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In the current situation, the virus is rapidly spreading worldwide, and the discovery of a vaccine and potential therapeutics are critically essential. The crystal structure for the main protease (Mpro) of SARS-CoV-2, 3-chymotrypsin-like cysteine protease (3CLpro), was recently made available and is considerably similar to the previously reported SARS-CoV. Due to its essentiality in viral replication, it represents a potential drug target. Herein, a computer-aided drug design (CADD) approach was implemented for the initial screening of 13 approved antiviral drugs. Molecular docking of 13 antivirals against the 3-chymotrypsin-like cysteine protease (3CLpro) enzyme was accomplished, and indinavir was described as a lead drug with a docking score of \u22128.824 and a XP Gscore of \u22129.466 kcal\/mol. Indinavir possesses an important pharmacophore, hydroxyethylamine (HEA), and thus, a new library of HEA compounds (&amp;gt;2500) was subjected to virtual screening that led to 25 hits with a docking score more than indinavir. Exclusively, compound 16 with a docking score of \u22128.955 adhered to drug-like parameters, and the structure\u2013activity relationship (SAR) analysis was demonstrated to highlight the importance of chemical scaffolds therein. Molecular dynamics (MD) simulation analysis performed at 100 ns supported the stability of 16 within the binding pocket. Largely, our results supported that this novel compound 16 binds with domains I and II, and the domain II\u2013III linker of the 3CLpro protein, suggesting its suitability as a strong candidate for therapeutic discovery against COVID-19.<\/jats:p>","DOI":"10.1021\/acs.jcim.0c00326","type":"journal-article","created":{"date-parts":[[2020,6,2]],"date-time":"2020-06-02T13:33:04Z","timestamp":1591104784000},"page":"5754-5770","source":"Crossref","is-referenced-by-count":122,"title":["Discovery of New Hydroxyethylamine Analogs against\n3CLpro Protein Target of SARS-CoV-2: Molecular Docking,\nMolecular Dynamics Simulation, and Structure\u2013Activity Relationship\nStudies"],"prefix":"10.1021","volume":"60","author":[{"given":"Sumit","family":"Kumar","sequence":"first","affiliation":[{"name":"University of Delhi , , ,","place":["Delhi, India, 110007"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Prem Prakash","family":"Sharma","sequence":"additional","affiliation":[{"name":"University of Delhi , , ,","place":["Delhi, India, 110007"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Uma","family":"Shankar","sequence":"additional","affiliation":[{"name":"Indian Institute of Technology , , ,","place":["Indore, Simrol, Indore, India, 453552"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dhruv","family":"Kumar","sequence":"additional","affiliation":[{"name":"Amity University Uttar Pradesh , , Sec-125 , ,","place":["Noida, India, 201313"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sanjeev K.","family":"Joshi","sequence":"additional","affiliation":[{"name":"Defence Research & Development Organization , , HQ, Rajaji Marg , ,","place":["New Delhi, India, 110011"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lindomar","family":"Pena","sequence":"additional","affiliation":[{"name":"Aggeu Magalhaes Institute (IAM), Oswaldo Cruz Foundation (Fiocruz) , , , ,","place":["Recife, Pernambuco, Brazil, 50670-420"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ravi","family":"Durvasula","sequence":"additional","affiliation":[{"name":"Loyola University Stritch School of Medicine , , 2160 South First Avenue , , ,","place":["Chicago, Illinois, United\nStates, 60153"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amit","family":"Kumar","sequence":"additional","affiliation":[{"name":"Indian Institute of Technology , , ,","place":["Indore, Simrol, Indore, India, 453552"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Prakasha","family":"Kempaiah","sequence":"additional","affiliation":[{"name":"Loyola