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Luo S, Wohl S, Zheng W, Yang S. Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery. Biomolecules 2023; 13:biom13030530. [PMID: 36979465 PMCID: PMC10046839 DOI: 10.3390/biom13030530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
Protein intrinsic disorder is increasingly recognized for its biological and disease-driven functions. However, it represents significant challenges for biophysical studies due to its high conformational flexibility. In addressing these challenges, we highlight the complementary and distinct capabilities of a range of experimental and computational methods and further describe integrative strategies available for combining these techniques. Integrative biophysics methods provide valuable insights into the sequence–structure–function relationship of disordered proteins, setting the stage for protein intrinsic disorder to become a promising target for drug discovery. Finally, we briefly summarize recent advances in the development of new small molecule inhibitors targeting the disordered N-terminal domains of three vital transcription factors.
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Affiliation(s)
- Shuqi Luo
- Center for Proteomics and Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Samuel Wohl
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Wenwei Zheng
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ 85212, USA
- Correspondence: (W.Z.); (S.Y.)
| | - Sichun Yang
- Center for Proteomics and Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
- Correspondence: (W.Z.); (S.Y.)
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52
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Candido MF, Medeiros M, Veronez LC, Bastos D, Oliveira KL, Pezuk JA, Valera ET, Brassesco MS. Drugging Hijacked Kinase Pathways in Pediatric Oncology: Opportunities and Current Scenario. Pharmaceutics 2023; 15:pharmaceutics15020664. [PMID: 36839989 PMCID: PMC9966033 DOI: 10.3390/pharmaceutics15020664] [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: 12/15/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/18/2023] Open
Abstract
Childhood cancer is considered rare, corresponding to ~3% of all malignant neoplasms in the human population. The World Health Organization (WHO) reports a universal occurrence of more than 15 cases per 100,000 inhabitants around the globe, and despite improvements in diagnosis, treatment and supportive care, one child dies of cancer every 3 min. Consequently, more efficient, selective and affordable therapeutics are still needed in order to improve outcomes and avoid long-term sequelae. Alterations in kinases' functionality is a trademark of cancer and the concept of exploiting them as drug targets has burgeoned in academia and in the pharmaceutical industry of the 21st century. Consequently, an increasing plethora of inhibitors has emerged. In the present study, the expression patterns of a selected group of kinases (including tyrosine receptors, members of the PI3K/AKT/mTOR and MAPK pathways, coordinators of cell cycle progression, and chromosome segregation) and their correlation with clinical outcomes in pediatric solid tumors were accessed through the R2: Genomics Analysis and Visualization Platform and by a thorough search of published literature. To further illustrate the importance of kinase dysregulation in the pathophysiology of pediatric cancer, we analyzed the vulnerability of different cancer cell lines against their inhibition through the Cancer Dependency Map portal, and performed a search for kinase-targeted compounds with approval and clinical applicability through the CanSAR knowledgebase. Finally, we provide a detailed literature review of a considerable set of small molecules that mitigate kinase activity under experimental testing and clinical trials for the treatment of pediatric tumors, while discuss critical challenges that must be overcome before translation into clinical options, including the absence of compounds designed specifically for childhood tumors which often show differential mutational burdens, intrinsic and acquired resistance, lack of selectivity and adverse effects on a growing organism.
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Affiliation(s)
- Marina Ferreira Candido
- Department of Cell Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil
| | - Mariana Medeiros
- Regional Blood Center, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil
| | - Luciana Chain Veronez
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil
| | - David Bastos
- Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-901, SP, Brazil
| | - Karla Laissa Oliveira
- Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-901, SP, Brazil
| | - Julia Alejandra Pezuk
- Departament of Biotechnology and Innovation, Anhanguera University of São Paulo, UNIAN/SP, São Paulo 04119-001, SP, Brazil
| | - Elvis Terci Valera
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil
| | - María Sol Brassesco
- Departament of Biotechnology and Innovation, Anhanguera University of São Paulo, UNIAN/SP, São Paulo 04119-001, SP, Brazil
- Correspondence: ; Tel.: +55-16-3315-9144; Fax: +55-16-3315-4886
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MDC1 maintains active elongation complexes of RNA polymerase II. Cell Rep 2023; 42:111979. [PMID: 36640322 DOI: 10.1016/j.celrep.2022.111979] [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: 12/14/2021] [Revised: 10/04/2022] [Accepted: 12/23/2022] [Indexed: 01/13/2023] Open
Abstract
The role of MDC1 in the DNA damage response has been extensively studied; however, its impact on other cellular processes is not well understood. Here, we describe the role of MDC1 in transcription as a regulator of RNA polymerase II (RNAPII). Depletion of MDC1 causes a genome-wide reduction in the abundance of actively engaged RNAPII elongation complexes throughout the gene body of protein-encoding genes under unperturbed conditions. Decreased engaged RNAPII subsequently alters the assembly of the spliceosome complex on chromatin, leading to changes in pre-mRNA splicing. Mechanistically, the S/TQ domain of MDC1 modulates RNAPII-mediated transcription. Upon genotoxic stress, MDC1 promotes the abundance of engaged RNAPII complexes at DNA breaks, thereby stimulating nascent transcription at the damaged sites. Of clinical relevance, cancer cells lacking MDC1 display hypersensitivity to RNAPII inhibitors. Overall, we unveil a role of MDC1 in RNAPII-mediated transcription with potential implications for cancer treatment.
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Patra D, Bhavya K, Ramprasad P, Kalia M, Pal D. Anti-cancer drug molecules targeting cancer cell cycle and proliferation. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 135:343-395. [PMID: 37061337 DOI: 10.1016/bs.apcsb.2022.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Cancer, a vicious clinical burden that potentiates maximum fatality for humankind, arises due to unregulated excessive cell division and proliferation through an eccentric expression of cell cycle regulator proteins. A set of evolutionarily conserved machinery controls the cell cycle in an extremely precise manner so that a cell that went through the cycle can produce a genetically identical copy. To achieve perfection, several checkpoints were placed in the cycle for surveillance; so, errors during the division were rectified by the repair strategies. However, irreparable damage leads to exit from the cell cycle and induces programmed cell death. In comparison to a normal cell, cancer cells facilitate the constitutive activation of many dormant proteins and impede negative regulators of the checkpoint. Extensive studies in the last few decades on cell division and proliferation of cancer cells elucidate the molecular mechanism of the cell-cycle regulators that are often targeted for the development of anti-cancer therapy. Each phase of the cell cycle has been regulated by a unique set of proteins including master regulators Cyclins, and CDKs, along with the accessory proteins such as CKI, Cdc25, error-responsive proteins, and various kinase proteins mainly WEE1 kinases, Polo-like kinases, and Aurora kinases that control cell division. Here in this chapter, we have analytically discussed the role of cell cycle regulators and proliferation factors in cancer progression and the rationale of using various cell cycle-targeting drug molecules as anti-cancer therapy.
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Affiliation(s)
- Debarun Patra
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India
| | - Kumari Bhavya
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India
| | - Palla Ramprasad
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India
| | - Moyna Kalia
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India
| | - Durba Pal
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India.
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55
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Donovan MG, Galbraith MD, Espinosa JM. Multi-omics investigation reveals functional specialization of transcriptional cyclin dependent kinases in cancer biology. Sci Rep 2022; 12:22505. [PMID: 36577800 PMCID: PMC9797569 DOI: 10.1038/s41598-022-26860-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/21/2022] [Indexed: 12/30/2022] Open
Abstract
Transcriptional addiction is recognized as a valid therapeutic target in cancer, whereby the dependency of cancer cells on oncogenic transcriptional regulators may be pharmacologically exploited. However, a comprehensive understanding of the key factors within the transcriptional machinery that might afford a useful therapeutic window remains elusive. Herein, we present a cross-omics investigation into the functional specialization of the transcriptional cyclin dependent kinases (tCDKs) through analysis of high-content genetic dependency, gene expression, patient survival, and drug response datasets. This analysis revealed specialization among tCDKs in terms of contributions to cancer cell fitness, clinical prognosis, and interaction with oncogenic signaling pathways. CDK7 and CDK9 stand out as the most relevant targets, albeit through distinct mechanisms of oncogenicity and context-dependent contributions to cancer survival and drug sensitivity. Genetic ablation of CDK9, but not CDK7, mimics the effect on cell viability the loss of key components of the transcriptional machinery. Pathway analysis of genetic co-dependency and drug sensitivity data show CDK7 and CDK9 have distinct relationships with major oncogenic signatures, including MYC and E2F targets, oxidative phosphorylation, and the unfolded protein response. Altogether, these results inform the improved design of therapeutic strategies targeting tCDKs in cancer.
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Affiliation(s)
- Micah G Donovan
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Matthew D Galbraith
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Joaquin M Espinosa
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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56
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Guo J, Huang X, Dou L, Yan M, Shen T, Tang W, Li J. Aging and aging-related diseases: from molecular mechanisms to interventions and treatments. Signal Transduct Target Ther 2022; 7:391. [PMID: 36522308 PMCID: PMC9755275 DOI: 10.1038/s41392-022-01251-0] [Citation(s) in RCA: 269] [Impact Index Per Article: 134.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/03/2022] [Accepted: 11/10/2022] [Indexed: 12/23/2022] Open
Abstract
Aging is a gradual and irreversible pathophysiological process. It presents with declines in tissue and cell functions and significant increases in the risks of various aging-related diseases, including neurodegenerative diseases, cardiovascular diseases, metabolic diseases, musculoskeletal diseases, and immune system diseases. Although the development of modern medicine has promoted human health and greatly extended life expectancy, with the aging of society, a variety of chronic diseases have gradually become the most important causes of disability and death in elderly individuals. Current research on aging focuses on elucidating how various endogenous and exogenous stresses (such as genomic instability, telomere dysfunction, epigenetic alterations, loss of proteostasis, compromise of autophagy, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, altered intercellular communication, deregulated nutrient sensing) participate in the regulation of aging. Furthermore, thorough research on the pathogenesis of aging to identify interventions that promote health and longevity (such as caloric restriction, microbiota transplantation, and nutritional intervention) and clinical treatment methods for aging-related diseases (depletion of senescent cells, stem cell therapy, antioxidative and anti-inflammatory treatments, and hormone replacement therapy) could decrease the incidence and development of aging-related diseases and in turn promote healthy aging and longevity.
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Affiliation(s)
- Jun Guo
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, China
| | - Xiuqing Huang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, China
| | - Lin Dou
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, China
| | - Mingjing Yan
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, China
| | - Tao Shen
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, China.
| | - Weiqing Tang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, China.
| | - Jian Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, China.
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Li ZM, Liu G, Gao Y, Zhao MG. Targeting CDK7 in oncology: The avenue forward. Pharmacol Ther 2022; 240:108229. [PMID: 35700828 DOI: 10.1016/j.pharmthera.2022.108229] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/02/2022] [Accepted: 06/07/2022] [Indexed: 12/14/2022]
Abstract
Cyclin-dependent kinase (CDK) 7 is best characterized for the ability to regulate biological processes, including the cell cycle and gene transcription. Abnormal CDK7 activity is observed in various tumours and represents a driving force for tumourigenesis. Therefore, CDK7 may be an appealing target for cancer treatment. Whereas, the enthusiasm for CDK7-targeted therapeutic strategy is mitigated due to the widely possessed belief that this protein is essential for normal cells. Indeed, the fact confronts the consensus. This is the first review to introduce the role of CDK7 in pan-cancers via a combined analysis of comprehensive gene information and (pre)clinical research results. We also discuss the recent advances in protein structure and summarize the understanding of mechanisms underlying CDK7 function. These endeavours highlight the pivotal roles of CDK7 in tumours and may contribute to the development of effective CDK7 inhibitors within the strategy of structure-based drug discovery for cancer therapy.
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Affiliation(s)
- Zhi-Mei Li
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Guan Liu
- Department of General Surgery, Tangdu Hospital, Fourth Military Medical University, Xinsi Road 1, Xi'an 710038, Shaanxi, PR China
| | - Ya Gao
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou 450001, Henan, PR China.
| | - Ming-Gao Zhao
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China; Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xinsi Road 1, Xi'an 710038, Shaanxi, PR China.
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58
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Li H, Muhetaer G, Xie Y, Yao K, Ma Q, Guan H, Xing S, Huang X, Zhou J. Identification of super-enhancer-driven peptidyl arginine deiminases as potential biomarkers and therapeutic targets for osimertinib-resistant non-small cell lung cancer. Front Pharmacol 2022; 13:1071365. [DOI: 10.3389/fphar.2022.1071365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 11/08/2022] [Indexed: 11/22/2022] Open
Abstract
Resistance to targeted drugs is now a challenging clinical problem in the treatment of non-small cell lung cancer (NSCLC). So far, there are no approved targeted therapeutic drugs for patients with disease progression after the third-generation epidermal growth factor receptor-tyrosine kinase inhibitor osimertinib resistance (OR). Super-enhancers (SEs) are large clusters of transcriptional enhancers that drive gene expression. In this study, we aimed to explore the potential pathogenic SEs and their driven genes in OR NSCLC. OR cell line was established by exposure of H1975 cells to incremental dosing of osimertinib. RNA-sequencing and H3K27ac ChIP-sequencing were used to identify the differential expressed genes (DEGs) and SEs in parental and resistant cells. Gene ontology analysis for the OR-specific SEs-associated genes showed that histone citrullination, protein citrullination, and peptidyl-arginine modification are the top three biological processes, and the DEGs involved in these biological processes, including peptidyl arginine deiminase 1 (PADI1), PADI2, and PADI3. Realtime-PCR and western blot detections confirmed these genes were highly expressed in OR cells. SE inhibitor decreases their expression, ensuring that SEs regulate their transcriptional expressions. The PADI inhibitor inhibited OR cells’ proliferation, invasion, and colony formation. This study demonstrates that SE-driven PADI family genes are potential biomarkers and targets for OR NSCLC.
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Insilico exploration of the potential inhibitory activity of DrugBank compounds against CDK7 kinase using structure-based virtual screening, molecular docking, and dynamics simulation approach. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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60
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Advances in the development of chordoma models for drug discovery and precision medicine. Biochim Biophys Acta Rev Cancer 2022; 1877:188812. [DOI: 10.1016/j.bbcan.2022.188812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/31/2022] [Accepted: 09/28/2022] [Indexed: 12/24/2022]
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Gu X, Shen H, Bai W, Xiang Z, Li X, Zhang R, Shi F, Li H, Zhu G, Guo S. Endometrial cancer prognosis prediction using correlation models based on CDK family genes. Front Genet 2022; 13:1021600. [PMID: 36299580 PMCID: PMC9589062 DOI: 10.3389/fgene.2022.1021600] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/27/2022] [Indexed: 11/17/2022] Open
Abstract
Cyclin-dependent kinases (CDKs) play an important role in cell division. Given that abnormal cell proliferation caused by dysregulation of cell division is one of the major causes of endometrial cancer (EC), it is important to elucidate the role of CDK family genes in the diagnosis and prognosis of EC. In this study, The Cancer Genome Atlas (TCGA) database was used to analyze the frequency of copy number variations and somatic mutations in 26 CDK family genes. Subsequently, the expression of these genes in EC was assessed, and their relationship with overall survival (OS) was examined via Kaplan–Meier analysis to assess their prognostic significance. A prognostic model based on seven CDK genes was constructed using Lasso and Cox regression, and the predictive performance of the model was analyzed using Kaplan–Meier analysis and column line plots. The correlation between CDK genes and immune cells was also examined. Patients with EC in the high-risk group had a poorer prognosis. The results of qRT-PCR and immunohistochemical analyses validated that CDK16 is highly expressed in EC tissues. Patients with EC with high CDK16 expression had worse 10-year OS than patients with low CDK16 expression. These findings suggest that the prognostic model constructed based on CDK genes can help to develop individualized and targeted treatment strategies for patients with EC.
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Affiliation(s)
- Xianhua Gu
- Department of Gynecological Oncology, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Honghong Shen
- Department of Medical Oncology, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Wenqi Bai
- Department of Gynecological Oncology, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Zheng Xiang
- Department of Surgical Oncology, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Xinwei Li
- Department of Medical Oncology, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Rong Zhang
- Department of Gynecological Oncology, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Fan Shi
- Department of Pathology, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Huiyuan Li
- Department of Medical Oncology, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Guangzheng Zhu
- Department of Surgical Oncology, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Suyang Guo
- Department of Gynecological Oncology, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
- *Correspondence: Suyang Guo,
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Dulińska-Litewka J, Felkle D, Dykas K, Handziuk Z, Krzysztofik M, Gąsiorkiewicz B. The role of cyclins in the development and progression of prostate cancer. Biomed Pharmacother 2022; 155:113742. [PMID: 36179490 DOI: 10.1016/j.biopha.2022.113742] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/10/2022] [Accepted: 09/21/2022] [Indexed: 11/02/2022] Open
Abstract
The role of cyclins in hormone-dependent neoplasms is crucial in the development of the disease that is resistant to first-line therapy, as the example of breast cancer shows. However, in prostate cancer, cyclins are studied to a lesser extent. There are some well-described molecular pathways, including cyclins A1 and D1 signaling, however the role of other cyclins, e.g., D2, D3, E, and H, still requires further investigation. Recent studies indicate that cyclins regulate various cellular processes, not only the cell cycle. Furthermore, they remain in cross-talk with many other signaling pathways, e.g., MAPK/ERK, PI3K/Akt, and Notch. The androgen signaling axis, which is pivotal in prostate cancer progression, interferes with cyclin pathways at many levels. This article summarizes current knowledge on the influence of cyclins on prostate cancer progression by describing interactions between the androgen receptor and cyclins, as well as mechanisms underlying the development of resistance to currently used therapies.
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Affiliation(s)
- Joanna Dulińska-Litewka
- Chair of Medical Biochemistry, Jagiellonian University Medical College, 31-034 Krakow, Mikołaja Kopernika Street 7C, Poland.
| | - Dominik Felkle
- Chair of Medical Biochemistry, Jagiellonian University Medical College, 31-034 Krakow, Mikołaja Kopernika Street 7C, Poland
| | - Kacper Dykas
- Chair of Medical Biochemistry, Jagiellonian University Medical College, 31-034 Krakow, Mikołaja Kopernika Street 7C, Poland
| | - Zuzanna Handziuk
- Chair of Medical Biochemistry, Jagiellonian University Medical College, 31-034 Krakow, Mikołaja Kopernika Street 7C, Poland
| | - Marta Krzysztofik
- Chair of Medical Biochemistry, Jagiellonian University Medical College, 31-034 Krakow, Mikołaja Kopernika Street 7C, Poland
| | - Bartosz Gąsiorkiewicz
- Chair of Medical Biochemistry, Jagiellonian University Medical College, 31-034 Krakow, Mikołaja Kopernika Street 7C, Poland
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Kuempers C, Jagomast T, Heidel C, Paulsen FO, Bohnet S, Schierholz S, Dreyer E, Kirfel J, Perner S. CDK7 is a prognostic biomarker for non-small cell lung cancer. Front Oncol 2022; 12:927140. [PMID: 36212402 PMCID: PMC9540232 DOI: 10.3389/fonc.2022.927140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
Aim Non-small cell lung cancer (NSCLC) remains the leading cause of cancer-related death globally despite promising progress of personalized therapy approaches. Cyclin-dependent kinase 7 (CDK7) is a kinase involved in transcription, overexpressed in a broad spectrum of cancer types and found to be associated with an unfavourable prognosis. In this study, we aimed to investigate the protein expression of CDK7 in a large cohort of NSCLC incorporating adenocarcinomas (adNSCLC) and squamous cell carcinomas (sqNSCLC) and to correlate its expression with clinicopathological data. Methods We performed immunohistochemical staining of CDK7 on our cohort of NSCLC including 258 adNSCLC and 101 sqNSCLC and measured protein expression via a semi-automated read out. According to the median value of CDK7 the cohort was stratified in a CDK7 high and low expressing group, respectively, and results were correlated with clinico-pathological data. Results CDK7 was significantly higher expressed in sqNSCLC than in adNSCLC. In the group of sqNSCLC, CDK7 expression was significantly higher in sqNSCLC with lymph node metastases than in sqNSCLC with N0 stage. We found a significantly worse overall survival and disease-free survival for patients with CDK7 high expressing NSCLC. Conclusion Since a high CDK7 expression seems to be linked with a poor prognosis it might serve as a promising novel prognostic biomarker and its assessment could be implied in future routine diagnostic workup of NSCLC samples. Considering that CDK7 inhibitors are currently tested in several trials for advanced solid malignancies, it may also be a new target for future anti-cancer therapy.
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Affiliation(s)
- Christiane Kuempers
- Institute of Pathology, University Hospital Schleswig-Holstein, Luebeck, Germany
- *Correspondence: Christiane Kuempers,
| | - Tobias Jagomast
- Institute of Pathology, University Hospital Schleswig-Holstein, Luebeck, Germany
| | - Carsten Heidel
- Institute of Pathology, University Hospital Schleswig-Holstein, Luebeck, Germany
- Department of Surgery, Schoen Klinik Neustadt, Holstein, Germany
| | - Finn-Ole Paulsen
- Institute of Pathology, University Hospital Schleswig-Holstein, Luebeck, Germany
- Department of Oncology, Hematology and Bone Marrow Transplantation with Division of Pneumology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sabine Bohnet
- Department of Pulmonology, University Hospital Schleswig-Holstein, Luebeck, Germany
| | - Stefanie Schierholz
- Department of Surgery, Medical University of Schleswig-Holstein, Luebeck, Germany
| | - Eva Dreyer
- Institute of Pathology, University Hospital Schleswig-Holstein, Luebeck, Germany
| | - Jutta Kirfel
- Institute of Pathology, University Hospital Schleswig-Holstein, Luebeck, Germany
| | - Sven Perner
- Institute of Pathology, University Hospital Schleswig-Holstein, Luebeck, Germany
- Pathology, Research Center Borstel-Leibniz Lung Center, Borstel, Germany
- German Center for Lung Research (DZL) Department Borstel, Borstel, Germany
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64
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Liu F, Qu R, Yang L, Shi G, Hao S, Hu C. Circular RNA Controls Tumor Occurrence and Development via Cell Cycle Regulation. Onco Targets Ther 2022; 15:993-1009. [PMID: 36134387 PMCID: PMC9484569 DOI: 10.2147/ott.s371629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 08/25/2022] [Indexed: 01/09/2023] Open
Abstract
Circular RNAs (circRNAs) participate in the occurrence and development of various diseases through different mechanisms, such as by acting as a microRNA (miRNA) sponge, interacting with RNA-binding proteins, and regulating gene transcription and protein translation. For example, the abnormal expression of specific circRNAs in tumor cells can alter key regulatory factors and the cell cycle network, resulting in cell cycle disorders and the development and metastasis of tumors. Here, we summarize the mechanisms involved in the circRNA-mediated processes that lead to uncontrolled cell cycle and tumor cell proliferation. Extensive studies investigating the abnormal expression of circRNAs in different cancer types have been conducted. The unique characteristics of circRNAs and their ability to regulate the cell cycle through diverse mechanisms is extremely valuable in tumor diagnosis, treatment, and prognosis. Our review may assist in further understanding the circRNA-mediated regulation of the cell cycle in tumors and provide insights for research on circRNA-based therapeutic strategies and biological diagnosis for cancer.
