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Yao X, Chen R, Chen H, Koleske A, Xiao X. Impact of Abl2/Arg deficiency on anxiety and depressive behaviors in mice. Behav Brain Res 2024; 468:115022. [PMID: 38697301 DOI: 10.1016/j.bbr.2024.115022] [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: 02/11/2024] [Revised: 04/19/2024] [Accepted: 04/26/2024] [Indexed: 05/04/2024]
Abstract
Abl2/Arg (ABL-related gene) is a member of the Abelson family of nonreceptor tyrosine kinases, known for its role in tumor progression, metastasis, tissue injury responses, inflammation, neural degeneration, and other diseases. In this study, we developed Abl2/Arg knockout (abl2-/-) mice to explore its impact on sensory/motor functions and emotion-related behaviors. Our findings show that abl2-/- mice exhibit normal growth and phenotypic characteristics, closely resembling their wild-type (WT) counterparts. Behavioral tests, including the elevated plus maze, marble-burying behavior test, and open field test, indicated pronounced anxiety-like behaviors in abl2-/- mice compared to WT mice. Furthermore, in the tail suspension test, abl2-/- mice showed a significant decrease in mobility time, suggesting depressive-like behavior. Conversely, in the Y-maze and cliff avoidance reaction tests, no notable differences were observed between abl2-/- and WT mice, suggesting the absence of working memory deficits and impulsivity in abl2-/- mice. Proteomic analysis of the hippocampus in abl2-/- mice highlighted significant alterations in proteins related to anxiety and depression, especially those associated with the GABAergic synapse in inhibitory neurotransmission. The expression of Gabbr2 was significantly reduced in the hippocampus of abl2-/- compared to WT mice, and intraperitoneal treatment of GABA receptor agonist Gaboxadol normalized anxiety/depression-related behaviors of abl2-/- mice. These findings underscore the potential role of Abl2/Arg in influencing anxiety and depressive-like behaviors, thereby contributing valuable insights into its broader physiological and pathological functions.
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Affiliation(s)
- Xiaojuan Yao
- Institute of Science and Technology for Brain-Inspired Intelligence, Behavioral and Cognitive Neuroscience Center, Fudan University, Shanghai 200433, China; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, Behavioral and Cognitive Neuroscience Center, Fudan University, Shanghai 200433, China
| | - Ruiying Chen
- Institute of Science and Technology for Brain-Inspired Intelligence, Behavioral and Cognitive Neuroscience Center, Fudan University, Shanghai 200433, China; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, Behavioral and Cognitive Neuroscience Center, Fudan University, Shanghai 200433, China
| | - Hongting Chen
- Institute of Science and Technology for Brain-Inspired Intelligence, Behavioral and Cognitive Neuroscience Center, Fudan University, Shanghai 200433, China; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, Behavioral and Cognitive Neuroscience Center, Fudan University, Shanghai 200433, China
| | - Anthony Koleske
- Departments of Molecular Biophysics and Biochemistry and Neuroscience, Yale University, New Haven, CT 06520, USA
| | - Xiao Xiao
- Institute of Science and Technology for Brain-Inspired Intelligence, Behavioral and Cognitive Neuroscience Center, Fudan University, Shanghai 200433, China; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, Behavioral and Cognitive Neuroscience Center, Fudan University, Shanghai 200433, China.
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2
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Rygiel KA, Elkins JM. Recent advances in the structural biology of tyrosine kinases. Curr Opin Struct Biol 2023; 82:102665. [PMID: 37562149 DOI: 10.1016/j.sbi.2023.102665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/08/2023] [Accepted: 07/10/2023] [Indexed: 08/12/2023]
Abstract
The past few years have seen exciting discoveries in the area of tyrosine kinase structural biology including the first high resolution models of full-length receptor tyrosine kinases and new mechanistic insights into the structural mechanisms of receptor tyrosine kinase activation. Despite being a mature area of research, the application of new technologies continues to advance our understanding. In this article we highlight a selection of recent studies that illustrate the current areas of research interest, focussing in particular on the exciting progress made possible by cryo-electron-microscopy. These new discoveries may herald a wave of new design ideas for therapeutics acting through novel mechanisms.
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Affiliation(s)
- Karolina A Rygiel
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Jonathan M Elkins
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, UK.
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3
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Shi K, Zhang J, Zhou E, Wang J, Wang Y. Small-Molecule Receptor-Interacting Protein 1 (RIP1) Inhibitors as Therapeutic Agents for Multifaceted Diseases: Current Medicinal Chemistry Insights and Emerging Opportunities. J Med Chem 2022; 65:14971-14999. [DOI: 10.1021/acs.jmedchem.2c01518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kunyu Shi
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Jifa Zhang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
- Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
- Tianfu Jincheng Laboratory, Chengdu, 610041 Sichuan, China
| | - Enda Zhou
- West China School of Pharmacy, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Yuxi Wang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
- Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
- Tianfu Jincheng Laboratory, Chengdu, 610041 Sichuan, China
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Preparation of Novel Pyrazolo[4,3- e]tetrazolo[1,5- b][1,2,4]triazine Sulfonamides and Their Experimental and Computational Biological Studies. Int J Mol Sci 2022; 23:ijms23115892. [PMID: 35682571 PMCID: PMC9180621 DOI: 10.3390/ijms23115892] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 02/04/2023] Open
Abstract
Pyrazolo[4,3-e]tetrazolo[1,5-b][1,2,4]triazine sulfonamides constitute a novel class of heterocyclic compounds with broad biological activity, including anticancer properties. Investigated in this study, MM-compounds (MM134, MM136, MM137, and MM139) exhibited cytotoxic and proapoptotic activity against cancer cell lines (BxPC-3, PC-3, and HCT-116) in nanomolar concentrations without causing cytotoxicity in normal cells (L929 and WI38). In silico predictions indicate that tested compounds exhibit favorable pharmacokinetic profiles and may exert anticancer activity through the inhibition of BTK kinase, the AKT-mTOR pathway and PD1-PD-L1 interaction. Our findings point out that these sulfonamide derivatives may constitute a source of new anticancer drugs after optimization.
