1
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Glenn IS, Hall LN, Khalid MM, Ott M, Shoichet BK. Colloidal Aggregation Confounds Cell-Based Covid-19 Antiviral Screens. J Med Chem 2024. [PMID: 38864383 DOI: 10.1021/acs.jmedchem.4c00597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Colloidal aggregation is one of the largest contributors to false positives in early drug discovery. Here, we consider aggregation's role in cell-based infectivity assays in Covid-19 drug repurposing. We investigated the potential aggregation of 41 drug candidates reported as SARs-CoV-2 entry inhibitors. Of these, 17 formed colloidal particles by dynamic light scattering and exhibited detergent-dependent enzyme inhibition. To evaluate the impact of aggregation on antiviral efficacy in cells, we presaturated the colloidal drug suspensions with BSA or spun them down by centrifugation and measured the effects on spike pseudovirus infectivity. Antiviral potencies diminished by at least 10-fold following both BSA and centrifugation treatments, supporting a colloid-based mechanism. Aggregates induced puncta of the labeled spike protein in fluorescence microscopy, consistent with sequestration of the protein on the colloidal particles. These observations suggest that colloidal aggregation is common among cell-based antiviral drug repurposing and offers rapid counter-screens to detect and eliminate these artifacts.
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Affiliation(s)
- Isabella S Glenn
- Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, California 94143, United States
| | - Lauren N Hall
- Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, California 94143, United States
| | - Mir M Khalid
- Gladstone Institutes, San Francisco, California 94158, United States
- Department of Medicine, University of California, San Francisco, San Francisco, California 94158, United States
| | - Melanie Ott
- Gladstone Institutes, San Francisco, California 94158, United States
- Department of Medicine, University of California, San Francisco, San Francisco, California 94158, United States
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, California 94143, United States
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2
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Shi S, Fu L, Yi J, Yang Z, Zhang X, Deng Y, Wang W, Wu C, Zhao W, Hou T, Zeng X, Lyu A, Cao D. ChemFH: an integrated tool for screening frequent false positives in chemical biology and drug discovery. Nucleic Acids Res 2024:gkae424. [PMID: 38783035 DOI: 10.1093/nar/gkae424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/25/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024] Open
Abstract
High-throughput screening rapidly tests an extensive array of chemical compounds to identify hit compounds for specific biological targets in drug discovery. However, false-positive results disrupt hit compound screening, leading to wastage of time and resources. To address this, we propose ChemFH, an integrated online platform facilitating rapid virtual evaluation of potential false positives, including colloidal aggregators, spectroscopic interference compounds, firefly luciferase inhibitors, chemical reactive compounds, promiscuous compounds, and other assay interferences. By leveraging a dataset containing 823 391 compounds, we constructed high-quality prediction models using multi-task directed message-passing network (DMPNN) architectures combining uncertainty estimation, yielding an average AUC value of 0.91. Furthermore, ChemFH incorporated 1441 representative alert substructures derived from the collected data and ten commonly used frequent hitter screening rules. ChemFH was validated with an external set of 75 compounds. Subsequently, the virtual screening capability of ChemFH was successfully confirmed through its application to five virtual screening libraries. Furthermore, ChemFH underwent additional validation on two natural products and FDA-approved drugs, yielding reliable and accurate results. ChemFH is a comprehensive, reliable, and computationally efficient screening pipeline that facilitates the identification of true positive results in assays, contributing to enhanced efficiency and success rates in drug discovery. ChemFH is freely available via https://chemfh.scbdd.com/.
