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Eastman RT, Rusinova R, Herold KF, Huang XP, Dranchak P, Voss TC, Rana S, Shrimp JH, White AD, Hemmings HC, Roth BL, Inglese J, Andersen OS, Dahlin JL. Nonspecific membrane bilayer perturbations by ivermectin underlie SARS-CoV-2 in vitro activity. bioRxiv 2023:2023.10.23.563088. [PMID: 37961094 PMCID: PMC10634736 DOI: 10.1101/2023.10.23.563088] [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: 11/15/2023]
Abstract
Since it was proposed as a potential host-directed antiviral agent for SARS-CoV-2, the antiparasitic drug ivermectin has been investigated thoroughly in clinical trials, which have provided insufficient support for its clinical efficacy. To examine the potential for ivermectin to be repurposed as an antiviral agent, we therefore undertook a series of preclinical studies. Consistent with early reports, ivermectin decreased SARS-CoV-2 viral burden in in vitro models at low micromolar concentrations, five- to ten-fold higher than the reported toxic clinical concentration. At similar concentrations, ivermectin also decreased cell viability and increased biomarkers of cytotoxicity and apoptosis. Further mechanistic and profiling studies revealed that ivermectin nonspecifically perturbs membrane bilayers at the same concentrations where it decreases the SARS-CoV-2 viral burden, resulting in nonspecific modulation of membrane-based targets such as G-protein coupled receptors and ion channels. These results suggest that a primary molecular mechanism for the in vitro antiviral activity of ivermectin may be nonspecific membrane perturbation, indicating that ivermectin is unlikely to be translatable into a safe and effective antiviral agent. These results and experimental workflow provide a useful paradigm for performing preclinical studies on (pandemic-related) drug repurposing candidates.
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Affiliation(s)
- Richard T. Eastman
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Radda Rusinova
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Karl F. Herold
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Patricia Dranchak
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Ty C. Voss
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Sandeep Rana
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Jonathan H. Shrimp
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Alex D. White
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Hugh C. Hemmings
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Bryan L. Roth
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Division of Chemical Biology and Medicinal Chemistry, University of North Carolina Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - James Inglese
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
- Metabolic Medicine Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Olaf S. Andersen
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Jayme L. Dahlin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
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Martin HJ, Melo-Filho CC, Korn D, Eastman RT, Rai G, Simeonov A, Zakharov AV, Muratov E, Tropsha A. Small molecule antiviral compound collection (SMACC): A comprehensive, highly curated database to support the discovery of broad-spectrum antiviral drug molecules. Antiviral Res 2023; 217:105620. [PMID: 37169224 PMCID: PMC11069349 DOI: 10.1016/j.antiviral.2023.105620] [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: 02/18/2023] [Revised: 04/13/2023] [Accepted: 04/27/2023] [Indexed: 05/13/2023]
Abstract
Diseases caused by new viruses cost thousands if not millions of human lives and trillions of dollars. We have identified, collected, curated, and integrated all chemogenomics data from ChEMBL for 13 emerging viruses that hold the greatest potential threat to global human health. By identifying and solving several challenges related to data annotation accuracy, we developed a highly curated and thoroughly annotated database of compounds tested in both phenotypic and target-based assays for these viruses that we dubbed SMACC (Small Molecule Antiviral Compound Collection). The pilot version of the SMACC database contains over 32,500 entries for 13 viruses. By analyzing data in SMACC, we have identified ∼50 compounds with polyviral inhibition profile, mostly covering flavi- and coronaviruses. The SMACC database may serve as a reference for virologists and medicinal chemists working on the development of novel BSA agents in preparation for future viral outbreaks. SMACC is publicly available at https://smacc.mml.unc.edu.
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Affiliation(s)
- Holli-Joi Martin
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Cleber C Melo-Filho
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Daniel Korn
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Richard T Eastman
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD, 20850, USA
| | - Ganesha Rai
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD, 20850, USA
| | - Anton Simeonov
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD, 20850, USA
| | - Alexey V Zakharov
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD, 20850, USA.
| | - Eugene Muratov
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA.
| | - Alexander Tropsha
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA.
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Yasgar A, Bougie D, Eastman RT, Huang R, Itkin M, Kouznetsova J, Lynch C, McKnight C, Miller M, Ngan DK, Peryea T, Shah P, Shinn P, Xia M, Xu X, Zakharov AV, Simeonov A. Quantitative Bioactivity Signatures of Dietary Supplements and Natural Products. ACS Pharmacol Transl Sci 2023; 6:683-701. [PMID: 37200814 PMCID: PMC10186358 DOI: 10.1021/acsptsci.2c00194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Indexed: 05/20/2023]
Abstract
Dietary supplements and natural products are often marketed as safe and effective alternatives to conventional drugs, but their safety and efficacy are not well regulated. To address the lack of scientific data in these areas, we assembled a collection of Dietary Supplements and Natural Products (DSNP), as well as Traditional Chinese Medicinal (TCM) plant extracts. These collections were then profiled in a series of in vitro high-throughput screening assays, including a liver cytochrome p450 enzyme panel, CAR/PXR signaling pathways, and P-glycoprotein (P-gp) transporter assay activities. This pipeline facilitated the interrogation of natural product-drug interaction (NaPDI) through prominent metabolizing pathways. In addition, we compared the activity profiles of the DSNP/TCM substances with those of an approved drug collection (the NCATS Pharmaceutical Collection or NPC). Many of the approved drugs have well-annotated mechanisms of action (MOAs), while the MOAs for most of the DSNP and TCM samples remain unknown. Based on the premise that compounds with similar activity profiles tend to share similar targets or MOA, we clustered the library activity profiles to identify overlap with the NPC to predict the MOAs of the DSNP/TCM substances. Our results suggest that many of these substances may have significant bioactivity and potential toxicity, and they provide a starting point for further research on their clinical relevance.
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Affiliation(s)
- Adam Yasgar
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Danielle Bougie
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Richard T Eastman
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Misha Itkin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Jennifer Kouznetsova
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Caitlin Lynch
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Crystal McKnight
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Mitch Miller
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Deborah K Ngan
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Tyler Peryea
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Pranav Shah
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Paul Shinn
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Xin Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Alexey V Zakharov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
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Calit J, Araújo JE, Deng B, Miura K, Gaitán XA, Araújo MDS, Medeiros JF, Long CA, Simeonov A, Eastman RT, Bargieri DY. Novel Transmission-Blocking Antimalarials Identified by High-Throughput Screening of Plasmodium berghei Ookluc. Antimicrob Agents Chemother 2023; 67:e0146522. [PMID: 36856421 PMCID: PMC10112123 DOI: 10.1128/aac.01465-22] [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: 10/31/2022] [Accepted: 02/09/2023] [Indexed: 03/02/2023] Open
Abstract
Safe and effective malaria transmission-blocking chemotherapeutics would allow a community-level approach to malaria control and eradication efforts by targeting the mosquito sexual stage of the parasite life cycle. However, only a single drug, primaquine, is currently approved for use in reducing transmission, and drug toxicity limits its widespread implementation. To address this limitation in antimalarial chemotherapeutics, we used a recently developed transgenic Plasmodium berghei line, Ookluc, to perform a series of high-throughput in vitro screens for compounds that inhibit parasite fertilization, the initial step of parasite development within the mosquito. Screens of antimalarial compounds, approved drug collections, and drug-like molecule libraries identified 185 compounds that inhibit parasite maturation to the zygote form. Seven compounds were further characterized to block gametocyte activation or to be cytotoxic to formed zygotes. These were further validated in mosquito membrane-feeding assays using Plasmodium falciparum and P. vivax. This work demonstrates that high-throughput screens using the Ookluc line can identify compounds that are active against the two most relevant human Plasmodium species and provides a list of compounds that can be explored for the development of new antimalarials to block transmission.
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Affiliation(s)
- Juliana Calit
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Jessica E. Araújo
- Plataforma de Produção e Infecção de Vetores da Malária-PIVEM, Laboratório de Entomologia, Fundação Oswaldo Cruz-Fiocruz Rondônia, Porto Velho, Rondônia, Brazil
- Programa de Pós-graduação em Biologia Experimental, Universidade Federal de Rondônia/Fiocruz Rondônia, Porto Velho, Rondônia, Brazil
| | - Bingbing Deng
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Kazutoyo Miura
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Xiomara A. Gaitán
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Maisa da Silva Araújo
- Plataforma de Produção e Infecção de Vetores da Malária-PIVEM, Laboratório de Entomologia, Fundação Oswaldo Cruz-Fiocruz Rondônia, Porto Velho, Rondônia, Brazil
| | - Jansen F. Medeiros
- Plataforma de Produção e Infecção de Vetores da Malária-PIVEM, Laboratório de Entomologia, Fundação Oswaldo Cruz-Fiocruz Rondônia, Porto Velho, Rondônia, Brazil
- Programa de Pós-graduação em Biologia Experimental, Universidade Federal de Rondônia/Fiocruz Rondônia, Porto Velho, Rondônia, Brazil
| | - Carole A. Long
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Anton Simeonov
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Richard T. Eastman
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Daniel Y. Bargieri
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
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Fu Y, da Fonseca Rezende e Mello J, Fleming BD, Renn A, Chen CZ, Hu X, Xu M, Gorshkov K, Hanson Q, Zheng W, Lee EM, Perera L, Petrovich R, Pradhan M, Eastman RT, Itkin Z, Stanley TB, Hsu A, Dandey V, Sharma K, Gillette W, Taylor T, Ramakrishnan N, Perkins S, Esposito D, Oh E, Susumu K, Wolak M, Ferrer M, Hall MD, Borgnia MJ, Simeonov A. A humanized nanobody phage display library yields potent binders of SARS CoV-2 spike. PLoS One 2022; 17:e0272364. [PMID: 35947606 PMCID: PMC9365158 DOI: 10.1371/journal.pone.0272364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/18/2022] [Indexed: 01/11/2023] Open
Abstract
Neutralizing antibodies targeting the SARS-CoV-2 spike protein have shown a great preventative/therapeutic potential. Here, we report a rapid and efficient strategy for the development and design of SARS-CoV-2 neutralizing humanized nanobody constructs with sub-nanomolar affinities and nanomolar potencies. CryoEM-based structural analysis of the nanobodies in complex with spike revealed two distinct binding modes. The most potent nanobody, RBD-1-2G(NCATS-BL8125), tolerates the N501Y RBD mutation and remains capable of neutralizing the B.1.1.7 (Alpha) variant. Molecular dynamics simulations provide a structural basis for understanding the neutralization process of nanobodies exclusively focused on the spike-ACE2 interface with and without the N501Y mutation on RBD. A primary human airway air-lung interface (ALI) ex vivo model showed that RBD-1-2G-Fc antibody treatment was effective at reducing viral burden following WA1 and B.1.1.7 SARS-CoV-2 infections. Therefore, this presented strategy will serve as a tool to mitigate the threat of emerging SARS-CoV-2 variants.
