Download MendeleyFragment Screening Hit Draws Attention to a Novel Transient Pocket Adjacent to the Recognition Site of the tRNA-Modifying Enzyme TGT.
Hassaan, E., Hohn, C., Ehrmann, F.R., Goetzke, F.W., Movsisyan, L., Hufner-Wulsdorf, T., Sebastiani, M., Hartsch, A., Reuter, K., Diederich, F., Klebe, G.(2020) J Med Chem 63: 6802-6820
- PubMed: 32515955
- DOI: https://doi.org/10.1021/acs.jmedchem.0c00115
- Primary Citation of Related Structures:
6RKQ, 6RKT - PubMed Abstract:
Fragment-based lead discovery was applied to tRNA-guanine transglycosylase, an enzyme modifying post-transcriptionally tRNAs in Shigella , the causative agent of shigellosis. TGT inhibition prevents translation of Shigella 's virulence factor VirF, hence reducing pathogenicity. One discovered fragment opens a transient subpocket in the preQ 1 -recognition site by pushing back an aspartate residue. This step is associated with reorganization of further amino acids structurally transforming a loop adjacent to the recognition site by duplicating the volume of the preQ 1 -recognition pocket. We synthesized 6-carboxamido-, 6-hydrazido-, and 4-guanidino-benzimidazoles to target the opened pocket, including a dihydro-imidazoquinazoline with a propyn-1-yl exit vector pointing into the transient pocket and displacing a conserved water network. MD simulations and hydration-site analysis suggest water displacement to contribute favorably to ligand binding. A cysteine residue, exclusively present in bacterial TGTs, serves as gatekeeper of the transient subpocket. It becomes accessible upon pocket opening for selective covalent attachment of electrophilic ligands in eubacterial TGTs.
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany.
Organizational Affiliation:
