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Mo C, Wei N, Li T, Ahmed Bhat M, Mohammadi M, Kuang C. CDK9 inhibitors for the treatment of solid tumors. Biochem Pharmacol 2024; 229:116470. [PMID: 39127153 DOI: 10.1016/j.bcp.2024.116470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 08/04/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024]
Abstract
Cyclin-dependent kinase 9 (CDK9) regulates mRNA transcription by promoting RNA Pol II elongation. CDK9 is now emerging as a potential therapeutic target for cancer, since its overexpression has been found to correlate with cancer development and worse clinical outcomes. While much work on CDK9 inhibition has focused on hematologic malignancies, the role of this cancer driver in solid tumors is starting to come into focus. Many solid cancers also overexpress CDK9 and depend on its activity to promote downstream oncogenic signaling pathways. In this review, we summarize the latest knowledge of CDK9 biology in solid tumors and the studies of small molecule CDK9 inhibitors. We discuss the results of the latest clinical trials of CDK9 inhibitors in solid tumors, with a focus on key issues to consider for improving the therapeutic impact of this drug class.
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Affiliation(s)
- Christiana Mo
- Department of Oncology, Montefiore Einstein, Bronx, NY, USA; Montefiore Einstein Comprehensive Cancer Center, Bronx, NY, USA
| | - Ning Wei
- Department of Oncology, Montefiore Einstein, Bronx, NY, USA; Montefiore Einstein Comprehensive Cancer Center, Bronx, NY, USA; Department of Molecular Pharmacology, Montefiore Einstein, Bronx, NY, USA
| | - Terence Li
- Department of Oncology, Montefiore Einstein, Bronx, NY, USA; Montefiore Einstein Comprehensive Cancer Center, Bronx, NY, USA; Department of Molecular Pharmacology, Montefiore Einstein, Bronx, NY, USA
| | - Muzaffer Ahmed Bhat
- Department of Oncology, Montefiore Einstein, Bronx, NY, USA; Montefiore Einstein Comprehensive Cancer Center, Bronx, NY, USA; Department of Molecular Pharmacology, Montefiore Einstein, Bronx, NY, USA
| | - Mahshid Mohammadi
- Department of Oncology, Montefiore Einstein, Bronx, NY, USA; Montefiore Einstein Comprehensive Cancer Center, Bronx, NY, USA; Department of Molecular Pharmacology, Montefiore Einstein, Bronx, NY, USA
| | - Chaoyuan Kuang
- Department of Oncology, Montefiore Einstein, Bronx, NY, USA; Montefiore Einstein Comprehensive Cancer Center, Bronx, NY, USA; Department of Molecular Pharmacology, Montefiore Einstein, Bronx, NY, USA.
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2
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Karimbayli J, Pellarin I, Belletti B, Baldassarre G. Insights into the structural and functional activities of forgotten Kinases: PCTAIREs CDKs. Mol Cancer 2024; 23:135. [PMID: 38951876 PMCID: PMC11218289 DOI: 10.1186/s12943-024-02043-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 06/12/2024] [Indexed: 07/03/2024] Open
Abstract
In cells, signal transduction heavily relies on the intricate regulation of protein kinases, which provide the fundamental framework for modulating most signaling pathways. Dysregulation of kinase activity has been implicated in numerous pathological conditions, particularly in cancer. The druggable nature of most kinases positions them into a focal point during the process of drug development. However, a significant challenge persists, as the role and biological function of nearly one third of human kinases remains largely unknown.Within this diverse landscape, cyclin-dependent kinases (CDKs) emerge as an intriguing molecular subgroup. In human, this kinase family encompasses 21 members, involved in several key biological processes. Remarkably, 13 of these CDKs belong to the category of understudied kinases, and only 5 having undergone broad investigation to date. This knowledge gap underscores the pressing need to delve into the study of these kinases, starting with a comprehensive review of the less-explored ones.Here, we will focus on the PCTAIRE subfamily of CDKs, which includes CDK16, CDK17, and CDK18, arguably among the most understudied CDKs members. To contextualize PCTAIREs within the spectrum of human pathophysiology, we conducted an exhaustive review of the existing literature and examined available databases. This approach resulted in an articulate depiction of these PCTAIREs, encompassing their expression patterns, 3D configurations, mechanisms of activation, and potential functions in normal tissues and in cancer.We propose that this effort offers the possibility of identifying promising areas of future research that extend from basic research to potential clinical and therapeutic applications.
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Affiliation(s)
- Javad Karimbayli
- Division of Molecular Oncology, Centro di Riferimento Oncologico (CRO) of Aviano, IRCCS, National Cancer Institute, Via Franco Gallini, Aviano, 33081, Italy
| | - Ilenia Pellarin
- Division of Molecular Oncology, Centro di Riferimento Oncologico (CRO) of Aviano, IRCCS, National Cancer Institute, Via Franco Gallini, Aviano, 33081, Italy
| | - Barbara Belletti
- Division of Molecular Oncology, Centro di Riferimento Oncologico (CRO) of Aviano, IRCCS, National Cancer Institute, Via Franco Gallini, Aviano, 33081, Italy
| | - Gustavo Baldassarre
- Division of Molecular Oncology, Centro di Riferimento Oncologico (CRO) of Aviano, IRCCS, National Cancer Institute, Via Franco Gallini, Aviano, 33081, Italy.
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3
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Zhang Y, Shan L, Tang W, Ge Y, Li C, Zhang J. Recent Discovery and Development of Inhibitors that Target CDK9 and Their Therapeutic Indications. J Med Chem 2024; 67:5185-5215. [PMID: 38564299 DOI: 10.1021/acs.jmedchem.4c00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
CDK9 is a cyclin-dependent kinase that plays pivotal roles in multiple cellular functions including gene transcription, cell cycle regulation, DNA damage repair, and cellular differentiation. Targeting CDK9 is considered an attractive strategy for antitumor therapy, especially for leukemia and lymphoma. Several potent small molecule inhibitors, exemplified by TG02 (4), have progressed to clinical trials. However, many of them face challenges such as low clinical efficacy and multiple adverse reactions and may necessitate the exploration of novel strategies to lead to success in the clinic. In this perspective, we present a comprehensive overview of the structural characteristics, biological functions, and preclinical status of CDK9 inhibitors. Our focus extends to various types of inhibitors, including pan-inhibitors, selective inhibitors, dual-target inhibitors, degraders, PPI inhibitors, and natural products. The discussion encompasses chemical structures, structure-activity relationships (SARs), biological activities, selectivity, and therapeutic potential, providing detailed insight into the diverse landscape of CDK9 inhibitors.
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Affiliation(s)
- Yuming Zhang
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
- West China College of Medicine, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Lianhai Shan
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031 Sichuan, China
| | - Wentao Tang
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Yating Ge
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - ChengXian Li
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Jifa Zhang
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
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4
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Wang H, Ba J, Kang Y, Gong Z, Liang T, Zhang Y, Qi J, Wang J. Recent Progress in CDK4/6 Inhibitors and PROTACs. Molecules 2023; 28:8060. [PMID: 38138549 PMCID: PMC10745860 DOI: 10.3390/molecules28248060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Cell division in eukaryotes is a highly regulated process that is critical to the life of a cell. Dysregulated cell proliferation, often driven by anomalies in cell Cyclin-dependent kinase (CDK) activation, is a key pathological mechanism in cancer. Recently, selective CDK4/6 inhibitors have shown clinical success, particularly in treating advanced-stage estrogen receptor (ER)-positive and human epidermal growth factor receptor 2 (HER2)-negative breast cancer. This review provides an in-depth analysis of the action mechanism and recent advancements in CDK4/6 inhibitors, categorizing them based on their structural characteristics and origins. Furthermore, it explores proteolysis targeting chimers (PROTACs) targeting CDK4/6. We hope that this review could be of benefit for further research on CDK4/6 inhibitors and PROTACs.
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Affiliation(s)
| | | | | | | | | | | | - Jianguo Qi
- Key Laboratory of Natural Medicine and Immuno-Engineering of Henan Province, Henan University Jinming Campus, Kaifeng 475004, China
| | - Jianhong Wang
- Key Laboratory of Natural Medicine and Immuno-Engineering of Henan Province, Henan University Jinming Campus, Kaifeng 475004, China
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Sarott R, Gourisankar S, Karim B, Nettles S, Yang H, Dwyer BG, Simanauskaite JM, Tse J, Abuzaid H, Krokhotin A, Zhang T, Hinshaw SM, Green MR, Crabtree GR, Gray NS. Borrowing Transcriptional Kinases to Activate Apoptosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563687. [PMID: 37961702 PMCID: PMC10634765 DOI: 10.1101/2023.10.23.563687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Protein kinases are disease drivers whose therapeutic targeting traditionally centers on inhibition of enzymatic activity. Here chemically induced proximity is leveraged to convert kinase inhibitors into context-specific activators of therapeutic genes. Bivalent molecules that link ligands of the transcription factor B-cell lymphoma 6 (BCL6) to ATP-competitive inhibitors of cyclin-dependent kinases (CDKs) were developed to re-localize CDK to BCL6-bound loci on chromatin and direct phosphorylation of RNA Pol II. The resulting BCL6-target proapoptotic gene expression translated into killing of diffuse large B-cell lymphoma (DLBCL) cells at 72 h with EC50s of 0.9 - 10 nM and highly specific ablation of the BCL6-regulated germinal center response in mice. The molecules exhibited 10,000-fold lower cytotoxicity in normal lymphocytes and are well tolerated in mice. Genomic and proteomic evidence corroborated a gain-of-function mechanism where, instead of global enzyme inhibition, a fraction of total kinase activity is borrowed and re-localized to BCL6-bound loci. The strategy demonstrates how kinase inhibitors can be used to context-specifically activate transcription, accessing new therapeutic space.