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Affiliation(s)
- Ying Fu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Juliana da Fonseca Rezende e Mello
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Bryan D. Fleming
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Alex Renn
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Catherine Z. Chen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Miao Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Kirill Gorshkov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Quinlin Hanson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Emily M. Lee
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Lalith Perera
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Robert Petrovich
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Manisha Pradhan
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Richard T. Eastman
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Zina Itkin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Thomas B. Stanley
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Allen Hsu
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Venkata Dandey
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Kedar Sharma
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - William Gillette
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Troy Taylor
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Nitya Ramakrishnan
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Shelley Perkins
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Dominic Esposito
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Eunkeu Oh
- Optical Sciences Division, Naval Research Laboratory, Washington, D.C., United States of America
| | - Kimihiro Susumu
- Optical Sciences Division, Naval Research Laboratory, Washington, D.C., United States of America
- Jacobs Corporation, Hanover, Maryland, United States of America
| | - Mason Wolak
- Optical Sciences Division, Naval Research Laboratory, Washington, D.C., United States of America
| | - Marc Ferrer
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
- * E-mail: (MDH); (MJB); (AS)
| | - Mario J. Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
- * E-mail: (MDH); (MJB); (AS)
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
- * E-mail: (MDH); (MJB); (AS)
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Martin H, Melo-filho CC, Korn D, Eastman RT, Rai G, Simeonov A, Zakharov AV, Muratov E, Tropsha A. Small Molecule Antiviral Compound Collection (SMACC): a database to support the discovery of broad-spectrum antiviral drug molecules.. [PMID: 35860225 PMCID: PMC9298133 DOI: 10.1101/2022.07.09.499397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Diseases caused by new viruses costs thousands if not millions of human lives and trillions of dollars in damage to the global economy. Despite the rapid development of vaccines for SARS-CoV-2, the lack of small molecule antiviral drugs that work against multiple viral families (broad-spectrum antivirals; BSAs) has left the entire world’s human population vulnerable to the infection between the beginning of the outbreak and the widespread availability of vaccines. Developing BSAs is an attractive, yet challenging, approach that could prevent the next, inevitable, viral outbreak from becoming a global catastrophe. To explore whether historical medicinal chemistry efforts suggest the possibility of discovering novel BSAs, we (i) identified, collected, curated, and integrated all chemical bioactivity data available in ChEMBL for molecules tested in respective assays for 13 emerging viruses that, based on published literature, hold the greatest potential threat to global human health; (ii) identified and solved the challenges related to data annotation accuracy including assay description ambiguity, missing cell or target information, and incorrect BioAssay Ontology (BAO) annotations; (iii) developed a highly curated and thoroughly annotated database of compounds tested in both phenotypic (21,392 entries) and target-based (11,123 entries) assays for these viruses; and (iv) identified a subset of compounds showing BSA activity. For the latter task, we eliminated inconclusive and annotated duplicative entries by checking the concordance between multiple assay results and identified eight compounds active against 3–4 viruses from the phenotypic data, 16 compounds active against two viruses from the target-based data, and 35 compounds active in at least one phenotypic and one target-based assay. The pilot version of our SMACC (Small Molecule Antiviral Compound Collection) database contains over 32,500 entries for 13 viruses. Our analysis indicates that previous research yielded very small number of BSA compounds. We posit that focused and coordinated efforts strategically targeting the discovery of such agents must be established and maintained going forward. The SMACC database publicly available at https://smacc.mml.unc.edu may serve as a reference for virologists and medicinal chemists working on the development of novel BSA agents in preparation for future viral outbreaks.
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Dorjsuren D, Eastman RT, Song MJ, Yasgar A, Chen Y, Bharti K, Zakharov AV, Jadhav A, Ferrer M, Shi PY, Simeonov A. A platform of assays for the discovery of anti-Zika small-molecules with activity in a 3D-bioprinted outer-blood-retina model. PLoS One 2022; 17:e0261821. [PMID: 35041689 PMCID: PMC8765781 DOI: 10.1371/journal.pone.0261821] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 12/10/2021] [Indexed: 01/24/2023] Open
Abstract
The global health emergency posed by the outbreak of Zika virus (ZIKV), an arthropod-borne flavivirus causing severe neonatal neurological conditions, has subsided, but there continues to be transmission of ZIKV in endemic regions. As such, there is still a medical need for discovering and developing therapeutical interventions against ZIKV. To identify small-molecule compounds that inhibit ZIKV disease and transmission, we screened multiple small-molecule collections, mostly derived from natural products, for their ability to inhibit wild-type ZIKV. As a primary high-throughput screen, we used a viral cytopathic effect (CPE) inhibition assay conducted in Vero cells that was optimized and miniaturized to a 1536-well format. Suitably active compounds identified from the primary screen were tested in a panel of orthogonal assays using recombinant Zika viruses, including a ZIKV Renilla luciferase reporter assay and a ZIKV mCherry reporter system. Compounds that were active in the wild-type ZIKV inhibition and ZIKV reporter assays were further evaluated for their inhibitory effects against other flaviviruses. Lastly, we demonstrated that wild-type ZIKV is able to infect a 3D-bioprinted outer-blood-retina barrier tissue model and disrupt its barrier function, as measured by electrical resistance. One of the identified compounds (3-Acetyl-13-deoxyphomenone, NCGC00380955) was able to prevent the pathological effects of the viral infection on this clinically relevant ZIKV infection model.
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Affiliation(s)
- Dorjbal Dorjsuren
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Richard T. Eastman
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Min Jae Song
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Adam Yasgar
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Yuchi Chen
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Kapil Bharti
- Unit on Ocular and Stem Cell Translational Research, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alexey V. Zakharov
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Ajit Jadhav
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Marc Ferrer
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Pei-Yong Shi
- University of Texas Medical Branch Galveston, Galveston, TX, United States of America
| | - Anton Simeonov
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
- * E-mail:
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8
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Fu Y, Mello JDFRE, Fleming BD, Renn A, Chen CZ, Hu X, Xu M, Gorshkov K, Hanson Q, Zheng W, Lee EM, Perera L, Petrovich R, Pradhan M, Eastman RT, Itkin Z, Stanley T, Hsu A, Dandey V, Gillette W, Taylor T, Ramakrishnan N, Perkins S, Esposito D, Oh E, Susumu K, Wolak M, Ferrer M, Hall MD, Borgnia MJ, Simeonov A. The humanized nanobody RBD-1-2G tolerates the spike N501Y mutation to neutralize SARS-CoV-2. bioRxiv 2021. [PMID: 34729560 DOI: 10.1101/2021.10.22.465476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Neutralizing antibodies targeting the SARS-CoV-2 spike protein have shown a great preventative/therapeutic potential. Here, we report a rapid and efficient strategy for the development and design of SARS-CoV-2 neutralizing humanized nanobody constructs with sub-nanomolar affinities and nanomolar potencies. CryoEM-based structural analysis of the nanobodies in complex with spike revealed two distinct binding modes. The most potent nanobody, RBD-1-2G(NCATS-BL8125), tolerates the N501Y RBD mutation and remains capable of neutralizing the B.1.1.7 (Alpha) variant. Molecular dynamics simulations provide a structural basis for understanding the neutralization process of nanobodies exclusively focused on the spike-ACE2 interface with and without the N501Y mutation on RBD. A primary human airway air-lung interface (ALI) ex vivo model showed that RBD-1-2G-Fc antibody treatment was effective at reducing viral burden following WA1 and B.1.1.7 SARS-CoV-2 infections. Therefore, this presented strategy will serve as a tool to mitigate the threat of emerging SARS-CoV-2 variants. One-Sentence Summary A cost-effective, high-throughput, adaptable pipeline capable of identifying effective humanized nanobodies against SARS-CoV-2.
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9
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Shamim K, Xu M, Hu X, Lee EM, Lu X, Huang R, Shah P, Xu X, Chen CZ, Shen M, Guo H, Chen L, Itkin Z, Eastman RT, Shinn P, Klumpp-Thomas C, Michael S, Simeonov A, Lo DC, Ming GL, Song H, Tang H, Zheng W, Huang W. Application of niclosamide and analogs as small molecule inhibitors of Zika virus and SARS-CoV-2 infection. Bioorg Med Chem Lett 2021; 40:127906. [PMID: 33689873 PMCID: PMC7936759 DOI: 10.1016/j.bmcl.2021.127906] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/15/2021] [Accepted: 02/21/2021] [Indexed: 12/12/2022]
Abstract
Zika virus has emerged as a potential threat to human health globally. A previous drug repurposing screen identified the approved anthelminthic drug niclosamide as a small molecule inhibitor of Zika virus infection. However, as antihelminthic drugs are generally designed to have low absorption when dosed orally, the very limited bioavailability of niclosamide will likely hinder its potential direct repurposing as an antiviral medication. Here, we conducted SAR studies focusing on the anilide and salicylic acid regions of niclosamide to improve physicochemical properties such as microsomal metabolic stability, permeability and solubility. We found that the 5-bromo substitution in the salicylic acid region retains potency while providing better drug-like properties. Other modifications in the anilide region with 2′-OMe and 2′-H substitutions were also advantageous. We found that the 4′-NO2 substituent can be replaced with a 4′-CN or 4′-CF3 substituents. Together, these modifications provide a basis for optimizing the structure of niclosamide to improve systemic exposure for application of niclosamide analogs as drug lead candidates for treating Zika and other viral infections. Indeed, key analogs were also able to rescue cells from the cytopathic effect of SARS-CoV-2 infection, indicating relevance for therapeutic strategies targeting the COVID-19 pandemic.
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Affiliation(s)
- Khalida Shamim
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA.
| | - Miao Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Emily M Lee
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA; Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Xiao Lu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Pranav Shah
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Xin Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Catherine Z Chen
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Hui Guo
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Lu Chen
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Zina Itkin
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Richard T Eastman
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Paul Shinn
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Carleen Klumpp-Thomas
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Sam Michael
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Donald C Lo
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hengli Tang
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Wenwei Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA.
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10
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Le Manach C, Dam J, Woodland JG, Kaur G, Khonde LP, Brunschwig C, Njoroge M, Wicht KJ, Horatscheck A, Paquet T, Boyle GA, Gibhard L, Taylor D, Lawrence N, Yeo T, Mok S, Eastman RT, Dorjsuren D, Talley DC, Guo H, Simeonov A, Reader J, van der Watt M, Erlank E, Venter N, Zawada JW, Aswat A, Nardini L, Coetzer TL, Lauterbach SB, Bezuidenhout BC, Theron A, Mancama D, Koekemoer LL, Birkholtz LM, Wittlin S, Delves M, Ottilie S, Winzeler EA, von Geldern TW, Smith D, Fidock DA, Street LJ, Basarab GS, Duffy J, Chibale K. Identification and Profiling of a Novel Diazaspiro[3.4]octane Chemical Series Active against Multiple Stages of the Human Malaria Parasite Plasmodium falciparum and Optimization Efforts. J Med Chem 2021; 64:2291-2309. [PMID: 33573376 DOI: 10.1021/acs.jmedchem.1c00034] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel diazaspiro[3.4]octane series was identified from a Plasmodium falciparum whole-cell high-throughput screening campaign. Hits displayed activity against multiple stages of the parasite lifecycle, which together with a novel sp3-rich scaffold provided an attractive starting point for a hit-to-lead medicinal chemistry optimization and biological profiling program. Structure-activity-relationship studies led to the identification of compounds that showed low nanomolar asexual blood-stage activity (<50 nM) together with strong gametocyte sterilizing properties that translated to transmission-blocking activity in the standard membrane feeding assay. Mechanistic studies through resistance selection with one of the analogues followed by whole-genome sequencing implicated the P. falciparum cyclic amine resistance locus in the mode of resistance.
