1
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Luo J, Li Y, Zhang Y, Wu D, Ren Y, Liu J, Wang C, Zhang J. An update on small molecule compounds targeting synthetic lethality for cancer therapy. Eur J Med Chem 2024; 278:116804. [PMID: 39241482 DOI: 10.1016/j.ejmech.2024.116804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 08/19/2024] [Accepted: 08/26/2024] [Indexed: 09/09/2024]
Abstract
Targeting cancer-specific vulnerabilities through synthetic lethality (SL) is an emerging paradigm in precision oncology. A SL strategy based on PARP inhibitors has demonstrated clinical efficacy. Advances in DNA damage response (DDR) uncover novel SL gene pairs. Beyond BRCA-PARP, emerging SL targets like ATR, ATM, DNA-PK, CHK1, WEE1, CDK12, RAD51, and RAD52 show clinical promise. Selective and bioavailable small molecule inhibitors have been developed to induce SL, but optimization for potency, specificity, and drug-like properties remains challenging. This article illuminated recent progress in the field of medicinal chemistry centered on the rational design of agents capable of eliciting SL specifically in neoplastic cells. It is envisioned that innovative strategies harnessing SL for small molecule design may unlock novel prospects for targeted cancer therapeutics going forward.
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Affiliation(s)
- Jiaxiang Luo
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Department of Pulmonary and Critical Care Medicine, Institute of Respiratory Health and Frontiers Science Center for Disease-related Molecular Network and Laboratory of Neuro-system and Multimorbidity, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yang Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Department of Pulmonary and Critical Care Medicine, Institute of Respiratory Health and Frontiers Science Center for Disease-related Molecular Network and Laboratory of Neuro-system and Multimorbidity, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yiwen Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Department of Pulmonary and Critical Care Medicine, Institute of Respiratory Health and Frontiers Science Center for Disease-related Molecular Network and Laboratory of Neuro-system and Multimorbidity, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Defa Wu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Department of Pulmonary and Critical Care Medicine, Institute of Respiratory Health and Frontiers Science Center for Disease-related Molecular Network and Laboratory of Neuro-system and Multimorbidity, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yijiu Ren
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Jie Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Department of Pulmonary and Critical Care Medicine, Institute of Respiratory Health and Frontiers Science Center for Disease-related Molecular Network and Laboratory of Neuro-system and Multimorbidity, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Chengdi Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Department of Pulmonary and Critical Care Medicine, Institute of Respiratory Health and Frontiers Science Center for Disease-related Molecular Network and Laboratory of Neuro-system and Multimorbidity, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Jifa Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Department of Pulmonary and Critical Care Medicine, Institute of Respiratory Health and Frontiers Science Center for Disease-related Molecular Network and Laboratory of Neuro-system and Multimorbidity, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
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2
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Huang Y, Liu W, Zhao C, Shi X, Zhao Q, Jia J, Wang A. Targeting cyclin-dependent kinases: From pocket specificity to drug selectivity. Eur J Med Chem 2024; 275:116547. [PMID: 38852339 DOI: 10.1016/j.ejmech.2024.116547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/11/2024]
Abstract
The development of selective modulators of cyclin-dependent kinases (CDKs), a kinase family with numerous members and functional variations, is a significant preclinical challenge. Recent advancements in crystallography have revealed subtle differences in the highly conserved CDK pockets. Exploiting these differences has proven to be an effective strategy for achieving excellent drug selectivity. While previous reports briefly discussed the structural features that lead to selectivity in individual CDK members, attaining inhibitor selectivity requires consideration of not only the specific structures of the target CDK but also the features of off-target members. In this review, we summarize the structure-activity relationships (SARs) that influence selectivity in CDK drug development and analyze the pocket features that lead to selectivity using molecular-protein binding models. In addition, in recent years, novel CDK modulators have been developed, providing more avenues for achieving selectivity. These cases were also included. We hope that these efforts will assist in the development of novel CDK drugs.
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Affiliation(s)
- Yaoguang Huang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Wenwu Liu
- School of Pharmaceutical Sciences, Tsinghua University, Haidian Dist., Beijing, 100084, People's Republic of China
| | - Changhao Zhao
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China
| | - Xiaoyu Shi
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Qingchun Zhao
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China; Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China.
| | - Jingming Jia
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
| | - Anhua Wang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
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3
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Lu KQ, Li ZL, Zhang Q, Yin Q, Zhang YL, Ni WJ, Jiang LZ, He W, Wang B. CDK12 is a potential biomarker for diagnosis, prognosis and immunomodulation in pan-cancer. Sci Rep 2024; 14:6574. [PMID: 38503865 PMCID: PMC10951204 DOI: 10.1038/s41598-024-56831-7] [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: 08/07/2023] [Accepted: 03/12/2024] [Indexed: 03/21/2024] Open
Abstract
Cell cycle-dependent protein kinase 12 (CDK12) plays a key role in a variety of carcinogenesis processes and represents a promising therapeutic target for cancer treatment. However, to date, there have been no systematic studies addressing its diagnostic, prognostic and immunological value across cancers. Here, we found that CDK12 was significantly upregulated in various types of cancers, and it expression increased with progression in ten cancer types, including breast cancer, cholangiocarcinoma and colon adenocarcinoma. Moreover, the ROC curves indicated that CDK12 showed diagnostic value in eight cancer types. High CDK12 expression was associated with poor prognosis in eight types of cancer, including low-grade glioma, mesothelioma, melanoma and pancreatic cancer. Furthermore, we conducted immunoassays to explore the exact mechanisms underlying CDK12-induced carcinogenesis, which revealed that increased expression of CDK12 allowed tumours to evade immune surveillance and upregulate immune checkpoint genes. Additionally, mutational studies have shown that amplification and missense mutations are the predominant mutational events affecting CDK12 across cancers. These findings establish CDK12 as a significant biological indicator of cancer diagnosis, prognosis, and immunotherapeutic targeting. Early surveillance and employment of CDK12 inhibitors, along with concomitant immunotherapy interventions, may enhance the clinical outcomes of cancer patients.
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Affiliation(s)
- Ke-Qi Lu
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Zuo-Lin Li
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Qian Zhang
- Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Qing Yin
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Yi-Lin Zhang
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Wei-Jie Ni
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - LiangYun-Zi Jiang
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Wei He
- Department of Gastroenterology, Jiangsu Province Geriatric Institute, and Jiangsu Province Official Hospital, Geriatric Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Bin Wang
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China.