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5
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Transport and metabolism of tyrosine kinase inhibitors associated with chronic myeloid leukemia therapy: a review. Mol Cell Biochem 2022; 477:1261-1279. [DOI: 10.1007/s11010-022-04376-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 01/27/2022] [Indexed: 12/14/2022]
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Xie T, Saleh T, Rossi P, Miller D, Kalodimos CG. Imatinib can act as an Allosteric Activator of Abl Kinase. J Mol Biol 2022; 434:167349. [PMID: 34774565 PMCID: PMC8752476 DOI: 10.1016/j.jmb.2021.167349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/15/2021] [Accepted: 11/05/2021] [Indexed: 02/01/2023]
Abstract
Imatinib is an ATP-competitive inhibitor of Bcr-Abl kinase and the first drug approved for chronic myelogenous leukemia (CML) treatment. Here we show that imatinib binds to a secondary, allosteric site located in the myristoyl pocket of Abl to function as an activator of the kinase activity. Abl transitions between an assembled, inhibited state and an extended, activated state. The equilibrium is regulated by the conformation of the αΙ helix, which is located nearby the allosteric pocket. Imatinib binding to the allosteric pocket elicits an αΙ helix conformation that is not compatible with the assembled state, thereby promoting the extended state and stimulating the kinase activity. Although in wild-type Abl the catalytic pocket has a much higher affinity for imatinib than the allosteric pocket does, the two binding affinities are comparable in Abl variants carrying imatinib-resistant mutations in the catalytic site. A previously isolated imatinib-resistant mutation in patients appears to be mediating its function by increasing the affinity of imatinib for the allosteric pocket, providing a hitherto unknown mechanism of drug resistance. Our results highlight the benefit of combining imatinib with allosteric inhibitors to maximize their inhibitory effect on Bcr-Abl.
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Affiliation(s)
- Tao Xie
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States
| | - Tamjeed Saleh
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States
| | - Paolo Rossi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States
| | - Darcie Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States
| | - Charalampos G Kalodimos
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States.
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Second-Generation Jak2 Inhibitors for Advanced Prostate Cancer: Are We Ready for Clinical Development? Cancers (Basel) 2021; 13:cancers13205204. [PMID: 34680353 PMCID: PMC8533841 DOI: 10.3390/cancers13205204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/05/2021] [Accepted: 10/11/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary Prostate Cancer (PC) is currently estimated to affect 1 in 9 men and is the second leading cause of cancer in men in the US. While androgen deprivation therapy, which targets the androgen receptor, is one of the front-line therapies for advanced PC and for recurrence of organ-confined PC treated with surgery, lethal castrate-resistant PC develops consistently in patients. PC is a multi-focal cancer with different grade carcinoma areas presenting simultaneously. Jak2-Stat5 signaling pathway has emerged as a potentially highly effective molecular target in PCs with positive areas for activated Stat5 protein. Activated Jak2-Stat5 signaling can be readily targeted by the second-generation Jak2-inhibitors that have been developed for myeloproliferative and autoimmune disorders and hematological malignancies. In this review, we analyze and summarize the Jak2 inhibitors that are currently in preclinical and clinical development. Abstract Androgen deprivation therapy (ADT) for metastatic and high-risk prostate cancer (PC) inhibits growth pathways driven by the androgen receptor (AR). Over time, ADT leads to the emergence of lethal castrate-resistant PC (CRPC), which is consistently caused by an acquired ability of tumors to re-activate AR. This has led to the development of second-generation anti-androgens that more effectively antagonize AR, such as enzalutamide (ENZ). However, the resistance of CRPC to ENZ develops rapidly. Studies utilizing preclinical models of PC have established that inhibition of the Jak2-Stat5 signaling leads to extensive PC cell apoptosis and decreased tumor growth. In large clinical cohorts, Jak2-Stat5 activity predicts PC progression and recurrence. Recently, Jak2-Stat5 signaling was demonstrated to induce ENZ-resistant PC growth in preclinical PC models, further emphasizing the importance of Jak2-Stat5 for therapeutic targeting for advanced PC. The discovery of the Jak2V617F somatic mutation in myeloproliferative disorders triggered the rapid development of Jak1/2-specific inhibitors for a variety of myeloproliferative and auto-immune disorders as well as hematological malignancies. Here, we review Jak2 inhibitors targeting the mutated Jak2V617F vs. wild type (WT)-Jak2 that are currently in the development pipeline. Among these 35 compounds with documented Jak2 inhibitory activity, those with potency against WT-Jak2 hold strong potential for advanced PC therapy.
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Kumar V, Kumar R, Parate S, Yoon S, Lee G, Kim D, Lee KW. Identification of ACK1 inhibitors as anticancer agents by using computer-aided drug designing. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130200] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Alam KA, Gani OASBM, Engh RA. Inhibitor binding to mutants of protein kinase A with
GGGxxG
and
GxGxxA
glycine‐rich loop motifs. J Mol Recognit 2020; 34:e2882. [DOI: 10.1002/jmr.2882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/28/2020] [Accepted: 10/20/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Kazi A. Alam
- The Norwegian Structural Biology Centre, Department of Chemistry UiT the Arctic University of Norway Tromsø Norway
| | - Osman A. S. B. M. Gani
- The Norwegian Structural Biology Centre, Department of Chemistry UiT the Arctic University of Norway Tromsø Norway
| | - Richard A. Engh
- The Norwegian Structural Biology Centre, Department of Chemistry UiT the Arctic University of Norway Tromsø Norway
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Manley PW, Barys L, Cowan-Jacob SW. The specificity of asciminib, a potential treatment for chronic myeloid leukemia, as a myristate-pocket binding ABL inhibitor and analysis of its interactions with mutant forms of BCR-ABL1 kinase. Leuk Res 2020; 98:106458. [DOI: 10.1016/j.leukres.2020.106458] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 12/26/2022]
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11
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Schröder M, Tan L, Wang J, Liang Y, Gray NS, Knapp S, Chaikuad A. Catalytic Domain Plasticity of MKK7 Reveals Structural Mechanisms of Allosteric Activation and Diverse Targeting Opportunities. Cell Chem Biol 2020; 27:1285-1295.e4. [DOI: 10.1016/j.chembiol.2020.07.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/08/2020] [Accepted: 07/21/2020] [Indexed: 01/19/2023]
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12
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Klümper T, Bruckmueller H, Diewock T, Kaehler M, Haenisch S, Pott C, Bruhn O, Cascorbi I. Expression differences of miR-142-5p between treatment-naïve chronic myeloid leukemia patients responding and non-responding to imatinib therapy suggest a link to oncogenic ABL2, SRI, cKIT and MCL1 signaling pathways critical for development of therapy resistance. Exp Hematol Oncol 2020; 9:26. [PMID: 32999756 PMCID: PMC7519530 DOI: 10.1186/s40164-020-00183-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/21/2020] [Indexed: 12/22/2022] Open
Abstract
Background Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm characterized by constitutive activity of the tyrosine kinase BCR-ABL1. Although the introduction of tyrosine kinase inhibitors (TKIs) has substantially improved patients’ prognosis, drug resistance remains one of the major challenges in CML therapy. MicroRNAs (miRNAs), a class of short non-coding RNAs acting as post-transcriptional regulators, are implicated in CML progression and drug resistance. The aim of the present study was to analyze the miRNA expression profiles of 45 treatment-naïve CML patients in chronic phase (28 peripheral blood and 17 bone marrow samples) with respect to future response to imatinib therapy. Methods TaqMan low density arrays were used to analyze the miRNA expression pattern of the patient samples. For selected microRNAs, reporter gene assays were performed to study their ability to regulate CML associated target genes. Results Significant lower expression levels of miR-142-5p were identified in both, peripheral blood and bone marrow samples of future non-responders suggesting a potential tumor suppressor role of this miRNA. This was supported by reporter gene assays that identified the survival, proliferation and invasion promoting CML related genes ABL2, cKIT, MCL1 and SRI as targets of miR-142-5p and miR-365a-3p, the latter identified as potential biomarker in peripheral blood samples. Conclusion MiR-142-5p and to a certain extend also miR-365a-3p were able to discriminate treatment-naïve CML patients not responding to imatinib in the course of their treatment from patients, who responded to therapy. However, further large-scale studies should clarify if the identified miRNAs have the potential as predictive biomarkers for TKI resistance.
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Affiliation(s)
- Theresa Klümper
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Henrike Bruckmueller
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Tobias Diewock
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Meike Kaehler
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Sierk Haenisch
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Christiane Pott
- Department of Medicine II, Haematology and Oncology, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Oliver Bruhn
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Ingolf Cascorbi
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
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Li Q. Application of Fragment-Based Drug Discovery to Versatile Targets. Front Mol Biosci 2020; 7:180. [PMID: 32850968 PMCID: PMC7419598 DOI: 10.3389/fmolb.2020.00180] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/10/2020] [Indexed: 12/14/2022] Open
Abstract
Fragment-based drug discovery (FBDD) is a powerful method to develop potent small-molecule compounds starting from fragments binding weakly to targets. As FBDD exhibits several advantages over high-throughput screening campaigns, it becomes an attractive strategy in target-based drug discovery. Many potent compounds/inhibitors of diverse targets have been developed using this approach. Methods used in fragment screening and understanding fragment-binding modes are critical in FBDD. This review elucidates fragment libraries, methods utilized in fragment identification/confirmation, strategies applied in growing the identified fragments into drug-like lead compounds, and applications of FBDD to different targets. As FBDD can be readily carried out through different biophysical and computer-based methods, it will play more important roles in drug discovery.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Guangdong Provincial Bioengineering Institute, Guangzhou Sugarcane Industry Research Institute, Guangdong Academy of Sciences, Guangzhou, China
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14
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Inhibitors Targeting RIPK1/RIPK3: Old and New Drugs. Trends Pharmacol Sci 2020; 41:209-224. [PMID: 32035657 DOI: 10.1016/j.tips.2020.01.002] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/13/2019] [Accepted: 01/02/2020] [Indexed: 12/26/2022]
Abstract
The scaffolding function of receptor-interacting protein kinase 1 (RIPK1) regulates prosurvival signaling and inflammatory gene expression, while its kinase activity mediates both apoptosis and necroptosis; the latter involving RIPK3 kinase activity. The mutual transition between the scaffold and kinase functions of RIPK1 is regulated by (de)ubiquitylation and (de)phosphorylation. RIPK1-mediated cell death leads to disruption of epithelial barriers and/or release of damage-associated molecular patterns (DAMPs), cytokines, and chemokines, propagating inflammatory and degenerative diseases. Many drug development programs have pursued targeting RIPK1, and to a lesser extent RIPK3 kinase activity. In this review, we classify existing and novel small-molecule drugs based on their pharmacodynamic (PD) type I, II, and III binding mode. Finally, we discuss their applicability and therapeutic potential in inflammatory and degenerative experimental disease models.
