1
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Wang J, Yang W, Zhao L, Wei B, Chen J. Binding Mechanism of Inhibitors to BRD4 and BRD9 Decoded by Multiple Independent Molecular Dynamics Simulations and Deep Learning. Molecules 2024; 29:1857. [PMID: 38675678 PMCID: PMC11054187 DOI: 10.3390/molecules29081857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/16/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Bromodomain 4 and 9 (BRD4 and BRD9) have been regarded as important targets of drug designs in regard to the treatment of multiple diseases. In our current study, molecular dynamics (MD) simulations, deep learning (DL) and binding free energy calculations are integrated to probe the binding modes of three inhibitors (H1B, JQ1 and TVU) to BRD4 and BRD9. The MD trajectory-based DL successfully identify significant functional function domains, such as BC-loop and ZA-loop. The information from the post-processing analysis of MD simulations indicates that inhibitor binding highly influences the structural flexibility and dynamic behavior of BRD4 and BRD9. The results of the MM-GBSA calculations not only suggest that the binding ability of H1B, JQ1 and TVU to BRD9 are stronger than to BRD4, but they also verify that van der Walls interactions are the primary forces responsible for inhibitor binding. The hot spots of BRD4 and BRD9 revealed by residue-based free energy estimation provide target sites of drug design in regard to BRD4 and BRD9. This work is anticipated to provide useful theoretical aids for the development of selective inhibitors over BRD family members.
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Affiliation(s)
- Jian Wang
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Wanchun Yang
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Lu Zhao
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Benzheng Wei
- Center for Medical Artificial Intelligence, Shandong University of Traditional Chinese Medicine, Qingdao 266112, China
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China
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2
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Zhang T, Sun S, Wang R, Li T, Gan B, Zhang Y. BioisoIdentifier: an online free tool to investigate local structural replacements from PDB. J Cheminform 2024; 16:7. [PMID: 38218937 PMCID: PMC10788035 DOI: 10.1186/s13321-024-00801-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/07/2024] [Indexed: 01/15/2024] Open
Abstract
Within the realm of contemporary medicinal chemistry, bioisosteres are empirically used to enhance potency and selectivity, improve adsorption, distribution, metabolism, excretion and toxicity profiles of drug candidates. It is believed that bioisosteric know-how may help bypass granted patents or generate novel intellectual property for commercialization. Beside the synthetic expertise, the drug discovery process also depends on efficient in silico tools. We hereby present BioisoIdentifier (BII), a web server aiming to uncover bioisosteric information for specific fragment. Using the Protein Data Bank as source, and specific substructures that the user attempt to surrogate as input, BII tries to find suitable fragments that fit well within the local protein active site. BII is a powerful computational tool that offers the ligand design ideas for bioisosteric replacing. For the validation of BII, catechol is conceived as model fragment attempted to be replaced, and many ideas are successfully offered. These outputs are hierarchically grouped according to structural similarity, and clustered based on unsupervised machine learning algorithms. In summary, we constructed a user-friendly interface to enable the viewing of top-ranking molecules for further experimental exploration. This makes BII a highly valuable tool for drug discovery. The BII web server is freely available to researchers and can be accessed at http://www.aifordrugs.cn/index/ . Scientific Contribution: By designing a more optimal computational process for mining bioisosteric replacements from the publicly accessible PDB database, then deployed on a web server for throughly free access for researchers. Additionally, machine learning methods are applied to cluster the bioisosteric replacements searched by the platform, making a scientific contribution to facilitate chemists' selection of appropriate bioisosteric replacements. The number of bioisosteric replacements obtained using BII is significantly larger than the currently available platforms, which expanding the search space for effective local structural replacements.