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4
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Schmitz M, Kaltheuner IH, Anand K, Düster R, Moecking J, Monastyrskyi A, Duckett DR, Roush WR, Geyer M. The reversible inhibitor SR-4835 binds Cdk12/cyclin K in a noncanonical G-loop conformation. J Biol Chem 2024; 300:105501. [PMID: 38016516 PMCID: PMC10767194 DOI: 10.1016/j.jbc.2023.105501] [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: 07/18/2023] [Revised: 10/23/2023] [Accepted: 11/08/2023] [Indexed: 11/30/2023] Open
Abstract
Inhibition of cyclin-dependent kinases (CDKs) has evolved as an emerging anticancer strategy. In addition to the cell cycle-regulating CDKs, the transcriptional kinases Cdk12 and Cdk13 have become the focus of interest as they mediate a variety of functions, including the transition from transcription initiation to elongation and termination, precursor mRNA splicing, and intronic polyadenylation. Here, we determine the crystal structure of the small molecular inhibitor SR-4835 bound to the Cdk12/cyclin K complex at 2.68 Å resolution. The compound's benzimidazole moiety is embedded in a unique hydrogen bond network mediated by the kinase hinge region with flanking hydroxy groups of the Y815 and D819 side chains. Whereas the SR-4835 head group targets the adenine-binding pocket, the kinase's glycine-rich loop is shifted down toward the activation loop. Additionally, the αC-helix adopts an inward conformation, and the phosphorylated T-loop threonine interacts with all three canonical arginines, a hallmark of CDK activation that is altered in Cdk12 and Cdk13. Dose-response inhibition measurements with recombinant CMGC kinases show that SR-4835 is highly specific for Cdk12 and Cdk13 following a 10-fold lower potency for Cdk10. Whereas other CDK-targeting compounds exhibit tighter binding affinities and higher potencies for kinase inhibition, SR-4835 can be considered a selective transcription elongation antagonist. Our results provide the basis for a rational improvement of SR-4835 toward Cdk12 inhibition and a gain in selectivity over other transcription regulating CDKs.
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Affiliation(s)
| | | | - Kanchan Anand
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Robert Düster
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Jonas Moecking
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | | | - Derek R Duckett
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, Florida, USA
| | - William R Roush
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, USA
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Bonn, Germany.
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5
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Zhang L, Zhen Y, Feng L, Li Z, Lu Y, Wang G, Ouyang L. Discovery of a novel dual-target inhibitor of CDK12 and PARP1 that induces synthetic lethality for treatment of triple-negative breast cancer. Eur J Med Chem 2023; 259:115648. [PMID: 37478560 DOI: 10.1016/j.ejmech.2023.115648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/07/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023]
Abstract
Triple negative breast cancer (TNBC) is one of the most aggressive breast tumors, with a high rate of recurrence and metastasis as well as a poor prognosis. Consequently, it is urgent to find new targeted therapeutic strategies and development of corresponding drugs. Previous studies have shown that CDK12 inhibitors in combination with PARP1 inhibitors is able to induce synthetic lethality in TNBC cells. Here, we reported simultaneously inhibition of CDK12 and PARP1 by genetic or pharmacological approaches synergistically inhibited the proliferation of TNBC cells. Then, a series of small molecule inhibitors targeting both CDK12 and PARP1 were designed and synthesized. The new dual-target inhibitor (12e) showed potent inhibitory activity against CDK12 (IC50 = 285 nM) and PARP1 (IC50 = 34 nM), as well as good anti-proliferative effects in TNBC cell lines. Meanwhile, compound 12e showed favorable synergistic anti-tumor efficacy in cells and xenografts by inhibiting DNA damage repair, promoting cell cycle arrest and apoptosis. Taken together, we successfully synthesized the first effective CDK12-PARP1 dual inhibitor, which is expected to be an attractive therapeutic strategy for TNBC.
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Affiliation(s)
- Lan Zhang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China.
| | - Yongqi Zhen
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China; Department of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China
| | - Lu Feng
- Department of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China
| | - Zhijia Li
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Yingying Lu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Guan Wang
- Department of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China.
| | - Liang Ouyang
- Department of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China.
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6
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Ghosh A, Jha PC, Manhas A. Computational studies to explore inhibitors against the cyclin-dependent kinase 12/13 enzyme: an insilco pharmacophore modeling, molecular docking and dynamics approach. J Biomol Struct Dyn 2023:1-14. [PMID: 37817503 DOI: 10.1080/07391102.2023.2266472] [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: 06/28/2023] [Accepted: 09/27/2023] [Indexed: 10/12/2023]
Abstract
Cancer is enlisted among the deadliest disease all over the world. The cyclin-dependent kinases 12 and 13 have been identified as cell cycle regulators. They conduct transcription and co-transcriptional processes by phosphorylating the C-terminal of RNA polymerase-II. Inhibition of CDK12 and 13 selectively presents a novel strategy to treat triple-negative breast cancer, but dual inhibitors are still lacking. Here, we report the screening of the natural product compound class against the dual CDK12/13 enzyme by employing various in silico methods. Complexes of CDK12 enzymes are used to form common feature pharmacophore models, whereas we perform receptor-based pharmacophore modelling on CDK13 enzyme owing to the availability of a single PDB. On conducting screening over the representative pharmacophores, the common drug-like screened natural products were shortlisted for conducting molecular docking studies. After molecular docking calculations, the candidates that showed crucial interaction with CDK12 and CDK13 enzymes were shortlisted for simulation studies. Five common docked candidates were selected for molecular dynamics simulations and free energy calculations. Based on the cut-off criteria of free energy calculations, one common hit was selected as the dual CDK12/13 inhibitor. The outcome concluded that the hit with ID CNP0386383 possesses drug-like properties, displays crucial interaction in the binding pocket, and shows stable dynamic behaviour and higher binding energy than the experimentally reported inhibitor of both CDK12 and CDK13 enzymes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amar Ghosh
- School of Applied Material Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India
| | - Prakash C Jha
- School of Applied Material Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India
| | - Anu Manhas
- Department of Chemistry, School of Energy Technology, Pandit Deendayal Energy University, Gandhinagar, Gujarat, India
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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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Pitolli C, Marini A, Guerra M, Pieraccioli M, Marabitti V, Palluzzi F, Giacò L, Tamburrini G, Cecconi F, Nazio F, Sette C, Pagliarini V. MYC up-regulation confers vulnerability to dual inhibition of CDK12 and CDK13 in high-risk Group 3 medulloblastoma. J Exp Clin Cancer Res 2023; 42:214. [PMID: 37599362 PMCID: PMC10440921 DOI: 10.1186/s13046-023-02790-2] [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: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/22/2023] Open
Abstract
BACKGROUND Medulloblastoma (MB) is the most common cerebellar malignancy during childhood. Among MB, MYC-amplified Group 3 tumors display the worst prognosis. MYC is an oncogenic transcription factor currently thought to be undruggable. Nevertheless, targeting MYC-dependent processes (i.e. transcription and RNA processing regulation) represents a promising approach. METHODS We have tested the sensitivity of MYC-driven Group 3 MB cells to a pool of transcription and splicing inhibitors that display a wide spectrum of targets. Among them, we focus on THZ531, an inhibitor of the transcriptional cyclin-dependent kinases (CDK) 12 and 13. High-throughput RNA-sequencing analyses followed by bioinformatics and functional analyses were carried out to elucidate the molecular mechanism(s) underlying the susceptibility of Group 3 MB to CDK12/13 chemical inhibition. Data from International Cancer Genome Consortium (ICGC) and other public databases were mined to evaluate the functional relevance of the cellular pathway/s affected by the treatment with THZ531 in Group 3 MB patients. RESULTS We found that pharmacological inhibition of CDK12/13 is highly selective for MYC-high Group 3 MB cells with respect to MYC-low MB cells. We identified a subset of genes enriched in functional terms related to the DNA damage response (DDR) that are up-regulated in Group 3 MB and repressed by CDK12/13 inhibition. Accordingly, MYC- and CDK12/13-dependent higher expression of DDR genes in Group 3 MB cells limits the toxic effects of endogenous DNA lesions in these cells. More importantly, chemical inhibition of CDK12/13 impaired the DDR and induced irreparable DNA damage exclusively in MYC-high Group 3 MB cells. The augmented sensitivity of MYC-high MB cells to CDK12/13 inhibition relies on the higher elongation rate of the RNA polymerase II in DDR genes. Lastly, combined treatments with THZ531 and DNA damage-inducing agents synergically suppressed viability of MYC-high Group 3 MB cells. CONCLUSIONS Our study demonstrates that CDK12/13 activity represents an exploitable vulnerability in MYC-high Group 3 MB and may pave the ground for new therapeutic approaches for this high-risk brain tumor.
