Integrated computational and experimental approaches to identify new papain-like protease inhibitors

Abstract

SARS-CoV-2 papain-like protease (PLpro), a key viral protease, plays a crucial role in the viral replication and pathogenesis, making it an attractive target for the development of antiviral therapies. Thus to target PLpro, the chlorogenic acid was chosen based on its well-established characteristics as a natural compound with inhibitory properties against viral proteases. The research strategy involved a synergistic combination of in-silico and in-vitro techniques, enabled successful identification of a natural inhibitor for PLpro. In the docking analysis, it was observed that chlorogenic acid exhibited a more pronounced interaction energy with PLpro compared to GRL0617. Additionally, the molecular dynamics simulations demonstrated remarkable stability of the chlorogenic acid-PLpro complex, along with close proximity in conformational dynamics. The assessment of post-processing end-state free energies indicated comparable affinities for both molecules. Furthermore, the enzymatic inhibition assay performed for dose-response analysis provided validation for chlorogenic acid as a potential inhibitor of PLpro. This experimental assessment strengthens the evidence supporting the inhibitory activity of chlorogenic acid against PLpro. Overall, this comprehensive analysis serves as a valuable platform for the development of potential therapeutic candidates targeting PLpro, offering promising prospects for combating SARS-CoV-2.