1
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Muli CS, Tarasov SG, Walters KJ. High-throughput assay exploiting disorder-to-order conformational switches: application to the proteasomal Rpn10:E6AP complex. Chem Sci 2024; 15:4041-4053. [PMID: 38487241 PMCID: PMC10935766 DOI: 10.1039/d3sc06370d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/05/2024] [Indexed: 03/17/2024] Open
Abstract
Conformational switching is pervasively driven by protein interactions, particularly for intrinsically disordered binding partners. We developed a dually orthogonal fluorescence-based assay to monitor such events, exploiting environmentally sensitive fluorophores. This assay is applied to E3 ligase E6AP, as its AZUL domain induces a disorder-to-order switch in an intrinsically disordered region of the proteasome, the so-named Rpn10 AZUL-binding domain (RAZUL). By testing various fluorophores, we developed an assay appropriate for high-throughput screening of Rpn10:E6AP-disrupting ligands. We found distinct positions in RAZUL for fluorophore labeling with either acrylodan or Atto610, which had disparate spectral responses to E6AP binding. E6AP caused a hypsochromic shift with increased fluorescence of acrylodan-RAZUL while decreasing fluorescence intensity of Atto610-RAZUL. Combining RAZUL labeled with either acrylodan or Atto610 into a common sample achieved robust and orthogonal measurement of the E6AP-induced conformational switch. This approach is generally applicable to disorder-to-order (or vice versa) transitions mediated by molecular interactions.
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Affiliation(s)
- Christine S Muli
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health Frederick MD 21702 USA
| | - Sergey G Tarasov
- Biophysics Resource, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health Frederick MD 21702 USA
| | - Kylie J Walters
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health Frederick MD 21702 USA
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2
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Allert MJ, Kumar S, Wang Y, Beese LS, Hellinga HW. Chromophore carbonyl twisting in fluorescent biosensors encodes direct readout of protein conformations with multicolor switching. Commun Chem 2023; 6:168. [PMID: 37598249 PMCID: PMC10439942 DOI: 10.1038/s42004-023-00982-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/11/2023] [Indexed: 08/21/2023] Open
Abstract
Fluorescent labeling of proteins is a powerful tool for probing structure-function relationships with many biosensing applications. Structure-based rules for systematically designing fluorescent biosensors require understanding ligand-mediated fluorescent response mechanisms which can be challenging to establish. We installed thiol-reactive derivatives of the naphthalene-based fluorophore Prodan into bacterial periplasmic glucose-binding proteins. Glucose binding elicited paired color exchanges in the excited and ground states of these conjugates. X-ray structures and mutagenesis studies established that glucose-mediated color switching arises from steric interactions that couple protein conformational changes to twisting of the Prodan carbonyl relative to its naphthalene plane. Mutations of residues contacting the carbonyl can optimize color switching by altering fluorophore conformational equilibria in the apo and glucose-bound proteins. A commonly accepted view is that Prodan derivatives report on protein conformations via solvatochromic effects due to changes in the dielectric of their local environment. Here we show that instead Prodan carbonyl twisting controls color switching. These insights enable structure-based biosensor design by coupling ligand-mediated protein conformational changes to internal chromophore twists through specific steric interactions between fluorophore and protein.
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Affiliation(s)
- Malin J Allert
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA
| | - Shivesh Kumar
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - You Wang
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA
| | - Lorena S Beese
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA
| | - Homme W Hellinga
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA.
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3
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La Sala G, Pfleger C, Käck H, Wissler L, Nevin P, Böhm K, Janet JP, Schimpl M, Stubbs CJ, De Vivo M, Tyrchan C, Hogner A, Gohlke H, Frolov AI. Combining structural and coevolution information to unveil allosteric sites. Chem Sci 2023; 14:7057-7067. [PMID: 37389247 PMCID: PMC10306073 DOI: 10.1039/d2sc06272k] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 06/02/2023] [Indexed: 07/01/2023] Open
Abstract
Understanding allosteric regulation in biomolecules is of great interest to pharmaceutical research and computational methods emerged during the last decades to characterize allosteric coupling. However, the prediction of allosteric sites in a protein structure remains a challenging task. Here, we integrate local binding site information, coevolutionary information, and information on dynamic allostery into a structure-based three-parameter model to identify potentially hidden allosteric sites in ensembles of protein structures with orthosteric ligands. When tested on five allosteric proteins (LFA-1, p38-α, GR, MAT2A, and BCKDK), the model successfully ranked all known allosteric pockets in the top three positions. Finally, we identified a novel druggable site in MAT2A confirmed by X-ray crystallography and SPR and a hitherto unknown druggable allosteric site in BCKDK validated by biochemical and X-ray crystallography analyses. Our model can be applied in drug discovery to identify allosteric pockets.
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Affiliation(s)
- Giuseppina La Sala
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca Gothenburg Sweden
| | - Christopher Pfleger
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf Germany
| | - Helena Käck
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Gothenburg Sweden
| | - Lisa Wissler
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Gothenburg Sweden
| | - Philip Nevin
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Gothenburg Sweden
| | - Kerstin Böhm
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Gothenburg Sweden
| | - Jon Paul Janet
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca Gothenburg Sweden
| | - Marianne Schimpl
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Cambridge UK
| | - Christopher J Stubbs
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Cambridge UK
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Design, Istituto Italiano di Tecnologia Via Morego 30 16163 Genoa Italy
| | - Christian Tyrchan
- Medicinal Chemistry, Research and Early Development, Respiratory & Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca Gothenburg Sweden
| | - Anders Hogner
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca Gothenburg Sweden
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Institute of Bio- and Geosciences (IBG-4: Bioinformatics) Forschungszentrum Jülich GmbH 52425 Jülich Germany
| | - Andrey I Frolov
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca Gothenburg Sweden
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4
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Cheng Z, Bhave M, Hwang SS, Rahman T, Chee XW. Identification of Potential p38γ Inhibitors via In Silico Screening, In Vitro Bioassay and Molecular Dynamics Simulation Studies. Int J Mol Sci 2023; 24:ijms24087360. [PMID: 37108523 PMCID: PMC10139033 DOI: 10.3390/ijms24087360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/06/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Protein kinase p38γ is an attractive target against cancer because it plays a pivotal role in cancer cell proliferation by phosphorylating the retinoblastoma tumour suppressor protein. Therefore, inhibition of p38γ with active small molecules represents an attractive alternative for developing anti-cancer drugs. In this work, we present a rigorous and systematic virtual screening framework to identify potential p38γ inhibitors against cancer. We combined the use of machine learning-based quantitative structure activity relationship modelling with conventional computer-aided drug discovery techniques, namely molecular docking and ligand-based methods, to identify potential p38γ inhibitors. The hit compounds were filtered using negative design techniques and then assessed for their binding stability with p38γ through molecular dynamics simulations. To this end, we identified a promising compound that inhibits p38γ activity at nanomolar concentrations and hepatocellular carcinoma cell growth in vitro in the low micromolar range. This hit compound could serve as a potential scaffold for further development of a potent p38γ inhibitor against cancer.
