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Zeng W, Han C, Mohammed S, Li S, Song Y, Sun F, Du Y. Indole-containing pharmaceuticals: targets, pharmacological activities, and SAR studies. RSC Med Chem 2024; 15:788-808. [PMID: 38516587 PMCID: PMC10953485 DOI: 10.1039/d3md00677h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/29/2024] [Indexed: 03/23/2024] Open
Abstract
Indole is a prestigious heterocyclic skeleton widely found in both naturally-occurring and biologically-active compounds. Pharmaceutical agents containing an indole skeleton in their framework possess a wide range of pharmacological properties, including antiviral, antitumor, analgesic, and other therapeutic activities, and many indole-containing drugs have been proven to have excellent pharmacokinetic and pharmacological effects. Over the past few decades, the FDA has approved over 40 indole-containing drugs for the treatment of various clinical conditions, and the development of indole-related drugs has attracted significant attention from medicinal chemists. This review aims to provide an overview of all the approved drugs that contain an indole nucleus, focusing on their targets, pharmacological activities, and SAR studies.
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Affiliation(s)
- Wei Zeng
- School of Pharmaceutical Science and Technology, Tianjin University Tianjin 300072 China
| | - Chi Han
- School of Pharmaceutical Science and Technology, Tianjin University Tianjin 300072 China
| | - Sarah Mohammed
- School of Pharmaceutical Science and Technology, Tianjin University Tianjin 300072 China
| | - Shanshan Li
- School of Pharmaceutical Science and Technology, Tianjin University Tianjin 300072 China
| | - Yixuan Song
- Department of Chemical Engineering & Biotechnology, University of Cambridge CB2 3RA Cambridge UK
| | - Fengxia Sun
- Research Center for Chemical Safety & Security and Verification Technology & College of Chemical and Pharmaceutical Engineering, Hebei University of Science and Technology Shijiazhuang 050018 China
| | - Yunfei Du
- School of Pharmaceutical Science and Technology, Tianjin University Tianjin 300072 China
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2
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Fontana C, de Meirelles JL, Verli H. Theoretical models of staurosporine and analogs uncover detailed structural information in biological solution. J Mol Graph Model 2024; 126:108653. [PMID: 37922640 DOI: 10.1016/j.jmgm.2023.108653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/12/2023] [Accepted: 10/12/2023] [Indexed: 11/07/2023]
Abstract
Staurosporine and its analogs (STA-analogs) are indolocarbazoles (ICZs) compounds able to inhibit kinase proteins in a non-specific way, while present antimicrobial and cytostatic properties. The knowledge of molecular features associated to the complexation, including the ligand shape in solution and thermodynamics of complexation, is substantial to the development of new bioactive ICZs with improved therapeutic properties. In this context, the empirical approach of GROMOS force field is able to accurately reproduce condensed phase physicochemical properties of molecular systems after parameterization. Hence, through parameterization under GROMOS force field and molecular simulations, we assessed STA-analogs dynamics in aqueous solution, as well as its interaction with water to probe conformational and structural features involved in complexation to therapeutic targets. The coexistence of multiple conformers observed in simulations, and confirmed by metadynamics calculations, expanding the conformational space knowledge of these ligands with potential implications in understanding the ligand conformational selection during complexation. Also, changes in availability to H-bonding concerning the different substituents and water can reflect on effects at complexation free energy due to variation at the desolvation energetic costs. Based on these results, we expect the obtained structural data provide systemic framework for rational chemical modification of STA-analogs.
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Affiliation(s)
- Crisciele Fontana
- Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Av. Bento Gonçalves, 9500 (Caixa Postal 15005), Porto Alegre, CEP 91501-970, RS, Brazil
| | - João Luiz de Meirelles
- Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Av. Bento Gonçalves, 9500 (Caixa Postal 15005), Porto Alegre, CEP 91501-970, RS, Brazil
| | - Hugo Verli
- Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Av. Bento Gonçalves, 9500 (Caixa Postal 15005), Porto Alegre, CEP 91501-970, RS, Brazil.
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3
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Yoon HR, Park GJ, Balupuri A, Kang NS. TWN-FS method: A novel fragment screening method for drug discovery. Comput Struct Biotechnol J 2023; 21:4683-4696. [PMID: 37841326 PMCID: PMC10568351 DOI: 10.1016/j.csbj.2023.09.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/17/2023] Open
Abstract
Fragment-based drug discovery (FBDD) is a well-established and effective method for generating diverse and novel hits in drug design. Kinases are suitable targets for FBDD due to their well-defined structure. Water molecules contribute to structure and function of proteins and also influence the environment within the binding pocket. Water molecules form a variety of hydrogen-bonded cyclic water-ring networks, collectively known as topological water networks (TWNs). Analyzing the TWNs in protein binding sites can provide valuable insights into potential locations and shapes for fragments within the binding site. Here, we introduce TWN-based fragment screening (TWN-FS) method, a novel screening method that suggests fragments through grouped TWN analysis within the protein binding site. We used this method to screen known CDK2, CHK1, IGF1R and ERBB4 inhibitors. Our findings suggest that TWN-FS method has the potential to effectively screen fragments. The TWN-FS method package is available on GitHub at https://github.com/pkj0421/TWN-FS.