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Affiliation(s)
- Claire Le Manach
- Drug Discovery and Development Center (H3D), University of Cape Town, Rondebosch 7701, South Africa
| | - Jean Dam
- Drug Discovery and Development Center (H3D), University of Cape Town, Rondebosch 7701, South Africa
| | - John G Woodland
- Drug Discovery and Development Center (H3D), University of Cape Town, Rondebosch 7701, South Africa
| | - Gurminder Kaur
- Drug Discovery and Development Center (H3D), University of Cape Town, Rondebosch 7701, South Africa
| | - Lutete P Khonde
- Drug Discovery and Development Center (H3D), University of Cape Town, Rondebosch 7701, South Africa
| | - Christel Brunschwig
- Drug Discovery and Development Center (H3D), Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Mathew Njoroge
- Drug Discovery and Development Center (H3D), Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Kathryn J Wicht
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - André Horatscheck
- Drug Discovery and Development Center (H3D), University of Cape Town, Rondebosch 7701, South Africa
| | - Tanya Paquet
- Drug Discovery and Development Center (H3D), University of Cape Town, Rondebosch 7701, South Africa
| | - Grant A Boyle
- Drug Discovery and Development Center (H3D), University of Cape Town, Rondebosch 7701, South Africa
| | - Liezl Gibhard
- Drug Discovery and Development Center (H3D), Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Dale Taylor
- Drug Discovery and Development Center (H3D), Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Nina Lawrence
- Drug Discovery and Development Center (H3D), Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Sachel Mok
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Richard T Eastman
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Dorjbal Dorjsuren
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Daniel C Talley
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Hui Guo
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Anton Simeonov
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Janette Reader
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Mariëtte van der Watt
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Erica Erlank
- Wits Research Institute for Malaria, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa.,Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2192, South Africa
| | - Nelius Venter
- Wits Research Institute for Malaria, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa.,Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2192, South Africa
| | - Jacek W Zawada
- Wits Research Institute for Malaria, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa.,Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2192, South Africa
| | - Ayesha Aswat
- Wits Research Institute for Malaria, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa.,Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2192, South Africa
| | - Luisa Nardini
- Wits Research Institute for Malaria, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa.,Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2192, South Africa
| | - Theresa L Coetzer
- Wits Research Institute for Malaria, School of Pathology, Department of Molecular Medicine and Haematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Sonja B Lauterbach
- Wits Research Institute for Malaria, School of Pathology, Department of Molecular Medicine and Haematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Belinda C Bezuidenhout
- Wits Research Institute for Malaria, School of Pathology, Department of Molecular Medicine and Haematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Anjo Theron
- Biosciences, Council for Scientific and Industrial Research, P.O. Box 395, Pretoria 0001, South Africa
| | - Dalu Mancama
- Biosciences, Council for Scientific and Industrial Research, P.O. Box 395, Pretoria 0001, South Africa
| | - Lizette L Koekemoer
- Wits Research Institute for Malaria, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa.,Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2192, South Africa
| | - Lyn-Marie Birkholtz
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland.,University of Basel, 4003 Basel, Switzerland
| | - Michael Delves
- Imperial College London, South Kensington, London SW7 2AZ, U.K.,London School of Hygiene and Tropical Medicine, London WC1E 7HT, U.K
| | - Sabine Ottilie
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, California 92093-076, United States
| | - Elizabeth A Winzeler
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, California 92093-076, United States
| | | | | | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States.,Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Leslie J Street
- Drug Discovery and Development Center (H3D), University of Cape Town, Rondebosch 7701, South Africa
| | - Gregory S Basarab
- Drug Discovery and Development Center (H3D), University of Cape Town, Rondebosch 7701, South Africa
| | - James Duffy
- Medicines for Malaria Venture, ICC, Route de Pré-Bois 20, P.O. Box 1826, 1215 Geneva, Switzerland
| | - Kelly Chibale
- Drug Discovery and Development Center (H3D), University of Cape Town, Rondebosch 7701, South Africa.,South African Medical Research Council, Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
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11
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Bobrowski T, Chen L, Eastman RT, Itkin Z, Shinn P, Chen CZ, Guo H, Zheng W, Michael S, Simeonov A, Hall MD, Zakharov AV, Muratov EN. Synergistic and Antagonistic Drug Combinations against SARS-CoV-2. Mol Ther 2021; 29:873-885. [PMID: 33333292 PMCID: PMC7834738 DOI: 10.1016/j.ymthe.2020.12.016] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [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: 09/03/2020] [Revised: 11/15/2020] [Accepted: 12/09/2020] [Indexed: 01/15/2023] Open
Abstract
Antiviral drug development for coronavirus disease 2019 (COVID-19) is occurring at an unprecedented pace, yet there are still limited therapeutic options for treating this disease. We hypothesized that combining drugs with independent mechanisms of action could result in synergy against SARS-CoV-2, thus generating better antiviral efficacy. Using in silico approaches, we prioritized 73 combinations of 32 drugs with potential activity against SARS-CoV-2 and then tested them in vitro. Sixteen synergistic and eight antagonistic combinations were identified; among 16 synergistic cases, combinations of the US Food and Drug Administration (FDA)-approved drug nitazoxanide with remdesivir, amodiaquine, or umifenovir were most notable, all exhibiting significant synergy against SARS-CoV-2 in a cell model. However, the combination of remdesivir and lysosomotropic drugs, such as hydroxychloroquine, demonstrated strong antagonism. Overall, these results highlight the utility of drug repurposing and preclinical testing of drug combinations for discovering potential therapies to treat COVID-19.
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Affiliation(s)
- Tesia Bobrowski
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Lu Chen
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Richard T Eastman
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Zina Itkin
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Paul Shinn
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Catherine Z Chen
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Hui Guo
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Wei Zheng
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Sam Michael
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Matthew D Hall
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Alexey V Zakharov
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD 20850, USA.
| | - Eugene N Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA.
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12
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Chen CZ, Shinn P, Itkin Z, Eastman RT, Bostwick R, Rasmussen L, Huang R, Shen M, Hu X, Wilson KM, Brooks BM, Guo H, Zhao T, Klump-Thomas C, Simeonov A, Michael SG, Lo DC, Hall MD, Zheng W. Drug Repurposing Screen for Compounds Inhibiting the Cytopathic Effect of SARS-CoV-2. Front Pharmacol 2021; 11:592737. [PMID: 33708112 PMCID: PMC7942396 DOI: 10.3389/fphar.2020.592737] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/04/2020] [Indexed: 11/23/2022] Open
Abstract
Drug repurposing is a rapid approach to identify therapeutics for the treatment of emerging infectious diseases such as COVID-19. To address the urgent need for treatment options, we carried out a quantitative high-throughput screen using a SARS-CoV-2 cytopathic assay with a compound collection of 8,810 approved and investigational drugs, mechanism-based bioactive compounds, and natural products. Three hundred and nineteen compounds with anti-SARS-CoV-2 activities were identified and confirmed, including 91 approved drugs and 49 investigational drugs. The anti-SARS-CoV-2 activities of 230 of these confirmed compounds, of which 38 are approved drugs, have not been previously reported. Chlorprothixene, methotrimeprazine, and piperacetazine were the three most potent FDA-approved drugs with anti-SARS-CoV-2 activities. These three compounds have not been previously reported to have anti-SARS-CoV-2 activities, although their antiviral activities against SARS-CoV and Ebola virus have been reported. These results demonstrate that this comprehensive data set is a useful resource for drug repurposing efforts, including design of new drug combinations for clinical trials for SARS-CoV-2.
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Affiliation(s)
- Catherine Z. Chen
- National Center for Advancing Translational Sciences, Rockville, MD, United States
| | - Paul Shinn
- National Center for Advancing Translational Sciences, Rockville, MD, United States
| | - Zina Itkin
- National Center for Advancing Translational Sciences, Rockville, MD, United States
| | - Richard T. Eastman
- National Center for Advancing Translational Sciences, Rockville, MD, United States
| | | | | | - Ruili Huang
- National Center for Advancing Translational Sciences, Rockville, MD, United States
| | - Min Shen
- National Center for Advancing Translational Sciences, Rockville, MD, United States
| | - Xin Hu
- National Center for Advancing Translational Sciences, Rockville, MD, United States
| | - Kelli M. Wilson
- National Center for Advancing Translational Sciences, Rockville, MD, United States
| | - Brianna M. Brooks
- National Center for Advancing Translational Sciences, Rockville, MD, United States
| | - Hui Guo
- National Center for Advancing Translational Sciences, Rockville, MD, United States
| | - Tongan Zhao
- National Center for Advancing Translational Sciences, Rockville, MD, United States
| | - Carleen Klump-Thomas
- National Center for Advancing Translational Sciences, Rockville, MD, United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, Rockville, MD, United States
| | - Samuel G. Michael
- National Center for Advancing Translational Sciences, Rockville, MD, United States
| | - Donald C. Lo
- National Center for Advancing Translational Sciences, Rockville, MD, United States
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences, Rockville, MD, United States
| | - Wei Zheng
- National Center for Advancing Translational Sciences, Rockville, MD, United States
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13
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Ansbro MR, Itkin Z, Chen L, Zahoranszky-Kohalmi G, Amaratunga C, Miotto O, Peryea T, Hobbs CV, Suon S, Sá JM, Dondorp AM, van der Pluijm RW, Wellems TE, Simeonov A, Eastman RT. Modulation of Triple Artemisinin-Based Combination Therapy Pharmacodynamics by Plasmodium falciparum Genotype. ACS Pharmacol Transl Sci 2020; 3:1144-1157. [PMID: 33344893 PMCID: PMC7737215 DOI: 10.1021/acsptsci.0c00110] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Indexed: 01/19/2023]
Abstract
The first-line treatments for uncomplicated Plasmodium falciparum malaria are artemisinin-based combination therapies (ACTs), consisting of an artemisinin derivative combined with a longer acting partner drug. However, the spread of P. falciparum with decreased susceptibility to artemisinin and partner drugs presents a significant challenge to malaria control efforts. To stem the spread of drug resistant parasites, novel chemotherapeutic strategies are being evaluated, including the implementation of triple artemisinin-based combination therapies (TACTs). Currently, there is limited knowledge on the pharmacodynamic and pharmacogenetic interactions of proposed TACT drug combinations. To evaluate these interactions, we established an in vitro high-throughput process for measuring the drug concentration-response to three distinct antimalarial drugs present in a TACT. Sixteen different TACT combinations were screened against 15 parasite lines from Cambodia, with a focus on parasites with differential susceptibilities to piperaquine and artemisinins. Analysis revealed drug-drug interactions unique to specific genetic backgrounds, including antagonism between piperaquine and pyronaridine associated with gene amplification of plasmepsin II/III, two aspartic proteases that localize to the parasite digestive vacuole. From this initial study, we identified parasite genotypes with decreased susceptibility to specific TACTs, as well as potential TACTs that display antagonism in a genotype-dependent manner. Our assay and analysis platform can be further leveraged to inform drug implementation decisions and evaluate next-generation TACTs.
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Affiliation(s)
- Megan R. Ansbro
- Laboratory of Malaria
and Vector Research, National Institute of Allergy and Infectious
Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
- Wellcome Sanger Institute, Hinxton CB10 1SA, U.K.
| | - Zina Itkin
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Lu Chen
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Gergely Zahoranszky-Kohalmi
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Chanaki Amaratunga
- Laboratory of Malaria
and Vector Research, National Institute of Allergy and Infectious
Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Olivo Miotto
- Wellcome Sanger Institute, Hinxton CB10 1SA, U.K.
- Mahidol-Oxford Tropical Medicine Research
Unit, Faculty of Tropical Medicine, Mahidol
University, Bangkok 10400, Thailand
- Centre
for Tropical Medicine and Global Health, Nuffield Department of Medicine
Research, University of Oxford, Oxford OX3 7LF, U.K.
- Medical Research Council (MRC) Centre for Genomics and
Global Health, University of Oxford, Oxford OX3 7BN, U.K.
| | - Tyler Peryea
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Charlotte V. Hobbs
- Division of Infectious Diseases, Children’s
Hospital, University of Mississippi Medical
Center, Jackson, Mississippi 39216, United States
| | - Seila Suon
- National Center for Parasitology, Entomology,
and Malaria Control, Phnom Penh, Cambodia
| | - Juliana M. Sá
- Laboratory of Malaria
and Vector Research, National Institute of Allergy and Infectious
Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Arjen M. Dondorp
- Mahidol-Oxford Tropical Medicine Research
Unit, Faculty of Tropical Medicine, Mahidol
University, Bangkok 10400, Thailand
- Centre
for Tropical Medicine and Global Health, Nuffield Department of Medicine
Research, University of Oxford, Oxford OX3 7LF, U.K.
| | - Rob W. van der Pluijm
- Mahidol-Oxford Tropical Medicine Research
Unit, Faculty of Tropical Medicine, Mahidol
University, Bangkok 10400, Thailand
- Centre
for Tropical Medicine and Global Health, Nuffield Department of Medicine
Research, University of Oxford, Oxford OX3 7LF, U.K.
| | - Thomas E. Wellems
- Laboratory of Malaria
and Vector Research, National Institute of Allergy and Infectious
Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Anton Simeonov
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Richard T. Eastman
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
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14
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Hanson QM, Wilson KM, Shen M, Itkin Z, Eastman RT, Shinn P, Hall MD. Targeting ACE2-RBD Interaction as a Platform for COVID-19 Therapeutics: Development and Drug-Repurposing Screen of an AlphaLISA Proximity Assay. ACS Pharmacol Transl Sci 2020; 3:1352-1360. [PMID: 33330843 PMCID: PMC7688046 DOI: 10.1021/acsptsci.0c00161] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [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: 10/02/2020] [Indexed: 12/11/2022]
Abstract
![]()
The
COVID-19 pandemic, caused by SARS-CoV-2, is a pressing public
health emergency garnering a rapid response from scientists across
the globe. Host cell invasion is initiated through direct binding
of the viral spike protein to the host receptor angiotensin-converting
enzyme 2 (ACE2). Disrupting the spike protein–ACE2 interaction
is a potential therapeutic target for treating COVID-19. We have developed
a proximity-based AlphaLISA assay to measure the binding of SARS-CoV-2
spike protein receptor binding domain (RBD) to ACE2. Utilizing this
assay platform, a drug-repurposing screen against 3384 small-molecule
drugs and preclinical compounds was carried out, yielding 25 high-quality
primary hits, of which only corilagin was validated in cherry-picking.
This established AlphaLISA RBD–ACE2 platform can facilitate
evaluation of biologics or small molecules that can perturb this essential
viral–host interaction to further the development of interventions
to address the global health pandemic.
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Affiliation(s)
- Quinlin M Hanson
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20852, United States
| | - Kelli M Wilson
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20852, United States
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20852, United States
| | - Zina Itkin
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20852, United States
| | - Richard T Eastman
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20852, United States
| | - Paul Shinn
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20852, United States
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20852, United States
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15
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Chen CZ, Shinn P, Itkin Z, Eastman RT, Bostwick R, Rasmussen L, Huang R, Shen M, Hu X, Wilson KM, Brooks B, Guo H, Zhao T, Klump-Thomas C, Simeonov A, Michael SG, Lo DC, Hall MD, Zheng W. Drug Repurposing Screen for Compounds Inhibiting the Cytopathic Effect of SARS-CoV-2. bioRxiv 2020:2020.08.18.255877. [PMID: 32839771 PMCID: PMC7444282 DOI: 10.1101/2020.08.18.255877] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 12/11/2022]
Abstract
Drug repurposing is a rapid approach to identifying therapeutics for the treatment of emerging infectious diseases such as COVID-19. To address the urgent need for treatment options, we carried out a quantitative high-throughput screen using a SARS-CoV-2 cytopathic assay with a compound collection of 8,810 approved and investigational drugs, mechanism-based bioactive compounds, and natural products. Three hundred and nineteen compounds with anti-SARS-CoV-2 activities were identified and confirmed, including 91 approved drug and 49 investigational drugs. Among these confirmed compounds, the anti-SARS-CoV-2 activities of 230 compounds, including 38 approved drugs, have not been previously reported. Chlorprothixene, methotrimeprazine, and piperacetazine were the three most potent FDA approved drugs with anti-SARS-CoV-2 activities. These three compounds have not been previously reported to have anti-SARS-CoV-2 activities, although their antiviral activities against SARS-CoV and Ebola virus have been reported. These results demonstrate that this comprehensive data set of drug repurposing screen for SARS-CoV-2 is useful for drug repurposing efforts including design of new drug combinations for clinical trials.
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Affiliation(s)
- Catherine Z. Chen
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, MD, 20850
| | - Paul Shinn
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, MD, 20850
| | - Zina Itkin
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, MD, 20850
| | - Richard T. Eastman
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, MD, 20850
| | - Robert Bostwick
- Southern Research, 2000 Ninth Avenue South, Birmingham, Alabama, 35205
| | - Lynn Rasmussen
- Southern Research, 2000 Ninth Avenue South, Birmingham, Alabama, 35205
| | - Ruili Huang
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, MD, 20850
| | - Min Shen
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, MD, 20850
| | - Xin Hu
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, MD, 20850
| | - Kelli M. Wilson
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, MD, 20850
| | - Brianna Brooks
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, MD, 20850
| | - Hui Guo
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, MD, 20850
| | - Tongan Zhao
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, MD, 20850
| | - Carleen Klump-Thomas
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, MD, 20850
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, MD, 20850
| | - Samuel G. Michael
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, MD, 20850
| | - Donald C. Lo
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, MD, 20850
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, MD, 20850
| | - Wei Zheng
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, MD, 20850
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16
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Bobrowski T, Chen L, Eastman RT, Itkin Z, Shinn P, Chen C, Guo H, Zheng W, Michael S, Simeonov A, Hall MD, Zakharov AV, Muratov EN. Discovery of Synergistic and Antagonistic Drug Combinations against SARS-CoV-2 In Vitro. bioRxiv 2020:2020.06.29.178889. [PMID: 32637956 PMCID: PMC7337386 DOI: 10.1101/2020.06.29.178889] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
COVID-19 is undoubtedly the most impactful viral disease of the current century, afflicting millions worldwide. As yet, there is not an approved vaccine, as well as limited options from existing drugs for treating this disease. We hypothesized that combining drugs with independent mechanisms of action could result in synergy against SARS-CoV-2. Using in silico approaches, we prioritized 73 combinations of 32 drugs with potential activity against SARS-CoV-2 and then tested them in vitro . Overall, we identified 16 synergistic and 8 antagonistic combinations, 4 of which were both synergistic and antagonistic in a dose-dependent manner. Among the 16 synergistic cases, combinations of nitazoxanide with three other compounds (remdesivir, amodiaquine and umifenovir) were the most notable, all exhibiting significant synergy against SARS-CoV-2. The combination of nitazoxanide, an FDA-approved drug, and remdesivir, FDA emergency use authorization for the treatment of COVID-19, demonstrate a strong synergistic interaction. Notably, the combination of remdesivir and hydroxychloroquine demonstrated strong antagonism. Overall, our results emphasize the importance of both drug repurposing and preclinical testing of drug combinations for potential therapeutic use against SARS-CoV-2 infections.
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Affiliation(s)
- Tesia Bobrowski
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Lu Chen
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Richard T. Eastman
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Zina Itkin
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Paul Shinn
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Catherine Chen
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Hui Guo
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Wei Zheng
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Sam Michael
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Alexey V. Zakharov
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Eugene N. Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
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17
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Eastman RT, Roth JS, Brimacombe KR, Simeonov A, Shen M, Patnaik S, Hall MD. Correction to Remdesivir: A Review of Its Discovery and Development Leading to Human Clinical Trials for Treatment of COVID-19. ACS Cent Sci 2020; 6:1009. [PMID: 32607448 PMCID: PMC7318059 DOI: 10.1021/acscentsci.0c00747] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Indexed: 05/04/2023]
Abstract
[This corrects the article DOI: 10.1021/acscentsci.0c00489.].
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18
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Hanson QM, Wilson KM, Shen M, Itkin Z, Eastman RT, Shinn P, Hall MD. Targeting ACE2-RBD interaction as a platform for COVID19 therapeutics: Development and drug repurposing screen of an AlphaLISA proximity assay. bioRxiv 2020. [PMID: 32577632 PMCID: PMC7301901 DOI: 10.1101/2020.06.16.154708] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, is a pressing public health emergency garnering rapid response from scientists across the globe. Host cell invasion is initiated through direct binding of the viral spike protein to the host receptor angiotensin-converting enzyme 2 (ACE2). Disrupting the spike-ACE2 interaction is a potential therapeutic target for treating COVID-19. We have developed a proximity-based AlphaLISA assay to measure binding of SARS-CoV-2 spike protein Receptor Binding Domain (RBD) to ACE2. Utilizing this assay platform, a drug-repurposing screen against 3,384 small molecule drugs and pre-clinical compounds was performed, yielding 25 high-quality, small-molecule hits that can be evaluated in cell-based models. This established AlphaLISA RBD-ACE2 platform can facilitate evaluation of biologics or small molecules that can perturb this essential viral-host interaction to further the development of interventions to address the global health pandemic.
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Affiliation(s)
- Quinlin M Hanson
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Kelli M Wilson
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Zina Itkin
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Richard T Eastman
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Paul Shinn
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health
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19
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Brimacombe KR, Zhao T, Eastman RT, Hu X, Wang K, Backus M, Baljinnyam B, Chen CZ, Chen L, Eicher T, Ferrer M, Fu Y, Gorshkov K, Guo H, Hanson QM, Itkin Z, Kales SC, Klumpp-Thomas C, Lee EM, Michael S, Mierzwa T, Patt A, Pradhan M, Renn A, Shinn P, Shrimp JH, Viraktamath A, Wilson KM, Xu M, Zakharov AV, Zhu W, Zheng W, Simeonov A, Mathé EA, Lo DC, Hall MD, Shen M. An OpenData portal to share COVID-19 drug repurposing data in real time. bioRxiv 2020:2020.06.04.135046. [PMID: 32511420 PMCID: PMC7276055 DOI: 10.1101/2020.06.04.135046] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The National Center for Advancing Translational Sciences (NCATS) has developed an online open science data portal for its COVID-19 drug repurposing campaign - named OpenData - with the goal of making data across a range of SARS-CoV-2 related assays available in real-time. The assays developed cover a wide spectrum of the SARS-CoV-2 life cycle, including both viral and human (host) targets. In total, over 10,000 compounds are being tested in full concentration-response ranges from across multiple annotated small molecule libraries, including approved drug, repurposing candidates and experimental therapeutics designed to modulate a wide range of cellular targets. The goal is to support research scientists, clinical investigators and public health officials through open data sharing and analysis tools to expedite the development of SARS-CoV-2 interventions, and to prioritize promising compounds and repurposed drugs for further development in treating COVID-19.
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Affiliation(s)
- Kyle R. Brimacombe
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Tongan Zhao
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Richard T. Eastman
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Ke Wang
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Mark Backus
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Bolormaa Baljinnyam
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Catherine Z. Chen
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Lu Chen
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Tara Eicher
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Marc Ferrer
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Ying Fu
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Kirill Gorshkov
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Hui Guo
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Quinlin M. Hanson
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Zina Itkin
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Stephen C. Kales
- National Center for Advancing Translational Sciences, National Institutes of Health
| | | | - Emily M. Lee
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Sam Michael
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Tim Mierzwa
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Andrew Patt
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Manisha Pradhan
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Alex Renn
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Paul Shinn
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Jonathan H. Shrimp
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Amit Viraktamath
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Kelli M. Wilson
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Miao Xu
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Alexey V. Zakharov
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Wei Zhu
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Ewy A. Mathé
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Donald C. Lo
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences, National Institutes of Health
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health
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20
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Sá JM, Kaslow SR, Moraes Barros RR, Brazeau NF, Parobek CM, Tao D, Salzman RE, Gibson TJ, Velmurugan S, Krause MA, Melendez-Muniz V, Kite WA, Han PK, Eastman RT, Kim A, Kessler EG, Abebe Y, James ER, Chakravarty S, Orr-Gonzalez S, Lambert LE, Engels T, Thomas ML, Fasinu PS, Serre D, Gwadz RW, Walker L, DeConti DK, Mu J, Bailey JA, Sim BKL, Hoffman SL, Fay MP, Dinglasan RR, Juliano JJ, Wellems TE. Plasmodium vivax chloroquine resistance links to pvcrt transcription in a genetic cross. Nat Commun 2019; 10:4300. [PMID: 31541097 PMCID: PMC6754410 DOI: 10.1038/s41467-019-12256-9] [Citation(s) in RCA: 30] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 08/26/2019] [Indexed: 12/30/2022] Open
Abstract
Mainstay treatment for Plasmodium vivax malaria has long relied on chloroquine (CQ) against blood-stage parasites plus primaquine against dormant liver-stage forms (hypnozoites), however drug resistance confronts this regimen and threatens malaria control programs. Understanding the basis of P. vivax chloroquine resistance (CQR) will inform drug discovery and malaria control. Here we investigate the genetics of P. vivax CQR by a cross of parasites differing in drug response. Gametocytogenesis, mosquito infection, and progeny production are performed with mixed parasite populations in nonhuman primates, as methods for P. vivax cloning and in vitro cultivation remain unavailable. Linkage mapping of progeny surviving >15 mg/kg CQ identifies a 76 kb region in chromosome 1 including pvcrt, an ortholog of the Plasmodium falciparum CQR transporter gene. Transcriptional analysis supports upregulated pvcrt expression as a mechanism of CQR.