University Stritch School of Medicine , , 2160 South First Avenue , , ,","place":["Chicago, Illinois, United\nStates, 60153"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3759-1057","authenticated-orcid":true,"family":"Poonam","sequence":"additional","affiliation":[{"name":"University of Delhi , , ,","place":["Delhi, India, 110007"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2133-8847","authenticated-orcid":true,"given":"Brijesh","family":"Rathi","sequence":"additional","affiliation":[{"name":"University of Delhi , , ,","place":["Delhi, India, 110007"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2020,6,2]]},"reference":[{"key":"2026081804364446700_cit1","doi-asserted-by":"publisher","first-page":"929","DOI":"10.1086\/377612","article-title":"Coronavirus 229E-Related\nPneumonia in Immunocompromised Patients","volume":"37","author":"Pene","year":"2003","journal-title":"Clin.\nInfect. Dis."},{"key":"2026081804364446700_cit2","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1038\/nrmicro1343","article-title":"Coronavirus infection of the central\nnervous system: host\u2013virus stand-off","volume":"4","author":"Bergmann","year":"2006","journal-title":"Nat. Rev. Microbiol."},{"key":"2026081804364446700_cit3","doi-asserted-by":"publisher","first-page":"4508","DOI":"10.1128\/JVI.72.5.4508-4514.1998","article-title":"Feline Coronavirus Type II Strains 79\u20131683 and\n79\u20131146 Originate from a Double Recombination between Feline\nCoronavirus Type I and Canine Coronavirus","volume":"72","author":"Herrewegh","year":"1998","journal-title":"J.\nVirol."},{"key":"2026081804364446700_cit4","doi-asserted-by":"publisher","first-page":"1456","DOI":"10.1021\/cb500917m","article-title":"Inhibitor Recognition\nSpecificity of MERS-CoV Papain-like Protease May Differ from That\nof SARS-CoV","volume":"10","author":"Lee","year":"2015","journal-title":"ACS Chem. Biol."},{"key":"2026081804364446700_cit5","doi-asserted-by":"publisher","first-page":"3485","DOI":"10.1021\/jm050852f","article-title":"Discovery\nof a Novel\nFamily of SARS-CoV Protease Inhibitors by Virtual Screening and 3D-QSAR\nStudies","volume":"49","author":"Tsai","year":"2006","journal-title":"J. Med. Chem."},{"key":"2026081804364446700_cit6","doi-asserted-by":"publisher","first-page":"2018","DOI":"10.1021\/acs.jmedchem.7b01732","article-title":"Discovery of Hydrocarbon-Stapled\nShort \u03b1-Helical Peptides as Promising Middle East Respiratory\nSyndrome Coronavirus (MERS-CoV) Fusion Inhibitors","volume":"61","author":"Wang","year":"2018","journal-title":"J. Med. Chem."},{"key":"2026081804364446700_cit7","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1038\/d41573-020-00016-0","article-title":"Therapeutic options for the 2019 novel coronavirus\n(2019-nCoV)","volume":"19","author":"Li","year":"2020","journal-title":"Nat. Rev. Drug Discovery"},{"key":"2026081804364446700_cit8","first-page":"63","article-title":"Corona virus SARS-CoV-2\ndisease COVID-19:\nInfection, prevention and clinical advances of the prospective chemical\ndrug therapeutics","volume":"7","author":"Chhikara","year":"2020","journal-title":"Chem. Biol. Lett."},{"key":"2026081804364446700_cit9","doi-asserted-by":"publisher","first-page":"599","DOI":"10.2174\/1568026620999200305144319","article-title":"Coronavirus\nDisease COVID-19: A New Threat to Public Health","volume":"20","author":"Kumar","year":"2020","journal-title":"Curr. Top. Med. Chem."},{"key":"2026081804364446700_cit10","unstructured":"Coronavirus disease (COVID-2019): Situation Report\n40. World\nHealth Organizationhttps:\/\/www.who.int\/docs\/default-source\/coronaviruse\/situation-reports\/20200229-sitrep-40-covid-19.pdf?sfvrsn=849d0665_2 (accessed 29 Feburary 2020)."},{"key":"2026081804364446700_cit11","unstructured":"Coronavirus\ndisease (COVID-2019): Situation Report 51. 