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Affiliation(s)
- Hye Ree Yoon
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea
| | - Gyoung Jin Park
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea
| | - Anand Balupuri
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea
| | - Nam Sook Kang
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea
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4
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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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5
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Xu Y, Zhang S, Lindahl E, Friedman R, Wu W, Su P. A general tight-binding based energy decomposition analysis scheme for intermolecular interactions in large molecules. J Chem Phys 2022; 157:034104. [DOI: 10.1063/5.0091781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, a general tight-binding based energy decomposition analysis (EDA) scheme for intermolecular interactions is proposed. Different from the earlier version [Xu et al., J. Chem. Phys. 154, 194106 (2021)], the current tight-binding based density functional theory (DFTB)-EDA is capable of performing interaction analysis with all the self-consistent charge (SCC) type DFTB methods, including SCC-DFTB2/3 and GFN1/2-xTB, despite their different formulas and parameterization schemes. In DFTB-EDA, the total interaction energy is divided into frozen, polarization, and dispersion terms. The performance of DFTB-EDA with SCC-DFTB2/3 and GFN1/2-xTB for various interaction systems is discussed and assessed.
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Affiliation(s)
- Yuan Xu
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Shu Zhang
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Erik Lindahl
- Department of Chemistry and Biomedical Sciences, Linnaeus University, 39182 Kalmar, Sweden
| | - Ran Friedman
- Department of Chemistry and Biomedical Sciences, Linnaeus University, 39182 Kalmar, Sweden
| | - Wei Wu
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Peifeng Su
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
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6
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Ferng TT, Terada D, Ando M, Tarver TC, Chaudhary F, Lin KC, Logan AC, Smith CC. The Irreversible FLT3 Inhibitor FF-10101 Is Active Against a Diversity of FLT3 Inhibitor Resistance Mechanisms. Mol Cancer Ther 2022; 21:844-854. [PMID: 35395091 DOI: 10.1158/1535-7163.mct-21-0317] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 11/02/2021] [Accepted: 02/24/2022] [Indexed: 11/16/2022]
Abstract
Small-molecule FLT3 inhibitors have recently improved clinical outcomes for patients with FLT3-mutant acute myeloid leukemia (AML) after many years of development, but resistance remains an important clinical problem. FF-10101 is the first irreversible, covalent inhibitor of FLT3 which has previously shown activity against FLT3 tyrosine kinase inhibitor resistance-causing FLT3 F691L and D835 mutations. We report that FF-10101 is also active against an expanded panel of clinically identified FLT3 mutations associated with resistance to other FLT3 inhibitors. We also demonstrate that FF-10101 can potentially address resistance mechanisms associated with growth factors present in the bone marrow microenvironment but is vulnerable to mutation at C695, the amino acid required for covalent FLT3 binding. These data suggest that FF-10101 possesses a favorable resistance profile that may contribute to improved single-agent efficacy when used in patients with FLT3-mutant AML.
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Affiliation(s)
- Timothy T Ferng
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
| | - Daisuke Terada
- Analysis Technology Center, FUJIFILM Corporation, Kanagawa, Japan
| | - Makoto Ando
- Pharmaceutical Products Division, FUJIFILM Corporation, Tokyo, Japan
| | - Theodore C Tarver
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Fihr Chaudhary
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Kimberly C Lin
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Aaron C Logan
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
| | - Catherine C Smith
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
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7
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Shi W, Singha M, Srivastava G, Pu L, Ramanujam J, Brylinski M. Pocket2Drug: An Encoder-Decoder Deep Neural Network for the Target-Based Drug Design. Front Pharmacol 2022; 13:837715. [PMID: 35359869 PMCID: PMC8962739 DOI: 10.3389/fphar.2022.837715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/10/2022] [Indexed: 11/13/2022] Open
Abstract
Computational modeling is an essential component of modern drug discovery. One of its most important applications is to select promising drug candidates for pharmacologically relevant target proteins. Because of continuing advances in structural biology, putative binding sites for small organic molecules are being discovered in numerous proteins linked to various diseases. These valuable data offer new opportunities to build efficient computational models predicting binding molecules for target sites through the application of data mining and machine learning. In particular, deep neural networks are powerful techniques capable of learning from complex data in order to make informed drug binding predictions. In this communication, we describe Pocket2Drug, a deep graph neural network model to predict binding molecules for a given a ligand binding site. This approach first learns the conditional probability distribution of small molecules from a large dataset of pocket structures with supervised training, followed by the sampling of drug candidates from the trained model. Comprehensive benchmarking simulations show that using Pocket2Drug significantly improves the chances of finding molecules binding to target pockets compared to traditional drug selection procedures. Specifically, known binders are generated for as many as 80.5% of targets present in the testing set consisting of dissimilar data from that used to train the deep graph neural network model. Overall, Pocket2Drug is a promising computational approach to inform the discovery of novel biopharmaceuticals.
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Affiliation(s)
- Wentao Shi
- Division of Electrical and Computer Engineering, Louisiana State University, Baton Rouge, LA, United States
| | - Manali Singha
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States
| | - Gopal Srivastava
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States
| | - Limeng Pu
- Center for Computation and Technology, Louisiana State University, Baton Rouge, LA, United States
| | - J. Ramanujam
- Division of Electrical and Computer Engineering, Louisiana State University, Baton Rouge, LA, United States
- Center for Computation and Technology, Louisiana State University, Baton Rouge, LA, United States
| | - Michal Brylinski
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States
- Center for Computation and Technology, Louisiana State University, Baton Rouge, LA, United States
- *Correspondence: Michal Brylinski,
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8
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Atas-Ozcan H, Brault V, Duchon A, Herault Y. Dyrk1a from Gene Function in Development and Physiology to Dosage Correction across Life Span in Down Syndrome. Genes (Basel) 2021; 12:1833. [PMID: 34828439 PMCID: PMC8624927 DOI: 10.3390/genes12111833] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 01/12/2023] Open
Abstract
Down syndrome is the main cause of intellectual disabilities with a large set of comorbidities from developmental origins but also that appeared across life span. Investigation of the genetic overdosage found in Down syndrome, due to the trisomy of human chromosome 21, has pointed to one main driver gene, the Dual-specificity tyrosine-regulated kinase 1A (Dyrk1a). Dyrk1a is a murine homolog of the drosophila minibrain gene. It has been found to be involved in many biological processes during development and in adulthood. Further analysis showed its haploinsufficiency in mental retardation disease 7 and its involvement in Alzheimer's disease. DYRK1A plays a role in major developmental steps of brain development, controlling the proliferation of neural progenitors, the migration of neurons, their dendritogenesis and the function of the synapse. Several strategies targeting the overdosage of DYRK1A in DS with specific kinase inhibitors have showed promising evidence that DS cognitive conditions can be alleviated. Nevertheless, providing conditions for proper temporal treatment and to tackle the neurodevelopmental and the neurodegenerative aspects of DS across life span is still an open question.
