CovidChloroV1, Main, Exploration, bibRecordById, pubmed:33051297

Identify potent SARS-CoV-2 main protease inhibitors via accelerated free energy perturbation-based virtual screening of existing drugs.

Identifieur interne : 001113 ( Main/Exploration ); précédent : 001112; suivant : 001114

Identify potent SARS-CoV-2 main protease inhibitors via accelerated free energy perturbation-based virtual screening of existing drugs.

Source :

Proceedings of the National Academy of Sciences of the United States of America [ 1091-6490 ] ; 2020.

RBID : pubmed:33051297

Descripteurs français

KwdFr :
- Antiviraux (pharmacologie), Betacoronavirus (effets des médicaments et des substances chimiques), Chloroquine (pharmacologie), Cysteine endopeptidases (MeSH), Dipyridamole (pharmacologie), Humains (MeSH), Hydroxychloroquine (pharmacologie), Infections à coronavirus (traitement médicamenteux), Inhibiteurs de protéases (pharmacologie), Pandémies (MeSH), Pneumopathie virale (traitement médicamenteux), Protéines virales non structurales (antagonistes et inhibiteurs), Repositionnement des médicaments (MeSH), Simulation de docking moléculaire (MeSH), Structure moléculaire (MeSH).
MESH :
- antagonistes et inhibiteurs : Protéines virales non structurales.
- effets des médicaments et des substances chimiques : Betacoronavirus.
- pharmacologie : Antiviraux, Chloroquine, Dipyridamole, Hydroxychloroquine, Inhibiteurs de protéases.
- traitement médicamenteux : Infections à coronavirus, Pneumopathie virale.
- Cysteine endopeptidases, Humains, Pandémies, Repositionnement des médicaments, Simulation de docking moléculaire, Structure moléculaire.

English descriptors

KwdEn :
- Antiviral Agents (pharmacology), Betacoronavirus (drug effects), COVID-19 (MeSH), Chloroquine (pharmacology), Coronavirus 3C Proteases (MeSH), Coronavirus Infections (drug therapy), Cysteine Endopeptidases (MeSH), Dipyridamole (pharmacology), Drug Repositioning (MeSH), Humans (MeSH), Hydroxychloroquine (pharmacology), Molecular Docking Simulation (MeSH), Molecular Structure (MeSH), Pandemics (MeSH), Pneumonia, Viral (drug therapy), Protease Inhibitors (pharmacology), SARS-CoV-2 (MeSH), Viral Nonstructural Proteins (antagonists & inhibitors).
MESH :
- chemical , antagonists & inhibitors : Viral Nonstructural Proteins.
- chemical , pharmacology : Antiviral Agents, Chloroquine, Dipyridamole, Hydroxychloroquine, Protease Inhibitors.
- drug effects : Betacoronavirus.
- drug therapy : Coronavirus Infections, Pneumonia, Viral.
- COVID-19, Coronavirus 3C Proteases, Cysteine Endopeptidases, Drug Repositioning, Humans, Molecular Docking Simulation, Molecular Structure, Pandemics, SARS-CoV-2.

Abstract

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global crisis. There is no therapeutic treatment specific for COVID-19. It is highly desirable to identify potential antiviral agents against SARS-CoV-2 from existing drugs available for other diseases and thus repurpose them for treatment of COVID-19. In general, a drug repurposing effort for treatment of a new disease, such as COVID-19, usually starts from a virtual screening of existing drugs, followed by experimental validation, but the actual hit rate is generally rather low with traditional computational methods. Here we report a virtual screening approach with accelerated free energy perturbation-based absolute binding free energy (FEP-ABFE) predictions and its use in identifying drugs targeting SARS-CoV-2 main protease (M^pro). The accurate FEP-ABFE predictions were based on the use of a restraint energy distribution (RED) function, making the practical FEP-ABFE-based virtual screening of the existing drug library possible. As a result, out of 25 drugs predicted, 15 were confirmed as potent inhibitors of SARS-CoV-2 M^pro The most potent one is dipyridamole (inhibitory constant K_i = 0.04 µM) which has shown promising therapeutic effects in subsequently conducted clinical studies for treatment of patients with COVID-19. Additionally, hydroxychloroquine (K_i = 0.36 µM) and chloroquine (K_i = 0.56 µM) were also found to potently inhibit SARS-CoV-2 M^pro We anticipate that the FEP-ABFE prediction-based virtual screening approach will be useful in many other drug repurposing or discovery efforts.

