101
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Bagal SK, Omoto K, Blakemore DC, Bungay PJ, Bilsland JG, Clarke PJ, Corbett MS, Cronin CN, Cui JJ, Dias R, Flanagan NJ, Greasley SE, Grimley R, Johnson E, Fengas D, Kitching L, Kraus ML, McAlpine I, Nagata A, Waldron GJ, Warmus JS. Discovery of Allosteric, Potent, Subtype Selective, and Peripherally Restricted TrkA Kinase Inhibitors. J Med Chem 2018; 62:247-265. [PMID: 29672039 DOI: 10.1021/acs.jmedchem.8b00280] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Tropomyosin receptor kinases (TrkA, TrkB, TrkC) are activated by hormones of the neurotrophin family: nerve growth factor (NGF), brain derived neurotrophic factor (BDNF), neurotrophin 3 (NT3), and neurotrophin 4 (NT4). Moreover, the NGF antibody tanezumab has provided clinical proof of concept for inhibition of the TrkA kinase pathway in pain leading to significant interest in the development of small molecule inhibitors of TrkA. However, achieving TrkA subtype selectivity over TrkB and TrkC via a Type I and Type II inhibitor binding mode has proven challenging and Type III or Type IV allosteric inhibitors may present a more promising selectivity design approach. Furthermore, TrkA inhibitors with minimal brain availability are required to deliver an appropriate safety profile. Herein, we describe the discovery of a highly potent, subtype selective, peripherally restricted, efficacious, and well-tolerated series of allosteric TrkA inhibitors that culminated in the delivery of candidate quality compound 23.
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Affiliation(s)
- Sharan K Bagal
- Worldwide Medicinal Chemistry , Pfizer Global R&D U.K. , The Portway Building, Granta Park , Cambridge CB21 6GS , U.K
| | - Kiyoyuki Omoto
- Worldwide Medicinal Chemistry , Pfizer Global R&D U.K. , The Portway Building, Granta Park , Cambridge CB21 6GS , U.K
| | - David C Blakemore
- Worldwide Medicinal Chemistry , Pfizer Global R&D U.K. , The Portway Building, Granta Park , Cambridge CB21 6GS , U.K
| | - Peter J Bungay
- Pharmacokinetics, Dynamics & Metabolism , Pfizer Global R&D U.K. , The Portway Building, Granta Park , Cambridge CB21 6GS , U.K
| | - James G Bilsland
- Pfizer Global R&D U.K. , The Portway Building, Granta Park , Cambridge CB21 6GS , U.K
| | - Philip J Clarke
- Peakdale Molecular , Discovery Park House, Ramsgate Road , Sandwich , Kent CT13 9ND , U.K
| | - Matthew S Corbett
- Pfizer Global R&D, Groton Laboratories , Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Ciaran N Cronin
- Pfizer Global R&D, La Jolla Laboratories , 10770 Science Center Drive, San Diego , California 92121 , United States
| | - J Jean Cui
- Pfizer Global R&D, La Jolla Laboratories , 10770 Science Center Drive, San Diego , California 92121 , United States
| | - Rebecca Dias
- Pfizer Global R&D U.K. , The Portway Building, Granta Park , Cambridge CB21 6GS , U.K
| | - Neil J Flanagan
- Pfizer Global R&D U.K. , The Portway Building, Granta Park , Cambridge CB21 6GS , U.K
| | - Samantha E Greasley
- Pfizer Global R&D, La Jolla Laboratories , 10770 Science Center Drive, San Diego , California 92121 , United States
| | - Rachel Grimley
- Pfizer Global R&D U.K. , The Portway Building, Granta Park , Cambridge CB21 6GS , U.K
| | - Eric Johnson
- Pfizer Global R&D, La Jolla Laboratories , 10770 Science Center Drive, San Diego , California 92121 , United States
| | - David Fengas
- Peakdale Molecular , Discovery Park House, Ramsgate Road , Sandwich , Kent CT13 9ND , U.K
| | - Linda Kitching
- Pfizer Global R&D U.K. , The Portway Building, Granta Park , Cambridge CB21 6GS , U.K
| | - Michelle L Kraus
- Pfizer Global R&D, La Jolla Laboratories , 10770 Science Center Drive, San Diego , California 92121 , United States
| | - Indrawan McAlpine
- Pfizer Global R&D, La Jolla Laboratories , 10770 Science Center Drive, San Diego , California 92121 , United States
| | - Asako Nagata
- Pfizer Global R&D, La Jolla Laboratories , 10770 Science Center Drive, San Diego , California 92121 , United States
| | - Gareth J Waldron
- Pfizer Global R&D U.K. , The Portway Building, Granta Park , Cambridge CB21 6GS , U.K
| | - Joseph S Warmus
- Pfizer Global R&D, Groton Laboratories , Eastern Point Road , Groton , Connecticut 06340 , United States
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Abstract
Allosteric modulation provides exciting opportunities for drug discovery of enzymes, ion channels, and G protein-coupled receptors. As cation channels gated by extracellular ATP, P2X receptors have attracted wide attention as new drug targets. Although small molecules targeting P2X receptors have entered into clinical trials for rheumatoid arthritis, cough, and pain, negative allosteric modulation of these receptors remains largely unexplored. Here, combining X-ray crystallography, computational modeling, and functional studies of channel mutants, we identified a negative allosteric site on P2X3 receptors, fostered by the left flipper (LF), lower body (LB), and dorsal fin (DF) domains. Using two structurally analogous subtype-specific allosteric inhibitors of P2X3, AF-353 and AF-219, the latter being a drug candidate under phase II clinical trials for refractory chronic cough and idiopathic pulmonary fibrosis, we defined the molecular interactions between the drugs and receptors and the mechanism by which allosteric changes in the LF, DF, and LB domains modulate ATP activation of P2X3. Our detailed characterization of this druggable allosteric site should inspire new strategies to develop P2X3-specific allosteric modulators for clinical use.
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103
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Billot K, Coquil C, Villiers B, Josselin-Foll B, Desban N, Delehouzé C, Oumata N, Le Meur Y, Boletta A, Weimbs T, Grosch M, Witzgall R, Saunier S, Fischer E, Pontoglio M, Fautrel A, Mrug M, Wallace D, Tran PV, Trudel M, Bukanov N, Ibraghimov-Beskrovnaya O, Meijer L. Casein kinase 1ε and 1α as novel players in polycystic kidney disease and mechanistic targets for (R)-roscovitine and (S)-CR8. Am J Physiol Renal Physiol 2018. [PMID: 29537311 DOI: 10.1152/ajprenal.00489.2017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Following the discovery of (R)-roscovitine's beneficial effects in three polycystic kidney disease (PKD) mouse models, cyclin-dependent kinases (CDKs) inhibitors have been investigated as potential treatments. We have used various affinity chromatography approaches to identify the molecular targets of roscovitine and its more potent analog (S)-CR8 in human and murine polycystic kidneys. These methods revealed casein kinases 1 (CK1) as additional targets of the two drugs. CK1ε expression at the mRNA and protein levels is enhanced in polycystic kidneys of 11 different PKD mouse models as well as in human polycystic kidneys. A shift in the pattern of CK1α isoforms is observed in all PKD mouse models. Furthermore, the catalytic activities of both CK1ε and CK1α are increased in mouse polycystic kidneys. Inhibition of CK1ε and CK1α may thus contribute to the long-lasting attenuating effects of roscovitine and (S)-CR8 on cyst development. CDKs and CK1s may constitute a dual therapeutic target to develop kinase inhibitory PKD drug candidates.
