1
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Ogawa N, Ohta M, Ikeguchi M. Conformational Selectivity of ITK Inhibitors: Insights from Molecular Dynamics Simulations. J Chem Inf Model 2023; 63:7860-7872. [PMID: 38069816 PMCID: PMC10751800 DOI: 10.1021/acs.jcim.3c01352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/26/2023]
Abstract
Interleukin-2-inducible T-cell kinase (ITK) regulates the response to T-cell receptor signaling and is a drug target for inflammatory and immunological diseases. Molecules that bind preferentially to the active form of ITK have low selectivity between kinases, whereas those that bind preferentially to the inactive form have high selectivity for ITK. Therefore, computational methods to predict the conformational selectivity of compounds are required to design highly selective ITK inhibitors. In this study, we performed absolute binding free-energy perturbation (ABFEP) simulations for 11 compounds on both active and inactive forms of ITK, and the calculated binding free energies were compared with experimental data. The conformational selectivity of 10 of the 11 compounds was correctly predicted using ABFEP. To investigate the mechanism underlying the stabilization of the active and inactive structures by the compounds, we performed extensive, conventional molecular dynamics simulations, which revealed that the compound-induced stabilization of the P-loop and linkage of conformational changes in L489, V419, F501, and M410 upon compound binding were critical factors. A guideline for designing inactive-form binders is proposed based on these key structural factors. The ABFEP and the created guidelines are expected to facilitate the discovery of highly selective ITK inhibitors.
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Affiliation(s)
- Naoki Ogawa
- Graduate
School of Medicinal Life Science, Yokohama
City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- Central
Pharmaceutical Research Institute, Japan
Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Masateru Ohta
- HPC-
and AI-Driven Drug Development Platform Division, Center for Computational
Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mitsunori Ikeguchi
- Graduate
School of Medicinal Life Science, Yokohama
City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- HPC-
and AI-Driven Drug Development Platform Division, Center for Computational
Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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2
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Sahoo AK, Rakshit A, Pan A, Dhara HN, Patel BK. Visible/solar-light-driven thiyl-radical-triggered synthesis of multi-substituted pyridines. Org Biomol Chem 2023; 21:1680-1691. [PMID: 36723155 DOI: 10.1039/d3ob00009e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A light-triggered synthesis of thio-functionalized pyridines is demonstrated using γ-ketodinitriles, thiols, and eosin Y as the photocatalyst. The reaction proceeds via the selective attack on one of the cyano groups by an in situ generated thiyl radical. The reaction also proceeds with nearly equal efficiency using direct sunlight. Large-scale synthesis and a few useful synthetic transformations of the substituted pyridines are also performed.
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Affiliation(s)
- Ashish Kumar Sahoo
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India.
| | - Amitava Rakshit
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India.
| | - Avishek Pan
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India.
| | - Hirendra Nath Dhara
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India.
| | - Bhisma K Patel
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India.
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3
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Xu M, Huang S, Chen J, Xu W, Xiang R, Piao Y, Zhao S. Cytotoxic lymphocytes-related gene ITK from a systematic CRISPR screen could predict prognosis of ovarian cancer patients with distant metastasis. J Transl Med 2021; 19:447. [PMID: 34702300 PMCID: PMC8549276 DOI: 10.1186/s12967-021-03119-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 10/15/2021] [Indexed: 11/10/2022] Open
Abstract
Background Ovarian cancer, a highly metastatic malignancy, has benefited tremendously from advances in modern human genomics. However, the genomic variations related to the metastasis remains unclear. Methods We filtered various significant genes (n = 6722) associated with metastasis within a large-scale functional genomic CRISPR/Cas9 knock-out library including 122,756 single guide RNAs, and identified ITK (IL2 Inducible T Cell Kinase) as a potential cancer suppressor gene for ovarian cancer metastasis. Downstream bioinformatic analysis was performed for ITK using public databases. Results We found that patients in low-ITK group had poor prognosis and more distant metastasis than those in high-ITK group in TCGA and GEO databases. We also demonstrated that ITK combined with the clinical factors could accurately predict prognosis through multiple Cox regression analysis and ROC analysis. Moreover, alterations correlated with distant metastasis emereged with significantly increased expression in SAMRCD1 in low-ITK group, but CD244 and SOCS1 in high-ITK group. Integrated analysis revealed dysregulated molecular processes including predominantly oncogenic signaling pathways in low-ITK group but immune related pathways in high-ITK group, which suggested ITK might inhibit distant metastasis in ovarian cancer. Furtherly, deconvolution of the cellular composition of all samples validated the close correlation between ITK and immune related function especially for cytotoxic lymphocytes. Conclusions Together, these data provide insights into the potential role of ITK, with implications for the future development of tansformative ovarian cancer therapeutics. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-03119-3.
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Affiliation(s)
- Mengyao Xu
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Shan Huang
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Jiahui Chen
- Department of Nuclear Medicine and PET/CT-MRI Center, The First Affiliated Hospital of Jinan University, Tianhe District, 613 West Huangpu Road, Guangzhou, 510630, China
| | - Wanxue Xu
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Rong Xiang
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Yongjun Piao
- School of Medicine, Nankai University, Tianjin, 300071, China. .,Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University Affiliated Hospital of Obstetrics and Gynecology, Tianjin, China.
| | - Shuangtao Zhao
- Department of Thoracic Surgery, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China.
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4
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Mudasani G, Paidikondala K, Gurská S, Maddirala SJ, Džubák P, Das V, Gundla R. C‐5 Aryl Substituted Azaspirooxindolinones Derivatives: Synthesis and Biological Evaluation as Potential Inhibitors of Tec Family Kinases. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Gopal Mudasani
- Department of Chemistry, School of Science GITAM (Deemed to be University) Hyderabad 502102 Telangana India
- Medicinal Chemistry Laboratory Division AragenLifesciences Pvt. Ltd Survey No: 125(Part) & 126, IDA Mallapur Hyderabad 500 076 India
| | - Kalyani Paidikondala
- Department of Chemistry, School of Science GITAM (Deemed to be University) Hyderabad 502102 Telangana India
| | - Soňa Gurská
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry Czech Advanced Technology and Research Institute Palacký University Olomouc Hněvotínská 1333/5 77900 Olomouc Czech Republic
| | - Shambabu Joseph Maddirala
- Medicinal Chemistry Laboratory Division AragenLifesciences Pvt. Ltd Survey No: 125(Part) & 126, IDA Mallapur Hyderabad 500 076 India
| | - Petr Džubák
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry Czech Advanced Technology and Research Institute Palacký University Olomouc Hněvotínská 1333/5 77900 Olomouc Czech Republic
| | - Viswanath Das
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry Czech Advanced Technology and Research Institute Palacký University Olomouc Hněvotínská 1333/5 77900 Olomouc Czech Republic
| | - Rambabu Gundla
- Department of Chemistry, School of Science GITAM (Deemed to be University) Hyderabad 502102 Telangana India
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5
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Rankine-Wilson LI, Shapira T, Sao Emani C, Av-Gay Y. From infection niche to therapeutic target: the intracellular lifestyle of Mycobacterium tuberculosis. MICROBIOLOGY (READING, ENGLAND) 2021; 167:001041. [PMID: 33826491 PMCID: PMC8289223 DOI: 10.1099/mic.0.001041] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/15/2021] [Indexed: 12/16/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is an obligate human pathogen killing millions of people annually. Treatment for tuberculosis is lengthy and complicated, involving multiple drugs and often resulting in serious side effects and non-compliance. Mtb has developed numerous complex mechanisms enabling it to not only survive but replicate inside professional phagocytes. These mechanisms include, among others, overcoming the phagosome maturation process, inhibiting the acidification of the phagosome and inhibiting apoptosis. Within the past decade, technologies have been developed that enable a more accurate understanding of Mtb physiology within its intracellular niche, paving the way for more clinically relevant drug-development programmes. Here we review the molecular biology of Mtb pathogenesis offering a unique perspective on the use and development of therapies that target Mtb during its intracellular life stage.
