Homology modeling and in silico toxicity assessment of potential inhibitors of cytidylate kinase from Mycobacterium tuberculosis

Abstract

Cytidylate kinase (CMK) plays a central role in the phosphorylation of ATP to nucleoside diphosphates in the purine and pyrimidine pathway in Mycobacterium tuberculosis (MTB). The enzyme is specific to bacteria, fungi, and plants and it shares the same pathway with a DNA-directed RNA polymerase subunit beta, the known target of rifampicin (RIF). Therefore, it serves as an attractive alternative target to inhibit the purine and pyrimidine pathway in MTB. In this study, the novel inhibitors of CMK were identified using in silico approach. Homology modeling was used to build the three-dimensional (3D) structure of CMK using program implemented in Modeller 9.16 and based on the template (3R20) obtained from Mycobacterium smegmatis. Structural analysis of CMK showed that it has P-loop or core in the ATP binding domain, nucleoside monophosphate binding (NMP) site, and a LID domain. Inhibition of any of the residues that formed the nucleoside binding site or ATP binding site blocks the catalytic activity of the CMK. Eleven thousand four hundred and fifty-four compounds that had an affinity to bind to the CMK with minimum binding energies were obtained through virtual screening from Zinc and PubChem databases using PyRx 8.0. These compounds were further filtered for Lipinski rule of five, molecular docking analysis, and ADMET properties (absorption distribution, metabolism, excretion, and toxicity). Four compounds (ZINC95485891 = − 8.80 kcal/mol, ZINC95485880 = − 8.44 kcal/mol, ZINC95485900 = − 8.24 kcal/mol, and ZINC95486231 = − 8.20 kcal/mol) with good binding energies and desirable pharmacokinetic properties were selected. These compounds were further subjected to molecular dynamic (MD) simulation and molecular mechanics generalized Born and surface area (MM-GBSA) analyses. The results of the analyses showed that all the four ligands formed a stable complex and had good free binding energy after 50 ns MD simulation. Therefore, these compounds were considered as possible inhibitors of MTB after experimental validation.