1
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Ortiz Jordan LM, Vega VF, Shumate J, Peles A, Zeiger J, Scampavia L, Spicer TP. Protocol for high throughput 3D drug screening of patient derived melanoma and renal cell carcinoma. SLAS Discov 2024; 29:100141. [PMID: 38218316 DOI: 10.1016/j.slasd.2024.01.002] [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] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/29/2023] [Accepted: 01/10/2024] [Indexed: 01/15/2024]
Abstract
High Throughput Screening (HTS) with 3D cell models is possible thanks to the recent progress and development in 3D cell culture technologies. Results from multiple studies have demonstrated different drug responses between 2D and 3D cell culture. It is now widely accepted that 3D cell models more accurately represent the physiologic conditions of tumors over 2D cell models. However, there is still a need for more accurate tests that are scalable and better imitate the complex conditions in living tissues. Here, we describe ultrahigh throughput 3D methods of drug response profiling in patient derived primary tumors including melanoma as well as renal cell carcinoma that were tested against the NCI oncologic set of FDA approved drugs. We also tested their autologous patient derived cancer associated fibroblasts, varied the in-vitro conditions using matrix vs matrix free methods and completed this in both 3D vs 2D rendered cancer cells. The result indicates a heterologous response to the drugs based on their genetic background, but not on their maintenance condition. Here, we present the methods and supporting results of the HTS efforts using these 3D of organoids derived from patients. This demonstrated the possibility of using patient derived 3D cells for HTS and expands on our screening capabilities for testing other types of cancer using clinically approved anti-cancer agents to find drugs for potential off label use.
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Affiliation(s)
- Luis M Ortiz Jordan
- High-Throughput Molecular Screening Center, Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 130 Scripps Way #1A1, Jupiter, FL 33458, USA
| | - Virneliz Fernández Vega
- High-Throughput Molecular Screening Center, Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 130 Scripps Way #1A1, Jupiter, FL 33458, USA
| | - Justin Shumate
- High-Throughput Molecular Screening Center, Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 130 Scripps Way #1A1, Jupiter, FL 33458, USA
| | - Adam Peles
- High-Throughput Molecular Screening Center, Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 130 Scripps Way #1A1, Jupiter, FL 33458, USA
| | - Jordan Zeiger
- High-Throughput Molecular Screening Center, Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 130 Scripps Way #1A1, Jupiter, FL 33458, USA
| | - Louis Scampavia
- High-Throughput Molecular Screening Center, Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 130 Scripps Way #1A1, Jupiter, FL 33458, USA
| | - Timothy P Spicer
- High-Throughput Molecular Screening Center, Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 130 Scripps Way #1A1, Jupiter, FL 33458, USA.
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2
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Smith E, Dickson L, Pickford P, Rowland A, Shumate J, Perez K, Scampavia L, Hernandez D, Spicer TP. Protocol for kinetic mode potassium channel assays on common plate readers and microscopes. SLAS Discov 2024; 29:100148. [PMID: 38677875 DOI: 10.1016/j.slasd.2024.100148] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/02/2024] [Accepted: 03/01/2024] [Indexed: 04/29/2024]
Abstract
Fluorescence-based potassium channel assays are typically run on expensive, hard to obtain, fluorescence imaging kinetic plate readers that are uncommon in most laboratories. Here we describe the use of the Brilliant Thallium Snapshot assay to conduct an endpoint potassium channel assay, so that it can be used across multiple plate reader platforms that are more common in many labs. These methods will allow users to identify modulators of potassium channels. For this work, we have taken a kinetic mode Molecular Devices FLIPR based protocol and adapted it to be utilized on endpoint plate readers, such as the BMG Labtech PHERAstar, to identify activators of GIRK channels in CHO cells. We demonstrate that both plate readers are functionally competent at generating excellent Z' values which makes them ideally suited to finding corollary hits from the Sigma LOPAC 1,280 screening collection. Importantly, this assay has also been validated using a high content reader, demonstrating the possibility of spatially resolving signals from individual cells within a mixed cell population. The compendium of these results shows the flexibility, accessibility and functionality of endpoint-compatible potassium channel assay readouts on more common plate readers.
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Affiliation(s)
- Emery Smith
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Department of Molecular Medicine, 130 Scripps Way #1A1, Jupiter, FL 33458, United States
| | - Louise Dickson
- Cerevance Ltd., 418 Cambridge Science Park Milton Rd, Milton, Cambridge CB4 0PZ, United Kingdom
| | - Philip Pickford
- Cerevance Ltd., 418 Cambridge Science Park Milton Rd, Milton, Cambridge CB4 0PZ, United Kingdom
| | - Anna Rowland
- Cerevance Ltd., 418 Cambridge Science Park Milton Rd, Milton, Cambridge CB4 0PZ, United Kingdom
| | - Justin Shumate
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Department of Molecular Medicine, 130 Scripps Way #1A1, Jupiter, FL 33458, United States
| | - Katherine Perez
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Department of Molecular Medicine, 130 Scripps Way #1A1, Jupiter, FL 33458, United States
| | - Louis Scampavia
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Department of Molecular Medicine, 130 Scripps Way #1A1, Jupiter, FL 33458, United States
| | | | - Timothy P Spicer
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Department of Molecular Medicine, 130 Scripps Way #1A1, Jupiter, FL 33458, United States.
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3
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Aziz F, Reddy K, Fernandez Vega V, Dey R, Hicks KA, Rao S, Jordan LO, Smith E, Shumate J, Scampavia L, Carpino N, Spicer TP, French JB. Rebamipide and Derivatives are Potent, Selective Inhibitors of Histidine Phosphatase Activity of the Suppressor of T Cell Receptor Signaling Proteins. J Med Chem 2024; 67:1949-1960. [PMID: 38252624 DOI: 10.1021/acs.jmedchem.3c01763] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The suppressor of T cell receptor signaling (Sts) proteins are negative regulators of immune signaling. Genetic inactivation of these proteins leads to significant resistance to infection. From a 590,000 compound high-throughput screen, we identified the 2-(1H)-quinolinone derivative, rebamipide, as a putative inhibitor of Sts phosphatase activity. Rebamipide, and a small library of derivatives, are competitive, selective inhibitors of Sts-1 with IC50 values from low to submicromolar. SAR analysis indicates that the quinolinone, the acid, and the amide moieties are all essential for activity. A crystal structure confirmed the SAR and reveals key interactions between this class of compound and the protein. Although rebamipide has poor cell permeability, we demonstrated that a liposomal preparation can inactivate the phosphatase activity of Sts-1 in cells. These studies demonstrate that Sts-1 enzyme activity can be pharmacologically inactivated and provide foundational tools and insights for the development of immune-enhancing therapies that target the Sts proteins.
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Affiliation(s)
- Faisal Aziz
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
| | - Kanamata Reddy
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
| | - Virneliz Fernandez Vega
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute, Jupiter, Florida 33458, United States
| | - Raja Dey
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
| | - Katherine A Hicks
- Department of Chemistry, State University of New York at Cortland, Cortland, New York 13045, United States
| | - Sumitha Rao
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute, Jupiter, Florida 33458, United States
| | - Luis Ortiz Jordan
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute, Jupiter, Florida 33458, United States
| | - Emery Smith
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute, Jupiter, Florida 33458, United States
| | - Justin Shumate
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute, Jupiter, Florida 33458, United States
| | - Louis Scampavia
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute, Jupiter, Florida 33458, United States
| | - Nicholas Carpino
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York 11790, United States
| | - Timothy P Spicer
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute, Jupiter, Florida 33458, United States
| | - Jarrod B French
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
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4
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Coant N, Bickel JD, Rahaim R, Otsuka Y, Choi YM, Xu R, Simoes M, Cariello C, Mao C, Saied EM, Arenz C, Spicer TP, Bannister TD, Tonge PJ, Airola MV, Scampavia L, Hannun YA, Rizzo RC, Haley JD. Neutral ceramidase-active site inhibitor chemotypes and binding modes. Bioorg Chem 2023; 139:106747. [PMID: 37531819 PMCID: PMC10681040 DOI: 10.1016/j.bioorg.2023.106747] [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: 06/21/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 08/04/2023]
Abstract
Ceramides impact a diverse array of biological functions and have been implicated in disease pathogenesis. The enzyme neutral ceramidase (nCDase) is a zinc-containing hydrolase and mediates the metabolism of ceramide to sphingosine (Sph), both in cells and in the intestinal lumen. nCDase inhibitors based on substrate mimetics, for example C6-urea ceramide, have limited potency, aqueous solubility, and micelle-free fraction. To identify non-ceramide mimetic nCDase inhibitors, hit compounds from an HTS campaign were evaluated in biochemical, cell based and in silico modeling approaches. A majority of small molecule nCDase inhibitors contained pharmacophores capable of zinc interaction but retained specificity for nCDase over zinc-containing acid and alkaline ceramidases, as well as matrix metalloprotease-3 and histone deacetylase-1. nCDase inhibitors were refined by SAR, were shown to be substrate competitive and were active in cellular assays. nCDase inhibitor compounds were modeled by in silico DOCK screening and by molecular simulation. Modeling data supports zinc interaction and a similar compound binding pose with ceramide. nCDase inhibitors were identified with notably improved activity and solubility in comparison with the reference lipid-mimetic C6-urea ceramide.
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Affiliation(s)
- Nicolas Coant
- Stony Brook University Cancer Center, Stony Brook University, Stony Brook, NY 11794, USA
| | - John D Bickel
- Department of Applied Mathematics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Ronald Rahaim
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL 33458, USA
| | - Yuka Otsuka
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL 33458, USA
| | - Yong-Mi Choi
- Department of Biochemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Ruijuan Xu
- Stony Brook University Cancer Center, Stony Brook University, Stony Brook, NY 11794, USA
| | - Michael Simoes
- Renaissance School of Medicine, Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Chris Cariello
- Renaissance School of Medicine, Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Cungui Mao
- Stony Brook University Cancer Center, Stony Brook University, Stony Brook, NY 11794, USA
| | - Essa M Saied
- Chemistry Department, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Christoph Arenz
- Institute for Chemistry, Humboldt Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - Timothy P Spicer
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL 33458, USA
| | - Thomas D Bannister
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL 33458, USA
| | - Peter J Tonge
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Michael V Airola
- Department of Biochemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Louis Scampavia
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL 33458, USA
| | - Yusuf A Hannun
- Stony Brook University Cancer Center, Stony Brook University, Stony Brook, NY 11794, USA.
| | - Robert C Rizzo
- Department of Applied Mathematics, Stony Brook University, Stony Brook, NY 11794, USA.
| | - John D Haley
- Stony Brook University Cancer Center, Stony Brook University, Stony Brook, NY 11794, USA; Renaissance School of Medicine, Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA.
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5
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Sprague DJ, Park SK, Gramberg S, Bauer L, Rohr CM, Chulkov EG, Smith E, Scampavia L, Spicer TP, Haeberlein S, Marchant JS. Target-based discovery of a broad spectrum flukicide. bioRxiv 2023:2023.09.22.559026. [PMID: 37790347 PMCID: PMC10542552 DOI: 10.1101/2023.09.22.559026] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Diseases caused by parasitic flatworms impart a considerable healthcare burden worldwide. Many of these diseases - for example, the parasitic blood fluke infection, schistosomiasis - are treated with the drug praziquantel (PZQ). However, PZQ is ineffective against disease caused by liver flukes from the genus Fasciola. This is due to a single amino acid change within the target of PZQ, a transient receptor potential ion channel (TRPMPZQ), in Fasciola species. Here we identify benzamidoquinazolinone analogs that are active against Fasciola TRPMPZQ. Structure-activity studies define an optimized ligand (BZQ) that caused protracted paralysis and damage to the protective tegument of these liver flukes. BZQ also retained activity against Schistosoma mansoni comparable to PZQ and was active against TRPMPZQ orthologs in all profiled species of parasitic fluke. This broad spectrum activity was manifest as BZQ adopts a pose within the binding pocket of TRPMPZQ dependent on a ubiquitously conserved residue. BZQ therefore acts as a universal activator of trematode TRPMPZQ and a first-in-class, broad spectrum flukicide.
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Affiliation(s)
- Daniel J. Sprague
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Program in Chemical Biology, Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Sang-Kyu Park
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Svenja Gramberg
- BFS, Institute of Parasitology, Justus Liebig University Giessen, Schubertstr. 81, 35392, Giessen, Germany
| | - Lisa Bauer
- BFS, Institute of Parasitology, Justus Liebig University Giessen, Schubertstr. 81, 35392, Giessen, Germany
| | - Claudia M. Rohr
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Evgeny G. Chulkov
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Emery Smith
- UF Scripps Molecular Screening Center, Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL, 33458, USA
| | - Louis Scampavia
- UF Scripps Molecular Screening Center, Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL, 33458, USA
| | - Timothy P. Spicer
- UF Scripps Molecular Screening Center, Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL, 33458, USA
| | - Simone Haeberlein
- BFS, Institute of Parasitology, Justus Liebig University Giessen, Schubertstr. 81, 35392, Giessen, Germany
| | - Jonathan S. Marchant
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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6
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Lee E, Archasappawat S, Ji K, Pena J, Fernandez-Vega V, Gangaraju R, Beesabathuni NS, Kim MJ, Tian Q, Shah PS, Scampavia L, Spicer TP, Hwang CI. A new vulnerability to BET inhibition due to enhanced autophagy in BRCA2 deficient pancreatic cancer. Cell Death Dis 2023; 14:620. [PMID: 37735513 PMCID: PMC10514057 DOI: 10.1038/s41419-023-06145-9] [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: 05/30/2023] [Revised: 09/06/2023] [Accepted: 09/12/2023] [Indexed: 09/23/2023]
Abstract
Pancreatic cancer is one of the deadliest diseases in human malignancies. Among total pancreatic cancer patients, ~10% of patients are categorized as familial pancreatic cancer (FPC) patients, carrying germline mutations of the genes involved in DNA repair pathways (e.g., BRCA2). Personalized medicine approaches tailored toward patients' mutations would improve patients' outcome. To identify novel vulnerabilities of BRCA2-deficient pancreatic cancer, we generated isogenic Brca2-deficient murine pancreatic cancer cell lines and performed high-throughput drug screens. High-throughput drug screening revealed that Brca2-deficient cells are sensitive to Bromodomain and Extraterminal Motif (BET) inhibitors, suggesting that BET inhibition might be a potential therapeutic approach. We found that BRCA2 deficiency increased autophagic flux, which was further enhanced by BET inhibition in Brca2-deficient pancreatic cancer cells, resulting in autophagy-dependent cell death. Our data suggests that BET inhibition can be a novel therapeutic strategy for BRCA2-deficient pancreatic cancer.
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Affiliation(s)
- EunJung Lee
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, 95616, USA
| | - Suyakarn Archasappawat
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, 95616, USA
- Graduate Group in Integrative Pathobiology, University of California, Davis, Davis, CA, 95616, USA
| | - Keely Ji
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, 95616, USA
| | - Jocelyn Pena
- The Herbert Wertheim UF Scripps Institute, High-Throughput Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, FL, 33458, USA
| | - Virneliz Fernandez-Vega
- The Herbert Wertheim UF Scripps Institute, High-Throughput Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, FL, 33458, USA
| | - Ritika Gangaraju
- Department of Chemical Engineering, College of Engineering, University of California, Davis, Davis, CA, 95616, USA
| | - Nitin Sai Beesabathuni
- Department of Chemical Engineering, College of Engineering, University of California, Davis, Davis, CA, 95616, USA
| | - Martin Jean Kim
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, 95616, USA
| | - Qi Tian
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, 95616, USA
| | - Priya S Shah
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, 95616, USA
- Department of Chemical Engineering, College of Engineering, University of California, Davis, Davis, CA, 95616, USA
| | - Louis Scampavia
- The Herbert Wertheim UF Scripps Institute, High-Throughput Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, FL, 33458, USA
| | - Timothy P Spicer
- The Herbert Wertheim UF Scripps Institute, High-Throughput Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, FL, 33458, USA
| | - Chang-Il Hwang
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, 95616, USA.
