{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T15:39:18Z","timestamp":1772120358216,"version":"3.50.1"},"reference-count":55,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2021,2,1]],"date-time":"2021-02-01T00:00:00Z","timestamp":1612137600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2021,2,1]],"date-time":"2021-02-01T00:00:00Z","timestamp":1612137600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2021,2,1]],"date-time":"2021-02-01T00:00:00Z","timestamp":1612137600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2021,2,1]],"date-time":"2021-02-01T00:00:00Z","timestamp":1612137600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2021,2,1]],"date-time":"2021-02-01T00:00:00Z","timestamp":1612137600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2021,2,1]],"date-time":"2021-02-01T00:00:00Z","timestamp":1612137600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2021,2,1]],"date-time":"2021-02-01T00:00:00Z","timestamp":1612137600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Biophysical Chemistry"],"published-print":{"date-parts":[[2021,2]]},"DOI":"10.1016\/j.bpc.2020.106510","type":"journal-article","created":{"date-parts":[[2020,11,27]],"date-time":"2020-11-27T20:42:22Z","timestamp":1606509742000},"page":"106510","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":16,"special_numbering":"C","title":["An insight into the interaction between \u03b1-ketoamide- based inhibitor and coronavirus main protease: A detailed in silico study"],"prefix":"10.1016","volume":"269","author":[{"given":"Snehasis","family":"Banerjee","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/j.bpc.2020.106510_bb0005","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1126\/science.abb3405","article-title":"Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved \u03b1-ketoamide inhibitors","volume":"368","author":"Zhang","year":"2020","journal-title":"Science"},{"key":"10.1016\/j.bpc.2020.106510_bb0010","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1038\/s41594-020-0440-6","article-title":"Structural basis for the inhibition of SARS-CoV-2 main protease by antineoplastic drug carmofur","volume":"27","author":"Jin","year":"2020","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.bpc.2020.106510_bb0015","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1038\/s41586-020-2008-3","article-title":"A new coronavirus associated with human respiratory disease in China","volume":"579","author":"Wu","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.bpc.2020.106510_bb0020","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1038\/s41586-020-2012-7","article-title":"A pneumonia outbreak associated with a new coronavirus of probable bat origin","volume":"579","author":"Zhou","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.bpc.2020.106510_bb0025","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1038\/s41586-020-2223-y","article-title":"Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors","volume":"582","author":"Jin","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.bpc.2020.106510_bb0030","doi-asserted-by":"crossref","first-page":"3202","DOI":"10.1038\/s41467-020-16954-7","article-title":"Structural plasticity of SARS-CoV-2 3CL Mpro active site cavity revealed by room temperature X-ray crystallography","volume":"11","author":"Kneller","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.bpc.2020.106510_bb0035","doi-asserted-by":"crossref","DOI":"10.1021\/acs.jpcb.0c04317","article-title":"Critical differences between the binding features of the spike proteins of SARS-CoV-2 and SARS-CoV","author":"Bai","year":"2020","journal-title":"J. Phys. Chem B"},{"key":"10.1016\/j.bpc.2020.106510_bb0040","doi-asserted-by":"crossref","first-page":"4413","DOI":"10.1021\/acs.jpclett.0c00994","volume":"11","year":"2020","journal-title":"J. Phys. Chem. Lett."