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Affiliation(s)
- Shaohua Shi
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, P.R. China
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, 999077, P.R. China
| | - Li Fu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, P.R. China
| | - Jiacai Yi
- School of Computer Science, National University of Defense Technology, Changsha, Hunan 410073, P.R. China
| | - Ziyi Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, P.R. China
| | - Xiaochen Zhang
- School of Information Technology, Shangqiu Normal University, Shangqiu, Henan 476000, P.R. China
| | - Youchao Deng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, P.R. China
| | - Wenxuan Wang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, P.R. China
| | - Chengkun Wu
- School of Computer Science, National University of Defense Technology, Changsha, Hunan 410073, P.R. China
| | - Wentao Zhao
- School of Computer Science, National University of Defense Technology, Changsha, Hunan 410073, P.R. China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
| | - Xiangxiang Zeng
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, Hunan 410082, P.R. China
| | - Aiping Lyu
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, 999077, P.R. China
| | - Dongsheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, P.R. China
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3
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Tan L, Hirte S, Palmacci V, Stork C, Kirchmair J. Tackling assay interference associated with small molecules. Nat Rev Chem 2024; 8:319-339. [PMID: 38622244 DOI: 10.1038/s41570-024-00593-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/29/2024] [Indexed: 04/17/2024]
Abstract
Biochemical and cell-based assays are essential to discovering and optimizing efficacious and safe drugs, agrochemicals and cosmetics. However, false assay readouts stemming from colloidal aggregation, chemical reactivity, chelation, light signal attenuation and emission, membrane disruption, and other interference mechanisms remain a considerable challenge in screening synthetic compounds and natural products. To address assay interference, a range of powerful experimental approaches are available and in silico methods are now gaining traction. This Review begins with an overview of the scope and limitations of experimental approaches for tackling assay interference. It then focuses on theoretical methods, discusses strategies for their integration with experimental approaches, and provides recommendations for best practices. The Review closes with a summary of the critical facts and an outlook on potential future developments.
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Affiliation(s)
- Lu Tan
- Drug Discovery Sciences, Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Steffen Hirte
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Vienna Doctoral School of Pharmaceutical, Nutritional and Sport Sciences (PhaNuSpo), University of Vienna, Vienna, Austria
| | - Vincenzo Palmacci
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Vienna Doctoral School of Pharmaceutical, Nutritional and Sport Sciences (PhaNuSpo), University of Vienna, Vienna, Austria
| | - Conrad Stork
- Department of Informatics, Center for Bioinformatics, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Hamburg, Germany
- BASF SE, Ludwigshafen am Rhein, Germany
| | - Johannes Kirchmair
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria.
- Christian Doppler Laboratory for Molecular Informatics in the Biosciences, Department for Pharmaceutical Sciences, University of Vienna, Vienna, Austria.
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4
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Zhang R, Zhou J, Yan H, Liu X, Shang C, Chen Y. Manidipine is not a potential inhibitor against SARS-CoV-2 main protease. Antimicrob Agents Chemother 2024; 68:e0129723. [PMID: 38294235 PMCID: PMC10916385 DOI: 10.1128/aac.01297-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024] Open
Affiliation(s)
- Rui Zhang
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Jiahao Zhou
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Haohao Yan
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Xiaoping Liu
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Chao Shang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yunyu Chen
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
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5
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Zhang R, Yan H, Zhou J, Yan G, Liu X, Shang C, Chen Y. Improved fluorescence-based assay for rapid screening and evaluation of SARS-CoV-2 main protease inhibitors. J Med Virol 2024; 96:e29498. [PMID: 38436148 DOI: 10.1002/jmv.29498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/07/2024] [Accepted: 02/20/2024] [Indexed: 03/05/2024]
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global threat to human health. In parallel with vaccines, efficacious antivirals are urgently needed. SARS-CoV-2 main protease (Mpro) is an attractive drug target for antiviral development owing to its key roles in virus replication and host immune evasion. Due to the limitations of currently available methods, the development of novel high-throughput screening assays is of the highest importance for the discovery of Mpro inhibitors. In this study, we first developed an improved fluorescence-based assay for rapid screening of Mpro inhibitors from an anti-infection compound library using a versatile dimerization-dependent red fluorescent protein (ddRFP) biosensor. Utilizing this assay, we identified MG-101 as a competitive Mpro inhibitor in vitro. Moreover, our results revealed that ensitrelvir is a potent Mpro inhibitor, but baicalein, chloroquine, ebselen, echinatin, and silibinin are not. Therefore, this robust ddRFP assay provides a faithful avenue for rapid screening and evaluation of Mpro inhibitors to fight against COVID-19.
