1
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Wang L, Fang Y, Ma Y, Zhao Z, Ma R, Zhang Y, Qiao Y, Wang X, Zhang Y. A novel natural Syk inhibitor suppresses IgE-mediated mast cell activation and passive cutaneous anaphylaxis. Bioorg Chem 2024; 146:107320. [PMID: 38569323 DOI: 10.1016/j.bioorg.2024.107320] [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: 01/23/2024] [Revised: 03/20/2024] [Accepted: 03/28/2024] [Indexed: 04/05/2024]
Abstract
Spleen tyrosine kinase (Syk) plays a crucial role as a target for allergy treatment due to its involvement in immunoreceptor signaling. The purpose of this study was to identify natural inhibitors of Syk and assess their effects on the IgE-mediated allergic response in mast cells and ICR mice. A list of eight compounds was selected based on pharmacophore and molecular docking, showing potential inhibitory effects through virtual screening. Among these compounds, sophoraflavanone G (SFG) was found to inhibit Syk activity in an enzymatic assay, with an IC50 value of 2.2 μM. To investigate the conformational dynamics of the SYK-SFG system, we performed molecular dynamics simulations. The stability of the binding between SFG and Syk was evaluated using root mean square deviation (RMSD) and root mean square fluctuation (RMSF). In RBL-2H3 cells, SFG demonstrated a dose-dependent suppression of IgE/BSA-induced mast cell degranulation, with no significant cytotoxicity observed at concentrations below 10.0 μM within 24 h. Furthermore, SFG reduced the production of TNF-α and IL-4 in RBL-2H3 cells. Mechanistic investigations revealed that SFG inhibited downstream signaling proteins, including phospholipase Cγ1 (PLCγ1), as well as mitogen-activated protein kinases (AKT, Erk1/2, p38, and JNK), in mast cells in a dose-dependent manner. Passive cutaneous anaphylaxis (PCA) experiments demonstrated that SFG could reduce ear swelling, mast cell degranulation, and the expression of COX-2 and IL-4. Overall, our findings identify naturally occurring SFG as a direct inhibitor of Syk that effectively suppresses mast cell degranulation both in vitro and in vivo.
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Affiliation(s)
- Lele Wang
- Key Laboratory of Ethnomedicine in Ministry of Education, School of Pharmacy, Minzu University of China, Haidian District, Beijing 100081, China
| | - Yuzhen Fang
- Key Laboratory of Ethnomedicine in Ministry of Education, School of Pharmacy, Minzu University of China, Haidian District, Beijing 100081, China
| | - Yuqing Ma
- Beijing Key Lab of Traditional Chinese Medicine Collateral Disease Theory Research, School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Zixi Zhao
- Beijing Key Lab of Traditional Chinese Medicine Collateral Disease Theory Research, School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Ruonan Ma
- Beijing Key Lab of Traditional Chinese Medicine Collateral Disease Theory Research, School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Yanling Zhang
- Key Laboratory of TCM-information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Yanjiang Qiao
- Key Laboratory of TCM-information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China.
| | - Xing Wang
- Beijing Key Lab of Traditional Chinese Medicine Collateral Disease Theory Research, School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China.
| | - Yuxin Zhang
- Key Laboratory of Ethnomedicine in Ministry of Education, School of Pharmacy, Minzu University of China, Haidian District, Beijing 100081, China.
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2
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Lee S, Dao PDQ, Lim HJ, Cho CS. Recyclable Magnetic Cu-MOF-74-Catalyzed C(sp 2)-N Coupling and Cyclization under Microwave Irradiation: Synthesis of Imidazo[1,2- c]quinazolines and Their Analogues. ACS OMEGA 2023; 8:16218-16227. [PMID: 37179653 PMCID: PMC10173347 DOI: 10.1021/acsomega.3c00680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/06/2023] [Indexed: 05/15/2023]
Abstract
Magnetic Cu-MOF-74 (Fe3O4@SiO2@Cu-MOF-74) was synthesized for the first time by grafting MOF-74 (copper as the metal center) on the surface of core-shell magnetic carboxyl-functionalized silica gel (Fe3O4@SiO2-COOH), which was prepared by coating core Fe3O4 nanoparticles with hydrolyzed 2-(3-(triethoxysilyl)propyl)succinic anhydride and tetraethyl orthosilicate. The structure of Fe3O4@SiO2@Cu-MOF-74 nanoparticles was characterized by Fourier transform infrared (FT-IR) spectroscopy, scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), and transmission electron microscopy (TEM). The prepared Fe3O4@SiO2@Cu-MOF-74 nanoparticles could be applied as a recyclable catalyst to the synthesis of N-fused hybrid scaffolds. 2-(2-Bromoaryl)imidazoles and 2-(2-bromovinyl)imidazoles were coupled and cyclized with cyanamide in DMF in the presence of a catalytic amount of Fe3O4@SiO2@Cu-MOF-74 along with a base to give imidazo[1,2-c]quinazolines and imidazo[1,2-c]pyrimidines, respectively, in good yields. The Fe3O4@SiO2@Cu-MOF-74 catalyst could be easily recovered by a super magnetic bar and recycled more than four times while almost maintaining catalytic activity.