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Zeng Y, Xiao J, Xu Y, Wei F, Tian L, Gao Y, Chen Y, Hu Y. Degradation of Cyclin-Dependent Kinase 9/Cyclin T1 by Optimized Microtubule-Associated Protein 1 Light Chain 3 Beta-Recruiting Coumarin Analogs. J Med Chem 2023; 66:12877-12893. [PMID: 37671907 DOI: 10.1021/acs.jmedchem.3c00828] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Autophagy is an efficient and attractive protein degradation pathway in addition to the ubiquitin-proteasome system. Herein, systematic optimization of coumarin analogs linked with the CDK9 inhibitor SNS-032 is reported that may bind to cyclin-dependent kinase 9 (CDK9) and microtubule-associated protein 1 light chain 3 beta (LC3B) simultaneously, which leads to the selective autophagic degradation of targeted CDK9/cyclin T1 and is different from the PROTAC degrader THAL-SNS-032. Further mechanism studies revealed an autophagy-lysosome pathway, where the degraders possibly formed a ternary complex with CDK9 and LC3B. In addition, degrader 10 showed antitumor efficacy in vivo. Our work optimized a potent LC3B recruiter and demonstrated the feasibility of autophagy-tethering compounds (ATTECs), which could be applied for the degradation of diverse intracellular pathogenic proteins to treat related diseases.
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Affiliation(s)
- Yanping Zeng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu-Chong-Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Jian Xiao
- Division of Anti-Tumor Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Yuanxin Xu
- Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210046, China
| | - Fan Wei
- Division of Anti-Tumor Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lina Tian
- Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210046, China
| | - Yinglei Gao
- Division of Anti-Tumor Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yi Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu-Chong-Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
- Division of Anti-Tumor Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai 264117, Shandong, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Youhong Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu-Chong-Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
- Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210046, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai 264117, Shandong, China
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
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7
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Yan Z, Du Y, Zhang H, Zheng Y, Lv H, Dong N, He F. Research progress of anticancer drugs targeting CDK12. RSC Med Chem 2023; 14:1629-1644. [PMID: 37731700 PMCID: PMC10507796 DOI: 10.1039/d3md00004d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 05/17/2023] [Indexed: 09/22/2023] Open
Abstract
Cyclin-dependent kinase 12 (CDK12) is a transcription-associated CDK that plays key roles in transcription, translation, mRNA splicing, the cell cycle, and DNA damage repair. Research has identified that high expression of CDK12 in organs such as the breast, stomach, and uterus can lead to HER2-positive breast cancer, gastric cancer and cervical cancer. Inhibiting high expression of CDK12 suppresses tumor growth and proliferation, suggesting that it is both a biomarker for cancer and a potential target for cancer therapy. CDK12 inhibitors can competitively bind the CDK12 hydrophobic pocket with ATP to avoid CDK12 phosphorylation, blocking subsequent signaling pathways. The development of CDK12 inhibitors is challenging due to the high homology of CDK12 with other CDKs. This review summarizes the research progress of CDK12 inhibitors, their mechanism of action and the structure-activity relationship, providing new insights into the design of CDK12 selective inhibitors.
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Affiliation(s)
- Zhijia Yan
- School of Chemistry & Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences) 3501 Da Xue Road Jinan 250353 China
| | - Yongli Du
- School of Chemistry & Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences) 3501 Da Xue Road Jinan 250353 China
| | - Haibin Zhang
- School of Chemistry & Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences) 3501 Da Xue Road Jinan 250353 China
| | - Yong Zheng
- School of Chemistry & Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences) 3501 Da Xue Road Jinan 250353 China
| | - Huiting Lv
- School of Chemistry & Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences) 3501 Da Xue Road Jinan 250353 China
| | - Ning Dong
- School of Chemistry & Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences) 3501 Da Xue Road Jinan 250353 China
| | - Fang He
- School of Water Conservancy and Environment, University of Jinan 336 Nanxinzhuang West Road Jinan 250022 China
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8
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Quintela M, James DW, Garcia J, Edwards K, Margarit L, Das N, Lutchman-Singh K, Beynon AL, Rioja I, Prinjha RK, Harker NR, Gonzalez D, Steven Conlan R, Francis LW. In silico enhancer mining reveals SNS-032 and EHMT2 inhibitors as therapeutic candidates in high-grade serous ovarian cancer. Br J Cancer 2023:10.1038/s41416-023-02274-2. [PMID: 37120667 DOI: 10.1038/s41416-023-02274-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/29/2023] [Accepted: 04/06/2023] [Indexed: 05/01/2023] Open
Abstract
BACKGROUND Epigenomic dysregulation has been linked to solid tumour malignancies, including ovarian cancers. Profiling of re-programmed enhancer locations associated with disease has the potential to improve stratification and thus therapeutic choices. Ovarian cancers are subdivided into histological subtypes that have significant molecular and clinical differences, with high-grade serous carcinoma representing the most common and aggressive subtype. METHODS We interrogated the enhancer landscape(s) of normal ovary and subtype-specific ovarian cancer states using publicly available data. With an initial focus on H3K27ac histone mark, we developed a computational pipeline to predict drug compound activity based on epigenomic stratification. Lastly, we substantiated our predictions in vitro using patient-derived clinical samples and cell lines. RESULTS Using our in silico approach, we highlighted recurrent and privative enhancer landscapes and identified the differential enrichment of a total of 164 transcription factors involved in 201 protein complexes across the subtypes. We pinpointed SNS-032 and EHMT2 inhibitors BIX-01294 and UNC0646 as therapeutic candidates in high-grade serous carcinoma, as well as probed the efficacy of specific inhibitors in vitro. CONCLUSION Here, we report the first attempt to exploit ovarian cancer epigenomic landscapes for drug discovery. This computational pipeline holds enormous potential for translating epigenomic profiling into therapeutic leads.
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Affiliation(s)
- Marcos Quintela
- Swansea University Medical School, Swansea University, Swansea, SA2 8PP, UK
| | - David W James
- Swansea University Medical School, Swansea University, Swansea, SA2 8PP, UK
| | - Jetzabel Garcia
- Swansea University Medical School, Swansea University, Swansea, SA2 8PP, UK
| | - Kadie Edwards
- Swansea University Medical School, Swansea University, Swansea, SA2 8PP, UK
| | - Lavinia Margarit
- Swansea University Medical School, Swansea University, Swansea, SA2 8PP, UK
- Cwm Taf Morgannwg University Health Board, Swansea, SA2 8QA, UK
| | - Nagindra Das
- Swansea Bay University Health Board, Swansea, SA12 7BR, UK
| | | | | | - Inmaculada Rioja
- Immunology Research Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage, SG1 2NY, UK
| | - Rab K Prinjha
- Immunology Research Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage, SG1 2NY, UK
| | - Nicola R Harker
- Immunology Research Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage, SG1 2NY, UK
| | - Deyarina Gonzalez
- Swansea University Medical School, Swansea University, Swansea, SA2 8PP, UK
| | - R Steven Conlan
- Swansea University Medical School, Swansea University, Swansea, SA2 8PP, UK
| | - Lewis W Francis
- Swansea University Medical School, Swansea University, Swansea, SA2 8PP, UK.
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9
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Zhao HY, Xin M, Zhang SQ. Progress of small molecules for targeted protein degradation: PROTACs and other technologies. Drug Dev Res 2023; 84:337-394. [PMID: 36606428 DOI: 10.1002/ddr.22026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 12/01/2022] [Accepted: 12/17/2022] [Indexed: 01/07/2023]
Abstract
Recent years have witnessed the rapid development of targeted protein degradation (TPD), especially proteolysis targeting chimeras. These degraders have manifested many advantages over small molecule inhibitors. To date, a huge number of degraders have been excavated against over 70 disease-related targets. In particular, degraders against estrogen receptor and androgen receptor have crowded into phase II clinical trial. TPD technologies largely expand the scope of druggable targets, and provide powerful tools for addressing intractable problems that can not be tackled by traditional small molecule inhibitors. In this review, we mainly focus on the structures and biological activities of small molecule degraders as well as the elucidation of mechanisms of emerging TPD technologies. We also propose the challenges that exist in the TPD field at present.
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Affiliation(s)
- Hong-Yi Zhao
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Minhang Xin
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - San-Qi Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
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10
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He XL, Hu YH, Chen JM, Zhang DQ, Yang HL, Zhang LZ, Mu YP, Zhang H, Chen GF, Liu W, Liu P. SNS-032 attenuates liver fibrosis by anti-active hepatic stellate cells via inhibition of cyclin dependent kinase 9. Front Pharmacol 2022; 13:1016552. [PMID: 36313366 PMCID: PMC9597511 DOI: 10.3389/fphar.2022.1016552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
Liver fibrosis is a common pathological process of all chronic liver diseases. Hepatic stellate cells (HSCs) play a central role in the development of liver fibrosis. Cyclin-dependent kinase 9 (CDK9) is a cell cycle kinase that regulates mRNA transcription and elongation. A CDK9 inhibitor SNS-032 has been reported to have good effects in anti-tumor. However, the role of SNS-032 in the development of liver fibrosis is unclear. In this study, SNS-032 was found to alleviate hepatic fibrosis by inhibiting the activation and inducing the apoptosis of active HSCs in carbon tetrachloride-induced model mice. In vitro, SNS-032 inhibited the activation and proliferation of active HSCs and induced the apoptosis of active HSCs by downregulating the expression of CDK9 and its downstream signal transductors, such phosphorylated RNA polymerase II and Bcl-2. CDK9 short hairpin RNA was transfected into active HSCs to further elucidate the mechanism of the above effects. Similar results were observed in active HSCs after CDK9 knockdown. In active HSCs with CDK9 knockdown, the expression levels of CDK9, phosphorylated RNA polymerase II, XIAP, Bcl-2, Mcl-1, and ɑ-SMA significantly decreased, whereas those of cleaved-PARP1 and Bax decreased prominently. These results indicated that SNS-032 is a potential drug and CDK9 might be a new prospective target for the treatment of liver fibrosis.