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Affiliation(s)
- Zixuan Cheng
- School of Engineering and Science, Swinburne University of Technology Sarawak, Kuching 93350, Malaysia
| | - Mrinal Bhave
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Melbourne, VIC 3122, Australia
| | - Siaw San Hwang
- School of Engineering and Science, Swinburne University of Technology Sarawak, Kuching 93350, Malaysia
| | - Taufiq Rahman
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK
| | - Xavier Wezen Chee
- School of Engineering and Science, Swinburne University of Technology Sarawak, Kuching 93350, Malaysia
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5
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Nguyen HT, Truong MNH, Le TV, Vo NT, Nguyen HD, Tran PH. A New Pathway for the Preparation of Pyrano[2,3- c]pyrazoles and molecular Docking as Inhibitors of p38 MAP Kinase. ACS OMEGA 2022; 7:17432-17443. [PMID: 35647469 PMCID: PMC9134431 DOI: 10.1021/acsomega.2c01814] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/27/2022] [Indexed: 05/09/2023]
Abstract
We report a new pathway to synthesize pyrano[2,3-c]pyrazoles and their binding mode to p38 MAP kinase. Pyrano[2,3-c]pyrazole derivatives have been prepared through a four-component reaction of benzyl alcohols, ethyl acetoacetate, phenylhydrazine, and malononitrile in the presence of sulfonated amorphous carbon and eosin Y as catalysts. All products were characterized by melting point, 1H and 13C NMR, and HRMS (ESI). The products were screened in silico for their binding activities to both the ATP-binding pocket and the lipid-binding pocket of p38 MAP kinase, using a structure-based flexible docking provided by the engine ADFR. The results showed that eight synthesized compounds had a higher affinity to the lipid pocket than to the other target site, which implied potential applications as allosteric inhibitors. Finally, the most biologically active compound, 5, had a binding affinity comparable to those of other proven lipid pocket inhibitors, with affinity to the target pocket reaching -10.9932 kcal/mol, and also had the best binding affinity to the ATP-binding pockets in all of our products. Thus, our research provides a novel pathway for synthesizing pyrano[2,3-c]pyrazoles and bioinformatic evidence for their biological capability to block p38 MAP kinase pockets, which could be useful for developing cancer or immune drugs.
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Affiliation(s)
- Hai Truong Nguyen
- Department
of Organic Chemistry, Faculty of Chemistry, University of Science, Ho Chi
Minh City 700000, Vietnam
- Vietnam
National University, Ho Chi
Minh City 700000, Vietnam
| | - Minh-Nhat Ha Truong
- Center
for Bioscience and Biotechnology, University
of Science, Ho Chi Minh City 700000, Vietnam
- Vietnam
National University, Ho Chi
Minh City 700000, Vietnam
| | - Tan Van Le
- Department
of Organic Chemistry, Faculty of Chemistry, University of Science, Ho Chi
Minh City 700000, Vietnam
- Vietnam
National University, Ho Chi
Minh City 700000, Vietnam
| | - Nam Tri Vo
- Center
for Bioscience and Biotechnology, University
of Science, Ho Chi Minh City 700000, Vietnam
- Vietnam
National University, Ho Chi
Minh City 700000, Vietnam
| | - Hoang Duc Nguyen
- Center
for Bioscience and Biotechnology, University
of Science, Ho Chi Minh City 700000, Vietnam
- Vietnam
National University, Ho Chi
Minh City 700000, Vietnam
- Email for H.D.N.:
| | - Phuong Hoang Tran
- Department
of Organic Chemistry, Faculty of Chemistry, University of Science, Ho Chi
Minh City 700000, Vietnam
- Vietnam
National University, Ho Chi
Minh City 700000, Vietnam
- Email for P.H.T.:
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6
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Zhang XH, Chen CH, Li H, Hsiang J, Wu X, Hu W, Horne D, Nam S, Shively J, Rosen ST. Targeting the non-ATP-binding pocket of the MAP kinase p38γ mediates a novel mechanism of cytotoxicity in cutaneous T-cell lymphoma (CTCL). FEBS Lett 2021; 595:2570-2592. [PMID: 34455585 PMCID: PMC8577799 DOI: 10.1002/1873-3468.14186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/31/2021] [Accepted: 08/19/2021] [Indexed: 02/01/2023]
Abstract
We describe here for the first time a lipid‐binding‐domain (LBD) in p38γ mitogen‐activated protein kinase (MAPK) involved in the response of T cells to a newly identified inhibitor, CSH71. We describe how CSH71, which binds to both the LBD and the ATP‐binding pocket of p38γ, is selectively cytotoxic to CTCL Hut78 cells but spares normal healthy peripheral blood mononuclear (PBMC) cells, and propose possible molecular mechanisms for its action. p38γ is a key player in CTCL development, and we expect that the ability to regulate its expression by specifically targeting the lipid‐binding domain will have important clinical relevance. Our findings characterize novel mechanisms of gene regulation in T lymphoma cells and validate the use of computational screening techniques to identify inhibitors for therapeutic development.
