1
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Wah Tan Z, Tee WV, Berezovsky IN. Learning about allosteric drugs and ways to design them. J Mol Biol 2022; 434:167692. [PMID: 35738428 DOI: 10.1016/j.jmb.2022.167692] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 05/23/2022] [Accepted: 06/15/2022] [Indexed: 11/16/2022]
Abstract
While the accelerating quest for precision medicine requires new individually targeting and selective drugs, and the ability to work with so-called undruggable targets, the realm of allosteric drugs meeting this need remains largely uncharted. Generalizing the observations on two major drug targets with widely observed inherent allostery, GPCRs and kinases, we describe and discuss basic allosteric modes of action that are universally applicable in all types of structures and functions. Using examples of Class A GPCRs and CMGC protein kinases, we show how Allosteric Signalling and Probing Fingerprints can be used to identify potential allosteric sites and reveal effector-leads that may serve as a starting point for the development of allosteric drugs targeting these regulatory sites. A set of distinct characteristics of allosteric ligands was established, which highlights the versatility of their design and make them advantageous before their orthosteric counterparts in personalized medicine. We argue that rational design of allosteric drugs should begin with the search for latent sites or design of non-natural binding sites followed by fragment-based design of allosteric ligands and by the mutual adjustment of the site-ligand pair in order to achieve required effects. On the basis of the perturbative nature and reversibility of allosteric communication, we propose a generic protocol for computational design of allosteric effectors, enabling also the allosteric tuning of biologics, in obtaining allosteric control over protein functions.
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Affiliation(s)
- Zhen Wah Tan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671
| | - Wei-Ven Tee
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671
| | - Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671; Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117579, Singapore.
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2
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Miller D, Reuillon T, Molyneux L, Blackburn T, Cook SJ, Edwards N, Endicott JA, Golding BT, Griffin RJ, Hardcastle I, Harnor SJ, Heptinstall A, Lochhead P, Martin MP, Martin NC, Myers S, Newell DR, Noble RA, Phillips N, Rigoreau L, Thomas H, Tucker JA, Wang LZ, Waring MJ, Wong AC, Wedge SR, Noble MEM, Cano C. Parallel Optimization of Potency and Pharmacokinetics Leading to the Discovery of a Pyrrole Carboxamide ERK5 Kinase Domain Inhibitor. J Med Chem 2022; 65:6513-6540. [PMID: 35468293 PMCID: PMC9109144 DOI: 10.1021/acs.jmedchem.1c01756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Indexed: 11/29/2022]
Abstract
The nonclassical extracellular signal-related kinase 5 (ERK5) mitogen-activated protein kinase pathway has been implicated in increased cellular proliferation, migration, survival, and angiogenesis; hence, ERK5 inhibition may be an attractive approach for cancer treatment. However, the development of selective ERK5 inhibitors has been challenging. Previously, we described the development of a pyrrole carboxamide high-throughput screening hit into a selective, submicromolar inhibitor of ERK5 kinase activity. Improvement in the ERK5 potency was necessary for the identification of a tool ERK5 inhibitor for target validation studies. Herein, we describe the optimization of this series to identify nanomolar pyrrole carboxamide inhibitors of ERK5 incorporating a basic center, which suffered from poor oral bioavailability. Parallel optimization of potency and in vitro pharmacokinetic parameters led to the identification of a nonbasic pyrazole analogue with an optimal balance of ERK5 inhibition and oral exposure.
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Affiliation(s)
- Duncan
C. Miller
- Cancer
Research UK Newcastle Drug Discovery Unit, Newcastle University Centre
for Cancer, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K.
| | - Tristan Reuillon
- Cancer
Research UK Newcastle Drug Discovery Unit, Newcastle University Centre
for Cancer, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K.
| | - Lauren Molyneux
- Cancer
Research UK Newcastle Drug Discovery Unit, Newcastle University Centre
for Cancer, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K.
| | - Timothy Blackburn
- Cancer
Research UK Newcastle Drug Discovery Unit, Newcastle University Centre
for Cancer, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K.
| | - Simon J. Cook
- Signalling
Laboratory, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, U.K.