- University of California Davis Comprehensive Cancer Center, Sacramento, CA, 95817, USA.
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7
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Rajan RG, Fernandez-Vega V, Sperry J, Nakashima J, Do LH, Andrews W, Boca S, Islam R, Chowdhary SA, Seldin J, Souza GR, Scampavia L, Hanafy KA, Vrionis FD, Spicer TP. In Vitro and In Vivo Drug-Response Profiling Using Patient-Derived High-Grade Glioma. Cancers (Basel) 2023; 15:3289. [PMID: 37444398 PMCID: PMC10339991 DOI: 10.3390/cancers15133289] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Genomic profiling cannot solely predict the complexity of how tumor cells behave in their in vivo microenvironment and their susceptibility to therapies. The aim of the study was to establish a functional drug prediction model utilizing patient-derived GBM tumor samples for in vitro testing of drug efficacy followed by in vivo validation to overcome the disadvantages of a strict pharmacogenomics approach. METHODS High-throughput in vitro pharmacologic testing of patient-derived GBM tumors cultured as 3D organoids offered a cost-effective, clinically and phenotypically relevant model, inclusive of tumor plasticity and stroma. RNAseq analysis supplemented this 128-compound screening to predict more efficacious and patient-specific drug combinations with additional tumor stemness evaluated using flow cytometry. In vivo PDX mouse models rapidly validated (50 days) and determined mutational influence alongside of drug efficacy. We present a representative GBM case of three tumors resected at initial presentation, at first recurrence without any treatment, and at a second recurrence following radiation and chemotherapy, all from the same patient. RESULTS Molecular and in vitro screening helped identify effective drug targets against several pathways as well as synergistic drug combinations of cobimetinib and vemurafenib for this patient, supported in part by in vivo tumor growth assessment. Each tumor iteration showed significantly varying stemness and drug resistance. CONCLUSIONS Our integrative model utilizing molecular, in vitro, and in vivo approaches provides direct evidence of a patient's tumor response drifting with treatment and time, as demonstrated by dynamic changes in their tumor profile, which may affect how one would address that drift pharmacologically.
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Affiliation(s)
- Robin G. Rajan
- Helene and Stephen Weicholz Cell Therapy Laboratory, Marcus Neuroscience Institute, Boca Raton Regional Hospital, 800 Meadows Road, Boca Raton, FL 33486, USA; (R.G.R.); (S.A.C.); (K.A.H.)
| | - Virneliz Fernandez-Vega
- The Herbert Wertheim UF Scripps Institute Molecular Screening Center, Department of Molecular Medicine, UF Scripps Biomedical Research, 130 Scripps Way, Jupiter, FL 33458, USA; (V.F.-V.); (L.S.)
| | - Jantzen Sperry
- Certis Oncology, 5626 Oberlin Dr. Suite 110, San Diego, CA 92121, USA; (J.S.); (J.N.); (L.H.D.); (W.A.)
| | - Jonathan Nakashima
- Certis Oncology, 5626 Oberlin Dr. Suite 110, San Diego, CA 92121, USA; (J.S.); (J.N.); (L.H.D.); (W.A.)
| | - Long H. Do
- Certis Oncology, 5626 Oberlin Dr. Suite 110, San Diego, CA 92121, USA; (J.S.); (J.N.); (L.H.D.); (W.A.)
| | - Warren Andrews
- Certis Oncology, 5626 Oberlin Dr. Suite 110, San Diego, CA 92121, USA; (J.S.); (J.N.); (L.H.D.); (W.A.)
| | - Simina Boca
- Innovation Center for Biomedical Informatics (ICBI), Departments of Oncology and Biostatistics, Bioinformatics and Biomathematics, Georgetown University Medical Center, 2115 Wisconsin Ave NW, Suite G100, Washington, DC 20007, USA;
| | - Rezwanul Islam
- Florida Atlantic University College of Medicine, 777 Glades Road, Boca Raton, FL 33431, USA;
| | - Sajeel A. Chowdhary
- Helene and Stephen Weicholz Cell Therapy Laboratory, Marcus Neuroscience Institute, Boca Raton Regional Hospital, 800 Meadows Road, Boca Raton, FL 33486, USA; (R.G.R.); (S.A.C.); (K.A.H.)
| | - Jan Seldin
- Greiner Bio-One North America, Inc., 4238 Capital Drive, Monroe, NC 28110, USA; (J.S.); (G.R.S.)
| | - Glauco R. Souza
- Greiner Bio-One North America, Inc., 4238 Capital Drive, Monroe, NC 28110, USA; (J.S.); (G.R.S.)
| | - Louis Scampavia
- The Herbert Wertheim UF Scripps Institute Molecular Screening Center, Department of Molecular Medicine, UF Scripps Biomedical Research, 130 Scripps Way, Jupiter, FL 33458, USA; (V.F.-V.); (L.S.)
| | - Khalid A. Hanafy
- Helene and Stephen Weicholz Cell Therapy Laboratory, Marcus Neuroscience Institute, Boca Raton Regional Hospital, 800 Meadows Road, Boca Raton, FL 33486, USA; (R.G.R.); (S.A.C.); (K.A.H.)
- Florida Atlantic University College of Medicine, 777 Glades Road, Boca Raton, FL 33431, USA;
| | - Frank D. Vrionis
- Helene and Stephen Weicholz Cell Therapy Laboratory, Marcus Neuroscience Institute, Boca Raton Regional Hospital, 800 Meadows Road, Boca Raton, FL 33486, USA; (R.G.R.); (S.A.C.); (K.A.H.)
- Florida Atlantic University College of Medicine, 777 Glades Road, Boca Raton, FL 33431, USA;
| | - Timothy P. Spicer
- The Herbert Wertheim UF Scripps Institute Molecular Screening Center, Department of Molecular Medicine, UF Scripps Biomedical Research, 130 Scripps Way, Jupiter, FL 33458, USA; (V.F.-V.); (L.S.)
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8
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Lee E, Archasappawat S, Ji K, Pena J, Fernandez-Vega V, Gangaraju R, Beesabathuni NS, Kim MJ, Tian Q, Shah P, Scampavia L, Spicer T, Hwang CI. A new vulnerability to BET inhibition due to enhanced autophagy in BRCA2 deficient pancreatic cancer. bioRxiv 2023:2023.05.30.542934. [PMID: 37398312 PMCID: PMC10312597 DOI: 10.1101/2023.05.30.542934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Pancreatic cancer is one of the deadliest diseases in human malignancies. Among total pancreatic cancer patients, ∼10% of patients are categorized as familial pancreatic cancer (FPC) patients, carrying germline mutations of the genes involved in DNA repair pathways ( e.g., BRCA2 ). Personalized medicine approaches tailored toward patients' mutations would improve patients' outcome. To identify novel vulnerabilities of BRCA2 -deficient pancreatic cancer, we generated isogenic Brca2 -deficient murine pancreatic cancer cell lines and performed high-throughput drug screens. High-throughput drug screening revealed that Brca2 -deficient cells are sensitive to Bromodomain and Extraterminal Motif (BET) inhibitors, suggesting that BET inhibition might be a potential therapeutic approach. We found that BRCA2 deficiency increased autophagic flux, which was further enhanced by BET inhibition in Brca2 -deficient pancreatic cancer cells, resulting in autophagy-dependent cell death. Our data suggests that BET inhibition can be a novel therapeutic strategy for BRCA2 -deficient pancreatic cancer.
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9
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Liao GY, Xu H, Shumate J, Scampavia L, Spicer T, Xu B. High throughput assay for compounds that boost BDNF expression in neurons. SLAS Discov 2023; 28:88-94. [PMID: 36842668 PMCID: PMC10759152 DOI: 10.1016/j.slasd.2023.02.005] [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] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/30/2023] [Accepted: 02/21/2023] [Indexed: 02/27/2023]
Abstract
Deficiencies in brain-derived neurotrophic factor (BDNF) have been linked to several brain disorders, making compounds that can boost neuronal BDNF synthesis attractive as potential therapeutics. However, a sensitive and quantitative BDNF assay for high-throughput screening (HTS) is still missing. Here we report the generation of a new mouse Bdnf allele, BdnfNLuc, in which the sequence encoding nano luciferase (NLuc) is inserted into the Bdnf locus immediately before the stop codon so that the allele will produce a BDNF-NLuc fusion protein. BDNF-NLuc protein appears to function like BDNF as BdnfNLuc/NLuc homozygous mice grew and behaved almost normally. We were able to establish and optimize cultures of cortical and hippocampal BdnfNLuc/+ neurons isolated from mouse embryos in 384-well plates. We used the cultures as a phenotypic assay to detect the ability of 10 mM KCl to stimulate BDNF synthesis and achieved a reproducible Z' factor > 0.50 for the assay, a measure considered suitable for HTS. We successfully scaled up the assay to screen the 1280-compound LOPAC library (Library of Pharmacologically Active Compounds). The screen identified several BDNF-boosting compounds, one of which is Bay K8644, a L-type voltage-gated calcium channel (L-VGCC) agonist, which was previously shown to stimulate BDNF synthesis. These results indicate that our phenotypic neuronal assay is ready for HTS to identify novel BDNF-boosting compounds.
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Affiliation(s)
- Guey-Ying Liao
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Haifei Xu
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Justin Shumate
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Louis Scampavia
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Timothy Spicer
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Baoji Xu
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, 130 Scripps Way, Jupiter, FL 33458, USA.
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10
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Smith E, Davis-Gardner ME, Garcia-Ordonez RD, Nguyen TT, Hull M, Chen E, Yu X, Bannister TD, Baillargeon P, Scampavia L, Griffin P, Farzan M, Spicer TP. High throughput screening for drugs that inhibit 3C-like protease in SARS-CoV-2. SLAS Discov 2023; 28:95-101. [PMID: 36646172 PMCID: PMC9839384 DOI: 10.1016/j.slasd.2023.01.001] [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] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/14/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023]
Abstract
The SARS coronavirus 2 (SARS-CoV-2) pandemic remains a major problem in many parts of the world and infection rates remain at extremely high levels. This high prevalence drives the continued emergence of new variants, and possibly ones that are more vaccine-resistant and that can drive infections even in highly vaccinated populations. The high rate of variant evolution makes clear the need for new therapeutics that can be clinically applied to minimize or eliminate the effects of COVID-19. With a hurdle of 10 years, on average, for first in class small molecule therapeutics to achieve FDA approval, the fastest way to identify therapeutics is by drug repurposing. To this end, we developed a high throughput cell-based screen that incorporates the essential viral 3C-like protease and its peptide cleavage site into a luciferase complementation assay to evaluate the efficacy of known drugs encompassing approximately 15,000 clinical-stage or FDA-approved small molecules. Confirmed inhibitors were also tested to determine their cytotoxic properties. Medicinal chemistry efforts to optimize the hits identified Tranilast as a potential lead. Here, we report the rapid screening and identification of potentially relevant drugs that exhibit selective inhibition of the SARS-CoV-2 viral 3C-like protease.
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Affiliation(s)
- Emery Smith
- Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL 33458, United States
| | | | - Ruben D Garcia-Ordonez
- Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL 33458, United States
| | - Tu-Trinh Nguyen
- Calibr at Scripps Research, La Jolla, CA 92037, United States
| | - Mitchell Hull
- Calibr at Scripps Research, La Jolla, CA 92037, United States
| | - Emily Chen
- Calibr at Scripps Research, La Jolla, CA 92037, United States
| | - Xuerong Yu
- Department of Chemistry, UF Scripps Biomedical Research, Jupiter, FL 33458, United States
| | - Thomas D Bannister
- Department of Chemistry, UF Scripps Biomedical Research, Jupiter, FL 33458, United States
| | - Pierre Baillargeon
- Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL 33458, United States
| | - Louis Scampavia
- Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL 33458, United States
| | - Patrick Griffin
- Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL 33458, United States
| | - Michael Farzan
- Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, FL 33458, United States
| | - Timothy P Spicer
- Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL 33458, United States.
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11
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Vega VF, Yang D, Jordán LO, Ye F, Conway L, Chen LY, Shumate J, Baillargeon P, Scampavia L, Parker C, Shen B, Spicer TP. Protocol for 3D screening of lung cancer spheroids using natural products. SLAS Discov 2023; 28:20-28. [PMID: 36681384 PMCID: PMC10291515 DOI: 10.1016/j.slasd.2023.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/23/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023]
Abstract
Non-small cell lung cancer (NSCLC) is the most common type of lung cancer and accounts for ∼84% of all lung cancer cases. NSCLC remains one of the leading causes of cancer-associated death, with a 5-year survival rate less than 25%. This type of cancer begins with healthy cells that change and start growing out of control, leading to the formation of lesions or tumors. Understanding the dynamics of how the tumor microenvironment promotes cancer initiation and progression that leads to cancer metastasis is crucial to help identify new molecular therapies. 3D primary cell tumor models have received renewed recognition due to their ability to better mimic the complexity of in vivo tumors and as a potential bridge between traditional 2D culture and in vivo studies. Vast improvements in 3D cell culture technologies make them much more cost effective and efficient largely because of the use of a cell-repellent surfaces and a novel angle plate adaptor technology. To exploit this technology, we accessed the Natural Products Library (NPL) at UF Scripps, which consists of crude extracts, partially purified fractions, and pure natural products (NPs). NPs generally are not very well represented in most drug discovery libraries and thus provide new insights to discover leads that could potentially emerge as novel molecular therapies. Herein we describe how we combined these technologies for 3D screening in 1536 well format using a panel of ten NSCLC cells lines (5 wild type and 5 mutant) against ∼1280 selected members of the NPL. After further evaluation, the selected active hits were prioritized to be screened against all 10 NSCLC cell lines as concentration response curves to determine the efficacy and selectivity of the compounds between wild type and mutant 3D cell models. Here, we demonstrate the methods needed for automated 3D screening using microbial NPs, exemplified by crude extracts, partially purified fractions, and pure NPs, that may lead to future use targeting human cancer.
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Affiliation(s)
- Virneliz Fernández Vega
- Molecular Screening Center, Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL, USA
| | - Dong Yang
- Department of Chemistry, UF Scripps Biomedical Research, Jupiter, FL, USA; Natural Products Discovery Center, UF Scripps Biomedical Research, Jupiter, FL, USA
| | - Luis Ortiz Jordán
- Molecular Screening Center, Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL, USA
| | - Fei Ye
- Department of Chemistry, UF Scripps Biomedical Research, Jupiter, FL, USA
| | - Louis Conway
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Li Yun Chen
- Department of Chemistry, UF Scripps Biomedical Research, Jupiter, FL, USA
| | - Justin Shumate
- Molecular Screening Center, Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL, USA
| | - Pierre Baillargeon
- Molecular Screening Center, Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL, USA
| | - Louis Scampavia
- Molecular Screening Center, Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL, USA
| | - Christopher Parker
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Ben Shen
- Department of Chemistry, UF Scripps Biomedical Research, Jupiter, FL, USA; Natural Products Discovery Center, UF Scripps Biomedical Research, Jupiter, FL, USA
| | - Timothy P Spicer
- Molecular Screening Center, Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL, USA.