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Affiliation(s)
| | - Chih-Hong Chen
- Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Hongzhi Li
- Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Jack Hsiang
- Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Xiwei Wu
- Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Weidong Hu
- Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - David Horne
- Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Sangkil Nam
- Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Jack Shively
- Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Steven T Rosen
- Beckman Research Institute of City of Hope, Duarte, CA, USA
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7
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Wei S, Zhao T, Wang J, Zhai X. Approach in Improving Potency and Selectivity of Kinase Inhibitors: Allosteric Kinase Inhibitors. Mini Rev Med Chem 2021; 21:991-1003. [PMID: 33355051 DOI: 10.2174/1389557521666201222144355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/21/2020] [Accepted: 10/16/2020] [Indexed: 11/22/2022]
Abstract
Allostery is an efficient and particular regulatory mechanism to regulate protein functions. Different from conserved orthosteric sites, allosteric sites have a distinctive functional mechanism to form the complex regulatory network. In drug discovery, kinase inhibitors targeting the allosteric pockets have received extensive attention for the advantages of high selectivity and low toxicity. The approval of trametinib as the first allosteric inhibitor validated that allosteric inhibitors could be used as effective therapeutic drugs for the treatment of diseases. To date, a wide range of allosteric inhibitors have been identified. In this perspective, we outline different binding modes and potential advantages of allosteric inhibitors. In the meantime, the research processes of typical and novel allosteric inhibitors are described briefly in terms of structure-activity relationships, ligand-protein interactions, and in vitro and in vivo activity. Additionally, challenges, as well as opportunities, are also presented.
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Affiliation(s)
- Shangfei Wei
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Tianming Zhao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Jie Wang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xin Zhai
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
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8
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Agnew C, Liu L, Liu S, Xu W, You L, Yeung W, Kannan N, Jablons D, Jura N. The crystal structure of the protein kinase HIPK2 reveals a unique architecture of its CMGC-insert region. J Biol Chem 2019; 294:13545-13559. [PMID: 31341017 PMCID: PMC6746438 DOI: 10.1074/jbc.ra119.009725] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/11/2019] [Indexed: 01/07/2023] Open
Abstract
The homeodomain-interacting protein kinase (HIPK) family is comprised of four nuclear protein kinases, HIPK1-4. HIPK proteins phosphorylate a diverse range of transcription factors involved in cell proliferation, differentiation, and apoptosis. HIPK2, thus far the best-characterized member of this largely understudied family of protein kinases, plays a role in the activation of p53 in response to DNA damage. Despite this tumor-suppressor function, HIPK2 is also found overexpressed in several cancers, and its hyperactivation causes chronic fibrosis. There are currently no structures of HIPK2 or of any other HIPK kinase. Here, we report the crystal structure of HIPK2's kinase domain bound to CX-4945, a casein kinase 2α (CK2α) inhibitor currently in clinical trials against several cancers. The structure, determined at 2.2 Å resolution, revealed that CX-4945 engages the HIPK2 active site in a hybrid binding mode between that seen in structures of CK2α and Pim1 kinases. The HIPK2 kinase domain crystallized in the active conformation, which was stabilized by phosphorylation of the activation loop. We noted that the overall kinase domain fold of HIPK2 closely resembles that of evolutionarily related dual-specificity tyrosine-regulated kinases (DYRKs). Most significant structural differences between HIPK2 and DYRKs included an absence of the regulatory N-terminal domain and a unique conformation of the CMGC-insert region and of a newly defined insert segment in the αC-β4 loop. This first crystal structure of HIPK2 paves the way for characterizing the understudied members of the HIPK family and for developing HIPK2-directed therapies for managing cancer and fibrosis.
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Affiliation(s)
- Christopher Agnew
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94158
| | - Lijun Liu
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94158
| | - Shu Liu
- Thoracic Oncology Laboratory, Department of Surgery, Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94115
| | - Wei Xu
- Thoracic Oncology Laboratory, Department of Surgery, Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94115
| | - Liang You
- Thoracic Oncology Laboratory, Department of Surgery, Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94115
| | - Wayland Yeung
- Institute of Bioinformatics and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Natarajan Kannan
- Institute of Bioinformatics and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - David Jablons
- Thoracic Oncology Laboratory, Department of Surgery, Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94115, Supported by the Kazan McClain Partners' Foundation and the H. N. and Frances C. Berger Foundation. To whom correspondence may be addressed:
1600 Divisadero St., A745, San Francisco, CA 94115. Tel.:
415-353-7502; E-mail:
| | - Natalia Jura
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94158,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, To whom correspondence may be addressed:
555 Mission Bay Blvd. S., Rm. 452W, San Francisco, CA 94158. Tel.:
415-514-1133; E-mail:
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9
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Panicker RC, Chattopadhaya S, Coyne AG, Srinivasan R. Allosteric Small-Molecule Serine/Threonine Kinase Inhibitors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:253-278. [PMID: 31707707 DOI: 10.1007/978-981-13-8719-7_11] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Deregulation of protein kinase activity has been linked to many diseases ranging from cancer to AIDS and neurodegenerative diseases. Not surprisingly, drugging the human kinome - the complete set of kinases encoded by the human genome - has been one of the major drug discovery pipelines. Majority of the approved clinical kinase inhibitors target the ATP binding site of kinases. However, the remarkable sequence and structural similarity of ATP binding pockets of kinases make selective inhibition of kinases a daunting task. To circumvent these issues, allosteric inhibitors that target sites other than the orthosteric ATP binding pocket have been developed. The structural diversity of the allosteric sites allows these inhibitors to have higher selectivity, lower toxicity and improved physiochemical properties and overcome drug resistance associated with the use of conventional kinase inhibitors. In this chapter, we will focus on the allosteric inhibitors of selected serine/threonine kinases, outline the benefits of using these inhibitors and discuss the challenges and future opportunities.
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Affiliation(s)
- Resmi C Panicker
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, People's Republic of China
| | | | - Anthony G Coyne
- University Chemical Laboratory, University of Cambridge, Cambridge, UK
| | - Rajavel Srinivasan
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, People's Republic of China.
