1
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Lindberg MF, Deau E, Arfwedson J, George N, George P, Alfonso P, Corrionero A, Meijer L. Comparative Efficacy and Selectivity of Pharmacological Inhibitors of DYRK and CLK Protein Kinases. J Med Chem 2023; 66:4106-4130. [PMID: 36876904 DOI: 10.1021/acs.jmedchem.2c02068] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Dual-specificity, tyrosine phosphorylation-regulated kinases (DYRKs) and cdc2-like kinases (CLKs) play a large variety of cellular functions and are involved in several diseases (cognitive disorders, diabetes, cancers, etc.). There is, thus, growing interest in pharmacological inhibitors as chemical probes and potential drug candidates. This study presents an unbiased evaluation of the kinase inhibitory activity of a library of 56 reported DYRK/CLK inhibitors on the basis of comparative, side-by-side, catalytic activity assays on a panel of 12 recombinant human kinases, enzyme kinetics (residence time and Kd), in-cell inhibition of Thr-212-Tau phosphorylation, and cytotoxicity. The 26 most active inhibitors were modeled in the crystal structure of DYRK1A. The results show a rather large diversity of potencies and selectivities among the reported inhibitors and emphasize the difficulties to avoid "off-targets" in this area of the kinome. The use of a panel of DYRKs/CLKs inhibitors is suggested to analyze the functions of these kinases in cellular processes.
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Affiliation(s)
| | - Emmanuel Deau
- Perha Pharmaceuticals, Perharidy Peninsula, 29680 Roscoff, France
| | - Jonas Arfwedson
- Perha Pharmaceuticals, Perharidy Peninsula, 29680 Roscoff, France
| | - Nicolas George
- Oncodesign, 25-27 avenue du Québec, 91140 Villebon-sur-Yvette, France
| | - Pascal George
- Perha Pharmaceuticals, Perharidy Peninsula, 29680 Roscoff, France
| | - Patricia Alfonso
- Enzymlogic, Qube Technology Park, C/Santiago Grisolía, 2, 28760 Madrid, Spain
| | - Ana Corrionero
- Enzymlogic, Qube Technology Park, C/Santiago Grisolía, 2, 28760 Madrid, Spain
| | - Laurent Meijer
- Perha Pharmaceuticals, Perharidy Peninsula, 29680 Roscoff, France
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2
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Dammann M, Stahlecker J, Zimmermann MO, Klett T, Rotzinger K, Kramer M, Coles M, Stehle T, Boeckler FM. Screening of a Halogen-Enriched Fragment Library Leads to Unconventional Binding Modes. J Med Chem 2022; 65:14539-14552. [DOI: 10.1021/acs.jmedchem.2c00951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marcel Dammann
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
| | - Jason Stahlecker
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
| | - Markus O. Zimmermann
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
| | - Theresa Klett
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
| | - Kilian Rotzinger
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
| | - Markus Kramer
- Institute of Organic Chemistry, Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
| | - Murray Coles
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, 72076Tübingen, Germany
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
| | - Frank M. Boeckler
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
- Interfaculty Institute for Biomedical Informatics (IBMI), Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
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3
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Stensen W, Rothweiler U, Engh RA, Stasko MR, Bederman I, Costa ACS, Fugelli A, Svendsen JSM. Novel DYRK1A Inhibitor Rescues Learning and Memory Deficits in a Mouse Model of Down Syndrome. Pharmaceuticals (Basel) 2021; 14:ph14111170. [PMID: 34832952 PMCID: PMC8617627 DOI: 10.3390/ph14111170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/05/2021] [Accepted: 11/13/2021] [Indexed: 01/20/2023] Open
Abstract
Down syndrome (DS) is a complex genetic disorder associated with substantial physical, cognitive, and behavioral challenges. Due to better treatment options for the physical co-morbidities of DS, the life expectancy of individuals with DS is beginning to approach that of the general population. However, the cognitive deficits seen in individuals with DS still cannot be addressed pharmacologically. In young individuals with DS, the level of intellectual disability varies from mild to severe, but cognitive ability generally decreases with increasing age, and all individuals with DS have early onset Alzheimer’s disease (AD) pathology by the age of 40. The present study introduces a novel inhibitor for the protein kinase DYRK1A, a key controlling kinase whose encoding gene is located on chromosome 21. The novel inhibitor is well characterized for use in mouse models and thus represents a valuable tool compound for further DYRK1A research.
