In silico analysis and characterization of potential inhibitors of MmaA3, a methoxy mycolic acid synthase from Mycobacterium tuberculosis

Abstract

The emergence of the multi-and extensively drug-resistant (MDR and XDR) strains of Mycobacterium tuberculosis (M.tb), necessitates paradigm-shifting therapeutic approaches. The impermeable waxy lipid layer, primarily composed of mycolic acids, is a key factor in conferring resistance to conventional drugs. This study introduces a novel strategy to combat drug resistance by targeting Methoxy mycolic acid synthase 3 (MmaA3), a critical enzyme in the mycolic acid biosynthesis pathway. MmaA3 is responsible for the O-methylation of hydroxymycolate precursors and emerges as a promising therapeutic target. Through homology-based modeling, we generated a three-dimensional structure of MmaA3, providing crucial insights into its structural characteristics. High throughput virtual screening was performed against the MmaA3 model, using diverse sources: knowledge-based, FDA-approved Drugbank, and Asinex-Elite libraries. Through rigorous computational analyses, including binding affinity assessments, molecular interactions analysis, and binding free energy calculations, potential inhibitors of MmaA3 have been identified. Subsequent validation studies evaluated the stability of top protein-ligand complexes, and free energy calculations using molecular dynamics simulations. The stability of complexes within the catalytic site was confirmed through RMSD and RMSF profile analyses. Furthermore, binding free energy calculations using the MM-GBSA approach revealed significant binding affinity of identified ligands for MmaA3 target protein, comparable to its substrate/cofactors. These findings underscore the potential of the proposed molecules as candidates for further experimental exploration, offering promising avenues for the development of effective inhibitors against M.tb. Overall, our research contributes to significantly advancing the formulation of progressive therapeutic strategies in combating drug-resistant tuberculosis.

Communicated by Ramaswamy H. Sarma

Keywords:

• MmaA3
• Mycobacterium tuberculosis
• Methyl transferases
• MD simulations
• MMGBSA
• virtual screening

Acknowledgments

C.M. and B.C. thank the Schrӧdinger team of Ms. Shelvia Malik, Mr. Prajwal Nandekar, Mr. Pritesh Bhat, and Mr. Kishore Venkatesh for access to the facilities and excellent training sessions. B.C. thanks Dr. Anandita Singh, Dr. Ramakrishnan Sitaraman, Dr. Shashi Bhushan Tripathi, Dr. Udit Soni, and Dr. Som Mondal for crucial inputs as part of the Student Research Committee (SRC), TERI SAS.

Author contributions

B.C. designed, conducted the experiments, and analyzed the outcomes. D.S. conducted MDS experiments and S.A. provided expertise in MDS. B.C. and R.S. analyzed and drafted the preliminary results. P.A.M. provided intellectual inputs and contributed to experimental design and analyses. C.M. conceived, designed, and coordinated the study, analyzed the results, and drafted the manuscript. All authors contributed to edit and review the final manuscript.

Data availability statement

Any data that is generated within the report will be available if required from the corresponding author.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

R.S. thanks the CSIR-HRDG for the fellowship (grant no. 09/995(0004)/2019-EMR-1). The study is supported by the grants received from the Department of Biotechnology (DBT), New Delhi, India [Grant ID: No. BT/RLF/Re-entry/47/2014].