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10
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Wolle P, Weisner J, Keul M, Landel I, Lategahn J, Rauh D. RASPELD to Perform High-End Screening in an Academic Environment toward the Development of Cancer Therapeutics. ChemMedChem 2018; 13:2065-2072. [DOI: 10.1002/cmdc.201800477] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Patrik Wolle
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Jörn Weisner
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Marina Keul
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Ina Landel
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Jonas Lategahn
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Daniel Rauh
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
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11
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Bührmann M, Hardick J, Weisner J, Quambusch L, Rauh D. Kovalente Liganden zur Adressierung einer lipophilen Bindetasche in der MAPK p38 α. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mike Bührmann
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Julia Hardick
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Jörn Weisner
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Lena Quambusch
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Daniel Rauh
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
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12
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Bührmann M, Hardick J, Weisner J, Quambusch L, Rauh D. Covalent Lipid Pocket Ligands Targeting p38α MAPK Mutants. Angew Chem Int Ed Engl 2017; 56:13232-13236. [DOI: 10.1002/anie.201706345] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Mike Bührmann
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Julia Hardick
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Jörn Weisner
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Lena Quambusch
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Daniel Rauh
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
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13
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Bührmann M, Wiedemann BM, Müller MP, Hardick J, Ecke M, Rauh D. Structure-based design, synthesis and crystallization of 2-arylquinazolines as lipid pocket ligands of p38α MAPK. PLoS One 2017; 12:e0184627. [PMID: 28892510 PMCID: PMC5593189 DOI: 10.1371/journal.pone.0184627] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/28/2017] [Indexed: 12/27/2022] Open
Abstract
In protein kinase research, identifying and addressing small molecule binding sites other than the highly conserved ATP-pocket are of intense interest because this line of investigation extends our understanding of kinase function beyond the catalytic phosphotransfer. Such alternative binding sites may be involved in altering the activation state through subtle conformational changes, control cellular enzyme localization, or in mediating and disrupting protein-protein interactions. Small organic molecules that target these less conserved regions might serve as tools for chemical biology research and to probe alternative strategies in targeting protein kinases in disease settings. Here, we present the structure-based design and synthesis of a focused library of 2-arylquinazoline derivatives to target the lipophilic C-terminal binding pocket in p38α MAPK, for which a clear biological function has yet to be identified. The interactions of the ligands with p38α MAPK was analyzed by SPR measurements and validated by protein X-ray crystallography.
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Affiliation(s)
- Mike Bührmann
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Bianca M. Wiedemann
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Matthias P. Müller
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Julia Hardick
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Maria Ecke
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Daniel Rauh
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
- * E-mail:
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14
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Halekotte J, Witt L, Ianes C, Krüger M, Bührmann M, Rauh D, Pichlo C, Brunstein E, Luxenburger A, Baumann U, Knippschild U, Bischof J, Peifer C. Optimized 4,5-Diarylimidazoles as Potent/Selective Inhibitors of Protein Kinase CK1δ and Their Structural Relation to p38α MAPK. Molecules 2017; 22:molecules22040522. [PMID: 28338621 PMCID: PMC6154583 DOI: 10.3390/molecules22040522] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/17/2017] [Accepted: 03/20/2017] [Indexed: 02/07/2023] Open
Abstract
The involvement of protein kinase CK1δ in the pathogenesis of severe disorders such as Alzheimer’s disease, amyotrophic lateral sclerosis, familial advanced sleep phase syndrome, and cancer has dramatically increased interest in the development of effective small molecule inhibitors for both therapeutic application and basic research. Unfortunately, the design of CK1 isoform-specific compounds has proved to be highly complicated due to the existence of six evolutionarily conserved human CK1 members that possess similar, different, or even opposite physiological and pathophysiological implications. Consequently, only few potent and selective CK1δ inhibitors have been reported so far and structurally divergent approaches are urgently needed in order to establish SAR that might enable complete discrimination of CK1 isoforms and related p38α MAPK. In this study we report on design and characterization of optimized 4,5-diarylimidazoles as highly effective ATP-competitive inhibitors of CK1δ with compounds 11b (IC50 CK1δ = 4 nM, IC50 CK1ε = 25 nM), 12a (IC50 CK1δ = 19 nM, IC50 CK1ε = 227 nM), and 16b (IC50 CK1δ = 8 nM, IC50 CK1ε = 81 nM) being among the most potent CK1δ-targeting agents published to date. Inhibitor compound 11b, displaying potential as a pharmacological tool, has further been profiled over a panel of 321 protein kinases exhibiting high selectivity. Cellular efficacy has been evaluated in human pancreatic cancer cell lines Colo357 (EC50 = 3.5 µM) and Panc89 (EC50 = 1.5 µM). SAR is substantiated by X-ray crystallographic analysis of 16b in CK1δ and 11b in p38α.
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Affiliation(s)
- Jakob Halekotte
- Institute of Pharmacy, Christian-Albrechts-University of Kiel, Gutenbergstraße 76, D-24118 Kiel, Germany.
| | - Lydia Witt
- Institute of Pharmacy, Christian-Albrechts-University of Kiel, Gutenbergstraße 76, D-24118 Kiel, Germany.
| | - Chiara Ianes
- Department of General and Visceral Surgery, Ulm University Hospital, Albert-Einstein-Allee 23, D-89081 Ulm, Germany.
| | - Marc Krüger
- Department of General and Visceral Surgery, Ulm University Hospital, Albert-Einstein-Allee 23, D-89081 Ulm, Germany.
| | - Mike Bührmann
- Institute of Chemical Biology, Dortmund University of Technology, Otto-Hahn-Straße 4a, D-44227 Dortmund, Germany.
| | - Daniel Rauh
- Institute of Chemical Biology, Dortmund University of Technology, Otto-Hahn-Straße 4a, D-44227 Dortmund, Germany.
| | - Christian Pichlo
- Department for Chemistry, University of Cologne, Otto-Fischer-Straße 12-14, D-50674 Cologne, Germany.
| | - Elena Brunstein
- Department for Chemistry, University of Cologne, Otto-Fischer-Straße 12-14, D-50674 Cologne, Germany.
| | - Andreas Luxenburger
- The Ferrier Research Institute, Victoria University of Wellington, Gracefield Research Centre, 69 Gracefield Road, Lower Hutt P.O. Box 33-436, New Zealand.
| | - Ulrich Baumann
- Department for Chemistry, University of Cologne, Otto-Fischer-Straße 12-14, D-50674 Cologne, Germany.
| | - Uwe Knippschild
- Department of General and Visceral Surgery, Ulm University Hospital, Albert-Einstein-Allee 23, D-89081 Ulm, Germany.
| | - Joachim Bischof
- Department of General and Visceral Surgery, Ulm University Hospital, Albert-Einstein-Allee 23, D-89081 Ulm, Germany.
| | - Christian Peifer
- Institute of Pharmacy, Christian-Albrechts-University of Kiel, Gutenbergstraße 76, D-24118 Kiel, Germany.