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Affiliation(s)
- Wenche Stensen
- Department of Chemistry, UiT, The Arctic University of Norway, 9037 Tromsø, Norway; (W.S.); (U.R.); (R.A.E.)
- Pharmasum Therapeutics AS, Gaustadalleen 21, 0349 Oslo, Norway;
| | - Ulli Rothweiler
- Department of Chemistry, UiT, The Arctic University of Norway, 9037 Tromsø, Norway; (W.S.); (U.R.); (R.A.E.)
- Pharmasum Therapeutics AS, Gaustadalleen 21, 0349 Oslo, Norway;
| | - Richard Alan Engh
- Department of Chemistry, UiT, The Arctic University of Norway, 9037 Tromsø, Norway; (W.S.); (U.R.); (R.A.E.)
| | - Melissa R. Stasko
- Departments of Pediatrics, Psychiatry, Macromolecular Science and Engineering, Case Western Reserve University, 11100 Euclid Avenue, Cleveland, OH 44106, USA; (M.R.S.); (I.B.); (A.C.S.C.)
| | - Ilya Bederman
- Departments of Pediatrics, Psychiatry, Macromolecular Science and Engineering, Case Western Reserve University, 11100 Euclid Avenue, Cleveland, OH 44106, USA; (M.R.S.); (I.B.); (A.C.S.C.)
| | - Alberto C. S. Costa
- Departments of Pediatrics, Psychiatry, Macromolecular Science and Engineering, Case Western Reserve University, 11100 Euclid Avenue, Cleveland, OH 44106, USA; (M.R.S.); (I.B.); (A.C.S.C.)
| | - Anders Fugelli
- Pharmasum Therapeutics AS, Gaustadalleen 21, 0349 Oslo, Norway;
| | - John S. Mjøen Svendsen
- Department of Chemistry, UiT, The Arctic University of Norway, 9037 Tromsø, Norway; (W.S.); (U.R.); (R.A.E.)
- Pharmasum Therapeutics AS, Gaustadalleen 21, 0349 Oslo, Norway;
- Correspondence:
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4
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Pucelik B, Barzowska A, Dąbrowski JM, Czarna A. Diabetic Kinome Inhibitors-A New Opportunity for β-Cells Restoration. Int J Mol Sci 2021; 22:9083. [PMID: 34445786 PMCID: PMC8396662 DOI: 10.3390/ijms22169083] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/13/2021] [Accepted: 08/18/2021] [Indexed: 01/03/2023] Open
Abstract
Diabetes, and several diseases related to diabetes, including cancer, cardiovascular diseases and neurological disorders, represent one of the major ongoing threats to human life, becoming a true pandemic of the 21st century. Current treatment strategies for diabetes mainly involve promoting β-cell differentiation, and one of the most widely studied targets for β-cell regeneration is DYRK1A kinase, a member of the DYRK family. DYRK1A has been characterized as a key regulator of cell growth, differentiation, and signal transduction in various organisms, while further roles and substrates are the subjects of extensive investigation. The targets of interest in this review are implicated in the regulation of β-cells through DYRK1A inhibition-through driving their transition from highly inefficient and death-prone populations into efficient and sufficient precursors of islet regeneration. Increasing evidence for the role of DYRK1A in diabetes progression and β-cell proliferation expands the potential for pharmaceutical applications of DYRK1A inhibitors. The variety of new compounds and binding modes, determined by crystal structure and in vitro studies, may lead to new strategies for diabetes treatment. This review provides recent insights into the initial self-activation of DYRK1A by tyrosine autophosphorylation. Moreover, the importance of developing novel DYRK1A inhibitors and their implications for the treatment of diabetes are thoroughly discussed. The evolving understanding of DYRK kinase structure and function and emerging high-throughput screening technologies have been described. As a final point of this work, we intend to promote the term "diabetic kinome" as part of scientific terminology to emphasize the role of the synergistic action of multiple kinases in governing the molecular processes that underlie this particular group of diseases.
