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Thienopyrimidinone Derivatives That Inhibit Bacterial tRNA (Guanine37-N¹)-Methyltransferase (TrmD) by Restructuring the Active Site with a Tyrosine-Flipping Mechanism

Author(s)
Zhong, Wenhe; Pasunooti, Kalyan Kumar; Balamkundu, Seetharamsing; Wong, Yee Hwa; Nah, Qianhui; Gadi, Vinod; Gnanakalai, Shanmugavel; Chionh, Yok Hian; McBee, Megan E.; Gopal, Pooja; Lim, Siau Hoi; Olivier, Nelson; Buurman, Ed T.; Dick, Thomas; Liu, Chuan Fa; Lescar, Julien; Dedon, Peter C; ... Show more Show less
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Creative Commons Attribution-NonCommercial-NoDerivs License http://creativecommons.org/licenses/by-nc-nd/4.0/
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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 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.
Date issued
2019-08
URI
https://hdl.handle.net/1721.1/122276
Department
Massachusetts Institute of Technology. Department of Biological Engineering
Journal
Journal of Medicinal Chemistry
Publisher
American Chemical Society (ACS)
Citation
Zhong, Wenhe et al. "Thienopyrimidinone Derivatives That Inhibit Bacterial tRNA (Guanine37-N¹)-Methyltransferase (TrmD) by Restructuring the Active Site with a Tyrosine-Flipping Mechanism." Journal of Medicinal Chemistry 62, 17 (August 2019): 7788-7805 © 2019 American Chemical Society
Version: Final published version
ISSN
0022-2623
1520-4804

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