Identification of novel Mycobacterium tuberculosis dihydrofolate reductase inhibitors through rational drug design

Dihydrofolate reductase (DHFR) is one of the validated drug targets in Mycobacterium tuberculosis (Mtb) infection. DHFR inhibitors have been used to treat various life-threatening diseases such as cancer, malaria, and several bacterial infections. However, all clinically effective DHFR inhibitors are non-selective, and inhibit both human and pathogenic DHFRs more or less to a similar extent. The crystal structure of various DHFRs complexed with nicotinamide adenine dinucleotide phosphate and different inhibitors is available in the protein data bank. The crystal structures are validated and have been used for new drug designing. M. tuberculosis DHFRs and human (h) DHFRs show 26% structure similarity, but their active sites are not identical and this characteristic forms the basis of this study. Because most of the reported inhibitors of M. tuberculosis DHFR are pteridine based and nonselective in nature, that is, they inhibit both microbial and host DHFRs, this study aimed to design and develop selective nonpteridine M. tuberculosis DHFR inhibitors.

In the ternary complex of methotrexate with M. tuberculosis DHFR, whose structure is also available in the protein data bank, the side of the aminopterin ring is accessible to the solvent; additionally, a glycerol "A" molecule is found in a depression nearby. This glycerol molecule interacts with the side chains of Trp22, Asp27, and Gln28, which form a pocket in M. tuberculosis DHFR; by contrast, glycerol is absent in h-DHFR. In the h-DHFRs (complexed with folate or N-(4-carboxy-{-[(2, 4-diamino pteridine-6-yl methyl)-amino]-benzoyl amino} -butyl) pthalamic acid (COP)), the site is well packed with three hydrophobic residue side chains, Leu22, Pro26, and Phe31, which correspond to Leu20, Arg23, and Gln28, respectively, found in M. tuberculosis DHFR. Therefore, compounds with side chain, which could mimic the binding mode of glycerol to protein, may bind to M. tuberculosis DHFR selectively. Such a derivative should be sterically and chemically hindered from forming a complex with h-DHFR. This assumption forms the basis of this study and this understanding has been used for designing selective inhibitors of M. tuberculosis DHFR.

A number of novel nonpteridine-based molecules have been identified after the virtual screening of three databases (MDPI, NCI and inhouse databases). The best molecules identified after screening the three databases have been synthesized and tested for antitubercular activity. The results are promising and require further work in this direction.

Structure based drug design can be used as an effective tool for the design of new cheiocal entity. Number of novel agents have been identified as antitubercular agents whose mechanism of action needs to be ascertained.