Tuberculosis (TB) continues to pose a global health challenge, exacerbated by the rise of drug-resistant strains. The development of new TB therapies is an arduous and time-consuming process. To expedite the discovery of effective treatments, computational structure-based drug repurposing has emerged as a promising strategy. From this perspective, conditionally essential targets present a valuable opportunity, and the mycobactin biosynthesis pathway stands out as a prime example highlighting the intricate response of Mycobacterium tuberculosis (Mtb) to changes in iron availability. This study focuses on the repurposing and revival of FDA-approved drugs (library) as potential inhibitors of MbtA, a crucial enzyme in mycobactin biosynthesis in Mtb conserved among all species of mycobacteria. The literature suggests this pathway to be associated with drug efflux pumps, which potentially contribute to drug resistance. This makes it a potential target for antitubercular drug discovery. Herein, we utilized cheminformatics and structure-based drug repurposing approaches, viz., molecular docking, dynamics, and PCA analysis, to decode the intermolecular interactions and binding affinity of the FDA-reported molecules against MbtA. Virtual screening revealed ten molecules with significant binding affinities and interactions with MbtA. These drugs, originally designed for different therapeutic indications (four antiviral, three anticancer, one CYP450 inhibitor, one ACE inhibitor, and one leukotriene antagonist), were repurposed as potential MbtA inhibitors. Furthermore, our study explores the binding modes and interactions between these drugs and MbtA, shedding light on the structural basis of their inhibitory potential. Principal component analysis highlighted significant motions in MbtA-bound ligands, emphasizing the stability of the top protein–ligand complexes (PLCs). This computational approach provides a swift and cost-effective method for identifying new MbtA inhibitors, which can subsequently undergo validation through experimental assays. This streamlined process is facilitated by the fact that these compounds are already FDA-approved and have established safety and efficacy profiles. This study has the potential to lay the groundwork for addressing the urgent global health challenge at hand, specifically in the context of combating antimicrobial resistance (AMR) and tuberculosis (TB).

The pathogenicity and virulence of Mycobacterium tuberculosis has further potentiated its infectiousness, making it a killer disease, as is evident from the WHO database. Eradicating the TB epidemic by 2030 is amongst the major health targets of the United Nations Sustainable Development Goals (SDGs). The increase in multidrug-resistant TB (MDR-TB) cases has challenged and prompted the scientific community to develop novel chemotherapeutic agents with novel mechanisms of action. The goal can be achieved by “conditionally essential target” (CET)-based drug design. The research pertaining to the mycobactin biosynthesis pathway (MBP) relating to iron acquisition is in a nascent stage; the pathway serves as a promising endogenous target for novel lead compound discoveries (non-specific MBP inhibitors). As a continuation of our previous research, reported by Stirret et al., 2008 and Ferreras et al., 2011, in this study we further aim to explore the structural diversity of the previously identified active molecules as this could lead to the discovery of a more potent analog. Eventually, we designed a small library of mycobactin analogs retaining diaryl-substituted pyrazoline (DAP) as the basic scaffold and tested their in silico stabilities by molecular docking (AutoDock 4.2.6). Docking of the designed molecules was performed in the active site of the MbtA receptor (by analogy with the related structure, PDB: 1MDB) to evaluate the binding modes and inhibitory profiles. The lowest energy conformation of each docked ligand was analyzed with the BIOVIA Discovery Studio Visualizer. The docking results identified GM08 and GM09 as potent inhibitors which could therefore serve as good leads. The ADMET profile also revealed satisfactory results. Furthermore, what remains to be seen is the stability of each molecule by employing MD simulation along with intracellular activity.

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.

Tuberculosis (TB) continues to pose a global health challenge, exacerbated by the rise of drug-resistant strains. The development of new TB therapies is an arduous and time-consuming process. To expedite the discovery of effective treatments, computational structure-based drug re-purposing has emerged as a promising strategy. From this perspective, conditionally essential targets present a valuable opportunity, and the mycobactin biosynthesis pathway stands out as a prime example highlighting the intricate response of Mycobacterium tuberculosis (Mtb) to changes in iron availability. This study focuses on the re-purposing and revival of FDA-approved drugs (library) as potential inhibitors of MbtA, a crucial enzyme in mycobactin biosynthesis in Mtb conserved among all species of mycobacteria. Literature suggests this pathway to be associated with drug efflux pumps, which potentially contribute to drug resistance. This makes it a potential target for antitubercular drug discovery. Herein we utilized cheminformatics and structure-based drug repurposing approaches, viz., molecular docking, dynamics, and PCA analysis, to decode the intermolecular interactions and binding affinity of the FDA-reported molecules against MbtA. The virtual screening revealed ten molecules with significant binding affinities and interactions with MbtA. These drugs, originally designed for different therapeutic indications (4: antiviral, 3: anticancer, 1: CYP450 inhibitor, 1: ACE inhibitor, and 1: leukotriene antagonist), are repurposed as potential MbtA inhibitors. Furthermore, our study explores the binding modes and interactions between these drugs and MbtA, shedding light on the structural basis of their inhibitory potential. Principal component analysis highlighted significant motions in MbtA-bound ligands, emphasizing the stability of the top Protein-Ligand Complexes (PLCs). This computational approach provides a swift and cost-effective method for identifying new MbtA inhibitors, which can subsequently undergo validation through experimental assays. This streamlined process is facilitated by the fact that these compounds are already FDA-approved and have established safety and efficacy profiles. This study has the potential to lay the groundwork for addressing the urgent global health challenge at hand, specifically in the context of combating Antimicrobial Resistance (AMR) and Tuberculosis (TB).