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Affiliation(s)
- Helin Atas-Ozcan
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (H.A.-O.); (V.B.); (A.D.)
| | - Véronique Brault
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (H.A.-O.); (V.B.); (A.D.)
| | - Arnaud Duchon
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (H.A.-O.); (V.B.); (A.D.)
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (H.A.-O.); (V.B.); (A.D.)
- Université de Strasbourg, CNRS, INSERM, Celphedia, Phenomin-Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France
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9
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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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10
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Ayala-Aguilera CC, Valero T, Lorente-Macías Á, Baillache DJ, Croke S, Unciti-Broceta A. Small Molecule Kinase Inhibitor Drugs (1995-2021): Medical Indication, Pharmacology, and Synthesis. J Med Chem 2021; 65:1047-1131. [PMID: 34624192 DOI: 10.1021/acs.jmedchem.1c00963] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The central role of dysregulated kinase activity in the etiology of progressive disorders, including cancer, has fostered incremental efforts on drug discovery programs over the past 40 years. As a result, kinase inhibitors are today one of the most important classes of drugs. The FDA approved 73 small molecule kinase inhibitor drugs until September 2021, and additional inhibitors were approved by other regulatory agencies during that time. To complement the published literature on clinical kinase inhibitors, we have prepared a review that recaps this large data set into an accessible format for the medicinal chemistry community. Along with the therapeutic and pharmacological properties of each kinase inhibitor approved across the world until 2020, we provide the synthesis routes originally used during the discovery phase, many of which were only available in patent applications. In the last section, we also provide an update on kinase inhibitor drugs approved in 2021.
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Affiliation(s)
- Cecilia C Ayala-Aguilera
- Cancer Research UK Edinburgh Centre, Institute of Genetics & Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, United Kingdom
| | - Teresa Valero
- Cancer Research UK Edinburgh Centre, Institute of Genetics & Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, United Kingdom
| | - Álvaro Lorente-Macías
- Cancer Research UK Edinburgh Centre, Institute of Genetics & Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, United Kingdom
| | - Daniel J Baillache
- Cancer Research UK Edinburgh Centre, Institute of Genetics & Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, United Kingdom
| | - Stephen Croke
- Cancer Research UK Edinburgh Centre, Institute of Genetics & Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, United Kingdom
| | - Asier Unciti-Broceta
- Cancer Research UK Edinburgh Centre, Institute of Genetics & Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, United Kingdom
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11
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Lorenz R, Wu J, Herberg FW, Taylor SS, Engh RA. Drugging the Undruggable: How Isoquinolines and PKA Initiated the Era of Designed Protein Kinase Inhibitor Therapeutics. Biochemistry 2021; 60:3470-3484. [PMID: 34370450 DOI: 10.1021/acs.biochem.1c00359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In 1984, Japanese researchers led by the biochemist Hiroyoshi Hidaka described the first synthetic protein kinase inhibitors based on an isoquinoline sulfonamide structure (Hidaka et al. Biochemistry, 1984 Oct 9; 23(21): 5036-41. doi: 10.1021/bi00316a032). These led to the first protein kinase inhibitor approved for medical use (fasudil), an inhibitor of the AGC subfamily Rho kinase. With potencies strong enough to compete against endogenous ATP, the isoquinoline compounds established the druggability of the ATP binding site. Crystal structures of their protein kinase complexes, including with cAMP-dependent protein kinase (PKA), showed interactions that, on the one hand, could mimic ATP but, on the other hand, could be optimized for high potency binding, kinase selectivity, and diversification away from adenosine. They also showed the flexibility of the glycine-rich loop, and PKA became a major prototype for crystallographic and nuclear magnetic resonance (NMR) studies of protein kinase mechanism and dynamic activity control. Since fasudil, more than 70 kinase inhibitors have been approved for clinical use, involving efforts that progressively have introduced new paradigms of data-driven drug discovery. Publicly available data alone comprise over 5000 protein kinase crystal structures and hundreds of thousands of binding data. Now, new methods, including artificial intelligence techniques and expansion of protein kinase targeting approaches, together with the expiration of patent protection for optimized inhibitor scaffolds, promise even greater advances in drug discovery. Looking back to the time of the first isoquinoline hinge binders brings the current state-of-the-art into stark contrast. Appropriately for this Perspective article, many of the milestone papers during this time were published in Biochemistry (now ACS Biochemistry).