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Affiliation(s)
| | - Tirosh Shapira
- Division of Infectious Disease, Department of Medicine, The University of British Columbia, Vancouver, Canada
| | - Carine Sao Emani
- Division of Infectious Disease, Department of Medicine, The University of British Columbia, Vancouver, Canada
| | - Yossef Av-Gay
- Department of Microbiology & Immunology, The University of British Columbia, Vancouver, Canada
- Division of Infectious Disease, Department of Medicine, The University of British Columbia, Vancouver, Canada
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6
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Sofi FA, Bharatam PV. Synthesis of Drugs and Biorelevant N-heterocycles Employing Recent Advances in C-N Bond Formation. CURR ORG CHEM 2020. [DOI: 10.2174/1385272824999200909114144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
C-N bond formation is a particularly important step in the generation of many
biologically relevant heterocyclic molecules. Several methods have been reported for this
purpose over the past few decades. Well-known named reactions like Ullmann-Goldberg
coupling, Buchwald-Hartwig coupling and Chan-Lam coupling are associated with the C-N
bond formation reactions. Several reviews covering this topic have already been published.
However, no comprehensive review covering the synthesis of drugs/ lead compounds using
the C-N bond formation reactions was reported. In this review, we cover many modern
methods of the C-N bond formation reactions, with special emphasis on metal-free and
green chemistry methods. We also report specific strategies adopted for the synthesis of
drugs, which involve the C-N bond formation reactions. Examples include anti-cancer,
antidepressant, anti-inflammatory, anti-atherosclerotic, anti-histaminic, antibiotics, antibacterial, anti-rheumatic,
antiepileptic and anti-diabetic agents. Many recently developed lead compounds generated using the C-N bond
formation reactions are also covered in this review. Examples include MAP kinase inhibitors, TRKs inhibitors,
Polo-like Kinase inhibitors and MPS1 inhibitors.
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Affiliation(s)
- Firdoos Ahmad Sofi
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S Nagar 160 062, Punjab, India
| | - Prasad V. Bharatam
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S Nagar 160 062, Punjab, India
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7
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Deniston CK, Salogiannis J, Mathea S, Snead DM, Lahiri I, Matyszewski M, Donosa O, Watanabe R, Böhning J, Shiau AK, Knapp S, Villa E, Reck-Peterson SL, Leschziner AE. Structure of LRRK2 in Parkinson's disease and model for microtubule interaction. Nature 2020; 588:344-349. [PMID: 32814344 PMCID: PMC7726071 DOI: 10.1038/s41586-020-2673-2] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 08/12/2020] [Indexed: 12/22/2022]
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is the most commonly mutated gene in familial Parkinson's disease1 and is also linked to its idiopathic form2. LRRK2 has been proposed to function in membrane trafficking3 and colocalizes with microtubules4. Despite the fundamental importance of LRRK2 for understanding and treating Parkinson's disease, structural information on the enzyme is limited. Here we report the structure of the catalytic half of LRRK2, and an atomic model of microtubule-associated LRRK2 built using a reported cryo-electron tomography in situ structure5. We propose that the conformation of the LRRK2 kinase domain regulates its interactions with microtubules, with a closed conformation favouring oligomerization on microtubules. We show that the catalytic half of LRRK2 is sufficient for filament formation and blocks the motility of the microtubule-based motors kinesin 1 and cytoplasmic dynein 1 in vitro. Kinase inhibitors that stabilize an open conformation relieve this interference and reduce the formation of LRRK2 filaments in cells, whereas inhibitors that stabilize a closed conformation do not. Our findings suggest that LRRK2 can act as a roadblock for microtubule-based motors and have implications for the design of therapeutic LRRK2 kinase inhibitors.
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Affiliation(s)
- C K Deniston
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Genomics Institute of the Novartis Research Foundation, La Jolla, CA, USA
| | - J Salogiannis
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - S Mathea
- Institute of Pharmaceutical Chemistry, Goethe-Universität, Frankfurt, Germany
| | - D M Snead
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - I Lahiri
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Mohali, India
| | - M Matyszewski
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - O Donosa
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - R Watanabe
- Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, CA, USA
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - J Böhning
- Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, CA, USA
- Sir William Dunn School of Pathology, Oxford University, Oxford, UK
| | - A K Shiau
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA, USA
| | - S Knapp
- Institute of Pharmaceutical Chemistry, Goethe-Universität, Frankfurt, Germany
| | - E Villa
- Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, CA, USA
| | - S L Reck-Peterson
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA, USA.
| | - A E Leschziner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, CA, USA.
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8
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Rakshit A, Kumar P, Alam T, Dhara H, Patel BK. Visible-Light-Accelerated Pd-Catalyzed Cascade Addition/Cyclization of Arylboronic Acids to γ- and β-Ketodinitriles for the Construction of 3-Cyanopyridines and 3-Cyanopyrrole Analogues. J Org Chem 2020; 85:12482-12504. [DOI: 10.1021/acs.joc.0c01703] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Amitava Rakshit
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Prashant Kumar
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Tipu Alam
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Hirendranath Dhara
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Bhisma K. Patel
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, India
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9
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Wu F, Zhuo L, Wang F, Huang W, Hao G, Yang G. Auto In Silico Ligand Directing Evolution to Facilitate the Rapid and Efficient Discovery of Drug Lead. iScience 2020; 23:101179. [PMID: 32498019 PMCID: PMC7267738 DOI: 10.1016/j.isci.2020.101179] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/25/2020] [Accepted: 05/13/2020] [Indexed: 12/21/2022] Open
Abstract
Motivated by the growing demand for reducing the chemical optimization burden of H2L, we developed auto in silico ligand directing evolution (AILDE, http://chemyang.ccnu.edu.cn/ccb/server/AILDE), an efficient and general approach for the rapid identification of drug leads in accessible chemical space. This computational strategy relies on minor chemical modifications on the scaffold of a hit compound, and it is primarily intended for identifying new lead compounds with minimal losses or, in some cases, even increases in ligand efficiency. We also described how AILDE greatly reduces the chemical optimization burden in the design of mesenchymal-epithelial transition factor (c-Met) kinase inhibitors. We only synthesized eight compounds and found highly efficient compound 5g, which showed an ∼1,000-fold improvement in in vitro activity compared with the hit compound. 5g also displayed excellent in vivo antitumor efficacy as a drug lead. We believe that AILDE may be applied to a large number of studies for rapid design and identification of drug leads. AILDE was developed for the rapid identification of drug leads A potent drug lead targeted to c-Met was found by synthesizing only eight compounds
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Affiliation(s)
- Fengxu Wu
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China
| | - Linsheng Zhuo
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China
| | - Fan Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China
| | - Wei Huang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China.
| | - Gefei Hao
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China.
| | - Guangfu Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, P. R. China.