| | - Noel Edwards
- Cancer
Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Paul O’Gorman Building, Medical School,
Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Jane A. Endicott
- Cancer
Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Paul O’Gorman Building, Medical School,
Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Bernard T. Golding
- Cancer
Research UK Newcastle Drug Discovery Unit, Newcastle University Centre
for Cancer, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K.
| | - Roger J. Griffin
- Cancer
Research UK Newcastle Drug Discovery Unit, Newcastle University Centre
for Cancer, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K.
| | - Ian Hardcastle
- Cancer
Research UK Newcastle Drug Discovery Unit, Newcastle University Centre
for Cancer, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K.
| | - Suzannah J. Harnor
- Cancer
Research UK Newcastle Drug Discovery Unit, Newcastle University Centre
for Cancer, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K.
| | - Amy Heptinstall
- Cancer
Research UK Newcastle Drug Discovery Unit, Newcastle University Centre
for Cancer, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K.
| | - Pamela Lochhead
- Signalling
Laboratory, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, U.K.
| | - Mathew P. Martin
- Cancer
Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Paul O’Gorman Building, Medical School,
Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Nick C. Martin
- Cancer
Research UK Newcastle Drug Discovery Unit, Newcastle University Centre
for Cancer, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K.
| | - Stephanie Myers
- Cancer
Research UK Newcastle Drug Discovery Unit, Newcastle University Centre
for Cancer, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K.
| | - David R. Newell
- Cancer
Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Paul O’Gorman Building, Medical School,
Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Richard A. Noble
- Cancer
Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Paul O’Gorman Building, Medical School,
Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Nicole Phillips
- Cancer
Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Paul O’Gorman Building, Medical School,
Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Laurent Rigoreau
- Cancer
Research UK Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Campus, Babraham, Cambridgeshire CB22 3AT, U.K.
| | - Huw Thomas
- Cancer
Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Paul O’Gorman Building, Medical School,
Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Julie A. Tucker
- Cancer
Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Paul O’Gorman Building, Medical School,
Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Lan-Zhen Wang
- Cancer
Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Paul O’Gorman Building, Medical School,
Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Michael J. Waring
- Cancer
Research UK Newcastle Drug Discovery Unit, Newcastle University Centre
for Cancer, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K.
| | - Ai-Ching Wong
- Cancer
Research UK Therapeutic Discovery Laboratories, London Bioscience Innovation Centre, 2 Royal College Street, London NW1 0NH, U.K.
| | - Stephen R. Wedge
- Cancer
Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Paul O’Gorman Building, Medical School,
Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Martin E. M. Noble
- Cancer
Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Paul O’Gorman Building, Medical School,
Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Celine Cano
- Cancer
Research UK Newcastle Drug Discovery Unit, Newcastle University Centre
for Cancer, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K.
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3
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Abstract
With several marketed drugs, allosteric inhibition of kinases has translated to pharmacological effects and clinical benefits comparable to those from orthosteric inhibition. However, despite much effort over more than 20 years, the number of kinase targets associated with FDA-approved allosteric drugs is limited, suggesting the challenges in identifying and validating allosteric inhibitors. Here we review the principles of allosteric inhibition, summarize the discovery of allosteric MEK1/2 and BCR-ABL1 inhibitors, and discuss the approaches to screening and demonstrating the functional activity of allosteric pocket ligands.
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Affiliation(s)
- Yue Pan
- Relay Therapeutics, 399 Binney Street, Cambridge, Massachusetts 02139, United States
| | - Mary M Mader
- Relay Therapeutics, 399 Binney Street, Cambridge, Massachusetts 02139, United States
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4
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Structural basis for small molecule targeting of Doublecortin Like Kinase 1 with DCLK1-IN-1. Commun Biol 2021; 4:1105. [PMID: 34545159 PMCID: PMC8452690 DOI: 10.1038/s42003-021-02631-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/01/2021] [Indexed: 02/03/2023] Open
Abstract
Doublecortin-like kinase 1 (DCLK1) is an understudied bi-functional kinase with a proven role in tumour growth and development. However, the presence of tissue-specific spliced DCLK1 isoforms with distinct biological functions have challenged the development of effective strategies to understand the role of DCLK1 in oncogenesis. Recently, DCLK1-IN-1 was reported as a highly selective DCLK1 inhibitor, a powerful tool to dissect DCLK1 biological functions. Here, we report the crystal structures of DCLK1 kinase domain in complex with DCLK1-IN-1 and its precursors. Combined, our data rationalises the structure-activity relationship that informed the development of DCLK1-IN-1 and provides the basis for the high selectivity of DCLK1-IN-1, with DCLK1-IN-1 inducing a drastic conformational change of the ATP binding site. We demonstrate that DCLK1-IN-1 binds DCLK1 long isoforms but does not prevent DCLK1's Microtubule-Associated Protein (MAP) function. Together, our work provides an invaluable structural platform to further the design of isoform-specific DCLK1 modulators for therapeutic intervention.