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Affiliation(s)
- Robin Lorenz
- Department of Biochemistry, Institute for Biology, University of Kassel, Kassel 34132, Germany
| | - Jian Wu
- Department of Pharmacology, University of California, San Diego, 9400 Gilman Drive, La Jolla, California 92093-0654, United States
| | - Friedrich W Herberg
- Department of Biochemistry, Institute for Biology, University of Kassel, Kassel 34132, Germany
| | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, 9400 Gilman Drive, La Jolla, California 92093-0654, United States.,Department of Chemistry and Biochemistry, University of California, San Diego, 9400 Gilman Drive, La Jolla, California 92093-0654, United States
| | - Richard A Engh
- The Norwegian Structural Biology Centre, Department of Chemistry, UiT the Arctic University of Norway, Tromsø 9012, Norway
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12
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Lindberg MF, Meijer L. Dual-Specificity, Tyrosine Phosphorylation-Regulated Kinases (DYRKs) and cdc2-Like Kinases (CLKs) in Human Disease, an Overview. Int J Mol Sci 2021; 22:6047. [PMID: 34205123 PMCID: PMC8199962 DOI: 10.3390/ijms22116047] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 01/09/2023] Open
Abstract
Dual-specificity tyrosine phosphorylation-regulated kinases (DYRK1A, 1B, 2-4) and cdc2-like kinases (CLK1-4) belong to the CMGC group of serine/threonine kinases. These protein kinases are involved in multiple cellular functions, including intracellular signaling, mRNA splicing, chromatin transcription, DNA damage repair, cell survival, cell cycle control, differentiation, homocysteine/methionine/folate regulation, body temperature regulation, endocytosis, neuronal development, synaptic plasticity, etc. Abnormal expression and/or activity of some of these kinases, DYRK1A in particular, is seen in many human nervous system diseases, such as cognitive deficits associated with Down syndrome, Alzheimer's disease and related diseases, tauopathies, dementia, Pick's disease, Parkinson's disease and other neurodegenerative diseases, Phelan-McDermid syndrome, autism, and CDKL5 deficiency disorder. DYRKs and CLKs are also involved in diabetes, abnormal folate/methionine metabolism, osteoarthritis, several solid cancers (glioblastoma, breast, and pancreatic cancers) and leukemias (acute lymphoblastic leukemia, acute megakaryoblastic leukemia), viral infections (influenza, HIV-1, HCMV, HCV, CMV, HPV), as well as infections caused by unicellular parasites (Leishmania, Trypanosoma, Plasmodium). This variety of pathological implications calls for (1) a better understanding of the regulations and substrates of DYRKs and CLKs and (2) the development of potent and selective inhibitors of these kinases and their evaluation as therapeutic drugs. This article briefly reviews the current knowledge about DYRK/CLK kinases and their implications in human disease.
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Affiliation(s)
| | - Laurent Meijer
- Perha Pharmaceuticals, Perharidy Peninsula, 29680 Roscoff, France;
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13
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The role of small molecule Flt3 receptor protein-tyrosine kinase inhibitors in the treatment of Flt3-positive acute myelogenous leukemias. Pharmacol Res 2020; 155:104725. [DOI: 10.1016/j.phrs.2020.104725] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 02/24/2020] [Indexed: 02/08/2023]
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14
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Westbrook JD, Soskind R, Hudson BP, Burley SK. Impact of the Protein Data Bank on antineoplastic approvals. Drug Discov Today 2020; 25:837-850. [PMID: 32068073 DOI: 10.1016/j.drudis.2020.02.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/08/2020] [Accepted: 02/07/2020] [Indexed: 12/14/2022]
Abstract
Open access to 3D structure information from the Protein Data Bank (PDB) facilitated discovery and development of >90% of the 79 new antineoplastic agents (54 small molecules, 25 biologics) with known molecular targets approved by the FDA 2010-2018. Analyses of PDB holdings, the scientific literature and related documents for each drug-target combination revealed that the impact of public-domain 3D structure data was broad and substantial, ranging from understanding target biology (∼95% of all targets) to identifying a given target as probably druggable (∼95% of all targets) to structure-guided lead optimization (>70% of all small-molecule drugs). In addition to aggregate impact assessments, illustrative case studies are presented for three protein kinase inhibitors, an allosteric enzyme inhibitor and seven advanced-stage melanoma therapeutics.
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Affiliation(s)
- John D Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Rose Soskind
- Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Brian P Hudson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Stephen K Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA; Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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15
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Zhao C, Wang D, Gao Z, Kan H, Qiu F, Chen L, Li H. Licocoumarone induces BxPC-3 pancreatic adenocarcinoma cell death by inhibiting DYRK1A. Chem Biol Interact 2020; 316:108913. [PMID: 31838052 DOI: 10.1016/j.cbi.2019.108913] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/23/2019] [Accepted: 12/03/2019] [Indexed: 12/16/2022]
Abstract
Protein kinases play an indispensable role in signaling pathways that regulate tumor cell functions, which represent potent therapeutic targets in cancers. Dual-specificity tyrosine phosphorylation regulated kinase 1A (DYRK1A) as a serine/threonine kinase has recently been reported to be upregulated in pancreatic ductal adenocarcinoma (PDAC) and show protumorigenic effect. By activity-guided phytochemical investigation of the extracts from Glycyrrhiza uralensis Fisch, we expect to find the effective constituents that can suppress pancreatic cancer cell proliferation and/or induce cells apoptotic by inhibiting DYRK1A. Eight isopentenyl-substituted compounds (1-8), including four coumarins (1-4), one benzofuran (5), and three flavonoids (6-8), were isolated and identified from G. uralensis Fisch. Among them, licocoumarone (LC, 5) showed effective inhibitory activity against DYRK1A with an IC50 value of 12.56 μM. Molecular docking analysis suggested that LC completely occupied the whole pocket of DYRK1A and formed obvious hydrophobic interactions and hydrogen bonds with DYRK1A residues. Further in vitro validation, including Microscale Thermophoresis (MST) and drug affinity responsive target stability (DARTS) techniques, demonstrated the specific combining capacity of LC to DYRK1A. Meanwhile, LC induced significant cytotoxicity against DYRK1A-overexpressing BxPC-3 cells with an IC50 value of 50.77 μM. Mechanism studies revealed that LC reduced c-MET protein level by inhibiting DYRK1A. These findings provide preliminary evidences that LC as a natural DYRK1A inhibitor suppresses human pancreatic adenocarcinoma BxPC-3 cell proliferation and induces cell apoptotic, which might present new options and possibilities for targeted therapies in pancreatic cancer therapy.
