A structure-based strategy to identify new molecular scaffolds targeting the bacterial ribosomal A-site.
The need for novel antibiotics is widely recognized. A well validated target of antibiotics is the bacterial ribosome. Recent X-ray structures of the ribosome bound to antibiotics have shed new light on the binding sites of these antibiotics, providing fresh impetus for structure-based strategies aiming at identifying new ribosomal ligands. In that respect, the ribosomal decoding region of the aminoacyl-tRNA acceptor site (A-site) is of particular interest because oligonucleotide model systems of this site are available for crystallography, NMR and compound binding assays. This work presents how these different resources can be combined in a hierarchical screening strategy which has led to the identification of new A-site ligands. The approach exploits an X-ray structure of the A-site against which large and diverse libraries of compounds were computationally docked. The complementarity of the compounds to the A-site was assessed using a scoring function specifically calibrated for RNA targets. Starting from approximately 1 million compounds, the computational selection of candidate ligands allowed us to focus the experimental work on 129 compounds, 34 of which showed affinity for the A-site in a FRET-based binding assay. NMR experiments confirmed binding to the A-site for some compounds. For the most potent compound in the FRET assay, a tentative binding mode is suggested, which is compatible with the NMR data and the limited SAR in this series. Overall, the results validate the screening strategy.
Foloppe
Nicolas
N
Vernalis (R&D) Ltd, Granta Park, Abington, Cambridge CB1 6GB, UK. n.foloppe@vernalis.com
Chen
I-Jen
IJ
Davis
Ben
B
Hold
Adam
A
Morley
Dave
D
Howes
Rob
R
D000900:Anti-Bacterial Agents / Q000737:chemistry* / Q000378:metabolism*; D001665:Binding Sites / Q000187:drug effects; D003198:Computer Simulation; D015195:Drug Design; D004353:Drug Evaluation, Preclinical / Q000379:methods*; D008024:Ligands; D009682:Magnetic Resonance Spectroscopy; D015394:Molecular Structure; D012329:RNA, Bacterial / Q000737:chemistry / Q000187:drug effects*; D012335:RNA, Ribosomal / Q000737:chemistry / Q000187:drug effects*; D012343:RNA, Transfer; D013050:Spectrometry, Fluorescence; D013329:Structure-Activity Relationship; D014961:X-Ray Diffraction
D000900:Anti-Bacterial Agents; D008024:Ligands; D012329:RNA, Bacterial; D012335:RNA, Ribosomal; D012343:RNA, Transfer