1
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Huang Y, Liu W, Zhao C, Shi X, Zhao Q, Jia J, Wang A. Targeting cyclin-dependent kinases: From pocket specificity to drug selectivity. Eur J Med Chem 2024; 275:116547. [PMID: 38852339 DOI: 10.1016/j.ejmech.2024.116547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/11/2024]
Abstract
The development of selective modulators of cyclin-dependent kinases (CDKs), a kinase family with numerous members and functional variations, is a significant preclinical challenge. Recent advancements in crystallography have revealed subtle differences in the highly conserved CDK pockets. Exploiting these differences has proven to be an effective strategy for achieving excellent drug selectivity. While previous reports briefly discussed the structural features that lead to selectivity in individual CDK members, attaining inhibitor selectivity requires consideration of not only the specific structures of the target CDK but also the features of off-target members. In this review, we summarize the structure-activity relationships (SARs) that influence selectivity in CDK drug development and analyze the pocket features that lead to selectivity using molecular-protein binding models. In addition, in recent years, novel CDK modulators have been developed, providing more avenues for achieving selectivity. These cases were also included. We hope that these efforts will assist in the development of novel CDK drugs.
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Affiliation(s)
- Yaoguang Huang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Wenwu Liu
- School of Pharmaceutical Sciences, Tsinghua University, Haidian Dist., Beijing, 100084, People's Republic of China
| | - Changhao Zhao
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China
| | - Xiaoyu Shi
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Qingchun Zhao
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China; Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China.
| | - Jingming Jia
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
| | - Anhua Wang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
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2
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Rahman R, Rahaman MH, Hanson AR, Choo N, Xie J, Townley SL, Shrestha R, Hassankhani R, Islam S, Ramm S, Simpson KJ, Risbridger GP, Best G, Centenera MM, Balk SP, Kichenadasse G, Taylor RA, Butler LM, Tilley WD, Conn SJ, Lawrence MG, Wang S, Selth LA. CDK9 inhibition inhibits multiple oncogenic transcriptional and epigenetic pathways in prostate cancer. Br J Cancer 2024:10.1038/s41416-024-02810-8. [PMID: 39117800 DOI: 10.1038/s41416-024-02810-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 07/18/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Cyclin-dependent kinase 9 (CDK9) stimulates oncogenic transcriptional pathways in cancer and CDK9 inhibitors have emerged as promising therapeutic candidates. METHODS The activity of an orally bioavailable CDK9 inhibitor, CDKI-73, was evaluated in prostate cancer cell lines, a xenograft mouse model, and patient-derived tumor explants and organoids. Expression of CDK9 was evaluated in clinical specimens by mining public datasets and immunohistochemistry. Effects of CDKI-73 on prostate cancer cells were determined by cell-based assays, molecular profiling and transcriptomic/epigenomic approaches. RESULTS CDKI-73 inhibited proliferation and enhanced cell death in diverse in vitro and in vivo models of androgen receptor (AR)-driven and AR-independent models. Mechanistically, CDKI-73-mediated inhibition of RNA polymerase II serine 2 phosphorylation resulted in reduced expression of BCL-2 anti-apoptotic factors and transcriptional defects. Transcriptomic and epigenomic approaches revealed that CDKI-73 suppressed signaling pathways regulated by AR, MYC, and BRD4, key drivers of dysregulated transcription in prostate cancer, and reprogrammed cancer-associated super-enhancers. These latter findings prompted the evaluation of CDKI-73 with the BRD4 inhibitor AZD5153, a combination that was synergistic in patient-derived organoids and in vivo. CONCLUSION Our work demonstrates that CDK9 inhibition disrupts multiple oncogenic pathways and positions CDKI-73 as a promising therapeutic agent for prostate cancer, particularly aggressive, therapy-resistant subtypes.
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Affiliation(s)
- Razia Rahman
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia
| | - Muhammed H Rahaman
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Adrienne R Hanson
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia
| | - Nicholas Choo
- Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - Jianling Xie
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia
| | - Scott L Townley
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia
| | - Raj Shrestha
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia
- Flinders University, Freemasons Centre for Male Health and Wellbeing, Bedford Park, SA, Australia
| | - Ramin Hassankhani
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Saiful Islam
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Susanne Ramm
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Kaylene J Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia
| | - Gail P Risbridger
- Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Cabrini Institute, Cabrini Health, Malvern, Melbourne, VIC, Australia
- Melbourne Urological Research Alliance (MURAL), Monash Biomedicine Discovery Institute Cancer Program, Monash University, Clayton, VIC, Australia
| | - Giles Best
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia
| | - Margaret M Centenera
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Steven P Balk
- Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Ganessan Kichenadasse
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia
- Department of Medical Oncology, Flinders Medical Centre, Southern Adelaide Local Health Network, Adelaide, SA, South Australia
| | - Renea A Taylor
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Cabrini Institute, Cabrini Health, Malvern, Melbourne, VIC, Australia
- Melbourne Urological Research Alliance (MURAL), Monash Biomedicine Discovery Institute Cancer Program, Monash University, Clayton, VIC, Australia
- Biomedicine Discovery Institute Cancer Program, Department of Physiology, Monash University, Clayton, VIC, Australia
| | - Lisa M Butler
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Wayne D Tilley
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
| | - Simon J Conn
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia
| | - Mitchell G Lawrence
- Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Cabrini Institute, Cabrini Health, Malvern, Melbourne, VIC, Australia
- Melbourne Urological Research Alliance (MURAL), Monash Biomedicine Discovery Institute Cancer Program, Monash University, Clayton, VIC, Australia
| | - Shudong Wang
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Luke A Selth
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia.
- Flinders University, Freemasons Centre for Male Health and Wellbeing, Bedford Park, SA, Australia.
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia.
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3
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Ahmad Sheikh K, Parveen D, Mumtaz Alam M, Azam F, Ahmed Khan M, Akhter M, Tasneem S, Meenu, Parvez S, Imtiyaz K, Rizvi MA, Shaquiquzzaman M. Exploring cyclopropylamine containing cyanopyrimidines as LSD1 inhibitors: Design, synthesis, ADMET, MD analysis and anticancer activity profiling. Bioorg Chem 2024; 147:107336. [PMID: 38636431 DOI: 10.1016/j.bioorg.2024.107336] [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: 10/25/2023] [Revised: 03/31/2024] [Accepted: 04/04/2024] [Indexed: 04/20/2024]
Abstract
In this series we report the structure-based design, synthesis and anticancer activity evaluation of a series of eighteen cyclopropylamine containing cyanopyrimidine derivatives. The computational predictions of ADMET properties revealed appropriate aqueous solubility, high GI absorption, no BBB permeability, no Lipinski rule violations, medium total clearance and no mutagenic, tumorigenic, irritant and reproductive toxic risks for most of the compounds. Compounds VIIb, VIIi and VIIm emerged as the most potent anticancer agents among all compounds evaluated against 60 cancer cell lines through the one-dose (10 µM) sulforhodamine B assay. Further, the multiple dose cell viability studies against cancer cell lines MOLT-4, A549 and HCT-116 revealed results consistent with the one-dose assay, besides sparing normal cell line HEK-293. The three potent compounds also displayed potent LSD1 inhibitory activity with IC50 values of 2.25, 1.80 and 6.08 µM. The n-propyl-thio/isopropyl-thio group bonded to the pyrimidine ring and unsubstituted/ electron donating group (at the para- position) attached to the phenyl ring resulted in enhanced anticancer activity. However, against leukemia cancer, the electron donating isopropyl group remarkably enhanced anti-cancer activity. Our findings provide important leads, which merit further optimization to result in better cancer therapeutics.
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Affiliation(s)
- Khursheed Ahmad Sheikh
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi 110062, India
| | - Darakhshan Parveen
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi 110062, India
| | - M Mumtaz Alam
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi 110062, India.
| | - Faizul Azam
- Department of Pharmaceutical Chemistry and Pharmacognosy, Unaizah College of Pharmacy, Qassim University, Saudi Arabia
| | - Mohammad Ahmed Khan
- Department of Pharmacology, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi 110062, India
| | - Mymoona Akhter
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi 110062, India
| | - Sharba Tasneem
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi 110062, India
| | - Meenu
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi 110062, India
| | - Suhel Parvez
- Department of Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Khalid Imtiyaz
- Genome Biology Lab, Department of Bioscience, Jamia Millia Islamia, New Delhi 110025, India
| | - Moshahid A Rizvi
- Genome Biology Lab, Department of Bioscience, Jamia Millia Islamia, New Delhi 110025, India
| | - M Shaquiquzzaman
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi 110062, India.
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4
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Zhang Y, Shan L, Tang W, Ge Y, Li C, Zhang J. Recent Discovery and Development of Inhibitors that Target CDK9 and Their Therapeutic Indications. J Med Chem 2024; 67:5185-5215. [PMID: 38564299 DOI: 10.1021/acs.jmedchem.4c00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
CDK9 is a cyclin-dependent kinase that plays pivotal roles in multiple cellular functions including gene transcription, cell cycle regulation, DNA damage repair, and cellular differentiation. Targeting CDK9 is considered an attractive strategy for antitumor therapy, especially for leukemia and lymphoma. Several potent small molecule inhibitors, exemplified by TG02 (4), have progressed to clinical trials. However, many of them face challenges such as low clinical efficacy and multiple adverse reactions and may necessitate the exploration of novel strategies to lead to success in the clinic. In this perspective, we present a comprehensive overview of the structural characteristics, biological functions, and preclinical status of CDK9 inhibitors. Our focus extends to various types of inhibitors, including pan-inhibitors, selective inhibitors, dual-target inhibitors, degraders, PPI inhibitors, and natural products. The discussion encompasses chemical structures, structure-activity relationships (SARs), biological activities, selectivity, and therapeutic potential, providing detailed insight into the diverse landscape of CDK9 inhibitors.
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Affiliation(s)
- Yuming Zhang
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
- West China College of Medicine, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Lianhai Shan
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031 Sichuan, China
| | - Wentao Tang
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Yating Ge
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - ChengXian Li
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Jifa Zhang
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
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5
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Wang S, Liu F, Li P, Wang JN, Mo Y, Lin B, Mei Y. Potent inhibitors targeting cyclin-dependent kinase 9 discovered via virtual high-throughput screening and absolute binding free energy calculations. Phys Chem Chem Phys 2024; 26:5377-5386. [PMID: 38269624 DOI: 10.1039/d3cp05582e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Due to the crucial regulatory mechanism of cyclin-dependent kinase 9 (CDK9) in mRNA transcription, the development of kinase inhibitors targeting CDK9 holds promise as a potential treatment strategy for cancer. A structure-based virtual screening approach has been employed for the discovery of potential novel CDK9 inhibitors. First, compounds with kinase inhibitor characteristics were identified from the ZINC15 database via virtual high-throughput screening. Next, the predicted binding modes were optimized by molecular dynamics simulations, followed by precise estimation of binding affinities using absolute binding free energy calculations based on the free energy perturbation scheme. The binding mode of molecule 006 underwent an inward-to-outward flipping, and the new binding mode exhibited binding affinity comparable to the small molecule T6Q in the crystal structure (PDB ID: 4BCF), highlighting the essential role of molecular dynamics simulation in capturing a plausible binding pose bridging docking and absolute binding free energy calculations. Finally, structural modifications based on these findings further enhanced the binding affinity with CDK9. The results revealed that enhancing the molecule's rigidity through ring formation, while maintaining the major interactions, reduced the entropy loss during the binding process and, thus, enhanced binding affinities.
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Affiliation(s)
- Shipeng Wang
- School of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China.
| | - Fengjiao Liu
- School of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China.
| | - Pengfei Li
- Single Particle, LLC, 10531 4S Commons Dr 166-629, San Diego, CA 92127, USA
| | - Jia-Ning Wang
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
| | - Yan Mo
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Bin Lin
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China.
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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6
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Stecoza CE, Nitulescu GM, Draghici C, Caproiu MT, Hanganu A, Olaru OT, Mihai DP, Bostan M, Mihaila M. Synthesis of 1,3,4-Thiadiazole Derivatives and Their Anticancer Evaluation. Int J Mol Sci 2023; 24:17476. [PMID: 38139304 PMCID: PMC10743895 DOI: 10.3390/ijms242417476] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Thiadiazole derivatives have garnered significant attention in the field of medicinal chemistry due to their diverse pharmacological activities, including anticancer properties. This article presents the synthesis of a series of thiadiazole derivatives and investigates their chemical characterization and potential anticancer effects on various cell lines. The results of the nuclear magnetic resonance (NMR) analyses confirmed the successful formation of the target compounds. The anticancer potential was evaluated through in silico and in vitro cell-based assays using LoVo and MCF-7 cancer lines. The assays included cell viability, proliferation, apoptosis, and cell cycle analysis to assess the compounds' effects on cancer cell growth and survival. Daphnia magna was used as an invertebrate model for the toxicity evaluation of the compounds. The results revealed promising anticancer activity for several of the synthesized derivatives, suggesting their potential as lead compounds for further drug development. The novel compound 2g, 5-[2-(benzenesulfonylmethyl)phenyl]-1,3,4-thiadiazol-2-amine, demonstrated good anti-proliferative effects, exhibiting an IC50 value of 2.44 µM against LoVo and 23.29 µM against MCF-7 after a 48-h incubation and little toxic effects in the Daphnia test.