DOI: 10.1073/pnas.2010470117
PubMed: 33051297
PubMed Central: PMC7959488

Affiliations:

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Le document en format XML

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<affiliation wicri:level="2"><nlm:affiliation>Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536.</nlm:affiliation>
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<author><name sortKey="Wang, Xin" sort="Wang, Xin" uniqKey="Wang X" first="Xin" last="Wang">Xin Wang</name>
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<affiliation wicri:level="1"><nlm:affiliation>Marine Biomedical Research Institute of Qingdao, 266100 Qingdao, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Marine Biomedical Research Institute of Qingdao, 266100 Qingdao</wicri:regionArea>
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<author><name sortKey="Luo, Hai Bin" sort="Luo, Hai Bin" uniqKey="Luo H" first="Hai-Bin" last="Luo">Hai-Bin Luo</name>
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<placeName><settlement type="city">Jiangmen</settlement>
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<affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 570228 Haikou, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 570228 Haikou</wicri:regionArea>
<wicri:noRegion>570228 Haikou</wicri:noRegion>
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<sourceDesc><biblStruct><analytic><title xml:lang="en">Identify potent SARS-CoV-2 main protease inhibitors via accelerated free energy perturbation-based virtual screening of existing drugs.</title>
<author><name sortKey="Li, Zhe" sort="Li, Zhe" uniqKey="Li Z" first="Zhe" last="Li">Zhe Li</name>
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<author><name sortKey="Li, Xin" sort="Li, Xin" uniqKey="Li X" first="Xin" last="Li">Xin Li</name>
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<affiliation wicri:level="1"><nlm:affiliation>School of Life Sciences, Lanzhou University, 734000 Lanzhou, China.</nlm:affiliation>
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<author><name sortKey="Huang, Yi You" sort="Huang, Yi You" uniqKey="Huang Y" first="Yi-You" last="Huang">Yi-You Huang</name>
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<author><name sortKey="Wu, Yaoxing" sort="Wu, Yaoxing" uniqKey="Wu Y" first="Yaoxing" last="Wu">Yaoxing Wu</name>
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<author><name sortKey="Liu, Runduo" sort="Liu, Runduo" uniqKey="Liu R" first="Runduo" last="Liu">Runduo Liu</name>
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<author><name sortKey="Zhou, Lingli" sort="Zhou, Lingli" uniqKey="Zhou L" first="Lingli" last="Zhou">Lingli Zhou</name>
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<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Ministry of Education (MOE) Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510006 Guangzhou</wicri:regionArea>
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<author><name sortKey="Lin, Yuxi" sort="Lin, Yuxi" uniqKey="Lin Y" first="Yuxi" last="Lin">Yuxi Lin</name>
<affiliation wicri:level="1"><nlm:affiliation>Center for Innovative Marine Drug Screening & Evaluation, School of Medicine and Pharmacy, Ocean University of China, 266100 Qingdao, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Center for Innovative Marine Drug Screening & Evaluation, School of Medicine and Pharmacy, Ocean University of China, 266100 Qingdao</wicri:regionArea>
<wicri:noRegion>266100 Qingdao</wicri:noRegion>
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<affiliation wicri:level="1"><nlm:affiliation>School of Life Sciences, Lanzhou University, 734000 Lanzhou, China.</nlm:affiliation>
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<wicri:regionArea>School of Life Sciences, Lanzhou University, 734000 Lanzhou</wicri:regionArea>
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<author><name sortKey="Wu, Deyan" sort="Wu, Deyan" uniqKey="Wu D" first="Deyan" last="Wu">Deyan Wu</name>