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10
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Jayarajan R, Satheeshkumar R, Kottha T, Subbaramanian S, Sayin K, Vasuki G. Water mediated synthesis of 6-amino-5-cyano-2-oxo-N-(pyridin-2-yl)-4-(p-tolyl)-2H-[1,2'-bipyridine]-3-carboxamide and 6-amino-5-cyano-4-(4-fluorophenyl)-2-oxo-N-(pyridin-2-yl)-2H-[1,2'-bipyridine]-3-carboxamide - An experimental and computational studies with non-linear optical (NLO) and molecular docking analyses. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 229:117861. [PMID: 31806479 DOI: 10.1016/j.saa.2019.117861] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/23/2019] [Accepted: 11/24/2019] [Indexed: 06/10/2023]
Abstract
6-Amino-5-cyano-2-oxo-N-(pyridin-2-yl)-4-(p-tolyl)-2H-[1,2'-bipyridine]-3-carboxamide and 6-amino-5-cyano-4-(4-fluorophenyl)-2-oxo-N-(pyridin-2-yl)-2H-[1,2'-bipyridine]-3-carboxamide were synthesized through three-component reaction between N1,N3-di(pyridin-2-yl)-malonamide, aldehyde and malononitrile in water using triethylamine as a base at room temperature. Synthesized compounds were characterized by using different techniques (FT-IR, NMR and X-ray diffraction). Additionally, the mentioned compounds were investigated by computational chemistry methods. Obtained results were supported with calculated results. Additionally, NLO properties and molecular docking analyses of related compounds were examined in detail. The binding modes of the compounds 4a and 4b were explored with the colchicine binding site of tubulin, from molecular docking studies, remarkable interactions have been observed for 4a and 4b near to the colchicines binding site of tubulin that may contribute to the inhibition of tubulin polymerization and anticancer activity.
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Affiliation(s)
- Ramasamy Jayarajan
- Department of Chemistry, Pondicherry University, Pondicherry 605014, India; Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Rajendran Satheeshkumar
- Departamento de Química Orgánica, Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, 702843 Santiago, Chile
| | | | - Sabarinathan Subbaramanian
- Department of Chemistry, Pondicherry University, Pondicherry 605014, India; Department of Chemistry, SRM Institute of Science and Technology (SRMIST), Vadapalani, Chennai-600026, TamilNadu, India
| | - Koray Sayin
- Department of Chemistry, Faculty of Science, Sivas Cumhuriyet University, 58140 Sivas, Turkey; Sivas Cumhuriyet University Advanced Research and Application Center (CUTAM), 58140 Sivas, Turkey.
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11
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Design, synthesis and structure-activity relationship of indolylindazoles as potent and selective covalent inhibitors of interleukin-2 inducible T-cell kinase (ITK). Eur J Med Chem 2019; 187:111918. [PMID: 31830635 DOI: 10.1016/j.ejmech.2019.111918] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/29/2019] [Accepted: 11/25/2019] [Indexed: 11/23/2022]
Abstract
Interleukin-2 inducible T-cell kinase (ITK), a member of the Tec family of tyrosine kinases, plays an important role in T cell signaling downstream of the T-cell receptor (TCR). Herein we report the discovery of a series of indolylindazole based covalent ITK inhibitors with nanomolar inhibitory potency against ITK, good kinase selectivity and potent inhibition of the phosphorylation of PLCγ1 and ERK1/2 in living cells. A computational study provided insight into the interactions between inhibitors and Phe437 at the ATP binding pocket of ITK, suggesting that both edge-to-face π-π interaction and the dihedral torsion angle contribute to inhibitors' potency. Compounds 43 and 55 stood out as selective covalent inhibitors with potent cellular activity, which could be used as chemical tools for further study of ITK functions.
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12
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Hantani R, Hanawa S, Oie S, Umetani K, Sato T, Hantani Y. Identification of a New Inhibitor That Stabilizes Interleukin-2-Inducible T-Cell Kinase in Its Inactive Conformation. SLAS DISCOVERY 2019; 24:854-862. [PMID: 31247148 DOI: 10.1177/2472555219857542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Interleukin-2-inducible T-cell kinase (ITK) plays an important role in T-cell signaling and is considered a promising drug target. As the ATP binding sites of protein kinases are highly conserved, the design of selective kinase inhibitors remains a challenge. Targeting inactive kinase conformations can address the issue of kinase inhibitor selectivity. It is important for selectivity considerations to identify compounds that stabilize inactive conformations from the primary screen hits. Here we screened a library of 390,000 compounds with an ADP-Glo assay using dephosphorylated ITK. After a surface plasmon resonance (SPR) assay was used to filter out promiscuous inhibitors, 105 hits were confirmed. Next, we used a fluorescent biosensor to enable the detection of conformational changes to identify inactive conformation inhibitors. A single-cysteine-substituted ITK mutant was labeled with acrylodan, and fluorescence emission was monitored. Using a fluorescent biosensor assay, we identified 34 inactive conformation inhibitors from SPR hits. Among them, one compound was bound to a site other than the ATP pocket and exhibited excellent selectivity against a kinase panel. Overall, (1) biochemical screening using dephosphorylated kinase, (2) hit confirmation by SPR assay, and (3) fluorescent biosensor assay that can distinguish inactive compounds provide a useful platform and offer opportunities to identify selective kinase inhibitors.
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Affiliation(s)
- Rie Hantani
- 1 Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco, Takatsuki, Osaka, Japan
| | - Saya Hanawa
- 1 Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco, Takatsuki, Osaka, Japan
| | - Shohei Oie
- 1 Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco, Takatsuki, Osaka, Japan
| | - Kayo Umetani
- 1 Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco, Takatsuki, Osaka, Japan
| | - Toshihiro Sato
- 1 Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco, Takatsuki, Osaka, Japan
| | - Yoshiji Hantani
- 1 Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco, Takatsuki, Osaka, Japan
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13
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Discovery of 7H-pyrrolo[2,3-d]pyrimidine derivatives as selective covalent irreversible inhibitors of interleukin-2-inducible T-cell kinase (Itk). Eur J Med Chem 2019; 173:167-183. [PMID: 30999237 DOI: 10.1016/j.ejmech.2019.03.055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/10/2019] [Accepted: 03/23/2019] [Indexed: 01/30/2023]
Abstract
Interleukin-2-inducible T-cell kinase (Itk) plays an important role in multiple signal transduction pathways in T and mast cells, and is a potential drug target for treating inflammatory diseases, autoimmune diseases, and T cell leukemia/lymphoma. Herein, we describe the discovery of a series of covalent Itk inhibitors based on the 7H-pyrrolo[2,3-d]pyrimidine scaffold. Placing an appropriate substitution group at a hydration site of the ATP binding pocket of Itk and using a saturated heterocyclic ring as a linker to the reactive group were crucial for selectivity. The optimized compound 9 showed potent activity against Itk, excellent selectivity for Itk over Btk and other structurally related kinases, inhibition of phospholipase C-γ1 (PLC-γ1) phosphorylation in cells, and anti-proliferative effects against multiple T leukemia/lymphoma cell lines. Compound 9 can serve as a valuable compound for further determination of functions of Itk.
