1
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Arora C, Madaan K, Mehta S, Singh R. Exploring isoindolin-1-ones as potential CDK7 inhibitors using cheminformatic tools. In Silico Pharmacol 2024; 12:51. [PMID: 38845825 PMCID: PMC11150237 DOI: 10.1007/s40203-024-00225-0] [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: 04/11/2024] [Accepted: 05/24/2024] [Indexed: 06/09/2024] Open
Abstract
In women who die from cancer, breast cancer is the most common cause of death. The development of small molecular scaffolds as specific Cyclin-dependent kinase (CDK) inhibitors is a promising strategy in the discovery of anti-breast cancer drugs. Isoindolin-1-ones are heterocyclic compounds with useful therapeutic properties. In this study, a library of 48 isoindolinones has been virtually screened by molecular docking that showed high binding affinity up to - 10.1 kcal/mol and conventional hydrogen bonding interactions with active amino acid residues of CDK7. The molecular dynamics simulation (MDS), fragment molecular orbital (FMO), density functional theory (DFT), and pharmacokinetics studies of the best two docked scored ligands 7 and 14 have been studied. Examining the ligand root mean square deviation and hydrogen bonding occupancy of the 100 ns MDS trajectory, both ligands 7 and 14 showed docked pose stability. FMO calculations displayed that LYS139 and LYS41 are majorly contributing to the binding interactions with ligands 7 and 14 in the docked poses. DFT studies of ligands 7 and 14 showed high values of global softness and low values of global hardness and chemical potential thus displaying chemically reactive soft molecules and this influences their anti-cancer activity. Our hits exhibited superior qualities to known CDK7 inhibitors, according to the comprehensive pharmacokinetic parameters that were predicted. The results indicate that isoindolin-1-one moieties are good candidates for anti-cancer action and could serve as effective CDK7 inhibitors. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-024-00225-0.
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Affiliation(s)
- Chahat Arora
- Department of Applied Chemistry, Delhi Technological University, Delhi, 110042 India
| | - Kunal Madaan
- Department of Applied Chemistry, Delhi Technological University, Delhi, 110042 India
| | - Saurabh Mehta
- Department of Applied Chemistry, Delhi Technological University, Delhi, 110042 India
| | - Ram Singh
- Department of Applied Chemistry, Delhi Technological University, Delhi, 110042 India
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2
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Zhang H, Lin G, Jia S, Wu J, Zhang Y, Tao Y, Huang W, Song M, Ding K, Ma D, Fan M. Design, synthesis and evaluation of thieno[3,2-d]pyrimidine derivatives as novel potent CDK7 inhibitors. Bioorg Chem 2024; 148:107456. [PMID: 38761706 DOI: 10.1016/j.bioorg.2024.107456] [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: 01/11/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
The targeting of cyclin-dependent kinase 7 (CDK7) has become a highly desirable therapeutic approach in the field of oncology due to its dual role in regulating essential biological processes, encompassing cell cycle progression and transcriptional control. We have previously identified a highly selective thieno[3,2-d]pyrimidine-based CDK7 inhibitor with demonstrated efficacy and safety in animal model. In this study, we sought to optimize the thieno[3,2-d]pyrimidine core to discover a novel series of CDK7 inhibitors with improved potency and pharmacokinetic (PK) properties. Through extensive structure-activity relationship (SAR) studies, compound 20 has emerged as the lead candidate due to its potent inhibitory activity against CDK7 and remarkable efficacy on MDA-MB-453 cells, a representative triple negative breast cancer (TNBC) cell line. Furthermore, 20 has demonstrated favorable oral bioavailability and exhibited highly desirable pharmacokinetic (PK) properties, making it a promising lead candidate for further structural optimization.