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Affiliation(s)
- Xiao-Li He
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Endocrinology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yong-Hong Hu
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jia-Mei Chen
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ding-Qi Zhang
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hai-Lin Yang
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lin-Zhang Zhang
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yong-Ping Mu
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hua Zhang
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Gao-Feng Chen
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wei Liu
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Wei Liu, ; Ping Liu,
| | - Ping Liu
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Wei Liu, ; Ping Liu,
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11
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Moser R, Annis J, Nikolova O, Whatcott C, Gurley K, Mendez E, Moran-Jones K, Dorrell C, Sears RC, Kuo C, Han H, Biankin A, Grandori C, Von Hoff DD, Kemp CJ. Pharmacologic Targeting of TFIIH Suppresses KRAS-Mutant Pancreatic Ductal Adenocarcinoma and Synergizes with TRAIL. Cancer Res 2022; 82:3375-3393. [PMID: 35819261 PMCID: PMC9481717 DOI: 10.1158/0008-5472.can-21-4222] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 04/26/2022] [Accepted: 07/05/2022] [Indexed: 02/07/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) typically presents as metastatic disease at diagnosis and remains refractory to treatment. Next-generation sequencing efforts have described the genomic landscape, classified molecular subtypes, and confirmed frequent alterations in major driver genes, with coexistent alterations in KRAS and TP53 correlating with the highest metastatic burden and poorest outcomes. However, translating this information to guide therapy remains a challenge. By integrating genomic analysis with an arrayed RNAi druggable genome screen and drug profiling of a KRAS/TP53 mutant PDAC cell line derived from a patient-derived xenograft (PDCL), we identified numerous targetable vulnerabilities that reveal both known and novel functional aspects of pancreatic cancer biology. A dependence on the general transcription and DNA repair factor TFIIH complex, particularly the XPB subunit and the CAK complex (CDK7/CyclinH/MAT1), was identified and further validated utilizing a panel of genomically subtyped KRAS mutant PDCLs. TFIIH function was inhibited with a covalent inhibitor of CDK7/12/13 (THZ1), a CDK7/CDK9 kinase inhibitor (SNS-032), and a covalent inhibitor of XPB (triptolide), which led to disruption of the protein stability of the RNA polymerase II subunit RPB1. Loss of RPB1 following TFIIH inhibition led to downregulation of key transcriptional effectors of KRAS-mutant signaling and negative regulators of apoptosis, including MCL1, XIAP, and CFLAR, initiating caspase-8 dependent apoptosis. All three drugs exhibited synergy in combination with a multivalent TRAIL, effectively reinforcing mitochondrial-mediated apoptosis. These findings present a novel combination therapy, with direct translational implications for current clinical trials on metastatic pancreatic cancer patients. Significance: This study utilizes functional genetic and pharmacological profiling of KRAS-mutant pancreatic adenocarcinoma to identify therapeutic strategies and finds that TFIIH inhibition synergizes with TRAIL to induce apoptosis in KRAS-driven pancreatic cancer.
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Affiliation(s)
- Russell Moser
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - James Annis
- Quellos High Throughput Facility, Institute for Stem Cell and Regenerative Medicine, University of Washington Medicine Research, Seattle, Washington
| | - Olga Nikolova
- Department of Computational Biology, Oregon Health and Science University, Portland, Oregon
| | - Cliff Whatcott
- Translational Genomics Research Institute, Molecular Medicine Division, Phoenix, Arizona
| | - Kay Gurley
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Eduardo Mendez
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Kim Moran-Jones
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Craig Dorrell
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, Oregon
| | - Rosalie C Sears
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, Oregon
| | - Calvin Kuo
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California
| | - Haiyong Han
- Translational Genomics Research Institute, Molecular Medicine Division, Phoenix, Arizona
| | - Andrew Biankin
- Translational Genomics Research Institute, Molecular Medicine Division, Phoenix, Arizona
| | | | - Daniel D Von Hoff
- Translational Genomics Research Institute, Molecular Medicine Division, Phoenix, Arizona
| | - Christopher J Kemp
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
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12
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Arndt S, Kohlpaintner PJ, Donsbach K, Waldvogel SR. Synthesis and Applications of Periodate for Fine Chemicals and Important Pharmaceuticals. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.2c00161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sebastian Arndt
- Department of Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Philipp J. Kohlpaintner
- Department of Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Kai Donsbach
- Virginia Commonwealth University, College of Engineering, Medicines for All Institute, 601 West Main Street, Richmond, Virginia 23284-3068, United States
| | - Siegfried R. Waldvogel
- Department of Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
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13
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Li J, Liu T, Song Y, Wang M, Liu L, Zhu H, Li Q, Lin J, Jiang H, Chen K, Zhao K, Wang M, Zhou H, Lin H, Luo C. Discovery of Small-Molecule Degraders of the CDK9-Cyclin T1 Complex for Targeting Transcriptional Addiction in Prostate Cancer. J Med Chem 2022; 65:11034-11057. [PMID: 35925880 DOI: 10.1021/acs.jmedchem.2c00257] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aberrant hyperactivation of cyclins results in carcinogenesis and therapy resistance in cancers. Direct degradation of the specific cyclin or cyclin-dependent kinase (CDK)-cyclin complex by small-molecule degraders remains a great challenge. Here, we applied the first application of hydrophobic tagging to induce degradation of CDK9-cyclin T1 heterodimer, which is required to keep productive transcription of oncogenes in cancers. LL-K9-3 was identified as a potent small-molecule degrader of CDK9-cyclin T1. Quantitative and time-resolved proteome profiling exhibited LL-K9-3 induced selective and synchronous degradation of CDK9 and cyclin T1. The expressions of androgen receptor (AR) and cMyc were reduced by LL-K9-3 in 22RV1 cells. LL-K9-3 exhibited enhanced anti-proliferative and pro-apoptotic effects compared with its parental CDK9 inhibitor SNS032 and suppressed downstream signaling of CDK9 and AR more effectively than SNS032. Moreover, LL-K9-3 inhibited AR and Myc-driven oncogenic transcriptional programs and exerted stronger inhibitory effects on several intrinsic target genes of AR than the monomeric CDK9 PROTAC (Thal-SNS032).
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Affiliation(s)
- Jiacheng Li
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Ting Liu
- School of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Yuanli Song
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China.,Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Mingyu Wang
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Liping Liu
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Hongwen Zhu
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China.,Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Qi Li
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Jin Lin
- School of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Hualiang Jiang
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Kaixian Chen
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Kehao Zhao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China
| | - Mingliang Wang
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hu Zhou
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China.,Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Hua Lin
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China
| | - Cheng Luo
- School of Pharmacy, Fujian Medical University, Fuzhou 350122, China.,The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China.,School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China
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14
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Chen R, Chen Y, Xiong P, Zheleva D, Blake D, Keating MJ, Wierda WG, Plunkett W. Cyclin-dependent kinase inhibitor fadraciclib (CYC065) depletes anti-apoptotic protein and synergizes with venetoclax in primary chronic lymphocytic leukemia cells. Leukemia 2022; 36:1596-1608. [PMID: 35383271 PMCID: PMC9162916 DOI: 10.1038/s41375-022-01553-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 03/10/2022] [Accepted: 03/18/2022] [Indexed: 12/24/2022]
Abstract
Fadraciclib (CYC065) is a second-generation aminopurine CDK2/9 inhibitor with increased potency and selectivity toward CDK2 and CDK9 compared to seliciclib (R-roscovitine). In chronic lymphocytic leukemia (CLL), a disease that depends on the over-expression of anti-apoptotic proteins for its survival, inhibition of CDK9 by fadraciclib reduced phosphorylation of the C-terminal domain of RNA polymerase II and blocked transcription in vitro; these actions depleted the intrinsically short-lived anti-apoptotic protein Mcl-1 and induced apoptosis. While the simulated bone marrow and lymph node microenvironments induced Mcl-1 expression and protected CLL cells from apoptosis, these conditions did not prolong the turnover rate of Mcl-1, and fadraciclib efficiently abrogated the protective effect. Further, fadraciclib was synergistic with the Bcl-2 antagonist venetoclax, inducing more profound CLL cell death, especially in samples with 17p deletion. While fadraciclib, venetoclax, and the combination each had distinct kinetics of cell death induction, their activities were reversible, as no additional cell death was induced upon removal of the drugs. The best combination effects were achieved when both drugs were maintained together. Altogether, this study provides a rationale for the clinical development of fadraciclib in CLL, either alone or in combination with a Bcl-2 antagonist.
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Affiliation(s)
- Rong Chen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuling Chen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ping Xiong
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Michael J Keating
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - William G Wierda
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - William Plunkett
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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15
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Shi Z, Tian L, Qiang T, Li J, Xing Y, Ren X, Liu C, Liang C. From Structure Modification to Drug Launch: A Systematic Review of the Ongoing Development of Cyclin-Dependent Kinase Inhibitors for Multiple Cancer Therapy. J Med Chem 2022; 65:6390-6418. [PMID: 35485642 DOI: 10.1021/acs.jmedchem.1c02064] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Herein, we discuss more than 50 cyclin-dependent kinase (CDK) inhibitors that have been approved or have undergone clinical trials and their therapeutic application in multiple cancers. This review discusses the design strategies, structure-activity relationships, and efficacy performances of these selective or nonselective CDK inhibitors. The theoretical basis of early broad-spectrum CDK inhibitors is similar to the scope of chemotherapy, but because their toxicity is greater than the benefit, there is no clinical therapeutic window. The notion that selective CDK inhibitors have a safer therapeutic potential than pan-CDK inhibitors has been widely recognized during the research process. Four CDK4/6 inhibitors have been approved for the treatment of breast cancer or for prophylactic administration during chemotherapy to protect bone marrow and immune system function. Furthermore, the emerging strategies in the field of CDK inhibitors are summarized briefly, and CDKs continue to be widely pursued as emerging anticancer drug targets for drug discovery.
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Affiliation(s)
- Zhenfeng Shi
- Department of Urology Surgery Center, The People's Hospital of Xinjiang Uyghur Autonomous Region, Urumqi 830002, P. R. China
| | - Lei Tian
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China.,Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Taotao Qiang
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Jingyi Li
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Yue Xing
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Xiaodong Ren
- Medical College, Guizhou University, Guiyang 550025, P. R. China
| | - Chang Liu
- Zhuhai Jinan Selenium Source Nanotechnology Co., Ltd., Zhuhai 519030, P. R. China
| | - Chengyuan Liang
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
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16
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Huang Z, Wang T, Wang C, Fan Y. CDK9 Inhibitors in Cancer Research. RSC Med Chem 2022; 13:688-710. [PMID: 35814933 PMCID: PMC9215160 DOI: 10.1039/d2md00040g] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/16/2022] [Indexed: 11/21/2022] Open
Abstract
Cyclin dependent kinase 9 (CDK9) played an essential role in regulating transcriptional elongation. Aberrations in CDK9 activity have been observed in various cancers, which made CDK9 was an attractive therapeutic...