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Fearon D, Westwood IM, van Montfort RLM, Bayliss R, Jones K, Bavetsias V. Synthesis and profiling of a 3-aminopyridin-2-one-based kinase targeted fragment library: Identification of 3-amino-5-(pyridin-4-yl)pyridin-2(1H)-one scaffold for monopolar spindle 1 (MPS1) and Aurora kinases inhibition. Bioorg Med Chem 2018; 26:3021-3029. [PMID: 29764757 PMCID: PMC6008489 DOI: 10.1016/j.bmc.2018.04.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/13/2018] [Accepted: 04/15/2018] [Indexed: 12/24/2022]
Abstract
Screening a 3-aminopyridin-2-one based fragment library against a 26-kinase panel representative of the human kinome identified 3-amino-5-(1-methyl-1H-pyrazol-4-yl)pyridin-2(1H)-one (2) and 3-amino-5-(pyridin-4-yl)pyridin-2(1H)-one (3) as ligand efficient inhibitors of the mitotic kinase Monopolar Spindle 1 (MPS1) and the Aurora kinase family. These kinases are well recognised as attractive targets for therapeutic intervention for treating cancer. Elucidation of the binding mode of these fragments and their analogues has been carried out by X-ray crystallography. Structural studies have identified key interactions with a conserved lysine residue and have highlighted potential regions of MPS1 which could be targeted to improve activity and selectivity.
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Affiliation(s)
- Daren Fearon
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SM2 5NG, UK
| | - Isaac M Westwood
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SM2 5NG, UK
| | - Rob L M van Montfort
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SM2 5NG, UK
| | - Richard Bayliss
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, UK
| | - Keith Jones
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SM2 5NG, UK.
| | - Vassilios Bavetsias
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SM2 5NG, UK.
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15
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Stankevičiūtė J, Vaitekūnas J, Petkevičius V, Gasparavičiūtė R, Tauraitė D, Meškys R. Oxyfunctionalization of pyridine derivatives using whole cells of Burkholderia sp. MAK1. Sci Rep 2016; 6:39129. [PMID: 27982075 PMCID: PMC5159870 DOI: 10.1038/srep39129] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 11/17/2016] [Indexed: 11/20/2022] Open
Abstract
Pyridinols and pyridinamines are important intermediates with many applications in chemical industry. The pyridine derivatives are in great demand as synthons for pharmaceutical products. Moreover, pyridines are used either as biologically active substances or as building blocks for polymers with unique physical properties. Application of enzymes or whole cells is an attractive strategy for preparation of hydroxylated pyridines since the methods for chemical synthesis of pyridinols, particularly aminopyridinols, are usually limited or inefficient. Burkholderia sp. MAK1 (DSM102049), capable of using pyridin-2-ol as the sole carbon and energy source, was isolated from soil. Whole cells of Burkholderia sp. MAK1 were confirmed to possess a good ability to convert different pyridin-2-amines and pyridin-2-ones into their 5-hydroxy derivatives. Moreover, several methylpyridines as well as methylated pyrazines were converted to appropriate N-oxides. In conclusion, regioselective oxyfunctionalization of pyridine derivatives using whole cells of Burkholderia sp. MAK1 is a promising method for the preparation of various pyridin-5-ols and pyridin-N-oxides.
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Affiliation(s)
- Jonita Stankevičiūtė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, the Life Sciences Centre, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Justas Vaitekūnas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, the Life Sciences Centre, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Vytautas Petkevičius
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, the Life Sciences Centre, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Renata Gasparavičiūtė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, the Life Sciences Centre, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Daiva Tauraitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, the Life Sciences Centre, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, the Life Sciences Centre, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
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16
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Wo J, Kong D, Brock NL, Xu F, Zhou X, Deng Z, Lin S. Transformation of Streptonigrin to Streptonigrone: Flavin Reductase-Mediated Flavin-Catalyzed Concomitant Oxidative Decarboxylation of Picolinic Acid Derivatives. ACS Catal 2016. [DOI: 10.1021/acscatal.6b00154] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Jing Wo
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Dekun Kong
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Nelson L. Brock
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Fei Xu
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xiufen Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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17
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Heifetz A, Trani G, Aldeghi M, MacKinnon CH, McEwan PA, Brookfield FA, Chudyk EI, Bodkin M, Pei Z, Burch JD, Ortwine DF. Fragment Molecular Orbital Method Applied to Lead Optimization of Novel Interleukin-2 Inducible T-Cell Kinase (ITK) Inhibitors. J Med Chem 2016; 59:4352-63. [PMID: 26950250 DOI: 10.1021/acs.jmedchem.6b00045] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Inhibition of inducible T-cell kinase (ITK), a nonreceptor tyrosine kinase, may represent a novel treatment for allergic asthma. In our previous reports, we described the discovery of sulfonylpyridine (SAP), benzothiazole (BZT), indazole (IND), and tetrahydroindazole (THI) series as novel ITK inhibitors and how computational tools such as dihedral scans and docking were used to support this process. X-ray crystallography and modeling were applied to provide essential insight into ITK-ligand interactions. However, "visual inspection" traditionally used for the rationalization of protein-ligand affinity cannot always explain the full complexity of the molecular interactions. The fragment molecular orbital (FMO) quantum-mechanical (QM) method provides a complete list of the interactions formed between the ligand and protein that are often omitted from traditional structure-based descriptions. FMO methodology was successfully used as part of a rational structure-based drug design effort to improve the ITK potency of high-throughput screening hits, ultimately delivering ligands with potency in the subnanomolar range.
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Affiliation(s)
- Alexander Heifetz
- Evotec (U.K.) Ltd. , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Giancarlo Trani
- Evotec (U.K.) Ltd. , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Matteo Aldeghi
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Colin H MacKinnon
- Evotec (U.K.) Ltd. , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Paul A McEwan
- Evotec (U.K.) Ltd. , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Frederick A Brookfield
- Evotec (U.K.) Ltd. , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Ewa I Chudyk
- Evotec (U.K.) Ltd. , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Mike Bodkin
- Evotec (U.K.) Ltd. , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Zhonghua Pei
- Discovery Chemistry, Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Jason D Burch
- Discovery Chemistry, Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel F Ortwine
- Discovery Chemistry, Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
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18
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Khalifa NM, Al-Omar MA, Sediek AA. Synthesis and characterization of some novel substituted pyridones and iminopyridines derived from pyrene moiety. RUSS J GEN CHEM+ 2016. [DOI: 10.1134/s1070363215120336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Burch JD, Barrett K, Chen Y, DeVoss J, Eigenbrot C, Goldsmith R, Ismaili MHA, Lau K, Lin Z, Ortwine DF, Zarrin AA, McEwan PA, Barker JJ, Ellebrandt C, Kordt D, Stein DB, Wang X, Chen Y, Hu B, Xu X, Yuen PW, Zhang Y, Pei Z. Tetrahydroindazoles as Interleukin-2 Inducible T-Cell Kinase Inhibitors. Part II. Second-Generation Analogues with Enhanced Potency, Selectivity, and Pharmacodynamic Modulation in Vivo. J Med Chem 2015; 58:3806-16. [PMID: 25844760 DOI: 10.1021/jm501998m] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The medicinal chemistry community has directed considerable efforts toward the discovery of selective inhibitors of interleukin-2 inducible T-cell kinase (ITK), given its role in T-cell signaling downstream of the T-cell receptor (TCR) and the implications of this target for inflammatory disorders such as asthma. We have previously disclosed a structure- and property-guided lead optimization effort which resulted in the discovery of a new series of tetrahydroindazole-containing selective ITK inhibitors. Herein we disclose further optimization of this series that resulted in further potency improvements, reduced off-target receptor binding liabilities, and reduced cytotoxicity. Specifically, we have identified a correlation between the basicity of solubilizing elements in the ITK inhibitors and off-target antiproliferative effects, which was exploited to reduce cytotoxicity while maintaining kinase selectivity. Optimized analogues were shown to reduce IL-2 and IL-13 production in vivo following oral or intraperitoneal dosing in mice.