},{"key":"10.1016\/j.bpc.2020.106510_bb0045","doi-asserted-by":"crossref","first-page":"5871","DOI":"10.1021\/acscatal.0c00110","article-title":"Comprehensive insights into the catalytic mechanism of middle east respiratory syndrome 3C-like protease and severe acute respiratory syndrome 3C-like protease","volume":"10","author":"Wang","year":"2020","journal-title":"ACS Catal."},{"key":"10.1016\/j.bpc.2020.106510_bb0050","doi-asserted-by":"crossref","DOI":"10.1038\/s41586-020-2286-9","article-title":"A SARS-CoV-2 protein interaction map reveals targets for drug repurposing","author":"Gordon","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.bpc.2020.106510_bb0055","doi-asserted-by":"crossref","first-page":"5764","DOI":"10.1039\/c2ob00034b","article-title":"Tuning and predicting biological affinity: arylnitriles as cysteine protease inhibitors","volume":"10","author":"Ehmke","year":"2012","journal-title":"Org. Biomol. Chem"},{"key":"10.1016\/j.bpc.2020.106510_bb0060","doi-asserted-by":"crossref","first-page":"13408","DOI":"10.1002\/anie.201601091","article-title":"Targeted covalent inhibitors for drug design","volume":"55","author":"Baillie","year":"2016","journal-title":"Angew. Chem. Int. Ed."},{"key":"10.1016\/j.bpc.2020.106510_bb0065","first-page":"1330","article-title":"Reversible Michael additions: covalent inhibitors and prodrugs","volume":"12","author":"Johansson","year":"2012","journal-title":"Mini Rev. Med. Chem."},{"key":"10.1016\/j.bpc.2020.106510_bb0070","doi-asserted-by":"crossref","first-page":"6911","DOI":"10.1021\/acs.jmedchem.7b00405","article-title":"Development of novel peptide-based Michael acceptors targeting rhodesain and falcipain-2 for the treatment of Neglected Tropical Diseases (NTDs)","volume":"60","author":"Ettari","year":"2017","journal-title":"J. Med. Chem."},{"key":"10.1016\/j.bpc.2020.106510_bb0075","doi-asserted-by":"crossref","first-page":"1951","DOI":"10.1021\/jm900946n","article-title":"Michael acceptor based antiplasmodial and antitrypanosomal cysteine protease inhibitors with unusual amino acids","volume":"53","author":"Breuning","year":"2010","journal-title":"J. Med. Chem."},{"key":"10.1016\/j.bpc.2020.106510_bb0080","doi-asserted-by":"crossref","first-page":"1228","DOI":"10.1002\/cmdc.201100093","article-title":"Development of novel peptidomimetics containing a vinyl sulfone moiety as proteasome inhibitors","volume":"6","author":"Ettari","year":"2011","journal-title":"ChemMedChem"},{"key":"10.1016\/j.bpc.2020.106510_bb0085","doi-asserted-by":"crossref","first-page":"3816","DOI":"10.1039\/C7CS00220C","article-title":"Structure-based design of targeted covalent inhibitors","volume":"47","author":"Lonsdale","year":"2018","journal-title":"Chem. Soc. Rev."},{"key":"10.1016\/j.bpc.2020.106510_bb0090","doi-asserted-by":"crossref","first-page":"3241","DOI":"10.1021\/acs.chemrev.5b00443","article-title":"Recent developments in general methodologies for the synthesis of \u03b1-ketoamides","volume":"116","author":"De Risi","year":"2016","journal-title":"Chem. Rev."},{"key":"10.1016\/j.bpc.2020.106510_bb0095","doi-asserted-by":"crossref","first-page":"1679","DOI":"10.1002\/anie.201308984","article-title":"Systematic comparison of peptidic proteasome inhibitors highlights the \u03b1-ketoamide electrophile as an auspicious reversible lead motif","volume":"53","author":"Stein","year":"2014","journal-title":"Angew. Chem., Int. Ed."},{"key":"10.1016\/j.bpc.2020.106510_bb0100","doi-asserted-by":"crossref","first-page":"107292","DOI":"10.1016\/j.compbiolchem.2020.107292","article-title":"Interaction of the prototypical \u03b1-ketoamide inhibitor with the SARS-CoV-2 main protease active site in silico: molecular dynamic simulations highlight the stability of the ligand-protein complex","volume":"87","author":"Liang","year":"2020","journal-title":"Comput. Biol. Chem."},{"issue":"12","key":"10.1016\/j.bpc.2020.106510_bb0105","doi-asserted-by":"crossref","first-page":"5099","DOI":"10.1021\/acs.jcim.9b00966","article-title":"Density functional theory transition-state modeling for the prediction of ames mutagenicity in 1,4 Michael acceptors","volume":"59","author":"Townsend","year":"2019","journal-title":"J. Chem. Inf. Model."