Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL pro) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates
Identifieur interne : 000469 ( Main/Exploration ); précédent : 000468; suivant : 000470Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL pro) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates
Auteurs : Yu Wai Chen [Hong Kong] ; Chin-Pang Bennu Yiu [Hong Kong] ; Kwok-Yin Wong [Hong Kong]Source :
- F1000Research [ 2046-1402 ] ; 2020.
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Abstract
We prepared the three-dimensional model of the SARS-CoV-2 (aka 2019-nCoV) 3C-like protease (3CL pro) using the crystal structure of the highly similar (96% identity) ortholog from the SARS-CoV. All residues involved in the catalysis, substrate binding and dimerisation are 100% conserved. Comparison of the polyprotein PP1AB sequences showed 86% identity. The 3C-like cleavage sites on the coronaviral polyproteins are highly conserved. Based on the near-identical substrate specificities and high sequence identities, we are of the opinion that some of the previous progress of specific inhibitors development for the SARS-CoV enzyme can be conferred on its SARS-CoV-2 counterpart. With the 3CL pro molecular model, we performed virtual screening for purchasable drugs and proposed 16 candidates for consideration. Among these, the antivirals ledipasvir or velpatasvir are particularly attractive as therapeutics to combat the new coronavirus with minimal side effects, commonly fatigue and headache. The drugs Epclusa (velpatasvir/sofosbuvir) and Harvoni (ledipasvir/sofosbuvir) could be very effective owing to their dual inhibitory actions on two viral enzymes.
Url:
DOI: 10.12688/f1000research.22457.1
PubMed: 32194944
PubMed Central: 7062204
Affiliations:
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<sup>pro</sup>) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates</title><author><name sortKey="Chen, Yu Wai" sort="Chen, Yu Wai" uniqKey="Chen Y" first="Yu Wai" last="Chen">Yu Wai Chen</name><affiliation wicri:level="1"><nlm:aff id="a1">Department of Applied Biology & Chemical Technology, Hong Kong Polytechnic University, Hunghom, Hong Kong</nlm:aff><country xml:lang="fr">Hong Kong</country><wicri:regionArea>Department of Applied Biology & Chemical Technology, Hong Kong Polytechnic University, Hunghom</wicri:regionArea><wicri:noRegion>Hunghom</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="a2">State Key Laboratory of Chemical Biology and Drug Discovery, Hunghom, Hong Kong</nlm:aff><country xml:lang="fr">Hong Kong</country><wicri:regionArea>State Key Laboratory of Chemical Biology and Drug Discovery, Hunghom</wicri:regionArea><wicri:noRegion>Hunghom</wicri:noRegion></affiliation></author><author><name sortKey="Yiu, Chin Pang Bennu" sort="Yiu, Chin Pang Bennu" uniqKey="Yiu C" first="Chin-Pang Bennu" last="Yiu">Chin-Pang Bennu Yiu</name><affiliation wicri:level="1"><nlm:aff id="a3">Independent Researcher, La Costa, Ma On Shan, Hong Kong</nlm:aff><country xml:lang="fr">Hong Kong</country><wicri:regionArea>Independent Researcher, La Costa, Ma On Shan</wicri:regionArea><wicri:noRegion>Ma On Shan</wicri:noRegion></affiliation></author><author><name sortKey="Wong, Kwok Yin" sort="Wong, Kwok Yin" uniqKey="Wong K" first="Kwok-Yin" last="Wong">Kwok-Yin Wong</name><affiliation wicri:level="1"><nlm:aff id="a1">Department of Applied Biology & Chemical Technology, Hong Kong Polytechnic University, Hunghom, Hong Kong</nlm:aff><country xml:lang="fr">Hong Kong</country><wicri:regionArea>Department of Applied Biology & Chemical Technology, Hong Kong Polytechnic University, Hunghom</wicri:regionArea><wicri:noRegion>Hunghom</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="a2">State Key Laboratory of Chemical Biology and Drug Discovery, Hunghom, Hong Kong</nlm:aff><country xml:lang="fr">Hong Kong</country><wicri:regionArea>State Key Laboratory of Chemical Biology and Drug Discovery, Hunghom</wicri:regionArea><wicri:noRegion>Hunghom</wicri:noRegion></affiliation></author></analytic><series><title level="j">F1000Research</title><idno type="eISSN">2046-1402</idno><imprint><date when="2020">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Benzimidazoles</term><term>Betacoronavirus</term><term>Carbamates</term><term>Cysteine