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12
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Hou S, Li Z, Chen X, Wang W, Duan T, Scampavia L, Yuan Y, Spicer TP, Chen X, Xie T. Elemene sensitizes pancreatic cancer cells to bortezomib by enhancing proteasome inhibition via molecular patch mechanism. Signal Transduct Target Ther 2023; 8:87. [PMID: 36849489 PMCID: PMC9971206 DOI: 10.1038/s41392-023-01373-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 02/04/2023] [Accepted: 02/16/2023] [Indexed: 03/01/2023] Open
Affiliation(s)
- Shurong Hou
- School of Pharmacy, Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Zhenzhen Li
- School of Pharmacy, Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Xiaoling Chen
- School of Pharmacy, Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Wenxin Wang
- School of Pharmacy, Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
- Department of Pharmacology, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, China
| | - Ting Duan
- School of Pharmacy, Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Louis Scampavia
- UF Scripps Molecular Screening Center, Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL, 33458, USA
| | - Yaxia Yuan
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Timothy P Spicer
- UF Scripps Molecular Screening Center, Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL, 33458, USA.
| | - Xiabin Chen
- School of Pharmacy, Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China.
| | - Tian Xie
- School of Pharmacy, Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China.
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13
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Liu Z, Chen K, Dai J, Xu P, Sun W, Liu W, Zhao Z, Bennett SP, Li P, Ma T, Lin Y, Kawakami A, Yu J, Wang F, Wang C, Li M, Chase P, Hodder P, Spicer TP, Scampavia L, Cao C, Pan L, Dong J, Chen Y, Yu B, Guo M, Fang P, Fisher DE, Wang J. A unique hyperdynamic dimer interface permits small molecule perturbation of the melanoma oncoprotein MITF for melanoma therapy. Cell Res 2023; 33:55-70. [PMID: 36588115 PMCID: PMC9810709 DOI: 10.1038/s41422-022-00744-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 08/16/2021] [Accepted: 10/17/2022] [Indexed: 01/03/2023] Open
Abstract
Microphthalmia transcription factor (MITF) regulates melanocyte development and is the "lineage-specific survival" oncogene of melanoma. MITF is essential for melanoma initiation, progression, and relapse and has been considered an important therapeutic target; however, direct inhibition of MITF through small molecules is considered impossible, due to the absence of a ligand-binding pocket for drug design. Here, our structural analyses show that the structure of MITF is hyperdynamic because of its out-of-register leucine zipper with a 3-residue insertion. The dynamic MITF is highly vulnerable to dimer-disrupting mutations, as we observed that MITF loss-of-function mutations in human Waardenburg syndrome type 2 A are frequently located on the dimer interface and disrupt the dimer forming ability accordingly. These observations suggest a unique opportunity to inhibit MITF with small molecules capable of disrupting the MITF dimer. From a high throughput screening against 654,650 compounds, we discovered compound TT-012, which specifically binds to dynamic MITF and destroys the latter's dimer formation and DNA-binding ability. Using chromatin immunoprecipitation assay and RNA sequencing, we showed that TT-012 inhibits the transcriptional activity of MITF in B16F10 melanoma cells. In addition, TT-012 inhibits the growth of high-MITF melanoma cells, and inhibits the tumor growth and metastasis with tolerable toxicity to liver and immune cells in animal models. Together, this study demonstrates a unique hyperdynamic dimer interface in melanoma oncoprotein MITF, and reveals a novel approach to therapeutically suppress MITF activity.
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Affiliation(s)
- Zaizhou Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Kaige Chen
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, Guangdong, China
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Jun Dai
- Department of Dermatology, Cutaneous Biology Research Center, Mass. General Hospital, Harvard Medical School, Boston, MA, USA
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Peng Xu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Wei Sun
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wanlin Liu
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhixin Zhao
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | - Peifeng Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Tiancheng Ma
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yuqi Lin
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Akinori Kawakami
- Department of Dermatology, Cutaneous Biology Research Center, Mass. General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jing Yu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fei Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chunxi Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Miao Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Peter Chase
- Scripps Research, Jupiter, FL, USA
- BMS Inc., Lawrenceville, NJ, USA
| | - Peter Hodder
- Scripps Research, Jupiter, FL, USA
- Amgen Inc., Thousand Oaks, CA, USA
| | | | | | - Chunyang Cao
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lifeng Pan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Jiajia Dong
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yong Chen
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Biao Yu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China.
| | - Min Guo
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- Kangma-Healthcode Biotech Co., Ltd., Shanghai, China.
| | - Pengfei Fang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China.
| | - David E Fisher
- Department of Dermatology, Cutaneous Biology Research Center, Mass. General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Jing Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China.
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14
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Reed A, Ichu TA, Milosevich N, Melillo B, Schafroth MA, Otsuka Y, Scampavia L, Spicer TP, Cravatt BF. LPCAT3 Inhibitors Remodel the Polyunsaturated Phospholipid Content of Human Cells and Protect from Ferroptosis. ACS Chem Biol 2022; 17:1607-1618. [PMID: 35658397 DOI: 10.1021/acschembio.2c00317] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
LPCAT3 is an integral membrane acyltransferase in the Lands cycle responsible for generating C20:4 phospholipids and has been implicated in key biological processes such as intestinal lipid absorption, lipoprotein assembly, and ferroptosis. Small-molecule inhibitors of LPCAT3 have not yet been described and would offer complementary tools to genetic models of LPCAT3 loss, which causes neonatal lethality in mice. Here, we report the discovery by high-throughput screening of a class of potent, selective, and cell-active inhibitors of LPCAT3. We provide evidence that these compounds inhibit LPCAT3 in a biphasic manner, possibly reflecting differential activity at each subunit of the LPCAT3 homodimer. LPCAT3 inhibitors cause rapid rewiring of polyunsaturated phospholipids in human cells that mirrors the changes observed in LPCAT3-null cells. Notably, these changes include not only the suppression of C20:4 phospholipids but also corresponding increases in C22:4 phospholipids, providing a potential mechanistic explanation for the partial but incomplete protection from ferroptosis observed in cells with pharmacological or genetic disruption of LPCAT3.
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Affiliation(s)
- Alex Reed
- Department of Chemistry, The Scripps Research Institute, La Jolla, San Diego, California 92037, United States
| | - Taka-Aki Ichu
- Department of Chemistry, The Scripps Research Institute, La Jolla, San Diego, California 92037, United States
| | - Natalia Milosevich
- Department of Chemistry, The Scripps Research Institute, La Jolla, San Diego, California 92037, United States
| | - Bruno Melillo
- Department of Chemistry, The Scripps Research Institute, La Jolla, San Diego, California 92037, United States
| | - Michael A Schafroth
- Department of Chemistry, The Scripps Research Institute, La Jolla, San Diego, California 92037, United States
| | - Yuka Otsuka
- UF Scripps HTS Facility, UF Scripps, Jupiter, Florida 33458, United States
| | - Louis Scampavia
- UF Scripps HTS Facility, UF Scripps, Jupiter, Florida 33458, United States
| | - Timothy P Spicer
- UF Scripps HTS Facility, UF Scripps, Jupiter, Florida 33458, United States
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, San Diego, California 92037, United States
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15
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Fernandez-Vega V, Hou S, Plenker D, Tiriac H, Baillargeon P, Shumate J, Scampavia L, Seldin J, Souza GR, Tuveson DA, Spicer TP. Lead identification using 3D models of pancreatic cancer. SLAS Discov 2022; 27:159-166. [PMID: 35306207 PMCID: PMC10258910 DOI: 10.1016/j.slasd.2022.03.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 03/14/2022] [Indexed: 01/07/2023]
Abstract
Recent technological advances have enabled 3D tissue culture models for fast and affordable HTS. We are no longer bound to 2D models for anti-cancer agent discovery, and it is clear that 3D tumor models provide more predictive data for translation of preclinical studies. In a previous study, we validated a microplate 3D spheroid-based technology for its compatibility with HTS automation. Small-scale screens using approved drugs have demonstrated that drug responses tend to differ between 2D and 3D cancer cell proliferation models. Here, we applied this 3D technology to the first ever large-scale screening effort completing HTS on over 150K molecules against primary pancreatic cancer cells. It is the first demonstration that a screening campaign of this magnitude using clinically relevant, ex-vivo 3D pancreatic tumor models established directly from biopsy, can be readily achieved in a fashion like traditional drug screen using 2D cell models. We identified four unique series of compounds with sub micromolar and even low nanomolar potency against a panel of patient derived pancreatic organoids. We also applied the 3D technology to test lead efficacy in autologous cancer associated fibroblasts and found a favorable profile for better efficacy in the cancer over wild type primary cells, an important milestone towards better leads. Importantly, the initial leads have been further validated in across multiple institutes with concordant outcomes. The work presented here represents the genesis of new small molecule leads found using 3D models of primary pancreas tumor cells.
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Affiliation(s)
- Virneliz Fernandez-Vega
- The Scripps Research Institute Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA
| | - Shurong Hou
- The Scripps Research Institute Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA
| | - Dennis Plenker
- Cancer Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Hervé Tiriac
- University of San Diego, California, Moores Cancer Center, Department of Surgery, San Diego, CA, USA
| | - Pierre Baillargeon
- The Scripps Research Institute Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA
| | - Justin Shumate
- The Scripps Research Institute Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA
| | - Louis Scampavia
- The Scripps Research Institute Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA
| | - Jan Seldin
- Greiner Bio-One North America, Inc., Monroe, NC, USA
| | | | - David A Tuveson
- Cancer Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Timothy P Spicer
- The Scripps Research Institute Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA.
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16
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Rao SR, Kostic A, Baillargeon P, Fernandez-Vega V, de Anda MR, Fletcher K, Shumate J, Scampavia L, Buxbaum JD, Spicer TP. Screening for modulators of autism spectrum disorder using induced human neurons. SLAS Discov 2022; 27:128-139. [PMID: 35123134 DOI: 10.1016/j.slasd.2022.01.004] [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] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Autism Spectrum Disorder (ASD) is a heterogeneous neurodevelopmental disorder. There are no drugs to treat the core symptoms. De novo mutations often play an important role in ASD and multiple high-risk loci have been identified in the last decade. These mutations range from copy number variants to small insertion/deletion and single nucleotide variants. Large-scale exome sequencing has identified over 100 risk genes that are associated with ASD. Both etiological heterogeneity and unavailability of human neurons remain major hurdles in understanding the pathophysiology of ASD and testing of new drug candidates. Hence, the most achievable and relevant model to screen for potential drugs is human neurons from inducible pluripotent stem cells (iPSCs), including those from individuals with genetic mutations. In this study, we tested stem cells from individuals carrying mutations in ADNP, FOXP1 or SHANK3. They were scaled and reprogrammed to glutamatergic neurons and assessed for the effects of their specific mutations on neurite outgrowth. High Content Analysis allowed us to observe phenotypic differences between ASD neurons compared to controls, in terms of neuron number, neurite number and neurite length per neuron. Further, neurons were derived from both patient derived and genetically modified iPSCs with DDX3X mutation which were tested against 5088 drug like compounds. We assessed individual compound effects on the induced neurons to determine if they elicited changes that would indicate neurite growth (neuroprotection) or, alternatively, reduce outgrowth and hence appear neurotoxic. This report includes all methods, phenotypic outcomes, and results for the largest ASD small molecule screening effort done to date.
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Affiliation(s)
- Sumitha Rajendra Rao
- The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Ana Kostic
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Pierre Baillargeon
- The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Virneliz Fernandez-Vega
- The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Mitzy Rios de Anda
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Kelty Fletcher
- The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Justin Shumate
- The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Louis Scampavia
- The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Timothy P Spicer
- The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA.
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17
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Mediouni S, Mou H, Otsuka Y, Jablonski JA, Adcock RS, Batra L, Chung DH, Rood C, de Vera IMS, Rahaim R, Ullah S, Yu X, Getmanenko YA, Kennedy NM, Wang C, Nguyen TT, Hull M, Chen E, Bannister TD, Baillargeon P, Scampavia L, Farzan M, Valente ST, Spicer TP. Identification of potent small molecule inhibitors of SARS-CoV-2 entry. SLAS Discov 2022; 27:8-19. [PMID: 35058179 PMCID: PMC8577999 DOI: 10.1016/j.slasd.2021.10.012] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 responsible for COVID-19 remains a persistent threat to mankind, especially for the immunocompromised and elderly for which the vaccine may have limited effectiveness. Entry of SARS-CoV-2 requires a high affinity interaction of the viral spike protein with the cellular receptor angiotensin-converting enzyme 2. Novel mutations on the spike protein correlate with the high transmissibility of new variants of SARS-CoV-2, highlighting the need for small molecule inhibitors of virus entry into target cells. We report the identification of such inhibitors through a robust high-throughput screen testing 15,000 small molecules from unique libraries. Several leads were validated in a suite of mechanistic assays, including whole cell SARS-CoV-2 infectivity assays. The main lead compound, calpeptin, was further characterized using SARS-CoV-1 and the novel SARS-CoV-2 variant entry assays, SARS-CoV-2 protease assays and molecular docking. This study reveals calpeptin as a potent and specific inhibitor of SARS-CoV-2 and some variants.
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Affiliation(s)
- Sonia Mediouni
- Scripps Research, Department of Immunology and Microbiology, Scripps Research, Jupiter, FL 33458, USA
| | - Huihui Mou
- Scripps Research, Department of Immunology and Microbiology, Scripps Research, Jupiter, FL 33458, USA
| | - Yuka Otsuka
- Scripps Research, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Joseph Anthony Jablonski
- Scripps Research, Department of Immunology and Microbiology, Scripps Research, Jupiter, FL 33458, USA
| | - Robert Scott Adcock
- Center for Predictive Medicine, Department of Microbiology Immunology, School of Medicine, University of Louisville, KY 40202, USA
| | - Lalit Batra
- Center for Predictive Medicine, Department of Microbiology Immunology, School of Medicine, University of Louisville, KY 40202, USA
| | - Dong-Hoon Chung
- Center for Predictive Medicine, Department of Microbiology Immunology, School of Medicine, University of Louisville, KY 40202, USA
| | - Christopher Rood
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Ian Mitchelle S de Vera
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Ronald Rahaim
- Scripps Research, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Sultan Ullah
- Scripps Research, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Xuerong Yu
- Scripps Research, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Yulia A Getmanenko
- Scripps Research, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Nicole M Kennedy
- Scripps Research, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Chao Wang
- Scripps Research, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Tu-Trinh Nguyen
- CALIBR, Scripps Research, 11119N Torrey Pines Rd, La Jolla, CA 9203, USA
| | - Mitchell Hull
- CALIBR, Scripps Research, 11119N Torrey Pines Rd, La Jolla, CA 9203, USA
| | - Emily Chen
- CALIBR, Scripps Research, 11119N Torrey Pines Rd, La Jolla, CA 9203, USA
| | - Thomas D Bannister
- Scripps Research, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Pierre Baillargeon
- Scripps Research, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Louis Scampavia
- Scripps Research, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Michael Farzan
- Scripps Research, Department of Immunology and Microbiology, Scripps Research, Jupiter, FL 33458, USA
| | - Susana T Valente
- Scripps Research, Department of Immunology and Microbiology, Scripps Research, Jupiter, FL 33458, USA
| | - Timothy P Spicer
- Scripps Research, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA.
