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Dynamics of human protein kinase Aurora A linked to drug selectivity

Journal Article · · eLife
DOI:https://doi.org/10.7554/eLife.36656· OSTI ID:1454323

Protein kinases are major drug targets, but the development of highly-selective inhibitors has been challenging due to the similarity of their active sites. The observation of distinct structural states of the fully-conserved Asp-Phe-Gly (DFG) loop has put the concept of conformational selection for the DFG-state at the center of kinase drug discovery. Recently, it was shown that Gleevec selectivity for the Tyr-kinase Abl was instead rooted in conformational changes after drug binding. Here, we investigate whether protein dynamics after binding is a more general paradigm for drug selectivity by characterizing the binding of several approved drugs to the Ser/Thr-kinase Aurora A. Using a combination of biophysical techniques, we propose a universal drug-binding mechanism, that rationalizes selectivity, affinity and long on-target residence time for kinase inhibitors. These new concepts, where protein dynamics in the drug-bound state plays the crucial role, can be applied to inhibitor design of targets outside the kinome.

Sponsoring Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
Grant/Contract Number:
FG02-05ER15699
OSTI ID:
1454323
Alternate ID(s):
OSTI ID: 1509825
OSTI ID: 1509835
OSTI ID: 1509836
OSTI ID: 1454324
Journal Information:
eLife, Journal Name: eLife Vol. 7; ISSN 2050-084X
Publisher:
eLife Sciences Publications, Ltd.Copyright Statement
Country of Publication:
United States
Language:
English

References (95)