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15
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Shang J, Lu S, Jiang Y, Zhang J. Allosteric modulators of MEK1: drug design and discovery. Chem Biol Drug Des 2016; 88:485-97. [PMID: 27115708 DOI: 10.1111/cbdd.12780] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 04/01/2016] [Accepted: 04/18/2016] [Indexed: 12/20/2022]
Abstract
Mitogen-activated protein kinase kinase (MAPKK, MEK) mediates signal transduction, controlling cell proliferation and survival. MEK occupies a key downstream position in the Ras-Raf-MEK-ERK signaling pathway, implying that inhibition of MEK will potently suppress tumor cell growth, with potential applications in cancer therapy. Based on the promising therapeutic effects of MEK modulators, continued efforts have been made in this class. Here, we review the discovery and development of MEK1 allosteric modulators, classifying them into four structural groups. The allosteric mechanisms and recent clinical progress involving these modulators are also reviewed.
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Affiliation(s)
- Jialin Shang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Yongjun Jiang
- School of Biotechnology and Chemical Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China. .,Medicinal Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai, China.
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16
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Becker C, Öcal S, Nguyen HD, Phan T, Keul M, Simard JR, Rauh D. Monitoring Conformational Changes in the Receptor Tyrosine Kinase EGFR. Chembiochem 2016; 17:990-4. [DOI: 10.1002/cbic.201600115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Christian Becker
- Technische Universität Dortmund; Fakultät für Chemie und Chemische Biologie; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Sinan Öcal
- Chemical Genomics Centre; Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 15 44227 Dortmund Germany
- University of Cologne; Department of Mathematics and Natural Sciences; Institute of Biochemistry; Otto-Fischer-Strasse 12-14 50674 Köln Germany
| | - Hoang D. Nguyen
- Chemical Genomics Centre; Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 15 44227 Dortmund Germany
- University of Science; Vietnam National University-Ho Chi Minh City; 227 Nguyen Van Cu Str., Dist. 5 Ho Chi Minh City Vietnam
| | - Trang Phan
- Chemical Genomics Centre; Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 15 44227 Dortmund Germany
- University of Science; Vietnam National University-Ho Chi Minh City; 227 Nguyen Van Cu Str., Dist. 5 Ho Chi Minh City Vietnam
| | - Marina Keul
- Technische Universität Dortmund; Fakultät für Chemie und Chemische Biologie; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Jeffrey R. Simard
- Chemical Genomics Centre; Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 15 44227 Dortmund Germany
- Amgen Inc.; 360 Binney Street Cambridge MA 02142 USA
| | - Daniel Rauh
- Technische Universität Dortmund; Fakultät für Chemie und Chemische Biologie; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
- Chemical Genomics Centre; Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 15 44227 Dortmund Germany
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17
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González-Vera JA, Morris MC. Fluorescent Reporters and Biosensors for Probing the Dynamic Behavior of Protein Kinases. Proteomes 2015; 3:369-410. [PMID: 28248276 PMCID: PMC5217393 DOI: 10.3390/proteomes3040369] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/30/2015] [Accepted: 10/23/2015] [Indexed: 12/20/2022] Open
Abstract
Probing the dynamic activities of protein kinases in real-time in living cells constitutes a major challenge that requires specific and sensitive tools tailored to meet the particular demands associated with cellular imaging. The development of genetically-encoded and synthetic fluorescent biosensors has provided means of monitoring protein kinase activities in a non-invasive fashion in their native cellular environment with high spatial and temporal resolution. Here, we review existing technologies to probe different dynamic features of protein kinases and discuss limitations where new developments are required to implement more performant tools, in particular with respect to infrared and near-infrared fluorescent probes and strategies which enable improved signal-to-noise ratio and controlled activation of probes.
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Affiliation(s)
- Juan A González-Vera
- Cell Cycle Biosensors & Inhibitors, Department of Amino Acids, Peptides and Proteins, Institute of Biomolecules Max Mousseron (IBMM) CNRS-UMR 5247, 15 Avenue Charles Flahault, Montpellier 34093, France.
| | - May C Morris
- Cell Cycle Biosensors & Inhibitors, Department of Amino Acids, Peptides and Proteins, Institute of Biomolecules Max Mousseron (IBMM) CNRS-UMR 5247, 15 Avenue Charles Flahault, Montpellier 34093, France.
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18
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Brummond KM, Kocsis LS. Intramolecular didehydro-Diels-Alder reaction and its impact on the structure-function properties of environmentally sensitive fluorophores. Acc Chem Res 2015. [PMID: 26207414 DOI: 10.1021/acs.accounts.5b00126] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Reaction discovery plays a vital role in accessing new chemical entities and materials possessing important function.1 In this Account, we delineate our reaction discovery program regarding the [4 + 2] cycloaddition reaction of styrene-ynes. In particular, we highlight our studies that lead to the realization of the diverging reaction mechanisms of the intramolecular didehydro-Diels-Alder (IMDDA) reaction to afford dihydronaphthalene and naphthalene products. Formation of the former involves an intermolecular hydrogen atom abstraction and isomerization, whereas the latter is formed via an unexpected elimination of H2. Forming aromatic compounds by a unimolecular elimination of H2 offers an environmentally benign alternative to typical oxidation protocols. We also include in this Account ongoing work focused on expanding the scope of this reaction, mainly its application to the preparation of cyclopenta[b]naphthalenes. Finally, we showcase the synthetic utility of the IMDDA reaction by preparing novel environmentally sensitive fluorophores. The choice to follow this path was largely influenced by the impact this reaction could have on our understanding of the structure-function relationships of these molecular sensors by taking advantage of a de novo construction and functionalization of the aromatic portion of these compounds. We were also inspired by the fact that, despite the advances that have been made in the construction of small molecule fluorophores, access to rationally designed fluorescent probes or sensors possessing varied and tuned photophysical, spectral, and chemical properties are still needed. To this end, we report our studies to correlate fluorophore structure with photophysical property relationships for a series of solvatochromic PRODAN analogs and viscosity-sensitive cyanoacrylate analogs. The versatility of this de novo strategy for fluorophore synthesis was demonstrated by showing that a number of functional groups could be installed at various locations, including handles for eventual biomolecule attachment or water-solubilizing groups. Further, biothiol sensors were designed, and we expect these to be of general utility for the study of lipid dynamics in cellular membranes and for the detection of protein-binding interactions, ideal applications for these relatively hydrophobic fluorophores. Future studies will be directed toward expanding this chemistry-driven approach to the rational preparation of fluorophores with enhanced photophysical and chemical properties for application in biological systems.