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15
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Mayfield JE, Irani S, Escobar EE, Zhang Z, Burkholder NT, Robinson MR, Mehaffey MR, Sipe SN, Yang W, Prescott NA, Kathuria KR, Liu Z, Brodbelt JS, Zhang Y. Tyr1 phosphorylation promotes phosphorylation of Ser2 on the C-terminal domain of eukaryotic RNA polymerase II by P-TEFb. eLife 2019; 8:48725. [PMID: 31385803 PMCID: PMC6715403 DOI: 10.7554/elife.48725] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 08/05/2019] [Indexed: 12/18/2022] Open
Abstract
The Positive Transcription Elongation Factor b (P-TEFb) phosphorylates Ser2 residues of the C-terminal domain (CTD) of the largest subunit (RPB1) of RNA polymerase II and is essential for the transition from transcription initiation to elongation in vivo. Surprisingly, P-TEFb exhibits Ser5 phosphorylation activity in vitro. The mechanism garnering Ser2 specificity to P-TEFb remains elusive and hinders understanding of the transition from transcription initiation to elongation. Through in vitro reconstruction of CTD phosphorylation, mass spectrometry analysis, and chromatin immunoprecipitation sequencing (ChIP-seq) analysis, we uncover a mechanism by which Tyr1 phosphorylation directs the kinase activity of P-TEFb and alters its specificity from Ser5 to Ser2. The loss of Tyr1 phosphorylation causes an accumulation of RNA polymerase II in the promoter region as detected by ChIP-seq. We demonstrate the ability of Tyr1 phosphorylation to generate a heterogeneous CTD modification landscape that expands the CTD’s coding potential. These findings provide direct experimental evidence for a combinatorial CTD phosphorylation code wherein previously installed modifications direct the identity and abundance of subsequent coding events by influencing the behavior of downstream enzymes. DNA contains the instructions for making proteins, which build and maintain our cells. So that the information encoded in DNA can be used, a molecular machine called RNA polymerase II makes copies of specific genes. These copies, in the form of a molecule called RNA, convey the instructions for making proteins to the rest of the cell. To ensure that RNA polymerase II copies the correct genes at the correct time, a group of regulatory proteins are needed to control its activity. Many of these proteins interact with RNA polymerase II at a region known as the C-terminal domain, or CTD for short. For example, before RNA polymerase can make a full copy of a gene, a small molecule called a phosphate group must first be added to CTD at specific units known as Ser2. The regulatory protein P-TEFb was thought to be responsible for phosphorylating Ser2. However, it was previously not known how P-TEFb added this phosphate group, and why it did not also add phosphate groups to other positions in the CTD domain that are structurally similar to Ser2. To investigate this, Mayfield, Irani et al. mixed the CTD domain with different regulatory proteins, and used various biochemical approaches to examine which specific positions of the domain had phosphate groups attached. These experiments revealed a previously unknown aspect of P-TEFb activity: its specificity for Ser2 increased dramatically if a different regulatory protein first added a phosphate group to a nearby location in CTD. This additional phosphate group directed P-TEFb to then add its phosphate specifically at Ser2. To confirm the activity of this mechanism in living human cells, Mayfield, Irani et al. used a drug that prevented the first phosphate from being added. In the drug treated cells, RNA polymerase II was found more frequently ‘stalled’ at positions on the DNA just before a gene starts. This suggests that living cells needs this two-phosphate code system in order for RNA polymerase II to progress and make copies of specific genes. These results are a step forward in understanding the complex control mechanisms cells use to make proteins from their DNA. Moreover, the model presented here – one phosphate addition priming a second specific phosphate addition – provides a template that may underlie similar regulatory processes.
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Affiliation(s)
- Joshua E Mayfield
- Department of Molecular Biosciences, University of Texas at Austin, Austin, United States
| | - Seema Irani
- Department of Chemical Engineering, University of Texas at Austin, Austin, United States
| | - Edwin E Escobar
- Department of Chemistry, University of Texas at Austin, Austin, United States
| | - Zhao Zhang
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, United States
| | - Nathaniel T Burkholder
- Department of Molecular Biosciences, University of Texas at Austin, Austin, United States
| | - Michelle R Robinson
- Department of Chemistry, University of Texas at Austin, Austin, United States
| | - M Rachel Mehaffey
- Department of Chemistry, University of Texas at Austin, Austin, United States
| | - Sarah N Sipe
- Department of Chemistry, University of Texas at Austin, Austin, United States
| | - Wanjie Yang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, United States
| | - Nicholas A Prescott
- Department of Molecular Biosciences, University of Texas at Austin, Austin, United States
| | - Karan R Kathuria
- Department of Molecular Biosciences, University of Texas at Austin, Austin, United States
| | - Zhijie Liu
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, United States
| | - Yan Zhang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, United States.,Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, United States
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Efficacy of Tyrosine Kinase Inhibitor Therapy in a Chemotherapy-refractory B-cell Precursor Acute Lymphoblastic Leukemia With ZC3HAV1-ABL2 Fusion. Hemasphere 2019; 3:e193. [PMID: 31723830 PMCID: PMC6746024 DOI: 10.1097/hs9.0000000000000193] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 11/26/2022] Open
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17
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Hanson SM, Georghiou G, Thakur MK, Miller WT, Rest JS, Chodera JD, Seeliger MA. What Makes a Kinase Promiscuous for Inhibitors? Cell Chem Biol 2019; 26:390-399.e5. [PMID: 30612951 DOI: 10.1016/j.chembiol.2018.11.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 09/13/2018] [Accepted: 11/06/2018] [Indexed: 10/27/2022]
Abstract
ATP-competitive kinase inhibitors often bind several kinases due to the high conservation of the ATP binding pocket. Through clustering analysis of a large kinome profiling dataset, we found a cluster of eight promiscuous kinases that on average bind more than five times more kinase inhibitors than the other 398 kinases in the dataset. To understand the structural basis of promiscuous inhibitor binding, we determined the co-crystal structure of the receptor tyrosine kinase DDR1 with the type I inhibitors dasatinib and VX-680. Surprisingly, we find that DDR1 binds these type I inhibitors in an inactive conformation typically reserved for type II inhibitors. Our computational and biochemical studies show that DDR1 is unusually stable in this inactive conformation, giving a mechanistic explanation for inhibitor promiscuity. This phenotypic clustering analysis provides a strategy to obtain functional insights not available by sequence comparison alone.
