1
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Shekhar M, Smith Z, Seeliger MA, Tiwary P. Protein Flexibility and Dissociation Pathway Differentiation Can Explain Onset of Resistance Mutations in Kinases. Angew Chem Int Ed Engl 2022; 61:e202200983. [PMID: 35486370 DOI: 10.1002/anie.202200983] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Indexed: 12/14/2022]
Abstract
Understanding how mutations render a drug ineffective is a problem of immense relevance. Often the mechanism through which mutations cause drug resistance can be explained purely through thermodynamics. However, the more perplexing situation is when two proteins have the same drug binding affinities but different residence times. In this work, we demonstrate how all-atom molecular dynamics simulations using recent developments grounded in statistical mechanics can provide a detailed mechanistic rationale for such variances. We discover dissociation mechanisms for the anti-cancer drug Imatinib (Gleevec) against wild-type and the N368S mutant of Abl kinase. We show how this point mutation triggers far-reaching changes in the protein's flexibility and leads to a different, much faster, drug dissociation pathway. We believe that this work marks an efficient and scalable approach to obtain mechanistic insight into resistance mutations in biomolecular receptors that are hard to explain using a structural perspective.
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Affiliation(s)
- Mrinal Shekhar
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Zachary Smith
- Biophysics Program and Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Markus A Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA
| | - Pratyush Tiwary
- Department of Chemistry and Biochemistry and Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
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2
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Shekhar M, Smith Z, Seeliger M, Tiwary P. Protein Flexibility and Dissociation Pathway Differentiation Can Explain Onset Of Resistance Mutations in Kinases. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Mrinal Shekhar
- Broad Institute Center for Development of Therapeutics UNITED STATES
| | - Zachary Smith
- University of Maryland at College Park Institute for Physical Science and Technology UNITED STATES
| | - Markus Seeliger
- Stony Brook University Department of Pharmacological Sciences UNITED STATES
| | - Pratyush Tiwary
- university of maryland chemistry and biochemistry university of maryland 20740 college park UNITED STATES
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3
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Tröster A, Heinzlmeir S, Berger BT, Gande SL, Saxena K, Sreeramulu S, Linhard V, Nasiri AH, Bolte M, Müller S, Kuster B, Médard G, Kudlinzki D, Schwalbe H. NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. ChemMedChem 2018; 13:1629-1633. [PMID: 29928781 DOI: 10.1002/cmdc.201800398] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Indexed: 01/14/2023]
Abstract
Erythropoietin-producing hepatocellular (EPH) receptors are transmembrane receptor tyrosine kinases. Their extracellular domains bind specifically to ephrin A/B ligands, and this binding modulates intracellular kinase activity. EPHs are key players in bidirectional intercellular signaling, controlling cell morphology, adhesion, and migration. They are increasingly recognized as cancer drug targets. We analyzed the binding of NVP-BHG712 (NVP) to EPHA2 and EPHB4. Unexpectedly, all tested commercially available NVP samples turned out to be a regioisomer (NVPiso) of the inhibitor, initially described in a Novartis patent application. They only differ by the localization of a single methyl group on either one of two adjacent nitrogen atoms. The two compounds of identical mass revealed different binding modes. Furthermore, both in vitro and in vivo experiments showed that the isomers differ in their kinase affinity and selectivity.