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Affiliation(s)
- Barbara Pucelik
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland; (B.P.); (A.B.)
| | - Agata Barzowska
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland; (B.P.); (A.B.)
| | - Janusz M. Dąbrowski
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Anna Czarna
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland; (B.P.); (A.B.)
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Shi C, Killoran MP, Hall MP, Otto P, Wood MG, Strauss E, Encell LP, Machleidt T, Wood KV, Kirkland TA. 5,5-Dialkylluciferins are thermal stable substrates for bioluminescence-based detection systems. PLoS One 2020; 15:e0243747. [PMID: 33315907 PMCID: PMC7735563 DOI: 10.1371/journal.pone.0243747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/26/2020] [Indexed: 11/18/2022] Open
Abstract
Firefly luciferase-based ATP detection assays are frequently used as a sensitive, cost-efficient method for monitoring hygiene in many industrial settings. Solutions of detection reagent, containing a mixture of a substrate and luciferase enzyme that produces photons in the presence of ATP, are relatively unstable and maintain only a limited shelf life even under refrigerated conditions. It is therefore common for the individual performing a hygiene test to manually prepare fresh reagent at the time of monitoring. To simplify sample processing, a liquid detection reagent with improved thermal stability is needed. The engineered firefly luciferase, Ultra-Glo™, fulfills one aspect of this need and has been valuable for hygiene monitoring because of its high resistance to chemical and thermal inactivation. However, solutions containing both Ultra-Glo™ luciferase and its substrate luciferin gradually lose the ability to effectively detect ATP over time. We demonstrate here that dehydroluciferin, a prevalent oxidative breakdown product of luciferin, is a potent inhibitor of Ultra-Glo™ luciferase and that its formation in the detection reagent is responsible for the decreased ability to detect ATP. We subsequently found that dialkylation at the 5-position of luciferin (e.g., 5,5-dimethylluciferin) prevents degradation to dehydroluciferin and improves substrate thermostability in solution. However, since 5,5-dialkylluciferins are poorly utilized by Ultra-Glo™ luciferase as substrates, we used structural optimization of the luciferin dialkyl modification and protein engineering of Ultra-Glo™ to develop a luciferase/luciferin pair that shows improved total reagent stability in solution at ambient temperature. The results of our studies outline a novel luciferase/luciferin system that could serve as foundations for the next generation of bioluminescence ATP detection assays with desirable reagent stability.
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Affiliation(s)
- Ce Shi
- Promega Biosciences, Inc., San Luis Obispo, California, United States of America
| | | | - Mary P. Hall
- Promega Corporation, Madison, Wisconsin, United States of America
| | - Paul Otto
- Promega Corporation, Madison, Wisconsin, United States of America
| | - Monika G. Wood
- Promega Corporation, Madison, Wisconsin, United States of America
| | - Ethan Strauss
- Promega Corporation, Madison, Wisconsin, United States of America
| | - Lance P. Encell
- Promega Corporation, Madison, Wisconsin, United States of America
| | - Thomas Machleidt
- Promega Corporation, Madison, Wisconsin, United States of America
| | - Keith V. Wood
- Promega Corporation, Madison, Wisconsin, United States of America
| | - Thomas A. Kirkland
- Promega Biosciences, Inc., San Luis Obispo, California, United States of America
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6
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7
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Katigbak J, Li H, Rooklin D, Zhang Y. AlphaSpace 2.0: Representing Concave Biomolecular Surfaces Using β-Clusters. J Chem Inf Model 2020; 60:1494-1508. [PMID: 31995373 PMCID: PMC7093224 DOI: 10.1021/acs.jcim.9b00652] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Modern rational modulator design and structure-function characterization often concentrate on concave regions of biomolecular surfaces, ranging from well-defined small-molecule binding sites to large protein-protein interaction interfaces. Here, we introduce a β-cluster as a pseudomolecular representation of fragment-centric pockets detected by AlphaSpace [J. Chem. Inf. Model. 2015, 55, 1585], a recently developed computational analysis tool for topographical mapping of biomolecular concavities. By mimicking the shape as well as atomic details of potential molecular binders, this new β-cluster representation allows direct pocket-to-ligand shape comparison and can be used to guide ligand optimization. Furthermore, we defined the β-score, the optimal Vina score of the β-cluster, as an indicator of pocket ligandability and developed an ensemble β-cluster approach, which allows one-to-one pocket mapping and comparison among aligned protein structures. We demonstrated the utility of β-cluster representation by applying the approach to a wide variety of problems including binding site detection and comparison, characterization of protein-protein interactions, and fragment-based ligand optimization. These new β-cluster functionalities have been implemented in AlphaSpace 2.0, which is freely available on the web at http://www.nyu.edu/projects/yzhang/AlphaSpace2.