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5
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Small molecule ERK5 kinase inhibitors paradoxically activate ERK5 signalling: be careful what you wish for…. Biochem Soc Trans 2021; 48:1859-1875. [PMID: 32915196 PMCID: PMC7609025 DOI: 10.1042/bst20190338] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/06/2020] [Accepted: 08/10/2020] [Indexed: 12/15/2022]
Abstract
ERK5 is a protein kinase that also contains a nuclear localisation signal and a transcriptional transactivation domain. Inhibition of ERK5 has therapeutic potential in cancer and inflammation and this has prompted the development of ERK5 kinase inhibitors (ERK5i). However, few ERK5i programmes have taken account of the ERK5 transactivation domain. We have recently shown that the binding of small molecule ERK5i to the ERK5 kinase domain stimulates nuclear localisation and paradoxical activation of its transactivation domain. Other kinase inhibitors paradoxically activate their intended kinase target, in some cases leading to severe physiological consequences highlighting the importance of mitigating these effects. Here, we review the assays used to monitor ERK5 activities (kinase and transcriptional) in cells, the challenges faced in development of small molecule inhibitors to the ERK5 pathway, and classify the molecular mechanisms of paradoxical activation of protein kinases by kinase inhibitors.
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6
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Liu Y, Ferguson FM, Li L, Kuljanin M, Mills CE, Subramanian K, Harshbarger W, Gondi S, Wang J, Sorger PK, Mancias JD, Gray NS, Westover KD. Chemical Biology Toolkit for DCLK1 Reveals Connection to RNA Processing. Cell Chem Biol 2020; 27:1229-1240.e4. [PMID: 32755567 PMCID: PMC8053042 DOI: 10.1016/j.chembiol.2020.07.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 06/02/2020] [Accepted: 06/24/2020] [Indexed: 12/27/2022]
Abstract
Doublecortin-like kinase 1 (DCLK1) is critical for neurogenesis, but overexpression is also observed in multiple cancers and is associated with poor prognosis. Nevertheless, the function of DCLK1 in cancer, especially the context-dependent functions, are poorly understood. We present a "toolkit" that includes the DCLK1 inhibitor DCLK1-IN-1, a complementary DCLK1-IN-1-resistant mutation G532A, and kinase dead mutants D511N and D533N, which can be used to investigate signaling pathways regulated by DCLK1. Using a cancer cell line engineered to be DCLK1 dependent for growth and cell migration, we show that this toolkit can be used to discover associations between DCLK1 kinase activity and biological processes. In particular, we show an association between DCLK1 and RNA processing, including the identification of CDK11 as a potential substrate of DCLK1 using phosphoproteomics.
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Affiliation(s)
- Yan Liu
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA; Department of Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Fleur M Ferguson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Lianbo Li
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA; Department of Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Miljan Kuljanin
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Caitlin E Mills
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA 02115, USA
| | - Kartik Subramanian
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA 02115, USA
| | - Wayne Harshbarger
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA; Department of Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Sudershan Gondi
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA; Department of Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Jinhua Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA 02115, USA
| | - Joseph D Mancias
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kenneth D Westover
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA; Department of Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA.