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Protein Data\nBank. https:\/\/www.rcsb.org\/structure\/6lu7 (accessed June 2020).","DOI":"10.2210\/pdb7bqy\/pdb"},{"key":"2026081804364446700_cit17","doi-asserted-by":"publisher","first-page":"22677","DOI":"10.1038\/srep22677","article-title":"Structure\nof Main Protease from Human Coronavirus NL63: Insights for Wide Spectrum\nAnti-Coronavirus Drug Design","volume":"6","author":"Wang","year":"2016","journal-title":"Sci. Rep."},{"key":"2026081804364446700_cit18","doi-asserted-by":"publisher","first-page":"248","DOI":"10.1007\/s13238-013-2841-3","article-title":"The newly emerged SARS-like\ncoronavirus HCoV-EMC also has an \u2033Achilles\u2019\nheel\u2033: current effective inhibitor targeting a 3C-like protease","volume":"4","author":"Ren","year":"2013","journal-title":"Protein Cell"},{"key":"2026081804364446700_cit19","doi-asserted-by":"publisher","first-page":"2515","DOI":"10.1128\/JVI.02114-07","article-title":"Structures of Two Coronavirus\nMain Proteases: Implications for Substrate Binding and Antiviral Drug\nDesign","volume":"82","author":"Xue","year":"2008","journal-title":"J. Virol."},{"key":"2026081804364446700_cit20","doi-asserted-by":"publisher","first-page":"13190","DOI":"10.1073\/pnas.1835675100","article-title":"The crystal structures of severe\nacute respiratory syndrome virus main protease and its complex with\nan inhibitor","volume":"100","author":"Yang","year":"2003","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"2026081804364446700_cit21","doi-asserted-by":"publisher","first-page":"3213","DOI":"10.1093\/emboj\/cdf327","article-title":"Structure\nof coronavirus main proteinase reveals combination\nof a chymotrypsin fold with an extra alpha-helical domain","volume":"21","author":"Anand","year":"2002","journal-title":"EMBO J."},{"key":"2026081804364446700_cit22","doi-asserted-by":"publisher","first-page":"1376","DOI":"10.1021\/ci1004916","article-title":"Inhibitors of SARS-3CLpro:\nVirtual Screening, Biological Evaluation, and Molecular Dynamics Simulation\nStudies","volume":"51","author":"Mukherjee","year":"2011","journal-title":"J. Chem. Inf. Model."},{"key":"2026081804364446700_cit23","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1021\/ci049809b","article-title":"Virtual Screening of\nNovel Noncovalent Inhibitors for\nSARS-CoV 3C-like Proteinase","volume":"45","author":"Liu","year":"2005","journal-title":"J. Chem. Inf. Model."},{"key":"2026081804364446700_cit24","doi-asserted-by":"publisher","first-page":"719","DOI":"10.1016\/j.bbrc.2004.04.083","article-title":"HIV protease\ninhibitor nelfinavir inhibits replication of SARS-associated coronavirus","volume":"318","author":"Yamamoto","year":"2004","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"2026081804364446700_cit25","doi-asserted-by":"publisher","first-page":"581","DOI":"10.3201\/eid1004.030458","article-title":"Inhibition\nof SARS coronavirus infection in vitro with\nclinically approved antiviral drugs","volume":"10","author":"Tan","year":"2004","journal-title":"Emerging\nInfect. Dis."},{"key":"2026081804364446700_cit26","unstructured":"Protein\nPreparation Wizard, Schro\u0308dinger Release 2020-1; Schro\u0308dinger, LLC: New York, 2020."},{"key":"2026081804364446700_cit27","unstructured":"Prime, Schro\u0308dinger\nRelease 2020-1: Schro\u0308dinger, LLC: New York, 2020."},{"key":"2026081804364446700_cit28","doi-asserted-by":"publisher","first-page":"137489","DOI":"10.1016\/j.cplett.2020.137489","article-title":"Identification of potential\nbinders\nof the main protease 3CLpro of the COVID-19 via structure-based ligand\ndesign and molecular modeling","volume":"750","author":"Macchiagodena","year":"2020","journal-title":"Chem. Phys. Lett."},{"key":"2026081804364446700_cit29","doi-asserted-by":"publisher","first-page":"31420","DOI":"10.1038\/srep31420","article-title":"Understanding the structural\nbasis of substrate recognition\nby Plasmodium falciparum plasmepsin V to aid in the design of potent\ninhibitors","volume":"6","author":"Bedi","year":"2016","journal-title":"Sci. Rep."