Insights into anti-tuberculosis drug design on the scaffold of nitroimidazole derivatives using structure-based computer-aided approaches†

Deazaflavin-dependent nitroreductase (Ddn) is a crucial enzyme involved in mycolic acid biosynthesis, a vital component of the cell wall in Mycobacterium tuberculosis (MTB)—the bacterial pathogen responsible for tuberculosis. Over the past two decades, nitroimidazole oxazine scaffold (NOS) derivatives have been investigated as potential therapeutic agents targeting Ddn in MTB, with a focus on enhancing drug efficacy, minimizing toxicity, and combating drug resistance. In this study, we performed an extensive theoretical investigation combining three-dimensional quantitative structure–activity relationship (3D-QSAR) studies, all-atom molecular docking, and atomic-level molecular dynamics (MD) simulations. Additionally, we analyzed the binding free energies and their decomposed terms between inhibitors and Ddn to elucidate the structure–activity relationships (SARs) and mechanisms of a series of NOS derivatives developed for MTB inhibition. The CoMFA and CoMSIA models demonstrated strong performance, with cross-validation coefficients (R_cv²) of 0.591 and 0.629, respectively, and prediction coefficients (R_pred²) of 0.7698 and 0.6848 for CoMFA and CoMSIA, respectively. These models effectively predicted the minimum inhibitory concentration (MIC) values of the compounds against MTB based on the NOS scaffold. Molecular docking followed by MD simulations was employed to validate the binding modes of these derivatives at the active site of Ddn, providing detailed insights into their interaction patterns. Notably, our analysis revealed that residues Tyr65, Ser78, Tyr130, Tyr133, and Tyr136 played critical roles in determining the potency of the compounds by contributing significantly to their binding energies. These findings provide valuable guidance for the rational design of novel NOS inhibitors with enhanced potential as effective anti-tuberculosis agents.