Computer-aided drug design based on comparative modeling, molecular docking and molecular dynamic simulation of Polyphosphate kinase (PPK) from Mycobacterium tuberculosis

Abstract

This study aimed to identify compounds that are capable of inhibiting polyphosphate kinase (PPK), the protein that shares a similar pathway with the target of isoniazid (INH) in the oxidative phosphorylation pathway of Mycobacterium tuberculosis (MTB). The three-dimensional structure of the PPK was predicted based on the homology modeling principle via Modeller9.16. Structural analysis revealed that the PPK has three active sites—metal ion-binding site (Arg431 and Arg461), ATP-binding site (Asn91, Tyr524, Arg624, and His652), and phosphohistidine intermediate active site (His491). The amino acids mentioned earlier play an essential role in the activity of the PPK, and their inhibition would block the function of the PPK. Ten thousand one hundred and six (10,106) ligands were obtained through virtual screening against Zinc database. These compounds were filtered by Lipinski rule of five and molecular docking analysis. A total of ten compounds with good AutoDock binding energy that varied between − 9.92 and − 8.01 kcal/mol which was lower than the binding energy of − 1.13 kcal/mol of Mg2+ (metallic cofactor) were selected. These compounds were further filtered for their pharmacokinetic and toxicity properties to further remove the compounds with unwanted properties. Three ligands—ZINC41125011, ZINC20318248, and ZINC20321877 with desired pharmacokinetic and toxicity properties were selected for molecular dynamic (MD) simulation and molecular generalized Born surface area (MM-GBSA) analysis. The result of the studies shows that all the three complexes are relatively stable in the binding site of the PPK, after 50 ns MD simulation. Therefore, these identified compounds are regarded as prospective inhibitors of MTB after positive experimental validation.