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18
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Chulkov EG, Smith E, Rohr CM, Yahya NA, Park SK, Scampavia L, Spicer TP, Marchant JS. Identification of novel modulators of a schistosome transient receptor potential channel targeted by praziquantel. PLoS Negl Trop Dis 2021; 15:e0009898. [PMID: 34731172 PMCID: PMC8565742 DOI: 10.1371/journal.pntd.0009898] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 06/17/2021] [Accepted: 10/11/2021] [Indexed: 12/24/2022] Open
Abstract
Given the worldwide burden of neglected tropical diseases, there is ongoing need to develop novel anthelmintic agents to strengthen the pipeline of drugs to combat these burdensome infections. Many diseases caused by parasitic flatworms are treated using the anthelmintic drug praziquantel (PZQ), employed for decades as the key clinical agent to treat schistosomiasis. PZQ activates a flatworm transient receptor potential (TRP) channel within the melastatin family (TRPMPZQ) to mediate sustained Ca2+ influx and worm paralysis. As a druggable target present in many parasitic flatworms, TRPMPZQ is a promising target for a target-based screening campaign with the goal of discovering novel regulators of this channel complex. Here, we have optimized methods to miniaturize a Ca2+-based reporter assay for Schistosoma mansoni TRPMPZQ (Sm.TRPMPZQ) activity enabling a high throughput screening (HTS) approach. This methodology will enable further HTS efforts against Sm.TRPMPZQ as well as other flatworm ion channels. A pilot screen of ~16,000 compounds yielded a novel activator of Sm.TRPMPZQ, and numerous potential blockers. The new activator of Sm.TRPMPZQ represented a distinct chemotype to PZQ, but is a known chemical entity previously identified by phenotypic screening. The fact that a compound prioritized from a phenotypic screening campaign is revealed to act, like PZQ, as an Sm.TRPMPZQ agonist underscores the validity of TRPMPZQ as a druggable target for antischistosomal ligands.
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Affiliation(s)
- Evgeny G. Chulkov
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Emery Smith
- Department of Molecular Medicine, Scripps Research, Jupiter, Florida, United States of America
| | - Claudia M. Rohr
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Nawal A. Yahya
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Sang-Kyu Park
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Louis Scampavia
- Department of Molecular Medicine, Scripps Research, Jupiter, Florida, United States of America
| | - Timothy P. Spicer
- Department of Molecular Medicine, Scripps Research, Jupiter, Florida, United States of America
| | - Jonathan S. Marchant
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
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19
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Stoveken HM, Fernandez-Vega V, Muntean BS, Patil DN, Shumate J, Bannister TD, Scampavia L, Spicer TP, Martemyanov KA. Identification of Potential Modulators of the RGS7/Gβ5/R7BP Complex. SLAS Discov 2021; 26:1177-1188. [PMID: 34112017 DOI: 10.1177/24725552211020679] [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] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Regulators of G protein signaling (RGS) proteins serve as critical regulatory nodes to limit the lifetime and extent of signaling via G protein-coupled receptors (GPCRs). Previously, approaches to pharmacologically inhibit RGS activity have mostly focused on the inhibition of GTPase activity by interrupting the interaction of RGS proteins with the G proteins they regulate. However, several RGS proteins are also regulated by association with binding partners. A notable example is the mammalian RGS7 protein, which has prominent roles in metabolic control, vision, reward, and actions of opioid analgesics. In vivo, RGS7 exists in complex with the binding partners type 5 G protein β subunit (Gβ5) and R7 binding protein (R7BP), which control its stability and activity, respectively. Targeting the whole RGS7/Gβ5/R7BP protein complex affords the opportunity to allosterically tune opioid receptor signaling following opioid engagement while potentially bypassing undesirable side effects. Hence, we implemented a novel strategy to pharmacologically target the interaction between RGS7/Gβ5 and R7BP. To do so, we searched for protein complex inhibitors using a time-resolved fluorescence resonance energy transfer (FRET)-based high-throughput screening (HTS) assay that measures compound-mediated alterations in the FRET signal between RGS7/Gβ5 and R7BP. We performed two HTS campaigns, each screening ~100,000 compounds from the Scripps Drug Discovery Library (SDDL). Each screen yielded more than 100 inhibitors, which will be described herein.
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Affiliation(s)
- Hannah M Stoveken
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL, USA
| | | | - Brian S Muntean
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL, USA
| | - Dipak N Patil
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL, USA
| | - Justin Shumate
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Thomas D Bannister
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Louis Scampavia
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Timothy P Spicer
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
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20
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Smith E, Davis-Gardner ME, Garcia-Ordonez RD, Nguyen TT, Hull M, Chen E, Baillargeon P, Scampavia L, Strutzenberg T, Griffin PR, Farzan M, Spicer TP. High-Throughput Screening for Drugs That Inhibit Papain-Like Protease in SARS-CoV-2. SLAS Discov 2020; 25:1152-1161. [PMID: 33043784 PMCID: PMC7550789 DOI: 10.1177/2472555220963667] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in late 2019 has triggered an ongoing global pandemic whereby infection may result in a lethal severe pneumonia-like disease designated as coronavirus disease 2019 (COVID-19). To date, millions of confirmed cases and hundreds of thousands of deaths have been reported worldwide, and there are currently no medical countermeasures available to prevent or treat the disease. The purported development of a vaccine could require at least 1–4 years, while the typical timeline from hit finding to drug registration of an antiviral is >10 years. Thus, repositioning of known drugs can significantly accelerate the development and deployment of therapies for COVID-19. To identify therapeutics that can be repurposed as SARS-CoV-2 antivirals, we developed and initiated a high-throughput cell-based screen that incorporates the essential viral papain-like protease (PLpro) and its peptide cleavage site into a luciferase complementation assay to evaluate the efficacy of known drugs encompassing approximately 15,000 clinical-stage or US Food and Drug Administration (FDA)-approved small molecules. Confirmed inhibitors were also tested to determine their cytotoxic properties. Here, we report the identification of four clinically relevant drugs that exhibit selective inhibition of the SARS-CoV-2 viral PLpro.
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Affiliation(s)
- Emery Smith
- Department of Molecular Medicine, Scripps Research Institute, Scripps Florida, Jupiter, FL, USA
| | | | - Ruben D Garcia-Ordonez
- Department of Molecular Medicine, Scripps Research Institute, Scripps Florida, Jupiter, FL, USA
| | | | | | - Emily Chen
- Calibr at Scripps Research, La Jolla, CA, USA
| | - Pierre Baillargeon
- Department of Molecular Medicine, Scripps Research Institute, Scripps Florida, Jupiter, FL, USA
| | - Louis Scampavia
- Department of Molecular Medicine, Scripps Research Institute, Scripps Florida, Jupiter, FL, USA
| | - Timothy Strutzenberg
- Department of Molecular Medicine, Scripps Research Institute, Scripps Florida, Jupiter, FL, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, Scripps Research Institute, Scripps Florida, Jupiter, FL, USA
| | - Michael Farzan
- Immunology and Microbiology, Scripps Research Institute, Scripps Florida, Jupiter, FL, USA
| | - Timothy P Spicer
- Department of Molecular Medicine, Scripps Research Institute, Scripps Florida, Jupiter, FL, USA
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21
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Smith E, Dukovski D, Shumate J, Scampavia L, Miller JP, Spicer TP. Identification of Compounds That Promote Readthrough of Premature Termination Codons in the CFTR. SLAS Discov 2020; 26:205-215. [PMID: 33016182 PMCID: PMC7838340 DOI: 10.1177/2472555220962001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Cystic fibrosis (CF) is caused by a mutation of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene, which disrupts an ion channel involved in hydration maintenance via anion homeostasis. Nearly 5% of CF patients possess one or more copies of the G542X allele, which results in a stop codon at residue 542, preventing full-length CFTR protein synthesis. Identifying small-molecule modulators of mutant CFTR biosynthesis that affect the readthrough of this and other premature termination codons to synthesize a fully functional CFTR protein represents a novel target area of drug discovery. We describe the implementation and integration for large-scale screening of a homogeneous, 1536-well functional G542X-CFTR readthrough assay. The assay uses HEK 293 cells engineered to overexpress the G542X-CFTR mutant, whose functional activity is monitored with a membrane potential dye. Cells are co-incubated with a CFTR amplifier and CFTR corrector to maximize mRNA levels and trafficking of CFTR to the cell surface. Compounds that allow translational readthrough and synthesis of functional CFTR chloride channels are reflected by changes in membrane potential in response to cAMP stimulation with forskolin and CFTR channel potentiation with genistein. Assay statistics yielded Z′ values of 0.69 ± 0.06. As further evidence of its suitability for high-throughput screening, we completed automated screening of approximately 666,000 compounds, identifying 7761 initial hits. Following secondary and tertiary assays, we identified 188 confirmed hit compounds with low and submicromolar potencies. Thus, this approach takes advantage of a phenotypic screen with high-throughput scalability to identify new small-molecule G542X-CFTR readthrough modulators.
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Affiliation(s)
- Emery Smith
- Department of Molecular Medicine, Scripps Florida, The Scripps Research Institute Molecular Screening Center, Jupiter, FL, USA
| | | | - Justin Shumate
- Department of Molecular Medicine, Scripps Florida, The Scripps Research Institute Molecular Screening Center, Jupiter, FL, USA
| | - Louis Scampavia
- Department of Molecular Medicine, Scripps Florida, The Scripps Research Institute Molecular Screening Center, Jupiter, FL, USA
| | | | - Timothy P Spicer
- Department of Molecular Medicine, Scripps Florida, The Scripps Research Institute Molecular Screening Center, Jupiter, FL, USA
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22
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Grandjean JMD, Madhavan A, Cech L, Seguinot BO, Paxman RJ, Smith E, Scampavia L, Powers ET, Cooley CB, Plate L, Spicer TP, Kelly JW, Wiseman RL. Pharmacologic IRE1/XBP1s activation confers targeted ER proteostasis reprogramming. Nat Chem Biol 2020; 16:1052-1061. [PMID: 32690944 PMCID: PMC7502540 DOI: 10.1038/s41589-020-0584-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [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: 07/23/2019] [Accepted: 06/05/2020] [Indexed: 12/14/2022]
Abstract
Activation of the IRE1/XBP1s signaling arm of the unfolded protein response (UPR) is a promising strategy to correct defects in endoplasmic reticulum (ER) proteostasis implicated in diverse diseases. However, no pharmacologic activators of this pathway identified to date are suitable for ER proteostasis remodeling through selective activation of IRE1/XBP1s signaling. Here, we use high-throughput screening to identify non-toxic compounds that induce ER proteostasis remodeling through IRE1/XBP1s activation. We employ transcriptional profiling to stringently confirm that our prioritized compounds selectively activate IRE1/XBP1s signaling without activating other cellular stress-responsive signaling pathways. Furthermore, we demonstrate that our compounds improve ER proteostasis of destabilized variants of amyloid precursor protein (APP) through an IRE1-dependent mechanism and reduce APP-associated mitochondrial toxicity in cellular models. These results establish highly selective IRE1/XBP1s activating compounds that can be widely employed to define the functional importance of IRE1/XBP1s activity for ER proteostasis regulation in the context of health and disease.
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Affiliation(s)
- Julia M D Grandjean
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Aparajita Madhavan
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Lauren Cech
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Bryan O Seguinot
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Ryan J Paxman
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Emery Smith
- Scripps Research Molecular Screening Center, The Scripps Research Institute, Jupiter, FL, USA
| | - Louis Scampavia
- Scripps Research Molecular Screening Center, The Scripps Research Institute, Jupiter, FL, USA
| | - Evan T Powers
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Lars Plate
- Departments of Chemistry and Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Timothy P Spicer
- Scripps Research Molecular Screening Center, The Scripps Research Institute, Jupiter, FL, USA
| | - Jeffery W Kelly
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - R Luke Wiseman
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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23
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Pan C, Otsuka Y, Sridharan B, Woo M, Leiton CV, Babu S, Torrente Gonçalves M, Kawalerski RR, K. Bai JD, Chang DK, Biankin AV, Scampavia L, Spicer T, Escobar‐Hoyos LF, Shroyer KR. An unbiased high-throughput drug screen reveals a potential therapeutic vulnerability in the most lethal molecular subtype of pancreatic cancer. Mol Oncol 2020; 14:1800-1816. [PMID: 32533886 PMCID: PMC7400780 DOI: 10.1002/1878-0261.12743] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 10/07/2019] [Revised: 03/26/2020] [Accepted: 06/03/2020] [Indexed: 01/05/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is predicted to become the second leading cause of cancer-related deaths in the United States by 2020, due in part to innate resistance to widely used chemotherapeutic agents and limited knowledge about key molecular factors that drive tumor aggression. We previously reported a novel negative prognostic biomarker, keratin 17 (K17), whose overexpression in cancer results in shortened patient survival. In this study, we aimed to determine the predictive value of K17 and explore the therapeutic vulnerability in K17-expressing PDAC, using an unbiased high-throughput drug screen. Patient-derived data analysis showed that K17 expression correlates with resistance to gemcitabine (Gem). In multiple in vitro and in vivo models of PDAC, spanning human and murine PDAC cells, and orthotopic xenografts, we determined that the expression of K17 results in a more than twofold increase in resistance to Gem and 5-fluorouracil, key components of current standard-of-care chemotherapeutic regimens. Furthermore, through an unbiased drug screen, we discovered that podophyllotoxin (PPT), a microtubule inhibitor, showed significantly higher sensitivity in K17-positive compared to K17-negative PDAC cell lines and animal models. In the clinic, another microtubule inhibitor, paclitaxel (PTX), is used in combination with Gem as a first-line chemotherapeutic regimen for PDAC. Surprisingly, we found that when combined with Gem, PPT, but not PTX, was synergistic in inhibiting the viability of K17-expressing PDAC cells. Importantly, in preclinical models, PPT in combination with Gem effectively decreased tumor growth and enhanced the survival of mice bearing K17-expressing tumors. This provides evidence that PPT and its derivatives could potentially be combined with Gem to enhance treatment efficacy for the ~ 50% of PDACs that express high levels of K17. In summary, we reported that K17 is a novel target for developing a biomarker-based personalized treatment for PDAC.
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Affiliation(s)
- Chun‐Hao Pan
- Department of PathologyRenaissance School of MedicineStony Brook UniversityNYUSA
- Molecular and Cellular Biology Graduate ProgramStony Brook UniversityNYUSA
| | | | | | - Melissa Woo
- Department of PathologyRenaissance School of MedicineStony Brook UniversityNYUSA
- Simons Summer Research ProgramStony Brook UniversityNYUSA
| | - Cindy V. Leiton
- Department of PathologyRenaissance School of MedicineStony Brook UniversityNYUSA
| | - Sruthi Babu
- Department of PathologyRenaissance School of MedicineStony Brook UniversityNYUSA
- Department of Family, Population & Preventive MedicineRenaissance School of MedicineStony Brook UniversityNYUSA
| | | | - Ryan R. Kawalerski
- Department of PathologyRenaissance School of MedicineStony Brook UniversityNYUSA
| | - Ji Dong K. Bai
- Department of PathologyRenaissance School of MedicineStony Brook UniversityNYUSA
| | - David K. Chang
- Wolfson Wohl Cancer Research CentreInstitute of Cancer SciencesUniversity of GlasgowUK
- West of Scotland Pancreatic UnitGlasgow Royal InfirmaryUK
| | - Andrew V. Biankin
- Wolfson Wohl Cancer Research CentreInstitute of Cancer SciencesUniversity of GlasgowUK
- West of Scotland Pancreatic UnitGlasgow Royal InfirmaryUK
| | | | | | - Luisa F. Escobar‐Hoyos
- Department of PathologyRenaissance School of MedicineStony Brook UniversityNYUSA
- Department of Therapeutic RadiologySchool of MedicineYale UniversityNew HavenCTUSA
- David M. Rubenstein Center for Pancreatic Cancer ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Genetic Toxicology and Cytogenetics Research GroupDepartment of BiologySchool of Natural Sciences and EducationUniversidad del CaucaPopayánColombia
| | - Kenneth R. Shroyer
- Department of PathologyRenaissance School of MedicineStony Brook UniversityNYUSA
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24
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Otsuka Y, Airola MV, Choi YM, Coant N, Snider J, Cariello C, Saied EM, Arenz C, Bannister T, Rahaim R, Hannun YA, Shumate J, Scampavia L, Haley JD, Spicer TP. Identification of Small-Molecule Inhibitors of Neutral Ceramidase (nCDase) via Target-Based High-Throughput Screening. SLAS Discov 2020; 26:113-121. [PMID: 32734807 DOI: 10.1177/2472555220945283] [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] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
There is interest in developing inhibitors of human neutral ceramidase (nCDase) because this enzyme plays a critical role in colon cancer. There are currently no potent or clinically effective inhibitors for nCDase reported to date, so we adapted a fluorescence-based enzyme activity method to a high-throughput screening format. We opted to use an assay whereby nCDase hydrolyzes the substrate RBM 14-16, and the addition of NaIO4 acts as an oxidant that releases umbelliferone, resulting in a fluorescent signal. As designed, test compounds that act as ceramidase inhibitors will prevent the hydrolysis of RBM 14-16, thereby decreasing fluorescence. This assay uses a 1536-well plate format with excitation in the blue spectrum of light energy, which could be a liability, so we incorporated a counterscreen that allows for rapid selection against fluorescence artifacts to minimize false-positive hits. The high-throughput screen of >650,000 small molecules found several lead series of hits. Multiple rounds of chemical optimization ensued with improved potency in terms of IC50 and selectivity over counterscreen assays. This study describes the first large-scale high-throughput optical screening assay for nCDase inhibitors that has resulted in leads that are now being pursued in crystal docking studies and in vitro drug metabolism and pharmacokinetics (DMPK).