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Affiliation(s)
- Kay M. Brummond
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15206, United States
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19
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Astolfi A, Iraci N, Manfroni G, Barreca ML, Cecchetti V. A Comprehensive Structural Overview of p38α MAPK in Complex with Type I Inhibitors. ChemMedChem 2015; 10:957-69. [PMID: 26012502 DOI: 10.1002/cmdc.201500030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/05/2015] [Indexed: 12/12/2022]
Abstract
p38α mitogen-activated protein kinase (MAPK) is a well-recognized therapeutic target for the treatment of autoimmune and inflammatory diseases. Over the past two decades, tremendous efforts have been focused on the discovery and development of small-molecule p38α MAPK inhibitors, although currently no drugs targeting this protein are clinically available. Therefore, the identification of novel chemotypes that are able to inhibit p38α MAPK function is still of great therapeutic significance. With the objective to support drug discovery programs aimed at identifying new immunomodulators acting on p38α MAPK, herein we present a complete overview of the available crystal structures of this protein in complex with ATP-site type I inhibitors. The 85 available complexes are classified by chemotype and experimental binding mode, and the ligand-protein interactions are discussed using the most representative inhibitors. The type and frequency of key inhibitor features are analyzed to give a final summary of the chemical requirements of promising p38α MAPK inhibitors. The proposed pharmacophore can be exploited to enhance the opportunities to identify novel type I inhibitors of p38α MAPK.
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Affiliation(s)
- Andrea Astolfi
- Department of Pharmaceutical Sciences, University of Perugia, Via A. Fabretti 48, 06123 Perugia (Italy)
| | - Nunzio Iraci
- Department of Pharmaceutical Sciences, University of Perugia, Via A. Fabretti 48, 06123 Perugia (Italy)
| | - Giuseppe Manfroni
- Department of Pharmaceutical Sciences, University of Perugia, Via A. Fabretti 48, 06123 Perugia (Italy)
| | - Maria Letizia Barreca
- Department of Pharmaceutical Sciences, University of Perugia, Via A. Fabretti 48, 06123 Perugia (Italy).
| | - Violetta Cecchetti
- Department of Pharmaceutical Sciences, University of Perugia, Via A. Fabretti 48, 06123 Perugia (Italy)
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20
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Fang Z, Simard JR, Plenker D, Nguyen HD, Phan T, Wolle P, Baumeister S, Rauh D. Discovery of inter-domain stabilizers-a novel assay system for allosteric akt inhibitors. ACS Chem Biol 2015; 10:279-88. [PMID: 24959717 DOI: 10.1021/cb500355c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In addition to the catalytically active kinase domain, most kinases feature regulatory domains that govern their activity. Modulating and interfering with these interdomain interactions presents a major opportunity for understanding biological systems and developing novel therapeutics. Therefore, small molecule inhibitors that target these interactions through an allosteric mode of action have high intrinsic selectivity, as these interactions are often unique to a single kinase or kinase family. Here we report the development of iFLiK (interface-Fluorescent Labels in Kinases), a fluorescence-based assay that can monitor such interdomain interactions. Using iFLiK, we have demonstrated selective detection of allosteric Akt inhibitors that induce an inactive closed conformation unique to Akt. This methodology easily distinguished small molecule allosteric inhibitors from classic ATP-competitive inhibitors. Screening an in-house compound library with iFLiK, we were able to identify novel compounds with a scaffold that has not been previously described for allosteric Akt inhibitors.
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Affiliation(s)
- Zhizhou Fang
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
- Chemical
Genomics
Centre of the Max Planck Society, Otto-Hahn-Strasse
15, 44227 Dortmund, Germany
| | - Jeffrey R. Simard
- Chemical
Genomics
Centre of the Max Planck Society, Otto-Hahn-Strasse
15, 44227 Dortmund, Germany
| | - Dennis Plenker
- University of Cologne, Medical Faculty, Department
of Translational Genomics, Weyertal 115b, 50931 Cologne, Germany
| | - Hoang D. Nguyen
- Chemical
Genomics
Centre of the Max Planck Society, Otto-Hahn-Strasse
15, 44227 Dortmund, Germany
| | - Trang Phan
- Chemical
Genomics
Centre of the Max Planck Society, Otto-Hahn-Strasse
15, 44227 Dortmund, Germany
| | - Patrik Wolle
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Stefan Baumeister
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Daniel Rauh
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
- Chemical
Genomics
Centre of the Max Planck Society, Otto-Hahn-Strasse
15, 44227 Dortmund, Germany
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21
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Lennarz S, Heider E, Blind M, Mayer G. An aptamer to the MAP kinase insert region. ACS Chem Biol 2015; 10:320-7. [PMID: 25184543 DOI: 10.1021/cb5005756] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Targeting functional, non-catalytic domains of protein kinases or other proteins is an emerging field in chemical biology research. Non-ATP competitive kinase inhibitors allow for the investigation of active-site independent functions, e.g., the biological role of protein-protein interactions. These inhibitors also serve as a starting point for developing novel therapeutic strategies. However, the identification of such inhibitors by means of conventional low molecular weight compounds represents a great challenge in modern drug discovery. Employing the mitogen-activated protein (MAP) kinase Erk2, we show that RNA aptamers have the capacity to be a novel, promising class of protein kinase inhibitors that can be applied to target individual subdomains and block domain specific functions without affecting kinase activity per se.
