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Wang K, Jiang M, Liu H, Meng C, Li M, Lu H. Discovery of novel co-degradation CK1α and CDK7/9 PROTACs with p53 activation for treating acute myeloid leukemia. Bioorg Chem 2024; 147:107319. [PMID: 38593529 DOI: 10.1016/j.bioorg.2024.107319] [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: 01/14/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/11/2024]
Abstract
Reactivating p53 activity to restore its anticancer function is an attractive cancer treatment strategy. In this study, we designed and synthesized a series of novel PROTACs to reactivate p53 via the co-degradation of CK1α and CDK7/9 proteins. Bioactivity studies showed that the selected PROTAC 13i exhibited potency antiproliferative activity in MV4-11 (IC50 = 0.096 ± 0.012 μM) and MOLM-13 (IC50 = 0.072 ± 0.014 μM) cells, and induced apoptosis of MV4-11 cells. Western-blot analysis showed that PROTAC 13i triple CK1α and CDK7/9 protein degradation resulted in the significantly increased expression of p53. At the same time, the transcriptional repression due to the degradation significantly reduced downstream gene expression of MYC, MDM2, BCL-2 and MCL-1, and reduced the inflammatory cytokine levels of TNF-α, IL-1β and IL-6 in PMBCs. These results indicate the beneficial impact of simultaneous CK1α and CDK7/9 degradation for acute myeloid leukemia therapy.
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MESH Headings
- Humans
- Tumor Suppressor Protein p53/metabolism
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/chemical synthesis
- Casein Kinase Ialpha/metabolism
- Casein Kinase Ialpha/antagonists & inhibitors
- Cell Proliferation/drug effects
- Drug Screening Assays, Antitumor
- Cyclin-Dependent Kinase 9/antagonists & inhibitors
- Cyclin-Dependent Kinase 9/metabolism
- Structure-Activity Relationship
- Molecular Structure
- Cyclin-Dependent Kinases/antagonists & inhibitors
- Cyclin-Dependent Kinases/metabolism
- Dose-Response Relationship, Drug
- Apoptosis/drug effects
- Drug Discovery
- Cell Line, Tumor
- Proteolysis/drug effects
- Tumor Cells, Cultured
- Proteolysis Targeting Chimera
- Cyclin-Dependent Kinase-Activating Kinase
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Affiliation(s)
- Kai Wang
- College of Pharmacy, Jilin University, Changchun 130021, China
| | - Meixu Jiang
- College of Pharmacy, Jilin University, Changchun 130021, China
| | - Huimin Liu
- College of Pharmacy, Jilin University, Changchun 130021, China
| | - Chen Meng
- College of Pharmacy, Jilin University, Changchun 130021, China
| | - Mengyuan Li
- College of Pharmacy, Jilin University, Changchun 130021, China
| | - Haibin Lu
- College of Pharmacy, Jilin University, Changchun 130021, China.
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Wu M, Han J, Liu Z, Zhang Y, Huang C, Li J, Li Z. Identification of novel CDK 9 inhibitors based on virtual screening, molecular dynamics simulation, and biological evaluation. Life Sci 2020; 258:118228. [PMID: 32781071 DOI: 10.1016/j.lfs.2020.118228] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 11/24/2022]
Abstract
AIMS Cyclin-dependent kinase 9 (CDK9) is a member of the CDK subfamily and plays a major role in the regulation of transcriptional elongation. It has attracted widespread attention as a therapeutic target for cancer. Here, we aimed to explore novel CDK 9 inhibitors by using a hybrid virtual screening strategy. MAIN METHODS A hybrid virtual screening strategy was constructed with computer-aided drug design (CADD). First, compounds were filtered in accordance with Lipinski's rule of five and adsorption, distribution, metabolism, excretion, and toxicity (ADMET) properties. Second, a 3D-QSAR pharmacophore model was built and used as a 3D query to screen the obtained hit compounds. Third, the hit compounds were subjected to molecular docking studies. Fourth, molecular dynamics (MD) simulations were performed on CDK9 in complex with the final hits to examine the structural stability. Finally, CDK9 kinase biochemical assay was performed to identify the biological activity of the hit compounds. KEY FINDINGS Seven hit compounds were screened out. These hit compounds showed drug-like properties in accordance with Lipinski's rule of five and ADMET. Complexes involving the six hit compounds bound to CDK9 exhibited good structural stability in the MD simulation. Furthermore, these six hit compounds had strong inhibitory activity against CDK9 kinase. In particular, hit 3 showed the most promising activity with the percentage of 71%. SIGNIFICANCE The six hit compounds may be promising novel CDK9 inhibitors, and the hybrid virtual screening strategy designed in this study provides an important reference for the design and synthesis of novel CDK9 inhibitors.