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Affiliation(s)
- Fang Liu
- Department of Hematology and Oncology, The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Rongfeng Qu
- Department of Hematology and Oncology, The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Limin Yang
- Department of Hematology and Oncology, The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Guang Shi
- Department of Hematology and Oncology, The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Shuhong Hao
- Department of Hematology and Oncology, The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Chunmei Hu
- Department of Hematology and Oncology, The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
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Wang Y, Zhang Z, Mi X, Li M, Huang D, Song T, Qi X, Yang M. Elevation of effective p53 expression sensitizes wild-type p53 breast cancer cells to CDK7 inhibitor THZ1. Cell Commun Signal 2022; 20:96. [PMID: 36058938 PMCID: PMC9442925 DOI: 10.1186/s12964-022-00837-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 02/03/2022] [Indexed: 12/02/2022] Open
Abstract
Background The cyclin-dependent kinase 7 (CDK7) inhibitor THZ1 represses multiple cancer cells. However, its tumor-repressive efficiency in wild-type p53 breast cancer cells remains controversial. Methods We conducted various assays, including CCK8, colony formation, flow cytometry, western blotting, and lactate dehydrogenase release detection, to clarify whether p53 elevation sensitizes breast cancer cells to THZ1. Results We found that upregulating functional p53 contributes to the increased sensitivity of breast cancer cells to THZ1. Increased THZ1 sensitivity requires active p53 and an intact p53 pathway, which was confirmed by introducing exogenous wild-type p53 and the subsequent elevation of THZ1-mediated tumor suppression in breast cancer cells carrying mutant p53. We confirmed that p53 accumulates in the nucleus and mitochondria during cell death. Furthermore, we identified extensive transcriptional disruption, rather than solely CDK7 inhibition, as the mechanism underlying the nutlin-3 and THZ1-induced death of breast cancer cells. Finally, we observed the combined nutlin-3 and THZ1 treatment amplified gasdermin E cleavage. Conclusion Enhanced sensitivity of breast cancer cells to THZ1 can be achieved by increasing effective p53 expression. Our approach may serve as a potential treatment for patients with breast cancer resistant to regular therapies. Video Abstract
Supplementary Information The online version contains supplementary material available at 10.1186/s12964-022-00837-z.
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Affiliation(s)
- Yueyuan Wang
- Department of Breast Surgery, The First Hospital of Jilin University, Changchun, People's Republic of China
| | - Zhihao Zhang
- Department of Breast Surgery, The First Hospital of Jilin University, Changchun, People's Republic of China
| | - Xuguang Mi
- Tumor Biotherapy Center, Jilin Province People's Hospital, Changchun, 130021, Jilin, Republic of China
| | - Mingxi Li
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, People's Republic of China
| | - Dan Huang
- Department of Breast Surgery, The First Hospital of Jilin University, Changchun, People's Republic of China
| | - Tingting Song
- Department of Breast Surgery, The First Hospital of Jilin University, Changchun, People's Republic of China
| | - Xiaoyan Qi
- Department of Breast Surgery, The First Hospital of Jilin University, Changchun, People's Republic of China
| | - Ming Yang
- Department of Breast Surgery, The First Hospital of Jilin University, Changchun, People's Republic of China.
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CDK7/GRP78 signaling axis contributes to tumor growth and metastasis in osteosarcoma. Oncogene 2022; 41:4524-4536. [PMID: 36042349 DOI: 10.1038/s41388-022-02446-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 11/08/2022]
Abstract
Osteosarcoma derives from primitive bone-forming mesenchymal cells and is the most common primary bone malignancy. Therapeutic targeting of osteosarcoma has been unsuccessful; therefore, identifying novel osteosarcoma pathogenesis could offer new therapeutic options. CDK7 is a subunit within the general transcription factor TFIIH. We aim to explore the new mechanism by which CDK7 regulates osteosarcoma and our studies may provide new theoretical support for the use of CDK7 inhibitors in the treatment of osteosarcoma. Here, we investigate the molecular mechanism underlying the association between CDK7 and GRP78 in osteosarcoma. Specifically, we find that an E3 ubiquitin ligase TRIM21 binds and targets GRP78 for ubiquitination and degradation, whereas CDK7 phosphorylates GRP78 at T69 to inhibit TRIM21 recruitment, leading to GRP78 stabilization. Notably, a CDK7-specific inhibitor, THZ1, blunts osteosarcoma growth and metastasis. Combination treatment with CDK7 and GRP78 inhibitors yield additive effects on osteosarcoma growth and progression inhibition. Thus, simultaneous suppression of CDK7 and GRP78 activity represents a potential new approach for the treatment of osteosarcoma. In conclusion, the discovery of this previously unknown CDK7/GRP78 signaling axis provides the molecular basis and the rationale to target human osteosarcoma.
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Krause W. Resistance to prostate cancer treatments. IUBMB Life 2022; 75:390-410. [PMID: 35978491 DOI: 10.1002/iub.2665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 07/09/2022] [Indexed: 12/14/2022]
Abstract
A review of the current treatment options for prostate cancer and the formation of resistance to these regimens has been compiled including primary, acquired, and cross-resistance. The diversification of the pathways involved and the escape routes the tumor is utilizing have been addressed. Whereas early stages of tumor can be cured, there is no treatment available after a point of no return has been reached, leaving palliative treatment as the only option. The major reasons for this outcome are the heterogeneity of tumors, both inter- and intra-individually and the nearly endless number of escape routes, which the tumor can select to overcome the effects of treatment. This means that more focus should be applied to the individualization of both diagnosis and therapy of prostate cancer. In addition to current treatment options, novel drugs and ongoing clinical trials have been addressed in this review.
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How does age determine the development of human immune-mediated arthritis? Nat Rev Rheumatol 2022; 18:501-512. [PMID: 35948692 PMCID: PMC9363867 DOI: 10.1038/s41584-022-00814-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2022] [Indexed: 11/08/2022]
Abstract
Does age substantially affect the emergence of human immune-mediated arthritis? Children do not usually develop immune-mediated articular inflammation during their first year of life. In patients with juvenile idiopathic arthritis, this apparent ‘immune privilege’ disintegrates, and chronic inflammation is associated with variable autoantibody signatures and patterns of disease that resemble adult arthritis phenotypes. Numerous mechanisms might be involved in this shift, including genetic and epigenetic predisposing factors, maturation of the immune system with a progressive modulation of putative tolerogenic controls, parallel development of microbial dysbiosis, accumulation of a pro-inflammatory burden driven by environmental exposures (the exposome) and comorbidity-related drivers. By exploring these mechanisms, we expand the discussion of three (not mutually exclusive) hypotheses on how these factors can contribute to the differences and similarities between the loss of immune tolerance in children and the development of established immune-mediated arthritis in adults. These three hypotheses relate to a critical window in genetics and epigenetics, immune maturation, and the accumulation of burden. The varied manifestation of the underlying mechanisms among individuals is only beginning to be clarified, but the establishment of a framework can facilitate the development of an integrated understanding of the pathogenesis of arthritis across all ages. In this Review, the authors discuss age-related arthropathy and the similarities and differences between childhood loss of immune tolerance and adult development of immune-mediated arthritis, and develop three hypotheses describing age-related mechanisms that contribute to the onset of arthritis. The arthritis-free ‘immune privilege’ of early childhood is overridden by multiple mechanisms, progressively and age-dependently, generating recognizable patterns of chronic inflammatory arthritis. The emergence of arthritis involves interconnected mechanisms related to immune priming, to a situational susceptibility and to the accumulation of an inflammatory burden. The accumulation of epigenetic drift may contribute to differences across ages. The exposome is expected to contribute to arthritis emergence in adults as well as in children.
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Zeng S, Lan B, Ren X, Zhang S, Schreyer D, Eckstein M, Yang H, Britzen-Laurent N, Dahl A, Mukhopadhyay D, Chang D, Kutschick I, Pfeffer S, Bailey P, Biankin A, Grützmann R, Pilarsky C. CDK7 inhibition augments response to multidrug chemotherapy in pancreatic cancer. J Exp Clin Cancer Res 2022; 41:241. [PMID: 35945614 PMCID: PMC9364549 DOI: 10.1186/s13046-022-02443-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 07/19/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with a dismal prognosis. Although combined treatment with gemcitabine and albumin-bound paclitaxel has improved the prognosis of PDAC, both intrinsic and acquired chemoresistance remain as severe hurtles towards improved prognosis. Thus, new therapeutic targets and innovative strategies are urgently needed. METHODS In this study, we used the KPC mouse model-derived PDAC cell line TB32047 to perform kinome-wide CRISPR-Cas9 loss-of-function screening. Next-generation sequencing and MAGeCK-VISPR analysis were performed to identify candidate genes. We then conducted cell viability, clonogenic, and apoptosis assays and evaluated the synergistic therapeutic effects of cyclin-dependent kinase 7 (CDK7) depletion or inhibition with gemcitabine (GEM) and paclitaxel (PTX) in a murine orthotopic pancreatic cancer model. For mechanistic studies, we performed genome enrichment analysis (GSEA) and Western blotting to identify and verify the pathways that render PDAC sensitive to GEM/PTX therapy. RESULTS We identified several cell cycle checkpoint kinases and DNA damage-related kinases as targets for overcoming chemoresistance. Among them, CDK7 ranked highly in both screenings. We demonstrated that both gene knockout and pharmacological inhibition of CDK7 by THZ1 result in cell cycle arrest, apoptosis induction, and DNA damage at least predominantly through the STAT3-MCL1-CHK1 axis. Furthermore, THZ1 synergized with GEM and PTX in vitro and in vivo, resulting in enhanced antitumor effects. CONCLUSIONS Our findings support the application of CRISPR-Cas9 screening in identifying novel therapeutic targets and suggest new strategies for overcoming chemoresistance in pancreatic cancer.
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Affiliation(s)
- Siyuan Zeng
- Department of Surgery, Universitätsklinikum Erlangen, Translational Research Center, Schwabachanlage 12, 91054, Erlangen, Germany
| | - Bin Lan
- Department of Surgery, Universitätsklinikum Erlangen, Translational Research Center, Schwabachanlage 12, 91054, Erlangen, Germany
| | - Xiaofan Ren
- Department of Surgery, Universitätsklinikum Erlangen, Translational Research Center, Schwabachanlage 12, 91054, Erlangen, Germany
| | - Shuman Zhang
- Department of Surgery, Universitätsklinikum Erlangen, Translational Research Center, Schwabachanlage 12, 91054, Erlangen, Germany
| | - Daniel Schreyer
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Glasgow, Scotland, UK
| | - Markus Eckstein
- Institute of Pathology, Universitätsklinikum Erlangen, 91054, Erlangen, Germany
| | - Hai Yang
- Department of Surgery, Universitätsklinikum Erlangen, Translational Research Center, Schwabachanlage 12, 91054, Erlangen, Germany
| | - Nathalie Britzen-Laurent
- Department of Surgery, Universitätsklinikum Erlangen, Translational Research Center, Schwabachanlage 12, 91054, Erlangen, Germany
| | - Andreas Dahl
- DRESDEN-Concept Genome Center a DFG NGS Competence Center, TU Dresden, 01307, Dresden, Germany
| | - Debabrata Mukhopadhyay
- Departments of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Jacksonville, USA
| | - David Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
| | - Isabella Kutschick
- Department of Surgery, Universitätsklinikum Erlangen, Translational Research Center, Schwabachanlage 12, 91054, Erlangen, Germany
| | - Susanne Pfeffer
- Department of Surgery, Universitätsklinikum Erlangen, Translational Research Center, Schwabachanlage 12, 91054, Erlangen, Germany
| | - Peter Bailey
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Glasgow, Scotland, UK
| | - Andrew Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
| | - Robert Grützmann
- Department of Surgery, Universitätsklinikum Erlangen, Translational Research Center, Schwabachanlage 12, 91054, Erlangen, Germany
| | - Christian Pilarsky
- Department of Surgery, Universitätsklinikum Erlangen, Translational Research Center, Schwabachanlage 12, 91054, Erlangen, Germany.
