Identification of potential inhibitors of dihydrofolate reductase (DHFR) through blocking the folate biosynthetic pathway of Mycobacterium tuberculosis utilizing structure-based virtual screening

Abstract

Tuberculosis (TB) has emerged as a leading cause of death due to a single infectious agent—Mycobacterium tuberculosis (Mt). This situation is exacerbated by delayed diagnosis, inadequate administration of effective TB medications, prolonged duration of treatment, shortage of toxin-free TB drugs, and frequent increases in resistance to most TB drugs. In an urge to find potential drug candidates for the treatment of fatal infectious TB disease, we targeted the folate biosynthetic pathway that involves the ubiquitous enzyme dihydrofolate reductase (DHFR), which catalyzes the NADPH-dependent reduction of dihydrofolate with the generation of tetrahydrofolate (THF). Blocking the enzymatic activity of DHFR exhausts the cellular pool of THF, which results in cessation of DNA synthesis in rapidly proliferating cells and ultimately cell death. Herein, a total of 1026 drug-like molecules with antibacterial activities were tested using several in silico tools for determining drug-likeness features, ADMET (absorption, distribution, metabolism, excretion, and toxicity) profiling, binding affinity, and conformation analysis using Autodock Vina and Schrodinger Suite. This exhaustive investigation identified CHEMBL577, CHEMBL161702, and CHEMBL1770248 as potential drug candidates for the inhibition of M. tuberculosis DHFR protein. Root mean square deviation, root mean square fluctuation, hydrogen bond, and MMGBSA evaluation by 100 ns molecular dynamics simulation (MDS) confirmed their molecular stability with the target protein. All of these drug-like compounds outperformed the control drugs trimethoprim and methotrexate in molecular docking and molecular dynamics simulation tests. Therefore, our study suggests these M. tuberculosis DHFR inhibitors as promising drug candidates. However, additional wet-lab experiments are required to verify their potential therapeutic potency as novel drugs against M. tuberculosis.