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Affiliation(s)
- Katy Billot
- ManRos Therapeutics, Centre de Perharidy , Roscoff , France
| | | | | | - Béatrice Josselin-Foll
- CNRS "Protein Phosphorylation and Human Disease Group, Station Biologique, Roscoff Cedex, Bretagne , France
| | - Nathalie Desban
- CNRS "Protein Phosphorylation and Human Disease Group, Station Biologique, Roscoff Cedex, Bretagne , France
| | - Claire Delehouzé
- CNRS "Protein Phosphorylation and Human Disease Group, Station Biologique, Roscoff Cedex, Bretagne , France
| | - Nassima Oumata
- ManRos Therapeutics, Centre de Perharidy , Roscoff , France
| | - Yannick Le Meur
- Service de Néphrologie, Centre Hospitalier Universitaire La Cavale Blanche, Rue Tanguy Prigent, Brest Cedex, France
| | - Alessandra Boletta
- Division of Genetics and Cell Biology, DIBIT San Raffaele Scientific Institute , Milan , Italy
| | - Thomas Weimbs
- Department of Molecular, Cellular, and Developmental Biology, Neuroscience Research Institute, University of California Santa Barbara , Santa Barbara, California
| | - Melanie Grosch
- University of Regensburg, Institute for Molecular and Cellular Anatomy, Universitätsstr 31, Regensburg , Germany
| | - Ralph Witzgall
- University of Regensburg, Institute for Molecular and Cellular Anatomy, Universitätsstr 31, Regensburg , Germany
| | | | - Evelyne Fischer
- "Expression Génique, Développement et Maladies", Equipe 26/INSERM U1016/CNRS UMR 8104/Université Paris-Descartes, Institut Cochin, Département Génétique & Développement, Paris , France
| | - Marco Pontoglio
- "Expression Génique, Développement et Maladies", Equipe 26/INSERM U1016/CNRS UMR 8104/Université Paris-Descartes, Institut Cochin, Département Génétique & Développement, Paris , France
| | - Alain Fautrel
- Université de Rennes 1, H2P2 Histopathology Core Facility, Rennes Cedex, France
| | - Michal Mrug
- Division of Nephrology, University of Alabama at Birmingham , Birmingham, Alabama.,Department of Veterans Affairs Medical Center , Birmingham, Alabama
| | - Darren Wallace
- University of Kansas Medical Center, The Jared Grantham Kidney Institute , Kansas City, Kansas
| | - Pamela V Tran
- University of Kansas Medical Center, The Jared Grantham Kidney Institute , Kansas City, Kansas.,University of Kansas Medical Center, Department of Anatomy and Cell Biology , Kansas City, Kansas
| | - Marie Trudel
- Institut de Recherches Cliniques de Montréal, Molecular Genetics and Development, Montreal, Quebec , Canada
| | - Nikolay Bukanov
- Sanofi Genzyme, Rare Renal and Bone Diseases, Framingham, Massachusetts
| | | | - Laurent Meijer
- ManRos Therapeutics, Centre de Perharidy , Roscoff , France
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104
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Lu S, Ji M, Ni D, Zhang J. Discovery of hidden allosteric sites as novel targets for allosteric drug design. Drug Discov Today 2018; 23:359-365. [DOI: 10.1016/j.drudis.2017.10.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 09/27/2017] [Accepted: 10/05/2017] [Indexed: 02/07/2023]
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105
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Progress with covalent small-molecule kinase inhibitors. Drug Discov Today 2018; 23:727-735. [PMID: 29337202 DOI: 10.1016/j.drudis.2018.01.035] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/23/2017] [Accepted: 01/09/2018] [Indexed: 01/07/2023]
Abstract
With reduced risk of toxicity and high selectivity, covalent small-molecule kinase inhibitors (CSKIs) have emerged rapidly. Through the lens of structural system pharmacology, here we review this rapid progress by considering design strategies and the challenges and opportunities offered by current CSKIs.
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106
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Wilson LJ, Linley A, Hammond DE, Hood FE, Coulson JM, MacEwan DJ, Ross SJ, Slupsky JR, Smith PD, Eyers PA, Prior IA. New Perspectives, Opportunities, and Challenges in Exploring the Human Protein Kinome. Cancer Res 2017; 78:15-29. [DOI: 10.1158/0008-5472.can-17-2291] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/22/2017] [Accepted: 10/31/2017] [Indexed: 11/16/2022]
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107
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Matissek KJ, Onozato ML, Sun S, Zheng Z, Schultz A, Lee J, Patel K, Jerevall PL, Saladi SV, Macleay A, Tavallai M, Badovinac-Crnjevic T, Barrios C, Beşe N, Chan A, Chavarri-Guerra Y, Debiasi M, Demirdögen E, Egeli Ü, Gökgöz S, Gomez H, Liedke P, Tasdelen I, Tolunay S, Werutsky G, St Louis J, Horick N, Finkelstein DM, Le LP, Bardia A, Goss PE, Sgroi DC, Iafrate AJ, Ellisen LW. Expressed Gene Fusions as Frequent Drivers of Poor Outcomes in Hormone Receptor-Positive Breast Cancer. Cancer Discov 2017; 8:336-353. [PMID: 29242214 DOI: 10.1158/2159-8290.cd-17-0535] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 11/09/2017] [Accepted: 12/11/2017] [Indexed: 11/16/2022]
Abstract
We sought to uncover genetic drivers of hormone receptor-positive (HR+) breast cancer, using a targeted next-generation sequencing approach for detecting expressed gene rearrangements without prior knowledge of the fusion partners. We identified intergenic fusions involving driver genes, including PIK3CA, AKT3, RAF1, and ESR1, in 14% (24/173) of unselected patients with advanced HR+ breast cancer. FISH confirmed the corresponding chromosomal rearrangements in both primary and metastatic tumors. Expression of novel kinase fusions in nontransformed cells deregulates phosphoprotein signaling, cell proliferation, and survival in three-dimensional culture, whereas expression in HR+ breast cancer models modulates estrogen-dependent growth and confers hormonal therapy resistance in vitro and in vivo Strikingly, shorter overall survival was observed in patients with rearrangement-positive versus rearrangement-negative tumors. Correspondingly, fusions were uncommon (<5%) among 300 patients presenting with primary HR+ breast cancer. Collectively, our findings identify expressed gene fusions as frequent and potentially actionable drivers in HR+ breast cancer.Significance: By using a powerful clinical molecular diagnostic assay, we identified expressed intergenic fusions as frequent contributors to treatment resistance and poor survival in advanced HR+ breast cancer. The prevalence and biological and prognostic significance of these alterations suggests that their detection may alter clinical management and bring to light new therapeutic opportunities. Cancer Discov; 8(3); 336-53. ©2017 AACR.See related commentary by Natrajan et al., p. 272See related article by Liu et al., p. 354This article is highlighted in the In This Issue feature, p. 253.