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Affiliation(s)
- Chao Zhao
- Wuya College of Innovation, School of Pharmaceutical Engineering, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Dun Wang
- Wuya College of Innovation, School of Pharmaceutical Engineering, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Zexuan Gao
- Wuya College of Innovation, School of Pharmaceutical Engineering, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Hongfeng Kan
- Wuya College of Innovation, School of Pharmaceutical Engineering, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Feng Qiu
- School of Chinese Materia Medica and Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.
| | - Lixia Chen
- Wuya College of Innovation, School of Pharmaceutical Engineering, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China.
| | - Hua Li
- Wuya College of Innovation, School of Pharmaceutical Engineering, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China; Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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16
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Gomha SM, Muhammad ZA, Ezz El-Arab E, Elmetwally AM, El-Sayed AA, Matar IK. Design, Synthesis, Molecular Docking Study and Anti-Hepatocellular Carcinoma Evaluation of New Bis-Triazolothiadiazines. Mini Rev Med Chem 2020; 20:788-800. [PMID: 31613728 DOI: 10.2174/1389557519666191015130037] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/12/2018] [Accepted: 07/10/2019] [Indexed: 11/22/2022]
Abstract
OBJECTIVE The reaction of bis(4-amino-4H-1,2,4-triazole-3-thiol) with hydrazonoyl halides and α-halo-ketones gave a new series of bis-1,2,4-triazolo[3,4-b]thiadiazine derivatives. METHODS The structure of the new products was established on the basis of their elemental and spectral data (mass, 1H NMR, 13C NMR and IR) and an alternate method. RESULTS Several of the synthesized products were subjected to in vitro anticancer screening against human hepatocellular carcinoma (HepG-2) and the results showed that compounds 16, 14 and 12 have promising activities (IC50 value of 24.8±9.1, 28.3±0.5, and 31±2.9μM, respectively) compared with Harmine reference drug (IC50 value of 22.4±1.11 μM). CONCLUSION Moreover, molecular docking studies were performed to analyze the binding modes of the discovered hits into the active site of DYRK1A using iGEMDOCK.
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Affiliation(s)
- Sobhi M Gomha
- Chemistry Department, Faculty of Science, Cairo University, Giza 12613, Egypt
- Department of Chemistry, Faculty of Science, Islamic University in Almadinah Almonawara, Almadinah Almonawara, 42351, Saudi Arabia
| | - Zeinab A Muhammad
- Organic Chemistry Department, National Organization for Drug Control and Research (NODCAR), Giza 12311, Egypt
| | - Elham Ezz El-Arab
- Organic Chemistry Department, National Organization for Drug Control and Research (NODCAR), Giza 12311, Egypt
| | - Amira M Elmetwally
- Organic Chemistry Department, National Organization for Drug Control and Research (NODCAR), Giza 12311, Egypt
| | - Abdelaziz A El-Sayed
- Department of Chemistry, Faculty of Science, Islamic University in Almadinah Almonawara, Almadinah Almonawara, 42351, Saudi Arabia
- Department of Zoology, Faculty of Science, Zagazig University, Zagazig 44519, Egypt
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17
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Apsel Winger B, Cortopassi WA, Garrido Ruiz D, Ding L, Jang K, Leyte-Vidal A, Zhang N, Esteve-Puig R, Jacobson MP, Shah NP. ATP-Competitive Inhibitors Midostaurin and Avapritinib Have Distinct Resistance Profiles in Exon 17-Mutant KIT. Cancer Res 2019; 79:4283-4292. [PMID: 31270078 DOI: 10.1158/0008-5472.can-18-3139] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 05/05/2019] [Accepted: 06/26/2019] [Indexed: 01/08/2023]
Abstract
KIT is a type-3 receptor tyrosine kinase that is frequently mutated at exon 11 or 17 in a variety of cancers. First-generation KIT tyrosine kinase inhibitors (TKI) are ineffective against KIT exon 17 mutations, which favor an active conformation that prevents these TKIs from binding. The ATP-competitive inhibitors, midostaurin and avapritinib, which target the active kinase conformation, were developed to inhibit exon 17-mutant KIT. Because secondary kinase domain mutations are a common mechanism of TKI resistance and guide ensuing TKI design, we sought to define problematic KIT kinase domain mutations for these emerging therapeutics. Midostaurin and avapritinib displayed different vulnerabilities to secondary kinase domain substitutions, with the T670I gatekeeper mutation being selectively problematic for avapritinib. Although gatekeeper mutations often directly disrupt inhibitor binding, we provide evidence that T670I confers avapritinib resistance indirectly by inducing distant conformational changes in the phosphate-binding loop. These findings suggest combining midostaurin and avapritinib may forestall acquired resistance mediated by secondary kinase domain mutations. SIGNIFICANCE: This study identifies potential problematic kinase domain mutations for next-generation KIT inhibitors midostaurin and avapritinib.
