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Sun Y, Hao M, Wu H, Zhang C, Wei D, Li S, Song Z, Tao Y. Unveiling the role of CaMKII in retinal degeneration: from biological mechanism to therapeutic strategies. Cell Biosci 2024; 14:59. [PMID: 38725013 PMCID: PMC11084033 DOI: 10.1186/s13578-024-01236-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 04/18/2024] [Indexed: 05/12/2024] Open
Abstract
Ca2+/calmodulin-dependent protein kinase II (CaMKII) is a family of broad substrate specificity serine (Ser)/threonine (Thr) protein kinases that play a crucial role in the Ca2+-dependent signaling pathways. Its significance as an intracellular Ca2+ sensor has garnered abundant research interest in the domain of neurodegeneration. Accumulating evidences suggest that CaMKII is implicated in the pathology of degenerative retinopathies such as diabetic retinopathy (DR), age-related macular degeneration (AMD), retinitis pigmentosa (RP) and glaucoma optic neuropathy. CaMKII can induce the aberrant proliferation of retinal blood vessels, influence the synaptic signaling, and exert dual effects on the survival of retinal ganglion cells and pigment epithelial cells. Researchers have put forth multiple therapeutic agents, encompassing small molecules, peptides, and nucleotides that possess the capability to modulate CaMKII activity. Due to its broad range isoforms and splice variants therapeutic strategies seek to inhibit specifically the CaMKII are confronted with considerable challenges. Therefore, it becomes crucial to discern the detrimental and advantageous aspects of CaMKII, thereby facilitating the development of efficacious treatment. In this review, we summarize recent research findings on the cellular and molecular biology of CaMKII, with special emphasis on its metabolic and regulatory mechanisms. We delve into the involvement of CaMKII in the retinal signal transduction pathways and discuss the correlation between CaMKII and calcium overload. Furthermore, we elaborate the therapeutic trials targeting CaMKII, and introduce recent developments in the zone of CaMKII inhibitors. These findings would enrich our knowledge of CaMKII, and shed light on the development of a therapeutic target for degenerative retinopathy.
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Affiliation(s)
- Yuxin Sun
- Department of Ophthalmology, Henan Eye Hospital, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, 450003, China
- College of Medicine, Zhengzhou University, Zhengzhou, 450001, China
| | - Mengyu Hao
- Department of Ophthalmology, Henan Eye Hospital, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, 450003, China
- College of Medicine, Zhengzhou University, Zhengzhou, 450001, China
| | - Hao Wu
- Department of Ophthalmology, Henan Eye Hospital, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, 450003, China
- College of Medicine, Zhengzhou University, Zhengzhou, 450001, China
| | - Chengzhi Zhang
- Department of Ophthalmology, Henan Eye Hospital, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, 450003, China
- College of Medicine, Zhengzhou University, Zhengzhou, 450001, China
| | - Dong Wei
- Department of Ophthalmology, Henan Eye Hospital, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, 450003, China
- College of Medicine, Zhengzhou University, Zhengzhou, 450001, China
| | - Siyu Li
- Department of Ophthalmology, Henan Eye Hospital, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, 450003, China
- College of Medicine, Zhengzhou University, Zhengzhou, 450001, China
| | - Zongming Song
- Department of Ophthalmology, Henan Eye Hospital, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, 450003, China.
| | - Ye Tao
- Department of Ophthalmology, Henan Eye Hospital, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, 450003, China.
- College of Medicine, Zhengzhou University, Zhengzhou, 450001, China.
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2
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Soragni C, Queiroz K, Ng CP, Stok A, Olivier T, Tzagkaraki D, Heijmans J, Suijker J, de Ruiter SPM, Olczyk A, Bokkers M, Schavemaker F, Trietsch SJ, Lanz HL, Vulto P, Joore J. Phenotypic screening in Organ-on-a-Chip systems: a 1537 kinase inhibitor library screen on a 3D angiogenesis assay. Angiogenesis 2024; 27:37-49. [PMID: 37493987 PMCID: PMC10881651 DOI: 10.1007/s10456-023-09888-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/13/2023] [Indexed: 07/27/2023]
Abstract
Modern drug development increasingly requires comprehensive models that can be utilized in the earliest stages of compound and target discovery. Here we report a phenotypic screening exercise in a high-throughput Organ-on-a-Chip setup. We assessed the inhibitory effect of 1537 protein kinase inhibitors in an angiogenesis assay. Over 4000 micro-vessels were grown under perfusion flow in microfluidic chips, exposed to a cocktail of pro-angiogenic factors and subsequently exposed to the respective kinase inhibitors. Efficacy of compounds was evaluated by reduced angiogenic sprouting, whereas reduced integrity of the main micro-vessel was taken as a measure for toxicity. The screen yielded 53 hits with high anti-angiogenicity and low toxicity, of which 44 were previously unassociated with angiogenic pathways. This study demonstrates that Organ-on-a-Chip models can be screened in high numbers to identify novel compounds and targets. This will ultimately reduce bias in early-stage drug development and increases probability to identify first in class compounds and targets for today's intractable diseases.
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Affiliation(s)
- Camilla Soragni
- MIMETAS BV, De Limes 7, 2342 DH, Oegstgeest, The Netherlands
- Department of Cardiology, Maastricht University, Maastricht, The Netherlands
| | - Karla Queiroz
- MIMETAS BV, De Limes 7, 2342 DH, Oegstgeest, The Netherlands
| | - Chee Ping Ng
- MIMETAS BV, De Limes 7, 2342 DH, Oegstgeest, The Netherlands
| | - Arthur Stok
- MIMETAS BV, De Limes 7, 2342 DH, Oegstgeest, The Netherlands
| | - Thomas Olivier
- MIMETAS BV, De Limes 7, 2342 DH, Oegstgeest, The Netherlands
| | - Dora Tzagkaraki
- MIMETAS BV, De Limes 7, 2342 DH, Oegstgeest, The Netherlands
| | - Jeroen Heijmans
- MIMETAS BV, De Limes 7, 2342 DH, Oegstgeest, The Netherlands
| | - Johnny Suijker
- MIMETAS BV, De Limes 7, 2342 DH, Oegstgeest, The Netherlands
| | | | | | - Marleen Bokkers
- MIMETAS BV, De Limes 7, 2342 DH, Oegstgeest, The Netherlands
| | | | | | | | - Paul Vulto
- MIMETAS BV, De Limes 7, 2342 DH, Oegstgeest, The Netherlands
| | - Jos Joore
- MIMETAS BV, De Limes 7, 2342 DH, Oegstgeest, The Netherlands.
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3
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Stephenson EH, Higgins JMG. Pharmacological approaches to understanding protein kinase signaling networks. Front Pharmacol 2023; 14:1310135. [PMID: 38164473 PMCID: PMC10757940 DOI: 10.3389/fphar.2023.1310135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024] Open
Abstract
Protein kinases play vital roles in controlling cell behavior, and an array of kinase inhibitors are used successfully for treatment of disease. Typical drug development pipelines involve biological studies to validate a protein kinase target, followed by the identification of small molecules that effectively inhibit this target in cells, animal models, and patients. However, it is clear that protein kinases operate within complex signaling networks. These networks increase the resilience of signaling pathways, which can render cells relatively insensitive to inhibition of a single kinase, and provide the potential for pathway rewiring, which can result in resistance to therapy. It is therefore vital to understand the properties of kinase signaling networks in health and disease so that we can design effective multi-targeted drugs or combinations of drugs. Here, we outline how pharmacological and chemo-genetic approaches can contribute to such knowledge, despite the known low selectivity of many kinase inhibitors. We discuss how detailed profiling of target engagement by kinase inhibitors can underpin these studies; how chemical probes can be used to uncover kinase-substrate relationships, and how these tools can be used to gain insight into the configuration and function of kinase signaling networks.
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Affiliation(s)
| | - Jonathan M. G. Higgins
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle uponTyne, United Kingdom
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4
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Gu S, Liu H, Liu L, Hou T, Kang Y. Artificial intelligence methods in kinase target profiling: Advances and challenges. Drug Discov Today 2023; 28:103796. [PMID: 37805065 DOI: 10.1016/j.drudis.2023.103796] [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: 07/12/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 10/09/2023]
Abstract
Kinases have a crucial role in regulating almost the full range of cellular processes, making them essential targets for therapeutic interventions against various diseases. Accurate kinase-profiling prediction is vital for addressing the selectivity/specificity challenges in kinase drug discovery, which is closely related to lead optimization, drug repurposing, and the understanding of potential drug side effects. In this review, we provide an overview of the latest advancements in machine learning (ML)-based and deep learning (DL)-based quantitative structure-activity relationship (QSAR) models for kinase profiling. We highlight current trends in this rapidly evolving field and discuss the existing challenges and future directions regarding experimental data set construction and model architecture design. Our aim is to offer practical insights and guidance for the development and utilization of these approaches.
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Affiliation(s)
- Shukai Gu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Huanxiang Liu
- Faculty of Applied Science, Macao Polytechnic University, Macao 999078
| | - Liwei Liu
- Advanced Computing and Storage Laboratory, Central Research Institute, 2012 Laboratories, Huawei Technologies Co. Ltd, Nanjing 210000, Jiangsu, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.
| | - Yu Kang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.
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5
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Zhang H, Guo Y, Yang Y, Wang Y, Zhang Y, Zhuang J, Zhang Y, Shen M, Zhao J, Zhang R, Qiu Y, Li S, Hu J, Li W, Wu J, Xu H, Fliesler SJ, Liao Y, Liu Z. MAP4Ks inhibition promotes retinal neuron regeneration from Müller glia in adult mice. NPJ Regen Med 2023; 8:36. [PMID: 37443319 DOI: 10.1038/s41536-023-00310-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Mammalian Müller glia (MG) possess limited regenerative capacities. However, the intrinsic capacity of mammalian MG to transdifferentiate to generate mature neurons without transgenic manipulations remains speculative. Here we show that MAP4K4, MAP4K6 and MAP4K7, which are conserved Misshapen subfamily of ste20 kinases homologs, repress YAP activity in mammalian MG and therefore restrict their ability to be reprogrammed. However, by treating with a small molecule inhibitor of MAP4K4/6/7, mouse MG regain their ability to proliferate and enter into a retinal progenitor cell (RPC)-like state after NMDA-induced retinal damage; such plasticity was lost in YAP knockout MG. Moreover, spontaneous trans-differentiation of MG into retinal neurons expressing both amacrine and retinal ganglion cell (RGC) markers occurs after inhibitor withdrawal. Taken together, these findings suggest that MAP4Ks block the reprogramming capacity of MG in a YAP-dependent manner in adult mammals, which provides a novel avenue for the pharmaceutical induction of retinal regeneration in vivo.
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Affiliation(s)
- Houjian Zhang
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
- Xiamen University Affiliated Xiamen Eye Center, School of Medicine, Xiamen University, Xiamen, China
- Department of Ophthalmology, the First Affiliated Hospital of University of South China, Hengyang, Hunan, 421001, China
| | - Yuli Guo
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
- Xiamen University Affiliated Xiamen Eye Center, School of Medicine, Xiamen University, Xiamen, China
- Department of Ophthalmology, the First Affiliated Hospital of University of South China, Hengyang, Hunan, 421001, China
| | - Yaqiong Yang
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
| | - Yuqian Wang
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
| | - Youwen Zhang
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
| | - Jingbin Zhuang
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
| | - Yuting Zhang
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
| | - Mei Shen
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
| | - Jiankai Zhao
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
| | - Rongrong Zhang
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
| | - Yan Qiu
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
| | - Shiying Li
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
| | - Jiaoyue Hu
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
| | - Wei Li
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
| | - Jianfeng Wu
- Laboratory animal research center, Xiamen University, Xiamen, Fujian, 361102, China
| | - Haiwei Xu
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, 400038, China
| | - Steven J Fliesler
- Departments of Ophthalmology and Biochemistry and Neuroscience Graduate School, Jacobs School of Medicine and Biomedical Sciences, SUNY- University at Buffalo, Buffalo, NY, USA
- Research Service, VA Western New York Healthcare System, Buffalo, NY, USA
| | - Yi Liao
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China.
| | - Zuguo Liu
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China.
