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Georgi V, Schiele F, Berger BT, Steffen A, Marin Zapata PA, Briem H, Menz S, Preusse C, Vasta JD, Robers MB, Brands M, Knapp S, Fernández-Montalván A. Binding Kinetics Survey of the Drugged Kinome. J Am Chem Soc 2018; 140:15774-15782. [PMID: 30362749 DOI: 10.1021/jacs.8b08048] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Target residence time is emerging as an important optimization parameter in drug discovery, yet target and off-target engagement dynamics have not been clearly linked to the clinical performance of drugs. Here we developed high-throughput binding kinetics assays to characterize the interactions of 270 protein kinase inhibitors with 40 clinically relevant targets. Analysis of the results revealed that on-rates are better correlated with affinity than off-rates and that the fraction of slowly dissociating drug-target complexes increases from early/preclinical to late stage and FDA-approved compounds, suggesting distinct contributions by each parameter to clinical success. Combining binding parameters with PK/ADME properties, we illustrate in silico and in cells how kinetic selectivity could be exploited as an optimization strategy. Furthermore, using bio- and chemoinformatics we uncovered structural features influencing rate constants. Our results underscore the value of binding kinetics information in rational drug design and provide a resource for future studies on this subject.
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Affiliation(s)
- Victoria Georgi
- Bayer AG, Drug Discovery, Pharmaceuticals , Müllerstraße 178 , 13353 Berlin , Germany.,Structural Genomics Consortium, Institute for Pharmaceutical Chemistry , Johann Wolfgang Goethe-University , Max-von-Laue-Straße 9 , 60438 Frankfurt am Main , Germany
| | - Felix Schiele
- Bayer AG, Drug Discovery, Pharmaceuticals , Müllerstraße 178 , 13353 Berlin , Germany
| | - Benedict-Tilman Berger
- Bayer AG, Drug Discovery, Pharmaceuticals , Müllerstraße 178 , 13353 Berlin , Germany.,Structural Genomics Consortium, Institute for Pharmaceutical Chemistry , Johann Wolfgang Goethe-University , Max-von-Laue-Straße 9 , 60438 Frankfurt am Main , Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences , Johann Wolfgang Goethe-University , Max-von-Laue-Straße 15 , 60438 Frankfurt am Main , Germany
| | - Andreas Steffen
- Bayer AG, Drug Discovery, Pharmaceuticals , Müllerstraße 178 , 13353 Berlin , Germany
| | - Paula A Marin Zapata
- Bayer AG, Drug Discovery, Pharmaceuticals , Müllerstraße 178 , 13353 Berlin , Germany
| | - Hans Briem
- Bayer AG, Drug Discovery, Pharmaceuticals , Müllerstraße 178 , 13353 Berlin , Germany
| | - Stephan Menz
- Bayer AG, Drug Discovery, Pharmaceuticals , Müllerstraße 178 , 13353 Berlin , Germany
| | - Cornelia Preusse
- Bayer AG, Drug Discovery, Pharmaceuticals , Müllerstraße 178 , 13353 Berlin , Germany
| | - James D Vasta
- Promega Corporation , 2800 Woods Hollow Road , Fitchburg , Wisconsin 53711 , United States
| | - Matthew B Robers
- Promega Corporation , 2800 Woods Hollow Road , Fitchburg , Wisconsin 53711 , United States
| | - Michael Brands
- Bayer AG, Drug Discovery, Pharmaceuticals , Müllerstraße 178 , 13353 Berlin , Germany
| | - Stefan Knapp
- Structural Genomics Consortium, Institute for Pharmaceutical Chemistry , Johann Wolfgang Goethe-University , Max-von-Laue-Straße 9 , 60438 Frankfurt am Main , Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences , Johann Wolfgang Goethe-University , Max-von-Laue-Straße 15 , 60438 Frankfurt am Main , Germany
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