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Affiliation(s)
- Juliana M Sá
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sarah R Kaslow
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Roberto R Moraes Barros
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nicholas F Brazeau
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Christian M Parobek
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Dingyin Tao
- W Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Rebecca E Salzman
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tyler J Gibson
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Michael A Krause
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Viviana Melendez-Muniz
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Whitney A Kite
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Paul K Han
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Richard T Eastman
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Adam Kim
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Evan G Kessler
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | | | | | - Sachy Orr-Gonzalez
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lynn E Lambert
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Theresa Engels
- Division of Veterinary Resources, Office of Research Services, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Marvin L Thomas
- Division of Veterinary Resources, Office of Research Services, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Pius S Fasinu
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Campbell University, Buies Creek, NC, 27506, USA
| | - David Serre
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Robert W Gwadz
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Larry Walker
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Campbell University, Buies Creek, NC, 27506, USA
| | - Derrick K DeConti
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01655, USA
| | - Jianbing Mu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jeffrey A Bailey
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Campbell University, Buies Creek, NC, 27506, USA
- Division of Transfusion Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, 01655, USA
| | | | | | - Michael P Fay
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Rhoel R Dinglasan
- W Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- Emerging Pathogens Institute, Department of Infectious Diseases & Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Jonathan J Juliano
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Thomas E Wellems
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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21
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Mason DJ, Eastman RT, Lewis RPI, Stott IP, Guha R, Bender A. Using Machine Learning to Predict Synergistic Antimalarial Compound Combinations With Novel Structures. Front Pharmacol 2018; 9:1096. [PMID: 30333748 PMCID: PMC6176478 DOI: 10.3389/fphar.2018.01096] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/07/2018] [Indexed: 01/28/2023] Open
Abstract
The parasite Plasmodium falciparum is the most lethal species of Plasmodium to cause serious malaria infection in humans, and with resistance developing rapidly novel treatment modalities are currently being sought, one of which being combinations of existing compounds. The discovery of combinations of antimalarial drugs that act synergistically with one another is hence of great importance; however an exhaustive experimental screen of large drug space in a pairwise manner is not an option. In this study we apply our machine learning approach, Combination Synergy Estimation (CoSynE), which can predict novel synergistic drug interactions using only prior experimental combination screening data and knowledge of compound molecular structures, to a dataset of 1,540 antimalarial drug combinations in which 22.2% were synergistic. Cross validation of our model showed that synergistic CoSynE predictions are enriched 2.74 × compared to random selection when both compounds in a predicted combination are known from other combinations among the training data, 2.36 × when only one compound is known from the training data, and 1.5 × for entirely novel combinations. We prospectively validated our model by making predictions for 185 combinations of 23 entirely novel compounds. CoSynE predicted 20 combinations to be synergistic, which was experimentally validated for nine of them (45%), corresponding to an enrichment of 1.70 × compared to random selection from this prospective data set. Such enrichment corresponds to a 41% reduction in experimental effort. Interestingly, we found that pairwise screening of the compounds CoSynE individually predicted to be synergistic would result in an enrichment of 1.36 × compared to random selection, indicating that synergy among compound combinations is not a random event. The nine novel and correctly predicted synergistic compound combinations mainly (where sufficient bioactivity information is available) consist of efflux or transporter inhibitors (such as hydroxyzine), combined with compounds exhibiting antimalarial activity alone (such as sorafenib, apicidin, or dihydroergotamine). However, not all compound synergies could be rationalized easily in this way. Overall, this study highlights the potential for predictive modeling to expedite the discovery of novel drug combinations in fight against antimalarial resistance, while the underlying approach is also generally applicable.
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Affiliation(s)
- Daniel J Mason
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Cambridge, United Kingdom.,Healx Ltd., Cambridge, United Kingdom
| | - Richard T Eastman
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Richard P I Lewis
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Cambridge, United Kingdom
| | - Ian P Stott
- Unilever Research and Development, Wirral, United Kingdom
| | - Rajarshi Guha
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Andreas Bender
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Cambridge, United Kingdom
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22
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Kasule J, Gabriel EE, Anok A, Neal J, Eastman RT, Penzak S, Newell K, Serwadda D, Duffy PE, Reynolds SJ, Hobbs CV. Sulfamethoxazole Levels in HIV-Exposed Uninfected Ugandan Children. Am J Trop Med Hyg 2018; 98:1718-1721. [PMID: 29692311 PMCID: PMC6086194 DOI: 10.4269/ajtmh.17-0933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Trimethoprim–sulfamethoxazole (TMP–SMX) prophylaxis in HIV-uninfected, exposed (HUE) children variably reduces clinical malaria burden despite antifolate resistance, but data regarding achieved serum levels and adherence are lacking. Serum samples from 70 HUE children aged 3–12 months from Rakai, Uganda, enrolled in an observational study were assayed for random SMX levels using a colorimetric assay. Adherence with TMP–SMX prophylaxis data (yes/no) was also collected. Of 148 visits with concurrent SMX levels available, 56% had self-reported adherence with TMP–SMX therapy. Among these 82 visits, mean (standard deviation) level was 19.78 (19.22) µg/mL, but 33% had SMX levels below half maximal inhibitory concentrations (IC50) for Plasmodium falciparum with some, but not all, of the reported antifolate resistance mutations reported in Uganda. With TMP–SMX prophylaxis, suboptimal adherence is concerning. Sulfamethoxazole levels below IC50s required to overcome malaria parasites with multiple antifolate resistance mutations may be significant. Further study of TMP–SMX in this context is needed.
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Affiliation(s)
- Jingo Kasule
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland.,Rakai Health Sciences Program, Kalisizo, Uganda
| | - Erin E Gabriel
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Aggrey Anok
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland.,Rakai Health Sciences Program, Kalisizo, Uganda
| | - Jillian Neal
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Richard T Eastman
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland
| | - Scott Penzak
- College of Pharmacy, University of North Texas, Fort Worth, Texas
| | - Kevin Newell
- Clinical Research Directorate/Clinical Monitoring Research Program, Leidos Biomedical Research, Inc., National Cancer Institute Campus at Frederick, Frederick, Maryland
| | - David Serwadda
- School of Public Health, Makerere College of Health Sciences, Kampala, Uganda.,Rakai Health Sciences Program, Kalisizo, Uganda
| | - Patrick E Duffy
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Steven J Reynolds
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland.,Rakai Health Sciences Program, Kalisizo, Uganda
| | - Charlotte V Hobbs
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland.,University of Mississippi Medical Center, Batson Children's Hospital, Jackson, Mississippi
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23
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KalantarMotamedi Y, Eastman RT, Guha R, Bender A. A systematic and prospectively validated approach for identifying synergistic drug combinations against malaria. Malar J 2018; 17:160. [PMID: 29642892 PMCID: PMC5896032 DOI: 10.1186/s12936-018-2294-5] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 03/24/2018] [Indexed: 01/01/2023] Open
Abstract
Background Nearly half of the world’s population (3.2 billion people) were at risk of malaria in 2015, and resistance to current therapies is a major concern. While the standard of care includes drug combinations, there is a pressing need to identify new combinations that can bypass current resistance mechanisms. In the work presented here, a combined transcriptional drug repositioning/discovery and machine learning approach is proposed. Methods The integrated approach utilizes gene expression data from patient-derived samples, in combination with large-scale anti-malarial combination screening data, to predict synergistic compound combinations for three Plasmodium falciparum strains (3D7, DD2 and HB3). Both single compounds and combinations predicted to be active were prospectively tested in experiment. Results One of the predicted single agents, apicidin, was active with the AC50 values of 74.9, 84.1 and 74.9 nM in 3D7, DD2 and HB3 P. falciparum strains while its maximal safe plasma concentration in human is 547.6 ± 136.6 nM. Apicidin at the safe dose of 500 nM kills on average 97% of the parasite. The synergy prediction algorithm exhibited overall precision and recall of 83.5 and 65.1% for mild-to-strong, 48.8 and 75.5% for moderate-to-strong and 12.0 and 62.7% for strong synergies. Some of the prospectively predicted combinations, such as tacrolimus-hydroxyzine and raloxifene-thioridazine, exhibited significant synergy across the three P. falciparum strains included in the study. Conclusions Systematic approaches can play an important role in accelerating discovering novel combinational therapies for malaria as it enables selecting novel synergistic compound pairs in a more informed and cost-effective manner. Electronic supplementary material The online version of this article (10.1186/s12936-018-2294-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yasaman KalantarMotamedi
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Richard T Eastman
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20852, USA
| | - Rajarshi Guha
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20852, USA.
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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24
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Zhang S, Zhu J, Zechel DL, Jessen-Trefzer C, Eastman RT, Paululat T, Bechthold A. New WS9326A Derivatives and One New Annimycin Derivative with Antimalarial Activity are Produced by Streptomyces asterosporus DSM 41452 and Its Mutant. Chembiochem 2017; 19:272-279. [PMID: 29148157 DOI: 10.1002/cbic.201700428] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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: 08/08/2017] [Indexed: 11/10/2022]
Abstract
In this study, we report that Streptomyces asterosporus DSM 41452 is a producer of new molecules related to the nonribosomal cyclodepsipeptide WS9326A and the polyketide annimycin. S. asterosporus DSM 41452 is shown to produce six cyclodepsipeptides and peptides, WS9326A to G. Notably, the compounds WS9326F and WS9326G have not been described before. The genome of S. asterosporus DSM 41452 was sequenced, and a putative WS9326A gene cluster was identified. Gene-deletion experiments confirmed that this cluster was responsible for the biosynthesis of WS9326A to G. Additionally, a gene-deletion experiment demonstrated that sas16 encoding a cytochrome P450 monooxygenase was involved in the synthesis of the novel (E)-2,3-dehydrotyrosine residue found in WS9326A and its derivatives. An insertion mutation within the putative annimycin gene cluster led to the production of a new annimycin derivative, annimycin B, which exhibited modest inhibitory activity against Plasmodium falciparum.
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Affiliation(s)
- Songya Zhang
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Stefan-Meier-Strasse 19 VF, 79104, Freiburg im Breisgau, Germany
| | - Jing Zhu
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Stefan-Meier-Strasse 19 VF, 79104, Freiburg im Breisgau, Germany
| | - David L Zechel
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario, K7L 3N6, Canada
| | - Claudia Jessen-Trefzer
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Stefan-Meier-Strasse 19 VF, 79104, Freiburg im Breisgau, Germany
| | - Richard T Eastman
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences/NIH, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Thomas Paululat
- Department of Chemistry and Biology, Universität Siegen, Adolf-Reichwein-Strasse 2, 57068, Siegen, Germany
| | - Andreas Bechthold
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Stefan-Meier-Strasse 19 VF, 79104, Freiburg im Breisgau, Germany
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25
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Nair SC, Xu R, Pattaradilokrat S, Wu J, Qi Y, Zilversmit M, Ganesan S, Nagarajan V, Eastman RT, Orandle MS, Tan JC, Myers TG, Liu S, Long CA, Li J, Su XZ. A Plasmodium yoelii HECT-like E3 ubiquitin ligase regulates parasite growth and virulence. Nat Commun 2017; 8:223. [PMID: 28790316 PMCID: PMC5548792 DOI: 10.1038/s41467-017-00267-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 02/08/2016] [Accepted: 06/12/2017] [Indexed: 01/18/2023] Open
Abstract
Infection of mice with strains of Plasmodium yoelii parasites can result in different pathology, but molecular mechanisms to explain this variation are unclear. Here we show that a P. yoelii gene encoding a HECT-like E3 ubiquitin ligase (Pyheul) influences parasitemia and host mortality. We genetically cross two lethal parasites with distinct disease phenotypes, and identify 43 genetically diverse progeny by typing with microsatellites and 9230 single-nucleotide polymorphisms. A genome-wide quantitative trait loci scan links parasite growth and host mortality to two major loci on chromosomes 1 and 7 with LOD (logarithm of the odds) scores = 6.1 and 8.1, respectively. Allelic exchange of partial sequences of Pyheul in the chromosome 7 locus and modification of the gene expression alter parasite growth and host mortality. This study identifies a gene that may have a function in parasite growth, virulence, and host–parasite interaction, and therefore could be a target for drug or vaccine development. Many strains of Plasmodium differ in virulence, but factors that control these distinctions are not known. Here the authors comparatively map virulence loci using the offspring from a P. yoelii YM and N67 genetic cross, and identify a putative HECT E3 ubiquitin ligase that may explain the variance.