- Xiamen University Affiliated Xiamen Eye Center, School of Medicine, Xiamen University, Xiamen, China.
- Department of Ophthalmology, the First Affiliated Hospital of University of South China, Hengyang, Hunan, 421001, China.
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6
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Bhoir S, De Benedetti A. Targeting Prostate Cancer, the 'Tousled Way'. Int J Mol Sci 2023; 24:11100. [PMID: 37446279 DOI: 10.3390/ijms241311100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/01/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Androgen deprivation therapy (ADT) has been the mainstay of prostate cancer (PCa) treatment, with success in developing more effective inhibitors of androgen synthesis and antiandrogens in clinical practice. However, hormone deprivation and AR ablation have caused an increase in ADT-insensitive PCas associated with a poor prognosis. Resistance to ADT arises through various mechanisms, and most castration-resistant PCas still rely on the androgen axis, while others become truly androgen receptor (AR)-independent. Our research identified the human tousled-like kinase 1 (TLK1) as a crucial early mediator of PCa cell adaptation to ADT, promoting androgen-independent growth, inhibiting apoptosis, and facilitating cell motility and metastasis. Although explicit, the growing role of TLK1 biology in PCa has remained underrepresented and elusive. In this review, we aim to highlight the diverse functions of TLK1 in PCa, shed light on the molecular mechanisms underlying the transition from androgen-sensitive (AS) to an androgen-insensitive (AI) disease mediated by TLK1, and explore potential strategies to counteract this process. Targeting TLK1 and its associated signaling could prevent PCa progression to the incurable metastatic castration-resistant PCa (mCRPC) stage and provide a promising approach to treating PCa.
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Affiliation(s)
- Siddhant Bhoir
- Department of Biochemistry and Molecular Biology, LSU Health Shreveport, Shreveport, LA 71103, USA
| | - Arrigo De Benedetti
- Department of Biochemistry and Molecular Biology, LSU Health Shreveport, Shreveport, LA 71103, USA
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7
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Reyes Gaido OE, Nkashama LJ, Schole KL, Wang Q, Umapathi P, Mesubi OO, Konstantinidis K, Luczak ED, Anderson ME. CaMKII as a Therapeutic Target in Cardiovascular Disease. Annu Rev Pharmacol Toxicol 2023; 63:249-272. [PMID: 35973713 PMCID: PMC11019858 DOI: 10.1146/annurev-pharmtox-051421-111814] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
CaMKII (the multifunctional Ca2+ and calmodulin-dependent protein kinase II) is a highly validated signal for promoting a variety of common diseases, particularly in the cardiovascular system. Despite substantial amounts of convincing preclinical data, CaMKII inhibitors have yet to emerge in clinical practice. Therapeutic inhibition is challenged by the diversity of CaMKII isoforms and splice variants and by physiological CaMKII activity that contributes to learning and memory. Thus, uncoupling the harmful and beneficial aspects of CaMKII will be paramount to developing effective therapies. In the last decade, several targeting strategies have emerged, including small molecules, peptides, and nucleotides, which hold promise in discriminating pathological from physiological CaMKII activity. Here we review the cellular and molecular biology of CaMKII, discuss its role in physiological and pathological signaling, and consider new findings and approaches for developing CaMKII therapeutics.
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Affiliation(s)
- Oscar E Reyes Gaido
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA;
| | | | - Kate L Schole
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA;
| | - Qinchuan Wang
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA;
| | - Priya Umapathi
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA;
| | - Olurotimi O Mesubi
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA;
| | - Klitos Konstantinidis
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA;
| | - Elizabeth D Luczak
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA;
| | - Mark E Anderson
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA;
- Departments of Physiology and Genetic Medicine and Program in Cellular and Molecular Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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8
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Wells CI, Drewry DH. Developing a Kinase Chemogenomic Set: Facilitating Investigation into Kinase Biology by Linking Phenotypes to Targets. Methods Mol Biol 2023; 2706:11-24. [PMID: 37558938 DOI: 10.1007/978-1-0716-3397-7_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Advances in increasingly complex phenotypic screening with lower throughput have necessitated the screening of smaller more highly annotated sets. One such collection of compounds which has been recently assembled is the kinase chemogenomic set. This is a set of curated kinase inhibitors built upon previous iterations, PKIS and PKIS2, and donations from our partners. Each compound in the set has been carefully selected based on selectivity, potency, and kinome coverage. These compounds as a set have been made available to the scientific community, enabling phenotypic screens to identify kinases that drive novel biology. Additionally, the associated data deposited in the public domain have also been used to inform new inhibitor design. Further expansion of this set to complete kinome coverage will allow for a greater understanding of kinase biology and its role in disease.
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Affiliation(s)
- Carrow I Wells
- Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC-CH), Chapel Hill, NC, USA.
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC-CH, Chapel Hill, NC, USA.
| | - David H Drewry
- Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC-CH), Chapel Hill, NC, USA
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC-CH, Chapel Hill, NC, USA
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9
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Decoding kinase-adverse event associations for small molecule kinase inhibitors. Nat Commun 2022; 13:4349. [PMID: 35896580 PMCID: PMC9329312 DOI: 10.1038/s41467-022-32033-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 07/14/2022] [Indexed: 11/08/2022] Open
Abstract
Small molecule kinase inhibitors (SMKIs) are being approved at a fast pace under expedited programs for anticancer treatment. In this study, we construct a multi-domain dataset from a total of 4638 patients in the registrational trials of 16 FDA-approved SMKIs and employ a machine-learning model to examine the relationships between kinase targets and adverse events (AEs). Internal and external (datasets from two independent SMKIs) validations have been conducted to verify the usefulness of the established model. We systematically evaluate the potential associations between 442 kinases with 2145 AEs and made publicly accessible an interactive web application “Identification of Kinase-Specific Signal” (https://gongj.shinyapps.io/ml4ki). The developed model (1) provides a platform for experimentalists to identify and verify undiscovered KI-AE pairs, (2) serves as a precision-medicine tool to mitigate individual patient safety risks by forecasting clinical safety signals and (3) can function as a modern drug development tool to screen and compare SMKI target therapies from the safety perspective. Small molecule kinase inhibitors (SMKIs) are being approved at a fast pace under expedited programs for anticancer treatment. Here, the authors employ a machine-learning model to examine the relationships between kinase targets and adverse events in the trials of 16 FDA-approved SMKIs.
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10
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Dissecting the roles of Haspin and VRK1 in histone H3 phosphorylation during mitosis. Sci Rep 2022; 12:11210. [PMID: 35778595 PMCID: PMC9249732 DOI: 10.1038/s41598-022-15339-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/22/2022] [Indexed: 12/12/2022] Open
Abstract
Protein kinases that phosphorylate histones are ideally-placed to influence the behavior of chromosomes during cell division. Indeed, a number of conserved histone phosphorylation events occur prominently during mitosis and meiosis in most eukaryotes, including on histone H3 at threonine-3 (H3T3ph). At least two kinases, Haspin and VRK1 (NHK-1/ballchen in Drosophila), have been proposed to carry out this modification. Phosphorylation of H3 by Haspin has defined roles in mitosis, but the significance of VRK1 activity towards histones in dividing cells has been unclear. Here, using in vitro kinase assays, KiPIK screening, RNA interference, and CRISPR/Cas9 approaches, we were unable to substantiate a direct role for VRK1, or its paralogue VRK2, in the phosphorylation of threonine-3 or serine-10 of Histone H3 in mitosis, although loss of VRK1 did slow cell proliferation. We conclude that the role of VRKs, and their more recently identified association with neuromuscular disease and importance in cancers of the nervous system, are unlikely to involve mitotic histone kinase activity. In contrast, Haspin is required to generate H3T3ph during mitosis.
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11
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Small Molecule Arranged Thermal Proximity Co aggregation (smarTPCA)-A Novel Approach to Characterize Protein-Protein Interactions in Living Cells by Similar Isothermal Dose-Responses. Int J Mol Sci 2022; 23:ijms23105605. [PMID: 35628420 PMCID: PMC9147192 DOI: 10.3390/ijms23105605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 11/17/2022] Open
Abstract
Chemical biology and the application of small molecules has proven to be a potent perturbation strategy, especially for the functional elucidation of proteins, their networks, and regulators. In recent years, the cellular thermal shift assay (CETSA) and its proteome-wide extension, thermal proteome profiling (TPP), have proven to be effective tools for identifying interactions of small molecules with their target proteins, as well as off-targets in living cells. Here, we asked the question whether isothermal dose-response (ITDR) CETSA can be exploited to characterize secondary effects downstream of the primary binding event, such as changes in post-translational modifications or protein-protein interactions (PPI). By applying ITDR-CETSA to MAPK14 kinase inhibitor treatment of living HL-60 cells, we found similar dose-responses for the direct inhibitor target and its known interaction partners MAPKAPK2 and MAPKAPK3. Extension of the dose-response similarity comparison to the proteome wide level using TPP with compound concentration range (TPP-CCR) revealed not only the known MAPK14 interaction partners MAPKAPK2 and MAPKAPK3, but also the potentially new intracellular interaction partner MYLK. We are confident that dose-dependent small molecule treatment in combination with ITDR-CETSA or TPP-CCR similarity assessment will not only allow discrimination between primary and secondary effects, but will also provide a novel method to study PPI in living cells without perturbation by protein modification, which we named "small molecule arranged thermal proximity coaggregation" (smarTPCA).
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12
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Ferreira A, Rivera A, Wohlgemuth JG, Dlott JS, Snyder LM, Alper SL, Romero JR. Dysregulated Erythroid Mg2+ Efflux in Type 2 Diabetes. Front Cell Dev Biol 2022; 10:861644. [PMID: 35445032 PMCID: PMC9013827 DOI: 10.3389/fcell.2022.861644] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/09/2022] [Indexed: 12/23/2022] Open
Abstract
Hyperglycemia is associated with decreased Mg2+ content in red blood cells (RBC), but mechanisms remain unclear. We characterized the regulation of Mg2+ efflux by glucose in ex vivo human RBC. We observed that hemoglobin A1C (HbA1C) values correlated with Na+-dependent Mg2+ efflux (Na+/Mg2+ exchange) and inversely correlated with cellular Mg content. Treatment of cells with 50 mM D-glucose, but not with sorbitol, lowered total cellular Mg (2.2 ± 0.1 to 2.0 ± 0.1 mM, p < 0.01) and enhanced Na+/Mg2+ exchange activity [0.60 ± 0.09 to 1.12 ± 0.09 mmol/1013 cell × h (flux units, FU), p < 0.05]. In contrast, incubation with selective Src family kinase inhibitors PP2 or SU6656 reduced glucose-stimulated exchange activation (p < 0.01). Na+/Mg2+ exchange activity was also higher in RBC from individuals with type 2 diabetes (T2D, 1.19 ± 0.13 FU) than from non-diabetic individuals (0.58 ± 0.05 FU, p < 0.01). Increased Na+/Mg2+ exchange activity in RBC from T2D subjects was associated with lower intracellular Mg content. Similarly increased exchange activity was evident in RBC from the diabetic db/db mouse model as compared to its non-diabetic control (p < 0.03). Extracellular exposure of intact RBC from T2D subjects to recombinant peptidyl-N-glycosidase F (PNGase F) reduced Na+/Mg2+ exchange activity from 0.98 ± 0.14 to 0.59 ± 0.13 FU (p < 0.05) and increased baseline intracellular Mg content (1.8 ± 0.1 mM) to normal values (2.1 ± 0.1 mM, p < 0.05). These data suggest that the reduced RBC Mg content of T2D RBC reflects enhanced RBC Na+/Mg2+ exchange subject to regulation by Src family kinases and by the N-glycosylation state of one or more membrane proteins. The data extend our understanding of dysregulated RBC Mg2+ homeostasis in T2D.
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Affiliation(s)
- Ana Ferreira
- Interdisciplinary Centre of Social Sciences (CICS.NOVA), Faculty of Social Sciences and Humanities (NOVA FCSH), Lisbon, Portugal
| | - Alicia Rivera
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, United States
- *Correspondence: Alicia Rivera,
| | | | | | | | - Seth L. Alper
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, United States
| | - Jose R. Romero
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
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13
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Bata N, Chaikuad A, Bakas NA, Limpert AS, Lambert LJ, Sheffler DJ, Berger LM, Liu G, Yuan C, Wang L, Peng Y, Dong J, Celeridad M, Layng F, Knapp S, Cosford NDP. Inhibitors of the Hippo Pathway Kinases STK3/MST2 and STK4/MST1 Have Utility for the Treatment of Acute Myeloid Leukemia. J Med Chem 2022; 65:1352-1369. [PMID: 34807584 PMCID: PMC10149138 DOI: 10.1021/acs.jmedchem.1c00804] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Serine/threonine-protein kinases 3 and 4 (STK3 and STK4, respectively) are key components of the Hippo signaling pathway, which regulates cell proliferation and death and provides a potential therapeutic target for acute myeloid leukemia (AML). Herein, we report the structure-based design of a series of pyrrolopyrimidine derivatives as STK3 and STK4 inhibitors. In an initial screen, the compounds exhibited low nanomolar potency against both STK3 and STK4. Crystallization of compound 6 with STK4 revealed two-point hinge binding in the ATP-binding pocket. Further characterization and analysis demonstrated that compound 20 (SBP-3264) specifically inhibited the Hippo signaling pathway in cultured mammalian cells and possessed favorable pharmacokinetic and pharmacodynamic properties in mice. We show that genetic knockdown and pharmacological inhibition of STK3 and STK4 suppress the proliferation of AML cells in vitro. Thus, SBP-3264 is a valuable chemical probe for understanding the roles of STK3 and STK4 in AML and is a promising candidate for further advancement as a potential therapy.
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Affiliation(s)
- Nicole Bata
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Apirat Chaikuad
- Buchmann Institute for Molecular Life Sciences, Structural Genomics Consortium, Johann Wolfgang Goethe-University, D-60438 Frankfurt am Main, Germany.,Institute for Pharmaceutical Chemistry, Max von Lauestrasse 9, Johann Wolfgang Goethe-University, D-60438 Frankfurt am Main, Germany
| | - Nicole A Bakas
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Allison S Limpert
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Lester J Lambert
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Douglas J Sheffler
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Lena M Berger
- Buchmann Institute for Molecular Life Sciences, Structural Genomics Consortium, Johann Wolfgang Goethe-University, D-60438 Frankfurt am Main, Germany.,Institute for Pharmaceutical Chemistry, Max von Lauestrasse 9, Johann Wolfgang Goethe-University, D-60438 Frankfurt am Main, Germany
| | - Guoxiong Liu
- Chemistry Department, Viva Biotech Ltd., 581 Shen Kuo Road, Shanghai 201203, China
| | - Cunxiang Yuan
- Chemistry Department, Viva Biotech Ltd., 581 Shen Kuo Road, Shanghai 201203, China
| | - Li Wang
- Chemistry Department, Viva Biotech Ltd., 581 Shen Kuo Road, Shanghai 201203, China
| | - Yi Peng
- Chemistry Department, Viva Biotech Ltd., 581 Shen Kuo Road, Shanghai 201203, China
| | - Jing Dong
- Chemistry Department, Viva Biotech Ltd., 581 Shen Kuo Road, Shanghai 201203, China
| | - Maria Celeridad
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Fabiana Layng
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Stefan Knapp
- Buchmann Institute for Molecular Life Sciences, Structural Genomics Consortium, Johann Wolfgang Goethe-University, D-60438 Frankfurt am Main, Germany.,Institute for Pharmaceutical Chemistry, Max von Lauestrasse 9, Johann Wolfgang Goethe-University, D-60438 Frankfurt am Main, Germany.,Translational cancer network DKTK site Frankfurt/Mainz and Frankfurt Cancer Institute (FCI), Johann Wolfgang Goethe-University, D-60438 Frankfurt am Main, Germany
| | - Nicholas D P Cosford
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
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14
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Lee SB, Chang TY, Lee NZ, Yu ZY, Liu CY, Lee HY. Design, synthesis and biological evaluation of bisindole derivatives as anticancer agents against Tousled-like kinases. Eur J Med Chem 2022; 227:113904. [PMID: 34662748 DOI: 10.1016/j.ejmech.2021.113904] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 10/02/2021] [Accepted: 10/03/2021] [Indexed: 11/03/2022]
Abstract
This study presents the design, synthesis, and characterization of bisindole molecules as anti-cancer agents against Tousled-like kinases (TLKs). We show that compound 2 composed of an indirubin-3'-oxime group linked with a (N-methylpiperidin-2-yl)ethyl moiety possessed inhibitory activity toward both TLK1 and TLK2 in vitro and diminished the phosphorylation level of the downstream substrate anti-silencing function 1 (ASF1) in replicating cells. The treatment of compound 2 impaired DNA replication, slowed S-phase progression, and triggered DNA damage response in replicating cells. Structure optimization further discovered six derivatives exhibiting potent TLK inhibitory activity and revealed the importance of the tertiary amine-containing moiety of the side chain. Moreover, the derivatives 6, 17, 19, and 20 strongly suppressed the growth of triple-negative breast cancer MDA-MB-231 cells, non-small cell lung cancer A549 cells, and colorectal cancer HCT-116 cells, while normal lung fibroblast MRC5 and IMR90 cells showed a lower response to these compounds. Taken together, this study identifies tertiary amine-linked indirubin-3'-oximes as potent anticancer agents that inhibit TLK activity.
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Affiliation(s)
- Sung-Bau Lee
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan; Master Program in Clinical Genomics and Proteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Ting-Yu Chang
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Nian-Zhe Lee
- Master Program in Clinical Genomics and Proteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Zih-Yao Yu
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Chi-Yuan Liu
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Hsueh-Yun Lee
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan; Master Program in Clinical Genomics and Proteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan; School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.
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Non-canonical role of Hippo tumor suppressor serine/threonine kinase 3 STK3 in prostate cancer. Mol Ther 2022; 30:485-500. [PMID: 34450249 PMCID: PMC8753456 DOI: 10.1016/j.ymthe.2021.08.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 07/14/2021] [Accepted: 08/20/2021] [Indexed: 01/07/2023] Open
Abstract
Serine/threonine kinase 3 (STK3) is an essential member of the highly conserved Hippo tumor suppressor pathway that regulates Yes-associated protein 1 (YAP1) and TAZ. STK3 and its paralog STK4 initiate a phosphorylation cascade that regulates YAP1/TAZ inhibition and degradation, which is important for regulated cell growth and organ size. Deregulation of this pathway leads to hyperactivation of YAP1 in various cancers. Counter to the canonical tumor suppression role of STK3, we report that in the context of prostate cancer (PC), STK3 has a pro-tumorigenic role. Our investigation started with the observation that STK3, but not STK4, is frequently amplified in PC. Additionally, high STK3 expression is associated with decreased overall survival and positively correlates with androgen receptor (AR) activity in metastatic castrate-resistant PC. XMU-MP-1, an STK3/4 inhibitor, slowed cell proliferation, spheroid growth, and Matrigel invasion in multiple models. Genetic depletion of STK3 decreased proliferation in several PC cell lines. In a syngeneic allograft model, STK3 loss slowed tumor growth kinetics in vivo, and biochemical analysis suggests a mitotic growth arrest phenotype. To further probe the role of STK3 in PC, we identified and validated a new set of selective STK3 inhibitors, with enhanced kinase selectivity relative to XMU-MP-1, that inhibited tumor spheroid growth and invasion. Consistent with the canonical role, inhibition of STK3 induced cardiomyocyte growth and had chemoprotective effects. Our results indicate that STK3 has a non-canonical role in PC progression and that inhibition of STK3 may have a therapeutic potential for PC that merits further investigation.
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16
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Inhibition of SYK and cSrc kinases can protect bone and cartilage in preclinical models of osteoarthritis and rheumatoid arthritis. Sci Rep 2021; 11:23120. [PMID: 34848799 PMCID: PMC8632988 DOI: 10.1038/s41598-021-02568-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 10/26/2021] [Indexed: 11/08/2022] Open
Abstract
The pathophysiology of osteoarthritis (OA) includes the destruction of subchondral bone tissue and inflammation of the synovium. Thus, an effective disease-modifying treatment should act on both of these pathogenetic components. It is known that cSrc kinase is involved in bone and cartilage remodeling, and SYK kinase is associated with the inflammatory component. Thus the aim of this study was to characterize the mechanism of action and efficacy of a small molecule multikinase inhibitor MT-SYK-03 targeting SYK and cSrc kinases among others in different in vitro and in vivo arthritis models. The selectivity of MT-SYK-03 kinase inhibition was assayed on a panel of 341 kinases. The compound was evaluated in a set of in vitro models of OA and in vivo OA and RA models: surgically-induced arthritis (SIA), monosodium iodoacetate-induced arthritis (MIA), collagen-induced arthritis (CIA), adjuvant-induced arthritis (AIA). MT-SYK-03 inhibited cSrc and SYK with IC50 of 14.2 and 23 nM respectively. Only five kinases were inhibited > 90% at 500 nM of MT-SYK-03. In in vitro OA models MT-SYK-03 reduced hypertrophic changes of chondrocytes, bone resorption, and inhibited SYK-mediated inflammatory signaling. MT-SYK-03 showed preferential distribution to joint and bone tissue (in rats) and revealed disease-modifying activity in vivo by halving the depth of cartilage erosion in rat SIA model, and increasing the pain threshold in rat MIA model. Chondroprotective and antiresorptive effects were shown in a monotherapy regime and in combination with methotrexate (MTX) in murine and rat CIA models; an immune-mediated inflammation in rat AIA model was decreased. The obtained preclinical data support inhibition of cSrc and SYK as a viable strategy for disease-modifying treatment of OA. A Phase 2 clinical study of MT-SYK-03 is to be started.
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Islam S, Wang S, Bowden N, Martin J, Head R. Repurposing existing therapeutics, its importance in oncology drug development: Kinases as a potential target. Br J Clin Pharmacol 2021; 88:64-74. [PMID: 34192364 PMCID: PMC9292808 DOI: 10.1111/bcp.14964] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/04/2021] [Accepted: 06/19/2021] [Indexed: 12/13/2022] Open
Abstract
Repurposing the large arsenal of existing non‐cancer drugs is an attractive proposition to expand the clinical pipelines for cancer therapeutics. The earlier successes in repurposing resulted primarily from serendipitous findings, but more recently, drug or target‐centric systematic identification of repurposing opportunities continues to rise. Kinases are one of the most sought‐after anti‐cancer drug targets over the last three decades. There are many non‐cancer approved drugs that can inhibit kinases as “off‐targets” as well as many existing kinase inhibitors that can target new additional kinases in cancer. Identifying cancer‐associated kinase inhibitors through mining commercial drug databases or new kinase targets for existing inhibitors through comprehensive kinome profiling can offer more effective trial‐ready options to rapidly advance drugs for clinical validation. In this review, we argue that drug repurposing is an important approach in modern drug development for cancer therapeutics. We have summarized the advantages of repurposing, the rationale behind this approach together with key barriers and opportunities in cancer drug development. We have also included examples of non‐cancer drugs that inhibit kinases or are associated with kinase signalling as a basis for their anti‐cancer action.
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Affiliation(s)
- Saiful Islam
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 500, Australia
| | - Shudong Wang
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 500, Australia
| | - Nikola Bowden
- Centre for Human Drug Repurposing and Medicines Research, University of Newcastle, NSW, 2305, Australia
| | - Jennifer Martin
- Centre for Human Drug Repurposing and Medicines Research, University of Newcastle, NSW, 2305, Australia
| | - Richard Head
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 500, Australia
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18
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Negi P, Cheke RS, Patil VM. Recent advances in pharmacological diversification of Src family kinase inhibitors. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2021. [DOI: 10.1186/s43042-021-00172-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Abstract
Background
Src kinase, a nonreceptor protein-tyrosine kinase is composed of 11 members (in human) and is involved in a wide variety of essential functions required to sustain cellular homeostasis and survival.