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Affiliation(s)
- Alix Tröster
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Stephanie Heinzlmeir
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil-Erlenmeyer-Forum 5, 85354, Freising, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Benedict-Tilman Berger
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany.,Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany
| | - Santosh L Gande
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Krishna Saxena
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Sridhar Sreeramulu
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Verena Linhard
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Amir H Nasiri
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Michael Bolte
- Institute for Inorganic Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Susanne Müller
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil-Erlenmeyer-Forum 5, 85354, Freising, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Guillaume Médard
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil-Erlenmeyer-Forum 5, 85354, Freising, Germany
| | - Denis Kudlinzki
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
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4
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Gilburt JAH, Sarkar H, Sheldrake P, Blagg J, Ying L, Dodson CA. Dynamic Equilibrium of the Aurora A Kinase Activation Loop Revealed by Single-Molecule Spectroscopy. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- James A. H. Gilburt
- National Heart & Lung Institute; SAF Building; Imperial College London; London SW7 2AZ UK
| | - Hajrah Sarkar
- National Heart & Lung Institute; SAF Building; Imperial College London; London SW7 2AZ UK
| | - Peter Sheldrake
- Cancer Research UK Cancer Therapeutics Unit; The Institute of Cancer Research; 15 Cotswold Road Sutton Surrey SM2 5NG UK
| | - Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit; The Institute of Cancer Research; 15 Cotswold Road Sutton Surrey SM2 5NG UK
| | - Liming Ying
- National Heart & Lung Institute; SAF Building; Imperial College London; London SW7 2AZ UK
| | - Charlotte A. Dodson
- National Heart & Lung Institute; SAF Building; Imperial College London; London SW7 2AZ UK
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5
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Gilburt JAH, Sarkar H, Sheldrake P, Blagg J, Ying L, Dodson CA. Dynamic Equilibrium of the Aurora A Kinase Activation Loop Revealed by Single-Molecule Spectroscopy. Angew Chem Int Ed Engl 2017; 56:11409-11414. [PMID: 28700101 PMCID: PMC5601181 DOI: 10.1002/anie.201704654] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Indexed: 12/14/2022]
Abstract
The conformation of the activation loop (T-loop) of protein kinases underlies enzymatic activity and influences the binding of small-molecule inhibitors. By using single-molecule fluorescence spectroscopy, we have determined that phosphorylated Aurora A kinase is in dynamic equilibrium between a DFG-in-like active T-loop conformation and a DFG-out-like inactive conformation, and have measured the rate constants of interconversion. Addition of the Aurora A activating protein TPX2 shifts the equilibrium towards an active T-loop conformation whereas addition of the inhibitors MLN8054 and CD532 favors an inactive T-loop. We show that Aurora A binds TPX2 and MLN8054 simultaneously and provide a new model for kinase conformational behavior. Our approach will enable conformation-specific effects to be integrated into inhibitor discovery across the kinome, and we outline some immediate consequences for structure-based drug discovery.
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Affiliation(s)
- James A. H. Gilburt
- National Heart & Lung InstituteSAF BuildingImperial College LondonLondonSW7 2AZUK
| | - Hajrah Sarkar
- National Heart & Lung InstituteSAF BuildingImperial College LondonLondonSW7 2AZUK
| | - Peter Sheldrake
- Cancer Research UK Cancer Therapeutics UnitThe Institute of Cancer Research15 Cotswold RoadSuttonSurreySM2 5NGUK
| | - Julian Blagg
- Cancer Research UK Cancer Therapeutics UnitThe Institute of Cancer Research15 Cotswold RoadSuttonSurreySM2 5NGUK
| | - Liming Ying
- National Heart & Lung InstituteSAF BuildingImperial College LondonLondonSW7 2AZUK
| | - Charlotte A. Dodson
- National Heart & Lung InstituteSAF BuildingImperial College LondonLondonSW7 2AZUK
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6