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Affiliation(s)
- Seong
Weon Lee
- Department
of Applied Chemistry, Kyungpook National
University, 80 Daehakro, Bukgu, Daegu 41566, Republic of Korea
| | - Pham Duy Quang Dao
- Department
of Applied Chemistry, Kyungpook National
University, 80 Daehakro, Bukgu, Daegu 41566, Republic of Korea
| | - Ho-Jin Lim
- Department
of Environmental Engineering, Kyungpook
National University, 80 Daehakro, Bukgu, Daegu 41566, Republic of Korea
| | - Chan Sik Cho
- Department
of Applied Chemistry, Kyungpook National
University, 80 Daehakro, Bukgu, Daegu 41566, Republic of Korea
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3
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Kumar V, Parate S, Danishuddin, Zeb A, Singh P, Lee G, Jung TS, Lee KW, Ha MW. 3D-QSAR-Based Pharmacophore Modeling, Virtual Screening, and Molecular Dynamics Simulations for the Identification of Spleen Tyrosine Kinase Inhibitors. Front Cell Infect Microbiol 2022; 12:909111. [PMID: 35846777 PMCID: PMC9280624 DOI: 10.3389/fcimb.2022.909111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Spleen tyrosine kinase (SYK) is an essential mediator of immune cell signaling and has been anticipated as a therapeutic target for autoimmune diseases, notably rheumatoid arthritis, allergic rhinitis, asthma, and cancers. Significant attempts have been undertaken in recent years to develop SYK inhibitors; however, limited success has been achieved due to poor pharmacokinetics and adverse effects of inhibitors. The primary goal of this research was to identify potential inhibitors having high affinity, selectivity based on key molecular interactions, and good drug-like properties than the available inhibitor, fostamatinib. In this study, a 3D-QSAR model was built for SYK based on known inhibitor IC50 values. The best pharmacophore model was then used as a 3D query to screen a drug-like database to retrieve hits with novel chemical scaffolds. The obtained compounds were subjected to binding affinity prediction using the molecular docking approach, and the results were subsequently validated using molecular dynamics (MD) simulations. The simulated compounds were ranked according to binding free energy (ΔG), and the binding affinity was compared with fostamatinib. The binding mode analysis of selected compounds revealed that the hit compounds form hydrogen bond interactions with hinge region residue Ala451, glycine-rich loop residue Lys375, Ser379, and DFG motif Asp512. Identified hits were also observed to form a desirable interaction with Pro455 and Asn457, the rare feature observed in SYK inhibitors. Therefore, we argue that identified hit compounds ZINC98363745, ZINC98365358, ZINC98364133, and ZINC08789982 may help in drug design against SYK.
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4
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Raauf AMR, Al-Smaism RF, Thejeel KA, Rasheed HAM. Synthesis, characterization and antimicrobial study via new heterocyclic derivatives of trimethoprim. Nat Prod Res 2018; 33:1277-1283. [PMID: 29726729 DOI: 10.1080/14786419.2018.1470516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
New compounds of trimethoprim heterocyclic derivatives were synthesized. These compounds were synthesized through the condensation reaction between trimethoprim with bromoacetic acid to yield compound 1. Several Schiff bases 2-7 have been synthesized by the condensation different aromatic aldehydes with compound 1. Compound 8 were formed from the reaction of sodium nitrite and acetyl acetone in presence of conc. hydrogen chloride to obtain the hydrazono derivative; then, Cyclocondensation of compound 8 with hydrazine hydrate, phenyl hydrazine and dinitrophenyl hydrazine respectively to yield compounds 9-11 in ethanol affording the pyrazoline derivatives. This work involves the synthesis of some 1,2,3-Triazoles derived from compound 1 by the action of sodium azide on the diazonium chloride salt to yield 5-azido-8-(3,4,5-trimethoxybenzyl)imidazo[1,2-c]pyrimidin-3(2H)-one 12. Finally, by reaction of 12 with acetyl acetone and ethyacetoacetate; respectively in sodium ethoxide/ethanol as a solvent to form compounds 13, 14. The structures of the compounds 1-14 were characterized by elemental analysis, spectral data and antimicrobial evaluation of the some newly synthesized compounds and found that the synthesized compounds are active against tested Gram positive and Gram negative bacteria like Staphylococcus aureus, Bacillus subtilis, Escherichia coli and Proteus.