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Affiliation(s)
- Jason D Burch
- †Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Kathy Barrett
- †Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Yuan Chen
- †Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jason DeVoss
- †Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Charles Eigenbrot
- †Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Richard Goldsmith
- †Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - M Hicham A Ismaili
- †Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Kevin Lau
- †Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Zhonghua Lin
- †Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel F Ortwine
- †Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Ali A Zarrin
- †Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Paul A McEwan
- ‡Evotec (U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - John J Barker
- ‡Evotec (U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Claire Ellebrandt
- §Evotec AG, Manfred Eigen Campus, Essener Bogen 7, D-22419 Hamburg, Germany
| | - Daniel Kordt
- §Evotec AG, Manfred Eigen Campus, Essener Bogen 7, D-22419 Hamburg, Germany
| | - Daniel B Stein
- §Evotec AG, Manfred Eigen Campus, Essener Bogen 7, D-22419 Hamburg, Germany
| | - Xiaolu Wang
- §Evotec AG, Manfred Eigen Campus, Essener Bogen 7, D-22419 Hamburg, Germany
| | - Yong Chen
- ∥Pharmaron Beijing Ltd. Co., No. 6 TaiHe Road BDA, 100176 Beijing, P. R. China
| | - Baihua Hu
- ∥Pharmaron Beijing Ltd. Co., No. 6 TaiHe Road BDA, 100176 Beijing, P. R. China
| | - Xiaofeng Xu
- ∥Pharmaron Beijing Ltd. Co., No. 6 TaiHe Road BDA, 100176 Beijing, P. R. China
| | - Po-Wai Yuen
- ∥Pharmaron Beijing Ltd. Co., No. 6 TaiHe Road BDA, 100176 Beijing, P. R. China
| | - Yamin Zhang
- ∥Pharmaron Beijing Ltd. Co., No. 6 TaiHe Road BDA, 100176 Beijing, P. R. China
| | - Zhonghua Pei
- †Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
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20
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Bruton's TK inhibitors: structural insights and evolution of clinical candidates. Future Med Chem 2015; 6:675-95. [PMID: 24895895 DOI: 10.4155/fmc.14.24] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Bruton's TK (BTK) is a promising biological target for therapeutic intervention of several diseases including inflammatory diseases and cancer/B cell malignancies. Numerous research groups are actively engaged in investigating the functions of BTK, and discovering potent and selective BTK inhibitors as drug candidates. Revealed by x-ray crystal structures with ligands of diverse chemical structures, the ability of BTK kinase domain to adopt various inactive conformations offers unique opportunities to identify highly potent and exquisitely selective inhibitors. Both reversible and covalent inhibitor approaches have yielded candidates demonstrating safety profiles and efficacies in multiple preclinical models of autoimmunity and oncology. Two BTK inhibitors have entered human clinical trials for oncology indications. Ibrutinib won the US FDA approval in November 2013 to become the first-in-class BTK inhibitor for treating mantle cell lymphoma. This encouraging outcome and the other on-going human studies could ultimately expand the utility of BTK inhibitors to broader autoimmune disease areas.
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21
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Zhong Y, Dong S, Strattan E, Ren L, Butchar JP, Thornton K, Mishra A, Porcu P, Bradshaw JM, Bisconte A, Owens TD, Verner E, Brameld KA, Funk JO, Hill RJ, Johnson AJ, Dubovsky JA. Targeting interleukin-2-inducible T-cell kinase (ITK) and resting lymphocyte kinase (RLK) using a novel covalent inhibitor PRN694. J Biol Chem 2015; 290:5960-78. [PMID: 25593320 DOI: 10.1074/jbc.m114.614891] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Interleukin-2-inducible T-cell kinase (ITK) and resting lymphocyte kinase (RLK or TXK) are essential mediators of intracellular signaling in both normal and neoplastic T-cells and natural killer (NK) cells. Thus, ITK and RLK inhibitors have therapeutic potential in a number of human autoimmune, inflammatory, and malignant diseases. Here we describe a novel ITK/RLK inhibitor, PRN694, which covalently binds to cysteine residues 442 of ITK and 350 of RLK and blocks kinase activity. Molecular modeling was utilized to design molecules that interact with cysteine while binding to the ATP binding site in the kinase domain. PRN694 exhibits extended target residence time on ITK and RLK and is highly selective for a subset of the TEC kinase family. In vitro cellular assays confirm that PRN694 prevents T-cell receptor- and Fc receptor-induced cellular and molecular activation, inhibits T-cell receptor-induced T-cell proliferation, and blocks proinflammatory cytokine release as well as activation of Th17 cells. Ex vivo assays demonstrate inhibitory activity against T-cell prolymphocytic leukemia cells, and in vivo assays demonstrate durable pharmacodynamic effects on ITK, which reduces an oxazolone-induced delayed type hypersensitivity reaction. These data indicate that PRN694 is a highly selective and potent covalent inhibitor of ITK and RLK, and its extended target residence time enables durable attenuation of effector cells in vitro and in vivo. The results from this study highlight potential applications of this dual inhibitor for the treatment of T-cell- or NK cell-mediated inflammatory, autoimmune, and malignant diseases.
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Affiliation(s)
- Yiming Zhong
- From the Division of Hematology, College of Medicine, Ohio State University, Columbus, Ohio 43210
| | - Shuai Dong
- the Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, Ohio State University, Columbus, Ohio 43210, and
| | - Ethan Strattan
- From the Division of Hematology, College of Medicine, Ohio State University, Columbus, Ohio 43210
| | - Li Ren
- From the Division of Hematology, College of Medicine, Ohio State University, Columbus, Ohio 43210
| | - Jonathan P Butchar
- From the Division of Hematology, College of Medicine, Ohio State University, Columbus, Ohio 43210
| | - Kelsey Thornton
- From the Division of Hematology, College of Medicine, Ohio State University, Columbus, Ohio 43210
| | - Anjali Mishra
- From the Division of Hematology, College of Medicine, Ohio State University, Columbus, Ohio 43210
| | - Pierluigi Porcu
- From the Division of Hematology, College of Medicine, Ohio State University, Columbus, Ohio 43210
| | | | | | | | - Erik Verner
- Principia Biopharma, South San Francisco, California 94080
| | - Ken A Brameld
- Principia Biopharma, South San Francisco, California 94080
| | | | - Ronald J Hill
- Principia Biopharma, South San Francisco, California 94080
| | - Amy J Johnson
- From the Division of Hematology, College of Medicine, Ohio State University, Columbus, Ohio 43210
| | - Jason A Dubovsky
- From the Division of Hematology, College of Medicine, Ohio State University, Columbus, Ohio 43210,
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22
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Norman P. Inducible tyrosine kinase inhibitors: a review of the patent literature (2010 - 2013). Expert Opin Ther Pat 2014; 24:979-91. [PMID: 24990480 DOI: 10.1517/13543776.2014.936381] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION The non-receptor tyrosine kinase, inducible tyrosine kinase (Itk), plays an important role in thymus(T)-cell signalling and the production of pro-inflammatory cytokines. Itk, and the other Tec family members, Rlk and Tec, are viewed as attractive drug targets for new agents for the treatment of autoimmune and inflammatory diseases. Interest in Itk inhibitors is still modest compared to other kinases such as the Janus kinase (JAK) family or Syk. AREAS COVERED This article reviews the patent filings published from January 2010 to April 2014 that claim Itk inhibitors. It first considers those applications that claim selective, or apparently selective, Itk inhibitors. It then considers those applications that claim less-selective Itk inhibitors. The recent interest in irreversible Itk inhibitors is also discussed. EXPERT OPINION There is a difference of opinion as to the preferred utility for Itk inhibitors. Progress has been made in designing selective Itk inhibitors but little clinical progress. Until clinical data are available, it remains difficult to assess how well Itk inhibitors compare with JAK inhibitors as potential treatments for rheumatoid arthritis. However, animal data suggest that irreversible Itk inhibitors could be useful in treating asthma, whereas dual Itk inhibitors may have more utility in treating rheumatoid arthritis.