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Xiao Q, Xiao Y, Li LY, Chen MK, Wu M. Multifaceted regulation of enhancers in cancer. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194839. [PMID: 35750313 DOI: 10.1016/j.bbagrm.2022.194839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/24/2022] [Accepted: 06/14/2022] [Indexed: 12/12/2022]
Abstract
Enhancer is one kind of cis-elements regulating gene transcription, whose activity is tightly controlled by epigenetic enzymes and histone modifications. Active enhancers are classified into typical enhancers, super-enhancers and over-active enhancers, according to the enrichment and location of histone modifications. Epigenetic factors control the level of histone modifications on enhancers to determine their activity, such as histone methyltransferases and acetylases. Transcription factors, cofactors and mediators co-operate together and are required for enhancer functions. In turn, abnormalities in these trans-acting factors affect enhancer activity. Recent studies have revealed enhancer dysregulation as one of the important features for cancer. Variations in enhancer regions and mutations of enhancer regulatory genes are frequently observed in cancer cells, and altering the activity of onco-enhancers is able to repress oncogene expression, and suppress tumorigenesis and metastasis. Here we summarize the recent discoveries about enhancer regulation in cancer and discuss their potential application in diagnosis and treatment.
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Affiliation(s)
- Qiong Xiao
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430072, China
| | - Yong Xiao
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430072, China
| | - Lian-Yun Li
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430072, China
| | - Ming-Kai Chen
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430072, China.
| | - Min Wu
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430072, China.
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Guo X, Chen H, Zhou Y, Shen L, Wu S, Chen Y. Cyclin-dependent kinase inhibition and its intersection with immunotherapy in breast cancer: more than CDK4/6 inhibition. Expert Opin Investig Drugs 2022; 31:933-944. [PMID: 35786092 DOI: 10.1080/13543784.2022.2097067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Cyclin-dependent kinase (CDK) 4/6 inhibitors (CDK4/6i) have had clinical success in treating hormone receptor-positive, human epidermal growth factor receptor 2-negative metastatic breast cancer. Notably, CDK4/6i have expanded to the neoadjuvant setting for early breast cancer and other cancer types and potently synergize with immunotherapy. Other CDKs, including CDK7, CDK9, and CDK12/13, mainly function in transcriptional processes as well as cell cycle regulation, RNA splicing, and DNA damage response. Inhibiting these CDKs aids in suppressing tumors, reversing drug resistance, increasing drug sensitivity, and enhancing anti-tumor immunity in breast cancer. AREAS COVERED We reviewed the applications of CDK4/6i, CDK7i, CDK9i and CDK12/13i for various breast cancer subtypes and their potentials for combination with immunotherapy. A literature search of PubMed, Embase, and Web of Science was conducted in April 2022. EXPERT OPINION The use of CDK4/6i represents a major milestone in breast cancer treatment. Moreover, transcription-related CDKs play critical roles in tumor development and are promising therapeutic targets for breast cancer. Some relevant clinical studies are underway. More specific and efficient CDKis will undoubtedly be developed and clinically tested. Characterization of their immune-priming effects will promote the development of combination therapies consisting of CDKi and immunotherapy.
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Affiliation(s)
- Xianan Guo
- Department of Breast Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Huihui Chen
- Department of Breast Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yunxiang Zhou
- Department of Breast Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lu Shen
- Department of Breast Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shijie Wu
- Department of Breast Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yiding Chen
- Department of Breast Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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Cyclin-dependent kinases as potential targets for colorectal cancer: past, present and future. Future Med Chem 2022; 14:1087-1105. [PMID: 35703127 DOI: 10.4155/fmc-2022-0064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Colorectal cancer (CRC) is a common cancer in the world and its prevalence is increasing in developing countries. Deregulated cell cycle traverse is a hallmark of malignant transformation and is often observed in CRC as a result of imprecise activity of cell cycle regulatory components, viz. cyclins and cyclin-dependent kinases (CDKs). Apart from cell cycle regulation, some CDKs also regulate processes such as transcription and have also been shown to be involved in colorectal carcinogenesis. This article aims to review cyclin-dependent kinases as potential targets for CRC. Furthermore, therapeutic candidates to target CDKs are also discussed.
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Chuanhui Huang, Wang S, Ma W. Design, Synthesis, and Antitumor Activity of New N4-Alkyl-N2-Phenyl-Pyrrolo[3,2-d]Pyrimidine-2,4-Diamine Derivatives as CDK6 Inhibitors. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022030062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Benot-Dominguez R, Cimini A, Barone D, Giordano A, Pentimalli F. The Emerging Role of Cyclin-Dependent Kinase Inhibitors in Treating Diet-Induced Obesity: New Opportunities for Breast and Ovarian Cancers? Cancers (Basel) 2022; 14:2709. [PMID: 35681689 PMCID: PMC9179653 DOI: 10.3390/cancers14112709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/26/2022] [Accepted: 05/26/2022] [Indexed: 12/24/2022] Open
Abstract
Overweight and obesity constitute the most impactful lifestyle-dependent risk factors for cancer and have been tightly linked to a higher number of tumor-related deaths nowadays. The excessive accumulation of energy can lead to an imbalance in the level of essential cellular biomolecules that may result in inflammation and cell-cycle dysregulation. Nutritional strategies and phytochemicals are gaining interest in the management of obesity-related cancers, with several ongoing and completed clinical studies that support their effectiveness. At the same time, cyclin-dependent kinases (CDKs) are becoming an important target in breast and ovarian cancer treatment, with various FDA-approved CDK4/6 inhibitors that have recently received more attention for their potential role in diet-induced obesity (DIO). Here we provide an overview of the most recent studies involving nutraceuticals and other dietary strategies affecting cell-cycle pathways, which might impact the management of breast and ovarian cancers, as well as the repurposing of already commercialized chemotherapeutic options to treat DIO.
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Affiliation(s)
- Reyes Benot-Dominguez
- Sbarro Institute for Cancer Research and Molecular Medicine and Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA; (R.B.-D.); (A.G.)
| | - Annamaria Cimini
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Daniela Barone
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori, IRCCS, Fondazione G. Pascale, 80131 Napoli, Italy;
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine and Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA; (R.B.-D.); (A.G.)
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
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Said MA, Abdelrahman MA, Abourehab MAS, Fares M, Eldehna WM. A patent review of anticancer CDK2 inhibitors (2017-present). Expert Opin Ther Pat 2022; 32:885-898. [PMID: 35583393 DOI: 10.1080/13543776.2022.2078193] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION : The success of the CDK4/6 inhibitor Ibrance™ (Palbociclib) as an anticancer agent inspired and directed more efforts towards the discovery of selective cyclin-dependent kinase (CDKs) inhibitors. CDK2 is a member of the CDKs family that plays an important role in regulating the progression of cells into both S- and M-phases of the cell cycle. Studies suggest that overexpression of CDK2 may be implicated in tumor growth in cancer. AREAS COVERED : This review covers the patent literature of CDK2 inhibitors published between 2017 and 2021. We searched the online databases of the European Patent Office, American Chemical Society, and Google patents. EXPERT OPINION Developing selective CDK2 inhibitors is challenging due to the absence of a previously approved selective CDK2 inhibitor. However, ongoing efforts by Incyte Corporation and Pfizer Inc., which are reported herein, may stand out as a new starting point and bring novel information critical for the medicinal chemistry and drug design scientists in the field of CDK2 inhibitors development.
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Affiliation(s)
- Mohamed A Said
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo, 11829, Egypt
| | - Mohamed A Abdelrahman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo, 11829, Egypt
| | - Mohammed A S Abourehab
- Department of Pharmaceutics, Faculty of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia.,Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Minia University, Minia 61519, Egypt
| | - Mohamed Fares
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo, 11829, Egypt.,School of Chemistry, The University of Sydney, NSW 2006, Australia
| | - Wagdy M Eldehna
- School of Biotechnology, Badr University in Cairo, Badr City, Cairo 11829, Egypt.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt
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Le Goff E, Martinand-Mari C, Belkhir K, Vacelet J, Nidelet S, Godefroy N, Baghdiguian S. Molecular complexity and gene expression controlling cell turnover during a digestive cycle of carnivorous sponge Lycopodina hypogea. Cell Tissue Res 2022; 388:399-416. [PMID: 35260936 DOI: 10.1007/s00441-022-03610-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 02/28/2022] [Indexed: 11/30/2022]
Abstract
Lycopodina hypogea is a carnivorous sponge that tolerates laboratory husbandry very well. During a digestion cycle, performed without any digestive cavity, this species undergoes spectacular morphological changes leading to a total regression of long filaments that ensure the capture of prey and their reformation at the end of the cycle. This phenomenon is a unique opportunity to analyze the molecular and cellular determinants that ensure digestion in the sister group of all other metazoans. Using differential transcriptomic analysis coupled with cell biology studies of proliferation, differentiation, and programmed cell deaths (i.e., autophagy and the destructive/constructive function of apoptosis), we demonstrate that the molecular and cellular actors that ensure digestive homeostasis in a sister group of all remaining animals are similar in variety and complexity to those controlling tissue homeostasis in higher vertebrates. During a digestion cycle, most of these actors are finely tuned in a coordinated manner. Our data benefits from complementary approaches coupling in silico and cell biology studies and demonstrate that the nutritive function is provided by the coordination of molecular network that impacts the cells turnover in the entire organism.
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Affiliation(s)
- Emilie Le Goff
- ISEM, CNRS, EPHE, Université Montpellier, Montpellier, IRD, France
| | | | - Khalid Belkhir
- ISEM, CNRS, EPHE, Université Montpellier, Montpellier, IRD, France
| | - Jean Vacelet
- IMBE, CNRS, Station Marine d'Endoume, Université Aix-Marseille, Université d'Avignon, 13007, Marseille, IRD, France
| | - Sabine Nidelet
- Montpellier GenomiX, Université Montpellier, CNRS, INSERM, Montpellier, France
- New Affiliation: CBGP, INRA, CIRAD, Université Montpellier, Montpellier SupAgroMontpellier, IRD, France
| | - Nelly Godefroy
- ISEM, CNRS, EPHE, Université Montpellier, Montpellier, IRD, France.
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Shi Z, Tian L, Qiang T, Li J, Xing Y, Ren X, Liu C, Liang C. From Structure Modification to Drug Launch: A Systematic Review of the Ongoing Development of Cyclin-Dependent Kinase Inhibitors for Multiple Cancer Therapy. J Med Chem 2022; 65:6390-6418. [PMID: 35485642 DOI: 10.1021/acs.jmedchem.1c02064] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Herein, we discuss more than 50 cyclin-dependent kinase (CDK) inhibitors that have been approved or have undergone clinical trials and their therapeutic application in multiple cancers. This review discusses the design strategies, structure-activity relationships, and efficacy performances of these selective or nonselective CDK inhibitors. The theoretical basis of early broad-spectrum CDK inhibitors is similar to the scope of chemotherapy, but because their toxicity is greater than the benefit, there is no clinical therapeutic window. The notion that selective CDK inhibitors have a safer therapeutic potential than pan-CDK inhibitors has been widely recognized during the research process. Four CDK4/6 inhibitors have been approved for the treatment of breast cancer or for prophylactic administration during chemotherapy to protect bone marrow and immune system function. Furthermore, the emerging strategies in the field of CDK inhibitors are summarized briefly, and CDKs continue to be widely pursued as emerging anticancer drug targets for drug discovery.
