Identification of irreversible protein splicing inhibitors as potential anti-TB drugs: insight from hybrid non-covalent/covalent docking virtual screening and molecular dynamics simulations

Abstract

Tuberculosis is responsible for ~3 million deaths annually and is one of the most prevalent infectious diseases known to mankind. Despite ongoing developments in medicine, the emergence of drug resistant Mycobacterium tuberculosis remains of great interest, specifically in developing countries where medical treatment is not readily available. The aim of this study is to identify and explore the binding affinities of novel potential inhibitors that can irreversibly inhibit the intein protein via a covalent bond formation with its active site cysteine. Our search for new leads as potential protein splicing inhibitors is based on Michael acceptor-like structures since they are strong electrophiles which react covalently with the nucleophilic cysteine SH group in the enzyme active site. Structure-based virtual screening using a hybrid non-covalent/covalent docking was performed. Furthermore, molecular dynamic simulations (MD) and extensive post-dynamic analysis were performed in order to ensure the stability of the docked ligand-enzyme complexes and provide insight into the binding affinities and interaction patterns of the screened inhibitors. Interestingly, three novel hits have shown better binding affinity in comparison to experimentally determined compounds with known protein splicing inhibitory activity. MD simulations also revealed that the docked compounds are fairly stable in the protein active site. Per-residue interaction analysis has highlighted the most important active site residues contributing to the inhibitor binding.