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7
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Ferguson FM, Liu Y, Harshbarger W, Huang L, Wang J, Deng X, Capuzzi SJ, Muratov EN, Tropsha A, Muthuswamy S, Westover KD, Gray NS. Synthesis and Structure-Activity Relationships of DCLK1 Kinase Inhibitors Based on a 5,11-Dihydro-6 H-benzo[ e]pyrimido[5,4- b][1,4]diazepin-6-one Scaffold. J Med Chem 2020; 63:7817-7826. [PMID: 32530623 DOI: 10.1021/acs.jmedchem.0c00596] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Doublecortin-like kinase 1 (DCLK1) is a serine/threonine kinase that is overexpressed in gastrointestinal cancers, including esophageal, gastric, colorectal, and pancreatic cancers. DCLK1 is also used as a marker of tuft cells, which regulate type II immunity in the gut. However, the substrates and functions of DCLK1 are understudied. We recently described the first selective DCLK1/2 inhibitor, DCLK1-IN-1, developed to aid the functional characterization of this important kinase. Here we describe the synthesis and structure-activity relationships of 5,11-dihydro-6H-benzo[e]pyrimido[5,4-b][1,4]diazepin-6-one DCLK1 inhibitors, resulting in the identification of DCLK1-IN-1.
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Affiliation(s)
- Fleur M Ferguson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Yan Liu
- Departments of Radiation Oncology and Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, United States
| | - Wayne Harshbarger
- Departments of Radiation Oncology and Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, United States
| | - Ling Huang
- Cancer Research Institute and Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Jinhua Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Xianming Deng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Stephen J Capuzzi
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Eugene N Muratov
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Alexander Tropsha
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Senthil Muthuswamy
- Cancer Research Institute and Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States.,Departments of Medicine and Pathology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Kenneth D Westover
- Departments of Radiation Oncology and Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, United States
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
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8
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Ferguson FM, Nabet B, Raghavan S, Liu Y, Leggett AL, Kuljanin M, Kalekar RL, Yang A, He S, Wang J, Ng RWS, Sulahian R, Li L, Poulin EJ, Huang L, Koren J, Dieguez-Martinez N, Espinosa S, Zeng Z, Corona CR, Vasta JD, Ohi R, Sim T, Kim ND, Harshbarger W, Lizcano JM, Robers MB, Muthaswamy S, Lin CY, Look AT, Haigis KM, Mancias JD, Wolpin BM, Aguirre AJ, Hahn WC, Westover KD, Gray NS. Discovery of a selective inhibitor of doublecortin like kinase 1. Nat Chem Biol 2020; 16:635-643. [PMID: 32251410 PMCID: PMC7246176 DOI: 10.1038/s41589-020-0506-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 02/05/2020] [Accepted: 02/24/2020] [Indexed: 12/16/2022]
Abstract
Doublecortin like kinase 1 (DCLK1) is an understudied kinase that is upregulated in a wide range of cancers, including pancreatic ductal adenocarcinoma (PDAC). However, little is known about its potential as a therapeutic target. We used chemoproteomic profiling and structure-based design to develop a selective, in vivo-compatible chemical probe of the DCLK1 kinase domain, DCLK1-IN-1. We demonstrate activity of DCLK1-IN-1 against clinically relevant patient-derived PDAC organoid models and use a combination of RNA-sequencing, proteomics and phosphoproteomics analysis to reveal that DCLK1 inhibition modulates proteins and pathways associated with cell motility in this context. DCLK1-IN-1 will serve as a versatile tool to investigate DCLK1 biology and establish its role in cancer.
