Dynamic undocking and the quasi-bound state as tools for drug discovery.Ruiz-Carmona, S., Schmidtke, P., Luque, F.J., Baker, L., Matassova, N., Davis, B., Roughley, S., Murray, J., Hubbard, R., Barril, X.
(2017) Nat Chem 9: 201-206
- PubMed: 28221352
- DOI: 10.1038/nchem.2660
- Primary Citation of Related Structures:
- PubMed Abstract:
There is a pressing need for new technologies that improve the efficacy and efficiency of drug discovery. Structure-based methods have contributed towards this goal but they focus on predicting the binding affinity of protein-ligand complexes, which ...
There is a pressing need for new technologies that improve the efficacy and efficiency of drug discovery. Structure-based methods have contributed towards this goal but they focus on predicting the binding affinity of protein-ligand complexes, which is notoriously difficult. We adopt an alternative approach that evaluates structural, rather than thermodynamic, stability. As bioactive molecules present a static binding mode, we devised dynamic undocking (DUck), a fast computational method to calculate the work necessary to reach a quasi-bound state at which the ligand has just broken the most important native contact with the receptor. This non-equilibrium property is surprisingly effective in virtual screening because true ligands form more-resilient interactions than decoys. Notably, DUck is orthogonal to docking and other 'thermodynamic' methods. We demonstrate the potential of the docking-undocking combination in a fragment screening against the molecular chaperone and oncology target Hsp90, for which we obtain novel chemotypes and a hit rate that approaches 40%.
Vernalis (R&D) Ltd, Granta Park, Cambridge CB21 6GB, UK.,YSBL, University of York, Heslington, York YO10 5DD, UK.,Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain.,Discngine, 33 rue du Fauburg Saint-Antoine, 75011 Paris, France.,Institut de Biomedicina de la Universitat de Barcelona (IBUB) and Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain.