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Chandía-Cristi A, Gutiérrez DA, Dulcey AE, Lara M, Vargas L, Lin YH, Jimenez-Muñoz P, Larenas G, Xu X, Wang A, Owens A, Dextras C, Chen Y, Pinto C, Marín T, Almarza-Salazar H, Acevedo K, Cancino GI, Hu X, Rojas P, Ferrer M, Southall N, Henderson MJ, Zanlungo S, Marugan JJ, Álvarez R A. Prophylactic treatment with the c-Abl inhibitor, neurotinib, diminishes neuronal damage and the convulsive state in pilocarpine-induced mice. Cell Rep 2024; 43:114144. [PMID: 38656874 DOI: 10.1016/j.celrep.2024.114144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 03/13/2024] [Accepted: 04/09/2024] [Indexed: 04/26/2024] Open
Abstract
The molecular mechanisms underlying seizure generation remain elusive, yet they are crucial for developing effective treatments for epilepsy. The current study shows that inhibiting c-Abl tyrosine kinase prevents apoptosis, reduces dendritic spine loss, and maintains N-methyl-d-aspartate (NMDA) receptor subunit 2B (NR2B) phosphorylated in in vitro models of excitotoxicity. Pilocarpine-induced status epilepticus (SE) in mice promotes c-Abl phosphorylation, and disrupting c-Abl activity leads to fewer seizures, increases latency toward SE, and improved animal survival. Currently, clinically used c-Abl inhibitors are non-selective and have poor brain penetration. The allosteric c-Abl inhibitor, neurotinib, used here has favorable potency, selectivity, pharmacokinetics, and vastly improved brain penetration. Neurotinib-administered mice have fewer seizures and improved survival following pilocarpine-SE induction. Our findings reveal c-Abl kinase activation as a key factor in ictogenesis and highlight the impact of its inhibition in preventing the insurgence of epileptic-like seizures in rodents and humans.
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Affiliation(s)
- América Chandía-Cristi
- Department of Cellular and Molecular Biology, Pontificia Universidad Católica de Chile, Portugal 49, Santiago, Chile
| | - Daniela A Gutiérrez
- Department of Cellular and Molecular Biology, Pontificia Universidad Católica de Chile, Portugal 49, Santiago, Chile; Millennium Institute on Immunology and Immunotherapy, Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Portugal 49, Santiago, Chile
| | - Andrés E Dulcey
- Early Translation Branch, National Center for Advancing Translational Sciences (NCATS), NIH, 9800 Medical Center Drive, Rockville, MD, USA
| | - Marcelo Lara
- Neuroscience Laboratory, Biology and Chemistry Faculty, Universidad de Santiago de Chile, Avenue Libertador Bernardo O'Higgins, Santiago 3363, Chile
| | - Lina Vargas
- Department of Cellular and Molecular Biology, Pontificia Universidad Católica de Chile, Portugal 49, Santiago, Chile
| | - Yi-Han Lin
- Early Translation Branch, National Center for Advancing Translational Sciences (NCATS), NIH, 9800 Medical Center Drive, Rockville, MD, USA
| | - Pablo Jimenez-Muñoz
- Department of Cellular and Molecular Biology, Pontificia Universidad Católica de Chile, Portugal 49, Santiago, Chile
| | - Gabriela Larenas
- Department of Cellular and Molecular Biology, Pontificia Universidad Católica de Chile, Portugal 49, Santiago, Chile
| | - Xin Xu
- Early Translation Branch, National Center for Advancing Translational Sciences (NCATS), NIH, 9800 Medical Center Drive, Rockville, MD, USA
| | - Amy Wang
- Early Translation Branch, National Center for Advancing Translational Sciences (NCATS), NIH, 9800 Medical Center Drive, Rockville, MD, USA
| | - Ashley Owens
- Early Translation Branch, National Center for Advancing Translational Sciences (NCATS), NIH, 9800 Medical Center Drive, Rockville, MD, USA
| | - Christopher Dextras
- Early Translation Branch, National Center for Advancing Translational Sciences (NCATS), NIH, 9800 Medical Center Drive, Rockville, MD, USA
| | - YuChi Chen
- Early Translation Branch, National Center for Advancing Translational Sciences (NCATS), NIH, 9800 Medical Center Drive, Rockville, MD, USA
| | - Claudio Pinto
- Department of Cellular and Molecular Biology, Pontificia Universidad Católica de Chile, Portugal 49, Santiago, Chile
| | - Tamara Marín
- Department of Cellular and Molecular Biology, Pontificia Universidad Católica de Chile, Portugal 49, Santiago, Chile; Millennium Institute on Immunology and Immunotherapy, Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Portugal 49, Santiago, Chile
| | - Hugo Almarza-Salazar
- Department of Cellular and Molecular Biology, Pontificia Universidad Católica de Chile, Portugal 49, Santiago, Chile; Millennium Institute on Immunology and Immunotherapy, Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Portugal 49, Santiago, Chile
| | - Keryma Acevedo
- Neurology Unit of Pediatric Division, Pontificia Universidad Católica de Chile, Avenue Libertador Bernardo O'Higgins 340, Santiago, Chile
| | - Gonzalo I Cancino
- Department of Cellular and Molecular Biology, Pontificia Universidad Católica de Chile, Portugal 49, Santiago, Chile
| | - Xin Hu
- Early Translation Branch, National Center for Advancing Translational Sciences (NCATS), NIH, 9800 Medical Center Drive, Rockville, MD, USA
| | - Patricio Rojas
- Neuroscience Laboratory, Biology and Chemistry Faculty, Universidad de Santiago de Chile, Avenue Libertador Bernardo O'Higgins, Santiago 3363, Chile
| | - Marc Ferrer
- Early Translation Branch, National Center for Advancing Translational Sciences (NCATS), NIH, 9800 Medical Center Drive, Rockville, MD, USA
| | - Noel Southall
- Early Translation Branch, National Center for Advancing Translational Sciences (NCATS), NIH, 9800 Medical Center Drive, Rockville, MD, USA
| | - Mark J Henderson
- Early Translation Branch, National Center for Advancing Translational Sciences (NCATS), NIH, 9800 Medical Center Drive, Rockville, MD, USA
| | - Silvana Zanlungo
- Department of Gastroenterology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Avenue Libertador Bernardo O'Higgins 340, Santiago, Chile.
| | - Juan J Marugan
- Early Translation Branch, National Center for Advancing Translational Sciences (NCATS), NIH, 9800 Medical Center Drive, Rockville, MD, USA.
| | - Alejandra Álvarez R
- Department of Cellular and Molecular Biology, Pontificia Universidad Católica de Chile, Portugal 49, Santiago, Chile; Millennium Institute on Immunology and Immunotherapy, Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Portugal 49, Santiago, Chile.
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2
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Sarkar R, Bolel P, Kapoor A, Eliseeva E, Dulcey AE, Templin JS, Wang AQ, Xu X, Southall N, Klubo-Gwiezdzinska J, Neumann S, Marugan JJ, Gershengorn MC. An Orally Efficacious Thyrotropin Receptor Ligand Inhibits Growth and Metastatic Activity of Thyroid Cancers. J Clin Endocrinol Metab 2024:dgae114. [PMID: 38421044 DOI: 10.1210/clinem/dgae114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 02/06/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
CONTEXT Thyroid-stimulating hormone (or thyrotropin) receptor (TSHR) could be a selective target for small molecule ligands to treat thyroid cancer (TC). OBJECTIVE We report a novel, orally efficacious ligand for TSHR that exhibits proliferation inhibitory activity against human TC in vitro and in vivo, and inhibition of metastasis in vivo. DESIGN A35 (NCATS-SM4420; NCGC00241808) was selected from a sub-library of >200 TSHR ligands. Cell proliferation assays including BrdU incorporation and WST-1, along with molecular docking studies were done. In vivo activity of A35 was assessed in TC cell-derived xenograft (CDX) models with immunocompromised (NSG) mice. FFPE sections of tumor and lung tissues were observed for the extent of cell death and metastasis. RESULTS A35 was shown to stimulate cAMP production in some cell types by activating TSHR but not in TC cells, MDA-T32 and MDA-T85. A35 inhibited proliferation of MDA-T32 & MDA-T85 in vitro and in vivo, and pulmonary metastasis of MDA-T85F1 in mice. In vitro, A35 inhibition of proliferation was reduced by a selective TSHR antagonist. Inhibition of CDX tumor growth without decreases in mouse weights and liver function showed A35 to be efficacious without apparent toxicity. Lastly, A35 reduced levels of Ki67 in the tumors and metastatic markers in lung tissues. CONCLUSION We conclude that A35 is a TSHR-selective inhibitor of TC cell proliferation and metastasis, and suggest that A35 may be a promising lead drug candidate for the treatment of differentiated thyroid cancer in humans.
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Affiliation(s)
- Rhitajit Sarkar
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Priyanka Bolel
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Abhijeet Kapoor
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Elena Eliseeva
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrés E Dulcey
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Jay S Templin
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Amy Q Wang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Xin Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Noel Southall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Joanna Klubo-Gwiezdzinska
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Susanne Neumann
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Juan J Marugan
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Marvin C Gershengorn
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
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Simms AM, Kanakia A, Sipra M, Dutta B, Southall N. A patient safety knowledge graph supporting vaccine product development. BMC Med Inform Decis Mak 2024; 24:10. [PMID: 38178113 PMCID: PMC10768450 DOI: 10.1186/s12911-023-02409-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/14/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Knowledge graphs are well-suited for modeling complex, unstructured, and multi-source data and facilitating their analysis. During the COVID-19 pandemic, adverse event data were integrated into a knowledge graph to support vaccine safety surveillance and nimbly respond to urgent health authority questions. Here, we provide details of this post-marketing safety system using public data sources. In addition to challenges with varied data representations, adverse event reporting on the COVID-19 vaccines generated an unprecedented volume of data; an order of magnitude larger than adverse events for all previous vaccines. The Patient Safety Knowledge Graph (PSKG) is a robust data store to accommodate the volume of adverse event data and harmonize primary surveillance data sources. METHODS We designed a semantic model to represent key safety concepts. We built an extract-transform-load (ETL) data pipeline to parse and import primary public data sources; align key elements such as vaccine names; integrated the Medical Dictionary for Regulatory Activities (MedDRA); and applied quality metrics. PSKG is deployed in a Neo4J graph database, and made available via a web interface and Application Programming Interfaces (APIs). RESULTS We import and align adverse event data and vaccine exposure data from 250 countries on a weekly basis, producing a graph with 4,340,980 nodes and 30,544,475 edges as of July 1, 2022. PSKG is used for ad-hoc analyses and periodic reporting for several widely available COVID-19 vaccines. Analysis code using the knowledge graph is 80% shorter than an equivalent implementation written entirely in Python, and runs over 200 times faster. CONCLUSIONS Organizing safety data into a concise model of nodes, properties, and edge relationships has greatly simplified analysis code by removing complex parsing and transformation algorithms from individual analyses and instead managing these centrally. The adoption of the knowledge graph transformed how the team answers key scientific and medical questions. Whereas previously an analysis would involve aggregating and transforming primary datasets from scratch to answer a specific question, the team can now iterate easily and respond as quickly as requests evolve (e.g., "Produce vaccine-X safety profile for adverse event-Y by country instead of age-range").
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Affiliation(s)
- Andrew M Simms
- Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, USA.
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4
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Park J, Djelassi M, Chima D, Hernandez R, Poroshin V, Iliescu AM, Domalik D, Southall N. Validation of a Natural Language Machine Learning Model for Safety Literature Surveillance. Drug Saf 2024; 47:71-80. [PMID: 37938539 DOI: 10.1007/s40264-023-01367-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2023] [Indexed: 11/09/2023]
Abstract
INTRODUCTION As part of routine safety surveillance, thousands of articles of potential interest are manually triaged for review by safety surveillance teams. This manual triage task is an interesting candidate for automation based on the abundance of process data available for training, the performance of natural language processing algorithms for this type of cognitive task, and the small number of safety signals that originate from literature review, resulting in its lower risk profile. However, deep learning algorithms introduce unique risks and the validation of such models for use in Good Pharmacovigilance Practice remains an open question. OBJECTIVE Qualifying an automated, deep learning approach to literature surveillance for use at AstraZeneca. METHODS The study is a prospective validation of a literature surveillance triage model, comparing its real-world performance with that of human surveillance teams working in parallel. The biggest risk in modifying this triage process is missing a safety signal (resulting in model false negatives) and hence model recall is the main evaluation metric considered. RESULTS The model demonstrates consistent global performance from training through testing, with recall rates comparable to that of existing surveillance teams. The model is accepted for use specifically for those products where non-inferiority to the manual process is rigorously demonstrated. CONCLUSION Characterizing model performance prospectively, under real-world conditions, allows us to thoroughly examine model consistency and failure modes, qualifying it for use in our surveillance processes. We also identify potential future improvements and recognize the opportunity for the community to collaborate on this shared task.
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Affiliation(s)
- Jiyoon Park
- Global Patient Safety, Chief Medical Office, AstraZeneca, Gaithersburg, MD, USA
| | - Malek Djelassi
- Enterprise AI Services, IGNITE IT, AstraZeneca, Mölndal, Sweden
| | - Daniel Chima
- Global Patient Safety, Chief Medical Office, AstraZeneca, Gaithersburg, MD, USA
| | | | | | - Ana-Maria Iliescu
- Global Patient Safety, Chief Medical Office, AstraZeneca, Mölndal, Sweden
| | - Douglas Domalik
- Global Patient Safety, Chief Medical Office, AstraZeneca, Gaithersburg, MD, USA
| | - Noel Southall
- Global Patient Safety, Chief Medical Office, AstraZeneca, Gaithersburg, MD, USA.
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Sayedyahossein S, Smith J, Barnaeva E, Li Z, Choe J, Ronzetti M, Dextras C, Hu X, Marugan J, Southall N, Baljinnyam B, Thines L, Tran AD, Ferrer M, Sacks DB. Discovery of small molecule inhibitors that effectively disrupt IQGAP1-Cdc42 interaction in breast cancer cells. Sci Rep 2022; 12:17372. [PMID: 36253497 PMCID: PMC9576799 DOI: 10.1038/s41598-022-21342-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/26/2022] [Indexed: 01/10/2023] Open
Abstract
The small GTPase Cdc42 is an integral component of the cytoskeleton, and its dysregulation leads to pathophysiological conditions, such as cancer. Binding of Cdc42 to the scaffold protein IQGAP1 stabilizes Cdc42 in its active form. The interaction between Cdc42 and IQGAP1 enhances migration and invasion of cancer cells. Disrupting this association could impair neoplastic progression and metastasis; however, no effective means to achieve this has been described. Here, we screened 78,500 compounds using a homogeneous time resolved fluorescence-based assay to identify small molecules that disrupt the binding of Cdc42 to IQGAP1. From the combined results of the validation assay and counter-screens, we selected 44 potent compounds for cell-based experiments. Immunoprecipitation and cell viability analysis rendered four lead compounds, namely NCGC00131308, NCGC00098561, MLS000332963 and NCGC00138812, three of which inhibited proliferation and migration of breast carcinoma cells. Microscale thermophoresis revealed that two compounds bind directly to Cdc42. One compound reduced the amount of active Cdc42 in cells and effectively impaired filopodia formation. Docking analysis provided plausible models of the compounds binding to the hydrophobic pocket adjacent to the GTP binding site of Cdc42. In conclusion, we identified small molecules that inhibit binding between Cdc42 and IQGAP1, which could potentially yield chemotherapeutic agents.
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Affiliation(s)
- Samar Sayedyahossein
- grid.94365.3d0000 0001 2297 5165Department of Laboratory Medicine, National Institutes of Health, Bethesda, MD 20892 USA ,grid.39381.300000 0004 1936 8884Present Address: Department of Physiology and Pharmacology, University of Western Ontario, London, ON Canada
| | - Jessica Smith
- grid.94365.3d0000 0001 2297 5165Department of Laboratory Medicine, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Present Address: Center for Scientific Review, National Institutes of Health, Bethesda, MD USA
| | - Elena Barnaeva
- grid.94365.3d0000 0001 2297 5165National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD USA
| | - Zhigang Li
- grid.94365.3d0000 0001 2297 5165Department of Laboratory Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Jun Choe
- grid.94365.3d0000 0001 2297 5165National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD USA
| | - Michael Ronzetti
- grid.94365.3d0000 0001 2297 5165National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD USA
| | - Christopher Dextras
- grid.94365.3d0000 0001 2297 5165National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD USA
| | - Xin Hu
- grid.94365.3d0000 0001 2297 5165National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD USA
| | - Juan Marugan
- grid.94365.3d0000 0001 2297 5165National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD USA
| | - Noel Southall
- grid.94365.3d0000 0001 2297 5165National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD USA
| | - Bolormaa Baljinnyam
- grid.94365.3d0000 0001 2297 5165National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD USA
| | - Louise Thines
- grid.94365.3d0000 0001 2297 5165Department of Laboratory Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Andy D. Tran
- grid.48336.3a0000 0004 1936 8075Confocal Microscopy Core Facility, Laboratory of Cancer Biology and Genetics, NCI, National Institutes of Health, Rockville, MD USA
| | - Marc Ferrer
- grid.94365.3d0000 0001 2297 5165National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD USA
| | - David B. Sacks
- grid.94365.3d0000 0001 2297 5165Department of Laboratory Medicine, National Institutes of Health, Bethesda, MD 20892 USA
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Sanchez TW, Ronzetti MH, Owens AE, Antony M, Voss T, Wallgren E, Talley D, Balakrishnan K, Leyes Porello SE, Rai G, Marugan JJ, Michael SG, Baljinnyam B, Southall N, Simeonov A, Henderson MJ. Real-Time Cellular Thermal Shift Assay to Monitor Target Engagement. ACS Chem Biol 2022; 17:2471-2482. [PMID: 36049119 PMCID: PMC9486815 DOI: 10.1021/acschembio.2c00334] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Determining a molecule's mechanism of action is paramount during chemical probe development and drug discovery. The cellular thermal shift assay (CETSA) is a valuable tool to confirm target engagement in cells for a small molecule that demonstrates a pharmacological effect. CETSA directly detects biophysical interactions between ligands and protein targets, which can alter a protein's unfolding and aggregation properties in response to thermal challenge. In traditional CETSA experiments, each temperature requires an individual sample, which restricts throughput and requires substantial optimization. To capture the full aggregation profile of a protein from a single sample, we developed a prototype real-time CETSA (RT-CETSA) platform by coupling a real-time PCR instrument with a CCD camera to detect luminescence. A thermally stable Nanoluciferase variant (ThermLuc) was bioengineered to withstand unfolding at temperatures greater than 90 °C and was compatible with monitoring target engagement events when fused to diverse targets. Utilizing well-characterized inhibitors of lactate dehydrogenase alpha, RT-CETSA showed significant correlation with enzymatic, biophysical, and other cell-based assays. A data analysis pipeline was developed to enhance the sensitivity of RT-CETSA to detect on-target binding. RT-CETSA technology advances capabilities of the CETSA method and facilitates the identification of ligand-target engagement in cells, a critical step in assessing the mechanism of action of a small molecule.