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Affiliation(s)
- Zhenfeng Shi
- Department of Urology Surgery Center, The People's Hospital of Xinjiang Uyghur Autonomous Region, Urumqi 830002, P. R. China
| | - Lei Tian
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China.,Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Taotao Qiang
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Jingyi Li
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Yue Xing
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Xiaodong Ren
- Medical College, Guizhou University, Guiyang 550025, P. R. China
| | - Chang Liu
- Zhuhai Jinan Selenium Source Nanotechnology Co., Ltd., Zhuhai 519030, P. R. China
| | - Chengyuan Liang
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
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78
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Jeronimo C, Robert F. The histone chaperone FACT: a guardian of chromatin structure integrity. Transcription 2022; 13:16-38. [PMID: 35485711 PMCID: PMC9467567 DOI: 10.1080/21541264.2022.2069995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The identification of FACT as a histone chaperone enabling transcription through chromatin in vitro has strongly shaped how its roles are envisioned. However, FACT has been implicated in essentially all aspects of chromatin biology, from transcription to DNA replication, DNA repair, and chromosome segregation. In this review, we focus on recent literature describing the role and mechanisms of FACT during transcription. We highlight the prime importance of FACT in preserving chromatin integrity during transcription and challenge its role as an elongation factor. We also review evidence for FACT's role as a cell-type/gene-specificregulator of gene expression and briefly summarize current efforts at using FACT inhibition as an anti-cancerstrategy.
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Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada.,Département de Médecine, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada.,Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
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79
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Funke K, Düster R, Wilson PDG, Arévalo L, Geyer M, Schorle H. Transcriptional CDK Inhibitors as Potential Treatment Option for Testicular Germ Cell Tumors. Cancers (Basel) 2022; 14:1690. [PMID: 35406461 PMCID: PMC8997165 DOI: 10.3390/cancers14071690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 02/04/2023] Open
Abstract
Type II testicular germ cell tumors (TGCT) are the most frequently diagnosed solid malignancy in young men. Up to 15% of patients with metastatic non-seminomas show cisplatin resistance and a very poor survival rate due to lacking treatment options. Transcriptional cyclin-dependent kinases (CDK) have been shown to be effective targets in the treatment of different types of cancer. Here, we investigated the effects of the CDK inhibitors dinaciclib, flavopiridol, YKL-5-124, THZ1, NVP2, SY0351 and THZ531. An XTT viability assay revealed a strong cytotoxic impact of CDK7/12/13 inhibitor SY0351 and CDK9 inhibitor NVP2 on the TGCT wild-type cell lines (2102EP, NCCIT, TCam2) and the cisplatin-resistant cell lines (2102EP-R, NCCIT-R). The CDK7 inhibitor YKL-5-124 showed a strong impact on 2102EP, 2102EP-R, NCCIT and NCCIT-R cell lines, leaving the MPAF control cell line mostly unaffected. FACS-based analysis revealed mild effects on the cell cycle of 2102EP and TCam2 cells after SY0351, YKL-5-124 or NVP2 treatment. Molecular analysis showed a cell-line-specific response for SY0351 and NVP2 inhibition while YKL-5-124 induced similar molecular changes in 2102EP, TCam2 and MPAF cells. Thus, after TGCT subtype determination, CDK inhibitors might be a potential alternative for optimized and individualized therapy independent of chemotherapy sensitivity.
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Affiliation(s)
- Kai Funke
- Department of Developmental Pathology, Institute of Pathology, University Hospital Bonn, 53127 Bonn, Germany; (K.F.); (P.D.-G.W.); (L.A.)
| | - Robert Düster
- The Institute of Structural Biology, University of Bonn, 53127 Bonn, Germany; (R.D.); (M.G.)
| | - Prince De-Graft Wilson
- Department of Developmental Pathology, Institute of Pathology, University Hospital Bonn, 53127 Bonn, Germany; (K.F.); (P.D.-G.W.); (L.A.)
| | - Lena Arévalo
- Department of Developmental Pathology, Institute of Pathology, University Hospital Bonn, 53127 Bonn, Germany; (K.F.); (P.D.-G.W.); (L.A.)
| | - Matthias Geyer
- The Institute of Structural Biology, University of Bonn, 53127 Bonn, Germany; (R.D.); (M.G.)
| | - Hubert Schorle
- Department of Developmental Pathology, Institute of Pathology, University Hospital Bonn, 53127 Bonn, Germany; (K.F.); (P.D.-G.W.); (L.A.)
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80
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Cyclin-Dependent Kinase Synthetic Lethality Partners in DNA Damage Response. Int J Mol Sci 2022; 23:ijms23073555. [PMID: 35408915 PMCID: PMC8998982 DOI: 10.3390/ijms23073555] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/16/2022] [Accepted: 03/23/2022] [Indexed: 02/07/2023] Open
Abstract
Cyclin-dependent kinases (CDKs) are pivotal mediators and effectors of the DNA damage response (DDR) that regulate both the pathway components and proteins involved in repair processes. Synthetic lethality (SL) describes a situation in which two genes are linked in such a way that the lack of functioning of just one maintains cell viability, while depletion of both triggers cell death. Synthetic lethal interactions involving CDKs are now emerging, and this can be used to selectively target tumor cells with DNA repair defects. In this review, SL interactions of CDKs with protooncogene products MYC, poly (ADP-ribose) polymerase (PARP-1), and cellular tumor antigen p53 (TP53) are discussed. The individual roles of each of the SL partners in DDR are described.
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81
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Liu Q, Guo L, Lou Z, Xiang X, Shao J. Super-enhancers and novel therapeutic targets in colorectal cancer. Cell Death Dis 2022; 13:228. [PMID: 35277481 PMCID: PMC8917125 DOI: 10.1038/s41419-022-04673-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 02/12/2022] [Accepted: 02/18/2022] [Indexed: 12/24/2022]
Abstract
Transcription factors, cofactors, chromatin regulators, and transcription apparatuses interact with transcriptional regulatory elements, including promoters, enhancers, and super-enhancers (SEs), to coordinately regulate the transcription of target genes and thereby control cell behaviors. Among these transcriptional regulatory components and related elements, SEs often play a central role in determining cell identity and tumor initiation and progression. Therefore, oncogenic SEs, which are generated within cancer cells in oncogenes and other genes important in tumor pathogenesis, have emerged as attractive targets for novel cancer therapeutic strategies in recent years. Herein, we review the identification, formation and activation modes, and regulatory mechanisms for downstream genes and pathways of oncogenic SEs. We also review the therapeutic strategies and compounds targeting oncogenic SEs in colorectal cancer and other malignancies.
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Affiliation(s)
- Qian Liu
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lijuan Guo
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhiyuan Lou
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
| | - Xueping Xiang
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China.
| | - Jimin Shao
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China.
- Cancer Center, Zhejiang University, Hangzhou, China.
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82
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Xie Z, Hou S, Yang X, Duan Y, Han J, Wang Q, Liao C. Lessons Learned from Past Cyclin-Dependent Kinase Drug Discovery Efforts. J Med Chem 2022; 65:6356-6389. [PMID: 35235745 DOI: 10.1021/acs.jmedchem.1c02190] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Inhibition of cyclin-dependent kinases (CDKs) has become an effective therapeutic strategy for treating various diseases, especially cancer. Over almost three decades, although great efforts have been made to discover CDK inhibitors, many of which have entered clinical trials, only four CDK inhibitors have been approved. In the process of CDK inhibitor development, many difficulties and misunderstandings have hampered their discovery and clinical applications, which mainly include inadequate understanding of the biological functions of CDKs, less attention paid to pan- and multi-CDK inhibitors, nonideal isoform selectivity of developed selective CDK inhibitors, overlooking the metabolic stability of early discovered CDK inhibitors, no effective resistance solutions, and a lack of available combination therapy and effective biomarkers for CDK therapies. After reviewing the mechanisms of CDKs and the research progress of CDK inhibitors, this perspective summarizes and discusses these difficulties or lessons, hoping to facilitate the successful discovery of more useful CDK inhibitors.
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Affiliation(s)
- Zhouling Xie
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Shuzeng Hou
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Xiaoxiao Yang
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Yajun Duan
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Jihong Han
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Qin Wang
- Department of Otolaryngology─Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, P. R. China
| | - Chenzhong Liao
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
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83
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Zhong S, Peng S, Chen Z, Chen Z, Luo JL. Choosing Kinase Inhibitors for Androgen Deprivation Therapy-Resistant Prostate Cancer. Pharmaceutics 2022; 14:498. [PMID: 35335873 PMCID: PMC8950316 DOI: 10.3390/pharmaceutics14030498] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/26/2022] [Accepted: 02/22/2022] [Indexed: 11/25/2022] Open
Abstract
Androgen deprivation therapy (ADT) is a systemic therapy for advanced prostate cancer (PCa). Although most patients initially respond to ADT, almost all cancers eventually develop castration resistance. Castration-resistant PCa (CRPC) is associated with a very poor prognosis, and the treatment of which is a serious clinical challenge. Accumulating evidence suggests that abnormal expression and activation of various kinases are associated with the emergence and maintenance of CRPC. Many efforts have been made to develop small molecule inhibitors to target the key kinases in CRPC. These inhibitors are designed to suppress the kinase activity or interrupt kinase-mediated signal pathways that are associated with PCa androgen-independent (AI) growth and CRPC development. In this review, we briefly summarize the roles of the kinases that are abnormally expressed and/or activated in CRPC and the recent advances in the development of small molecule inhibitors that target kinases for the treatment of CRPC.
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Affiliation(s)
- Shangwei Zhong
- Department of General Surgery, Xiangya Hospital, Central South University, Hunan 410008, China; (S.Z.); (S.P.); (Z.C.)
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33459, USA
| | - Shoujiao Peng
- Department of General Surgery, Xiangya Hospital, Central South University, Hunan 410008, China; (S.Z.); (S.P.); (Z.C.)
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33459, USA
| | - Zihua Chen
- Department of General Surgery, Xiangya Hospital, Central South University, Hunan 410008, China; (S.Z.); (S.P.); (Z.C.)
| | - Zhikang Chen
- Department of General Surgery, Xiangya Hospital, Central South University, Hunan 410008, China; (S.Z.); (S.P.); (Z.C.)
| | - Jun-Li Luo
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33459, USA
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84
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Zheng Y, Zhang W, Xu L, Zhou H, Yuan M, Xu H. Recent Progress in Understanding the Action of Natural Compounds at Novel Therapeutic Drug Targets for the Treatment of Liver Cancer. Front Oncol 2022; 11:795548. [PMID: 35155196 PMCID: PMC8825370 DOI: 10.3389/fonc.2021.795548] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/27/2021] [Indexed: 12/11/2022] Open
Abstract
Liver cancer is the third most common cause of cancer-related death following lung and stomach cancers. As a highly lethal disease, liver cancer is diagnosed frequently in less developed countries. Natural compounds extracted from herbs, animals and natural materials have been adopted by traditional Chinese medicine (TCM) practices and reported to be effective in the development of new medications for the treatment of diseases. It is important to focus on the mechanisms of action of natural compounds against hepatocellular carcinoma (HCC), particularly in terms of cell cycle regulation, apoptosis induction, autophagy mediation and cell migration and invasion. In this review, we characterize novel representative natural compounds according to their pharmacologic effects based on recently published studies. The aim of this review is to summarize and explore novel therapeutic drug targets of natural compounds, which could accelerate the discovery of new anticancer drugs.
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Affiliation(s)
- Yannan Zheng
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Engineering Research Center of Shanghai Colleges for Traditional Chinese Medicine (TCM) New Drug Discovery, Shanghai, China
| | - Wenhui Zhang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Engineering Research Center of Shanghai Colleges for Traditional Chinese Medicine (TCM) New Drug Discovery, Shanghai, China
| | - Lin Xu
- Engineering Research Center of Shanghai Colleges for Traditional Chinese Medicine (TCM) New Drug Discovery, Shanghai, China.,School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Hua Zhou
- Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Man Yuan
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Engineering Research Center of Shanghai Colleges for Traditional Chinese Medicine (TCM) New Drug Discovery, Shanghai, China
| | - Hongxi Xu
- Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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85
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Marineau JJ, Hamman KB, Hu S, Alnemy S, Mihalich J, Kabro A, Whitmore KM, Winter DK, Roy S, Ciblat S, Ke N, Savinainen A, Wilsily A, Malojcic G, Zahler R, Schmidt D, Bradley MJ, Waters NJ, Chuaqui C. Discovery of SY-5609: A Selective, Noncovalent Inhibitor of CDK7. J Med Chem 2022; 65:1458-1480. [PMID: 34726887 DOI: 10.1021/acs.jmedchem.1c01171] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
CDK7 has emerged as an exciting target in oncology due to its roles in two important processes that are misregulated in cancer cells: cell cycle and transcription. This report describes the discovery of SY-5609, a highly potent (sub-nM CDK7 Kd) and selective, orally available inhibitor of CDK7 that entered the clinic in 2020 (ClinicalTrials.gov Identifier: NCT04247126). Structure-based design was leveraged to obtain high selectivity (>4000-times the closest off target) and slow off-rate binding kinetics desirable for potent cellular activity. Finally, incorporation of a phosphine oxide as an atypical hydrogen bond acceptor helped provide the required potency and metabolic stability. The development candidate SY-5609 displays potent inhibition of CDK7 in cells and demonstrates strong efficacy in mouse xenograft models when dosed as low as 2 mg/kg.