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Affiliation(s)
- Camelia Elena Stecoza
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (C.E.S.); (O.T.O.); (D.P.M.)
| | - George Mihai Nitulescu
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (C.E.S.); (O.T.O.); (D.P.M.)
| | - Constantin Draghici
- “Costin D. Neniţescu” Institute of Organic and Supramolecular Chemistry, Romanian Academy, 202B Splaiul Independenţei, 060023 Bucharest, Romania (A.H.)
| | - Miron Teodor Caproiu
- “Costin D. Neniţescu” Institute of Organic and Supramolecular Chemistry, Romanian Academy, 202B Splaiul Independenţei, 060023 Bucharest, Romania (A.H.)
| | - Anamaria Hanganu
- “Costin D. Neniţescu” Institute of Organic and Supramolecular Chemistry, Romanian Academy, 202B Splaiul Independenţei, 060023 Bucharest, Romania (A.H.)
| | - Octavian Tudorel Olaru
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (C.E.S.); (O.T.O.); (D.P.M.)
| | - Dragos Paul Mihai
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (C.E.S.); (O.T.O.); (D.P.M.)
| | - Marinela Bostan
- Stefan S. Nicolau Institute of Virology, 285 Mihai Bravu Street, 030304 Bucharest, Romania; (M.B.); (M.M.)
| | - Mirela Mihaila
- Stefan S. Nicolau Institute of Virology, 285 Mihai Bravu Street, 030304 Bucharest, Romania; (M.B.); (M.M.)
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Husseiny EM, Abulkhair HS, El-Hddad SS, Osama N, El-Zoghbi MS. Aminopyridone-linked benzimidazoles: a fragment-based drug design for the development of CDK9 inhibitors. Future Med Chem 2023; 15:1213-1232. [PMID: 37584185 DOI: 10.4155/fmc-2023-0139] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023] Open
Abstract
Aim: A fragment-based design and synthesis of three novel series of aminopyridone-linked benzimidazoles as potential anticancer candidates with significant CDK9 inhibition was implemented. Materials & methods: All synthesized compounds were submitted to National Cancer Institute, 60 cell lines and seven-dose cytotoxicity toward three cancer cells. Results: Compounds 2, 4a, 4c, 4d, 6a and 8a exhibited significant cytotoxicity and selectivity with IC50 range of 7.61-57.75 μM. Regarding the mechanism either in vitro or in silico, 4a, 6a and 8a displayed potent CDK9 inhibition with IC50 value of 0.424-8.461 μM. Compound 6a arrested the cell cycle at S phase and induced apoptosis in MCF-7 cells. Conclusion: Compound 6a is a promising CDK9 inhibitor that warrants additional research for cancer treatment.
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Affiliation(s)
- Ebtehal M Husseiny
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy (Girls), Al-Azhar University, Nasr City, Cairo, 11754, Egypt
| | - Hamada S Abulkhair
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Nasr City, Cairo, 11884, Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Horus University - Egypt, New Damietta, 34518, Egypt
| | - Sanadelaslam Sa El-Hddad
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Omar Almukhtar University, Al Bayda, 102345, Libya
| | - Nada Osama
- Biochemistry Department, Faculty of Pharmacy, Menoufia University, Shibin Elkom, Menoufia, 32511, Egypt
| | - Mona S El-Zoghbi
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Menoufia University, Shebin El-Koum, 32511, Egypt
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8
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Fanta BS, Lenjisa J, Teo T, Kou L, Mekonnen L, Yang Y, Basnet SKC, Hassankhani R, Sykes MJ, Yu M, Wang S. Discovery of N,4-Di(1H-pyrazol-4-yl)pyrimidin-2-amine-Derived CDK2 Inhibitors as Potential Anticancer Agents: Design, Synthesis, and Evaluation. Molecules 2023; 28:molecules28072951. [PMID: 37049714 PMCID: PMC10096391 DOI: 10.3390/molecules28072951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/16/2023] [Accepted: 03/19/2023] [Indexed: 03/29/2023] Open
Abstract
Cyclin-dependent kinase 2 (CDK2) has been garnering considerable interest as a target to develop new cancer treatments and to ameliorate resistance to CDK4/6 inhibitors. However, a selective CDK2 inhibitor has yet to be clinically approved. With the desire to discover novel, potent, and selective CDK2 inhibitors, the phenylsulfonamide moiety of our previous lead compound 1 was bioisosterically replaced with pyrazole derivatives, affording a novel series of N,4-di(1H-pyrazol-4-yl)pyrimidin-2-amines that exhibited potent CDK2 inhibitory activity. Among them, 15 was the most potent CDK2 inhibitor (Ki = 0.005 µM) with a degree of selectivity over other CDKs tested. Meanwhile, this compound displayed sub-micromolar antiproliferative activity against a panel of 13 cancer cell lines (GI50 = 0.127–0.560 μM). Mechanistic studies in ovarian cancer cells revealed that 15 reduced the phosphorylation of retinoblastoma at Thr821, arrested cells at the S and G2/M phases, and induced apoptosis. These results accentuate the potential of the N,4-di(1H-pyrazol-4-yl)pyrimidin-2-amine scaffold to be developed into potent and selective CDK2 inhibitors for the treatment of cancer.