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Affiliation(s)
- Tinghao Zhang
- Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, China
| | - Shaohua Sun
- Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, China
| | - Runzhou Wang
- School of Management, Xi'an University of Architecture and Technology, Xi'an, 710055, China
| | - Ting Li
- Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, China
| | - Bicheng Gan
- College of Petroleum Engineering, Northeast Petroleum University, Daqing, 163318, Heilongjiang, China
| | - Yuezhou Zhang
- Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, China.
- Ningbo Institute of Northwestern Polytechnical University, Frontiers Science Center for Flexible Electronics (FSCFE), Key Laboratory of Flexible Electronics of Zhejiang Province, Ningbo Institute of Northwestern Polytechnical University, 218 Qingyi Road, Ningbo, 315103, China.
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3
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Huang J, Wu Y, Hu Z, Han S, Rong L, Xie X, Chen W, Peng X. Mn(OAc) 2-promoted [3+2] cyclization of enaminone with isocyanoacetate: Rapid access to pyrrole-2-carboxylic ester derivatives with potent anticancer activity. Bioorg Chem 2023; 140:106748. [PMID: 37562314 DOI: 10.1016/j.bioorg.2023.106748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 07/15/2023] [Accepted: 07/20/2023] [Indexed: 08/12/2023]
Abstract
The practical and facile Mn(OAc)2-promoted [3+2] cycloaddition reaction of enaminones with isocyanoacetate was developed, that delivered a diversity of 3-aroyl pyrrole-2-carboxylic esters with broad substrates scope. The most of the newly synthesized compounds exhibit moderate antiproliferative activity against four cancer cells. Notably, compound 2n demonstrate the most potent activity with average IC50 values of 5.61 μM against four distinct cancer cell lines. Moreover, 2n exhibit favorable anti-migration activity and drug-like properties. The further investigation suggests that compound 2n possesses the ability to inhibit ERK5 activity and exhibits effective binding with the ERK5 protein, making it a promising candidate as a lead compound for a new class of ERK5 inhibitors discovery.
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Affiliation(s)
- Jiuzhong Huang
- School of Pharmacy, Gannan Medical University, Ganzhou 341000, PR China
| | - Yi Wu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, PR China
| | - Zhihao Hu
- School of Pharmacy, Gannan Medical University, Ganzhou 341000, PR China
| | - Shihong Han
- School of Pharmacy, Gannan Medical University, Ganzhou 341000, PR China
| | - Lanlan Rong
- School of Pharmacy, Gannan Medical University, Ganzhou 341000, PR China
| | - Xin Xie
- School of Pharmacy, Gannan Medical University, Ganzhou 341000, PR China
| | - Weiming Chen
- School of Pharmacy, Gannan Medical University, Ganzhou 341000, PR China.
| | - Xiaopeng Peng
- School of Pharmacy, Gannan Medical University, Ganzhou 341000, PR China.
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4
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Sánchez-Fdez A, Matilla-Almazán S, Del Carmen S, Abad M, Arconada-Luque E, Jiménez-Suárez J, Chinchilla-Tábora LM, Ruíz-Hidalgo MJ, Sánchez-Prieto R, Pandiella A, Esparís-Ogando A. Etiopathogenic role of ERK5 signaling in sarcoma: prognostic and therapeutic implications. Exp Mol Med 2023; 55:1247-1257. [PMID: 37332046 PMCID: PMC10317974 DOI: 10.1038/s12276-023-01008-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 02/28/2023] [Accepted: 03/07/2023] [Indexed: 06/20/2023] Open
Abstract
Sarcomas constitute a heterogeneous group of rare and difficult-to-treat tumors that can affect people of all ages, representing one of the most common forms of cancer in childhood and adolescence. Little is known about the molecular entities involved in sarcomagenesis. Therefore, the identification of processes that lead to the development of the disease may uncover novel therapeutic opportunities. Here, we show that the MEK5/ERK5 signaling pathway plays a critical role in the pathogenesis of sarcomas. By developing a mouse model engineered to express a constitutively active form of MEK5, we demonstrate that the exclusive activation of the MEK5/ERK5 pathway can promote sarcomagenesis. Histopathological analyses identified these tumors as undifferentiated pleomorphic sarcomas. Bioinformatic studies revealed that sarcomas are the tumors in which ERK5 is most frequently amplified and overexpressed. Moreover, analysis of the impact of ERK5 protein expression on overall survival in patients diagnosed with different sarcoma types in our local hospital showed a 5-fold decrease in median survival in patients with elevated ERK5 expression compared with those with low expression. Pharmacological and genetic studies revealed that targeting the MEK5/ERK5 pathway drastically affects the proliferation of human sarcoma cells and tumor growth. Interestingly, sarcoma cells with knockout of ERK5 or MEK5 were unable to form tumors when engrafted into mice. Taken together, our results reveal a role of the MEK5/ERK5 pathway in sarcomagenesis and open a new scenario to be considered in the treatment of patients with sarcoma in which the ERK5 pathway is pathophysiologically involved.
