101
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Discovery of imidazo[1,2-b]pyridazine derivatives as IKKbeta inhibitors. Part 1: Hit-to-lead study and structure-activity relationship. Bioorg Med Chem Lett 2010; 20:5113-8. [PMID: 20675134 DOI: 10.1016/j.bmcl.2010.07.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2010] [Revised: 07/05/2010] [Accepted: 07/07/2010] [Indexed: 01/03/2023]
Abstract
Imidazo[1,2-b]pyridazine derivatives from high-throughput screening were developed as IKKbeta inhibitors. By the optimization of the 3- and 6-position of imidazo[1,2-b]pyridazine scaffold, cell-free IKKbeta inhibitory activity and TNFalpha inhibitory activity in THP-1 cell increased. Also, these compounds showed high kinase selectivity. The structure-activity relationship was revealed and the interaction model of imidazo[1,2-b]pyridazine compounds with IKKbeta was constructed.
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102
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Nemecek C, Metz WA, Wentzler S, Ding FX, Venot C, Souaille C, Dagallier A, Maignan S, Guilloteau JP, Bernard F, Henry A, Grapinet S, Lesuisse D. Design of Potent IGF1-R Inhibitors Related to Bis-azaindoles. Chem Biol Drug Des 2010; 76:100-6. [DOI: 10.1111/j.1747-0285.2010.00991.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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103
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Sakiyama Y. The use of machine learning and nonlinear statistical tools for ADME prediction. Expert Opin Drug Metab Toxicol 2010; 5:149-69. [PMID: 19239395 DOI: 10.1517/17425250902753261] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Absorption, distribution, metabolism and excretion (ADME)-related failure of drug candidates is a major issue for the pharmaceutical industry today. Prediction of ADME by in silico tools has now become an inevitable paradigm to reduce cost and enhance efficiency in pharmaceutical research. Recently, machine learning as well as nonlinear statistical tools has been widely applied to predict routine ADME end points. To achieve accurate and reliable predictions, it would be a prerequisite to understand the concepts, mechanisms and limitations of these tools. Here, we have devised a small synthetic nonlinear data set to help understand the mechanism of machine learning by 2D-visualisation. We applied six new machine learning methods to four different data sets. The methods include Naive Bayes classifier, classification and regression tree, random forest, Gaussian process, support vector machine and k nearest neighbour. The results demonstrated that ensemble learning and kernel machine displayed greater accuracy of prediction than classical methods irrespective of the data set size. The importance of interaction with the engineering field is also addressed. The results described here provide insights into the mechanism of machine learning, which will enable appropriate usage in the future.
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Affiliation(s)
- Yojiro Sakiyama
- Pharmacokinetics Dynamics Metabolism, Pfizer Global Research and Development, Sandwich Laboratories, Kent, UK.
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104
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Mortier J, Frederick R, Ganeff C, Remouchamps C, Talaga P, Pochet L, Wouters J, Piette J, Dejardin E, Masereel B. Pyrazolo[4,3-c]isoquinolines as potential inhibitors of NF-κB activation. Biochem Pharmacol 2010; 79:1462-72. [DOI: 10.1016/j.bcp.2010.01.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 01/12/2010] [Accepted: 01/12/2010] [Indexed: 10/19/2022]
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105
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Egert-Schmidt AM, Dreher J, Dunkel U, Kohfeld S, Preu L, Weber H, Ehlert JE, Mutschler B, Totzke F, Schächtele C, Kubbutat MHG, Baumann K, Kunick C. Identification of 2-anilino-9-methoxy-5,7-dihydro-6H-pyrimido[5,4-d][1]benzazepin-6-ones as dual PLK1/VEGF-R2 kinase inhibitor chemotypes by structure-based lead generation. J Med Chem 2010; 53:2433-42. [PMID: 20170163 DOI: 10.1021/jm901388c] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
To develop multikinase inhibitors with dual PLK1/VEGF-R2 inhibitory activity, the d-annulated 1-benzazepin-2-one scaffold present in the paullone family of kinase inhibitors was investigated as a general structure template suitable for anchoring annulated heterocycles at the hinge region of the ATP binding site. For this purpose, the indole substructure of the paullones was replaced by other nitrogen containing heteroaromatics. The designed scaffolds were synthesized and tested on the indicated kinases. The 2-anilino-5,7-dihydro-6H-pyrimido[5,4-d][1]benzazepin-6-ones were found to be VEGF-R2 inhibitors with selectivity against the insulin receptor kinase. The attachment of a methoxy group to the 9-position of the scaffold led to additional PLK1 inhibitory activity, which was explained by an alternative binding mode of the 9-methoxy derivatives. Selected members of the compound class inhibited the VEGF-R2 autophosphorylation in human umbilical vein endothelial cells, the sprouting of human umbilical vein endothelial cell speroids, and the proliferation of diverse cancer cell lines.