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9
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Liu Y, Wei Y, Wang X, Ma L, Li X, Sun Y, Wu Y, Zhang L, Wang J, Li M, Zhang K, Wei M, Yang G, Yang C. Discovery of novel and bioavailable histone deacetylases and cyclin-dependent kinases dual inhibitor to impair the stemness of leukemia cells. Eur J Med Chem 2023; 249:115140. [PMID: 36736154 DOI: 10.1016/j.ejmech.2023.115140] [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: 10/19/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Acute myeloid leukemia (AML) has been confirmed as one of the most lethal heterogeneous clonal diseases. In addition to being essential for the development and progression of leukemia, leukemic stem cells (LSCs), a subpopulation of leukemia cells with stem cell characteristics, are also primarily responsible for the development of leukemia relapse and drug resistance. Elimination of stemness and induction of AML cell differentiation would become a promising and effective therapeutic strategy. In the present study, a novel class of HDACs/CDKs dual inhibitors was prepared and optimized. An active compound 33a has been identified, which exhibited potent and selective inhibition of CDK9, CDK12, CDK13, HDAC1, HDAC2 and HDAC3 at low nanomolar concentrations and significantly induced differentiation of leukemic stem-like cells and inhibited AML proliferation. Furthermore, the lead compound has relatively adequate oral bioavailability, suggesting that it might be used as a novel strategy to reduce the burden of LSCs and improve the prognosis for AML.
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Affiliation(s)
- Yulin Liu
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, PR China
| | - Yujiao Wei
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, PR China
| | - Xuan Wang
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, PR China
| | - Lan Ma
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, PR China
| | - Xuechun Li
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, PR China
| | - Yue Sun
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, PR China
| | - Yanjie Wu
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, PR China
| | - Li Zhang
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen, Guangdong, 518000, PR China
| | - Jiefu Wang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, PR China.
| | - Ming Li
- Cangzhou Institutes for Food and Drug Control, Cangzhou, 061000, PR China.
| | - Kun Zhang
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, PR China.
| | - Mingming Wei
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, PR China.
| | - Guang Yang
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, PR China.
| | - Cheng Yang
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, PR China.
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10
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Fanta BS, Mekonnen L, Basnet SKC, Teo T, Lenjisa J, Khair NZ, Kou L, Tadesse S, Sykes MJ, Yu M, Wang S. 2-Anilino-4-(1-methyl-1H-pyrazol-4-yl)pyrimidine-derived CDK2 inhibitors as anticancer agents: Design, synthesis & evaluation. Bioorg Med Chem 2023; 80:117158. [PMID: 36706608 DOI: 10.1016/j.bmc.2023.117158] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/03/2023] [Accepted: 01/07/2023] [Indexed: 01/12/2023]
Abstract
Deregulation of cyclin-dependent kinase 2 (CDK2) and its activating partners, cyclins A and E, is associated with the pathogenesis of a myriad of human cancers and with resistance to anticancer drugs including CDK4/6 inhibitors. Thus, CDK2 has become an attractive target for the development of new anticancer therapies and for the amelioration of the resistance to CDK4/6 inhibitors. Bioisosteric replacement of the thiazole moiety of CDKI-73, a clinically trialled CDK inhibitor, by a pyrazole group afforded 9 and 19 that displayed potent CDK2-cyclin E inhibition (Ki = 0.023 and 0.001 μM, respectively) with submicromolar antiproliferative activity against a panel of cancer cell lines (GI50 = 0.025-0.780 μM). Mechanistic studies on 19 with HCT-116 colorectal cancer cells revealed that the compound reduced the phosphorylation of retinoblastoma at Ser807/811, arrested the cells at the G2/M phase, and induced apoptosis. These results highlight the potential of the 2-anilino-4-(1-methyl-1H-pyrazol-4-yl)pyrimidine series in developing potent and selective CDK2 inhibitors to combat cancer.