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Affiliation(s)
- Sabine Lennarz
- Life and Medical Sciences Institute, Gerhard-Domagk-Str.1, 53121 Bonn, Germany
| | - Elena Heider
- Life and Medical Sciences Institute, Gerhard-Domagk-Str.1, 53121 Bonn, Germany
| | - Michael Blind
- Life and Medical Sciences Institute, Gerhard-Domagk-Str.1, 53121 Bonn, Germany
| | - Günter Mayer
- Life and Medical Sciences Institute, Gerhard-Domagk-Str.1, 53121 Bonn, Germany
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22
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Abstract
The quest for ever more selective kinase inhibitors as potential future drugs has yielded a large repertoire of chemical probes that are selective for specific kinase conformations. These probes have been useful tools to obtain structural snapshots of kinase conformational plasticity. Similarly, kinetic and thermodynamic inhibitor binding experiments provide glimpses at the time scales and energetics of conformational interconversions. These experimental insights are complemented by computational predictions of conformational energy landscapes and simulations of conformational transitions and of the process of inhibitors binding to the protein kinase domain. A picture emerges in which highly selective inhibitors capitalize on the dynamic nature of kinases.
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Affiliation(s)
- Michael Tong
- Department
of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, United States
| | - Markus A. Seeliger
- Department
of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, United States
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23
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Novel approaches for targeting kinases: allosteric inhibition, allosteric activation and pseudokinases. Future Med Chem 2014; 6:541-61. [PMID: 24649957 DOI: 10.4155/fmc.13.216] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Protein kinases are involved in many essential cellular processes and their deregulation can lead to a variety of diseases, including cancer. The pharmaceutical industry has invested heavily in the identification of kinase inhibitors to modulate these disease-promoting pathways, resulting in several successful drugs. However, the field is challenging as it is difficult to identify novel selective inhibitors with good pharmacokinetic/pharmacodynamic properties. In addition, resistance to kinase inhibitor treatment frequently arises. The identification of non-ATP site targeting ('allosteric') inhibitors, the identification of kinase activators and the expansion of kinase target space to include the less studied members of the family, including atypical- and pseudo-kinases, are potential avenues to overcome these challenges. In this perspective, the opportunities and challenges of following these approaches and others will be discussed.
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24
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Fluorescent biosensors for drug discovery new tools for old targets--screening for inhibitors of cyclin-dependent kinases. Eur J Med Chem 2014; 88:74-88. [PMID: 25314935 DOI: 10.1016/j.ejmech.2014.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 09/29/2014] [Accepted: 10/01/2014] [Indexed: 12/12/2022]
Abstract
Cyclin-dependent kinases play central roles in regulation of cell cycle progression, transcriptional regulation and other major biological processes such as neuronal differentiation and metabolism. These kinases are hyperactivated in most human cancers and constitute attractive pharmacological targets. A large number of ATP-competitive inhibitors of CDKs have been identified from natural substances, in high throughput screening assays, or through structure-guided approaches. Alternative strategies have been explored to target essential protein/protein interfaces and screen for allosteric inhibitors that trap inactive intermediates or prevent conformational activation. However this remains a major challenge given the highly conserved structural features of these kinases, and calls for new and alternative screening technologies. Fluorescent biosensors constitute powerful tools for the detection of biomolecules in complex biological samples, and are well suited to study dynamic processes and highlight molecular alterations associated with pathological disorders. They further constitute sensitive and selective tools which can be readily implemented to high throughput and high content screens in drug discovery programmes. Our group has developed fluorescent biosensors to probe cyclin-dependent kinases and gain insight into their molecular behaviour in vitro and in living cells. These tools provide a means of monitoring subtle alterations in the abundance and activity of CDK/Cyclins and can respond to compounds that interfere with the conformational dynamics of these kinases. In this review we discuss the different strategies which have been devised to target CDK/Cyclins, and describe the implementation of our CDK/Cyclin biosensors to develop HTS/HCS assays in view of identifying new classes of inhibitors for cancer therapeutics.
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25
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Richters A, Nguyen HD, Phan T, Simard JR, Grütter C, Engel J, Rauh D. Identification of Type II and III DDR2 Inhibitors. J Med Chem 2014; 57:4252-62. [DOI: 10.1021/jm500167q] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- André Richters
- Department
of Chemistry and Chemical Biology, Technical University of Dortmund, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Hoang D. Nguyen
- Chemical
Genomics Centre of the Max Planck Society, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Trang Phan
- Chemical
Genomics Centre of the Max Planck Society, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Jeffrey R. Simard
- Chemical
Genomics Centre of the Max Planck Society, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Christian Grütter
- Department
of Chemistry and Chemical Biology, Technical University of Dortmund, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Julian Engel
- Department
of Chemistry and Chemical Biology, Technical University of Dortmund, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Daniel Rauh
- Department
of Chemistry and Chemical Biology, Technical University of Dortmund, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
- Chemical
Genomics Centre of the Max Planck Society, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
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26
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Simard JR, Rauh D. FLiK: a direct-binding assay for the identification and kinetic characterization of stabilizers of inactive kinase conformations. Methods Enzymol 2014; 548:147-71. [PMID: 25399645 DOI: 10.1016/b978-0-12-397918-6.00006-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Despite the hundreds of kinase inhibitors currently in discovery and preclinical phases, the number of FDA-approved kinase inhibitors remains very low by comparison, a discrepancy which reflects the challenges which accompanies kinase inhibitor development. Targeting protein kinases with ATP-competitive inhibitors has been the classical approach to inhibit kinase activity, but the highly conserved nature of the ATP-binding site often contributes to the poor inhibitor selectivity. To address this problem, we developed a high-throughput screening technology that can discriminate for inhibitors, which stabilize inactive kinase conformations by binding within allosteric pockets in the kinase domain. Here, we describe how to use the Fluorescence Labels in Kinases approach to measure the K(d) of ligands as well as how to kinetically characterize the binding and dissociation of ligands to the kinase. We also describe how this technology can be used to rapidly screen small molecule libraries in high throughput.
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Affiliation(s)
- Jeffrey R Simard
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany.
| | - Daniel Rauh
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany; Fakultät Chemie, Chemische Biologie, Technische Universität Dortmund, Dortmund, Germany.