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Affiliation(s)
- Adrián Sánchez-Fdez
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC)-CSIC, Salamanca, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-Universidad de Salamanca, Salamanca, Spain
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Sofía Matilla-Almazán
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC)-CSIC, Salamanca, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-Universidad de Salamanca, Salamanca, Spain
| | - Sofía Del Carmen
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Departmento de Patología, Hospital Universitario de Salamanca, Universidad de Salamanca, Salamanca, Spain
| | - Mar Abad
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Departmento de Patología, Hospital Universitario de Salamanca, Universidad de Salamanca, Salamanca, Spain
| | - Elena Arconada-Luque
- Universidad de Castilla-La Mancha, Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Unidad Asociada de Biomedicina UCLM, Unidad asociada al CSIC, Albacete, Spain
| | - Jaime Jiménez-Suárez
- Universidad de Castilla-La Mancha, Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Unidad Asociada de Biomedicina UCLM, Unidad asociada al CSIC, Albacete, Spain
| | - Luis Miguel Chinchilla-Tábora
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Departmento de Patología, Hospital Universitario de Salamanca, Universidad de Salamanca, Salamanca, Spain
| | - Mª José Ruíz-Hidalgo
- Universidad de Castilla-La Mancha, Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Unidad Asociada de Biomedicina UCLM, Unidad asociada al CSIC, Albacete, Spain
- Universidad de Castilla-La Mancha, Departamento de Química Inorgánica, Orgánica y Bioquímica, Área de Bioquímica y Biología Molecular. Facultad de Medicina, Albacete, Spain
| | - Ricardo Sánchez-Prieto
- Universidad de Castilla-La Mancha, Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Unidad Asociada de Biomedicina UCLM, Unidad asociada al CSIC, Albacete, Spain
- Universidad de Castilla-La Mancha, Departamento de Ciencias Médicas, Facultad de Medicina, Albacete, Spain
- Departamento de Biología del Cáncer, Instituto de Investigaciones Biomédicas 'Alberto Sols' (CSIC-UAM), Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, Madrid, Spain
- Instituto de Investigaciones Biomédicas 'Alberto Sols', Consejo Superior de Investigaciones Científicas (IIBM-CSIC)-Universidad de Castilla-La Mancha (UCLM), Albacete, Spain
| | - Atanasio Pandiella
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC)-CSIC, Salamanca, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-Universidad de Salamanca, Salamanca, Spain
| | - Azucena Esparís-Ogando
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain.
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC)-CSIC, Salamanca, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-Universidad de Salamanca, Salamanca, Spain.
