1
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Gallego RA, Cho-Schultz S, Del Bel M, Dechert-Schmitt AM, Donaldson JS, He M, Jalaie M, Kania R, Matthews J, McTigue M, Tuttle JB, Risley H, Zhou D, Zhou R, Ahmad OK, Bernier L, Berritt S, Braganza J, Chen Z, Cianfrogna JA, Collins M, Costa Jones C, Cronin CN, Davis C, Dress K, Edwards M, Farrell W, France SP, Grable N, Johnson E, Johnson TW, Jones R, Knauber T, Lafontaine J, Loach RP, Maestre M, Miller N, Moen M, Monfette S, Morse P, Nager AR, Niosi M, Richardson P, Rohner AK, Sach NW, Timofeevski S, Tucker JW, Vetelino B, Zhang L, Nair SK. Discovery of PF-07265028, A Selective Small Molecule Inhibitor of Hematopoietic Progenitor Kinase 1 (HPK1) for the Treatment of Cancer. J Med Chem 2024; 67:22002-22038. [PMID: 39651809 DOI: 10.1021/acs.jmedchem.4c01930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2024]
Abstract
Hematopoietic progenitor kinase 1 (HPK1/MAP4K1) represents a high interest target for the treatment of cancer through an immune-mediated mechanism. Herein we present highlights of the drug discovery campaign within the lactam/azalactam series of inhibitors that yielded a small molecule (21, PF-07265028), which was advanced to a phase 1 clinical trial (NCT05233436). Key components of the discovery effort included optimization of potency through mitigation of ligand strain as guided by the use of cocrystal structures, mitigation of ADME liabilities (plasma instability and fraction metabolism by CYP2D6), and optimization of kinase selectivity, particularly over immune-modulating kinases with high homology to HPK1. Structure-based drug design via leveraging cocrystal structures and lipophilic efficiency analysis proved to be valuable tools that ultimately enabled the delivery of a clinical-quality small molecule inhibitor of HPK1.
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Affiliation(s)
- Rebecca A Gallego
- Oncology Medicinal Chemistry Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Sujin Cho-Schultz
- Oncology Medicinal Chemistry Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Matthew Del Bel
- Oncology Medicinal Chemistry Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | | | - Joyann S Donaldson
- Oncology Medicinal Chemistry Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Mingying He
- Oncology Medicinal Chemistry Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Mehran Jalaie
- Oncology Medicinal Chemistry Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Rob Kania
- Oncology Medicinal Chemistry Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Jean Matthews
- Oncology Medicinal Chemistry Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Michele McTigue
- Oncology Medicinal Chemistry Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Jamison B Tuttle
- Worldwide Research and Development, Pfizer, Inc., Cambridge, Massachusetts 02139, United States
| | - Hud Risley
- Worldwide Research and Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Dahui Zhou
- Worldwide Research and Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Ru Zhou
- Oncology Medicinal Chemistry Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Omar K Ahmad
- Worldwide Research and Development, Pfizer, Inc., Cambridge, Massachusetts 02139, United States
| | - Louise Bernier
- Oncology Medicinal Chemistry Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Simon Berritt
- Worldwide Research and Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - John Braganza
- Oncology Medicinal Chemistry Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Zecheng Chen
- Worldwide Research and Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Julie A Cianfrogna
- Pharmacokinetics, Dynamics and Metabolism Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Michael Collins
- Oncology Medicinal Chemistry Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Cinthia Costa Jones
- Oncology Research Unit Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Ciaran N Cronin
- Oncology Medicinal Chemistry Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Carl Davis
- Pharmacokinetics, Dynamics and Metabolism Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Klaus Dress
- Oncology Medicinal Chemistry Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Martin Edwards
- Oncology Medicinal Chemistry Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - William Farrell
- Oncology Medicinal Chemistry Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Scott P France
- Worldwide Research and Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Nicole Grable
- Oncology Medicinal Chemistry Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Eric Johnson
- Oncology Medicinal Chemistry Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Ted W Johnson
- Oncology Medicinal Chemistry Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Rhys Jones
- Pharmacokinetics, Dynamics and Metabolism Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Thomas Knauber
- Worldwide Research and Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Jennifer Lafontaine
- Oncology Medicinal Chemistry Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Richard P Loach
- Worldwide Research and Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Michael Maestre
- Oncology Research Unit Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Nichol Miller
- Oncology Research Unit Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Mark Moen
- Worldwide Research and Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Sebastien Monfette
- Worldwide Research and Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Peter Morse
- Pharmacokinetics, Dynamics and Metabolism Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Andrew Ross Nager
- Oncology Research Unit Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Mark Niosi
- Worldwide Research and Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Paul Richardson
- Oncology Medicinal Chemistry Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Allison K Rohner
- Oncology Medicinal Chemistry Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Neal W Sach
- Oncology Medicinal Chemistry Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Sergei Timofeevski
- Oncology Research Unit Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Joseph W Tucker
- Worldwide Research and Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Beth Vetelino
- Worldwide Research and Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Lei Zhang
- Worldwide Research and Development, Pfizer, Inc., Cambridge, Massachusetts 02139, United States
| | - Sajiv K Nair
- Oncology Medicinal Chemistry Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
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2
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Ong HW, de Silva C, Avalani K, Kwarcinski F, Mansfield CR, Chirgwin M, Truong A, Derbyshire ER, Zutshi R, Drewry DH. Characterization of 2,4-Dianilinopyrimidines Against Five P. falciparum Kinases PfARK1, PfARK3, PfNEK3, PfPK9, and PfPKB. ACS Med Chem Lett 2023; 14:1774-1784. [PMID: 38116430 PMCID: PMC10726455 DOI: 10.1021/acsmedchemlett.3c00354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023] Open
Abstract
Plasmodium kinases are increasingly recognized as potential novel antiplasmodial targets for the treatment of malaria, but only a small subset of these kinases have had structure-activity relationship (SAR) campaigns reported. Herein we report the discovery of CZC-54252 (1) as an inhibitor of five P. falciparum kinases PfARK1, PfARK3, PfNEK3, PfPK9, and PfPKB. 39 analogues were evaluated against all five kinases to establish SAR at three regions of the kinase active site. Nanomolar inhibitors of each kinase were discovered. We identified common and divergent SAR trends across all five kinases, highlighting substituents in each region that improve potency and selectivity for each kinase. Potent analogues were evaluated against the P. falciparum blood stage. Eight submicromolar inhibitors were discovered, of which 37 demonstrated potent antiplasmodial activity (EC50 = 0.16 μM). Our results provide an understanding of features needed to inhibit each individual kinase and lay groundwork for future optimization efforts toward novel antimalarials.
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Affiliation(s)
- Han Wee Ong
- Structural
Genomics Consortium and Division of Chemical Biology and Medicinal
Chemistry, Eshelman School of Pharmacy,
University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Chandi de Silva
- Luceome
Biotechnologies, LLC, 1665 East 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Krisha Avalani
- Luceome
Biotechnologies, LLC, 1665 East 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Frank Kwarcinski
- Luceome
Biotechnologies, LLC, 1665 East 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Christopher R. Mansfield
- Department
of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, North Carolina 27710, United States
| | - Michael Chirgwin
- Department
of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Anna Truong
- Department
of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Emily R. Derbyshire
- Department
of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, North Carolina 27710, United States
- Department
of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Reena Zutshi
- Luceome
Biotechnologies, LLC, 1665 East 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - David H. Drewry
- Structural
Genomics Consortium and Division of Chemical Biology and Medicinal
Chemistry, Eshelman School of Pharmacy,
University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger
Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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3
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Zhao Z, Bourne PE. How Ligands Interact with the Kinase Hinge. ACS Med Chem Lett 2023; 14:1503-1508. [PMID: 37974950 PMCID: PMC10641887 DOI: 10.1021/acsmedchemlett.3c00212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 10/03/2023] [Indexed: 11/19/2023] Open
Abstract
ATP-competitive kinase inhibitors form hydrogen bond interactions with the kinase hinge region at the adenine binding site. Thus, it is crucial to explore hinge-ligand recognition as part of a rational drug design strategy. Here, harnessing known ligand-bound kinase structures and experimental assay resources, we first created a kinase structure-assay database (KSAD) containing 2705 nM ligand-bound kinase complexes. Then, using KSAD, we systematically investigate hinge-ligand binding patterns using interaction fingerprints, thereby delineating 15 different hydrogen-bond interaction modes. We believe these results will be valuable for de novo drug design and/or scaffold hopping of kinase-targeted drugs.