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Affiliation(s)
- Anne-Marie Egert-Schmidt
- Technische Universitat Braunschweig, Institut für Pharmazeutische Chemie, Beethovenstrasse 55, 38106 Braunschweig, Germany
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106
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Pagano N, Wong EY, Breiding T, Liu H, Wilbuer A, Bregman H, Shen Q, Diamond SL, Meggers E. From imide to lactam metallo-pyridocarbazoles: distinct scaffolds for the design of selective protein kinase inhibitors. J Org Chem 2010; 74:8997-9009. [PMID: 19886617 DOI: 10.1021/jo901641k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Organometallic pyridocarbazole scaffolds are investigated as protein kinase inhibitors. Whereas our previous designs employed solely a maleimide pharmacophore for achieving the two crucial canonical hydrogen bonds to the hinge region of the ATP binding site, we have now extended our investigations to include the related lactam metallo-pyridocarbazoles. The synthetic access of the two regioisomeric lactam pyridocarbazoles is described, and the distinct biological properties of the two lactam scaffolds are revealed by employing a ruthenium half sandwich complex as a model system, resulting in organometallic lead structures for the inhibition of the protein kinases TrkA and CLK2. These new lactam metallo-pyridocarbazoles expand our existing molecular toolbox and assist toward the generation of metal complex scaffolds as lead structures for the design of selective inhibitors for numerous kinases of the human kinome.
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Affiliation(s)
- Nicholas Pagano
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35032 Marburg, Germany
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107
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Asses Y, Leroux V, Tairi-Kellou S, Dono R, Maina F, Maigret B. Analysis of c-Met kinase domain complexes: a new specific catalytic site receptor model for defining binding modes of ATP-competitive ligands. Chem Biol Drug Des 2010; 74:560-70. [PMID: 19909299 DOI: 10.1111/j.1747-0285.2009.00895.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The receptor tyrosine kinase c-Met have multiple roles during cancer development and is currently considered as an important target for molecularly targeted therapies. Structural knowledge of how compounds interact on c-Met catalytic site could guide structure-based drug design strategies towards more effective and selective anticancer drug candidates. However, although 17 crystal structures of c-Met complexed with adenosine triphosphate (ATP)-competitive kinase inhibitors are publicly available (August 2009), there are still open questions regarding the prediction of ligand binding modes. We have applied molecular modeling and molecular mechanics to analyze the distribution of ligands interaction energy on c-Met residues, and deduced a new model of the active site allowing for an unambiguous identification of ligand binding modes. We demonstrate that the binding of known ligands on the c-Met catalytic site involves seven identified structurally-distinct areas. Five of these match the generic kinase ATP binding site model built by Novartis scientists in the 1990s, while the two others are distinct allosteric regions that can be exploited by second generation kinase inhibitors such as Gleevec. We show here that c-Met can accept both such kinds of allosteric inhibitors, a very unusual feature in the kinase family that opens new grounds for highly specific drug design.