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Affiliation(s)
- Joseph Katigbak
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Haotian Li
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - David Rooklin
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, New York 10003, United States
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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8
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Biological Evaluation of Arylsemicarbazone Derivatives as Potential Anticancer Agents. Pharmaceuticals (Basel) 2019; 12:ph12040169. [PMID: 31744203 PMCID: PMC6958387 DOI: 10.3390/ph12040169] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/14/2019] [Accepted: 11/14/2019] [Indexed: 12/24/2022] Open
Abstract
Fourteen arylsemicarbazone derivatives were synthesized and evaluated in order to find agents with potential anticancer activity. Cytotoxic screening was performed against K562, HL-60, MOLT-4, HEp-2, NCI-H292, HT-29 and MCF-7 tumor cell lines. Compounds 3c and 4a were active against the tested cancer cell lines, being more cytotoxic for the HL-60 cell line with IC50 values of 13.08 μM and 11.38 μM, respectively. Regarding the protein kinase inhibition assay, 3c inhibited seven different kinases and 4a strongly inhibited the CK1δ/ε kinase. The studied kinases are involved in several cellular functions such as proliferation, migration, cell death and cell cycle progression. Additional analysis by flow cytometry revealed that 3c and 4a caused depolarization of the mitochondrial membrane, suggesting apoptosis mediated by the intrinsic pathway. Compound 3c induced arrest in G1 phase of the cell cycle on HL-60 cells, and in the annexin V assay approximately 50% of cells were in apoptosis at the highest concentration tested (26 μM). Compound 4a inhibited cell cycle by accumulation of abnormal postmitotic cells at G1 phase and induced DNA fragmentation at the highest concentration (22 μM).
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9
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Yueh C, Rettenmaier J, Xia B, Hall DR, Alekseenko A, Porter KA, Barkovich K, Keseru G, Whitty A, Wells JA, Vajda S, Kozakov D. Kinase Atlas: Druggability Analysis of Potential Allosteric Sites in Kinases. J Med Chem 2019; 62:6512-6524. [PMID: 31274316 DOI: 10.1021/acs.jmedchem.9b00089] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The inhibition of kinases has been pursued by the pharmaceutical industry for over 20 years. While the locations of the sites that bind type II and III inhibitors at or near the adenosine 5'-triphosphate binding sites are well defined, the literature describes 10 different regions that were reported as regulatory hot spots in some kinases and thus are potential target sites for type IV inhibitors. Kinase Atlas is a systematic collection of binding hot spots located at the above ten sites in 4910 structures of 376 distinct kinases available in the Protein Data Bank. The hot spots are identified by FTMap, a computational analogue of experimental fragment screening. Users of Kinase Atlas ( https://kinase-atlas.bu.edu ) may view summarized results for all structures of a particular kinase, such as which binding sites are present and how druggable they are, or they may view hot spot information for a particular kinase structure of interest.
