In Vitro Screening of Anti-Viral and Virucidal Effects Against SARS-CoV-2 by Phenylamino-Phenoxy-Quinoline Derivatives: An Integrative Computational Approach

Abstract

This study investigated the binding interactions between three groups of 2,4-disubstituted phenylamino-phenoxyquinoline derivatives 1-3(a-d) and four readily available drugs (ritonavir, ensitrelvir, nirmatrelvir, and paxlovid) with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using cytotoxicity, virucidal activity testing, molecular docking, and molecular dynamic methods. Between the concentration range of 500 to 31.25 µg/mL, 1-3(a-d) demonstrated that none of the investigated substances had any harmful effects on Vero E6 cells. The virucidal activity testing demonstrated that ritonavir, ensitrelvir, nirmatrelvir, paxlovid, and 3c had log reduction values ranging from 2.99 to 3.50 when treated with concentrations between 62.5 to 125 µg/mL. Ritonavir and 3c had exceptional log reduction values that surpassed those of the other substances examined. 3c exhibited the highest log reduction value when compared to the other 2,4-disubstituted quinoline derivatives evaluated at the same concentration. The molecular docking approach revealed that all analyzed compounds interacted with the active site of the SARS-CoV-2 main protease (Mpro) through hydrogen bonds and π-sulfur interactions. Furthermore, molecular dynamics simulations, combined with binding free energy calculations using MM-PBSA and MM-GBSA techniques, demonstrated the binding free energy of Mpro-ensitrelvir and Mpro-3c was greater than that of Mpro-1a. To validate our computational results, we conducted Mpro inhibitor screening assay. The analysis was confirmed that compound 3c exhibits strong inhibitory activity (IC50 = 2.71 μM), consistent with our virucidal testing and computational approaches. The results emphasize the potential of 2,4-disubstituted quinoline derivatives as promising candidates for inhibiting SARS-CoV-2. This provides crucial insights for developing effective antiviral drugs.