However, emerging evidence demonstrates that ATP-competitive inhibitors can affect kinase interactions and functions in ways beyond blocking catalytic activity. Overall, these studies underscore the relationship between the ATP-binding and regulatory sites of MAPKs and provide insight into how ATP-competitive ligands can be designed to confer graded control over protein kinase function. Zhang, Jianming; Adrian, Francisco J. In an effort to find new pharmacol. Here, using soln.
NMR, X-ray crystallog. GNF-5, an analog of GNF-2 with improved pharmacokinetic properties, when used in combination with the ATP-competitive inhibitors imatinib or nilotinib, suppressed the emergence of resistance mutations in vitro, displayed additive inhibitory activity in biochem.
These results show that therapeutically relevant inhibition of Bcr-Abl activity can be achieved with inhibitors that bind to the myristate-binding site and that combining allosteric and ATP-competitive inhibitors can overcome resistance to either agent alone. Successful treatment of chronic myelogenous leukemia is based on inhibitors binding to the ATP site of the deregulated breakpoint cluster region Bcr -Abelson tyrosine kinase Abl fusion protein.
Recently, a new type of allosteric inhibitors targeting the Abl myristoyl pocket was shown in preclin. Using NMR and small-angle x-ray scattering, we have analyzed the soln. Binding of the ATP-site inhibitor imatinib leads to an unexpected open conformation of the multidomain SH3-SH2-kinase c-Abl core, whose relevance is confirmed by cellular assays on Bcr-Abl.
The combination of imatinib with the allosteric inhibitor GNF-5 restores the closed, inactivated state. Our data provide detailed insights on the poorly understood combined effect of the two inhibitor types, which is able to overcome drug resistance.
Rabindran, Sridhar K. HER-2 belongs to the ErbB family of receptor tyrosine kinases, which has been implicated in a variety of cancers. Blocking HER-2 function by a small mol. HKI reduces HER-2 receptor autophosphorylation in cells at doses consistent with inhibition of cell proliferation and functions as an irreversible binding inhibitor, most likely by targeting a cysteine residue in the ATP-binding pocket of the receptor.
In agreement with the predicted effects of HER-2 inactivation, HKI treatment of cells results in inhibition of downstream signal transduction events and cell cycle regulatory pathways. On the basis of its favorable preclin. Honigberg, Lee A. Activation of the B-cell antigen receptor BCR signaling pathway contributes to the initiation and maintenance of B-cell malignancies and autoimmune diseases.
The Bruton tyrosine kinase Btk is specifically required for BCR signaling as demonstrated by human and mouse mutations that disrupt Btk function and prevent B-cell maturation at steps that require a functional BCR pathway. Herein we describe a selective and irreversible Btk inhibitor, PCI, that is currently under clin. We have used this inhibitor to investigate the biol. In mice with collagen-induced arthritis, orally administered PCI reduced the level of circulating autoantibodies and completely suppressed disease.
PCI also inhibited autoantibody prodn. Occupancy of the Btk active site by PCI was monitored in vitro and in vivo using a fluorescent affinity probe for Btk. Active site occupancy of Btk was tightly correlated with the blockade of BCR signaling and in vivo efficacy.
Finally, PCI induced objective clin. These findings support Btk inhibition as a therapeutic approach for the treatment of human diseases assocd. Protein kinases are a large family of approx. The clin. To date, the majority of clin. Recently, there has been renewed interest in the development of irreversible inhibitors that form covalent bonds with cysteine or other nucleophilic residues in the ATP-binding pocket.
Irreversible kinase inhibitors have a no. Here, we review recent efforts to develop cysteine-targeted irreversible protein kinase inhibitors and discuss their modes of recognizing the ATP-binding pocket and their biol.
Shan, Yibing; Seeliger, Markus A. In many protein kinases, a characteristic conformational change the "DFG flip" connects catalytically active and inactive conformations. Many kinase inhibitors - including the cancer drug imatinib - selectively target a specific DFG conformation, but the function and mechanism of the flip remain unclear.
Using long mol. Consistent with our model's predictions, we demonstrated exptl. Our model suggests a possible explanation for the high degree of conservation of the DFG motif: that the flip, modulated by electrostatic changes inherent to the catalytic cycle, allows the kinase to access flexible conformations facilitating nucleotide binding and release.
Miller, Duncan C. Royal Society of Chemistry. A database of binding kinetic data across multiple targets has been created. Hurst, Dow P. Recent isothiocyanate covalent labeling studies have suggested that a classical cannabinoid, - -7'-isothiocyanatohydroxy-1',1'dimethylheptyl-hexahydrocannabinol AM ,enters the cannabinoid CB2 receptor via the lipid bilayer.