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Affiliation(s)
- Peter Norman
- Norman Consulting , 18 Pink Lane, Burnham, Bucks, SL1 8JW , UK
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23
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Burch JD, Lau K, Barker JJ, Brookfield F, Chen Y, Chen Y, Eigenbrot C, Ellebrandt C, Ismaili MHA, Johnson A, Kordt D, MacKinnon CH, McEwan PA, Ortwine DF, Stein DB, Wang X, Winkler D, Yuen PW, Zhang Y, Zarrin AA, Pei Z. Property- and structure-guided discovery of a tetrahydroindazole series of interleukin-2 inducible T-cell kinase inhibitors. J Med Chem 2014; 57:5714-27. [PMID: 24918870 DOI: 10.1021/jm500550e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Interleukin-2 inducible T-cell kinase (ITK), a member of the Tec family of tyrosine kinases, plays a major role in T-cell signaling downstream of the T-cell receptor (TCR), and considerable efforts have been directed toward discovery of ITK-selective inhibitors as potential treatments of inflammatory disorders such as asthma. Using a previously disclosed indazole series of inhibitors as a starting point, and using X-ray crystallography and solubility forecast index (SFI) as guides, we evolved a series of tetrahydroindazole inhibitors with improved potency, selectivity, and pharmaceutical properties. Highlights include identification of a selectivity pocket above the ligand plane, and identification of appropriate lipophilic substituents to occupy this space. This effort culminated in identification of a potent and selective ITK inhibitor (GNE-9822) with good ADME properties in preclinical species.
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Affiliation(s)
- Jason D Burch
- Genentech Inc. , 1 DNA Way, South San Francisco, California 94080, United States
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24
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Zhong Y, Johnson AJ, Byrd JC, Dubovsky JA. Targeting Interleukin-2-Inducible T-cell Kinase (ITK) in T-Cell Related Diseases. ACTA ACUST UNITED AC 2014; 2:1-11. [PMID: 27917390 DOI: 10.14304/surya.jpr.v2n6.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
IL2-inducible T-cell kinase (ITK), a member of the Tec family tyrosine kinases, is the predominant Tec kinase in T cells and natural killer (NK) cells mediating T cell receptor (TCR) and Fc receptor (Fc R) initiated signal transduction. ITK deficiency results in impaired T and NK cell functions, leading to various disorders including malignancies, inflammation, and autoimmune diseases. In this mini-review, the role of ITK in T cell signaling and the development of small molecule inhibitors of ITK for the treatment of T-cell related disorders is examined.
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Affiliation(s)
- Yiming Zhong
- Division of Hematology, Department of Internal Medicine, The Ohio State University, 320 W. 10th Avenue, Columbus, OH 43210, USA
| | - Amy J Johnson
- Division of Hematology, Department of Internal Medicine, The Ohio State University, 320 W. 10th Avenue, Columbus, OH 43210, USA
| | - John C Byrd
- Division of Hematology, Department of Internal Medicine, The Ohio State University, 320 W. 10th Avenue, Columbus, OH 43210, USA
| | - Jason A Dubovsky
- Division of Hematology, Department of Internal Medicine, The Ohio State University, 320 W. 10th Avenue, Columbus, OH 43210, USA
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25
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Woods CJ, Malaisree M, Michel J, Long B, McIntosh-Smith S, Mulholland AJ. Rapid decomposition and visualisation of protein-ligand binding free energies by residue and by water. Faraday Discuss 2014; 169:477-99. [PMID: 25340314 DOI: 10.1039/c3fd00125c] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Recent advances in computational hardware, software and algorithms enable simulations of protein-ligand complexes to achieve timescales during which complete ligand binding and unbinding pathways can be observed. While observation of such events can promote understanding of binding and unbinding pathways, it does not alone provide information about the molecular drivers for protein-ligand association, nor guidance on how a ligand could be optimised to better bind to the protein. We have developed the waterswap (C. J. Woods et al., J. Chem. Phys., 2011, 134, 054114) absolute binding free energy method that calculates binding affinities by exchanging the ligand with an equivalent volume of water. A significant advantage of this method is that the binding free energy is calculated using a single reaction coordinate from a single simulation. This has enabled the development of new visualisations of binding affinities based on free energy decompositions to per-residue and per-water molecule components. These provide a clear picture of which protein-ligand interactions are strong, and which active site water molecules are stabilised or destabilised upon binding. Optimisation of the algorithms underlying the decomposition enables near-real-time visualisation, allowing these calculations to be used either to provide interactive feedback to a ligand designer, or to provide run-time analysis of protein-ligand molecular dynamics simulations.
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26
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Discovery and optimization of indazoles as potent and selective interleukin-2 inducible T cell kinase (ITK) inhibitors. Bioorg Med Chem Lett 2014; 24:2448-52. [PMID: 24767842 DOI: 10.1016/j.bmcl.2014.04.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 04/06/2014] [Accepted: 04/07/2014] [Indexed: 11/23/2022]
Abstract
There is evidence that small molecule inhibitors of the non-receptor tyrosine kinase ITK, a component of the T-cell receptor signaling cascade, could represent a novel asthma therapeutic class. Moreover, given the expected chronic dosing regimen of any asthma treatment, highly selective as well as potent inhibitors would be strongly preferred in any potential therapeutic. Here we report hit-to-lead optimization of a series of indazoles that demonstrate sub-nanomolar inhibitory potency against ITK with strong cellular activity and good kinase selectivity. We also elucidate the binding mode of these inhibitors by solving the X-ray crystal structures of the complexes.
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Structure-functional prediction and analysis of cancer mutation effects in protein kinases. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2014; 2014:653487. [PMID: 24817905 PMCID: PMC4000980 DOI: 10.1155/2014/653487] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 12/31/2013] [Accepted: 02/28/2014] [Indexed: 12/17/2022]
Abstract
A central goal of cancer research is to discover and characterize the functional effects of mutated genes that contribute to tumorigenesis. In this study, we provide a detailed structural classification and analysis of functional dynamics for members of protein kinase families that are known to harbor cancer mutations. We also present a systematic computational analysis that combines sequence and structure-based prediction models to characterize the effect of cancer mutations in protein kinases. We focus on the differential effects of activating point mutations that increase protein kinase activity and kinase-inactivating mutations that decrease activity. Mapping of cancer mutations onto the conformational mobility profiles of known crystal structures demonstrated that activating mutations could reduce a steric barrier for the movement from the basal “low” activity state to the “active” state. According to our analysis, the mechanism of activating mutations reflects a combined effect of partial destabilization of the kinase in its inactive state and a concomitant stabilization of its active-like form, which is likely to drive tumorigenesis at some level. Ultimately, the analysis of the evolutionary and structural features of the major cancer-causing mutational hotspot in kinases can also aid in the correlation of kinase mutation effects with clinical outcomes.
