Towards the development of better therapeutic agents for Mycobacterium Tuberculosis: Computational design and evaluation of pyrazinone derivatives as inhibitors of enoyl acyl carrier protein reductase

Abstract

The treatment of tuberculosis (TB) has become challenging due to the emergence of multidrug-resistant strains of Mycobacterium tuberculosis. Consequently, new, and efficient therapies need to be developed to combat this dreaded disease. In this study, we apply in-silico techniques to analyse the potential inhibitory role of pyrazinone derivatives for enoyl-acyl carrier protein reductase (InhA), an important component protein involved in the synthesis of mycolic acids, the major components of the mycobacterial cell wall. Specifically, we amalgamated molecular docking, molecular dynamics (MD) simulations and quantum mechanical (QM) calculations to analyse the interaction of InhA with eight distinct pyrazinone derivatives, that contain thiophenyl, phenyl, or chloro substitutions at C6, ethyl or methoxybenzyl substitutions at N4, and carboxylate group (hydrolysed form of the parent carbonitrile group) at C2 position of the pyrazinone skeleton and compared our results with isoniazid, a well-known first-line TB drug that potentially inhibits InhA. Docking suggests that despite binding within the same pocket (albeit with different residues), pyrazinone derivatives interact more strongly with InhA than isoniazid. This points towards the potentially greater efficacy of these compounds than isoniazid towards InhA inhibition. Further, although C6 substitution does not significantly affect the ligand binding, N4-methoxybenzyl derivatives exhibit higher docking scores than their N4-ethyl counterparts, thereby suggesting their promising inhibitory potential against InhA. Extended (500 ns) all-atom explicit solvent MD simulations, amounting to a total of 9 µs of the simulation time, provide a refined picture of ligand binding in the explicit-solvent environment, and suggest that the crucial interaction with Arg 194 observed in the docked structures is mostly retained. Analysis of the hydrogen bond occupancies and binding-site linear interaction energies reiterate that the binding of the pyrazinone derivatives with InhA is stronger than isoniazid. In synchrony with MMGBSA binding energy calculations and QM calculations, these analyses reveal that irrespective of the nature of C6 substitution, pyrazinone derivatives with N4-methoxybenzyl substitution exhibit stronger binding to InhA, compared to those containing N4-ethyl substitution. Overall, this study identifies promising candidate compounds that should be experimentally tested for their potential inhibitory effects towards InhA.