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Affiliation(s)
- Hongjin Zhang
- Academy of Medical Engineering and Translational Medicine (AMT), Tianjin University, Tianjin 300072, China; Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China
| | - Guohao Lin
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China; Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China
| | - Suyun Jia
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China; School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China; Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 20032, China
| | - Jianbo Wu
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China; College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Ying Zhang
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China; College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Yanxin Tao
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China; School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Weixue Huang
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 20032, China
| | - Meiru Song
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China; Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China; Institute of Chemistry, Henan Academy of Sciences, Zhengzhou, Henan 450046, China
| | - Ke Ding
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 20032, China.
| | - Dawei Ma
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 20032, China.
| | - Mengyang Fan
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China; Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China.
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3
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Song X, Fang C, Dai Y, Sun Y, Qiu C, Lin X, Xu R. Cyclin-dependent kinase 7 (CDK7) inhibitors as a novel therapeutic strategy for different molecular types of breast cancer. Br J Cancer 2024; 130:1239-1248. [PMID: 38355840 PMCID: PMC11014910 DOI: 10.1038/s41416-024-02589-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 01/06/2024] [Accepted: 01/16/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Cyclin-dependent kinase (CDK) 7 is aberrantly overexpressed in many types of cancer and is an attractive target for cancer therapy due to its dual role in transcription and cell cycle progression. Moreover, CDK7 can directly modulate the activities of estrogen receptor (ER), which is a major driver in breast cancer. Breast cancer cells have exhibited high sensitivity to CDK7 inhibition in pre-clinical studies. METHODS In this review, we provide a comprehensive summary of the latest insights into CDK7 biology and recent advancements in CDK7 inhibitor development for breast cancer treatment. We also discuss the current application of CDK7 inhibitors in different molecular types of breast cancer to provide potential strategies for the treatment of breast cancer. RESULTS Significant progress has been made in the development of selective CDK7 inhibitors, which show efficacy in both triple-negative breast cancer (TNBC) and hormone receptor-positive breast cancer (HR+). Moreover, combined with other agents, CDK7 inhibitors may provide synergistic effects for endocrine therapy and chemotherapy. Thus, high-quality studies for developing potent CDK7 inhibitors and investigating their applications in breast cancer therapy are rapidly emerging. CONCLUSION CDK7 inhibitors have emerged as a promising therapeutic strategy and have demonstrated significant anti-cancer activity in different subtypes of breast cancer, especially those that have been resistant to current therapies.
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Affiliation(s)
- Xue Song
- Department of Breast Cancer, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, 510120, China
| | - Chen Fang
- Department of Breast Cancer, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, 510120, China
| | - Yan Dai
- Department of Breast Cancer, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, 510120, China
| | - Yang Sun
- Department of Breast Cancer, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, 510120, China
| | - Chang Qiu
- Department of Breast Cancer, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, 510120, China
| | - Xiaojie Lin
- Department of Breast Cancer, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, 510120, China
| | - Rui Xu
- Department of Breast Cancer, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, 510120, China.
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4
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Zhang H, Lin G, Jia S, Zhang Y, Wu J, Tao Y, Huang W, Song M, Ding K, Ma D, Fan M. Discovery and optimization of thieno[3,2-d]pyrimidine derivatives as highly selective inhibitors of cyclin-dependent kinase 7. Eur J Med Chem 2024; 263:115955. [PMID: 38000213 DOI: 10.1016/j.ejmech.2023.115955] [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: 09/21/2023] [Revised: 11/05/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023]
Abstract
Targeting cyclin-dependent kinase 7 (CDK7) has emerged as a highly sought-after therapeutic strategy in oncology due to its duality of function in regulating biological processes, including cell cycle progression and transcriptional control. Herein, we describe the design, optimization and characterization of a series of thieno[3,2-d]pyrimidine derivatives as potent CDK7 inhibitors. The involvement of thiophene as core structure plays critical role in leading to the remarkable selectivity and incorporation of a fluorine atom into the piperidine ring enhances metabolic stability. Structure-activity relationship (SAR) study generated compound 36 as lead compound with potent inhibitory activity against CDK7 and good kinome selectivity in vitro. Compound 36 demonstrated strong efficacy against a triple negative breast cancer (TNBC) cell line-derived xenograft (CDX) mouse model upon oral administration at 5 mg/kg once daily. Therefore, it exhibits immense potential as a lead candidate for further exploration in the development of cancer therapy.