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Affiliation(s)
- Ayad M R Raauf
- a Department of Pharmaceutical Chemistry, College of Pharmacy , Al-Mustansiriyah University , Baghdad , Iraq
| | - Rafah F Al-Smaism
- a Department of Pharmaceutical Chemistry, College of Pharmacy , Al-Mustansiriyah University , Baghdad , Iraq
| | - Khalida A Thejeel
- b Department of Geophysics, College of Remote Sensing and Geophysics , AL-Karkh University for Science , Baghdad , Iraq
| | - Hala Ayad M Rasheed
- c Department of Clinical Laboratory Science, Collage of Pharmacy , Al-Mustansiriyah University , Baghdad , Iraq
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5
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Ajani H, Jansa J, Köprülüoğlu C, Hobza P, Kryštof V, Lyčka A, Lepsik M. Imidazo[1,2-c
]pyrimidin-5(6H
)-one as a novel core of cyclin-dependent kinase 2 inhibitors: Synthesis, activity measurement, docking, and quantum mechanical scoring. J Mol Recognit 2018; 31:e2720. [DOI: 10.1002/jmr.2720] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/26/2018] [Accepted: 03/21/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Haresh Ajani
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry; Palacký University; Olomouc Czech Republic
| | - Josef Jansa
- Research Institute for Organic Syntheses (VUOS); Pardubice-Rybitví Czech Republic
- Department of Organic Chemistry, Faculty of Science; Palacký University; Olomouc Czech Republic
| | - Cemal Köprülüoğlu
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry; Palacký University; Olomouc Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry; Palacký University; Olomouc Czech Republic
| | - Vladimír Kryštof
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science; Palacký University and Institute of Experimental Botany; Olomouc Czech Republic
| | - Antonín Lyčka
- Research Institute for Organic Syntheses (VUOS); Pardubice-Rybitví Czech Republic
- Faculty of Science; University of Hradec Králové; Hradec Králové Czech Republic
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6
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Kaur M, Silakari O. Ligand-based and e-pharmacophore modeling, 3D-QSAR and hierarchical virtual screening to identify dual inhibitors of spleen tyrosine kinase (Syk) and janus kinase 3 (JAK3). J Biomol Struct Dyn 2016; 35:3043-3060. [PMID: 27678281 DOI: 10.1080/07391102.2016.1240108] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The clinical efficacy of multiple kinase inhibitors has caught the interest of Pharmaceutical and Biotech researchers to develop potential drugs with multi-kinase inhibitory activity for complex diseases. In the present work, we attempted to identify dual inhibitors of spleen tyrosine kinase (Syk) and janus kinase 3 (JAK3), keys players in immune signaling, by developing ideal pharmacophores integrating Ligand-based pharmacophore models (LBPMs) and Structure-based pharmacophore models (SBPMs), thereby projecting the optimum pharmacophoric required for inhibition of both the kinases. The four point LBPM; ADPR.14 suggested the presence of one hydrogen bond acceptor, one hydrogen bond donor, one positive ionizable, and one ring aromatic feature for Syk inhibitory activity and AADH.54 proposed the necessity of two hydrogen bond acceptor, one hydrogen bond donor, and one hydrophobic feature for JAK3 inhibitory activity. To our interest, SBPMs identified additional ring aromatic features required for inhibition of both the kinases. For Syk inhibitory activity, the hydrogen bond acceptor feature indicated by LBPM was devoid of forming hydrogen bonding interaction with the hinge region amino acid residue (Ala451). Thus merging the information revealed by both LBPMs and SBPMs, ideal pharmacophore models i.e. ADPRR.14 (Syk) and AADHR.54 (JAK3) were generated. These models after rigorous statistical validation were used for screening of Asinex database. The systematic virtual screening protocol, including pharmacophore and docking-based screening, ADME property, and MM-GBSA energy calculations, retrieved final 10 hits as dual inhibitors of Syk and JAK3. Final 10 hits thus obtained can aid in the development of potential therapeutic agents for autoimmune disorders. Also the top two hits were evaluated against both the enzymes.