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Affiliation(s)
- Consuelo Pitolli
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy
| | - Alberto Marini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168, Rome, Italy
| | - Marika Guerra
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy
| | - Marco Pieraccioli
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168, Rome, Italy
| | - Veronica Marabitti
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Fernando Palluzzi
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168, Rome, Italy
- Present Address: Integrated Omics Department, Novo Nordisk, 2860, Søborg, Denmark
| | - Luciano Giacò
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168, Rome, Italy
| | - Gianpiero Tamburrini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy
- Pediatric Neurosurgery, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168, Rome, Italy
| | - Francesco Cecconi
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Department of Basic Biotechnological Sciences, Intensive Care and Perioperative Clinics Research, Catholic University of the Sacred Heart, 00168, Rome, Italy
- Unit of Cell Stress and Survival, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Francesca Nazio
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy.
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168, Rome, Italy.
| | - Vittoria Pagliarini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy.
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168, Rome, Italy.
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9
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Hartung IV, Rudolph J, Mader MM, Mulder MPC, Workman P. Expanding Chemical Probe Space: Quality Criteria for Covalent and Degrader Probes. J Med Chem 2023; 66:9297-9312. [PMID: 37403870 PMCID: PMC10388296 DOI: 10.1021/acs.jmedchem.3c00550] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Indexed: 07/06/2023]
Abstract
Within druggable target space, new small-molecule modalities, particularly covalent inhibitors and targeted degraders, have expanded the repertoire of medicinal chemists. Molecules with such modes of action have a large potential not only as drugs but also as chemical probes. Criteria have previously been established to describe the potency, selectivity, and properties of small-molecule probes that are qualified to enable the interrogation and validation of drug targets. These definitions have been tailored to reversibly acting modulators but fall short in their applicability to other modalities. While initial guidelines have been proposed, we delineate here a full set of criteria for the characterization of covalent, irreversible inhibitors as well as heterobifunctional degraders ("proteolysis-targeting chimeras", or PROTACs) and molecular glue degraders. We propose modified potency and selectivity criteria compared to those for reversible inhibitors. We discuss their relevance and highlight examples of suitable probe and pathfinder compounds.
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Affiliation(s)
- Ingo V. Hartung
- Medicinal
Chemistry, Global Research & Development, Merck Healthcare KGaA, 64293 Darmstadt, Germany
| | - Joachim Rudolph
- Discovery
Chemistry, Genentech, South San Francisco, California 94080, United States
| | - Mary M. Mader
- Molecular
Innovation, Indiana Biosciences Research
Institute, Indianapolis, Indiana 64202, United States
| | - Monique P. C. Mulder
- Department
of Cell and Chemical Biology, Leiden University
Medical Center, 2333 ZA Leiden, The Netherlands
| | - Paul Workman
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London, Sutton SM2 5NG, United Kingdom
- Chemical
Probes Portal, https://www.chemicalprobes.org/
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10
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Savoy L, Long N, Lee H, Chen R, Allen B, Lin HY, Tognon C, Malhotra SV, Tyner JW, Zhang H. CDK12/13 dual inhibitors are potential therapeutics for acute myeloid leukemia. Br J Haematol 2023; 202:195-198. [PMID: 37182843 PMCID: PMC10330638 DOI: 10.1111/bjh.18843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/17/2023] [Accepted: 04/23/2023] [Indexed: 05/16/2023]
Affiliation(s)
- Lindsey Savoy
- Division of Oncological Sciences, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | - Nicola Long
- Division of Hematology and Medical Oncology, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | - Hyunjung Lee
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | - Reid Chen
- Division of Oncological Sciences, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | - Basil Allen
- Division of Oncological Sciences, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | - Hsin-Yun Lin
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | - Cristina Tognon
- Division of Hematology and Medical Oncology, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | - Sanjay V. Malhotra
- Center for Experimental Therapeutics, Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | - Jeffrey W. Tyner
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | - Haijiao Zhang
- Division of Oncological Sciences, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
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11
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Bai Y, Liu Z, Li Y, Zhao H, Lai C, Zhao S, Chen K, Luo C, Yang X, Wang F. Structural Mass Spectrometry Probes the Inhibitor-Induced Allosteric Activation of CDK12/CDK13-Cyclin K Dissociation. J Am Chem Soc 2023; 145:11477-11481. [PMID: 37207290 DOI: 10.1021/jacs.3c01697] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The rational design and development of effective inhibitors for cyclin-dependent kinases 12 and 13 (CDK12 and CDK13) are largely dependent on the understanding of the dynamic inhibition conformations but are difficult to be achieved by conventional characterization tools. Herein, we integrate the structural mass spectrometry (MS) methods of lysine reactivity profiling (LRP) and native MS (nMS) to systematically interrogate both the dynamic molecular interactions and overall protein assembly of CDK12/CDK13-cyclin K (CycK) complexes under the modulation of small molecule inhibitors. The essential structure insights, including inhibitor binding pocket, binding strength, interfacial molecular details, and dynamic conformation changes, can be derived from the complementary results of LRP and nMS. We find the inhibitor SR-4835 binding can greatly destabilize the CDK12/CDK13-CycK interactions in an unusual allosteric activation way, thereby providing a novel alternative for the kinase activity inhibition. Our results underscore the great potential of LRP combination with nMS for the evaluation and rational design of effective kinase inhibitors at the molecular level.
