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 : 000530 ( Pmc/Corpus ); précédent : 000529; suivant : 000531Prediction 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 ; Chin-Pang Bennu Yiu ; Kwok-Yin WongSource :
- F1000Research [ 2046-1402 ] ; 2020.
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
Links to Exploration step
PMC:7062204Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL
<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><nlm:aff id="a1">Department of Applied Biology & Chemical Technology, Hong Kong Polytechnic University, Hunghom, Hong Kong</nlm:aff></affiliation><affiliation><nlm:aff id="a2">State Key Laboratory of Chemical Biology and Drug Discovery, Hunghom, Hong Kong</nlm:aff></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><nlm:aff id="a3">Independent Researcher, La Costa, Ma On Shan, Hong Kong</nlm:aff></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><nlm:aff id="a1">Department of Applied Biology & Chemical Technology, Hong Kong Polytechnic University, Hunghom, Hong Kong</nlm:aff></affiliation><affiliation><nlm:aff id="a2">State Key Laboratory of Chemical Biology and Drug Discovery, Hunghom, Hong Kong</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">32194944</idno><idno type="pmc">7062204</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7062204</idno><idno type="RBID">PMC:7062204</idno><idno type="doi">10.12688/f1000research.22457.1</idno><date when="2020">2020</date><idno type="wicri:Area/Pmc/Corpus">000530</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000530</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL
<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><nlm:aff id="a1">Department of Applied Biology & Chemical Technology, Hong Kong Polytechnic University, Hunghom, Hong Kong</nlm:aff></affiliation><affiliation><nlm:aff id="a2">State Key Laboratory of Chemical Biology and Drug Discovery, Hunghom, Hong Kong</nlm:aff></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><nlm:aff id="a3">Independent Researcher, La Costa, Ma On Shan, Hong Kong</nlm:aff></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><nlm:aff id="a1">Department of Applied Biology & Chemical Technology, Hong Kong Polytechnic University, Hunghom, Hong Kong</nlm:aff></affiliation><affiliation><nlm:aff id="a2">State Key Laboratory of Chemical Biology and Drug Discovery, Hunghom, Hong Kong</nlm:aff></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></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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<front><journal-meta><journal-id journal-id-type="nlm-ta">F1000Res</journal-id><journal-id journal-id-type="iso-abbrev">F1000Res</journal-id><journal-id journal-id-type="pmc">F1000Research</journal-id><journal-title-group><journal-title>F1000Research</journal-title></journal-title-group><issn pub-type="epub">2046-1402</issn><publisher><publisher-name>F1000 Research Limited</publisher-name><publisher-loc>London, UK</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">32194944</article-id><article-id pub-id-type="pmc">7062204</article-id><article-id pub-id-type="doi">10.12688/f1000research.22457.1</article-id><article-categories><subj-group subj-group-type="heading"><subject>Brief Report</subject></subj-group><subj-group><subject>Articles</subject></subj-group></article-categories><title-group><article-title>Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL
<sup>pro</sup>) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates</article-title><fn-group content-type="pub-status"><fn><p>[version 1; peer review: 3 approved]</p></fn></fn-group></title-group><contrib-group><contrib contrib-type="author"><name><surname>Chen</surname><given-names>Yu Wai</given-names></name><role content-type="http://credit.casrai.org/">Conceptualization</role><role content-type="http://credit.casrai.org/">Data Curation</role><role content-type="http://credit.casrai.org/">Formal Analysis</role><role content-type="http://credit.casrai.org/">Investigation</role><role content-type="http://credit.casrai.org/">Methodology</role><role content-type="http://credit.casrai.org/">Project Administration</role><role content-type="http://credit.casrai.org/">Resources</role><role content-type="http://credit.casrai.org/">Supervision</role><role content-type="http://credit.casrai.org/">Validation</role><role content-type="http://credit.casrai.org/">Visualization</role><role content-type="http://credit.casrai.org/">Writing – Original Draft Preparation</role><role content-type="http://credit.casrai.org/">Writing – Review & Editing</role><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0001-7833-7533</contrib-id><xref ref-type="corresp" rid="c1">a</xref><xref ref-type="aff" rid="a1">1</xref><xref ref-type="aff" rid="a2">2</xref></contrib><contrib contrib-type="author"><name><surname>Yiu</surname><given-names>Chin-Pang Bennu</given-names></name><role content-type="http://credit.casrai.org/">Conceptualization</role><role content-type="http://credit.casrai.org/">Formal Analysis</role><role content-type="http://credit.casrai.org/">Investigation</role><role content-type="http://credit.casrai.org/">Methodology</role><role content-type="http://credit.casrai.org/">Project Administration</role><role content-type="http://credit.casrai.org/">Resources</role><role content-type="http://credit.casrai.org/">Validation</role><role content-type="http://credit.casrai.org/">Visualization</role><role content-type="http://credit.casrai.org/">Writing – Original Draft Preparation</role><role content-type="http://credit.casrai.org/">Writing – Review & Editing</role><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0003-3965-3992</contrib-id><xref ref-type="aff" rid="a3">3</xref></contrib><contrib contrib-type="author"><name><surname>Wong</surname><given-names>Kwok-Yin</given-names></name><role content-type="http://credit.casrai.org/">Funding Acquisition</role><role content-type="http://credit.casrai.org/">Project Administration</role><role content-type="http://credit.casrai.org/">Resources</role><role content-type="http://credit.casrai.org/">Supervision</role><role content-type="http://credit.casrai.org/">Visualization</role><role content-type="http://credit.casrai.org/">Writing – Review & Editing</role><xref ref-type="corresp" rid="c2">b</xref><xref ref-type="aff" rid="a1">1</xref><xref ref-type="aff" rid="a2">2</xref></contrib><aff id="a1"><label>1</label>Department of Applied Biology & Chemical Technology, Hong Kong Polytechnic University, Hunghom, Hong Kong</aff><aff id="a2"><label>2</label>State Key Laboratory of Chemical Biology and Drug Discovery, Hunghom, Hong Kong</aff><aff id="a3"><label>3</label>Independent Researcher, La Costa, Ma On Shan, Hong Kong</aff></contrib-group><author-notes><corresp id="c1"><label>a</label><email xlink:href="mailto:yu-wai.chen@polyu.edu.hk">yu-wai.chen@polyu.edu.hk</email></corresp><corresp id="c2"><label>b</label><email xlink:href="mailto:kwok-yin.wong@polyu.edu.hk">kwok-yin.wong@polyu.edu.hk</email></corresp><fn fn-type="COI-statement"><p>No competing interests were disclosed.</p></fn></author-notes><pub-date pub-type="epub"><day>21</day><month>2</month><year>2020</year></pub-date><pub-date pub-type="collection"><year>2020</year></pub-date><volume>9</volume><elocation-id>129</elocation-id><history><date date-type="accepted"><day>19</day><month>2</month><year>2020</year></date></history><permissions><copyright-statement>Copyright: © 2020 Chen YW et al.</copyright-statement><copyright-year>2020</copyright-year><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><self-uri content-type="pdf" xlink:href="f1000research-9-24784.pdf"></self-uri><abstract><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></abstract><kwd-group kwd-group-type="author"><kwd>COVID-19</kwd><kwd>SARS</kwd><kwd>2019-nCoV</kwd><kwd>3C-like protease</kwd><kwd>drug repurpose</kwd><kwd>antiviral</kwd><kwd>coronavirus</kwd><kwd>virtual screening</kwd><kwd>molecular modelling</kwd><kwd>ledipasvir</kwd><kwd>velpatasvir</kwd><kwd>Hepatitis C virus</kwd><kwd>HCV</kwd></kwd-group><funding-group><award-group id="fund-1" xlink:href="http://dx.doi.org/10.13039/501100004377"><funding-source>Hong Kong Polytechnic University</funding-source><award-id>1-ZVH9</award-id></award-group><award-group id="fund-2" xlink:href="http://dx.doi.org/10.13039/501100007156"><funding-source>Innovation and Technology Commission - Hong Kong</funding-source></award-group><funding-statement>We acknowledge support from the Innovation and Technology Commission of Hong Kong, the Hong Kong Polytechnic University and the Life Science Area of Strategic Fund 1-ZVH9.</funding-statement><funding-statement><italic>The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</italic></funding-statement></funding-group></article-meta></front><body><sec sec-type="intro"><title>Introduction</title><p>On 7 January 2020, a new coronavirus, 2019-nCoV (now officially named SARS-CoV-2) was implicated in an alarming outbreak of a pneumonia-like illness COVID-19, originating from Wuhan City, Hubei, China. Human-to-human transmission was first confirmed in Guangdong, China