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5
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Miller D, Harnor SJ, Martin MP, Noble RA, Wedge SR, Cano C. Modulation of ERK5 Activity as a Therapeutic Anti-Cancer Strategy. J Med Chem 2023; 66:4491-4502. [PMID: 37002872 PMCID: PMC10108346 DOI: 10.1021/acs.jmedchem.3c00072] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Indexed: 04/03/2023]
Abstract
The extracellular signal-regulated kinase 5 (ERK5) signaling pathway is one of four conventional mitogen-activated protein (MAP) kinase pathways. Genetic perturbation of ERK5 has suggested that modulation of ERK5 activity may have therapeutic potential in cancer chemotherapy. This Miniperspective examines the evidence for ERK5 as a drug target in cancer, the structure of ERK5, and the evolution of structurally distinct chemotypes of ERK5 kinase domain inhibitors. The emerging complexities of ERK5 pharmacology are discussed, including the confounding phenomenon of paradoxical ERK5 activation by small-molecule ERK5 inhibitors. The impact of the recent development and biological evaluation of potent and selective bifunctional degraders of ERK5 and future opportunities in ERK modulation are also explored.
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Affiliation(s)
- Duncan
C. Miller
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Group, Newcastle University Centre for Cancer, School of Natural and
Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Suzannah J. Harnor
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Group, Newcastle University Centre for Cancer, School of Natural and
Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Mathew P. Martin
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Group, Translational and Clinical Research
Institute, Paul O’Gorman Building, Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Richard A. Noble
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Group, Translational and Clinical Research
Institute, Paul O’Gorman Building, Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Stephen R. Wedge
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Group, Translational and Clinical Research
Institute, Paul O’Gorman Building, Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Celine Cano
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Group, Newcastle University Centre for Cancer, School of Natural and
Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, United Kingdom
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6
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Arconada-Luque E, Jiménez-Suarez J, Pascual-Serra R, Nam-Cha SH, Moline T, Cimas FJ, Fliquete G, Ortega-Muelas M, Roche O, Fernández-Aroca DM, Muñoz Velasco R, García-Flores N, Garnés-García C, Sánchez-Fdez A, Matilla-Almazán S, Sánchez-Arévalo Lobo VJ, Hernández-Losa J, Belandia B, Pandiella A, Esparís-Ogando A, Ramón y Cajal S, del Peso L, Sánchez-Prieto R, Ruiz-Hidalgo MJ. ERK5 Is a Major Determinant of Chemical Sarcomagenesis: Implications in Human Pathology. Cancers (Basel) 2022; 14:cancers14143509. [PMID: 35884568 PMCID: PMC9316148 DOI: 10.3390/cancers14143509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/11/2022] [Accepted: 07/16/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Sarcoma is a heterogeneous group of tumors poorly studied with few therapeutic opportunities. Interestingly, the role of MAPKs still remains unclear in sarcomatous pathology. Here, we describe for the first time the critical role of ERK5 in the biology of soft tissue sarcoma by using in vitro and in vivo approaches in a murine experimental model of chemical sarcomagenesis. Indeed, our observations were extrapolated to a short series of human leiomyosarcoma and rhabdomyosarcomas. Furthermore, transcriptome analysis allows us to demonstrate the critical role of KLF2 in the biological effects of ERK5. Therefore, the data presented here open new windows in the diagnosis and therapy of soft tissue sarcomas. Abstract Sarcomas are a heterogeneous group of tumors in which the role of ERK5 is poorly studied. To clarify the role of this MAPK in sarcomatous pathology, we used a murine 3-methyl-cholanthrene (3MC)-induced sarcoma model. Our data show that 3MC induces pleomorphic sarcomas with muscle differentiation, showing an increased expression of ERK5. Indeed, this upregulation was also observed in human sarcomas of muscular origin, such as leiomyosarcoma or rhabdomyosarcoma. Moreover, in cell lines derived from these 3MC-induced tumors, abrogation of Mapk7 expression by using specific shRNAs decreased in vitro growth and colony-forming capacity and led to a marked loss of tumor growth in vivo. In fact, transcriptomic profiling in ERK5 abrogated cell lines by RNAseq showed a deregulated gene expression pattern for key biological processes such as angiogenesis, migration, motility, etc., correlating with a better prognostic in human pathology. Finally, among the various differentially expressed genes, Klf2 is a key mediator of the biological effects of ERK5 as indicated by its specific interference, demonstrating that the ERK5–KLF2 axis is an important determinant of sarcoma biology that should be further studied in human pathology.