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Affiliation(s)
- Zheng Zhao
- School of Data Science and Department
of Biomedical Engineering, University of
Virginia, Charlottesville, Virginia 22904, United States
| | - Philip E. Bourne
- School of Data Science and Department
of Biomedical Engineering, University of
Virginia, Charlottesville, Virginia 22904, United States
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4
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Zhang J, Li W, Wang W, Chen Q, Xu Z, Deng M, Zhou L, He G. Dual roles of FAK in tumor angiogenesis: A review focused on pericyte FAK. Eur J Pharmacol 2023; 947:175694. [PMID: 36967077 DOI: 10.1016/j.ejphar.2023.175694] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/16/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023]
Abstract
Focal adhesion kinase (FAK), also known as protein tyrosine kinase 2 (PTK2), is a ubiquitously expressed non-receptor tyrosine kinase, that plays a pivotal role in integrin-mediated signal transduction. Endothelial FAK is upregulated in many types of cancer and promotes tumorigenesis and tumor progression. However, recent studies have shown that pericyte FAK has the opposite effect. This review article dissects the mechanisms, by which endothelial cells (ECs) and pericyte FAK regulate angiogenesis, with an emphasis on the Gas6/Axl pathway. In particular, this article discusses the role of pericyte FAK loss on angiogenesis during tumorigenesis and metastasis. In addition, the existing challenges and future application of drug-based anti-FAK targeted therapies will be discussed to provide a theoretical basis for further development and use of FAK inhibitors.
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5
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Schröder M, Leiendecker M, Grädler U, Braun J, Blum A, Wanior M, Berger BT, Krämer A, Müller S, Esdar C, Knapp S, Heinrich T. MSC-1186, a Highly Selective Pan-SRPK Inhibitor Based on an Exceptionally Decorated Benzimidazole-Pyrimidine Core. J Med Chem 2023; 66:837-854. [PMID: 36516476 DOI: 10.1021/acs.jmedchem.2c01705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The highly conserved catalytic sites in protein kinases make it difficult to identify ATP competitive inhibitors with kinome-wide selectivity. Serendipitously, during a dedicated fragment campaign for the focal adhesion kinase (FAK), a scaffold that had lost its initial FAK affinity showed remarkable potency and selectivity for serine-arginine-protein kinases 1-3 (SRPK1-3). Non-conserved interactions with the uniquely structured hinge region of the SRPK family were the key drivers of the exclusive selectivity of the discovered fragment hit. Structure-guided medicinal chemistry efforts led to the SRPK inhibitor MSC-1186, which fulfills all hallmarks of a reversible chemical probe, including nanomolar cellular potency and excellent kinome-wide selectivity. The combination of MSC-1186 with CDC2-like kinase (CLK) inhibitors showed additive attenuation of SR-protein phosphorylation compared to the single agents. MSC-1186 and negative control (MSC-5360) are chemical probes available via the Structural Genomics Consortium chemical probe program (https://www.sgc-ffm.uni-frankfurt.de/).
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Affiliation(s)
- Martin Schröder
- SGC Frankfurt, Goethe University Frankfurt, Buchmann Institute for Life Sciences (BMLS), Riedberg Campus, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | | | - Ulrich Grädler
- Merck Healthcare KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Juliane Braun
- Merck Healthcare KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Andreas Blum
- Merck Healthcare KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Marek Wanior
- SGC Frankfurt, Goethe University Frankfurt, Buchmann Institute for Life Sciences (BMLS), Riedberg Campus, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Benedict-Tilman Berger
- SGC Frankfurt, Goethe University Frankfurt, Buchmann Institute for Life Sciences (BMLS), Riedberg Campus, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Andreas Krämer
- SGC Frankfurt, Goethe University Frankfurt, Buchmann Institute for Life Sciences (BMLS), Riedberg Campus, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Susanne Müller
- SGC Frankfurt, Goethe University Frankfurt, Buchmann Institute for Life Sciences (BMLS), Riedberg Campus, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Christina Esdar
- Merck Healthcare KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Stefan Knapp
- SGC Frankfurt, Goethe University Frankfurt, Buchmann Institute for Life Sciences (BMLS), Riedberg Campus, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Timo Heinrich
- Merck Healthcare KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
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6
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Chemical space docking enables large-scale structure-based virtual screening to discover ROCK1 kinase inhibitors. Nat Commun 2022; 13:6447. [PMID: 36307407 PMCID: PMC9616902 DOI: 10.1038/s41467-022-33981-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/05/2022] [Indexed: 12/25/2022] Open
Abstract
With the ever-increasing number of synthesis-on-demand compounds for drug lead discovery, there is a great need for efficient search technologies. We present the successful application of a virtual screening method that combines two advances: (1) it avoids full library enumeration (2) products are evaluated by molecular docking, leveraging protein structural information. Crucially, these advances enable a structure-based technique that can efficiently explore libraries with billions of molecules and beyond. We apply this method to identify inhibitors of ROCK1 from almost one billion commercially available compounds. Out of 69 purchased compounds, 27 (39%) have Ki values < 10 µM. X-ray structures of two leads confirm their docked poses. This approach to docking scales roughly with the number of reagents that span a chemical space and is therefore multiple orders of magnitude faster than traditional docking.
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7
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Subbaiah MAM, Meanwell NA. Bioisosteres of the Phenyl Ring: Recent Strategic Applications in Lead Optimization and Drug Design. J Med Chem 2021; 64:14046-14128. [PMID: 34591488 DOI: 10.1021/acs.jmedchem.1c01215] [Citation(s) in RCA: 273] [Impact Index Per Article: 68.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The benzene moiety is the most prevalent ring system in marketed drugs, underscoring its historic popularity in drug design either as a pharmacophore or as a scaffold that projects pharmacophoric elements. However, introspective analyses of medicinal chemistry practices at the beginning of the 21st century highlighted the indiscriminate deployment of phenyl rings as an important contributor to the poor physicochemical properties of advanced molecules, which limited their prospects of being developed into effective drugs. This Perspective deliberates on the design and applications of bioisosteric replacements for a phenyl ring that have provided practical solutions to a range of developability problems frequently encountered in lead optimization campaigns. While the effect of phenyl ring replacements on compound properties is contextual in nature, bioisosteric substitution can lead to enhanced potency, solubility, and metabolic stability while reducing lipophilicity, plasma protein binding, phospholipidosis potential, and inhibition of cytochrome P450 enzymes and the hERG channel.
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Affiliation(s)
- Murugaiah A M Subbaiah
- Department of Medicinal Chemistry, Biocon-Bristol Myers Squibb Research and Development Centre, Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bangalore, Karnataka 560099, India
| | - Nicholas A Meanwell
- Department of Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
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8
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Lorenz R, Wu J, Herberg FW, Taylor SS, Engh RA. Drugging the Undruggable: How Isoquinolines and PKA Initiated the Era of Designed Protein Kinase Inhibitor Therapeutics. Biochemistry 2021; 60:3470-3484. [PMID: 34370450 DOI: 10.1021/acs.biochem.1c00359] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In 1984, Japanese researchers led by the biochemist Hiroyoshi Hidaka described the first synthetic protein kinase inhibitors based on an isoquinoline sulfonamide structure (Hidaka et al. Biochemistry, 1984 Oct 9; 23(21): 5036-41. doi: 10.1021/bi00316a032). These led to the first protein kinase inhibitor approved for medical use (fasudil), an inhibitor of the AGC subfamily Rho kinase. With potencies strong enough to compete against endogenous ATP, the isoquinoline compounds established the druggability of the ATP binding site. Crystal structures of their protein kinase complexes, including with cAMP-dependent protein kinase (PKA), showed interactions that, on the one hand, could mimic ATP but, on the other hand, could be optimized for high potency binding, kinase selectivity, and diversification away from adenosine. They also showed the flexibility of the glycine-rich loop, and PKA became a major prototype for crystallographic and nuclear magnetic resonance (NMR) studies of protein kinase mechanism and dynamic activity control. Since fasudil, more than 70 kinase inhibitors have been approved for clinical use, involving efforts that progressively have introduced new paradigms of data-driven drug discovery. Publicly available data alone comprise over 5000 protein kinase crystal structures and hundreds of thousands of binding data. Now, new methods, including artificial intelligence techniques and expansion of protein kinase targeting approaches, together with the expiration of patent protection for optimized inhibitor scaffolds, promise even greater advances in drug discovery. Looking back to the time of the first isoquinoline hinge binders brings the current state-of-the-art into stark contrast. Appropriately for this Perspective article, many of the milestone papers during this time were published in Biochemistry (now ACS Biochemistry).