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Affiliation(s)
- Zhi Huang
- Department of Medicinal Chemistry, School of Medicine, Nankai University 94 Weijin Road Tianjin 300071 China
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences Hefei 230031 China
| | - Tianqi Wang
- Department of Medicinal Chemistry, School of Medicine, Nankai University 94 Weijin Road Tianjin 300071 China
| | - Cheng Wang
- Department of Medicinal Chemistry, School of Medicine, Nankai University 94 Weijin Road Tianjin 300071 China
| | - Yan Fan
- Department of Medicinal Chemistry, School of Medicine, Nankai University 94 Weijin Road Tianjin 300071 China
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17
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Abstract
Proteolysis-targeting chimeras are a new modality of chemical tools and potential therapeutics involving the induction of protein degradation. Cyclin-dependent kinase (CDK) protein, which is involved in cycles and transcription cycles, participates in regulation of the cell cycle, transcription and splicing. Proteolysis-targeting chimeras targeting CDKs show several advantages over traditional CDK small-molecule inhibitors in potency, selectivity and drug resistance. In addition, the discovery of molecule glues promotes the development of CDK degraders. Herein, the authors describe the existing CDK degraders and focus on the discussion of the structural characteristics and design of these degraders.
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18
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King A, Blackledge MS. Evaluation of small molecule kinase inhibitors as novel antimicrobial and antibiofilm agents. Chem Biol Drug Des 2021; 98:1038-1064. [PMID: 34581492 PMCID: PMC8616828 DOI: 10.1111/cbdd.13962] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/24/2021] [Accepted: 09/15/2021] [Indexed: 12/25/2022]
Abstract
Antibiotic resistance is a global and pressing concern. Our current therapeutic arsenal is increasingly limited as bacteria are developing resistance at a rate that far outpaces our ability to create new treatments. Novel approaches to treating and curing bacterial infections are urgently needed. Bacterial kinases have been increasingly explored as novel drug targets and are poised for development into novel therapeutic agents to combat bacterial infections. This review describes several general classes of bacterial kinases that play important roles in bacterial growth, antibiotic resistance, and biofilm formation. General features of these kinase classes are discussed and areas of particular interest for the development of inhibitors will be highlighted. Small molecule kinase inhibitors are described and organized by phenotypic effect, spotlighting particularly interesting inhibitors with novel functions and potential therapeutic benefit. Finally, we provide our perspective on the future of bacterial kinase inhibition as a viable strategy to combat bacterial infections and overcome the pressures of increasing antibiotic resistance.
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Affiliation(s)
- Ashley King
- Department of Chemistry, High Point University, One University Parkway, High Point, NC 27268
| | - Meghan S. Blackledge
- Department of Chemistry, High Point University, One University Parkway, High Point, NC 27268
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19
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Rana S, Mallareddy JR, Singh S, Boghean L, Natarajan A. Inhibitors, PROTACs and Molecular Glues as Diverse Therapeutic Modalities to Target Cyclin-Dependent Kinase. Cancers (Basel) 2021; 13:5506. [PMID: 34771669 PMCID: PMC8583118 DOI: 10.3390/cancers13215506] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 12/25/2022] Open
Abstract
The cyclin-dependent kinase (CDK) family of proteins play prominent roles in transcription, mRNA processing, and cell cycle regulation, making them attractive cancer targets. Palbociclib was the first FDA-approved CDK inhibitor that non-selectively targets the ATP binding sites of CDK4 and CDK6. In this review, we will briefly inventory CDK inhibitors that are either part of over 30 active clinical trials or recruiting patients. The lack of selectivity among CDKs and dose-limiting toxicities are major challenges associated with the development of CDK inhibitors. Proteolysis Targeting Chimeras (PROTACs) and Molecular Glues have emerged as alternative therapeutic modalities to target proteins. PROTACs and Molecular glues utilize the cellular protein degradation machinery to destroy the target protein. PROTACs are heterobifunctional molecules that form a ternary complex with the target protein and E3-ligase by making two distinct small molecule-protein interactions. On the other hand, Molecular glues function by converting the target protein into a "neo-substrate" for an E3 ligase. Unlike small molecule inhibitors, preclinical studies with CDK targeted PROTACs have exhibited improved CDK selectivity. Moreover, the efficacy of PROTACs and molecular glues are not tied to the dose of these molecular entities but to the formation of the ternary complex. Here, we provide an overview of PROTACs and molecular glues that modulate CDK function as emerging therapeutic modalities.
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Affiliation(s)
- Sandeep Rana
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA;
| | - Jayapal Reddy Mallareddy
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA; (J.R.M.); (S.S.); (L.B.)
| | - Sarbjit Singh
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA; (J.R.M.); (S.S.); (L.B.)
| | - Lidia Boghean
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA; (J.R.M.); (S.S.); (L.B.)
| | - Amarnath Natarajan
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA; (J.R.M.); (S.S.); (L.B.)
- Pharmaceutical Sciences and University of Nebraska Medical Center, Omaha, NE 68198, USA
- Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
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20
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Bhurta D, Bharate SB. Analyzing the scaffold diversity of cyclin-dependent kinase inhibitors and revisiting the clinical and preclinical pipeline. Med Res Rev 2021; 42:654-709. [PMID: 34605036 DOI: 10.1002/med.21856] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 07/04/2021] [Accepted: 09/21/2021] [Indexed: 12/17/2022]
Abstract
Kinases have gained an important place in the list of vital therapeutic targets because of their overwhelming clinical success in the last two decades. Among various clinically validated kinases, the cyclin-dependent kinases (CDK) are one of the extensively studied drug targets for clinical development. Food and Drug Administration has approved three CDK inhibitors for therapeutic use, and at least 27 inhibitors are under active clinical development. In the last decade, research and development in this area took a rapid pace, and thus the analysis of scaffold diversity is essential for future drug design. Available reviews lack the systematic study and discussion on the scaffold diversity of CDK inhibitors. Herein we have reviewed and critically analyzed the chemical diversity present in the preclinical and clinical pipeline of CDK inhibitors. Our analysis has shown that although several scaffolds represent CDK inhibitors, only the amino-pyrimidine is a well-represented scaffold. The three-nitrogen framework of amino-pyrimidine is a fundamental hinge-binding unit. Further, we have discussed the selectivity aspects among CDKs, the clinical trial dose-limiting toxicities, and highlighted the most advanced clinical candidates. We also discuss the changing paradigm towards selective inhibitors and an overview of ATP-binding pockets of all druggable CDKs. We carefully analyzed the clinical pipeline to unravel the candidates that are currently under active clinical development. In addition to the plenty of dual CDK4/6 inhibitors, there are many selective CDK7, CDK9, and CDK8/19 inhibitors in the clinical pipeline.
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Affiliation(s)
- Deendyal Bhurta
- Natural Products & Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, India
| | - Sandip B Bharate
- Natural Products & Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, India
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21
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Ketley A, Wojciechowska M, Ghidelli-Disse S, Bamborough P, Ghosh TK, Morato ML, Sedehizadeh S, Malik NA, Tang Z, Powalowska P, Tanner M, Billeter-Clark R, Trueman RC, Geiszler PC, Agostini A, Othman O, Bösche M, Bantscheff M, Rüdiger M, Mossakowska DE, Drewry DH, Zuercher WJ, Thornton CA, Drewes G, Uings I, Hayes CJ, Brook JD. CDK12 inhibition reduces abnormalities in cells from patients with myotonic dystrophy and in a mouse model. Sci Transl Med 2021; 12:12/541/eaaz2415. [PMID: 32350131 DOI: 10.1126/scitranslmed.aaz2415] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/16/2019] [Accepted: 02/25/2020] [Indexed: 12/17/2022]
Abstract
Myotonic dystrophy type 1 (DM1) is an RNA-based disease with no current treatment. It is caused by a transcribed CTG repeat expansion within the 3' untranslated region of the dystrophia myotonica protein kinase (DMPK) gene. Mutant repeat expansion transcripts remain in the nuclei of patients' cells, forming distinct microscopically detectable foci that contribute substantially to the pathophysiology of the condition. Here, we report small-molecule inhibitors that remove nuclear foci and have beneficial effects in the HSALR mouse model, reducing transgene expression, leading to improvements in myotonia, splicing, and centralized nuclei. Using chemoproteomics in combination with cell-based assays, we identify cyclin-dependent kinase 12 (CDK12) as a druggable target for this condition. CDK12 is a protein elevated in DM1 cell lines and patient muscle biopsies, and our results showed that its inhibition led to reduced expression of repeat expansion RNA. Some of the inhibitors identified in this study are currently the subject of clinical trials for other indications and provide valuable starting points for a drug development program in DM1.
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Affiliation(s)
- Ami Ketley
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Marzena Wojciechowska
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Sonja Ghidelli-Disse
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 61997 Heidelberg, Germany
| | - Paul Bamborough
- Computational and Modelling Sciences, GlaxoSmithKline, Medicines Research Centre, Hertfordshire SG1 2NY, UK
| | - Tushar K Ghosh
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Marta Lopez Morato
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Saam Sedehizadeh
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Naveed Altaf Malik
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Zhenzhi Tang
- Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642-0001, USA
| | - Paulina Powalowska
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK.,School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Matthew Tanner
- Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642-0001, USA
| | - Rudolf Billeter-Clark
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Rebecca C Trueman
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Philippine C Geiszler
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Alessandra Agostini
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Othman Othman
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Markus Bösche
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 61997 Heidelberg, Germany
| | - Marcus Bantscheff
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 61997 Heidelberg, Germany
| | - Martin Rüdiger
- Screening Profiling and Mechanistic Biology, GlaxoSmithKline, Medicines Research Centre, Hertfordshire SG1 2NY, UK
| | - Danuta E Mossakowska
- Discovery Partnerships with Academia, GlaxoSmithKline, Medicines Research Centre, Hertfordshire SG1 2NY, UK.,Malopolska Centre of Biotechnology, Jagiellonian University, 30-348 Krakow, Poland
| | - David H Drewry
- Department of Chemical Biology, GlaxoSmithKline, Research Triangle Park, NC 27709-3398, USA
| | - William J Zuercher
- Department of Chemical Biology, GlaxoSmithKline, Research Triangle Park, NC 27709-3398, USA.,SGC Center for Chemical Biology, UNC, Eshelman School of Pharmacy, Chapel Hill, NC 27599, USA
| | - Charles A Thornton
- Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642-0001, USA
| | - Gerard Drewes
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 61997 Heidelberg, Germany
| | - Iain Uings
- Discovery Partnerships with Academia, GlaxoSmithKline, Medicines Research Centre, Hertfordshire SG1 2NY, UK
| | - Christopher J Hayes
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - J David Brook
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK.