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Affiliation(s)
- Karina J Matissek
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Maristela L Onozato
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Sheng Sun
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Zongli Zheng
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Andrew Schultz
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Jesse Lee
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Kristofer Patel
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Piiha-Lotta Jerevall
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Srinivas Vinod Saladi
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Allison Macleay
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Mehrad Tavallai
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | | | - Carlos Barrios
- Latin America Cooperative Oncology Group (LACOG) and Pontificia Universidade Catolica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Nuran Beşe
- Department of Radiation Oncology, Acibadem Breast Research Institute, Istanbul, Turkey
| | | | - Yanin Chavarri-Guerra
- Instituto Nacional de Ciencias Medicas y Nutrición Salvador Zubiran, México City D.F., México
| | - Marcio Debiasi
- Latin America Cooperative Oncology Group (LACOG) and Pontificia Universidade Catolica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Elif Demirdögen
- Departments of Medical Biology, General Surgery, Pathology of Medical Faculty of Uludag University, Bursa, Turkey
| | - Ünal Egeli
- Departments of Medical Biology, General Surgery, Pathology of Medical Faculty of Uludag University, Bursa, Turkey
| | - Sahsuvar Gökgöz
- Departments of Medical Biology, General Surgery, Pathology of Medical Faculty of Uludag University, Bursa, Turkey
| | - Henry Gomez
- Instituto Nacional de Enfermedades Neoplasicas, Lima, Perú
| | - Pedro Liedke
- Latin America Cooperative Oncology Group (LACOG) and Pontificia Universidade Catolica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Ismet Tasdelen
- Departments of Medical Biology, General Surgery, Pathology of Medical Faculty of Uludag University, Bursa, Turkey
| | - Sahsine Tolunay
- Departments of Medical Biology, General Surgery, Pathology of Medical Faculty of Uludag University, Bursa, Turkey
| | - Gustavo Werutsky
- Latin America Cooperative Oncology Group (LACOG) and Pontificia Universidade Catolica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Jessica St Louis
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Nora Horick
- Biostatistics Center, Massachusetts General Hospital, Boston, Massachusetts
| | - Dianne M Finkelstein
- Harvard Medical School, Boston, Massachusetts
- Biostatistics Center, Massachusetts General Hospital, Boston, Massachusetts
| | - Long Phi Le
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Aditya Bardia
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Paul E Goss
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Dennis C Sgroi
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - A John Iafrate
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Leif W Ellisen
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.
- Harvard Medical School, Boston, Massachusetts
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108
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Stetz G, Tse A, Verkhivker GM. Ensemble-based modeling and rigidity decomposition of allosteric interaction networks and communication pathways in cyclin-dependent kinases: Differentiating kinase clients of the Hsp90-Cdc37 chaperone. PLoS One 2017; 12:e0186089. [PMID: 29095844 PMCID: PMC5667858 DOI: 10.1371/journal.pone.0186089] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 09/25/2017] [Indexed: 12/24/2022] Open
Abstract
The overarching goal of delineating molecular principles underlying differentiation of protein kinase clients and chaperone-based modulation of kinase activity is fundamental to understanding activity of many oncogenic kinases that require chaperoning of Hsp70 and Hsp90 systems to attain a functionally competent active form. Despite structural similarities and common activation mechanisms shared by cyclin-dependent kinase (CDK) proteins, members of this family can exhibit vastly different chaperone preferences. The molecular determinants underlying chaperone dependencies of protein kinases are not fully understood as structurally similar kinases may often elicit distinct regulatory responses to the chaperone. The regulatory divergences observed for members of CDK family are of particular interest as functional diversification among these kinases may be related to variations in chaperone dependencies and can be exploited in drug discovery of personalized therapeutic agents. In this work, we report the results of a computational investigation of several members of CDK family (CDK5, CDK6, CDK9) that represented a broad repertoire of chaperone dependencies—from nonclient CDK5, to weak client CDK6, and strong client CDK9. By using molecular simulations of multiple crystal structures we characterized conformational ensembles and collective dynamics of CDK proteins. We found that the elevated dynamics of CDK9 can trigger imbalances in cooperative collective motions and reduce stability of the active fold, thus creating a cascade of favorable conditions for chaperone intervention. The ensemble-based modeling of residue interaction networks and community analysis determined how differences in modularity of allosteric networks and topography of communication pathways can be linked with the client status of CDK proteins. This analysis unveiled depleted modularity of the allosteric network in CDK9 that alters distribution of communication pathways and leads to impaired signaling in the client kinase. According to our results, these network features may uniquely define chaperone dependencies of CDK clients. The perturbation response scanning and rigidity decomposition approaches identified regulatory hotspots that mediate differences in stability and cooperativity of allosteric interaction networks in the CDK structures. By combining these synergistic approaches, our study revealed dynamic and network signatures that can differentiate kinase clients and rationalize subtle divergences in the activation mechanisms of CDK family members. The therapeutic implications of these results are illustrated by identifying structural hotspots of pathogenic mutations that preferentially target regions of the increased flexibility to enable modulation of activation changes. Our study offers a network-based perspective on dynamic kinase mechanisms and drug design by unravelling relationships between protein kinase dynamics, allosteric communications and chaperone dependencies.
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Affiliation(s)
- Gabrielle Stetz
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Amanda Tse
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Gennady M. Verkhivker
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California, United States of America
- * E-mail:
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109
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Nguyen TL, Fruit C, Hérault Y, Meijer L, Besson T. Dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) inhibitors: a survey of recent patent literature. Expert Opin Ther Pat 2017; 27:1183-1199. [PMID: 28766366 DOI: 10.1080/13543776.2017.1360285] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) is a eukaryotic serine-threonine protein kinase belonging to the CMGC group. DYRK1A hyperactivity appears to contribute to the development of a number of human malignancies and to cognitive deficits observed in Down syndrome and Alzheimer's disease. As a result, the DYRK1A kinase represents an attractive target for the synthesis and optimization of pharmacological inhibitors of potential therapeutic interest. Like most tyrosine kinase inhibitors developed up to the market, DYRK1A inhibitors are essentially acting by competing with ATP for binding at the catalytic site of the kinase. Areas covered: This paper reviews patent activity associated with the discovery of synthetic novel heterocyclic molecules inhibiting the catalytic activity of DYRK1A. Expert opinion: Despite the important role of DYRK1A in biological processes and the growing interest in the design of new therapeutic drugs, there are only few patented synthetic DYRK1A inhibitors and most of them were and are still developed by academic research groups, sometimes with industrial partners.