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Affiliation(s)
- Rui Zhang
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Haohao Yan
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Jiahao Zhou
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Gangan Yan
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Xiaoping Liu
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Chao Shang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yunyu Chen
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
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6
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Li X, Song Y. Structure and function of SARS-CoV and SARS-CoV-2 main proteases and their inhibition: A comprehensive review. Eur J Med Chem 2023; 260:115772. [PMID: 37659195 PMCID: PMC10529944 DOI: 10.1016/j.ejmech.2023.115772] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/04/2023]
Abstract
Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) identified in 2003 infected ∼8000 people in 26 countries with 800 deaths, which was soon contained and eradicated by syndromic surveillance and enhanced quarantine. A closely related coronavirus SARS-CoV-2, the causative agent of COVID-19 identified in 2019, has been dramatically more contagious and catastrophic. It has infected and caused various flu-like symptoms of billions of people in >200 countries, including >6 million people died of or with the virus. Despite the availability of several vaccines and antiviral drugs against SARS-CoV-2, finding new therapeutics is needed because of viral evolution and a possible emerging coronavirus in the future. The main protease (Mpro) of these coronaviruses plays important roles in their life cycle and is essential for the viral replication. This article represents a comprehensive review of the function, structure and inhibition of SARS-CoV and -CoV-2 Mpro, including structure-activity relationships, protein-inhibitor interactions and clinical trial status.
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Affiliation(s)
- Xin Li
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
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7
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Glenn IS, Hall LN, Khalid MM, Ott M, Shoichet BK. Colloidal aggregation confounds cell-based Covid-19 antiviral screens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.27.564435. [PMID: 37961552 PMCID: PMC10634915 DOI: 10.1101/2023.10.27.564435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Colloidal aggregation is one of the largest contributors to false-positives in early drug discovery and chemical biology. Much work has focused on its impact on pure-protein screens; here we consider aggregations role in cell-based infectivity assays in Covid-19 drug repurposing. We began by investigating the potential aggregation of 41 drug candidates reported as SARs-CoV-2 entry inhibitors. Of these, 17 formed colloidal-particles by dynamic light scattering and exhibited detergent-dependent enzyme inhibition. To evaluate antiviral efficacy of the drugs in cells we used spike pseudotyped lentivirus and pre-saturation of the colloids with BSA. The antiviral potency of the aggregators was diminished by at least 10-fold and often entirely eliminated in the presence of BSA, suggesting antiviral activity can be attributed to the non-specific nature of the colloids. In confocal microscopy, the aggregates induced fluorescent puncta of labeled spike protein, consistent with sequestration of the protein on the colloidal particles. Addition of either non-ionic detergent or of BSA disrupted these puncta. These observations suggest that colloidal aggregation is common among cell-based anti-viral drug repurposing, and perhaps cell-based assays more broadly, and offers rapid counter-screens to detect and eliminate these artifacts, allowing the community invest resources in compounds with true potential as a Covid-19 therapeutic.
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Affiliation(s)
- Isabella S Glenn
- Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Lauren N Hall
- Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Mir M Khalid
- Gladstone Institutes, San Francisco, California, United States
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States
| | - Melanie Ott
- Gladstone Institutes, San Francisco, California, United States
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States
- Chan Zuckerberg Biohub, San Francisco, California, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, CA, USA
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8
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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9
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Mader MM, Rudolph J, Hartung IV, Uehling D, Workman P, Zuercher W. Which Small Molecule? Selecting Chemical Probes for Use in Cancer Research and Target Validation. Cancer Discov 2023; 13:2150-2165. [PMID: 37712569 DOI: 10.1158/2159-8290.cd-23-0536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/17/2023] [Accepted: 08/08/2023] [Indexed: 09/16/2023]
Abstract
Small-molecule chemical "probes" complement the use of molecular biology techniques to explore, validate, and generate hypotheses on the function of proteins in diseases such as cancer. Unfortunately, the poor selection and use of small-molecule reagents can lead to incorrect conclusions. Here, we illustrate examples of poor chemical tools and suggest best practices for the selection, validation, and use of high-quality chemical probes in cancer research. We also note the complexity associated with tools for novel drug modalities, exemplified by protein degraders, and provide advice and resources to facilitate the independent identification of appropriate small-molecule probes by researchers. SIGNIFICANCE Validation of biological targets and pathways will be aided by a shared understanding of the criteria of potency, selectivity, and target engagement associated with small-molecule reagents ("chemical probes") that enable that work. Interdisciplinary collaboration between cancer biologists, medicinal chemists, and chemical biologists and the awareness of available resources will reduce misleading data generation and interpretation, strengthen data robustness, and improve productivity in academic and industrial research.