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22
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Ghosh S, Ramarao TA, Samanta PK, Jha A, Satpati P, Sen A. Triazole based isatin derivatives as potential inhibitor of key cancer promoting kinases- insight from electronic structure, docking and molecular dynamics simulations. J Mol Graph Model 2021; 107:107944. [PMID: 34091175 DOI: 10.1016/j.jmgm.2021.107944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 04/07/2021] [Accepted: 05/11/2021] [Indexed: 01/22/2023]
Abstract
Computer Aided Drug Design approaches have been applied to predict potential inhibitors for two different kinases, namely, cyclin-dependent kinase 2 (CDK2) and Epidermal Growth Factor Receptor (EGFR) which are known to play crucial role in cancer growth. We have designed alkyl and aryl substituted isatin-triazole ligands and performed molecular docking to rank and predict possible binding pockets in CDK2 and EGFR kinases. Best-scoring ligands in the kinase-binding pocket were selected from the docking study and subjected to molecular dynamics simulation. Absolute binding affinities were estimated from the MD trajectories using the MM/PBSA approach. The results suggest that aryl substituted isatin-triazole ligands are better binder to the kinases relative to its alkyl analogue. Furthermore, aryl substituted isatin-triazole ligands prefer binding to EGFR kinases relative to CDK2. The ligand binding pockets of the kinases are primarily hydrophobic in nature. Ligand-kinase binding is favoured by electrostatic and Van der Waals interactions, later being the major contributor. Large estimated negative binding affinities (~ -10 to -25 kcal/mol) indicate that the ligands might inhibit the kinases. Physicochemical property analysis suggests that the proposed ligands could be orally bio-available.
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Affiliation(s)
- Suvankar Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - T Atchuta Ramarao
- Department of Chemistry, GIS, GITAM Deemed to Be University, Rushikonda, Visakhapatnam, 530045, AP, India
| | - Pralok K Samanta
- Department of Chemistry, GSS, GITAM Deemed to Be University, Rudaram, Hyderabad, 502329, Telangana, India
| | - Anjali Jha
- Department of Chemistry, GIS, GITAM Deemed to Be University, Rushikonda, Visakhapatnam, 530045, AP, India.
| | - Priyadarshi Satpati
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
| | - Anik Sen
- Department of Chemistry, GIS, GITAM Deemed to Be University, Rushikonda, Visakhapatnam, 530045, AP, India.
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23
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Goel B, Tripathi N, Bhardwaj N, Jain SK. Small Molecule CDK Inhibitors for the Therapeutic Management of Cancer. Curr Top Med Chem 2021; 20:1535-1563. [PMID: 32416692 DOI: 10.2174/1568026620666200516152756] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/14/2020] [Accepted: 04/17/2020] [Indexed: 01/03/2023]
Abstract
Cyclin-dependent kinases (CDKs) are a group of multifunctional enzymes consisting of catalytic and regulatory subunits. The regulatory subunit, cyclin, remains dissociated under normal circumstances, and complexation of cyclin with the catalytic subunit of CDK leads to its activation for phosphorylation of protein substrates. The primary role of CDKs is in the regulation of the cell cycle. Retinoblastoma protein (Rb) is one of the widely investigated tumor suppressor protein substrates of CDK, which prevents cells from entering into cell-cycle under normal conditions. Phosphorylation of Rb by CDKs causes its inactivation and ultimately allows cells to enter a new cell cycle. Many cancers are associated with hyperactivation of CDKs as a result of mutation of the CDK genes or CDK inhibitor genes. Therefore, CDK modulators are of great interest to explore as novel therapeutic agents against cancer and led to the discovery of several CDK inhibitors to clinics. This review focuses on the current progress and development of anti-cancer CDK inhibitors from preclinical to clinical and synthetic to natural small molecules.
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Affiliation(s)
- Bharat Goel
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi-221005, India
| | - Nancy Tripathi
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi-221005, India
| | - Nivedita Bhardwaj
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi-221005, India
| | - Shreyans K Jain
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi-221005, India
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24
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Wróbel A, Drozdowska D. Recent Design and Structure-Activity Relationship Studies on the Modifications of DHFR Inhibitors as Anticancer Agents. Curr Med Chem 2021; 28:910-939. [PMID: 31622199 DOI: 10.2174/0929867326666191016151018] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/25/2019] [Accepted: 09/27/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Dihydrofolate reductase (DHFR) has been known for decades as a molecular target for antibacterial, antifungal and anti-malarial treatments. This enzyme is becoming increasingly important in the design of new anticancer drugs, which is confirmed by numerous studies including modelling, synthesis and in vitro biological research. This review aims to present and discuss some remarkable recent advances in the research of new DHFR inhibitors with potential anticancer activity. METHODS The scientific literature of the last decade on the different types of DHFR inhibitors has been searched. The studies on design, synthesis and investigation structure-activity relationships were summarized and divided into several subsections depending on the leading molecule and its structural modification. Various methods of synthesis, potential anticancer activity and possible practical applications as DHFR inhibitors of new chemical compounds were described and discussed. RESULTS This review presents the current state of knowledge on the modification of known DHFR inhibitors and the structures and searches for about eighty new molecules, designed as potential anticancer drugs. In addition, DHFR inhibitors acting on thymidylate synthase (TS), carbon anhydrase (CA) and even DNA-binding are presented in this paper. CONCLUSION Thorough physicochemical characterization and biological investigations highlight the structure-activity relationship of DHFR inhibitors. This will enable even better design and synthesis of active compounds, which would have the expected mechanism of action and the desired activity.
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Affiliation(s)
- Agnieszka Wróbel
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University, Białystok, Poland
| | - Danuta Drozdowska
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University, Białystok, Poland
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25
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Yang X, Luo W, Li L, Hu X, Xu M, Wang Y, Feng J, Qian J, Guan X, Zhao Y, Liang G. CDK9 inhibition improves diabetic nephropathy by reducing inflammation in the kidneys. Toxicol Appl Pharmacol 2021; 416:115465. [PMID: 33631230 DOI: 10.1016/j.taap.2021.115465] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/06/2021] [Accepted: 02/18/2021] [Indexed: 12/15/2022]
Abstract
Diabetic nephropathy (DN) is a chronic inflammatory renal disease induced by hyperglycemia. Recent studies have implicated cyclin-dependent kinase 9 (CDK9) in inflammatory responses and renal fibrosis. In this study, we explored a potential role of CDK9 in DN by using cultured mouse mesangial cell line SV40 MES-13 and streptozotocin-induced type 1 mouse model of diabetes. We inhibited CDK9 in mice and in cultured cells by a highly selective CDK9 inhibitor, LDC000067 (LDC), and evaluated inflammatory and fibrogenic outcome by mRNA and protein analyses. Our studies show that treatment of diabetic mice with LDC significantly inhibits the levels of inflammatory cytokines and fibrogenic genes in kidney specimens. These reductions were associated with improved renal function. We also found that LDC treatment suppressed MAPK-AP1 activation. We then confirmed the involvement of CDK9 in cultured SV40 MES-13 cells and showed that deficiency in CDK9 prevents glucose-induced inflammatory and fibrogenic proteins. This protection was also afforded by suppression of MAPK-AP1. Taken together, our results how that hyperglycemia activates CDK9-MAPK-AP1 axis in kidneys to induce inflammation and fibrosis, leading to renal dysfunction. Our findings also suggest that CDK9 may serve as a potential therapeutic target for DN.
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Affiliation(s)
- Xiaojing Yang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Wu Luo
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Li Li
- Department of Anesthesiology, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Xiang Hu
- Department of Endocrinology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Mingjiang Xu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yi Wang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jianpeng Feng
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jianchang Qian
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xinfu Guan
- The Affiliated Cangnan Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yunjie Zhao
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Guang Liang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China; The Affiliated Cangnan Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China.
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26
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Chen R, Tsai J, Thompson PA, Chen Y, Xiong P, Liu C, Burrows F, Sivina M, Burger JA, Keating MJ, Wierda WG, Plunkett W. The multi-kinase inhibitor TG02 induces apoptosis and blocks B-cell receptor signaling in chronic lymphocytic leukemia through dual mechanisms of action. Blood Cancer J 2021; 11:57. [PMID: 33714981 PMCID: PMC7956145 DOI: 10.1038/s41408-021-00436-0] [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: 10/07/2020] [Revised: 01/13/2021] [Accepted: 01/25/2021] [Indexed: 02/06/2023] Open
Abstract
The constitutive activation of B-cell receptor (BCR) signaling, together with the overexpression of the Bcl-2 family anti-apoptotic proteins, represents two hallmarks of chronic lymphocytic leukemia (CLL) that drive leukemia cell proliferation and sustain their survival. TG02 is a small molecule multi-kinase inhibitor that simultaneously targets both of these facets of CLL pathogenesis. First, its inhibition of cyclin-dependent kinase 9 blocked the activation of RNA polymerase II and transcription. This led to the depletion of Mcl-1 and rapid induction of apoptosis in the primary CLL cells. This mechanism of apoptosis was independent of CLL prognostic factors or prior treatment history, but dependent on the expression of BAX and BAK. Second, TG02, which inhibits the members of the BCR signaling pathway such as Lck and Fyn, blocked BCR-crosslinking-induced activation of NF-κB and Akt, indicating abrogation of BCR signaling. Finally, the combination of TG02 and ibrutinib demonstrated moderate synergy, suggesting a future combination of TG02 with ibrutinib, or use in patients that are refractory to the BCR antagonists. Thus, the dual inhibitory activity on both the CLL survival pathway and BCR signaling identifies TG02 as a unique compound for clinical development in CLL and possibly other B cell malignancies.
