Discovery of Putative GyrB Inhibitors against Mycobacterium tuberculosis: A Combined Virtual Screening and Experimental Study

Introduction: With the rapid emergence of drug-resistant strains of tuberculosis, resistance to current first-line and second-line anti-tuberculosis drugs is becoming increasingly prevalent. Consequently, the discovery of new lead compounds is essential to address this challenge. GyrB has emerged as a promising target for tuberculosis treatment due to its pivotal role in DNA replication and topology regulation in Mycobacterium tuberculosis. Methods: In this study, a multi-conformational virtual screening approach, complemented by antibacterial activity assays, was utilized to identify novel GyrB inhibitors from the ChemDiv database. Results: Among the 27 compounds purchased, 10 exhibited significant inhibitory effects against the H37Rv strain, with 8 featuring novel core scaffolds. Notably, three compounds (V027-7669, V017-8710, and 5132-0213) demonstrated a minimum inhibitory concentration (MIC) of 8 μg/mL. Compounds V027-7669 and V017-8710, in particular, showed antibacterial activity against a multidrug-resistant tuberculosis strain, with MIC values of 32 μg/mL and 16 μg/mL, respectively. Molecular dynamics simulations revealed that both V027-7669 and V017-8710 bind stably to GyrB, which are primarily driven by nonpolar interactions. Furthermore, both of them occupy a novel sub-pocket formed by residues Val99, Gly106, Val123, Gly124, and Val125, where they establish hydrogen bonds with Val125. Conclusion: Our study underscores the effectiveness of a multi-conformational virtual screening strategy in identifying novel GyrB inhibitors and suggests V027-7669 and V017-8710 as promising lead compounds for the development of treatments against multidrug- resistant tuberculosis.