Endopeptidases</term><term>Drug Repositioning</term><term>Fluorenes</term><term>Heterocyclic Compounds, 4 or More Rings</term><term>Viral Nonstructural Proteins</term><term>Viral Proteins</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Benzimidazoles</term><term>Carbamates</term><term>Composés hétérocycliques avec 4 noyaux ou plus</term><term>Cysteine endopeptidases</term><term>Fluorènes</term><term>Protéines virales</term><term>Protéines virales non structurales</term><term>Repositionnement des médicaments</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Benzimidazoles</term><term>Carbamates</term><term>Cysteine Endopeptidases</term><term>Fluorenes</term><term>Heterocyclic Compounds, 4 or More Rings</term><term>Viral Nonstructural Proteins</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Betacoronavirus</term><term>Drug Repositioning</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Benzimidazoles</term><term>Carbamates</term><term>Composés hétérocycliques avec 4 noyaux ou plus</term><term>Cysteine endopeptidases</term><term>Fluorènes</term><term>Protéines virales</term><term>Protéines virales non structurales</term><term>Repositionnement des médicaments</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>We prepared the three-dimensional model of the SARS-CoV-2 (aka 2019-nCoV) 3C-like protease (3CL
<sup>pro</sup>) using the crystal structure of the highly similar (96% identity) ortholog from the SARS-CoV. All residues involved in the catalysis, substrate binding and dimerisation are 100% conserved. Comparison of the polyprotein PP1AB sequences showed 86% identity. The 3C-like cleavage sites on the coronaviral polyproteins are highly conserved. Based on the near-identical substrate specificities and high sequence identities, we are of the opinion that some of the previous progress of specific inhibitors development for the SARS-CoV enzyme can be conferred on its SARS-CoV-2 counterpart. With the 3CL
<sup>pro</sup> molecular model, we performed virtual screening for purchasable drugs and proposed 16 candidates for consideration. Among these, the antivirals ledipasvir or velpatasvir are particularly attractive as therapeutics to combat the new coronavirus with minimal side effects, commonly fatigue and headache. The drugs Epclusa (velpatasvir/sofosbuvir) and Harvoni (ledipasvir/sofosbuvir) could be very effective owing to their dual inhibitory actions on two viral enzymes.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Chan, Jf" uniqKey="Chan J">JF Chan</name></author><author><name sortKey="Yuan, S" uniqKey="Yuan S">S Yuan</name></author><author><name sortKey="Kok, Kh" uniqKey="Kok K">KH Kok</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Muramatsu, T" uniqKey="Muramatsu T">T Muramatsu</name></author><author><name sortKey="Takemoto, C" uniqKey="Takemoto C">C Takemoto</name></author><author><name sortKey="Kim, Yt" uniqKey="Kim Y">YT Kim</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Krivov, Gg" uniqKey="Krivov G">GG Krivov</name></author><author><name sortKey="Shapovalov, Mv" uniqKey="Shapovalov M">MV Shapovalov</name></author><author><name sortKey="Dunbrack, Rl" 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Li</name></author><author><name sortKey="Zhang, J" uniqKey="Zhang J">J Zhang</name></author><author><name sortKey="Wang, N" uniqKey="Wang N">N Wang</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Hong Kong</li></country></list><tree><country name="Hong Kong"><noRegion><name sortKey="Chen, Yu Wai" sort="Chen, Yu Wai" uniqKey="Chen Y" first="Yu Wai" last="Chen">Yu Wai Chen</name></noRegion><name sortKey="Chen, Yu Wai" sort="Chen, Yu Wai" uniqKey="Chen Y" first="Yu Wai" last="Chen">Yu Wai Chen</name><name sortKey="Wong, Kwok Yin" sort="Wong, Kwok Yin" uniqKey="Wong K" first="Kwok-Yin" last="Wong">Kwok-Yin Wong</name><name sortKey="Wong, Kwok Yin" sort="Wong, Kwok Yin" uniqKey="Wong K" first="Kwok-Yin" last="Wong">Kwok-Yin Wong</name><name sortKey="Yiu, Chin Pang Bennu" sort="Yiu, Chin Pang Bennu" uniqKey="Yiu C" first="Chin-Pang Bennu" last="Yiu">Chin-Pang Bennu Yiu</name></country></tree></affiliations></record>Pour manipuler ce 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