SARS-COV-2 M-pro conformational changes induced by covalently bound ligands

Autor(es)

Ferreira, Glaucio Monteiro ^{[1, 2]} ; Kronenberger, Thales ^{[3, 2]} ; Tonduru, Arun Kumar ^[3] ; Crespo Hirata, Rosario Dominguez ^[1] ; Hirata, Mario Hiroyuki ^[1] ; Poso, Antti ^{[3, 2]}

Afiliação do(s) autor(es)

^[1] Univ Sao Paulo, Sch Pharmaceut Sci, Dept Clin & Toxicol Anal, Sao Paulo - Brazil

^[2] Univ Hosp Tubingen, Dept Oncol & Pneumonol, Internal Med 8, Tubingen - Germany

^[3] Univ Eastern Finland, Fac Hlth Sci, Sch Pharm, Kuopio - Finland

• Tipo de documento: Artigo Científico
• Fonte: JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS; AUG 2021.
• Citações Web of Science: 2

Resumo

SARS-CoV-2's main protease (M-pro) interaction with ligands has been explored with a myriad of crystal structures, most of the monomers. Nonetheless, M-pro is known to be active as a dimer but the relevance of the dimerization in the ligand-induced conformational changes has not been fully elucidated. We systematically simulated different M-pro-ligand complexes aiming to study their conformational changes and interactions, through molecular dynamics (MD). We focused on covalently bound ligands (N1 and N3, similar to 9 mu s per system both monomers and dimers) and compared these trajectories against the apostructure. Our results suggest that the monomeric simulations led to an unrealistically flexible active site. In contrast, the M-pro dimer displayed a stable oxyanion-loop conformation along the trajectory. Also, ligand interactions with residues His41, Gly143, His163, Glu166 and Gln189 are postulated to impact the ligands' inhibitory activity significantly. In dimeric simulations, especially Gly143 and His163 have increased interaction frequencies. In conclusion, long-timescale MD is a more suitable tool for exploring in silico the activity of bioactive compounds that potentially inhibit the dimeric form of SARS-CoV-2 M-pro. Communicated by Ramaswamy H. Sarma (AU)

• 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: 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