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

• Published in: Journal of biomolecular structure & dynamics 2022-01, Vol.40 (21), p.11339-11356
• Main Authors: de Souza, Anacleto Silva, de Souza, Robson Francisco, Guzzo, Cristiane Rodrigues
• Format: Article
• Language: English
• Subjects: Acarbose; Angiotensin Amide; Antiviral Agents - pharmacology; Dihydrostreptomycin Sulfate; Drug Repositioning; Enviomycin; Fenoterol; high-throughput virtual screening; Molecular Docking Simulation; Molecular Dynamics Simulation; molecular dynamics simulations; prediction; Protease Inhibitors - pharmacology; QSAR models; Quantitative Structure-Activity Relationship; SARS-CoV-2; SARS-CoV-2 - drug effects
• ISSN: 0739-1102; 1538-0254
• DOI: 10.1080/07391102.2021.1958700

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 2 LOO = 0.60, r 2 = 0.80 and r 2 pred = 0.91), partial-least-square (PLS) regression (q 2 LOO = 0.83, r 2 = 0.62 and r 2 pred = 0.70) and sequential minimal optimization (SMO) regression (q 2 LOO = 0.70, r 2 = 0.80 and r 2 pred = 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