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<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-Sen University, 510006 Guangzhou</wicri:regionArea>
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<author><name sortKey="Zhang, Lei" sort="Zhang, Lei" uniqKey="Zhang L" first="Lei" last="Zhang">Lei Zhang</name>
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<country xml:lang="fr">République populaire de Chine</country>
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<author><name sortKey="Liu, Hao" sort="Liu, Hao" uniqKey="Liu H" first="Hao" last="Liu">Hao Liu</name>
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<country xml:lang="fr">République populaire de Chine</country>
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<author><name sortKey="Xu, Ximing" sort="Xu, Ximing" uniqKey="Xu X" first="Ximing" last="Xu">Ximing Xu</name>
<affiliation wicri:level="1"><nlm:affiliation>Center for Innovative Marine Drug Screening & Evaluation, School of Medicine and Pharmacy, Ocean University of China, 266100 Qingdao, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Center for Innovative Marine Drug Screening & Evaluation, School of Medicine and Pharmacy, Ocean University of China, 266100 Qingdao</wicri:regionArea>
<wicri:noRegion>266100 Qingdao</wicri:noRegion>
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<affiliation wicri:level="1"><nlm:affiliation>Marine Biomedical Research Institute of Qingdao, 266100 Qingdao, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Marine Biomedical Research Institute of Qingdao, 266100 Qingdao</wicri:regionArea>
<wicri:noRegion>266100 Qingdao</wicri:noRegion>
</affiliation>
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<author><name sortKey="Yu, Kunqian" sort="Yu, Kunqian" uniqKey="Yu K" first="Kunqian" last="Yu">Kunqian Yu</name>
<affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai</wicri:regionArea>
<wicri:noRegion>201203 Shanghai</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:affiliation>University of Chinese Academy of Sciences, 100049 Beijing, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>University of Chinese Academy of Sciences, 100049 Beijing</wicri:regionArea>
<placeName><settlement type="city">Pékin</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Zhang, Yuxia" sort="Zhang, Yuxia" uniqKey="Zhang Y" first="Yuxia" last="Zhang">Yuxia Zhang</name>
<affiliation wicri:level="1"><nlm:affiliation>Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, 510623 Guangzhou, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, 510623 Guangzhou</wicri:regionArea>
<placeName><settlement type="city">Jiangmen</settlement>
<region type="province">Guangdong</region>
</placeName>
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<author><name sortKey="Cui, Jun" sort="Cui, Jun" uniqKey="Cui J" first="Jun" last="Cui">Jun Cui</name>
<affiliation wicri:level="1"><nlm:affiliation>Ministry of Education (MOE) Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510006 Guangzhou, China; cuij5@mail.sysu.edu.cn zhan@uky.edu wx8399@ouc.edu.cn luohb77@mail.sysu.edu.cn.</nlm:affiliation>
<country wicri:rule="url">République populaire de Chine</country>
<wicri:regionArea>Ministry of Education (MOE) Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510006 Guangzhou</wicri:regionArea>
<placeName><settlement type="city">Jiangmen</settlement>
<region type="province">Guangdong</region>
</placeName>
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<author><name sortKey="Zhan, Chang Guo" sort="Zhan, Chang Guo" uniqKey="Zhan C" first="Chang-Guo" last="Zhan">Chang-Guo Zhan</name>
<affiliation wicri:level="1"><nlm:affiliation>Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, Lexington, KY 40536; cuij5@mail.sysu.edu.cn zhan@uky.edu wx8399@ouc.edu.cn luohb77@mail.sysu.edu.cn.</nlm:affiliation>
<country wicri:rule="url">République populaire de Chine</country>
<wicri:regionArea>Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, Lexington</wicri:regionArea>
<wicri:noRegion>Lexington</wicri:noRegion>
</affiliation>
<affiliation wicri:level="2"><nlm:affiliation>Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Kentucky</region>