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Chen FW, Davies JP, Calvo R, Chaudhari J, Dolios G, Taylor MK, Patnaik S, Dehdashti J, Mull R, Dranchack P, Wang A, Xu X, Hughes E, Southall N, Ferrer M, Wang R, Marugan JJ, Ioannou YA. Activation of mitochondrial TRAP1 stimulates mitochondria-lysosome crosstalk and correction of lysosomal dysfunction. iScience 2022; 25:104941. [PMID: 36065186 PMCID: PMC9440283 DOI: 10.1016/j.isci.2022.104941] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 04/27/2022] [Accepted: 08/11/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- Fannie W. Chen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joanna P. Davies
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Raul Calvo
- Early Translation Branch, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Jagruti Chaudhari
- Cell Therapy and Cell Engineering Facility, Memorial Sloan Kettering Cancer Center, 1250 1st Avenue, New York, NY 10065, USA
| | - Georgia Dolios
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mercedes K. Taylor
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Samarjit Patnaik
- Early Translation Branch, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Jean Dehdashti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rebecca Mull
- Early Translation Branch, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Patricia Dranchack
- Early Translation Branch, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Amy Wang
- Early Translation Branch, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Xin Xu
- Early Translation Branch, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Emma Hughes
- Early Translation Branch, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Noel Southall
- Early Translation Branch, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Marc Ferrer
- Early Translation Branch, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Rong Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Juan J. Marugan
- Early Translation Branch, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
- Corresponding author
| | - Yiannis A. Ioannou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Corresponding author
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Frankowski KJ, Patnaik S, Wang C, Southall N, Dutta D, De S, Li D, Dextras C, Lin YH, Bryant-Connah M, Davis D, Wang F, Wachsmuth LM, Shah P, Williams J, Kabir M, Zhu E, Baljinnyam B, Wang A, Xu X, Norton J, Ferrer M, Titus S, Simeonov A, Zheng W, Mathews Griner LA, Jadhav A, Aubé J, Henderson MJ, Rudloff U, Schoenen FJ, Huang S, Marugan JJ. Discovery and Optimization of Pyrrolopyrimidine Derivatives as Selective Disruptors of the Perinucleolar Compartment, a Marker of Tumor Progression toward Metastasis. J Med Chem 2022; 65:8303-8331. [PMID: 35696646 PMCID: PMC10024865 DOI: 10.1021/acs.jmedchem.2c00204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The perinucleolar compartment (PNC) is a dynamic subnuclear body found at the periphery of the nucleolus. The PNC is enriched with RNA transcripts and RNA-binding proteins, reflecting different states of genome organization. PNC prevalence positively correlates with cancer progression and metastatic capacity, making it a useful marker for metastatic cancer progression. A high-throughput, high-content assay was developed to identify novel small molecules that selectively reduce PNC prevalence in cancer cells. We identified and further optimized a pyrrolopyrimidine series able to reduce PNC prevalence in PC3M cancer cells at submicromolar concentrations without affecting cell viability. Structure-activity relationship exploration of the structural elements necessary for activity resulted in the discovery of several potent compounds. Analysis of in vitro drug-like properties led to the discovery of the bioavailable analogue, metarrestin, which has shown potent antimetastatic activity with improved survival in rodent models and is currently being evaluated in a first-in-human phase 1 clinical trial.
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Affiliation(s)
- Kevin J Frankowski
- KU Specialized Chemistry Center, University of Kansas, 2034 Becker Drive, Lawrence, Kansas 66047, United States.,Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Samarjit Patnaik
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Chen Wang
- Department of Cell and Molecular Biology, Northwestern University, Chicago, Illinois 60611, United States
| | - Noel Southall
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Dipannita Dutta
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Soumitta De
- Rare Tumor Initiative, Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20892, United States
| | - Dandan Li
- Rare Tumor Initiative, Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20892, United States
| | - Christopher Dextras
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Yi-Han Lin
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Marthe Bryant-Connah
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Danielle Davis
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Feijun Wang
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Leah M Wachsmuth
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Pranav Shah
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Jordan Williams
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Md Kabir
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Edward Zhu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Bolormaa Baljinnyam
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Amy Wang
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Xin Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - John Norton
- Department of Cell and Molecular Biology, Northwestern University, Chicago, Illinois 60611, United States
| | - Marc Ferrer
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Steve Titus
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Lesley A Mathews Griner
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Jeffrey Aubé
- KU Specialized Chemistry Center, University of Kansas, 2034 Becker Drive, Lawrence, Kansas 66047, United States.,Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Mark J Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Udo Rudloff
- Rare Tumor Initiative, Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20892, United States
| | - Frank J Schoenen
- KU Specialized Chemistry Center, University of Kansas, 2034 Becker Drive, Lawrence, Kansas 66047, United States
| | - Sui Huang
- Department of Cell and Molecular Biology, Northwestern University, Chicago, Illinois 60611, United States
| | - Juan J Marugan
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
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9
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Unni DR, Moxon SAT, Bada M, Brush M, Bruskiewich R, Caufield JH, Clemons PA, Dancik V, Dumontier M, Fecho K, Glusman G, Hadlock JJ, Harris NL, Joshi A, Putman T, Qin G, Ramsey SA, Shefchek KA, Solbrig H, Soman K, Thessen AE, Haendel MA, Bizon C, Mungall CJ, Acevedo L, Ahalt SC, Alden J, Alkanaq A, Amin N, Avila R, Balhoff J, Baranzini SE, Baumgartner A, Baumgartner W, Belhu B, Brandes M, Brandon N, Burtt N, Byrd W, Callaghan J, Cano MA, Carrell S, Celebi R, Champion J, Chen Z, Chen M, Chung L, Cohen K, Conlin T, Corkill D, Costanzo M, Cox S, Crouse A, Crowder C, Crumbley ME, Dai C, Dančík V, De Miranda Azevedo R, Deutsch E, Dougherty J, Duby MP, Duvvuri V, Edwards S, Emonet V, Fehrmann N, Flannick J, Foksinska AM, Gardner V, Gatica E, Glen A, Goel P, Gormley J, Greyber A, Haaland P, Hanspers K, He K, He K, Henrickson J, Hinderer EW, Hoatlin M, Hoffman A, Huang S, Huang C, Hubal R, Huellas‐Bruskiewicz K, Huls FB, Hunter L, Hyde G, Issabekova T, Jarrell M, Jenkins L, Johs A, Kang J, Kanwar R, Kebede Y, Kim KJ, Kluge A, Knowles M, Koesterer R, Korn D, Koslicki D, Krishnamurthy A, Kvarfordt L, Lee J, Leigh M, Lin J, Liu Z, Liu S, Ma C, Magis A, Mamidi T, Mandal M, Mantilla M, Massung J, Mauldin D, McClelland J, McMurry J, Mease P, Mendoza L, Mersmann M, Mesbah A, Might M, Morton K, Muller S, Muluka AT, Osborne J, Owen P, Patton M, Peden DB, Peene RC, Persaud B, Pfaff E, Pico A, Pollard E, Price G, Raj S, Reilly J, Riutta A, Roach J, Roper RT, Rosenblatt G, Rubin I, Rucka S, Rudavsky‐Brody N, Sakaguchi R, Santos E, Schaper K, Schmitt CP, Schurman S, Scott E, Seitanakis S, Sharma P, Shmulevich I, Shrestha M, Shrivastava S, Sinha M, Smith B, Southall N, Southern N, Stillwell L, Strasser M"M, Su AI, Ta C, Thessen AE, Tinglin J, Tonstad L, Tran‐Nguyen T, Tropsha A, Vaidya G, Veenhuis L, Viola A, Grotthuss M, Wang M, Wang P, Watkins PB, Weber R, Wei Q, Weng C, Whitlock J, Williams MD, Williams A, Womack F, Wood E, Wu C, Xin JK, Xu H, Xu C, Yakaboski C, Yao Y, Yi H, Yilmaz A, Zheng M, Zhou X, Zhou E, Zhu Q, Zisk T. Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science. Clin Transl Sci 2022; 15:1848-1855. [PMID: 36125173 PMCID: PMC9372416 DOI: 10.1111/cts.13302] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/27/2022] [Accepted: 05/02/2022] [Indexed: 12/12/2022] Open
Abstract
Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph‐based data models elucidate the interconnectedness among core biomedical concepts, enable data structures to be easily updated, and support intuitive queries, visualizations, and inference algorithms. However, knowledge discovery across these “knowledge graphs” (KGs) has remained difficult. Data set heterogeneity and complexity; the proliferation of ad hoc data formats; poor compliance with guidelines on findability, accessibility, interoperability, and reusability; and, in particular, the lack of a universally accepted, open‐access model for standardization across biomedical KGs has left the task of reconciling data sources to downstream consumers. Biolink Model is an open‐source data model that can be used to formalize the relationships between data structures in translational science. It incorporates object‐oriented classification and graph‐oriented features. The core of the model is a set of hierarchical, interconnected classes (or categories) and relationships between them (or predicates) representing biomedical entities such as gene, disease, chemical, anatomic structure, and phenotype. The model provides class and edge attributes and associations that guide how entities should relate to one another. Here, we highlight the need for a standardized data model for KGs, describe Biolink Model, and compare it with other models. We demonstrate the utility of Biolink Model in various initiatives, including the Biomedical Data Translator Consortium and the Monarch Initiative, and show how it has supported easier integration and interoperability of biomedical KGs, bringing together knowledge from multiple sources and helping to realize the goals of translational science.
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Affiliation(s)
- Deepak R. Unni
- Genome Biology Unit, European Molecular Biology Laboratory Heidelberg Germany
- Division of Environmental Genomics and Systems Biology Lawrence Berkeley National Laboratory Berkeley California USA
| | - Sierra A. T. Moxon
- Division of Environmental Genomics and Systems Biology Lawrence Berkeley National Laboratory Berkeley California USA
| | - Michael Bada
- Center for Health AI University of Colorado Anschutz Medical Campus Aurora Colorado USA
| | - Matthew Brush
- Center for Health AI University of Colorado Anschutz Medical Campus Aurora Colorado USA
| | | | - J. Harry Caufield
- Division of Environmental Genomics and Systems Biology Lawrence Berkeley National Laboratory Berkeley California USA
| | - Paul A. Clemons
- Chemical Biology and Therapeutics Science Program Broad Institute Cambridge Massachusetts USA
| | - Vlado Dancik
- Chemical Biology and Therapeutics Science Program Broad Institute Cambridge Massachusetts USA
| | - Michel Dumontier
- Institute of Data Science Maastricht University Maastricht The Netherlands
| | - Karamarie Fecho
- Renaissance Computing Institute University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
| | | | | | - Nomi L. Harris
- Division of Environmental Genomics and Systems Biology Lawrence Berkeley National Laboratory Berkeley California USA
| | - Arpita Joshi
- Institute for Systems Biology Seattle Washington USA
| | - Tim Putman
- Center for Health AI University of Colorado Anschutz Medical Campus Aurora Colorado USA
| | - Guangrong Qin
- Institute for Systems Biology Seattle Washington USA
| | - Stephen A. Ramsey
- Department of Biomedical Sciences Oregon State University Corvallis Oregon USA
| | - Kent A. Shefchek
- Center for Health AI University of Colorado Anschutz Medical Campus Aurora Colorado USA
| | | | - Karthik Soman
- Department of Neurology University of California San Francisco San Francisco California USA
| | - Anne E. Thessen
- Center for Health AI University of Colorado Anschutz Medical Campus Aurora Colorado USA
| | - Melissa A. Haendel
- Center for Health AI University of Colorado Anschutz Medical Campus Aurora Colorado USA
| | - Chris Bizon
- Renaissance Computing Institute University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
| | - Christopher J. Mungall
- Division of Environmental Genomics and Systems Biology Lawrence Berkeley National Laboratory Berkeley California USA
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10
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Fecho K, Thessen AE, Baranzini SE, Bizon C, Hadlock JJ, Huang S, Roper RT, Southall N, Ta C, Watkins PB, Williams MD, Xu H, Byrd W, Dančík V, Duby MP, Dumontier M, Glusman G, Harris NL, Hinderer EW, Hyde G, Johs A, Su AI, Qin G, Zhu Q. Progress toward a universal biomedical data translator. Clin Transl Sci 2022; 15:1838-1847. [PMID: 35611543 PMCID: PMC9372428 DOI: 10.1111/cts.13301] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/27/2022] [Accepted: 05/02/2022] [Indexed: 11/28/2022] Open
Abstract
Clinical, biomedical, and translational science has reached an inflection point in the breadth and diversity of available data and the potential impact of such data to improve human health and well-being. However, the data are often siloed, disorganized, and not broadly accessible due to discipline-specific differences in terminology and representation. To address these challenges, the Biomedical Data Translator Consortium has developed and tested a pilot knowledge graph-based "Translator" system capable of integrating existing biomedical data sets and "translating" those data into insights intended to augment human reasoning and accelerate translational science. Having demonstrated feasibility of the Translator system, the Translator program has since moved into development, and the Translator Consortium has made significant progress in the research, design, and implementation of an operational system. Herein, we describe the current system's architecture, performance, and quality of results. We apply Translator to several real-world use cases developed in collaboration with subject-matter experts. Finally, we discuss the scientific and technical features of Translator and compare those features to other state-of-the-art, biomedical graph-based question-answering systems.
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Grants
- OT3TR002019 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- ZIA TR000276-05 National Center for Advancing Translational Sciences, Intramural Research Program
- OT2TR003449 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- U01 DK065201 NIDDK NIH HHS
- OT2TR002515 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR003443 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR002584 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR003434 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2 TR003449 NCATS NIH HHS
- OT2TR003433 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR003435 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR002517 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT3TR002027 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR003422 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR003441 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT3TR002020 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR003448 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR003428 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR003445 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- I75N95021P00636 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR002520 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR003427 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR003436 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- ZIA TR000276 Intramural NIH HHS
- OT2TR002514 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT3TR002025 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2 TR003428 NCATS NIH HHS
- 5U01DK065201 NIDDK NIH HHS
- OT2TR003437 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR003450 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT3TR002026 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR003430 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- National Institute of Diabetes and Digestive and Kidney Diseases
- National Center for Advancing Translational Sciences, Biomedical Data Translator Program
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Affiliation(s)
- Karamarie Fecho
- Renaissance Computing InstituteUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Anne E. Thessen
- Center for Health AIUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Sergio E. Baranzini
- Weill Institute for Neurosciences, Department of NeurologyUniversity of California at San FranciscoSan FranciscoCaliforniaUSA
| | - Chris Bizon
- Renaissance Computing InstituteUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | | | - Sui Huang
- Institute for Systems BiologySeattleWashingtonUSA
| | | | - Noel Southall
- Division of Preclinical Innovation, National Center for Advancing Translational SciencesNational Institutes of HealthRockvilleMarylandUSA
| | - Casey Ta
- Department of Biomedical InformaticsColumbia UniversityNew YorkNew YorkUSA
| | - Paul B. Watkins
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of PharmacyUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Mark D. Williams
- Division of Preclinical Innovation, National Center for Advancing Translational SciencesNational Institutes of HealthRockvilleMarylandUSA
| | - Hao Xu
- Renaissance Computing InstituteUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - William Byrd
- Hugh Kaul Precision Medicine InstituteUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Vlado Dančík
- Chemical Biology and Therapeutics Science ProgramBroad InstituteCambridgeMassachusettsUSA
| | - Marc P. Duby
- Medical and Population Genetics ProgramBroad InstituteCambridgeMassachusettsUSA
| | - Michel Dumontier
- Institute of Data ScienceMaastricht UniversityMaastrichtThe Netherlands
| | | | - Nomi L. Harris
- Division of Environmental Genomics and Systems BiologyLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Eugene W. Hinderer
- Tufts Clinical and Translational Science InstituteTufts Medical CenterBostonMassachusettsUSA
| | - Greg Hyde
- Thayer School of EngineeringDartmouth CollegeHanoverNew HampshireUSA
| | - Adam Johs
- Department of Information Science, College of Computing and InformaticsDrexel UniversityPhiladelphiaPennsylvaniaUSA
| | - Andrew I. Su
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCaliforniaUSA
| | | | - Qian Zhu
- Division of Preclinical Innovation, National Center for Advancing Translational SciencesNational Institutes of HealthRockvilleMarylandUSA
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11
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Esteban-Lopez M, Wilson K, Myhr C, Kaftanovskaya E, Henderson M, Southall N, Hu X, Barnaeva E, Ferrer M, Kim D, Ye W, Morello R, Agoulnik I, Marugan J, Agoulnik A. RXFP2 Small Molecule Agonists: Potential Therapeutics for Osteoporosis. FASEB J 2022. [PMID: 35554639 DOI: 10.1096/fasebj.2022.36.s1.r2398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Osteoporosis is a chronic bone disease characterized by decreased bone mass and increased risk of developing fractures, predominantly observed in the elderly. Osteoporosis affects approximately 10 million people in the US, and the number is expected to increase exponentially as the elderly population continues to grow. The pathophysiological cause of the disease is a decrease in the activity of the bone-forming cells (osteoblasts) that alters bone remodeling in favor of bone resorption, leading to a decrease in bone mass. Recent studies identified the G protein-coupled receptor (GPCR) for insulin-like 3 peptide (INSL3), relaxin family peptide receptor 2 (RXFP2), as an attractive target for the treatment of osteoporosis. The goal of this study is to develop small molecule agonists of RXFP2, expressed in osteoblast cells, to promote bone growth and counteract the deleterious effects of osteoporosis. Currently, the most effective available treatment for osteoporosis is an expensive hormone therapy that requires daily injections. We aim to create drugs that are stable and can be delivered orally. Several low molecular weight compounds were identified as agonists of the RXFP2 receptor using a high-throughput screen of the NCATS small molecule library. The screening assay measured cAMP response in RXFP2-transfected HEK293T cells. An extensive structure-activity relationship campaign resulted in highly potent and efficient full RXFP2 agonists. The selectivity and specificity of the compounds for human and mouse RXFP2 was shown using orthogonal cAMP assays, counter-screening against the related relaxin receptor RXFP1, and a GPCRome screen using the PRESTO-Tango assay. The drug candidates were further tested in primary human osteoblasts to demonstrate that they promote mineralization by measuring hydroxyapatite deposition in the cell matrix. We showed that the compounds had low cytotoxicity in various cell types. Using a series of RXFP2/RXFP1 chimeric receptors, we established that the compounds are allosteric agonists of the RXFP2 receptor and identified the GPCR transmembrane domains as the specific region for compound interaction. The RXFP2 agonist with the highest activity in vitro was selected for pharmacokinetics (PK) profiling in mice, showing optimal oral bioavailability and bone exposure. An efficacy study using 2-month-old WT female mice treated orally with 10 mg/kg of compound 3 times a week for 8 weeks showed a significant increase of the vertebral trabecular number and thickness by micro-CT analysis compared to vehicle treated controls. We expect that the further characterization of these compounds may lead to the development of a new class of cost-effective drugs for the treatment of osteoporosis and other diseases associated with bone loss.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Roy Morello
- Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR
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12
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Marín T, Dulcey AE, Campos F, de la Fuente C, Acuña M, Castro J, Pinto C, Yañez MJ, Cortez C, McGrath DW, Sáez PJ, Gorshkov K, Zheng W, Southall N, Carmo-Fonseca M, Marugán J, Alvarez AR, Zanlungo S. c-Abl Activation Linked to Autophagy-Lysosomal Dysfunction Contributes to Neurological Impairment in Niemann-Pick Type A Disease. Front Cell Dev Biol 2022; 10:844297. [PMID: 35399514 PMCID: PMC8985125 DOI: 10.3389/fcell.2022.844297] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 02/25/2022] [Indexed: 12/05/2022] Open
Abstract
Niemann-Pick type A (NPA) disease is a fatal lysosomal neurodegenerative disorder caused by the deficiency in acid sphingomyelinase (ASM) activity. NPA patients present severe and progressive neurodegeneration starting at an early age. Currently, there is no effective treatment for this disease and NPA patients die between 2 and 3 years of age. NPA is characterized by an accumulation of sphingomyelin in lysosomes and dysfunction in the autophagy-lysosomal pathway. Recent studies show that c-Abl tyrosine kinase activity downregulates autophagy and the lysosomal pathway. Interestingly, this kinase is also activated in other lysosomal neurodegenerative disorders. Here, we describe that c-Abl activation contributes to the mechanisms of neuronal damage and death in NPA disease. Our data demonstrate that: 1) c-Abl is activated in-vitro as well as in-vivo NPA models; 2) imatinib, a clinical c-Abl inhibitor, reduces autophagy-lysosomal pathway alterations, restores autophagy flux, and lowers sphingomyelin accumulation in NPA patient fibroblasts and NPA neuronal models and 3) chronic treatment with nilotinib and neurotinib, two c-Abl inhibitors with differences in blood-brain barrier penetrance and target binding mode, show further benefits. While nilotinib treatment reduces neuronal death in the cerebellum and improves locomotor functions, neurotinib decreases glial activation, neuronal disorganization, and loss in hippocampus and cortex, as well as the cognitive decline of NPA mice. Our results support the participation of c-Abl signaling in NPA neurodegeneration and autophagy-lysosomal alterations, supporting the potential use of c-Abl inhibitors for the clinical treatment of NPA patients.