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Affiliation(s)
- Yu Bai
- School of Pharmacy, China Medical University, Shenyang 110122, China
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanqing Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Heng Zhao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Can Lai
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shan Zhao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Kaixian Chen
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Luo
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xueming Yang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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12
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Wood GE, Graves LA, Rubin EM, Reed DR, Riedel RF, Strauss SJ. Bad to the Bone: Emerging Approaches to Aggressive Bone Sarcomas. Am Soc Clin Oncol Educ Book 2023; 43:e390306. [PMID: 37220319 DOI: 10.1200/edbk_390306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Bone sarcomas are rare heterogeneous tumors that affect patients of all ages including children, adolescent young adults, and older adults. They include many aggressive subtypes and patient groups with poor outcomes, poor access to clinical trials, and lack of defined standard therapeutic strategies. Conventional chondrosarcoma remains a surgical disease, with no defined role for cytotoxic therapy and no approved targeted systemic therapies. Here, we discuss promising novel targets and strategies undergoing evaluation in clinical trials. Multiagent chemotherapy has greatly improved outcomes for patients with Ewing sarcoma (ES) and osteosarcoma, but management of those with high-risk or recurrent disease remains challenging and controversial. We describe the impact of international collaborative trials, such as the rEECur study, that aim to define optimal treatment strategies for those with recurrent, refractory ES, and evidence for high-dose chemotherapy with stem-cell support. We also discuss current and emerging strategies for other small round cell sarcomas, such as CIC-rearranged, BCOR-rearranged tumors, and the evaluation of emerging novel therapeutics and trial designs that may offer a new paradigm to improve survival in these aggressive tumors with notoriously bad (to the bone) outcomes.
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Affiliation(s)
- Georgina E Wood
- Department of Oncology, University College London Hospitals NHS Trust, UCL Cancer Institute, London, United Kingdom
| | - Laurie A Graves
- Division of Hematology/Oncology, Department of Pediatrics, Duke University, Durham, NC
| | - Elyssa M Rubin
- Division of Oncology, Children's Hospital of Orange County, Orange, CA
| | - Damon R Reed
- Department of Individualized Cancer Management, Moffitt Cancer Center, Tampa, FL
| | - Richard F Riedel
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Durham, NC
| | - Sandra J Strauss
- Department of Oncology, University College London Hospitals NHS Trust, UCL Cancer Institute, London, United Kingdom
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13
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Wu W, Yu S, Yu X. Transcription-associated cyclin-dependent kinase 12 (CDK12) as a potential target for cancer therapy. Biochim Biophys Acta Rev Cancer 2023; 1878:188842. [PMID: 36460141 DOI: 10.1016/j.bbcan.2022.188842] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022]
Abstract
Cyclin-dependent kinase 12 (CDK12), a transcription-related cyclin dependent kinase (CDK), plays a momentous part in multitudinous biological functions, such as replication, transcription initiation to elongation and termination, precursor mRNA (pre-mRNA) splicing, intron polyadenylation (IPA), and translation. CDK12 can act as a tumour suppressor or oncogene in disparate cellular environments, and its dysregulation likely provokes tumorigenesis. A comprehensive understanding of CDK12 will tremendously facilitate the exploitation of novel tactics for the treatment and precaution of cancer. Currently, CDK12 inhibitors are nonspecific and nonselective, which profoundly hinders the pharmacological target validation and drug exploitation process. Herein, we summarize the newly comprehension of the biological functions of CDK12 with a focus on recently emerged advancements of CDK12-associated therapeutic approaches in cancers.
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Affiliation(s)
- Wence Wu
- Departments of Orthopedics, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Beijing Key Laboratory for Carcinogenesis and Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shengji Yu
- Departments of Orthopedics, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Xiying Yu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Beijing Key Laboratory for Carcinogenesis and Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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14
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Gai C, Harnor SJ, Zhang S, Cano C, Zhuang C, Zhao Q. Advanced approaches of developing targeted covalent drugs. RSC Med Chem 2022; 13:1460-1475. [PMID: 36561076 PMCID: PMC9749957 DOI: 10.1039/d2md00216g] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022] Open
Abstract
In recent years, the development of targeted covalent inhibitors has gained popularity around the world. Specific groups (electrophilic warheads) form irreversible bonds with the side chain of nucleophilic amino acid residues, thus changing the function of biological targets such as proteins. Since the first targeted covalent inhibitor was disclosed in the 1990s, great efforts have been made to develop covalent ligands from known reversible leads or drugs by addition of tolerated electrophilic warheads. However, high reactivity and "off-target" toxicity remain challenging issues. This review covers the concept of targeted covalent inhibition to diseases, discusses traditional and interdisciplinary strategies of cysteine-focused covalent drug discovery, and exhibits newly disclosed electrophilic warheads majorly targeting the cysteine residue. Successful applications to address the challenges of designing effective covalent drugs are also introduced.
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Affiliation(s)
- Conghao Gai
- Organic Chemistry Group, College of Pharmacy, Naval Medical University Shanghai 200433 P. R. China
| | - Suzannah J Harnor
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, School of Natural and Environmental Sciences, Bedson Building, Newcastle University Newcastle upon Tyne NE1 7RU UK
| | - Shihao Zhang
- Organic Chemistry Group, College of Pharmacy, Naval Medical University Shanghai 200433 P. R. China
| | - Céline Cano
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, School of Natural and Environmental Sciences, Bedson Building, Newcastle University Newcastle upon Tyne NE1 7RU UK
| | - Chunlin Zhuang
- Organic Chemistry Group, College of Pharmacy, Naval Medical University Shanghai 200433 P. R. China
| | - Qingjie Zhao
- Organic Chemistry Group, College of Pharmacy, Naval Medical University Shanghai 200433 P. R. China
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15
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The mechanism of BUD13 m6A methylation mediated MBNL1-phosphorylation by CDK12 regulating the vasculogenic mimicry in glioblastoma cells. Cell Death Dis 2022; 13:1017. [PMID: 36463205 PMCID: PMC9719550 DOI: 10.1038/s41419-022-05426-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 12/04/2022]
Abstract
Vasculogenic mimicry (VM) is an endothelium-independent tumor microcirculation that provides adequate blood supply for tumor growth. The presence of VM greatly hinders the treatment of glioblastoma (GBM) with anti-angiogenic drugs. Therefore, targeting VM formation may be a feasible therapeutic strategy for GBM. The research aimed to evaluate the roles of BUD13, CDK12, MBNL1 in regulating VM formation of GBM. BUD13 and CDK12 were upregulated and MBNL1 was downregulated in GBM tissues and cells. Knockdown of BUD13, CDK12, or overexpression of MBNL1 inhibited GBM VM formation. METTL3 enhanced the stability of BUD13 mRNA and upregulated its expression through m6A methylation. BUD13 enhanced the stability of CDK12 mRNA and upregulated its expression. CDK12 phosphorylated MBNL1, thereby regulating VM formation of GBM. The simultaneous knockdown of BUD13, CDK12, and overexpression of MBNL1 reduced the volume of subcutaneously transplanted tumors in nude mice and prolonged the survival period. Thus, the BUD13/CDK12/MBNL1 axis plays a crucial role in regulating VM formation of GBM and provides a potential target for GBM therapy.