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Affiliation(s)
- Sonya M Hanson
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA; Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065-1115, USA
| | - George Georghiou
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA
| | - Manish K Thakur
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA
| | - W Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY 11794-8651, USA
| | - Joshua S Rest
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
| | - John D Chodera
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065-1115, USA.
| | - Markus A Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA.
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18
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Trosset JY, Cavé C. In Silico Target Druggability Assessment: From Structural to Systemic Approaches. Methods Mol Biol 2019; 1953:63-88. [PMID: 30912016 DOI: 10.1007/978-1-4939-9145-7_5] [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] [Indexed: 01/10/2023]
Abstract
This chapter will focus on today's in silico direct and indirect approaches to assess therapeutic target druggability. The direct approach tries to infer from the 3D structure the capacity of the target protein to bind small molecule in order to modulate its biological function. Algorithms to recognize and characterize the quality of the ligand interaction sites whether within buried protein cavities or within large protein-protein interface will be reviewed in the first part of the paper. In the case a ligand-binding site is already identified, indirect aspects of target druggability can be assessed. These indirect approaches focus first on target promiscuity and the potential difficulties in developing specific drugs. It is based on large-scale comparison of protein-binding sites. The second aspect concerns the capacity of the target to induce resistant pathway once it is inhibited or activated by a drug. The emergence of drug-resistant pathways can be assessed through systemic analysis of biological networks implementing metabolism and/or cell regulation signaling.
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Affiliation(s)
| | - Christian Cavé
- BioCIS UFR Pharmacie UMR CNRS 8076, Université Paris Saclay, Orsay, France
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19
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Cho H, Shin I, Ju E, Choi S, Hur W, Kim H, Hong E, Kim ND, Choi HG, Gray NS, Sim T. First SAR Study for Overriding NRAS Mutant Driven Acute Myeloid Leukemia. J Med Chem 2018; 61:8353-8373. [PMID: 30153003 DOI: 10.1021/acs.jmedchem.8b00882] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
GNF-7, a multitargeted kinase inhibitor, served as a dual kinase inhibitor of ACK1 and GCK, which provided a novel therapeutic strategy for overriding AML expressing NRAS mutation. This SAR study with GNF-7 derivatives, designed to target NRAS mutant-driven AML, led to identification of the extremely potent inhibitors, 10d, 10g, and 11i, which possess single-digit nanomolar inhibitory activity against both ACK1 and GCK. These substances strongly suppress proliferation of mutant NRAS expressing AML cells via apoptosis and AKT/mTOR signaling blockade. Compound 11i is superior to GNF-7 in terms of kinase inhibitory activity, cellular activity, and differential cytotoxicity. Moreover, 10k possessing a favorable mouse pharmacokinetic profile prolonged life-span of Ba/F3-NRAS-G12D injected mice and significantly delayed tumor growth of OCI-AML3 xenograft model without causing the prominent level of toxicity found with GNF-7. Taken together, this study provides insight into the design of novel ACK1 and GCK dual inhibitors for overriding NRAS mutant-driven AML.