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Affiliation(s)
- Mary M Mader
- Indiana Biosciences Research Institute, Indianapolis, Indiana
- Chemistry in Cancer Research (CICR) Working Group of the American Association for Cancer Research, Philadelphia, Pennsylvania
| | - Joachim Rudolph
- Chemistry in Cancer Research (CICR) Working Group of the American Association for Cancer Research, Philadelphia, Pennsylvania
- Genentech, Inc., South San Francisco, California
| | - Ingo V Hartung
- Chemistry in Cancer Research (CICR) Working Group of the American Association for Cancer Research, Philadelphia, Pennsylvania
- Merck Healthcare KGaA, Darmstadt, Germany
| | - David Uehling
- Chemistry in Cancer Research (CICR) Working Group of the American Association for Cancer Research, Philadelphia, Pennsylvania
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Paul Workman
- Chemistry in Cancer Research (CICR) Working Group of the American Association for Cancer Research, Philadelphia, Pennsylvania
- Centre for Cancer Drug Discovery, The Institute of Cancer Research (London), Sutton, United Kingdom
- Chemical Probes Portal (www.chemicalprobes.org)
| | - William Zuercher
- Chemistry in Cancer Research (CICR) Working Group of the American Association for Cancer Research, Philadelphia, Pennsylvania
- F. Hoffmann-La Roche Ltd., Basel, Switzerland
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10
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Fink EA, Bardine C, Gahbauer S, Singh I, Detomasi TC, White K, Gu S, Wan X, Chen J, Ary B, Glenn I, O'Connell J, O'Donnell H, Fajtová P, Lyu J, Vigneron S, Young NJ, Kondratov IS, Alisoltani A, Simons LM, Lorenzo‐Redondo R, Ozer EA, Hultquist JF, O'Donoghue AJ, Moroz YS, Taunton J, Renslo AR, Irwin JJ, García‐Sastre A, Shoichet BK, Craik CS. Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors. Protein Sci 2023; 32:e4712. [PMID: 37354015 PMCID: PMC10364469 DOI: 10.1002/pro.4712] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/29/2023] [Accepted: 06/21/2023] [Indexed: 06/25/2023]
Abstract
Antiviral therapeutics to treat SARS-CoV-2 are needed to diminish the morbidity of the ongoing COVID-19 pandemic. A well-precedented drug target is the main viral protease (MPro ), which is targeted by an approved drug and by several investigational drugs. Emerging viral resistance has made new inhibitor chemotypes more pressing. Adopting a structure-based approach, we docked 1.2 billion non-covalent lead-like molecules and a new library of 6.5 million electrophiles against the enzyme structure. From these, 29 non-covalent and 11 covalent inhibitors were identified in 37 series, the most potent having an IC50 of 29 and 20 μM, respectively. Several series were optimized, resulting in low micromolar inhibitors. Subsequent crystallography confirmed the docking predicted binding modes and may template further optimization. While the new chemotypes may aid further optimization of MPro inhibitors for SARS-CoV-2, the modest success rate also reveals weaknesses in our approach for challenging targets like MPro versus other targets where it has been more successful, and versus other structure-based techniques against MPro itself.
