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33 Publications visible to you, out of a total of 33
Structure-Kinetic-Relationship Reveals the Mechanism of Selectivity of FAK Inhibitors Over PYK2

Abstract

Not specified

Authors: Benedict-Tilman Berger, Marta Amaral, Daria B. Kokh, Ariane Nunes-Alves, Djordje Musil, Timo Heinrich, Martin Schröder, Rebecca Neil, Jing Wang, Iva Navratilova, Joerg Bomke, Jonathan M. Elkins, Susanne Müller, Matthias Frech, Rebecca C. Wade, Stefan Knapp

Date Published: 2020

Publication Type: Journal

Machine Learning Analysis of τRAMD Trajectories to Decipher Molecular Determinants of Drug-Target Residence Times

Abstract

Not specified

Authors: Daria B. Kokh, Tom Kaufmann, Bastian Kister, Rebecca C. Wade

Date Published: 24th May 2019

Publication Type: Journal

Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations

Abstract

Not specified

Authors: Daria B. Kokh, Marta Amaral, Joerg Bomke, Ulrich Grädler, Djordje Musil, Hans-Peter Buchstaller, Matthias K. Dreyer, Matthias Frech, Maryse Lowinski, Francois Vallee, Marc Bianciotto, Alexey Rak, Rebecca C. Wade

Date Published: 24th May 2018

Publication Type: Journal

New approaches for computing ligand–receptor binding kinetics

Abstract

Not specified

Authors: Neil J Bruce, Gaurav K Ganotra, Daria B Kokh, S Kashif Sadiq, Rebecca C Wade

Date Published: 1st Apr 2018

Publication Type: Journal

Protein conformational flexibility modulates kinetics and thermodynamics of drug binding

Abstract (Expand)

Structure-based drug design has often been restricted by the rather static picture of protein–ligand complexes presented by crystal structures, despite the widely accepted importance of protein flexibility …y in biomolecular recognition. Here we report a detailed experimental and computational study of the drug target, human heat shock protein 90, to explore the contribution of protein dynamics to the binding thermodynamics and kinetics of drug-like compounds. We observe that their binding properties depend on whether the protein has a loop or a helical conformation in the binding site of the ligand-bound state. Compounds bound to the helical conformation display slow association and dissociation rates, high-affinity and high cellular efficacy, and predominantly entropically driven binding. An important entropic contribution comes from the greater flexibility of the helical relative to the loop conformation in the ligand-bound state. This unusual mechanism suggests increasing target flexibility in the bound state by ligand design as a new strategy for drug discovery.

Authors: M. Amaral, D. B. Kokh, J. Bomke, A. Wegener, H. P. Buchstaller, H. M. Eggenweiler, P. Matias, C. Sirrenberg, R. C. Wade, M. Frech

Date Published: 1st Dec 2017

Publication Type: Journal

TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets.

Abstract

Not specified

Authors: Antonia Stank, Daria B. Kokh, Max Horn, Elena Sizikova, Rebecca Neil, Joanna Panecka, Stefan Richter, Rebecca C. Wade

Date Published: 3rd Jul 2017

Publication Type: Journal

Kinetics for Drug Discovery: an industry-driven effort to target drug residence time

Abstract (Expand)

A considerable number of approved drugs show non-equilibrium binding characteristics, emphasizing the potential role of drug residence times for in vivo efficacy. Therefore, a detailed understanding … of the kinetics of association and dissociation of a target–ligand complex might provide crucial insight into the molecular mechanism-of-action of a compound. This deeper understanding will help to improve decision making in drug discovery, thus leading to a better selection of interesting compounds to be profiled further. In this review, we highlight the contributions of the Kinetics for Drug Discovery (K4DD) Consortium, which targets major open questions related to binding kinetics in an industry-driven public-private partnership.

Authors: Doris A. Schuetz, Wilhelmus Egbertus Arnout de Witte, Yin Cheong Wong, Bernhard Knasmueller, Lars Richter, Daria B. Kokh, S. Kashif Sadiq, Reggie Bosma, Indira Nederpelt, Laura H. Heitman, Elena Segala, Marta Amaral, Dong Guo, Dorothee Andres, Victoria Georgi, Leigh A. Stoddart, Steve Hill, Robert M. Cooke, Chris De Graaf, Rob Leurs, Matthias Frech, Rebecca C. Wade, Elizabeth Cunera Maria de Lange, Adriaan P. IJzerman, Anke Müller-Fahrnow, Gerhard F. Ecker

Date Published: 1st Jun 2017

Publication Type: Journal

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