</placeName>
<wicri:cityArea>Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Wang, Xin" sort="Wang, Xin" uniqKey="Wang X" first="Xin" last="Wang">Xin Wang</name>
<affiliation wicri:level="1"><nlm:affiliation>Center for Innovative Marine Drug Screening & Evaluation, School of Medicine and Pharmacy, Ocean University of China, 266100 Qingdao, China; cuij5@mail.sysu.edu.cn zhan@uky.edu wx8399@ouc.edu.cn luohb77@mail.sysu.edu.cn.</nlm:affiliation>
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<wicri:regionArea>Center for Innovative Marine Drug Screening & Evaluation, School of Medicine and Pharmacy, Ocean University of China, 266100 Qingdao</wicri:regionArea>
<wicri:noRegion>266100 Qingdao</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:affiliation>Marine Biomedical Research Institute of Qingdao, 266100 Qingdao, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Marine Biomedical Research Institute of Qingdao, 266100 Qingdao</wicri:regionArea>
<wicri:noRegion>266100 Qingdao</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Luo, Hai Bin" sort="Luo, Hai Bin" uniqKey="Luo H" first="Hai-Bin" last="Luo">Hai-Bin Luo</name>
<affiliation wicri:level="1"><nlm:affiliation>Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-Sen University, 510006 Guangzhou, People's Republic of China; cuij5@mail.sysu.edu.cn zhan@uky.edu wx8399@ouc.edu.cn luohb77@mail.sysu.edu.cn.</nlm:affiliation>
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<wicri:regionArea>Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-Sen University, 510006 Guangzhou</wicri:regionArea>
<placeName><settlement type="city">Jiangmen</settlement>
<region type="province">Guangdong</region>
</placeName>
</affiliation>
<affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 570228 Haikou, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 570228 Haikou</wicri:regionArea>
<wicri:noRegion>570228 Haikou</wicri:noRegion>
</affiliation>
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<series><title level="j">Proceedings of the National Academy of Sciences of the United States of America</title>
<idno type="eISSN">1091-6490</idno>
<imprint><date when="2020" type="published">2020</date>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Antiviral Agents (pharmacology)</term>
<term>Betacoronavirus (drug effects)</term>
<term>COVID-19 (MeSH)</term>
<term>Chloroquine (pharmacology)</term>
<term>Coronavirus 3C Proteases (MeSH)</term>
<term>Coronavirus Infections (drug therapy)</term>
<term>Cysteine Endopeptidases (MeSH)</term>
<term>Dipyridamole (pharmacology)</term>
<term>Drug Repositioning (MeSH)</term>
<term>Humans (MeSH)</term>
<term>Hydroxychloroquine (pharmacology)</term>
<term>Molecular Docking Simulation (MeSH)</term>
<term>Molecular Structure (MeSH)</term>
<term>Pandemics (MeSH)</term>
<term>Pneumonia, Viral (drug therapy)</term>
<term>Protease Inhibitors (pharmacology)</term>
<term>SARS-CoV-2 (MeSH)</term>
<term>Viral Nonstructural Proteins (antagonists & inhibitors)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Antiviraux (pharmacologie)</term>
<term>Betacoronavirus (effets des médicaments et des substances chimiques)</term>
<term>Chloroquine (pharmacologie)</term>
<term>Cysteine endopeptidases (MeSH)</term>
<term>Dipyridamole (pharmacologie)</term>
<term>Humains (MeSH)</term>
<term>Hydroxychloroquine (pharmacologie)</term>
<term>Infections à coronavirus (traitement médicamenteux)</term>
<term>Inhibiteurs de protéases (pharmacologie)</term>
<term>Pandémies (MeSH)</term>
<term>Pneumopathie virale (traitement médicamenteux)</term>
<term>Protéines virales non structurales (antagonistes et inhibiteurs)</term>
<term>Repositionnement des médicaments (MeSH)</term>
<term>Simulation de docking moléculaire (MeSH)</term>
<term>Structure moléculaire (MeSH)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="antagonists & inhibitors" xml:lang="en"><term>Viral Nonstructural Proteins</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="pharmacology" xml:lang="en"><term>Antiviral Agents</term>
<term>Chloroquine</term>
