Exploring the binding sites of Staphylococcus aureus phenylalanine tRNA synthetase: A homology model approach

Abstract

Increased resistance of MRSA (multidrug resistance Staphylococcus aureus) to anti-infective drugs is a threat to global health necessitating the development of anti-infectives with novel mechanisms of action. Phenylalanine tRNA synthetase (PheRS) is a unique enzyme of the aminoacyl-tRNA synthetases (aaRSs), which are essential enzymes for protein biosynthesis. PheRS is an (αb) tetrameric enzyme composed of two alpha subunits (PheS) and two larger beta subunits (PheT). Our potential target in the drug development for the treatment of MRSA infections is the phenylalanine tRNA synthetase alpha subunit that contains the binding site for the natural substrate. There is no crystal structure available for S. aureus PheRS, therefore comparative structure modeling is required to establish a putative 3D structure for the required enzyme enabling development of new inhibitors with greater selectivity. The S. aureus PheRS alpha subunit homology model was constructed using Molecular Operating Environment (MOE) software. Staphylococcus haemolyticus PheRS was the main template while Thermus thermophilus PheRS was utilised to predict the enzyme binding with tRNA. The model has been evaluated and compared with the main template through Ramachandran plots, Verify 3D and Protein Statistical Analysis (ProSA). The query protein active site was predicted from its sequence using a conservation analysis tool. Docking suitable ligands using MOE into the constructed model were used to assess the predicted active sites. The docked ligands involved the PheRS natural substrate (phenylalanine), phenylalanyl-adenylate and several described S. aureus PheRS inhibitors.

Impact of the Stringent Stress Response on the Expression of Methicillin Resistance in Staphylococcaceae Strains Carrying mecA, mecA1 and mecC

“…– RUSA239HRC2 carries an SNP mutation that led to the substitution of phenylalanine residue by a serine at amino acid 254 of PheS—the alpha subunit of the phenylalanyl-tRNA synthase, a residue that has different chemical properties. Phe254 is part of the large hydrophobic pocket that forms the active site of this essential enzyme for protein biosynthesis [ 37 ]. Thus, mutations in this location can influence cellular growth.…”

Phenylalanyl tRNA synthetase (PheRS) substrate mimics: design, synthesis, molecular dynamics and antimicrobial evaluation

“…The corresponding N,N-dimethyl-7-deazapurine derivatives of series 4 (16) were prepared in a 6-step pathway starting with 7chloro-6-deazapurine (10), which was converted into 7 N,Ndimethyl-7-deazapurine (11) by reaction with DMF and 10 M aqueous KOH at 95 C. 23 The thiadiazol-2-amine ( 14) was prepared as described in Scheme 1 from the hydrazide (13), which was obtained on reaction of 3-(4-(dimethylamino)-7Hpyrrolo[2,3-d]pyrimidin-7-yl)propanoate (12) with hydrazine hydrate. The thiadiazol-2-amine ( 14) was coupled with the N-Boc protected L-amino acids using TBTU and HOBt to form the amides (15), which were subsequently deprotected using excess TFA to give the series 4 derivatives (16).…”

“…15 Bacterial PheRS is structurally different from human PheRSs (cytoplasmic and mitochondrial) with low homology allowing for design of selective PheRS inhibitors. 16 PheRS inhibitors with varying structure design have been described such as the ethanolamines, 17 phenyl-thiazolyl-urea sulfonamides 18 and bicyclic azetidines 19 ( Fig. 2 ).…”

Design, computational studies, synthesis and in vitro antimicrobial evaluation of benzimidazole based thio-oxadiazole and thio-thiadiazole analogues

“…All the compounds from the two series showed weak inhibitory activity against E. faecalis and P. aeruginosa (MIC 128 μg/mL) and were inactive against both E. coli and K. pneumoniae. To provide a clearer insight of these unexpected results on a molecular level a published homology model of S. aureus PheRS [34] was used to study the interactions between 8b and the S. aureus PheRS enzyme using MD simulation. On visualising the final frame 2D interactions of the simulation using MOE software (Fig.…”

“…Molecular dynamic simulations were run using either the crystal structure of Th. thermophilus PheRS [PDB ID: 1JJC] [32] or S. aureus PheRS previously published homology model [34]. PDB files were first optimised using protein preparation wizard in Maestro [49] version 11.8.012 by assigning bond orders, adding hydrogen, and correcting incorrect bond types.…”