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28
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Mortenson PN, Berdini V, O'Reilly M. Fragment-based approaches to the discovery of kinase inhibitors. Methods Enzymol 2014; 548:69-92. [PMID: 25399642 DOI: 10.1016/b978-0-12-397918-6.00003-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Protein kinases are one of the most important families of drug targets, and aberrant kinase activity has been linked to a large number of disease areas. Although eminently targetable using small molecules, kinases present a number of challenges as drug targets, not least obtaining selectivity across such a large and relatively closely related target family. Fragment-based drug discovery involves screening simple, low-molecular weight compounds to generate initial hits against a target. These hits are then optimized to more potent compounds via medicinal chemistry, usually facilitated by structural biology. Here, we will present a number of recent examples of fragment-based approaches to the discovery of kinase inhibitors, detailing the construction of fragment-screening libraries, the identification and validation of fragment hits, and their optimization into potent and selective lead compounds. The advantages of fragment-based methodologies will be discussed, along with some of the challenges associated with using this route. Finally, we will present a number of key lessons derived both from our own experience running fragment screens against kinases and from a large number of published studies.
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29
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Alder CM, Ambler M, Campbell AJ, Champigny AC, Deakin AM, Harling JD, Harris CA, Longstaff T, Lynn S, Maxwell AC, Mooney CJ, Scullion C, Singh OMP, Smith IED, Somers DO, Tame CJ, Wayne G, Wilson C, Woolven JM. Identification of a Novel and Selective Series of Itk Inhibitors via a Template-Hopping Strategy. ACS Med Chem Lett 2013; 4:948-52. [PMID: 24900590 DOI: 10.1021/ml400206q] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 08/12/2013] [Indexed: 12/23/2022] Open
Abstract
Inhibition of Itk potentially constitutes a novel, nonsteroidal treatment for asthma and other T-cell mediated diseases. In-house kinase cross-screening resulted in the identification of an aminopyrazole-based series of Itk inhibitors. Initial work on this series highlighted selectivity issues with several other kinases, particularly AurA and AurB. A template-hopping strategy was used to identify a series of aminobenzothiazole Itk inhibitors, which utilized an inherently more selective hinge binding motif. Crystallography and modeling were used to rationalize the observed selectivity. Initial exploration of the SAR around this series identified potent Itk inhibitors in both enzyme and cellular assays.
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Affiliation(s)
- Catherine M. Alder
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Martin Ambler
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Amanda J. Campbell
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Aurelie C. Champigny
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Angela M. Deakin
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - John D. Harling
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Carol A. Harris
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Tim Longstaff
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Sean Lynn
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Aoife C. Maxwell
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Chris J. Mooney
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Callum Scullion
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Onkar M. P. Singh
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Ian E. D. Smith
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Donald O. Somers
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Christopher J. Tame
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Gareth Wayne
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Caroline Wilson
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - James M. Woolven
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
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30
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MacKinnon CH, Lau K, Burch JD, Chen Y, Dines J, Ding X, Eigenbrot C, Heifetz A, Jaochico A, Johnson A, Kraemer J, Kruger S, Krülle TM, Liimatta M, Ly J, Maghames R, Montalbetti CAGN, Ortwine DF, Pérez-Fuertes Y, Shia S, Stein DB, Trani G, Vaidya DG, Wang X, Bromidge SM, Wu LC, Pei Z. Structure-based design and synthesis of potent benzothiazole inhibitors of interleukin-2 inducible T cell kinase (ITK). Bioorg Med Chem Lett 2013; 23:6331-5. [PMID: 24138940 DOI: 10.1016/j.bmcl.2013.09.069] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/17/2013] [Accepted: 09/23/2013] [Indexed: 11/17/2022]
Abstract
Inhibition of the non-receptor tyrosine kinase ITK, a component of the T-cell receptor signalling cascade, may represent a novel treatment for allergic asthma. Here we report the structure-based optimization of a series of benzothiazole amides that demonstrate sub-nanomolar inhibitory potency against ITK with good cellular activity and kinase selectivity. We also elucidate the binding mode of these inhibitors by solving the X-ray crystal structures of several inhibitor-ITK complexes.
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Affiliation(s)
- Colin H MacKinnon
- Evotec (UK) Ltd, 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
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31
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Harling JD, Deakin AM, Campos S, Grimley R, Chaudry L, Nye C, Polyakova O, Bessant CM, Barton N, Somers D, Barrett J, Graves RH, Hanns L, Kerr WJ, Solari R. Discovery of novel irreversible inhibitors of interleukin (IL)-2-inducible tyrosine kinase (Itk) by targeting cysteine 442 in the ATP pocket. J Biol Chem 2013; 288:28195-206. [PMID: 23935099 DOI: 10.1074/jbc.m113.474114] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
IL-2-inducible tyrosine kinase (Itk) plays a key role in antigen receptor signaling in T cells and is considered an important target for anti-inflammatory drug discovery. In order to generate inhibitors with the necessary potency and selectivity, a compound that targeted cysteine 442 in the ATP binding pocket and with an envisaged irreversible mode of action was designed. We incorporated a high degree of molecular recognition and specific design features making the compound suitable for inhaled delivery. This study confirms the irreversible covalent binding of the inhibitor to the kinase by x-ray crystallography and enzymology while demonstrating potency, selectivity, and prolonged duration of action in in vitro biological assays. The biosynthetic turnover of the kinase was also examined as a critical factor when designing irreversible inhibitors for extended duration of action. The exemplified Itk inhibitor demonstrated inhibition of both TH1 and TH2 cytokines, was additive with fluticasone propionate, and inhibited cytokine release from human lung fragments. Finally, we describe an in vivo pharmacodynamic assay that allows rapid preclinical development without animal efficacy models.