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Affiliation(s)
- Thu Lan Nguyen
- a Manros Therapeutics , Centre de Perharidy , Roscoff , France
- b Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch , Illkirch , France
- c Centre National de la Recherche Scientifique, UMR7104 , Illkirch , France
- d Institut National de la Santé et de la Recherche Médicale, U964 , Illkirch , France
- e Université de Strasbourg , Illkirch , France
| | - Corinne Fruit
- f Normandie Univ , UNIROUEN, INSA Rouen, CNRS, COBRA UMR 6014 , Rouen , France
| | - Yann Hérault
- a Manros Therapeutics , Centre de Perharidy , Roscoff , France
- b Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch , Illkirch , France
- c Centre National de la Recherche Scientifique, UMR7104 , Illkirch , France
- d Institut National de la Santé et de la Recherche Médicale, U964 , Illkirch , France
- e Université de Strasbourg , Illkirch , France
| | - Laurent Meijer
- a Manros Therapeutics , Centre de Perharidy , Roscoff , France
| | - Thierry Besson
- f Normandie Univ , UNIROUEN, INSA Rouen, CNRS, COBRA UMR 6014 , Rouen , France
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110
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Research advances in kinase enzymes and inhibitors for cardiovascular disease treatment. Future Sci OA 2017; 3:FSO204. [PMID: 29134113 PMCID: PMC5674217 DOI: 10.4155/fsoa-2017-0010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 03/29/2017] [Indexed: 12/13/2022] Open
Abstract
The targeting of protein kinases has great future potential for the design of new drugs against cardiovascular diseases (CVDs). Enormous efforts have been made toward achieving this aim. Unfortunately, kinase inhibitors designed to treat CVDs have suffered from numerous limitations such as poor selectivity, bad permeability and toxicity. So, where are we now in terms of discovering effective kinase targeting drugs to treat CVDs? Various drug design techniques have been approached for this purpose since the discovery of the inhibitory activity of Staurosporine against protein kinase C in 1986. This review aims to provide context for the status of several emerging classes of direct kinase modulators to treat CVDs and discuss challenges that are preventing scientists from finding new kinase drugs to treat heart disease.
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111
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Berndt N, Karim RM, Schönbrunn E. Advances of small molecule targeting of kinases. Curr Opin Chem Biol 2017; 39:126-132. [PMID: 28732278 DOI: 10.1016/j.cbpa.2017.06.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 06/12/2017] [Accepted: 06/14/2017] [Indexed: 12/21/2022]
Abstract
Reversible protein phosphorylation regulates virtually all aspects of life in the cell. As a result, dysregulation of protein kinases, the enzymes responsible for transferring phosphate groups from ATP to proteins, are often the cause or consequence of many human diseases including cancer. Almost three dozen protein kinase inhibitors (PKIs) have been approved for clinical applications since 1995, the vast majority of them for the treatment of cancer. According to the NCI, there are more than 100 types of cancer. However, FDA-approved PKIs only target 14 of them. Importantly, of the more than 500 protein kinases encoded by the human genome, only 22 are targets for currently approved PKIs, suggesting that the reservoir of PKIs still has room to grow significantly. In this short review we will discuss the most recent advances, challenges, and alternatives to currently adopted strategies in this burgeoning field.
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Affiliation(s)
- Norbert Berndt
- Drug Discovery Department, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Rezaul M Karim
- Drug Discovery Department, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Ernst Schönbrunn
- Drug Discovery Department, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.
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112
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Zhao Z, Xie L, Bourne PE. Insights into the binding mode of MEK type-III inhibitors. A step towards discovering and designing allosteric kinase inhibitors across the human kinome. PLoS One 2017; 12:e0179936. [PMID: 28628649 PMCID: PMC5476283 DOI: 10.1371/journal.pone.0179936] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/06/2017] [Indexed: 11/18/2022] Open
Abstract
Protein kinases are critical drug targets for treating a large variety of human diseases. Type-III kinase inhibitors have attracted increasing attention as highly selective therapeutics. Thus, understanding the binding mechanism of existing type-III kinase inhibitors provides useful insights into designing new type-III kinase inhibitors. In this work, we have systematically studied the binding mode of MEK-targeted type-III inhibitors using structural systems pharmacology and molecular dynamics simulation. Our studies provide detailed sequence, structure, interaction-fingerprint, pharmacophore and binding-site information on the binding characteristics of MEK type-III kinase inhibitors. We hypothesize that the helix-folding activation loop is a hallmark allosteric binding site for type-III inhibitors. Subsequently, we screened and predicted allosteric binding sites across the human kinome, suggesting other kinases as potential targets suitable for type-III inhibitors.
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Affiliation(s)
- Zheng Zhao
- National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, Maryland, United States of America
| | - Lei Xie
- Department of Computer Science, Hunter College, The City University of New York, New York, United States of America
- The Graduate Center, The City University of New York, New York, United States of America
| | - Philip E. Bourne
- National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, Maryland, United States of America
- Office of the Director, National Institutes of Health, Bethesda, Maryland, United States of America
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113
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Albanaz ATS, Rodrigues CHM, Pires DEV, Ascher DB. Combating mutations in genetic disease and drug resistance: understanding molecular mechanisms to guide drug design. Expert Opin Drug Discov 2017; 12:553-563. [PMID: 28490289 DOI: 10.1080/17460441.2017.1322579] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Mutations introduce diversity into genomes, leading to selective changes and driving evolution. These changes have contributed to the emergence of many of the current major health concerns of the 21st century, from the development of genetic diseases and cancers to the rise and spread of drug resistance. The experimental systematic testing of all mutations in a system of interest is impractical and not cost-effective, which has created interest in the development of computational tools to understand the molecular consequences of mutations to aid and guide rational experimentation. Areas covered: Here, the authors discuss the recent development of computational methods to understand the effects of coding mutations to protein function and interactions, particularly in the context of the 3D structure of the protein. Expert opinion: While significant progress has been made in terms of innovative tools to understand and quantify the different range of effects in which a mutation or a set of mutations can give rise to a phenotype, a great gap still exists when integrating these predictions and drawing causality conclusions linking variants. This often requires a detailed understanding of the system being perturbed. However, as part of the drug development process it can be used preemptively in a similar fashion to pharmacokinetics predictions, to guide development of therapeutics to help guide the design and analysis of clinical trials, patient treatment and public health policy strategies.
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Affiliation(s)
- Amanda T S Albanaz
- a Centro de Pesquisas René Rachou, FIOCRUZ , Belo Horizonte , MG , Brazil.,b Department of Biochemistry and Immunology , Universidade Federal de Minas Gerais , Belo Horizonte , Minas Gerais , Brazil
| | - Carlos H M Rodrigues
- a Centro de Pesquisas René Rachou, FIOCRUZ , Belo Horizonte , MG , Brazil.,b Department of Biochemistry and Immunology , Universidade Federal de Minas Gerais , Belo Horizonte , Minas Gerais , Brazil
| | - Douglas E V Pires
- a Centro de Pesquisas René Rachou, FIOCRUZ , Belo Horizonte , MG , Brazil
| | - David B Ascher
- a Centro de Pesquisas René Rachou, FIOCRUZ , Belo Horizonte , MG , Brazil.,c Department of Biochemistry , University of Cambridge , Cambridge , Cambridgeshire , UK.,d Department of Biochemistry and Molecular Biology , University of Melbourne , Melbourne , Victoria , Australia
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114
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Bayraktar O, Ozkirimli E, Ulgen K. Sphingosine kinase 1 (SK1) allosteric inhibitors that target the dimerization site. Comput Biol Chem 2017; 69:64-76. [PMID: 28587987 DOI: 10.1016/j.compbiolchem.2017.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/29/2017] [Accepted: 05/24/2017] [Indexed: 02/03/2023]
Abstract
The sphingosine kinase 1 (SK1)/sphingosine-1-phosphate (S1P) signaling pathway is a crucial target for numerous human diseases from cancer to cardiovascular diseases. However, available SK1 inhibitors that target the active site suffer from poor potency, selectivity and pharmacokinetic properties. The selectivity issue of the kinases, which share a highly-conserved ATP-pocket, can be overcome by targeting the less-conserved allosteric sites. SK1 is known to function minimally as a dimer; however, the crystal structure of the SK1 dimer has not been determined. In this study, a template-based algorithm implemented in PRISM was used to predict the SK1 dimer structure and then the possible allosteric sites at the dimer interface were determined via SiteMap. These sites were used in a virtual screening campaign that includes an integrated workflow of structure-based pharmacophore modeling, virtual screening, molecular docking, re-screening of common scaffolds to propose a series of compounds with different scaffolds as potential allosteric SK1 inhibitors. Finally, the stability of the SK1-ligand complexes was analyzed by molecular dynamics simulations. As a final outcome, ligand 7 having a 4,9-dihydro-1H-purine scaffold and ligand 12 having a 2,3,4,9-tetrahydro-1H-β-carboline scaffold were found to be potential selective inhibitors for SK1.