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Affiliation(s)
- Maninder Kaur
- a Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research , Punjabi University , Patiala , Punjab 147002 , India
| | - Om Silakari
- a Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research , Punjabi University , Patiala , Punjab 147002 , India
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7
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Kaur M, Silakari O. Identification of new dual spleen tyrosine kinase (Syk) and phosphoionositide-3-kinase δ (PI3Kδ) inhibitors using ligand and structure-based integrated ideal pharmacophore models. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2016; 27:469-499. [PMID: 27431536 DOI: 10.1080/1062936x.2016.1209555] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/01/2016] [Indexed: 06/06/2023]
Abstract
Owing to the complex pathophysiology of autoimmune disorders, it is very challenging to develop successful treatment strategies. Single-target agents are not desired therapeutics for such multi-factorial disorders. Considering the current need for the treatment of complex autoimmune disorders, dual inhibitors of Syk and PI3Kδ have been designed using ligand and structure-based molecular modelling strategies. In the present work, structure and ligand-based pharmacophore modelling was implemented for a varied set of Syk and PI3Kδ inhibitors. Ligand-based pharmacophore models (LBPMs) were developed for two kinases: ADPR.14 (r(2)train = 0.809) for Syk, comprising one hydrogen bond acceptor, one hydrogen bond donor, one positive ionisable and one ring aromatic feature, and for PI3Kδ: AAARR.45 (r(2)train = 0.942) consisting of three hydrogen bond acceptor and two ring aromatic features. The generated e-pharmacophore models revealed an additional ring aromatic and hydrophobic feature important for Syk and PI3Kδ inhibition, respectively. Subsequently, LBPMs were modified resulting in APDRR.14 hypothesis for Syk inhibitors and AAAHRR.45 hypothesis for PI3Kδ inhibitors employed for virtual screening. Thus, the combination of ligand and structure-based pharmacophore modelling helped in developing ideal pharmacophore models that may be an efficient tool for the designing of novel dual inhibitors of Syk and PI3Kδ.
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Affiliation(s)
- M Kaur
- a Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research , Punjabi University , Patiala , India
| | - O Silakari
- a Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research , Punjabi University , Patiala , India
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8
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Insight into the therapeutic aspects of ‘Zeta-Chain Associated Protein Kinase 70kDa’ inhibitors: A review. Cell Signal 2014; 26:2481-92. [DOI: 10.1016/j.cellsig.2014.06.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 06/27/2014] [Indexed: 01/06/2023]
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9
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Jansa J, Lyčka A, Padělková Z, Grepl M, Konečný P, Hajdúch M, Džubák P. New Imidazo[1,2-c]pyrimidin-5(6H)-Ones Derived from Cytosine: Synthesis, Structure, and Cytotoxic Activity. J Heterocycl Chem 2014. [DOI: 10.1002/jhet.2243] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Josef Jansa
- Research Institute for Organic Syntheses (VUOS); Rybitví 296 CZ-533 54 Pardubice-Rybitví Czech Republic
- Department of Organic Chemistry, Faculty of Science; Palacký University; 17. listopadu 1192/12 CZ-771 46 Olomouc Czech Republic
| | - Antonín Lyčka
- Research Institute for Organic Syntheses (VUOS); Rybitví 296 CZ-533 54 Pardubice-Rybitví Czech Republic
| | - Zdeňka Padělková
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology; University of Pardubice; Studentská 573 CZ-532 10 Pardubice Czech Republic
| | - Martin Grepl
- Farmak, a.s.; Na Vlčinci 16/3 CZ-771 17 Olomouc Czech Republic
| | - Petr Konečný
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry; Palacký University, Olomouc; Puškinova 6 CZ-775 20 Olomouc Czech Republic
- University Hospital Olomouc; Ivana Petroviče Pavlova 6 CZ-77520 Olomouc Czech Republic
| | - Marián Hajdúch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry; Palacký University, Olomouc; Puškinova 6 CZ-775 20 Olomouc Czech Republic
- University Hospital Olomouc; Ivana Petroviče Pavlova 6 CZ-77520 Olomouc Czech Republic
| | - Petr Džubák
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry; Palacký University, Olomouc; Puškinova 6 CZ-775 20 Olomouc Czech Republic
- University Hospital Olomouc; Ivana Petroviče Pavlova 6 CZ-77520 Olomouc Czech Republic
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10
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Zhao H, Caflisch A. Discovery of ZAP70 inhibitors by high-throughput docking into a conformation of its kinase domain generated by molecular dynamics. Bioorg Med Chem Lett 2013; 23:5721-6. [DOI: 10.1016/j.bmcl.2013.08.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 07/30/2013] [Accepted: 08/01/2013] [Indexed: 12/19/2022]
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11
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Inhibitors of switch kinase 'spleen tyrosine kinase' in inflammation and immune-mediated disorders: a review. Eur J Med Chem 2013; 67:434-46. [PMID: 23917087 DOI: 10.1016/j.ejmech.2013.04.070] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 04/17/2013] [Accepted: 04/18/2013] [Indexed: 12/29/2022]
Abstract
Spleen tyrosine kinase (Syk), a member of Syk family of non-receptor protein tyrosine kinases plays a significant role in the immune cell signaling in B cells, mast cells, macrophages and neutrophils. Anomalous regulation of this kinase can lead to different allergic disorders and antibody-mediated autoimmune diseases such as rheumatoid arthritis, asthma, psoriasis and allergic rhinitis. Being involved in the growth and survive mechanism of B cells, its inhibition can be beneficial in B-cell lymphoma. Thus, Syk can be sited as a therapeutically relevant target for various allergic and autoimmune disorders. This review article describes the structure of Syk and its role in B-cell signaling. In addition to this, data regarding small molecule inhibitors of Syk has also been reviewed from different papers and patents published.
