Structural Analysis and Identification of Potential Inhibitors for Phosphophoglucosamine Mutase From Mycobacterium Tuberculosis
Posted: 13 Feb 2020 Last revised: 20 Feb 2020
Date Written: February 11, 2020
Phosphoglucosamine mutase (GlmM) belonging to the superfamily of proteins called α-D-phosphohexomutases is involved in the UDP-N-acetylglucosamine (UDP-GlcNAc) biosynthetic pathway by converting glucosamine-6-phosphate (G6P) to glucosamine-1-phosphate (G1P) leading to the synthesis of UDP-GlcNAc which is an essential precursor in peptidoglycan layer synthesis in Mycobacterium sp. Our study is to target GlmM from Mycobacterium tuberculosis and scrutinize lead compounds computationally which can be tested experimentally for the inhibition of this key protein. Homology modelling of the protein 3D structure was performed using Modeller followed by the validation using PROCHECK. The utilities of SAVES and the data about active site residues were obtained from the literatures on the α-D-phosphohexomutase superfamily proteins whose active sites are conserved. Docking studies were carried out by Autodock Vina and then MD simulations were done using GROMACS5.2. Virtual screening studies are being carried out using softwares like OpenBabel and PyRx.
Crystal structure of Francisella tularensis GlmM has been used as the template to obtain the three-dimensional structure of MtGlmM. The validated models with lesser outliers in the Ramachandran plot are used for docking studies. Docking of the protein with its substrate G6P has shown very less RMSD in comparison to crystal structure of GlmM containing substrate (G6P) from Pseudomonas aueroginosa. The stability of the substrate bound MtGlmM was further analyzed by MD simulations and RMSD, RMSF, RG plots verified the stability of the substrate in the protein. Additionally, the structural analysis of the protein provided insights on the domain movements which seems to be important for the protein function where the fourth domain of the protein consisting of antiparallel β-sheets connected to the other three domains via a loop showed less flexibility when bound to substrate and more flexibility in the apo form which were analyzed from the MD simulation trajectories.
Further, virtual screening is being carried out from compounds extracted from drug databases, which are filtered by ligand based similarity search using OpenBabel and then structure based screening will be carried out using PyRx software. Structural analysis proved that the closed conformation of the fourth domain is important for the product formation, hence inhibition of the flexibility of this domain by binding to drug molecules with high affinity may inhibit the activity of the protein to counter deadly tuberculosis organism.
Keywords: Modelling, Model validation, Docking, Simulation, virtual screening
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