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Affiliation(s)
- Hanna Cho
- KU-KIST Graduate School of Converging Science and Technology , Korea University , 145 Anam-ro, Seongbuk-gu , Seoul 02841 , Republic of Korea
| | - Injae Shin
- KU-KIST Graduate School of Converging Science and Technology , Korea University , 145 Anam-ro, Seongbuk-gu , Seoul 02841 , Republic of Korea
| | - Eunhye Ju
- KU-KIST Graduate School of Converging Science and Technology , Korea University , 145 Anam-ro, Seongbuk-gu , Seoul 02841 , Republic of Korea
| | - Seunghye Choi
- KU-KIST Graduate School of Converging Science and Technology , Korea University , 145 Anam-ro, Seongbuk-gu , Seoul 02841 , Republic of Korea
| | - Wooyoung Hur
- Chemical Kinomics Research Center , Korea Institute of Science and Technology (KIST) , 5 Hwarangro 14-gil, Seongbuk-gu , Seoul 02792 , Republic of Korea
| | - Haelee Kim
- Daegu-Gyeongbuk Medical Innovation Foundation , 2387 dalgubeol-daero, Suseong-gu , Daegu 42019 , Republic of Korea
| | - Eunmi Hong
- Daegu-Gyeongbuk Medical Innovation Foundation , 2387 dalgubeol-daero, Suseong-gu , Daegu 42019 , Republic of Korea
| | - Nam Doo Kim
- Daegu-Gyeongbuk Medical Innovation Foundation , 2387 dalgubeol-daero, Suseong-gu , Daegu 42019 , Republic of Korea.,NDBio Therapeutics Inc. , 32 Songdogwahak-ro, Yeonsu-gu , Incheon 21984 , Republic of Korea
| | - Hwan Geun Choi
- Daegu-Gyeongbuk Medical Innovation Foundation , 2387 dalgubeol-daero, Suseong-gu , Daegu 42019 , Republic of Korea
| | - Nathanael S Gray
- Department of Cancer Biology , Dana-Farber Cancer Institute , Boston , Massachusetts 02215 , United States.,Department of Biological Chemistry & Molecular Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Taebo Sim
- KU-KIST Graduate School of Converging Science and Technology , Korea University , 145 Anam-ro, Seongbuk-gu , Seoul 02841 , Republic of Korea.,Chemical Kinomics Research Center , Korea Institute of Science and Technology (KIST) , 5 Hwarangro 14-gil, Seongbuk-gu , Seoul 02792 , Republic of Korea
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20
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Meirson T, Genna A, Lukic N, Makhnii T, Alter J, Sharma VP, Wang Y, Samson AO, Condeelis JS, Gil-Henn H. Targeting invadopodia-mediated breast cancer metastasis by using ABL kinase inhibitors. Oncotarget 2018; 9:22158-22183. [PMID: 29774130 PMCID: PMC5955141 DOI: 10.18632/oncotarget.25243] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 04/08/2018] [Indexed: 12/14/2022] Open
Abstract
Metastatic dissemination of cancer cells from the primary tumor and their spread to distant sites in the body is the leading cause of mortality in breast cancer patients. While researchers have identified treatments that shrink or slow metastatic tumors, no treatment that permanently eradicates metastasis exists at present. Here, we show that the ABL kinase inhibitors imatinib, nilotinib, and GNF-5 impede invadopodium precursor formation and cortactin-phosphorylation dependent invadopodium maturation, leading to decreased actin polymerization in invadopodia, reduced extracellular matrix degradation, and impaired matrix proteolysis-dependent invasion. Using a mouse xenograft model we demonstrate that, while primary tumor size is not affected by ABL kinase inhibitors, the in vivo matrix metalloproteinase (MMP) activity, tumor cell invasion, and consequent spontaneous metastasis to lungs are significantly impaired in inhibitor-treated mice. Further proteogenomic analysis of breast cancer patient databases revealed co-expression of the Abl-related gene (Arg) and cortactin across all hormone- and human epidermal growth factor receptor 2 (HER2)-receptor status tumors, which correlates synergistically with distant metastasis and poor patient prognosis. Our findings establish a prognostic value for Arg and cortactin as predictors of metastatic dissemination and suggest that therapeutic inhibition of ABL kinases may be used for blocking breast cancer metastasis.
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Affiliation(s)
- Tomer Meirson
- Laboratory of Cell Migration and Invasion, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel.,Drug Discovery Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
| | - Alessandro Genna
- Laboratory of Cell Migration and Invasion, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
| | - Nikola Lukic
- Laboratory of Cell Migration and Invasion, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
| | - Tetiana Makhnii
- Laboratory of Cell Migration and Invasion, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
| | - Joel Alter
- Laboratory of Cell Migration and Invasion, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
| | - Ved P Sharma
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Integrated Imaging Program, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Yarong Wang
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Integrated Imaging Program, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Abraham O Samson
- Drug Discovery Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
| | - John S Condeelis
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Integrated Imaging Program, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Hava Gil-Henn
- Laboratory of Cell Migration and Invasion, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
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21
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The Intersection of Structural and Chemical Biology - An Essential Synergy. Cell Chem Biol 2016; 23:173-182. [PMID: 26933743 DOI: 10.1016/j.chembiol.2015.12.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 12/04/2015] [Accepted: 12/04/2015] [Indexed: 12/22/2022]
Abstract
The continual improvement in our ability to generate high resolution structural models of biological molecules has stimulated and supported innovative chemical biology projects that target increasingly challenging ligand interaction sites. In this review we outline some of the recent developments in chemical biology and rational ligand design and show selected examples that illustrate the synergy between these research areas.
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22
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Abstract
The Abelson tyrosine kinases were initially identified as drivers of leukemia in mice and humans. The Abl family kinases Abl1 and Abl2 regulate diverse cellular processes during development and normal homeostasis, and their functions are subverted during inflammation, cancer and other pathologies. Abl kinases can be activated by multiple stimuli leading to cytoskeletal reorganization required for cell morphogenesis, motility, adhesion and polarity. Depending on the cellular context, Abl kinases regulate cell survival and proliferation. Emerging data support important roles for Abl kinases in pathologies linked to inflammation. Among these are neurodegenerative diseases and inflammatory pathologies. Unexpectedly, Abl kinases have also been identified as important players in mammalian host cells during microbial pathogenesis. Thus, the use of Abl kinase inhibitors might prove to be effective in the treatment of pathologies beyond leukemia and solid tumors. In this Cell Science at a Glance article and in the accompanying poster, we highlight the emerging roles of Abl kinases in the regulation of cellular processes in normal cells and diverse pathologies ranging from cancer to microbial pathogenesis.