<sup><xref rid="ref-1" ref-type="bibr">1</xref></sup>. The World Health Organisation has declared this a global public health emergency — on 15 February 2020, there are more than 65,000 confirmed cases reported, and the death toll is over 1500. In the height of the crisis, this virus is spreading at a rate and scale far worse than previous coronaviral epidemics.</p><p> It was immediately evident from its genome that the coronavirus is evolutionarily related (80% identity) to the beta-coronavirus implicated in the severe acute respiratory syndrome (SARS), which originated in bats and was causative of a global outbreak in 2003. The momentum of research on developing antiviral agents against the SARS-CoV carried on after the epidemic subsided. Despite this, no SARS treatment has yet come to fruition; however, knowledge acquired from the extensive research and development efforts may be of use to inform the current therapeutic options. </p><p> The viral genome encodes more than 20 proteins, among which are two proteases (PL
<sup>pro</sup> and 3CL
<sup>pro</sup>) that are vital to virus replication; they cleave the two translated polyproteins (PP1A and PP1AB) into individual functional components. The 3-chymotrypsin-like protease (3CL
<sup>pro</sup>, aka main protease, M
<sup>pro</sup>) is considered to be a promising drug target. Tremendous effort has been spent on studying this protein in order to identify therapeutics against the SARS-CoV in particular and other pathogenic coronaviruses (e.g. MERS-CoV, the Middle East respiratory syndrome coronavirus) in general because they share similar active sites and enzymatic mechanisms. The purpose of this study is to build a molecular model of the 3CL
<sup>pro</sup> of the SARS-CoV-2 and to carry out virtual screening to identify readily usable therapeutics. It was not our intention, however, to comment on other structure-based drug design research as these will not be timely for the current epidemic.</p></sec><sec sec-type="methods"><title>Methods</title><sec><title>Analysis of protein sequences</title><p>The translated polyprotein (PP1AB) sequence was obtained from the annotation of the GenBank entry of the SARS-CoV-2 genome (accession number
<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN908947">MN908947</ext-link>). By comparing this sequence with the SARS-CoV PP1AB sequence (accession number
<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/protein/ABI96956.1">ABI96956</ext-link>), the protease cleavage sites and all mature protein sequences were obtained. Sequence comparison and alignment were performed with
<ext-link ext-link-type="uri" xlink:href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins">BLASTp</ext-link>.</p></sec><sec><title>Preparation of structural model</title><p>The high-resolution apo-enzyme structure of SARS-CoV 3CL
<sup>pro</sup> (PDBID:
<ext-link ext-link-type="uri" xlink:href="https://www.rcsb.org/structure/2duc">2DUC</ext-link>)
<sup><xref rid="ref-2" ref-type="bibr">2</xref></sup> was employed as the template. The variant residues were “mutated”
<italic>in silico</italic> by
<ext-link ext-link-type="uri" xlink:href="http://dunbrack.fccc.edu/SCWRL3.php/">SCWRL4</ext-link><sup><xref rid="ref-3" ref-type="bibr">3</xref></sup>, followed by manual adjustment to ensure that the best side-chain rotamer was employed (
<xref rid="T2" ref-type="table">Table 2</xref>). The rebuilt model was subjected to steepest descent energy minimisation by
<ext-link ext-link-type="uri" xlink:href="http://www.gromacs.org/">Gromacs</ext-link> 2018.4 using the Gromos 54A7 forcefield, with a restraint force constant of 1000 kJ mol
<sup>-1</sup> nm
<sup>-2</sup> applied on all backbone atoms and all atoms of the vital residues (
<xref rid="T1" ref-type="table">Table 1</xref>). Accessible surface area of residues were calculated with
<italic>areaimol</italic> of the
<ext-link ext-link-type="uri" xlink:href="http://www.ccp4.ac.uk/">CCP4 suite</ext-link> v7.0.</p><table-wrap id="T1" orientation="portrait" position="anchor"><label>Table 1. </label><caption><title>SARS-CoV 3CL
<sup>pro</sup> important residues and SARS-CoV-2 variant residues.</title></caption><table frame="hsides" rules="groups" content-type="article-table"><thead><tr><th align="left" valign="top" rowspan="1" colspan="1">Function</th><th align="left" valign="top" rowspan="1" colspan="1">Residue Number</th><th align="left" valign="top" rowspan="1" colspan="1">Reference</th></tr></thead><tbody><tr><td align="left" valign="top" rowspan="1" colspan="1">Catalytic</td><td align="left" valign="top" rowspan="1" colspan="1">41, 145</td><td align="left" valign="top" rowspan="1" colspan="1"><sup><xref rid="ref-8" ref-type="bibr">8</xref></sup></td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">Substrate binding</td><td align="left" valign="top" rowspan="1" colspan="1">41, 49, 143–144, 163–167, 187–192</td><td align="left" valign="top" rowspan="1" colspan="1"><xref rid="ref-2" ref-type="bibr">2</xref>,
<xref rid="ref-9" ref-type="bibr">9</xref></td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">Dimerisation</td><td align="left" valign="top" rowspan="1" colspan="1">10, 11, 14, 28, 139, 140, 147, 298</td><td align="left" valign="top" rowspan="1" colspan="1"><xref rid="ref-10" ref-type="bibr">10</xref>–
<xref rid="ref-13" ref-type="bibr">13 </xref></td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">SARS-CoV-2 variants</td><td align="left" valign="top" rowspan="1" colspan="1">35, 46, 65, 86, 88, 94, 134, 180, 202, 267, 285, 286</td><td align="left" valign="top" rowspan="1" colspan="1">This work</td></tr></tbody></table></table-wrap><table-wrap id="T2" orientation="portrait" position="anchor"><label>Table 2. </label><caption><title><italic>In silico</italic> mutagenesis of the SARS-CoV-2 3CL
<sup>pro</sup>.</title><p>The 12 variant residues with reference to the SARS-CoV enzyme are shown with the respective treatment of rotamer. “A” and “B” refers to the individual chains of the dimeric model. Both chains are in the crystal asymmetric unit and are not identical. The rotamer symbol (bracketed) is defined according to the conventions of Richardson
<sup><xref rid="ref-15" ref-type="bibr">15</xref></sup>, followed by its respective rank of popularity. ASA: accessible surface area (average of A and B chains) of the residue in the SARS-CoV 3CL
<sup>pro</sup> structure, in Å
<sup>2</sup> and in % relative to the ASA of a residue X in the Gly-X-Gly conformation.</p></caption><table frame="hsides" rules="groups" content-type="article-table"><thead><tr><th align="left" valign="top" rowspan="1" colspan="1">Residue</th><th align="left" valign="top" rowspan="1" colspan="1">Rotamer</th><th align="left" valign="top" rowspan="1" colspan="1">ASA, Å