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Affiliation(s)
- Robin Lorenz
- Department of Biochemistry, Institute for Biology, University of Kassel, Kassel 34132, Germany
| | - Jian Wu
- Department of Pharmacology, University of California, San Diego, 9400 Gilman Drive, La Jolla, California 92093-0654, United States
| | - Friedrich W Herberg
- Department of Biochemistry, Institute for Biology, University of Kassel, Kassel 34132, Germany
| | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, 9400 Gilman Drive, La Jolla, California 92093-0654, United States.,Department of Chemistry and Biochemistry, University of California, San Diego, 9400 Gilman Drive, La Jolla, California 92093-0654, United States
| | - Richard A Engh
- The Norwegian Structural Biology Centre, Department of Chemistry, UiT the Arctic University of Norway, Tromsø 9012, Norway
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9
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Brullo C, Tasso B. New Insights on Fak and Fak Inhibitors. Curr Med Chem 2021; 28:3318-3338. [PMID: 33143618 DOI: 10.2174/0929867327666201103162239] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/08/2020] [Accepted: 09/19/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Focal adhesion kinase (Fak) is a cytoplasmic protein tyrosine kinase overexpressed and activated in different solid cancers; it has shown an important role in metastasis formation, cell migration, invasion and angiogenesis and consequently it has been proposed as a potential target in cancer therapy, particularly in a metastatic phase. In recent years, different investigations have highlighted the importance of new Fak inhibitors as potential anti-cancer drugs, but other studies evidenced its role in different pathologies related to the cardiac function or viral infection. METHODS An extensive bibliographic research (104 references) has been done concerning the structure of Fak, its importance in tumor development, but also in other pathologies currently under study. The compounds currently subjected to clinical studies were therefore treated using the appropriate databases. Finally, the main chemical scaffolds currently under preclinical investigation were analyzed, focusing on their molecular structures and on the activity structure relationships (SAR). RESULTS At the moment, only a few reversible ATP-competitive inhibitors are under investigation in pre-clinical studies and clinical trials. Other compounds, with different chemical scaffolds, are investigated to obtain more active and selective Fak inhibitors. This mini-review is a summary of different Fak functions in cancer and other pathologies; the compounds today in clinical trials and the recent chemical scaffolds (also included in patents) giving the most interesting results are investigated. In addition, PROTAC molecules are reported. CONCLUSION All reported results evidenced that additional studies are necessary to design and synthesize new selective and more active compounds, although promising information has been obtained from associations between Fak inhibitors and other different anti- cancer drugs. In addition, the other important roles evidenced, both at the nuclear level and in non-cancerous cells, make this protein an increasingly important target in pharmaceutical chemistry.
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Affiliation(s)
- Chiara Brullo
- Department of Pharmacy, University of Genova, Viale Benedetto XV, 3-I16132 Genova, Italy
| | - Bruno Tasso
- Department of Pharmacy, University of Genova, Viale Benedetto XV, 3-I16132 Genova, Italy
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10
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Arendse LB, Wyllie S, Chibale K, Gilbert IH. Plasmodium Kinases as Potential Drug Targets for Malaria: Challenges and Opportunities. ACS Infect Dis 2021; 7:518-534. [PMID: 33590753 PMCID: PMC7961706 DOI: 10.1021/acsinfecdis.0c00724] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Indexed: 12/30/2022]
Abstract
Protein and phosphoinositide kinases have been successfully exploited as drug targets in various disease areas, principally in oncology. In malaria, several protein kinases are under investigation as potential drug targets, and an inhibitor of Plasmodium phosphatidylinositol 4-kinase type III beta (PI4KIIIβ) is currently in phase 2 clinical studies. In this Perspective, we review the potential of kinases as drug targets for the treatment of malaria. Kinases are known to be readily druggable, and many are essential for parasite survival. A key challenge in the design of Plasmodium kinase inhibitors is obtaining selectivity over the corresponding human orthologue(s) and other human kinases due to the highly conserved nature of the shared ATP binding site. Notwithstanding this, there are some notable differences between the Plasmodium and human kinome that may be exploitable. There is also the potential for designed polypharmacology, where several Plasmodium kinases are inhibited by the same drug. Prior to starting the drug discovery process, it is important to carefully assess potential kinase targets to ensure that the inhibition of the desired kinase will kill the parasites in the required life-cycle stages with a sufficiently fast rate of kill. Here, we highlight key target attributes and experimental approaches to consider and summarize the progress that has been made targeting Plasmodium PI4KIIIβ, cGMP-dependent protein kinase, and cyclin-dependent-like kinase 3.
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Affiliation(s)
- Lauren B. Arendse
- Drug
Discovery and Development Centre (H3D), South African Medical Research
Council Drug Discovery and Development Research Unit, Department of
Chemistry, and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, Cape Town, Western Cape 7701, South Africa
| | - Susan Wyllie
- Wellcome
Centre for Anti-Infectives Research, Division of Biological Chemistry
and Drug Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Kelly Chibale
- Drug
Discovery and Development Centre (H3D), South African Medical Research
Council Drug Discovery and Development Research Unit, Department of
Chemistry, and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, Cape Town, Western Cape 7701, South Africa
| | - Ian H. Gilbert
- Wellcome
Centre for Anti-Infectives Research, Division of Biological Chemistry
and Drug Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
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11
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Picado A, Chaikuad A, Wells CI, Shrestha S, Zuercher WJ, Pickett JE, Kwarcinski FE, Sinha P, de Silva CS, Zutshi R, Liu S, Kannan N, Knapp S, Drewry DH, Willson TM. A Chemical Probe for Dark Kinase STK17B Derives Its Potency and High Selectivity through a Unique P-Loop Conformation. J Med Chem 2020; 63:14626-14646. [PMID: 33215924 PMCID: PMC7816213 DOI: 10.1021/acs.jmedchem.0c01174] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
STK17B is a member of the death-associated protein kinase family and has been genetically linked to the development of diverse diseases. However, the role of STK17B in normal and disease pathology is poorly defined. Here, we present the discovery of thieno[3,2-d] pyrimidine SGC-STK17B-1 (11s), a high-quality chemical probe for this understudied "dark" kinase. 11s is an ATP-competitive inhibitor that showed remarkable selectivity over other kinases including the closely related STK17A. X-ray crystallography of 11s and related thieno[3,2-d]pyrimidines bound to STK17B revealed a unique P-loop conformation characterized by a salt bridge between R41 and the carboxylic acid of the inhibitor. Molecular dynamic simulations of STK17B revealed the flexibility of the P-loop and a wide range of R41 conformations available to the apo-protein. The isomeric thieno[2,3-d]pyrimidine SGC-STK17B-1N (19g) was identified as a negative control compound. The >100-fold lower activity of 19g on STK17B was attributed to the reduced basicity of its pyrimidine N1.