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Affiliation(s)
- Elissa A. Fink
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
- Graduate Program in BiophysicsUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Conner Bardine
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
- Graduate Program in Chemistry and Chemical BiologyUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Stefan Gahbauer
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Isha Singh
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Tyler C. Detomasi
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Kris White
- Department of MicrobiologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Global Health and Emerging Pathogens InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Shuo Gu
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Xiaobo Wan
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Jun Chen
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Beatrice Ary
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Isabella Glenn
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Joseph O'Connell
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Henry O'Donnell
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California‐San DiegoSan DiegoCaliforniaUSA
| | - Jiankun Lyu
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Seth Vigneron
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Nicholas J. Young
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Ivan S. Kondratov
- Enamine Ltd.KyïvUkraine
- V.P. Kukhar Institute of Bioorganic Chemistry and PetrochemistryNational Academy of Sciences of UkraineKyïvUkraine
| | - Arghavan Alisoltani
- Division of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Lacy M. Simons
- Division of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Ramon Lorenzo‐Redondo
- Division of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Egon A. Ozer
- Division of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Judd F. Hultquist
- Division of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Anthony J. O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California‐San DiegoSan DiegoCaliforniaUSA
| | - Yurii S. Moroz
- National Taras Shevchenko University of KyïvKyïvUkraine
- Chemspace LLCKyïvUkraine
| | - Jack Taunton
- Department of Cellular and Molecular PharmacologyUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Adam R. Renslo
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - John J. Irwin
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Adolfo García‐Sastre
- Department of MicrobiologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Global Health and Emerging Pathogens InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Medicine, Division of Infectious DiseasesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Tisch Cancer Institute, Icahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Pathology, Molecular and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- QBI COVID‐19 Research Group (QCRG)San FranciscoCaliforniaUSA
| | - Brian K. Shoichet
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
- QBI COVID‐19 Research Group (QCRG)San FranciscoCaliforniaUSA
| | - Charles S. Craik
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
- QBI COVID‐19 Research Group (QCRG)San FranciscoCaliforniaUSA
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11
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Szal T, Chauhan SS, Lewe P, Rachad FZ, Madre M, Paunina L, Witt S, Parthasarathi R, Windshügel B. Efflux Pump-Binding 4(3-Aminocyclobutyl)Pyrimidin-2-Amines Are Colloidal Aggregators. Biomolecules 2023; 13:1000. [PMID: 37371580 DOI: 10.3390/biom13061000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/02/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Efflux pumps are a relevant factor in antimicrobial resistance. In E. coli, the tripartite efflux pump AcrAB-TolC removes a chemically diverse set of antibiotics from the bacterium. Therefore, small molecules interfering with efflux pump function are considered adjuvants for improving antimicrobial therapies. Several compounds targeting the periplasmic adapter protein AcrA and the efflux pump AcrB have been identified to act synergistically with different antibiotics. Among those, several 4(3-aminocyclobutyl)pyrimidin-2-amines have been shown to bind to both proteins. In this study, we intended to identify analogs of these substances with improved binding affinity to AcrA using virtual screening followed by experimental validation. While we succeeded in identifying several compounds showing a synergistic effect with erythromycin on E. coli, biophysical studies suggested that 4(3-aminocyclobutyl)pyrimidin-2-amines form colloidal aggregates that do not bind specifically to AcrA. Therefore, these substances are not suited for further development. Our study emphasizes the importance of implementing additional control experiments to identify aggregators among bioactive compounds.
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Affiliation(s)
- Tania Szal
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, 22525 Hamburg, Germany
- School of Science, Constructor University, 28759 Bremen, Germany
| | - Shweta Singh Chauhan
- Computational Toxicology Facility, Toxicoinformatics & Industrial Research CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Philipp Lewe
- Centre for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf (UKE), 22607 Hamburg, Germany
| | - Fatima-Zahra Rachad
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, 22525 Hamburg, Germany
| | - Marina Madre
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia
| | - Laura Paunina
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia
| | - Susanne Witt
- Centre for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf (UKE), 22607 Hamburg, Germany
| | - Ramakrishnan Parthasarathi
- Computational Toxicology Facility, Toxicoinformatics & Industrial Research CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Björn Windshügel
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, 22525 Hamburg, Germany
- School of Science, Constructor University, 28759 Bremen, Germany
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12
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Hong SH, Xi SY, Johns AC, Tang LC, Li A, Hum MN, Chartier CA, Jovanovic M, Shah NH. Mapping the Chemical Space of Active-Site Targeted Covalent Ligands for Protein Tyrosine Phosphatases. Chembiochem 2023; 24:e202200706. [PMID: 36893077 PMCID: PMC10192133 DOI: 10.1002/cbic.202200706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/05/2023] [Accepted: 03/09/2023] [Indexed: 03/10/2023]
Abstract
Protein tyrosine phosphatases (PTPs) are an important class of enzymes that modulate essential cellular processes through protein dephosphorylation and are dysregulated in various disease states. There is demand for new compounds that target the active sites of these enzymes, for use as chemical tools to dissect their biological roles or as leads for the development of new therapeutics. In this study, we explore an array of electrophiles and fragment scaffolds to investigate the required chemical parameters for covalent inhibition of tyrosine phosphatases. Our analysis juxtaposes the intrinsic electrophilicity of these compounds with their potency against several classical PTPs, revealing chemotypes that inhibit tyrosine phosphatases while minimizing excessive, potentially non-specific reactivity. We also assess sequence divergence at key residues in PTPs to explain their differential susceptibility to covalent inhibition. We anticipate that our study will inspire new strategies to develop covalent probes and inhibitors for tyrosine phosphatases.