<sup>2</sup> (%)</th><th align="left" valign="top" rowspan="1" colspan="1">Remarks on replacement</th></tr></thead><tbody><tr><td align="left" valign="top" rowspan="1" colspan="1">T35V </td><td align="left" valign="top" rowspan="1" colspan="1">AB: (t-), top</td><td align="right" valign="top" rowspan="1" colspan="1">19 (14%)</td><td align="left" valign="top" rowspan="1" colspan="1">conservative</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">A46S</td><td align="left" valign="top" rowspan="1" colspan="1">A: (t-), 3rd; B: (p-), top</td><td align="right" valign="top" rowspan="1" colspan="1">73 (63%)</td><td align="left" valign="top" rowspan="1" colspan="1">A chain disordered, rotamer chosen to minimise steric clash</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">S65N </td><td align="left" valign="top" rowspan="1" colspan="1">AB: (m-20), top</td><td align="right" valign="top" rowspan="1" colspan="1">38 (28%)</td><td rowspan="1" colspan="1"></td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">L86V</td><td align="left" valign="top" rowspan="1" colspan="1">A: (m), 2nd; B: (t), top </td><td align="right" valign="top" rowspan="1" colspan="1">0 (0%)</td><td align="left" valign="top" rowspan="1" colspan="1">A chain rotamer to avoid clash</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">R88K</td><td align="left" valign="top" rowspan="1" colspan="1">A: (mtpt), 9th; B: (mtpp), 19th</td><td align="right" valign="top" rowspan="1" colspan="1">81 (33%)</td><td align="left" valign="top" rowspan="1" colspan="1">AB: real-space refined with good fit to arginine densities</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">S94A</td><td align="left" valign="top" rowspan="1" colspan="1">not applicable</td><td align="right" valign="top" rowspan="1" colspan="1">64 (51%)</td><td rowspan="1" colspan="1"></td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">H134F</td><td align="left" valign="top" rowspan="1" colspan="1">AB: (m-85), top</td><td align="right" valign="top" rowspan="1" colspan="1">57 (29%)</td><td align="left" valign="top" rowspan="1" colspan="1">occupy similar but larger space</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">K180N </td><td align="left" valign="top" rowspan="1" colspan="1">AB: (m-20), top</td><td align="right" valign="top" rowspan="1" colspan="1">102 (50%)</td><td rowspan="1" colspan="1"></td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">L202V </td><td align="left" valign="top" rowspan="1" colspan="1">AB: (p), 3rd</td><td align="right" valign="top" rowspan="1" colspan="1">22 (12%)</td><td align="left" valign="top" rowspan="1" colspan="1">avoid steric clash</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">A267S </td><td align="left" valign="top" rowspan="1" colspan="1">AB: (m), 2nd</td><td align="right" valign="top" rowspan="1" colspan="1">0 (0%)</td><td align="left" valign="top" rowspan="1" colspan="1">avoid steric clash</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">T285A </td><td align="left" valign="top" rowspan="1" colspan="1">not applicable</td><td align="right" valign="top" rowspan="1" colspan="1">68 (44%)</td><td align="left" valign="top" rowspan="1" colspan="1">at dimeric interface</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">I286L</td><td align="left" valign="top" rowspan="1" colspan="1">(mt), top </td><td align="right" valign="top" rowspan="1" colspan="1">75 (46%)</td><td align="left" valign="top" rowspan="1" colspan="1">at dimeric interface</td></tr></tbody></table></table-wrap></sec><sec><title>Virtual screening</title><p><ext-link ext-link-type="uri" xlink:href="https://bioserv.rpbs.univ-paris-diderot.fr/services/MTiOpenScreen/">MTiOpenScreen</ext-link> web service
<sup><xref rid="ref-4" ref-type="bibr">4</xref></sup> was used for screening against its library of 7173 purchasable drugs (Drugs-lib), with the binding site grid specified by the active-site residues. The active sites on chain A and chain B were screened independently with
<ext-link ext-link-type="uri" xlink:href="http://vina.scripps.edu/">AutoDock Vina</ext-link><sup><xref rid="ref-5" ref-type="bibr">5</xref></sup>. When the crystal structure was released, it was stripped of its inhibitor and subjected to a screening. A list of 4,500 target:ligand docking combinations ranked by binding energies was produced for each screen. The top 10 or 11 (ranked using a binding energy cut-off) hits for chains A and B were examined visually in
<ext-link ext-link-type="uri" xlink:href="https://sourceforge.net/projects/pymol/files/pymol/1.7/">PyMOL (version 1.7.X)</ext-link><sup><xref rid="ref-6" ref-type="bibr">6</xref></sup>.</p><p>An earlier version of this article can be found on ChemRxiv (DOI:
<ext-link ext-link-type="uri" xlink:href="https://doi.org/10.26434/chemrxiv.11831103.v2">10.26434/chemrxiv.11831103.v2</ext-link>).</p></sec></sec><sec sec-type="results"><title>Results</title><sec><title>High sequence homology with SARS-CoV</title><p>The first available genome was GenBank MN908947, now NCBI Reference Sequence NC_045512. From it, the PP1AB sequence of SARS-CoV-2 was extracted and aligned with that of SARS-CoV. The overall amino-acid sequence identity is very high (86%). The conservation is noticeable at the polyprotein cleavage sites. All 11 3CL
<sup>pro</sup> sites
<sup><xref rid="ref-2" ref-type="bibr">2</xref></sup> are highly conserved or identical (
<italic>Extended data</italic><sup><xref rid="ref-7" ref-type="bibr">7</xref></sup>, Table S1), inferring that their respective proteases have very similar specificities. The 3CL
<sup>pro</sup> sequence of SARS-CoV-2 has only 12 out of 306 residues different from that of SARS-CoV (identity = 96%). </p></sec><sec><title>Conserved sequence identity among SARS-CoV-2</title><p>We compared the polyprotein PP1AB and the 3CL
<sup>pro</sup> sequences among all 11 SARS-CoV-2 genomes (GenBank
<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN908947">MN908947</ext-link>,
<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN938384">MN938384</ext-link>,
<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN975262">MN975262</ext-link>,
<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN985325">MN985325</ext-link>,
<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN988668">MN988668</ext-link>,
<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN988669">MN988669</ext-link>,
<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN988713">MN988713</ext-link>,
<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN994467">MN994467</ext-link>,
<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN994468">MN994468</ext-link>,
<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN996527">MN996527</ext-link> and
<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN996528">MN996528</ext-link>) that were available on 1 February 2020. With reference to MN908947 (NC_045512), among the 7096 residues, there is only one variable residue in each of MN975262 (in NSP-4), MN994467 (in NSP-2), MN994468 (in NSP-13), MN996527 (in NSP-16); and two in MN988713 (in NSP-1 and NSP-3). The remaining five have no difference. To summarise, all SARS-CoV-2 3CL
<sup>pro</sup> sequences and all their cleavage junctions on their polyproteins are 100% conserved.</p></sec><sec><title>3D model of the SARS-CoV-2 3CL
<sup>pro</sup></title><p>The amino acids that are known to be important for the enzyme’s functions are listed in
<xref rid="T1" ref-type="table">Table 1</xref>. Not unexpectedly, none of the 12 variant positions are involved in major roles. Therefore, we are confident to prepare a structural model of the SARS-CoV-2 3CL
<sup>pro</sup> by molecular modelling (
<italic>Extended data</italic><sup><xref rid="ref-7" ref-type="bibr">7</xref></sup>, Figure S1), which will be immediately useful for
<italic>in silico</italic> development of targeted treatment. After we submitted the first draft of this study, the crystal structure of SARS-CoV-2 3CL
<sup>pro</sup> was solved and released (PDB ID
<ext-link ext-link-type="uri" xlink:href="https://www.rcsb.org/structure/6LU7">6LU7</ext-link>), which confirms that the predicted model is good within experimental errors (
