Computational Elucidation of Structural Basis for Ligand Binding with Mycobacterium tuberculosis Glucose-1-Phosphate Thymidylyltransferase (RmlA)

Abstract

Glucose-1-Phosphate Thymidylyltransferase (RmlA) is one of the enzymes in rhamnose biosynthesis pathway, where rhamnose acts as linker of peptidoglycan and arabinogalacton in the cell wall, therefore RmlA is a potential enzyme for the survival of Mycobacterium tuberculosis (Mtb). To go into the depth of the structure for exploring binding regions, homology model of RmlA was built in Prime, Schrodinger v9.2. The model with lowest Discrete Optimized Potential Energy (DOPE) score of -35524.17 kcal/mol and RMSD of 0.1 Å with the template (1H5R_B) was subjected to Molecular Dynamics Simulation (MDS) for 5 ns to achieve its stable folding state. The tertiary structure of the proposed model is composed of α/β/α sandwich type protein with quasi-Rossmann type folding pattern. The substrate, deoxy Thymidine tri phosphate (dTTP) comprises of triphosphate (R1) and methyl (R2) side chains where, R1 is highly essential for the survival of Mtb. Therefore, nineteen side chain analogues of dTTP were designed by substituting R1 and R2 chain of dTTP using Combi Glide, Schrodinger v9.2 and docked with the target RmlA protein. Out of which two analogues such as, 6-[(2R,3S,5R)-5-[5-(2- aminoethyl)-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl]-3-hydroxyoxolan-2 yl] hexanoic acid (COMP- 11) and 4-(2-{1-[(1S,3S,4S)-3-(5-carboxypentyl)-4-hydroxy-2-methylidenecyclopentyl]-2,4-dioxo- 1,2,3,4-tetrahydropyrimidin-5-yl}ethyl)morpholin-4-ium (COMP-12) showed the highest GLIDE score (-12.55 Kcal/mol and -11.58 Kcal/mol respectively) than that of substrate (-9.725 Kcal/mol). During simulations, hydrogen bonding profile between the two top hits and protein ranges up to 5 strong polar contacts which were much stronger than that of substrate. Similarly, the computational binding free energy of both the analogues was found to be less than -70 Kcal/mol which is much lower than that of substrate (-52.84 Kcal/mol). All these results suggest that these two compounds have more stable interaction than that of substrate inside the solvent condition and can be used as competitive inhibitors.

Comparative genomic analysis of Myroides odoratimimus isolates

“…Undecaprenyl diphosphate synthase (UPPS) is involved in cell wall biosynthesis (peptidoglycan and wall teichoic acid synthesis) by catalyzing the synthesis of a polyisoprenoid, becoming an attractive antibacterial drug target (Farha et al, 2015). Glucose-1phosphate thymidylyltransferase (RmlA) is vital for bacteria survival (Mansuri et al, 2016). It participates in L-rhamnose synthesis (Alphey et al, 2013;Mansuri et al, 2016), a critical linker of peptidoglycan and arabinogalacton in bacterial cell wall (Mansuri et al, 2016), by catalyzing the generation of dTDP-D-glucose and pyrophosphate (PPi) (Alphey et al, 2013;Mansuri et al, 2016).…”

“…Glucose-1phosphate thymidylyltransferase (RmlA) is vital for bacteria survival (Mansuri et al, 2016). It participates in L-rhamnose synthesis (Alphey et al, 2013;Mansuri et al, 2016), a critical linker of peptidoglycan and arabinogalacton in bacterial cell wall (Mansuri et al, 2016), by catalyzing the generation of dTDP-D-glucose and pyrophosphate (PPi) (Alphey et al, 2013;Mansuri et al, 2016). dTDP-D-glucose 4,6-dehydratase (RmlB) is also involved in L-rhamnose biosynthesis, by catalyzing the conversion of dTDP-D-glucose into dTDP-4-keto-6-deoxy-D-glucose in cell wall (Allard et al, 2002).…”

Investigation of Plant Antimicrobial Peptides against Selected Pathogenic Bacterial Species Using a Peptide-Protein Docking Approach

“…Glucose-1-phosphate thymidylyltransferase (RmlA) serves as the leading enzyme of the rhamnose biosynthesis pathway and is therefore essential for the survival of M . tuberculosis [ 32 ]. The glucose-1-phosphate thymidylyltransferase (RmlA) also plays an essential role in bacterial cell wall viability, and therefore, RmlA could serve as a major target in the prevention of this infection.…”

The structure of glucose‐1‐phosphate thymidylyltransferase from Mycobacterium tuberculosis reveals the location of an essential magnesium ion in the RmlA‐type enzymes

“… Comparison of the experimentally determined RmlA model presented here with that based on the homology modeling previously described . A superposition of the ribbon representations for the two models in stereo is presented in (A) with the experimentally determined model highlighted in violet.…”

“…Given that the rmlA gene has been shown to be essential for mycobacterial growth, it is somewhat surprising that the crystal structure of the enzyme from M. tuberculosis has never been described . Indeed, two recent reports focusing on possible inhibitors of the enzyme from M. tuberculosis relied solely upon molecular modeling procedures . Here we report a functional and structural investigation of M. tuberculosis RmlA.…”