Main body of the abstract
Deregulated activity of Src family kinase is related to malignant transformation. In 2001, Food and Drug Administration approved imatinib for the treatment of chronic myeloid leukemia followed by approval of various other inhibitors from this category as effective therapeutics for cancer patients. In the past decade, Src family kinase has been investigated for the treatment of diverse pathologies in addition to cancer. In this regard, we provide a systematic evaluation of Src kinase regarding its mechanistic role in cancer and other diseases. Here we comment on preclinical and clinical success of Src kinase inhibitors in cancer followed by diabetes, hypertension, tuberculosis, and inflammation.
Short conclusion
Studies focusing on the diversified role of Src kinase as potential therapeutical target for the development of medicinally active agents might produce significant advances in the management of not only various types of cancer but also other diseases which are in demand for potent and safe therapeutics.
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Gally JM, Bourg S, Fogha J, Do QT, Aci-Sèche S, Bonnet P. VSPrep: A KNIME Workflow for the Preparation of Molecular Databases for Virtual Screening. Curr Med Chem 2021; 27:6480-6494. [PMID: 31242833 DOI: 10.2174/0929867326666190614160451] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 04/11/2019] [Accepted: 05/24/2019] [Indexed: 01/21/2023]
Abstract
Drug discovery is a challenging and expensive field. Hence, novel in silico tools have been developed in early discovery stage to identify and prioritize novel molecules with suitable physicochemical properties. In many in silico drug design projects, molecular databases are screened by virtual screening tools to search for potential bioactive molecules. The preparation of the molecules is therefore a key step in the success of well-established techniques such as docking, similarity or pharmacophore searching. We review here the lists of several toolkits used in different steps during the cleaning of molecular databases, integrated within a KNIME workflow. During the first step of the automatic workflow, salts are removed, and mixtures are split to get one compound per entry. Then compounds with unwanted features are filtered. Duplicated entries are then deleted while considering stereochemistry. As a compromise between exhaustiveness and computational time, most distributed tautomers at physiological pH are computed. Additionally, various flags are applied to molecules by using either classical molecular descriptors, similarity search to known libraries or substructure search rules. Moreover, stereoisomers are enumerated depending on the unassigned chiral centers. Then, three-dimensional coordinates, and optionally conformers, are generated. This workflow has been already applied to several drug design projects and can be used for molecular database preparation upon request.
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Affiliation(s)
- José-Manuel Gally
- Institut de Chimie Organique et Analytique (ICOA), Universite d'Orleans, UMR CNRS 7311, BP 6759, 45067 Orleans, France
| | - Stéphane Bourg
- Institut de Chimie Organique et Analytique (ICOA), Universite d'Orleans, UMR CNRS 7311, BP 6759, 45067 Orleans, France
| | - Jade Fogha
- Institut de Chimie Organique et Analytique (ICOA), Universite d'Orleans, UMR CNRS 7311, BP 6759, 45067 Orleans, France
| | - Quoc-Tuan Do
- Greenpharma S.A.S. 3, allee du Titane, 45100 Orleans, France
| | - Samia Aci-Sèche
- Institut de Chimie Organique et Analytique (ICOA), Universite d'Orleans, UMR CNRS 7311, BP 6759, 45067 Orleans, France
| | - Pascal Bonnet
- Institut de Chimie Organique et Analytique (ICOA), Universite d'Orleans, UMR CNRS 7311, BP 6759, 45067 Orleans, France
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Enriched conditioning expands the regenerative ability of sensory neurons after spinal cord injury via neuronal intrinsic redox signaling. Nat Commun 2020; 11:6425. [PMID: 33349630 PMCID: PMC7752916 DOI: 10.1038/s41467-020-20179-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 11/06/2020] [Indexed: 12/13/2022] Open
Abstract
Overcoming the restricted axonal regenerative ability that limits functional repair following a central nervous system injury remains a challenge. Here we report a regenerative paradigm that we call enriched conditioning, which combines environmental enrichment (EE) followed by a conditioning sciatic nerve axotomy that precedes a spinal cord injury (SCI). Enriched conditioning significantly increases the regenerative ability of dorsal root ganglia (DRG) sensory neurons compared to EE or a conditioning injury alone, propelling axon growth well beyond the spinal injury site. Mechanistically, we established that enriched conditioning relies on the unique neuronal intrinsic signaling axis PKC-STAT3-NADPH oxidase 2 (NOX2), enhancing redox signaling as shown by redox proteomics in DRG. Finally, NOX2 conditional deletion or overexpression respectively blocked or phenocopied enriched conditioning-dependent axon regeneration after SCI leading to improved functional recovery. These studies provide a paradigm that drives the regenerative ability of sensory neurons offering a potential redox-dependent regenerative model for mechanistic and therapeutic discoveries. Pre conditioning injury or environmental enrichment have been shown to promote axon regeneration. Here the authors show that environmental enrichment, combined with preconditioning injury promotes regeneration via a redox signalling dependent mechanism.
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Picado A, Chaikuad A, Wells CI, Shrestha S, Zuercher WJ, Pickett JE, Kwarcinski FE, Sinha P, de Silva CS, Zutshi R, Liu S, Kannan N, Knapp S, Drewry DH, Willson TM. A Chemical Probe for Dark Kinase STK17B Derives Its Potency and High Selectivity through a Unique P-Loop Conformation. J Med Chem 2020; 63:14626-14646. [PMID: 33215924 DOI: 10.1021/acs.jmedchem.0c01174] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
STK17B is a member of the death-associated protein kinase family and has been genetically linked to the development of diverse diseases. However, the role of STK17B in normal and disease pathology is poorly defined. Here, we present the discovery of thieno[3,2-d] pyrimidine SGC-STK17B-1 (11s), a high-quality chemical probe for this understudied "dark" kinase. 11s is an ATP-competitive inhibitor that showed remarkable selectivity over other kinases including the closely related STK17A. X-ray crystallography of 11s and related thieno[3,2-d]pyrimidines bound to STK17B revealed a unique P-loop conformation characterized by a salt bridge between R41 and the carboxylic acid of the inhibitor. Molecular dynamic simulations of STK17B revealed the flexibility of the P-loop and a wide range of R41 conformations available to the apo-protein. The isomeric thieno[2,3-d]pyrimidine SGC-STK17B-1N (19g) was identified as a negative control compound. The >100-fold lower activity of 19g on STK17B was attributed to the reduced basicity of its pyrimidine N1.
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Affiliation(s)
- Alfredo Picado
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7264, United States
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, Frankfurt 60438, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Straße 15, Frankfurt 60438, Germany
| | - Carrow I Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7264, United States
| | - Safal Shrestha
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
| | - William J Zuercher
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7264, United States
| | - Julie E Pickett
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7264, United States
| | - Frank E Kwarcinski
- Luceome Biotechnologies, 1665 E. 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Parvathi Sinha
- Luceome Biotechnologies, 1665 E. 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Chandi S de Silva
- Luceome Biotechnologies, 1665 E. 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Reena Zutshi
- Luceome Biotechnologies, 1665 E. 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, United States
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, Frankfurt 60438, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Straße 15, Frankfurt 60438, Germany.,German Translational Cancer Network (DKTK) site Frankfurt/Mainz, Frankfurt am Main 60596, Germany.,Frankfurt Cancer Institute (FCI), Paul-Ehrlich-Straße 42-44, Frankfurt am Main 60596, Germany
| | - David H Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7264, United States
| | - Timothy M Willson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7264, United States
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22
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Karasev D, Sobolev B, Lagunin A, Filimonov D, Poroikov V. Prediction of Protein-ligand Interaction Based on Sequence Similarity and Ligand Structural Features. Int J Mol Sci 2020; 21:ijms21218152. [PMID: 33142754 PMCID: PMC7663273 DOI: 10.3390/ijms21218152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 01/09/2023] Open
Abstract
Computationally predicting the interaction of proteins and ligands presents three main directions: the search of new target proteins for ligands, the search of new ligands for targets, and predicting the interaction of new proteins and new ligands. We proposed an approach providing the fuzzy classification of protein sequences based on the ligand structural features to analyze the latter most complicated case. We tested our approach on five protein groups, which represented promised targets for drug-like ligands and differed in functional peculiarities. The training sets were built with the original procedure overcoming the data ambiguity. Our study showed the effective prediction of new targets for ligands with an average accuracy of 0.96. The prediction of new ligands for targets displayed the average accuracy 0.95; accuracy estimates were close to our previous results, comparable in accuracy to those of other methods or exceeded them. Using the fuzzy coefficients reflecting the target-to-ligand specificity, we provided predicting interactions for new proteins and new ligands; the obtained accuracy values from 0.89 to 0.99 were acceptable for such a sophisticated task. The protein kinase family case demonstrated the ability to account for subtle features of proteins and ligands required for the specificity of protein–ligand interaction.
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Affiliation(s)
- Dmitry Karasev
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow 119121, Russia; (B.S.); (A.L.); (D.F.); (V.P.)
- Correspondence:
| | - Boris Sobolev
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow 119121, Russia; (B.S.); (A.L.); (D.F.); (V.P.)
| | - Alexey Lagunin
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow 119121, Russia; (B.S.); (A.L.); (D.F.); (V.P.)
- Department of Bioinformatics, Russian National Research Medical University, Moscow 117997, Russia
| | - Dmitry Filimonov
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow 119121, Russia; (B.S.); (A.L.); (D.F.); (V.P.)
| | - Vladimir Poroikov
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow 119121, Russia; (B.S.); (A.L.); (D.F.); (V.P.)
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23
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Qhobosheane MA, Legoabe LJ, Josselin B, Bach S, Ruchaud S, Beteck RM. Synthesis and evaluation of C3 substituted chalcone‐based derivatives of 7‐azaindole as protein kinase inhibitors. Chem Biol Drug Des 2020; 96:1395-1407. [DOI: 10.1111/cbdd.13748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/01/2020] [Accepted: 06/05/2020] [Indexed: 01/01/2023]
Affiliation(s)
- Malikotsi A. Qhobosheane
- Centre of Excellence for Pharmaceutical Sciences North‐West University Potchefstroom South Africa
| | - Lesetja J. Legoabe
- Centre of Excellence for Pharmaceutical Sciences North‐West University Potchefstroom South Africa
| | - Béatrice Josselin
- Sorbonne Université CNRS UMR 8227 Integrative Biology of Marine Models Laboratory (LBI2M) Station Biologique de Roscoff Roscoff Cedex France
- Sorbonne Université CNRS FR2424 Plateforme de criblage KISSf (Kinase Inhibitor Specialized Screening facility) Station Biologique de Roscoff Roscoff France
| | - Stéphane Bach
- Sorbonne Université CNRS UMR 8227 Integrative Biology of Marine Models Laboratory (LBI2M) Station Biologique de Roscoff Roscoff Cedex France
- Sorbonne Université CNRS FR2424 Plateforme de criblage KISSf (Kinase Inhibitor Specialized Screening facility) Station Biologique de Roscoff Roscoff France
| | - Sandrine Ruchaud
- Sorbonne Université CNRS UMR 8227 Integrative Biology of Marine Models Laboratory (LBI2M) Station Biologique de Roscoff Roscoff Cedex France
| | - Richard M. Beteck
- Centre of Excellence for Pharmaceutical Sciences North‐West University Potchefstroom South Africa
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24
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Zhong Y, Qiu RZ, Sun SL, Zhao C, Fan TY, Chen M, Li NG, Shi ZH. Small-Molecule Fms-like Tyrosine Kinase 3 Inhibitors: An Attractive and Efficient Method for the Treatment of Acute Myeloid Leukemia. J Med Chem 2020; 63:12403-12428. [PMID: 32659083 DOI: 10.1021/acs.jmedchem.0c00696] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Fms-like tyrosine kinase 3 (FLT3) is an important member of the class III receptor tyrosine kinase (RTK) family, which is involved in the proliferation of hematopoietic cells and lymphocytes. In recent years, increasing evidence have demonstrated that the activation and mutation of FLT3 is closely implicated in the occurrence and development of acute myeloid leukemia (AML). The exploration of small-molecule inhibitors targeting FLT3 has aroused wide interest of pharmaceutical chemists and is expected to bring new hope for AML therapy. In this review, we specifically highlighted FLT3 mediated JAK/STAT, RAS/MAPK, and PI3K/AKT/mTOR signaling. The structural properties and biological activities of representative FLT3 inhibitors reported from 2014 to the present were also summarized. In addition, the major challenges in the current advance of novel FLT3 inhibitors were further analyzed, with the aim to guide future drug discovery.