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Affiliation(s)
- Ozge Bayraktar
- Department of Computational Science and Engineering, Bogazici University, 34342 Bebek, Istanbul, Turkey
| | - Elif Ozkirimli
- Department of Computational Science and Engineering, Bogazici University, 34342 Bebek, Istanbul, Turkey; Department of Chemical Engineering, Bogazici University, 34342 Bebek, Istanbul, Turkey.
| | - Kutlu Ulgen
- Department of Computational Science and Engineering, Bogazici University, 34342 Bebek, Istanbul, Turkey; Department of Chemical Engineering, Bogazici University, 34342 Bebek, Istanbul, Turkey.
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115
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Mejuch T, Garivet G, Hofer W, Kaiser N, Fansa EK, Ehrt C, Koch O, Baumann M, Ziegler S, Wittinghofer A, Waldmann H. Small-Molecule Inhibition of the UNC119-Cargo Interaction. Angew Chem Int Ed Engl 2017; 56:6181-6186. [DOI: 10.1002/anie.201701905] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 03/30/2017] [Indexed: 01/10/2023]
Affiliation(s)
- Tom Mejuch
- Department of Chemical Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Guillaume Garivet
- Department of Chemical Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Walter Hofer
- Department of Chemical Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Nadine Kaiser
- Department of Chemical Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Eyad K. Fansa
- Department of Structural Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Christiane Ehrt
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Oliver Koch
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Matthias Baumann
- Lead Discovery Center GmbH; Otto-Hahn-Strasse 15 44227 Dortmund Germany
| | - Slava Ziegler
- Department of Chemical Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Alfred Wittinghofer
- Department of Structural Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Herbert Waldmann
- Department of Chemical Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
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116
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Mejuch T, Garivet G, Hofer W, Kaiser N, Fansa EK, Ehrt C, Koch O, Baumann M, Ziegler S, Wittinghofer A, Waldmann H. Small-Molecule Inhibition of the UNC119-Cargo Interaction. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701905] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Tom Mejuch
- Department of Chemical Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Guillaume Garivet
- Department of Chemical Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Walter Hofer
- Department of Chemical Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Nadine Kaiser
- Department of Chemical Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Eyad K. Fansa
- Department of Structural Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Christiane Ehrt
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Oliver Koch
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Matthias Baumann
- Lead Discovery Center GmbH; Otto-Hahn-Strasse 15 44227 Dortmund Germany
| | - Slava Ziegler
- Department of Chemical Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Alfred Wittinghofer
- Department of Structural Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Herbert Waldmann
- Department of Chemical Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
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117
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Barnes PJ. Kinases as Novel Therapeutic Targets in Asthma and Chronic Obstructive Pulmonary Disease. Pharmacol Rev 2017; 68:788-815. [PMID: 27363440 DOI: 10.1124/pr.116.012518] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Multiple kinases play a critical role in orchestrating the chronic inflammation and structural changes in the respiratory tract of patients with asthma and chronic obstructive pulmonary disease (COPD). Kinases activate signaling pathways that lead to contraction of airway smooth muscle and release of inflammatory mediators (such as cytokines, chemokines, growth factors) as well as cell migration, activation, and proliferation. For this reason there has been great interest in the development of kinase inhibitors as anti-inflammatory therapies, particular where corticosteroids are less effective, as in severe asthma and COPD. However, it has proven difficult to develop selective kinase inhibitors that are both effective and safe after oral administration and this has led to a search for inhaled kinase inhibitors, which would reduce systemic exposure. Although many kinases have been implicated in inflammation and remodeling of airway disease, very few classes of drug have reached the stage of clinical studies in these diseases. The most promising drugs are p38 MAP kinases, isoenzyme-selective PI3-kinases, Janus-activated kinases, and Syk-kinases, and inhaled formulations of these drugs are now in development. There has also been interest in developing inhibitors that block more than one kinase, because these drugs may be more effective and with less risk of losing efficacy with time. No kinase inhibitors are yet on the market for the treatment of airway diseases, but as kinase inhibitors are improved from other therapeutic areas there is hope that these drugs may eventually prove useful in treating refractory asthma and COPD.
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Affiliation(s)
- Peter J Barnes
- National Heart and Lung Institute, Imperial College, London, United Kingdom
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118
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Biochemical analysis of leishmanial and human GDP-Mannose Pyrophosphorylases and selection of inhibitors as new leads. Sci Rep 2017; 7:751. [PMID: 28389670 PMCID: PMC5429698 DOI: 10.1038/s41598-017-00848-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 03/16/2017] [Indexed: 12/12/2022] Open
Abstract
Leishmaniases are an ensemble of diseases caused by the protozoan parasite of the genus Leishmania. Current antileishmanial treatments are limited and present main issues of toxicity and drug resistance emergence. Therefore, the generation of new inhibitors specifically directed against a leishmanial target is an attractive strategy to expand the chemotherapeutic arsenal. GDP-Mannose Pyrophosphorylase (GDP-MP) is a prominent therapeutic target involved in host-parasite recognition which has been described to be essential for parasite survival. In this work, we produced and purified GDP-MPs from L. mexicana (LmGDP-MP), L. donovani (LdGDP-MP), and human (hGDP-MP), and compared their enzymatic properties. From a rationale design of 100 potential inhibitors, four compounds were identified having a promising and specific inhibitory effect on parasite GDP-MP and antileishmanial activities, one of them exhibits a competitive inhibition on LdGDP-MP and belongs to the 2-substituted quinoline series.
