Quantitative structure-activity relationships, molecular docking and molecular dynamics simulations reveal drug repurposing candidates as potent SARS-CoV-2 main protease inhibitors

Autor(es)

de Souza, Anacleto Silva ^[1] ; de Souza, Robson Francisco ^[1] ; Guzzo, Cristiane Rodrigues ^[1]

Afiliação do(s) autor(es)

^[1] Univ Sao Paulo, Inst Biomed Sci, Dept Microbiol, Av Prof Lineu Prestes 1374, Cidade Univ, BR-5508900 Sao Paulo - Brazil

• Tipo de documento: Artigo Científico
• Fonte: JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS; JUL 2021.
• Citações Web of Science: 0

Resumo

The current outbreak of COVID-19 is leading an unprecedented scientific effort focusing on targeting SARS-CoV-2 proteins critical for its viral replication. Herein, we performed high-throughput virtual screening of more than eleven thousand FDA-approved drugs using backpropagation-based artificial neural networks (q(LOO)(2) = 0.60, r(2) = 0.80 and r(pred)(2) = 0.91), partial-least-square (PLS) regression (q(LOO)(2) = 0.83, r(2) = 0.62 and r(pred)(2) = 0.70) and sequential minimal optimization (SMO) regression (q(LOO)(2) = 0.70, r(2) = 0.80 and r(pred)(2) = 0.89). We simulated the stability of Acarbose-derived hexasaccharide, Naratriptan, Peramivir, Dihydrostreptomycin, Enviomycin, Rolitetracycline, Viomycin, Angiotensin II, Angiotensin 1-7, Angiotensinamide, Fenoterol, Zanamivir, Laninamivir and Laninamivir octanoate with 3CL(pro) by 100 ns and calculated binding free energy using molecular mechanics combined with Poisson-Boltzmann surface area (MM-PBSA). Our QSAR models and molecular dynamics data suggest that seven repurposed-drug candidates such as Acarbose-derived Hexasaccharide, Angiotensinamide, Dihydrostreptomycin, Enviomycin, Fenoterol, Naratriptan and Viomycin are potential SARS-CoV-2 main protease inhibitors. In addition, our QSAR models and molecular dynamics simulations revealed that His41, Asn142, Cys145, Glu166 and Gln189 are potential pharmacophoric centers for 3CL(pro) inhibitors. Glu166 is a potential pharmacophore for drug design and inhibitors that interact with this residue may be critical to avoid dimerization of 3CL(pro). Our results will contribute to future investigations of novel chemical scaffolds and the discovery of novel hits in high-throughput screening as potential anti-SARS-CoV-2 properties. Communicated by Ramaswamy H. Sarma (AU)

• Processo FAPESP: 20/04680-0 - Desenho de diferentes fragmentos da proteína de superfície, spike, do SARS-CoV-2, para desenvolvimento de testes rápidos e de vacina
• Beneficiário: Cristiane Rodrigues Guzzo Carvalho
• Modalidade de apoio: Auxílio à Pesquisa - Regular
• Processo FAPESP: 19/00195-2 - Compreensão das redes de sinalização c-di-GMP e do sistema de secreção tipo II presentes no patógeno humano Leptospira interrogans Copenhageni
• Beneficiário: Cristiane Rodrigues Guzzo Carvalho
• Modalidade de apoio: Auxílio à Pesquisa - Regular
• Processo FAPESP: 16/09047-8 - Genômica comparativa de toxinas bacterianas associadas ao sistema secretório do tipo IV
• Beneficiário: Robson Francisco de Souza
• Modalidade de apoio: Auxílio à Pesquisa - Regular