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Affiliation(s)
- John D Harling
- From the Allergic Inflammation Discovery Performance Unit and
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32
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Vargas L, Hamasy A, Nore BF, E. Smith CI. Inhibitors of BTK and ITK: State of the New Drugs for Cancer, Autoimmunity and Inflammatory Diseases. Scand J Immunol 2013; 78:130-9. [DOI: 10.1111/sji.12069] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 05/05/2013] [Indexed: 01/01/2023]
Affiliation(s)
- L. Vargas
- Department of Laboratory Medicine; Clinical Research Center; Karolinska Institutet; Karolinska University Hospital; Huddinge; Sweden
| | | | | | - C. I. E. Smith
- Department of Laboratory Medicine; Clinical Research Center; Karolinska Institutet; Karolinska University Hospital; Huddinge; Sweden
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33
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34
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3D-QSAR analysis of benzimidazole inhibitors of interleukin-2 inducible T cell kinase (ITK) considering receptor flexibility and water importance for molecular alignment. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0548-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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35
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Affiliation(s)
- Jean-Damien Charrier
- Chemistry Department at Vertex Pharmaceuticals (Europe) Ltd, 86-88 Jubilee Avenue, Milton Park, Abingdon, Oxfordshire OX14 4RW, UK
| | - Ronald MA Knegtel
- Chemistry Department at Vertex Pharmaceuticals (Europe) Ltd, 86-88 Jubilee Avenue, Milton Park, Abingdon, Oxfordshire OX14 4RW, UK
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36
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Harker WR, Delaney PM, Simms M, Tozer MJ, Harrity JP. Scalable synthesis of functionalised 2-pyridones via [4+2] cycloaddition reactions of 2-pyrazinones and alkynylboronates. Tetrahedron 2013. [DOI: 10.1016/j.tet.2012.12.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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37
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Yang Y, Lightstone FC, Wong SE. Approaches to efficiently estimate solvation and explicit water energetics in ligand binding: the use of WaterMap. Expert Opin Drug Discov 2013; 8:277-87. [DOI: 10.1517/17460441.2013.749853] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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38
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Xie Q, Joseph RE, Fulton DB, Andreotti AH. Substrate recognition of PLCγ1 via a specific docking surface on Itk. J Mol Biol 2012; 425:683-96. [PMID: 23219468 DOI: 10.1016/j.jmb.2012.10.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 10/29/2012] [Accepted: 10/31/2012] [Indexed: 12/15/2022]
Abstract
Itk (interleukin-2 inducible T cell kinase) is a non-receptor protein tyrosine kinase expressed primarily in T cells. Itk catalyzes phosphorylation on tyrosine residues within a number of its natural substrates, including the well-characterized Y783 of PLCγ1. However, the molecular mechanisms Itk exploits to recognize its substrates are not completely understood. We have previously identified a specific docking interaction between the kinase domain of Itk and the C-terminal Src homology 2 (SH2C) domain of PLCγ1 that promotes substrate specificity for this enzyme/substrate pair. In the current study, we identify and map the interaction surface on the Itk kinase domain as an acidic patch centered on the G helix. Mutation of the residues on and adjacent to the G helix within the Itk kinase domain impairs the catalytic efficacy of PLCγ1 substrate phosphorylation by specifically altering the protein-protein interaction interface and not the inherent catalytic activity of Itk. NMR titration experiments using a Btk (Bruton's tyrosine kinase) kinase domain as a surrogate for the Itk kinase domain provide further support for an Itk/PLCγ1 SH2C interaction surrounding the G helix of the kinase domain. The work presented here provides structural insight into how the Itk kinase uses the G helix to single out Y783 of PLCγ1 for specific phosphorylation. Comparing these results to other well-characterized kinase/substrate systems suggests that the G helix is a general structural feature used by kinases for substrate recognition during signaling.
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Affiliation(s)
- Qian Xie
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
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39
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Zapf CW, Gerstenberger BS, Xing L, Limburg DC, Anderson DR, Caspers N, Han S, Aulabaugh A, Kurumbail R, Shakya S, Li X, Spaulding V, Czerwinski RM, Seth N, Medley QG. Covalent Inhibitors of Interleukin-2 Inducible T Cell Kinase (Itk) with Nanomolar Potency in a Whole-Blood Assay. J Med Chem 2012; 55:10047-63. [DOI: 10.1021/jm301190s] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Christoph W. Zapf
- BioTherapeutics Chemistry, Pfizer Worldwide Medicinal Chemistry, 200 Cambridgepark Drive, Cambridge, Massachusetts
02140, United States
| | - Brian S. Gerstenberger
- BioTherapeutics
Chemistry, Pfizer Worldwide Medicinal Chemistry, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Li Xing
- BioTherapeutics Chemistry, Pfizer Worldwide Medicinal Chemistry, 200 Cambridgepark Drive, Cambridge, Massachusetts
02140, United States
| | - David C. Limburg
- BioTherapeutics
Chemistry, Pfizer Worldwide Medicinal Chemistry, Eastern Point Road, Groton, Connecticut 06340, United States
| | - David R. Anderson
- BioTherapeutics
Chemistry, Pfizer Worldwide Medicinal Chemistry, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Nicole Caspers
- Structure Biology and Biophysics, Pfizer Worldwide Medicinal Chemistry, Eastern Point
Road, Groton, Connecticut 06340, United States
| | - Seungil Han
- Structure Biology and Biophysics, Pfizer Worldwide Medicinal Chemistry, Eastern Point
Road, Groton, Connecticut 06340, United States
| | - Ann Aulabaugh
- Structure Biology and Biophysics, Pfizer Worldwide Medicinal Chemistry, Eastern Point
Road, Groton, Connecticut 06340, United States
| | - Ravi Kurumbail
- Structure Biology and Biophysics, Pfizer Worldwide Medicinal Chemistry, Eastern Point
Road, Groton, Connecticut 06340, United States
| | - Subarna Shakya
- Inflammation and Autoimmunity, Pfizer Research, 200 Cambridgepark Drive, Cambridge,
Massachusetts 02140, United States
| | - Xin Li
- Inflammation and Autoimmunity, Pfizer Research, 200 Cambridgepark Drive, Cambridge,
Massachusetts 02140, United States
| | - Vikki Spaulding
- Inflammation and Autoimmunity, Pfizer Research, 200 Cambridgepark Drive, Cambridge,
Massachusetts 02140, United States
| | - Robert M. Czerwinski
- Inflammation and Autoimmunity, Pfizer Research, 200 Cambridgepark Drive, Cambridge,
Massachusetts 02140, United States
| | - Nilufer Seth
- Inflammation and Autoimmunity, Pfizer Research, 200 Cambridgepark Drive, Cambridge,
Massachusetts 02140, United States
| | - Quintus G. Medley
- Inflammation and Autoimmunity, Pfizer Research, 200 Cambridgepark Drive, Cambridge,
Massachusetts 02140, United States
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40
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Zhou Q, Chu X, Tang W, Lu T. An efficient one-pot synthesis of 1,4-disubstituted 3-amino-2-pyridone derivatives via three-component reactions of alkynyl aldehydes and amines with ethyl 2-((diphenylmethylene)amino)acetate. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.03.106] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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41
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X-ray crystallographic structure-based design of selective thienopyrazole inhibitors for interleukin-2-inducible tyrosine kinase. Bioorg Med Chem Lett 2012; 22:3296-300. [DOI: 10.1016/j.bmcl.2012.03.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 03/02/2012] [Accepted: 03/05/2012] [Indexed: 11/22/2022]
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42
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Murray CW, Verdonk ML, Rees DC. Experiences in fragment-based drug discovery. Trends Pharmacol Sci 2012; 33:224-32. [PMID: 22459076 DOI: 10.1016/j.tips.2012.02.006] [Citation(s) in RCA: 176] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 02/28/2012] [Accepted: 02/28/2012] [Indexed: 11/17/2022]
Abstract
Fragment-based drug discovery (FBDD) has become established in both industry and academia as an alternative approach to high-throughput screening for the generation of chemical leads for drug targets. In FBDD, specialised detection methods are used to identify small chemical compounds (fragments) that bind to the drug target, and structural biology is usually employed to establish their binding mode and to facilitate their optimisation. In this article, we present three recent and successful case histories in FBDD. We then re-examine the key concepts and challenges of FBDD with particular emphasis on recent literature and our own experience from a substantial number of FBDD applications. Our opinion is that careful application of FBDD is living up to its promise of delivering high quality leads with good physical properties and that in future many drug molecules will be derived from fragment-based approaches.
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Affiliation(s)
- Christopher W Murray
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, UK.
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43
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P. Mahajan M, Singh P, Singh P, Kumar K, Kumar V, Bisetty K. Synthetic Studies on the Role of Substituents at C-3 Position on C3-C4 Bond Cleavage of β-Lactam Ring: Convenient Route for Diastereoselective Synthesis of Pyridin-2-ones. HETEROCYCLES 2012. [DOI: 10.3987/com-12-s(n)83] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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44
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Knegtel RMA, Robinson DD. A Role for Hydration in Interleukin-2 Inducible T Cell Kinase (Itk) Selectivity. Mol Inform 2011; 30:950-9. [DOI: 10.1002/minf.201100086] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 09/09/2011] [Indexed: 11/07/2022]
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