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119
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Bailey JJ, Schirrmacher R, Farrell K, Bernard-Gauthier V. Tropomyosin receptor kinase inhibitors: an updated patent review for 2010-2016 - Part I. Expert Opin Ther Pat 2017; 27:733-751. [PMID: 28270010 DOI: 10.1080/13543776.2017.1297796] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
INTRODUCTION Tropomyosin receptor kinases (TrkA/B/C) play crucial roles in the development and maintenance of the nervous system, and aberrant expression of Trk has been implicated in neurological disorders as well as neural and non-neural neoplasms. Patent activity encompassing Trk inhibitors has grown substantially over the last 6 years, recognized by a rise in the number of pharmaceutical entrants to the field and the escalation of novel inhibitor chemotypes. Area covered: In Part I of this two part review, a biological and structural overview of Trk is provided in the context of Trk as a therapeutic target for cancer and pain, followed by the report of recent patent literature claiming small molecule inhibitors of Trk family kinases or which describe inhibitors developed for other kinase targets but include noteworthy Trk inhibition/application. The discussion of the patent literature continues in Part II of this review, which includes an in-depth view of the current clinical applications of Trk inhibitors. Expert opinion: Substantial synthetic efforts in Trk inhibitor development has propagated numerous and diverse inhibitor chemotypes, including TrkA-specific inhibitors. While many novel Trk inhibitors remain the original progeny of Trk-specific development programs, kinase inhibitors initially developed for other kinases have also been successfully repositioned for Trk.
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Affiliation(s)
- Justin J Bailey
- a Faculty of Medicine & Dentistry , University of Alberta, Department of Oncology , Edmonton , AB , Canada
| | - Ralf Schirrmacher
- a Faculty of Medicine & Dentistry , University of Alberta, Department of Oncology , Edmonton , AB , Canada
| | - Kristen Farrell
- a Faculty of Medicine & Dentistry , University of Alberta, Department of Oncology , Edmonton , AB , Canada
| | - Vadim Bernard-Gauthier
- a Faculty of Medicine & Dentistry , University of Alberta, Department of Oncology , Edmonton , AB , Canada
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120
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Roskoski R. Allosteric MEK1/2 inhibitors including cobimetanib and trametinib in the treatment of cutaneous melanomas. Pharmacol Res 2017; 117:20-31. [PMID: 27956260 DOI: 10.1016/j.phrs.2016.12.009] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 02/07/2023]
Abstract
The Ras-Raf-MEK-ERK (Map kinase) cellular pathway is a highly conserved eukaryotic signaling module that transduces extracellular signals from growth factors and cytokines into intracellular regulatory events that are involved in cell growth and proliferation or the contrary pathway of cell differentiation. Dysregulation of this pathway occurs in more than one-third of all malignancies, a process that has fostered the development of targeted Map kinase pathway inhibitors. Cutaneous melanomas, which arise from skin melanocytes, are the most aggressive form of skin cancer. Mutations that activate the Map kinase pathway occur in more than 90% of these melanomas. This has led to the development of the combination of dabrafenib and trametinib or vemurafenib and cobimetanib for the treatment of BRAF V600E mutant melanomas. Dabrafenib and vemurafenib target V600E/K BRAF mutants while trametinib and cobimetanib target MEK1/2. The latter two agents bind to MEK1/2 at a site that is adjacent to, but separate from, the ATP-binding site and are therefore classified as type III allosteric protein kinase inhibitors. These agents form a hydrogen bond with a conserved β3-lysine and they make numerous hydrophobic contacts with residues within the αC-helix, the β5 strand, and within the activation segment, regions of the protein kinase domain that exhibit greater diversity than those found within the ATP-binding site. One advantage of such allosteric inhibitors is that they do not have to compete with millimolar concentrations of cellular ATP, which most FDA-approved small molecule competitive inhibitors such as imatinib must do. Owing to the wide spread activation of this pathway in numerous neoplasms, trametinib and cobimetinib are being studied in combination with other targeted and cytotoxic drugs in a variety of clinical situations. Except for BRAF and NRAS mutations, there are no other biomarkers correlated with treatment responses following MEK1/2 inhibition and the discovery of such biomarkers would represent an important therapeutic breakthrough.
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Affiliation(s)
- Robert Roskoski
- Blue Ridge Institute for Medical Research, 3754 Brevard Road, Suite 116, Box 19, Horse Shoe, NC 28742-8814, United States.
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121
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Hanold LE, Fulton MD, Kennedy EJ. Targeting kinase signaling pathways with constrained peptide scaffolds. Pharmacol Ther 2017; 173:159-170. [PMID: 28185915 DOI: 10.1016/j.pharmthera.2017.02.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Kinases are amongst the largest families in the human proteome and serve as critical mediators of a myriad of cell signaling pathways. Since altered kinase activity is implicated in a variety of pathological diseases, kinases have become a prominent class of proteins for targeted inhibition. Although numerous small molecule and antibody-based inhibitors have already received clinical approval, several challenges may still exist with these strategies including resistance, target selection, inhibitor potency and in vivo activity profiles. Constrained peptide inhibitors have emerged as an alternative strategy for kinase inhibition. Distinct from small molecule inhibitors, peptides can provide a large binding surface area that allows them to bind shallow protein surfaces rather than defined pockets within the target protein structure. By including chemical constraints within the peptide sequence, additional benefits can be bestowed onto the peptide scaffold such as improved target affinity and target selectivity, cell permeability and proteolytic resistance. In this review, we highlight examples of diverse chemistries that are being employed to constrain kinase-targeting peptide scaffolds and highlight their application to modulate kinase signaling as well as their potential clinical implications.
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Affiliation(s)
- Laura E Hanold
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, United States
| | - Melody D Fulton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, United States
| | - Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, United States.
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122
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Lu S, Zhang J. Designed covalent allosteric modulators: an emerging paradigm in drug discovery. Drug Discov Today 2017; 22:447-453. [DOI: 10.1016/j.drudis.2016.11.013] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/04/2016] [Accepted: 11/15/2016] [Indexed: 12/11/2022]
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123
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Miller MS, Maheshwari S, McRobb FM, Kinzler KW, Amzel LM, Vogelstein B, Gabelli SB. Identification of allosteric binding sites for PI3Kα oncogenic mutant specific inhibitor design. Bioorg Med Chem 2017; 25:1481-1486. [PMID: 28129991 DOI: 10.1016/j.bmc.2017.01.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 01/06/2017] [Accepted: 01/11/2017] [Indexed: 10/20/2022]
Abstract
PIK3CA, the gene that encodes the catalytic subunit of phosphatidylinositol 3-kinase α (PI3Kα), is frequently mutated in breast and other types of cancer. A specific inhibitor that targets the mutant forms of PI3Kα could maximize treatment efficiency while minimizing side-effects. Herein we describe the identification of novel binding pockets that may provide an opportunity for the design of mutant selective inhibitors. Using a fragment-based approach, we screened a library of 352 fragments (MW<300Da) for binding to PI3Kα by X-ray crystallography. Five novel binding pockets were identified, each providing potential opportunities for inhibitor design. Of particular interest was a binding pocket near Glu542, which is located in one of the two most frequently mutated domains.
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Affiliation(s)
- Michelle S Miller
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Sweta Maheshwari
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Fiona M McRobb
- Schrödinger, Inc., 120 West 45th Street, New York, NY 10036, United States
| | - Kenneth W Kinzler
- Ludwig Center and Howard Hughes Medical Institutions, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
| | - L Mario Amzel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Bert Vogelstein
- Ludwig Center and Howard Hughes Medical Institutions, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
| | - Sandra B Gabelli
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States; Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States.
