Structure-based hit-to-lead design, optimization, and synthesis of tetrahydro-1,3,5-triazine-2-amine derivatives as potential inhibitors of Mycobacterium tuberculosis Dihydrofolate Reductase (MtbDHFR).

Abstract

Among several Mycobacterium tuberculosis potential drug targets, Mycobacterium tuberculosis Dihydrofolate Reductase (MtbDHFR) is a key enzyme involved in folate metabolism. It is an important target in which its inhibition results in mycobacterial cell death. Several successful anti-folates against infectious diseases exist, but none have been developed to combat tuberculosis. Previously, two potent anti-tuberculosis phenotypic hits belonging to the tetrahydro-1,3,5-triazine-2-amine (THT) family, were predicted and confirmed as inhibitors of MtbDHFR. Therefore, optimizing these confirmed hits can lead to a new class of anti-tuberculosis compounds that are target specific and highly potent. The study aims to design and synthesize tetrahydro-1,3,5-triazine-2-amine derivatives as potential anti-TB hit based on the 3D structure of MtbDHFR. Structure-activity relationship (SAR) was applied in the design of 113 tetrahydro-1,3,5-triazine-2-amine based on the 3D structure of MtbDHFR. The rest of the compounds were designed by scaffold hopping via the synergy of Marvin Sketch (manual design) and Spark software program to inflate the library to a capacity of 1700 compounds. By considering the key distinguishing features between human-DHFR and MtbDHFR, the matter of selectivity was well addressed. Resultantly 23 out of 40 tested compounds favored MtbDHFR inhibition over Human DHFR in terms of selectivity. The generated compound library was subjected to virtual screening using Auto-Dock Vina to predict the binding affinities and the best binding pose of each compound inside the binding site of the MtbDHFR target. Next, ADMET studies were then performed to predict the pharmacokinetics and toxicity profiles of the designed compounds. Furthermore, Molecular Dynamics (MD) simulations were done on four ligand complexes where conformational stability, residue flexibility (RMSF), compactness (Rg), and hydrogen bonding were analyzed. The Molecular Dynamics (MD) simulation results support excellent binding affinities of these ligands observed earlier by molecular docking. The study demonstrated a successful hit to lead optimization and all compounds were identified with, binding affinities ranging from -6.5 to -14.1 kcal/mol, improved drug-like, and ADMET properties. Two of the high-ranked compounds were selected for synthesis. The carbodiimide, DCC-mediated coupling reaction was used to synthesize two of the pre-qualified compounds AZ01 and TB1 which had a percentage yield of 74 and 67% respectively, paving the way for further exploration and experimentation work such as biological assays and potentially preclinical testing. Conclusively it is imperative to mention that 1,3,5-triazine scaffolds holds a great promise to the design of novel effective anti-TB leads and may be a beacon of hope for the eradication of this global burdensome TB disease. vi Furthermore, the inter-disciplinary project has advanced basic science at CUT and boosted molecule design and synthesis in addition to encouraging inter-disciplinary collaborations.