Virtual Screening, pharmacophore development and structure based similarity search to identify inhibitors against IdeR, a transcription factor of Mycobacterium tuberculosis

Akshay Rohilla,Anil K Tyagi,Garima Khare

doi:10.1038/s41598-017-04748-9

Abstract

ideR, an essential gene of Mycobacterium tuberculosis, is an attractive drug target as its conditional knockout displayed attenuated growth phenotype in vitro and in vivo. To the best of our knowledge, no inhibitors of IdeR are identified. We carried out virtual screening of NCI database against the IdeR DNA binding domain followed by inhibition studies using EMSA. Nine compounds exhibited potent inhibition with NSC 281033 (I-20) and NSC 12453 (I-42) exhibiting IC50 values of 2 µg/ml and 1 µg/ml, respectively. We then attempted to optimize the leads firstly by structure based similarity search resulting in a class of inhibitors based on I-42 containing benzene sulfonic acid, 4-hydroxy-3-[(2-hydroxy-1-naphthalenyl) azo] scaffold with 4 molecules exhibiting IC50 ≤ 10 µg/ml. Secondly, optimization included development of energy based pharmacophore and screening of ZINC database followed by docking studies, yielding a molecule with IC50 of 60 µg/ml. More importantly, a five-point pharmacophore model provided insight into the features essential for IdeR inhibition. Five molecules with promising IC50 values also inhibited M. tuberculosis growth in broth culture with MIC90 ranging from 17.5 µg/ml to 100 µg/ml and negligible cytotoxicity in various cell lines. We believe our work opens up avenues for further optimization studies.

Highlights

Binding domain followed by inhibition studies using Electrophoretic Mobility Shift Assay (EMSA)
M. tuberculosis upregulates its iron acquisition machinery, which synthesizes small molecules known as mycobactins and carboxymycobactins that function as iron chelators[8, 9]
These molecules bind iron from the host proteins and with the help of various transporters, this iron is transported to the M. tuberculosis cytosol, where it is utilized for many crucial processes[10,11,12,13,14]

Summary

Introduction

Binding domain followed by inhibition studies using EMSA. Nine compounds exhibited potent inhibition with NSC 281033 (I-20) and NSC 12453 (I-42) exhibiting IC50 values of 2 μg/ml and 1 μg/ml, respectively. A series of studies carried out by Hol et al on the crystal structures of M. tuberculosis IdeR in monomer and DNA bound forms identified Ser 37, Pro 39 and Gln 43 as few of the residues crucial for the binding of IdeR to the DNA molecule[18,19,20,21]. Studies of the crystal structure determination, iron binding kinetics and molecular dynamics simulation[23] of IdeR have provided insights into the binding mechanism of IdeR with iron and its cognate DNA sequences and have established a starting point for carrying out structure based identification of potent inhibitory molecules against IdeR

Methods

Results

Conclusion