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Affiliation(s)
| | - Justin Rettenmaier
- Departments of Pharmaceutical Chemistry and Cellular and Molecular Pharmacology , University of California , 1700 Fourth Street , San Francisco , California 9415 , United States
| | | | - David R Hall
- Acpharis Incorporated , Holliston , Massachusetts 01746 , United States
| | | | | | - Krister Barkovich
- Departments of Pharmaceutical Chemistry and Cellular and Molecular Pharmacology , University of California , 1700 Fourth Street , San Francisco , California 9415 , United States
| | - Gyorgy Keseru
- Medicinal Chemistry Research Group , Research Center for Natural Sciences , Magyar tudósok krt. 2 , H-1117 Budapest , Hungary
| | | | - James A Wells
- Departments of Pharmaceutical Chemistry and Cellular and Molecular Pharmacology , University of California , 1700 Fourth Street , San Francisco , California 9415 , United States
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10
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Chen J, Pang L, Wang W, Wang L, Zhang JZH, Zhu T. Decoding molecular mechanism of inhibitor bindings to CDK2 using molecular dynamics simulations and binding free energy calculations. J Biomol Struct Dyn 2019; 38:985-996. [PMID: 30843759 DOI: 10.1080/07391102.2019.1591304] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
CDK2 can be used as an attractive target for development of efficient inhibitors curing multiple disease relating with CDK2. In this work, molecular dynamics (MD) simulations and binding free energy calculations were coupled to probe conformational changes of CDK2 due to inhibitor associations and binding mechanisms of inhibitors PM1, FMD and X64 to CDK2. The results suggest that the binding strength of FMD and X64 to CDK2 is stronger than that of PM1. Principal component (PC) analysis and cross-correlation map calculations based on the equilibrated MD trajectories demonstrate that the structural difference in inhibitors exerts important impact on motion modes and dynamics behavior of CDK2. Residue-based free energy decomposition method was adopted to estimate the inhibitor-residue spectrum. The results not only efficiently identify the hot interaction spot of inhibitors with CDK2 but also show that the hydrophobic rings R1, R2 and R3 as well as polar groups of three inhibitors play key roles in favorably binding of inhibitors to CDK2. This work is expected to contribute energetic basis and dynamics information to development of promising inhibitors toward CDK2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, China
| | - Laixue Pang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - Wei Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - Lifei Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - John Z H Zhang
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China.,Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Tong Zhu
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China.,Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
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11
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Czarna A, Wang J, Zelencova D, Liu Y, Deng X, Choi HG, Zhang T, Zhou W, Chang JW, Kildalsen H, Seternes OM, Gray NS, Engh RA, Rothweiler U. Novel Scaffolds for Dual Specificity Tyrosine-Phosphorylation-Regulated Kinase (DYRK1A) Inhibitors. J Med Chem 2018; 61:7560-7572. [PMID: 30095246 DOI: 10.1021/acs.jmedchem.7b01847] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
DYRK1A is one of five members of the dual-specificity tyrosine (Y) phosphorylation-regulated kinase (DYRK) family. The DYRK1A gene is located in the Down syndrome critical region and regulates cellular processes related to proliferation and differentiation of neuronal progenitor cells during early development. This has focused research on its role in neuronal degenerative diseases, including Alzheimer's and Down syndrome. Recent studies have also shown a possible role of DYRK1A in diabetes. Here we report a variety of scaffolds not generally known for DYRK1A inhibition, demonstrating their effects in in vitro assays and also in cell cultures. These inhibitors effectively block the tau phosphorylation that is a hallmark of Alzheimer's disease. The crystal structures of these inhibitors support the design of optimized and novel therapeutics.