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Affiliation(s)
- Fleur M Ferguson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Behnam Nabet
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Srivatsan Raghavan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yan Liu
- Departments of Biochemistry and Radiation Oncology, the University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Alan L Leggett
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Miljan Kuljanin
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Radha L Kalekar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Annan Yang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shuning He
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jinhua Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Raymond W S Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rita Sulahian
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lianbo Li
- Departments of Biochemistry and Radiation Oncology, the University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Emily J Poulin
- Cancer Research Institute and Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Ling Huang
- Cancer Research Institute and Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jost Koren
- Department of Molecular and Human Genetics, Therapeutic Innovation Center Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Nora Dieguez-Martinez
- Departament de Bioquímica i Biologia Molecular & Institut de Neurociencies, Facultat de Medicina. Universitat Autonoma de Barcelona, Bellaterra, Spain
| | - Sergio Espinosa
- Departament de Bioquímica i Biologia Molecular & Institut de Neurociencies, Facultat de Medicina. Universitat Autonoma de Barcelona, Bellaterra, Spain
| | | | | | | | - Ryoma Ohi
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Taebo Sim
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea and KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, Republic of Korea
| | - Nam Doo Kim
- NDBio Therapeutics Inc, Incheon, Republic of Korea
| | - Wayne Harshbarger
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- GSK Vaccines, Rockville, MD, USA
| | - Jose M Lizcano
- Departament de Bioquímica i Biologia Molecular & Institut de Neurociencies, Facultat de Medicina. Universitat Autonoma de Barcelona, Bellaterra, Spain
| | | | - Senthil Muthaswamy
- Cancer Research Institute and Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Departments of Medicine and Pathology, Harvard Medical School, Boston, MA, USA
| | - Charles Y Lin
- Department of Molecular and Human Genetics, Therapeutic Innovation Center Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Kevin M Haigis
- Cancer Research Institute and Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Harvard Digestive Disease Center, Harvard Medical School, Boston, MA, USA
| | - Joseph D Mancias
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Andrew J Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kenneth D Westover
- Departments of Biochemistry and Radiation Oncology, the University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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9
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Moreira B, Armstrong T, Batista ICA, Clemente Tavares N, Pires CV, de Moraes Mourão M, Falcone FH, Dekker LV. Use of BODIPY-Labeled ATP Analogues in the Development and Validation of a Fluorescence Polarization-Based Assay for Screening of Kinase Inhibitors. ACS OMEGA 2020; 5:9064-9070. [PMID: 32363258 PMCID: PMC7191558 DOI: 10.1021/acsomega.9b03344] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/10/2020] [Indexed: 05/14/2023]
Abstract
The screening of compound libraries to identify small-molecule modulators of specific biological targets is crucial in the process for the discovery of novel therapeutics and molecular probes. Considering the need for simple single-tool assay technologies with which one could monitor "all" kinases, we developed a fluorescence polarization (FP)-based assay to monitor the binding capabilities of protein kinases to ATP. We used BODIPY ATP-y-S as a probe to measure the shift in the polarization of a light beam when passed through the sample. We were able to optimize the assay using commercial Protein Kinase A (PKA) and H7 efficiently inhibited the binding of the probe when added to the reaction. Furthermore, we were able to employ the assay in a high-throughput fashion and validate the screening of a set of small molecules predicted to dock into the ATP-binding site of PKA. This will be useful to screen larger libraries of compounds that may target protein kinases by blocking ATP binding.
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Affiliation(s)
- Bernardo
Pereira Moreira
- Biomedizinisches
Forschungszentrum Seltersberg, Institut für Parasitologie, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
- Instituto
de Pesquisas René Rachou, Fundação
Oswaldo Cruz—FIOCRUZ, Belo Horizonte 30190-002, Minas Gerais, Brazil
- School
of Pharmacy, Division of Molecular Therapeutics and Formulation, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Tom Armstrong
- School
of Chemistry, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Izabella Cristina Andrade Batista
- Instituto
de Pesquisas René Rachou, Fundação
Oswaldo Cruz—FIOCRUZ, Belo Horizonte 30190-002, Minas Gerais, Brazil