},{"key":"2026081804364446700_cit30","volume-title":"LigPrep, Schro\u0308dinger Release 2020-1","year":"2020"},{"key":"2026081804364446700_cit31","volume-title":"Epik,\nSchro\u0308dinger Release 2020-1","year":"2020"},{"key":"2026081804364446700_cit32","volume-title":"Glide, Schro\u0308dinger\nRelease 2020-1","year":"2020"},{"key":"2026081804364446700_cit33","doi-asserted-by":"publisher","first-page":"42717","DOI":"10.1038\/srep42717","article-title":"SwissADME: a free web\ntool to evaluate\npharmacokinetics, drug-likeness and medicinal chemistry friendliness\nof small molecules","volume":"7","author":"Daina","year":"2017","journal-title":"Sci. Rep."},{"key":"2026081804364446700_cit34","doi-asserted-by":"publisher","first-page":"4066","DOI":"10.1021\/acs.jmedchem.5b00104","article-title":"pkCSM:\nPredicting Small-Molecule\nPharmacokinetic and Toxicity Properties Using Graph-Based Signatures","volume":"58","author":"Pires","year":"2015","journal-title":"J. Med. Chem."},{"key":"2026081804364446700_cit35a","unstructured":"(a)\n          Desmond Molecular Dynamics System,\nSchro\u0308dinger\nRelease 2020-1; D. E. Shaw Research: New York, 2020."},{"key":"2026081804364446700_cit35b","unstructured":"(b)\n          Maestro-Desmond Interoperability Tools; Schro\u0308dinger: New York, 2020."},{"key":"2026081804364446700_cit36","doi-asserted-by":"publisher","first-page":"929","DOI":"10.1056\/NEJMoa2001191","article-title":"First Case of 2019 Novel Coronavirus\nin the United States","volume":"382","author":"Holshue","year":"2020","journal-title":"N. Engl. J. Med."},{"key":"2026081804364446700_cit37","doi-asserted-by":"publisher","first-page":"1787","DOI":"10.1056\/NEJMoa2001282","article-title":"A trial of lopinavir\u2013ritonavir in adults\nhospitalized with\nsevere Covid-19","volume":"382","author":"Cao","year":"2020","journal-title":"N. Engl. J. Med."},{"key":"2026081804364446700_cit38","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciaa237","article-title":"In Vitro Antiviral\nActivity and Projection of Optimized Dosing Design of Hydroxychloroquine\nfor the Treatment of Severe Acute Respiratory Syndrome Coronavirus\n2 (SARS-CoV-2)","author":"Yao","year":"2020","journal-title":"Clin. Infect. Dis."},{"key":"2026081804364446700_cit39","doi-asserted-by":"publisher","first-page":"105949","DOI":"10.1016\/j.ijantimicag.2020.105949","article-title":"Hydroxychloroquine\nand azithromycin\nas a treatment of COVID-19: results of an open-label non-randomized\nclinical trial","author":"Gautret","year":"2020","journal-title":"Int. J. Antimicrob. Agents"},{"key":"2026081804364446700_cit40","doi-asserted-by":"publisher","first-page":"1750","DOI":"10.1021\/jm030644s","article-title":"Glide:\nA New Approach for Rapid,\nAccurate Docking and Scoring. 2. Enrichment Factors in Database Screening","volume":"47","author":"Halgren","year":"2004","journal-title":"J. Med. Chem."},{"key":"2026081804364446700_cit41","doi-asserted-by":"crossref","unstructured":"Chang, Y. C.; Tung, Y. A.; Lee, K. H.; Chen, T. F.; Hsiao, Y. C.; Chang, H. C.; Hsieh, T. T.; Su, C.\nH.; Wang, S.\nS.; Yu, J. Y.; Shih, S. S.; Lin, Y. H.; Lin, Y. H.; Tu, Y. C. E.; Tung, C. W.; Chen, C. Y.\n          Potential Therapeutic Agents\nfor COVID-19 Based on the Analysis of Protease and RNA Polymerase\nDocking. Preprints, 2020. https:\/\/www.preprints.org\/manuscript\/202002.0242\/v1 (accessed\nJune 2020).","DOI":"10.20944\/preprints202002.0242.v1"},{"key":"2026081804364446700_cit42","doi-asserted-by":"publisher","first-page":"1511","DOI":"10.1002\/med.21486","article-title":"Multistage inhibitors\nof the malaria parasite: Emerging hope for\nchemoprotection and malaria eradication","volume":"38","author":"Poonam","year":"2018","journal-title":"Med.\nRes. Rev."