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12
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Li BK, Cong Y, Yang XG, Xue Y, Chen YZ. In silico prediction of spleen tyrosine kinase inhibitors using machine learning approaches and an optimized molecular descriptor subset generated by recursive feature elimination method. Comput Biol Med 2013; 43:395-404. [DOI: 10.1016/j.compbiomed.2013.01.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Revised: 12/31/2012] [Accepted: 01/21/2013] [Indexed: 11/16/2022]
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13
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Synthesis, characterization, electrochemical behavior and in vitro protein tyrosine kinase inhibitory activity of the cymene-halogenobenzohydroxamato [Ru(η6-cymene)(bha)Cl] complexes. J Organomet Chem 2013. [DOI: 10.1016/j.jorganchem.2012.12.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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14
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Kaur M, Kumari A, Bahia MS, Silakari O. Designing of new multi-targeted inhibitors of spleen tyrosine kinase (Syk) and zeta-associated protein of 70kDa (ZAP-70) using hierarchical virtual screening protocol. J Mol Graph Model 2012; 39:165-75. [PMID: 23280414 DOI: 10.1016/j.jmgm.2012.11.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 11/09/2012] [Accepted: 11/17/2012] [Indexed: 12/19/2022]
Abstract
In the present study, diverse inhibitor molecules of two protein tyrosine kinases i.e. Syk and ZAP-70 were considered for the pharmacophore and docking analyses to design new multi-targeted agents for these enzymes. These enzymes are non-receptor protein tyrosine kinases and both are expressed mainly in B and T-lymphocytes where they play a crucial role in immune signaling. The role of these two enzymes in inflammatory and autoimmune diseases makes them potential therapeutic targets for the designing of new multi-targeted agents to combat disease conditions associated with them. The pharmacophore models were developed for Syk and ZAP-70 inhibitors using PHASE module of Schrödinger software. The generated pharmacophore models for both enzymes were clustered and top five models for each target were selected on the basis of survival minus inactive score that were subsequently used for the 3D-QSAR analysis. The best model for Syk (ADHR.45-5) and ZAP-70 (AADRR.265-3) were selected corresponding to highest value of Q(2). Both models were employed for the screening of a PHASE database of approximately 1.5 million compounds, subsequently the retrieved hits were screened employing docking simulations with Syk and ZAP-70 proteins. Finally, the screened compounds having structural features of both pharmacophore models and displaying essential interactions with both proteins were investigated for ADME properties. Thus, the new leads obtained in this way would show inhibitory activity against Syk and ZAP-70, and may serve as novel therapeutic agents for the treatment of inflammatory disorders.