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Affiliation(s)
- Tamara Marín
- Department of Gastroenterology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Andrés E. Dulcey
- Early Translation Branch, National Center for Advancing Translational Sciences (NCATS), NIH, Rockville, MD, United States
| | - Fabián Campos
- Department of Gastroenterology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Catalina de la Fuente
- Laboratory of Cell Signaling, Center for Aging and Regeneration (CARE), Millennium Institute on Immunology and Immunotherapy (IMII), Department of Cellular and Molecular Biology, Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Mariana Acuña
- Department of Gastroenterology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Juan Castro
- Department of Gastroenterology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Claudio Pinto
- Laboratory of Cell Signaling, Center for Aging and Regeneration (CARE), Millennium Institute on Immunology and Immunotherapy (IMII), Department of Cellular and Molecular Biology, Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - María José Yañez
- School of Medical Technology, Health Sciences Faculty, Universidad San Sebastián, Santiago, Chile
| | - Cristian Cortez
- Center for Genomics and Bioinformatics, Faculty of Science, Universidad Mayor, Santiago, Chile
| | - David W. McGrath
- Cell Communication and Migration Laboratory, Institute of Biochemistry and Molecular Cell Biology, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Pablo J. Sáez
- Cell Communication and Migration Laboratory, Institute of Biochemistry and Molecular Cell Biology, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kirill Gorshkov
- Early Translation Branch, National Center for Advancing Translational Sciences (NCATS), NIH, Rockville, MD, United States
| | - Wei Zheng
- Early Translation Branch, National Center for Advancing Translational Sciences (NCATS), NIH, Rockville, MD, United States
| | - Noel Southall
- Early Translation Branch, National Center for Advancing Translational Sciences (NCATS), NIH, Rockville, MD, United States
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular Joȧo Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Juan Marugán
- Early Translation Branch, National Center for Advancing Translational Sciences (NCATS), NIH, Rockville, MD, United States
- *Correspondence: Juan Marugán, ; Alejandra R. Alvarez, ; Silvana Zanlungo,
| | - Alejandra R. Alvarez
- Laboratory of Cell Signaling, Center for Aging and Regeneration (CARE), Millennium Institute on Immunology and Immunotherapy (IMII), Department of Cellular and Molecular Biology, Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago, Chile
- *Correspondence: Juan Marugán, ; Alejandra R. Alvarez, ; Silvana Zanlungo,
| | - Silvana Zanlungo
- Department of Gastroenterology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- *Correspondence: Juan Marugán, ; Alejandra R. Alvarez, ; Silvana Zanlungo,
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13
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Owens AE, Iannotti MJ, Sanchez TW, Voss T, Kapoor A, Hall MD, Marugan JJ, Michael S, Southall N, Henderson MJ. High-Throughput Cellular Thermal Shift Assay Using Acoustic Transfer of Protein Lysates. ACS Chem Biol 2022; 17:322-330. [PMID: 35119255 PMCID: PMC10026039 DOI: 10.1021/acschembio.1c00760] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cellular thermal shift assay (CETSA) is a valuable method to confirm target engagement within a complex cellular environment, by detecting changes in a protein's thermal stability upon ligand binding. The classical CETSA method measures changes in the thermal stability of endogenous proteins using immunoblotting, which is low-throughput and laborious. Reverse-phase protein arrays (RPPAs) have been demonstrated as a detection modality for CETSA; however, the reported procedure requires manual processing steps that limit throughput and preclude screening applications. We developed a high-throughput CETSA using an acoustic RPPA (HT-CETSA-aRPPA) protocol that is compatible with 96- and 384-well microplates from start-to-finish, using low speed centrifugation to remove thermally destabilized proteins. The utility of HT-CETSA-aRPPA for guiding structure-activity relationship studies was demonstrated for inhibitors of lactate dehydrogenase A. Additionally, a collection of kinase inhibitors was screened to identify compounds that engage MEK1, a clinically relevant kinase target.
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Affiliation(s)
- Ashley E. Owens
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Michael J. Iannotti
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Tino W. Sanchez
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Ty Voss
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Abhijeet Kapoor
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Juan J. Marugan
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Sam Michael
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Noel Southall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Mark J. Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
- Corresponding Author: Mark Henderson;
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14
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Kapoor A, Henderson MJ, Marugan J, Southall N. Membrane recognition and substrate binding mechanism of PIP4Kγ kinase from molecular simulations. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.2278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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15
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Mansouri K, Karmaus AL, Fitzpatrick J, Patlewicz G, Pradeep P, Alberga D, Alepee N, Allen TEH, Allen D, Alves VM, Andrade CH, Auernhammer TR, Ballabio D, Bell S, Benfenati E, Bhattacharya S, Bastos JV, Boyd S, Brown JB, Capuzzi SJ, Chushak Y, Ciallella H, Clark AM, Consonni V, Daga PR, Ekins S, Farag S, Fedorov M, Fourches D, Gadaleta D, Gao F, Gearhart JM, Goh G, Goodman JM, Grisoni F, Grulke CM, Hartung T, Hirn M, Karpov P, Korotcov A, Lavado GJ, Lawless M, Li X, Luechtefeld T, Lunghini F, Mangiatordi GF, Marcou G, Marsh D, Martin T, Mauri A, Muratov EN, Myatt GJ, Nguyen DT, Nicolotti O, Note R, Pande P, Parks AK, Peryea T, Polash AH, Rallo R, Roncaglioni A, Rowlands C, Ruiz P, Russo DP, Sayed A, Sayre R, Sheils T, Siegel C, Silva AC, Simeonov A, Sosnin S, Southall N, Strickland J, Tang Y, Teppen B, Tetko IV, Thomas D, Tkachenko V, Todeschini R, Toma C, Tripodi I, Trisciuzzi D, Tropsha A, Varnek A, Vukovic K, Wang Z, Wang L, Waters KM, Wedlake AJ, Wijeyesakere SJ, Wilson D, Xiao Z, Yang H, Zahoranszky-Kohalmi G, Zakharov AV, Zhang FF, Zhang Z, Zhao T, Zhu H, Zorn KM, Casey W, Kleinstreuer NC. Erratum: CATMoS: Collaborative Acute Toxicity Modeling Suite. Environ Health Perspect 2021; 129:109001. [PMID: 34647794 PMCID: PMC8516060 DOI: 10.1289/ehp10369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 05/21/2023]
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16
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Sheils T, Mathias SL, Siramshetty VB, Bocci G, Bologa CG, Yang JJ, Waller A, Southall N, Nguyen DT, Oprea TI. How to Illuminate the Druggable Genome Using Pharos. ACTA ACUST UNITED AC 2021; 69:e92. [PMID: 31898878 DOI: 10.1002/cpbi.92] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Pharos is an integrated web-based informatics platform for the analysis of data aggregated by the Illuminating the Druggable Genome (IDG) Knowledge Management Center, an NIH Common Fund initiative. The current version of Pharos (as of October 2019) spans 20,244 proteins in the human proteome, 19,880 disease and phenotype associations, and 226,829 ChEMBL compounds. This resource not only collates and analyzes data from over 60 high-quality resources to generate these types, but also uses text indexing to find less apparent connections between targets, and has recently begun to collaborate with institutions that generate data and resources. Proteins are ranked according to a knowledge-based classification system, which can help researchers to identify less studied "dark" targets that could be potentially further illuminated. This is an important process for both drug discovery and target validation, as more knowledge can accelerate target identification, and previously understudied proteins can serve as novel targets in drug discovery. Two basic protocols illustrate the levels of detail available for targets and several methods of finding targets of interest. An Alternate Protocol illustrates the difference in available knowledge between less and more studied targets. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Search for a target and view details Alternate Protocol: Search for dark target and view details Basic Protocol 2: Filter a target list to get refined results.
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Affiliation(s)
- Timothy Sheils
- National Center for Advancing Translational Sciences, Rockville, Maryland
| | - Stephen L Mathias
- Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, New Mexico
| | | | - Giovanni Bocci
- Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, New Mexico
| | - Cristian G Bologa
- Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, New Mexico
| | - Jeremy J Yang
- Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, New Mexico
| | - Anna Waller
- Department of Pathology, University of New Mexico School of Medicine, Albuquerque, New Mexico
| | - Noel Southall
- National Center for Advancing Translational Sciences, Rockville, Maryland
| | - Dac-Trung Nguyen
- National Center for Advancing Translational Sciences, Rockville, Maryland
| | - Tudor I Oprea
- Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, New Mexico.,UNM Comprehensive Cancer Center, Albuquerque, New Mexico.,Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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17
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Mansouri K, Karmaus A, Fitzpatrick J, Patlewicz G, Pradeep P, Alberga D, Alepee N, Allen TEH, Allen D, Alves VM, Andrade CH, Auernhammer TR, Ballabio D, Bell S, Benfenati E, Bhattacharya S, Bastos JV, Boyd S, Brown JB, Capuzzi SJ, Chushak Y, Ciallella H, Clark AM, Consonni V, Daga PR, Ekins S, Farag S, Fedorov M, Fourches D, Gadaleta D, Gao F, Gearhart JM, Goh G, Goodman JM, Grisoni F, Grulke CM, Hartung T, Hirn M, Karpov P, Korotcov A, Lavado GJ, Lawless M, Li X, Luechtefeld T, Lunghini F, Mangiatordi GF, Marcou G, Marsh D, Martin T, Mauri A, Muratov EN, Myatt GJ, Nguyen DT, Nicolotti O, Note R, Pande P, Parks AK, Peryea T, Polash A, Rallo R, Roncaglioni A, Rowlands C, Ruiz P, Russo D, Sayed A, Sayre R, Sheils T, Siegel C, Silva AC, Simeonov A, Sosnin S, Southall N, Strickland J, Tang Y, Teppen B, Tetko IV, Thomas D, Tkachenko V, Todeschini R, Toma C, Tripodi I, Trisciuzzi D, Tropsha A, Varnek A, Vukovic K, Wang Z, Wang L, Waters KM, Wedlake AJ, Wijeyesakere SJ, Wilson D, Xiao Z, Yang H, Zahoranszky-Kohalmi G, Zakharov AV, Zhang FF, Zhang Z, Zhao T, Zhu H, Zorn KM, Casey W, Kleinstreuer NC. Erratum: CATMoS: Collaborative Acute Toxicity Modeling Suite. Environ Health Perspect 2021; 129:79001. [PMID: 34242083 PMCID: PMC8270350 DOI: 10.1289/ehp9883] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 05/28/2023]
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18
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Rolt A, Talley DC, Park SB, Hu Z, Dulcey A, Ma C, Irvin P, Leek M, Wang AQ, Stachulski AV, Xu X, Southall N, Ferrer M, Liang TJ, Marugan JJ. Discovery and Optimization of a 4-Aminopiperidine Scaffold for Inhibition of Hepatitis C Virus Assembly. J Med Chem 2021; 64:9431-9443. [PMID: 34184537 DOI: 10.1021/acs.jmedchem.1c00696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The majority of FDA-approved HCV therapeutics target the viral replicative machinery. An automated high-throughput phenotypic screen identified several small molecules as potent inhibitors of hepatitis C virus replication. Here, we disclose the discovery and optimization of a 4-aminopiperidine (4AP) scaffold targeting the assembly stages of the HCV life cycle. The original screening hit (1) demonstrates efficacy in the HCVcc assay but does not show potency prior to or during viral replication. Colocalization and infectivity studies indicate that the 4AP chemotype inhibits the assembly and release of infectious HCV. Compound 1 acts synergistically with FDA-approved direct-acting antiviral compounds Telaprevir and Daclatasvir, as well as broad spectrum antivirals Ribavirin and cyclosporin A. Following an SAR campaign, several derivatives of the 4AP series have been identified with increased potency against HCV, reduced in vitro toxicity, as well as improved in vitro and in vivo ADME properties.
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Affiliation(s)
- Adam Rolt
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20892, United States
| | - Daniel C Talley
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Seung Bum Park
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20892, United States
| | - Zongyi Hu
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20892, United States
| | - Andrés Dulcey
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Christopher Ma
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20892, United States
| | - Parker Irvin
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20892, United States
| | - Madeleine Leek
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20892, United States
| | - Amy Q Wang
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Andrew V Stachulski
- The Robert Robinson Laboratories, Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, U.K
| | - Xin Xu
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Noel Southall
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Marc Ferrer
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - T Jake Liang
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20892, United States
| | - Juan J Marugan
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
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19
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Siramshetty V, Williams J, Nguyễn ÐT, Neyra J, Southall N, Mathé E, Xu X, Shah P. Validating ADME QSAR Models Using Marketed Drugs. SLAS Discov 2021; 26:1326-1336. [PMID: 34176369 DOI: 10.1177/24725552211017520] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Problems with drug ADME are responsible for many clinical failures. By understanding the ADME properties of marketed drugs and modeling how chemical structure contributes to these inherent properties, we can help new projects reduce their risk profiles. Kinetic aqueous solubility, the parallel artificial membrane permeability assay (PAMPA), and rat liver microsomal stability constitute the Tier I ADME assays at the National Center for Advancing Translational Sciences (NCATS). Using recent data generated from in-house lead optimization Tier I studies, we update quantitative structure-activity relationship (QSAR) models for these three endpoints and validate in silico performance against a set of marketed drugs (balanced accuracies range between 71% and 85%). Improved models and experimental datasets are of direct relevance to drug discovery projects and, together with the prediction services that have been made publicly available at the ADME@NCATS web portal (https://opendata.ncats.nih.gov/adme/), provide important tools for the drug discovery community. The results are discussed in light of our previously reported ADME models and state-of-the-art models from scientific literature.Graphical Abstract[Figure: see text].
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Affiliation(s)
- Vishal Siramshetty
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Rockville, MD, USA
| | - Jordan Williams
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Rockville, MD, USA
| | - Ðắc-Trung Nguyễn
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Rockville, MD, USA
| | - Jorge Neyra
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Rockville, MD, USA
| | - Noel Southall
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Rockville, MD, USA
| | - Ewy Mathé
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Rockville, MD, USA
| | - Xin Xu
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Rockville, MD, USA
| | - Pranav Shah
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Rockville, MD, USA
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20
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Jaynes JM, Sable R, Ronzetti M, Bautista W, Knotts Z, Abisoye-Ogunniyan A, Li D, Calvo R, Dashnyam M, Singh A, Guerin T, White J, Ravichandran S, Kumar P, Talsania K, Chen V, Ghebremedhin A, Karanam B, Bin Salam A, Amin R, Odzorig T, Aiken T, Nguyen V, Bian Y, Zarif JC, de Groot AE, Mehta M, Fan L, Hu X, Simeonov A, Pate N, Abu-Asab M, Ferrer M, Southall N, Ock CY, Zhao Y, Lopez H, Kozlov S, de Val N, Yates CC, Baljinnyam B, Marugan J, Rudloff U. Mannose receptor (CD206) activation in tumor-associated macrophages enhances adaptive and innate antitumor immune responses. Sci Transl Med 2021; 12:12/530/eaax6337. [PMID: 32051227 DOI: 10.1126/scitranslmed.aax6337] [Citation(s) in RCA: 175] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 10/11/2019] [Indexed: 02/06/2023]
Abstract
Solid tumors elicit a detectable immune response including the infiltration of tumor-associated macrophages (TAMs). Unfortunately, this immune response is co-opted into contributing toward tumor growth instead of preventing its progression. We seek to reestablish an antitumor immune response by selectively targeting surface receptors and endogenous signaling processes of the macrophage subtypes driving cancer progression. RP-182 is a synthetic 10-mer amphipathic analog of host defense peptides that selectively induces a conformational switch of the mannose receptor CD206 expressed on TAMs displaying an M2-like phenotype. RP-182-mediated activation of this receptor in human and murine M2-like macrophages elicits a program of endocytosis, phagosome-lysosome formation, and autophagy and reprograms M2-like TAMs to an antitumor M1-like phenotype. In syngeneic and autochthonous murine cancer models, RP-182 suppressed tumor growth, extended survival, and was an effective combination partner with chemo- or immune checkpoint therapy. Antitumor activity of RP-182 was also observed in CD206high patient-derived xenotransplantation models. Mechanistically, via selective reduction of immunosuppressive M2-like TAMs, RP-182 improved adaptive and innate antitumor immune responses, including increased cancer cell phagocytosis by reprogrammed TAMs.