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Affiliation(s)
- Yue Zhong
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Run-Ze Qiu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Shan-Liang Sun
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Chao Zhao
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Tian-Yuan Fan
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Min Chen
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Nian-Guang Li
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Zhi-Hao Shi
- Department of Organic Chemistry, China Pharmaceutical University, Nanjing 211198, China
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25
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Fromont C, Atzori A, Kaur D, Hashmi L, Greco G, Cabanillas A, Nguyen HV, Jones DH, Garzón M, Varela A, Stevenson B, Iacobini GP, Lenoir M, Rajesh S, Box C, Kumar J, Grant P, Novitskaya V, Morgan J, Sorrell FJ, Redondo C, Kramer A, Harris CJ, Leighton B, Vickers SP, Cheetham SC, Kenyon C, Grabowska AM, Overduin M, Berditchevski F, Weston CJ, Knapp S, Fischer PM, Butterworth S. Discovery of Highly Selective Inhibitors of Calmodulin-Dependent Kinases That Restore Insulin Sensitivity in the Diet-Induced Obesity in Vivo Mouse Model. J Med Chem 2020; 63:6784-6801. [PMID: 32433887 PMCID: PMC7445743 DOI: 10.1021/acs.jmedchem.9b01803] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Polymorphisms
in the region of the calmodulin-dependent kinase
isoform D (CaMK1D) gene are associated with increased incidence of
diabetes, with the most common polymorphism resulting in increased
recognition by transcription factors and increased protein expression.
While reducing CaMK1D expression has a potentially beneficial effect
on glucose processing in human hepatocytes, there are no known selective
inhibitors of CaMK1 kinases that can be used to validate or translate
these findings. Here we describe the development of a series of potent,
selective, and drug-like CaMK1 inhibitors that are able to provide
significant free target cover in mouse models and are therefore useful
as in vivo tool compounds. Our results show that
a lead compound from this series improves insulin sensitivity and
glucose control in the diet-induced obesity mouse model after both
acute and chronic administration, providing the first in vivo validation of CaMK1D as a target for diabetes therapeutics.
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Affiliation(s)
- Christophe Fromont
- Centre for Biomolecular Sciences and School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Alessio Atzori
- Centre for Biomolecular Sciences and School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Divneet Kaur
- Centre for Biomolecular Sciences and School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Lubna Hashmi
- Centre for Biomolecular Sciences and School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Graziella Greco
- School of Pharmacy, College of Medical and Dental Sciences, University of Birmingham, Edgbaston B15 2TT, U.K
| | - Alejandro Cabanillas
- School of Pharmacy, College of Medical and Dental Sciences, University of Birmingham, Edgbaston B15 2TT, U.K
| | - Huy Van Nguyen
- School of Pharmacy, College of Medical and Dental Sciences, University of Birmingham, Edgbaston B15 2TT, U.K
| | - D Heulyn Jones
- Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PL, U.K
| | - Miguel Garzón
- Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PL, U.K
| | - Ana Varela
- Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PL, U.K
| | - Brett Stevenson
- Sygnature Discovery, BioCity, Pennyfoot Street, Nottingham NG1 1GF, U.K
| | - Greg P Iacobini
- Sygnature Discovery, BioCity, Pennyfoot Street, Nottingham NG1 1GF, U.K
| | - Marc Lenoir
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Sundaresan Rajesh
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Clare Box
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Jitendra Kumar
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Paige Grant
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Vera Novitskaya
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Juliet Morgan
- Sygnature Discovery, BioCity, Pennyfoot Street, Nottingham NG1 1GF, U.K
| | - Fiona J Sorrell
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, U.K
| | - Clara Redondo
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, U.K
| | - Andreas Kramer
- Structural Genomics Consortium and Buchmann Institute for Molecular Life Sciences, Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - C John Harris
- CJH Consultants, Ford Cottage, South Weirs, Burley Road, Brockenhurst, Hants SO42 7UQ, U.K
| | - Brendan Leighton
- The Research Network, IPC 600 Discovery Park, Ramsgate Road, Sandwich CT13 9NJ, U.K
| | - Steven P Vickers
- RenaSci Limited, BioCity, Pennyfoot Street, Nottingham NG1 1GF, U.K
| | | | - Colin Kenyon
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa
| | - Anna M Grabowska
- Ex Vivo Cancer Pharmacology Centre of Excellence, Cancer Biology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Fedor Berditchevski
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Chris J Weston
- Centre for Liver Research, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K.,NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, B15 2TT, U.K
| | - Stefan Knapp
- Structural Genomics Consortium and Buchmann Institute for Molecular Life Sciences, Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Peter M Fischer
- Centre for Biomolecular Sciences and School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Sam Butterworth
- Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PL, U.K
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26
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Watson NA, Cartwright TN, Lawless C, Cámara-Donoso M, Sen O, Sako K, Hirota T, Kimura H, Higgins JMG. Kinase inhibition profiles as a tool to identify kinases for specific phosphorylation sites. Nat Commun 2020; 11:1684. [PMID: 32245944 PMCID: PMC7125195 DOI: 10.1038/s41467-020-15428-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 03/06/2020] [Indexed: 01/08/2023] Open
Abstract
There are thousands of known cellular phosphorylation sites, but the paucity of ways to identify kinases for particular phosphorylation events remains a major roadblock for understanding kinase signaling. To address this, we here develop a generally applicable method that exploits the large number of kinase inhibitors that have been profiled on near-kinome-wide panels of protein kinases. The inhibition profile for each kinase provides a fingerprint that allows identification of unknown kinases acting on target phosphosites in cell extracts. We validate the method on diverse known kinase-phosphosite pairs, including histone kinases, EGFR autophosphorylation, and Integrin β1 phosphorylation by Src-family kinases. We also use our approach to identify the previously unknown kinases responsible for phosphorylation of INCENP at a site within a commonly phosphorylated motif in mitosis (a non-canonical target of Cyclin B-Cdk1), and of BCL9L at S915 (PKA). We show that the method has clear advantages over in silico and genetic screening.
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Affiliation(s)
- Nikolaus A Watson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Tyrell N Cartwright
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Conor Lawless
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Marcos Cámara-Donoso
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Onur Sen
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Kosuke Sako
- The Cancer Institute, Japanese Foundation for Cancer Research, Koto, Tokyo, 135-8550, Japan
| | - Toru Hirota
- The Cancer Institute, Japanese Foundation for Cancer Research, Koto, Tokyo, 135-8550, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8503, Japan
| | - Jonathan M G Higgins
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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27
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Hickman KA, Hariharan S, De Melo J, Ylanko J, Lustig LC, Penn LZ, Andrews DW. Image-Based Analysis of Protein Stability. Cytometry A 2020; 97:363-377. [PMID: 31774248 PMCID: PMC7187295 DOI: 10.1002/cyto.a.23928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 12/14/2022]
Abstract
Short half-life proteins regulate many essential processes, including cell cycle, transcription, and apoptosis. However, few well-characterized protein-turnover pathways have been identified because traditional methods to measure protein half-life are time and labor intensive. To overcome this barrier, we developed a protein stability probe and high-content screening pipeline for novel regulators of short half-life proteins using automated image analysis. Our pilot probe consists of the short half-life protein c-MYC (MYC) fused to Venus fluorescent protein (MYC-Venus). This probe enables protein half-life to be scored as a function of fluorescence intensity and distribution. Rapid turnover prevents maximal fluorescence of the probe due to the relatively longer maturation time of the fluorescent protein. Cells expressing the MYC-Venus probe were analyzed using a pipeline in which automated confocal microscopy and image analyses were used to score MYC-Venus stability by two strategies: assaying the percentage of cells with Venus fluorescence above background, and phenotypic comparative analysis. To evaluate this high-content screening pipeline and our probe, a kinase inhibitor library was screened by confocal microscopy to identify known and novel kinases that regulate MYC stability. Compounds identified were shown to increase the half-life of both MYC-Venus and endogenous MYC, validating the probe and pipeline. Fusion of another short half-life protein, myeloid cell leukemia 1 (MCL1), with Venus also demonstrated an increase in percent Venus-positive cells after treatment with inhibitors known to stabilize MCL1. Together, the results validate the use of our automated microscopy and image analysis pipeline of stability probe-expressing cells to rapidly and quantitatively identify regulators of short half-life proteins. © 2019 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.
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Affiliation(s)
- K. Ashley Hickman
- Sunnybrook Research InstituteTorontoON M4N 3M5Canada
- Princess Margaret Cancer CenterTorontoON M5G 1L7Canada
- Faculty of Medicine, Department of Medical BiophysicsUniversity of TorontoTorontoON M5G 1L7Canada
| | - Santosh Hariharan
- Sunnybrook Research InstituteTorontoON M4N 3M5Canada
- Faculty of Medicine, Department of Medical BiophysicsUniversity of TorontoTorontoON M5G 1L7Canada
| | - Jason De Melo
- Princess Margaret Cancer CenterTorontoON M5G 1L7Canada
| | - Jarkko Ylanko
- Sunnybrook Research InstituteTorontoON M4N 3M5Canada
| | - Lindsay C. Lustig
- Princess Margaret Cancer CenterTorontoON M5G 1L7Canada
- Faculty of Medicine, Department of Medical BiophysicsUniversity of TorontoTorontoON M5G 1L7Canada
| | - Linda Z. Penn
- Princess Margaret Cancer CenterTorontoON M5G 1L7Canada
- Faculty of Medicine, Department of Medical BiophysicsUniversity of TorontoTorontoON M5G 1L7Canada
| | - David W. Andrews
- Sunnybrook Research InstituteTorontoON M4N 3M5Canada
- Faculty of Medicine, Department of Medical BiophysicsUniversity of TorontoTorontoON M5G 1L7Canada
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28
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McGill MM, Sabikunnahar B, Fang Q, Teuscher C, Krementsov DN. The sex-specific role of p38 MAP kinase in CNS autoimmunity is regulated by estrogen receptor alpha. J Neuroimmunol 2020; 342:577209. [PMID: 32200131 PMCID: PMC8978838 DOI: 10.1016/j.jneuroim.2020.577209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 12/30/2022]
Abstract
Biological sex is a critical factor in regulating immune function. A striking example of this is the higher prevalence of autoimmune diseases such as multiple sclerosis (MS) and lupus in females compared to males. While many studies have implicated the role of sex hormones such as estrogens and androgens in these sex differences, surprisingly little is known about other molecular pathways that underlie sex differences or interact with sex hormones. We have previously shown that conditional ablation of p38α MAP kinase signaling in myeloid cells (p38αCKO) was protective in a mouse model of MS, experimental autoimmune encephalomyelitis (EAE), in female but not male mice. This sex difference was dependent on the presence of sex hormones, leading us to hypothesize that the pathogenic function of p38α in EAE depends on estrogen signaling via one of the two nuclear estrogen receptors, encoded by Esr1 and Esr2 . To test this hypothesis, we performed experiments with p38αCKO macrophages, which demonstrated that the effects of estradiol and p38α were independent of one another in vitro . Since many sex hormone effects are lost in vitro, we generated p38αCKO mice lacking either Esr1 or Esr2 , and evaluated their EAE susceptibility in vivo . Myeloid-specific deletion of Esr1 abrogated protection in p38αCKO females, although global deletion of Esr1 and Esr2 did not. Moreover, global or myeloid-specific disruption of Esr1 unexpectedly promoted protection from EAE in p38αCKO males. Mechanistically, Esr1 deletion resulted in partial reprogramming of p38α-dependent transcriptional modules in male macrophages, in particular those regulated by TGFβ, BRD4, and SMARCA4. These results demonstrate that estrogen signaling in myeloid cells plays an important sex-specific role in programming their dependence on specific intracellular signaling pathways in the context of autoimmune disease pathogenesis, suggesting potential avenues for sex-specific therapeutics or combinatorial approaches for the treatment of such diseases.
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Affiliation(s)
- Mahalia M McGill
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA
| | - Bristy Sabikunnahar
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA
| | - Qian Fang
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA
| | - Cory Teuscher
- Department of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Dimitry N Krementsov
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA.