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Affiliation(s)
- Aaditya Khatri
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jun Wang
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ann Marie Pendergast
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
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23
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Assessing protein kinase target similarity: Comparing sequence, structure, and cheminformatics approaches. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1605-16. [PMID: 26001898 DOI: 10.1016/j.bbapap.2015.05.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 05/08/2015] [Accepted: 05/11/2015] [Indexed: 11/22/2022]
Abstract
In just over two decades, structure based protein kinase inhibitor discovery has grown from trial and error approaches, using individual target structures, to structure and data driven approaches that may aim to optimize inhibition properties across several targets. This is increasingly enabled by the growing availability of potent compounds and kinome-wide binding data. Assessing the prospects for adapting known compounds to new therapeutic uses is thus a key priority for current drug discovery efforts. Tools that can successfully link the diverse information regarding target sequence, structure, and ligand binding properties now accompany a transformation of protein kinase inhibitor research, away from single, block-buster drug models, and toward "personalized medicine" with niche applications and highly specialized research groups. Major hurdles for the transformation to data driven drug discovery include mismatches in data types, and disparities of methods and molecules used; at the core remains the problem that ligand binding energies cannot be predicted precisely from individual structures. However, there is a growing body of experimental data for increasingly successful focussing of efforts: focussed chemical libraries, drug repurposing, polypharmacological design, to name a few. Protein kinase target similarity is easily quantified by sequence, and its relevance to ligand design includes broad classification by key binding sites, evaluation of resistance mutations, and the use of surrogate proteins. Although structural evaluation offers more information, the flexibility of protein kinases, and differences between the crystal and physiological environments may make the use of crystal structures misleading when structures are considered individually. Cheminformatics may enable the "calibration" of sequence and crystal structure information, with statistical methods able to identify key correlates to activity but also here, "the devil is in the details." Examples from specific repurposing and polypharmacology applications illustrate these points. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases.
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24
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Ha BH, Simpson MA, Koleske AJ, Boggon TJ. Structure of the ABL2/ARG kinase in complex with dasatinib. Acta Crystallogr F Struct Biol Commun 2015; 71:443-8. [PMID: 25849507 PMCID: PMC4388181 DOI: 10.1107/s2053230x15004793] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/09/2015] [Indexed: 12/26/2022] Open
Abstract
ABL2/ARG (ABL-related gene) belongs to the ABL (Abelson tyrosine-protein kinase) family of tyrosine kinases. ARG plays important roles in cell morphogenesis, motility, growth and survival, and many of these biological roles overlap with the cellular functions of the ABL kinase. Chronic myeloid leukemia (CML) is associated with constitutive ABL kinase activation resulting from fusion between parts of the breakpoint cluster region (BCR) and ABL1 genes. Similarly, fusion of the ETV6 (Tel) and ARG genes drives some forms of T-cell acute lymphoblastic leukemia (T-ALL) and acute myeloid leukemia (AML). Dasatinib is a tyrosine kinase inhibitor used for the treatment of CML by inhibiting ABL, and while it also inhibits ARG, there is currently no structure of ARG in complex with dasatinib. Here, the co-crystal structure of the mouse ARG catalytic domain with dasatinib at 2.5 Å resolution is reported. Dasatinib-bound ARG is found in the DFG-in conformation although it is nonphosphorylated on the activation-loop tyrosine. In this structure the glycine-rich P-loop is found in a relatively open conformation compared with other known ABL family-inhibitor complex structures.
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Affiliation(s)
- Byung Hak Ha
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Mark Adam Simpson
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Anthony J. Koleske
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Titus J. Boggon
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
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25
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Novel approaches for targeting kinases: allosteric inhibition, allosteric activation and pseudokinases. Future Med Chem 2014; 6:541-61. [PMID: 24649957 DOI: 10.4155/fmc.13.216] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Protein kinases are involved in many essential cellular processes and their deregulation can lead to a variety of diseases, including cancer. The pharmaceutical industry has invested heavily in the identification of kinase inhibitors to modulate these disease-promoting pathways, resulting in several successful drugs. However, the field is challenging as it is difficult to identify novel selective inhibitors with good pharmacokinetic/pharmacodynamic properties. In addition, resistance to kinase inhibitor treatment frequently arises. The identification of non-ATP site targeting ('allosteric') inhibitors, the identification of kinase activators and the expansion of kinase target space to include the less studied members of the family, including atypical- and pseudo-kinases, are potential avenues to overcome these challenges. In this perspective, the opportunities and challenges of following these approaches and others will be discussed.
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26
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Mura C, McAnany CE. An introduction to biomolecular simulations and docking. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.935372] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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27
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Hutterer C, Wandinger SK, Wagner S, Müller R, Stamminger T, Zeitträger I, Godl K, Baumgartner R, Strobl S, Marschall M. Profiling of the kinome of cytomegalovirus-infected cells reveals the functional importance of host kinases Aurora A, ABL and AMPK. Antiviral Res 2013; 99:139-48. [PMID: 23648710 DOI: 10.1016/j.antiviral.2013.04.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 04/19/2013] [Accepted: 04/24/2013] [Indexed: 12/20/2022]
Abstract
Human cytomegalovirus infection can lead to life-threatening clinical manifestations particularly in the immunocompromised host. Current therapy options face severe limitations leading to a continued search for alternative drug candidates. Viral replication is dependent on a balanced interaction between viral and cellular proteins. Especially protein kinases are important regulators of virus-host interaction indicated by remarkable kinome alterations induced upon HCMV infection. Here we report a novel approach of kinome profiling with an outcome that suggests an important role of specific cellular protein kinases, such as AMPK, ABL2 and Aurora A. Inhibition of AMPK and ABL kinases showed a significant reduction, whereas inhibition of Aurora A kinase led to a slight activation of HCMV replication, as measured in a GFP reporter-based replication assay. Furthermore, analysis of the mode of antiviral action suggested a substantial benefit for the efficiency of viral replication at the immediate early (AMPK) or early-late (ABL) phases of HCMV gene expression. In contrast, inhibition of Aurora A kinase promoted an enhancement of viral early-late gene expression, suggesting a putative role of Aurora A signaling in host defense. Thus, the combined data provide new information on host cell kinases involved in viral replication and uncovered potential targets for future antiviral strategies.