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Affiliation(s)
- Jesse M Jaynes
- College of Agriculture, Environment and Nutrition Sciences, Integrative Biosciences Program, Tuskegee University, Tuskegee, AL 36088, USA.,Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, AL 36088, USA
| | - Rushikesh Sable
- Rare Tumor Initiative, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael Ronzetti
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Wendy Bautista
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Zachary Knotts
- Rare Tumor Initiative, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Abisola Abisoye-Ogunniyan
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, AL 36088, USA.,Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Dandan Li
- Rare Tumor Initiative, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Raul Calvo
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Myagmarjav Dashnyam
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Anju Singh
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Theresa Guerin
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Jason White
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, AL 36088, USA
| | - Sarangan Ravichandran
- Advanced Biomedical Computing Center, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Parimal Kumar
- Sequencing Facility and Single Cell Analysis Facility, Advanced Technology Research Facility, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | - Keyur Talsania
- CCR-SF Bioinformatics Group, Advanced Biomedical and Computational Sciences, Biomedical Informatics and Data Science, Advanced Technology Research Facility, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | - Vicky Chen
- CCR-SF Bioinformatics Group, Advanced Biomedical and Computational Sciences, Biomedical Informatics and Data Science, Advanced Technology Research Facility, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | - Anghesom Ghebremedhin
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, AL 36088, USA
| | - Balasubramanyam Karanam
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, AL 36088, USA
| | - Ahmad Bin Salam
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, AL 36088, USA
| | - Ruksana Amin
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, AL 36088, USA
| | - Taivan Odzorig
- Rare Tumor Initiative, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Taylor Aiken
- Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.,Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
| | - Victoria Nguyen
- Rare Tumor Initiative, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Yansong Bian
- Rare Tumor Initiative, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jelani C Zarif
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA.,Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Amber E de Groot
- James Buchanan Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA.,Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Monika Mehta
- Sequencing Facility and Single Cell Analysis Facility, Advanced Technology Research Facility, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer Research, SAXS Core Facility, Center for Cancer Research of the National Cancer Institute, Frederick, MD 21701, USA
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Nathan Pate
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Mones Abu-Asab
- Section of Histopathology, National Eye Institute, Bethesda, MD 20892, USA
| | - Marc Ferrer
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Noel Southall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Chan-Young Ock
- Department of Hemato Oncology, Seoul National University Hospital, Seoul 03080, Korea
| | - Yongmei Zhao
- CCR-SF Bioinformatics Group, Advanced Biomedical and Computational Sciences, Biomedical Informatics and Data Science, Advanced Technology Research Facility, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | | | - Serguei Kozlov
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Natalia de Val
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA.,Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 21701, USA
| | - Clayton C Yates
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, AL 36088, USA.
| | - Bolormaa Baljinnyam
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA.
| | - Juan Marugan
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA.
| | - Udo Rudloff
- Rare Tumor Initiative, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
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21
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Rocereta J, Free R, Dulcey Garcia A, Southall N, Shi L, Lane J, Wetsel W, Marugan J, Sibley D. Optimization of ML321: a D
2
dopamine receptor‐selective antagonist for the treatment of neuropsychiatric disorders. FASEB J 2021. [DOI: 10.1096/fasebj.2021.35.s1.02466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Julia Rocereta
- Molecular Neuropharmacology SectionNational Institute of Neurological Disorders and StrokeBethesdaMD
| | - R. Free
- Molecular Neuropharmacology SectionNational Institute of Neurological Disorders and StrokeBethesdaMD
| | | | - Noel Southall
- National Center for Advancing Translational SciencesRockvilleMD
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics UnitNational Institute on Drug AbuseBaltimoreMD
| | - J. Lane
- University of NottinghamNottingham
| | - William Wetsel
- Duke University School of MedicineDuke UniversityDurhamNC
| | - Juan Marugan
- National Center for Advancing Translational SciencesRockvilleMD
| | - David Sibley
- Molecular Neuropharmacology SectionNational Institute of Neurological Disorders and StrokeBethesdaMD
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22
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Mansouri K, Karmaus AL, Fitzpatrick J, Patlewicz G, Pradeep P, Alberga D, Alepee N, Allen TE, Allen D, Alves VM, Andrade CH, Auernhammer TR, Ballabio D, Bell S, Benfenati E, Bhattacharya S, Bastos JV, Boyd S, Brown J, Capuzzi SJ, Chushak Y, Ciallella H, Clark AM, Consonni V, Daga PR, Ekins S, Farag S, Fedorov M, Fourches D, Gadaleta D, Gao F, Gearhart JM, Goh G, Goodman JM, Grisoni F, Grulke CM, Hartung T, Hirn M, Karpov P, Korotcov A, Lavado GJ, Lawless M, Li X, Luechtefeld T, Lunghini F, Mangiatordi GF, Marcou G, Marsh D, Martin T, Mauri A, Muratov EN, Myatt GJ, Nguyen DT, Nicolotti O, Note R, Pande P, Parks AK, Peryea T, Polash AH, Rallo R, Roncaglioni A, Rowlands C, Ruiz P, Russo DP, Sayed A, Sayre R, Sheils T, Siegel C, Silva AC, Simeonov A, Sosnin S, Southall N, Strickland J, Tang Y, Teppen B, Tetko IV, Thomas D, Tkachenko V, Todeschini R, Toma C, Tripodi I, Trisciuzzi D, Tropsha A, Varnek A, Vukovic K, Wang Z, Wang L, Waters KM, Wedlake AJ, Wijeyesakere SJ, Wilson D, Xiao Z, Yang H, Zahoranszky-Kohalmi G, Zakharov AV, Zhang FF, Zhang Z, Zhao T, Zhu H, Zorn KM, Casey W, Kleinstreuer NC. CATMoS: Collaborative Acute Toxicity Modeling Suite. Environ Health Perspect 2021; 129:47013. [PMID: 33929906 PMCID: PMC8086800 DOI: 10.1289/ehp8495] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
BACKGROUND Humans are exposed to tens of thousands of chemical substances that need to be assessed for their potential toxicity. Acute systemic toxicity testing serves as the basis for regulatory hazard classification, labeling, and risk management. However, it is cost- and time-prohibitive to evaluate all new and existing chemicals using traditional rodent acute toxicity tests. In silico models built using existing data facilitate rapid acute toxicity predictions without using animals. OBJECTIVES The U.S. Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM) Acute Toxicity Workgroup organized an international collaboration to develop in silico models for predicting acute oral toxicity based on five different end points: Lethal Dose 50 (LD50 value, U.S. Environmental Protection Agency hazard (four) categories, Globally Harmonized System for Classification and Labeling hazard (five) categories, very toxic chemicals [LD50 (LD50≤50mg/kg)], and nontoxic chemicals (LD50>2,000mg/kg). METHODS An acute oral toxicity data inventory for 11,992 chemicals was compiled, split into training and evaluation sets, and made available to 35 participating international research groups that submitted a total of 139 predictive models. Predictions that fell within the applicability domains of the submitted models were evaluated using external validation sets. These were then combined into consensus models to leverage strengths of individual approaches. RESULTS The resulting consensus predictions, which leverage the collective strengths of each individual model, form the Collaborative Acute Toxicity Modeling Suite (CATMoS). CATMoS demonstrated high performance in terms of accuracy and robustness when compared with in vivo results. DISCUSSION CATMoS is being evaluated by regulatory agencies for its utility and applicability as a potential replacement for in vivo rat acute oral toxicity studies. CATMoS predictions for more than 800,000 chemicals have been made available via the National Toxicology Program's Integrated Chemical Environment tools and data sets (ice.ntp.niehs.nih.gov). The models are also implemented in a free, standalone, open-source tool, OPERA, which allows predictions of new and untested chemicals to be made. https://doi.org/10.1289/EHP8495.
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Affiliation(s)
- Kamel Mansouri
- Integrated Laboratory Systems, LLC, Morrisville, North Carolina, USA
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, Research Triangle Park, North Carolina, USA
| | - Agnes L. Karmaus
- Integrated Laboratory Systems, LLC, Morrisville, North Carolina, USA
| | | | - Grace Patlewicz
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Prachi Pradeep
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
- Oak Ridge Institute for Science and Education (ORISE) Research Participation Program, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Domenico Alberga
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
| | | | - Timothy E.H. Allen
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Dave Allen
- Integrated Laboratory Systems, LLC, Morrisville, North Carolina, USA
| | - Vinicius M. Alves
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
- Laboratory for Molecular Modeling and Design, Faculty of Pharmacy, Federal University of Goiás, Goiania, Brazil
| | - Carolina H. Andrade
- Laboratory for Molecular Modeling and Design, Faculty of Pharmacy, Federal University of Goiás, Goiania, Brazil
| | | | - Davide Ballabio
- Milano Chemometrics & QSAR Research Group, Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Shannon Bell
- Integrated Laboratory Systems, LLC, Morrisville, North Carolina, USA
| | - Emilio Benfenati
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Sudin Bhattacharya
- Institute for Quantitative Health Science and Engineering, Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan, USA
| | - Joyce V. Bastos
- Laboratory for Molecular Modeling and Design, Faculty of Pharmacy, Federal University of Goiás, Goiania, Brazil
| | - Stephen Boyd
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - J.B. Brown
- Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Stephen J. Capuzzi
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Yaroslav Chushak
- Aeromedical Research Department, Force Health Protection, USAFSAM, Dayton, Ohio, USA
- Henry M Jackson Foundation for the Advancement of Military Medicine, Dayton, Ohio, USA
| | - Heather Ciallella
- Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey, USA
| | - Alex M. Clark
- Collaborations Pharmaceuticals, Inc., Raleigh, North Carolina, USA
| | - Viviana Consonni
- Milano Chemometrics & QSAR Research Group, Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | | | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., Raleigh, North Carolina, USA
| | - Sherif Farag
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Maxim Fedorov
- Skoltech, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Denis Fourches
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | - Domenico Gadaleta
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Feng Gao
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Jeffery M. Gearhart
- Aeromedical Research Department, Force Health Protection, USAFSAM, Dayton, Ohio, USA
- Henry M Jackson Foundation for the Advancement of Military Medicine, Dayton, Ohio, USA
| | - Garett Goh
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jonathan M. Goodman
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Francesca Grisoni
- Milano Chemometrics & QSAR Research Group, Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Christopher M. Grulke
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | | | - Matthew Hirn
- Department of Computational Mathematics, Science & Engineering, Department of Mathematics, Michigan State University, East Lansing, Michigan, USA
| | - Pavel Karpov
- Institute of Structural Biology, Helmholtz Zentrum München (GmbH), Neuherberg, Germany
| | | | - Giovanna J. Lavado
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | | | - Xinhao Li
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA
| | | | - Filippo Lunghini
- Laboratoire de Chemoinformatique, URM7140, Université de Strasbourg, Strasbourg, France
| | - Giuseppe F. Mangiatordi
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
| | - Gilles Marcou
- Laboratoire de Chemoinformatique, URM7140, Université de Strasbourg, Strasbourg, France
| | - Dan Marsh
- Underwriters Laboratories, Northbrook, Illinois, USA
| | - Todd Martin
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Cincinnati, Ohio, USA
| | | | - Eugene N. Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
- Laboratory for Molecular Modeling and Design, Faculty of Pharmacy, Federal University of Goiás, Goiania, Brazil
| | | | - Dac-Trung Nguyen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Orazio Nicolotti
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
| | - Reine Note
- L’Oréal Research & Innovation, Aulnay-sous-Bois, France
| | - Paritosh Pande
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | | | - Tyler Peryea
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | | | - Robert Rallo
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Alessandra Roncaglioni
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | | | - Patricia Ruiz
- Office of Innovation and Analytics, Agency for Toxic Substances and Disease Registry, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Daniel P. Russo
- Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey, USA
| | - Ahmed Sayed
- Rosettastein Consulting UG, Freising, Germany
| | - Risa Sayre
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
- Oak Ridge Institute for Science and Education (ORISE) Research Participation Program, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Timothy Sheils
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Charles Siegel
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Arthur C. Silva
- Laboratory for Molecular Modeling and Design, Faculty of Pharmacy, Federal University of Goiás, Goiania, Brazil
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Sergey Sosnin
- Skoltech, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Noel Southall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Judy Strickland
- Integrated Laboratory Systems, LLC, Morrisville, North Carolina, USA
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Brian Teppen
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Igor V. Tetko
- Institute of Structural Biology, Helmholtz Zentrum München (GmbH), Neuherberg, Germany
- BIGCHEM GmbH, Unterschleissheim, Germany
| | - Dennis Thomas
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | | | - Roberto Todeschini
- Milano Chemometrics & QSAR Research Group, Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Cosimo Toma
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Ignacio Tripodi
- Computer Science/Interdisciplinary Quantitative Biology, University of Colorado, Boulder, Colorado, USA
| | - Daniela Trisciuzzi
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Alexandre Varnek
- Laboratoire de Chemoinformatique, URM7140, Université de Strasbourg, Strasbourg, France
| | - Kristijan Vukovic
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Zhongyu Wang
- School of Environmental Sciences and Technology, Dalian University of Technology; Dalian, Liaoning, China
| | - Liguo Wang
- School of Environmental Sciences and Technology, Dalian University of Technology; Dalian, Liaoning, China
| | | | - Andrew J. Wedlake
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | - Dan Wilson
- The Dow Chemical Company, Midland, Michigan, USA
| | - Zijun Xiao
- School of Environmental Sciences and Technology, Dalian University of Technology; Dalian, Liaoning, China
| | - Hongbin Yang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Gergely Zahoranszky-Kohalmi
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Alexey V. Zakharov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | | | - Zhen Zhang
- Dow Agrosciences, Indianapolis, Indiana, USA
| | - Tongan Zhao
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Hao Zhu
- Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey, USA
| | | | - Warren Casey
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, Research Triangle Park, North Carolina, USA
| | - Nicole C. Kleinstreuer
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, Research Triangle Park, North Carolina, USA
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Peryea T, Southall N, Miller M, Katzel D, Anderson N, Neyra J, Stemann S, Nguyễn ÐT, Amugoda D, Newatia A, Ghazzaoui R, Johanson E, Diederik H, Callahan L, Switzer F. Global Substance Registration System: consistent scientific descriptions for substances related to health. Nucleic Acids Res 2021; 49:D1179-D1185. [PMID: 33137173 DOI: 10.1093/nar/gkaa962] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 12/18/2022] Open
Abstract
The US Food and Drug Administration (FDA) and the National Center for Advancing Translational Sciences (NCATS) have collaborated to publish rigorous scientific descriptions of substances relevant to regulated products. The FDA has adopted the global ISO 11238 data standard for the identification of substances in medicinal products and has populated a database to organize the agency's regulatory submissions and marketed products data. NCATS has worked with FDA to develop the Global Substance Registration System (GSRS) and produce a non-proprietary version of the database for public benefit. In 2019, more than half of all new drugs in clinical development were proteins, nucleic acid therapeutics, polymer products, structurally diverse natural products or cellular therapies. While multiple databases of small molecule chemical structures are available, this resource is unique in its application of regulatory standards for the identification of medicinal substances and its robust support for other substances in addition to small molecules. This public, manually curated dataset provides unique ingredient identifiers (UNIIs) and detailed descriptions for over 100 000 substances that are particularly relevant to medicine and translational research. The dataset can be accessed and queried at https://gsrs.ncats.nih.gov/app/substances.
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Affiliation(s)
- Tyler Peryea
- Office of the Commissioner, US Food and Drug Administration, Silver Spring, MD 20993, USA.,Informatics, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Noel Southall
- Informatics, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mitch Miller
- Informatics, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel Katzel
- Informatics, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Niko Anderson
- Informatics, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jorge Neyra
- Informatics, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sarah Stemann
- Informatics, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ðắc-Trung Nguyễn
- Informatics, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dammika Amugoda
- Informatics, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Archana Newatia
- Office of the Commissioner, US Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Ramez Ghazzaoui
- Office of the Commissioner, US Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Elaine Johanson
- Office of the Commissioner, US Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Herman Diederik
- College ter Beoordeling van Geneesmiddelen, 3531 AH Utrecht, Netherlands
| | - Larry Callahan
- Office of the Commissioner, US Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Frank Switzer
- Office of the Commissioner, US Food and Drug Administration, Silver Spring, MD 20993, USA
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24
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Sheils TK, Mathias SL, Kelleher KJ, Siramshetty VB, Nguyen DT, Bologa CG, Jensen LJ, Vidović D, Koleti A, Schürer SC, Waller A, Yang JJ, Holmes J, Bocci G, Southall N, Dharkar P, Mathé E, Simeonov A, Oprea TI. TCRD and Pharos 2021: mining the human proteome for disease biology. Nucleic Acids Res 2021; 49:D1334-D1346. [PMID: 33156327 PMCID: PMC7778974 DOI: 10.1093/nar/gkaa993] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/09/2020] [Accepted: 10/14/2020] [Indexed: 12/13/2022] Open
Abstract
In 2014, the National Institutes of Health (NIH) initiated the Illuminating the Druggable Genome (IDG) program to identify and improve our understanding of poorly characterized proteins that can potentially be modulated using small molecules or biologics. Two resources produced from these efforts are: The Target Central Resource Database (TCRD) (http://juniper.health.unm.edu/tcrd/) and Pharos (https://pharos.nih.gov/), a web interface to browse the TCRD. The ultimate goal of these resources is to highlight and facilitate research into currently understudied proteins, by aggregating a multitude of data sources, and ranking targets based on the amount of data available, and presenting data in machine learning ready format. Since the 2017 release, both TCRD and Pharos have produced two major releases, which have incorporated or expanded an additional 25 data sources. Recently incorporated data types include human and viral-human protein-protein interactions, protein-disease and protein-phenotype associations, and drug-induced gene signatures, among others. These aggregated data have enabled us to generate new visualizations and content sections in Pharos, in order to empower users to find new areas of study in the druggable genome.