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Affiliation(s)
- Maninder Kaur
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
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15
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Dokla EM, Mahmoud AH, Elsayed MSA, El-Khatib AH, Linscheid MW, Abouzid KA. Applying ligands profiling using multiple extended electron distribution based field templates and feature trees similarity searching in the discovery of new generation of urea-based antineoplastic kinase inhibitors. PLoS One 2012. [PMID: 23185312 PMCID: PMC3502486 DOI: 10.1371/journal.pone.0049284] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study provides a comprehensive computational procedure for the discovery of novel urea-based antineoplastic kinase inhibitors while focusing on diversification of both chemotype and selectivity pattern. It presents a systematic structural analysis of the different binding motifs of urea-based kinase inhibitors and the corresponding configurations of the kinase enzymes. The computational model depends on simultaneous application of two protocols. The first protocol applies multiple consecutive validated virtual screening filters including SMARTS, support vector-machine model (ROC = 0.98), Bayesian model (ROC = 0.86) and structure-based pharmacophore filters based on urea-based kinase inhibitors complexes retrieved from literature. This is followed by hits profiling against different extended electron distribution (XED) based field templates representing different kinase targets. The second protocol enables cancericidal activity verification by using the algorithm of feature trees (Ftrees) similarity searching against NCI database. Being a proof-of-concept study, this combined procedure was experimentally validated by its utilization in developing a novel series of urea-based derivatives of strong anticancer activity. This new series is based on 3-benzylbenzo[d]thiazol-2(3H)-one scaffold which has interesting chemical feasibility and wide diversification capability. Antineoplastic activity of this series was assayed in vitro against NCI 60 tumor-cell lines showing very strong inhibition of GI50 as low as 0.9 uM. Additionally, its mechanism was unleashed using KINEX™ protein kinase microarray-based small molecule inhibitor profiling platform and cell cycle analysis showing a peculiar selectivity pattern against Zap70, c-src, Mink1, csk and MeKK2 kinases. Interestingly, it showed activity on syk kinase confirming the recent studies finding of the high activity of diphenyl urea containing compounds against this kinase. Allover, the new series, which is based on a new kinase scaffold with interesting chemical diversification capabilities, showed that it exhibits its “emergent” properties by perturbing multiple unexplored kinase pathways.
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Affiliation(s)
- Eman M Dokla
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt.
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16
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Genc M, Yılmaz E, Ilhan S, Karagoz Z. Synthesis, antihistaminic action and theoretical studies of (4-methoxybenzyl)(1,4,5,6-tetrahydropirimidin-2-yl)amine hydroiodide. RESEARCH ON CHEMICAL INTERMEDIATES 2012. [DOI: 10.1007/s11164-012-0813-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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17
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Kaur M, Bahia MS, Silakari O. Exploring the role of water molecules for docking and receptor guided 3D-QSAR analysis of naphthyridine derivatives as spleen tyrosine kinase (Syk) inhibitors. J Chem Inf Model 2012; 52:2619-30. [PMID: 22900966 DOI: 10.1021/ci300227f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In the present study, 3D-QSAR analysis was performed utilizing docking based alignment of [1,6]-naphthyridine derivatives as Syk enzyme inhibitors. The role of the water molecules was explored for the docking based alignment that revealed two conserved water molecules important for proper orientation and alignment of naphthyridine inhibitors in the active site of Syk enzyme. The QSAR model was selected having highest value of Q(2) (0.624) and Pearson-r (0.862). The selected model also displayed the highest values of R(2) (0.978) and F-value (184.5) and the lowest SD (0.862). The contour plots developed on the basis of the best model helped to reveal the essential structural features of naphthyridines derivatives responsible for inhibition of Syk enzyme. The generated model and information revealed from it was utilized to design and predict new congeneric molecules that can be used as potential therapeutic agents.
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Affiliation(s)
- Maninder Kaur
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
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18
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Singh R, Masuda ES, Payan DG. Discovery and development of spleen tyrosine kinase (SYK) inhibitors. J Med Chem 2012; 55:3614-43. [PMID: 22257213 DOI: 10.1021/jm201271b] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Rajinder Singh
- Rigel, Inc., 1180 Veterans Boulevard, South San Francisco, California 94080, USA.
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19
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Hall J, Aulabaugh A, Rajamohan F, Liu S, Kaila N, Wan ZK, Ryan M, Magyar R, Qiu X. Biophysical and mechanistic insights into novel allosteric inhibitor of spleen tyrosine kinase. J Biol Chem 2012; 287:7717-27. [PMID: 22219190 DOI: 10.1074/jbc.m111.311993] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Extracellular stimulation of the B cell receptor or mast cell FcεRI receptor activates a cascade of protein kinases, ultimately leading to antigenic or inflammation immune responses, respectively. Syk is a soluble kinase responsible for transmission of the receptor activation signal from the membrane to cytosolic targets. Control of Syk function is, therefore, critical to the human antigenic and inflammation immune response, and an inhibitor of Syk could provide therapy for autoimmune or inflammation diseases. We report here a novel allosteric Syk inhibitor, X1, that is noncompetitive against ATP (K(i) 4 ± 1 μM) and substrate peptide (K(i) 5 ± 1 μM), and competitive against activation of Syk by its upstream regulatory kinase LynB (K(i) 4 ± 1 μM). The inhibition mechanism was interrogated using a combination of structural, biophysical, and kinetic methods, which suggest the compound inhibits Syk by reinforcing the natural regulatory interactions between the SH2 and kinase domains. This novel mode of inhibition provides a new opportunity to improve the selectivity profile of Syk inhibitors for the development of safer drug candidates.
