6AFK

Crystal structure of TrmD from Pseudomonas aeruginosa in complex with active-site inhibitor

Summary for 6AFK

• Entry DOI: 10.2210/pdb6afk/pdb
• Descriptor: tRNA (guanine-N(1)-)-methyltransferase, S-ADENOSYLMETHIONINE, N-{(3S)-1-[3-(pyridin-4-yl)-1H-pyrazol-5-yl]piperidin-3-yl}-1H-indole-2-carboxamide, ... (4 entities in total)
• Functional Keywords: trna methyltransferase, transferase
• Biological source: Pseudomonas aeruginosa UCBPP-PA14
• Total number of polymer chains: 2
• Total formula weight: 61457.21

Authors

Zhong, W.,Koay, A.,Wong, Y.W.,Sahili, A.E.,Nah, Q.,Kang, C.,Poulsen, A.,Chionh, Y.K.,McBee, M.,Matter, A.,Hill, J.,Lescar, J.,Dedon, P.C. (deposition date: 2018-08-08, release date: 2019-08-14, Last modification date: 2023-11-22)

Primary citation

Zhong, W.,Koay, A.,Ngo, A.,Li, Y.,Nah, Q.,Wong, Y.H.,Chionh, Y.H.,Ng, H.Q.,Koh-Stenta, X.,Poulsen, A.,Foo, K.,McBee, M.,Choong, M.L.,El Sahili, A.,Kang, C.,Matter, A.,Lescar, J.,Hill, J.,Dedon, P.
Targeting the Bacterial Epitranscriptome for Antibiotic Development: Discovery of Novel tRNA-(N1G37) Methyltransferase (TrmD) Inhibitors.
Acs Infect Dis., 5:326-335, 2019

PubMed Abstract: Bacterial tRNA modification synthesis pathways are critical to cell survival under stress and thus represent ideal mechanism-based targets for antibiotic development. One such target is the tRNA-(NG37) methyltransferase (TrmD), which is conserved and essential in many bacterial pathogens. Here we developed and applied a widely applicable, radioactivity-free, bioluminescence-based high-throughput screen (HTS) against 116350 compounds from structurally diverse small-molecule libraries to identify inhibitors of Pseudomonas aeruginosa TrmD ( PaTrmD). Of 285 compounds passing primary and secondary screens, a total of 61 TrmD inhibitors comprised of more than 12 different chemical scaffolds were identified, all showing submicromolar to low micromolar enzyme inhibitor constants, with binding affinity confirmed by thermal stability and surface plasmon resonance. S-Adenosyl-l-methionine (SAM) competition assays suggested that compounds in the pyridine-pyrazole-piperidine scaffold were substrate SAM-competitive inhibitors. This was confirmed in structural studies, with nuclear magnetic resonance analysis and crystal structures of PaTrmD showing pyridine-pyrazole-piperidine compounds bound in the SAM-binding pocket. Five hits showed cellular activities against Gram-positive bacteria, including mycobacteria, while one compound, a SAM-noncompetitive inhibitor, exhibited broad-spectrum antibacterial activity. The results of this HTS expand the repertoire of TrmD-inhibiting molecular scaffolds that show promise for antibiotic development.

PubMed: 30682246
DOI: 10.1021/acsinfecdis.8b00275

Experimental method

X-RAY DIFFRACTION (2.75 Å)