- School
of Pharmacy, Division of Molecular Therapeutics and Formulation, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Naiara Clemente Tavares
- Instituto
de Pesquisas René Rachou, Fundação
Oswaldo Cruz—FIOCRUZ, Belo Horizonte 30190-002, Minas Gerais, Brazil
- School
of Pharmacy, Division of Molecular Therapeutics and Formulation, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Camilla Valente Pires
- Instituto
de Pesquisas René Rachou, Fundação
Oswaldo Cruz—FIOCRUZ, Belo Horizonte 30190-002, Minas Gerais, Brazil
- School
of Pharmacy, Division of Molecular Therapeutics and Formulation, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Marina de Moraes Mourão
- Instituto
de Pesquisas René Rachou, Fundação
Oswaldo Cruz—FIOCRUZ, Belo Horizonte 30190-002, Minas Gerais, Brazil
| | - Franco H. Falcone
- Biomedizinisches
Forschungszentrum Seltersberg, Institut für Parasitologie, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
- School
of Pharmacy, Division of Molecular Therapeutics and Formulation, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Lodewijk V. Dekker
- School
of Pharmacy, Division of Biomolecular Science and Medicinal Chemistry, University of Nottingham, Nottingham NG7 2RD, United Kingdom
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10
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Lochhead PA, Tucker JA, Tatum NJ, Wang J, Oxley D, Kidger AM, Johnson VP, Cassidy MA, Gray NS, Noble MEM, Cook SJ. Paradoxical activation of the protein kinase-transcription factor ERK5 by ERK5 kinase inhibitors. Nat Commun 2020; 11:1383. [PMID: 32170057 PMCID: PMC7069993 DOI: 10.1038/s41467-020-15031-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 02/11/2020] [Indexed: 12/20/2022] Open
Abstract
The dual protein kinase-transcription factor, ERK5, is an emerging drug target in cancer and inflammation, and small-molecule ERK5 kinase inhibitors have been developed. However, selective ERK5 kinase inhibitors fail to recapitulate ERK5 genetic ablation phenotypes, suggesting kinase-independent functions for ERK5. Here we show that ERK5 kinase inhibitors cause paradoxical activation of ERK5 transcriptional activity mediated through its unique C-terminal transcriptional activation domain (TAD). Using the ERK5 kinase inhibitor, Compound 26 (ERK5-IN-1), as a paradigm, we have developed kinase-active, drug-resistant mutants of ERK5. With these mutants, we show that induction of ERK5 transcriptional activity requires direct binding of the inhibitor to the kinase domain. This in turn promotes conformational changes in the kinase domain that result in nuclear translocation of ERK5 and stimulation of gene transcription. This shows that both the ERK5 kinase and TAD must be considered when assessing the role of ERK5 and the effectiveness of anti-ERK5 therapeutics.
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Affiliation(s)
- Pamela A Lochhead
- Signalling Laboratory, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
| | - Julie A Tucker
- York Biomedical Research Institute and Department of Biology, University of York, York, YO10 5DD, UK
| | - Natalie J Tatum
- CRUK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Newcastle University, Newcastle, NE2 4HH, UK
| | - Jinhua Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - David Oxley
- Signalling Laboratory, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Andrew M Kidger
- Signalling Laboratory, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Victoria P Johnson
- Signalling Laboratory, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
- Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK
| | - Megan A Cassidy
- Signalling Laboratory, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Martin E M Noble
- CRUK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Newcastle University, Newcastle, NE2 4HH, UK
| | - Simon J Cook
- Signalling Laboratory, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
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11
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Targeted Avenues for Cancer Treatment: The MEK5-ERK5 Signaling Pathway. Trends Mol Med 2020; 26:394-407. [PMID: 32277933 DOI: 10.1016/j.molmed.2020.01.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/20/2019] [Accepted: 01/21/2020] [Indexed: 12/13/2022]
Abstract
Twenty years have passed since extracellular signal-regulated kinase 5 (ERK5) and its upstream activator, mitogen-activated protein kinase 5 (MEK5), first emerged onto the cancer research scene. Although we have come a long way in defining the liaison between dysregulated MEK5-ERK5 signaling and the pathogenesis of epithelial and nonepithelial malignancies, selective targeting of this unique pathway remains elusive. Here, we provide an updated review of the existing evidence for a correlation between aberrant MEK5-ERK5 (phospho)proteomic/transcriptomic profiles, aggressive cancer states, and poor patient outcomes. We then focus on emerging insights from preclinical models regarding the relevance of upregulated ERK5 activity in promoting tumor growth, metastasis, therapy resistance, undifferentiated traits, and immunosuppression, highlighting the opportunities, prospects, and challenges of selectively blocking this cascade for antineoplastic treatment and chemosensitization.