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Affiliation(s)
- Mingfei Wu
- The Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The key laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Hefei 230032, China
| | - Jianfei Han
- The Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The key laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Hefei 230032, China
| | - Zhicheng Liu
- The Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The key laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Hefei 230032, China
| | - Yilong Zhang
- The Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The key laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Hefei 230032, China
| | - Cheng Huang
- The Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The key laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Hefei 230032, China
| | - Jun Li
- The Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The key laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Hefei 230032, China.
| | - Zeng Li
- The Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The key laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Hefei 230032, China.
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Boffo S, Damato A, Alfano L, Giordano A. CDK9 inhibitors in acute myeloid leukemia. J Exp Clin Cancer Res 2018; 37:36. [PMID: 29471852 PMCID: PMC5824552 DOI: 10.1186/s13046-018-0704-8] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 02/12/2018] [Indexed: 02/07/2023] Open
Abstract
Current treatment for acute myeloid leukemia (AML) is less than optimal, but increased understanding of disease pathobiology and genomics has led to clinical investigation of novel targeted therapies and rational combinations. Targeting the cyclin-dependent kinase 9 (CDK9) pathway, which is dysregulated in AML, is an attractive approach. Inhibition of CDK9 leads to downregulation of cell survival genes regulated by super enhancers such as MCL-1, MYC, and cyclin D1. As CDK9 inhibitors are nonselective, predictive biomarkers that may help identify patients most likely to respond to CDK9 inhibitors are now being utilized, with the goal of improving efficacy and safety.
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Affiliation(s)
- Silvia Boffo
- Sbarro Institute for Cancer Research and Molecular Medicine, Department of Biology, Temple University, 1900 N. 12th St., Room 431, Philadelphia, PA 19122-6017 USA
| | - Angela Damato
- Sbarro Institute for Cancer Research and Molecular Medicine, Department of Biology, Temple University, 1900 N. 12th St., Room 431, Philadelphia, PA 19122-6017 USA
- Medical Oncology Unit, Clinical Cancer Centre, IRCCS–Arcispedale S. Maria Nuova, Reggio Emilia, Italy
| | - Luigi Alfano
- Oncology Research Center of Mercogliano (CROM), Istituto Nazionale Per Lo Studio E La Cura Dei Tumori “Fondazione Giovanni Pascale”, IRCCS, Naples, Italy
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine, Department of Biology, Temple University, 1900 N. 12th St., Room 431, Philadelphia, PA 19122-6017 USA
- Department of Medicine, Surgery, and Neuroscience, University of Siena, Siena, Italy
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Asamitsu K, Hirokawa T, Okamoto T. MD simulation of the Tat/Cyclin T1/CDK9 complex revealing the hidden catalytic cavity within the CDK9 molecule upon Tat binding. PLoS One 2017; 12:e0171727. [PMID: 28178316 PMCID: PMC5298246 DOI: 10.1371/journal.pone.0171727] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/24/2017] [Indexed: 02/02/2023] Open
Abstract
In this study, we applied molecular dynamics (MD) simulation to analyze the dynamic behavior of the Tat/CycT1/CDK9 tri-molecular complex and revealed the structural changes of P-TEFb upon Tat binding. We found that Tat could deliberately change the local flexibility of CycT1. Although the structural coordinates of the H1 and H2 helices did not substantially change, H1', H2', and H3' exhibited significant changes en masse. Consequently, the CycT1 residues involved in Tat binding, namely Tat-recognition residues (TRRs), lost their flexibility with the addition of Tat to P-TEFb. In addition, we clarified the structural variation of CDK9 in complex with CycT1 in the presence or absence of Tat. Interestingly, Tat addition significantly reduced the structural variability of the T-loop, thus consolidating the structural integrity of P-TEFb. Finally, we deciphered the formation of the hidden catalytic cavity of CDK9 upon Tat binding. MD simulation revealed that the PITALRE signature sequence of CDK9 flips the inactive kinase cavity of CDK9 into the active form by connecting with Thr186, which is crucial for its activity, thus presumably recruiting the substrate peptide such as the C-terminal domain of RNA pol II. These findings provide vital information for the development of effective novel anti-HIV drugs with CDK9 catalytic activity as the target.
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Grants
- Ministry of Education, Culture, Sports, Science, and Technology "The Platform Project for Supporting Drug Discovery and Life Science Research (Platform for Drug Discovery, Informatics, and Structural Life Science)"
- Ministry of Education, Culture, Sports, Science, and Technology
- Asahi Grass Foundation
- Japan Agency for Medical Research and Development
- Junwakai Foundation
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Affiliation(s)
- Kaori Asamitsu
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, Japan
| | - Takatsugu Hirokawa
- Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
- * E-mail: (TH); (TO)
| | - Takashi Okamoto
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, Japan
- * E-mail: (TH); (TO)
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