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Affiliation(s)
- Yuka Otsuka
- Department of Molecular Medicine, Scripps Research, The Scripps Research Molecular Screening Center, Jupiter, FL, USA
| | - Michael V Airola
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | - Yong-Mi Choi
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | - Nicolas Coant
- Stony Brook University Cancer Center, Stony Brook, NY, USA
| | - Justin Snider
- Stony Brook University Cancer Center, Stony Brook, NY, USA
| | - Chris Cariello
- Department of Pathology, Stony Brook Renaissance School of Medicine, Stony Brook, NY, USA
| | - Essa M Saied
- Chemistry Department, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Christoph Arenz
- Institute for Chemistry, Humboldt Universität zu Berlin, Berlin, Germany
| | - Thomas Bannister
- Department of Molecular Medicine, Scripps Research, The Scripps Research Molecular Screening Center, Jupiter, FL, USA
| | - Ron Rahaim
- Department of Molecular Medicine, Scripps Research, The Scripps Research Molecular Screening Center, Jupiter, FL, USA
| | - Yusuf A Hannun
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA.,Stony Brook University Cancer Center, Stony Brook, NY, USA
| | - Justin Shumate
- Department of Molecular Medicine, Scripps Research, The Scripps Research Molecular Screening Center, Jupiter, FL, USA
| | - Louis Scampavia
- Department of Molecular Medicine, Scripps Research, The Scripps Research Molecular Screening Center, Jupiter, FL, USA
| | - John D Haley
- Stony Brook University Cancer Center, Stony Brook, NY, USA.,Department of Pathology, Stony Brook Renaissance School of Medicine, Stony Brook, NY, USA
| | - Timothy P Spicer
- Department of Molecular Medicine, Scripps Research, The Scripps Research Molecular Screening Center, Jupiter, FL, USA
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25
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Boca S, Bhuvaneshwar K, Fernandez-Vega V, Kancherla J, Rao S, Madhavan S, Riggins R, Beckman RA, Corrada Bravo H, Scampavia L, Spicer T. Prioritizing targeted therapies in an evidence-based manner, integrating biological context and functional precision medicine. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.e14065] [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: 11/20/2022] Open
Abstract
e14065 Background: It is becoming increasingly common for cancer patients to undergo molecular profiling of their tumors in order to see whether there are any actionable DNA, gene expression, or protein expression signatures. For example, individuals with ER+ or HER2+ breast cancer or KRAS wild type (non-mutated) colorectal cancer are prescribed specific targeted therapies. When an individual’s molecular alterations do not match any currently-approved recommendations for their tumor type, their clinician may consider prescribing a therapy approved in a different tumor type. Unfortunately, tumors often eventually become resistant to the therapies they are exposed to, leading to a narrowing of options after each therapy line. Methods: We previously developed CDGnet, an evidence-based approach and web-based tool for prioritizing targeted therapies based on tumor molecular profiles based on known pathways which provide biological context. CDGnet considers approved therapies with biomarkers among the alterations for the individual’s tumor type and other tumor types as the first and second evidence level categories respectively. These are followed by therapies that target or have as biomarkers genes or proteins downstream of altered oncogenes, considering curated pathways for the individual’s tumor type and other tumor types as the third and fourth evidence level categories respectively. We are currently expanding CDGnet in order to include data from high-throughput screening (HTS) experiments of NCI oncologic drugs performed on patient-derived organoids. The concept of “functional precision medicine” consists of using functional drug efficacy determination directly on individual patients, in this case by considering drugs with low half maximal effective concentrations (EC50) which are tested on tissues derived from the actual patients. Results: We will present extensions to CDGnet that allow users to upload both the molecular profiles and the HTS data to see whether any drugs are predicted by both approaches or whether specific combinations appear promising for further testing. Preliminary results on a set of glioblastoma samples will be presented. Conclusions: We hope that extending CDGnet to also include HTS data will eventually allow a truly multi-factorial personalized oncology approach, whereby both molecular alterations at the DNA, RNA, and protein levels and patient-derived organoids will be considered in deciding on treatment plans for individuals.
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Affiliation(s)
- Simina Boca
- Georgetown Innovation Center for Biomedical Informatics, Washington, DC
| | | | | | | | - Shruti Rao
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC
| | | | - Rebecca Riggins
- Georgetown Lombardi Comprehensive Cancer Center, Washington, DC
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Wang L, Cheng CM, Qin J, Xu M, Kao CY, Shi J, You E, Gong W, Rosa LP, Chase P, Scampavia L, Madoux F, Spicer T, Hodder P, Xu HE, Tsai SY, Tsai MJ. Small-molecule inhibitor targeting orphan nuclear receptor COUP-TFII for prostate cancer treatment. Sci Adv 2020; 6:eaaz8031. [PMID: 32494682 PMCID: PMC7190335 DOI: 10.1126/sciadv.aaz8031] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 02/04/2020] [Indexed: 06/01/2023]
Abstract
The orphan nuclear receptor COUP-TFII is expressed at a low level in adult tissues, but its expression is increased and shown to promote progression of multiple diseases, including prostate cancer, heart failure, and muscular dystrophy. Suppression of COUP-TFII slows disease progression, making it an intriguing therapeutic target. Here, we identified a potent and specific COUP-TFII inhibitor through high-throughput screening. The inhibitor specifically suppressed COUP-TFII activity to regulate its target genes. Mechanistically, the inhibitor directly bound to the COUP-TFII ligand-binding domain and disrupted COUP-TFII interaction with transcription regulators, including FOXA1, thus repressing COUP-TFII activity on target gene regulation. Through blocking COUP-TFII's oncogenic activity in prostate cancer, the inhibitor efficiently exerted a potent antitumor effect in xenograft mouse models and patient-derived xenograft models. Our study identified a potent and specific COUP-TFII inhibitor that may be useful for the treatment of prostate cancer and possibly other diseases.
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Affiliation(s)
- Leiming Wang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chiang-Min Cheng
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jun Qin
- CAS Key Laboratory of Tissue Microenvironment and Tumor, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Mafei Xu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chung-Yang Kao
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jingjing Shi
- CAS Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Erli You
- CAS Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wanchun Gong
- CAS Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Laura Pedro Rosa
- Scripps Research, Molecular Screening Center, Jupiter, FL 33458, USA
| | - Peter Chase
- Scripps Research, Molecular Screening Center, Jupiter, FL 33458, USA
| | - Louis Scampavia
- Scripps Research, Molecular Screening Center, Jupiter, FL 33458, USA
| | - Franck Madoux
- Scripps Research, Molecular Screening Center, Jupiter, FL 33458, USA
| | - Timothy Spicer
- Scripps Research, Molecular Screening Center, Jupiter, FL 33458, USA
| | - Peter Hodder
- Scripps Research, Molecular Screening Center, Jupiter, FL 33458, USA
| | - H. Eric Xu
- CAS Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Sophia Y. Tsai
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine and Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ming-Jer Tsai
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine and Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
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Nieto A, Fernández-Vega V, Spicer TP, Sturchler E, Adhikari P, Kennedy N, Mandat S, Chase P, Scampavia L, Bannister T, Hodder P, McDonald PH. Identification of Novel, Structurally Diverse, Small Molecule Modulators of GPR119. Assay Drug Dev Technol 2019; 16:278-288. [PMID: 30019946 DOI: 10.1089/adt.2018.849] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
GPR119 drug discovery efforts in the pharmaceutical industry for the treatment of type 2 diabetes mellitus (T2DM) and obesity, were initiated based on its restricted distribution in pancreas and GI tract, and its possible role in glucose homeostasis. While a number of lead series have emerged, the pharmacological endpoints they provide have not been clear. In particular, many lead series have demonstrated loss of efficacy and significant toxic side effects. Thus, we sought to identify novel, potent, positive modulators of GPR119. In this study, we have successfully developed and optimized a high-throughput screening strategy to identify GPR119 modulators using a live cell assay format that utilizes a cyclic nucleotide-gated channel as a biosensor for cAMP production. Our high-throughput screening (HTS) approach is unique to that of previous HTS approaches targeting this receptor, as changes in cAMP were measured both in the presence and absence of an EC10 of the endogenous ligand, oleoylethanolamide, enabling detection of both agonists and potential allosteric modulators in a single assay. From these efforts, we have identified positive modulators of GPR119 with similar as well as unique scaffolds compared to existing compounds and similar as well as unique signaling properties. Our compounds will not only serve as novel molecular probes to better understand GPR119 pleiotropic signaling and the underlying physiological consequences of receptor activation, but are also well-suited for translation as potential therapeutic agents.
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Affiliation(s)
- Ainhoa Nieto
- 1 Department of Molecular Medicine, The Scripps Research Institute , Jupiter, Florida
| | | | - Timothy P Spicer
- 1 Department of Molecular Medicine, The Scripps Research Institute , Jupiter, Florida
| | - Emmanuel Sturchler
- 1 Department of Molecular Medicine, The Scripps Research Institute , Jupiter, Florida
| | - Pramisha Adhikari
- 1 Department of Molecular Medicine, The Scripps Research Institute , Jupiter, Florida
| | - Nicole Kennedy
- 2 Department of Chemistry, The Scripps Research Institute , Jupiter, Florida
| | - Sean Mandat
- 1 Department of Molecular Medicine, The Scripps Research Institute , Jupiter, Florida
| | - Peter Chase
- 1 Department of Molecular Medicine, The Scripps Research Institute , Jupiter, Florida
| | - Louis Scampavia
- 1 Department of Molecular Medicine, The Scripps Research Institute , Jupiter, Florida
| | - Thomas Bannister
- 2 Department of Chemistry, The Scripps Research Institute , Jupiter, Florida
| | - Peter Hodder
- 1 Department of Molecular Medicine, The Scripps Research Institute , Jupiter, Florida
| | - Patricia H McDonald
- 1 Department of Molecular Medicine, The Scripps Research Institute , Jupiter, Florida
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Baillargeon P, Spicer TP, Scampavia L. Applications for Open Source Microplate-Compatible Illumination Panels. J Vis Exp 2019. [PMID: 31633701 DOI: 10.3791/60088] [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: 10/31/2022] Open
Abstract
Microplates are commonly used in the modern laboratory environment for a wide variety of tasks both in small-scale laboratory benchtop operations as well as large-scale high-throughput screening (HTS) campaigns. Though laboratory automation has greatly increased the utility of microplates there remain instances where automation-based instrumentation is not feasible, cost-effective or compatible with microplate formatting needs. In these cases, microplates must be manually prepared. Problematic to manual microplate manipulations is that a number of difficulties can arise pertaining to the accurate tracking of sample operations, data record keeping and quality control (QC) inspection for well artifacts or formatting errors. As microplate well densities increase (i.e., 96-well, 384-well, 1536-well) the potential for introducing errors also drastically increases. Moreover, for small bench-top laboratory operations there exists a need to improve the ease and accuracy of sample handling in a cost-effective fashion. Herein, we describe a system that acts as a semi-automated pipetting guide referred to as the Microplate Assistive Pipetting Light Emitter (M.A.P.L.E.). M.A.P.L.E. has multiple uses for supporting compound hit-picking and microplate preparation for assay development in high-throughput screening or laboratory benchtop operations, as well as QC/quality assurance (QA) diagnostic evaluation of microplate quality or visualizing well formatting errors.
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Affiliation(s)
- Pierre Baillargeon
- The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Florida
| | - Timothy P Spicer
- The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Florida
| | - Louis Scampavia
- The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Florida;
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29
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Muntean BS, Patil DN, Madoux F, Fossetta J, Scampavia L, Spicer TP, Martemyanov KA. A High-Throughput Time-Resolved Fluorescence Energy Transfer Assay to Screen for Modulators of RGS7/Gβ5/R7BP Complex. Assay Drug Dev Technol 2019; 16:150-161. [PMID: 29658790 DOI: 10.1089/adt.2017.839] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 01/15/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are excellent drug targets exploited by majority of the Food and Drug Administration-approved medications, but when modulated, are often accompanied by significant adverse effects. Targeting of other elements in GPCR pathways for improved safety and efficacy is thus an unmet need. The strength of GPCR signaling is tightly regulated by regulators of G protein signaling (RGS) proteins, making them attractive drug targets. We focused on a prominent RGS complex in the brain consisting of RGS7 and its binding partners Gβ5 and R7BP. These complexes play critical roles in regulating multiple GPCRs and essential physiological processes, yet no small molecule modulators are currently available to modify its function. In this study, we report a novel high-throughput approach to screen for small molecule modulators of the intramolecular transitions in the RGS7/Gβ5/R7BP complex known to be involved in its allosteric regulation. We developed a time-resolved fluorescence energy transfer-based in vitro assay that utilizes full-length recombinant proteins and shows consistency, excellent assay statistics, and high level of sensitivity. We demonstrated the potential of this approach by screening two compound libraries (LOPAC 1280 and MicroSource Spectrum). This study confirms the feasibility of the chosen strategy for identifying small molecule modulators of RGS7/Gβ5/R7BP complex for impacting signaling downstream of the GPCRs.
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Affiliation(s)
- Brian S Muntean
- 1 Department of Neuroscience, The Scripps Research Institute , Jupiter, Florida
| | - Dipak N Patil
- 1 Department of Neuroscience, The Scripps Research Institute , Jupiter, Florida
| | - Franck Madoux
- 2 Department of Molecular Medicine, The Scripps Research Institute , Jupiter, Florida
| | | | - Louis Scampavia
- 2 Department of Molecular Medicine, The Scripps Research Institute , Jupiter, Florida
| | - Timothy P Spicer
- 2 Department of Molecular Medicine, The Scripps Research Institute , Jupiter, Florida
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30
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Baillargeon P, Shumate J, Hou S, Fernandez-Vega V, Marques N, Souza G, Seldin J, Spicer TP, Scampavia L. Automating a Magnetic 3D Spheroid Model Technology for High-Throughput Screening. SLAS Technol 2019; 24:420-428. [PMID: 31225974 DOI: 10.1177/2472630319854337] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [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: 01/09/2023]
Abstract
Affordable and physiologically relevant three-dimensional (3D) cell-based assays used in high-throughput screening (HTS) are on the rise in early drug discovery. These technologies have been aided by the recent adaptation of novel microplate treatments and spheroid culturing techniques. One such technology involves the use of nanoparticle (NanoShuttle-PL) labeled cells and custom magnetic drives to assist in cell aggregation to ensure rapid 3D structure formation after the cells have been dispensed into microtiter plates. Transitioning this technology from a low-throughput manual benchtop application, as previously published by our lab, into a robotically enabled format achieves orders of magnitude greater throughput but required the development of specialized support hardware. This effort included in-house development, fabrication, and testing of ancillary devices that assist robotic handing and high-precision placement of microtiter plates into an incubator embedded with magnetic drives. Utilizing a "rapid prototyping" approach facilitated by cloud-based computer-aided design software, we built the necessary components using hobby-grade 3D printers with turnaround times that rival those of traditional manufacturing/development practices at a substantially reduced cost. This approach culminated in a first-in-class HTS-compatible 3D system in which we have coupled 3D bioprinting to a fully automated HTS robotic platform utilizing our novel magnetic incubator shelf assemblies.