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Affiliation(s)
- Elena Arconada-Luque
- Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (E.A.-L.); (J.J.-S.); (R.P.-S.); (M.O.-M.); (O.R.); (D.M.F.-A.); (N.G.-F.); (C.G.-G.); (M.J.R.-H.)
| | - Jaime Jiménez-Suarez
- Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (E.A.-L.); (J.J.-S.); (R.P.-S.); (M.O.-M.); (O.R.); (D.M.F.-A.); (N.G.-F.); (C.G.-G.); (M.J.R.-H.)
| | - Raquel Pascual-Serra
- Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (E.A.-L.); (J.J.-S.); (R.P.-S.); (M.O.-M.); (O.R.); (D.M.F.-A.); (N.G.-F.); (C.G.-G.); (M.J.R.-H.)
| | - Syong Hyun Nam-Cha
- Servicio de Anatomía Patológica, Hospital General de Albacete, 02008 Albacete, Spain;
| | - Teresa Moline
- Grupo de Patología Molecular Traslacional, Vall d’Hebron Institut de Recerca, Universitat Autònoma de Barcelona Centro de Investigación Biomédica en RED de Cancer CIBERONC, 08035 Barcelona, Spain; (T.M.); (G.F.); (J.H.-L.); (S.R.y.C.)
| | - Francisco J. Cimas
- Unidad de Bioquímica y Biología Molecular, Servicio de Instrumentación Biomédica, Universidad de Castilla-La Mancha, 02008 Albacete, Spain;
| | - Germán Fliquete
- Grupo de Patología Molecular Traslacional, Vall d’Hebron Institut de Recerca, Universitat Autònoma de Barcelona Centro de Investigación Biomédica en RED de Cancer CIBERONC, 08035 Barcelona, Spain; (T.M.); (G.F.); (J.H.-L.); (S.R.y.C.)
| | - Marta Ortega-Muelas
- Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (E.A.-L.); (J.J.-S.); (R.P.-S.); (M.O.-M.); (O.R.); (D.M.F.-A.); (N.G.-F.); (C.G.-G.); (M.J.R.-H.)
| | - Olga Roche
- Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (E.A.-L.); (J.J.-S.); (R.P.-S.); (M.O.-M.); (O.R.); (D.M.F.-A.); (N.G.-F.); (C.G.-G.); (M.J.R.-H.)
- Departamento de Ciencias Médicas, Facultad de Medicina, Universidad de Castilla-La Mancha, 02008 Albacete, Spain
| | - Diego M. Fernández-Aroca
- Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (E.A.-L.); (J.J.-S.); (R.P.-S.); (M.O.-M.); (O.R.); (D.M.F.-A.); (N.G.-F.); (C.G.-G.); (M.J.R.-H.)
| | - Raúl Muñoz Velasco
- Grupo de Oncología Molecular, Facultad de Ciencias Experimentales, Instituto de Investigación Biosanitaria, Universidad Francisco de Vitoria, Pozuelo de Alarcón, 28223 Madrid, Spain; (R.M.V.); (V.J.S.-A.L.)
