Structure Elucidation and Identification of Novel Lead Molecules against Sulfur Import Protein cysA of Mycobacterium tuberculosis.

AIMS: The present work considers the Sulphate import ABC transporter protein (cysA) as a potential drug target for the identification of inhibitors for the protein. BACKGROUND: The ABC (ATP binding cassette) transporters play a crucial role in the survival and virulence of Mycobacterium tuberculosis by the acquisition of micronutrients from host tissue. OBJECTIVES: The 3D structural features of the cysA protein are built. Molecular scaffolds are identified by implementing active site identification, ADME properties, Virtual Screening, and a few other computational techniques. METHODS: The theoretical model of cysA is predicted using homology modeling protocols, and the structure is validated by various validation methods. The prediction of partial dimer formation through protein-protein docking methods gave insight into the conformational changes taking place in the cysA protein. The natural substrate ATP is docked with cysA protein that confirms the ATP binding site. To find the drug-like compounds, virtual screening studies were carried out around the active site by several ligand databases. RESULTS: The findings demonstrate the significance of residues SER41, GLY42, ARG50, GLN85, HIS86, LYS91, ARG142, and ASP161 in drug-target interactions. The docking studies of existing TB drugs against cysA were also performed. The result analysis shows that none of the existing drugs inhibits the ATP active site, which confirms cysA as a promising drug target. Using in-silico methods, the ADME parameters of a few chosen ligand molecules are predicted and contrasted with the ADME characteristics of the available TB medications. CONCLUSION: The results revealed the values of ADME parameters of selected ligand molecules are more permissible than existing TB drugs, which emphasizes the drug-like activity of ligand molecules by inhibition of cysA proteins. The structural data, active site information, and selected ligand molecules help in the identification of new therapeutic scaffolds for Tuberculosis.

Structure-based drug design, synthesis and screening of MmaA1 inhibitors as novel anti-TB agents.

Tuberculosis is one of the leading causes of death across the world. The treatment regimens for tuberculosis are well established, but still the control of the disease faces many challenges such as lengthy treatment protocols, drug resistance and toxicity. In the present work, mycolic acid methyl transferase (MmaA1), a protein involved in the maturation of mycolic acids in the biochemical pathway of the Mycobacterium, was studied for novel drug discovery. The homology model of the MmaA1 protein was built and validated by using computational techniques. The MmaA1 protein has 286 amino acid residues consisting of 10 α-helices and 7 ß-sheets. The active site of the MmaA1 protein was identified using CASTp, SiteMap and PatchDock. Virtual screening studies were performed with two small molecule ligand databases: Asinex synergy and Diverse_Elite_Gold_Platinum databases having a total of 43,446 molecules and generated 1,30,814 conformers against the predicted and validated active site of the MmaA1 protein. Binding analysis showed that the residues ASP 19, PHE 22, TRP 30, TYR 32, TRP 74 and ALA 77 of MmaA1 protein have consistent interactions with the ligands. The hit ligands were further filtered by in silico ADME properties to eliminate potentially toxic molecules. Of the top 10 molecules, 3-(2-morpholinoacetamido)-N-(1,4-dihydro-4-oxoquinazolin-6-yl) benzamide was synthesised and screened for in vitro anti-TB activity against Mtb H37Rv using MABA assay. The compound and its intermediates exhibited good in vitro anti-TB activity which can be taken up for future lead optimisation studies. Structure based virtual screening study was performed using a validated homology model against small molecules from two virtual compound libraries. Synthesised the lead compound 3-(2-morpholinoacetamido)-N-(1,4-dihydro-4-oxoquinazolin-6-yl)benzamide obtained from virtual screening. In vitro activity against Mtb H37Rv has given a promising result.

Identification of small molecular inhibitors for efflux protein Rv2688c of Mycobacterium tuberculosis.

Mycobacterium tuberculosis (Mtb) is the pathogen, which causes tuberculosis. The development of multidrug-resistant and extensively drug-resistant strains in Mtb is due to an efflux mechanism of antibiotics in the bacteria. The efflux pump proteins in the bacteria are implicated in the active efflux of antibiotics. The efflux pump protein, "fluoroquinolones export ATP-binding protein Rv2688c" (FEAB), is considered as a potential therapeutic target to prevent tuberculosis. In the present work, in silico protocols are applied to identify inhibitors for the FEAB protein to arrest the efflux mechanism. Comparative modeling techniques are used to build the protein structure. The generated structure consists of 9 helices, 13 beta strands, and 3 ß sheets. The active site is predicted using active site prediction server tools. The virtual screening protocols are carried out to generate small ligand inhibitor structures. The identified ligand molecules show selective binding with Ser97, Glu99, Lys149, Asp171, Glu172, and Ser175 amino acid residues of the protein. The ligand molecules are subjected to in silico prediction of pharmaco kinetic properties, and the predicted IC50 (HERG) of all the molecules are less than -5.0, which is indicative of the identified ligand molecules is being potentially good FEAB inhibitors.