<italic>Extended data</italic><sup><xref rid="ref-7" ref-type="bibr">7</xref></sup>, Figure S2).</p></sec><sec><title>Virtual screening for readily available drugs</title><p>When examined in molecular graphics
<sup><xref rid="ref-6" ref-type="bibr">6</xref></sup>, all solutions were found to fit into their respective active sites convincingly. The binding energies of chain A complexes were generally higher than those of chain B by approximately 1.4 kcal mol
<sup>-1</sup> (
<xref rid="T3" ref-type="table">Table 3</xref>). This presumably demonstrates the intrinsic conformational variability between the A- and B-chain active sites in the crystal structure (the average root-mean-square deviation (rmsd) in Cα atomic positions of active-site residues is 0.83 Å). In each screen, the differences in binding energies are small, suggesting that the ranking is not discriminatory, and all top scorers should be examined. We combined the two screens and found 16 candidates which give promising binding models (etoposide and its phosphate counted as one) (
<xref rid="T3" ref-type="table">Table 3</xref>).</p><table-wrap id="T3" orientation="portrait" position="anchor"><label>Table 3. </label><caption><title>The results of virtual screening of drugs on the active sites of SARS-CoV-2 3CL
<sup>pro</sup> model.</title><p>The left and right columns are the results of A and B chains, respectively. The top scorers are listed first, then the equivalent top scorers of the other chain listed at the lower half. B.E.: AutoDock Vina binding energy in kcal mol
<sup>-1</sup>. The number of hits of a drug is the times it appears among all results within a screen regardless of rank, only the binding energy of the top-ranking hit was shown. Etoposide and its phosphate are listed separately in the screens. Approved and pre-approved drugs are shown in green and orange, respectively. Except dihydroergocristine and ditercalinium, all approved drugs have undergone post-market surveillance, i.e. Phase 4.</p></caption><table frame="hsides" rules="groups" content-type="article-table"><thead><tr><th align="left" valign="top" rowspan="1" colspan="1">A Chain</th><th rowspan="1" colspan="1"></th><th rowspan="1" colspan="1"></th><th align="left" valign="top" rowspan="1" colspan="1">B Chain</th><th rowspan="1" colspan="1"></th><th rowspan="1" colspan="1"></th></tr><tr><th align="left" valign="top" rowspan="1" colspan="1">A Top scorers</th><th align="right" valign="top" rowspan="1" colspan="1">B.E.</th><th align="right" valign="top" rowspan="1" colspan="1">Hits</th><th align="left" valign="top" rowspan="1" colspan="1">B Top scorers</th><th align="right" valign="top" rowspan="1" colspan="1">B.E.</th><th align="right" valign="top" rowspan="1" colspan="1">Hits</th></tr></thead><tbody><tr><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#F37421" style-type="color">diosmin</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-10.1</td><td align="right" valign="top" rowspan="1" colspan="1">1</td><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#00B050" style-type="color">etoposide</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-8.7</td><td align="right" valign="top" rowspan="1" colspan="1">32</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#00B050" style-type="color">hesperidin</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-10.1</td><td align="right" valign="top" rowspan="1" colspan="1">38</td><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#F37421" style-type="color">R428</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-8.6</td><td align="right" valign="top" rowspan="1" colspan="1">2</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#F37421" style-type="color">MK-3207</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-10.1</td><td align="right" valign="top" rowspan="1" colspan="1">4</td><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#F37421" style-type="color">MK-3207</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-8.6</td><td align="right" valign="top" rowspan="1" colspan="1">4</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#00B050" style-type="color">venetoclax</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-10.0</td><td align="right" valign="top" rowspan="1" colspan="1">1</td><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#00B050" style-type="color">teniposide</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-8.5</td><td align="right" valign="top" rowspan="1" colspan="1">34</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#00B050" style-type="color">dihydroergocristine</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-9.8</td><td align="right" valign="top" rowspan="1" colspan="1">6</td><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#F37421" style-type="color">UK-432097</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-8.5</td><td align="right" valign="top" rowspan="1" colspan="1">2</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#00B050" style-type="color">bolazine</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-9.8</td><td align="right" valign="top" rowspan="1" colspan="1">1</td><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#00B050" style-type="color">eluxadoline</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-8.4</td><td align="right" valign="top" rowspan="1" colspan="1">1</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#F37421" style-type="color">R428</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-9.8</td><td align="right" valign="top" rowspan="1" colspan="1">2</td><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#00B050" style-type="color">venetoclax</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-8.4</td><td align="right" valign="top" rowspan="1" colspan="1">1</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#00B050" style-type="color">ditercalinium</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-9.8</td><td align="right" valign="top" rowspan="1" colspan="1">1</td><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#00B050" style-type="color">ledipasvir</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-8.4</td><td align="right" valign="top" rowspan="1" colspan="1">3</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#00B050" style-type="color">etoposide-phosphate</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-9.8</td><td align="right" valign="top" rowspan="1" colspan="1">21</td><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#00B050" style-type="color">irinotecan</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-8.4</td><td align="right" valign="top" rowspan="1" colspan="1">1</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#00B050" style-type="color">lumacaftor</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-8.4</td><td align="right" valign="top" rowspan="1" colspan="1">1</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#00B050" style-type="color">velpatasvir</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-8.4</td><td align="right" valign="top" rowspan="1" colspan="1">5</td></tr><tr><th align="left" valign="top" rowspan="1" colspan="1">(B Top scorers)</th><th rowspan="1" colspan="1"></th><th rowspan="1" colspan="1"></th><th align="left" valign="top" rowspan="1" colspan="1">(A Top scorers)</th><th rowspan="1" colspan="1"></th><th rowspan="1" colspan="1"></th></tr><tr><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#00B050" style-type="color">teniposide</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-9.7 </td><td align="right" valign="top" rowspan="1" colspan="1">34</td><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#00B050" style-type="color">hesperidin</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-8.3</td><td align="right" valign="top" rowspan="1" colspan="1">38</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#00B050" style-type="color">etoposide</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-9.7</td><td align="right" valign="top" rowspan="1" colspan="1">32</td><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#00B050" style-type="color">etoposide-phosphate</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-8.3</td><td