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Affiliation(s)
- Hongjin Zhang
- Academy of Medical Engineering and Translational Medicine (AMT), Tianjin University, Tianjin, 300072, China; Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310018, China
| | - Guohao Lin
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310018, China; Zhejiang Cancer Hospital, Hangzhou, Zhejiang, 310022, China
| | - Suyun Jia
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310018, China; School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, 310024, China; Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 20032, China
| | - Ying Zhang
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310018, China; College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China
| | - Jianbo Wu
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310018, China; College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China
| | - Yanxin Tao
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310018, China; School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, 310024, China; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Weixue Huang
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 20032, China
| | - Meiru Song
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310018, China; Zhejiang Cancer Hospital, Hangzhou, Zhejiang, 310022, China
| | - Ke Ding
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 20032, China.
| | - Dawei Ma
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 20032, China.
| | - Mengyang Fan
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310018, China; Zhejiang Cancer Hospital, Hangzhou, Zhejiang, 310022, China.
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5
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Charles Coombes R, Howell S, Lord SR, Kenny L, Mansi J, Mitri Z, Palmieri C, Chap LI, Richards P, Gradishar W, Sardesai S, Melear J, O'Shaughnessy J, Ward P, Chalasani P, Arkenau T, Baird RD, Jeselsohn R, Ali S, Clack G, Bahl A, McIntosh S, Krebs MG. Dose escalation and expansion cohorts in patients with advanced breast cancer in a Phase I study of the CDK7-inhibitor samuraciclib. Nat Commun 2023; 14:4444. [PMID: 37488191 PMCID: PMC10366102 DOI: 10.1038/s41467-023-40061-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 07/11/2023] [Indexed: 07/26/2023] Open
Abstract
Samuraciclib is a selective oral CDK7-inhibitor. A multi-modular, open-label Phase I study to evaluate safety and tolerability of samuraciclib in patients with advanced malignancies was designed (ClinicalTrials.gov: NCT03363893). Here we report results from dose escalation and 2 expansion cohorts: Module 1A dose escalation with paired biopsy cohort in advanced solid tumor patients, Module 1B-1 triple negative breast cancer (TNBC) monotherapy expansion, and Module 2A fulvestrant combination in HR+/HER2- breast cancer patients post-CDK4/6-inhibitor. Core study primary endpoints are safety and tolerability, and secondary endpoints are pharmacokinetics (PK), pharmacodynamic (PD) activity, and anti-tumor activity. Common adverse events are low grade nausea, vomiting, and diarrhea. Maximum tolerated dose is 360 mg once daily. PK demonstrates dose proportionality (120 mg-480 mg), a half-life of approximately 75 hours, and no fulvestrant interaction. In dose escalation, one partial response (PR) is identified with disease control rate of 53% (19/36) and reduction of phosphorylated RNA polymerase II, a substrate of CDK7, in circulating lymphocytes and tumor tissue. In TNBC expansion, one PR (duration 337 days) and clinical benefit rate at 24 weeks (CBR) of 20.0% (4/20) is achieved. In combination with fulvestrant, 3 patients achieve PR with CBR 36.0% (9/25); in patients without detectable TP53-mutation CBR is 47.4% (9/19). In this study, samuraciclib exhibits tolerable safety and PK is supportive of once-daily oral administration. Clinical activity in TNBC and HR+/HER2-breast cancer post-CDK4/6-inhibitor settings warrants further evaluation.
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Affiliation(s)
| | - Sacha Howell
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester and The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Simon R Lord
- Early Phase Clinical Trials Unit, Department of Oncology, University of Oxford, Oxford, UK
| | - Laura Kenny
- Imperial College, South Kensington, London, UK
| | - Janine Mansi
- Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Zahi Mitri
- OHSU Knight Cancer Institute, Portland, OR, USA
| | | | | | | | | | | | - Jason Melear
- Baylor University Medical Center, Texas Oncology, Dallas, TX, USA
| | | | | | | | | | | | | | - Simak Ali
- Imperial College, South Kensington, London, UK
| | | | | | | | - Matthew G Krebs
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester and The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK.