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Affiliation(s)
- Sethu C Nair
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ruixue Xu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, China
| | - Sittiporn Pattaradilokrat
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA.,Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Jian Wu
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yanwei Qi
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA.,State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, China
| | - Martine Zilversmit
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sundar Ganesan
- Biological Imaging Section, Research Technology Branch, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Vijayaraj Nagarajan
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Richard T Eastman
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Marlene S Orandle
- Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - John C Tan
- The Eck Institute of Global Health, Department of Biological Sciences, University of Notre Dame, Indiana, 46556, USA
| | - Timothy G Myers
- Genomic Technologies Section, Research Technologies Branch, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Shengfa Liu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, China
| | - Carole A Long
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jian Li
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, China.
| | - Xin-Zhuan Su
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA. .,State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, China.
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26
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Eastman RT, Khine P, Huang R, Thomas CJ, Su XZ. PfCRT and PfMDR1 modulate interactions of artemisinin derivatives and ion channel blockers. Sci Rep 2016; 6:25379. [PMID: 27147113 PMCID: PMC4857081 DOI: 10.1038/srep25379] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/15/2016] [Indexed: 01/01/2023] Open
Abstract
Treatment of the symptomatic asexual stage of Plasmodium falciparum relies almost exclusively on artemisinin (ART) combination therapies (ACTs) in endemic regions. ACTs combine ART or its derivative with a long-acting partner drug to maximize efficacy during the typical three-day regimen. Both laboratory and clinical studies have previously demonstrated that the common drug resistance determinants P. falciparum chloroquine resistance transporter (PfCRT) and multidrug resistance transporter (PfMDR1) can modulate the susceptibility to many current antimalarial drugs and chemical compounds. Here we investigated the parasite responses to dihydroartemisinin (DHA) and various Ca2+ and Na+ channel blockers and showed positively correlated responses between DHA and several channel blockers, suggesting potential shared transport pathways or mode of action. Additionally, we demonstrated that PfCRT and PfMDR1 could also significantly modulate the pharmacodynamic interactions of the compounds and that the interactions were influenced by the parasite genetic backgrounds. These results provide important information for better understanding of drug resistance and for assessing the overall impact of drug resistance markers on parasite response to ACTs.
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Affiliation(s)
- Richard T Eastman
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.,Division of Preclinical Development, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Pwint Khine
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Ruili Huang
- Division of Preclinical Development, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Craig J Thomas
- Division of Preclinical Development, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Xin-Zhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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27
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Cheng KCC, Cao S, Raveh A, MacArthur R, Dranchak P, Chlipala G, Okoneski MT, Guha R, Eastman RT, Yuan J, Schultz PJ, Su XZ, Tamayo-Castillo G, Matainaho T, Clardy J, Sherman DH, Inglese J. Actinoramide A Identified as a Potent Antimalarial from Titration-Based Screening of Marine Natural Product Extracts. J Nat Prod 2015; 78:2411-2422. [PMID: 26465675 PMCID: PMC4633019 DOI: 10.1021/acs.jnatprod.5b00489] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Methods to identify the bioactive diversity within natural product extracts (NPEs) continue to evolve. NPEs constitute complex mixtures of chemical substances varying in structure, composition, and abundance. NPEs can therefore be challenging to evaluate efficiently with high-throughput screening approaches designed to test pure substances. Here we facilitate the rapid identification and prioritization of antimalarial NPEs using a pharmacologically driven, quantitative high-throughput-screening (qHTS) paradigm. In qHTS each NPE is tested across a concentration range from which sigmoidal response, efficacy, and apparent EC50s can be used to rank order NPEs for subsequent organism reculture, extraction, and fractionation. Using an NPE library derived from diverse marine microorganisms we observed potent antimalarial activity from two Streptomyces sp. extracts identified from thousands tested using qHTS. Seven compounds were isolated from two phylogenetically related Streptomyces species: Streptomyces ballenaensis collected from Costa Rica and Streptomyces bangulaensis collected from Papua New Guinea. Among them we identified actinoramides A and B, belonging to the unusually elaborated nonproteinogenic amino-acid-containing tetrapeptide series of natural products. In addition, we characterized a series of new compounds, including an artifact, 25-epi-actinoramide A, and actinoramides D, E, and F, which are closely related biosynthetic congeners of the previously reported metabolites.
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Affiliation(s)
- Ken Chih-Chien Cheng
- National Center of Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Shugeng Cao
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawai'i at Hilo, Hilo, HI 96720, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, C-643, Boston, Massachusetts 021151, USA
| | - Avi Raveh
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - Ryan MacArthur
- National Center of Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Patricia Dranchak
- National Center of Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - George Chlipala
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - Matthew T. Okoneski
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA
- Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - Rajarshi Guha
- National Center of Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Richard T. Eastman
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20852, USA
| | - Jing Yuan
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20852, USA
| | - Pamela J. Schultz
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - Xin-zhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20852, USA
| | - Giselle Tamayo-Castillo
- Unidad Estrategica de Bioprospección, Instituto Nacional de Biodiversidad (INBio), Santo Domingo de Heredia, Costa Rica & CIPRONA-Escuela de Química, Universidad de Costa Rica, 2060 San Pedro, Costa Rica
| | - Teatulohi Matainaho
- School of Medicine and Health Sciences, University of Papua New Guinea, Boroko, Papua New Guinea
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, C-643, Boston, Massachusetts 021151, USA
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA
- Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - James Inglese
- National Center of Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
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28
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Mott BT, Eastman RT, Guha R, Sherlach KS, Siriwardana A, Shinn P, McKnight C, Michael S, Lacerda-Queiroz N, Patel PR, Khine P, Sun H, Kasbekar M, Aghdam N, Fontaine SD, Liu D, Mierzwa T, Mathews-Griner LA, Ferrer M, Renslo AR, Inglese J, Yuan J, Roepe PD, Su XZ, Thomas CJ. High-throughput matrix screening identifies synergistic and antagonistic antimalarial drug combinations. Sci Rep 2015; 5:13891. [PMID: 26403635 PMCID: PMC4585899 DOI: 10.1038/srep13891] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [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: 04/07/2015] [Accepted: 08/07/2015] [Indexed: 01/22/2023] Open
Abstract
Drug resistance in Plasmodium parasites is a constant threat. Novel therapeutics, especially new drug combinations, must be identified at a faster rate. In response to the urgent need for new antimalarial drug combinations we screened a large collection of approved and investigational drugs, tested 13,910 drug pairs, and identified many promising antimalarial drug combinations. The activity of known antimalarial drug regimens was confirmed and a myriad of new classes of positively interacting drug pairings were discovered. Network and clustering analyses reinforced established mechanistic relationships for known drug combinations and identified several novel mechanistic hypotheses. From eleven screens comprising >4,600 combinations per parasite strain (including duplicates) we further investigated interactions between approved antimalarials, calcium homeostasis modulators, and inhibitors of phosphatidylinositide 3-kinases (PI3K) and the mammalian target of rapamycin (mTOR). These studies highlight important targets and pathways and provide promising leads for clinically actionable antimalarial therapy.
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Affiliation(s)
- Bryan T. Mott
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD
| | - Richard T. Eastman
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Rajarshi Guha
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD
| | - Katy S. Sherlach
- Department of Chemistry, Georgetown University, 37th and O St., NW, Washington, DC
| | - Amila Siriwardana
- Department of Chemistry, Georgetown University, 37th and O St., NW, Washington, DC
| | - Paul Shinn
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD
| | - Crystal McKnight
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD
| | - Sam Michael
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD
| | - Norinne Lacerda-Queiroz
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Paresma R. Patel
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD
| | - Pwint Khine
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Hongmao Sun
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD
| | - Monica Kasbekar
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD
| | - Nima Aghdam
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD
- Department of Chemistry, Georgetown University, 37th and O St., NW, Washington, DC
| | - Shaun D. Fontaine
- Department of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, CA
| | - Dongbo Liu
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD
| | - Tim Mierzwa
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD
| | - Lesley A. Mathews-Griner
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD
| | - Marc Ferrer
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD
| | - Adam R. Renslo
- Department of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, CA
| | - James Inglese
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Jing Yuan
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Paul D. Roepe
- Department of Chemistry, Georgetown University, 37th and O St., NW, Washington, DC
- Department of Biochemistry, Cellular and Molecular Biology and Center for Infectious Diseases, Georgetown University, 37th and O St., NW, Washington, DC
| | - Xin-zhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Craig J. Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD
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29
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Lisewski AM, Quiros JP, Ng CL, Adikesavan AK, Miura K, Putluri N, Eastman RT, Scanfeld D, Regenbogen SJ, Altenhofen L, Llinás M, Sreekumar A, Long C, Fidock DA, Lichtarge O. Supergenomic network compression and the discovery of EXP1 as a glutathione transferase inhibited by artesunate. Cell 2014; 158:916-928. [PMID: 25126794 DOI: 10.1016/j.cell.2014.07.011] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 01/02/2014] [Accepted: 07/07/2014] [Indexed: 01/01/2023]
Abstract
A central problem in biology is to identify gene function. One approach is to infer function in large supergenomic networks of interactions and ancestral relationships among genes; however, their analysis can be computationally prohibitive. We show here that these biological networks are compressible. They can be shrunk dramatically by eliminating redundant evolutionary relationships, and this process is efficient because in these networks the number of compressible elements rises linearly rather than exponentially as in other complex networks. Compression enables global network analysis to computationally harness hundreds of interconnected genomes and to produce functional predictions. As a demonstration, we show that the essential, but functionally uncharacterized Plasmodium falciparum antigen EXP1 is a membrane glutathione S-transferase. EXP1 efficiently degrades cytotoxic hematin, is potently inhibited by artesunate, and is associated with artesunate metabolism and susceptibility in drug-pressured malaria parasites. These data implicate EXP1 in the mode of action of a frontline antimalarial drug.
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Affiliation(s)
- Andreas Martin Lisewski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Joel P Quiros
- Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Caroline L Ng
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Anbu Karani Adikesavan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kazutoyo Miura
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Nagireddy Putluri
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX 77030, USA; Verna and Marrs McLean Department of Biochemistry and Alkek Center for Molecular Discovery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard T Eastman
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA; Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Daniel Scanfeld
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Sam J Regenbogen
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lindsey Altenhofen
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Biochemistry and Molecular Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, State College, PA 16802, USA
| | - Manuel Llinás
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Biochemistry and Molecular Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, State College, PA 16802, USA
| | - Arun Sreekumar
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX 77030, USA; Verna and Marrs McLean Department of Biochemistry and Alkek Center for Molecular Discovery, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Carole Long
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX 77030, USA; Verna and Marrs McLean Department of Biochemistry and Alkek Center for Molecular Discovery, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA.
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Ojo KK, Eastman RT, Vidadala R, Zhang Z, Rivas KL, Choi R, Lutz JD, Reid MC, Fox AMW, Hulverson MA, Kennedy M, Isoherranen N, Kim LM, Comess KM, Kempf DJ, Verlinde CLMJ, Su XZ, Kappe SHI, Maly DJ, Fan E, Van Voorhis WC. A specific inhibitor of PfCDPK4 blocks malaria transmission: chemical-genetic validation. J Infect Dis 2013; 209:275-84. [PMID: 24123773 DOI: 10.1093/infdis/jit522] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [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] [Indexed: 01/03/2023] Open
Abstract
Malaria parasites are transmitted by mosquitoes, and blocking parasite transmission is critical in reducing or eliminating malaria in endemic regions. Here, we report the pharmacological characterization of a new class of malaria transmission-blocking compounds that acts via the inhibition of Plasmodia CDPK4 enzyme. We demonstrate that these compounds achieved selectivity over mammalian kinases by capitalizing on a small serine gatekeeper residue in the active site of the Plasmodium CDPK4 enzyme. To directly confirm the mechanism of action of these compounds, we generated P. falciparum parasites that express a drug-resistant methionine gatekeeper (S147 M) CDPK4 mutant. Mutant parasites showed a shift in exflagellation EC50 relative to the wild-type strains in the presence of compound 1294, providing chemical-genetic evidence that CDPK4 is the target of the compound. Pharmacokinetic analyses suggest that coformulation of this transmission-blocking agent with asexual stage antimalarials such as artemisinin combination therapy (ACT) is a promising option for drug delivery that may reduce transmission of malaria including drug-resistant strains. Ongoing studies include refining the compounds to improve efficacy and toxicological properties for efficient blocking of malaria transmission.