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Wentsch HK, Walter NM, Bührmann M, Mayer-Wrangowski S, Rauh D, Zaman GJR, Willemsen-Seegers N, Buijsman RC, Henning M, Dauch D, Zender L, Laufer S. Optimierte Bindungsdauer am Zielenzym: Typ-I1/2
-Inhibitoren der p38α-MAP-Kinase mit verbesserter Bindungskinetik durch direkte Interaktion mit der R-Spine. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Heike K. Wentsch
- Pharmazeutisches Institut; Pharmazeutische und Medizinische Chemie; Eberhard Karls Universität Tübingen; Auf der Morgenstelle 8 72076 Tübingen Deutschland
| | - Niklas M. Walter
- Pharmazeutisches Institut; Pharmazeutische und Medizinische Chemie; Eberhard Karls Universität Tübingen; Auf der Morgenstelle 8 72076 Tübingen Deutschland
| | - Mike Bührmann
- Fakultät für Chemie und Chemische Biologie; TU Dortmund; Deutschland
| | | | - Daniel Rauh
- Fakultät für Chemie und Chemische Biologie; TU Dortmund; Deutschland
| | - Guido J. R. Zaman
- Netherlands Translational Research Center B.V. (NTRC); Oss Niederlande
| | | | | | - Melanie Henning
- Klinische Tumorbiologie; Abteilung Innere Medizin VIII; Universitätsklinikum Tübingen; Deutschland
- Institut für Physiologie; Abteilung Physiologie I; Eberhard Karls Universität Tübingen; Deutschland
| | - Daniel Dauch
- Klinische Tumorbiologie; Abteilung Innere Medizin VIII; Universitätsklinikum Tübingen; Deutschland
- Institut für Physiologie; Abteilung Physiologie I; Eberhard Karls Universität Tübingen; Deutschland
| | - Lars Zender
- Klinische Tumorbiologie; Abteilung Innere Medizin VIII; Universitätsklinikum Tübingen; Deutschland
- Institut für Physiologie; Abteilung Physiologie I; Eberhard Karls Universität Tübingen; Deutschland
| | - Stefan Laufer
- Pharmazeutisches Institut; Pharmazeutische und Medizinische Chemie; Eberhard Karls Universität Tübingen; Auf der Morgenstelle 8 72076 Tübingen Deutschland
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7
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Wentsch HK, Walter NM, Bührmann M, Mayer-Wrangowski S, Rauh D, Zaman GJR, Willemsen-Seegers N, Buijsman RC, Henning M, Dauch D, Zender L, Laufer S. Optimized Target Residence Time: Type I1/2
Inhibitors for p38α MAP Kinase with Improved Binding Kinetics through Direct Interaction with the R-Spine. Angew Chem Int Ed Engl 2017; 56:5363-5367. [DOI: 10.1002/anie.201701185] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/09/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Heike K. Wentsch
- Institute of Pharmaceutical Sciences; Pharmaceutical and Medicinal Chemistry; Eberhard Karls Universität Tübingen; Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Niklas M. Walter
- Institute of Pharmaceutical Sciences; Pharmaceutical and Medicinal Chemistry; Eberhard Karls Universität Tübingen; Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Mike Bührmann
- Faculty of Chemistry and Chemical Biology; Technische Universität Dortmund; Germany
| | | | - Daniel Rauh
- Faculty of Chemistry and Chemical Biology; Technische Universität Dortmund; Germany
| | - Guido J. R. Zaman
- Netherlands Translational Research Center B.V. (NTRC); Oss The Netherlands
| | | | - Rogier C. Buijsman
- Netherlands Translational Research Center B.V. (NTRC); Oss The Netherlands
| | - Melanie Henning
- Department of Internal Medicine VIII; University Hospital Tübingen (Germany)
- Institute of Physiology; Department of Physiology I; Eberhard Karls Universität Tübingen; Germany
| | - Daniel Dauch
- Department of Internal Medicine VIII; University Hospital Tübingen (Germany)
- Institute of Physiology; Department of Physiology I; Eberhard Karls Universität Tübingen; Germany
| | - Lars Zender
- Department of Internal Medicine VIII; University Hospital Tübingen (Germany)
- Institute of Physiology; Department of Physiology I; Eberhard Karls Universität Tübingen; Germany
| | - Stefan Laufer
- Institute of Pharmaceutical Sciences; Pharmaceutical and Medicinal Chemistry; Eberhard Karls Universität Tübingen; Auf der Morgenstelle 8 72076 Tübingen Germany
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8
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Gande SL, Saxena K, Sreeramulu S, Linhard V, Kudlinzki D, Heinzlmeir S, Reichert AJ, Skerra A, Kuster B, Schwalbe H. Expression and Purification of EPHA2 Tyrosine Kinase Domain for Crystallographic and NMR Studies. Chembiochem 2016; 17:2257-2263. [DOI: 10.1002/cbic.201600483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Indexed: 01/12/2023]
Affiliation(s)
- Santosh L. Gande