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12
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MacKerell AD, Jo S, Lakkaraju SK, Lind C, Yu W. Identification and characterization of fragment binding sites for allosteric ligand design using the site identification by ligand competitive saturation hotspots approach (SILCS-Hotspots). Biochim Biophys Acta Gen Subj 2020; 1864:129519. [PMID: 31911242 DOI: 10.1016/j.bbagen.2020.129519] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/21/2019] [Accepted: 12/31/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Fragment-based ligand design is used for the development of novel ligands that target macromolecules, most notably proteins. Central to its success is the identification of fragment binding sites that are spatially adjacent such that fragments occupying those sites may be linked to create drug-like ligands. Current experimental and computational approaches that address this problem typically identify only a limited number of sites as well as use a limited number of fragment types. METHODS The site-identification by ligand competitive saturation (SILCS) approach is extended to the identification of fragment bindings sites, with the method termed SILCS-Hotspots. The approach involves precomputation of the SILCS FragMaps following which the identification of Hotspots, performed by identifying of all possible fragment binding sites on the full 3D structure of the protein followed by spatial clustering. RESULTS The SILCS-Hotspots approach identifies a large number of sites on the target protein, including many sites not accessible in experimental structures due to low binding affinities and binding sites on the protein interior. The identified sites are shown to recapitulate the location of known drug-like molecules in both allosteric and orthosteric binding sites on seven proteins including the androgen receptor, the CDK2 and Erk5 kinases, PTP1B phosphatase and three GPCRs; the β2-adrenergic, GPR40 fatty-acid binding and M2-muscarinic receptors. Analysis indicates the importance of considering all possible fragment binding sites, and not just those accessible to experimental methods, when identifying novel binding sites and performing ligand design versus just considering the most favorable sites. The approach is shown to identify a larger number of known binding sites of drug-like molecules versus the commonly used FTMap and Fpocket methods. GENERAL SIGNIFICANCE The present results indicate the potential utility of the SILCS-Hotspots approach for fragment-based rational design of ligands, including allosteric modulators.
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Affiliation(s)
- Alexander D MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, United States of America.
| | - Sunhwan Jo
- SilcsBio, LLC, 8 Market Place, Suite 300, Baltimore, MD 21202, United States of America
| | | | - Christoffer Lind
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, United States of America
| | - Wenbo Yu
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, United States of America
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13
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Myers SM, Miller DC, Molyneux L, Arasta M, Bawn RH, Blackburn TJ, Cook SJ, Edwards N, Endicott JA, Golding BT, Griffin RJ, Hammonds T, Hardcastle IR, Harnor SJ, Heptinstall AB, Lochhead PA, Martin MP, Martin NC, Newell DR, Owen PJ, Pang LC, Reuillon T, Rigoreau LJM, Thomas HD, Tucker JA, Wang LZ, Wong AC, Noble MEM, Wedge SR, Cano C. Identification of a novel orally bioavailable ERK5 inhibitor with selectivity over p38α and BRD4. Eur J Med Chem 2019; 178:530-543. [PMID: 31212132 DOI: 10.1016/j.ejmech.2019.05.057] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/30/2019] [Accepted: 05/20/2019] [Indexed: 11/18/2022]
Abstract
Extracellular regulated kinase 5 (ERK5) signalling has been implicated in driving a number of cellular phenotypes including endothelial cell angiogenesis and tumour cell motility. Novel ERK5 inhibitors were identified using high throughput screening, with a series of pyrrole-2-carboxamides substituted at the 4-position with an aroyl group being found to exhibit IC50 values in the micromolar range, but having no selectivity against p38α MAP kinase. Truncation of the N-substituent marginally enhanced potency (∼3-fold) against ERK5, but importantly attenuated inhibition of p38α. Systematic variation of the substituents on the aroyl group led to the selective inhibitor 4-(2-bromo-6-fluorobenzoyl)-N-(pyridin-3-yl)-1H-pyrrole-2-carboxamide (IC50 0.82 μM for ERK5; IC50 > 120 μM for p38α). The crystal structure (PDB 5O7I) of this compound in complex with ERK5 has been solved. This compound was orally bioavailable and inhibited bFGF-driven Matrigel plug angiogenesis and tumour xenograft growth. The selective ERK5 inhibitor described herein provides a lead for further development into a tool compound for more extensive studies seeking to examine the role of ERK5 signalling in cancer and other diseases.