- Departamento de Anatomía Patológica, Instituto de Investigación Hospital 12 de Octubre, Av. Córdoba, s/n, 28041 Madrid, Spain
| | - Natalia García-Flores
- Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (E.A.-L.); (J.J.-S.); (R.P.-S.); (M.O.-M.); (O.R.); (D.M.F.-A.); (N.G.-F.); (C.G.-G.); (M.J.R.-H.)
| | - Cristina Garnés-García
- Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (E.A.-L.); (J.J.-S.); (R.P.-S.); (M.O.-M.); (O.R.); (D.M.F.-A.); (N.G.-F.); (C.G.-G.); (M.J.R.-H.)
| | - Adrián Sánchez-Fdez
- Instituto de Biología Molecular y Celular del Cáncer-CSIC, 37007 Salamanca, Spain; (A.S.-F.); (S.M.-A.); (A.P.); (A.E.-O.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Universidad de Salamanca, CSIC, 37007 Salamanca, Spain
- Centro de Investigación Biomédica en RED de Cancer CIBERONC, 37007 Salamanca, Spain
| | - Sofía Matilla-Almazán
- Instituto de Biología Molecular y Celular del Cáncer-CSIC, 37007 Salamanca, Spain; (A.S.-F.); (S.M.-A.); (A.P.); (A.E.-O.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Universidad de Salamanca, CSIC, 37007 Salamanca, Spain
- Centro de Investigación Biomédica en RED de Cancer CIBERONC, 37007 Salamanca, Spain
| | - Víctor J. Sánchez-Arévalo Lobo
- Grupo de Oncología Molecular, Facultad de Ciencias Experimentales, Instituto de Investigación Biosanitaria, Universidad Francisco de Vitoria, Pozuelo de Alarcón, 28223 Madrid, Spain; (R.M.V.); (V.J.S.-A.L.)
- Departamento de Anatomía Patológica, Instituto de Investigación Hospital 12 de Octubre, Av. Córdoba, s/n, 28041 Madrid, Spain
| | - Javier Hernández-Losa
- Grupo de Patología Molecular Traslacional, Vall d’Hebron Institut de Recerca, Universitat Autònoma de Barcelona Centro de Investigación Biomédica en RED de Cancer CIBERONC, 08035 Barcelona, Spain; (T.M.); (G.F.); (J.H.-L.); (S.R.y.C.)
| | - Borja Belandia
- Departamento de Biología del Cáncer, Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC-UAM), Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, 28029 Madrid, Spain;
| | - Atanasio Pandiella
- Instituto de Biología Molecular y Celular del Cáncer-CSIC, 37007 Salamanca, Spain; (A.S.-F.); (S.M.-A.); (A.P.); (A.E.-O.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Universidad de Salamanca, CSIC, 37007 Salamanca, Spain
- Centro de Investigación Biomédica en RED de Cancer CIBERONC, 37007 Salamanca, Spain
| | - Azucena Esparís-Ogando
- Instituto de Biología Molecular y Celular del Cáncer-CSIC, 37007 Salamanca, Spain; (A.S.-F.); (S.M.-A.); (A.P.); (A.E.-O.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Universidad de Salamanca, CSIC, 37007 Salamanca, Spain
- Centro de Investigación Biomédica en RED de Cancer CIBERONC, 37007 Salamanca, Spain
| | - Santiago Ramón y Cajal
- Grupo de Patología Molecular Traslacional, Vall d’Hebron Institut de Recerca, Universitat Autònoma de Barcelona Centro de Investigación Biomédica en RED de Cancer CIBERONC, 08035 Barcelona, Spain; (T.M.); (G.F.); (J.H.-L.); (S.R.y.C.)
| | - Luis del Peso
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC-UAM), 28029 Madrid, Spain;
- Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, 28029 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias CIBERES, 28029 Madrid, Spain
| | - Ricardo Sánchez-Prieto
- Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (E.A.-L.); (J.J.-S.); (R.P.-S.); (M.O.-M.); (O.R.); (D.M.F.-A.); (N.G.-F.); (C.G.-G.); (M.J.R.-H.)