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Affiliation(s)
- Kayode K Ojo
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
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31
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Lemieux JE, Kyes SA, Otto TD, Feller AI, Eastman RT, Pinches RA, Berriman M, Su XZ, Newbold CI. Genome-wide profiling of chromosome interactions in Plasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation. Mol Microbiol 2013; 90:519-37. [PMID: 23980881 PMCID: PMC3894959 DOI: 10.1111/mmi.12381] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [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] [Accepted: 08/25/2013] [Indexed: 12/31/2022]
Abstract
Spatial relationships within the eukaryotic nucleus are essential for proper nuclear function. In Plasmodium falciparum, the repositioning of chromosomes has been implicated in the regulation of the expression of genes responsible for antigenic variation, and the formation of a single, peri-nuclear nucleolus results in the clustering of rDNA. Nevertheless, the precise spatial relationships between chromosomes remain poorly understood, because, until recently, techniques with sufficient resolution have been lacking. Here we have used chromosome conformation capture and second-generation sequencing to study changes in chromosome folding and spatial positioning that occur during switches in var gene expression. We have generated maps of chromosomal spatial affinities within the P. falciparum nucleus at 25 Kb resolution, revealing a structured nucleolus, an absence of chromosome territories, and confirming previously identified clustering of heterochromatin foci. We show that switches in var gene expression do not appear to involve interaction with a distant enhancer, but do result in local changes at the active locus. These maps reveal the folding properties of malaria chromosomes, validate known physical associations, and characterize the global landscape of spatial interactions. Collectively, our data provide critical information for a better understanding of gene expression regulation and antigenic variation in malaria parasites.
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Affiliation(s)
- Jacob E Lemieux
- Weatherall Institute of Molecular Medicine, Headington, Oxford, OX3 9DS, UK; National Institute of Allergy and Infectious Disease, NIH, Rockville, MD, 20892, USA
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32
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Abstract
Plasmodium falciparum resistance to chloroquine and sulphadoxine-pyrimethamine has led to the recent adoption of artemisinin-based combination therapies (ACTs) as the first line of treatment against malaria. ACTs comprise semisynthetic artemisinin derivatives paired with distinct chemical classes of longer acting drugs. These artemisinins are exceptionally potent against the pathogenic asexual blood stages of Plasmodium parasites and also act on the transmissible sexual stages. These combinations increase the rates of clinical and parasitological cures and decrease the selection pressure for the emergence of antimalarial resistance. This Review article discusses our current knowledge about the mode of action of ACTs, their pharmacological properties and the proposed mechanisms of drug resistance.
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Affiliation(s)
- Richard T Eastman
- Department of Microbiology & Immunology, Columbia University College of Physicians and Surgeons, Hammer Health Sciences Center, Room 1502, 701 West 168th Street, New York 10032, New York, USA.
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Fidock DA, Eastman RT, Ward SA, Meshnick SR. Recent highlights in antimalarial drug resistance and chemotherapy research. Trends Parasitol 2008; 24:537-44. [PMID: 18938106 DOI: 10.1016/j.pt.2008.09.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Revised: 09/15/2008] [Accepted: 09/16/2008] [Indexed: 01/07/2023]
Abstract
This review summarizes recent investigations into antimalarial drug resistance and chemotherapy, including reports of some of the many exciting talks and posters on this topic that were presented at the third Molecular Approaches to Malaria meeting held in Lorne, Australia, in February 2008 (MAM 2008). After surveying this area of research, we focus on two important questions: what is the molecular contribution of pfcrt to chloroquine resistance, and what is the mechanism of action of artemisinin? We conclude with thoughts about the current state of antimalarial chemotherapy and priorities moving forward.
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Affiliation(s)
- David A Fidock
- Department of Microbiology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA.
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Gillespie JR, Yokoyama K, Lu K, Eastman RT, Bollinger JG, Van Voorhis WC, Gelb MH, Buckner FS. C-terminal proteolysis of prenylated proteins in trypanosomatids and RNA interference of enzymes required for the post-translational processing pathway of farnesylated proteins. Mol Biochem Parasitol 2007; 153:115-24. [PMID: 17397944 DOI: 10.1016/j.molbiopara.2007.02.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Revised: 02/17/2007] [Accepted: 02/26/2007] [Indexed: 11/23/2022]
Abstract
The C-terminal "CaaX"-motif-containing proteins usually undergo three sequential post-translational processing steps: (1) attachment of a prenyl group to the cysteine residue; (2) proteolytic removal of the last three amino acids "aaX"; (3) methyl esterification of the exposed alpha-carboxyl group of the prenyl-cysteine residue. The Trypanosoma brucei and Leishmania major Ras converting enzyme 1 (RCE1) orthologs of 302 and 285 amino acids-proteins, respectively, have only 13-20% sequence identity to those from other species but contain the critical residues for the activity found in other orthologs. The Trypanosoma brucei a-factor converting enzyme 1 (AFC1) ortholog consists of 427 amino acids with 29-33% sequence identity to those of other species and contains the consensus HExxH zinc-binding motif. The trypanosomatid RCE1 and AFC1 orthologs contain predicted transmembrane regions like other species. Membranes from Sf9 cells expressing the RCE1 ortholog of T. brucei or L. major showed proteolytic activity against farnesylated RAS-CVIM, whereas membranes containing T. brucei AFC1 ortholog were inactive. The results suggest that RCE1 is responsible for proteolytic removal of the C-terminal aaX from prenyl-CaaX proteins in these parasites. All the three enzymatic post-translational processes are thought to be required for proper cellular functioning of CaaX-proteins in eukaryotic cells. We carried out RNA interference experiments in Trypanosoma brucei of the enzymes involved in farnesyl protein post-translational modification to evaluate their importance in cell proliferation. Knockdown of T. brucei PFT beta subunit and RCE1 mRNAs resulted in >20-fold suppression of cell growth and dramatic morphologic changes. Knockdown of PPMT mRNA caused less dramatic effects on growth but induced noticeable changes in cell morphology.
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Affiliation(s)
- John R Gillespie
- Department of Medicine, University of Washington, 1959 N.E. Pacific St., Seattle, WA 98195, USA
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35
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Eastman RT, White J, Hucke O, Yokoyama K, Verlinde CLMJ, Hast MA, Beese LS, Gelb MH, Rathod PK, Van Voorhis WC. Resistance mutations at the lipid substrate binding site of Plasmodium falciparum protein farnesyltransferase. Mol Biochem Parasitol 2006; 152:66-71. [PMID: 17208314 PMCID: PMC2875941 DOI: 10.1016/j.molbiopara.2006.11.012] [Citation(s) in RCA: 23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2006] [Revised: 11/30/2006] [Accepted: 11/30/2006] [Indexed: 11/23/2022]
Abstract
The post-translational farnesylation of proteins serves to anchor a subset of intracellular proteins to membranes in eukaryotic organisms and also promotes protein-protein interactions. This enzymatic reaction is carried out by protein farnesyltransferase (PFT), which catalyzes the transfer of a 15-carbon isoprenoid lipid unit, a farnesyl group, from farnesyl pyrophosphate to the C-termini of proteins containing a CaaX motif. Inhibition of PFT is lethal to the pathogenic protozoa Plasmodium falciparum. Previously, we have shown that parasites resistant to a tetrahydroquinoline (THQ)-based PFT inhibitor BMS-388891 have mutations leading to amino acid substitutions in PFT that map to the peptide substrate binding domain. We now report the selection of parasites resistant to another THQ PFT inhibitor BMS-339941. In whole cell assays sensitivity to BMS-339941 was reduced by 33-fold in a resistant clone, and biochemical analysis demonstrated a corresponding 33-fold increase in the BMS-339941 K(i) for the mutant PFT enzyme. More detailed kinetic analysis revealed that the mutant enzyme required higher concentration of peptide and farnesyl pyrophosphate substrates for optimum catalysis. Unlike previously characterized parasites resistant to BMS-388891, the resistant parasites have a mutation which is predicted to be in a distinct location of the enzymatic pocket, near the farnesyl pyrophosphate binding pocket. This is the first description of a mutation from any species affecting the farnesyl pyrophosphate binding pocket with reduced efficacy of PFT inhibitors. These data provide further support that PFT is the target of THQ inhibitors in P. falciparum and suggest that PFT inhibitors should be combined with other antimalarial agents to minimize the development of resistant parasites.
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Affiliation(s)
| | - John White
- Department of Pathobiology, University of Washington, Seattle, WA, USA
| | - Oliver Hucke
- Biochemistry, University of Washington, Seattle, WA, USA
| | | | | | - Michael A. Hast
- Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Lorena S. Beese
- Biochemistry, Duke University Medical Center, Durham, NC, USA
| | | | - Pradipsinh K. Rathod
- Department of Pathobiology, University of Washington, Seattle, WA, USA
- Chemistry, University of Washington, Seattle, WA, USA
| | - Wesley C. Van Voorhis
- Department of Pathobiology, University of Washington, Seattle, WA, USA
- Medicine, University of Washington, Seattle, WA, USA
- Corresponding author: Wesley C. Van Voorhis, Dept. of Medicine, University of Washington, Box 357185, 1959 N.E. Pacific, Seattle, WA 98195-7185, Tel.: + 1-206-543-2447; fax: + 1-206-685-8681, E. mail addresses:
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Eastman RT, Buckner FS, Yokoyama K, Gelb MH, Van Voorhis WC. Thematic review series: lipid posttranslational modifications. Fighting parasitic disease by blocking protein farnesylation. J Lipid Res 2005; 47:233-40. [PMID: 16339110 DOI: 10.1194/jlr.r500016-jlr200] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [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: 11/20/2022] Open
Abstract
Protein farnesylation is a form of posttranslational modification that occurs in most, if not all, eukaryotic cells. Inhibitors of protein farnesyltransferase (PFTIs) have been developed as anticancer chemotherapeutic agents. Using the knowledge gained from the development of PFTIs for the treatment of cancer, researchers are currently investigating the use of PFTIs for the treatment of eukaryotic pathogens. This "piggy-back" approach not only accelerates the development of a chemotherapeutic agent for protozoan pathogens but is also a means of mitigating the costs associated with de novo drug design. PFTIs have already been shown to be efficacious in the treatment of eukaryotic pathogens in animal models, including both Trypanosoma brucei, the causative agent of African sleeping sickness, and Plasmodium falciparum, one of the causative agents of malaria. Here, current evidence and progress are summarized that support the targeting of protein farnesyltransferase for the treatment of parasitic diseases.