align="right" valign="top" rowspan="1" colspan="1">21</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#F37421" style-type="color">UK-432097</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-9.6</td><td align="right" valign="top" rowspan="1" colspan="1">2</td><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#00B050" style-type="color">bolazine</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-8.3</td><td align="right" valign="top" rowspan="1" colspan="1">1</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#00B050" style-type="color">irinotecan</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-9.5</td><td align="right" valign="top" rowspan="1" colspan="1">1</td><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#00B050" style-type="color">dihydroergocristine</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-8.1</td><td align="right" valign="top" rowspan="1" colspan="1">6</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#00B050" style-type="color">lumacaftor</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-8.9</td><td align="right" valign="top" rowspan="1" colspan="1">1</td><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#F37421" style-type="color">diosmin</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-7.9</td><td align="right" valign="top" rowspan="1" colspan="1">1</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#00B050" style-type="color">velpatasvir</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-8.5</td><td align="right" valign="top" rowspan="1" colspan="1">2</td><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#00B050" style-type="color">ditercalinium</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-7.7</td><td align="right" valign="top" rowspan="1" colspan="1">1</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#00B050" style-type="color">eluxadoline</styled-content></td><td align="right" valign="top" rowspan="1" colspan="1">-8.0</td><td align="right" valign="top" rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1"><styled-content style="#00B050" style-type="color">ledipasvir</styled-content></td><td rowspan="1" colspan="1"></td><td align="right" valign="top" rowspan="1" colspan="1">0</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td></tr></tbody></table></table-wrap></sec><sec><title>Assessment of the candidate drugs</title><p>We checked the actions, targets and side effects of the 16 candidates. Among these, we first noticed velpatasvir (
<xref ref-type="fig" rid="f1">Figure 1A, D</xref>) and ledipasvir, which are inhibitors of the NS5A protein of the hepatitis C virus (HCV). Both are marketed as approved drugs in combination with sofosbuvir, which is a prodrug nucleotide analogue inhibitor of RNA-dependent RNA polymerase (RdRp, or NS5B). Interestingly, sofosbuvir has recently been proposed as an antiviral for the SARS-CoV-2 based on the similarity between the replication mechanisms of the HCV and the coronaviruses
<sup><xref rid="ref-14" ref-type="bibr">14</xref></sup>. Our results further strengthen that these dual-component HCV drugs, Epclusa (velpatasvir/sofosbuvir) and Harvoni (ledipasvir/sofosbuvir), may be attractive candidates to repurpose because they may inhibit two coronaviral enzymes. A drug that can target two viral proteins substantially reduces the ability of the virus to develop resistance. These direct-acting antiviral drugs are also associated with very minimal side effects and are conveniently orally administered (
<xref rid="T4" ref-type="table">Table 4</xref>).</p><fig fig-type="figure" id="f1" orientation="portrait" position="anchor"><label>Figure 1. </label><caption><title>Virtual screening results for the SARS-CoV-2 3CL
<sup>pro</sup> protease.</title><p>Docking of representative drugs into the active sites of A chain (
<bold>A</bold>,
<bold>B</bold>,
<bold>C</bold>) and that of
<bold>B</bold> chain (
<bold>D</bold>,
<bold>E</bold>,
<bold>F</bold>). The catalytic residue surfaces are coloured in yellow. Atom colours of drug: C: cyan; O: red; N: blue; H: white; S: yellow; only polar hydrogens are shown. Prepared with PyMOL.</p></caption><graphic xlink:href="f1000research-9-24784-g0000"></graphic></fig><table-wrap id="T4" orientation="portrait" position="anchor"><label>Table 4. </label><caption><title>Possible side effects and routes of administration of the drugs identified from virtual screening for SARS-CoV-2 3CL
<sup>pro</sup>.</title></caption><table frame="hsides" rules="groups" content-type="article-table"><thead><tr><th align="left" valign="top" rowspan="1" colspan="1">Drug</th><th align="left" valign="top" rowspan="1" colspan="1">Possible side effects (adverse reactions)</th><th align="left" valign="top" rowspan="1" colspan="1">Admin.</th></tr></thead><tbody><tr><td align="left" valign="top" rowspan="1" colspan="1">Diosmin
<sup><xref ref-type="other" rid="TFN1">a</xref>,
<xref ref-type="other" rid="TFN1">b</xref></sup></td><td align="left" valign="top" rowspan="1" colspan="1">Mild gastrointestinal disorders; skin irritations; nausea; heart arrhythmias</td><td align="left" valign="top" rowspan="1" colspan="1">Topical; oral</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">Hesperidin
<sup><xref ref-type="other" rid="TFN1">a</xref>,
<xref ref-type="other" rid="TFN1">d</xref></sup></td><td align="left" valign="top" rowspan="1" colspan="1">Stomach pain and upset; diarrhea; headache</td><td align="left" valign="top" rowspan="1" colspan="1">Oral</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">MK-3207
<sup><xref ref-type="other" rid="TFN1">c</xref></sup></td><td align="left" valign="top" rowspan="1" colspan="1">No information</td><td align="left" valign="top" rowspan="1" colspan="1">Oral</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">Venetoclax
<sup><xref ref-type="other" rid="TFN1">a</xref>,
<xref ref-type="other" rid="TFN1">b</xref></sup></td><td align="left" valign="top" rowspan="1" colspan="1">Neutropenia; nausea; anaemia, diarrhea; upper respiratory tract infection</td><td align="left" valign="top" rowspan="1" colspan="1">Oral</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">Dihydroergocristine
<sup><xref ref-type="other" rid="TFN1">a</xref></sup></td><td align="left" valign="top" rowspan="1" colspan="1">No information</td><td align="left" valign="top" rowspan="1" colspan="1">Oral</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">Bolazine
<sup><xref ref-type="other" rid="TFN1">b</xref></sup></td><td align="left" valign="top" rowspan="1" colspan="1">No information</td><td align="left" valign="top" rowspan="1" colspan="1">Intramuscular</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">R428
<sup><xref ref-type="other" rid="TFN1">b</xref></sup></td><td align="left" valign="top" rowspan="1" colspan="1">No information</td><td align="left" valign="top" rowspan="1" colspan="1">Oral</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">Ditercalinium</td><td align="left" valign="top" rowspan="1" colspan="1">No information</td><td align="left" valign="top" rowspan="1" colspan="1">No info</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">Etoposide
<sup><xref ref-type="other" rid="TFN1">a</xref>,
<xref ref-type="other" rid="TFN1">b</xref></sup></td><td align="left" valign="top" rowspan="1" colspan="1">Alopecia; constipation; diarrhea; nausea; vomiting; secondary malignancies</td><td align="left" valign="top" rowspan="1" colspan="1">Intravenous</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">Teniposide
<sup><xref ref-type="other" rid="TFN1">a</xref>,
<xref ref-type="other" rid="TFN1">b</xref></sup></td><td align="left" valign="top" rowspan="1" colspan="1">Gastrointestinal toxicity; hypersensitivity reactions; reversible alopecia</td><td align="left" valign="top" rowspan="1" colspan="1">Intravenous</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">UK-432097