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Affiliation(s)
- Corina Hutterer
- Institute for Clinical and Molecular Virology, University of Erlangen-Nuremberg, Erlangen, Germany.
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28
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Lemeer S, Zörgiebel C, Ruprecht B, Kohl K, Kuster B. Comparing immobilized kinase inhibitors and covalent ATP probes for proteomic profiling of kinase expression and drug selectivity. J Proteome Res 2013; 12:1723-31. [PMID: 23495751 DOI: 10.1021/pr301073j] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Kinases are involved in the regulation of many cellular processes and aberrant kinase signaling has been implicated in human disease. As a consequence, kinases are attractive drug targets. Assessing kinase function and drug selectivity in a more physiological context is challenging and often hampered by the generally low expression level of kinases and the extensive post-translation modification in vivo. Kinase drug selectivity screens by chemical proteomics have gained attention because they allow the profiling of hundreds of kinases against one drug at the same time. Here, we directly compared two such methods, notably, immobilized broad spectrum kinase inhibitors (kinobeads) and active site labeling using desthiobiotin-ATP and -ADP probes. Affinity purification of ∼ 100 kinases by either kinobeads or ATP/ADP probes was readily achieved using 1 mg of cellular protein. Bioinformatic analysis revealed a high degree of complementarity of the two techniques. Kinobeads covered the Tyrosine Kinase family particularly well and ATP probes enriched higher numbers of STE family kinases. A consecutive combination of both enrichment strategies therefore allowed for the coverage of a larger part of the kinome than any one technique alone. While kinobeads are very selective for kinases, the ATP/ADP probes also enriched a large number of other nucleotide binding proteins. Both methods were applied to the selectivity profiling of the small molecular Aurora kinase inhibitor tozasertib in K562 cells. Our data confirmed Aurora A, B, and BCR-ABL as the main targets of tozasertib and identified TNK1, STK2, RPS6KA1, and RPS6KA3 as submicromolar off targets.
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Affiliation(s)
- Simone Lemeer
- Chair of Proteomics and Bioanalytics, Technische Universität München , Emil Erlenmeyer Forum 5, 85354 Freising, Germany
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29
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Abstract
The focus of this chapter is on the important concepts behind the in silico techniques that are used today to assess target druggability. The first step of the assessment consists of finding cavity space in the protein using 2D and/or 3D topological concepts. These concepts underlie the geometry and energy-based pocketfinder algorithms. Analysis pursues on the physico-chemical complementarity between the binding site and the drug like molecule. Geometrical and molecular flexibility aspect are also included in this assessment. The presence of hot interaction spots are shown to be particularly important for targeting protein-protein interactions. Finally, binding site promiscuity can be assessed by large scale structural comparison with other targets. Common chemical features amongst protein cavities can predict potential cross-reactivity with unwanted targets.
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30
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Divergent allosteric control of the IRE1α endoribonuclease using kinase inhibitors. Nat Chem Biol 2012; 8:982-9. [PMID: 23086298 PMCID: PMC3508346 DOI: 10.1038/nchembio.1094] [Citation(s) in RCA: 153] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 09/10/2012] [Indexed: 11/08/2022]
Abstract
Under endoplasmic reticulum stress, unfolded protein accumulation leads to activation of the endoplasmic reticulum transmembrane kinase/endoRNase (RNase) IRE1α. IRE1α oligomerizes, autophosphorylates and initiates splicing of XBP1 mRNA, thus triggering the unfolded protein response (UPR). Here we show that IRE1α's kinase-controlled RNase can be regulated in two distinct modes with kinase inhibitors: one class of ligands occupies IRE1α's kinase ATP-binding site to activate RNase-mediated XBP1 mRNA splicing even without upstream endoplasmic reticulum stress, whereas a second class can inhibit the RNase through the same ATP-binding site, even under endoplasmic reticulum stress. Thus, alternative kinase conformations stabilized by distinct classes of ATP-competitive inhibitors can cause allosteric switching of IRE1α's RNase--either on or off. As dysregulation of the UPR has been implicated in a variety of cell degenerative and neoplastic disorders, small-molecule control over IRE1α should advance efforts to understand the UPR's role in pathophysiology and to develop drugs for endoplasmic reticulum stress-related diseases.
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31
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Elkins JM, Santaguida S, Musacchio A, Knapp S. Crystal structure of human aurora B in complex with INCENP and VX-680. J Med Chem 2012; 55:7841-8. [PMID: 22920039 PMCID: PMC3621106 DOI: 10.1021/jm3008954] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
![]()
We present the structure of the human Aurora B kinase
domain in
complex with the C-terminal Aurora-binding region of human INCENP
and the Aurora kinase inhibitor VX-680. The structure unexpectedly
reveals a dimeric arrangement of the Aurora B:INCENP complex, which
was confirmed to exist in solution by analytical ultracentrifugation.
The dimerization involves a domain swap of the activation loop, resulting
in a different conformation of the DFG motif as compared to that seen
in other kinase complexes with VX-680. The binding of INCENP differs
significantly from that seen in the Xenopus laevis Aurora B:INCENP complex currently used as a model for structure-based
design for this important oncology target.
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Affiliation(s)
- Jonathan M Elkins
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom.
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