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Affiliation(s)
- Justin Hall
- Structural Biology and Biophysics Group, Pfizer, Groton, Connecticut 06340, USA.
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20
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Feng XE, Zhao WY, Ban SR, Zhao CX, Li QS, Lin WH. Structure-activity relationship of halophenols as a new class of protein tyrosine kinase inhibitors. Int J Mol Sci 2011; 12:6104-15. [PMID: 22016647 PMCID: PMC3189771 DOI: 10.3390/ijms12096104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 09/14/2011] [Accepted: 09/15/2011] [Indexed: 01/15/2023] Open
Abstract
A series of new benzophenone and diphenylmethane halophenol derivatives were prepared. Their structures were established based on (1)H NMR, (13)C NMR and HRMS data. All prepared compounds were screened for their in vitro protein tyrosine kinase (PTK) inhibitory activities. The effects of modification of the linker, functional groups and substituted positions at the phenyl ring on PTK inhibitory activity were investigated. Twelve halophenols showed significant PTK inhibitory activity. Among them, compounds 6c, 6d, 7d, 9d, 10d, 11d and 13d exhibited stronger activities than that of genistein, the positive reference compound. The results gave a relatively full and definite description of the structure-activity relationship and provided a foundation for further design and structure optimization of the halophenols.
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Affiliation(s)
- Xiu E. Feng
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan 030001, Shanxi, China; E-Mails: (X.E.F.); (W.Y.Z.); (S.R.B.); (C.X.Z.)
- School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China
| | - Wan Yi Zhao
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan 030001, Shanxi, China; E-Mails: (X.E.F.); (W.Y.Z.); (S.R.B.); (C.X.Z.)
| | - Shu Rong Ban
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan 030001, Shanxi, China; E-Mails: (X.E.F.); (W.Y.Z.); (S.R.B.); (C.X.Z.)
| | - Cheng Xiao Zhao
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan 030001, Shanxi, China; E-Mails: (X.E.F.); (W.Y.Z.); (S.R.B.); (C.X.Z.)
| | - Qing Shan Li
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan 030001, Shanxi, China; E-Mails: (X.E.F.); (W.Y.Z.); (S.R.B.); (C.X.Z.)
- School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100083, China; E-Mail:
| | - Wen Han Lin
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100083, China; E-Mail:
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21
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Liddle J, Atkinson FL, Barker MD, Carter PS, Curtis NR, Davis RP, Douault C, Dickson MC, Elwes D, Garton NS, Gray M, Hayhow TG, Hobbs CI, Jones E, Leach S, Leavens K, Lewis HD, McCleary S, Neu M, Patel VK, Preston AGS, Ramirez-Molina C, Shipley TJ, Skone PA, Smithers N, Somers DO, Walker AL, Watson RJ, Weingarten GG. Discovery of GSK143, a highly potent, selective and orally efficacious spleen tyrosine kinase inhibitor. Bioorg Med Chem Lett 2011; 21:6188-94. [PMID: 21903390 DOI: 10.1016/j.bmcl.2011.07.082] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 07/20/2011] [Accepted: 07/22/2011] [Indexed: 11/19/2022]
Abstract
The lead optimisation of the diaminopyrimidine carboxamide series of spleen tyrosine kinase inhibitors is described. The medicinal chemistry strategy was focused on optimising the human whole blood activity whilst achieving a sufficient margin over liability kinases and hERG activity. GSK143 is a potent and highly selective SYK inhibitor showing good efficacy in the rat Arthus model.
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Affiliation(s)
- John Liddle
- GlaxoSmithKline R&D, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, UK.