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Affiliation(s)
- Pierre Baillargeon
- 1 The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA
| | - Justin Shumate
- 1 The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA
| | - Shurong Hou
- 1 The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA.,2 Holistic Integrative Pharmacy Institutes, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Virneliz Fernandez-Vega
- 1 The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA
| | - Nicholas Marques
- 1 The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA
| | | | | | - Timothy P Spicer
- 1 The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA
| | - Louis Scampavia
- 1 The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA
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Sridharan B, Hubbs C, Llamosas N, Kilinc M, Singhera FU, Willems E, Piper DR, Scampavia L, Rumbaugh G, Spicer TP. A Simple Procedure for Creating Scalable Phenotypic Screening Assays in Human Neurons. Sci Rep 2019; 9:9000. [PMID: 31227747 PMCID: PMC6588600 DOI: 10.1038/s41598-019-45265-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 01/11/2019] [Accepted: 06/04/2019] [Indexed: 02/08/2023] Open
Abstract
Neurons created from human induced pluripotent stem cells (hiPSCs) provide the capability of identifying biological mechanisms that underlie brain disorders. IPSC-derived human neurons, or iNs, hold promise for advancing precision medicine through drug screening, though it remains unclear to what extent iNs can support early-stage drug discovery efforts in industrial-scale screening centers. Despite several reported approaches to generate iNs from iPSCs, each suffer from technological limitations that challenge their scalability and reproducibility, both requirements for successful screening assays. We addressed these challenges by initially removing the roadblocks related to scaling of iNs for high throughput screening (HTS)-ready assays. We accomplished this by simplifying the production and plating of iNs and adapting them to a freezer-ready format. We then tested the performance of freezer-ready iNs in an HTS-amenable phenotypic assay that measured neurite outgrowth. This assay successfully identified small molecule inhibitors of neurite outgrowth. Importantly, we provide evidence that this scalable iN-based assay was both robust and highly reproducible across different laboratories. These streamlined approaches are compatible with any iPSC line that can produce iNs. Thus, our findings indicate that current methods for producing iPSCs are appropriate for large-scale drug-discovery campaigns (i.e. >10e5 compounds) that read out simple neuronal phenotypes. However, due to the inherent limitations of currently available iN differentiation protocols, technological advances are required to achieve similar scalability for screens that require more complex phenotypes related to neuronal function.
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Affiliation(s)
- BanuPriya Sridharan
- The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Research, Jupiter, Florida, 33458, USA
| | - Christopher Hubbs
- Department of Neuroscience, Scripps Research, Jupiter, Florida, 33458, USA
| | - Nerea Llamosas
- Department of Neuroscience, Scripps Research, Jupiter, Florida, 33458, USA
| | - Murat Kilinc
- Graduate School of Chemical and Biological Sciences, Scripps Research, Jupiter, Florida, 33458, USA
| | - Fakhar U Singhera
- The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Research, Jupiter, Florida, 33458, USA
| | - Erik Willems
- Cell Biology, Thermo Fisher Scientific, Carlsbad, California, 92008, USA
| | - David R Piper
- Cell Biology, Thermo Fisher Scientific, Carlsbad, California, 92008, USA
| | - Louis Scampavia
- The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Research, Jupiter, Florida, 33458, USA
| | - Gavin Rumbaugh
- The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Research, Jupiter, Florida, 33458, USA.
- Department of Neuroscience, Scripps Research, Jupiter, Florida, 33458, USA.
- Graduate School of Chemical and Biological Sciences, Scripps Research, Jupiter, Florida, 33458, USA.
| | - Timothy P Spicer
- The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Research, Jupiter, Florida, 33458, USA.
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Baillargeon P, Fernandez-Vega V, Sridharan BP, Brown S, Griffin PR, Rosen H, Cravatt B, Scampavia L, Spicer TP. The Scripps Molecular Screening Center and Translational Research Institute. SLAS Discov 2019; 24:386-397. [PMID: 30682260 PMCID: PMC7724958 DOI: 10.1177/2472555218820809] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The Scripps Research Molecular Screening Center (SRMSC) was founded in 2004 and comprises more than $22 million of specialized automation. As part of the Translational Research Institute (TRI), it comprises early drug discovery labs and medicinal chemistry. Together with Scripps Research at the La Jolla, California, campus, this represents one of the most competitive academic industrial screening centers worldwide. The SRMSC uses automated platforms, one a screening cell and the other a cherry-picking platform. Matched technologies are available throughout Scripps to allow scientists to develop assays and prepare them for automated screening. The library comprises more than 1 million drug-like compounds, including a proprietary collection of >665,000 molecules. Internal chemistry has included ~40,000 unique compounds that are not found elsewhere. These collections are screened against a myriad of disease targets, including cell-based and biochemical assays that are provided by Scripps faculty or from global investigators. Scripps has proven competence in all detection formats, including high-content analysis, fluorescence, bioluminescence resonance energy transfer (BRET), time-resolved fluorescence resonance energy transfer (TR-FRET), fluorescence polarization (FP), luminescence, absorbance, AlphaScreen, and Ca++ signaling. These technologies are applied to NIH-derived collaborations as well as biotech and pharma initiatives. The SRMSC and TRI are recognized for discovering multiple leads, including Ozanimod.
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Affiliation(s)
- Pierre Baillargeon
- Department of Molecular Medicine, Scripps Research Florida, 130 Scripps Way, Jupiter, Florida, USA
| | - Virneliz Fernandez-Vega
- Department of Molecular Medicine, Scripps Research Florida, 130 Scripps Way, Jupiter, Florida, USA
| | - Banu Priya Sridharan
- Department of Molecular Medicine, Scripps Research Florida, 130 Scripps Way, Jupiter, Florida, USA
| | - Steven Brown
- Department of Molecular Medicine, Scripps Research California, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Patrick R. Griffin
- Department of Molecular Medicine, Scripps Research Florida, 130 Scripps Way, Jupiter, Florida, USA
| | - Hugh Rosen
- Department of Molecular Medicine, Scripps Research California, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Benjamin Cravatt
- Department of Molecular Medicine, Scripps Research California, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Louis Scampavia
- Department of Molecular Medicine, Scripps Research Florida, 130 Scripps Way, Jupiter, Florida, USA
| | - Timothy P. Spicer
- Department of Molecular Medicine, Scripps Research Florida, 130 Scripps Way, Jupiter, Florida, USA
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Zhou W, Yin Y, Smith E, Chou J, Shumate J, Scampavia L, Spicer TP, Carpino N, French JB. Discovery and Characterization of Two Classes of Selective Inhibitors of the Suppressor of the TCR Signaling Family of Proteins. ACS Infect Dis 2019; 5:250-259. [PMID: 30485744 DOI: 10.1021/acsinfecdis.8b00238] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 11/29/2022]
Abstract
The suppressor of T-cell receptor signaling (Sts) proteins, Sts-1, has recently emerged as a potential immunostimulatory target for drug development. Genetic inactivation of the Sts proteins dramatically increases host survival of systemic infection and leads to improved pathogen clearance. The protein tyrosine phosphatase (PTP) activity of these proteins arises from a C-terminal 2-histidine phosphatase (HP) domain. To identify new inhibitors of the HP activity of Sts-1, we miniaturized a phosphatase assay to a 1536-well format and conducted a 20 580 compound screen. Among the hits were two classes of structurally related compounds, tetracycline variants and sulfonated azo dyes. These hits had low micromolar to nanomolar IC50 values. Orthogonal screening confirmed the validity of these inhibitors and demonstrated that both act competitively on Sts-1 phosphatase activity. When tested on other PTPs, PTP1B and SHP1, it was found that the tetracycline PTP1B, SHP1, the tetracycline variant (doxycycline), and the sulfonated azo dye (Congo red) are selective inhibitors of Sts-1HP, with selectivity indices ranging from 19 to as high as 200. The planar polyaromatic moieties present in both classes of compounds suggested a common binding mode. The mutation of either tryptophan 494 or tyrosine 596, located near the active site of the protein, reduced the Ki of the inhibitors from 3- to 18-fold, indicating that these residues may help to promote the binding of substrates with aromatic groups. This work provides new insights into substrate selectivity mechanisms and describes two classes of compounds that can serve as probes of function or as a basis for future drug discovery.
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Affiliation(s)
| | | | - Emery Smith
- Department of Molecular Medicine, Scripps Research Molecular Screening Center, Scripps Research, 130 Scripps Way, Jupiter, Florida 33458, United States
| | | | - Justin Shumate
- Department of Molecular Medicine, Scripps Research Molecular Screening Center, Scripps Research, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Louis Scampavia
- Department of Molecular Medicine, Scripps Research Molecular Screening Center, Scripps Research, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Timothy P. Spicer
- Department of Molecular Medicine, Scripps Research Molecular Screening Center, Scripps Research, 130 Scripps Way, Jupiter, Florida 33458, United States
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Baillargeon P, Coss-Flores K, Singhera F, Shumate J, Williams H, DeLuca L, Spicer TP, Scampavia L. Design of Microplate-Compatible Illumination Panels for a Semiautomated Benchtop Pipetting System. SLAS Technol 2019; 24:399-407. [PMID: 30698997 DOI: 10.1177/2472630318822476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Microplates are an essential tool used in laboratories for storing research materials and performing assays. Many types of laboratory automation exist that greatly reduce the effort needed to utilize microplates; however, there are cases where the use of such automation is not feasible or practical. In these instances, researchers must work in an environment where liquid handling operations are performed manually with handheld pipetting devices. This type of work is tedious and error-prone as it relies on researchers to manually track a significant amount of metadata, including transfer volumes, plate barcodes, well contents, and well locations. To address this challenge, we have developed an open-source, semiautomated benchtop system that facilitates manual pipetting using visual indicators. This device streamlines the process of identifying the location of wells so that the researcher can perform manual transfers in a more efficient, reliable, and accurate manner. This system utilizes a graphical user interface that allows the user to load worklists and then issues commands to illuminate wells of interest, providing a visual indicator for users to follow in real time. The software and hardware tools utilized for development, along with the implementation techniques used to produce this system, are described within.
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Affiliation(s)
- Pierre Baillargeon
- 1 The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, Florida, USA
| | - Kervin Coss-Flores
- 1 The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, Florida, USA
| | - Fakhar Singhera
- 1 The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, Florida, USA
| | - Justin Shumate
- 1 The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, Florida, USA
| | - Hannah Williams
- 1 The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, Florida, USA
| | - Lina DeLuca
- 1 The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, Florida, USA
| | - Timothy P Spicer
- 1 The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, Florida, USA
| | - Louis Scampavia
- 1 The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, Florida, USA
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Spicer TP, Vega VF, Scampavia L, Willetts L, Vessels M. A Novel 3D Culture System for High-Throughput Hepatoxicity Screening. Bioprocess Int 2018; 16:1-5. [PMID: 35431667 PMCID: PMC9012168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Timothy P Spicer
- Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida
| | | | - Louis Scampavia
- Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida
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Spicer TP, Gardiner DL, Schoenen FJ, Roy S, Griffin PR, Chase P, Scampavia L, Hodder P, Trenholme KR. Identification of Antimalarial Inhibitors Using Late-Stage Gametocytes in a Phenotypic Live/Dead Assay. SLAS Discov 2018; 24:38-46. [PMID: 30142014 DOI: 10.1177/2472555218796410] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Malaria remains a major cause of morbidity and mortality worldwide with ~3.3 billion people at risk of contracting malaria and an estimated 450,000 deaths each year. While tools to reduce the infection prevalence to low levels are currently under development, additional efforts will be required to interrupt transmission. Transmission between human host and vector by the malaria parasite involves gametogenesis in the host and uptake of gametocytes by the mosquito vector. This stage is a bottleneck for reproduction of the parasite, making it a target for small-molecule drug discovery. Targeting this stage, we used whole Plasmodium falciparum gametocytes from in vitro culture and implemented them into 1536-well plates to create a live/dead phenotypic antigametocyte assay. Using specialized equipment and upon further validation, we screened ~150,000 compounds from the NIH repository currently housed at Scripps Florida. We identified 100 primary screening hits that were tested for concentration response. Additional follow-up studies to determine specificity, potency, and increased efficacy of the antigametocyte candidate compounds resulted in a starting point for initial medicinal chemistry intervention. From this, 13 chemical analogs were subsequently tested as de novo powders, which confirmed original activity from the initial analysis and now provide a point of future engagement.
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Affiliation(s)
- Timothy P Spicer
- 1 Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL, USA.,2 School of Medicine, University of Queensland, Herston, Queensland, Australia
| | - Donald L Gardiner
- 2 School of Medicine, University of Queensland, Herston, Queensland, Australia
| | - Frank J Schoenen
- 3 The University of Kansas Specialized Chemistry Center, Lawrence, KS,USA
| | - Sudeshna Roy
- 3 The University of Kansas Specialized Chemistry Center, Lawrence, KS,USA.,4 The University of Mississippi, Oxford, MS
| | - Patrick R Griffin
- 1 Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL, USA
| | - Peter Chase
- 1 Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL, USA.,5 BMS, Hopewell, NJ
| | - Louis Scampavia
- 1 Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL, USA
| | - Peter Hodder
- 1 Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL, USA.,6 Amgen, Inc., Thousand Oaks, CA, USA
| | - Katharine R Trenholme
- 2 School of Medicine, University of Queensland, Herston, Queensland, Australia.,7 Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
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37
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Hou S, Tiriac H, Sridharan BP, Scampavia L, Madoux F, Seldin J, Souza GR, Watson D, Tuveson D, Spicer TP. Advanced Development of Primary Pancreatic Organoid Tumor Models for High-Throughput Phenotypic Drug Screening. SLAS Discov 2018; 23:574-584. [PMID: 29673279 PMCID: PMC6013403 DOI: 10.1177/2472555218766842] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [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] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/26/2018] [Accepted: 03/05/2018] [Indexed: 12/30/2022]
Abstract
Traditional high-throughput drug screening in oncology routinely relies on two-dimensional (2D) cell models, which inadequately recapitulate the physiologic context of cancer. Three-dimensional (3D) cell models are thought to better mimic the complexity of in vivo tumors. Numerous methods to culture 3D organoids have been described, but most are nonhomogeneous and expensive, and hence impractical for high-throughput screening (HTS) purposes. Here we describe an HTS-compatible method that enables the consistent production of organoids in standard flat-bottom 384- and 1536-well plates by combining the use of a cell-repellent surface with a bioprinting technology incorporating magnetic force. We validated this homogeneous process by evaluating the effects of well-characterized anticancer agents against four patient-derived pancreatic cancer KRAS mutant-associated primary cells, including cancer-associated fibroblasts. This technology was tested for its compatibility with HTS automation by completing a cytotoxicity pilot screen of ~3300 approved drugs. To highlight the benefits of the 3D format, we performed this pilot screen in parallel in both the 2D and 3D assays. These data indicate that this technique can be readily applied to support large-scale drug screening relying on clinically relevant, ex vivo 3D tumor models directly harvested from patients, an important milestone toward personalized medicine.