},{"key":"10.1016\/j.bpc.2020.106510_bb0110","doi-asserted-by":"crossref","first-page":"2557","DOI":"10.1002\/cmdc.201402244","article-title":"\u03b1-Keto phenylamides as P1\u2019-extended proteasome inhibitors","volume":"9","author":"Voss","year":"2014","journal-title":"ChemMedChem"},{"key":"10.1016\/j.bpc.2020.106510_bb0115","doi-asserted-by":"crossref","first-page":"1086","DOI":"10.1021\/acsmedchemlett.9b00233","article-title":"Synthesis and biological activity of peptide \u03b1-Ketoamide derivatives as proteasome inhibitors","volume":"10","author":"Pacifico","year":"2019","journal-title":"ACS Med. Chem. Lett."},{"key":"10.1016\/j.bpc.2020.106510_bb0120","doi-asserted-by":"crossref","first-page":"6326","DOI":"10.1021\/jm901221v","article-title":"Peptidyl \u03b1-ketoamides with nucleobases, methylpiperazine, and dimethylaminoalkyl substituents as calpain inhibitors","volume":"53","author":"Ovat","year":"2010","journal-title":"J. Med. Chem."},{"key":"10.1016\/j.bpc.2020.106510_bb0125","doi-asserted-by":"crossref","first-page":"4545","DOI":"10.1021\/jm100089e","article-title":"Design and synthesis of \u03b1-ketoamides as cathepsin S inhibitors with potential applications against tumor invasion and angiogenesis","volume":"53","author":"Chen","year":"2010","journal-title":"J. Med. Chem."},{"key":"10.1016\/j.bpc.2020.106510_bb0130","doi-asserted-by":"crossref","first-page":"17716","DOI":"10.1038\/s41598-020-74468-0","article-title":"Rational approach toward COVID-19 main protease inhibitors via molecular docking, molecular dynamics simulation and free energy calculation","volume":"10","author":"Keretsu","year":"2020","journal-title":"Sci. Rep."},{"key":"10.1016\/j.bpc.2020.106510_bb0135","doi-asserted-by":"crossref","first-page":"876","DOI":"10.1021\/acschembio.7b00988","article-title":"Thienyl-substituted \u03b1-ketoamide: a less hydrophobic reactive group for photo-affinity labeling","volume":"13","author":"Ota","year":"2018","journal-title":"ACS Chem. Biol."},{"key":"10.1016\/j.bpc.2020.106510_bb0140","doi-asserted-by":"crossref","first-page":"4562","DOI":"10.1021\/acs.jmedchem.9b01828","article-title":"\u03b1-Ketoamides as broad-spectrum inhibitors of coronavirus and enterovirus replication: structure-based design, synthesis, and activity assessment","volume":"63","author":"Zhang","year":"2020","journal-title":"J. Med. Chem."},{"key":"10.1016\/j.bpc.2020.106510_bb0145","doi-asserted-by":"crossref","first-page":"39","DOI":"10.3389\/fchem.2013.00039","article-title":"Cysteine protease inhibition by nitrile-based inhibitors: a computational study","volume":"1","author":"Quesne","year":"2013","journal-title":"Front. Chem."},{"key":"10.1016\/j.bpc.2020.106510_bb0150","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1016\/j.jmgm.2017.10.012","article-title":"Reaction profiling of a set of acrylamide-based human tissue transglutaminase inhibitors","volume":"79","author":"Jasim","year":"2018","journal-title":"J. Mol. Graph. Model."},{"key":"10.1016\/j.bpc.2020.106510_bb0155","doi-asserted-by":"crossref","first-page":"1765","DOI":"10.1021\/ct301082y","article-title":"Benchmark study for the cysteine\u2212histidine proton transfer reaction in a protein environment: gas phase, COSMO, QM\/MM approaches","volume":"9","author":"Paasche","year":"2013","journal-title":"J. Chem. Theory Comput."},{"key":"10.1016\/j.bpc.2020.106510_bb0160","doi-asserted-by":"crossref","first-page":"869","DOI":"10.1002\/cmdc.201000020","article-title":"Mechanistic study of the reaction of thiol-containing enzymes with \u03b1,\u03b2-unsaturated carbonyl substrates by computation and chemoassays","volume":"5","author":"Paasche","year":"2010","journal-title":"ChemMedChem"},{"key":"10.1016\/j.bpc.2020.106510_bb0165","doi-asserted-by":"crossref","first-page":"2064","DOI":"10.3390\/molecules25092064","article-title":"Naphthoquinones as covalent reversible inhibitors of cysteine proteases\u2014studies on inhibition mechanism and kinetics","volume":"25","author":"Klein","year":"2020","journal-title":"Molecules"},{"key":"10.1016\/j.bpc.2020.106510_bb0170","doi-asserted-by":"crossref","first-page":"2872","DOI":"10.1021\/acscatal.9b04690","article-title":"How the destabilization of a reaction intermediate affects enzymatic efficiency: the case of human Transketolase","volume":"10","author":"Mario","year":"2020","journal-title":"ACS Catal."