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Affiliation(s)
- Jason J Marineau
- Syros Pharmaceuticals Inc., 35 Cambridge Park Drive, Fourth Floor, Cambridge, Massachusetts 02140, United States
| | - Kristin B Hamman
- Syros Pharmaceuticals Inc., 35 Cambridge Park Drive, Fourth Floor, Cambridge, Massachusetts 02140, United States
| | - Shanhu Hu
- Syros Pharmaceuticals Inc., 35 Cambridge Park Drive, Fourth Floor, Cambridge, Massachusetts 02140, United States
| | - Sydney Alnemy
- Syros Pharmaceuticals Inc., 35 Cambridge Park Drive, Fourth Floor, Cambridge, Massachusetts 02140, United States
| | - Janessa Mihalich
- Syros Pharmaceuticals Inc., 35 Cambridge Park Drive, Fourth Floor, Cambridge, Massachusetts 02140, United States
| | - Anzhelika Kabro
- Paraza Pharma Inc., 2525 Avenue Marie-Curie, Montreal, Quebec H4S 2E1, Canada
| | | | - Dana K Winter
- Paraza Pharma Inc., 2525 Avenue Marie-Curie, Montreal, Quebec H4S 2E1, Canada
| | - Stephanie Roy
- Paraza Pharma Inc., 2525 Avenue Marie-Curie, Montreal, Quebec H4S 2E1, Canada
| | - Stephane Ciblat
- Paraza Pharma Inc., 2525 Avenue Marie-Curie, Montreal, Quebec H4S 2E1, Canada
| | - Nan Ke
- Syros Pharmaceuticals Inc., 35 Cambridge Park Drive, Fourth Floor, Cambridge, Massachusetts 02140, United States
| | - Anneli Savinainen
- Syros Pharmaceuticals Inc., 35 Cambridge Park Drive, Fourth Floor, Cambridge, Massachusetts 02140, United States
| | - Ashraf Wilsily
- Syros Pharmaceuticals Inc., 35 Cambridge Park Drive, Fourth Floor, Cambridge, Massachusetts 02140, United States
| | - Goran Malojcic
- Syros Pharmaceuticals Inc., 35 Cambridge Park Drive, Fourth Floor, Cambridge, Massachusetts 02140, United States
| | - Robert Zahler
- Syros Pharmaceuticals Inc., 35 Cambridge Park Drive, Fourth Floor, Cambridge, Massachusetts 02140, United States
| | - Darby Schmidt
- Syros Pharmaceuticals Inc., 35 Cambridge Park Drive, Fourth Floor, Cambridge, Massachusetts 02140, United States
| | - Michael J Bradley
- Syros Pharmaceuticals Inc., 35 Cambridge Park Drive, Fourth Floor, Cambridge, Massachusetts 02140, United States
| | - Nigel J Waters
- Syros Pharmaceuticals Inc., 35 Cambridge Park Drive, Fourth Floor, Cambridge, Massachusetts 02140, United States
| | - Claudio Chuaqui
- Syros Pharmaceuticals Inc., 35 Cambridge Park Drive, Fourth Floor, Cambridge, Massachusetts 02140, United States
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86
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Jagomast T, Idel C, Klapper L, Kuppler P, Offermann A, Dreyer E, Bruchhage KL, Ribbat-Idel J, Perner S. CDK7 Predicts Worse Outcome in Head and Neck Squamous-Cell Cancer. Cancers (Basel) 2022; 14:492. [PMID: 35158760 PMCID: PMC8833595 DOI: 10.3390/cancers14030492] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/03/2022] [Accepted: 01/17/2022] [Indexed: 02/04/2023] Open
Abstract
HNSCC is the sixth most common cancer worldwide and the prognosis is still poor. Here, we investigated the prognostic implications of CDK7 and pMED1. Both proteins affect transcription, and their expression is altered throughout different tumor entities. pMED1 is phosphorylated by CDK7. Importantly, CDK7 and MED1 have been ascribed prognostic implications by various studies. However, their prognostic value in head and neck squamous-cell cancer (HNSCC) remains elusive. We applied immunohistochemical staining of CDK7 and pMED1 on our large and clinically well-characterized HNSCC tissue cohort comprising 419 patients. Software-aided quantification of staining intensity was performed as a measure of protein expression. The following results were linked to the clinicopathological features of our cohort and correlated in different tissue types (primary tumor, lymph node metastasis, distant metastasis, recurrence). Upregulation CDK7 was associated with worse 5-year overall survival as well as disease-free survival in HNSCC while being independent of other known prognostic factors such as p16-status. Also, CDK7 expression was significantly elevated in immune cell infiltrated tumors. In HNSCC CDK7 might serve as a novel prognostic marker to indicate the prognosis of patients. Furthermore, in vitro studies proved the feasibility of CDK7 inhibition with attenuating effects on cell proliferation underlining its remarkable translational potential for future therapeutic regimes.
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Affiliation(s)
- Tobias Jagomast
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Ratzeburger Allee 160, 23538 Luebeck, Germany; (L.K.); (P.K.); (A.O.); (E.D.); (S.P.)
| | - Christian Idel
- Department of Otorhinolaryngology, University of Luebeck, Ratzeburger Allee 160, 23538 Luebeck, Germany; (C.I.); (K.-L.B.)
| | - Luise Klapper
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Ratzeburger Allee 160, 23538 Luebeck, Germany; (L.K.); (P.K.); (A.O.); (E.D.); (S.P.)
| | - Patrick Kuppler
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Ratzeburger Allee 160, 23538 Luebeck, Germany; (L.K.); (P.K.); (A.O.); (E.D.); (S.P.)
| | - Anne Offermann
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Ratzeburger Allee 160, 23538 Luebeck, Germany; (L.K.); (P.K.); (A.O.); (E.D.); (S.P.)
| | - Eva Dreyer
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Ratzeburger Allee 160, 23538 Luebeck, Germany; (L.K.); (P.K.); (A.O.); (E.D.); (S.P.)
| | - Karl-Ludwig Bruchhage
- Department of Otorhinolaryngology, University of Luebeck, Ratzeburger Allee 160, 23538 Luebeck, Germany; (C.I.); (K.-L.B.)
| | - Julika Ribbat-Idel
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Ratzeburger Allee 160, 23538 Luebeck, Germany; (L.K.); (P.K.); (A.O.); (E.D.); (S.P.)
| | - Sven Perner
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Ratzeburger Allee 160, 23538 Luebeck, Germany; (L.K.); (P.K.); (A.O.); (E.D.); (S.P.)
- Pathology, Research Center Borstel, Leibniz Lung Center, Parkallee 1-40, 23845 Borstel, Germany
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87
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Yuan J, Li X, Yu S. CDK7-dependent transcriptional addiction in bone and soft tissue sarcomas: Present and Future. Biochim Biophys Acta Rev Cancer 2022; 1877:188680. [PMID: 35051528 DOI: 10.1016/j.bbcan.2022.188680] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 12/25/2022]
Abstract
Cancer arises from genetic alterations that invariably contribute to dysregulated transcriptional programs. These dysregulated programs establish and maintain specific cancer cell states, leading to an intensive dependence on a set of certain regulators of gene expression. The CDK7 functions as the core of transcription, and governs RNA polymerase II and the downstream oncogenes expression in cancers. CDK7 inhibition leads to reduced recruitment of super-enhancers-driven oncogenic transcription factors, and the depression of these associated oncogenes expression, which indicates the dependence of transcriptional addiction of cancers on CDK7. Given that specified oncoproteins of sarcomas commonly function at oncogenic transcription, targeting CDK7-denpendent transcriptional addiction may be of guiding significance for the treatment of sarcomas. In this review, we summarize the advances in mechanism of targeted CDK7-dependent transcriptional addiction and discuss the path ahead to potential application discovery in bone and soft tissue sarcomas, providing theoretical considerations for bio-orthogonal therapeutic strategies.
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Affiliation(s)
- Jin Yuan
- Department 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
| | - Xiaoyang Li
- Department 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.
| | - Shengji Yu
- Department 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.
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88
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Control of Expression of Key Cell Cycle Enzymes Drives Cell Line-Specific Functions of CDK7 in Human PDAC Cells. Int J Mol Sci 2022; 23:ijms23020812. [PMID: 35054996 PMCID: PMC8775745 DOI: 10.3390/ijms23020812] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/30/2021] [Accepted: 01/08/2022] [Indexed: 01/16/2023] Open
Abstract
Inhibition of the dual function cell cycle and transcription kinase CDK7 is known to affect the viability of cancer cells, but the mechanisms underlying cell line-specific growth control remain poorly understood. Here, we employed a previously developed, highly specific small molecule inhibitor that non-covalently blocks ATP binding to CDK7 (LDC4297) to study the mechanisms underlying cell line-specific growth using a panel of genetically heterogeneous human pancreatic tumor lines as model system. Although LDC4297 diminished both transcription rates and CDK T-loop phosphorylation in a comparable manner, some PDAC lines displayed significantly higher sensitivity than others. We focused our analyses on two well-responsive lines (Mia-Paca2 and Panc89) that, however, showed significant differences in their viability upon extended exposure to limiting LDC4297 concentrations. Biochemical and RNAseq analysis revealed striking differences in gene expression and cell cycle control. Especially the downregulation of a group of cell cycle control genes, among them CDK1/2 and CDC25A/C, correlated well to the observed viability differences in Panc89 versus Mia-Paca2 cells. A parallel downregulation of regulatory pathways supported the hypothesis of a feedforward programmatic effect of CDK7 inhibitors, eventually causing hypersensitivity of PDAC lines.
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89
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OUP accepted manuscript. Carcinogenesis 2022; 43:779-786. [DOI: 10.1093/carcin/bgac036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 04/04/2022] [Accepted: 04/21/2022] [Indexed: 11/14/2022] Open
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90
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Abstract
Cancer is a group of diseases in which cells divide continuously and excessively. Cell division is tightly regulated by multiple evolutionarily conserved cell cycle control mechanisms, to ensure the production of two genetically identical cells. Cell cycle checkpoints operate as DNA surveillance mechanisms that prevent the accumulation and propagation of genetic errors during cell division. Checkpoints can delay cell cycle progression or, in response to irreparable DNA damage, induce cell cycle exit or cell death. Cancer-associated mutations that perturb cell cycle control allow continuous cell division chiefly by compromising the ability of cells to exit the cell cycle. Continuous rounds of division, however, create increased reliance on other cell cycle control mechanisms to prevent catastrophic levels of damage and maintain cell viability. New detailed insights into cell cycle control mechanisms and their role in cancer reveal how these dependencies can be best exploited in cancer treatment.
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Affiliation(s)
- Helen K Matthews
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
- Department of Biomedical Science, University of Sheffield, Sheffield, UK
| | - Cosetta Bertoli
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Robertus A M de Bruin
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK.
- UCL Cancer Institute, University College London, London, UK.