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22
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Moore WJ, Richard D, Thorarensen A. An analysis of the diaminopyrimidine patent estates describing spleen tyrosine kinase inhibitors by Rigel and Portola. Expert Opin Ther Pat 2010; 20:1703-22. [DOI: 10.1517/13543776.2010.534459] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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23
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Spleen tyrosine kinases: biology, therapeutic targets and drugs. Drug Discov Today 2010; 15:517-30. [PMID: 20553955 DOI: 10.1016/j.drudis.2010.05.001] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Revised: 04/02/2010] [Accepted: 05/14/2010] [Indexed: 12/30/2022]
Abstract
Spleen tyrosine kinase (Syk) is an intriguing protein tyrosine kinase involved in signal transduction in a variety of cell types, and its aberrant regulation is associated with different allergic disorders and antibody-mediated autoimmune diseases such as rheumatoid arthritis, asthma and allergic rhinitis. Syk also plays an important part in the uncontrolled growth of tumor cells, particularly B cells. For these reasons, Syk is considered one of the most interesting biological targets of the last decade, as proved by the great number of papers and patents published, and the possibility of treating these pathologies by means of Syk kinase inhibitors has led to a great interest from the pharmaceutical and biotech industry.
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24
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Targeting B-cells in Inflammatory Disease. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2010. [DOI: 10.1016/s0065-7743(10)45011-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
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25
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Sasada T, Moriuchi M, Sakai N, Konakahara T. An Unprecedented Approach to the Single-Step Synthesis of 3,4-Fused Pyrimidin-2-one and Pyrimidin-2-thione Derivatives by a [3+2+1] Annulation. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900639] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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26
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Xie HZ, Li LL, Ren JX, Zou J, Yang L, Wei YQ, Yang SY. Pharmacophore modeling study based on known spleen tyrosine kinase inhibitors together with virtual screening for identifying novel inhibitors. Bioorg Med Chem Lett 2009; 19:1944-9. [PMID: 19254842 DOI: 10.1016/j.bmcl.2009.02.049] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2008] [Revised: 01/20/2009] [Accepted: 02/12/2009] [Indexed: 02/05/2023]
Abstract
In this investigation, chemical features based 3D pharmacophore models were developed based on the known inhibitors of Spleen tyrosine kinase (Syk) with the aid of hiphop and hyporefine modules within catalyst. The best quantitative pharmacophore model, Hypo1, was used as a 3D structural query for retrieving potential inhibitors from chemical databases including Specs, NCI, MayBridge, and Chinese Nature Product Database (CNPD). The hit compounds were subsequently subjected to filtering by Lipinski's rule of five and docking studies to refine the retrieved hits. Finally 30 compounds were selected from the top ranked hit compounds and conducted an in vitro kinase inhibitory assay. Six compounds showed a good inhibitory potency against Syk, which have been selected for further investigation.
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Affiliation(s)
- Huan-Zhang Xie
- State Key Laboratory of Biotherapy, West China Hospital, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
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27
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Manlove A, Groziak MP. Chapter 6.2: Six-Membered Ring Systems: Diazines and Benzo Derivatives. PROGRESS IN HETEROCYCLIC CHEMISTRY 2009. [DOI: 10.1016/s0959-6380(09)70040-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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28
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Hirabayashi A, Mukaiyama H, Kobayashi H, Shiohara H, Nakayama S, Ozawa M, Miyazawa K, Misawa K, Ohnota H, Isaji M. Structure-activity relationship studies of 5-benzylaminoimidazo[1,2-c]pyrimidine-8-carboxamide derivatives as potent, highly selective ZAP-70 kinase inhibitors. Bioorg Med Chem 2008; 17:284-94. [PMID: 19010686 DOI: 10.1016/j.bmc.2008.10.070] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Revised: 10/30/2008] [Accepted: 10/31/2008] [Indexed: 11/18/2022]
Abstract
Zeta-associated protein, 70 kDa (ZAP-70), a spleen tyrosine kinase (Syk) family kinase, is normally expressed on T cells and natural killer cells and plays a crucial role in activation of the T cell immunoresponse. Thus, selective ZAP-70 inhibitors might be useful not only for treating autoimmune diseases, but also for suppressing organ transplant rejection. In our recent study on the synthesis of Syk family kinase inhibitors, we discovered that novel imidazo[1,2-c]pyrimidine-8-carboxamide derivatives possessed potent ZAP-70 inhibitory activity with good selectivity for ZAP-70 over other kinases. In particular, compound 26 showed excellent ZAP-70 kinase inhibition and high selectivity for ZAP-70 over structurally related Syk. The discovery of a potent, highly selective ZAP-70 inhibitor would contribute a new therapeutic tool for autoimmune diseases and organ transplant medication.
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Affiliation(s)
- Akihito Hirabayashi
- Central Research Laboratory, Kissei Pharmaceutical Company, 4365-1 Kashiwabara, Hotaka, Azumino, Nagano Prefecture 399-8304, Japan.
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