<sup><xref ref-type="other" rid="TFN1">c</xref></sup></td><td align="left" valign="top" rowspan="1" colspan="1">No information</td><td align="left" valign="top" rowspan="1" colspan="1">Inhaled</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">Irinotecan
<sup><xref ref-type="other" rid="TFN1">a</xref>,
<xref ref-type="other" rid="TFN1">b</xref></sup></td><td align="left" valign="top" rowspan="1" colspan="1">Gastrointestinal complication</td><td align="left" valign="top" rowspan="1" colspan="1">Intravenous</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">Lumacaftor
<sup><xref ref-type="other" rid="TFN1">a</xref></sup></td><td align="left" valign="top" rowspan="1" colspan="1">Dyspnea; nasopharyngitis; nausea; diarrhea; upper respiratory tract infection</td><td align="left" valign="top" rowspan="1" colspan="1">Oral</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">Velpatasvir
<sup><xref ref-type="other" rid="TFN1">a</xref>,
<xref ref-type="other" rid="TFN1">b</xref></sup></td><td align="left" valign="top" rowspan="1" colspan="1">Headache; fatigue; nausea</td><td align="left" valign="top" rowspan="1" colspan="1">Oral</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">Eluxadoline
<sup><xref ref-type="other" rid="TFN1">a</xref>,
<xref ref-type="other" rid="TFN1">b</xref></sup></td><td align="left" valign="top" rowspan="1" colspan="1">Constipation; nausea; fatigue, bronchitis, viral gastroenteritis; pancreatitis</td><td align="left" valign="top" rowspan="1" colspan="1">Oral</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">Ledipasvir
<sup><xref ref-type="other" rid="TFN1">a</xref></sup></td><td align="left" valign="top" rowspan="1" colspan="1">Fatigue; headache</td><td align="left" valign="top" rowspan="1" colspan="1">Oral</td></tr></tbody></table><table-wrap-foot><fn><p id="TFN1">Sources of information:
<sup>a</sup> DrugBank.ca (main),
<sup>b</sup> Wikipedia.org,
<sup>c</sup> ClinicalTrials.gov and
<sup>d </sup>WebMD.com.</p></fn></table-wrap-foot></table-wrap><p> The flavonoid glycosides diosmin (
<xref ref-type="fig" rid="f1">Figure 1B</xref>) and hesperidin (
<xref ref-type="fig" rid="f1">Figure 1E</xref>), obtained from citrus fruits, fit very well into and block the substrate binding site. Yet, these compounds cause mild adverse reactions (
<xref rid="T4" ref-type="table">Table 4</xref>). Hesperidin hits showed up multiple times, suggesting it has many modes of binding (
<xref ref-type="fig" rid="f1">Figure 1A</xref>). Teniposide and etoposide (and its phosphate) are chemically related and turned up in multiple hits with good binding models (
<xref ref-type="fig" rid="f1">Figure 1F</xref>). However, these chemotherapy drugs have a lot of strong side effects and need intravenous administration (
<xref rid="T4" ref-type="table">Table 4</xref>). The approved drug venetoclax (
<xref ref-type="fig" rid="f1">Figure 1C</xref>) and investigational drugs MK-3207 and R428 scored well in both screens. Venetoclax is another chemotherapy drug that is burdened by side effects including upper respiratory tract infection (
<xref rid="T4" ref-type="table">Table 4</xref>). Not much has been disclosed about MK-3207 and R428.</p><p>We subjected the crystal structure to the same virtual screening procedures. A very similar list of candidates showed up consistently (
<italic>Extended data</italic><sup><xref rid="ref-7" ref-type="bibr">7</xref></sup>, Table S2) with high scores although ledipasvir was not found.</p><p>We noticed that most of the compounds on the list have molecular weights (MW) over 500, except lumacaftor (MW=452). The largest one is ledipasvir (MW=889). This is because the size of the peptide substrate and the deeply buried protease active site demand a large molecule that has many rotatable dynamics to fit into it.</p></sec></sec><sec sec-type="discussion"><title>Discussion</title><p>We identified five trials on
<ext-link ext-link-type="uri" xlink:href="https://clinicaltrials.gov/">ClinicalTrials.gov</ext-link> involving antiviral and immunomodulatory drug treatments for SARS (
<xref rid="T5" ref-type="table">Table 5</xref>), all without reported results; i.e., at present, there are no safe and effective drug candidates against SARS-CoV. This is because once the epidemic is over, there are no patients to recruit for clinical trials. Only the study with streptokinase succeeded in completion of phase 3. It is disappointing that little progress in SARS drug development has been made in the past 17 years. After the 2003 outbreak, numerous inhibitors for the 3CL
<sup>pro</sup> enzyme have been proposed
<sup><xref rid="ref-16" ref-type="bibr">16</xref>,
<xref rid="ref-17" ref-type="bibr">17</xref></sup>, yet no new drug candidates have succeeded to enter the clinical phase 1.</p><table-wrap id="T5" orientation="portrait" position="anchor"><label>Table 5. </label><caption><title>Drugs targeting SARS that are registered for the U.S. Food and Drug Administration (USFDA) clinical trials.</title></caption><table frame="hsides" rules="groups" content-type="article-table"><thead><tr><th align="left" valign="top" rowspan="1" colspan="1">Drug</th><th align="left" valign="top" rowspan="1" colspan="1">Condition</th><th align="left" valign="top" rowspan="1" colspan="1">Phase</th><th align="left" valign="top" rowspan="1" colspan="1">Status</th><th align="left" valign="top" rowspan="1" colspan="1">From</th><th align="left" valign="top" rowspan="1" colspan="1">To</th><th align="left" valign="top" rowspan="1" colspan="1">Location</th></tr></thead><tbody><tr><td align="left" valign="top" rowspan="1" colspan="1">Lopinavir / Ritonavir + Ribavirin</td><td align="left" valign="top" rowspan="1" colspan="1">SARS</td><td align="left" valign="top" rowspan="1" colspan="1">Unknown</td><td align="left" valign="top" rowspan="1" colspan="1">Unknown</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td align="left" valign="top" rowspan="1" colspan="1">Hong Kong</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">Alferon LDO</td><td align="left" valign="top" rowspan="1" colspan="1">SARS</td><td align="left" valign="top" rowspan="1" colspan="1">Phase 2</td><td align="left" valign="top" rowspan="1" colspan="1">Completed</td><td align="left" valign="top" rowspan="1" colspan="1">Nov 04</td><td align="left" valign="top" rowspan="1" colspan="1">Apr 06</td><td align="left" valign="top" rowspan="1" colspan="1">Hong Kong</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">Poly-ICLC</td><td align="left" valign="top" rowspan="1" colspan="1">Respiratory viruses
<sup><xref ref-type="other" rid="TFN2">a</xref></sup></td><td align="left" valign="top" rowspan="1" colspan="1">Phase 1</td><td align="left" valign="top" rowspan="1" colspan="1">Completed</td><td align="left" valign="top" rowspan="1" colspan="1">Mar 08</td><td align="left" valign="top" rowspan="1" colspan="1">Dec 09</td><td align="left" valign="top" rowspan="1" colspan="1">USA</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">Streptokinase</td><td align="left" valign="top" rowspan="1" colspan="1">SARS, ARDS</td><td align="left" valign="top" rowspan="1" colspan="1">Phase 3</td><td align="left" valign="top" rowspan="1" colspan="1">Completed</td><td align="left" valign="top" rowspan="1" colspan="1">Feb 16</td><td align="left" valign="top" rowspan="1" colspan="1">Jan 18</td><td rowspan="1" colspan="1"></td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">Glucocorticoid
<break></break>(methylprednisolone) therapy</td><td align="left" valign="top" rowspan="1" colspan="1">Coronavirus
<break></break>infections
<sup><xref ref-type="other" rid="TFN2">b</xref></sup></td><td align="left" valign="top" rowspan="1" colspan="1">Phase 2,
<break></break>Phase 3</td><td align="left" valign="top" rowspan="1" colspan="1">Unknown</td><td align="left" valign="top" rowspan="1" colspan="1">Jan 20</td><td align="left" valign="top" rowspan="1" colspan="1">Dec 20
<break></break>(Est.)</td><td align="left" valign="top" rowspan="1" colspan="1">China</td></tr></tbody></table><table-wrap-foot><fn><p id="TFN2"><sup>a</sup> This covers unknown respiratory viruses.