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Affiliation(s)
- Suk ho Hong
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Sarah Y. Xi
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Andrew C. Johns
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Lauren C. Tang
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Allyson Li
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Madeleine N. Hum
- Department of Chemistry, Columbia University, New York, NY 10027
| | | | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Neel H. Shah
- Department of Chemistry, Columbia University, New York, NY 10027
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13
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Zhang H, Liang B, Sang X, An J, Huang Z. Discovery of Potential Inhibitors of SARS-CoV-2 Main Protease by a Transfer Learning Method. Viruses 2023; 15:v15040891. [PMID: 37112871 PMCID: PMC10143255 DOI: 10.3390/v15040891] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 remains a global public health threat and has prompted the development of antiviral therapies. Artificial intelligence may be one of the strategies to facilitate drug development for emerging and re-emerging diseases. The main protease (Mpro) of SARS-CoV-2 is an attractive drug target due to its essential role in the virus life cycle and high conservation among SARS-CoVs. In this study, we used a data augmentation method to boost transfer learning model performance in screening for potential inhibitors of SARS-CoV-2 Mpro. This method appeared to outperform graph convolution neural network, random forest and Chemprop on an external test set. The fine-tuned model was used to screen for a natural compound library and a de novo generated compound library. By combination with other in silico analysis methods, a total of 27 compounds were selected for experimental validation of anti-Mpro activities. Among all the selected hits, two compounds (gyssypol acetic acid and hyperoside) displayed inhibitory effects against Mpro with IC50 values of 67.6 μM and 235.8 μM, respectively. The results obtained in this study may suggest an effective strategy of discovering potential therapeutic leads for SARS-CoV-2 and other coronaviruses.
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14
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Pidugu LS, Servius HW, Sevdalis SE, Cook ME, Varney KM, Pozharski E, Drohat AC. Characterizing inhibitors of human AP endonuclease 1. PLoS One 2023; 18:e0280526. [PMID: 36652434 PMCID: PMC9847973 DOI: 10.1371/journal.pone.0280526] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 12/30/2022] [Indexed: 01/19/2023] Open
Abstract
AP endonuclease 1 (APE1) processes DNA lesions including apurinic/apyrimidinic sites and 3´-blocking groups, mediating base excision repair and single strand break repair. Much effort has focused on developing specific inhibitors of APE1, which could have important applications in basic research and potentially lead to clinical anticancer agents. We used structural, biophysical, and biochemical methods to characterize several reported inhibitors, including 7-nitroindole-2-carboxylic acid (CRT0044876), given its small size, reported potency, and widespread use for studying APE1. Intriguingly, NMR chemical shift perturbation (CSP) experiments show that CRT0044876 and three similar indole-2-carboxylic acids bind a pocket distal from the APE1 active site. A crystal structure confirms these findings and defines the pose for 5-nitroindole-2-carboxylic acid. However, dynamic light scattering experiments show the indole compounds form colloidal aggregates that could bind (sequester) APE1, causing nonspecific inhibition. Endonuclease assays show the compounds lack significant APE1 inhibition under conditions (detergent) that disrupt aggregation. Thus, binding of the indole-2-carboxylic acids at the remote pocket does not inhibit APE1 repair activity. Myricetin also forms aggregates and lacks APE1 inhibition under aggregate-disrupting conditions. Two other reported compounds (MLS000552981, MLS000419194) inhibit APE1 in vitro with low micromolar IC50 and do not appear to aggregate in this concentration range. However, NMR CSP experiments indicate the compounds do not bind specifically to apo- or Mg2+-bound APE1, pointing to a non-specific mode of inhibition, possibly DNA binding. Our results highlight methods for rigorous interrogation of putative APE1 inhibitors and should facilitate future efforts to discover compounds that specifically inhibit this important repair enzyme.
