Thienopyrimidinone Derivatives That Inhibit Bacterial tRNA (Guanine37-
N1)-Methyltransferase (TrmD) by Restructuring the Active Site with a Tyrosine-Flipping Mechanism.
J Med Chem 2019;
62:7788-7805. [PMID:
31442049 PMCID:
PMC6748665 DOI:
10.1021/acs.jmedchem.9b00582]
[Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
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Among the >120
modified ribonucleosides in the prokaryotic epitranscriptome,
many tRNA modifications are critical to bacterial survival, which
makes their synthetic enzymes ideal targets for antibiotic development.
Here we performed a structure-based design of inhibitors of tRNA-(N1G37) methyltransferase, TrmD, which is an essential enzyme
in many bacterial pathogens. On the basis of crystal structures of
TrmDs from Pseudomonas aeruginosa and Mycobacterium tuberculosis, we synthesized a series
of thienopyrimidinone derivatives with nanomolar potency against TrmD
in vitro and discovered a novel active site conformational change
triggered by inhibitor binding. This tyrosine-flipping mechanism is
uniquely found in P. aeruginosa TrmD
and renders the enzyme inaccessible to the cofactor S-adenosyl-l-methionine (SAM) and probably to the substrate
tRNA. Biophysical and biochemical structure–activity relationship
studies provided insights into the mechanisms underlying the potency
of thienopyrimidinones as TrmD inhibitors, with several derivatives
found to be active against Gram-positive and mycobacterial pathogens.
These results lay a foundation for further development of TrmD inhibitors
as antimicrobial agents.
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