<sup>b</sup> This includes the COVID-19. Est. = estimated.</p></fn></table-wrap-foot></table-wrap><p>One record which receives a lot of attention amid the current outbreak is the lopinavir/ritonavir combination
<sup><xref rid="ref-18" ref-type="bibr">18</xref></sup>. They are protease inhibitors originally developed against HIV. During the 2003 SARS outbreak, despite lacking a clinical trial, they were tried as an emergency measure and found to offer improved clinical outcome
<sup><xref rid="ref-18" ref-type="bibr">18</xref></sup>. However, some scientists did express scepticism
<sup><xref rid="ref-19" ref-type="bibr">19</xref></sup>. By analogy, these compounds were speculated to act on SARS-CoV 3CL
<sup>pro</sup> specifically, but there is as yet no crystal structure to support that, although docking studies were carried out to propose various binding modes
<sup><xref rid="ref-20" ref-type="bibr">20</xref>–
<xref rid="ref-23" ref-type="bibr">23</xref></sup>. The IC
<sub>50</sub> value of lopinavir is 50 μM (
<italic>K</italic><sub>i</sub> = 14 μM) and that for ritonavir cannot be established
<sup><xref rid="ref-24" ref-type="bibr">24</xref></sup>. Although this is far from a cure, based on our results that the two CoV 3CL
<sup>pro</sup> enzymes are identical as far as protein sequences and substrate specificities are concerned, we are of the opinion that this is still one of the recommended routes for immediate treatment at the time of writing (early February 2020). </p><p>If we look beyond the 3CL
<sup>pro</sup>, an earlier screen produced 27 candidates that could be repurposed against both SARS-CoV and MERS-CoV
<sup><xref rid="ref-25" ref-type="bibr">25</xref></sup>. In addition, the other coronaviral proteins could be targeted for screening. Treatment of the COVID-19 with remdesivir (a repurposed drug in development targeting the RdRp) showing improved clinical outcome has just been reported and clinical trial is now underway
<sup><xref rid="ref-26" ref-type="bibr">26</xref></sup>.</p><p>We consider this work part of the global efforts responding in a timely fashion to fight this deadly communicable disease. We are aware that there are similar modelling, screening and repurposing exercises targeting 3CL
<sup>pro</sup> reported or announced
<sup><xref rid="ref-20" ref-type="bibr">20</xref>,
<xref rid="ref-27" ref-type="bibr">27</xref>–
<xref rid="ref-33" ref-type="bibr">33</xref></sup>. Our methods did not overlap, and we share no common results with these studies.</p></sec><sec sec-type="data-availability"><title>Data availability</title><sec><title>Source data</title><p>The 11 SARS-CoV-2 polyprotein PP1AB and 3CL
<sup>pro</sup> sequences used in this study were obtained from NCBI GenBank, accession numbers
<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN908947">MN908947</ext-link> ,
<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN938384">MN938384</ext-link>,
<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN975262">MN975262</ext-link>,
<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN985325">MN985325</ext-link>,
<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN988668">MN988668</ext-link>,
<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN988669">MN988669</ext-link>,
<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN988713">MN988713</ext-link>,
<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN994467">MN994467</ext-link>,
<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN994468">MN994468</ext-link>,
<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN996527">MN996527</ext-link> and
<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN996528">MN996528</ext-link>, available on 1 February 2020.</p><p>The SARS-CoV PP1AB sequence wsa obtained from NCBI Protein, accession number
<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/protein/ABI96956.1">ABI96956.</ext-link></p><p>The two coronavirus protease structures used were obtained from Protein Data Bank, ID
<ext-link ext-link-type="uri" xlink:href="https://www.rcsb.org/structure/2DUC">2DUC</ext-link> and
<ext-link ext-link-type="uri" xlink:href="https://www.rcsb.org/structure/6LU7">6LU7.</ext-link></p></sec><sec><title>Extended data</title><p>Open Science Framework: SARS-CoV-2 (2019-nCoV) 3CLpro Model and Screening.
<ext-link ext-link-type="uri" xlink:href="https://doi.org/10.17605/OSF.IO/HCU8X">https://doi.org/10.17605/OSF.IO/HCU8X</ext-link><sup><xref rid="ref-7" ref-type="bibr">7</xref></sup>.</p><p>The “Virtual Screening” folder contains the following extended data:</p><list list-type="bullet"><list-item><p>2019-nCoV-3CLpro.pdb. (3D model of the 3CL
<sup>pro</sup>: A and B chains.)</p></list-item><list-item><p>A-screen4500.pdbqt, B-screen4500.pdbqt, X-screen4500.pdbqt. (Virtual screening 3D results of Model A chain, Model B chain and the crystal-structure (A chain) in PDBQT format (can be viewed by any text editor). Use the software PyMOL to open these files. Each result file contains 4500 drug-to-protein docking hits ranked by AutoDock Vina binding energies in kcal mol
<sup>-1</sup>.)</p></list-item><list-item><p>A-screen1500.table.csv, B-screen1500.table.csv, X-screen1500.table.csv. (Virtual screening results (names only) of Model A chain, Model B chain and the crystal-structure (A chain) in CSV format (can be opened by Excel or any text editor). This is a summary of the top 1500 drug-to-protein docking hits ranked by AutoDock Vina binding energies in kcal mol
<sup>-1</sup>.)</p></list-item></list><p>The “Extended Results” folder contains the following extended data:</p><list list-type="bullet"><list-item><p>Tab S1.docx (Sequence homology of the 3CL
<sup>pro</sup> cleavage junctions of PP1AB between SARS-CoV-2 and SARS-CoV).</p></list-item><list-item><p>Tab S2.docx (The results of virtual screening of drugs on the active site of SARS-CoV-2 3CL
<sup>pro</sup> crystal structure).</p></list-item><list-item><p>Fig S1.pptx (The structural model of the SARS-CoV-2 3CL
<sup>pro</sup> protease).</p></list-item><list-item><p>Compare Crystal.docx (A comparison, with Figure S2, of the active sites of model chains A, B and the crystal structure).</p></list-item></list><p>Data are available under the terms of the
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<article-title>Therapeutic drugs targeting 2019-nCoV main protease by high-throughput screening.</article-title><source><italic toggle="yes">bioRxiv.</italic></source><year>2020</year><pub-id pub-id-type="doi">10.1101/2020.01.28.922922</pub-id></mixed-citation></ref></ref-list></back><sub-article id="report60415" article-type="peer-review"><front-stub><article-id pub-id-type="doi">10.5256/f1000research.24784.r60415</article-id><title-group><article-title>Reviewer response for version 1</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Viprakasit</surname><given-names>Vip</given-names></name><xref ref-type="aff" rid="r60415a1">1</xref><role>Referee</role></contrib><contrib contrib-type="author"><name><surname>Tulalamba</surname><given-names>Warut</given-names></name><xref ref-type="aff" rid="r60415a2">2</xref><role>Co-referee</role></contrib><aff id="r60415a1"><label>1</label>Division of Pediatric Haematology and Oncology, Thalassemia Center, Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand</aff><aff id="r60415a2"><label>2</label>Research Division and Thalassemia Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand</aff></contrib-group><author-notes><fn fn-type="COI-statement"><p><bold>Competing interests: </bold>No competing interests were disclosed.</p></fn></author-notes><pub-date pub-type="epub"><day>17</day><month>3</month><year>2020</year></pub-date><permissions><copyright-statement>Copyright: © 2020 Viprakasit V and Tulalamba W</copyright-statement><copyright-year>2020</copyright-year><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><related-article related-article-type="peer-reviewed-article" id="d35e3251" ext-link-type="doi" xlink:href="10.12688/f1000research.22457.1">Version 1</related-article><custom-meta-group><custom-meta><meta-name>recommendation</meta-name><meta-value>approve</meta-value></custom-meta></custom-meta-group></front-stub><body><p>In this article, Chen YW and his colleagues carried out virtual screening using the computational molecular modeling of the viral protein from SARS-CoV-2 or COVID-19 to identify therapeutics targets. The authors presented that 3CLpro protease enzyme of the SARS-CoV-2 is considered to be a promising drug target and repurposing accessible drugs to challenge the globally outbreaking of the SARS-CoV-2. The authors initially used the translated polyprotein (PP1AB) sequence of SARS-CoV-2 and SARS-CoV to prepare for protein structural model. Subsequently, they performed computational virtual screening against this against its using a library of purchasable drugs with the binding site grid. Among > 7,000 repurposing drugs in the screening with their known side effects, the antivirals ledipasir or velpatasvir are potentially used against SARS-CoV-2 infection with minimal side effects. The manuscript is straightforward in both terminology and structure. The manuscript can be considered to be accepted with a minor revision and could be further improved with following points:
<list list-type="order"><list-item><p>Table 2 is mentioned prior Table 1 in the manuscript.</p></list-item><list-item><p>More details of the setting and cut-off used in the virtual screening and analysis should be provided in the Method section.</p></list-item><list-item><p>Table 1 is quite confusing. The importance residues of the SARS-CoV 3CLpro previously reported and the variant residues found in SARS-CoV-2 (this work) should be separated. The amino acid variants of each position should be included. Using the image with the annotation could be an alternative and more informative presentation.</p></list-item><list-item><p>In Table 3, some information should be included in the table, such as molecular weight. In addition, the authors should discuss more about the results shown in the Table 3 to compare the binding energy different between A and B chains.</p></list-item><list-item><p>In the conclusion, the authors proposed velpatasvir and ledipasvir as an attractive candidate. However, based on the virtual screening on the active sites of SARS-CoV-2 3CLpro model, both of them are not ranked as the top list in Chain A screening. Could you please explain this scenario? The results from other virtual screening package (such as Glide or FlexX) should be compared?</p></list-item><list-item><p>To extend the interest of the topic as well as to compare the potential for using repurposing drug in COVID-19 treatment, the drug virtual screening with other viral enzymes might be performed and compared. In this case, since there are several clinical researches for using this drug family (e.g. Lopinavir/ritonavir) in COVID-19 treatment, therefore, the authors can compare the virtual screening model with the clinical outcomes.</p></list-item></list></p><p>We confirm that we have read this submission and believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.</p></body></sub-article><sub-article id="report60414" article-type="peer-review"><front-stub><article-id pub-id-type="doi">10.5256/f1000research.24784.r60414</article-id><title-group><article-title>Reviewer response for version 1</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Ng</surname><given-names>Wai-Lung</given-names></name><xref ref-type="aff" rid="r60414a1">1</xref><role>Referee</role><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0003-2892-6318</contrib-id></contrib><aff id="r60414a1"><label>1</label>School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong (CUHK), Hong Kong, Hong Kong</aff></contrib-group><author-notes><fn fn-type="COI-statement"><p><bold>Competing interests: </bold>No competing interests were disclosed.</p></fn></author-notes><pub-date pub-type="epub"><day>6</day><month>3</month><year>2020</year></pub-date><permissions><copyright-statement>Copyright: © 2020 Ng WL</copyright-statement><copyright-year>2020</copyright-year><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><related-article related-article-type="peer-reviewed-article" id="d35e3330" ext-link-type="doi" xlink:href="10.12688/f1000research.22457.1">Version 1</related-article><custom-meta-group><custom-meta><meta-name>recommendation</meta-name><meta-value>approve</meta-value></custom-meta></custom-meta-group></front-stub><body><p>Since December 2019, a plethora of cases resembling viral pneumonia has emerged exponentially in Wuhan, China, which is now coined Coronavirus Disease 2019 (COVID-19; formerly known as 2019-nCoV).</p><p> Chen
<italic>et. al.</italic> reported the computational modelling and virtual screening results of the 3C-like protease (3CLpro) of SARS-CoV-2. This study is timely in view of the recent outbreak of COVID-19. The rationale of repurposing existing drugs to tackle the global viral outbreak is sound. The manuscript is also well-written and structured. It should be noted that:
<list list-type="bullet"><list-item><p>The authors compared their model with the recently published crystal structure of 3CLpro and found a high similarity between the two structures. They also obtained a similar list of top-ranked drug candidates when the crystal structure was subjected to the same screening protocol.</p></list-item><list-item><p>Several studies using similar modeling and virtual screening approaches have also been published recently. </p></list-item></list> Some suggestions for improving the manuscript:
<list list-type="bullet"><list-item><p>The authors proposed that the HCV drugs velpatasvir and ledipasvir, and thus Epclusa and Harvoni, could be attractive drug candidates for treating SARS-CoV-2 infection. However, there is no direct evidence to support this claim. To support this claim, the authors should connect the computational results with experimental data. To test their hypothesis, the authors should at least prove (or disprove) that the two HCV drugs could inhibit the biochemical activity of 3CLpro of SARS-CoV-2.</p></list-item><list-item><p>To further test the hypothesis, the two NS5A inhibitors should be tested using in vitro assays such as viral RNA PCR assay.</p></list-item><list-item><p>If there are no such experimental data to support the claim, the authors may consider revising their conclusion to "the computational results provide a rationale for further experimental validation of treating SARS-CoV-2 with velpatasvir and ledipasvir".</p></list-item></list></p><p>I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.</p></body></sub-article><sub-article id="report60688" article-type="peer-review"><front-stub><article-id pub-id-type="doi">10.5256/f1000research.24784.r60688</article-id><title-group><article-title>Reviewer response for version 1</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Huang</surname><given-names>Jing</given-names></name><xref ref-type="aff" rid="r60688a1">1</xref><role>Referee</role><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0001-9639-2907</contrib-id></contrib><contrib contrib-type="author"><name><surname>Tan</surname><given-names>Qiaozhu</given-names></name><xref ref-type="aff" rid="r60688a1">1</xref><role>Co-referee</role></contrib><aff id="r60688a1"><label>1</label>School of Life Sciences, Westlake University, Hangzhou, China</aff></contrib-group><author-notes><fn fn-type="COI-statement"><p><bold>Competing interests: </bold>No competing interests were disclosed.</p></fn></author-notes><pub-date pub-type="epub"><day>6</day><month>3</month><year>2020</year></pub-date><permissions><copyright-statement>Copyright: © 2020 Tan Q and Huang J</copyright-statement><copyright-year>2020</copyright-year><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><related-article related-article-type="peer-reviewed-article" id="d35e3425" ext-link-type="doi" xlink:href="10.12688/f1000research.22457.1">Version 1</related-article><custom-meta-group><custom-meta><meta-name>recommendation</meta-name><meta-value>approve</meta-value></custom-meta></custom-meta-group></front-stub><body><p>Yu Wai Chen and co-workers presented a molecular modeling and docking study of the 3CL protease in the SARS-CoV-2 virus. The manuscript started with comparing polyprotein PP1AB sequences of SARS-CoV-2 and SARS-CoV, based on which the 3D structure of SARS-CoV-2 3CLPro protein was constructed. The authors then performed virtual screening against SARS-CoV-2 3CLPro using a library of 7173 purchasable drugs. Considering both binding affinities and known side effects, the authors recommend velpatasvir and ledipasvir, and further suggest combining them with another HCV RdRp inhibitor sofosbuvir, aka repurposing the Epclusa and Harvoni for treating the coronavirus. This is a concise and timely report, and has proposed new therapeutic possibilities for the SARS-CoV-2 virus. The manuscript could be further improved by addressing the following comments.
<list list-type="order"><list-item><p>More details of the docking should be provided. What's the binding energy cutoff used? How is the hits (reported in Table 3) used? 3CLpro is catalytically active as a dimer. How is this considered in the virtual screening? What does the "(B Top scorers)" mean?</p></list-item><list-item><p>In the extended data of virtual screening, one compound could have multiple entries with different ZINC numbers. For example hesperidin corresponds to at least 20 different compounds. What are the difference? And how are different results assembled?</p></list-item><list-item><p>Table 1 is not clear. Please do a column-by-column comparison between different sites of SARS-CoV and SARS-CoV-2. Also please add one-letter amino acid codes for the residues.</p></list-item><list-item><p>The constructed protein structure is very similar to the recently solved crystal structure (6LU7), as "... confirms that the predicted model is good within experimental errors", but the docking results seem to differ significantly. Could the authors explain?</p></list-item></list></p><p>We confirm that we have read this submission and believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.</p></body></sub-article></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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