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6
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Bhurta D, Hossain MM, Bhardwaj M, Showket F, Nandi U, Dar MJ, Bharate SB. Orally bioavailable styryl derivative of rohitukine-N-oxide inhibits CDK9/T1 and the growth of pancreatic cancer cells. Eur J Med Chem 2023; 258:115533. [PMID: 37302342 DOI: 10.1016/j.ejmech.2023.115533] [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: 03/17/2023] [Revised: 05/14/2023] [Accepted: 05/28/2023] [Indexed: 06/13/2023]
Abstract
The chromone alkaloid is one of the classical pharmacophores for cyclin-dependent kinases (CDKs) and represents the first CDK inhibitor to reach clinical trials. Rohitukine (1), a chromone alkaloid isolated from Dysoxylum binectariferum inspired the discovery of several clinical candidates. The N-oxide derivative of rohitukine occurs naturally, with no reports on its biological activity. Herein, we report isolation, biological evaluation, and synthetic modification of rohitukine N-oxide for CDK9/T1 inhibition and antiproliferative activity in cancer cells. Rohitukine N-oxide (2) inhibits CDK9/T1 (IC50 7.6 μM) and shows antiproliferative activity in the colon and pancreatic cancer cells. The chloro-substituted styryl derivatives, 2b, and 2l, inhibit CDK9/T1 with IC50 values of 0.17 and 0.15 μM, respectively. These derivatives display cellular antiproliferative activity in HCT 116 (colon) and MIA PaCa-2 (pancreatic) cancer cells with GI50 values of 2.5-9.7 μM with excellent selectivity over HEK293 (embryonic kidney) cells. Both analogs induce cell death in MIA PaCa-2 cells via inducing intracellular ROS production, reducing mitochondrial membrane potential, and inducing apoptosis. These analogs are metabolically stable in liver microsomes and have a decent oral pharmacokinetics in BALB/c mice. The molecular modeling studies indicated their strong binding at the ATP-binding site of CDK7/H and CDK9/T1.
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Affiliation(s)
- Deendyal Bhurta
- Natural Products & Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India; Academy of Scientific & Innovative Research, Ghaziabad, 201002, India
| | - Md Mehedi Hossain
- Academy of Scientific & Innovative Research, Ghaziabad, 201002, India; Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Mahir Bhardwaj
- Academy of Scientific & Innovative Research, Ghaziabad, 201002, India; Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Farheen Showket
- Academy of Scientific & Innovative Research, Ghaziabad, 201002, India; Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Utpal Nandi
- Academy of Scientific & Innovative Research, Ghaziabad, 201002, India; Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Mohd Jamal Dar
- Academy of Scientific & Innovative Research, Ghaziabad, 201002, India; Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Sandip B Bharate
- Natural Products & Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India; Academy of Scientific & Innovative Research, Ghaziabad, 201002, India; Department of Natural Products & Medicinal Chemistry, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500007, India.
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7
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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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8
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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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9
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Dion V, Schumacher N, Masar N, Pieltain A, Tocquin P, Lesoinne P, Malgrange B, Vandenbosch R, Franzen R. Cyclin-dependent kinase 7 contributes to myelin maintenance in the adult central nervous system and promotes myelin gene expression. Glia 2022; 70:1652-1665. [PMID: 35488490 DOI: 10.1002/glia.24186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 04/08/2022] [Accepted: 04/21/2022] [Indexed: 11/08/2022]
Abstract
Mechanisms regulating oligodendrocyte differentiation, developmental myelination and myelin maintenance in adulthood are complex and still not completely described. Their understanding is crucial for the development of new protective or therapeutic strategies in demyelinating pathologies such as multiple sclerosis. In this perspective, we have investigated the role of Cyclin-dependent kinase 7 (Cdk7), a kinase involved in cell-cycle progression and transcription regulation, in the oligodendroglial lineage. We generated a conditional knock-out mouse model in which Cdk7 is invalidated in post-mitotic oligodendrocytes. At the end of developmental myelination, the number and diameter of myelinated axons, as well as the myelin structure, thickness and protein composition, were normal. However, in young adult and in aged mice, there was a higher number of small caliber myelinated axons associated with a decreased mean axonal diameter, myelin sheaths of large caliber axons were thinner, and the level of some major myelin-associated proteins was reduced. These defects were accompanied by the appearance of an abnormal clasping phenotype. We also used an in vitro oligodendroglial model and showed that Cdk7 pharmacological inhibition led to an altered myelination-associated morphological modification combined with a decreased expression of myelin-specific genes. Altogether, we identified novel functions for Cdk7 in CNS myelination.
