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.
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Furthermore, the inter-disciplinary project has advanced basic science at CUT and boosted
molecule design and synthesis in addition to encouraging inter-disciplinary collaborations.