- Center for Biomolecular Magnetic Resonance (BMRZ); Institute for Organic Chemistry and Chemical Biology; Johann Wolfgang Goethe-Universität; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
- German Cancer Consortium (DKTK); In Neuenheimer Feld 280 69120 Heidelberg Germany
- German Cancer Research Center (DKFZ); In Neuenheimer Feld 280 69120 Heidelberg Germany
| | - Krishna Saxena
- Center for Biomolecular Magnetic Resonance (BMRZ); Institute for Organic Chemistry and Chemical Biology; Johann Wolfgang Goethe-Universität; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
- German Cancer Consortium (DKTK); In Neuenheimer Feld 280 69120 Heidelberg Germany
- German Cancer Research Center (DKFZ); In Neuenheimer Feld 280 69120 Heidelberg Germany
| | - Sridhar Sreeramulu
- Center for Biomolecular Magnetic Resonance (BMRZ); Institute for Organic Chemistry and Chemical Biology; Johann Wolfgang Goethe-Universität; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Verena Linhard
- Center for Biomolecular Magnetic Resonance (BMRZ); Institute for Organic Chemistry and Chemical Biology; Johann Wolfgang Goethe-Universität; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Denis Kudlinzki
- Center for Biomolecular Magnetic Resonance (BMRZ); Institute for Organic Chemistry and Chemical Biology; Johann Wolfgang Goethe-Universität; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
- German Cancer Consortium (DKTK); In Neuenheimer Feld 280 69120 Heidelberg Germany
- German Cancer Research Center (DKFZ); In Neuenheimer Feld 280 69120 Heidelberg Germany
| | - Stephanie Heinzlmeir
- German Cancer Consortium (DKTK); In Neuenheimer Feld 280 69120 Heidelberg Germany
- German Cancer Research Center (DKFZ); In Neuenheimer Feld 280 69120 Heidelberg Germany
- Chair of Proteomics and Bioanalytics; Technical University of Munich; Emil-Erlenmeyer-Forum 5 85354 Freising Germany
| | - Andreas J. Reichert
- Chair of Biological Chemistry; Technical University of Munich; Emil-Erlenmeyer-Forum 5 85354 Freising Germany
| | - Arne Skerra
- Chair of Biological Chemistry; Technical University of Munich; Emil-Erlenmeyer-Forum 5 85354 Freising Germany
| | - Bernhard Kuster
- German Cancer Consortium (DKTK); In Neuenheimer Feld 280 69120 Heidelberg Germany
- German Cancer Research Center (DKFZ); In Neuenheimer Feld 280 69120 Heidelberg Germany
- Chair of Proteomics and Bioanalytics; Technical University of Munich; Emil-Erlenmeyer-Forum 5 85354 Freising Germany
- Center for integrated Protein Science Munich (CIPSM); Technical University of Munich; Arcisstrasse 21 80333 München Germany
- Bavarian Biomolecular Mass Spectrometry Center; Technical University of Munich; Gregor-Mendel-Strasse 4 85354 Freising Germany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ); Institute for Organic Chemistry and Chemical Biology; Johann Wolfgang Goethe-Universität; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
- German Cancer Consortium (DKTK); In Neuenheimer Feld 280 69120 Heidelberg Germany
- German Cancer Research Center (DKFZ); In Neuenheimer Feld 280 69120 Heidelberg Germany
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9
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Larion M, Hansen AL, Zhang F, Bruschweiler-Li L, Tugarinov V, Miller BG, Brüschweiler R. Kinetic Cooperativity in Human Pancreatic Glucokinase Originates from Millisecond Dynamics of the Small Domain. Angew Chem Int Ed Engl 2015; 54:8129-32. [PMID: 26013420 PMCID: PMC4587531 DOI: 10.1002/anie.201501204] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 04/15/2015] [Indexed: 11/06/2022]
Abstract
The hallmark of glucokinase (GCK), which catalyzes the phosphorylation of glucose during glycolysis, is its kinetic cooperativity, whose understanding at atomic detail has remained open since its discovery over 40 years ago. Herein, by using kinetic CPMG NMR spectroscopic data for 17 isoleucine side chains distributed over all parts of GCK, we show that the origin of kinetic cooperativity is rooted in intramolecular protein dynamics. Residues of glucose-free GCK located in the small domain displayed distinct exchange behavior involving multiple conformers that are substantially populated (p>17 %) with a kex value of 509±51 s(-1) , whereas in the glucose-bound form these exchange processes were quenched. This exchange behavior directly competes with the enzymatic turnover rate at physiological glucose concentrations, thereby generating the sigmoidal rate dependence that defines kinetic cooperativity.