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Affiliation(s)
- Lakshmi S. Pidugu
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Hardler W. Servius
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Spiridon E. Sevdalis
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Mary E. Cook
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Kristen M. Varney
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Edwin Pozharski
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Center for Biomolecular Therapeutics, Institute for Bioscience and Biotechnology Research, Rockville, Maryland, United States of America
- * E-mail: (EP); (ACD)
| | - Alexander C. Drohat
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (EP); (ACD)
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15
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Yang P, Zhu Y, Zheng Q, Meng S, Wu Y, Shuai W, Sun Q, Wang G. Recent advances of β-catenin small molecule inhibitors for cancer therapy: Current development and future perspectives. Eur J Med Chem 2022; 243:114789. [DOI: 10.1016/j.ejmech.2022.114789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/17/2022] [Accepted: 09/18/2022] [Indexed: 11/28/2022]
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16
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Sheridan R, Spelman K. Polyphenolic promiscuity, inflammation-coupled selectivity: Whether PAINs filters mask an antiviral asset. Front Pharmacol 2022; 13:909945. [PMID: 36339544 PMCID: PMC9634583 DOI: 10.3389/fphar.2022.909945] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/03/2022] [Indexed: 11/26/2023] Open
Abstract
The Covid-19 pandemic has elicited much laboratory and clinical research attention on vaccines, mAbs, and certain small-molecule antivirals against SARS-CoV-2 infection. By contrast, there has been comparatively little attention on plant-derived compounds, especially those that are understood to be safely ingested at common doses and are frequently consumed in the diet in herbs, spices, fruits and vegetables. Examining plant secondary metabolites, we review recent elucidations into the pharmacological activity of flavonoids and other polyphenolic compounds and also survey their putative frequent-hitter behavior. Polyphenols, like many drugs, are glucuronidated post-ingestion. In an inflammatory milieu such as infection, a reversion back to the active aglycone by the release of β-glucuronidase from neutrophils and macrophages allows cellular entry of the aglycone. In the context of viral infection, virions and intracellular virus particles may be exposed to promiscuous binding by the polyphenol aglycones resulting in viral inhibition. As the mechanism's scope would apply to the diverse range of virus species that elicit inflammation in infected hosts, we highlight pre-clinical studies of polyphenol aglycones, such as luteolin, isoginkgetin, quercetin, quercetagetin, baicalein, curcumin, fisetin and hesperetin that reduce virion replication spanning multiple distinct virus genera. It is hoped that greater awareness of the potential spatial selectivity of polyphenolic activation to sites of pathogenic infection will spur renewed research and clinical attention for natural products antiviral assaying and trialing over a wide array of infectious viral diseases.
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Affiliation(s)
| | - Kevin Spelman
- Massachusetts College of Pharmacy and Health Sciences, Boston, MA, United States
- Health Education and Research, Driggs, ID, United States
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17
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Yazdi AK, Pakarian P, Perveen S, Hajian T, Santhakumar V, Bolotokova A, Li F, Vedadi M. Kinetic Characterization of SARS-CoV-2 nsp13 ATPase Activity and Discovery of Small-Molecule Inhibitors. ACS Infect Dis 2022; 8:1533-1542. [PMID: 35822715 PMCID: PMC9305828 DOI: 10.1021/acsinfecdis.2c00165] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Indexed: 11/29/2022]
Abstract
SARS-CoV-2 non-structural protein 13 (nsp13) is a highly conserved helicase and RNA 5'-triphosphatase. It uses the energy derived from the hydrolysis of nucleoside triphosphates for directional movement along the nucleic acids and promotes the unwinding of double-stranded nucleic acids. Nsp13 is essential for replication and propagation of all human and non-human coronaviruses. Combined with its defined nucleotide binding site and druggability, nsp13 is one of the most promising candidates for the development of pan-coronavirus therapeutics. Here, we report the development and optimization of bioluminescence assays for kinetic characterization of nsp13 ATPase activity in the presence and absence of single-stranded DNA. Screening of a library of 5000 small molecules in the presence of single-stranded DNA resulted in the discovery of six nsp13 small-molecule inhibitors with IC50 values ranging from 6 ± 0.5 to 50 ± 6 μM. In addition to providing validated methods for high-throughput screening of nsp13 in drug discovery campaigns, the reproducible screening hits we present here could potentially be chemistry starting points toward the development of more potent and selective nsp13 inhibitors, enabling the discovery of antiviral therapeutics.
