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The Active Site of a Prototypical “Rigid” Drug Target is Marked by Extensive Conformational Dynamics

Drug discovery, in particular optimization of candidates using medicinal chemistry, is generally guided by structural biology. However, for optimizing binding kinetics, relevant for efficacy and off‐target effects, information on protein motion is important. Herein, we demonstrate for the prototypic...

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Autores principales: Singh, Himanshu, Das, Chandan K., Vasa, Suresh K., Grohe, Kristof, Schäfer, Lars V., Linser, Rasmus
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7756556/
https://www.ncbi.nlm.nih.gov/pubmed/32965765
http://dx.doi.org/10.1002/anie.202009348
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author Singh, Himanshu
Das, Chandan K.
Vasa, Suresh K.
Grohe, Kristof
Schäfer, Lars V.
Linser, Rasmus
author_facet Singh, Himanshu
Das, Chandan K.
Vasa, Suresh K.
Grohe, Kristof
Schäfer, Lars V.
Linser, Rasmus
author_sort Singh, Himanshu
collection PubMed
description Drug discovery, in particular optimization of candidates using medicinal chemistry, is generally guided by structural biology. However, for optimizing binding kinetics, relevant for efficacy and off‐target effects, information on protein motion is important. Herein, we demonstrate for the prototypical textbook example of an allegedly “rigid protein” that substantial active‐site dynamics have generally remained unrecognized, despite thousands of medicinal‐chemistry studies on this model over decades. Comparing cryogenic X‐ray structures, solid‐state NMR on micro‐crystalline protein at room temperature, and solution NMR structure and dynamics, supported by MD simulations, we show that under physiologically relevant conditions the pocket is in fact shaped by pronounced open/close conformational‐exchange dynamics. The study, which is of general significance for pharmacological research, evinces a generic pitfall in drug discovery routines.
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spelling pubmed-77565562020-12-28 The Active Site of a Prototypical “Rigid” Drug Target is Marked by Extensive Conformational Dynamics Singh, Himanshu Das, Chandan K. Vasa, Suresh K. Grohe, Kristof Schäfer, Lars V. Linser, Rasmus Angew Chem Int Ed Engl Communications Drug discovery, in particular optimization of candidates using medicinal chemistry, is generally guided by structural biology. However, for optimizing binding kinetics, relevant for efficacy and off‐target effects, information on protein motion is important. Herein, we demonstrate for the prototypical textbook example of an allegedly “rigid protein” that substantial active‐site dynamics have generally remained unrecognized, despite thousands of medicinal‐chemistry studies on this model over decades. Comparing cryogenic X‐ray structures, solid‐state NMR on micro‐crystalline protein at room temperature, and solution NMR structure and dynamics, supported by MD simulations, we show that under physiologically relevant conditions the pocket is in fact shaped by pronounced open/close conformational‐exchange dynamics. The study, which is of general significance for pharmacological research, evinces a generic pitfall in drug discovery routines. John Wiley and Sons Inc. 2020-11-16 2020-12-14 /pmc/articles/PMC7756556/ /pubmed/32965765 http://dx.doi.org/10.1002/anie.202009348 Text en © 2020 The Authors. Published by Wiley-VCH GmbH This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Communications
Singh, Himanshu
Das, Chandan K.
Vasa, Suresh K.
Grohe, Kristof
Schäfer, Lars V.
Linser, Rasmus
The Active Site of a Prototypical “Rigid” Drug Target is Marked by Extensive Conformational Dynamics
title The Active Site of a Prototypical “Rigid” Drug Target is Marked by Extensive Conformational Dynamics
title_full The Active Site of a Prototypical “Rigid” Drug Target is Marked by Extensive Conformational Dynamics
title_fullStr The Active Site of a Prototypical “Rigid” Drug Target is Marked by Extensive Conformational Dynamics
title_full_unstemmed The Active Site of a Prototypical “Rigid” Drug Target is Marked by Extensive Conformational Dynamics
title_short The Active Site of a Prototypical “Rigid” Drug Target is Marked by Extensive Conformational Dynamics
title_sort active site of a prototypical “rigid” drug target is marked by extensive conformational dynamics
topic Communications
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7756556/
https://www.ncbi.nlm.nih.gov/pubmed/32965765
http://dx.doi.org/10.1002/anie.202009348
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