Marine Pyrrole Imidazole Alkaloids as Anti-Cathepsins Agents for SARS-CoV-2 Entry Inhibition: Insights from in silico Docking and Molecular Dynamic Simulations

Abstract

The emergence of SARS-CoV-2 variants poses a significant threat to public health, highlighting the urgent need for novel therapeutic agents to address gaps in current healthcare solutions. Although several preventive vaccines have been developed and approved, their long-term efficacy remains uncertain, and the spike protein targeted by these vaccines is highly susceptible to mutation. Consequently, targeting host proteases such as Cathepsins L and B, which are implicated in viral entry, could provide a potent antiviral strategy against SARS-CoV-2. These Cathepsins are appealing drug targets because of their well-defined substrate-binding pockets, which can be utilized as binding sites for drug enzyme inhibitors. In this study, we present an integrated computer-aided drug discovery approach for a selection of 14 pyrrole-imidazole alkaloids targeting Cathepsins L and B. This approach employs a combination of modern computational methodologies, including molecular docking and molecular dynamics (MD) simulations. Our molecular docking studies identified a promising marine alkaloid, Mauritiamine, which exhibited notable binding affinities for Cathepsin L (-9.35 kcal/mol) and Cathepsin B (-9.03 kcal/mol). Subsequently, MD simulations were conducted to investigate the interaction dynamics and structural stability of the docked complexes. The resulting analyses, including maps of structural deformability, b-factors, eigenvalues, variance and covariance matrices, along with elastic network models, confirmed the structural stability of both the Cathepsin L-Mauritiamine and Cathepsin B-Mauritiamine complexes. These results underscore the potential of Mauritiamine as a promising candidate for antiviral therapy against SARS-CoV-2. Further in vitro and in vivo studies will pave the way for the identification of clinically relevant antivirals inspired by marine pyrrole-imidazole alkaloids.