Download MendeleyNMR2-Based Drug Discovery Pipeline Presented on the Oncogenic Protein KRAS.
Butikofer, M., Torres, F., Kadavath, H., Gamperli, N., Abi Saad, M.J., Zindel, D., Coudevylle, N., Riek, R., Orts, J.(2025) J Am Chem Soc 147: 13200-13209
- PubMed: 40228104
- DOI: https://doi.org/10.1021/jacs.4c16762
- Primary Citation of Related Structures:
8PI0, 8PIY, 8QDK, 8QDN, 8QDP, 8QDS, 8QDT, 8QDW, 8QE6, 8QE7, 8QEI, 8QEJ - PubMed Abstract:
Fragment-based drug discovery has emerged as a powerful approach for developing therapeutics against challenging targets, including the GTPase KRAS. Here, we report an NMR-based screening campaign employing state-of-the-art techniques to evaluate a library of 890 fragments against the oncogenic KRAS G12V mutant bound to GMP-PNP. Further HSQC titration experiments identified hits with low millimolar affinities binding within the SI/SII switch region, which forms the binding interface for the effector proteins. To elucidate the binding modes, we applied NMR molecular replacement ( N MR 2 ) structure calculations, bypassing the need for a conventional protein resonance assignment. Traditionally, N MR 2 relies on isotope-filtered nuclear Overhauser effect spectroscopy experiments requiring double-labeled [ 13 C, 15 N]-protein. We introduce a cost-efficient alternative using a relaxation-based filter that eliminates isotope labeling while preserving structural accuracy. Validation against standard isotopically labeled workflows confirmed the equivalence of the derived protein-ligand structures. This approach enabled the determination of 12 N MR 2 KRAS-fragment complex structures, providing critical insights into structure-activity relationships to guide ligand optimization. These results demonstrate the streamlined integration of N MR 2 into a fragment-based drug discovery pipeline composed of screening, binding characterization, and rapid structural elucidation with or without isotopic labeling.
Organizational Affiliation:
Department of Pharmaceutical Sciences, University of Vienna, Josef-Holaubek-Platz 2, 2F 353, Vienna, A-1090, Austria.