},{"key":"2026081804364446700_cit43","doi-asserted-by":"publisher","first-page":"705","DOI":"10.1080\/17460441.2020.1740203","article-title":"Fluorinated scaffolds for antimalarial\ndrug discovery","volume":"15","author":"Upadhyay","year":"2020","journal-title":"Expert Opin. Drug Discovery"},{"key":"2026081804364446700_cit44","first-page":"14","article-title":"Chemical libraries\ntargeting Liver Stage Malarial infection","volume":"6","author":"Sharma","year":"2019","journal-title":"Chem.\nBiol. Lett."},{"key":"2026081804364446700_cit45","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1021\/acsinfecdis.8b00197","article-title":"Fast-Acting Small Molecules\nTargeting Malarial Aspartyl Proteases, Plasmepsins, Inhibit Malaria\nInfection at Multiple Life Stages","volume":"5","author":"Singh","year":"2019","journal-title":"ACS Infect.\nDis."},{"key":"2026081804364446700_cit46","doi-asserted-by":"publisher","first-page":"3837","DOI":"10.1016\/j.bmc.2018.06.037","article-title":"Antiplasmodial activity\nof hydroxyethylamine analogs: Synthesis, biological activity and structure\nactivity relationship of plasmepsin inhibitors","volume":"26","author":"Kumar\nSingh","year":"2018","journal-title":"Bioorg. Med. Chem."},{"key":"2026081804364446700_cit47","doi-asserted-by":"publisher","first-page":"973","DOI":"10.1080\/1062936X.2017.1388281","article-title":"Hydroxyethylamine derivatives as\nHIV-1 protease inhibitors: a predictive\nQSAR modelling study based on Monte Carlo optimization","volume":"28","author":"Bhargava","year":"2017","journal-title":"SAR QSAR Environ. Res."},{"key":"2026081804364446700_cit48","doi-asserted-by":"publisher","first-page":"2565","DOI":"10.1016\/j.bmcl.2019.08.006","article-title":"Potent HIV-1\nprotease inhibitors incorporating squaramide-derived P2 ligands: Design,\nsynthesis, and biological evaluation","volume":"29","author":"Ghosh","year":"2019","journal-title":"Bioorg.\nMed. Chem. Lett."},{"key":"2026081804364446700_cit49","doi-asserted-by":"publisher","first-page":"111940","DOI":"10.1016\/j.ejmech.2019.111940","article-title":"Discovery of novel\n1,2,3-triazole\noseltamivir derivatives as potent influenza neuraminidase inhibitors\ntargeting the 430-cavity","volume":"187","author":"Ju","year":"2020","journal-title":"Eur. J. Med. Chem."},{"key":"2026081804364446700_cit50","doi-asserted-by":"publisher","first-page":"820","DOI":"10.1529\/biophysj.107.112045","article-title":"Ligand binding\nto the voltage-gated\nKv1.5 potassium channel in the open state-docking and computer simulations\nof a homology model","volume":"94","author":"Ande\u0301r","year":"2008","journal-title":"Biophys. J."},{"key":"2026081804364446700_cit51","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1006\/jmbi.2001.4551","article-title":"FlexE: efficient molecular\ndocking considering protein structure variations1 1Edited by J. Thornton","volume":"308","author":"Clau\u00dfen","year":"2001","journal-title":"J. Mol. Biol."}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.0c00326","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article-pdf\/60\/12\/5754\/9619460\/ci0c00326.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article-pdf\/60\/12\/5754\/9619460\/ci0c00326.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T09:00:32Z","timestamp":1787043632000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article\/60\/12\/5754\/890865\/Discovery-of-New-Hydroxyethylamine-Analogs-against"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,6,2]]},"references-count":52,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2020,6,2]]},"published-print":{"date-parts":[[2020,12,28]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.0c00326","relation":{"has-preprint":[{"id-type":"doi","id":"10.26434\/chemrxiv.12083004.v1","asserted-by":"object"},{"id-type":"doi","id":"10.26434\/chemrxiv.12083004","asserted-by":"object"}]},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,6,2]]}}}