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Affiliation(s)
- Rong Chen
- Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA.
| | - Jennifer Tsai
- Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA.,Department of Emergency Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Philip A Thompson
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Yuling Chen
- Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Ping Xiong
- Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Chaomei Liu
- Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Francis Burrows
- Tragara Pharmaceuticals, Carlsbad, CA, USA.,Kura Oncology, Inc., San Diego, CA, USA
| | - Mariela Sivina
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Jan A Burger
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Michael J Keating
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - William G Wierda
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - William Plunkett
- Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA.,Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
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27
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Khan FM, Abbasi MA, Aziz‐ur‐Rehman, Siddiqui SZ, Sadiq Butt AR, Raza H, Zafar A, Ali Shah SA, Shahid M, Seo S. Convergent synthesis of carbonic anhydrase inhibiting bi‐heterocyclic benzamides: Structure–activity relationship and mechanistic explorations through enzyme inhibition, kinetics, and computational studies. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Farhan M. Khan
- Department of Chemistry Government College University Lahore Pakistan
| | | | - Aziz‐ur‐Rehman
- Department of Chemistry Government College University Lahore Pakistan
| | | | | | - Hussain Raza
- College of Natural Sciences, Department of Biological Science Kongju National University Gongju South Korea
| | - Ayesha Zafar
- School of Chemical Sciences University of Auckland Auckland New Zealand
| | - Syed A. Ali Shah
- Faculty of Pharmacy and Atta‐ur‐Rahman Institute for Natural Products Discovery (AuRIns), Level 9, FF3 Universiti Teknologi MARA, Puncak Alam Campus Bandar Puncak Alam Malaysia
| | - Muhammad Shahid
- Department of Biochemistry University of Agriculture Faisalabad Pakistan
| | - Sung‐Yum Seo
- College of Natural Sciences, Department of Biological Science Kongju National University Gongju South Korea
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28
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Abstract
Cyclin-dependent kinase 7 (CDK7), along with cyclin H and MAT1, forms the CDK-activating complex (CAK), which directs progression through the cell cycle via T-loop phosphorylation of cell cycle CDKs. CAK is also a component of the general transcription factor, TFIIH. CDK7-mediated phosphorylation of RNA polymerase II (Pol II) at active gene promoters permits transcription. Cell cycle dysregulation is an established hallmark of cancer, and aberrant control of transcriptional processes, through diverse mechanisms, is also common in many cancers. Furthermore, CDK7 levels are elevated in a number of cancer types and are associated with clinical outcomes, suggestive of greater dependence on CDK7 activity, compared with normal tissues. These findings identify CDK7 as a cancer therapeutic target, and several recent publications report selective CDK7 inhibitors (CDK7i) with activity against diverse cancer types. Preclinical studies have shown that CDK7i cause cell cycle arrest, apoptosis and repression of transcription, particularly of super-enhancer-associated genes in cancer, and have demonstrated their potential for overcoming resistance to cancer treatments. Moreover, combinations of CDK7i with other targeted cancer therapies, including BET inhibitors, BCL2 inhibitors and hormone therapies, have shown efficacy in model systems. Four CDK7i, ICEC0942 (CT7001), SY-1365, SY-5609 and LY3405105, have now progressed to Phase I/II clinical trials. Here we describe the work that has led to the development of selective CDK7i, the current status of the most advanced clinical candidates, and discuss their potential importance as cancer therapeutics, both as monotherapies and in combination settings. ClinicalTrials.gov Identifiers: NCT03363893; NCT03134638; NCT04247126; NCT03770494.
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29
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Development and therapeutic potential of 2-aminothiazole derivatives in anticancer drug discovery. Med Chem Res 2021; 30:771-806. [PMID: 33469255 PMCID: PMC7809097 DOI: 10.1007/s00044-020-02686-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/06/2020] [Indexed: 11/01/2022]
Abstract
Currently, the development of anticancer drug resistance is significantly restricted the clinical efficacy of the most commonly prescribed anticancer drug. Malignant disease is widely prevalent and considered to be the major challenges of this century, which concerns the medical community all over the world. Consequently, investigating small molecule antitumor agents, which could decrease drug resistance and reduce unpleasant side effect is more desirable. 2-aminothiazole scaffold has emerged as a promising scaffold in medicinal chemistry and drug discovery research. This nucleus is a fundamental part of some clinically applied anticancer drugs such as dasatinib and alpelisib. Literature survey documented that different 2-aminothiazole analogs exhibited their potent and selective nanomolar inhibitory activity against a wide range of human cancerous cell lines such as breast, leukemia, lung, colon, CNS, melanoma, ovarian, renal, and prostate. In this paper, we have reviewed the progresses and structural modification of 2-aminothiazole to pursuit potent anticancers and also highlighted in vitro activities and in silico studies. The information will useful for future innovation. Representatives of 2-aminothiazole-containing compounds classification.
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30
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Liang H, Du J, Elhassan RM, Hou X, Fang H. Recent progress in development of cyclin-dependent kinase 7 inhibitors for cancer therapy. Expert Opin Investig Drugs 2021; 30:61-76. [PMID: 33183110 DOI: 10.1080/13543784.2021.1850693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Introduction: Cyclin-dependent kinase 7 (CDK7) is a part of the CDK-activating kinase family (CAK) which has a key role in the cell cycle and transcriptional regulation. Several lines of evidence suggest that CDK7 is a promising therapeutic target for cancer. CDK7 selective inhibitors such as SY-5609 and CT7001 are in clinical development. Areas covered: We explore the biology of CDK7 and its role in cancer and follow this with an evaluation of the preclinical and clinical progress of CDK7 inhibitors, and their potential in the clinic. We searched PubMed and ClinicalTrials to identify relevant data from the database inception to 14 October 2020. Expert opinion: CDK7 inhibitors are next generation therapeutics for cancer. However, there are still challenges which include selectively, side effects, and drug resistance. Nevertheless, with ongoing clinical development of these inhibitors and greater analysis of their target, CDK7 inhibitors will become a promising approach for treatment of cancer in the near future.
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Affiliation(s)
- Hanzhi Liang
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University , Jinan, Shandong, China
| | - Jintong Du
- Shandong Cancer Hospital and Institute, Shandong First Medical University , Jinan, Shandong, China
| | - Reham M Elhassan
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University , Jinan, Shandong, China
| | - Xuben Hou
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University , Jinan, Shandong, China
| | - Hao Fang
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University , Jinan, Shandong, China
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31
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Proteolysis targeting chimera (PROTAC) in drug discovery paradigm: Recent progress and future challenges. Eur J Med Chem 2020; 210:112981. [PMID: 33160761 DOI: 10.1016/j.ejmech.2020.112981] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/23/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023]
Abstract
Proteolysis targeting chimera (PROTAC), hijacking protein of interest (POI) and recruiting E3 ligase for target degradation via the ubiquitin-proteasome pathway, is a novel drug discovery paradigm which has been widely used as biological tools and medicinal molecules with the potential of clinical application value. Currently, ARV-110, an orally small molecule PROTAC was designed to specifically target Androgen receptor (AR), firstly enters clinical phase I trials for the treatment of metastatic castration-resistant prostate cancer, which turns a new avenue for the development of PROTAC. We herein provide a detail summary on the latest one year progress of PROTAC target various proteins and elucidate the advantages of PROTAC technology. Finally, the potential challenges of this vibrant field are also discussed.
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32
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2-aminothiazoles in drug discovery: Privileged structures or toxicophores? Chem Biol Interact 2020; 330:109244. [PMID: 32861748 DOI: 10.1016/j.cbi.2020.109244] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/15/2020] [Accepted: 08/26/2020] [Indexed: 01/11/2023]
Abstract
The 2-aminothiazole functionality has long been established as a privileged structural feature and therefore frequently exploited in the process of drug discovery and development. It has been introduced into numerous compounds due to its capacity for targeting a wide range of therapeutic target proteins. On the other hand, the aminothiazole group has also been classified as a toxicophore susceptible to metabolic activation and the ensuing reactive metabolite formation, hence caution is warranted when used in drug design. This review is divided into three parts entailing: (i) the general characteristics of the aminothiazole group, (ii) the advantages of the aminothiazole group in medicinal chemistry, and (iii) the impact of the integrated aminothiazole group on compound safety profile.
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33
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Nagarajaiah H, Prasad NL, Begum NS. Sequential One-Pot Synthesis of 2-Aminothiazoles Using Corresponding Ketones: Insights into Their Structural Features. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2020.1821228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- H. Nagarajaiah
- Department of Chemistry, REVA University, Bengaluru, India
| | - N. L. Prasad
- Department of Chemistry, Bangalore University, Bangalore, India
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34
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Liu Y, Hao M, Leggett AL, Gao Y, Ficarro SB, Che J, He Z, Olson CM, Marto JA, Kwiatkowski NP, Zhang T, Gray NS. Discovery of MFH290: A Potent and Highly Selective Covalent Inhibitor for Cyclin-Dependent Kinase 12/13. J Med Chem 2020; 63:6708-6726. [DOI: 10.1021/acs.jmedchem.9b01929] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yao Liu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Cancer Biology, Dana Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Mingfeng Hao
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Cancer Biology, Dana Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Alan L. Leggett
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Cancer Biology, Dana Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Yang Gao
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Cancer Biology, Dana Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Scott B. Ficarro
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Cancer Biology, Dana Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
- Blais Proteomics Center, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Jianwei Che
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Cancer Biology, Dana Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Zhixiang He
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Cancer Biology, Dana Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Calla M. Olson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Cancer Biology, Dana Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Jarrod A. Marto
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Cancer Biology, Dana Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
- Blais Proteomics Center, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Nicholas P. Kwiatkowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Cancer Biology, Dana Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Tinghu Zhang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Cancer Biology, Dana Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Nathanael S. Gray
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Cancer Biology, Dana Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
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35
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Therapeutic Targeting of the General RNA Polymerase II Transcription Machinery. Int J Mol Sci 2020; 21:ijms21093354. [PMID: 32397434 PMCID: PMC7246882 DOI: 10.3390/ijms21093354] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 12/27/2022] Open
Abstract
Inhibitors targeting the general RNA polymerase II (RNAPII) transcription machinery are candidate therapeutics in cancer and other complex diseases. Here, we review the molecular targets and mechanisms of action of these compounds, framing them within the steps of RNAPII transcription. We discuss the effects of transcription inhibitors in vitro and in cellular models (with an emphasis on cancer), as well as their efficacy in preclinical and clinical studies. We also discuss the rationale for inhibiting broadly acting transcriptional regulators or RNAPII itself in complex diseases.