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16
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Wang B, Wang Y, Wen Y, Zhang YL, Ni WJ, Tang TT, Cao JY, Yin Q, Jiang W, Yin D, Li ZL, Lv LL, Liu BC. Tubular-specific CDK12 knockout causes a defect in urine concentration due to premature cleavage of the slc12a1 gene. Mol Ther 2022; 30:3300-3312. [PMID: 35581939 PMCID: PMC9552909 DOI: 10.1016/j.ymthe.2022.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/21/2022] [Accepted: 05/11/2022] [Indexed: 11/27/2022] Open
Abstract
Cyclin-dependent kinase 12 (CDK12) plays a critical role in regulating gene transcription. CDK12 inhibition is a potential anticancer therapeutic strategy. However, several clinical trials have shown that CDK inhibitors might cause renal dysfunction and electrolyte disorders. CDK12 is abundant in renal tubular epithelial cells (RTECs), but the exact role of CDK12 in renal physiology remains unclear. Genetic knockout of CDK12 in mouse RTECs causes polydipsia, polyuria, and hydronephrosis. This phenotype is caused by defects in water reabsorption that are the result of reduced Na-K-2Cl cotransporter 2 (NKCC2) levels in the kidney. In addition, CKD12 knockout causes an increase in Slc12a1 (which encodes NKCC2) intronic polyadenylation events, which results in Slc12a1 truncated transcript production and NKCC2 downregulation. These findings provide novel insight into CDK12 being necessary for maintaining renal homeostasis by regulating NKCC2 transcription, which explains the critical water and electrolyte disturbance that occurs during the application of CDK12 inhibitors for cancer treatment. Therefore, there are safety concerns about the clinical use of these new anticancer drugs.
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Affiliation(s)
- Bin Wang
- Institute of Nephrology, Zhong da Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China
| | - Yao Wang
- Nanjing Medical University, Nanjing, Jiangsu, China; Department of Nephrology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yi Wen
- Institute of Nephrology, Zhong da Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China.
| | - Yi-Lin Zhang
- Institute of Nephrology, Zhong da Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China
| | - Wei-Jie Ni
- Institute of Nephrology, Zhong da Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China
| | - Tao-Tao Tang
- Institute of Nephrology, Zhong da Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China
| | - Jing-Yuan Cao
- Institute of Nephrology, Zhong da Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China
| | - Qing Yin
- Institute of Nephrology, Zhong da Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China
| | - Wei Jiang
- Institute of Nephrology, Zhong da Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China
| | - Di Yin
- Institute of Nephrology, Zhong da Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China
| | - Zuo-Lin Li
- Institute of Nephrology, Zhong da Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China
| | - Lin-Li Lv
- Institute of Nephrology, Zhong da Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China
| | - Bi-Cheng Liu
- Institute of Nephrology, Zhong da Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China; Nanjing Medical University, Nanjing, Jiangsu, China.
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17
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Tang R, Liu J, Li S, Zhang J, Yu C, Liu H, Chen F, Lv L, Zhang Q, Yuan K, Shao H. A patent and literature review of CDK12 inhibitors. Expert Opin Ther Pat 2022; 32:1055-1065. [PMID: 36120913 DOI: 10.1080/13543776.2022.2126765] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Cyclin-dependent kinase 12 (CDK12) belongs to the CDK family of serine/threonine protein kinases and associates with cyclin K to exert its biological functions, including regulating gene transcription, mRNA processing and translation. Increasing evidences demonstrate the importance of CDK12 in various human cancers, illustrating its potential as both biomarker and therapeutic target. In addition, CDK12 is also a promising target for the treatment of myotonic dystrophy type 1. Efforts have been taken to discover small molecule inhibitors to validate this important therapeutic target. AREAS COVERED This review covers the patented CDK12 inhibitors from 2016 to present, as well as these from peer-reviewed literature. It provides the reader an update of the discovery strategies, chemical structures and molecular profiling of all available CDK12 inhibitors. EXPERT OPINION CDK12 inhibitors with various mechanism of actions have been discovered and it is a great set of tools to evaluate the therapeutic potential of CDK12 in different disease models. CDK12 inhibitors have shown promising results in myotonic dystrophy type 1 mouse model and several preclinical cancer models either as single agent or combination with other anti-cancer agents. Its therapeutic value awaits more rigorous preclinical testing and further clinical investigation.
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Affiliation(s)
- Ruijun Tang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China.,Center for Clinical Biorepositories and Biospecimen & Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jing Liu
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China
| | - Shuyao Li
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China
| | - Junjie Zhang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China
| | - Chunhong Yu
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China
| | - Honglu Liu
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China
| | - Fang Chen
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China
| | - Lu Lv
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China
| | - Qian Zhang
- Department of Chemistry, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
| | - Kai Yuan
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China.,Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,The Biobank of Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China
| | - Hao Shao
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China
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18
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Yang J, Chang Y, Tien JCY, Wang Z, Zhou Y, Zhang P, Huang W, Vo J, Apel IJ, Wang C, Zeng VZ, Cheng Y, Li S, Wang GX, Chinnaiyan AM, Ding K. Discovery of a Highly Potent and Selective Dual PROTAC Degrader of CDK12 and CDK13. J Med Chem 2022; 65:11066-11083. [PMID: 35938508 PMCID: PMC9876424 DOI: 10.1021/acs.jmedchem.2c00384] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Indexed: 01/28/2023]
Abstract
Selective degradation of the cyclin-dependent kinases 12 and 13 (CDK12/13) presents a novel therapeutic opportunity for triple-negative breast cancer (TNBC), but there is still a lack of dual CDK12/13 degraders. Here, we report the discovery of the first series of highly potent and selective dual CDK12/13 degraders by employing the proteolysis-targeting chimera (PROTAC) technology. The optimal compound 7f effectively degraded CDK12 and CDK13 with DC50 values of 2.2 and 2.1 nM, respectively, in MDA-MB-231 breast cancer cells. Global proteomic profiling demonstrated the target selectivity of 7f. In vitro, 7f suppressed expression of core DNA damage response (DDR) genes in a time- and dose-dependent manner. Further, 7f markedly inhibited proliferation of multiple TNBC cell lines including MFM223, with an IC50 value of 47 nM. Importantly, 7f displayed a significantly improved antiproliferative activity compared to the structurally similar inhibitor 4, suggesting the potential advantage of a CDK12/13 degrader for TNBC targeted therapy.