},{"key":"10.1016\/j.bpc.2020.106510_bb0175","doi-asserted-by":"crossref","unstructured":"Arafet, K.; \u015awiderek K.; Moliner,V. Computational study of the Michaelis complex formation and the effect on the reaction mechanism of Cruzain cysteine protease, ACS Omega, 2018, 3, 18613\u201318622.","DOI":"10.1021\/acsomega.8b03010"},{"key":"10.1016\/j.bpc.2020.106510_bb0180","doi-asserted-by":"crossref","first-page":"5145","DOI":"10.1021\/bi400629r","article-title":"Reaction pathway and free energy profile for papain-catalyzed hydrolysis of N-acetyl-phe-gly 4-nitroanilide","volume":"52","author":"Wei","year":"2013","journal-title":"Biochemistry"},{"key":"10.1016\/j.bpc.2020.106510_bb0185","doi-asserted-by":"crossref","DOI":"10.1039\/D0SC02823A","article-title":"Revealing the molecular mechanisms of proteolysis of SARS-CoV-2 Mpro by QM\/MM computational methods","author":"\u015awiderek","year":"2020","journal-title":"Chem. Sci."},{"key":"10.1016\/j.bpc.2020.106510_bb0190","doi-asserted-by":"crossref","first-page":"1207","DOI":"10.1021\/acscatal.6b03096","article-title":"Computational study of the catalytic mechanism of the Cruzain cysteine protease","volume":"7","author":"Arafet","year":"2017","journal-title":"ACS Catal."},{"key":"10.1016\/j.bpc.2020.106510_bb0195","doi-asserted-by":"crossref","first-page":"975","DOI":"10.1002\/prot.22939","article-title":"The mechanism of papain inhibition by peptidyl aldehydes","volume":"79","author":"Shokhen","year":"2011","journal-title":"Proteins"},{"key":"10.1016\/j.bpc.2020.106510_bb0200","series-title":"Tuning Proton Transfer Thermodynamics in SARS-Cov-2 Main Protease: Implications for Catalysis and Inhibitor Design","author":"Zanetti-Polzi","year":"2020"},{"key":"10.1016\/j.bpc.2020.106510_bb0205","series-title":"Mechanism of Inhibition of SARS-CoV-2 Mpro by N3 Peptidyl Michael Acceptor Explained by QM\/MM Simulations and Design of New Derivatives with Tunable Chemical Reactivity","author":"Arafet","year":"2020"},{"key":"10.1016\/j.bpc.2020.106510_bb0210","doi-asserted-by":"crossref","first-page":"17945","DOI":"10.1021\/jacs.7b08938","article-title":"Can relative binding free energy predict selectivity of reversible covalent inhibitors?","volume":"139","author":"Chatterjee","year":"2017","journal-title":"J. Am. Chem. Soc."},{"key":"10.1016\/j.bpc.2020.106510_bb0215","doi-asserted-by":"crossref","first-page":"5648","DOI":"10.1063\/1.464913","article-title":"Density-functional thermochemistry. III. The role of exact exchange","volume":"98","author":"Becke","year":"1993","journal-title":"J. Chem. Phys."},{"key":"10.1016\/j.bpc.2020.106510_bb0220","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1103\/PhysRevB.37.785","article-title":"Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density","volume":"37","author":"Lee","year":"1988","journal-title":"Phys. Rev. B"},{"key":"10.1016\/j.bpc.2020.106510_bb0225","doi-asserted-by":"crossref","first-page":"1173","DOI":"10.1007\/s00894-007-0233-4","article-title":"Optimization of parameters for semiempirical methods. V. Modification of NDDO approximations and application to 70 elements","volume":"13","author":"Stewart","year":"2007","journal-title":"J. Mol. Model."},{"key":"10.1016\/j.bpc.2020.106510_bb0230","doi-asserted-by":"crossref","first-page":"760","DOI":"10.1002\/jcc.10156","article-title":"Geometry optimization with QM\/MM, ONIOM and other combined methods. I. Microiterations and constraints","volume":"24","author":"Vreven","year":"2003","journal-title":"J. Comp. Chem."