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27
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Prével C, Pellerano M, Van TNN, Morris MC. Fluorescent biosensors for high throughput screening of protein kinase inhibitors. Biotechnol J 2013; 9:253-65. [PMID: 24357625 DOI: 10.1002/biot.201300196] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 07/24/2013] [Accepted: 10/30/2013] [Indexed: 12/11/2022]
Abstract
High throughput screening assays aim to identify small molecules that interfere with protein function, activity, or conformation, which can serve as effective tools for chemical biology studies of targets involved in physiological processes or pathways of interest or disease models, as well as templates for development of therapeutics in medicinal chemistry. Fluorescent biosensors constitute attractive and powerful tools for drug discovery programs, from high throughput screening assays, to postscreen characterization of hits, optimization of lead compounds, and preclinical evaluation of candidate drugs. They provide a means of screening for inhibitors that selectively target enzymatic activity, conformation, and/or function in vitro. Moreover, fluorescent biosensors constitute useful tools for cell- and image-based, multiplex and multiparametric, high-content screening. Application of fluorescence-based sensors to screen large and complex libraries of compounds in vitro, in cell-based formats or whole organisms requires several levels of optimization to establish robust and reproducible assays. In this review, we describe the different fluorescent biosensor technologies which have been applied to high throughput screens, and discuss the prerequisite criteria underlying their successful application. Special emphasis is placed on protein kinase biosensors, since these enzymes constitute one of the most important classes of therapeutic targets in drug discovery.
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Affiliation(s)
- Camille Prével
- CRBM-CNRS-UMR 5237, Chemical Biology and Nanotechnology for Therapeutics, 1919 Route de Mende, 34293 Montpellier, France
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28
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Schneider R, Gohla A, Simard JR, Yadav DB, Fang Z, van Otterlo WAL, Rauh D. Overcoming compound fluorescence in the FLiK screening assay with red-shifted fluorophores. J Am Chem Soc 2013; 135:8400-8. [PMID: 23672540 DOI: 10.1021/ja403074j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In the attempt to discover novel chemical scaffolds that can modulate the activity of disease-associated enzymes, such as kinases, biochemical assays are usually deployed in high-throughput screenings. First-line assays, such as activity-based assays, often rely on fluorescent molecules by measuring a change in the total emission intensity, polarization state, or energy transfer to another fluorescent molecule. However, under certain conditions, intrinsic compound fluorescence can lead to difficult data analysis and to false-positive, as well as false-negative, hits. We have reported previously on a powerful direct binding assay called fluorescent labels in kinases ('FLiK'), which enables a sensitive measurement of conformational changes in kinases upon ligand binding. In this assay system, changes in the emission spectrum of the fluorophore acrylodan, induced by the binding of a ligand, are translated into a robust assay readout. However, under the excitation conditions of acrylodan, intrinsic compound fluorescence derived from highly conjugated compounds complicates data analysis. We therefore optimized this method by identifying novel fluorophores that excite in the far red, thereby avoiding compound fluorescence. With this advancement, even rigid compounds with multiple π-conjugated ring systems can now be measured reliably. This study was performed on three different kinase constructs with three different labeling sites, each undergoing distinct conformational changes upon ligand binding. It may therefore serve as a guideline for the establishment of novel fluorescence-based detection assays.
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Affiliation(s)
- Ralf Schneider
- Chemical Genomics Centre of the Max-Planck-Society , Otto-Hahn-Strasse 15, 44137 Dortmund, Germany
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Schneider R, Beumer C, Simard JR, Grütter C, Rauh D. Selective Detection of Allosteric Phosphatase Inhibitors. J Am Chem Soc 2013; 135:6838-41. [DOI: 10.1021/ja4030484] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Ralf Schneider
- Chemical Genomics Centre der Max-Planck-Gesellschaft, Otto-Hahn-Strasse 15, 44227
Dortmund, Germany
| | - Claudia Beumer
- Fakultät
Chemie−Chemische
Biologie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Jeffrey R. Simard
- Chemical Genomics Centre der Max-Planck-Gesellschaft, Otto-Hahn-Strasse 15, 44227
Dortmund, Germany
| | - Christian Grütter
- Fakultät
Chemie−Chemische
Biologie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Daniel Rauh
- Chemical Genomics Centre der Max-Planck-Gesellschaft, Otto-Hahn-Strasse 15, 44227
Dortmund, Germany
- Fakultät
Chemie−Chemische
Biologie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
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Fang Z, Grütter C, Rauh D. Strategies for the selective regulation of kinases with allosteric modulators: exploiting exclusive structural features. ACS Chem Biol 2013; 8:58-70. [PMID: 23249378 DOI: 10.1021/cb300663j] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The modulation of kinase function has become an important goal in modern drug discovery and chemical biology research. In cancer-targeted therapies, kinase inhibitors have been experiencing an upsurge, which can be measured by the increasing number of kinase inhibitors approved by the FDA in recent years. However, lack of efficacy, limited selectivity, and the emergence of acquired drug resistance still represent major bottlenecks in the clinic and challenge inhibitor development. Most known kinase inhibitors target the active kinase and are ATP competitive. A second class of small organic molecules, which address remote sites of the kinase and stabilize enzymatically inactive conformations, is rapidly moving to the forefront of kinase inhibitor research. Such allosteric modulators bind to sites that are less conserved across the kinome and only accessible upon conformational changes. These molecules are therefore thought to provide various advantages such as higher selectivity and extended drug target residence times. This review highlights various strategies that have been developed to utilizing exclusive structural features of kinases and thereby modulating their activity allosterically.
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Affiliation(s)
- Zhizhou Fang
- Technische Universität Dortmund, Fakultät
Chemie − Chemische Biologie, Otto-Hahn-Strasse
6, D-44227 Dortmund, Germany
| | - Christian Grütter
- Technische Universität Dortmund, Fakultät
Chemie − Chemische Biologie, Otto-Hahn-Strasse
6, D-44227 Dortmund, Germany
| | - Daniel Rauh
- Technische Universität Dortmund, Fakultät
Chemie − Chemische Biologie, Otto-Hahn-Strasse
6, D-44227 Dortmund, Germany
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