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Affiliation(s)
- Richard T Eastman
- Department of Pathobiology, University of Washington, Seattle, WA, USA
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37
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Eastman RT, Barrett LK, Dupuis K, Buckner FS, Van Voorhis WC. Leishmania inactivation in human pheresis platelets by a psoralen (amotosalen HCl) and long-wavelength ultraviolet irradiation. Transfusion 2005; 45:1459-63. [PMID: 16131378 DOI: 10.1111/j.1537-2995.2005.00552.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
BACKGROUND Leishmania spp. are protozoans that cause skin and visceral diseases. Leishmania are obligate intracellular parasites of mononuclear phagocytes and have been documented to be transmitted by blood transfusion. STUDY DESIGN AND METHODS This study examines whether Leishmania can be inactivated in human platelet (PLT) concentrates by a photochemical treatment process that is applicable to blood bank use. Human PLT concentrates were contaminated with Leishmania mexicana metacyclic promastigotes or mouse-derived Leishmania major amastigotes and were exposed to long-wavelength ultraviolet (UV) A light (320-400 nm) plus the psoralen amotosalen HCl. RESULTS Neither treatment with amotosalen nor UVA alone had an effect on Leishmania viability; however, treatment with 150 micromol per L amotosalen plus 3 J per cm(2) UVA inactivated both metacyclic promastigotes and amastigotes to undetectable levels, more than a 10,000-fold reduction in viability. CONCLUSIONS This study demonstrates the effectiveness of photochemical treatment to inactivate Leishmania in PLT concentrates intended for transfusion. Both metacylic promastigotes, which represent the infectious form from the sand fly vector, and amastigotes, which represent the form that grows in mononuclear phagocytes, were extremely susceptible to photochemical inactivation by this process. Thus, the photochemical treatment of PLT concentrates inactivates both forms of Leishmania that would be expected to circulate in blood products collected from infected donors.
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Affiliation(s)
- Richard T Eastman
- Departments of Pathobiology and Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA
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38
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Buckner FS, Eastman RT, Yokoyama K, Gelb MH, Van Voorhis WC. Protein farnesyl transferase inhibitors for the treatment of malaria and African trypanosomiasis. Curr Opin Investig Drugs 2005; 6:791-7. [PMID: 16121685] [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] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Protein farnesyl transferase inhibitors (PFTIs) have been developed as oncology therapeutics but recent studies have supported the use of PFTIs for the treatment of eukaryotic pathogens. Data supporting PFTIs for the treatment of African sleeping sickness caused by Trypanosoma brucei sp, and for the therapy of malaria caused by Plasmodium spp is reviewed. Protein prenylation in T. brucei and P. falciparum has been studied using a variety of techniques, including recombinant and native enzyme assays. Studies have demonstrated farnesylation and geranylgeranylation in these parasites. A variety of PFTIs have shown growth inhibition activity and killing of T. brucei and P. falciparum, yet not all mammalian PFTIs are active on parasitic PFTs. Protein farnesyl transferase as well as protein geranylgeranyl transferase type II enzymatic activities have been demonstrated in T brucei and P. falciparum, but protein geranylgeranyl transferase type I activity may be lacking from these parasites, perhaps explaining the extreme sensitivity of these organisms to PFTIs compared with mammalian cells. Given that PFTIs are relatively non-toxic in short-term administration to humans, PFTIs specific to parasites are not required for therapy. Thus, the challenge in PFTI drug development is not to identify selective antiparasite compounds, but to identify compounds with sufficient potency and pharmacokinetic properties to produce satisfactory drugs for malaria and African sleeping sickness.
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Affiliation(s)
- Frederick S Buckner
- Department of Medicine, University of Washington, Seattle, WA 98125-7185, USA
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39
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Eastman RT, White J, Hucke O, Bauer K, Yokoyama K, Nallan L, Chakrabarti D, Verlinde CLMJ, Gelb MH, Rathod PK, Van Voorhis WC. Resistance to a Protein Farnesyltransferase Inhibitor in Plasmodium falciparum. J Biol Chem 2005; 280:13554-9. [PMID: 15661734 DOI: 10.1074/jbc.m413556200] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [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: 11/06/2022] Open
Abstract
The post-translational farnesylation of proteins serves to anchor a subset of intracellular proteins to membranes in eukaryotic organisms and also promotes protein-protein interactions. Inhibition of protein farnesyltransferase (PFT) is lethal to the pathogenic protozoa Plasmodium falciparum. Parasites were isolated that were resistant to BMS-388891, a tetrahydroquinoline (THQ) PFT inhibitor. Resistance was associated with a 12-fold decrease in drug susceptibility. Genotypic analysis revealed a single point mutation in the beta subunit in resistant parasites. The resultant tyrosine 837 to cysteine alteration in the beta subunit corresponded to the binding site for the THQ and peptide substrate. Biochemical analysis of Y837C-PFT demonstrated a 13-fold increase in BMS-388891 concentration necessary for inhibiting 50% of the enzyme activity. These data are consistent with PFT as the target of BMS-388891 in P. falciparum and suggest that PFT inhibitors should be combined with other antimalarial agents for effective therapy.
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Affiliation(s)
- Richard T Eastman
- Department of Pathobiology, University of Washington, Seattle, Washington 98195, USA
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40
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Song JL, Harry JB, Eastman RT, Oliver BG, White TC. The Candida albicans lanosterol 14-alpha-demethylase (ERG11) gene promoter is maximally induced after prolonged growth with antifungal drugs. Antimicrob Agents Chemother 2004; 48:1136-44. [PMID: 15047513 PMCID: PMC375326 DOI: 10.1128/aac.48.4.1136-1144.2004] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [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: 11/20/2022] Open
Abstract
The azole antifungal drugs that target lanosterol 14-alpha-demethylase, encoded by the ERG11 gene, are used to treat a variety of infections caused by Candida albicans. Azoles are known to induce expression of ERG11 mRNA. The ERG11 promoter was cloned 5' of the luciferase-coding region, and the induction of ERG11 expression by azoles was monitored by luciferase assays. Maximal induction of the ERG11 promoter by azoles occurs not during logarithmic growth but after the diauxic shift and requires azoles to be present throughout logarithmic growth. The effects of pH, carbon source, and aerobic or anaerobic growth on induction of the ERG11 promoter by azoles were analyzed. Treatment with terbinafine and fenpropimorph, which target other enzymes in the ergosterol biosynthetic pathway, also resulted in a delayed induction of ERG11 promoter activity. Nascent sterol synthesis was shown to parallel ERG11 promoter activity, and total sterols were reduced coincident with the timing of ERG11 promoter activation. These results as a whole suggest that expression of the ERG11 promoter is regulated in response to sterol depletion.
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Affiliation(s)
- Jia L Song
- Department of Pathobiology, School of Public Health and Community Medicine, University of Washington, and Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
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41
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Abstract
Trypanosoma cruzi infection, transmitted by insect vectors or blood transfusions, is an important cause of morbidity and mortality in many Latin American countries. Treatments are toxic and frequently ineffective in curing patients with chronic manifestations of the infection (Chagas disease). Potentially exploitable chemotherapeutic targets of T. cruzi are enzymes of the sterol biosynthesis pathway. In particular, the P450 enzyme, lanosterol 14alpha-demethylase, has been implicated as the target of azole antifungal drugs that have potent anti-T. cruzi activity. In the work reported here, the T. cruzi lanosterol 14alpha-demethylase (Tc14DM) gene was cloned by degenerate PCR. The gene was found to be expressed in both insect and mammalian life-cycle stages of the parasite. Tc14DM was able to complement the function of the homologous gene in yeast (erg11) as demonstrated by restored ergosterol production in an erg11-deficient yeast strain. When the yeast strain was co-transfected with the P450 reductase gene from Trypanosoma brucei, the amount of ergosterol production was increased, indicating that the endogenous yeast P450 reductase was an inefficient partner with Tc14DM. Heterologous expression of Tc14DM in the baculovirus/Sf9 system resulted in a 52kDa product. The protein was observed to have the characteristic absorbance spectra of a P450 enzyme. A typical Type II binding spectrum was produced when the imidazole compound, ketoconazole, was mixed with the Tc14DM, demonstrating that ketoconazole binds the enzyme.
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Affiliation(s)
- Frederick S Buckner
- Department of Medicine, University of Washington, Box 357185, Seattle, WA 98195-7185, USA.
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42
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Hinshaw JC, Suh DY, Garnier P, Buckner FS, Eastman RT, Matsuda SPT, Joubert BM, Coppens I, Joiner KA, Merali S, Nash TE, Prestwich GD. Oxidosqualene cyclase inhibitors as antimicrobial agents. J Med Chem 2003; 46:4240-3. [PMID: 13678402 DOI: 10.1021/jm034126t] [Citation(s) in RCA: 28] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small-molecule oxidosqualene cyclase (OSC) inhibitors were found to be effective in assays against cloned OSC-like enzymes from human pathogens. A combinatorial library was prepared and used to identify lead compounds that inhibit the growth of Trypanosoma cruzi, Leishmania mexicana amazonensis, and Pneumocystis carinii in culture. Selectivity for the microorganisms in preference to mammalian cells was observed.
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Affiliation(s)
- Jerald C Hinshaw
- Department of Medicinal Chemistry, University of Utah, 419 Wakara Way, Suite 205, Salt Lake City, Utah 84108-1257, USA
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43
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Van Voorhis WC, Barrett LK, Eastman RT, Alfonso R, Dupuis K. Trypanosoma cruzi inactivation in human platelet concentrates and plasma by a psoralen (amotosalen HCl) and long-wavelength UV. Antimicrob Agents Chemother 2003; 47:475-9. [PMID: 12543646 PMCID: PMC151742 DOI: 10.1128/aac.47.2.475-479.2003] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Trypanosoma cruzi, the protozoan pathogen that causes Chagas' disease, can be found in the blood of infected individuals for their entire life span. This presents a serious challenge in safeguarding blood products. Transmission of T. cruzi from blood products is a frequent occurrence in Latin America, where Chagas' disease is endemic. This study was designed to determine whether T. cruzi could be inactivated in human platelet concentrates and plasma by a photochemical treatment process with long-wavelength UV A light (UVA, 320 to 400 nm) plus the psoralen amotosalen HCl (Cerus Corporation). Units of platelet concentrates (300 ml) and plasma (300 ml) were intentionally contaminated with approximately 10(6) T. cruzi trypomastigotes, the T. cruzi form found in the bloodstream, per ml. The viability of T. cruzi after photochemical inactivation was determined by their ability to replicate in 3T3 fibroblasts. Controls, including treatment with 150 micro M amotosalen or 3 J/cm(2) UVA alone, did not lead to reduction of the viability of T. cruzi in plasma or platelet concentrates. However, treatment with 150 micro M amotosalen plus 3 J/cm(2) UVA inactivated T. cruzi to undetectable levels in plasma and platelet concentrates. This represented a >5.4-log reduction of T. cruzi in platelet concentrates and >5.0-log reduction of T. cruzi in plasma. We conclude that the amotosalen plus UVA photochemical inactivation technology is effective in inactivating high levels of protozoan pathogens, such as T. cruzi, in platelet concentrates and plasma, as has been previously shown for numerous viruses and bacteria.
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Affiliation(s)
- Wesley C Van Voorhis
- Departments of Medicine. Pathobiology, University of Washington, Seattle, Washington, USA.
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Buckner FS, Eastman RT, Nepomuceno-Silva JL, Speelmon EC, Myler PJ, Van Voorhis WC, Yokoyama K. Cloning, heterologous expression, and substrate specificities of protein farnesyltransferases from Trypanosoma cruzi and Leishmania major. Mol Biochem Parasitol 2002; 122:181-8. [PMID: 12106872 DOI: 10.1016/s0166-6851(02)00099-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [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: 11/16/2022]
Abstract
Chagas disease and leishmaniasis are tropical diseases caused by the protozoan parasites, Trypanosoma cruzi and Leishmania species, respectively. Protein farnesyltransferase (PFT) is being investigated as a target for anti-trypanosomatid agents because inhibitors of this enzyme are highly toxic to these parasites compared to mammalian cells. Here, we report the cloning of the alpha- and beta-subunit genes of PFT from T. cruzi and Leishmania major. The proteins encoded by these genes are considerably larger than those of mammalian PFTs due to the presence of a number of inserts of >25 amino acids that map to junctions between helical structural elements. These inserts are not part of the active site or the interface between the two subunits. Northern blots demonstrate expression of messenger RNA for the PFT subunits in both mammalian and insect life-cycle stages of these parasites. The T. cruzi, Trypanosoma brucei, and L. major PFTs were overexpressed in the Sf9 cell/baculovirus system as active enzyme forms. Kinetic studies with a panel of CALX-containing peptides with all 20 amino acids in the X-position show that trypanosomatid PFTs have similar substrate specificities and these are different from the mammalian PFT substrate specificity patterns.
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