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Affiliation(s)
- Anna Czarna
- Department of Pharmacy, Faculty of Health Sciences , UiT The Arctic University of Norway , N-9037 Tromsø , Norway
| | - Jinhua Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston , Massachusetts 02115 , United States
| | - Diana Zelencova
- The Norwegian Structural Biology Centre, Department of Chemistry , UiT The Arctic University of Norway , N-9037 Tromsø , Norway
| | - Yao Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston , Massachusetts 02115 , United States
| | - Xianming Deng
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston , Massachusetts 02115 , United States
| | - Hwan Geun Choi
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston , Massachusetts 02115 , United States
| | - Tinghu Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston , Massachusetts 02115 , United States
| | - Wenjun Zhou
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston , Massachusetts 02115 , United States
| | - Jae Won Chang
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston , Massachusetts 02115 , United States
| | - Hanne Kildalsen
- Department of Pharmacy, Faculty of Health Sciences , UiT The Arctic University of Norway , N-9037 Tromsø , Norway
| | - Ole Morten Seternes
- Department of Pharmacy, Faculty of Health Sciences , UiT The Arctic University of Norway , N-9037 Tromsø , Norway
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston , Massachusetts 02115 , United States
| | - Richard A Engh
- The Norwegian Structural Biology Centre, Department of Chemistry , UiT The Arctic University of Norway , N-9037 Tromsø , Norway
| | - Ulli Rothweiler
- The Norwegian Structural Biology Centre, Department of Chemistry , UiT The Arctic University of Norway , N-9037 Tromsø , Norway
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12
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Lau ATY, Xu YM. Regulation of human mitogen-activated protein kinase 15 (extracellular signal-regulated kinase 7/8) and its functions: A recent update. J Cell Physiol 2018; 234:75-88. [PMID: 30070699 DOI: 10.1002/jcp.27053] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 06/25/2018] [Indexed: 02/05/2023]
Abstract
Mitogen-activated protein kinase 15 (MAPK15), originally also known as extracellular signal-regulated kinase 7/8, is the most recently identified atypical MAPK and the least studied so far. Examinations of the role of MAPK15 in various cell lines and model systems indicate that MAPK15 participates in a variety of cellular activities such as promoting cell proliferation, cell transformation, and apoptosis; stimulating autophagy; regulating cell division, ciliogenesis, and protein secretion; and maintaining genome stability. As multiple roles of MAPK15 were observed among these studies, therefore, it remains unclear whether MAPK15 acts as a proto-oncogene or tumor suppressor. Here, the recent literature on human MAPK15 and the resulting functions will be discussed.
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Affiliation(s)
- Andy T Y Lau
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, People's Republic of China
| | - Yan-Ming Xu
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, People's Republic of China
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13
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Nguyen TL, Fruit C, Hérault Y, Meijer L, Besson T. Dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) inhibitors: a survey of recent patent literature. Expert Opin Ther Pat 2017; 27:1183-1199. [PMID: 28766366 DOI: 10.1080/13543776.2017.1360285] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) is a eukaryotic serine-threonine protein kinase belonging to the CMGC group. DYRK1A hyperactivity appears to contribute to the development of a number of human malignancies and to cognitive deficits observed in Down syndrome and Alzheimer's disease. As a result, the DYRK1A kinase represents an attractive target for the synthesis and optimization of pharmacological inhibitors of potential therapeutic interest. Like most tyrosine kinase inhibitors developed up to the market, DYRK1A inhibitors are essentially acting by competing with ATP for binding at the catalytic site of the kinase. Areas covered: This paper reviews patent activity associated with the discovery of synthetic novel heterocyclic molecules inhibiting the catalytic activity of DYRK1A. Expert opinion: Despite the important role of DYRK1A in biological processes and the growing interest in the design of new therapeutic drugs, there are only few patented synthetic DYRK1A inhibitors and most of them were and are still developed by academic research groups, sometimes with industrial partners.