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91
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Scheidemann ER, Shajahan-Haq AN. Resistance to CDK4/6 Inhibitors in Estrogen Receptor-Positive Breast Cancer. Int J Mol Sci 2021; 22:12292. [PMID: 34830174 PMCID: PMC8625090 DOI: 10.3390/ijms222212292] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 12/12/2022] Open
Abstract
Estrogen receptor-positive (ER+) breast cancer is the most common form of breast cancer. Antiestrogens were the first therapy aimed at treating this subtype, but resistance to these warranted the development of a new treatment option. CDK4/6 inhibitors address this problem by halting cell cycle progression in ER+ cells, and have proven to be successful in the clinic. Unfortunately, both intrinsic and acquired resistance to CDK4/6 inhibitors are common. Numerous mechanisms of how resistance occurs have been identified to date, including the activation of prominent growth signaling pathways, the loss of tumor-suppressive genes, and noncanonical cell cycle function. Many of these have been successfully targeted and demonstrate the ability to overcome resistance to CDK4/6 inhibitors in preclinical and clinical trials. Future studies should focus on the development of biomarkers so that patients likely to be resistant to CDK4/6 inhibition can initially be given alternative methods of treatment.
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Affiliation(s)
| | - Ayesha N. Shajahan-Haq
- Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University Medical Center, Washington, DC 20057, USA;
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92
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Medina JR, Tian X, Li WH, Suarez D, Mack JF, LaFrance L, Martyr C, Brackley J, Di Marco C, Rivero R, Heerding DA, McHugh C, Minthorn E, Bhaskar A, Rubin J, Butticello M, Carpenter C, Nartey EN, Berrodin TJ, Kallal LA, Mangatt B. Cell-Based Drug Discovery: Identification and Optimization of Small Molecules that Reduce c-MYC Protein Levels in Cells. J Med Chem 2021; 64:16056-16087. [PMID: 34669409 DOI: 10.1021/acs.jmedchem.1c01416] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Elevated expression of the c-MYC oncogene is one of the most common abnormalities in human cancers. Unfortunately, efforts to identify pharmacological inhibitors that directly target MYC have not yet yielded a drug-like molecule due to the lack of any known small molecule binding pocket in the protein, which could be exploited to disrupt MYC function. We have recently described a strategy to target MYC indirectly, where a screening effort designed to identify compounds that can rapidly decrease endogenous c-MYC protein levels in a MYC-amplified cell line led to the discovery of a compound series that phenocopies c-MYC knockdown by siRNA. Herein, we describe our medicinal chemistry program that led to the discovery of potent, orally bioavailable c-MYC-reducing compounds. The development of a minimum pharmacophore model based on empirical structure activity relationship as well as the property-based approach used to modulate pharmacokinetics properties will be highlighted.
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Affiliation(s)
- Jesús R Medina
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Xinrong Tian
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - William H Li
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Dominic Suarez
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - James F Mack
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Louis LaFrance
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Cuthbert Martyr
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - James Brackley
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Christina Di Marco
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Ralph Rivero
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Dirk A Heerding
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Charles McHugh
- Oncology Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Elisabeth Minthorn
- Oncology Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Aishwarya Bhaskar
- Oncology Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Jacob Rubin
- Oncology Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Michael Butticello
- Oncology Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | | | - Eldridge N Nartey
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Thomas J Berrodin
- Oncology Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Lorena A Kallal
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Biju Mangatt
- Oncology Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
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93
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Arnold C, Demuth P, Seiwert N, Wittmann S, Boengler K, Rasenberger B, Christmann M, Huber M, Brunner T, Linnebacher M, Fahrer J. The mitochondrial disruptor devimistat (CPI-613®) synergizes with genotoxic anticancer drugs in colorectal cancer therapy in a Bim-dependent manner. Mol Cancer Ther 2021; 21:100-112. [PMID: 34750196 DOI: 10.1158/1535-7163.mct-21-0393] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 09/22/2021] [Accepted: 11/03/2021] [Indexed: 11/16/2022]
Abstract
Colorectal cancer (CRC) is one of the most frequent tumor entities, with an increasing incidence and mortality in younger adults in Europe and the US. 5-year survival rates for advanced CRC are still low, highlighting the need for novel targets in CRC therapy. Here, we investigated the therapeutic potential of the compound devimistat (CPI 613®) that targets altered mitochondrial cancer cell metabolism and its synergism with the antineoplastic drugs 5-fluorouracil (5-FU) and irinotecan (IT) in CRC. Devimistat exerted a comparable cytotoxicity in a panel of established CRC cell lines and patient-derived short-term culture independent of their genetic and epigenetic status, whereas human colonic epithelial cells were more resistant indicating tumor selectivity. These findings were corroborated in intestinal organoid and tumoroid models. Mechanistically, devimistat disrupted mitochondrial membrane potential and severely impaired mitochondrial respiration, resulting in CRC cell death induction independent of p53. Combination treatment of devimistat with 5-FU or IT demonstrated synergistic cell killing in CRC cells as shown by Combenefit modelling and Chou-Talalay analysis. Increased cell death induction was revealed as major mechanism involving downregulation of anti-apoptotic genes and accumulation of pro-apoptotic Bim, which was confirmed by its genetic knockdown. In human CRC xenograft mouse models, devimistat showed anti-tumor activity and synergized with IT, resulting in prolonged survival and enhanced therapeutic efficacy. In human tumor xenografts, devimistat prevented IT-triggered p53 stabilization and caused synergistic Bim induction. Taken together, our study revealed devimistat as a promising candidate in CRC therapy by synergizing with established antineoplastic drugs in vitro and in vivo.
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Affiliation(s)
- Carina Arnold
- Department of Chemistry, Division of Food Chemistry and Toxicology, University of Kaiserslautern
| | - Philipp Demuth
- Department of Chemistry, Division of Food Chemistry and Toxicology, University of Kaiserslautern
| | - Nina Seiwert
- Institute of Toxicology, Medical Center of the University Mainz
| | - Simon Wittmann
- Department of Chemistry, Division of Food Chemistry and Toxicology, University of Kaiserslautern
| | | | | | | | - Magdalena Huber
- Institute for Medical Microbiology and Hospital Hygiene, Philipp University of Marburg
| | | | - Michael Linnebacher
- Department of General Surgery, Division of Molecular Oncology and Immunotherapy, University of Rostock
| | - Jörg Fahrer
- Department of Chemistry, Division of Food Chemistry and Toxicology, University of Kaiserslautern
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94
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Chen X, Li Y, Dai H, Zhang H, Wan D, Zhou X, Situ C, Zhu H. Cyclin-dependent kinase 7 is essential for spermatogenesis by regulating retinoic acid signaling pathways and the STAT3 molecular pathway. IUBMB Life 2021; 73:1446-1459. [PMID: 34717033 DOI: 10.1002/iub.2574] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 10/20/2021] [Indexed: 12/28/2022]
Abstract
Spermatogenesis is a complex process that requires precise regulation. Phosphorylation plays a role in spermatogenesis by regulating protein structure and activity. This study focused on cyclin-dependent kinase 7 (CDK7), and explored its function and molecular mechanisms in spermatogenesis in vitro in a cell line and in vivo in a mouse model. Inhibition of CDK7 activity affected spermatogonia proliferation and differentiation, and we found that CDK7 regulates retinoic acid (RA)-mediated c-KIT expression to play a role in spermatogonia. Then, we demonstrated that inhibition of CDK7 affected meiosis initiation, DNA repair, and synaptonemal complex formation in meiosis progression, and CDK7 played this role by regulating RA-mediated STRA8 and REC8 signaling pathways. Moreover, inhibition of CDK7 impacted spermatid differentiation and resulted in decreased counts, decreased motility, and increased head deformity of sperm. We demonstrated that CDK7 affects germ cell apoptosis and sperm motility by activating STAT3 and that STAT3 further regulates Cortactin expression to influence the nuclear elongation, chromatin condensation, and acrosome formation of sperm. Additionally, EP300 was identified as another potential target phosphorylated by CDK7 that participates in chromatin condensation. Our results demonstrated the important role of CDK7 in all key aspects of spermatogenesis, potentially providing an effective target for clinical diagnosis and pathogenesis.
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Affiliation(s)
- Xu Chen
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Yan Li
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Haiqian Dai
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Hao Zhang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Danyang Wan
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Xinli Zhou
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Chenghao Situ
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Hui Zhu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
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95
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Parrello D, Vlasenok M, Kranz L, Nechaev S. Targeting the Transcriptome Through Globally Acting Components. Front Genet 2021; 12:749850. [PMID: 34603400 PMCID: PMC8481634 DOI: 10.3389/fgene.2021.749850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/02/2021] [Indexed: 11/13/2022] Open
Abstract
Transcription is a step in gene expression that defines the identity of cells and its dysregulation is associated with diseases. With advancing technologies revealing molecular underpinnings of the cell with ever-higher precision, our ability to view the transcriptomes may have surpassed our knowledge of the principles behind their organization. The human RNA polymerase II (Pol II) machinery comprises thousands of components that, in conjunction with epigenetic and other mechanisms, drive specialized programs of development, differentiation, and responses to the environment. Parts of these programs are repurposed in oncogenic transformation. Targeting of cancers is commonly done by inhibiting general or broadly acting components of the cellular machinery. The critical unanswered question is how globally acting or general factors exert cell type specific effects on transcription. One solution, which is discussed here, may be among the events that take place at genes during early Pol II transcription elongation. This essay turns the spotlight on the well-known phenomenon of promoter-proximal Pol II pausing as a step that separates signals that establish pausing genome-wide from those that release the paused Pol II into the gene. Concepts generated in this rapidly developing field will enhance our understanding of basic principles behind transcriptome organization and hopefully translate into better therapies at the bedside.
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Affiliation(s)
- Damien Parrello
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, United States
| | - Maria Vlasenok
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Lincoln Kranz
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, United States
| | - Sergei Nechaev
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, United States
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96
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Bhurta D, Bharate SB. Analyzing the scaffold diversity of cyclin-dependent kinase inhibitors and revisiting the clinical and preclinical pipeline. Med Res Rev 2021; 42:654-709. [PMID: 34605036 DOI: 10.1002/med.21856] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 07/04/2021] [Accepted: 09/21/2021] [Indexed: 12/17/2022]
Abstract
Kinases have gained an important place in the list of vital therapeutic targets because of their overwhelming clinical success in the last two decades. Among various clinically validated kinases, the cyclin-dependent kinases (CDK) are one of the extensively studied drug targets for clinical development. Food and Drug Administration has approved three CDK inhibitors for therapeutic use, and at least 27 inhibitors are under active clinical development. In the last decade, research and development in this area took a rapid pace, and thus the analysis of scaffold diversity is essential for future drug design. Available reviews lack the systematic study and discussion on the scaffold diversity of CDK inhibitors. Herein we have reviewed and critically analyzed the chemical diversity present in the preclinical and clinical pipeline of CDK inhibitors. Our analysis has shown that although several scaffolds represent CDK inhibitors, only the amino-pyrimidine is a well-represented scaffold. The three-nitrogen framework of amino-pyrimidine is a fundamental hinge-binding unit. Further, we have discussed the selectivity aspects among CDKs, the clinical trial dose-limiting toxicities, and highlighted the most advanced clinical candidates. We also discuss the changing paradigm towards selective inhibitors and an overview of ATP-binding pockets of all druggable CDKs. We carefully analyzed the clinical pipeline to unravel the candidates that are currently under active clinical development. In addition to the plenty of dual CDK4/6 inhibitors, there are many selective CDK7, CDK9, and CDK8/19 inhibitors in the clinical pipeline.
