The 3C protease is distinguished from most proteases due to the presence of cysteine nucleophile that plays an essential role in viral replication. This peculiar structure encompassed with its role in viral replication has promoted 3C protease as an interesting target for therapeutic agents in the treatment of diseases caused by human rhinovirus (HRV). Herein we present a comprehensive molecular dynamics study of the comparison of two potent inhibitors, sg85 and rupintrivir complexed with HRV-3C protease. The binding free energy studies revealed a higher binding affinity for sg85 −58.853 kcal/mol than for rupintrivir −54.0873 kcal/mol and this was found to be in correlation with the experimental data. The energy decomposition analysis showed that, residues Leu 127, Thr 142, Ser 144, Gly 145, Tyr 146, Cys 147, His 161, Val 162, Gly 163, Gly 164, Asn 165, Phe 170 largely contributed to the binding of sg85, whereas His 40, Leu 127 and Gly 163 impacted the binding of rupintrivir. It further showed that His 40, Glu 71, Leu 127, Cys 147 Gly 163 and Gyl 164 are crucial residues that play a key role in ligand-enzyme binding; amongst these residues are residues of the conserved active site (His 40, Glu 71 and Cys 147). These findings provide a comprehensive understanding of the dynamics and structural features and will serve as guidance in the design and development of potent novel inhibitors of HRV. Graphical Abstract
A molecular dynamic investigation of Human Rhinovirus 3C Protease Drug Target: Insights towards the design of potential Inhibitors