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Affiliation(s)
- Jianzhang Yang
- International
Cooperative Laboratory of Traditional Chinese Medicine Modernization
and Innovative Drug Discovery of Chinese Ministry of Education (MOE),
Guangzhou City Key Laboratory of Precision Chemical Drug Development,
College of Pharmacy, Jinan University, 855 Xingye Avenue East, Guangzhou 511400, People’s Republic of China
| | - Yu Chang
- International
Cooperative Laboratory of Traditional Chinese Medicine Modernization
and Innovative Drug Discovery of Chinese Ministry of Education (MOE),
Guangzhou City Key Laboratory of Precision Chemical Drug Development,
College of Pharmacy, Jinan University, 855 Xingye Avenue East, Guangzhou 511400, People’s Republic of China
- Michigan
Center for Translational Pathology, University
of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jean Ching-Yi Tien
- Michigan
Center for Translational Pathology, University
of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Zhen Wang
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy
of Sciences, #345 Ling Ling Road, Shanghai 200032, People’s Republic of China
| | - Yang Zhou
- International
Cooperative Laboratory of Traditional Chinese Medicine Modernization
and Innovative Drug Discovery of Chinese Ministry of Education (MOE),
Guangzhou City Key Laboratory of Precision Chemical Drug Development,
College of Pharmacy, Jinan University, 855 Xingye Avenue East, Guangzhou 511400, People’s Republic of China
| | - Pujuan Zhang
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy
of Sciences, #345 Ling Ling Road, Shanghai 200032, People’s Republic of China
| | - Weixue Huang
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy
of Sciences, #345 Ling Ling Road, Shanghai 200032, People’s Republic of China
| | - Josh Vo
- Michigan
Center for Translational Pathology, University
of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ingrid J. Apel
- Michigan
Center for Translational Pathology, University
of Michigan, Ann Arbor, Michigan 48109, United States
| | - Cynthia Wang
- Michigan
Center for Translational Pathology, University
of Michigan, Ann Arbor, Michigan 48109, United States
| | - Victoria Zhixuan Zeng
- Michigan
Center for Translational Pathology, University
of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yunhui Cheng
- Michigan
Center for Translational Pathology, University
of Michigan, Ann Arbor, Michigan 48109, United States
| | - Shuqin Li
- Michigan
Center for Translational Pathology, University
of Michigan, Ann Arbor, Michigan 48109, United States
| | - George Xiaoju Wang
- Michigan
Center for Translational Pathology, University
of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Arul M. Chinnaiyan
- Michigan
Center for Translational Pathology, University
of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
- Howard Hughes
Medical Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Urology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ke Ding
- International
Cooperative Laboratory of Traditional Chinese Medicine Modernization
and Innovative Drug Discovery of Chinese Ministry of Education (MOE),
Guangzhou City Key Laboratory of Precision Chemical Drug Development,
College of Pharmacy, Jinan University, 855 Xingye Avenue East, Guangzhou 511400, People’s Republic of China
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy
of Sciences, #345 Ling Ling Road, Shanghai 200032, People’s Republic of China
- Institute
of Basic Medicine and Cancer (IBMC), Chinese
Academy of Sciences, Hangzhou, Zhejiang 310022, People’s Republic of China
- The
First Affiliated Hospital (Huaqiao Hospital), Jinan University, 601
Huangpu Avenue West, Guangzhou 510632, China
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19
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Magnuson B, Bedi K, Narayanan IV, Bartkowiak B, Blinkiewicz H, Paulsen MT, Greenleaf A, Ljungman M. CDK12 regulates co-transcriptional splicing and RNA turnover in human cells. iScience 2022; 25:105030. [PMID: 36111258 PMCID: PMC9468413 DOI: 10.1016/j.isci.2022.105030] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/13/2022] [Accepted: 08/23/2022] [Indexed: 11/28/2022] Open
Abstract
The cyclin-dependent kinase CDK12 has garnered interest as a cancer therapeutic target as DNA damage response genes are particularly suppressed by loss of CDK12 activity. In this study, we assessed the acute effects of CDK12 inhibition on transcription and RNA processing using nascent RNA Bru-seq and BruChase-seq. Acute transcriptional changes were overall small after CDK12 inhibition but over 600 genes showed intragenic premature termination, including DNA repair and cell cycle genes. Furthermore, many genes showed reduced transcriptional readthrough past the end of genes in the absence of CDK12 activity. RNA turnover was dramatically affected by CDK12 inhibition and importantly, caused increased degradation of many transcripts from DNA damage response genes. We also show that co-transcriptional splicing was suppressed by CDK12 inhibition. Taken together, these studies reveal the roles of CDK12 in regulating transcription elongation, transcription termination, co-transcriptional splicing, and RNA turnover. Over 600 genes showed prematurely terminated transcription when CDK12 was inhibited CDK12 promotes transcriptional readthrough past transcription end sites (TESs) CDK12 promotes splicing and affects transcript stability
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Affiliation(s)
- Brian Magnuson
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center and Center for RNA Biomedicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Karan Bedi
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center and Center for RNA Biomedicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Bartlomiej Bartkowiak
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hailey Blinkiewicz
- Department of Radiation Oncology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michelle T. Paulsen
- Department of Radiation Oncology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Arno Greenleaf
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mats Ljungman
- Rogel Cancer Center and Center for RNA Biomedicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Radiation Oncology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Corresponding author
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20
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Maki RG, Grohar PJ, Antonescu CR. Ewing sarcoma and related FET family translocation-associated round cell tumors: A century of clinical and scientific progress. Genes Chromosomes Cancer 2022; 61:509-517. [PMID: 35443099 PMCID: PMC9197982 DOI: 10.1002/gcc.23050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 04/09/2022] [Accepted: 04/11/2022] [Indexed: 11/10/2022] Open
Abstract
The year 2021 marked the centenary of the first publication of a cancer termed diffuse endothelioma of bone by James Ewing. Its unique features were apparent even in the first case series he described. This new diagnosis was clearly distinct from osteogenic sarcoma and myeloma, which were already well recognized at the time. We undertake this summary to better understanding Ewing sarcoma, contrasting the logarithmic evolution of the standard of care of systemic therapy for this and related diagnoses to the exponential understanding of the molecular biology of this family of tumors. We also outline in this manuscript how the finding of genomic relatives within Ewing sarcoma itself and related tumors, first noted nearly 40 years ago, helps us appreciate the need to find therapeutic plans that are specific for each small round blue cell tumor subtype. The advent of next generation sequencing regarding previously unknown small round blue cell tumor subtypes in many ways puts us back in the shoes of James Ewing in 1921, searching anew for clues leading to better treatments for increasingly rare cancer subsets.
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Affiliation(s)
- Robert G Maki
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Patrick J Grohar
- Division of Oncology, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Cristina R Antonescu
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
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21
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Lei P, Zhang J, Liao P, Ren C, Wang J, Wang Y. Current progress and novel strategies that target CDK12 for drug discovery. Eur J Med Chem 2022; 240:114603. [PMID: 35868123 DOI: 10.1016/j.ejmech.2022.114603] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 02/05/2023]
Abstract
CDK12 is a cyclin-dependent kinase that plays critical roles in DNA replication, transcription, mRNA splicing, and DNA damage repair. CDK12 genomic changes, including mutation, amplification, deletion, and fusion, lead to various cancers, such as colorectal cancer, gastric cancer, and ovarian cancer. An increasing number of CDK12 inhibitors have been reported since CDK12 was identified as a biomarker and cancer therapeutic target. A major challenge lies in that CDK12 and CDK13 share highly similar sequences, which leads to great difficulties in the development of highly selective CDK12 inhibitors. In recent years, great efforts were made in developing selective CDK12 blockers. Techniques including PROTAC and molecular glue degraders were also applied to facilitate their development. Also, the drug combination strategy of CDK12 small molecule inhibitors were studied. This review discusses the latest studies on CDK12 inhibitors and analyzes their structure-activity relationships, shedding light on their further development.
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Affiliation(s)
- Peng Lei
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jifa Zhang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Tianfu Jincheng Laboratory, Chengdu, 610041, Sichuan, China
| | - Peiyu Liao
- School of Pharmacy, Chengdu Medical College, Chengdu, 610500, Sichuan, China
| | - Changyu Ren
- Department of Pharmacy, Chengdu Fifth People's Hospital, Chengdu, 611130, Sichuan, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, 38163, Tennessee, United States
| | - Yuxi Wang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Tianfu Jincheng Laboratory, Chengdu, 610041, Sichuan, China.