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Affiliation(s)
- Timothy K Sheils
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Stephen L Mathias
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Keith J Kelleher
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Vishal B Siramshetty
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Dac-Trung Nguyen
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Cristian G Bologa
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Dušica Vidović
- Institute for Data Science and Computing, University of Miami, Coral Gables, FL 33146, USA
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Amar Koleti
- Institute for Data Science and Computing, University of Miami, Coral Gables, FL 33146, USA
| | - Stephan C Schürer
- Institute for Data Science and Computing, University of Miami, Coral Gables, FL 33146, USA
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Anna Waller
- UNM Center for Molecular Discovery, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Jeremy J Yang
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Jayme Holmes
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Giovanni Bocci
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Noel Southall
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Poorva Dharkar
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Ewy Mathé
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Anton Simeonov
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Tudor I Oprea
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- UNM Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, 40530 Gothenburg, Sweden
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25
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Duggal M, Stone H, Paul P, Charles R, Sacks L, Southall N. 546. Capturing Clinician’s Experiences Repurposing Drugs to Inform Future Studies During COVID-19. Open Forum Infect Dis 2020. [PMCID: PMC7777160 DOI: 10.1093/ofid/ofaa439.740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
CURE ID is an internet-based repository developed collaboratively by FDA and NCATS/NIH, with the support of WHO and IDSA. It encourages clinicians globally to share novel uses of existing drugs for patients with difficult-to-treat infections. It is designed to serve as a rapid communication platform for healthcare providers during an outbreak, providing for systematic case-sharing, discussion, and the latest literature. Besides case reports, CURE ID offers a discussion platform for clinicians, disease-specific clinical trials curated from clincialtrials.gov, and a newsfeed that shows relevant journal articles and news related to COVID-19 and other infectious diseases.
Methods
The CURE ID team extracted individual case reports on patient-level treatments and outcomes of COVID-19 infection from the published literature and gathered clinician-submitted cases through the electronic case report form. Additionally, CURE ID partnered with the University of Pennsylvania’s CORONA database to further populate the CURE ID database with published cases.
Results
As of submission, lopinavir-Ritonavir (n=51) was the most commonly reported drug used. The following were also reported: hydroxychloroquine (n=31), azithromycin (n=28), arbidol (n=22), interferon alfa-2B (n=18), moxifloxacin (n=18), methylprednisolone (n=17), ivermectin (n=14), lopinavir (n=12), oseltamivir (n=12). The other drugs reported were danoprevir-ritonavir, intravenous immunoglobulins, interferon, interferon alfa, and tocilizumab. CURE ID currently includes more than 150 detailed COVID case reports of 65 repurposed drugs. We expect case reporting for specific drugs to be dynamic and additional data to accrue. Updated results will be presented.
Conclusion
Several drugs are being repurposed to treat COVID-19. CURE ID gives clinicians an opportunity to share their treatment experiences and discuss their questions with a global community of healthcare providers. By utilizing the CURE ID platform, in conjunction with data gathered from other registries, observational studies and clinical trials, hypotheses can be generated that may inform future clinical trials and ultimately, potentially find safe and effective treatments for this deadly disease.
Disclosures
All Authors: No reported disclosures
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26
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Ma CD, Imamura M, Talley DC, Rolt A, Xu X, Wang AQ, Le D, Uchida T, Osawa M, Teraoka Y, Li K, Hu X, Park SB, Chalasani N, Irvin PH, Dulcey AE, Southall N, Marugan JJ, Hu Z, Chayama K, Frankowski KJ, Liang TJ. Fluoxazolevir inhibits hepatitis C virus infection in humanized chimeric mice by blocking viral membrane fusion. Nat Microbiol 2020; 5:1532-1541. [PMID: 32868923 PMCID: PMC7677215 DOI: 10.1038/s41564-020-0781-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 07/27/2020] [Indexed: 12/16/2022]
Abstract
Fluoxazolevir is an aryloxazole-based entry inhibitor of hepatitis C virus (HCV). We show that fluoxazolevir inhibits fusion of HCV with hepatic cells by binding HCV envelope protein 1 to prevent fusion. Nine of ten fluoxazolevir resistance-associated substitutions are in envelope protein 1, and four are in a putative fusion peptide. Pharmacokinetic studies in mice, rats and dogs revealed that fluoxazolevir localizes to the liver. A 4-week intraperitoneal regimen of fluoxazolevir in humanized chimeric mice infected with HCV genotypes 1b, 2a or 3 resulted in a 2-log reduction in viraemia, without evidence of drug resistance. In comparison, daclatasvir, an approved HCV drug, suppressed more than 3 log of viraemia but is associated with the emergence of resistance-associated substitutions in mice. Combination therapy using fluoxazolevir and daclatasvir cleared HCV genotypes 1b and 3 in mice. Fluoxazolevir combined with glecaprevir and pibrentasvir was also effective in clearing multidrug-resistant HCV replication in mice. Fluoxazolevir may be promising as the next generation of combination drug cocktails for HCV treatment.
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Affiliation(s)
- Christopher D Ma
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michio Imamura
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical & Health Science, Hiroshima University, Hiroshima, Japan
| | - Daniel C Talley
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Adam Rolt
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Xin Xu
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Amy Q Wang
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Derek Le
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Takuro Uchida
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical & Health Science, Hiroshima University, Hiroshima, Japan
| | - Mitsutaka Osawa
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical & Health Science, Hiroshima University, Hiroshima, Japan
| | - Yuji Teraoka
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical & Health Science, Hiroshima University, Hiroshima, Japan
| | - Kelin Li
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Xin Hu
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Seung Bum Park
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Nishanth Chalasani
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Parker H Irvin
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andres E Dulcey
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Noel Southall
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Juan J Marugan
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Zongyi Hu
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kazuaki Chayama
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical & Health Science, Hiroshima University, Hiroshima, Japan
| | - Kevin J Frankowski
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Tsanyang Jake Liang
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
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27
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Siramshetty VB, Shah P, Kerns E, Nguyen K, Yu KR, Kabir M, Williams J, Neyra J, Southall N, Nguyễn ÐT, Xu X. Retrospective assessment of rat liver microsomal stability at NCATS: data and QSAR models. Sci Rep 2020; 10:20713. [PMID: 33244000 PMCID: PMC7693334 DOI: 10.1038/s41598-020-77327-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/04/2020] [Indexed: 11/09/2022] Open
Abstract
Hepatic metabolic stability is a key pharmacokinetic parameter in drug discovery. Metabolic stability is usually assessed in microsomal fractions and only the best compounds progress in the drug discovery process. A high-throughput single time point substrate depletion assay in rat liver microsomes (RLM) is employed at the National Center for Advancing Translational Sciences. Between 2012 and 2020, RLM stability data was generated for ~ 24,000 compounds from more than 250 projects that cover a wide range of pharmacological targets and cellular pathways. Although a crucial endpoint, little or no data exists in the public domain. In this study, computational models were developed for predicting RLM stability using different machine learning methods. In addition, a retrospective time-split validation was performed, and local models were built for projects that performed poorly with global models. Further analysis revealed inherent medicinal chemistry knowledge potentially useful to chemists in the pursuit of synthesizing metabolically stable compounds. In addition, we deposited experimental data for ~ 2500 compounds in the PubChem bioassay database (AID: 1508591). The global prediction models are made publicly accessible ( https://opendata.ncats.nih.gov/adme ). This is to the best of our knowledge, the first publicly available RLM prediction model built using high-quality data generated at a single laboratory.
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Affiliation(s)
- Vishal B Siramshetty
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Pranav Shah
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Edward Kerns
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Kimloan Nguyen
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD, 20850, USA.,NY State Public Health, DOHMH 42-09 28th St, Long Island City, NY, 11101, USA
| | - Kyeong Ri Yu
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD, 20850, USA.,School of Medicine, Virginia Commonwealth University, 1201 E Marshall St, Richmond, VA, 23298, USA
| | - Md Kabir
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD, 20850, USA.,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, 10029, USA
| | - Jordan Williams
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Jorge Neyra
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Noel Southall
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Ðắc-Trung Nguyễn
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Xin Xu
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD, 20850, USA.
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28
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Zhu Q, Nguyen DT, Grishagin I, Southall N, Sid E, Pariser A. An integrative knowledge graph for rare diseases, derived from the Genetic and Rare Diseases Information Center (GARD). J Biomed Semantics 2020; 11:13. [PMID: 33183351 PMCID: PMC7663894 DOI: 10.1186/s13326-020-00232-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/05/2020] [Indexed: 01/16/2023] Open
Abstract
Background The Genetic and Rare Diseases (GARD) Information Center was established by the National Institutes of Health (NIH) to provide freely accessible consumer health information on over 6500 genetic and rare diseases. As the cumulative scientific understanding and underlying evidence for these diseases have expanded over time, existing practices to generate knowledge from these publications and resources have not been able to keep pace. Through determining the applicability of computational approaches to enhance or replace manual curation tasks, we aim to both improve the sustainability and relevance of consumer health information, but also to develop a foundational database, from which translational science researchers may start to unravel disease characteristics that are vital to the research process. Results We developed a meta-ontology based integrative knowledge graph for rare diseases in Neo4j. This integrative knowledge graph includes a total of 3,819,623 nodes and 84,223,681 relations from 34 different biomedical data resources, including curated drug and rare disease associations. Semi-automatic mappings were generated for 2154 unique FDA orphan designations to 776 unique GARD diseases, and 3322 unique FDA designated drugs to UNII, as well as 180,363 associations between drug and indication from Inxight Drugs, which were integrated into the knowledge graph. We conducted four case studies to demonstrate the capabilities of this integrative knowledge graph in accelerating the curation of scientific understanding on rare diseases through the generation of disease mappings/profiles and pathogenesis associations. Conclusions By integrating well-established database resources, we developed an integrative knowledge graph containing a large volume of biomedical and research data. Demonstration of several immediate use cases and limitations of this process reveal both the potential feasibility and barriers of utilizing graph-based resources and approaches to support their use by providers of consumer health information, such as GARD, that may struggle with the needs of maintaining knowledge reliant on an evolving and growing evidence-base. Finally, the successful integration of these datasets into a freely accessible knowledge graph highlights an opportunity to take a translational science view on the field of rare diseases by enabling researchers to identify disease characteristics, which may play a role in the translation of discover across different research domains.
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Affiliation(s)
- Qian Zhu
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, 20850, USA.
| | - Dac-Trung Nguyen
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, 20850, USA
| | - Ivan Grishagin
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, 20850, USA
| | - Noel Southall
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, 20850, USA
| | - Eric Sid
- Office of Rare Disease Research, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Anne Pariser
- Office of Rare Disease Research, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
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29
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Hu Z, Rolt A, Hu X, Ma CD, Le DJ, Park SB, Houghton M, Southall N, Anderson DE, Talley DC, Lloyd JR, Marugan JC, Liang TJ. Chlorcyclizine Inhibits Viral Fusion of Hepatitis C Virus Entry by Directly Targeting HCV Envelope Glycoprotein 1. Cell Chem Biol 2020; 27:780-792.e5. [PMID: 32386595 PMCID: PMC7368827 DOI: 10.1016/j.chembiol.2020.04.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/04/2020] [Accepted: 04/13/2020] [Indexed: 12/22/2022]
Abstract
Chlorcyclizine (CCZ) is a potent hepatitis C virus (HCV) entry inhibitor, but its molecular mechanism is unknown. Here, we show that CCZ directly targets the fusion peptide of HCV E1 and interferes with the fusion process. Generation of CCZ resistance-associated substitutions of HCV in vitro revealed six missense mutations in the HCV E1 protein, five being in the putative fusion peptide. A viral fusion assay demonstrated that CCZ blocked HCV entry at the membrane fusion step and that the mutant viruses acquired resistance to CCZ's action in blocking membrane fusion. UV cross-linking of photoactivatable CCZ-diazirine-biotin in both HCV-infected cells and recombinant HCV E1/E2 protein demonstrated direct binding to HCV E1 glycoprotein. Mass spectrometry analysis revealed that CCZ cross-linked to an E1 sequence adjacent to the putative fusion peptide. Docking simulations demonstrate a putative binding model, wherein CCZ binds to a hydrophobic pocket of HCV E1 and forms extensive interactions with the fusion peptide.
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Affiliation(s)
- Zongyi Hu
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Adam Rolt
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Xin Hu
- Division of Pre-Clinical Innovations, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Christopher D Ma
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Derek J Le
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Seung Bum Park
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Michael Houghton
- Li Ka Shing Virology Institute, University of Alberta, Edmonton, Canada
| | - Noel Southall
- Division of Pre-Clinical Innovations, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - D Eric Anderson
- Advanced Mass Spectrometry Facility, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Daniel C Talley
- Division of Pre-Clinical Innovations, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - John R Lloyd
- Advanced Mass Spectrometry Facility, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Juan C Marugan
- Division of Pre-Clinical Innovations, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - T Jake Liang
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA.
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30
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Moritz AE, Free RB, Weiner WS, Akano EO, Gandhi D, Abramyan A, Keck TM, Ferrer M, Hu X, Southall N, Steiner J, Aubé J, Shi L, Frankowski KJ, Sibley DR. Discovery, Optimization, and Characterization of ML417: A Novel and Highly Selective D 3 Dopamine Receptor Agonist. J Med Chem 2020; 63:5526-5567. [PMID: 32342685 DOI: 10.1021/acs.jmedchem.0c00424] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
To identify novel D3 dopamine receptor (D3R) agonists, we conducted a high-throughput screen using a β-arrestin recruitment assay. Counterscreening of the hit compounds provided an assessment of their selectivity, efficacy, and potency. The most promising scaffold was optimized through medicinal chemistry resulting in enhanced potency and selectivity. The optimized compound, ML417 (20), potently promotes D3R-mediated β-arrestin translocation, G protein activation, and ERK1/2 phosphorylation (pERK) while lacking activity at other dopamine receptors. Screening of ML417 against multiple G protein-coupled receptors revealed exceptional global selectivity. Molecular modeling suggests that ML417 interacts with the D3R in a unique manner, possibly explaining its remarkable selectivity. ML417 was also found to protect against neurodegeneration of dopaminergic neurons derived from iPSCs. Together with promising pharmacokinetics and toxicology profiles, these results suggest that ML417 is a novel and uniquely selective D3R agonist that may serve as both a research tool and a therapeutic lead for the treatment of neuropsychiatric disorders.
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Affiliation(s)
- Amy E Moritz
- Molecular Neuropharmacology Section, National Institute of Neurological Disorders and Stroke, Intramural Research Program, National Institutes of Health, 35 Convent Drive, MSC-3723, Bethesda, Maryland 20892-3723, United States
| | - R Benjamin Free
- Molecular Neuropharmacology Section, National Institute of Neurological Disorders and Stroke, Intramural Research Program, National Institutes of Health, 35 Convent Drive, MSC-3723, Bethesda, Maryland 20892-3723, United States
| | - Warren S Weiner
- University of Kansas Specialized Chemistry Center, University of Kansas, Lawrence, Kansas 66047, United States
| | - Emmanuel O Akano
- Molecular Neuropharmacology Section, National Institute of Neurological Disorders and Stroke, Intramural Research Program, National Institutes of Health, 35 Convent Drive, MSC-3723, Bethesda, Maryland 20892-3723, United States
| | - Disha Gandhi
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, 125 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
| | - Ara Abramyan
- Computational Chemistry and Molecular Biophysics Unit, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Baltimore, Maryland, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Thomas M Keck
- Department of Chemistry & Biochemistry, Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
| | - Marc Ferrer
- NIH Chemical Genomics Center, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Xin Hu
- NIH Chemical Genomics Center, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Noel Southall
- NIH Chemical Genomics Center, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Joseph Steiner
- NeuroTherapeutics Development Unit, National Institute for Neurological Disorders and Stroke, Intramural Research Program, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Jeffrey Aubé
- University of Kansas Specialized Chemistry Center, University of Kansas, Lawrence, Kansas 66047, United States.,Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, 125 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Unit, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Baltimore, Maryland, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Kevin J Frankowski
- University of Kansas Specialized Chemistry Center, University of Kansas, Lawrence, Kansas 66047, United States.,Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, 125 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
| | - David R Sibley
- Molecular Neuropharmacology Section, National Institute of Neurological Disorders and Stroke, Intramural Research Program, National Institutes of Health, 35 Convent Drive, MSC-3723, Bethesda, Maryland 20892-3723, United States
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31
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Kapoor A, Ghosh AK, Forman M, Hu X, Ye W, Southall N, Marugan J, Keyes RF, Smith BC, Meyers DJ, Ferrer M, Arav-Boger R. Validation and Characterization of Five Distinct Novel Inhibitors of Human Cytomegalovirus. J Med Chem 2020; 63:3896-3907. [PMID: 32191456 PMCID: PMC7386824 DOI: 10.1021/acs.jmedchem.9b01501] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The critical consequences of human cytomegalovirus (HCMV) infection in the transplant population and in congenitally infected infants, the limited treatment options for HCMV, and the rise of resistant mutants toward existing therapies has fueled the search for new anti-HCMV agents. A pp28-luciferase recombinant HCMV was used as a reporter system for high-throughput screening of HCMV inhibitors. Approximately 400 000 compounds from existing libraries were screened. Subsequent validation assays using resynthesized compounds, several virus strains, and detailed virology assays resulted in the identification of five structurally unique and selective HCMV inhibitors, active at sub to low micromolar concentrations. Further characterization revealed that each compound inhibited a specific stage of HCMV replication. One compound was also active against herpes simplex virus (HSV1 and HSV2), and another compound was active against Epstein-Barr virus (EBV). Drug combination studies revealed that all five compounds were additive with ganciclovir or letermovir. Future studies will focus on optimization of these new anti-HCMV compounds along with mechanistic studies.