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29
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Nassal D, Gratz D, Hund TJ. Challenges and Opportunities for Therapeutic Targeting of Calmodulin Kinase II in Heart. Front Pharmacol 2020; 11:35. [PMID: 32116711 PMCID: PMC7012788 DOI: 10.3389/fphar.2020.00035] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/14/2020] [Indexed: 12/19/2022] Open
Abstract
Heart failure remains a major health burden around the world. Despite great progress in delineation of molecular mechanisms underlying development of disease, standard therapy has not advanced at the same pace. The multifunctional signaling molecule Ca2+/calmodulin-dependent protein kinase II (CaMKII) has received considerable attention over recent years for its central role in maladaptive remodeling and arrhythmias in the setting of chronic disease. However, these basic science discoveries have yet to translate into new therapies for human patients. This review addresses both the promise and barriers to developing translational therapies that target CaMKII signaling to abrogate pathologic remodeling in the setting of chronic disease. Efforts in small molecule design are discussed, as well as alternative targeting approaches that exploit novel avenues for compound delivery and/or genetic approaches to affect cardiac CaMKII signaling. These alternative strategies provide hope for overcoming some of the challenges that have limited the development of new therapies.
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Affiliation(s)
- Drew Nassal
- The Frick Center for Heart Failure and Arrhythmia and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Daniel Gratz
- The Frick Center for Heart Failure and Arrhythmia and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States.,Department of Biomedical Engineering, College of Engineering, The Ohio State University, Columbus, OH, United States
| | - Thomas J Hund
- The Frick Center for Heart Failure and Arrhythmia and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States.,Department of Biomedical Engineering, College of Engineering, The Ohio State University, Columbus, OH, United States.,Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States
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30
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Borisov DV, Veselovsky AV. [Ligand-receptor binding kinetics in drug design]. BIOMEDITSINSKAIA KHIMIIA 2020; 66:42-53. [PMID: 32116225 DOI: 10.18097/pbmc20206601042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Traditionally, the thermodynamic values of affinity are considered as the main criterion for the development of new drugs. Usually, these values for drugs are measured <i>in vitro</i> at steady concentrations of the receptor and ligand, which are differed from <i>in vivo</i> environment. Recent studies have shown that the kinetics of the process of drug binding to its receptor make significant contribution in the drug effectiveness. This has increased attention in characterizing and predicting the rate constants of association and dissociation of the receptor ligand at the stage of preclinical studies of drug candidates. A drug with a long residence time can determine ligand-receptor selectivity (kinetic selectivity), maintain pharmacological activity of the drug at its low concentration in vivo. The paper discusses the theoretical basis of protein-ligand binding, molecular determinants that control the kinetics of the drug-receptor binding. Understanding the molecular features underlying the kinetics of receptor-ligand binding will contribute to the rational design of drugs with desired properties.
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Affiliation(s)
- D V Borisov
- Institute of Biomedical Chemistry, Moscow, Russia
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31
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Pinzi L, Rastelli G. Identification of Target Associations for Polypharmacology from Analysis of Crystallographic Ligands of the Protein Data Bank. J Chem Inf Model 2019; 60:372-390. [PMID: 31800237 DOI: 10.1021/acs.jcim.9b00821] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The design of a chemical entity that potently and selectively binds to a biological target of therapeutic relevance has dominated the scene of drug discovery so far. However, recent findings suggest that multitarget ligands may be endowed with superior efficacy and be less prone to drug resistance. The Protein Data Bank (PDB) provides experimentally validated structural information about targets and bound ligands. Therefore, it represents a valuable source of information to help identifying active sites, understanding pharmacophore requirements, designing novel ligands, and inferring structure-activity relationships. In this study, we performed a large-scale analysis of the PDB by integrating different ligand-based and structure-based approaches, with the aim of identifying promising target associations for polypharmacology based on reported crystal structure information. First, the 2D and 3D similarity profiles of the crystallographic ligands were evaluated using different ligand-based methods. Then, activity data of pairs of similar ligands binding to different targets were inspected by comparing structural information with bioactivity annotations reported in the ChEMBL, BindingDB, BindingMOAD, and PDBbind databases. Afterward, extensive docking screenings of ligands in the identified cross-targets were made in order to validate and refine the ligand-based results. Finally, the therapeutic relevance of the identified target combinations for polypharmacology was evaluated from comparison with information on therapeutic targets reported in the Therapeutic Target Database (TTD). The results led to the identification of several target associations with high therapeutic potential for polypharmacology.
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Affiliation(s)
- Luca Pinzi
- Department of Life Sciences , University of Modena and Reggio Emilia , Via Giuseppe Campi 103 , 41125 Modena , Italy
| | - Giulio Rastelli
- Department of Life Sciences , University of Modena and Reggio Emilia , Via Giuseppe Campi 103 , 41125 Modena , Italy
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32
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Karasev D, Sobolev B, Lagunin A, Filimonov D, Poroikov V. Prediction of Protein-Ligand Interaction Based on the Positional Similarity Scores Derived from Amino Acid Sequences. Int J Mol Sci 2019; 21:ijms21010024. [PMID: 31861473 PMCID: PMC6981593 DOI: 10.3390/ijms21010024] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/13/2019] [Accepted: 12/16/2019] [Indexed: 12/14/2022] Open
Abstract
The affinity of different drug-like ligands to multiple protein targets reflects general chemical–biological interactions. Computational methods estimating such interactions analyze the available information about the structure of the targets, ligands, or both. Prediction of protein–ligand interactions based on pairwise sequence alignment provides reasonable accuracy if the ligands’ specificity well coincides with the phylogenic taxonomy of the proteins. Methods using multiple alignment require an accurate match of functionally significant residues. Such conditions may not be met in the case of diverged protein families. To overcome these limitations, we propose an approach based on the analysis of local sequence similarity within the set of analyzed proteins. The positional scores, calculated by sequence fragment comparisons, are used as input data for the Bayesian classifier. Our approach provides a prediction accuracy comparable or exceeding those of other methods. It was demonstrated on the popular Gold Standard test sets, presenting different sequence heterogeneity and varying from the group, including different protein families to the more specific groups. A reasonable prediction accuracy was also found for protein kinases, displaying weak relationships between sequence phylogeny and inhibitor specificity. Thus, our method can be applied to the broad area of protein–ligand interactions.
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Affiliation(s)
- Dmitry Karasev
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow 119121, Russia; (B.S.); (A.L.); (D.F.); (V.P.)
- Correspondence:
| | - Boris Sobolev
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow 119121, Russia; (B.S.); (A.L.); (D.F.); (V.P.)
| | - Alexey Lagunin
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow 119121, Russia; (B.S.); (A.L.); (D.F.); (V.P.)
- Department of Bioinformatics, Russian National Research Medical University, Moscow 117997, Russia
| | - Dmitry Filimonov
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow 119121, Russia; (B.S.); (A.L.); (D.F.); (V.P.)
| | - Vladimir Poroikov
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow 119121, Russia; (B.S.); (A.L.); (D.F.); (V.P.)
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miRNAs that Induce Human Cardiomyocyte Proliferation Converge on the Hippo Pathway. Cell Rep 2019; 23:2168-2174. [PMID: 29768213 PMCID: PMC6261450 DOI: 10.1016/j.celrep.2018.04.049] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 07/28/2017] [Accepted: 04/12/2018] [Indexed: 11/23/2022] Open
Abstract
Understanding the mechanisms that control human cardiomyocyte proliferation might be applicable to regenerative medicine. We screened a whole genome collection of human miRNAs, identifying 96 to be capable of increasing proliferation (DNA synthesis and cytokinesis) of human iPSC-derived cardiomyocytes. Chemical screening and computational approaches indicated that most of these miRNAs (67) target different components of the Hippo pathway and that their activity depends on the nuclear translocation of the Hippo transcriptional effector YAP. 53 of the 67 miRNAs are present in human iPSC cardiomyocytes, yet anti-miRNA screening revealed that none are individually essential for basal proliferation of hiPSC cardiomyocytes despite the importance of YAP for proliferation. We propose a model in which multiple endogenous miRNAs redundantly suppress Hippo signaling to sustain the cell cycle of immature cardiomyocytes.
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Downregulation of GRK5 hampers the migration of breast cancer cells. Sci Rep 2019; 9:15548. [PMID: 31664083 PMCID: PMC6820534 DOI: 10.1038/s41598-019-51923-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 10/07/2019] [Indexed: 12/20/2022] Open
Abstract
Sunitinib is a multispecific kinase inhibitor and one of its targets is the kinase GRK5, which is regulating a multitude of G protein-coupled receptors (GPCRs). In this study we demonstrate that a decreased GRK5 expression induced by knock-down experiments or sunitinib treatment hampers the migration of cancer cell lines. A proteomic analysis revealed many pathways related to cell migration which were down regulated upon the GRK5 knock-down. Furthermore, we found in MDA-MB-231 breast cancer cells that the inhibition of migration is mediated by the GPCR gastrin releasing peptide receptor (GRPR) leading to a reduced expression of migration regulating downstream targets like CDC42 and ROCK1. An in silico Kaplan Meier analysis revealed that GRK5 and GRPR overexpression reduces the distant metastasis free survival in triple-negative breast cancer (TNBC) patients. Thus, we suggest a novel anti-migratory effect of impaired GRK5 expression which induces a negative feedback loop on GRPR signalling.
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Kong YL, Wang YF, Zhu ZS, Deng ZW, Chen J, Zhang D, Jiang QH, Zhao SC, Zhang YD. Silencing of the MEKK2/MEKK3 Pathway Protects against Spinal Cord Injury via the Hedgehog Pathway and the JNK Pathway. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 17:578-589. [PMID: 31382189 PMCID: PMC6682310 DOI: 10.1016/j.omtn.2019.05.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/17/2019] [Indexed: 12/15/2022]
Abstract
Spinal cord injury (SCI) is a devastating medical condition, often accompanied by motor and sensory dysfunction. The Hedgehog (Hh) pathway has a protective role in pathological injury after SCI. However, the specific mechanism remains unclear. The present study aimed to confirm the effects of the mitogen-activated protein kinase kinase-2 (MEKK2)/MEKK3/JNK/Hh pathway on SCI. SCI rat models were established and then inoculated with plasmids overexpressing MEKK2/MEKK3 or with small interfering RNA (siRNA) against MEKK2/MEKK3. The expression of MEKK2 and -3 was detected in dorsal root ganglia (DRG) cells. The motor function of hindlimbs, the expression of the c-Jun N-terminal kinase (JNK)- and Hh-pathway-related genes, and the level of neurofilament-200 (NF-200) and glial fibrillary acidic protein (GFAP) were measured. MEKK2 and -3 were expressed at a high level in DRG cells. The silencing of MEKK2/MEKK3 in rats caused an increase in the expression of glioma-associated oncogene homolog-1 (Gli-1), Nestin, smoothened (Smo), and Sonic Hedgehog (Shh). The Basso, Beattie, and Bresnahan (BBB) rating and the level of NF-200 protein also increased. However, the expression of monocyte chemoattractant protein-1 (MCP-1), macrophage inflammatory protein-1β (MIP-1β), MIP-3α, p-JNK/JNK, and p-c-Jun/c-Jun and the level of GFAP were reduced. Downregulation of MEKK2/MEKK3 ameliorated the symptoms of SCI by promoting neural progenitor cell differentiation via activating the Hh pathway and disrupting the JNK pathway. The findings in this study reveal a potential biomarker for SCI treatment.
