The crystal structure of the drug targetMycobacterium tuberculosismethionyl-tRNA synthetase in complex with a catalytic intermediate

Abstract

Mycobacterium tuberculosis is a pathogenic bacterial infectious agent that is responsible for approximately 1.5 million human deaths annually. Current treatment requires the long-term administration of multiple medicines with substantial side effects. Lack of compliance, together with other factors, has resulted in a worrisome increase in resistance. New treatment options are therefore urgently needed. Here, the crystal structure of methionyl-tRNA synthetase (MetRS), an enzyme critical for protein biosynthesis and therefore a drug target, in complex with its catalytic intermediate methionyl adenylate is reported. Phenylalanine 292 of the M. tuberculosis enzyme is in an `out' conformation and barely contacts the adenine ring, in contrast to other MetRS structures where ring stacking occurs between the adenine and a protein side-chain ring in the `in' conformation. A comparison with human cytosolic MetRS reveals substantial differences in the active site as well as regarding the position of the connective peptide subdomain 1 (CP1) near the active site, which bodes well for arriving at selective inhibitors. Comparison with the human mitochondrial enzyme at the amino-acid sequence level suggests that arriving at inhibitors with higher affinity for the mycobacterial enzyme than for the mitochondrial enzyme might be achievable.

Structural characterization of free-state and product-stateMycobacterium tuberculosismethionyl-tRNA synthetase reveals an induced-fit ligand-recognition mechanism

“…In April 2018, Barros-Á lvarez and coworkers reported a crystal structure of MtMetRS complexed with the intermediate product Met-AMP (PDB entry 6ax8; Barros-Á lvarez et al, 2018). It has a lower resolution than PDB entry 5xet; thus, our crystallographic data may provide further structural details.…”

“…A collection of MetRS structures from Aquifex aeolicus, Thermus thermophilus, Pyrococcus abyssi, Escherichia coli and Mycobacterium smegmatis (Nakanishi et al, 2005;Sugiura et al, 2000;Crepin et al, 2004;Mechulam et al, 1999;Ingvarsson & Unge, 2010) have been determined. Very recently, the structure of M. tuberculosis MetRS (MtMetRS), which shares similar structural characteristics with MetRS from M. smegmatis, was reported in complex with the intermediate methionyl-adenylate ( Barros-Á lvarez et al, 2018). A comparative analysis of the unliganded structure (apo form or free-state enzyme; F-state) and structures complexed either with the intermediate product, analogues or inhibitors (denoted the product state; P-state) revealed conformation changes induced by the ligands.…”

Toward a structome of Acinetobacter baumannii drug targets

“…For example, Pro256 in A. baumannii MetRS is a threonine in human MetRS which offers different substrate interactions as well as structural rigidity associated (Figure ). Within the KMSKS and HIGH motifs exist more changes in conserved amino acids, like a His18 substitution to asparagine and a Met331 substitution to phenylalanine, both of which affect other unique interactions stabilizing substrate transition states …”

“…Within the KMSKS and HIGH motifs exist more changes in conserved amino acids, like a His18 substitution to asparagine and a Met331 substitution to phenylalanine, both of which affect other unique interactions stabilizing substrate transition states. 36 Tyrosyl-tRNA synthetase (TyrRS) is a member of the Class I tRNA synthetases, like MetRS, 34 TyrRS uses a two-step reaction to catalyze the aminoacylation of tRNA; first, recognition of the appropriately matching amino acid, Tyr, activates the reaction with ATP to produce an aminoacyladenylate, Tyr-AMP. The second step involves the transfer of the amino acid to its cognate tRNA and release of AMP.…”

Discovery of novel antituberculosis agents among 3-phenyl-5-(1-phenyl-1H-[1,2,3]triazol-4-yl)-[1,2,4]oxadiazole derivatives targeting aminoacyl-tRNA synthetases

“…With the fact that considerable selectivity between S. aureus and human mitochondrial enzymes was achieved, there are opportunities to develop inhibitors with higher selectivity toward M. tuberculosis MetRS than for both human homologs. Besides, recently several crystal structures of M. tuberculosis MetRS were reported 8 , 9 , which makes this enzyme promising for the receptor-oriented rational design of inhibitors with antituberculosis activity. Unfortunately, the frequency of resistance occurrence to aaRSs inhibitors is very high (10 –7 –10 –8 ) due to point mutations in the gene encoding enzyme which consequently affects ligand-binding interactions.…”