However, the sequence of steps involved in such a lipid pathway entry has not yet been elucidated. Here, we test the hypothesis that the endogenous cannabinoid snarachidonoylglycerol 2-AG attains access to the CB2 receptor via the lipid bilayer. To this end, we have employed microsecond time scale all-atom mol.
To our knowledge, this is the first demonstration via unbiased mol. Gleevec, a well-known cancer therapeutic agent, is an effective inhibitor of several tyrosine kinases, including Abl and c-Kit, but displays less potency to inhibit closely homologous tyrosine kinases, such as Lck and c-Src. Because many structural features of the binding site are highly conserved in these homologous kinases, the mol.
To address this issue, free energy perturbation mol. Dominant binding free energy contributions arises from the van der Waals dispersive interaction, compensating about two-thirds of the unfavorable free energy penalty assocd. In contrast, the contributions from electrostatic and repulsive interactions nearly cancel out due to solvent effects.
Furthermore, the calcns. Among the kinases examd. Tyrosine kinases present attractive drug targets for specific types of cancers. Gleevec, a well-known therapeutic agent against chronic myelogenous leukemia, is an effective inhibitor of Abl tyrosine kinase. However, Gleevec fails to inhibit closely homologous tyrosine kinases, such as c-Src. Because many structural features of the binding site are conserved, the mol. Some have attributed the difference in binding specificity of Gleevec to subtle variations in ligand-protein interactions binding affinity control , whereas others have proposed that it is the conformation of the DFG motif, in which ligand binding is only accessible to Abl and not to c-Src conformational selection control.
To address this issue, the abs. The results of the free energy simulations are in good agreement with expts. The latter is shown to be controlled by a conformational selection mechanism and also by differences in key van der Waals interactions responsible for the stabilization of Gleevec in the binding pocket of Abl. Hari, Sanjay B.
Over the past decade, an increasingly diverse array of potent and selective inhibitors that target the ATP-binding sites of protein kinases have been developed. Many of these inhibitors, like the clin. Imatinib is notable in that it is highly selective for its kinase target, Abl, over other closely related tyrosine kinases, such as Src. In this report, a systematic anal.
In contrast to imatinib, many of these inhibitors have very similar potencies against Src and Abl. Furthermore, only a subset of this class of inhibitors is sensitive to the phosphorylation state of the activation loop of these kinases.
In attempting to explain this observation, an unexpected correlation was uncovered between Abl's activation loop and another flexible active site feature, called the phosphate-binding loop p-loop. These studies shed light on how imatinib is able to obtain its high target selectivity and reveal how the conformational preference of flexible active site regions can vary between closely related kinases.
Cyclin-dependent kinases CDKs are key regulatory enzymes in cell cycle progression and transcription. Aberrant activity of CDKs has been implicated in a no. CDK inhibitors have been reported as potential drug leads. However, these inhibitors exclusively bind to the ATP site, which is largely conserved among protein kinases, and clin. CDKs are unique among protein kinases, as their functionality strictly depends on assocn.
In an effort to identify potential target sites for disruption of the CDK-cyclin interaction, we probed the extrinsic fluorophore 8-anilinonaphthalene sulfonate ANS with human CDK2 and cyclin A using fluorescence spectroscopy and protein crystallog.
These findings indicate the potential of the ANS binding pocket as a new target site for allosteric inhibitors disrupting the interaction of CDKs and cyclins. In press A dynamically coupled allosteric network underlies binding cooperativity in Src kinase , Nat.
Google Scholar There is no corresponding record for this reference. Lee, Kenneth P. Ire1 is an ancient transmembrane sensor of ER stress with dual protein kinase and RNase activities. We have detd. Dimerization of the kinase domain composes a large catalytic surface on the KEN domain which carries out RNase function. We further show that signal induced trans-autophosphorylation of the kinase domain permits unfettered binding of nucleotide, which in turn promotes dimerization to compose the RNase active site.
Comparison of Ire1 to a topol. Cited By. This article is cited by 52 publications. Yu Du, Renxiao Wang. Journal of Chemical Theory and Computation , 16 10 , Potter, Ames C. Register, Markus A. Seeliger, Dustin J. ACS Chemical Biology , 15 7 , Journal of the American Chemical Society , 38 , Timson, Meilan Huang. The Journal of Physical Chemistry B , 13 , The Journal of Physical Chemistry B , 17 , Gobillot , Ivan Lebedev , Micah J.
Gliedt , Sanjay B. Hari , Arinjay K. Mitra , Bradley J. Backes , Feroz R. Papa , Markus A. Seeliger , and Dustin J. ACS Chemical Biology , 11 8 , McDonald , Russell C. Petter , and K.