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Affiliation(s)
- Yan-Long Kong
- Department of Orthopaedics, Fengxian Hospital Affiliated to Anhui University of Science and Technology, 6600 Nanfeng Road, Shanghai 201499, People’s Republic of China
| | - Yi-Fei Wang
- Department of Orthopaedics, Fengxian Hospital Affiliated to Southern Medical University, 6600 Nanfeng Road, Shanghai 201499, People’s Republic of China
| | - Zhong-Sheng Zhu
- Department of Orthopaedics, Fengxian Hospital Affiliated to Southern Medical University, 6600 Nanfeng Road, Shanghai 201499, People’s Republic of China
| | - Zheng-Wei Deng
- Graduate School, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, People’s Republic of China
| | - Jing Chen
- Graduate School, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, People’s Republic of China
| | - Dong Zhang
- Department of Orthopaedics, Fengxian Hospital Affiliated to Southern Medical University, 6600 Nanfeng Road, Shanghai 201499, People’s Republic of China
| | - Qun-Hua Jiang
- Department of Orthopaedics, Fengxian Hospital Affiliated to Southern Medical University, 6600 Nanfeng Road, Shanghai 201499, People’s Republic of China
- Corresponding author: Qun-Hua Jiang, Department of Orthopaedics, Fengxian Hospital Affiliated to Southern Medical University, 6600 Nanfeng Road, Shanghai 201499, People’s Republic of China.
| | - Shi-Chang Zhao
- Department of Orthopedic Surgery, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai Jiao Tong University, 600 Yishan Road, Shanghai 200233, People’s Republic of China
- Corresponding author: Shi-Chang Zhao, Dr., Department of Orthopedic Surgery, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai Jiao Tong University, 600 Yishan Road, Shanghai 200233, People’s Republic of China.
| | - Ya-Dong Zhang
- Department of Orthopaedics, Fengxian Hospital Affiliated to Anhui University of Science and Technology, 6600 Nanfeng Road, Shanghai 201499, People’s Republic of China
- Department of Orthopaedics, Fengxian Hospital Affiliated to Southern Medical University, 6600 Nanfeng Road, Shanghai 201499, People’s Republic of China
- Corresponding author: Ya-Dong Zhang, Dr., Department of Orthopaedics, Fengxian Hospital Affiliated to Anhui University of Science and Technology, 6600 Nanfeng Road, Shanghai 201499, People’s Republic of China.
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Kinase Inhibitors with Antiepileptic Properties Identified with a Novel in Vitro Screening Platform. Int J Mol Sci 2019; 20:ijms20102502. [PMID: 31117204 PMCID: PMC6566965 DOI: 10.3390/ijms20102502] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 02/06/2023] Open
Abstract
Kinase signaling plays an important role in acquired epilepsy, but only a small percentage of the total kinome has been investigated in this context. A major roadblock that prevents the systematic investigation of the contributions of kinase signaling networks is the slow speed of experiments designed to test the chronic effects of target inhibition in epilepsy models. We developed a novel in vitro screening platform based on microwire recordings from an organotypic hippocampal culture model of acquired epilepsy. This platform enables the direct, parallel determination of the effects of compounds on spontaneous epileptiform activity. The platform also enables repeated recordings from the same culture over two-week long experiments. We screened 45 kinase inhibitors and quantified their effects on seizure duration, the frequency of paroxysmal activity, and electrographic load. We identified several inhibitors with previously unknown antiepileptic properties. We also used kinase inhibition profile cross-referencing to identify kinases that are inhibited by seizure-suppressing compounds, but not by compounds that had no effect on seizures.
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37
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Ashraf S, Bell S, O'Leary C, Canning P, Micu I, Fernandez JA, O'Hare M, Barabas P, McCauley H, Brazil DP, Stitt AW, McGeown JG, Curtis TM. CAMKII as a therapeutic target for growth factor-induced retinal and choroidal neovascularization. JCI Insight 2019; 4:122442. [PMID: 30721154 PMCID: PMC6482993 DOI: 10.1172/jci.insight.122442] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 01/31/2019] [Indexed: 12/14/2022] Open
Abstract
While anti-VEGF drugs are commonly used to inhibit pathological retinal and choroidal neovascularization, not all patients respond in an optimal manner. Mechanisms underpinning resistance to anti‑VEGF therapy include the upregulation of other proangiogenic factors. Therefore, therapeutic strategies that simultaneously target multiple growth factor signaling pathways would have significant value. Here, we show that Ca2+/calmodulin-dependent kinase II (CAMKII) mediates the angiogenic actions of a range of growth factors in human retinal endothelial cells and that this kinase acts as a key nodal point for the activation of several signal transduction cascades that are known to play a critical role in growth factor-induced angiogenesis. We also demonstrate that endothelial CAMKIIγ and -δ isoforms differentially regulate the angiogenic effects of different growth factors and that genetic deletion of these isoforms suppresses pathological retinal and choroidal neovascularization in vivo. Our studies suggest that CAMKII could provide a novel and efficacious target to inhibit multiple angiogenic signaling pathways for the treatment of vasoproliferative diseases of the eye. CAMKIIγ represents a particularly promising target, as deletion of this isoform inhibited pathological neovascularization, while enhancing reparative angiogenesis in the ischemic retina.
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Affiliation(s)
- Sadaf Ashraf
- Wellcome-Wolfson Institute for Experimental Medicine and
| | - Samuel Bell
- Wellcome-Wolfson Institute for Experimental Medicine and
| | | | - Paul Canning
- Wellcome-Wolfson Institute for Experimental Medicine and
| | - Ileana Micu
- Advanced Imaging Core Technology Unit, Faculty of Medicine, Health and Life Sciences, Queen's University of Belfast, Belfast, United Kingdom
| | | | - Michael O'Hare
- Wellcome-Wolfson Institute for Experimental Medicine and
| | - Peter Barabas
- Wellcome-Wolfson Institute for Experimental Medicine and
| | | | - Derek P Brazil
- Wellcome-Wolfson Institute for Experimental Medicine and
| | - Alan W Stitt
- Wellcome-Wolfson Institute for Experimental Medicine and
| | | | - Tim M Curtis
- Wellcome-Wolfson Institute for Experimental Medicine and
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38
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Comprehensive structure-activity-relationship of azaindoles as highly potent FLT3 inhibitors. Bioorg Med Chem 2019; 27:692-699. [DOI: 10.1016/j.bmc.2019.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 12/13/2022]
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39
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Dadashian EL, McAuley EM, Liu D, Shaffer AL, Young RM, Iyer JR, Kruhlak MJ, Staudt LM, Wiestner A, Herman SEM. TLR Signaling Is Activated in Lymph Node-Resident CLL Cells and Is Only Partially Inhibited by Ibrutinib. Cancer Res 2019; 79:360-371. [PMID: 30498085 PMCID: PMC6342512 DOI: 10.1158/0008-5472.can-18-0781] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 08/01/2018] [Accepted: 11/19/2018] [Indexed: 12/17/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is a malignancy of mature B cells driven by B-cell receptor (BCR) signaling and activated primarily in the lymph node. The Bruton's tyrosine kinase (BTK) inhibitor ibrutinib effectively inhibits BCR-dependent proliferation and survival signals and has emerged as a breakthrough therapy for CLL. However, complete remissions are uncommon and are achieved only after years of continuous therapy. We hypothesized that other signaling pathways that sustain CLL cell survival are only partially inhibited by ibrutinib. In normal B cells, Toll-like receptor (TLR) signaling cooperates with BCR signaling to activate prosurvival NF-κB. Here, we show that an experimentally validated gene signature of TLR activation is overexpressed in lymph node-resident CLL cells compared with cells in the blood. Consistent with TLR activation, we detected phosphorylation of NF-κB, STAT1, and STAT3 in lymph node-resident CLL cells and in cells stimulated with CpG oligonucleotides in vitro. CpG promoted IRAK1 degradation, secretion of IL10, and extended survival of CLL cells in culture. CpG-induced TLR signaling was significantly inhibited by both an IRAK1/4 inhibitor and ibrutinib. Although inhibition of TLR signaling was incomplete with either drug, the combination achieved superior results, including more effective inhibition of TLR-mediated survival signaling. Our data suggest an important role for TLR signaling in CLL pathogenesis and in sustaining the viability of CLL cells during ibrutinib therapy. The combination of ibrutinib with a TLR pathway inhibitor could provide superior antitumor activity and should be investigated in clinical studies. SIGNIFICANCE: CLL relies on the concomitant cooperation of B-cell receptor and Toll-like receptor signaling; inhibition of both pathways is superior to inhibition of either pathway alone. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/79/2/360/F1.large.jpg.
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MESH Headings
- Adenine/analogs & derivatives
- Agammaglobulinaemia Tyrosine Kinase/antagonists & inhibitors
- Agammaglobulinaemia Tyrosine Kinase/metabolism
- Cell Proliferation/drug effects
- Cell Survival/drug effects
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Lymph Nodes/drug effects
- Lymph Nodes/metabolism
- Lymph Nodes/pathology
- Oligodeoxyribonucleotides/pharmacology
- Piperidines
- Protein Kinase Inhibitors/pharmacology
- Pyrazoles/pharmacology
- Pyrimidines/pharmacology
- Receptor Cross-Talk
- Receptors, Antigen, B-Cell/antagonists & inhibitors
- Receptors, Antigen, B-Cell/metabolism
- Signal Transduction/drug effects
- Toll-Like Receptors/antagonists & inhibitors
- Toll-Like Receptors/metabolism
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Affiliation(s)
- Eman L Dadashian
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Erin M McAuley
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Delong Liu
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Arthur L Shaffer
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Ryan M Young
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Jessica R Iyer
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Michael J Kruhlak
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Louis M Staudt
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Adrian Wiestner
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Sarah E M Herman
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland.
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Jorda R, Hendrychová D, Voller J, Řezníčková E, Gucký T, Kryštof V. How Selective Are Pharmacological Inhibitors of Cell-Cycle-Regulating Cyclin-Dependent Kinases? J Med Chem 2018; 61:9105-9120. [PMID: 30234987 DOI: 10.1021/acs.jmedchem.8b00049] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cyclin-dependent kinases (CDKs) are an important and emerging class of drug targets for which many small-molecule inhibitors have been developed. However, there is often insufficient data available on the selectivity of CDK inhibitors (CDKi) to attribute the effects on the presumed target CDK to these inhibitors. Here, we highlight discrepancies between the kinase selectivity of CDKi and the phenotype exhibited; we evaluated 31 CDKi (claimed to target CDK1-4) for activity toward CDKs 1, 2, 4, 5, 7, 9 and for effects on the cell cycle. Our results suggest that most CDKi should be reclassified as pan-selective and should not be used as a tool. In addition, some compounds did not even inhibit CDKs as their primary cellular targets; for example, NU6140 showed potent inhibition of Aurora kinases. We also established an online database of commercially available CDKi for critical evaluation of their utility as molecular probes. Our results should help researchers select the most relevant chemical tools for their specific applications.
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Affiliation(s)
- Radek Jorda
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
| | - Denisa Hendrychová
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
| | - Jiří Voller
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
| | - Eva Řezníčková
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
| | - Tomáš Gucký
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
| | - Vladimír Kryštof
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
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KInhibition: A Kinase Inhibitor Selection Portal. iScience 2018; 8:49-53. [PMID: 30273912 PMCID: PMC6170255 DOI: 10.1016/j.isci.2018.09.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/21/2018] [Accepted: 09/10/2018] [Indexed: 01/27/2023] Open
Abstract
Protein kinases constitute a large class of signaling molecules frequently targeted in research and clinical uses. However, kinase inhibitors are notoriously non-specific, making it difficult to select an appropriate inhibitor for a given kinase. Available data from large-scale kinase inhibitor screens are often difficult to query. Here, we present KInhibition (https://kinhibition.fredhutch.org), an online portal that allows users to search publicly available datasets to find selective inhibitors for a chosen kinase or group of kinases. Compounds are sorted by a KInhibition Selectivity Score, calculated based on compounds' activity against the selected kinase(s) versus activity against all other kinases for which that compound has been profiled. The current version allows users to query four datasets, with a framework that can easily accommodate additional datasets. KInhibition represents a powerful platform through which researchers from broad areas of biology, chemistry, and pharmacology can easily interrogate large datasets to help guide their selection of kinase inhibitors. An easy-to-use tool that compiles datasets from kinase inhibitor screens A KInhibition Selectivity Score quantifies each compound's selectivity Users can select kinases, view compounds and selectivity, and download the results KInhibition is broadly applicable across life science disciplines
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Hazlitt RA, Teitz T, Bonga JD, Fang J, Diao S, Iconaru L, Yang L, Goktug AN, Currier DG, Chen T, Rankovic Z, Min J, Zuo J. Development of Second-Generation CDK2 Inhibitors for the Prevention of Cisplatin-Induced Hearing Loss. J Med Chem 2018; 61:7700-7709. [PMID: 30091915 DOI: 10.1021/acs.jmedchem.8b00669] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
There are currently no FDA-approved therapies to prevent the hearing loss associated with the usage of cisplatin in chemotherapeutic regimens. We recently demonstrated that the pharmacologic inhibition with kenpaullone or genetic deletion of CDK2 preserved hearing function in animal models treated with cisplatin, which suggests that CDK2 is a promising therapeutic target to prevent cisplatin-induced ototoxicity. In this study, we identified two lead compounds, AT7519 and AZD5438, from a focused library screen of 187 CDK2 inhibitors, performed in an immortalized cell line derived from neonatal mouse cochleae treated with cisplatin. Moreover, we screened 36 analogues of AT7519 and identified analogue 7, which exhibited an improved therapeutic index. When delivered locally, analogue 7 and AZD5438 both provided significant protection against cisplatin-induced ototoxicity in mice. Thus, we have identified two additional compounds that prevent cisplatin-induced ototoxicity in vivo and provided further evidence that CDK2 is a druggable target for treating cisplatin-induced ototoxicity.
