Thienopyrimidinone Derivatives That Inhibit Bacterial tRNA (Guanine37-N1)-Methyltransferase (TrmD) by Restructuring the Active Site with a Tyrosine-Flipping Mechanism.Zhong, W., Pasunooti, K.K., Balamkundu, S., Wong, Y.H., Nah, Q., Gadi, V., Gnanakalai, S., Chionh, Y.H., McBee, M.E., Gopal, P., Lim, S.H., Olivier, N., Buurman, E.T., Dick, T., Liu, C.F., Lescar, J., Dedon, P.C.
(2019) J Med Chem 62: 7788-7805
- PubMed: 31442049
- DOI: 10.1021/acs.jmedchem.9b00582
- Primary Citation of Related Structures:
5ZHL, 5ZHK, 5ZHN, 5ZHM, 5ZHJ, 5ZHI, 6JOF, 6JOE
- PubMed Abstract:
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 des ...
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-(N 1 G37) 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.
Department of Biological Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States.