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Affiliation(s)
- Thu Lan Nguyen
- a Manros Therapeutics , Centre de Perharidy , Roscoff , France
- b Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch , Illkirch , France
- c Centre National de la Recherche Scientifique, UMR7104 , Illkirch , France
- d Institut National de la Santé et de la Recherche Médicale, U964 , Illkirch , France
- e Université de Strasbourg , Illkirch , France
| | - Corinne Fruit
- f Normandie Univ , UNIROUEN, INSA Rouen, CNRS, COBRA UMR 6014 , Rouen , France
| | - Yann Hérault
- a Manros Therapeutics , Centre de Perharidy , Roscoff , France
- b Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch , Illkirch , France
- c Centre National de la Recherche Scientifique, UMR7104 , Illkirch , France
- d Institut National de la Santé et de la Recherche Médicale, U964 , Illkirch , France
- e Université de Strasbourg , Illkirch , France
| | - Laurent Meijer
- a Manros Therapeutics , Centre de Perharidy , Roscoff , France
| | - Thierry Besson
- f Normandie Univ , UNIROUEN, INSA Rouen, CNRS, COBRA UMR 6014 , Rouen , France
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Rothweiler U, Stensen W, Brandsdal BO, Isaksson J, Leeson FA, Engh RA, Svendsen JSM. Probing the ATP-Binding Pocket of Protein Kinase DYRK1A with Benzothiazole Fragment Molecules. J Med Chem 2016; 59:9814-9824. [PMID: 27736065 DOI: 10.1021/acs.jmedchem.6b01086] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
DYRK1A has emerged as a potential target for therapies of Alzheimer's disease using small molecules. On the basis of the observation of selective DYRK1A inhibition by firefly d-luciferin, we have explored static and dynamic structural properties of fragment sized variants of the benzothiazole scaffold with respect to DYRK1A using X-ray crystallography and NMR techniques. The compounds have excellent ligand efficiencies and show a remarkable diversity of binding modes in dynamic equilibrium. Binding geometries are determined in part by interactions often considered "weak", including "orthogonal multipolar" types represented by, for example, F-CO, sulfur-aromatic, and halogen-aromatic interactions, together with hydrogen bonds that are modulated by variation of electron withdrawing groups. These studies show how the benzothiazole scaffold is highly promising for the development of therapeutic DYRK1A inhibitors. In addition, the subtleties of the binding interactions, including dynamics, show how full structural studies are required to fully interpret the essential physical determinants of binding.
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Affiliation(s)
- Ulli Rothweiler
- The Norwegian Structural Biology Centre, Department of Chemistry, UiT The Arctic University of Norway , N-9037 Tromsø, Norway
- Pharmasum Therapeutics AS , Smørblomstvn. 36, N-9102 Kvaløysletta, Norway
| | - Wenche Stensen
- Pharmasum Therapeutics AS , Smørblomstvn. 36, N-9102 Kvaløysletta, Norway
- Department of Chemistry, UiT The Arctic University of Norway , N-9037 Tromsø, Norway
| | - Bjørn Olav Brandsdal
- The Centre of Theoretical and Computational Chemistry, Department of Chemistry, UiT The Arctic University of Norway , N-9037 Tromsø, Norway
| | - Johan Isaksson
- Department of Chemistry, UiT The Arctic University of Norway , N-9037 Tromsø, Norway
| | - Frederick Alan Leeson
- Pharmasum Therapeutics AS , Smørblomstvn. 36, N-9102 Kvaløysletta, Norway
- Department of Chemistry, UiT The Arctic University of Norway , N-9037 Tromsø, Norway
| | - Richard Alan Engh
- The Norwegian Structural Biology Centre, Department of Chemistry, UiT The Arctic University of Norway , N-9037 Tromsø, Norway
| | - John S Mjøen Svendsen
- Pharmasum Therapeutics AS , Smørblomstvn. 36, N-9102 Kvaløysletta, Norway
- Department of Chemistry, UiT The Arctic University of Norway , N-9037 Tromsø, Norway
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Stotani S, Giordanetto F, Medda F. DYRK1A inhibition as potential treatment for Alzheimer's disease. Future Med Chem 2016; 8:681-96. [PMID: 27073990 DOI: 10.4155/fmc-2016-0013] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
In total, 47,500,000 people worldwide are affected by dementia and this number is estimated to double by 2030 and triple within 2050 resulting in a huge burden on public health. Alzheimer's disease (AD), a progressive neurodegenerative disorder, is the most common cause of dementia, accounting for 60-70% of all the cases. The cause of AD is still poorly understood but several brain abnormalities (e.g., loss of neuronal connections and neuronal death) have been identified in affected patients. In addition to the accumulation of β-amyloid plaques in the brain tissue, aberrant phosphorylation of tau proteins has proved to increase neuronal death. DYRK1A phosphorylates tau on 11 different Ser/Thr residues, resulting in the formation of aggregates called 'neurofibrillary tangles' which, together with amyloid plaques, could be responsible for dementia, neuronal degeneration and cell death. Small molecule inhibition of DYRK1A could thus represent an interesting approach toward the treatment of Alzheimer's and other neurodegenerative diseases. Herein we review the current progress in the identification and development of DYRK1A inhibitors.