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Affiliation(s)
- Beth Apsel Winger
- Division of Hematology/Oncology, Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Wilian A Cortopassi
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
| | - Diego Garrido Ruiz
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
| | - Lucky Ding
- Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, California
| | - Kibeom Jang
- Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, California
| | - Ariel Leyte-Vidal
- Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, California
| | - Na Zhang
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California.,Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing, China
| | - Rosaura Esteve-Puig
- Department of Dermatology, University of California San Francisco, San Francisco, California
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
| | - Neil P Shah
- Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, California.
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18
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Arbones ML, Thomazeau A, Nakano-Kobayashi A, Hagiwara M, Delabar JM. DYRK1A and cognition: A lifelong relationship. Pharmacol Ther 2019; 194:199-221. [PMID: 30268771 DOI: 10.1016/j.pharmthera.2018.09.010] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The dosage of the serine threonine kinase DYRK1A is critical in the central nervous system (CNS) during development and aging. This review analyzes the functions of this kinase by considering its interacting partners and pathways. The role of DYRK1A in controlling the differentiation of prenatal newly formed neurons is presented separately from its role at the pre- and post-synaptic levels in the adult CNS; its effects on synaptic plasticity are also discussed. Because this kinase is positioned at the crossroads of many important processes, genetic dosage errors in this protein produce devastating effects arising from DYRK1A deficiency, such as in MRD7, an autism spectrum disorder, or from DYRK1A excess, such as in Down syndrome. Effects of these errors have been shown in various animal models including Drosophila, zebrafish, and mice. Dysregulation of DYRK1A levels also occurs in neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Finally, this review describes inhibitors that have been assessed in vivo. Accurate targeting of DYRK1A levels in the brain, with either inhibitors or activators, is a future research challenge.
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Affiliation(s)
- Maria L Arbones
- Department of Developmental Biology, Instituto de Biología Molecular de Barcelona, CSIC, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 08028 Barcelona, Spain.
| | - Aurore Thomazeau
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, United States
| | - Akiko Nakano-Kobayashi
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Jean M Delabar
- INSERM U1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMRS 1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
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19
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Manley PW, Caravatti G, Furet P, Roesel J, Tran P, Wagner T, Wartmann M. Comparison of the Kinase Profile of Midostaurin (Rydapt) with That of Its Predominant Metabolites and the Potential Relevance of Some Newly Identified Targets to Leukemia Therapy. Biochemistry 2018; 57:5576-5590. [PMID: 30148617 DOI: 10.1021/acs.biochem.8b00727] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The multitargeted protein kinase inhibitor midostaurin is approved for the treatment of both newly diagnosed FLT3-mutated acute myeloid leukemia (AML) and KIT-driven advanced systemic mastocytosis. AML is a heterogeneous malignancy, and investigational drugs targeting FLT3 have shown disparate effects in patients with FLT3-mutated AML, probably as a result of their inhibiting different targets and pathways at the administered doses. However, the efficacy and side effects of drugs do not just reflect the biochemical and pharmacodynamic properties of the parent compound but are often comprised of complex cooperative effects between the properties of the parent and active metabolites. Following chronic dosing, two midostaurin metabolites attain steady-state plasma trough levels greater than that of the parent drug. In this study, we characterized these metabolites and determined their profiles as kinase inhibitors using radiometric transphosphorylation assays. Like midostaurin, the metabolites potently inhibit mutant forms of FLT3 and KIT and several additional kinases that either are directly involved in the deregulated signaling pathways or have been implicated as playing a role in AML via stromal support, such as IGF1R, LYN, PDPK1, RET, SYK, TRKA, and VEGFR2. Consequently, a complex interplay between the kinase activities of midostaurin and its metabolites is likely to contribute to the efficacy of midostaurin in AML and helps to engender the distinctive effects of the drug compared to those of other FLT3 inhibitors in this malignancy.
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Affiliation(s)
- Paul W Manley
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research , Novartis International AG , CH-4002 Basel , Switzerland
| | - Giorgio Caravatti
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research , Novartis International AG , CH-4002 Basel , Switzerland
| | - Pascal Furet
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research , Novartis International AG , CH-4002 Basel , Switzerland
| | - Johannes Roesel
- Oncology Disease Area, Novartis Institutes for Biomedical Research , Novartis International AG , CH-4002 Basel , Switzerland
| | - Phi Tran
- Department of Drug Metabolism and Pharmacokinetics , Novartis Institutes for Biomedical Research , East Hanover , New Jersey 07936 , United States
| | - Trixie Wagner
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research , Novartis International AG , CH-4002 Basel , Switzerland
| | - Markus Wartmann
- Oncology Disease Area, Novartis Institutes for Biomedical Research , Novartis International AG , CH-4002 Basel , Switzerland
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20
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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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21
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Hiller NDJ, Silva NAAE, Faria RX, Souza ALA, Resende JALC, Borges Farias A, Correia Romeiro N, de Luna Martins D. Synthesis and Evaluation of the Anticancer and Trypanocidal Activities of Boronic Tyrphostins. ChemMedChem 2018; 13:1395-1404. [PMID: 29856519 DOI: 10.1002/cmdc.201800206] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/14/2018] [Indexed: 12/13/2022]
Abstract
Molecules containing an (cyanovinyl)arene moiety are known as tyrphostins because of their ability to inhibit proteins from the tyrosine kinase family, an interesting target for the development of anticancer and trypanocidal drugs. In the present work, (E)-(cyanovinyl)benzeneboronic acids were synthesized by Knoevenagel condensations without the use of any catalysts in water through a simple protocol that completely avoided the use of organic solvents in the synthesis and workup process. The in vitro anticancer and trypanocidal activities of the synthesized boronic acids were also evaluated, and it was discovered that the introduction of the boronic acid functionality improved the activity of the boronic tyrphostins. In silico target fishing with the use of a chemogenomic approach suggested that tyrosine-phosphorylation-regulated kinase 1a (DYRK1A) was a potential target for some of the designed compounds.