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Affiliation(s)
- Alfredo Picado
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7264
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Max-von-Laue-Straße 9, Goethe University Frankfurt, 60438 Frankfurt, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Straße 15, 60438 Frankfurt, Germany
| | - Carrow I. Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7264
| | - Safal Shrestha
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - William J. Zuercher
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7264
| | - Julie E. Pickett
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7264
| | | | - Parvathi Sinha
- Luceome Biotechnologies, 1665 E. 18th Street, Suite 106, Tucson, AZ 85719
| | - Chandi S. de Silva
- Luceome Biotechnologies, 1665 E. 18th Street, Suite 106, Tucson, AZ 85719
| | - Reena Zutshi
- Luceome Biotechnologies, 1665 E. 18th Street, Suite 106, Tucson, AZ 85719
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, NC 27599-3420
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Max-von-Laue-Straße 9, Goethe University Frankfurt, 60438 Frankfurt, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Straße 15, 60438 Frankfurt, Germany
- German Translational Cancer Network (DKTK) site Frankfurt/Mainz
- Frankfurt Cancer Institute (FCI), Paul-Ehrlich-Straße 42-44, 60596 Frankfurt am Main
| | - David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7264
| | - Timothy M. Willson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7264
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12
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Rodrigues DA, Pinheiro PSM, Fraga CAM. Multitarget Inhibition of Histone Deacetylase (HDAC) and Phosphatidylinositol-3-kinase (PI3K): Current and Future Prospects. ChemMedChem 2020; 16:448-457. [PMID: 33049098 DOI: 10.1002/cmdc.202000643] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/06/2020] [Indexed: 12/11/2022]
Abstract
The discovery of histone deacetylase (HDAC) inhibitors is a hot topic in the medicinal chemistry community regarding cancer research. This is related primarily to two factors: success in the clinic, e. g., the four FDA-approved HDAC inhibitors, and strong versatility to combine their pharmacophoric features to design new hybrid compounds with multitarget profiles. Thus, the selection of adequate pharmacophores to combine, i. e., combining targets that can result in a synergistic effect, is desirable, as it increases the probability of discovering a new useful therapeutic strategy. In this work, we highlight the design of multitarget HDAC/PI3K inhibitors. Although this approach is still in its early stages, many significant works have described the design and pharmacological evaluation of this new promising class of multitarget inhibitors, where compound CUDC-907, which is already in clinical trials, stands out. Therefore, the question emerges of whether there still space for the design and evaluation of new multitarget HDAC/PI3K inhibitors. When considering the selectivity profile of the described multitarget compounds, the answer appears to be in the affirmative, especially since the first examples of compounds with a certain selectivity profile only recently appeared in 2020.
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Affiliation(s)
- Daniel A Rodrigues
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, Brazil
| | - Pedro S M Pinheiro
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, Brazil.,Programa de Pós-Graduação em Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, Brazil
| | - Carlos A M Fraga
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, Brazil.,Programa de Pós-Graduação em Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, Brazil
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13
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Uko NE, Güner OF, Matesic DF, Bowen JP. Akt Pathway Inhibitors. Curr Top Med Chem 2020; 20:883-900. [DOI: 10.2174/1568026620666200224101808] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/24/2019] [Accepted: 12/24/2019] [Indexed: 12/14/2022]
Abstract
Cancer is a devastating disease that has plagued humans from ancient times to this day. After
decades of slow research progress, promising drug development, and the identification of new targets,
the war on cancer was launched, in 1972. The P13K/Akt pathway is a growth-regulating cellular signaling
pathway, which in many human cancers is over-activated. Studies have demonstrated that a decrease
in Akt activity by Akt inhibitors is associated with a reduction in tumor cell proliferation. There have
been several promising drug candidates that have been studied, including but not limited to ipatasertib
(RG7440), 1; afuresertib (GSK2110183), 2; uprosertib (GSK2141795), 3; capivasertib (AZD5363), 4;
which reportedly bind to the ATP active site and inhibit Akt activity, thus exerting cytotoxic and antiproliferative
activities against human cancer cells. For most of the compounds discussed in this review,
data from preclinical studies in various cancers suggest a mechanistic basis involving hyperactivated
Akt signaling. Allosteric inhibitors are also known to alter the activity of kinases. Perifosine (KRX-
0401), 5, an alkylphospholipid, is known as the first allosteric Akt inhibitor to enter clinical development
and is mechanistically characterized as a PH-domain dependent inhibitor, non-competitive with
ATP. This results in a reduction in Akt enzymatic and cellular activities. Other small molecule (MK-
2206, 6, PHT-427, Akti-1/2) inhibitors with a similar mechanism of action, alter Akt activity through the
suppression of cell growth mediated by the inhibition of Akt membrane localization and subsequent activation.
The natural product solenopsin has been identified as an inhibitor of Akt. A few promising solenopsin
derivatives have emerged through pharmacophore modeling, energy-based calculations, and
property predictions.
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Affiliation(s)
- Nne E. Uko
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University, Atlanta, GA 30341, United States
| | - Osman F. Güner
- Department of Chemistry and Physics, Santa Rosa Junior College, Santa Rosa, CA, United States
| | - Diane F. Matesic
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University, Atlanta, GA 30341, United States
| | - J. Phillip Bowen
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University, Atlanta, GA 30341, United States
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14
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IODVA1, a guanidinobenzimidazole derivative, targets Rac activity and Ras-driven cancer models. PLoS One 2020; 15:e0229801. [PMID: 32163428 PMCID: PMC7067412 DOI: 10.1371/journal.pone.0229801] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 02/13/2020] [Indexed: 12/17/2022] Open
Abstract
We report the synthesis and preliminary characterization of IODVA1, a potent small molecule that is active in xenograft mouse models of Ras-driven lung and breast cancers. In an effort to inhibit oncogenic Ras signaling, we combined in silico screening with inhibition of proliferation and colony formation of Ras-driven cells. NSC124205 fulfilled all criteria. HPLC analysis revealed that NSC124205 was a mixture of at least three compounds, from which IODVA1 was determined to be the active component. IODVA1 decreased 2D and 3D cell proliferation, cell spreading and ruffle and lamellipodia formation through downregulation of Rac activity. IODVA1 significantly impaired xenograft tumor growth of Ras-driven cancer cells with no observable toxicity. Immuno-histochemistry analysis of tumor sections suggests that cell death occurs by increased apoptosis. Our data suggest that IODVA1 targets Rac signaling to induce death of Ras-transformed cells. Therefore, IODVA1 holds promise as an anti-tumor therapeutic agent.
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15
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A small molecule inhibitor of PCSK9 that antagonizes LDL receptor binding via interaction with a cryptic PCSK9 binding groove. Bioorg Med Chem 2020; 28:115344. [DOI: 10.1016/j.bmc.2020.115344] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 01/17/2020] [Accepted: 01/23/2020] [Indexed: 12/11/2022]
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16
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Comprehensive structure-activity-relationship of azaindoles as highly potent FLT3 inhibitors. Bioorg Med Chem 2019; 27:692-699. [DOI: 10.1016/j.bmc.2019.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 12/13/2022]
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17
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Bagal SK, Andrews M, Bechle BM, Bian J, Bilsland J, Blakemore DC, Braganza JF, Bungay PJ, Corbett MS, Cronin CN, Cui JJ, Dias R, Flanagan NJ, Greasley SE, Grimley R, James K, Johnson E, Kitching L, Kraus ML, McAlpine I, Nagata A, Ninkovic S, Omoto K, Scales S, Skerratt SE, Sun J, Tran-Dubé M, Waldron GJ, Wang F, Warmus JS. Discovery of Potent, Selective, and Peripherally Restricted Pan-Trk Kinase Inhibitors for the Treatment of Pain. J Med Chem 2018; 61:6779-6800. [PMID: 29944371 DOI: 10.1021/acs.jmedchem.8b00633] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Hormones of the neurotrophin family, nerve growth factor (NGF), brain derived neurotrophic factor (BDNF), neurotrophin 3 (NT3), and neurotrophin 4 (NT4), are known to activate the family of Tropomyosin receptor kinases (TrkA, TrkB, and TrkC). Moreover, inhibition of the TrkA kinase pathway in pain has been clinically validated by the NGF antibody tanezumab, leading to significant interest in the development of small molecule inhibitors of TrkA. Furthermore, Trk inhibitors having an acceptable safety profile will require minimal brain availability. Herein, we discuss the discovery of two potent, selective, peripherally restricted, efficacious, and well-tolerated series of pan-Trk inhibitors which successfully delivered three candidate quality compounds 10b, 13b, and 19. All three compounds are predicted to possess low metabolic clearance in human that does not proceed via aldehyde oxidase-catalyzed reactions, thus addressing the potential clearance prediction liability associated with our current pan-Trk development candidate PF-06273340.