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Affiliation(s)
- Silvia Stotani
- Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Emil-Figge-Str. 76a, 44227 Dortmund, Germany
| | - Fabrizio Giordanetto
- Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Emil-Figge-Str. 76a, 44227 Dortmund, Germany
- DE Shaw Research, 120W 45th Street, New York, NY 10036, USA
| | - Federico Medda
- Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Emil-Figge-Str. 76a, 44227 Dortmund, Germany
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16
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Detection of secondary binding sites in proteins using fragment screening. Proc Natl Acad Sci U S A 2015; 112:15910-5. [PMID: 26655740 DOI: 10.1073/pnas.1518946112] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Proteins need to be tightly regulated as they control biological processes in most normal cellular functions. The precise mechanisms of regulation are rarely completely understood but can involve binding of endogenous ligands and/or partner proteins at specific locations on a protein that can modulate function. Often, these additional secondary binding sites appear separate to the primary binding site, which, for example for an enzyme, may bind a substrate. In previous work, we have uncovered several examples in which secondary binding sites were discovered on proteins using fragment screening approaches. In each case, we were able to establish that the newly identified secondary binding site was biologically relevant as it was able to modulate function by the binding of a small molecule. In this study, we investigate how often secondary binding sites are located on proteins by analyzing 24 protein targets for which we have performed a fragment screen using X-ray crystallography. Our analysis shows that, surprisingly, the majority of proteins contain secondary binding sites based on their ability to bind fragments. Furthermore, sequence analysis of these previously unknown sites indicate high conservation, which suggests that they may have a biological function, perhaps via an allosteric mechanism. Comparing the physicochemical properties of the secondary sites with known primary ligand binding sites also shows broad similarities indicating that many of the secondary sites may be druggable in nature with small molecules that could provide new opportunities to modulate potential therapeutic targets.
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Assessing protein kinase target similarity: Comparing sequence, structure, and cheminformatics approaches. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1605-16. [PMID: 26001898 DOI: 10.1016/j.bbapap.2015.05.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 05/08/2015] [Accepted: 05/11/2015] [Indexed: 11/22/2022]
Abstract
In just over two decades, structure based protein kinase inhibitor discovery has grown from trial and error approaches, using individual target structures, to structure and data driven approaches that may aim to optimize inhibition properties across several targets. This is increasingly enabled by the growing availability of potent compounds and kinome-wide binding data. Assessing the prospects for adapting known compounds to new therapeutic uses is thus a key priority for current drug discovery efforts. Tools that can successfully link the diverse information regarding target sequence, structure, and ligand binding properties now accompany a transformation of protein kinase inhibitor research, away from single, block-buster drug models, and toward "personalized medicine" with niche applications and highly specialized research groups. Major hurdles for the transformation to data driven drug discovery include mismatches in data types, and disparities of methods and molecules used; at the core remains the problem that ligand binding energies cannot be predicted precisely from individual structures. However, there is a growing body of experimental data for increasingly successful focussing of efforts: focussed chemical libraries, drug repurposing, polypharmacological design, to name a few. Protein kinase target similarity is easily quantified by sequence, and its relevance to ligand design includes broad classification by key binding sites, evaluation of resistance mutations, and the use of surrogate proteins. Although structural evaluation offers more information, the flexibility of protein kinases, and differences between the crystal and physiological environments may make the use of crystal structures misleading when structures are considered individually. Cheminformatics may enable the "calibration" of sequence and crystal structure information, with statistical methods able to identify key correlates to activity but also here, "the devil is in the details." Examples from specific repurposing and polypharmacology applications illustrate these points. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases.
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