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Affiliation(s)
- Yasmine Asses
- Nancy Université, LORIA-UMR 7503, Equipe-projet Orpailleur, Campus scientifique, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France
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108
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Oikawa M. An Improved Synthesis of Arylboronates toward Twenty Novel 1,3-Disubstituted 4-Amino-1H-pyrazolo[3,4-d]pyrimidine Analogs. HETEROCYCLES 2010. [DOI: 10.3987/com-09-11857] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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109
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Hilton S, Naud S, Caldwell JJ, Boxall K, Burns S, Anderson VE, Antoni L, Allen CE, Pearl LH, Oliver AW, Wynne Aherne G, Garrett MD, Collins I. Identification and characterisation of 2-aminopyridine inhibitors of checkpoint kinase 2. Bioorg Med Chem 2009; 18:707-18. [PMID: 20022510 DOI: 10.1016/j.bmc.2009.11.058] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Revised: 11/16/2009] [Accepted: 11/27/2009] [Indexed: 11/28/2022]
Abstract
5-(Hetero)aryl-3-(4-carboxamidophenyl)-2-aminopyridine inhibitors of CHK2 were identified from high throughput screening of a kinase-focussed compound library. Rapid exploration of the hits through straightforward chemistry established structure-activity relationships and a proposed ATP-competitive binding mode which was verified by X-ray crystallography of several analogues bound to CHK2. Variation of the 5-(hetero)aryl substituent identified bicyclic dioxolane and dioxane groups which improved the affinity and the selectivity of the compounds for CHK2 versus CHK1. The 3-(4-carboxamidophenyl) substituent could be successfully replaced by acyclic omega-aminoalkylamides, which made additional polar interactions within the binding site and led to more potent inhibitors of CHK2. Compounds from this series showed activity in cell-based mechanistic assays for inhibition of CHK2.
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Affiliation(s)
- Stephen Hilton
- Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
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110
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Congreve M, Marshall F. The impact of GPCR structures on pharmacology and structure-based drug design. Br J Pharmacol 2009; 159:986-96. [PMID: 19912230 DOI: 10.1111/j.1476-5381.2009.00476.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
After many years of effort, recent technical breakthroughs have enabled the X-ray crystal structures of three G-protein-coupled receptors (GPCRs) (beta1 and beta2 adrenergic and adenosine A(2a)) to be solved in addition to rhodopsin. GPCRs, like other membrane proteins, have lagged behind soluble drug targets such as kinases and proteases in the number of structures available and the level of understanding of these targets and their interaction with drugs. The availability of increasing numbers of structures of GPCRs is set to greatly increase our understanding of some of the key issues in GPCR biology. In particular, what constitutes the different receptor conformations that are involved in signalling and the molecular changes which occur upon receptor activation. How future GPCR structures might alter our views on areas such as agonist-directed signalling and allosteric regulation as well as dimerization is discussed. Knowledge of crystal structures in complex with small molecules will enable techniques in drug discovery and design, which have previously only been applied to soluble targets, to now be used for GPCR targets. These methods include structure-based drug design, virtual screening and fragment screening. This review considers how these methods have been used to address problems in drug discovery for kinase and protease targets and therefore how such methods are likely to impact GPCR drug discovery in the future.
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Affiliation(s)
- Miles Congreve
- Heptares Therapeutics Ltd, Welwyn Garden City, Hertfordshire, UK
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111
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Armen RS, Chen J, Brooks CL. An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics. J Chem Theory Comput 2009; 5:2909-2923. [PMID: 20160879 DOI: 10.1021/ct900262t] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and "noise" that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds.