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Affiliation(s)
- Sharan K Bagal
- Worldwide Medicinal Chemistry , Pfizer Worldwide R&D U.K. , The Portway Building, Granta Park , Cambridge CB21 6GS , U.K
| | - Mark Andrews
- Pfizer Worldwide R&D U.K. , Sandwich , Kent CT13 9NJ , U.K
| | - Bruce M Bechle
- Pfizer Worldwide R&D, Groton Laboratories , Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Jianwei Bian
- Pfizer Worldwide R&D, Groton Laboratories , Eastern Point Road , Groton , Connecticut 06340 , United States
| | - James Bilsland
- Pfizer Worldwide R&D U.K. , The Portway Building, Granta Park , Cambridge CB21 6GS , U.K
| | - David C Blakemore
- Worldwide Medicinal Chemistry , Pfizer Worldwide R&D U.K. , The Portway Building, Granta Park , Cambridge CB21 6GS , U.K
| | - John F Braganza
- Pfizer Worldwide R&D, La Jolla Laboratories , 10770 Science Center Drive , San Diego , California 92121 , United States
| | - Peter J Bungay
- Pharmacokinetics, Dynamics & Metabolism , Pfizer Worldwide R&D U.K. , The Portway Building, Granta Park , Cambridge CB21 6GS , U.K
| | - Matthew S Corbett
- Pfizer Worldwide R&D, Groton Laboratories , Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Ciaran N Cronin
- Pfizer Worldwide R&D, La Jolla Laboratories , 10770 Science Center Drive , San Diego , California 92121 , United States
| | - Jingrong Jean Cui
- Pfizer Worldwide R&D, La Jolla Laboratories , 10770 Science Center Drive , San Diego , California 92121 , United States
| | - Rebecca Dias
- Pfizer Worldwide R&D U.K. , The Portway Building, Granta Park , Cambridge CB21 6GS , U.K
| | - Neil J Flanagan
- Pfizer Worldwide R&D U.K. , The Portway Building, Granta Park , Cambridge CB21 6GS , U.K
| | - Samantha E Greasley
- Pfizer Worldwide R&D, La Jolla Laboratories , 10770 Science Center Drive , San Diego , California 92121 , United States
| | - Rachel Grimley
- Pfizer Worldwide R&D U.K. , The Portway Building, Granta Park , Cambridge CB21 6GS , U.K
| | - Kim James
- Peakdale Molecular , Discovery Park House, Ramsgate Road , Sandwich CT13 9ND , U.K
| | - Eric Johnson
- Pfizer Worldwide R&D, La Jolla Laboratories , 10770 Science Center Drive , San Diego , California 92121 , United States
| | - Linda Kitching
- Pfizer Worldwide R&D U.K. , The Portway Building, Granta Park , Cambridge CB21 6GS , U.K
| | - Michelle L Kraus
- Pfizer Worldwide R&D, La Jolla Laboratories , 10770 Science Center Drive , San Diego , California 92121 , United States
| | - Indrawan McAlpine
- Pfizer Worldwide R&D, La Jolla Laboratories , 10770 Science Center Drive , San Diego , California 92121 , United States
| | - Asako Nagata
- Pfizer Worldwide R&D, La Jolla Laboratories , 10770 Science Center Drive , San Diego , California 92121 , United States
| | - Sacha Ninkovic
- Pfizer Worldwide R&D, La Jolla Laboratories , 10770 Science Center Drive , San Diego , California 92121 , United States
| | - Kiyoyuki Omoto
- Worldwide Medicinal Chemistry , Pfizer Worldwide R&D U.K. , The Portway Building, Granta Park , Cambridge CB21 6GS , U.K
| | - Stephanie Scales
- Pfizer Worldwide R&D, La Jolla Laboratories , 10770 Science Center Drive , San Diego , California 92121 , United States
| | - Sarah E Skerratt
- Worldwide Medicinal Chemistry , Pfizer Worldwide R&D U.K. , The Portway Building, Granta Park , Cambridge CB21 6GS , U.K
| | - Jianmin Sun
- Pfizer Worldwide R&D, Groton Laboratories , Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Michelle Tran-Dubé
- Pfizer Worldwide R&D, La Jolla Laboratories , 10770 Science Center Drive , San Diego , California 92121 , United States
| | - Gareth J Waldron
- Pfizer Worldwide R&D U.K. , The Portway Building, Granta Park , Cambridge CB21 6GS , U.K
| | - Fen Wang
- Pfizer Worldwide R&D, La Jolla Laboratories , 10770 Science Center Drive , San Diego , California 92121 , United States
| | - Joseph S Warmus
- Pfizer Worldwide R&D, Groton Laboratories , Eastern Point Road , Groton , Connecticut 06340 , United States
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18
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Ung PMU, Rahman R, Schlessinger A. Redefining the Protein Kinase Conformational Space with Machine Learning. Cell Chem Biol 2018; 25:916-924.e2. [PMID: 29861272 DOI: 10.1016/j.chembiol.2018.05.002] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/28/2018] [Accepted: 05/01/2018] [Indexed: 02/07/2023]
Abstract
Protein kinases are dynamic, adopting different conformational states that are critical for their catalytic activity. We assess a range of structural features derived from the conserved αC helix and DFG motif to define the conformational space of the catalytic domain of protein kinases. We then construct Kinformation, a random forest classifier, to annotate the conformation of 3,708 kinase structures in the PDB. Our classification scheme captures known active and inactive kinase conformations and defines an additional conformational state, thereby refining the current understanding of the kinase conformational space. Furthermore, network analysis of the small molecules recognized by each conformation captures chemical substructures that are associated with each conformation type. Our description of the kinase conformational space is expected to improve modeling of protein kinase structures, as well as guide the development of conformation-specific kinase inhibitors with optimal pharmacological profiles.
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Affiliation(s)
- Peter Man-Un Ung
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Rayees Rahman
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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19
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Aouidate A, Ghaleb A, Ghamali M, Chtita S, Ousaa A, Choukrad M, Sbai A, Bouachrine M, Lakhlifi T. Structural basis of pyrazolopyrimidine derivatives as CAMKIIδ kinase inhibitors: insights from 3D QSAR, docking studies and in silico ADMET evaluation. CHEMICAL PAPERS 2018. [DOI: 10.1007/s11696-018-0510-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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20
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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: 5.7] [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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21
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Affiliation(s)
- Peng-Cheng Lv
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing P. R. China
- Nanjing Institute for the Comprehensive Utilization of Wild Plant, Nanjing, P. R. China
| | - Ai-Qin Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing P. R. China
- Nanjing Institute for the Comprehensive Utilization of Wild Plant, Nanjing, P. R. China
| | - Wei-Ming Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing P. R. China
- Nanjing Institute for the Comprehensive Utilization of Wild Plant, Nanjing, P. R. China
| | - Hai-Liang Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing P. R. China
- Nanjing Institute for the Comprehensive Utilization of Wild Plant, Nanjing, P. R. China
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22
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Mukherjee P, Bentzien J, Bosanac T, Mao W, Burke M, Muegge I. Kinase Crystal Miner: A Powerful Approach to Repurposing 3D Hinge Binding Fragments and Its Application to Finding Novel Bruton Tyrosine Kinase Inhibitors. J Chem Inf Model 2017; 57:2152-2160. [DOI: 10.1021/acs.jcim.7b00213] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Prasenjit Mukherjee
- Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877-0368, United States
| | - Jörg Bentzien
- Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877-0368, United States
| | - Todd Bosanac
- Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877-0368, United States
| | - Wang Mao
- Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877-0368, United States
| | - Michael Burke
- Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877-0368, United States
| | - Ingo Muegge
- Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877-0368, United States
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23
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Johannessen L, Sundberg TB, O'Connell DJ, Kolde R, Berstler J, Billings KJ, Khor B, Seashore-Ludlow B, Fassl A, Russell CN, Latorre IJ, Jiang B, Graham DB, Perez JR, Sicinski P, Phillips AJ, Schreiber SL, Gray NS, Shamji AF, Xavier RJ. Small-molecule studies identify CDK8 as a regulator of IL-10 in myeloid cells. Nat Chem Biol 2017; 13:1102-1108. [PMID: 28805801 DOI: 10.1038/nchembio.2458] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 07/17/2017] [Indexed: 12/27/2022]
Abstract
Enhancing production of the anti-inflammatory cytokine interleukin-10 (IL-10) is a promising strategy to suppress pathogenic inflammation. To identify new mechanisms regulating IL-10 production, we conducted a phenotypic screen for small molecules that enhance IL-10 secretion from activated dendritic cells. Mechanism-of-action studies using a prioritized hit from the screen, BRD6989, identified the Mediator-associated kinase CDK8, and its paralog CDK19, as negative regulators of IL-10 production during innate immune activation. The ability of BRD6989 to upregulate IL-10 is recapitulated by multiple, structurally differentiated CDK8 and CDK19 inhibitors and requires an intact cyclin C-CDK8 complex. Using a highly parallel pathway reporter assay, we identified a role for enhanced AP-1 activity in IL-10 potentiation following CDK8 and CDK19 inhibition, an effect associated with reduced phosphorylation of a negative regulatory site on c-Jun. These findings identify a function for CDK8 and CDK19 in regulating innate immune activation and suggest that these kinases may warrant consideration as therapeutic targets for inflammatory disorders.