- Departamento de Ciencias Médicas, Facultad de Medicina, Universidad de Castilla-La Mancha, 02008 Albacete, Spain
- Departamento de Biología del Cáncer, Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC-UAM), Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, 28029 Madrid, Spain;
- Instituto de Investigaciones Biomédicas ‘Alberto Sols’, Consejo Superior de Investigaciones Científicas (IIBM-CSIC)-Universidad de Castilla-La Mancha, 02008 Albacete, Spain
- Correspondence:
| | - María José Ruiz-Hidalgo
- Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (E.A.-L.); (J.J.-S.); (R.P.-S.); (M.O.-M.); (O.R.); (D.M.F.-A.); (N.G.-F.); (C.G.-G.); (M.J.R.-H.)
- Departamento de Química Inorgánica, Orgánica y Bioquímica, Área de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad de Castilla-La Mancha, 02008 Albacete, Spain
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7
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Cook SJ, Lochhead PA. ERK5 Signalling and Resistance to ERK1/2 Pathway Therapeutics: The Path Less Travelled? Front Cell Dev Biol 2022; 10:839997. [PMID: 35903549 PMCID: PMC9315226 DOI: 10.3389/fcell.2022.839997] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 06/13/2022] [Indexed: 12/01/2022] Open
Abstract
The RAS-regulated RAF-MEK1/2-ERK1/2 signalling pathway is frequently de-regulated in human cancer. Melanoma in particular exhibits a high incidence of activating BRAFV600E/K and NRASQ61L/K mutations and such cells are addicted to the activity of these mutant oncoproteins. As a result three different BRAF inhibitors (BRAFi) have now been approved for BRAFV600E/K- mutant melanoma and have transformed the treatment of this disease. Despite this, clinical responses are typically transient as tumour cells develop resistance. These resistance mechanisms frequently involve reinstatement of ERK1/2 signalling and BRAFi are now deployed in combination with one of three approved MEK1/2 inhibitors (MEKi) to provide more durable, but still transient, clinical responses. Furthermore, inhibitors to ERK1/2 (ERK1/2i) have also been developed to counteract ERK1/2 signalling. However, recent studies have suggested that BRAFi/MEKi and ERK1/2i resistance can arise through activation of a parallel signalling pathway leading to activation of ERK5, an unusual protein kinase that contains both a kinase domain and a transcriptional transactivation domain. Here we review the evidence supporting ERK5 as a mediator of BRAFi/MEKi and ERK1/2i resistance. We also review the challenges in targeting ERK5 signalling with small molecules, including paradoxical activation of the transcriptional transactivation domain, and discuss new therapeutic modalities that could be employed to target ERK5.
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Affiliation(s)
- Simon J. Cook
- Signalling Programme, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Pamela A. Lochhead
- Signalling Programme, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
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8
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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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9
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Pan X, Pei J, Wang A, Shuai W, Feng L, Bu F, Zhu Y, Zhang L, Wang G, Ouyang L. Development of small molecule extracellular signal-regulated kinases (ERKs) inhibitors for cancer therapy. Acta Pharm Sin B 2022; 12:2171-2192. [PMID: 35646548 PMCID: PMC9136582 DOI: 10.1016/j.apsb.2021.12.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/18/2021] [Accepted: 12/22/2021] [Indexed: 01/09/2023] Open
Abstract
The mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase 1/2 (ERK1/2) signaling pathway is widely activated by a variety of extracellular stimuli, and its dysregulation is associated with the proliferation, invasion, and migration of cancer cells. ERK1/2 is located at the distal end of this pathway and rarely undergoes mutations, making it an attractive target for anticancer drug development. Currently, an increasing number of ERK1/2 inhibitors have been designed and synthesized for antitumor therapy, among which representative compounds have entered clinical trials. When ERK1/2 signal transduction is eliminated, ERK5 may provide a bypass route to rescue proliferation, and weaken the potency of ERK1/2 inhibitors. Therefore, drug research targeting ERK5 or based on the compensatory mechanism of ERK5 for ERK1/2 opens up a new way for oncotherapy. This review provides an overview of the physiological and biological functions of ERKs, focuses on the structure-activity relationships of small molecule inhibitors targeting ERKs, with a view to providing guidance for future drug design and optimization, and discusses the potential therapeutic strategies to overcome drug resistance.