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Affiliation(s)
- Mioara Larion
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210 (USA)
| | - Alexandar L Hansen
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210 (USA)
| | - Fengli Zhang
- National High Magnetic Field Laboratory, Tallahassee, FL 32306 (USA)
| | - Lei Bruschweiler-Li
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210 (USA)
| | - Vitali Tugarinov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520 (USA)
| | - Brian G Miller
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306 (USA)
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210 (USA).
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10
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Larion M, Hansen AL, Zhang F, Bruschweiler-Li L, Tugarinov V, Miller BG, Brüschweiler R. Kinetic Cooperativity in Human Pancreatic Glucokinase Originates from Millisecond Dynamics of the Small Domain. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201501204] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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11
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Vinh NB, Devine SM, Munoz L, Ryan RM, Wang BH, Krum H, Chalmers DK, Simpson JS, Scammells PJ. Design, Synthesis, and Biological Evaluation of Tetra-Substituted Thiophenes as Inhibitors of p38α MAPK. ChemistryOpen 2014; 4:56-64. [PMID: 25861571 PMCID: PMC4380954 DOI: 10.1002/open.201402076] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Indexed: 12/30/2022] Open
Abstract
p38α mitogen-activated protein kinase (MAPK) plays a role in several cellular processes and consequently has been a therapeutic target in inflammatory diseases, cancer, and cardiovascular disease. A number of known p38α MAPK inhibitors contain vicinal 4-fluorophenyl/4-pyridyl rings connected to either a 5- or 6-membered heterocycle. In this study, a small library of substituted thiophene-based compounds bearing the vicinal 4-fluorophenyl/4-pyridyl rings was designed using computational docking as a visualisation tool. Compounds were synthesised and evaluated in a fluorescence polarisation binding assay. The synthesised analogues had a higher binding affinity to the active phosphorylated form of p38α MAPK than the inactive nonphosphorylated form of the protein. 4-(2-(4-fluorophenyl)thiophen-3-yl)pyridine had a Ki value of 0.6 μm to active p38α MAPK highlighting that substitution of the core ring to a thiophene retains affinity to the enzyme and can be utilised in p38α MAPK inhibitors. This compound was further elaborated using a substituted phenyl ring in order to probe the second hydrophobic pocket. Many of these analogues exhibited low micromolar affinity to active p38α MAPK. The suppression of neonatal rat fibroblast collagen synthesis was also observed suggesting that further development of these compounds may lead to potential therapeutics having cardioprotective properties.
