Analysis of critical protein-protein interactions of SARS-CoV-2 capping and proofreading molecular machineries towards designing dual target inhibitory peptides

Abstract

AbstractCoronaviruses (CoVs) have been the cause of human respiratory syndromes for many years. In recent years, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as the cause of the coronavirus disease (COVID-19) global pandemic has imposed enormous health care issues and economic burden. The recent emerging SARS-CoV-2 variants with higher transmissibility and substantial immune evasion, have highlighted the importance of sustainable and imperative solutions to develop novel therapeutics other than vaccination to combat CoVs infections. In the search for promising antivirals for coronaviruses, besides receptor recognition and virus entry, efforts have concentrated on targeting other molecular machineries of the virus, such as the replication/transcription complex (RTC). Here, the key interacting residues that mediate the protein-protein interactions (PPIs) of nsp10 with nsp16 and nsp14 have been comprehensively analyzed. Consequently, the key residues' interaction maps, interaction energies, structural networks, and dynamics were investigated. Nsp10 stimulates nsp14's exoribonuclease (ExoN) as well as nsp16's 2′O-methyltransferase (2′O-MTase). Nsp14 ExoN is an RNA proofreading enzyme that supports replication fidelity. Nsp16 2′O-MTase is responsible for completion of the RNA capping to ensure efficient replication and translation and escape from the host cell's innate immune system. The results of PPIs analysis proposed crucial information which was applicable to anti SARS-CoV-2 drug design. Based on the PPIs analysis, a set of dual-target peptide inhibitors were designed on the basis of the predicted shared protein-protein interfaces of the nsp16-nsp10 and nsp14-nsp10 interactions. The peptides were evaluated by molecular docking, peptide-protein interaction analysis, and molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) calculations, and then were further optimized byin silicosaturation mutagenesis. According to the predicted evolutionary conservation among CoVs for the target residues that interact with the designed peptides, the designed peptides have the potential to be developed as dual target pan-coronavirus inhibitors.