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22
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Transcription associated cyclin-dependent kinases as therapeutic targets for prostate cancer. Oncogene 2022; 41:3303-3315. [PMID: 35568739 PMCID: PMC9187515 DOI: 10.1038/s41388-022-02347-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/21/2022] [Accepted: 05/04/2022] [Indexed: 11/08/2022]
Abstract
Transcriptional deregulation has emerged as a hallmark of several cancer types. In metastatic castration-resistant prostate cancer, a stage in which systemic androgen deprivation therapies fail to show clinical benefit, transcriptional addiction to the androgen receptor is maintained in most patients. This has led to increased efforts to find novel therapies that prevent oncogenic transactivation of the androgen receptor. In this context, a group of druggable protein kinases, known as transcription associated cyclin-dependent kinases (tCDKs), show great potential as therapeutic targets. Despite initial reservations about targeting tCDKs due to their ubiquitous and prerequisite nature, preclinical studies showed that selectively inhibiting such kinases could provide sufficient therapeutic window to exert antitumour effects in the absence of systemic toxicity. As a result, several highly specific inhibitors are currently being trialled in solid tumours, including prostate cancer. This article summarises the roles of tCDKs in regulating gene transcription and highlights rationales for their targeting in prostate cancer. It provides an overview of the most recent developments in this therapeutic area, including the most recent clinical advances, and discusses the utility of tCDK inhibitors in combination with established cancer agents.
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23
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Borsari C, Keles E, McPhail JA, Schaefer A, Sriramaratnam R, Goch W, Schaefer T, De Pascale M, Bal W, Gstaiger M, Burke JE, Wymann MP. Covalent Proximity Scanning of a Distal Cysteine to Target PI3Kα. J Am Chem Soc 2022; 144:6326-6342. [PMID: 35353516 PMCID: PMC9011356 DOI: 10.1021/jacs.1c13568] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Covalent protein
kinase inhibitors exploit currently noncatalytic
cysteines in the adenosine 5′-triphosphate (ATP)-binding site
via electrophiles directly appended to a reversible-inhibitor scaffold.
Here, we delineate a path to target solvent-exposed cysteines at a
distance >10 Å from an ATP-site-directed core module and produce
potent covalent phosphoinositide 3-kinase α (PI3Kα) inhibitors.
First, reactive warheads are used to reach out to Cys862 on PI3Kα,
and second, enones are replaced with druglike warheads while linkers
are optimized. The systematic investigation of intrinsic warhead reactivity
(kchem), rate of covalent bond formation
and proximity (kinact and reaction space
volume Vr), and integration of structure
data, kinetic and structural modeling, led to the guided identification
of high-quality, covalent chemical probes. A novel stochastic approach
provided direct access to the calculation of overall reaction rates
as a function of kchem, kinact, Ki, and Vr, which was validated with compounds with varied linker
lengths. X-ray crystallography, protein mass spectrometry (MS), and
NanoBRET assays confirmed covalent bond formation of the acrylamide
warhead and Cys862. In rat liver microsomes, compounds 19 and 22 outperformed the rapidly metabolized CNX-1351,
the only known PI3Kα irreversible inhibitor. Washout experiments
in cancer cell lines with mutated, constitutively activated PI3Kα
showed a long-lasting inhibition of PI3Kα. In SKOV3 cells, compounds 19 and 22 revealed PI3Kβ-dependent signaling,
which was sensitive to TGX221. Compounds 19 and 22 thus qualify as specific chemical probes to explore PI3Kα-selective
signaling branches. The proposed approach is generally suited to develop
covalent tools targeting distal, unexplored Cys residues in biologically
active enzymes.
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Affiliation(s)
- Chiara Borsari
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Erhan Keles
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Jacob A McPhail
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Alexander Schaefer
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Rohitha Sriramaratnam
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Wojciech Goch
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Thorsten Schaefer
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Martina De Pascale
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Wojciech Bal
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Matthias P Wymann
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
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24
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Lee J, Ban JW, Kim J, Yang S, Lee G, Dhorma LP, Kim MH, Ha MW, Hong S, Park HG. Asymmetric Phase-Transfer Catalytic aza-Michael Addition to Cyclic Enone: Highly Enantioselective and Diastereoselective Synthesis of Cyclic 1,3-Aminoalcohols. Org Lett 2022; 24:1647-1651. [PMID: 35175781 DOI: 10.1021/acs.orglett.2c00192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The highly enantioselective aza-Michael reaction of tert-butyl β-naphthylmethoxycarbamate to cyclic enones has been accomplished by using a new cinchona alkaloid derived C(9)-urea ammonium catalyst under phase-transfer catalysis conditions with up to 98% ee at 0 °C. The resulting aza-Michael adducts can be converted to versatile intermediates by selective deprotection and the cyclic 1,3-aminoalcohols by diastereoselective reduction with up to 32:1, which have been widely used as important pharmacophores in pharmaceutical development.
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Affiliation(s)
- Jaeyong Lee
- Research Institute of Pharmaceutical Sciences and College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Jeong Woo Ban
- Research Institute of Pharmaceutical Sciences and College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Jeongseok Kim
- Research Institute of Pharmaceutical Sciences and College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Sehun Yang
- Research Institute of Pharmaceutical Sciences and College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Geumwoo Lee
- Research Institute of Pharmaceutical Sciences and College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Lama Prema Dhorma
- College of Pharmacy, Gachon University, 191 Hambakmoero, Yeonsu-gu, Incheon 21936, Republic of Korea
| | - Mi-Hyun Kim
- College of Pharmacy, Gachon University, 191 Hambakmoero, Yeonsu-gu, Incheon 21936, Republic of Korea
| | - Min Woo Ha
- Jeju Research Institute of Pharmaceutical Sciences, College of Pharmacy and Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, 102 Jejudaehak-ro, Jeju 63243, Republic of Korea
| | - Suckchang Hong
- Research Institute of Pharmaceutical Sciences and College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Hyeung-Geun Park
- Research Institute of Pharmaceutical Sciences and College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
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25
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Liu Y, Fu L, Wu J, Liu M, Wang G, Liu B, Zhang L. Transcriptional cyclin-dependent kinases: Potential drug targets in cancer therapy. Eur J Med Chem 2021; 229:114056. [PMID: 34942431 DOI: 10.1016/j.ejmech.2021.114056] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/14/2021] [Accepted: 12/14/2021] [Indexed: 02/08/2023]
Abstract
In the wake of the development of the concept of cell cycle and its limiting points, cyclin-dependent kinases (CDKs) are considered to play a central role in regulating cell cycle progression. Recent studies have strongly demonstrated that CDKs also has multiple functions, especially in response to extracellular and intracellular signals by interfering with transcriptional events. Consequently, how to inhibit their function has been a hot research topic. It is worth noting that the key role of CDKs in regulating transcription has been explored in recent years, but its related pharmacological targets are less developed, and most inhibitors have not entered the clinical stage. Accordingly, this perspective focus on the biological functions of transcription related CDKs and their complexes, some key upstream and downstream signals, and inhibitors for cancer treatment in recent years. In addition, some corresponding combined treatment strategies will provide a more novel perspective for future cancer remedy.