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Affiliation(s)
- Arun Kapoor
- Department of Pediatrics, Division of Infectious Disease, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ayan K. Ghosh
- Department of Pediatrics, Division of Infectious Disease, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Michael Forman
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Xin Hu
- National Center for Advancing Translational Sciences (NCATS), National Institute of Health, Bethesda, MD 20850, USA
| | - Wenjuan Ye
- National Center for Advancing Translational Sciences (NCATS), National Institute of Health, Bethesda, MD 20850, USA
| | - Noel Southall
- National Center for Advancing Translational Sciences (NCATS), National Institute of Health, Bethesda, MD 20850, USA
| | - Juan Marugan
- National Center for Advancing Translational Sciences (NCATS), National Institute of Health, Bethesda, MD 20850, USA
| | - Robert F. Keyes
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Brian C. Smith
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - David J. Meyers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Marc Ferrer
- National Center for Advancing Translational Sciences (NCATS), National Institute of Health, Bethesda, MD 20850, USA
| | - Ravit Arav-Boger
- Department of Pediatrics, Division of Infectious Disease, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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32
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Rocereta J, Free RB, Garcia AD, Southall N, Shi L, Lane R, Wetsel W, Marugan JJ, Sibley DR. Optimization of a novel D
2
dopamine receptor antagonist with unprecedented selectivity as a therapeutic to treat psychosis and other neuropsychiatric disorders. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.04066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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33
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Fontelonga TM, Jordan B, Nunes AM, Barraza-Flores P, Bolden N, Wuebbles RD, Griner LM, Hu X, Ferrer M, Marugan J, Southall N, Burkin DJ. Sunitinib promotes myogenic regeneration and mitigates disease progression in the mdx mouse model of Duchenne muscular dystrophy. Hum Mol Genet 2020; 28:2120-2132. [PMID: 30806670 DOI: 10.1093/hmg/ddz044] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/28/2019] [Accepted: 02/18/2019] [Indexed: 02/07/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a lethal, muscle degenerative disease causing premature death of affected children. DMD is characterized by mutations in the dystrophin gene that result in a loss of the dystrophin protein. Loss of dystrophin causes an associated reduction in proteins of the dystrophin glycoprotein complex, leading to contraction-induced sarcolemmal weakening, muscle tearing, fibrotic infiltration and rounds of degeneration and failed regeneration affecting satellite cell populations. The α7β1 integrin has been implicated in increasing myogenic capacity of satellite cells, therefore restoring muscle viability, increasing muscle force and preserving muscle function in dystrophic mouse models. In this study, we show that a Food and Drug Administration (FDA)-approved small molecule, Sunitinib, is a potent α7 integrin enhancer capable of promoting myogenic regeneration by stimulating satellite cell activation and increasing myofiber fusion. Sunitinib exerts its regenerative effects via transient inhibition of SHP-2 and subsequent activation of the STAT3 pathway. Treatment of mdx mice with Sunitinib demonstrated decreased membrane leakiness and damage owing to myofiber regeneration and enhanced support at the extracellular matrix. The decreased myofiber damage translated into a significant increase in muscle force production. This study identifies an already FDA-approved compound, Sunitinib, as a possible DMD therapeutic with the potential to treat other muscular dystrophies in which there is defective muscle repair.
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Affiliation(s)
- Tatiana M Fontelonga
- Department of Pharmacology, University of Nevada, Reno School of Medicine, , Reno, NV, USA
| | - Brennan Jordan
- Department of Pharmacology, University of Nevada, Reno School of Medicine, , Reno, NV, USA
| | - Andreia M Nunes
- Department of Pharmacology, University of Nevada, Reno School of Medicine, , Reno, NV, USA
| | - Pamela Barraza-Flores
- Department of Pharmacology, University of Nevada, Reno School of Medicine, , Reno, NV, USA
| | - Nicholas Bolden
- Department of Pharmacology, University of Nevada, Reno School of Medicine, , Reno, NV, USA
| | - Ryan D Wuebbles
- Department of Pharmacology, University of Nevada, Reno School of Medicine, , Reno, NV, USA
| | - Lesley Mathews Griner
- Division of Pre-clinical Innovation, NIH Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Xin Hu
- Division of Pre-clinical Innovation, NIH Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Marc Ferrer
- Division of Pre-clinical Innovation, NIH Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Juan Marugan
- Division of Pre-clinical Innovation, NIH Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Noel Southall
- Division of Pre-clinical Innovation, NIH Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Dean J Burkin
- Department of Pharmacology, University of Nevada, Reno School of Medicine, , Reno, NV, USA
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34
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Ellis CR, Racz R, Kruhlak NL, Kim MT, Zakharov AV, Southall N, Hawkins EG, Burkhart K, Strauss DG, Stavitskaya L. Evaluating kratom alkaloids using PHASE. PLoS One 2020; 15:e0229646. [PMID: 32126112 PMCID: PMC7053747 DOI: 10.1371/journal.pone.0229646] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 02/11/2020] [Indexed: 01/01/2023] Open
Abstract
Kratom is a botanical substance that is marketed and promoted in the US for pharmaceutical opioid indications despite having no US Food and Drug Administration approved uses. Kratom contains over forty alkaloids including two partial agonists at the mu opioid receptor, mitragynine and 7-hydroxymitragynine, that have been subjected to the FDA's scientific and medical evaluation. However, pharmacological and toxicological data for the remaining alkaloids are limited. Therefore, we applied the Public Health Assessment via Structural Evaluation (PHASE) protocol to generate in silico binding profiles for 25 kratom alkaloids to facilitate the risk evaluation of kratom. PHASE demonstrates that kratom alkaloids share structural features with controlled opioids, indicates that several alkaloids bind to the opioid, adrenergic, and serotonin receptors, and suggests that mitragynine and 7-hydroxymitragynine are the strongest binders at the mu opioid receptor. Subsequently, the in silico binding profiles of a subset of the alkaloids were experimentally verified at the opioid, adrenergic, and serotonin receptors using radioligand binding assays. The verified binding profiles demonstrate the ability of PHASE to identify potential safety signals and provide a tool for prioritizing experimental evaluation of high-risk compounds.
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MESH Headings
- Animals
- Binding Sites
- HEK293 Cells
- Humans
- In Vitro Techniques
- Mitragyna/chemistry
- Molecular Docking Simulation
- Plants, Medicinal/chemistry
- Radioligand Assay
- Receptors, Adrenergic/drug effects
- Receptors, Adrenergic/metabolism
- Receptors, Opioid/drug effects
- Receptors, Opioid/metabolism
- Receptors, Opioid, mu/drug effects
- Receptors, Opioid, mu/metabolism
- Receptors, Serotonin/drug effects
- Receptors, Serotonin/metabolism
- Secologanin Tryptamine Alkaloids/chemistry
- Secologanin Tryptamine Alkaloids/pharmacokinetics
- Secologanin Tryptamine Alkaloids/pharmacology
- Structure-Activity Relationship
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Affiliation(s)
- Christopher R. Ellis
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Rebecca Racz
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Naomi L. Kruhlak
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Marlene T. Kim
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Alexey V. Zakharov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Noel Southall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Edward G. Hawkins
- Controlled Substances Staff, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Keith Burkhart
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - David G. Strauss
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Lidiya Stavitskaya
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
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Singh A, Dashnyam M, Chim B, Escobar TM, Dulcey AE, Hu X, Wilson KM, Koganti PP, Spinner CA, Xu X, Jadhav A, Southall N, Marugan J, Selvaraj V, Lazarevic V, Muljo SA, Ferrer M. Anxiolytic Drug FGIN-1-27 Ameliorates Autoimmunity by Metabolic Reprogramming of Pathogenic Th17 Cells. Sci Rep 2020; 10:3766. [PMID: 32111885 PMCID: PMC7048748 DOI: 10.1038/s41598-020-60610-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 02/11/2020] [Indexed: 01/10/2023] Open
Abstract
Th17 cells are critical drivers of autoimmune diseases and immunopathology. There is an unmet need to develop therapies targeting pathogenic Th17 cells for the treatment of autoimmune disorders. Here, we report that anxiolytic FGIN-1-27 inhibits differentiation and pathogenicity of Th17 cells in vitro and in vivo using the experimental autoimmune encephalomyelitis (EAE) model of Th17 cell-driven pathology. Remarkably, we found that the effects of FGIN-1-27 were independent of translocator protein (TSPO), the reported target for this small molecule, and instead were driven by a metabolic switch in Th17 cells that led to the induction of the amino acid starvation response and altered cellular fatty acid composition. Our findings suggest that the small molecule FGIN-1-27 can be re-purposed to relieve autoimmunity by metabolic reprogramming of pathogenic Th17 cells.
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Affiliation(s)
- Anju Singh
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Rockville, MD, USA
| | - Myagmarjav Dashnyam
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Rockville, MD, USA
| | - Bryan Chim
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Thelma M Escobar
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Andrés E Dulcey
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Rockville, MD, USA
| | - Xin Hu
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Rockville, MD, USA
| | - Kelli M Wilson
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Rockville, MD, USA
| | - Prasanthi P Koganti
- Department of Animal Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York, USA
| | - Camille A Spinner
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xin Xu
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Rockville, MD, USA
| | - Ajit Jadhav
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Rockville, MD, USA
| | - Noel Southall
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Rockville, MD, USA
| | - Juan Marugan
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Rockville, MD, USA
| | - Vimal Selvaraj
- Department of Animal Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York, USA
| | - Vanja Lazarevic
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Stefan A Muljo
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
| | - Marc Ferrer
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Rockville, MD, USA.
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36
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Yu L, Zhang X, Yang Y, Li D, Tang K, Zhao Z, He W, Wang C, Sahoo N, Converso-Baran K, Davis CS, Brooks SV, Bigot A, Calvo R, Martinez NJ, Southall N, Hu X, Marugan J, Ferrer M, Xu H. Small-molecule activation of lysosomal TRP channels ameliorates Duchenne muscular dystrophy in mouse models. Sci Adv 2020; 6:eaaz2736. [PMID: 32128386 PMCID: PMC7032923 DOI: 10.1126/sciadv.aaz2736] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/22/2019] [Indexed: 05/12/2023]
Abstract
Duchenne muscular dystrophy (DMD) is a devastating disease caused by mutations in dystrophin that compromise sarcolemma integrity. Currently, there is no treatment for DMD. Mutations in transient receptor potential mucolipin 1 (ML1), a lysosomal Ca2+ channel required for lysosomal exocytosis, produce a DMD-like phenotype. Here, we show that transgenic overexpression or pharmacological activation of ML1 in vivo facilitates sarcolemma repair and alleviates the dystrophic phenotypes in both skeletal and cardiac muscles of mdx mice (a mouse model of DMD). Hallmark dystrophic features of DMD, including myofiber necrosis, central nucleation, fibrosis, elevated serum creatine kinase levels, reduced muscle force, impaired motor ability, and dilated cardiomyopathies, were all ameliorated by increasing ML1 activity. ML1-dependent activation of transcription factor EB (TFEB) corrects lysosomal insufficiency to diminish muscle damage. Hence, targeting lysosomal Ca2+ channels may represent a promising approach to treat DMD and related muscle diseases.
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MESH Headings
- Animals
- Biomarkers
- Biopsy
- Disease Models, Animal
- Dystrophin/genetics
- Fluorescent Antibody Technique
- Gene Expression
- Lysosomes/drug effects
- Lysosomes/metabolism
- Mice
- Mice, Inbred mdx
- Mice, Transgenic
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/pathology
- Muscle, Skeletal/physiopathology
- Muscular Dystrophy, Duchenne/drug therapy
- Muscular Dystrophy, Duchenne/genetics
- Muscular Dystrophy, Duchenne/metabolism
- Muscular Dystrophy, Duchenne/pathology
- Myocardium/metabolism
- Myocardium/pathology
- Transient Receptor Potential Channels/agonists
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Affiliation(s)
- Lu Yu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, 4114 Biological Sciences Building, 1105 North University, Ann Arbor, MI 48109, USA
| | - Xiaoli Zhang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, 4114 Biological Sciences Building, 1105 North University, Ann Arbor, MI 48109, USA
| | - Yexin Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, 4114 Biological Sciences Building, 1105 North University, Ann Arbor, MI 48109, USA
| | - Dan Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, 4114 Biological Sciences Building, 1105 North University, Ann Arbor, MI 48109, USA
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Kaiyuan Tang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, 4114 Biological Sciences Building, 1105 North University, Ann Arbor, MI 48109, USA
| | - Zifan Zhao
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, 4114 Biological Sciences Building, 1105 North University, Ann Arbor, MI 48109, USA
| | - Wanwan He
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, 4114 Biological Sciences Building, 1105 North University, Ann Arbor, MI 48109, USA
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Ce Wang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, 4114 Biological Sciences Building, 1105 North University, Ann Arbor, MI 48109, USA
| | - Nirakar Sahoo
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, 4114 Biological Sciences Building, 1105 North University, Ann Arbor, MI 48109, USA
- Department of Biology, The University of Texas Rio Grande Valley, 1201 W University Dr., Edinburg, TX 78539, USA
| | - Kimber Converso-Baran
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carol S. Davis
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Susan V. Brooks
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anne Bigot
- Sorbonne Université, INSERM, AIM, Center for Research in Myology, UMRS974, GH Pitié-Salpétrière, 75651 Paris Cedex 13, France
| | - Raul Calvo
- NIH/NCATS/NCGC, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | | | - Noel Southall
- NIH/NCATS/NCGC, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Xin Hu
- NIH/NCATS/NCGC, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Juan Marugan
- NIH/NCATS/NCGC, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Marc Ferrer
- NIH/NCATS/NCGC, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Haoxing Xu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, 4114 Biological Sciences Building, 1105 North University, Ann Arbor, MI 48109, USA
- Corresponding author.
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37
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Shah P, Siramshetty V, Tawa G, Nguyen DT, Zakharov A, Southall N, Isin EM, Obach RS, Xu X, Manevski N. P38 - Exploring species differences in aldehyde oxidase activity. Drug Metab Pharmacokinet 2020. [DOI: 10.1016/j.dmpk.2020.04.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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38
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Zhang X, Chen W, Li P, Calvo R, Southall N, Hu X, Bryant-Genevier M, Feng X, Geng Q, Gao C, Yang M, Tang K, Ferrer M, Marugan JJ, Xu H. Agonist-specific voltage-dependent gating of lysosomal two-pore Na + channels. eLife 2019; 8:e51423. [PMID: 31825310 PMCID: PMC6905855 DOI: 10.7554/elife.51423] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/23/2019] [Indexed: 12/12/2022] Open
Abstract
Mammalian two-pore-channels (TPC1, 2; TPCN1, TPCN2) are ubiquitously- expressed, PI(3,5)P2-activated, Na+-selective channels in the endosomes and lysosomes that regulate luminal pH homeostasis, membrane trafficking, and Ebola viral infection. Whereas the channel activity of TPC1 is strongly dependent on membrane voltage, TPC2 lacks such voltage dependence despite the presence of the presumed 'S4 voltage-sensing' domains. By performing high-throughput screening followed by lysosomal electrophysiology, here we identified a class of tricyclic anti-depressants (TCAs) as small-molecule agonists of TPC channels. TCAs activate both TPC1 and TPC2 in a voltage-dependent manner, referred to as Lysosomal Na+ channel Voltage-dependent Activators (LyNa-VAs). We also identified another compound which, like PI(3,5)P2, activates TPC2 independent of voltage, suggesting the existence of agonist-specific gating mechanisms. Our identification of small-molecule TPC agonists should facilitate the studies of the cell biological roles of TPCs and can also readily explain the reported effects of TCAs in the modulation of autophagy and lysosomal functions.
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Affiliation(s)
- Xiaoli Zhang
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborUnited States
| | - Wei Chen
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborUnited States
| | - Ping Li
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborUnited States
- Collaborative Innovation Center of Yangtze River Delta Region Green PharmaceuticalsZhejiang University of TechnologyHangzhouChina
| | - Raul Calvo
- National Center for Advancing Translational Sciences (NCATS)Medical Center DriveRockvilleUnited States
| | - Noel Southall
- National Center for Advancing Translational Sciences (NCATS)Medical Center DriveRockvilleUnited States
| | - Xin Hu
- National Center for Advancing Translational Sciences (NCATS)Medical Center DriveRockvilleUnited States
| | - Melanie Bryant-Genevier
- National Center for Advancing Translational Sciences (NCATS)Medical Center DriveRockvilleUnited States
| | - Xinghua Feng
- Collaborative Innovation Center of Yangtze River Delta Region Green PharmaceuticalsZhejiang University of TechnologyHangzhouChina
| | - Qi Geng
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborUnited States
| | - Chenlang Gao
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborUnited States
| | - Meimei Yang
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborUnited States
- Department of NeurologyThe Fourth Hospital of Harbin Medical UniversityHarbinChina
| | - Kaiyuan Tang
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborUnited States
| | - Marc Ferrer
- National Center for Advancing Translational Sciences (NCATS)Medical Center DriveRockvilleUnited States
| | - Juan Jose Marugan
- National Center for Advancing Translational Sciences (NCATS)Medical Center DriveRockvilleUnited States
| | - Haoxing Xu
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborUnited States
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39
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Zakharov AV, Zhao T, Nguyen DT, Peryea T, Sheils T, Yasgar A, Huang R, Southall N, Simeonov A. Novel Consensus Architecture To Improve Performance of Large-Scale Multitask Deep Learning QSAR Models. J Chem Inf Model 2019; 59:4613-4624. [PMID: 31584270 DOI: 10.1021/acs.jcim.9b00526] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Advances in the development of high-throughput screening and automated chemistry have rapidly accelerated the production of chemical and biological data, much of them freely accessible through literature aggregator services such as ChEMBL and PubChem. Here, we explore how to use this comprehensive mapping of chemical biology space to support the development of large-scale quantitative structure-activity relationship (QSAR) models. We propose a new deep learning consensus architecture (DLCA) that combines consensus and multitask deep learning approaches together to generate large-scale QSAR models. This method improves knowledge transfer across different target/assays while also integrating contributions from models based on different descriptors. The proposed approach was validated and compared with proteochemometrics, multitask deep learning, and Random Forest methods paired with various descriptors types. DLCA models demonstrated improved prediction accuracy for both regression and classification tasks. The best models together with their modeling sets are provided through publicly available web services at https://predictor.ncats.io .
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Affiliation(s)
- Alexey V Zakharov
- National Center for Advancing Translational Sciences (NCATS) , National Institutes of Health , 9800 Medical Center Drive , Rockville , Maryland 20850 , United States
| | - Tongan Zhao
- National Center for Advancing Translational Sciences (NCATS) , National Institutes of Health , 9800 Medical Center Drive , Rockville , Maryland 20850 , United States
| | - Dac-Trung Nguyen
- National Center for Advancing Translational Sciences (NCATS) , National Institutes of Health , 9800 Medical Center Drive , Rockville , Maryland 20850 , United States
| | - Tyler Peryea
- National Center for Advancing Translational Sciences (NCATS) , National Institutes of Health , 9800 Medical Center Drive , Rockville , Maryland 20850 , United States
| | - Timothy Sheils
- National Center for Advancing Translational Sciences (NCATS) , National Institutes of Health , 9800 Medical Center Drive , Rockville , Maryland 20850 , United States
| | - Adam Yasgar
- National Center for Advancing Translational Sciences (NCATS) , National Institutes of Health , 9800 Medical Center Drive , Rockville , Maryland 20850 , United States
| | - Ruili Huang
- National Center for Advancing Translational Sciences (NCATS) , National Institutes of Health , 9800 Medical Center Drive , Rockville , Maryland 20850 , United States
| | - Noel Southall
- National Center for Advancing Translational Sciences (NCATS) , National Institutes of Health , 9800 Medical Center Drive , Rockville , Maryland 20850 , United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences (NCATS) , National Institutes of Health , 9800 Medical Center Drive , Rockville , Maryland 20850 , United States
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40
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Huang R, Zhu H, Shinn P, Ngan D, Ye L, Thakur A, Grewal G, Zhao T, Southall N, Hall MD, Simeonov A, Austin CP. The NCATS Pharmaceutical Collection: a 10-year update. Drug Discov Today 2019; 24:2341-2349. [PMID: 31585169 DOI: 10.1016/j.drudis.2019.09.019] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 09/16/2019] [Accepted: 09/24/2019] [Indexed: 12/25/2022]
Abstract
The National Center for Advancing Translational Sciences (NCATS) Pharmaceutical Collection (NPC), a comprehensive collection of clinically approved drugs, was made a public resource in 2011. Over the past decade, the NPC has been systematically profiled for activity across an array of pathways and disease models, generating an unparalleled amount of data. These data have not only enabled the identification of new repurposing candidates with several in clinical trials, but also uncovered new biological insights into drug targets and disease mechanisms. This retrospective provides an update on the NPC in terms of both successes and lessons learned. We also report our efforts in bringing the NPC up-to-date with drugs approved in recent years.