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Affiliation(s)
- Stephanie M Myers
- Newcastle Drug Discovery, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Duncan C Miller
- Newcastle Drug Discovery, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Lauren Molyneux
- Newcastle Drug Discovery, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Mercedes Arasta
- Newcastle Drug Discovery, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK
| | - Ruth H Bawn
- Newcastle Drug Discovery, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Timothy J Blackburn
- Newcastle Drug Discovery, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Simon J Cook
- Signalling Laboratory, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Noel Edwards
- Newcastle Drug Discovery, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK
| | - Jane A Endicott
- Newcastle Drug Discovery, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK
| | - Bernard T Golding
- Newcastle Drug Discovery, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Roger J Griffin
- Newcastle Drug Discovery, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Tim Hammonds
- Cancer Research UK Therapeutic Discovery Laboratories, London Bioscience Innovation Centre, 2 Royal College Street, London, NW1 0NH, UK
| | - Ian R Hardcastle
- Newcastle Drug Discovery, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Suzannah J Harnor
- Newcastle Drug Discovery, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Amy B Heptinstall
- Newcastle Drug Discovery, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Pamela A Lochhead
- Signalling Laboratory, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Mathew P Martin
- Newcastle Drug Discovery, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK
| | - Nick C Martin
- Newcastle Drug Discovery, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - David R Newell
- Newcastle Drug Discovery, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK
| | - Paul J Owen
- Cancer Research UK Therapeutic Discovery Laboratories, London Bioscience Innovation Centre, 2 Royal College Street, London, NW1 0NH, UK
| | - Leon C Pang
- Cancer Research UK Therapeutic Discovery Laboratories, London Bioscience Innovation Centre, 2 Royal College Street, London, NW1 0NH, UK
| | - Tristan Reuillon
- Newcastle Drug Discovery, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Laurent J M Rigoreau
- Cancer Research UK Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Campus, Babraham, Cambridgeshire, CB22 3AT, UK
| | - Huw D Thomas
- Newcastle Drug Discovery, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK
| | - Julie A Tucker
- Newcastle Drug Discovery, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK
| | - Lan-Zhen Wang
- Newcastle Drug Discovery, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK
| | - Ai-Ching Wong
- Cancer Research UK Therapeutic Discovery Laboratories, London Bioscience Innovation Centre, 2 Royal College Street, London, NW1 0NH, UK
| | - Martin E M Noble
- Newcastle Drug Discovery, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK.
| | - Stephen R Wedge
- Newcastle Drug Discovery, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK.
| | - Celine Cano
- Newcastle Drug Discovery, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK.
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14
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Nguyen D, Lemos C, Wortmann L, Eis K, Holton SJ, Boemer U, Moosmayer D, Eberspaecher U, Weiske J, Lechner C, Prechtl S, Suelzle D, Siegel F, Prinz F, Lesche R, Nicke B, Nowak-Reppel K, Himmel H, Mumberg D, von Nussbaum F, Nising CF, Bauser M, Haegebarth A. Discovery and Characterization of the Potent and Highly Selective (Piperidin-4-yl)pyrido[3,2- d]pyrimidine Based in Vitro Probe BAY-885 for the Kinase ERK5. J Med Chem 2019; 62:928-940. [PMID: 30563338 DOI: 10.1021/acs.jmedchem.8b01606] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The availability of a chemical probe to study the role of a specific domain of a protein in a concentration- and time-dependent manner is of high value. Herein, we report the identification of a highly potent and selective ERK5 inhibitor BAY-885 by high-throughput screening and subsequent structure-based optimization. ERK5 is a key integrator of cellular signal transduction, and it has been shown to play a role in various cellular processes such as proliferation, differentiation, apoptosis, and cell survival. We could demonstrate that inhibition of ERK5 kinase and transcriptional activity with a small molecule did not translate into antiproliferative activity in different relevant cell models, which is in contrast to the results obtained by RNAi technology.
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Affiliation(s)
- Duy Nguyen
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Clara Lemos
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Lars Wortmann
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Knut Eis
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Simon J Holton
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Ulf Boemer
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Dieter Moosmayer
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Uwe Eberspaecher
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Joerg Weiske
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Christian Lechner
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Stefan Prechtl
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Detlev Suelzle
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Franziska Siegel
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Florian Prinz
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Ralf Lesche
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Barbara Nicke
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | | | - Herbert Himmel
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Dominik Mumberg
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Franz von Nussbaum
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Carl F Nising
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Marcus Bauser
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
| | - Andrea Haegebarth
- Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany
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15
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Yao B, Wang S, Xiao P, Wang Q, Hea Y, Zhang Y. MAPK signaling pathways in eye wounds: Multifunction and cooperation. Exp Cell Res 2017; 359:10-16. [DOI: 10.1016/j.yexcr.2017.06.024] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 06/29/2017] [Indexed: 12/12/2022]
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