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Affiliation(s)
- Liv Johannessen
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Thomas B Sundberg
- Center for the Development of Therapeutics, Broad Institute, Cambridge, Massachusetts, USA
| | - Daniel J O'Connell
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Raivo Kolde
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - James Berstler
- Center for the Development of Therapeutics, Broad Institute, Cambridge, Massachusetts, USA
| | - Katelyn J Billings
- Department of Chemistry, Yale University, New Haven, Connecticut, USA.,Center for the Science of Therapeutics, Broad Institute, Cambridge, Massachusetts, USA
| | - Bernard Khor
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | - Anne Fassl
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Caitlin N Russell
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Isabel J Latorre
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Baishan Jiang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Daniel B Graham
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA.,Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jose R Perez
- Center for the Development of Therapeutics, Broad Institute, Cambridge, Massachusetts, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew J Phillips
- Center for the Development of Therapeutics, Broad Institute, Cambridge, Massachusetts, USA
| | - Stuart L Schreiber
- Center for the Science of Therapeutics, Broad Institute, Cambridge, Massachusetts, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Cambridge, Massachusetts, USA
| | - Nathanael S Gray
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Alykhan F Shamji
- Center for the Science of Therapeutics, Broad Institute, Cambridge, Massachusetts, USA
| | - Ramnik J Xavier
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.,Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, Massachusetts, USA
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24
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Narayanan D, Gani OABSM, Gruber FXE, Engh RA. Data driven polypharmacological drug design for lung cancer: analyses for targeting ALK, MET, and EGFR. J Cheminform 2017; 9:43. [PMID: 29086093 PMCID: PMC5496928 DOI: 10.1186/s13321-017-0229-8] [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: 10/30/2016] [Accepted: 06/18/2017] [Indexed: 12/14/2022] Open
Abstract
Drug design of protein kinase inhibitors is now greatly enabled by thousands of publicly available X-ray structures, extensive ligand binding data, and optimized scaffolds coming off patent. The extensive data begin to enable design against a spectrum of targets (polypharmacology); however, the data also reveal heterogeneities of structure, subtleties of chemical interactions, and apparent inconsistencies between diverse data types. As a result, incorporation of all relevant data requires expert choices to combine computational and informatics methods, along with human insight. Here we consider polypharmacological targeting of protein kinases ALK, MET, and EGFR (and its drug resistant mutant T790M) in non small cell lung cancer as an example. Both EGFR and ALK represent sources of primary oncogenic lesions, while drug resistance arises from MET amplification and EGFR mutation. A drug which inhibits these targets will expand relevant patient populations and forestall drug resistance. Crizotinib co-targets ALK and MET. Analysis of the crystal structures reveals few shared interaction types, highlighting proton-arene and key CH–O hydrogen bonding interactions. These are not typically encoded into molecular mechanics force fields. Cheminformatics analyses of binding data show EGFR to be dissimilar to ALK and MET, but its structure shows how it may be co-targeted with the addition of a covalent trap. This suggests a strategy for the design of a focussed chemical library based on a pan-kinome scaffold. Tests of model compounds show these to be compatible with the goal of ALK, MET, and EGFR polypharmacology.
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Affiliation(s)
- Dilip Narayanan
- The Norwegian Structural Biology Center, Department of Chemistry, Faculty of Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Osman A B S M Gani
- The Norwegian Structural Biology Center, Department of Chemistry, Faculty of Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Franz X E Gruber
- The Norwegian Structural Biology Center, Department of Chemistry, Faculty of Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Richard A Engh
- The Norwegian Structural Biology Center, Department of Chemistry, Faculty of Science, UiT The Arctic University of Norway, Tromsø, Norway.
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25
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Xu D, Li L, Zhou D, Liu D, Hudmon A, Meroueh SO. Structure-Based Target-Specific Screening Leads to Small-Molecule CaMKII Inhibitors. ChemMedChem 2017; 12:660-677. [PMID: 28371191 PMCID: PMC5554713 DOI: 10.1002/cmdc.201600636] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/23/2017] [Indexed: 02/06/2023]
Abstract
Target-specific scoring methods are more commonly used to identify small-molecule inhibitors among compounds docked to a target of interest. Top candidates that emerge from these methods have rarely been tested for activity and specificity across a family of proteins. In this study we docked a chemical library into CaMKIIδ, a member of the Ca2+ /calmodulin (CaM)-dependent protein kinase (CaMK) family, and re-scored the resulting protein-compound structures using Support Vector Machine SPecific (SVMSP), a target-specific method that we developed previously. Among the 35 selected candidates, three hits were identified, such as quinazoline compound 1 (KIN-1; N4-[7-chloro-2-[(E)-styryl]quinazolin-4-yl]-N1,N1-diethylpentane-1,4-diamine), which was found to inhibit CaMKIIδ kinase activity at single-digit micromolar IC50 . Activity across the kinome was assessed by profiling analogues of 1, namely 6 (KIN-236; N4-[7-chloro-2-[(E)-2-(2-chloro-4,5-dimethoxyphenyl)vinyl]quinazolin-4-yl]-N1,N1-diethylpentane-1,4-diamine), and an analogue of hit compound 2 (KIN-15; 2-[4-[(E)-[(5-bromobenzofuran-2-carbonyl)hydrazono]methyl]-2-chloro-6-methoxyphenoxy]acetic acid), namely 14 (KIN-332; N-[(E)-[4-(2-anilino-2-oxoethoxy)-3-chlorophenyl]methyleneamino]benzofuran-2-carboxamide), against 337 kinases. Interestingly, for compound 6, CaMKIIδ and homologue CaMKIIγ were among the top ten targets. Among the top 25 targets of 6, IC50 values ranged from 5 to 22 μm. Compound 14 was found to be not specific toward CaMKII kinases, but it does inhibit two kinases with sub-micromolar IC50 values among the top 25. Derivatives of 1 were tested against several kinases including several members of the CaMK family. These data afforded a limited structure-activity relationship study. Molecular dynamics simulations with explicit solvent followed by end-point MM-GBSA free-energy calculations revealed strong engagement of specific residues within the ATP binding pocket, and also changes in the dynamics as a result of binding. This work suggests that target-specific scoring approaches such as SVMSP may hold promise for the identification of small-molecule kinase inhibitors that exhibit some level of specificity toward the target of interest across a large number of proteins.