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Affiliation(s)
- Shurong Hou
- The Scripps Research Institute Molecular
Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, FL,
USA
- These authors contributed equally to
this work
| | - Hervé Tiriac
- Cancer Center, Cold Spring Harbor
Laboratory, Cold Spring Harbor, NY, USA
- These authors contributed equally to
this work
| | - Banu Priya Sridharan
- The Scripps Research Institute Molecular
Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, FL,
USA
| | - Louis Scampavia
- The Scripps Research Institute Molecular
Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, FL,
USA
| | - Franck Madoux
- The Scripps Research Institute Molecular
Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, FL,
USA
- Amgen, Inc., Thousand Oaks, CA,
USA
| | - Jan Seldin
- Greiner Bio-One North America, Inc.,
Monroe, NC, USA
| | - Glauco R. Souza
- Nano3D Biosciences, Inc. and University
of Texas Health Science Center at Houston, Houston, TX, USA
| | | | - David Tuveson
- Cancer Center, Cold Spring Harbor
Laboratory, Cold Spring Harbor, NY, USA
- Co-communicated by D.T. and T.P.S
| | - Timothy P. Spicer
- The Scripps Research Institute Molecular
Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, FL,
USA
- Co-communicated by D.T. and T.P.S
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Quereda V, Hou S, Madoux F, Scampavia L, Spicer TP, Duckett D. A Cytotoxic Three-Dimensional-Spheroid, High-Throughput Assay Using Patient-Derived Glioma Stem Cells. SLAS Discov 2018; 23:842-849. [PMID: 29750582 DOI: 10.1177/2472555218775055] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Glioblastoma (GBM) is the most aggressive primary brain cancer with an average survival time after diagnosis of only 12-14 months, with few (<5%) long-term survivors. A growing body of work suggests that GBMs contain a small population of glioma stem cells (GSCs) that are thought to be major contributors to treatment resistance and disease relapse. Identifying compounds that modulate GSC proliferation would provide highly valuable molecular probes of GSC-directed signaling. However, targeting GSCs pharmacologically has been challenging. Patient-derived GSCs can be cultured as neurospheres, and in vivo these cells functionally recapitulate the heterogeneity of the original tumor. Using patient-derived GSC-enriched cultures, we have developed a 1536-well spheroid-based proliferation assay and completed a pilot screen, testing ~3300 compounds comprising approved drugs. This cytotoxic and automation-friendly assay yielded a signal-to-background (S/B) ratio of 161.3 ± 7.5 and Z' of 0.77 ± 0.02, demonstrating its robustness. Importantly, compounds were identified with anti-GSC activity, demonstrating the applicability of this assay for large-scale high-throughput screening (HTS).
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Affiliation(s)
- Victor Quereda
- 1 Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA
| | - Shurong Hou
- 2 The Scripps Research Institute Molecular Screening Center, Scripps Florida, Jupiter, FL, USA
| | | | - Louis Scampavia
- 2 The Scripps Research Institute Molecular Screening Center, Scripps Florida, Jupiter, FL, USA
| | - Timothy P Spicer
- 2 The Scripps Research Institute Molecular Screening Center, Scripps Florida, Jupiter, FL, USA
| | - Derek Duckett
- 1 Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA
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Kota S, Hou S, Guerrant W, Madoux F, Troutman S, Fernandez-Vega V, Alekseeva N, Madala N, Scampavia L, Kissil J, Spicer TP. A novel three-dimensional high-throughput screening approach identifies inducers of a mutant KRAS selective lethal phenotype. Oncogene 2018; 37:4372-4384. [PMID: 29743592 PMCID: PMC6138545 DOI: 10.1038/s41388-018-0257-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 01/09/2018] [Revised: 03/04/2018] [Accepted: 03/16/2018] [Indexed: 01/01/2023]
Abstract
The RAS proteins are the most frequently mutated oncogenes in cancer, with highest frequency found in pancreatic, lung, and colon tumors. Moreover, the activity of RAS is required for the proliferation and/or survival of these tumor cells and thus represents a high-value target for therapeutic development. Direct targeting of RAS has proven challenging for multiple reasons stemming from the biology of the protein, the complexity of downstream effector pathways and upstream regulatory networks. Thus, significant efforts have been directed at identifying downstream targets on which RAS is dependent. These efforts have proven challenging, in part due to confounding factors such as reliance on two-dimensional adherent monolayer cell cultures that inadequately recapitulate the physiologic context to which cells are exposed in vivo. To overcome these issues, we implemented a High Throughput Screening (HTS) approach using a spheroid-based 3-dimensional culture format, thought to more closely reflect conditions experienced by cells in vivo. Using isogenic cell pairs, differing in the status of KRAS, we identified Proscillaridin A as a selective inhibitor of cells harboring the oncogenic KRasG12V allele. Significantly, the identification of Proscillaridin A was facilitated by the 3D screening platform and would not have been discovered employing standard 2D culturing methods.
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Affiliation(s)
- Smitha Kota
- Department of Molecular Medicine, The Scripps Research Institute, Florida, USA
| | - Shurong Hou
- Department of Molecular Medicine, The Scripps Research Institute, Florida, USA
| | - William Guerrant
- Department of Molecular Medicine, The Scripps Research Institute, Florida, USA
| | - Franck Madoux
- Department of Molecular Medicine, The Scripps Research Institute, Florida, USA.,Amgen Inc., Thousand Oaks, CA, USA
| | - Scott Troutman
- Department of Molecular Medicine, The Scripps Research Institute, Florida, USA
| | | | - Nina Alekseeva
- Department of Molecular Medicine, The Scripps Research Institute, Florida, USA
| | - Neeharika Madala
- Department of Molecular Medicine, The Scripps Research Institute, Florida, USA
| | - Louis Scampavia
- Department of Molecular Medicine, The Scripps Research Institute, Florida, USA
| | - Joseph Kissil
- Department of Molecular Medicine, The Scripps Research Institute, Florida, USA.
| | - Timothy P Spicer
- Department of Molecular Medicine, The Scripps Research Institute, Florida, USA.
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Shumate J, Baillargeon P, Spicer TP, Scampavia L. IoT for Real-Time Measurement of High-Throughput Liquid Dispensing in Laboratory Environments. SLAS Technol 2018; 23:440-447. [PMID: 29649373 DOI: 10.1177/2472630318769454] [Citation(s) in RCA: 12] [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] [Indexed: 12/18/2022]
Abstract
Critical to maintaining quality control in high-throughput screening is the need for constant monitoring of liquid-dispensing fidelity. Traditional methods involve operator intervention with gravimetric analysis to monitor the gross accuracy of full plate dispenses, visual verification of contents, or dedicated weigh stations on screening platforms that introduce potential bottlenecks and increase the plate-processing cycle time. We present a unique solution using open-source hardware, software, and 3D printing to automate dispenser accuracy determination by providing real-time dispense weight measurements via a network-connected precision balance. This system uses an Arduino microcontroller to connect a precision balance to a local network. By integrating the precision balance as an Internet of Things (IoT) device, it gains the ability to provide real-time gravimetric summaries of dispensing, generate timely alerts when problems are detected, and capture historical dispensing data for future analysis. All collected data can then be accessed via a web interface for reviewing alerts and dispensing information in real time or remotely for timely intervention of dispense errors. The development of this system also leveraged 3D printing to rapidly prototype sensor brackets, mounting solutions, and component enclosures.
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Affiliation(s)
- Justin Shumate
- 1 The Scripps Research Institute Molecular Screening Center and Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA
| | - Pierre Baillargeon
- 1 The Scripps Research Institute Molecular Screening Center and Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA
| | - Timothy P Spicer
- 1 The Scripps Research Institute Molecular Screening Center and Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA
| | - Louis Scampavia
- 1 The Scripps Research Institute Molecular Screening Center and Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA
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41
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Wolff RA, Wang-Gillam A, Alvarez H, Tiriac H, Engle D, Hou S, Groff AF, San Lucas A, Bernard V, Allenson K, Castillo J, Kim D, Mulu F, Huang J, Stephens B, Wistuba II, Katz M, Varadhachary G, Park Y, Hicks J, Chinnaiyan A, Scampavia L, Spicer T, Gerhardinger C, Maitra A, Tuveson D, Rinn J, Lizee G, Yee C, Levine AJ. Dynamic changes during the treatment of pancreatic cancer. Oncotarget 2018; 9:14764-14790. [PMID: 29599906 PMCID: PMC5871077 DOI: 10.18632/oncotarget.24483] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 12/20/2017] [Accepted: 02/01/2018] [Indexed: 01/17/2023] Open
Abstract
This manuscript follows a single patient with pancreatic adenocarcinoma for a five year period, detailing the clinical record, pathology, the dynamic evolution of molecular and cellular alterations as well as the responses to treatments with chemotherapies, targeted therapies and immunotherapies. DNA and RNA samples from biopsies and blood identified a dynamic set of changes in allelic imbalances and copy number variations in response to therapies. Organoid cultures established from biopsies over time were employed for extensive drug testing to determine if this approach was feasible for treatments. When an unusual drug response was detected, an extensive RNA sequencing analysis was employed to establish novel mechanisms of action of this drug. Organoid cell cultures were employed to identify possible antigens associated with the tumor and the patient's T-cells were expanded against one of these antigens. Similar and identical T-cell receptor sequences were observed in the initial biopsy and the expanded T-cell population. Immunotherapy treatment failed to shrink the tumor, which had undergone an epithelial to mesenchymal transition prior to therapy. A warm autopsy of the metastatic lung tumor permitted an extensive analysis of tumor heterogeneity over five years of treatment and surgery. This detailed analysis of the clinical descriptions, imaging, pathology, molecular and cellular evolution of the tumors, treatments, and responses to chemotherapy, targeted therapies, and immunotherapies, as well as attempts at the development of personalized medical treatments for a single patient should provide a valuable guide to future directions in cancer treatment.
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Affiliation(s)
- Robert A Wolff
- Department of Gastrointestinal (GI) Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | | | - Hector Alvarez
- Department of Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Hervé Tiriac
- Cold Spring Harbor Laboratory, New York, NY, USA
| | | | - Shurong Hou
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL, USA
| | - Abigail F Groff
- Department of Molecular and Cellular Biology, Harvard University, The Broad Institute, Cambridge, MA, USA
| | - Anthony San Lucas
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Vincent Bernard
- Department of Radiation Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Kelvin Allenson
- Department of Surgical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Jonathan Castillo
- Department of Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Dong Kim
- Department of Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Feven Mulu
- Department of Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Jonathan Huang
- Department of Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Bret Stephens
- Department of Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Matthew Katz
- Department of Surgical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Gauri Varadhachary
- Department of Gastrointestinal (GI) Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | | | - James Hicks
- Cold Spring Harbor Laboratory, New York, NY, USA
| | - Arul Chinnaiyan
- Center for Translational Pathology, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - Louis Scampavia
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL, USA
| | - Timothy Spicer
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL, USA
| | - Chiara Gerhardinger
- Department of Molecular and Cellular Biology, Harvard University, The Broad Institute, Cambridge, MA, USA
| | - Anirban Maitra
- Department of Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | | | - John Rinn
- Department of Molecular and Cellular Biology, Harvard University, The Broad Institute, Cambridge, MA, USA.,Current address: University of Colorado Boulder, BioFrontiers Institute, Boulder, CO, USA
| | - Gregory Lizee
- Department of Melanoma Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Cassian Yee
- Department of Melanoma Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Arnold J Levine
- Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ, USA
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42
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Smith E, Giuliano KA, Shumate J, Baillargeon P, McEwan B, Cullen MD, Miller JP, Drew L, Scampavia L, Spicer TP. A Homogeneous Cell-Based Halide-Sensitive Yellow Fluorescence Protein Assay to Identify Modulators of the Cystic Fibrosis Transmembrane Conductance Regulator Ion Channel. Assay Drug Dev Technol 2017; 15:395-406. [DOI: 10.1089/adt.2017.810] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Emery Smith
- Department of Molecular Medicine, The Scripps Research Institute Molecular Screening Center, Scripps Florida, Jupiter, Florida
| | | | - Justin Shumate
- Department of Molecular Medicine, The Scripps Research Institute Molecular Screening Center, Scripps Florida, Jupiter, Florida
| | - Pierre Baillargeon
- Department of Molecular Medicine, The Scripps Research Institute Molecular Screening Center, Scripps Florida, Jupiter, Florida
| | - Brigid McEwan
- Proteostasis Therapeutics, Inc., Cambridge, Massachusetts
| | | | - John P. Miller
- Proteostasis Therapeutics, Inc., Cambridge, Massachusetts
| | - Lawrence Drew
- Proteostasis Therapeutics, Inc., Cambridge, Massachusetts
| | - Louis Scampavia
- Department of Molecular Medicine, The Scripps Research Institute Molecular Screening Center, Scripps Florida, Jupiter, Florida
| | - Timothy P. Spicer
- Department of Molecular Medicine, The Scripps Research Institute Molecular Screening Center, Scripps Florida, Jupiter, Florida
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43
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Spicer TP, Hubbs C, Vaissiere T, Collia D, Rojas C, Kilinc M, Vick K, Madoux F, Baillargeon P, Shumate J, Martemyanov KA, Page DT, Puthanveettil S, Hodder P, Davis R, Miller CA, Scampavia L, Rumbaugh G. Improved Scalability of Neuron-Based Phenotypic Screening Assays for Therapeutic Discovery in Neuropsychiatric Disorders. Mol Neuropsychiatry 2017; 3:141-150. [PMID: 29594133 DOI: 10.1159/000481731] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/08/2017] [Indexed: 02/05/2023]
Abstract
There is a pressing need to improve approaches for drug discovery related to neuropsychiatric disorders (NSDs). Therapeutic discovery in neuropsychiatric disorders would benefit from screening assays that can measure changes in complex phenotypes linked to disease mechanisms. However, traditional assays that track complex neuronal phenotypes, such as neuronal connectivity, exhibit poor scalability and are not compatible with high-throughput screening (HTS) procedures. Therefore, we created a neuronal phenotypic assay platform that focused on improving the scalability and affordability of neuron-based assays capable of tracking disease-relevant phenotypes. First, using inexpensive laboratory-level automation, we industrialized primary neuronal culture production, which enabled the creation of scalable assays within functioning neural networks. We then developed a panel of phenotypic assays based on culturing of primary neurons from genetically modified mice expressing HTS-compatible reporters that capture disease-relevant phenotypes. We demonstrated that a library of 1,280 compounds was quickly screened against both assays using only a few litters of mice in a typical academic laboratory setting. Finally, we implemented one assay in a fully automated high-throughput academic screening facility, illustrating the scalability of assays designed using this platform. These methodological improvements simplify the creation of highly scalable neuron-based phenotypic assays designed to improve drug discovery in CNS disorders.
