Designing and In Silico Evaluation of Some Non-Nucleoside <i>MbtA</i> Inhibitors: On Track to Tackle Tuberculosis

Abstract

The WHO database shows that mycobacterium tuberculosis has become an epidemic worldwide due to its pathogenicity and virulence, which have magnified its infectiousness. The situation becomes grimmer with the prevalence of MDR-TB, XDR-TB, emergence of cross-resistance, ineffectiveness of novel therapeutic targets, failure of novel medications in clinical trials, currently available drugs losing their therapeutic efficacy, lack of drug discovery efforts due to poor ROI, and the existence of co-infections; i.e., HIV, TB, COVID, and HIV-TB-COVID. Following our prior studies described by Stirret et al. in 2008, Ferreras et al. in 2011, and Shyam et al. in 2021, herein we focus on exploring pyrazoline-based mycobactin analogs (non-specific mycobactin biosynthesis inhibitors) targeting the MbtA enzyme (first step of mycobactin biosynthesis) with a hope of finding a more potent analog showing a high affinity for MbtA. The design strategy involves retaining the structural features of mycobacterial siderophores. Herein, a small library (12 molecules) of mycobactin analogs were designed, keeping the necessary skeleton (diaryl-substituted pyrazoline (DAP)) intact and assessed their stability using in silico tools. In order to determine the binding modes and inhibitory profiles of the designed ligands, docking was carried out in the active pocket of MbtA (analogous with the homologous structure with PDB ID: 1MDB). The best energy conformation (lowest score) of each docked ligand was represented graphically. The ADMET profile of each molecule was analyzed. The best molecule that revealed a good ADMET profile was taken up for MD simulation study (45 ns). Results revealed that the designed compounds GV08 (−8.80 kcal/mol, 352.58 nM), GV09 (−8.61 kcal/mol, 499.91 nM), GV03 (−8.59 kcal/mol, 508.51 nM), and GV07 (−8.54 kcal/mol, 553.44 nM) had a good docking score and inhibition constant. Of these, GV08 showed a good ADME profile with all the major parameters lying in the acceptable ranges. They also showed the least toxicity with no hepatotoxicity and skin sensitization. MD simulation studies of GV08 also suggest that it was stable throughout the course of simulation. This could be justified by RMSD, RMSF, and H-bond plots. The future scope invalidates these findings through synthesis, characterization, and intracellular activity.

Keywords

• antitubercular drug discovery
• <i>MbtA</i>
• molecular docking
• MD simulation
• mycobactin
• siderophores