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Affiliation(s)
- David Xu
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indianapolis, IN, 46202, USA
| | - Liwei Li
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Van Nuys Medical Science Building, MS 4023, 635 Barnhill Drive, Indianapolis, IN, 46202-5122, USA
| | - Donghui Zhou
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Van Nuys Medical Science Building, MS 4023, 635 Barnhill Drive, Indianapolis, IN, 46202-5122, USA
| | - Degang Liu
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Van Nuys Medical Science Building, MS 4023, 635 Barnhill Drive, Indianapolis, IN, 46202-5122, USA
| | - Andy Hudmon
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Van Nuys Medical Science Building, MS 4023, 635 Barnhill Drive, Indianapolis, IN, 46202-5122, USA
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Samy O Meroueh
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Van Nuys Medical Science Building, MS 4023, 635 Barnhill Drive, Indianapolis, IN, 46202-5122, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Indiana University Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
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26
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Koyama T, Yamaotsu N, Nakagome I, Ozawa SI, Yoshida T, Hayakawa D, Hirono S. Multi-step virtual screening to develop selective DYRK1A inhibitors. J Mol Graph Model 2017; 72:229-239. [PMID: 28129593 DOI: 10.1016/j.jmgm.2017.01.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 01/12/2017] [Accepted: 01/12/2017] [Indexed: 11/29/2022]
Abstract
Developing selective inhibitors for a particular kinase remains a major challenge in kinase-targeted drug discovery. Here we performed a multi-step virtual screening for dual-specificity tyrosine-phosphorylation-regulated kinase 1A (DYRK1A) inhibitors by focusing on the selectivity for DYRK1A over cyclin-dependent kinase 5 (CDK5). To examine the key factors contributing to the selectivity, we constructed logistic regression models to discriminate between actives and inactives for DYRK1A and CDK5, respectively, using residue-based binding free energies. The residue-based parameters were calculated by molecular mechanics-generalized Born surface area (MM-GBSA) decomposition methods for kinase-ligand complexes modeled by computer ligand docking. Based on the findings from the logistic regression models, we built a three-dimensional (3D) pharmacophore model and chose filter criteria for the multi-step virtual screening. The virtual hit compounds obtained from the screening were assessed for their inhibitory activities against DYRK1A and CDK5 by in vitro assay. Our screening identified two novel selective DYRK1A inhibitors with IC50 values of several μM for DYRK1A and >100μM for CDK5, which can be further optimized to develop more potent selective DYRK1A inhibitors.
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Affiliation(s)
- Tomoko Koyama
- School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan.
| | - Noriyuki Yamaotsu
- School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Izumi Nakagome
- School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Shin-Ichiro Ozawa
- School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Tomoki Yoshida
- School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Daichi Hayakawa
- School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Shuichi Hirono
- School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan.
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27
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Synthesis of (3-(2-Aminopyrimidin-4-yl)-4-hydroxyphenyl)phenyl Methanone Analogues as Inhibitors of Vascular Endothelial Growth Factor Receptor-2 Kinase. B KOREAN CHEM SOC 2017. [DOI: 10.1002/bkcs.11049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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28
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Farand J, Mai N, Chandrasekhar J, Newby ZE, Van Veldhuizen J, Loyer-Drew J, Venkataramani C, Guerrero J, Kwok A, Li N, Zherebina Y, Wilbert S, Zablocki J, Phillips G, Watkins WJ, Mourey R, Notte GT. Selectivity switch between FAK and Pyk2: Macrocyclization of FAK inhibitors improves Pyk2 potency. Bioorg Med Chem Lett 2016; 26:5926-5930. [PMID: 27876318 DOI: 10.1016/j.bmcl.2016.10.092] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 10/30/2016] [Accepted: 10/31/2016] [Indexed: 01/24/2023]
Abstract
Herein, we describe the synthesis of Pyk2 inhibitors via macrocyclization of FAK and dual Pyk2-FAK inhibitors. We identified macrocycle 25a as a highly potent Pyk2 inhibitor (IC50=0.7nM), with ∼175-fold improvement in Pyk2 potency as compared to its acyclic counterpart. In many cases, macrocyclization improved Pyk2 potency while weakening FAK potency, thereby improving the Pyk2/FAK selectivity ratio for this structural class of inhibitors. Various macrocyclic linkers were studied in an attempt to optimize Pyk2 selectivity. We observed macrocyclic atropisomerism during the synthesis of 19-membered macrocycles 10a-d, and successfully obtained crystallographic evidence of one atropisomer (10a-AtropB) preferentially bound to Pyk2.
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Affiliation(s)
- Julie Farand
- Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA.
| | - Nicholas Mai
- Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Jayaraman Chandrasekhar
- Department of Structural Chemistry, Gilead Sciences, Inc., 199 East Blaine Street, Seattle, WA 98102, USA
| | - Zachary E Newby
- Department of Structural Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Josh Van Veldhuizen
- Department of Medicinal Chemistry, Gilead Sciences, Inc., 199 East Blaine Street, Seattle, WA 98102, USA
| | - Jennifer Loyer-Drew
- Department of Medicinal Chemistry, Gilead Sciences, Inc., 199 East Blaine Street, Seattle, WA 98102, USA
| | - Chandrasekar Venkataramani
- Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Juan Guerrero
- Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Amy Kwok
- Department of Biology, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Ning Li
- Department of Biology, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Yelena Zherebina
- Department of Biology, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Sibylle Wilbert
- Department of Drug Metabolism, Gilead Sciences, Inc., 199 East Blaine Street, Seattle, WA 98102, USA
| | - Jeff Zablocki
- Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Gary Phillips
- Department of Medicinal Chemistry, Gilead Sciences, Inc., 199 East Blaine Street, Seattle, WA 98102, USA
| | - William J Watkins
- Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Robert Mourey
- Department of Biology, Gilead Sciences, Inc., 199 East Blaine Street, Seattle, WA 98102, USA
| | - Gregory T Notte
- Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
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29
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Wang Q, Amato SP, Rubitski DM, Hayward MM, Kormos BL, Verhoest PR, Xu L, Brandon NJ, Ehlers MD. Identification of Phosphorylation Consensus Sequences and Endogenous Neuronal Substrates of the Psychiatric Risk Kinase TNIK. J Pharmacol Exp Ther 2016; 356:410-23. [PMID: 26645429 DOI: 10.1124/jpet.115.229880] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 12/01/2015] [Indexed: 12/28/2022] Open
Abstract
Traf2- and Nck-interacting kinase (TNIK) is a serine/threonine kinase highly expressed in the brain and enriched in the postsynaptic density of glutamatergic synapses in the mammalian brain. Accumulating genetic evidence and functional data have implicated TNIK as a risk factor for psychiatric disorders. However, the endogenous substrates of TNIK in neurons are unknown. Here, we describe a novel selective small molecule inhibitor of the TNIK kinase family. Using this inhibitor, we report the identification of endogenous neuronal TNIK substrates by immunoprecipitation with a phosphomotif antibody followed by mass spectrometry. Phosphorylation consensus sequences were defined by phosphopeptide sequence analysis. Among the identified substrates were members of the delta-catenin family including p120-catenin, δ-catenin, and armadillo repeat gene deleted in velo-cardio-facial syndrome (ARVCF), each of which is linked to psychiatric or neurologic disorders. Using p120-catenin as a representative substrate, we show TNIK-induced p120-catenin phosphorylation in cells requires intact kinase activity and phosphorylation of TNIK at T181 and T187 in the activation loop. Addition of the small molecule TNIK inhibitor or knocking down TNIK by two shRNAs reduced endogenous p120-catenin phosphorylation in cells. Together, using a TNIK inhibitor and phosphomotif antibody, we identify endogenous substrates of TNIK in neurons, define consensus sequences for TNIK, and suggest signaling pathways by which TNIK influences synaptic development and function linked to psychiatric and neurologic disorders.