Journal of Chemical Theory and Computation , 12 4 , Warner , Michael P. Latham , Natalie G. Ahn , and Arthur Pardi. Biochemistry , 54 28 , ACS Chemical Biology , 10 1 , Pegram , Jake W.
Anderson , Natalie G. Dynamic equilibria in protein kinases. Current Opinion in Structural Biology , 71 , Protein kinase sensors: an overview of new designs for visualizing kinase dynamics in single plant cells.
Plant Physiology , 2 , Feldman , Rajarshi Ghosh , Vincent C. Auyeung , James L. Potter , Venkata N. Vidadala , B. Perera , Alina Olivier , Bradley J. Backes , Julie Zikherman , Feroz R. Papa , Dustin J. Biophysica , 1 2 , Cancers , 13 9 , Tokarski , Robert Borzilleri , William J. Pitts , Jonathan Lippy , Litao Zhang. An innovative kinome platform to accelerate small-molecule inhibitor discovery and optimization from hits to leads.
Drug Discovery Today , 26 5 , Madsen , Ole H. Biomolecules , 11 4 , Druggable Transient Pockets in Protein Kinases.
Molecules , 26 3 , Prognostic and immunological role of Fam20C in pan-cancer. Novel 2,6-disubstituted pyridine hydrazones: Synthesis, anticancer activity, docking studies and effects on caspasemediated apoptosis. Journal of Molecular Structure , , International Journal of Molecular Sciences , 22 1 , Lochhead , Julie A.
Tucker , Natalie J. Kidger , Victoria P. Johnson , Megan A. Cassidy , Nathanael S. Gray , Martin E. Noble , Simon J. Conformational states dynamically populated by a kinase determine its function. European Journal of Medicinal Chemistry , , Fowler , Dustin J. Cell Chemical Biology , 27 8 , Hamza , Mahmoud E. An analogue of a kinase inhibitor exhibits subjective characteristics that contribute to its inhibitory activities as a potential anti-cancer candidate: insights through computational biomolecular modelling of UM binding with lyn protein.
RSC Advances , 10 1 , In situ study of RSK2 kinase activity in a single living cell by combining single molecule spectroscopy with activity-based probes. The Analyst , 12 , Synthesis, anticancer activity, toxicity evaluation and molecular docking studies of novel phenylaminopyrimidine— thio urea hybrids as potential kinase inhibitors. Computational Biology and Chemistry , 78 , Protein Allostery in Rational Drug Design.
Pharmacophore and molecular dynamics based activity profiling of natural products for kinases involved in lung cancer. Crystal structures of the kinase domain of PpkA, a key regulatory component of T6SS, reveal a general inhibitory mechanism.
Biochemical Journal , 13 , Kinase Inhibitor Drugs. Effects of rigidity on the selectivity of protein kinase inhibitors. Computer-Aided Drug Discovery. Pelton , Michelle L. Survey of solution dynamics in Src kinase reveals allosteric cross talk between the ligand binding and regulatory sites. How and when does an anticancer drug leave its binding site?.
Engelman , Alice T. Annual Review of Cancer Biology , 1 1 , Impact of phosphoproteomics in the translation of kinase-targeted therapies. Manley , Nikolaus J. Physical Chemistry Chemical Physics , 19 2 , Wintrode , Franklin A. Imatinib binding to human c-Src is coupled to inter-domain allostery and suggests a novel kinase inhibition strategy. Aleem , George Georghiou , Ralph E.
Kleiner , Kip E. More effective drugs may be achieved by pursuing the following two strategies. First, conformational targeting of aggregates of misfolded proteins, rather than less specific binding that includes monomer subunits, which vastly outnumber the toxic targets.
Second, since neurodegenerative diseases frequently include more than one potential protein pathology, generic targeting of aggregates by shape might also be a crucial feature of a drug candidate. Based on the knowledge we obtained from our previous experimental study and computer modeling of amino acid residual level interactions between graphene and peptides, here we systemically redesigned an important protein for better conformational stability and desirable orientation on graphene.
In this paper, immunoglobulin G IgG antibody-binding domain of protein G protein GB1 was studied to demonstrate how we can preserve the protein native structure and control the protein orientation on graphene surface by redesigning protein mutants.
Various experimental tools including sum frequency generation vibrational spectroscopy, attenuated total refection-Fourier transform infrared spectroscopy, fluorescence spectroscopy, and circular dichroism spectroscopy were used to study the protein GB1 structure on graphene, supplemented by molecular dynamics simulations.
By carefully designing the protein GB1 mutant, we can avoid strong unfavorable interactions between protein and graphene to preserve protein conformation and to enable the protein to adopt a preferred orientation.