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Affiliation(s)
- Valérie Dion
- Laboratory of Nervous System Disorders and Therapies, GIGA Neurosciences, University of Liège, Liège, Belgium
| | - Nathalie Schumacher
- Laboratory of Nervous System Disorders and Therapies, GIGA Neurosciences, University of Liège, Liège, Belgium
| | - Nathalie Masar
- Laboratory of Nervous System Disorders and Therapies, GIGA Neurosciences, University of Liège, Liège, Belgium
| | - Alexandra Pieltain
- Laboratory of Nervous System Disorders and Therapies, GIGA Neurosciences, University of Liège, Liège, Belgium
| | - Pierre Tocquin
- CARE PhytoSYSTEMS, Integrative Biological Sciences, University of Liège, Liège, Belgium
| | - Pierre Lesoinne
- Laboratory of Nervous System Disorders and Therapies, GIGA Neurosciences, University of Liège, Liège, Belgium
| | - Brigitte Malgrange
- Laboratory of Developmental Neurobiology, GIGA Stem Cells & GIGA Neurosciences, University of Liège, Liège, Belgium
| | - Renaud Vandenbosch
- Laboratory of Developmental Neurobiology, GIGA Stem Cells & GIGA Neurosciences, University of Liège, Liège, Belgium.,Division of Histology, Department of Biomedical and Preclinical Sciences, University of Liège, Liège, Belgium
| | - Rachelle Franzen
- Laboratory of Nervous System Disorders and Therapies, GIGA Neurosciences, University of Liège, Liège, Belgium
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10
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Wei D, Wang H, Zeng Q, Wang W, Hao B, Feng X, Wang P, Song N, Kan W, Huang G, Zhou X, Tan M, Zhou Y, Huang R, Li J, Chen XH. Discovery of Potent and Selective CDK9 Degraders for Targeting Transcription Regulation in Triple-Negative Breast Cancer. J Med Chem 2021; 64:14822-14847. [PMID: 34538051 DOI: 10.1021/acs.jmedchem.1c01350] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Triple-negative breast cancer (TNBC) is highly aggressive with very limited treatment options due to the lack of efficient targeted therapies and thus still remains clinically challenging. Targeting transcription-associated cyclin-dependent kinases to remodel transcriptional regulation shows great promise in cancer therapy. Herein, we report the synthesis, optimization, and evaluation of new series of heterobifunctional molecules as highly selective and efficacious CDK9 degraders, enabling potent inhibition of TNBC cell growth and rapidly targeted degradation of CDK9. Moreover, the most potent CDK9 degrader (compound 45) induces cell apoptosis in vitro and inhibits tumor growth in the MDA-MB-231 TNBC model. Furthermore, the RNA-seq, immunohistochemistry assays demonstrate that the CDK9 degrader downregulates the downstream targets, such as MYC, at the transcriptional level, resulting apoptosis in TNBC cells. Our work establishes that 45 is a highly potent and efficacious CDK9 degrader for targeting transcription regulation, which represents an effective strategy and great potential as a new targeted therapy for TNBC.
