Inhibitor induced conformational changes in SARS-COV-2 papain-like protease

Autor(es)

Ferreira, Glaucio Monteiro ; Pillaiyar, Thanigaimalai ; Hirata, Mario Hiroyuki ; Poso, Antti ; Kronenberger, Thales

• Tipo de documento: Artigo Científico
• Fonte: SCIENTIFIC REPORTS; v. 12, n. 1, p. 13-pg., 2022-07-08.

Resumo

SARS-CoV-2's papain-like protease (PLpro) interaction with ligands has recently been explored with a myriad of crystal structures. We used molecular dynamics (MD) simulations to study different PLpro-ligand complexes, their ligand-induced conformational changes, and interactions. We focused on inhibitors reported with known IC50 against PLpro, namely GRL-0617, XR8-89, PLP_Snyder530, and Sander's recently published compound 7 (CPD7), and compared these trajectories against the apostructure (Apo), with a total of around 60 mu s worth simulation data. We aimed to study the conformational changes using molecular dynamics simulations for the inhibitors in the PLpro. PCA analyses and the MSM models revealed distinct conformations of PLpro in the absence/presence of ligands and proposed that BL2-loop contributes to the accessibility of these inhibitors. Further, bulkier substituents closer to Tyr268 and Gln269 could improve inhibition of SARS-CoV-2 PLpro by occupying the region between BL2-groove and BL2-loop, but we also expand on the relevance of exploring multiple PLpro sub-pockets to improve inhibition. (AU)

• Processo FAPESP: 16/12899-6 - Caracterização genômica, epigenômica e farmacogenômica de portadores de hipercolesterolemia familial na população brasileira
• Beneficiário: Mario Hiroyuki Hirata
• Modalidade de apoio: Auxílio à Pesquisa - Temático
• Processo FAPESP: 19/24112-9 - Desenvolvimento de novos inibidores da HMG-CoA redutase, integrando estudos genéticos e modelagem molecular de pacientes dislipidêmicos
• Beneficiário: Glaucio Monteiro Ferreira
• Modalidade de apoio: Bolsas no Exterior - Estágio de Pesquisa - Pós-Doutorado
• Processo FAPESP: 21/11205-9 - Desenvolvimento de novos fármacos baseados na estrutura de proteínas essenciais para síntese e metabolismo do colesterol, integrando estudos genéticos e modelagem molecular de pacientes dislipidêmicos
• Beneficiário: Glaucio Monteiro Ferreira
• Modalidade de apoio: Bolsas no Brasil - Pós-Doutorado