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Affiliation(s)
- Noemi de J Hiller
- Research Group on Catalysis and Synthesis (CSI), Universidade Federal Fluminense, Laboratório 413, Instituto de Química, Campus do Valonguinho, Centro, Niterói, RJ, 24020-141, Brazil
| | - Nayane A A E Silva
- Research Group on Catalysis and Synthesis (CSI), Universidade Federal Fluminense, Laboratório 413, Instituto de Química, Campus do Valonguinho, Centro, Niterói, RJ, 24020-141, Brazil
| | - Robson X Faria
- Laboratory of Toxoplasmosis and other Protozoan Diseases, Oswaldo Cruz Institute (Fiocruz), Brasil
| | - André Luís A Souza
- Laboratory of Biochemistry of Peptides, Oswaldo Cruz Institute (Fiocruz), Brazil
| | - Jackson A L C Resende
- Laboratory of Solid-State Chemistry, Universidade Federal do Mato Grosso, Instituto de Ciências Exatas e da Terra, Campus Universitário do Araguaia, Barra do Garças, MT, 78600-000, Brazil
| | - André Borges Farias
- Núcleo de Pesquisas em Ecologia e Desenvolvimento Social (NUPEM), Universidade Federal do Rio de Janeiro, Campus de Macaé, Av. Rotary Club s/n; São José do Barreto, Macaé, RJ, 27901-000, Brazil
| | - Nelilma Correia Romeiro
- Núcleo de Pesquisas em Ecologia e Desenvolvimento Social (NUPEM), Universidade Federal do Rio de Janeiro, Campus de Macaé, Av. Rotary Club s/n; São José do Barreto, Macaé, RJ, 27901-000, Brazil
| | - Daniela de Luna Martins
- Research Group on Catalysis and Synthesis (CSI), Universidade Federal Fluminense, Laboratório 413, Instituto de Química, Campus do Valonguinho, Centro, Niterói, RJ, 24020-141, Brazil
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22
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Widowati EW, Ernst S, Hausmann R, Müller-Newen G, Becker W. Functional characterization of DYRK1A missense variants associated with a syndromic form of intellectual deficiency and autism. Biol Open 2018; 7:7/4/bio032862. [PMID: 29700199 PMCID: PMC5936063 DOI: 10.1242/bio.032862] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Haploinsufficiency of DYRK1A is a cause of a neurodevelopmental syndrome termed mental retardation autosomal dominant 7 (MRD7). Several truncation mutations, microdeletions and missense variants have been identified and result in a recognizable phenotypic profile, including microcephaly, intellectual disability, epileptic seizures, autism spectrum disorder and language delay. DYRK1A is an evolutionary conserved protein kinase which achieves full catalytic activity through tyrosine autophosphorylation. We used a heterologous mammalian expression system to explore the functional characteristics of pathogenic missense variants that affect the catalytic domain of DYRK1A. Four of the substitutions eliminated tyrosine autophosphorylation (L245R, F308V, S311F, S346P), indicating that these variants lacked kinase activity. Tyrosine phosphorylation of DYRK1A-L295F in mammalian cells was comparable to wild type, although the mutant showed lower catalytic activity and reduced thermodynamic stability in cellular thermal shift assays. In addition, we observed that one variant (DYRK1A-T588N) with a mutation outside the catalytic domain did not differ from wild-type DYRK1A in tyrosine autophosphorylation, catalytic activity or subcellular localization. These results suggest that the pathogenic missense variants in the catalytic domain of DYRK1A impair enzymatic function by affecting catalytic residues or by compromising the structural integrity of the kinase domain. This article has an associated First Person interview with the first author of the paper. Summary: We have analyzed the functional consequences of amino acid substitutions in the protein kinase DYRK1A that have been identified as pathogenic in patients with microcephaly, intellectual disability and autism.
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Affiliation(s)
- Esti Wahyu Widowati
- Institute of Pharmacology and Toxicology, Medical Faculty, RWTH Aachen University, 52074 Aachen, Germany.,Chemistry Study Program, Faculty of Science and Technology, State Islamic University (UIN) Sunan Kalijaga, Yogyakarta 55281, Indonesia
| | - Sabrina Ernst
- Institute of Biochemistry and Molecular Biology, Medical Faculty, RWTH Aachen University, 52074 Aachen, Germany
| | - Ralf Hausmann
- Institute of Pharmacology and Toxicology, Medical Faculty, RWTH Aachen University, 52074 Aachen, Germany
| | - Gerhard Müller-Newen
- Institute of Biochemistry and Molecular Biology, Medical Faculty, RWTH Aachen University, 52074 Aachen, Germany
| | - Walter Becker
- Institute of Pharmacology and Toxicology, Medical Faculty, RWTH Aachen University, 52074 Aachen, Germany
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Kim K, Cha JS, Cho YS, Kim H, Chang N, Kim HJ, Cho HS. Crystal Structure of Human Dual-Specificity Tyrosine-Regulated Kinase 3 Reveals New Structural Features and Insights into its Auto-phosphorylation. J Mol Biol 2018; 430:1521-1530. [PMID: 29634919 DOI: 10.1016/j.jmb.2018.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/31/2018] [Accepted: 04/03/2018] [Indexed: 11/15/2022]
Abstract
Dual-specificity tyrosine-regulated kinases (DYRKs) auto-phosphorylate a critical tyrosine residue in their activation loop and phosphorylate their substrate on serine and threonine residues. The auto-phosphorylation occurs intramolecularly and is a one-off event. DYRK3 is selectively expressed at a high level in hematopoietic cells and attenuates erythroblast development, leading to anemia. In the present study, we determined the crystal structure of the mature form of human DYRK3 in complex with harmine, an ATP competitive inhibitor. The crystal structure revealed a phosphorylation site, residue S350, whose phosphorylation increases the stability of DYRK3 and enhances its kinase activity. In addition, our structural and biochemical assays suggest that the N-terminal auto-phosphorylation accessory domain stabilizes the DYRK3 protein, followed by auto-phosphorylation of the tyrosine of the activation loop, which is important for kinase activity. Finally, our docking analysis provides information for the design of novel and potent therapeutics to treat anemia.