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Affiliation(s)
- Deendyal Bhurta
- Natural Products & Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, India
| | - Sandip B Bharate
- Natural Products & Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, India
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97
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Cao L, Huang C, Cui Zhou D, Hu Y, Lih TM, Savage SR, Krug K, Clark DJ, Schnaubelt M, Chen L, da Veiga Leprevost F, Eguez RV, Yang W, Pan J, Wen B, Dou Y, Jiang W, Liao Y, Shi Z, Terekhanova NV, Cao S, Lu RJH, Li Y, Liu R, Zhu H, Ronning P, Wu Y, Wyczalkowski MA, Easwaran H, Danilova L, Mer AS, Yoo S, Wang JM, Liu W, Haibe-Kains B, Thiagarajan M, Jewell SD, Hostetter G, Newton CJ, Li QK, Roehrl MH, Fenyö D, Wang P, Nesvizhskii AI, Mani DR, Omenn GS, Boja ES, Mesri M, Robles AI, Rodriguez H, Bathe OF, Chan DW, Hruban RH, Ding L, Zhang B, Zhang H. Proteogenomic characterization of pancreatic ductal adenocarcinoma. Cell 2021; 184:5031-5052.e26. [PMID: 34534465 PMCID: PMC8654574 DOI: 10.1016/j.cell.2021.08.023] [Citation(s) in RCA: 241] [Impact Index Per Article: 80.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/19/2021] [Accepted: 08/18/2021] [Indexed: 02/07/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with poor patient survival. Toward understanding the underlying molecular alterations that drive PDAC oncogenesis, we conducted comprehensive proteogenomic analysis of 140 pancreatic cancers, 67 normal adjacent tissues, and 9 normal pancreatic ductal tissues. Proteomic, phosphoproteomic, and glycoproteomic analyses were used to characterize proteins and their modifications. In addition, whole-genome sequencing, whole-exome sequencing, methylation, RNA sequencing (RNA-seq), and microRNA sequencing (miRNA-seq) were performed on the same tissues to facilitate an integrated proteogenomic analysis and determine the impact of genomic alterations on protein expression, signaling pathways, and post-translational modifications. To ensure robust downstream analyses, tumor neoplastic cellularity was assessed via multiple orthogonal strategies using molecular features and verified via pathological estimation of tumor cellularity based on histological review. This integrated proteogenomic characterization of PDAC will serve as a valuable resource for the community, paving the way for early detection and identification of novel therapeutic targets.
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Affiliation(s)
- Liwei Cao
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Chen Huang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniel Cui Zhou
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - T Mamie Lih
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Sara R Savage
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - David J Clark
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Michael Schnaubelt
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Lijun Chen
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | | | | | - Weiming Yang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Jianbo Pan
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Bo Wen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yongchao Dou
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wen Jiang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yuxing Liao
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhiao Shi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nadezhda V Terekhanova
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Song Cao
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Rita Jui-Hsien Lu
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Ruiyang Liu
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Houxiang Zhu
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Peter Ronning
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Yige Wu
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Matthew A Wyczalkowski
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Hariharan Easwaran
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Ludmila Danilova
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Arvind Singh Mer
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Seungyeul Yoo
- Sema4, a Mount Sinai venture, Stamford, CT 06902, USA
| | - Joshua M Wang
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Wenke Liu
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Mathangi Thiagarajan
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Scott D Jewell
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | | | | | - Qing Kay Li
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Michael H Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David Fenyö
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Pei Wang
- Sema4, a Mount Sinai venture, Stamford, CT 06902, USA
| | | | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Emily S Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Oliver F Bathe
- Departments of Surgery and Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Daniel W Chan
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Ralph H Hruban
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21287, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA.
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21287, USA.
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Choi YJ, Lee H, Kim DS, Kim DH, Kang MH, Cho YH, Choi CM, Yoo J, Lee KO, Choi EK, Lee JC, Rho JK. Discovery of a novel CDK7 inhibitor YPN-005 in small cell lung cancer. Eur J Pharmacol 2021; 907:174298. [PMID: 34224696 DOI: 10.1016/j.ejphar.2021.174298] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/22/2021] [Accepted: 06/29/2021] [Indexed: 02/05/2023]
Abstract
In contrast to non-small cell lung cancer, there has been no significant progress in the development of therapies for the small cell lung cancer (SCLC) in recent decades. Although various targeted agents, including immunotherapies, have recently been developed for testing in clinical trials, novel therapeutic agents are still needed for SCLC. We developed a potent inhibitor of cyclin-dependent kinase 7 (CDK7), designated YPN-005, and sought to determine whether it showed any anticancer effects in SCLC cells, cisplatin or etoposide-resistant cells, or organoids derived from SCLC patients. In a panel of kinases assay, YPN-005 was highly selective for CDK7 and showed antiproliferative effects in SCLC and cells with acquired resistance to conventional anticancer drugs. Similar to other CDK7 inhibitors, YPN-005 treatment significantly decreased the phosphorylation of the carboxyl-terminal domain of RNA polymerase II. Consistent with the in vitro results, YPN-005 treatment showed a significant inhibition of tumor growth through the suppression of RNA polymerase II phosphorylation. Finally, YPN-005 showed potent anticancer effects in organoids derived from SCLC patients compared to another CDK7 inhibitor, THZ1. Therapeutic targeting of CDK7 in SCLC might be suitable for clinical investigation, and YPN-005 may be a promising therapeutic option for primary SCLC and SCLC with acquired resistance to conventional therapy.
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Affiliation(s)
- Yun Jung Choi
- Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan, College of Medicine, Seoul 05505, South Korea
| | - Hyeonjeong Lee
- Department of Biomedical Sciences, Asan Medical Center, AMIST, University of Ulsan, College of Medicine, Seoul 05505, South Korea
| | - Da-Som Kim
- Department of Biomedical Sciences, Asan Medical Center, AMIST, University of Ulsan, College of Medicine, Seoul 05505, South Korea
| | - Dong Ha Kim
- Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan, College of Medicine, Seoul 05505, South Korea
| | - Myoung-Hee Kang
- Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan, College of Medicine, Seoul 05505, South Korea
| | - Yong-Hee Cho
- Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan, College of Medicine, Seoul 05505, South Korea
| | - Chang-Min Choi
- Department of Pulmonology and Critical Care Medicine, Asan Medical Center, University of Ulsan, College of Medicine, Seoul 05505, South Korea; Department of Oncology, Asan Medical Center, University of Ulsan, College of Medicine, Seoul 05505, South Korea
| | - Jakyung Yoo
- R&D Institute, Yungjin Pharmaceutical Co., Ltd, 109, Suwon 16229, South Korea
| | - Kwang-Ok Lee
- R&D Institute, Yungjin Pharmaceutical Co., Ltd, 109, Suwon 16229, South Korea
| | - Eun Kyung Choi
- Department of Radiation Oncology, Asan Medical Center, University of Ulsan, College of Medicine, Seoul 05505, South Korea
| | - Jae Cheol Lee
- Department of Oncology, Asan Medical Center, University of Ulsan, College of Medicine, Seoul 05505, South Korea.
| | - Jin Kyung Rho
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan, College of Medicine, Seoul 05505, South Korea.
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99
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Kumar V, Parate S, Thakur G, Lee G, Ro HS, Kim Y, Kim HJ, Kim MO, Lee KW. Identification of CDK7 Inhibitors from Natural Sources Using Pharmacoinformatics and Molecular Dynamics Simulations. Biomedicines 2021; 9:1197. [PMID: 34572383 PMCID: PMC8468199 DOI: 10.3390/biomedicines9091197] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 02/02/2023] Open
Abstract
The cyclin-dependent kinase 7 (CDK7) plays a crucial role in regulating the cell cycle and RNA polymerase-based transcription. Overexpression of this kinase is linked with various cancers in humans due to its dual involvement in cell development. Furthermore, emerging evidence has revealed that inhibiting CDK7 has anti-cancer effects, driving the development of novel and more cost-effective inhibitors with enhanced selectivity for CDK7 over other CDKs. In the present investigation, a pharmacophore-based approach was utilized to identify potential hit compounds against CDK7. The generated pharmacophore models were validated and used as 3D queries to screen 55,578 natural drug-like compounds. The obtained compounds were then subjected to molecular docking and molecular dynamics simulations to predict their binding mode with CDK7. The molecular dynamics simulation trajectories were subsequently used to calculate binding affinity, revealing four hits-ZINC20392430, SN00112175, SN00004718, and SN00262261-having a better binding affinity towards CDK7 than the reference inhibitors (CT7001 and THZ1). The binding mode analysis displayed hydrogen bond interactions with the hinge region residues Met94 and Glu95, DFG motif residue Asp155, ATP-binding site residues Thr96, Asp97, and Gln141, and quintessential residue outside the kinase domain, Cys312 of CDK7. The in silico selectivity of the hits was further checked by docking with CDK2, the close homolog structure of CDK7. Additionally, the detailed pharmacokinetic properties were predicted, revealing that our hits have better properties than established CDK7 inhibitors CT7001 and THZ1. Hence, we argue that proposed hits may be crucial against CDK7-related malignancies.
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Affiliation(s)
- Vikas Kumar
- Department of Bio & Medical Big Data (BK4 Program), Division of Life Sciences, Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea;
| | - Shraddha Parate
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Division of Applied Life Science, Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (S.P.); (G.L.)
| | - Gunjan Thakur
- Department of Veterinary Medicine, Institute of Animal Medicine, Gyeongsang National University (GNU), Jinju 52828, Korea;
| | - Gihwan Lee
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Division of Applied Life Science, Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (S.P.); (G.L.)
| | - Hyeon-Su Ro
- Department of Bio & Medical Big Data (BK4 Program), Research Institute of Life Sciences, Gyeongsang National University (GNU), Jinju 52828, Korea;
| | - Yongseong Kim
- School of Cosmetics and Food Development, Kyungnam University, Masan 631-701, Korea;
| | - Hong Ja Kim
- Division of Life Sciences and Applied Life Science (BK21 Four), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea;
| | - Myeong Ok Kim
- Division of Life Sciences and Applied Life Science (BK21 Four), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea;
| | - Keun Woo Lee
- Department of Bio & Medical Big Data (BK4 Program), Division of Life Sciences, Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea;
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100
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Panagiotou E, Gomatou G, Trontzas IP, Syrigos N, Kotteas E. Cyclin-dependent kinase (CDK) inhibitors in solid tumors: a review of clinical trials. Clin Transl Oncol 2021; 24:161-192. [PMID: 34363593 DOI: 10.1007/s12094-021-02688-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/27/2021] [Indexed: 12/24/2022]
Abstract
Cyclin-dependent kinases (CDKs) play a key regulating role in the cell cycle, which is almost universally altered in cancer, leading to sustained proliferation. Early pan-CDK inhibitors showed poor results in clinical trials for solid malignancies, as the lack of selectivity produced significant toxicity. The production of more selective inhibitors led to significant developments in cancer therapy, as CDK4/6 inhibitors in combination with endocrine therapy changed the landscape of the treatment of hormone-receptor positive (HR +) metastatic breast cancer. Recently, Trilaciclib demonstrated benefits regarding hematological toxicity compared to placebo when administered in combination with chemotherapy in small cell lung cancer. Newer agents, such as SY-5609, a selective CDK7 inhibitor, have also shown promising results in early clinical trials. In this paper, we review the data from clinical trials of CDK inhibitors in solid tumors, either as a monotherapy or in combination with other agents, with an emphasis on novel agents and potential new indications for this drug class.
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Affiliation(s)
- E Panagiotou
- Oncology Unit, Sotiria General Hospital, Athens School of Medicine, 152 Mesogeion Avenue, 11527, Athens, Greece.
| | - G Gomatou
- Oncology Unit, Sotiria General Hospital, Athens School of Medicine, 152 Mesogeion Avenue, 11527, Athens, Greece
| | - I P Trontzas
- Oncology Unit, Sotiria General Hospital, Athens School of Medicine, 152 Mesogeion Avenue, 11527, Athens, Greece
| | - N Syrigos
- Oncology Unit, Sotiria General Hospital, Athens School of Medicine, 152 Mesogeion Avenue, 11527, Athens, Greece
| | - E Kotteas
- Oncology Unit, Sotiria General Hospital, Athens School of Medicine, 152 Mesogeion Avenue, 11527, Athens, Greece
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