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Affiliation(s)
- Dan Wei
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanlin Wang
- College of Pharmacy, Fudan University, Shanghai 201203, China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qinghe Zeng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjing Wang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bingbing Hao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xule Feng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Peipei Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ning Song
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weijuan Kan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Guifang Huang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xiaoyu Zhou
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yubo Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Zhongshan Institute for Drug Discovery, The Institutes of Drug Discovery and Development, CAS, Zhongshan, Guangdong 528400, China
| | - Ruimin Huang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jia Li
- College of Pharmacy, Fudan University, Shanghai 201203, China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Zhongshan Institute for Drug Discovery, The Institutes of Drug Discovery and Development, CAS, Zhongshan, Guangdong 528400, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Xiao-Hua Chen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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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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Development of New Meridianin/Leucettine-Derived Hybrid Small Molecules as Nanomolar Multi-Kinase Inhibitors with Antitumor Activity. Biomedicines 2021; 9:biomedicines9091131. [PMID: 34572319 PMCID: PMC8468039 DOI: 10.3390/biomedicines9091131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/23/2021] [Accepted: 08/27/2021] [Indexed: 12/31/2022] Open
Abstract
Although the sea ecosystem offers a broad range of bioactivities including anticancer, none of the FDA-approved antiproliferative protein kinase inhibitors are derived from a marine source. In a step to develop new marine-inspired potent kinase inhibitors with antiproliferative activities, a new series of hybrid small molecules (5a–5g) was designed and synthesized based on chemical moieties derived from two marine natural products (Meridianin E and Leucettamine B). Over a panel of 14 cancer-related kinases, a single dose of 10 µM of the parent hybrid 5a possessing the benzo[d][1,3]dioxole moiety of Leucettamine B was able to inhibit the activity of FMS, LCK, LYN, and DAPK1 kinases with 82.5 ± 0.6, 81.4 ± 0.6, 75.2 ± 0.0, and 55 ± 1.1%, respectively. Further optimization revealed the most potent multiple kinase inhibitor of this new series (5g) with IC50 values of 110, 87.7, and 169 nM against FMS, LCK, and LYN kinases, respectively. Compared to imatinib (FDA-approved multiple kinase inhibitor), compound 5g was found to be ~ 9- and 2-fold more potent than imatinib over both FMS and LCK kinases, respectively. In silico docking simulation models of the synthesized compounds within the active site of FMS, LCK, LYN, and DAPK1 kinases offered reasonable explanations of the elicited biological activities. In an in vitro anticancer assay using a library of 60 cancer cell lines that include blood, lung, colon, CNS, skin, ovarian, renal, prostate, and breast cancers, it was found that compound 5g was able to suppress 60 and 70% of tumor growth in leukemia SR and renal RXF 393 cell lines, respectively. Moreover, an ADME study indicated a suitable profile of compound 5g concerning cell permeability and blood-brain barrier (BBB) impermeability, avoiding possible CNS side effects. Accordingly, compound 5g is reported as a potential lead towards novel antiproliferative marine-derived kinase modulators.
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Cyclin B2 (CCNB2) Stimulates the Proliferation of Triple-Negative Breast Cancer (TNBC) Cells In Vitro and In Vivo. DISEASE MARKERS 2021; 2021:5511041. [PMID: 34354775 PMCID: PMC8331305 DOI: 10.1155/2021/5511041] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 07/10/2021] [Indexed: 02/06/2023]
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive type of breast cancer. Currently, targeting therapy makes great advances for the treatment of TNBC, whereas more effective therapeutic targets are urgently needed. Cyclin B2 (CCNB2), which belongs to B-type cyclins, is known as a cell cycle regulator. CCNB2 is synthesized at G1 phase in cancer cells and downregulated at anaphase. The defects of CCNB2 led to the abnormal cell cycle and tumorigenesis. Though there are wide effects of CCNB2 on multiple types of tumors, the potential role of CCNB2 in TNBC progression is still unclear. Herein, we found that CCNB2 was highly expressed in human TNBC tissues and correlated with the prognosis and clinical pathological features including tumor size (p = 0.022∗) and pTNM stage (p = 0.021∗) of patients with TNBC. CCNB2 could promote the proliferation of TNBC cells in vitro and in mice. Our findings therefore confirmed the involvement of CCNB2 in TNBC progression and provided the evidence that CCNB2 could serve as a promising molecular target of TNBC.
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