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Affiliation(s)
- Kuglae Kim
- Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Jeong Seok Cha
- Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Yong-Soon Cho
- Department of Clinical Pharmacology and Therapeutics, Asan Medical Center, 88 Olympic-ro, 43-gil, Songpa-gu, Seoul 05505, Republic of Korea
| | - Hoyoung Kim
- Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Nienping Chang
- Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Hye-Jung Kim
- New Drug Development Center, KBIO Osong Medical Innovation Foundation, Cheongju 28160, Republic of Korea
| | - Hyun-Soo Cho
- Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
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24
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Hutterer C, Milbradt J, Hamilton S, Zaja M, Leban J, Henry C, Vitt D, Steingruber M, Sonntag E, Zeitträger I, Bahsi H, Stamminger T, Rawlinson W, Strobl S, Marschall M. Inhibitors of dual-specificity tyrosine phosphorylation-regulated kinases (DYRK) exert a strong anti-herpesviral activity. Antiviral Res 2017; 143:113-121. [PMID: 28400201 DOI: 10.1016/j.antiviral.2017.04.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/26/2017] [Accepted: 04/07/2017] [Indexed: 11/26/2022]
Abstract
Infection with human cytomegalovirus (HCMV) is a serious medical problem, particularly in immunocompromised individuals and neonates. The success of (val)ganciclovir therapy is hampered by low drug compatibility and induction of viral resistance. A novel strategy of antiviral treatment is based on the exploitation of cell-directed signaling, e. g. pathways with a known relevance for carcinogenesis and tumor drug development. Here we describe a principle for putative antiviral drugs based on targeting dual-specificity tyrosine phosphorylation-regulated kinases (DYRKs). DYRKs constitute an evolutionarily conserved family of protein kinases with key roles in the control of cell proliferation and differentiation. Members of the DYRK family are capable of phosphorylating a number of substrate proteins, including regulators of the cell cycle, e.g. DYRK1B can induce cell cycle arrest, a critical step for the regulation of HCMV replication. Here we provide first evidence for a critical role of DYRKs during viral replication and the high antiviral potential of DYRK inhibitors (SC84227, SC97202 and SC97208, Harmine and AZ-191). Using established replication assays for laboratory and clinically relevant strains of HCMV, concentration-dependent profiles of inhibition were obtained. Mean inhibitory concentrations (EC50) of 0.98 ± 0.08 μM/SC84227, 0.60 ± 0.02 μM/SC97202, 6.26 ± 1.64 μM/SC97208, 0.71 ± 0.019 μM/Harmine and 0.63 ± 0.23 μM/AZ-191 were determined with HCMV strain AD169-GFP for the infection of primary human fibroblasts. A first analysis of the mode of antiviral action suggested a block of viral replication at the early-late stage of HCMV gene expression. Moreover, rhesus macaque cytomegalovirus (RhCMV), varicella-zoster virus (VZV) and herpes simplex virus (HSV-1) showed a similarly high sensitivity to these compounds. Thus, we conclude that DYRK signaling represents a promising target pathway for the development of novel anti-herpesviral strategies.
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Affiliation(s)
- Corina Hutterer
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Germany.
| | - Jens Milbradt
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Germany
| | - Stuart Hamilton
- Serology and Virology Division, SEALS Microbiology Prince of Wales Hospital Randwick NSW 2013 and SOMS and BABS, University of NSW, Sydney, Australia
| | - Mirko Zaja
- 4SC Discovery GmbH, Martinsried, Germany
| | | | | | | | - Mirjam Steingruber
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Germany
| | - Eric Sonntag
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Germany
| | - Isabel Zeitträger
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Germany
| | - Hanife Bahsi
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Germany
| | - Thomas Stamminger
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Germany
| | - William Rawlinson
- Serology and Virology Division, SEALS Microbiology Prince of Wales Hospital Randwick NSW 2013 and SOMS and BABS, University of NSW, Sydney, Australia
| | | | - Manfred Marschall
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Germany.
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25
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Lee CC, Chuang YC, Liu YL, Yang CN. A molecular dynamics simulation study for variant drug responses due to FMS-like tyrosine kinase 3 G697R mutation. RSC Adv 2017. [DOI: 10.1039/c7ra04099g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
FMS-like tyrosine kinase 3 (FLT3) is an attractive target for acute myeloid leukemia. This work provides a mechanism behind the severe and minor drug resistance experienced by PKC412 and sorafenib, respectively, in response to G697R mutation.
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Affiliation(s)
- Chien-Cheng Lee
- Department of Pharmacy
- Zuoying Armed Forces General Hospital
- Kaohsiung
- Taiwan
| | - Yu-Chung Chuang
- Department of Life Science
- National University of Kaohsiung
- Kaohsiung
- Taiwan
| | - Yu-Lin Liu
- Department of Life Science
- National University of Kaohsiung
- Kaohsiung
- Taiwan
| | - Chia-Ning Yang
- Department of Life Science
- National University of Kaohsiung
- Kaohsiung
- Taiwan
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26
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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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