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Affiliation(s)
| | - Christopher Hubbs
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL, USA
| | - Thomas Vaissiere
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL, USA
| | | | - Camilo Rojas
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL, USA
| | - Murat Kilinc
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL, USA
| | - Kyle Vick
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL, USA.,Department of Aerie Pharmaceuticals, Durham, NC, USA
| | - Franck Madoux
- Department of Molecular Medicine, Jupiter, FL, USA.,Department of Amgen, Thousand Oaks, CA, USA
| | | | | | | | - Damon T Page
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL, USA
| | | | - Peter Hodder
- Department of Molecular Medicine, Jupiter, FL, USA.,Department of Amgen, Thousand Oaks, CA, USA
| | - Ronald Davis
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL, USA
| | - Courtney A Miller
- Department of Molecular Medicine, Jupiter, FL, USA.,Department of Neuroscience, The Scripps Research Institute, Jupiter, FL, USA
| | | | - Gavin Rumbaugh
- Department of Molecular Medicine, Jupiter, FL, USA.,Department of Neuroscience, The Scripps Research Institute, Jupiter, FL, USA
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44
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Kong J, Fang P, Madoux F, Spicer TP, Scampavia L, Kim S, Guo M. High-Throughput Screening for Protein Synthesis Inhibitors Targeting Aminoacyl-tRNA Synthetases. SLAS Discov 2017; 23:174-182. [PMID: 29020503 DOI: 10.1177/2472555217734128] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Aminoacylation has been implicated in a wide variety of cancers. Aminoacyl-tRNA synthetases (ARSs) exist in large excess in tumor cells due to their increased demand for translation, whereas most other protein-synthesis apparatuses are quantitatively limited. Among other components that constitute the translation machinery-namely, tRNA, amino acid, ATP, and ARS-ARS is the only target that can be blocked by small molecules. No constitutively active ARSs have been reported, and mutations of ARS can cause inaccurate substrate recognition and malformation of the multi-ARS complex (MSC). Hence, interference of the activity is expected to be independent of genotype without developing resistance. Here, we report a high-throughput screening (HTS) system to find mammalian ARS inhibitors. The rabbit-reticulocyte lysate we used closely resembles both the individual and complexed structures of human ARSs, and it may predispose active compounds that are readily applicable for humankind. This assay was further validated because it identified familiar translational inhibitors from a pilot screen, such as emetine, proving its suitability for our purpose. The assay demonstrated excellent quality control (QC) parameters and reproducibility, and is proven ready for further HTS campaigns with large chemical libraries.
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Affiliation(s)
- Jiwon Kong
- 1 Medicinal Bioconvergence Research Center, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Pengfei Fang
- 2 Department of Cancer Biology, Scripps Research Institute, Scripps Florida, Jupiter, FL, USA.,3 State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Franck Madoux
- 4 Department of Molecular Medicine, Scripps Research Institute, Scripps Florida, Jupiter, FL, USA.,5 Discovery Technologies, Amgen, Thousand Oaks, CA, USA
| | - Timothy P Spicer
- 4 Department of Molecular Medicine, Scripps Research Institute, Scripps Florida, Jupiter, FL, USA
| | - Louis Scampavia
- 4 Department of Molecular Medicine, Scripps Research Institute, Scripps Florida, Jupiter, FL, USA
| | - Sunghoon Kim
- 1 Medicinal Bioconvergence Research Center, College of Pharmacy, Seoul National University, Seoul, Korea.,6 Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
| | - Min Guo
- 2 Department of Cancer Biology, Scripps Research Institute, Scripps Florida, Jupiter, FL, USA
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45
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Singhera F, Cooper E, Scampavia L, Spicer T. Using bead injection to model dispensing of 3-D multicellular spheroids into microtiter plates. Talanta 2017; 177:74-76. [PMID: 29108585 DOI: 10.1016/j.talanta.2017.09.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 08/01/2017] [Revised: 09/07/2017] [Accepted: 09/08/2017] [Indexed: 11/28/2022]
Abstract
Biomedical translational research has relied on two dimensional (2D) cell cultures for drug discovery over the decades, requiring cells to grow on a flat surface which does not always accurately model in vivo biological states. Three dimensional (3D) cell cultures, also known as 3D spheroids or organoids, grow as cellular tissues that are more physiologically relevant especially with respect to emulating cancer tumor-like structures [1]. While attractive, current methods for generating 3D spheroids has yet to replace 2D culturing methods used for drug discovery efforts that employ high-throughput screening (HTS), having limitations with scalability, reproducibility, and compatibility predominantly associated with conventional microtiter plate usage. Presented is a novel use of bead injection for the reproducible placement of spheroids and beads into high density microtiter plates of a 384- and 1536- well format.
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Affiliation(s)
- Fakhar Singhera
- The Scripps Research Institute Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, 130 Scripps Way, Jupiter, FL, USA
| | - Emily Cooper
- The Scripps Research Institute Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, 130 Scripps Way, Jupiter, FL, USA
| | - Louis Scampavia
- The Scripps Research Institute Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, 130 Scripps Way, Jupiter, FL, USA.
| | - Timothy Spicer
- The Scripps Research Institute Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, 130 Scripps Way, Jupiter, FL, USA
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Collia D, Bannister TD, Tan H, Jin S, Langaee T, Shumate J, Scampavia L, Spicer TP. A Rapid Phenotypic Whole-Cell Screening Approach for the Identification of Small-Molecule Inhibitors That Counter β-Lactamase Resistance in Pseudomonas aeruginosa. SLAS Discov 2017; 23:55-64. [PMID: 28850797 DOI: 10.1177/2472555217728489] [Citation(s) in RCA: 7] [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] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen that is prevalent in hospitals and continues to develop resistance to multiple classes of antibiotics. Historically, β-lactam antibiotics have been the first line of therapeutic defense. However, the emergence of multidrug-resistant (MDR) strains of P. aeruginosa, such as AmpC β-lactamase overproducing mutants, limits the effectiveness of current antibiotics. Among AmpC hyperproducing clinical isolates, inactivation of AmpG, which is essential for the expression of AmpC, increases bacterial sensitivity to β-lactam antibiotics. We hypothesize that inhibition of AmpG activity will enhance the efficacy of β-lactams against P. aeruginosa. Here, using a highly drug-resistant AmpC-inducible laboratory strain PAO1, we describe an ultra-high-throughput whole-cell turbidity assay designed to identify small-molecule inhibitors of the AmpG. We screened 645,000 compounds to identify compounds with the ability to inhibit bacterial growth in the presence of cefoxitin, an AmpC inducer, and identified 2663 inhibitors that were also tested in the absence of cefoxitin to determine AmpG specificity. The Z' and signal-to-background ratio were robust at 0.87 ± 0.05 and 2.2 ± 0.2, respectively. Through a series of secondary and tertiary studies, including a novel luciferase-based counterscreen, we ultimately identified eight potential AmpG-specific inhibitors.
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Affiliation(s)
- Deanna Collia
- 1 The Scripps Research Institute Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA
| | | | - Hao Tan
- 3 Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Shouguang Jin
- 3 Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Taimour Langaee
- 4 Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Justin Shumate
- 1 The Scripps Research Institute Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA
| | - Louis Scampavia
- 1 The Scripps Research Institute Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA
| | - Timothy P Spicer
- 1 The Scripps Research Institute Molecular Screening Center, Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA
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Janovick JA, Spicer TP, Bannister TD, Scampavia L, Conn PM. Pharmacoperone rescue of vasopressin 2 receptor mutants reveals unexpected constitutive activity and coupling bias. PLoS One 2017; 12:e0181830. [PMID: 28767678 PMCID: PMC5540481 DOI: 10.1371/journal.pone.0181830] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [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: 01/30/2017] [Accepted: 07/08/2017] [Indexed: 12/30/2022] Open
Abstract
Pharmacoperones are small molecules that diffuse into cells and rescue misfolded, mistrafficked protein mutants, restoring their function. These substances act with high target specificity, serving as templates to fold (or refold) receptors, enzymes, ion channels or other proteins and enable them to pass the scrutiny of the cellular quality control system ("rescue"). In the present study we demonstrate that a rescued mutant (L83Q) of the vasopressin type 2 receptor (V2R), shows a strong bias for Gs coupling unlike the WT V2 receptor, which couples to both Gs and Gq/11. Failure of the mutant to couple to Gq/11 was not due to a limiting quantity of G-proteins since other Gq/11-coupled receptors (WT V2R, histamine receptor and muscarinic receptor) responded appropriately to their ligands. Transfection with DNA encoding Gq enabled the V2 receptor mutant to couple to this G protein, but only modestly compared with the WT receptor. Fourteen V2R mutant pharmacoperones, of multiple chemical classes, obtained from a high throughput screen of a 660,000 structure library, and one V2R peptidomimetic antagonist rescues L83Q. The rescued mutant shows similar bias with all pharmacoperones identified, suggesting that the bias is intrinsic to the mutant protein's structure, rather than due to the chemical class of the pharmacoperone. In the case of V2R mutant Y128S, rescue with a pharmacoperone revealed constitutive activity, also with bias for Gs, although both IP and cAMP were produced in response to agonist. These results suggest that particular rescued receptor mutants show functional characteristics that differ from the WT receptor; a finding that may be important to consider as pharmacoperones are developed as therapeutic agents.
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Affiliation(s)
- Jo Ann Janovick
- Departments of Internal Medicine and Cell Biology/Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Timothy P. Spicer
- Lead Identification Division, Translational Research Institute and Department of Molecular Therapeutics, Scripps Research Institute, Jupiter, Florida, United States of America
| | - Thomas D. Bannister
- Department of Chemistry, Scripps Research Institute, Jupiter, Florida, United States of America
| | - Louis Scampavia
- Lead Identification Division, Translational Research Institute and Department of Molecular Therapeutics, Scripps Research Institute, Jupiter, Florida, United States of America
| | - P. Michael Conn
- Departments of Internal Medicine and Cell Biology/Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
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Hou S, Madoux F, Scampavia L, Janovick JA, Conn PM, Spicer TP. Drug Library Screening for the Identification of Ionophores That Correct the Mistrafficking Disorder Associated with Oxalosis Kidney Disease. SLAS Discov 2017; 22:887-896. [PMID: 28346094 DOI: 10.1177/2472555217689992] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Primary hyperoxaluria is the underlying cause of oxalosis and is a life-threatening autosomal recessive disease, for which treatment may require dialysis or dual liver-kidney transplantation. The most common primary hyperoxaluria type 1 (PH1) is caused by genetic mutations of a liver-specific enzyme alanine:glyoxylate aminotransferase (AGT), which results in the misrouting of AGT from the peroxisomes to the mitochondria. Pharmacoperones are small molecules with the ability to modify misfolded proteins and route them correctly within the cells, which may present an effective strategy to treat AGT misrouting in PH1 disorders. We miniaturized a cell-based high-content assay into 1536-well plate format and screened ~4200 pharmacologically relevant compounds including Food and Drug Administration, European Union, and Japanese-approved drugs. This assay employs CHO cells stably expressing AGT-170, a mutant that predominantly resides in the mitochondria, where we monitor for its relocation to the peroxisomes through automated image acquisition and analysis. The miniaturized 1536-well assay yielded a Z' averaging 0.70 ± 0.07. Three drugs were identified as potential pharmacoperones from this pilot screen, demonstrating the applicability of this assay for large-scale high-throughput screening.
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Affiliation(s)
- Shurong Hou
- 1 Department of Molecular Therapeutics, Scripps Research Institute Molecular Screening Center, Scripps Research Institute, Jupiter, FL, USA
| | - Franck Madoux
- 1 Department of Molecular Therapeutics, Scripps Research Institute Molecular Screening Center, Scripps Research Institute, Jupiter, FL, USA.,3 Amgen Inc., Thousand Oaks, CA
| | - Louis Scampavia
- 1 Department of Molecular Therapeutics, Scripps Research Institute Molecular Screening Center, Scripps Research Institute, Jupiter, FL, USA
| | - Jo Ann Janovick
- 2 Departments of Internal Medicine and Cell Biology/Biochemistry, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - P Michael Conn
- 2 Departments of Internal Medicine and Cell Biology/Biochemistry, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Timothy P Spicer
- 1 Department of Molecular Therapeutics, Scripps Research Institute Molecular Screening Center, Scripps Research Institute, Jupiter, FL, USA
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Madoux F, Tanner A, Vessels M, Willetts L, Hou S, Scampavia L, Spicer TP. A 1536-Well 3D Viability Assay to Assess the Cytotoxic Effect of Drugs on Spheroids. SLAS Discov 2017; 22:516-524. [PMID: 28346088 DOI: 10.1177/2472555216686308] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Evaluation of drug cytotoxicity traditionally relies on use of cell monolayers, which are easily miniaturized to the 1536-well plate format. Three-dimensional (3D) cell culture models have recently gained popularity thanks to their ability to better mimic the complexity of in vivo systems. Despite growing interest in these more physiologically relevant and highly predictive cell-based models for compound profiling and drug discovery, 3D assays are currently performed in a medium- to low-throughput format, either in 96-well or 384-well plates. Here, we describe the design and implementation of a novel high-throughput screening (HTS)-compatible 1536-well plate assay that enables the parallel formation, size monitoring and viability assessment of 3D spheroids in a highly consistent manner. Custom-made plates featuring an ultra-low-attachment surface and round-bottom wells were evaluated for their compatibility with HTS requirements through a luminescence-based cytotoxicity pilot screen of ~3300 drugs from approved drug and National Cancer Institute (NCI) collections. As anticipated, results from this screen were significantly different from a parallel screen performed on cell monolayers. With the ability to achieve an average Z' factor greater than 0.5, this automation-friendly assay can be implemented to either profile lead compounds in a more economical plate format or to interrogate large compound libraries by ultra-HTS (uHTS).
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Affiliation(s)
- Franck Madoux
- 1 Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA.,3 Amgen, One Amgen Center Drive, Thousand Oaks, CA, USA
| | - Allison Tanner
- 2 Corning Incorporated, Life Sciences, Tewksbury, MA, USA
| | | | | | - Shurong Hou
- 1 Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA
| | - Louis Scampavia
- 1 Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA
| | - Timothy P Spicer
- 1 Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA
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Wang J, Fang P, Chase P, Tshori S, Razin E, Spicer TP, Scampavia L, Hodder P, Guo M. Development of an HTS-Compatible Assay for Discovery of Melanoma-Related Microphthalmia Transcription Factor Disruptors Using AlphaScreen Technology. SLAS Discov 2016; 22:58-66. [PMID: 27827304 DOI: 10.1177/1087057116675274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Microphthalmia transcription factor (MITF) is a master transcription factor expressed in melanocytes, essential for melanocyte survival, differentiation, and pigment formation, and is a key oncogenic factor in melanoma initiation, migration, and treatment resistance. Although identified as an important therapeutic target for melanoma, clinical inhibitors directly targeting the MITF protein are not available. Based on the functional state of MITF, we have designed an MITF dimerization-based AlphaScreen (MIDAS) assay that sensitively and specifically mirrors the dimerization of MITF in vitro. This assay is further exploited for identification of the MITF dimer disruptor for high-throughput screening. A pilot screen against a library of 1280 pharmacologically active compounds indicates that the MIDAS assay performance exhibits exceptional results with a Z' factor of 0.81 and a signal-to-background (S/B) ratio of 3.92 while identifying initial hit compounds that yield an ability to disrupt MITF-DNA interaction. The results presented demonstrate that the MIDAS assay is ready to screen large chemical libraries in order to discover novel modulators of MITF for potential melanoma treatment.
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Affiliation(s)
- Jing Wang
- 1 Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL, USA.,2 State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Pengfei Fang
- 1 Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL, USA.,2 State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Peter Chase
- 4 Scripps Research Institute Molecular Screening Center, Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA.,PH-Amgen, Inc., Thousand Oaks, CA; PC-Bristol-Myers Squibb, Princeton, NJ
| | - Sagi Tshori
- 5 Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem 91120, Israel
| | - Ehud Razin
- 5 Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem 91120, Israel
| | - Timothy P Spicer
- 4 Scripps Research Institute Molecular Screening Center, Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Louis Scampavia
- 4 Scripps Research Institute Molecular Screening Center, Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Peter Hodder
- 4 Scripps Research Institute Molecular Screening Center, Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA.,PH-Amgen, Inc., Thousand Oaks, CA; PC-Bristol-Myers Squibb, Princeton, NJ
| | - Min Guo
- 1 Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL, USA.,2 State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.,3 Kangma BioTech Ltd., 781 Cailun Road, Shanghai 201203, China
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