The methodology developed in this study is general and can be applied to study different proteins on graphene and beyond. With the knowledge obtained from this research, one could apply this method to optimize protein function on surfaces e. Such files may be downloaded by article for research use if there is a public use license linked to the relevant article, that license may permit other uses. More by Shuai Wei.
More by Xingquan Zou. More by Jiayi Tian. More by Hao Huang. More by Wen Guo. More by Zhan Chen. Cite this: J. Article Views Altmetric -. Perturbation approaches for exploring protein binding site flexibility to predict transient binding pockets. Shiau, A. Structural Analysis of E. Cell , — Vogt, A. Conformational selection or induced fit?
A critical appraisal of the kinetic mechanism. Biochemistry 51 , — Klein, T. Structural and dynamic insights into the energetics of activation loop rearrangement in FGFR1 kinase. Heller, G. Targeting disordered proteins with small molecules using entropy. Trends Biochem. Kabsch, W. Acta Crystallogr D. Crystallogr 66 , — Bricogne, G.
Buster v. Lindorff-Larsen, K. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins Struct. Wang, J. Development and testing of a general amber force field. Dupradeau, F. The R. Abraham, M. Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers.
SoftwareX 1—2 , 19—25 Sanschagrin, P. Cluster analysis of consensus water sites in thrombin and trypsin shows conservation between serine proteases and contributions to ligand specificity.
Protein Sci. Nguyen, C. Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril. Case, D. Download references. We thank S. Kashif Sadiq and Neil Bruce for useful suggestion on the manuscript preparation.
You can also search for this author in PubMed Google Scholar. Correspondence to M. Amaral or R. Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Reprints and Permissions. Amaral, M. Protein conformational flexibility modulates kinetics and thermodynamics of drug binding. Nat Commun 8, Download citation. Received : 16 November Accepted : 16 November Published : 22 December Anyone you share the following link with will be able to read this content:.
Sorry, a shareable link is not currently available for this article. Provided by the Springer Nature SharedIt content-sharing initiative. Scientific Reports Journal of Biomolecular NMR Journal of Computer-Aided Molecular Design Nature Communications By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.
Advanced search. Skip to main content Thank you for visiting nature. Download PDF. Subjects Computational biophysics Enzyme mechanisms Kinetics Thermodynamics. Abstract 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 in biomolecular recognition.
Introduction Understanding protein—drug binding mechanisms, and characterizing their thermodynamics and kinetics are fundamental prerequisites to developing effective drug discovery procedures and, indeed, to developing effective drugs. Full size image. Table 1 Chemical structure of compounds 1—20 with R 1 and R 2 substitutions Full size table.
Discussion We have described an interdisciplinary study that elucidates the mechanism of drug binding to N-HSP Computation of desolvation free energies of compounds The desolvation free energy of a compound, was estimated as the hydration free energy taken with the opposite sign. Protein hydration shell analysis using MD simulations The structural and thermodynamic properties of the water molecules were analyzed using the Grid Inhomogeneous Solvation Theory GIST method 68 implemented in the Amber tools package Protein hydration shell analysis using 3D-RISM 3D-RISM analysis of the solvent density implemented in MOE software 66 was carried out using available structures with helical and loop-in conformations of the binding site 8, 14, 16, 20 and 1, 6 , respectively.
Computation of conformational entropy The computation model for estimation of relative binding entropy is schematically illustrated in Supplementary Fig. References 1. Article PubMed Google Scholar CAS Google Scholar Article Google Scholar Author information Author notes M. Amaral and D. Kokh contributed equally to this work. Amaral, A. Wade Authors M. Amaral View author publications. View author publications.
Ethics declarations Competing interests The authors declare no competing financial interests. Additional information Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material. Supplementary Information. About this article. Cite this article Amaral, M. Copy to clipboard. Katrine Wallis Scientific Reports A rebinding-assay for measuring extreme kinetics using label-free biosensors John G. Quinn Scientific Reports A simple approach for reconstruction of non-uniformly sampled pseudo-3D NMR data for accurate measurement of spin relaxation parameters Kyle W.
Ben-Shalom , Nathan M. Lim , Sam C. Gill , Michael K. Digwal , Hardik J. Patel , Weilin Sun , Brandon S. Imber , Stefan O. Ochiana , Maulik R. Patel , Liza Shrestha , Smit. Beattie , Pat Zanzonico , Jason S.
Comments By submitting a comment you agree to abide by our Terms and Community Guidelines. Publish with us For authors For Reviewers Submit manuscript.
Search Search articles by subject, keyword or author. Show results from All journals This journal.
0コメント