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Affiliation(s)
- Roger S Armen
- Department of Chemistry, 930 N. University Ave, University of Michigan, Ann Arbor, MI 48109
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112
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Goldberg FW, Ward RA, Powell SJ, Debreczeni JÉ, Norman RA, Roberts NJ, Dishington AP, Gingell HJ, Wickson KF, Roberts AL. Rapid Generation of a High Quality Lead for Transforming Growth Factor-β (TGF-β) Type I Receptor (ALK5). J Med Chem 2009; 52:7901-5. [DOI: 10.1021/jm900807w] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | - Richard A. Ward
- AstraZeneca, Mereside, Alderley Park, Macclesfield SK10 4TG, U.K
| | - Steven J. Powell
- AstraZeneca, Mereside, Alderley Park, Macclesfield SK10 4TG, U.K
| | | | | | | | | | - Helen J. Gingell
- AstraZeneca, Mereside, Alderley Park, Macclesfield SK10 4TG, U.K
| | - Kate F. Wickson
- AstraZeneca, Mereside, Alderley Park, Macclesfield SK10 4TG, U.K
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113
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Robert F, Williams C, Yan Y, Donohue E, Cencic R, Burley SK, Pelletier J. Blocking UV-induced eIF2alpha phosphorylation with small molecule inhibitors of GCN2. Chem Biol Drug Des 2009; 74:57-67. [PMID: 19519745 DOI: 10.1111/j.1747-0285.2009.00827.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The eIF2alpha kinase general control non-depressible 2 integrates translation initiation rates to amino acid availability. General control non-depressible 2 also regulates translation initiation during synaptic plasticity and GCN2(-/-) mice show improved memory compared with wild-type mice with a reduced threshold for triggering late long-term potentiation. This property suggests that inhibiting general control non-depressible 2 function might represent a therapeutic avenue for improving memory. We screened for general control non-depressible 2 inhibitors using a small library of known kinase inhibitors and ATP-analogs and identified three compounds--indirubin-3'-monoxime, SP600125 and a SyK inhibitor with activity against general control non-depressible 2. All three compounds inhibit the ability of general control non-depressible 2 to phosphorylate eIF2alphain vitro as well as in vivo following UV-treatment of mouse embryonic fibroblasts. Using computer-assisted modeling, we modeled the binding of the inhibitors in the ATP-binding site of general control non-depressible 2. This work provides the molecular basis for undertaking structure-activity relationships of these compounds in order to develop specific inhibitors of general control non-depressible 2.
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Affiliation(s)
- Francis Robert
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
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114
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Fufezan C, Specht M. p3d--Python module for structural bioinformatics. BMC Bioinformatics 2009; 10:258. [PMID: 19698094 PMCID: PMC2744707 DOI: 10.1186/1471-2105-10-258] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Accepted: 08/21/2009] [Indexed: 11/10/2022] Open
Abstract
Background High-throughput bioinformatic analysis tools are needed to mine the large amount of structural data via knowledge based approaches. The development of such tools requires a robust interface to access the structural data in an easy way. For this the Python scripting language is the optimal choice since its philosophy is to write an understandable source code. Results p3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files). p3d's strength arises from the combination of a) very fast spatial access to the structural data due to the implementation of a binary space partitioning (BSP) tree, b) set theory and c) functions that allow to combine a and b and that use human readable language in the search queries rather than complex computer language. All these factors combined facilitate the rapid development of bioinformatic tools that can perform quick and complex analyses of protein structures. Conclusion p3d is the perfect tool to quickly develop tools for structural bioinformatics using the Python scripting language.
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Affiliation(s)
- Christian Fufezan
- Westfälische Wilhelms-Universität Münster, Institute for Evolution and Biodiversity, Münster, Germany.