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Affiliation(s)
- Ruili Huang
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA.
| | - Hu Zhu
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Paul Shinn
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Deborah Ngan
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Lin Ye
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Ashish Thakur
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Gurmit Grewal
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Tongan Zhao
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Noel Southall
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Mathew D Hall
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Anton Simeonov
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Christopher P Austin
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
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41
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Frankowski KJ, Wang C, Patnaik S, Schoenen FJ, Southall N, Li D, Teper Y, Sun W, Kandela I, Hu D, Dextras C, Knotts Z, Bian Y, Norton J, Titus S, Lewandowska MA, Wen Y, Farley KI, Griner LM, Sultan J, Meng Z, Zhou M, Vilimas T, Powers AS, Kozlov S, Nagashima K, Quadri HS, Fang M, Long C, Khanolkar O, Chen W, Kang J, Huang H, Chow E, Goldberg E, Feldman C, Xi R, Kim HR, Sahagian G, Baserga SJ, Mazar A, Ferrer M, Zheng W, Shilatifard A, Aubé J, Rudloff U, Marugan JJ, Huang S. Metarrestin, a perinucleolar compartment inhibitor, effectively suppresses metastasis. Sci Transl Med 2019; 10:10/441/eaap8307. [PMID: 29769289 DOI: 10.1126/scitranslmed.aap8307] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 04/24/2018] [Indexed: 12/16/2022]
Abstract
Metastasis remains a leading cause of cancer mortality due to the lack of specific inhibitors against this complex process. To identify compounds selectively targeting the metastatic state, we used the perinucleolar compartment (PNC), a complex nuclear structure associated with metastatic behaviors of cancer cells, as a phenotypic marker for a high-content screen of over 140,000 structurally diverse compounds. Metarrestin, obtained through optimization of a screening hit, disassembles PNCs in multiple cancer cell lines, inhibits invasion in vitro, suppresses metastatic development in three mouse models of human cancer, and extends survival of mice in a metastatic pancreatic cancer xenograft model with no organ toxicity or discernable adverse effects. Metarrestin disrupts the nucleolar structure and inhibits RNA polymerase (Pol) I transcription, at least in part by interacting with the translation elongation factor eEF1A2. Thus, metarrestin represents a potential therapeutic approach for the treatment of metastatic cancer.
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Affiliation(s)
- Kevin J Frankowski
- Specialized Chemistry Center, The University of Kansas, Lawrence, KS 66047, USA
| | - Chen Wang
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Samarjit Patnaik
- NIH (National Institutes of Health) Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD, 20850, USA
| | - Frank J Schoenen
- Specialized Chemistry Center, The University of Kansas, Lawrence, KS 66047, USA
| | - Noel Southall
- NIH (National Institutes of Health) Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD, 20850, USA
| | - Dandan Li
- Thoracic and Gastrointestinal Oncology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yaroslav Teper
- Thoracic and Gastrointestinal Oncology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Wei Sun
- NIH (National Institutes of Health) Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD, 20850, USA
| | - Irawati Kandela
- Center for Developmental Therapeutics, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, USA
| | - Deqing Hu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Christopher Dextras
- NIH (National Institutes of Health) Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD, 20850, USA
| | - Zachary Knotts
- Thoracic and Gastrointestinal Oncology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yansong Bian
- Thoracic and Gastrointestinal Oncology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - John Norton
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Steve Titus
- NIH (National Institutes of Health) Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD, 20850, USA
| | - Marzena A Lewandowska
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Yiping Wen
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Katherine I Farley
- Departments of Molecular Biophysics and Biochemistry, Genetics, and Therapeutic Radiology, Yale University and Yale School of Medicine, New Haven, CT 06520, USA
| | - Lesley Mathews Griner
- NIH (National Institutes of Health) Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD, 20850, USA
| | - Jamey Sultan
- NIH (National Institutes of Health) Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD, 20850, USA
| | - Zhaojing Meng
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Ming Zhou
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Tomas Vilimas
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Fort Detrick, Frederick, MD 21702, USA
| | - Astin S Powers
- Laboratory of Pathology, Center for Cancer Research, NIH, Bethesda, MD 20892, USA
| | - Serguei Kozlov
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Fort Detrick, Frederick, MD 21702, USA
| | - Kunio Nagashima
- Electron Microscope Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Humair S Quadri
- Thoracic and Gastrointestinal Oncology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Min Fang
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Charles Long
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Ojus Khanolkar
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Warren Chen
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Jinsol Kang
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Helen Huang
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Eric Chow
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Esthermanya Goldberg
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Coral Feldman
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Romi Xi
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Hye Rim Kim
- Department of Human Genetics, Cancer Biology Graduate Program, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Gary Sahagian
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Susan J Baserga
- Departments of Molecular Biophysics and Biochemistry, Genetics, and Therapeutic Radiology, Yale University and Yale School of Medicine, New Haven, CT 06520, USA
| | - Andrew Mazar
- Center for Developmental Therapeutics, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, USA
| | - Marc Ferrer
- NIH (National Institutes of Health) Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD, 20850, USA
| | - Wei Zheng
- NIH (National Institutes of Health) Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD, 20850, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jeffrey Aubé
- Specialized Chemistry Center, The University of Kansas, Lawrence, KS 66047, USA
| | - Udo Rudloff
- Thoracic and Gastrointestinal Oncology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| | - Juan Jose Marugan
- NIH (National Institutes of Health) Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD, 20850, USA.
| | - Sui Huang
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA.
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Kaftanovskaya E, Ng HH, Rivas B, Myhr C, Shupe T, Hu X, Ferrer M, Southall N, Wilson K, Marugan J, Bishop C, Agoulnik I, Agoulnik A. SAT-035 Small Molecule Allosteric Agonist of Relaxin Receptor Ml290 Demonstrates Antifibrotic Properties in Liver Fibrosis. J Endocr Soc 2019. [PMCID: PMC6552156 DOI: 10.1210/js.2019-sat-035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Fibrosis is an underlying cause of cirrhosis and hepatic failure resulting in end stage liver disease with limited pharmacological therapeutic options. The beneficial effects of relaxin peptide treatment have been demonstrated previously in clinically relevant animal models of liver disease. However, the low stability of the recombinant relaxin peptide in vivo requires continuous intravenous delivery for chronic therapeutic application. We have recently identified a first series of small molecule allosteric biased agonists of the human relaxin receptor RXFP1 which showed efficacy similar to relaxin in several functional assays in vitro. Here we investigated the therapeutic effects of small molecule RXFP1 agonist on activated hepatic stellate cells, the main source of excessive collagen production in liver fibrosis. We have demonstrated that RXFP1 expression is increased in fibrotic mouse liver, specifically in activated hepatic stellate cells. The lead compound, ML290, was selected based on its effects on the expression of the genes involved in fibrosis in primary human stellate cells. RNA-Seq analysis of TGFβ1-activated LX-2 hepatic stellate cells showed that about 500 genes were misregulated by ML290. Gene Ontology analysis demonstrated that ML290 treatment primarily affects extracellular matrix remodeling and cytokine signaling, with expression profiles indicating an antifibrotic effect of ML290. ML290 treatment of human liver organoids with lipopolysaccharide-induced fibrotic phenotype resulted in dramatic reduction of type I collagen. The pharmacokinetics of ML290 in mice after multiple injections demonstrated its high stability in vivo, as evidenced by the sustained concentrations of compound in the liver. The ML290 treatment of mice expressing human RXFP1 gene with carbon tetrachloride-induced liver fibrosis resulted in significantly reduced collagen content, alpha-smooth muscle actin expression and cell proliferation around portal ducts, and the decrease of pro-fibrotic genes’ expression. In summary, ML290, the small molecule agonist of relaxin receptor, has anti-fibrotic effects in liver fibrosis. Funding source: NIH/NIDDK
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Affiliation(s)
- Elena Kaftanovskaya
- Human and Molecular Genetics, Florida Intl Univ College of Med, Miami, FL, United States
| | - Hooi Hooi Ng
- Florida Intl Univ College of Med, Miami, FL, United States
| | - Bryan Rivas
- Florida Intl Univ College of Med, Miami, FL, United States
| | - Courtney Myhr
- Florida Intl Univ College of Med, Miami, FL, United States
| | - Thomas Shupe
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Marc Ferrer
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Noel Southall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Kenneth Wilson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Juan Marugan
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Colin Bishop
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Irina Agoulnik
- Florida Intl Univ College of Med, Miami, FL, United States
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Huang R, Grishagin I, Wang Y, Zhao T, Greene J, Obenauer JC, Ngan D, Nguyen DT, Guha R, Jadhav A, Southall N, Simeonov A, Austin CP. The NCATS BioPlanet - An Integrated Platform for Exploring the Universe of Cellular Signaling Pathways for Toxicology, Systems Biology, and Chemical Genomics. Front Pharmacol 2019; 10:445. [PMID: 31133849 PMCID: PMC6524730 DOI: 10.3389/fphar.2019.00445] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 04/08/2019] [Indexed: 12/16/2022] Open
Abstract
Chemical genomics aims to comprehensively define, and ultimately predict, the effects of small molecule compounds on biological systems. Chemical activity profiling approaches must consider chemical effects on all pathways operative in mammalian cells. To enable a strategic and maximally efficient chemical profiling of pathway space, we have created the NCATS BioPlanet, a comprehensive integrated pathway resource that incorporates the universe of 1,658 human pathways sourced from publicly available, manually curated sources, which have been subjected to thorough redundancy and consistency cross-evaluation. BioPlanet supports interactive browsing, retrieval, and analysis of pathways, exploration of pathway connections, and pathway search by gene targets, category, and availability of corresponding bioactivity assay, as well as visualization of pathways on a 3-dimensional globe, in which the distance between any two pathways is proportional to their degree of gene component overlap. Using this resource, we propose a strategy to identify a minimal set of 362 biological assays that can interrogate the universe of human pathways. The NCATS BioPlanet is a public resource, which will be continually expanded and updated, for systems biology, toxicology, and chemical genomics, available at http://tripod.nih.gov/bioplanet/.
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Affiliation(s)
- Ruili Huang
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | | | - Yuhong Wang
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Tongan Zhao
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Jon Greene
- Rancho BioSciences, San Diego, CA, United States
| | | | - Deborah Ngan
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Dac-Trung Nguyen
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Rajarshi Guha
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Ajit Jadhav
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Noel Southall
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Anton Simeonov
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Christopher P Austin
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
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Patnaik S, Basu D, Southall N, Dehdashti S, Wan KK, Zheng W, Ferrer M, Taylor M, Engel DA, Marugan JJ. Identification, design and synthesis of novel pyrazolopyridine influenza virus nonstructural protein 1 antagonists. Bioorg Med Chem Lett 2019; 29:1113-1119. [PMID: 30852083 DOI: 10.1016/j.bmcl.2019.02.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 02/21/2019] [Accepted: 02/26/2019] [Indexed: 11/27/2022]
Abstract
Nonstructural protein 1 (NS1) plays a crucial function in the replication, spread, and pathogenesis of influenza virus by inhibiting the host innate immune response. Here we report the discovery and optimization of novel pyrazolopyridine NS1 antagonists that can potently inhibit influenza A/PR/8/34 replication in MDCK cells, rescue MDCK cells from cytopathic effects of seasonal influenza A strains, reverse NS1-dependent inhibition of IFN-β gene expression, and suppress the slow growth phenotype in NS1-expressing yeast. These pyrazolopyridines will enable researchers to investigate NS1 function during infection and how antagonists can be utilized in the next generation of treatments for influenza infection.
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Affiliation(s)
- Samarjit Patnaik
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States.
| | - Dipanwita Basu
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, 1300 Jefferson Park Ave., Charlottesville, VA 22908, United States
| | - Noel Southall
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - Seameen Dehdashti
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - Kanny K Wan
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - Wei Zheng
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - Marc Ferrer
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - Mercedes Taylor
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - Daniel A Engel
- Alexander BioDiscoveries, LLC, 530 Forrest Rd., Charlottesville, VA 22902, United States.
| | - Juan Jose Marugan
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States.
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45
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Sengupta N, Jović M, Barnaeva E, Kim DW, Hu X, Southall N, Dejmek M, Mejdrova I, Nencka R, Baumlova A, Chalupska D, Boura E, Ferrer M, Marugan J, Balla T. A large scale high-throughput screen identifies chemical inhibitors of phosphatidylinositol 4-kinase type II alpha. J Lipid Res 2019; 60:683-693. [PMID: 30626625 DOI: 10.1194/jlr.d090159] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/08/2019] [Indexed: 12/24/2022] Open
Abstract
The minor phospholipid, phosphatidylinositol 4-phosphate (PI4P), is emerging as a key regulator of lipid transfer in ER-membrane contact sites. Four different phosphatidylinositol 4-kinase (PI4K) enzymes generate PI4P in different membrane compartments supporting distinct cellular processes, many of which are crucial for the maintenance of cellular integrity but also hijacked by intracellular pathogens. While type III PI4Ks have been targeted by small molecular inhibitors, thus helping decipher their importance in cellular physiology, no inhibitors are available for the type II PI4Ks, which hinders investigations into their cellular functions. Here, we describe the identification of small molecular inhibitors of PI4K type II alpha (PI4K2A) by implementing a large scale small molecule high-throughput screening. A novel assay was developed that allows testing of selected inhibitors against PI4K2A in intact cells using a bioluminescence resonance energy transfer approach adapted to plate readers. The compounds disclosed here will pave the way to the optimization of PI4K2A inhibitors that can be used in cellular and animal studies to better understand the role of this enzyme in both normal and pathological states.
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Affiliation(s)
- Nivedita Sengupta
- Section on Molecular Signal Transduction, Program for Developmental Neuroscience, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Marko Jović
- Section on Molecular Signal Transduction, Program for Developmental Neuroscience, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Elena Barnaeva
- Division of Preclinical Innovation National Center for Advancing Translational Sciences, Rockville, MD 20850
| | - David W Kim
- Division of Preclinical Innovation National Center for Advancing Translational Sciences, Rockville, MD 20850
| | - Xin Hu
- Division of Preclinical Innovation National Center for Advancing Translational Sciences, Rockville, MD 20850
| | - Noel Southall
- Division of Preclinical Innovation National Center for Advancing Translational Sciences, Rockville, MD 20850
| | - Milan Dejmek
- Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic, 166 10 Prague 6, Czech Republic
| | - Ivana Mejdrova
- Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic, 166 10 Prague 6, Czech Republic
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic, 166 10 Prague 6, Czech Republic
| | - Adriana Baumlova
- Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic, 166 10 Prague 6, Czech Republic
| | - Dominika Chalupska
- Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic, 166 10 Prague 6, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic, 166 10 Prague 6, Czech Republic
| | - Marc Ferrer
- Division of Preclinical Innovation National Center for Advancing Translational Sciences, Rockville, MD 20850
| | - Juan Marugan
- Division of Preclinical Innovation National Center for Advancing Translational Sciences, Rockville, MD 20850
| | - Tamas Balla
- Section on Molecular Signal Transduction, Program for Developmental Neuroscience, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
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Chiang N, Barnaeva E, Hu X, Marugan J, Southall N, Ferrer M, Serhan CN. Identification of Chemotype Agonists for Human Resolvin D1 Receptor DRV1 with Pro-Resolving Functions. Cell Chem Biol 2018; 26:244-254.e4. [PMID: 30554914 DOI: 10.1016/j.chembiol.2018.10.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/20/2018] [Accepted: 10/26/2018] [Indexed: 12/14/2022]
Abstract
Resolution of acute inflammation is governed, in part, by specialized pro-resolving mediators, including lipoxins, resolvins, protectins, and maresins. Among them, resolvin D1 (RvD1) exhibits potent pro-resolving functions via activating human resolvin D1 receptor (DRV1/GPR32). RvD1 is a complex molecule that requires challenging organic synthesis, diminishing its potential as a therapeutic. Therefore, we implemented a high-throughput screening of small-molecule libraries and identified several chemotypes that activated recombinant DRV1, represented by NCGC00120943 (C1A), NCGC00135472 (C2A), pMPPF, and pMPPI. These chemotypes also elicited rapid impedance changes in cells overexpressing recombinant DRV1. With human macrophages, they each stimulated phagocytosis of serum-treated zymosan at concentrations comparable with that of RvD1, the endogenous DRV1 ligand. In addition, macrophage phagocytosis of live E. coli was significantly increased by these chemotypes in DRV1-transfected macrophages, compared with mock-transfected cells. Taken together, these chemotypes identified by unbiased screens act as RvD1 mimetics, exhibiting pro-resolving functions via interacting with human DRV1.
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Affiliation(s)
- Nan Chiang
- Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road BTM 3-016, Boston, MA 02115, USA
| | - Elena Barnaeva
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Juan Marugan
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Noel Southall
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Marc Ferrer
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA.
| | - Charles N Serhan
- Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road BTM 3-016, Boston, MA 02115, USA.
