Design, synthesis and biological evaluation of novel InhA inhibitors as anti-tuberculosis agents

In this research, molecular modeling and computer-aided molecular design approaches were applied to study and design novel inhibitors as anti-tuberculosis agents. Enoyl-ACP reductase (InhA) enzyme of Mycobacterium tuberculosis is one of the enzymes responsible for the synthesis of mycolic acid which is the main component in Mycobacterium tuberculosis cell walls. Moreover, it is also an attractive target of isoniazid, the first line drug for tuberculosis treatment. However, the efficiency of isoniazid has decreased due to KatG enzyme mutation, which is responsible for activation of isoniazid. Therefore, inhibitors with different isoniazid mechanisms that can directly inhibit InhA (direct InhA inhibitors) are a key to developing anti-tuberculosis drugs opposed to isoniazid drug resistance. Benzimidazole derivatives are the first target of direct InhA inhibitors. Benzimidazole derivatives were designed based on a structural modification of 2,3-dihydro-1H-indane group and converted oxygen atoms to nitrogen atoms using the bio-isostere principle. This screens for aromatic ring substitutions to increase hydrogen bonding,π-π, π-cation and π-sigma interactions between inhibitors with the binding pocket of InhA. Then, selected compounds were collected based on Lipinski’s rules of five, pharmacokinetic properties and toxicity. Molecular docking calculations, molecular dynamic simulations and binding energy calculations were studied and used to select potential compounds for further synthesis based on the good binding affinity and crucial interactions. Five compounds (AN19, AN25, AN30, AN55 and AN63) were selected for synthesis and characterization by 1H-NMR, 13C-NMR and DEPT-135 and mass spectrometry. The InhA inhibitory of compounds were evaluated in concentrations of 1 μM of the synthesis compounds. The results showed that compounds, AN19, AN25 and AN63 displayed inhibitory activity with 21.25, 18.83 and 18.53% respectively. Whereas, triclosan, a reference InhA inhibitor and compound 7, a reference benzimidazole, showed inhibitory activity at 28.36% and 44.34%, respectively. Three novel compounds showed statistically significant differences as compared to both reference compounds. The anti-Mycobacterium tuberculosis, caseum fraction unbound and maximum recommended tolerated doses (MRTD) using a mycoCSM prediction of five compounds and compound 7 were predicted. These values are not statistically significantly different as compared to compound 7 and compound AN19 showing the lowest MRTD. Moreover, hepatotoxicity was predicted using a pkCSM prediction. Compounds AN19, AN55 and 7 revealed no hepatotoxicity. Therefore, potential computer-aided molecular designs provided the outlines for a rational design of novel and more potent treatments of Mycobacterium tuberculosis based on benzimidazole derivatives. The second target in this study were pyrrolyl benzohydrazide derivatives. The results were derived from molecular docking calculations, molecular dynamic simulations and binding energy calculations aids to understand the binding mode and binding interactions in the binding pockets of InhA including hydrogen bonds and hydrophobic interactions. In addition, molecular dynamic simulations were used to investigate the key structural information. The obtained key interactions are hydrogen bond interactions with Gly96 as well as hydrophobic amino acid and NAD+ cofactor residues in the binding InhA pocket. Based on the results from this study both benzimidazole and pyrrolyl benzohydrazide derivatives can provide fruitful information for further design of novel inhibitors as highly potent approaches to solving the problem of resistance to isoniazid.