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dc.contributor.authorHernández González, Jorge E. [UNESP]
dc.contributor.authorEberle, Raphael J.
dc.contributor.authorWillbold, Dieter
dc.contributor.authorCoronado, Mônika A.
dc.date.accessioned2022-04-28T19:50:56Z
dc.date.available2022-04-28T19:50:56Z
dc.date.issued2022-01-24
dc.identifierhttp://dx.doi.org/10.3389/fmolb.2021.816166
dc.identifier.citationFrontiers in Molecular Biosciences, v. 8.
dc.identifier.issn2296-889X
dc.identifier.urihttp://hdl.handle.net/11449/223492
dc.description.abstractThe SARS-CoV-2 main protease, also known as 3-chymotrypsin-like protease (3CLpro), is a cysteine protease responsible for the cleavage of viral polyproteins pp1a and pp1ab, at least, at eleven conserved sites, which leads to the formation of mature nonstructural proteins essential for the replication of the virus. Due to its essential role, numerous studies have been conducted so far, which have confirmed 3CLpro as an attractive drug target to combat Covid-19 and have reported a vast number of inhibitors and their co-crystal structures. Despite all the ongoing efforts, D-peptides, which possess key advantages over L-peptides as therapeutic agents, have not been explored as potential drug candidates against 3CLpro. The current work fills this gap by reporting an in silico approach for the discovery of D-peptides capable of inhibiting 3CLpro that involves structure-based virtual screening (SBVS) of an in-house library of D-tripeptides and D-tetrapeptides into the protease active site and subsequent rescoring steps, including Molecular Mechanics Generalized-Born Surface Area (MM-GBSA) free energy calculations and molecular dynamics (MD) simulations. In vitro enzymatic assays conducted for the four top-scoring D-tetrapeptides at 20 μM showed that all of them caused 55–85% inhibition of 3CLpro activity, thus highlighting the suitability of the devised approach. Overall, our results present a promising computational strategy to identify D-peptides capable of inhibiting 3CLpro, with broader application in problems involving protein inhibition.en
dc.description.sponsorshipFundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ)
dc.language.isoeng
dc.relation.ispartofFrontiers in Molecular Biosciences
dc.sourceScopus
dc.subject3CLpro
dc.subjectD-peptide
dc.subjectmolecular dynamics simulation
dc.subjectSARS-CoV-2
dc.subjectvirtual screening
dc.titleA Computer-Aided Approach for the Discovery of D-Peptides as Inhibitors of SARS-CoV-2 Main Proteaseen
dc.typeArtigo
dc.contributor.institutionUniversidade Estadual Paulista (UNESP)
dc.contributor.institutionUniversidade Federal do Rio de Janeiro (UFRJ)
dc.contributor.institutionForschungszentrum Jülich
dc.contributor.institutionUniversitätsstraße
dc.description.affiliationMultiuser Center for Biomolecular Innovation IBILCE Universidade Estadual Paulista (UNESP), São Jose do Rio Preto
dc.description.affiliationLaboratory for Molecular Modeling and Dynamics Instituto de Biofísica Carlos Chagas Filho Universidade Federal do Rio de Janeiro Cidade Universitária Ilha do Fundão
dc.description.affiliationInstitute of Biological Information Processing (IBI-7 Structural Biochemistry) Forschungszentrum Jülich
dc.description.affiliationInstitut für Physikalische Biologie Heinrich-Heine-Universität Düsseldorf Universitätsstraße
dc.description.affiliationJuStruct: Jülich Centre for Structural Biology Forschungszentrum Jülich
dc.description.affiliationUnespMultiuser Center for Biomolecular Innovation IBILCE Universidade Estadual Paulista (UNESP), São Jose do Rio Preto
dc.identifier.doi10.3389/fmolb.2021.816166
dc.identifier.scopus2-s2.0-85124938065
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