},{"key":"10.1016\/j.bpc.2020.106510_bb0235","series-title":"Gaussian 09","author":"Frisch","year":"2016"},{"key":"10.1016\/j.bpc.2020.106510_bb0240","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1016\/0301-0104(81)85090-2","article-title":"Electrostatic interaction of a solute with a continuum. A direct utilization of ab initio molecular potentials for the prevision of solvent effects","volume":"55","author":"Miertu\u0161","year":"1981","journal-title":"Chem. Phys."},{"key":"10.1016\/j.bpc.2020.106510_bb0245","doi-asserted-by":"crossref","first-page":"8452","DOI":"10.1021\/ja960884f","article-title":"Charge screening and the dielectric constant of proteins: insights from molecular dynamics","volume":"118","author":"Simonson","year":"1996","journal-title":"J. Am. Chem. Soc."},{"key":"10.1016\/j.bpc.2020.106510_bb0250","doi-asserted-by":"crossref","first-page":"2778","DOI":"10.1021\/ci200227u","article-title":"LigPlot+: multiple ligand-protein interaction diagrams for drug discovery","volume":"51","author":"Laskowski","year":"2011","journal-title":"J. Chem. Inf. Model."},{"key":"10.1016\/j.bpc.2020.106510_bb0255","doi-asserted-by":"crossref","first-page":"899","DOI":"10.1021\/cr00088a005","article-title":"Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint","volume":"88","author":"Reed","year":"1988","journal-title":"Chem. Rev."},{"key":"10.1016\/j.bpc.2020.106510_bb0260","doi-asserted-by":"crossref","first-page":"1938","DOI":"10.1021\/acscatal.9b04002","article-title":"Exploring the origin of amidase substrate promiscuity in CALB by a computational approach","volume":"10","author":"Galm\u00e9s","year":"2020","journal-title":"ACS Catal."},{"key":"10.1016\/j.bpc.2020.106510_bb0265","doi-asserted-by":"crossref","first-page":"W537","DOI":"10.1093\/nar\/gks375","article-title":"H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulation","volume":"40","author":"Anandakrishnan","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.bpc.2020.106510_bb0270","series-title":"A Microscopic Description of SARS-CoV-2 Main Protease Inhibition with Michael Acceptors. Strategies for Improving Inhibitors Design","author":"Ramos-Guzm\u00e1n","year":"2020"},{"key":"10.1016\/j.bpc.2020.106510_bb0275","doi-asserted-by":"crossref","first-page":"2868","DOI":"10.1002\/jcc.26068","article-title":"Exploring nature and predicting strength of hydrogen bonds: a correlation analysis between atoms-in-molecules descriptors, binding energies, and energy components of symmetry-adapted perturbation theory","volume":"40","author":"Emamian","year":"2019","journal-title":"J. Comput. Chem."}],"container-title":["Biophysical Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0301462220302180?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0301462220302180?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,4]],"date-time":"2025-10-04T07:55:59Z","timestamp":1759564559000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0301462220302180"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,2]]},"references-count":55,"alternative-id":["S0301462220302180"],"URL":"https:\/\/doi.org\/10.1016\/j.bpc.2020.106510","relation":{"has-preprint":[{"id-type":"doi","id":"10.26434\/chemrxiv.12787463","asserted-by":"object"},{"id-type":"doi","id":"10.26434\/chemrxiv.12787463.v1","asserted-by":"object"}]},"ISSN":["0301-4622"],"issn-type":[{"value":"0301-4622","type":"print"}],"subject":[],"published":{"date-parts":[[2021,2]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"An insight into the interaction between \u03b1-ketoamide- based inhibitor and coronavirus main protease: A detailed in silico study","name":"articletitle","label":"Article Title"},{"value":"Biophysical Chemistry","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.bpc.2020.106510","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2020 Elsevier B.V. All rights reserved.","name":"copyright","label":"Copyright"}],"article-number":"106510"}}