<term>Dipyridamole</term>
<term>Hydroxychloroquine</term>
<term>Protease Inhibitors</term>
</keywords>
<keywords scheme="MESH" qualifier="antagonistes et inhibiteurs" xml:lang="fr"><term>Protéines virales non structurales</term>
</keywords>
<keywords scheme="MESH" qualifier="drug effects" xml:lang="en"><term>Betacoronavirus</term>
</keywords>
<keywords scheme="MESH" qualifier="drug therapy" xml:lang="en"><term>Coronavirus Infections</term>
<term>Pneumonia, Viral</term>
</keywords>
<keywords scheme="MESH" qualifier="effets des médicaments et des substances chimiques" xml:lang="fr"><term>Betacoronavirus</term>
</keywords>
<keywords scheme="MESH" qualifier="pharmacologie" xml:lang="fr"><term>Antiviraux</term>
<term>Chloroquine</term>
<term>Dipyridamole</term>
<term>Hydroxychloroquine</term>
<term>Inhibiteurs de protéases</term>
</keywords>
<keywords scheme="MESH" qualifier="traitement médicamenteux" xml:lang="fr"><term>Infections à coronavirus</term>
<term>Pneumopathie virale</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>COVID-19</term>
<term>Coronavirus 3C Proteases</term>
<term>Cysteine Endopeptidases</term>
<term>Drug Repositioning</term>
<term>Humans</term>
<term>Molecular Docking Simulation</term>
<term>Molecular Structure</term>
<term>Pandemics</term>
<term>SARS-CoV-2</term>
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<keywords scheme="MESH" xml:lang="fr"><term>Cysteine endopeptidases</term>
<term>Humains</term>
<term>Pandémies</term>
<term>Repositionnement des médicaments</term>
<term>Simulation de docking moléculaire</term>
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<front><div type="abstract" xml:lang="en">The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global crisis. There is no therapeutic treatment specific for COVID-19. It is highly desirable to identify potential antiviral agents against SARS-CoV-2 from existing drugs available for other diseases and thus repurpose them for treatment of COVID-19. In general, a drug repurposing effort for treatment of a new disease, such as COVID-19, usually starts from a virtual screening of existing drugs, followed by experimental validation, but the actual hit rate is generally rather low with traditional computational methods. Here we report a virtual screening approach with accelerated free energy perturbation-based absolute binding free energy (FEP-ABFE) predictions and its use in identifying drugs targeting SARS-CoV-2 main protease (M<sup>pro</sup>
). The accurate FEP-ABFE predictions were based on the use of a restraint energy distribution (RED) function, making the practical FEP-ABFE-based virtual screening of the existing drug library possible. As a result, out of 25 drugs predicted, 15 were confirmed as potent inhibitors of SARS-CoV-2 M<sup>pro</sup>
 The most potent one is dipyridamole (inhibitory constant K<sub>i</sub>
 = 0.04 µM) which has shown promising therapeutic effects in subsequently conducted clinical studies for treatment of patients with COVID-19. Additionally, hydroxychloroquine (K<sub>i</sub>
 = 0.36 µM) and chloroquine (K<sub>i</sub>
 = 0.56 µM) were also found to potently inhibit SARS-CoV-2 M<sup>pro</sup>
 We anticipate that the FEP-ABFE prediction-based virtual screening approach will be useful in many other drug repurposing or discovery efforts.</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">33051297</PMID>
<DateCompleted><Year>2020</Year>
<Month>11</Month>
<Day>11</Day>
</DateCompleted>
<DateRevised><Year>2021</Year>
<Month>03</Month>
<Day>24</Day>
</DateRevised>
<Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1091-6490</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>117</Volume>
<Issue>44</Issue>
<PubDate><Year>2020</Year>
<Month>11</Month>
<Day>03</Day>
</PubDate>
</JournalIssue>
<Title>Proceedings of the National Academy of Sciences of the United States of America</Title>
<ISOAbbreviation>Proc Natl Acad Sci U S A</ISOAbbreviation>
</Journal>
<ArticleTitle>Identify potent SARS-CoV-2 main protease inhibitors via accelerated free energy perturbation-based virtual screening of existing drugs.</ArticleTitle>
<Pagination><MedlinePgn>27381-27387</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1073/pnas.2010470117</ELocationID>
<Abstract><AbstractText>The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global crisis. There is no therapeutic treatment specific for COVID-19. It is highly desirable to identify potential antiviral agents against SARS-CoV-2 from existing drugs available for other diseases and thus repurpose them for treatment of COVID-19. In general, a drug repurposing effort for treatment of a new disease, such as COVID-19, usually starts from a virtual screening of existing drugs, followed by experimental validation, but the actual hit rate is generally rather low with traditional computational methods. Here we report a virtual screening approach with accelerated free energy perturbation-based absolute binding free energy (FEP-ABFE) predictions and its use in identifying drugs targeting SARS-CoV-2 main protease (M<sup>pro</sup>
). The accurate FEP-ABFE predictions were based on the use of a restraint energy distribution (RED) function, making the practical FEP-ABFE-based virtual screening of the existing drug library possible. As a result, out of 25 drugs predicted, 15 were confirmed as potent inhibitors of SARS-CoV-2 M<sup>pro</sup>
 The most potent one is dipyridamole (inhibitory constant K<sub>i</sub>
 = 0.04 µM) which has shown promising therapeutic effects in subsequently conducted clinical studies for treatment of patients with COVID-19. Additionally, hydroxychloroquine (K<sub>i</sub>
 = 0.36 µM) and chloroquine (K<sub>i</sub>
 = 0.56 µM) were also found to potently inhibit SARS-CoV-2 M<sup>pro</sup>
 We anticipate that the FEP-ABFE prediction-based virtual screening approach will be useful in many other drug repurposing or discovery efforts.</AbstractText>
<CopyrightInformation>Copyright © 2020 the Author(s). Published by PNAS.</CopyrightInformation>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Li</LastName>
<ForeName>Zhe</ForeName>
<Initials>Z</Initials>
<Identifier Source="ORCID">0000-0002-9357-6839</Identifier>
<AffiliationInfo><Affiliation>Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-Sen University, 510006 Guangzhou, People's Republic of China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Li</LastName>
<ForeName>Xin</ForeName>
<Initials>X</Initials>
<AffiliationInfo><Affiliation>Center for Innovative Marine Drug Screening & Evaluation, School of Medicine and Pharmacy, Ocean University of China, 266100 Qingdao, China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>School of Life Sciences, Lanzhou University, 734000 Lanzhou, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Huang</LastName>
<ForeName>Yi-You</ForeName>
<Initials>YY</Initials>
<AffiliationInfo><Affiliation>Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-Sen University, 510006 Guangzhou, People's Republic of China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Wu</LastName>
<ForeName>Yaoxing</ForeName>
<Initials>Y</Initials>
<AffiliationInfo><Affiliation>Ministry of Education (MOE) Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510006 Guangzhou, China.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Liu</LastName>
<ForeName>Runduo</ForeName>
<Initials>R</Initials>
<Identifier Source="ORCID">0000-0002-8446-0404</Identifier>
<AffiliationInfo><Affiliation>Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-Sen University, 510006 Guangzhou, People's Republic of China.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Zhou</LastName>
<ForeName>Lingli</ForeName>
<Initials>L</Initials>
<AffiliationInfo><Affiliation>Ministry of Education (MOE) Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510006 Guangzhou, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Lin</LastName>
<ForeName>Yuxi</ForeName>
<Initials>Y</Initials>
<AffiliationInfo><Affiliation>Center for Innovative Marine Drug Screening & Evaluation, School of Medicine and Pharmacy, Ocean University of China, 266100 Qingdao, China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>School of Life Sciences, Lanzhou University, 734000 Lanzhou, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Wu</LastName>
