The identification of novel Mycobacterium tuberculosis DHFR inhibitors and the investigation of their binding preferences by using molecular modelling.

Ian C Paterson,Tao Sun,Hunmin Jung,Jing Pu,Yanhui Yang,Hao Wang,Zhe Chang,Lee Fah Yap,Yun Fong Ngeow,Sargit Kaur,Wee Lin Wong,James C Sacchettini,Wei Hong,Yu Wang

doi:10.1038/srep15328

Abstract

It is an urgent need to develop new drugs for Mycobacterium tuberculosis (Mtb), and the enzyme, dihydrofolate reductase (DHFR) is a recognised drug target. The crystal structures of methotrexate binding to mt- and h-DHFR separately indicate that the glycerol (GOL) binding site is likely to be critical for the function of mt-DHFR selective inhibitors. We have used in silico methods to screen NCI small molecule database and a group of related compounds were obtained that inhibit mt-DHFR activity and showed bactericidal effects against a test Mtb strain. The binding poses were then analysed and the influence of GOL binding site was studied by using molecular modelling. By comparing the chemical structures, 4 compounds that might be able to occupy the GOL binding site were identified. However, these compounds contain large hydrophobic side chains. As the GOL binding site is more hydrophilic, molecular modelling indicated that these compounds were failed to occupy the GOL site. The most potent inhibitor (compound 6) demonstrated limited selectivity for mt-DHFR, but did contain a novel central core (7H-pyrrolo[3,2-f]quinazoline-1,3-diamine), which may significantly expand the chemical space of novel mt-DHFR inhibitors. Collectively, these observations will inform future medicinal chemistry efforts to improve the selectivity of compounds against mt-DHFR.

Highlights

Tuberculosis (TB) is a deadly infectious disease caused by Mycobacterium tuberculosis (Mtb) that is prevalent in South-East Asia and Africa
Analysis of the crystal structures of MTX binding to mt- and h-dihydrofolate reductase (DHFR) indicate that mycobacterial DHFR (mt-DHFR) binds with MTX, glycerol (GOL) and NADPH (PDB ID: 1DF7) (Fig. 2)[15], but the GOL binding site is essentially absent in human DHFR (h-DHFR) (PDB ID: 1OHJ, h-DHFR complexed with NADPH and PT523)[16]
After removal of duplicates and those molecules that have already been previously reported as mt-DHFR inhibitors, 213 compounds (158 molecules selected from the hit list based on vRocs searching, and 55 from Sybyl searching) were chosen from the final hit list

Summary

Introduction

Tuberculosis (TB) is a deadly infectious disease caused by Mycobacterium tuberculosis (Mtb) that is prevalent in South-East Asia and Africa. Potent inhibition of DHFR has been achieved with analogues of the substrate, dihydrofolate, and one of the most well-known inhibitors is Methotrexate (MTX, Fig. 1), which binds to both human DHFR (h-DHFR) and mt-DHFR without any significant selectivity[7,8]. Such inhibitors contain 2,4-Diaminopteridin as the central core and are referred to as classical inhibitors. In order to understand the relatively low selectivity (5 times vs h-DHFR for the most potent compound), the influence of GOL binding site was studied using molecular dynamic simulations and free energy calculations, as it was believed that the GOL binding site could be important for the selectivity

Methods

Results

Conclusion