Modes of Binding of Small Molecules Dictate the Interruption of RBD-ACE2 Complex of SARS-CoV-2

The spike protein is a vital target for therapeutic advancement to inhibit viral entrance. Given that the connection between Spike and ACE2 constitutes the initial phase of SARS-CoV-2 pathogenesis, obstructing this interaction presents a promising therapeutic approach. This work aims to find compounds from DrugBank that can modulate the stability of the spike RBD-ACE2 protein-protein complex. Employing a therapeutic repurposing strategy, we conducted molecular docking of over 9000 DrugBank compounds against the Spike RBD-ACE2 complex, on ten variants, including the wild-type. We also evaluated the intricate stability of the RBD-ACE2 proteins by molecular dynamics simulations, hydrogen bond analysis, RMSD analysis, radius of gyration analysis, and the QM-MM approach. We assessed the efficacy of the top ten candidates for each variant as an inhibitor. Our findings demonstrated for the first time that DrugBank small molecules can interact in three distinct modalities inside the extensive protein-protein interface of RBD and ACE2 complexes. The top ten analyses identified specific DrugBank candidates for each variant and molecules capable of binding to multiple variants. This comprehensive computational technique enables the screening and forecasting of hits for any big and shallow protein-protein interface drug targets.