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36
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Aasebø E, Berven FS, Bartaula-Brevik S, Stokowy T, Hovland R, Vaudel M, Døskeland SO, McCormack E, Batth TS, Olsen JV, Bruserud Ø, Selheim F, Hernandez-Valladares M. Proteome and Phosphoproteome Changes Associated with Prognosis in Acute Myeloid Leukemia. Cancers (Basel) 2020; 12:cancers12030709. [PMID: 32192169 PMCID: PMC7140113 DOI: 10.3390/cancers12030709] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/05/2020] [Accepted: 03/13/2020] [Indexed: 12/12/2022] Open
Abstract
Acute myeloid leukemia (AML) is a hematological cancer that mainly affects the elderly. Although complete remission (CR) is achieved for the majority of the patients after induction and consolidation therapies, nearly two-thirds relapse within a short interval. Understanding biological factors that determine relapse has become of major clinical interest in AML. We utilized liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify the protein changes and protein phosphorylation events associated with AML relapse in primary cells from 41 AML patients at time of diagnosis. Patients were defined as relapse-free if they had not relapsed within a five-year clinical follow-up after AML diagnosis. Relapse was associated with increased expression of RNA processing proteins and decreased expression of V-ATPase proteins. We also observed an increase in phosphorylation events catalyzed by cyclin-dependent kinases (CDKs) and casein kinase 2 (CSK2). The biological relevance of the proteome findings was supported by cell proliferation assays using inhibitors of V-ATPase (bafilomycin), CSK2 (CX-4945), CDK4/6 (abemaciclib) and CDK2/7/9 (SNS-032). While bafilomycin preferentially inhibited the cells from relapse patients, the kinase inhibitors were less efficient in these cells. This suggests that therapy against the upregulated kinases could also target the factors inducing their upregulation rather than their activity. This study, therefore, presents markers that could help predict AML relapse and direct therapeutic strategies.
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Affiliation(s)
- Elise Aasebø
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
| | - Frode S. Berven
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
- The Department of Biomedicine, University of Bergen, 5009 Bergen, Norway;
| | - Sushma Bartaula-Brevik
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
| | - Tomasz Stokowy
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
- Department for Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway;
| | - Randi Hovland
- Department for Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway;
- Department of Biological Sciences, University of Bergen, 5006 Bergen, Norway
| | - Marc Vaudel
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
| | | | - Emmet McCormack
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway;
| | - Tanveer S. Batth
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark; (T.S.B.); (J.V.O.)
| | - Jesper V. Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark; (T.S.B.); (J.V.O.)
| | - Øystein Bruserud
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
| | - Frode Selheim
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
- The Department of Biomedicine, University of Bergen, 5009 Bergen, Norway;
| | - Maria Hernandez-Valladares
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
- Correspondence: ; Tel.: +47-5558-6368
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37
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Banert K. Functionalized Allenes: Generation by Sigmatropic Rearrangement and Application in Heterocyclic Chemistry. CURR ORG CHEM 2020. [DOI: 10.2174/1385272823666191112102523] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The present review article summarizes the synthesis of allenes, which bear an adjacent functional group, by [3,3]- or [2,3]-sigmatropic rearrangement of appropriate propargyl substrates. Functionalized allenes, such as allenyl isothiocyanates, isoelenocyanates, isocyanates, thiocyanates, azides, azo compounds and others, are easily available by these methods. In several cases, however, the title compounds show high reactivity, which leads to rapid intermolecular or intramolecular successive reactions. Consequently, synthesis of the allenes by sigmatropic rearrangement has to be combined with special techniques, for example, flash vacuum pyrolysis or in situ generation and trapping reactions. The high tendency of the presented functionalized allenes to undergo cyclization reactions can be utilized to prepare heterocyclic products, for instance, thiazoles, selenazoles, 1,2,3-triazoles and pyrazoles. The synthesis of functionalized 1,3-butadienes by a second sigmatropic rearrangement of the title compounds is also successful.
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Affiliation(s)
- Klaus Banert
- Chemnitz University of Technology, Organic Chemistry, Strasse der Nationen 62, 09111 Chemnitz, Germany
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38
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Rashid M, Husain A, Mishra R, Karim S, Khan S, Ahmad M, Al-wabel N, Husain A, Ahmad A, Khan SA. Design and synthesis of benzimidazoles containing substituted oxadiazole, thiadiazole and triazolo-thiadiazines as a source of new anticancer agents. ARAB J CHEM 2019. [DOI: 10.1016/j.arabjc.2015.08.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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39
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Eberl HC, Werner T, Reinhard FB, Lehmann S, Thomson D, Chen P, Zhang C, Rau C, Muelbaier M, Drewes G, Drewry D, Bantscheff M. Chemical proteomics reveals target selectivity of clinical Jak inhibitors in human primary cells. Sci Rep 2019; 9:14159. [PMID: 31578349 PMCID: PMC6775116 DOI: 10.1038/s41598-019-50335-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 09/05/2019] [Indexed: 12/15/2022] Open
Abstract
Kinobeads are a set of promiscuous kinase inhibitors immobilized on sepharose beads for the comprehensive enrichment of endogenously expressed protein kinases from cell lines and tissues. These beads enable chemoproteomics profiling of kinase inhibitors of interest in dose-dependent competition studies in combination with quantitative mass spectrometry. We present improved bead matrices that capture more than 350 protein kinases and 15 lipid kinases from human cell lysates, respectively. A multiplexing strategy is suggested that enables determination of apparent dissociation constants in a single mass spectrometry experiment. Miniaturization of the procedure enabled determining the target selectivity of the clinical BCR-ABL inhibitor dasatinib in peripheral blood mononuclear cell (PBMC) lysates from individual donors. Profiling of a set of Jak kinase inhibitors revealed kinase off-targets from nearly all kinase families underpinning the need to profile kinase inhibitors against the kinome. Potently bound off-targets of clinical inhibitors suggest polypharmacology, e.g. through MRCK alpha and beta, which bind to decernotinib with nanomolar affinity.
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Affiliation(s)
- H Christian Eberl
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany.
| | - Thilo Werner
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Friedrich B Reinhard
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Stephanie Lehmann
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Douglas Thomson
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Peiling Chen
- GlaxoSmithKline, Upper Merion, 709 Swedeland Rd #1539, King of Prussia, PA, 19406, United States
| | - Cunyu Zhang
- GlaxoSmithKline, Upper Merion, 709 Swedeland Rd #1539, King of Prussia, PA, 19406, United States
| | - Christina Rau
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Marcel Muelbaier
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Gerard Drewes
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - David Drewry
- GlaxoSmithKline, Research Triangle Park, 5 Moore Drive, North Carolina, 27709, United States.,UNC Eshelman School of Pharmacy, Structural Genomics Consortium, University of North Carolina at Chapel Hill, 120 Mason Farm Rd, Chapel Hill, NC, 27599, United States
| | - Marcus Bantscheff
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany.
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40
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An Efficient Synthesis of Benzo[
g
]thiazolo[2,3‐
b
]quinazolin‐4‐ium and Benzo[
g
]benzo[4,5]thiazolo[2,3‐
b
]quinazolin‐14‐ium Hydroxides by a One‐pot, Three‐component Reaction under Green Conditions. J Heterocycl Chem 2019. [DOI: 10.1002/jhet.3685] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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41
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Sánchez-Martínez C, Lallena MJ, Sanfeliciano SG, de Dios A. Cyclin dependent kinase (CDK) inhibitors as anticancer drugs: Recent advances (2015-2019). Bioorg Med Chem Lett 2019; 29:126637. [PMID: 31477350 DOI: 10.1016/j.bmcl.2019.126637] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/22/2019] [Accepted: 08/23/2019] [Indexed: 12/15/2022]
Abstract
Sustained proliferative capacity and gene dysregulation are hallmarks of cancer. In mammalian cells, cyclin-dependent kinases (CDKs) control critical cell cycle checkpoints and key transcriptional events in response to extracellular and intracellular signals leading to proliferation. Significant clinical activity for the treatment of hormone receptor positive metastatic breast cancer has been demonstrated by palbociclib, ribociclib and abemaciclib, dual CDK4/6 inhibitors recently FDA-approved. SY-1365, a CDK7 inhibitor has shown initial encouraging data in phase I for solid tumors treatment. These results have rejuvenated the CDKs research field. This review provides an overview of relevant advances on CDK inhibitor research since 2015 to 2019, with special emphasis on transcriptional CDK inhibitors, new emerging strategies such as target protein degradation and compounds under clinical evaluation.
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Affiliation(s)
| | - María José Lallena
- Discovery Chemistry Research and Technologies, Eli Lilly and Company, Alcobendas (Madrid) 28108, Spain
| | | | - Alfonso de Dios
- Discovery Chemistry Research and Technologies, Eli Lilly and Company, Indianapolis, IN 46285, United States
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42
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Abstract
Cancer is known as one of the main causes of death in the world; and many compounds have been synthesized to date with potential use in cancer therapy. Thiazole is a versatile heterocycle, found in the structure of many drugs in use as well as anticancer agents. This review provides an overview of recent advances in thiazole-bearing compounds as anticancer agents with particular emphasis on their mechanism of action in cancerous cells. Chemical designs, structure–activity relationships and relevant preclinical properties have been comprehensively described.
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43
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Okimoto RA, Wu W, Nanjo S, Olivas V, Lin YK, Ponce RK, Oyama R, Kondo T, Bivona TG. CIC-DUX4 oncoprotein drives sarcoma metastasis and tumorigenesis via distinct regulatory programs. J Clin Invest 2019; 129:3401-3406. [PMID: 31329165 DOI: 10.1172/jci126366] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 05/24/2019] [Indexed: 12/31/2022] Open
Abstract
Transcription factor fusion genes create oncoproteins that drive oncogenesis and represent challenging therapeutic targets. Understanding the molecular targets by which such fusion oncoproteins promote malignancy offers an approach to develop rational treatment strategies to improve clinical outcomes. Capicua-double homeobox 4 (CIC-DUX4) is a transcription factor fusion oncoprotein that defines certain undifferentiated round cell sarcomas with high metastatic propensity and poor clinical outcomes. The molecular targets regulated by the CIC-DUX4 oncoprotein that promote this aggressive malignancy remain largely unknown. We demonstrated that increased expression of ETS variant 4 (ETV4) and cyclin E1 (CCNE1) occurs via neomorphic, direct effects of CIC-DUX4 and drives tumor metastasis and survival, respectively. We uncovered a molecular dependence on the CCNE-CDK2 cell cycle complex that renders CIC-DUX4-expressing tumors sensitive to inhibition of the CCNE-CDK2 complex, suggesting a therapeutic strategy for CIC-DUX4-expressing tumors. Our findings highlight a paradigm of functional diversification of transcriptional repertoires controlled by a genetically aberrant transcriptional regulator, with therapeutic implications.