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115
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Solowiej J, Bergqvist S, McTigue MA, Marrone T, Quenzer T, Cobbs M, Ryan K, Kania RS, Diehl W, Murray BW. Characterizing the effects of the juxtamembrane domain on vascular endothelial growth factor receptor-2 enzymatic activity, autophosphorylation, and inhibition by axitinib. Biochemistry 2009; 48:7019-31. [PMID: 19526984 DOI: 10.1021/bi900522y] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The catalytic domains of protein kinases are commonly treated as independent modular units with distinct biological functions. Here, the interactions between the catalytic and juxtamembrane domains of VEGFR2 are studied. Highly purified preparations of the receptor tyrosine kinase VEGFR2 catalytic domain without (VEGFR2-CD) and with (VEGFR2-CD/JM) the juxtamembrane (JM) domain were characterized by kinetic, biophysical, and structural methods. Although the catalytic parameters for both constructs were similar, the autophosphorylation rate of VEGFR2-CD/JM was substantially faster than VEGFR2-CD. The first event in the autophosphorylation reaction was phosphorylation of JM residue Y801 followed by phosphorylation of activation loop residues in the CD. The rates of activation loop autophosphorylation for the two constructs were determined to be similar. The autophosphorylation rate of Y801 was invariant on enzyme concentration, which is consistent with an intramolecular reaction. In addition, the first biochemical characterization of the advanced clinical compound axitinib is reported. Axitinib was found to have 40-fold enhanced biochemical potency toward VEGFR2-CD/JM (K(i) = 28 pM) compared to VEGFR2-CD, which correlates better with cellular potency. Calorimetric studies, including a novel ITC compound displacement method, confirmed the potency and provided insight into the thermodynamic origin of the potency differences. A structural model for the VEGFR2-CD/JM is proposed based on the experimental findings reported here and on the JM position in c-Kit, FLT3, and CSF1/cFMS. The described studies identify potential functions of the VEGFR2 JM domain with implications to both receptor biology and inhibitor design.
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Affiliation(s)
- James Solowiej
- Pfizer Global Research and Development, La Jolla, Pfizer Inc., 10777 Science Center Drive, San Diego, California 92121, USA
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116
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Smyth LA, Collins I. Measuring and interpreting the selectivity of protein kinase inhibitors. J Chem Biol 2009; 2:131-51. [PMID: 19568781 PMCID: PMC2725273 DOI: 10.1007/s12154-009-0023-9] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Revised: 05/08/2009] [Accepted: 05/15/2009] [Indexed: 12/23/2022] Open
Abstract
Protein kinase inhibitors are a well-established class of clinically useful drugs, particularly for the treatment of cancer. Achieving inhibitor selectivity for particular protein kinases often remains a significant challenge in the development of new small molecules as drugs or as tools for chemical biology research. This review summarises the methodologies available for measuring kinase inhibitor selectivity, both in vitro and in cells. The interpretation of kinase inhibitor selectivity data is discussed, particularly with reference to the structural biology of the protein targets. Measurement and prediction of kinase inhibitor selectivity will be important for the development of new multi-targeted kinase inhibitors.
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Affiliation(s)
- Lynette A Smyth
- Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK,
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117
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Wang T, Yu D, Lamb ML. Trk kinase inhibitors as new treatments for cancer and pain. Expert Opin Ther Pat 2009; 19:305-19. [PMID: 19441906 DOI: 10.1517/13543770902721261] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Tropomyosin-related kinases (Trks) are a family of receptor tyrosine kinases activated by neurotrophins. Trks play important roles in pain sensation as well as tumour cell growth and survival signaling. Thus, inhibitors of Trk receptor kinases might provide targeted treatments for pain and cancer. OBJECTIVE This paper reviews those patent applications since 2002 claiming small-molecule inhibitors of Trk receptor kinases. METHODS Primary literature and patents were searched with SciFinder and Google Scholar. Patents were selected based on their relevance to Trks and were evaluated and representative compounds were listed as examples. RESULTS/CONCLUSION Several series of Trk inhibitors with excellent in vitro potencies have been reported and a number of compounds have gone into the clinic. It should be noted that few of these inhibitors are Trk selective, demonstrating that targeting Trk kinases for treatment of pain and/or cancer offers a promising but also challenging approach.
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Affiliation(s)
- Tao Wang
- Cancer Discovery, AstraZeneca R&D Boston, Waltham, MA 02451, USA.