NMR Characterization of Kinase p38 Dynamics in Free and Ligand-Bound Forms journal January 2006
Dynamic Equilibrium of the Aurora A Kinase Activation Loop Revealed by Single-Molecule Spectroscopy journal August 2017
NMR Backbone Assignment of a Protein Kinase Catalytic Domain by a Combination of Several Approaches: Application to the Catalytic Subunit of cAMP-Dependent Protein Kinase journal October 2004
Aurora A, centrosome structure, and the centrosome cycle journal October 2009
UCSF Chimera?A visualization system for exploratory research and analysis journal January 2004
NMRPipe: A multidimensional spectral processing system based on UNIX pipes journal November 1995
Aurora A kinase (AURKA) in normal and pathological cell division journal August 2012
Aurora kinase inhibitors: Progress towards the clinic journal February 2012
Nmrglue: an open source Python package for the analysis of multidimensional NMR data journal March 2013
Backbone assignment of the tyrosine kinase Src catalytic domain in complex with imatinib journal April 2011
Chapter 23 Fitting Enzyme Kinetic Data with KinTek Global Kinetic Explorer book January 2009
Structures of the Cancer-Related Aurora-A, FAK, and EphA2 Protein Kinases from Nanovolume Crystallography journal December 2002
Structural Basis of Aurora-A Activation by TPX2 at the Mitotic Spindle journal October 2003
Global Kinetic Explorer: A new computer program for dynamic simulation and fitting of kinetic data journal April 2009
Aurora kinase inhibitors as anticancer molecules journal October 2010
Defining the conserved internal architecture of a protein kinase journal March 2010
Antimitotic drugs in cancer chemotherapy: Promises and pitfalls journal September 2013
SAR and inhibitor complex structure determination of a novel class of potent and specific Aurora kinase inhibitors journal March 2006
7-(Pyrazol-4-yl)-3H-imidazo[4,5-b]pyridine-based derivatives for kinase inhibition: Co-crystallisation studies with Aurora-A reveal distinct differences in the orientation of the pyrazole N1-substituent journal October 2015
Characterization of a highly selective inhibitor of the Aurora kinases journal September 2017
Drugging MYCN through an Allosteric Transition in Aurora Kinase A journal September 2014
Small Molecule Recognition of c-Src via the Imatinib-Binding Conformation journal October 2008
Ins and Outs of Kinase DFG Motifs journal June 2013
A comprehensive review on Aurora kinase: Small molecule inhibitors and clinical trial studies journal November 2017
Compound Selectivity and Target Residence Time of Kinase Inhibitors Studied with Surface Plasmon Resonance journal February 2017
Identification of a Major Determinant for Serine-Threonine Kinase Phosphoacceptor Specificity journal January 2014
Current applications of 19F NMR to studies of protein structure and dynamics journal April 2012
c-Src Binds to the Cancer Drug Imatinib with an Inactive Abl/c-Kit Conformation and a Distributed Thermodynamic Penalty journal March 2007
Dynamics-Driven Allostery in Protein Kinases journal November 2015
Tyrosine Kinase Activation and Conformational Flexibility: Lessons from Src-Family Tyrosine Kinases journal April 2017
Discovery of a Selective Aurora A Kinase Inhibitor by Virtual Screening journal March 2016
Characterization of Three Druggable Hot-Spots in the Aurora-A/TPX2 Interaction Using Biochemical, Biophysical, and Fragment-Based Approaches journal October 2017
Unactivated PKR Exists in an Open Conformation Capable of Binding Nucleotides journal August 2006
A Novel Mechanism by Which Small Molecule Inhibitors Induce the DFG Flip in Aurora A journal January 2012
The Different Flexibility of c-Src and c-Abl Kinases Regulates the Accessibility of a Druggable Inactive Conformation journal January 2012
Disabling ErbB Receptors with Rationally Designed Exocyclic Mimetics of Antibodies:  Structure−Function Analysis journal August 2001
1,4,5,6-Tetrahydropyrrolo[3,4- c ]pyrazoles:  Identification of a Potent Aurora Kinase Inhibitor with a Favorable Antitumor Kinase Inhibition Profile journal November 2006
Fragment-Based Discovery of the Pyrazol-4-yl Urea (AT9283), a Multitargeted Kinase Inhibitor with Potent Aurora Kinase Activity journal January 2009
Computational Study of the “DFG-Flip” Conformational Transition in c-Abl and c-Src Tyrosine Kinases journal January 2015
A Computational Model for Overcoming Drug Resistance Using Selective Dual-Inhibitors for Aurora Kinase A and Its T217D Variant journal November 2013
Three-dimensional structure of the tyrosine kinase c-Src journal February 1997
A water-mediated allosteric network governs activation of Aurora kinase A journal February 2017
Rational design of inhibitors that bind to inactive kinase conformations journal June 2006
Activation pathway of Src kinase reveals intermediate states as targets for drug design journal March 2014
Improved low-resolution crystallographic refinement with Phenix and Rosetta journal September 2013
Aurora-A — A guardian of poles journal January 2005
The drug–target residence time model: a 10-year retrospective journal December 2015
Drug–target residence time and its implications for lead optimization journal August 2006
Protein kinases — the major drug targets of the twenty-first century? journal April 2002
The druggable genome journal September 2002
A potent and highly specific FN3 monobody inhibitor of the Abl SH2 domain journal March 2010
Energetic dissection of Gleevec's selectivity toward human tyrosine kinases journal September 2014
Allosteric modulation of AURKA kinase activity by a small-molecule inhibitor of its protein-protein interaction with TPX2 journal June 2016
Simple and inexpensive incorporation of 19F-Tryptophan for protein NMR spectroscopy journal January 2012
Crystal structure of an Aurora-A mutant that mimics Aurora-B bound to MLN8054: insights into selectivity and drug design journal March 2010
Structure-kinetic relationship study of CDK8/CycC specific compounds journal April 2013
Crystal Structure of Aurora-2, an Oncogenic Serine/Threonine Kinase journal September 2002
Solution Conformations and Dynamics of ABL Kinase-Inhibitor Complexes Determined by NMR Substantiate the Different Binding Modes of Imatinib/Nilotinib and Dasatinib journal April 2008
Aurora kinase inhibitors as anti-cancer therapy journal January 2010
Allosteric inhibition of Aurora-A kinase by a synthetic vNAR domain journal July 2016
Evolution of the eukaryotic protein kinases as dynamic molecular switches journal September 2012
Phaser crystallographic software journal July 2007
xia2 : an expert system for macromolecular crystallography data reduction journal December 2009
Coot model-building tools for molecular graphics journal November 2004
MolProbity : all-atom structure validation for macromolecular crystallography journal December 2009
XDS journal January 2010
PHENIX: a comprehensive Python-based system for macromolecular structure solution journal January 2010
Features and development of Coot journal March 2010
Overview of the CCP 4 suite and current developments journal March 2011
iMOSFLM : a new graphical interface for diffraction-image processing with MOSFLM journal March 2011
Towards automated crystallographic structure refinement with phenix.refine journal March 2012
How good are my data and what is the resolution? journal June 2013
ACHESYM : an algorithm and server for standardized placement of macromolecular models in the unit cell journal November 2014
CheckMyMetal : a macromolecular metal-binding validation tool journal February 2017
Modulation of kinase-inhibitor interactions by auxiliary protein binding: Crystallography studies on Aurora A interactions with VX-680 and with TPX2 journal October 2008
Insights into nucleotide binding in protein kinase A using fluorescent adenosine derivatives journal January 2000
Switching Aurora-A kinase on and off at an allosteric site journal April 2017
Structural Mechanism for STI-571 Inhibition of Abelson Tyrosine Kinase journal September 2000
Using ancient protein kinases to unravel a modern cancer drug's mechanism journal February 2015
Imatinib: A Breakthrough of Targeted Therapy in Cancer journal January 2014
A Unique Structure for Epidermal Growth Factor Receptor Bound to GW572016 (Lapatinib): Relationships among Protein Conformation, Inhibitor Off-Rate, and Receptor Activity in Tumor Cells journal September 2004
Equally Potent Inhibition of c-Src and Abl by Compounds that Recognize Inactive Kinase Conformations journal March 2009
Aurora Kinases: New Targets for Cancer Therapy journal December 2006
Aurora Kinases as Anticancer Drug Targets journal March 2008
Targeting Aurora Kinases with Danusertib (PHA-739358) Inhibits Growth of Liver Metastases from Gastroenteropancreatic Neuroendocrine Tumors in an Orthotopic Xenograft Model journal July 2012
PHA-739358, a potent inhibitor of Aurora kinases with a selective target inhibition profile relevant to cancer journal December 2007
Roles of Aurora Kinases in Mitosis and Tumorigenesis journal January 2007
Phase I Pharmacokinetic and Pharmacodynamic Study of the Aurora Kinase Inhibitor Danusertib in Patients With Advanced or Metastatic Solid Tumors journal October 2009
A Src-Like Inactive Conformation in the Abl Tyrosine Kinase Domain journal May 2006
Specificity Rendering ‘Hot-Spots’ for Aurora Kinase Inhibitor Design: The Role of Non-Covalent Interactions and Conformational Transitions journal December 2014
Identification of small molecule inhibitors of the Aurora-A/TPX2 complex journal March 2017
Structural Biology Insight for the Design of Sub-type Selective Aurora Kinase Inhibitors journal July 2015
Aurora Kinase Inhibitors: Current Status and Outlook journal December 2015
Molecular mechanism of Aurora A kinase autophosphorylation and its allosteric activation by TPX2 journal May 2014
A dynamic mechanism for allosteric activation of Aurora kinase A by activation loop phosphorylation journal February 2018

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