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Affiliation(s)
- Ross A Okimoto
- Department of Medicine.,Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
| | | | | | | | | | | | - Rieko Oyama
- Division of Rare Cancer Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Tadashi Kondo
- Division of Rare Cancer Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Trever G Bivona
- Department of Medicine.,Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA.,Cellular and Molecular Pharmacology, UCSF, San Francisco, California, USA
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44
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Xu Y, Wang Q, Wu Y, Zeng Z, Rudolph M, Hashmi ASK. Gold‐Catalyzed Synthesis of 2,5‐Disubstituted Oxazoles from Carboxamides and Propynals. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201801386] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Yun Xu
- Institute of Organic ChemistryHeidelberg University Im Neuenheimer Feld 270 69120 Heidelberg Germany
- Department of Environmental ScienceSchool of Engineering, China Pharmaceutical University 211198 Nanjing China
| | - Qian Wang
- Institute of Organic ChemistryHeidelberg University Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Yufeng Wu
- Institute of Organic ChemistryHeidelberg University Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Zhongyi Zeng
- Institute of Organic ChemistryHeidelberg University Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Matthias Rudolph
- Institute of Organic ChemistryHeidelberg University Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - A. Stephen K. Hashmi
- Institute of Organic ChemistryHeidelberg University Im Neuenheimer Feld 270 69120 Heidelberg Germany
- Chemistry Department, Faculty of ScienceKing Abdulaziz University (KAU) 21589 Jeddah Saudi Arabia
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45
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Rubenstein R, Sharma DR, Chang B, Oumata N, Cam M, Vaucelle L, Lindberg MF, Chiu A, Wisniewski T, Wang KKW, Meijer L. Novel Mouse Tauopathy Model for Repetitive Mild Traumatic Brain Injury: Evaluation of Long-Term Effects on Cognition and Biomarker Levels After Therapeutic Inhibition of Tau Phosphorylation. Front Neurol 2019; 10:124. [PMID: 30915013 PMCID: PMC6421297 DOI: 10.3389/fneur.2019.00124] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 01/30/2019] [Indexed: 12/20/2022] Open
Abstract
Traumatic brain injury (TBI) is a risk factor for a group of neurodegenerative diseases termed tauopathies, which includes Alzheimer's disease and chronic traumatic encephalopathy (CTE). Although TBI is stratified by impact severity as either mild (m), moderate or severe, mTBI is the most common and the most difficult to diagnose. Tauopathies are pathologically related by the accumulation of hyperphosphorylated tau (P-tau) and increased total tau (T-tau). Here we describe: (i) a novel human tau-expressing transgenic mouse model, TghTau/PS1, to study repetitive mild closed head injury (rmCHI), (ii) quantitative comparison of T-tau and P-tau from brain and plasma in TghTau/PS1 mice over a 12 month period following rmCHI (and sham), (iii) the usefulness of P-tau as an early- and late-stage blood-based biochemical biomarker for rmCHI, (iii) the influence of kinase-targeted therapeutic intervention on rmCHI-associated cognitive deficits using a combination of lithium chloride (LiCl) and R-roscovitine (ros), and (iv) correlation of behavioral and cognitive changes with concentrations of the brain and blood-based T-tau and P-tau. Compared to sham-treated mice, behavior changes and cognitive deficits of rmCHI-treated TghTau/PS1 mice correlated with increases in both cortex and plasma T-tau and P-tau levels over 12 months. In addition, T-tau, but more predominantly P-tau, levels were significantly reduced in the cortex and plasma by LiCl + ros approaching the biomarker levels in sham and drug-treated sham mice (the drugs had only modest effects on the T-tau and P-tau levels in sham mice) throughout the 12 month study period. Furthermore, although we also observed a reversal of the abnormal behavior and cognitive deficits in the drug-treated rmCHI mice (compared to the untreated rmCHI mice) throughout the time course, these drug-treated effects were most pronounced up until 10 and 12 months where the abnormal behavior and cognition deficits began to gradually increase. These studies describe: (a) a translational relevant animal model for TBI-linked tauopathies, and (b) utilization of T-tau and P-tau as rmCHI biomarkers in plasma to monitor novel therapeutic strategies and treatment regimens for these neurodegenerative diseases.
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Affiliation(s)
- Richard Rubenstein
- Laboratory of Neurodegenerative Diseases and CNS Biomarker Discovery, Departments of Neurology and Physiology/Pharmacology, SUNY Downstate Medical Center, Brooklyn, NY, United States
| | - Deep R Sharma
- Laboratory of Neurodegenerative Diseases and CNS Biomarker Discovery, Departments of Neurology and Physiology/Pharmacology, SUNY Downstate Medical Center, Brooklyn, NY, United States
| | - Binggong Chang
- Laboratory of Neurodegenerative Diseases and CNS Biomarker Discovery, Departments of Neurology and Physiology/Pharmacology, SUNY Downstate Medical Center, Brooklyn, NY, United States
| | - Nassima Oumata
- ManRos Therapeutics, Centre de Perharidy, Roscoff, France
| | - Morgane Cam
- ManRos Therapeutics, Centre de Perharidy, Roscoff, France
| | - Lise Vaucelle
- ManRos Therapeutics, Centre de Perharidy, Roscoff, France
| | | | - Allen Chiu
- Laboratory of Neurodegenerative Diseases and CNS Biomarker Discovery, Departments of Neurology and Physiology/Pharmacology, SUNY Downstate Medical Center, Brooklyn, NY, United States
| | - Thomas Wisniewski
- Center for Cognitive Neurology and Departments of Neurology, Pathology and Psychiatry, New York University School of Medicine, New York, NY, United States
| | - Kevin K W Wang
- Program for Neurotrauma, Neuroproteomics and Biomarker Research, Departments of Emergency Medicine, Psychiatry and Neuroscience, University of Florida, Gainesville, FL, United States
| | - Laurent Meijer
- ManRos Therapeutics, Centre de Perharidy, Roscoff, France
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46
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Taguchi YH. Drug candidate identification based on gene expression of treated cells using tensor decomposition-based unsupervised feature extraction for large-scale data. BMC Bioinformatics 2019; 19:388. [PMID: 30717646 PMCID: PMC7394334 DOI: 10.1186/s12859-018-2395-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 09/25/2018] [Indexed: 02/08/2023] Open
Abstract
Background Although in silico drug discovery is necessary for drug development, two major strategies, a structure-based and ligand-based approach, have not been completely successful. Currently, the third approach, inference of drug candidates from gene expression profiles obtained from the cells treated with the compounds under study requires the use of a training dataset. Here, the purpose was to develop a new approach that does not require any pre-existing knowledge about the drug–protein interactions, but these interactions can be inferred by means of an integrated approach using gene expression profiles obtained from the cells treated with the analysed compounds and the existing data describing gene–gene interactions. Results In the present study, using tensor decomposition-based unsupervised feature extraction, which represents an extension of the recently proposed principal-component analysis-based feature extraction, gene sets and compounds with a significant dose-dependent activity were screened without any training datasets. Next, after these results were combined with the data showing perturbations in single-gene expression profiles, genes targeted by the analysed compounds were inferred. The set of target genes thus identified was shown to significantly overlap with known target genes of the compounds under study. Conclusions The method is specifically designed for large-scale datasets (including hundreds of treatments with compounds), not for conventional small-scale datasets. The obtained results indicate that two compounds that have not been extensively studied, WZ-3105 and CGP-60474, represent promising drug candidates targeting multiple cancers, including melanoma, adenocarcinoma, liver carcinoma, and breast, colon, and prostate cancers, which were analysed in this in silico study. Electronic supplementary material The online version of this article (10.1186/s12859-018-2395-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Y-H Taguchi
- Department of Physics, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan.
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47
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Bera P, Brandão P, Mondal G, Santra A, Jana A, Mokhamatam RB, Manna SK, Mandal TK, Bera P. An unusual iminoacylation of 2-amino pyridyl thiazole: Synthesis, X-ray crystallography and DFT study of copper(II) amidine complexes and their cytotoxicity, DNA binding and cleavage study. Polyhedron 2019. [DOI: 10.1016/j.poly.2018.11.069] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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48
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Banert K, Seifert J. Steric hindrance classified: treatment of isothiocyanatoallene with secondary amines bearing bulky substituents to generate 2-aminothiazoles. Org Chem Front 2019. [DOI: 10.1039/c9qo00312f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Based on the reaction of allenyl isothiocyanate with secondary amines, the influence of strong steric hindrance on the nucleophilicity of amines was measured.
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Affiliation(s)
- Klaus Banert
- Chemnitz University of Technology
- Organic Chemistry
- 09111 Chemnitz
- Germany
| | - Jennifer Seifert
- Chemnitz University of Technology
- Organic Chemistry
- 09111 Chemnitz
- Germany
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49
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Tadesse S, Caldon EC, Tilley W, Wang S. Cyclin-Dependent Kinase 2 Inhibitors in Cancer Therapy: An Update. J Med Chem 2018; 62:4233-4251. [PMID: 30543440 DOI: 10.1021/acs.jmedchem.8b01469] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cyclin-dependent kinase 2 (CDK2) drives the progression of cells into the S- and M-phases of the cell cycle. CDK2 activity is largely dispensable for normal development, but it is critically associated with tumor growth in multiple cancer types. Although the role of CDK2 in tumorigenesis has been controversial, emerging evidence proposes that selective CDK2 inhibition may provide a therapeutic benefit against certain tumors, and it continues to appeal as a strategy to exploit in anticancer drug development. Several small-molecule CDK2 inhibitors have progressed to the clinical trials. However, a CDK2-selective inhibitor is yet to be discovered. Here, we discuss the latest understandings of the role of CDK2 in normal and cancer cells, review the core pharmacophores used to target CDK2, and outline strategies for the rational design of CDK2 inhibitors. We attempt to provide an outlook on how CDK2-selective inhibitors may open new avenues for cancer therapy.
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Affiliation(s)
- Solomon Tadesse
- Centre for Drug Discovery and Development , University of South Australia Cancer Research Institute , Adelaide , SA 5000 , Australia
| | - Elizabeth C Caldon
- The Kinghorn Cancer Centre , Garvan Institute of Medical Research , Darlinghurst , NSW 2010 , Australia.,St Vincent's Clinical School, UNSW Medicine , UNSW Sydney , Darlinghurst , NSW 2010 , Australia
| | - Wayne Tilley
- Adelaide Medical School , University of Adelaide , Adelaide , SA 5000 , Australia
| | - Shudong Wang
- Centre for Drug Discovery and Development , University of South Australia Cancer Research Institute , Adelaide , SA 5000 , Australia
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50
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Zhu Y, Wang Q, Luo H, Zhang G, Yu Y. Efficient and facile strategy to substituted 2-aminothiazoles via ring opening of α-nitroepoxides. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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