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118
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Lu L, Ghose AK, Quail MR, Albom MS, Durkin JT, Holskin BP, Angeles TS, Meyer SL, Ruggeri BA, Cheng M. ALK Mutants in the Kinase Domain Exhibit Altered Kinase Activity and Differential Sensitivity to Small Molecule ALK Inhibitors. Biochemistry 2009; 48:3600-9. [PMID: 19249873 DOI: 10.1021/bi8020923] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Lihui Lu
- Worldwide Discovery Research, Cephalon Inc., West Chester, Pennsylvania 19380
| | - Arup K. Ghose
- Worldwide Discovery Research, Cephalon Inc., West Chester, Pennsylvania 19380
| | - Matthew R. Quail
- Worldwide Discovery Research, Cephalon Inc., West Chester, Pennsylvania 19380
| | - Mark S. Albom
- Worldwide Discovery Research, Cephalon Inc., West Chester, Pennsylvania 19380
| | - John T. Durkin
- Worldwide Discovery Research, Cephalon Inc., West Chester, Pennsylvania 19380
| | - Beverly P. Holskin
- Worldwide Discovery Research, Cephalon Inc., West Chester, Pennsylvania 19380
| | - Thelma S. Angeles
- Worldwide Discovery Research, Cephalon Inc., West Chester, Pennsylvania 19380
| | - Sheryl L. Meyer
- Worldwide Discovery Research, Cephalon Inc., West Chester, Pennsylvania 19380
| | - Bruce A. Ruggeri
- Worldwide Discovery Research, Cephalon Inc., West Chester, Pennsylvania 19380
| | - Mangeng Cheng
- Worldwide Discovery Research, Cephalon Inc., West Chester, Pennsylvania 19380
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119
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van Montfort RLM, Workman P. Structure-based design of molecular cancer therapeutics. Trends Biotechnol 2009; 27:315-28. [PMID: 19339067 DOI: 10.1016/j.tibtech.2009.02.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Revised: 02/16/2009] [Accepted: 02/18/2009] [Indexed: 01/16/2023]
Abstract
Structure-based approaches now impact across the whole continuum of drug discovery, from new target selection through the identification of hits to the optimization of lead compounds. Optimal application of structure-based design involves close integration with other discovery technologies, including fragment-based and virtual screening. Here, we illustrate the use of structural information and of structure-based drug design approaches in the discovery of small-molecule inhibitors for cancer drug targets and provide an outlook on the exploitation of structural information in future cancer drug discovery. Examples include high profile protein kinase targets and structurally related PI3 kinases, histone deacetylases, poly(ADP-ribose)polymerase and the molecular chaperone HSP90. Structure-based design approaches have also been successfully applied to the protein-protein interaction targets p53-MDM2 and the Bcl-2 family.
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Affiliation(s)
- Rob L M van Montfort
- Section of Structural Biology, The Institute of Cancer Research, Chester Beatty Laboratories, Chelsea, London SW3 6JB, UK.
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120
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Abstract
Purines are critical cofactors in the enzymatic reactions that create and maintain living organisms. In humans, there are approximately 3,266 proteins that utilize purine cofactors and these proteins constitute the so-called purinome. The human purinome encompasses a wide-ranging functional repertoire and many of these proteins are attractive drug targets. For example, it is estimated that 30% of modern drug discovery projects target protein kinases and that modulators of small G-proteins comprise more than 50% of currently marketed drugs. Given the importance of purine-binding proteins to drug discovery, the following review will discuss the forces that mediate protein:purine recognition, the factors that determine druggability of a protein target, and the process of structure-based drug design. A review of purine recognition in representatives of the various purine-binding protein families, as well as the challenges faced in targeting members of the purinome in drug discovery campaigns will also be given.
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Affiliation(s)
- Jeremy M Murray
- Department of Protein Engineering, Genentech, Inc., South San Francisco, CA, USA
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121
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Smith GF. Medicinal chemistry by the numbers: the physicochemistry, thermodynamics and kinetics of modern drug design. PROGRESS IN MEDICINAL CHEMISTRY 2009; 48:1-29. [PMID: 21544956 DOI: 10.1016/s0079-6468(09)04801-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Affiliation(s)
- Graham F Smith
- Merck Research Laboratories, 33 Avenue Louis Pasteur, Boston, MA 02115, USA
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