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Affiliation(s)
- Qi Wang
- Neuroscience & Pain Research Unit, BioTherapeutics Research and Development, Pfizer Inc. Cambridge, Massachusetts (Q.W., S.P.A., D.M.R., N.J.B., M.D.E.); Center of Chemistry Innovation and Excellence, Pfizer Inc., Groton, Connecticut (M.M.H.); Neuroscience Medicinal Chemistry, Pfizer Inc., Cambridge, Massachusetts (B.L.K., P.R.V.);and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts (L.X.)
| | - Stephen P Amato
- Neuroscience & Pain Research Unit, BioTherapeutics Research and Development, Pfizer Inc. Cambridge, Massachusetts (Q.W., S.P.A., D.M.R., N.J.B., M.D.E.); Center of Chemistry Innovation and Excellence, Pfizer Inc., Groton, Connecticut (M.M.H.); Neuroscience Medicinal Chemistry, Pfizer Inc., Cambridge, Massachusetts (B.L.K., P.R.V.);and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts (L.X.)
| | - David M Rubitski
- Neuroscience & Pain Research Unit, BioTherapeutics Research and Development, Pfizer Inc. Cambridge, Massachusetts (Q.W., S.P.A., D.M.R., N.J.B., M.D.E.); Center of Chemistry Innovation and Excellence, Pfizer Inc., Groton, Connecticut (M.M.H.); Neuroscience Medicinal Chemistry, Pfizer Inc., Cambridge, Massachusetts (B.L.K., P.R.V.);and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts (L.X.)
| | - Matthew M Hayward
- Neuroscience & Pain Research Unit, BioTherapeutics Research and Development, Pfizer Inc. Cambridge, Massachusetts (Q.W., S.P.A., D.M.R., N.J.B., M.D.E.); Center of Chemistry Innovation and Excellence, Pfizer Inc., Groton, Connecticut (M.M.H.); Neuroscience Medicinal Chemistry, Pfizer Inc., Cambridge, Massachusetts (B.L.K., P.R.V.);and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts (L.X.)
| | - Bethany L Kormos
- Neuroscience & Pain Research Unit, BioTherapeutics Research and Development, Pfizer Inc. Cambridge, Massachusetts (Q.W., S.P.A., D.M.R., N.J.B., M.D.E.); Center of Chemistry Innovation and Excellence, Pfizer Inc., Groton, Connecticut (M.M.H.); Neuroscience Medicinal Chemistry, Pfizer Inc., Cambridge, Massachusetts (B.L.K., P.R.V.);and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts (L.X.)
| | - Patrick R Verhoest
- Neuroscience & Pain Research Unit, BioTherapeutics Research and Development, Pfizer Inc. Cambridge, Massachusetts (Q.W., S.P.A., D.M.R., N.J.B., M.D.E.); Center of Chemistry Innovation and Excellence, Pfizer Inc., Groton, Connecticut (M.M.H.); Neuroscience Medicinal Chemistry, Pfizer Inc., Cambridge, Massachusetts (B.L.K., P.R.V.);and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts (L.X.)
| | - Lan Xu
- Neuroscience & Pain Research Unit, BioTherapeutics Research and Development, Pfizer Inc. Cambridge, Massachusetts (Q.W., S.P.A., D.M.R., N.J.B., M.D.E.); Center of Chemistry Innovation and Excellence, Pfizer Inc., Groton, Connecticut (M.M.H.); Neuroscience Medicinal Chemistry, Pfizer Inc., Cambridge, Massachusetts (B.L.K., P.R.V.);and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts (L.X.)
| | - Nicholas J Brandon
- Neuroscience & Pain Research Unit, BioTherapeutics Research and Development, Pfizer Inc. Cambridge, Massachusetts (Q.W., S.P.A., D.M.R., N.J.B., M.D.E.); Center of Chemistry Innovation and Excellence, Pfizer Inc., Groton, Connecticut (M.M.H.); Neuroscience Medicinal Chemistry, Pfizer Inc., Cambridge, Massachusetts (B.L.K., P.R.V.);and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts (L.X.)
| | - Michael D Ehlers
- Neuroscience & Pain Research Unit, BioTherapeutics Research and Development, Pfizer Inc. Cambridge, Massachusetts (Q.W., S.P.A., D.M.R., N.J.B., M.D.E.); Center of Chemistry Innovation and Excellence, Pfizer Inc., Groton, Connecticut (M.M.H.); Neuroscience Medicinal Chemistry, Pfizer Inc., Cambridge, Massachusetts (B.L.K., P.R.V.);and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts (L.X.)
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30
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Kinase hinge binding scaffolds and their hydrogen bond patterns. Bioorg Med Chem 2015; 23:6520-7. [DOI: 10.1016/j.bmc.2015.08.006] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/24/2015] [Accepted: 08/08/2015] [Indexed: 11/20/2022]
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31
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Zhao H, Caflisch A. Current kinase inhibitors cover a tiny fraction of fragment space. Bioorg Med Chem Lett 2015; 25:2372-6. [PMID: 25911301 DOI: 10.1016/j.bmcl.2015.04.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 04/02/2015] [Accepted: 04/04/2015] [Indexed: 01/18/2023]
Abstract
We analyze the chemical space coverage of kinase inhibitors in the public domain from a fragment point of view. A set of 26,668 kinase inhibitors from the ChEMBL database of bioactive molecules were decomposed automatically by fragmentation at rotatable bonds. Remarkably, about half of the resulting 10,302 fragments originate from inaccessible libraries, as they are not present in commercially available compounds. By mapping to the established kinase pharmacophore models, privileged fragments in sub-pockets are identified, for example, the 5681 ring-containing fragments capable of forming bi-dentate hydrogen bonds with the hinge region in the ATP binding site. Surprisingly, hinge-binding fragments in current kinase inhibitors cover only 1% of the potential hinge-binders obtained by decomposing a library of nearly 7.5 million commercially available compounds, which indicates that a large fraction of chemical space is unexplored.
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Affiliation(s)
- Hongtao Zhao
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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32
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Pirard B, Ertl P. Evaluation of a semi-automated workflow for fragment growing. J Chem Inf Model 2015; 55:180-93. [PMID: 25514394 DOI: 10.1021/ci5006355] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Intelligent Automatic Design (IADE) is an expert system developed at Novartis to identify nonclassical bioisosteres. In addition to bioisostere searching, one could also use IADE to grow a fragment bound to a protein. Here we report an evaluation of IADE as a tool for fragment growing. Three examples from the literature served as test cases. In all three cases, IADE generated close analogues of the published compounds and reproduced their crystallographic binding modes. This exercise validated the use of the IADE system for fragment growing. We have also gained experience in optimizing the performance of IADE for this type of application.
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Affiliation(s)
- Bernard Pirard
- Novartis Institutes for BioMedical Research , Novartis Campus, CH-4056 Basel, Switzerland
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33
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Goldberg FW, Kettle JG, Kogej T, Perry MW, Tomkinson NP. Designing novel building blocks is an overlooked strategy to improve compound quality. Drug Discov Today 2015; 20:11-7. [DOI: 10.1016/j.drudis.2014.09.023] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 07/28/2014] [Accepted: 09/26/2014] [Indexed: 12/19/2022]
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34
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Henderson JL, Kormos BL, Hayward MM, Coffman KJ, Jasti J, Kurumbail RG, Wager TT, Verhoest PR, Noell GS, Chen Y, Needle E, Berger Z, Steyn SJ, Houle C, Hirst WD, Galatsis P. Discovery and preclinical profiling of 3-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl]benzonitrile (PF-06447475), a highly potent, selective, brain penetrant, and in vivo active LRRK2 kinase inhibitor. J Med Chem 2014; 58:419-32. [PMID: 25353650 DOI: 10.1021/jm5014055] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Leucine rich repeat kinase 2 (LRRK2) has been genetically linked to Parkinson's disease (PD) by genome-wide association studies (GWAS). The most common LRRK2 mutation, G2019S, which is relatively rare in the total population, gives rise to increased kinase activity. As such, LRRK2 kinase inhibitors are potentially useful in the treatment of PD. We herein disclose the discovery and optimization of a novel series of potent LRRK2 inhibitors, focusing on improving kinome selectivity using a surrogate crystallography approach. This resulted in the identification of 14 (PF-06447475), a highly potent, brain penetrant and selective LRRK2 inhibitor which has been further profiled in in vivo safety and pharmacodynamic studies.
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Affiliation(s)
- Jaclyn L Henderson
- Worldwide Medicinal Chemistry, ‡Neuroscience Research Unit, and §Pharmacokinetics, Dynamics, and Metabolism, Pfizer Worldwide R&D , 610 Main Street, Cambridge, Massachusetts 02139, United States
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Chakravarti B, Akhtar T, Rai B, Yadav M, Akhtar Siddiqui J, Dhar Dwivedi SK, Thakur R, Singh AK, Singh AK, Kumar H, Khan K, Pal S, Rath SK, Lal J, Konwar R, Trivedi AK, Datta D, Mishra DP, Godbole MM, Sanyal S, Chattopadhyay N, Kumar A. Thioaryl Naphthylmethanone Oxime Ether Analogs as Novel Anticancer Agents. J Med Chem 2014; 57:8010-25. [DOI: 10.1021/jm500873e] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Madan Madhav Godbole
- Department
of Molecular Medicine and Biotechnology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, 226014, India
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