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Affiliation(s)
- Natalie B Vinh
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville, VIC 3052 (Australia)
| | - Shane M Devine
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville, VIC 3052 (Australia)
| | - Lenka Munoz
- Discipline of Pharmacology, School of Medical Sciences and Bosch Institute, The University of Sydney Sydney, NSW 2006 (Australia)
| | - Renae M Ryan
- Discipline of Pharmacology, School of Medical Sciences and Bosch Institute, The University of Sydney Sydney, NSW 2006 (Australia)
| | - Bing H Wang
- Centre of Cardiovascular Research and Education in Therapeutics, Department of Epidemiology and Preventative Medicine, Monash University 99 Commercial Road, Melbourne, VIC 3004 (Australia)
| | - Henry Krum
- Centre of Cardiovascular Research and Education in Therapeutics, Department of Epidemiology and Preventative Medicine, Monash University 99 Commercial Road, Melbourne, VIC 3004 (Australia)
| | - David K Chalmers
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville, VIC 3052 (Australia)
| | - Jamie S Simpson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville, VIC 3052 (Australia)
| | - Peter J Scammells
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville, VIC 3052 (Australia)
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12
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Nielsen G, Jonker HRA, Vajpai N, Grzesiek S, Schwalbe H. Kinase in Motion: Insights into the Dynamic Nature of p38α by High-Pressure NMR Spectroscopic Studies. Chembiochem 2013; 14:1799-806. [DOI: 10.1002/cbic.201300170] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Indexed: 11/11/2022]
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13
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Flick J, Tristram F, Wenzel W. Modeling loop backbone flexibility in receptor-ligand docking simulations. J Comput Chem 2012; 33:2504-15. [DOI: 10.1002/jcc.23087] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Revised: 06/15/2012] [Accepted: 07/09/2012] [Indexed: 12/20/2022]
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14
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Honndorf VS, Coudevylle N, Laufer S, Becker S, Griesinger C, Habeck M. Inferential NMR/X-ray-based structure determination of a dibenzo[a,d]cycloheptenone inhibitor-p38α MAP kinase complex in solution. Angew Chem Int Ed Engl 2012; 51:2359-62. [PMID: 22275118 DOI: 10.1002/anie.201105241] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 12/23/2011] [Indexed: 11/10/2022]
Affiliation(s)
- Valerie S Honndorf
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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15
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Honndorf VS, Coudevylle N, Laufer S, Becker S, Griesinger C, Habeck M. Inferential NMR/X-ray-Based Structure Determination of a Dibenzo[a,d]cycloheptenone Inhibitor-p38α MAP Kinase Complex in Solution. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201105241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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16
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Nielsen G, Schwalbe H. NMR spectroscopic investigations of the activated p38α mitogen-activated protein kinase. Chembiochem 2011; 12:2599-607. [PMID: 22012687 DOI: 10.1002/cbic.201100527] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Indexed: 11/11/2022]
Abstract
Phosphorylation of protein kinases is a central mechanism involved in numerous cellular regulatory circuits, both in prokaryotic and eukaryotic cells. An understanding of the structural and functional consequences of protein phosphorylation is of considerable importance for the design of selective, small-molecule kinase inhibitors. NMR spectroscopy is a central method to support structure-based drug design. Here, we present the NMR assignment of the activated p38α kinase and compare it to the NMR assignment of unphosphorylated p38α. Conformational changes in solution induced by activation can be located to the activation loop, an adjacent loop, and an insert part of the polypeptide chain that is specific for the family of mitogen-activated kinases. Deuterium-exchange experiments additionally revealed differences in exchange behavior for two residues in an alanine-rich helix-loop motif that becomes more flexible upon binding of an ATP analogue and a substrate peptide.
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Affiliation(s)
- Gerd Nielsen
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe University, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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Honndorf VS, Coudevylle N, Laufer S, Becker S, Griesinger C. Dynamics in the p38alpha MAP kinase-SB203580 complex observed by liquid-state NMR spectroscopy. Angew Chem Int Ed Engl 2008; 47:3548-51. [PMID: 18389508 DOI: 10.1002/anie.200705614] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Valerie S Honndorf
- Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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Honndorf V, Coudevylle N, Laufer S, Becker S, Griesinger C. Dynamics in the p38α MAP Kinase–SB203580 Complex Observed by Liquid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200705614] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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