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Affiliation(s)
- Yi Liu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, 610031, Chengdu, China
| | - Leilei Fu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, 610031, Chengdu, China
| | - Junhao Wu
- Department of Otolaryngology, Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Ming Liu
- Department of Orthopedics, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Guan Wang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, 610041, China.
| | - Bo Liu
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Lan Zhang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, 610031, Chengdu, China.
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26
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Decaesteker B, Durinck K, Van Roy N, De Wilde B, Van Neste C, Van Haver S, Roberts S, De Preter K, Vermeirssen V, Speleman F. From DNA Copy Number Gains and Tumor Dependencies to Novel Therapeutic Targets for High-Risk Neuroblastoma. J Pers Med 2021; 11:1286. [PMID: 34945759 PMCID: PMC8707517 DOI: 10.3390/jpm11121286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/19/2021] [Accepted: 11/20/2021] [Indexed: 12/15/2022] Open
Abstract
Neuroblastoma is a pediatric tumor arising from the sympatho-adrenal lineage and a worldwide leading cause of childhood cancer-related deaths. About half of high-risk patients die from the disease while survivors suffer from multiple therapy-related side-effects. While neuroblastomas present with a low mutational burden, focal and large segmental DNA copy number aberrations are highly recurrent and associated with poor survival. It can be assumed that the affected chromosomal regions contain critical genes implicated in neuroblastoma biology and behavior. More specifically, evidence has emerged that several of these genes are implicated in tumor dependencies thus potentially providing novel therapeutic entry points. In this review, we briefly review the current status of recurrent DNA copy number aberrations in neuroblastoma and provide an overview of the genes affected by these genomic variants for which a direct role in neuroblastoma has been established. Several of these genes are implicated in networks that positively regulate MYCN expression or stability as well as cell cycle control and apoptosis. Finally, we summarize alternative approaches to identify and prioritize candidate copy-number driven dependency genes for neuroblastoma offering novel therapeutic opportunities.
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Grants
- P30 CA008748 NCI NIH HHS
- G087221N, G.0507.12, G049720N,12U4718N, 11C3921N, 11J8313N, 12B5313N, 1514215N, 1197617N,1238420N, 12Q8322N, 3F018519, 12N6917N Fund for Scientific Research Flanders
- 2018-087, 2018-125, 2020-112 Belgian Foundation against Cancer
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Affiliation(s)
- Bieke Decaesteker
- Department for Biomolecular Medicine, Ghent University, Medical Research Building (MRB1), Corneel Heymanslaan 10, B-9000 Ghent, Belgium; (B.D.); (K.D.); (N.V.R.); (B.D.W.); (C.V.N.); (S.V.H.); (K.D.P.); (V.V.)
| | - Kaat Durinck
- Department for Biomolecular Medicine, Ghent University, Medical Research Building (MRB1), Corneel Heymanslaan 10, B-9000 Ghent, Belgium; (B.D.); (K.D.); (N.V.R.); (B.D.W.); (C.V.N.); (S.V.H.); (K.D.P.); (V.V.)
| | - Nadine Van Roy
- Department for Biomolecular Medicine, Ghent University, Medical Research Building (MRB1), Corneel Heymanslaan 10, B-9000 Ghent, Belgium; (B.D.); (K.D.); (N.V.R.); (B.D.W.); (C.V.N.); (S.V.H.); (K.D.P.); (V.V.)
| | - Bram De Wilde
- Department for Biomolecular Medicine, Ghent University, Medical Research Building (MRB1), Corneel Heymanslaan 10, B-9000 Ghent, Belgium; (B.D.); (K.D.); (N.V.R.); (B.D.W.); (C.V.N.); (S.V.H.); (K.D.P.); (V.V.)
- Department of Internal Medicine and Pediatrics, Ghent University Hospital, Corneel Heymanslaan 10, B-9000 Ghent, Belgium
| | - Christophe Van Neste
- Department for Biomolecular Medicine, Ghent University, Medical Research Building (MRB1), Corneel Heymanslaan 10, B-9000 Ghent, Belgium; (B.D.); (K.D.); (N.V.R.); (B.D.W.); (C.V.N.); (S.V.H.); (K.D.P.); (V.V.)
| | - Stéphane Van Haver
- Department for Biomolecular Medicine, Ghent University, Medical Research Building (MRB1), Corneel Heymanslaan 10, B-9000 Ghent, Belgium; (B.D.); (K.D.); (N.V.R.); (B.D.W.); (C.V.N.); (S.V.H.); (K.D.P.); (V.V.)
| | - Stephen Roberts
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Katleen De Preter
- Department for Biomolecular Medicine, Ghent University, Medical Research Building (MRB1), Corneel Heymanslaan 10, B-9000 Ghent, Belgium; (B.D.); (K.D.); (N.V.R.); (B.D.W.); (C.V.N.); (S.V.H.); (K.D.P.); (V.V.)
| | - Vanessa Vermeirssen
- Department for Biomolecular Medicine, Ghent University, Medical Research Building (MRB1), Corneel Heymanslaan 10, B-9000 Ghent, Belgium; (B.D.); (K.D.); (N.V.R.); (B.D.W.); (C.V.N.); (S.V.H.); (K.D.P.); (V.V.)
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, B-9052 Zwijnaarde, Belgium
| | - Frank Speleman
- Department for Biomolecular Medicine, Ghent University, Medical Research Building (MRB1), Corneel Heymanslaan 10, B-9000 Ghent, Belgium; (B.D.); (K.D.); (N.V.R.); (B.D.W.); (C.V.N.); (S.V.H.); (K.D.P.); (V.V.)
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27
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Serafim RAM, Elkins JM, Zuercher WJ, Laufer SA, Gehringer M. Chemical Probes for Understudied Kinases: Challenges and Opportunities. J Med Chem 2021; 65:1132-1170. [PMID: 34477374 DOI: 10.1021/acs.jmedchem.1c00980] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over 20 years after the approval of the first-in-class protein kinase inhibitor imatinib, the biological function of a significant fraction of the human kinome remains poorly understood while most research continues to be focused on few well-validated targets. Given the strong genetic evidence for involvement of many kinases in health and disease, the understudied fraction of the kinome holds a large and unexplored potential for future therapies. Specific chemical probes are indispensable tools to interrogate biology enabling proper preclinical validation of novel kinase targets. In this Perspective, we highlight recent case studies illustrating the development of high-quality chemical probes for less-studied kinases and their application in target validation. We spotlight emerging techniques and approaches employed in the generation of chemical probes for protein kinases and beyond and discuss the associated challenges and opportunities.
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Affiliation(s)
- Ricardo A M Serafim
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Jonathan M Elkins
- Centre for Medicines Discovery, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - William J Zuercher
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stefan A Laufer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany.,Tübingen Center for Academic Drug Discovery, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
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