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124
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Verkhivker GM. Network-based modelling and percolation analysis of conformational dynamics and activation in the CDK2 and CDK4 proteins: dynamic and energetic polarization of the kinase lobes may determine divergence of the regulatory mechanisms. MOLECULAR BIOSYSTEMS 2017; 13:2235-2253. [DOI: 10.1039/c7mb00355b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Network modeling and percolation analysis of conformational dynamics and energetics of regulatory mechanisms in cyclin-dependent kinases.
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Affiliation(s)
- G. M. Verkhivker
- Graduate Program in Computational and Data Sciences
- Department of Computational Biosciences
- Schmid College of Science and Technology
- Chapman University
- Orange
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125
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Kinetic characterization and molecular docking of novel allosteric inhibitors of aminoglycoside phosphotransferases. Biochim Biophys Acta Gen Subj 2017; 1861:3464-3473. [DOI: 10.1016/j.bbagen.2016.09.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/07/2016] [Accepted: 09/11/2016] [Indexed: 11/21/2022]
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126
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Miura T, Matsuo A, Muraoka T, Ide M, Morikami K, Kamikawa T, Nishihara M, Kashiwagi H. Identification of a selective inhibitor of transforming growth factor β-activated kinase 1 by biosensor-based screening of focused libraries. Bioorg Med Chem Lett 2016; 27:1031-1036. [PMID: 28109791 DOI: 10.1016/j.bmcl.2016.12.064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 12/20/2016] [Accepted: 12/27/2016] [Indexed: 01/07/2023]
Abstract
Transforming growth factor-β activated kinase 1 (TAK1), a member of the mitogen-activated protein kinase kinase kinase family, plays an essential role in mediating signals from various pro-inflammatory cytokines and therefore may be a good target for developing anti-inflammation agents. Herein, we report our efforts to identify TAK1 inhibitors with a good selectivity profile with which to initiate medicinal chemistry. Instead of resorting to a high-throughput screening campaign, we performed biosensor-based biophysical screening for a limited number of compounds by taking advantage of existing knowledge on kinase inhibitors. Rather than focusing on one specific inhibition mode, we searched for three different types, Type I (ATP-competitive, DFG-in), Type II (DFG-out), and Type III binders (non-ATP competitive) in parallel, and succeeded in identifying candidates in all three categories efficiently and rapidly. Finally, the biosensor-based binding kinetics for the active and inactive forms of TAK1 were measured to prioritize the Type I and Type II inhibitors. The effort resulted in the identification of a new TAK1-selective Type I compound with a thienopyrimidine scaffold that served as a good starting point for medicinal chemistry.
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Affiliation(s)
- Takaaki Miura
- Research Division, Chugai Pharmaceutical Co., Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan.
| | - Atsushi Matsuo
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Terushige Muraoka
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Mitsuaki Ide
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Kenji Morikami
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Takayuki Kamikawa
- Research Division, Chugai Pharmaceutical Co., Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Masamichi Nishihara
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Hirotaka Kashiwagi
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
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127
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Exploring Molecular Mechanisms of Paradoxical Activation in the BRAF Kinase Dimers: Atomistic Simulations of Conformational Dynamics and Modeling of Allosteric Communication Networks and Signaling Pathways. PLoS One 2016; 11:e0166583. [PMID: 27861609 PMCID: PMC5115767 DOI: 10.1371/journal.pone.0166583] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/31/2016] [Indexed: 12/14/2022] Open
Abstract
The recent studies have revealed that most BRAF inhibitors can paradoxically induce kinase activation by promoting dimerization and enzyme transactivation. Despite rapidly growing number of structural and functional studies about the BRAF dimer complexes, the molecular basis of paradoxical activation phenomenon is poorly understood and remains largely hypothetical. In this work, we have explored the relationships between inhibitor binding, protein dynamics and allosteric signaling in the BRAF dimers using a network-centric approach. Using this theoretical framework, we have combined molecular dynamics simulations with coevolutionary analysis and modeling of the residue interaction networks to determine molecular determinants of paradoxical activation. We have investigated functional effects produced by paradox inducer inhibitors PLX4720, Dabrafenib, Vemurafenib and a paradox breaker inhibitor PLX7904. Functional dynamics and binding free energy analyses of the BRAF dimer complexes have suggested that negative cooperativity effect and dimer-promoting potential of the inhibitors could be important drivers of paradoxical activation. We have introduced a protein structure network model in which coevolutionary residue dependencies and dynamic maps of residue correlations are integrated in the construction and analysis of the residue interaction networks. The results have shown that coevolutionary residues in the BRAF structures could assemble into independent structural modules and form a global interaction network that may promote dimerization. We have also found that BRAF inhibitors could modulate centrality and communication propensities of global mediating centers in the residue interaction networks. By simulating allosteric communication pathways in the BRAF structures, we have determined that paradox inducer and breaker inhibitors may activate specific signaling routes that correlate with the extent of paradoxical activation. While paradox inducer inhibitors may facilitate a rapid and efficient communication via an optimal single pathway, the paradox breaker may induce a broader ensemble of suboptimal and less efficient communication routes. The central finding of our study is that paradox breaker PLX7904 could mimic structural, dynamic and network features of the inactive BRAF-WT monomer that may be required for evading paradoxical activation. The results of this study rationalize the existing structure-functional experiments by offering a network-centric rationale of the paradoxical activation phenomenon. We argue that BRAF inhibitors that amplify dynamic features of the inactive BRAF-WT monomer and intervene with the allosteric interaction networks may serve as effective paradox breakers in cellular environment.
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128
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The Intersection of Structural and Chemical Biology - An Essential Synergy. Cell Chem Biol 2016; 23:173-182. [PMID: 26933743 DOI: 10.1016/j.chembiol.2015.12.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 12/04/2015] [Accepted: 12/04/2015] [Indexed: 12/22/2022]
Abstract
The continual improvement in our ability to generate high resolution structural models of biological molecules has stimulated and supported innovative chemical biology projects that target increasingly challenging ligand interaction sites. In this review we outline some of the recent developments in chemical biology and rational ligand design and show selected examples that illustrate the synergy between these research areas.
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Chilà R, Guffanti F, Damia G. Role and therapeutic potential of CDK12 in human cancers. Cancer Treat Rev 2016; 50:83-88. [PMID: 27662623 DOI: 10.1016/j.ctrv.2016.09.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 08/30/2016] [Accepted: 09/01/2016] [Indexed: 12/31/2022]
Abstract
Phosphorylation of the RNA polymerase II C-terminal domain by cyclin-dependent kinases (CDKs) is important for productive transcription. Deregulated transcription-CDKs have been reported in different human cancers. Until recently CDK9 was the only transcription-CDK with a causative role in cancer, but evidence is cumulating of the importance of CDK12. This review summarizes the role of CDK12 in transcription and RNA processing, in maintaining genomic stability/integrity and in tumorigenesis. CDK12 mutations have been reported in many cancers and have been suggested as a cause of defective DNA repair in ovarian carcinoma. CDK12 may have a role as a new therapeutic target in oncology.
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Affiliation(s)
- Rosaria Chilà
- Laboratory of Molecular Pharmacology, Oncology Department, IRCCS - Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Federica Guffanti
- Laboratory of Molecular Pharmacology, Oncology Department, IRCCS - Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Giovanna Damia
- Laboratory of Molecular Pharmacology, Oncology Department, IRCCS - Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy.