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Affiliation(s)
| | - Paknoosh Pakarian
- Structural Genomics Consortium,
University of Toronto, Toronto, Ontario M5G 1L7,
Canada
| | - Sumera Perveen
- Structural Genomics Consortium,
University of Toronto, Toronto, Ontario M5G 1L7,
Canada
| | - Taraneh Hajian
- Structural Genomics Consortium,
University of Toronto, Toronto, Ontario M5G 1L7,
Canada
| | | | - Albina Bolotokova
- Structural Genomics Consortium,
University of Toronto, Toronto, Ontario M5G 1L7,
Canada
| | - Fengling Li
- Structural Genomics Consortium,
University of Toronto, Toronto, Ontario M5G 1L7,
Canada
| | - Masoud Vedadi
- Structural Genomics Consortium,
University of Toronto, Toronto, Ontario M5G 1L7,
Canada
- Department of Pharmacology and Toxicology,
University of Toronto, Toronto, Ontario M5S 1A8,
Canada
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18
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McCoy MA, Spicer D, Wells N, Hoogewijs K, Fiedler M, Baud MGJ. Biophysical Survey of Small-Molecule β-Catenin Inhibitors: A Cautionary Tale. J Med Chem 2022; 65:7246-7261. [PMID: 35581674 PMCID: PMC9150122 DOI: 10.1021/acs.jmedchem.2c00228] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The canonical Wingless-related
integration site signaling pathway
plays a critical role in human physiology, and its dysregulation can
lead to an array of diseases. β-Catenin is a multifunctional
protein within this pathway and an attractive yet challenging therapeutic
target, most notably in oncology. This has stimulated the search for
potent small-molecule inhibitors binding directly to the β-catenin
surface to inhibit its protein–protein interactions and downstream
signaling. Here, we provide an account of the claimed (and some putative)
small-molecule ligands of β-catenin from the literature. Through
in silico analysis, we show that most of these molecules contain promiscuous
chemical substructures notorious for interfering with screening assays.
Finally, and in line with this analysis, we demonstrate using orthogonal
biophysical techniques that none of the examined small molecules bind
at the surface of β-catenin. While shedding doubts on their
reported mode of action, this study also reaffirms β-catenin
as a prominent target in drug discovery.
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Affiliation(s)
- Michael A McCoy
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Dominique Spicer
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Neil Wells
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Kurt Hoogewijs
- National University of Ireland, University Road, Galway H91 TK33, Ireland
| | - Marc Fiedler
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - Matthias G J Baud
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
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19
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Ma C, Tan H, Choza J, Wang Y, Wang J. Validation and invalidation of SARS-CoV-2 main protease inhibitors using the Flip-GFP and Protease-Glo luciferase assays. Acta Pharm Sin B 2022; 12:1636-1651. [PMID: 34745850 PMCID: PMC8558150 DOI: 10.1016/j.apsb.2021.10.026] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/24/2021] [Accepted: 10/14/2021] [Indexed: 12/14/2022] Open
Abstract
SARS-CoV-2 main protease (Mpro) is one of the most extensively exploited drug targets for COVID-19. Structurally disparate compounds have been reported as Mpro inhibitors, raising the question of their target specificity. To elucidate the target specificity and the cellular target engagement of the claimed Mpro inhibitors, we systematically characterize their mechanism of action using the cell-free FRET assay, the thermal shift-binding assay, the cell lysate Protease-Glo luciferase assay, and the cell-based FlipGFP assay. Collectively, our results have shown that majority of the Mpro inhibitors identified from drug repurposing including ebselen, carmofur, disulfiram, and shikonin are promiscuous cysteine inhibitors that are not specific to Mpro, while chloroquine, oxytetracycline, montelukast, candesartan, and dipyridamole do not inhibit Mpro in any of the assays tested. Overall, our study highlights the need of stringent hit validation at the early stage of drug discovery.
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20
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Perylene as a controversial antiviral scaffold. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2022. [DOI: 10.1016/bs.armc.2022.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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