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Affiliation(s)
- Xiaoli Pan
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Junping Pei
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Aoxue Wang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Wen Shuai
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Lu Feng
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Faqian Bu
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Yumeng Zhu
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Lan Zhang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
- Corresponding authors. Tel./fax: +86 28 85503817.
| | - Guan Wang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
- Corresponding authors. Tel./fax: +86 28 85503817.
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
- Corresponding authors. Tel./fax: +86 28 85503817.
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10
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Karim RM, Bikowitz MJ, Chan A, Zhu JY, Grassie D, Becker A, Berndt N, Gunawan S, Lawrence NJ, Schönbrunn E. Differential BET Bromodomain Inhibition by Dihydropteridinone and Pyrimidodiazepinone Kinase Inhibitors. J Med Chem 2021; 64:15772-15786. [PMID: 34710325 DOI: 10.1021/acs.jmedchem.1c01096] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BRD4 and other members of the bromodomain and extraterminal (BET) family of proteins are promising epigenetic targets for the development of novel therapeutics. Among the reported BRD4 inhibitors are dihydropteridinones and benzopyrimidodiazepinones originally designed to target the kinases PLK1, ERK5, and LRRK2. While these kinase inhibitors were identified as BRD4 inhibitors, little is known about their binding potential and structural details of interaction with the other BET bromodomains. We comprehensively characterized a series of known and newly identified dual BRD4-kinase inhibitors against all eight individual BET bromodomains. A detailed analysis of 23 novel cocrystal structures of BET-kinase inhibitor complexes in combination with direct binding assays and cell signaling studies revealed significant differences in molecular shape complementarity and inhibitory potential. Collectively, the data offer new insights into the action of kinase inhibitors across BET bromodomains, which may aid the development of drugs to inhibit certain BET proteins and kinases differentially.
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Affiliation(s)
- Rezaul Md Karim
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States.,Department of Molecular Medicine, USF Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Melissa J Bikowitz
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States.,Department of Molecular Medicine, USF Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Alice Chan
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Jin-Yi Zhu
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Dylan Grassie
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Andreas Becker
- Chemical Biology Core, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Norbert Berndt
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Steven Gunawan
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Nicholas J Lawrence
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Ernst Schönbrunn
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States
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11
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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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12
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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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13
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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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14
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Beyond Kinase Activity: ERK5 Nucleo-Cytoplasmic Shuttling as a Novel Target for Anticancer Therapy. Int J Mol Sci 2020; 21:ijms21030938. [PMID: 32023850 PMCID: PMC7038028 DOI: 10.3390/ijms21030938] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 01/18/2023] Open
Abstract
The importance of mitogen-activated protein kinases (MAPK) in human pathology is underlined by the relevance of abnormalities of MAPK-related signaling pathways to a number of different diseases, including inflammatory disorders and cancer. One of the key events in MAPK signaling, especially with respect to pro-proliferative effects that are crucial for the onset and progression of cancer, is MAPK nuclear translocation and its role in the regulation of gene expression. The extracellular signal-regulated kinase 5 (ERK5) is the most recently discovered classical MAPK and it is emerging as a possible target for cancer treatment. The bigger size of ERK5 when compared to other MAPK enables multiple levels of regulation of its expression and activity. In particular, the phosphorylation of kinase domain and C-terminus, as well as post-translational modifications and chaperone binding, are involved in ERK5 regulation. Likewise, different mechanisms control ERK5 nucleo-cytoplasmic shuttling, underscoring the key role of ERK5 in the nuclear compartment. In this review, we will focus on the mechanisms involved in ERK5 trafficking between cytoplasm and nucleus, and discuss how these processes might be exploited to design new strategies for cancer treatment.
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