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47
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Vilimas T, Wang AQ, Patnaik S, Hughes EA, Singleton MD, Knotts Z, Li D, Frankowski K, Schlomer JJ, Guerin TM, Springer S, Drennan C, Dextras C, Wang C, Gilbert D, Southall N, Ferrer M, Huang S, Kozlov S, Marugan J, Xu X, Rudloff U. Pharmacokinetic evaluation of the PNC disassembler metarrestin in wild-type and Pdx1-Cre;LSL-Kras G12D/+;Tp53 R172H/+ (KPC) mice, a genetically engineered model of pancreatic cancer. Cancer Chemother Pharmacol 2018; 82:1067-1080. [PMID: 30306263 PMCID: PMC6267684 DOI: 10.1007/s00280-018-3699-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 08/29/2018] [Indexed: 12/18/2022]
Abstract
PURPOSE Metarrestin is a first-in-class small molecule clinical candidate capable of disrupting the perinucleolar compartment, a subnuclear structure unique to metastatic cancer cells. This study aims to define the pharmacokinetic (PK) profile of metarrestin and the pharmacokinetic/pharmacodynamic relationship of metarrestin-regulated markers. METHODS PK studies included the administration of single or multiple dose of metarrestin at 3, 10, or 25 mg/kg via intravenous (IV) injection, gavage (PO) or with chow to wild-type C57BL/6 mice and KPC mice bearing autochthonous pancreatic tumors. Metarrestin concentrations were analyzed by UPLC-MS/MS. Pharmacodynamic assays included mRNA expression profiling by RNA-seq and qRT-PCR for KPC mice. RESULTS Metarrestin had a moderate plasma clearance of 48 mL/min/kg and a large volume of distribution of 17 L/kg at 3 mg/kg IV in C57BL/6 mice. The oral bioavailability after single-dose (SD) treatment was > 80%. In KPC mice treated with SD 25 mg/kg PO, plasma AUC0-∞ of 14400 ng h/mL, Cmax of 810 ng/mL and half-life (t1/2) of 8.5 h were observed. At 24 h after SD of 25 mg/kg PO, the intratumor concentration of metarrestin was high with a mean value of 6.2 µg/g tissue (or 13 µM), well above the cell-based IC50 of 0.4 µM. At multiple dose (MD) 25 mg/kg/day PO in KPC mice, mean tissue/plasma AUC0-24h ratio for tumor, spleen and liver was 37, 30 and 31, respectively. There was a good linear relationship of dosage to AUC0-24h and C24h. AUC0-24h MD to AUC0-24h SD ratios ranged from two for liver to five for tumor indicating additional accumulation in tumors. Dose-dependent normalization of FOXA1 and FOXO6 mRNA expression was observed in KPC tumors. CONCLUSIONS Metarrestin is an effective therapeutic candidate with a favorable PK profile achieving excellent intratumor tissue levels in a disease with known poor drug delivery.
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Affiliation(s)
- Tomas Vilimas
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, 21702, USA
| | - Amy Q Wang
- Therapeutics for Rare and Neglected Diseases (TRND) Program, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Samarjit Patnaik
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Emma A Hughes
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Marc D Singleton
- Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Zachary Knotts
- Rare Tumor Initiative (RTI), Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Hatfield Center, 10 Center Drive, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Dandan Li
- Rare Tumor Initiative (RTI), Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Hatfield Center, 10 Center Drive, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Kevin Frankowski
- Department of Medicinal Chemistry and Specialized Chemistry Center, University of Kansas, Lawrence, KS, USA
| | - Jerome J Schlomer
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, 21702, USA
| | - Theresa M Guerin
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, 21702, USA
| | - Stephanie Springer
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, 21702, USA
| | - Catherine Drennan
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, 21702, USA
| | - Christopher Dextras
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Chen Wang
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL, 60611, USA
| | - Debra Gilbert
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, 21702, USA
| | - Noel Southall
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Marc Ferrer
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Sui Huang
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL, 60611, USA
| | - Serguei Kozlov
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, 21702, USA
| | - Juan Marugan
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA.
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bldg B, Rockville, MD, 20850, USA.
| | - Xin Xu
- Therapeutics for Rare and Neglected Diseases (TRND) Program, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA.
| | - Udo Rudloff
- Rare Tumor Initiative (RTI), Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Hatfield Center, 10 Center Drive, 9000 Rockville Pike, Bethesda, MD, 20892, USA.
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Gorshkov K, Chen CZ, Marshall RE, Mihatov N, Choi Y, Nguyen DT, Southall N, Chen KG, Park JK, Zheng W. Advancing precision medicine with personalized drug screening. Drug Discov Today 2018; 24:272-278. [PMID: 30125678 DOI: 10.1016/j.drudis.2018.08.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/26/2018] [Accepted: 08/13/2018] [Indexed: 01/15/2023]
Abstract
Personalized drug screening (PDS) of approved drug libraries enables rapid development of specific small-molecule therapies for individual patients. With a multidisciplinary team including clinicians, researchers, ethicists, informaticians and regulatory professionals, patient treatment can be optimized with greater efficacy and fewer adverse effects by using PDS as an approach to find remedies. In addition, PDS has the potential to rapidly identify therapeutics for a patient suffering from a disease without an existing therapy. From cancer to bacterial infections, we review specific maladies addressed with PDS campaigns. We predict that PDS combined with personal genomic analyses will contribute to the development of future precision medicine endeavors.
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Affiliation(s)
- Kirill Gorshkov
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892-3375, USA
| | - Catherine Z Chen
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892-3375, USA
| | - Raisa E Marshall
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892-3375, USA
| | - Nino Mihatov
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892-3375, USA
| | - Yong Choi
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892-3375, USA
| | - Dac-Trung Nguyen
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892-3375, USA
| | - Noel Southall
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892-3375, USA
| | - Kevin G Chen
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892-3375, USA
| | - John K Park
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892-3375, USA
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892-3375, USA.
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49
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Wilson KJ, Xiao J, Chen CZ, Huang Z, Agoulnik IU, Ferrer M, Southall N, Hu X, Zheng W, Xu X, Wang A, Myhr C, Barnaeva E, George ER, Agoulnik AI, Marugan JJ. Optimization of the first small-molecule relaxin/insulin-like family peptide receptor (RXFP1) agonists: Activation results in an antifibrotic gene expression profile. Eur J Med Chem 2018; 156:79-92. [PMID: 30006176 PMCID: PMC6102074 DOI: 10.1016/j.ejmech.2018.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/25/2018] [Accepted: 06/02/2018] [Indexed: 01/08/2023]
Abstract
A dose responsive quantitative high throughput screen (qHTS) of >350,000 compounds against a human relaxin/insulin-like family peptide receptor (RXFP1) transfected HEK293 cell line identified 2-acetamido-N-phenylbenzamides 1 and 3 with modest agonist activity. An extensive structure-activity study has been undertaken to optimize the potency, efficacy, and physical properties of the series, resulting in the identification of compound 65 (ML-290), which has excellent in vivo PK properties with high levels of systemic exposure. This series, exemplified by 65, has produced first-in-class small-molecule agonists of RXFP1 and is a potent activator of anti-fibrotic genes.
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Affiliation(s)
- Kenneth J. Wilson
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850
| | - Jingbo Xiao
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850
| | - Catherine Z. Chen
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850
| | - Zaohua Huang
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th Street, HLSI 419B, Miami, FL 33199
| | - Irina U. Agoulnik
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th Street, HLSI 419B, Miami, FL 33199
| | - Marc Ferrer
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850
| | - Noel Southall
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850
| | - Xin Hu
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850
| | - Wei Zheng
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850
| | - Xin Xu
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850
| | - Amy Wang
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850
| | - Courtney Myhr
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th Street, HLSI 419B, Miami, FL 33199
| | - Elena Barnaeva
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850
| | - Emmett R. George
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850
| | - Alexander I. Agoulnik
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th Street, HLSI 419B, Miami, FL 33199
| | - Juan J. Marugan
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850
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Luderman KD, Conroy JL, Free RB, Southall N, Ferrer M, Sanchez-Soto M, Moritz AE, Willette BKA, Fyfe TJ, Jain P, Titus S, Hazelwood LA, Aubé J, Lane JR, Frankowski KJ, Sibley DR. Identification of Positive Allosteric Modulators of the D 1 Dopamine Receptor That Act at Diverse Binding Sites. Mol Pharmacol 2018; 94:1197-1209. [PMID: 30068735 DOI: 10.1124/mol.118.113175] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/27/2018] [Indexed: 01/11/2023] Open
Abstract
The D1 dopamine receptor is linked to a variety of neuropsychiatric disorders and represents an attractive drug target for the enhancement of cognition in schizophrenia, Alzheimer disease, and other disorders. Positive allosteric modulators (PAMs), with their potential for greater selectivity and larger therapeutic windows, may represent a viable drug development strategy, as orthosteric D1 receptor agonists possess known clinical liabilities. We discovered two structurally distinct D1 receptor PAMs, MLS6585 and MLS1082, via a high-throughput screen of the NIH Molecular Libraries program small-molecule library. Both compounds potentiate dopamine-stimulated G protein- and β-arrestin-mediated signaling and increase the affinity of dopamine for the D1 receptor with low micromolar potencies. Neither compound displayed any intrinsic agonist activity. Both compounds were also found to potentiate the efficacy of partial agonists. We tested maximally effective concentrations of each PAM in combination to determine if the compounds might act at separate or similar sites. In combination, MLS1082 + MLS6585 produced an additive potentiation of dopamine potency beyond that caused by either PAM alone for both β-arrestin recruitment and cAMP accumulation, suggesting diverse sites of action. In addition, MLS6585, but not MLS1082, had additive activity with the previously described D1 receptor PAM "Compound B," suggesting that MLS1082 and Compound B may share a common binding site. A point mutation (R130Q) in the D1 receptor was found to abrogate MLS1082 activity without affecting that of MLS6585, suggesting this residue may be involved in the binding/activity of MLS1082 but not that of MLS6585. Together, MLS1082 and MLS6585 may serve as important tool compounds for the characterization of diverse allosteric sites on the D1 receptor as well as the development of optimized lead compounds for therapeutic use.
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Affiliation(s)
- Kathryn D Luderman
- Molecular Neuropharmacology Section, National Institute of Neurologic Disorders and Stroke, Intramural Research Program, National Institutes of Health, Bethesda, Maryland (K.D.L., J.L.C., R.B.F., M.S.-S., A.E.M., B.K.A.W., L.A.H., D.R.S.); NIH Chemical Genomics Center, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland (N.S., M.F., S.T.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (T.J.F., J.R.L.); KU Specialized Chemistry Center, University of Kansas, Lawrence, Kansas (P.J., J.A., K.J.F.); and Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (J.A., K.J.F.)
| | - Jennie L Conroy
- Molecular Neuropharmacology Section, National Institute of Neurologic Disorders and Stroke, Intramural Research Program, National Institutes of Health, Bethesda, Maryland (K.D.L., J.L.C., R.B.F., M.S.-S., A.E.M., B.K.A.W., L.A.H., D.R.S.); NIH Chemical Genomics Center, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland (N.S., M.F., S.T.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (T.J.F., J.R.L.); KU Specialized Chemistry Center, University of Kansas, Lawrence, Kansas (P.J., J.A., K.J.F.); and Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (J.A., K.J.F.)
| | - R Benjamin Free
- Molecular Neuropharmacology Section, National Institute of Neurologic Disorders and Stroke, Intramural Research Program, National Institutes of Health, Bethesda, Maryland (K.D.L., J.L.C., R.B.F., M.S.-S., A.E.M., B.K.A.W., L.A.H., D.R.S.); NIH Chemical Genomics Center, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland (N.S., M.F., S.T.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (T.J.F., J.R.L.); KU Specialized Chemistry Center, University of Kansas, Lawrence, Kansas (P.J., J.A., K.J.F.); and Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (J.A., K.J.F.)
| | - Noel Southall
- Molecular Neuropharmacology Section, National Institute of Neurologic Disorders and Stroke, Intramural Research Program, National Institutes of Health, Bethesda, Maryland (K.D.L., J.L.C., R.B.F., M.S.-S., A.E.M., B.K.A.W., L.A.H., D.R.S.); NIH Chemical Genomics Center, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland (N.S., M.F., S.T.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (T.J.F., J.R.L.); KU Specialized Chemistry Center, University of Kansas, Lawrence, Kansas (P.J., J.A., K.J.F.); and Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (J.A., K.J.F.)
| | - Marc Ferrer
- Molecular Neuropharmacology Section, National Institute of Neurologic Disorders and Stroke, Intramural Research Program, National Institutes of Health, Bethesda, Maryland (K.D.L., J.L.C., R.B.F., M.S.-S., A.E.M., B.K.A.W., L.A.H., D.R.S.); NIH Chemical Genomics Center, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland (N.S., M.F., S.T.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (T.J.F., J.R.L.); KU Specialized Chemistry Center, University of Kansas, Lawrence, Kansas (P.J., J.A., K.J.F.); and Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (J.A., K.J.F.)
| | - Marta Sanchez-Soto
- Molecular Neuropharmacology Section, National Institute of Neurologic Disorders and Stroke, Intramural Research Program, National Institutes of Health, Bethesda, Maryland (K.D.L., J.L.C., R.B.F., M.S.-S., A.E.M., B.K.A.W., L.A.H., D.R.S.); NIH Chemical Genomics Center, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland (N.S., M.F., S.T.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (T.J.F., J.R.L.); KU Specialized Chemistry Center, University of Kansas, Lawrence, Kansas (P.J., J.A., K.J.F.); and Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (J.A., K.J.F.)
| | - Amy E Moritz
- Molecular Neuropharmacology Section, National Institute of Neurologic Disorders and Stroke, Intramural Research Program, National Institutes of Health, Bethesda, Maryland (K.D.L., J.L.C., R.B.F., M.S.-S., A.E.M., B.K.A.W., L.A.H., D.R.S.); NIH Chemical Genomics Center, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland (N.S., M.F., S.T.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (T.J.F., J.R.L.); KU Specialized Chemistry Center, University of Kansas, Lawrence, Kansas (P.J., J.A., K.J.F.); and Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (J.A., K.J.F.)
| | - Blair K A Willette
- Molecular Neuropharmacology Section, National Institute of Neurologic Disorders and Stroke, Intramural Research Program, National Institutes of Health, Bethesda, Maryland (K.D.L., J.L.C., R.B.F., M.S.-S., A.E.M., B.K.A.W., L.A.H., D.R.S.); NIH Chemical Genomics Center, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland (N.S., M.F., S.T.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (T.J.F., J.R.L.); KU Specialized Chemistry Center, University of Kansas, Lawrence, Kansas (P.J., J.A., K.J.F.); and Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (J.A., K.J.F.)
| | - Tim J Fyfe
- Molecular Neuropharmacology Section, National Institute of Neurologic Disorders and Stroke, Intramural Research Program, National Institutes of Health, Bethesda, Maryland (K.D.L., J.L.C., R.B.F., M.S.-S., A.E.M., B.K.A.W., L.A.H., D.R.S.); NIH Chemical Genomics Center, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland (N.S., M.F., S.T.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (T.J.F., J.R.L.); KU Specialized Chemistry Center, University of Kansas, Lawrence, Kansas (P.J., J.A., K.J.F.); and Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (J.A., K.J.F.)
| | - Prashi Jain
- Molecular Neuropharmacology Section, National Institute of Neurologic Disorders and Stroke, Intramural Research Program, National Institutes of Health, Bethesda, Maryland (K.D.L., J.L.C., R.B.F., M.S.-S., A.E.M., B.K.A.W., L.A.H., D.R.S.); NIH Chemical Genomics Center, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland (N.S., M.F., S.T.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (T.J.F., J.R.L.); KU Specialized Chemistry Center, University of Kansas, Lawrence, Kansas (P.J., J.A., K.J.F.); and Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (J.A., K.J.F.)
| | - Steve Titus
- Molecular Neuropharmacology Section, National Institute of Neurologic Disorders and Stroke, Intramural Research Program, National Institutes of Health, Bethesda, Maryland (K.D.L., J.L.C., R.B.F., M.S.-S., A.E.M., B.K.A.W., L.A.H., D.R.S.); NIH Chemical Genomics Center, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland (N.S., M.F., S.T.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (T.J.F., J.R.L.); KU Specialized Chemistry Center, University of Kansas, Lawrence, Kansas (P.J., J.A., K.J.F.); and Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (J.A., K.J.F.)
| | - Lisa A Hazelwood
- Molecular Neuropharmacology Section, National Institute of Neurologic Disorders and Stroke, Intramural Research Program, National Institutes of Health, Bethesda, Maryland (K.D.L., J.L.C., R.B.F., M.S.-S., A.E.M., B.K.A.W., L.A.H., D.R.S.); NIH Chemical Genomics Center, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland (N.S., M.F., S.T.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (T.J.F., J.R.L.); KU Specialized Chemistry Center, University of Kansas, Lawrence, Kansas (P.J., J.A., K.J.F.); and Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (J.A., K.J.F.)
| | - Jeffrey Aubé
- Molecular Neuropharmacology Section, National Institute of Neurologic Disorders and Stroke, Intramural Research Program, National Institutes of Health, Bethesda, Maryland (K.D.L., J.L.C., R.B.F., M.S.-S., A.E.M., B.K.A.W., L.A.H., D.R.S.); NIH Chemical Genomics Center, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland (N.S., M.F., S.T.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (T.J.F., J.R.L.); KU Specialized Chemistry Center, University of Kansas, Lawrence, Kansas (P.J., J.A., K.J.F.); and Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (J.A., K.J.F.)
| | - J Robert Lane
- Molecular Neuropharmacology Section, National Institute of Neurologic Disorders and Stroke, Intramural Research Program, National Institutes of Health, Bethesda, Maryland (K.D.L., J.L.C., R.B.F., M.S.-S., A.E.M., B.K.A.W., L.A.H., D.R.S.); NIH Chemical Genomics Center, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland (N.S., M.F., S.T.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (T.J.F., J.R.L.); KU Specialized Chemistry Center, University of Kansas, Lawrence, Kansas (P.J., J.A., K.J.F.); and Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (J.A., K.J.F.)
| | - Kevin J Frankowski
- Molecular Neuropharmacology Section, National Institute of Neurologic Disorders and Stroke, Intramural Research Program, National Institutes of Health, Bethesda, Maryland (K.D.L., J.L.C., R.B.F., M.S.-S., A.E.M., B.K.A.W., L.A.H., D.R.S.); NIH Chemical Genomics Center, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland (N.S., M.F., S.T.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (T.J.F., J.R.L.); KU Specialized Chemistry Center, University of Kansas, Lawrence, Kansas (P.J., J.A., K.J.F.); and Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (J.A., K.J.F.)
| | - David R Sibley
- Molecular Neuropharmacology Section, National Institute of Neurologic Disorders and Stroke, Intramural Research Program, National Institutes of Health, Bethesda, Maryland (K.D.L., J.L.C., R.B.F., M.S.-S., A.E.M., B.K.A.W., L.A.H., D.R.S.); NIH Chemical Genomics Center, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland (N.S., M.F., S.T.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (T.J.F., J.R.L.); KU Specialized Chemistry Center, University of Kansas, Lawrence, Kansas (P.J., J.A., K.J.F.); and Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (J.A., K.J.F.)
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