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43
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Molecular basis of Tousled-Like Kinase 2 activation. Nat Commun 2018; 9:2535. [PMID: 29955062 PMCID: PMC6023931 DOI: 10.1038/s41467-018-04941-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 06/06/2018] [Indexed: 12/21/2022] Open
Abstract
Tousled-like kinases (TLKs) are required for genome stability and normal development in numerous organisms and have been implicated in breast cancer and intellectual disability. In humans, the similar TLK1 and TLK2 interact with each other and TLK activity enhances ASF1 histone binding and is inhibited by the DNA damage response, although the molecular mechanisms of TLK regulation remain unclear. Here we describe the crystal structure of the TLK2 kinase domain. We show that the coiled-coil domains mediate dimerization and are essential for activation through ordered autophosphorylation that promotes higher order oligomers that locally increase TLK2 activity. We show that TLK2 mutations involved in intellectual disability impair kinase activity, and the docking of several small-molecule inhibitors of TLK activity suggest that the crystal structure will be useful for guiding the rationale design of new inhibition strategies. Together our results provide insights into the structure and molecular regulation of the TLKs. The Tousled-like kinase (TLKs) family belongs to a distinct branch of Ser/Thr kinases that exhibit the highest levels of activity during DNA replication. Here the authors present the crystal structure of the kinase domain from human TLK2 and propose an activation model for TLK2 based on biochemical and phosphoproteomics experiments.
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44
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Schneider P, Schneider G. Polypharmacological Drug−target Inference for Chemogenomics. Mol Inform 2018; 37:e1800050. [DOI: 10.1002/minf.201800050] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 04/24/2018] [Indexed: 01/10/2023]
Affiliation(s)
- Petra Schneider
- Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology (ETH); Vladimir-Prelog-Weg 4 CH-8093 Zurich Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology (ETH); Vladimir-Prelog-Weg 4 CH-8093 Zurich Switzerland
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45
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Pogodin PV, Lagunin AA, Rudik AV, Filimonov DA, Druzhilovskiy DS, Nicklaus MC, Poroikov VV. How to Achieve Better Results Using PASS-Based Virtual Screening: Case Study for Kinase Inhibitors. Front Chem 2018; 6:133. [PMID: 29755970 PMCID: PMC5935003 DOI: 10.3389/fchem.2018.00133] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/09/2018] [Indexed: 12/16/2022] Open
Abstract
Discovery of new pharmaceutical substances is currently boosted by the possibility of utilization of the Synthetically Accessible Virtual Inventory (SAVI) library, which includes about 283 million molecules, each annotated with a proposed synthetic one-step route from commercially available starting materials. The SAVI database is well-suited for ligand-based methods of virtual screening to select molecules for experimental testing. In this study, we compare the performance of three approaches for the analysis of structure-activity relationships that differ in their criteria for selecting of "active" and "inactive" compounds included in the training sets. PASS (Prediction of Activity Spectra for Substances), which is based on a modified Naïve Bayes algorithm, was applied since it had been shown to be robust and to provide good predictions of many biological activities based on just the structural formula of a compound even if the information in the training set is incomplete. We used different subsets of kinase inhibitors for this case study because many data are currently available on this important class of drug-like molecules. Based on the subsets of kinase inhibitors extracted from the ChEMBL 20 database we performed the PASS training, and then applied the model to ChEMBL 23 compounds not yet present in ChEMBL 20 to identify novel kinase inhibitors. As one may expect, the best prediction accuracy was obtained if only the experimentally confirmed active and inactive compounds for distinct kinases in the training procedure were used. However, for some kinases, reasonable results were obtained even if we used merged training sets, in which we designated as inactives the compounds not tested against the particular kinase. Thus, depending on the availability of data for a particular biological activity, one may choose the first or the second approach for creating ligand-based computational tools to achieve the best possible results in virtual screening.
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Affiliation(s)
- Pavel V. Pogodin
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
| | - Alexey A. Lagunin
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
- Department of Bioinformatics, Medical-Biological Department, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Anastasia V. Rudik
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
| | - Dmitry A. Filimonov
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
| | | | - Mark C. Nicklaus
- Computer-Aided Drug Design Group, Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, NIH, NCI-Frederick, Frederick, MD, United States
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46
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Klaeger S, Heinzlmeir S, Wilhelm M, Polzer H, Vick B, Koenig PA, Reinecke M, Ruprecht B, Petzoldt S, Meng C, Zecha J, Reiter K, Qiao H, Helm D, Koch H, Schoof M, Canevari G, Casale E, Depaolini SR, Feuchtinger A, Wu Z, Schmidt T, Rueckert L, Becker W, Huenges J, Garz AK, Gohlke BO, Zolg DP, Kayser G, Vooder T, Preissner R, Hahne H, Tõnisson N, Kramer K, Götze K, Bassermann F, Schlegl J, Ehrlich HC, Aiche S, Walch A, Greif PA, Schneider S, Felder ER, Ruland J, Médard G, Jeremias I, Spiekermann K, Kuster B. The target landscape of clinical kinase drugs. Science 2018; 358:358/6367/eaan4368. [PMID: 29191878 DOI: 10.1126/science.aan4368] [Citation(s) in RCA: 512] [Impact Index Per Article: 85.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 09/20/2017] [Indexed: 02/06/2023]
Abstract
Kinase inhibitors are important cancer therapeutics. Polypharmacology is commonly observed, requiring thorough target deconvolution to understand drug mechanism of action. Using chemical proteomics, we analyzed the target spectrum of 243 clinically evaluated kinase drugs. The data revealed previously unknown targets for established drugs, offered a perspective on the "druggable" kinome, highlighted (non)kinase off-targets, and suggested potential therapeutic applications. Integration of phosphoproteomic data refined drug-affected pathways, identified response markers, and strengthened rationale for combination treatments. We exemplify translational value by discovering SIK2 (salt-inducible kinase 2) inhibitors that modulate cytokine production in primary cells, by identifying drugs against the lung cancer survival marker MELK (maternal embryonic leucine zipper kinase), and by repurposing cabozantinib to treat FLT3-ITD-positive acute myeloid leukemia. This resource, available via the ProteomicsDB database, should facilitate basic, clinical, and drug discovery research and aid clinical decision-making.
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Affiliation(s)
- Susan Klaeger
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stephanie Heinzlmeir
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Harald Polzer
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Internal Medicine III, University Hospital, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Binje Vick
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, German Center for Environmental Health (HMGU), Munich, Germany
| | | | - Maria Reinecke
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Benjamin Ruprecht
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Svenja Petzoldt
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Chen Meng
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Jana Zecha
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Katrin Reiter
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Internal Medicine III, University Hospital, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Huichao Qiao
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Dominic Helm
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Heiner Koch
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Schoof
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | | | - Elena Casale
- Oncology, Nerviano Medical Sciences Srl, Milan, Italy
| | | | - Annette Feuchtinger
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Zhixiang Wu
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Tobias Schmidt
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | | | | | | | - Anne-Kathrin Garz
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Medicine III, Klinikum rechts der Isar, TUM, Munich, Germany
| | - Bjoern-Oliver Gohlke
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Structural Bioinformatics Group, Charité-Universitätsmedizin, Berlin, Germany
| | - Daniel Paul Zolg
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Gian Kayser
- Institute of Surgical Pathology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tonu Vooder
- Center of Thoracic Surgery, Krefeld, Germany.,Estonian Genome Center, University of Tartu, Tartu, Estonia.,Tartu University Hospital, Tartu, Estonia
| | - Robert Preissner
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Structural Bioinformatics Group, Charité-Universitätsmedizin, Berlin, Germany
| | - Hannes Hahne
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Neeme Tõnisson
- Estonian Genome Center, University of Tartu, Tartu, Estonia.,Tartu University Hospital, Tartu, Estonia
| | - Karl Kramer
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Katharina Götze
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Medicine III, Klinikum rechts der Isar, TUM, Munich, Germany
| | - Florian Bassermann
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Medicine III, Klinikum rechts der Isar, TUM, Munich, Germany
| | | | | | | | - Axel Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Philipp A Greif
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Internal Medicine III, University Hospital, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Sabine Schneider
- Department of Chemistry, TUM, Garching, Germany.,Center For Integrated Protein Science Munich (CIPSM), Munich, Germany
| | | | - Juergen Ruland
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institut für Klinische Chemie und Pathobiochemie, TUM, Munich, Germany
| | - Guillaume Médard
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Irmela Jeremias
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, German Center for Environmental Health (HMGU), Munich, Germany.,Department of Pediatrics, Dr von Hauner Children's Hospital, LMU, Munich, Germany
| | - Karsten Spiekermann
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Internal Medicine III, University Hospital, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany. .,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Center For Integrated Protein Science Munich (CIPSM), Munich, Germany.,Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), TUM, Freising, Germany
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47
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Cheminformatics Analysis of Dynamic WNK-Inhibitor Interactions. Mol Inform 2018; 37:e1700138. [DOI: 10.1002/minf.201700138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 02/05/2018] [Indexed: 11/07/2022]
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48
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Selective inhibition reveals cyclin-dependent kinase 2 as another kinase that phosphorylates the androgen receptor at serine 81. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:354-363. [DOI: 10.1016/j.bbamcr.2017.11.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 11/10/2017] [Accepted: 11/16/2017] [Indexed: 12/22/2022]
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49
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Wells CI, Kapadia NR, Couñago RM, Drewry DH. In depth analysis of kinase cross screening data to identify chemical starting points for inhibition of the Nek family of kinases. MEDCHEMCOMM 2018; 9:44-66. [PMID: 30108900 PMCID: PMC6071746 DOI: 10.1039/c7md00510e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 11/01/2017] [Indexed: 01/11/2023]
Abstract
Potent, selective, and cell active small molecule kinase inhibitors are useful tools to help unravel the complexities of kinase signaling. As the biological functions of individual kinases become better understood, they can become targets of drug discovery efforts. The small molecules used to shed light on function can also then serve as chemical starting points in these drug discovery efforts. The Nek family of kinases has received very little attention, as judged by number of citations in PubMed, yet they appear to play many key roles and have been implicated in disease. Here we present our work to identify high quality chemical starting points that have emerged due to the increased incidence of broad kinome screening. We anticipate that this analysis will allow the community to progress towards the generation of chemical probes and eventually drugs that target members of the Nek family.
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Affiliation(s)
- C I Wells
- Structural Genomics Consortium , Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , NC , 27599 USA .
| | - N R Kapadia
- Structural Genomics Consortium , Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , NC , 27599 USA .
| | - R M Couñago
- Structural Genomics Consortium , Universidade Estadual de Campinas - UNICAMP , Campinas , SP , 13083 Brazil
| | - D H Drewry
- Structural Genomics Consortium , Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , NC , 27599 USA .
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50
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Wei S, Li L, Shu Y, Zhao K, Ji Z. Synthesis, antifungal and antitumor activity of two new types of imidazolin-2-ones. Bioorg Med Chem 2017; 25:6501-6510. [DOI: 10.1016/j.bmc.2017.10.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/18/2017] [Accepted: 10/20/2017] [Indexed: 11/29/2022]
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