Pharmacophore model-based virtual screening, docking, biological evaluation and molecular dynamics simulations for inhibitors discovery against α-tryptophan synthase from Mycobacterium tuberculosis

Abstract

Discovery of new anti-tuberculosis drugs with novel mode of action is urgently needed. The tryptophan synthase is a genetically validated enzyme that catalyzes last step of tryptophan biosynthetic pathway required for growth and survival of Mycobacterium tuberculosis. Here, a ligand-based pharmacophore model was built using molecular operating environment (MOE) software (version 2010.12) and validation of generated pharmacophoric features was done using active, inactive and decoy set of molecules. The generated pharmacophore model was used for screening of 7,523,972 drug-like molecules of ZINC database. The best matches (RMSD < 1) retrieved as a result of screening were subjected to molecular docking studies into active pocket of α-subunit of tryptophan synthase from M. tuberculosis. The five hits were selected and validated through anti-tuberculosis activity analysis. Finally, a new inhibitor ZINC09150898 has been identified with best binding score −32.07 kcal/mol, showing 100% growth inhibition of M. tuberculosis (H37Rv strain) at 50 µg/mL. This identified inhibitor–protein complex was further subjected to MD simulations studies (50 ns) involving root mean square deviation, root mean square fluctuation, secondary structure analysis and pocket interaction analysis to explore its binding mode stability inside active pocket. The binding free energies of inhibitor–protein complex through MM-PBSA analysis suggested that van der Waals interactions play a vital role for retention of identified inhibitor inside the protein pocket. All these analyses confirmed retention of ligand inside pocket and no unfolding in protein structure was observed over explored time scale.

Communicated by Ramaswamy H. Sarma

Keywords:

• Pharmacophore
• RMSD
• molecular docking
• anti-tuberculosis
• MD simulations
• MMPBSA

Acknowledgments

We are thankful to provincial TB control program, Hayatabad Peshawar, Khyber Pakhtunkhwa who facilitated us to perform experiments at their highly equipped labs. The authors also extend their appreciation to the deanship of scientific research at King Khalid University for its funding this prolific research group No. R. G. P.2/23/41/2020.

Author contributions

S.N. and U.F. conceived, designed and performed the experiments, analyzed the data, and wrote the manuscript. Y.N.M., A.A. and A.M. contributed research materials and reviewed the drafts of manuscript. S.K., Z.U.H., M.S. and R.S. analyzed the data, prepared figures/tables and reviewed drafts of manuscript.

Disclosure statement

The authors declared that there is no conflict of interest.