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130
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Carlino L, Rastelli G. Dual Kinase-Bromodomain Inhibitors in Anticancer Drug Discovery: A Structural and Pharmacological Perspective. J Med Chem 2016; 59:9305-9320. [DOI: 10.1021/acs.jmedchem.6b00438] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Luca Carlino
- Department
of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Giulio Rastelli
- Department
of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy
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Lead Discovery of Type II BRAF V600E Inhibitors Targeting the Structurally Validated DFG-Out Conformation Based upon Selected Fragments. Molecules 2016; 21:molecules21070879. [PMID: 27438814 PMCID: PMC6272942 DOI: 10.3390/molecules21070879] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/13/2016] [Accepted: 06/28/2016] [Indexed: 11/17/2022] Open
Abstract
The success of the first approved kinase inhibitor imatinib has spurred great interest in the development of type II inhibitors targeting the inactive DFG-out conformation, wherein the Phe of the DFG motif at the start of the activation loop points into the ATP binding site. Nevertheless, kinase inhibitors launched so far are heavily biased toward type I inhibitors targeting the active DFG-in conformation, wherein the Phe of the DFG motif flips by approximately 180° relative to the inactive conformation, resulting in Phe and Asp swapping their positions. Data recently obtained with structurally validated type II inhibitors supported the conclusion that type II inhibitors are more selective than type I inhibitors. In our type II BRAF V600E inhibitor lead discovery effort, we identified phenylaminopyrimidine (PAP) and unsymmetrically disubstituted urea as two fragments that are frequently presented in FDA-approved protein kinase inhibitors. We therefore defined PAP and unsymmetrically disubstituted urea as privileged fragments for kinase drug discovery. A pharmacophore for type II inhibitors, 4-phenylaminopyrimidine urea (4-PAPU), was assembled based upon these privileged fragments. Lead compound SI-046 with BRAF V600E inhibitory activity comparable to the template compound sorafenib was in turn obtained through preliminary structure-activity relationship (SAR) study. Molecular docking suggested that SI-046 is a bona fide type II kinase inhibitor binding to the structurally validated "classical DFG-out" conformation of BRAF V600E. Our privileged fragments-based approach was shown to efficiently deliver a bona fide type II kinase inhibitor lead. In essence, the theme of this article is to showcase the strategy and rationale of our approach.
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Moarbess G, Guichou JF, Paniagua-Gayraud S, Chouchou A, Marcadet O, Leroy F, Ruédas R, Cuq P, Deleuze-Masquéfa C, Bonnet PA. New IKK inhibitors: Synthesis of new imidazo[1,2-a]quinoxaline derivatives using microwave assistance and biological evaluation as IKK inhibitors. Eur J Med Chem 2016; 115:268-74. [PMID: 27017554 DOI: 10.1016/j.ejmech.2016.03.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Revised: 03/01/2016] [Accepted: 03/02/2016] [Indexed: 12/12/2022]
Abstract
The inhibition of the NF-κB-dependent pathways by IKK inhibitors plays an important role in immunity, inflammation, and cancer. New imidazoquinoxalines tricyclic derivatives are prepared using microwave assistance and their biological activities as IKK inhibitors are described. Compounds 6a present a potent inhibition activity and selectivity for IKK2. Docking studies in the IKK2 binding site allowed identification of residues most likely to interact with theses inhibitors and explain their potent IKK2 inhibition activity and selectivity.
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Affiliation(s)
- Georges Moarbess
- Lebanese University, Faculty of Sciences II, Department of Chemistry and Biochemistry, Campus Fanar, BP 90656 Jdeideh, Lebanon
| | - Jean-François Guichou
- CNRS, UMR5048 - Université de Montpellier, Centre de Biochimie Structurale, F-34090 Montpellier, France; INSERM, U1054, F-34090 Montpellier, France
| | - Stéphanie Paniagua-Gayraud
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université Montpellier, ENSCM, Faculté de Pharmacie, 15, avenue Charles Flahault,BP14491, 34093 Montpellier cedex 5, France
| | - Adrien Chouchou
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université Montpellier, ENSCM, Faculté de Pharmacie, 15, avenue Charles Flahault,BP14491, 34093 Montpellier cedex 5, France
| | - Olivier Marcadet
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université Montpellier, ENSCM, Faculté de Pharmacie, 15, avenue Charles Flahault,BP14491, 34093 Montpellier cedex 5, France
| | - Fiona Leroy
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université Montpellier, ENSCM, Faculté de Pharmacie, 15, avenue Charles Flahault,BP14491, 34093 Montpellier cedex 5, France
| | - Rémi Ruédas
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université Montpellier, ENSCM, Faculté de Pharmacie, 15, avenue Charles Flahault,BP14491, 34093 Montpellier cedex 5, France
| | - Pierre Cuq
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université Montpellier, ENSCM, Faculté de Pharmacie, 15, avenue Charles Flahault,BP14491, 34093 Montpellier cedex 5, France
| | - Carine Deleuze-Masquéfa
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université Montpellier, ENSCM, Faculté de Pharmacie, 15, avenue Charles Flahault,BP14491, 34093 Montpellier cedex 5, France.
| | - Pierre-Antoine Bonnet
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université Montpellier, ENSCM, Faculté de Pharmacie, 15, avenue Charles Flahault,BP14491, 34093 Montpellier cedex 5, France
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Yan M, Wang H, Wang Q, Zhang Z, Zhang C. Allosteric inhibition of c-Met kinase in sub-microsecond molecular dynamics simulations induced by its inhibitor, tivantinib. Phys Chem Chem Phys 2016; 18:10367-74. [DOI: 10.1039/c5cp07001e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Molecular dynamics simulations showed that conformation transition of c-Met from DFG-in to DFG-out may accomplish rapidly in the presence of tivantinib. A unique binding mode of tivantinib was found to be critical for this “DFG-flip”.
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Affiliation(s)
- Maocai Yan
- School of Pharmacy
- Jining Medical University
- Rizhao
- P. R. China
| | - Huiyun Wang
- School of Pharmacy
- Jining Medical University
- Rizhao
- P. R. China
| | - Qibao Wang
- School of Pharmacy
- Jining Medical University
- Rizhao
- P. R. China
| | - Zhen Zhang
- School of Pharmacy
- Jining Medical University
- Rizhao
- P. R. China
| | - Chunyan Zhang
- School of Pharmacy
- Jining Medical University
- Rizhao
- P. R. China
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134
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Verkhivker GM. Molecular dynamics simulations and modelling of the residue interaction networks in the BRAF kinase complexes with small molecule inhibitors: probing the allosteric effects of ligand-induced kinase dimerization and paradoxical activation. MOLECULAR BIOSYSTEMS 2016; 12:3146-65. [DOI: 10.1039/c6mb00298f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The computational analysis of residue interaction networks dissects the allosteric effects of inhibitor-induced BRAF kinase dimerization and paradoxical activation.
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Affiliation(s)
- G. M. Verkhivker
- Graduate Program in Computational and Data Sciences
- Department of Computational Sciences
- Schmid College of Science and Technology
- Chapman University
- Orange
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