<ForeName>Deyan</ForeName>
<Initials>D</Initials>
<AffiliationInfo><Affiliation>Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-Sen University, 510006 Guangzhou, People's Republic of China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Zhang</LastName>
<ForeName>Lei</ForeName>
<Initials>L</Initials>
<AffiliationInfo><Affiliation>Ministry of Education (MOE) Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510006 Guangzhou, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Liu</LastName>
<ForeName>Hao</ForeName>
<Initials>H</Initials>
<AffiliationInfo><Affiliation>High Performance Computing Center, Pilot National Laboratory for Marine Science and Technology, 266237 Qingdao, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Xu</LastName>
<ForeName>Ximing</ForeName>
<Initials>X</Initials>
<AffiliationInfo><Affiliation>Center for Innovative Marine Drug Screening & Evaluation, School of Medicine and Pharmacy, Ocean University of China, 266100 Qingdao, China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Marine Biomedical Research Institute of Qingdao, 266100 Qingdao, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Yu</LastName>
<ForeName>Kunqian</ForeName>
<Initials>K</Initials>
<AffiliationInfo><Affiliation>State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>University of Chinese Academy of Sciences, 100049 Beijing, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Zhang</LastName>
<ForeName>Yuxia</ForeName>
<Initials>Y</Initials>
<AffiliationInfo><Affiliation>Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, 510623 Guangzhou, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Cui</LastName>
<ForeName>Jun</ForeName>
<Initials>J</Initials>
<AffiliationInfo><Affiliation>Ministry of Education (MOE) Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510006 Guangzhou, China; cuij5@mail.sysu.edu.cn zhan@uky.edu wx8399@ouc.edu.cn luohb77@mail.sysu.edu.cn.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Zhan</LastName>
<ForeName>Chang-Guo</ForeName>
<Initials>CG</Initials>
<Identifier Source="ORCID">0000-0002-4128-7269</Identifier>
<AffiliationInfo><Affiliation>Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, Lexington, KY 40536; cuij5@mail.sysu.edu.cn zhan@uky.edu wx8399@ouc.edu.cn luohb77@mail.sysu.edu.cn.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Wang</LastName>
<ForeName>Xin</ForeName>
<Initials>X</Initials>
<Identifier Source="ORCID">0000-0001-7467-6060</Identifier>
<AffiliationInfo><Affiliation>Center for Innovative Marine Drug Screening & Evaluation, School of Medicine and Pharmacy, Ocean University of China, 266100 Qingdao, China; cuij5@mail.sysu.edu.cn zhan@uky.edu wx8399@ouc.edu.cn luohb77@mail.sysu.edu.cn.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Marine Biomedical Research Institute of Qingdao, 266100 Qingdao, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Luo</LastName>
<ForeName>Hai-Bin</ForeName>
<Initials>HB</Initials>
<Identifier Source="ORCID">0000-0002-2163-0509</Identifier>
<AffiliationInfo><Affiliation>Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-Sen University, 510006 Guangzhou, People's Republic of China; cuij5@mail.sysu.edu.cn zhan@uky.edu wx8399@ouc.edu.cn luohb77@mail.sysu.edu.cn.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 570228 Haikou, China.</Affiliation>
</AffiliationInfo>
</Author>
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<PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType>
<PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType>
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<Month>10</Month>
<Day>13</Day>
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Identify potent SARS-CoV-2 main protease inhibitors via accelerated free energy perturbation-based virtual screening of existing drugs.

Identify potent SARS-CoV-2 main protease inhibitors via accelerated free energy perturbation-based virtual screening of existing drugs.

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