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Affiliation(s)
- Biruk Sintayehu Fanta
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Laychiluh Mekonnen
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Sunita K C Basnet
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Theodosia Teo
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Jimma Lenjisa
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Nishat Z Khair
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Lianmeng Kou
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Solomon Tadesse
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Matthew J Sykes
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Mingfeng Yu
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia.
| | - Shudong Wang
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia.
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11
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Chen R, Hassankhani R, Long Y, Basnet SKC, Teo T, Yang Y, Mekonnen L, Yu M, Wang S. Discovery of Potent Inhibitors of Cyclin-Dependent Kinases 7 and 9: Design, Synthesis, Structure-Activity Relationship Analysis and Biological Evaluation. ChemMedChem 2023; 18:e202200582. [PMID: 36400715 DOI: 10.1002/cmdc.202200582] [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: 10/31/2022] [Revised: 11/17/2022] [Indexed: 11/21/2022]
Abstract
Cyclin-dependent kinases (CDKs) 7 and 9 are deregulated in various types of human cancer and are thus viewed as therapeutic targets. Accordingly, small-molecule inhibitors of both CDKs are highly sought-after. Capitalising on our previous discovery of CDKI-73, a potent CDK9 inhibitor, medicinal chemistry optimisation was pursued. A number of N-pyridinylpyrimidin-2-amines were rationally designed, chemically synthesised and biologically assessed. Among them, N-(6-(4-cyclopentylpiperazin-1-yl)pyridin-3-yl)-4-(imidazo[1,2-a]pyrimidin-3-yl)pyrimidin-2-amine was found to be one of the most potent inhibitors of CDKs 7 and 9 as well as the most effective anti-proliferative agent towards multiple human cancer cell lines. The cellular mode of action of this compound was investigated in MV4-11 acute myeloid leukaemia cells, revealing that the compound dampened the kinase activity of cellular CDKs 7 and 9, arrested the cell cycle at sub-G1 phase and induced apoptosis.
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Affiliation(s)
- Renjie Chen
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | - Ramin Hassankhani
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | - Yi Long
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | - Sunita K C Basnet
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | - Theodosia Teo
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | - Yuchao Yang
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | - Laychiluh Mekonnen
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | - Mingfeng Yu
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | - Shudong Wang
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
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12
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D'costa M, Bothe A, Das S, Udhaya Kumar S, Gnanasambandan R, George Priya Doss C. CDK regulators—Cell cycle progression or apoptosis—Scenarios in normal cells and cancerous cells. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 135:125-177. [PMID: 37061330 DOI: 10.1016/bs.apcsb.2022.11.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Serine/threonine kinases called cyclin-dependent kinases (CDKs) interact with cyclins and CDK inhibitors (CKIs) to control the catalytic activity. CDKs are essential controllers of RNA transcription and cell cycle advancement. The ubiquitous overactivity of the cell cycle CDKs is caused by a number of genetic and epigenetic processes in human cancer, and their suppression can result in both cell cycle arrest and apoptosis. This review focused on CDKs, describing their kinase activity, their role in phosphorylation inhibition, and CDK inhibitory proteins (CIP/KIP, INK 4, RPIC). We next compared the role of different CDKs, mainly p21, p27, p57, p16, p15, p18, and p19, in the cell cycle and apoptosis in cancer cells with respect to normal cells. The current work also draws attention to the use of CDKIs as therapeutics, overcoming the pharmacokinetic barriers of pan-CDK inhibitors, analyze new chemical classes that are effective at attacking the CDKs that control the cell cycle (cdk4/6 or cdk2). It also discusses CDKI's drawbacks and its combination therapy against cancer patients. These findings collectively demonstrate the complexity of cancer cell cycles and the need for targeted therapeutic intervention. In order to slow the progression of the disease or enhance clinical outcomes, new medicines may be discovered by researching the relationship between cell death and cell proliferation.
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Affiliation(s)
- Maria D'costa
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Anusha Bothe
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Soumik Das
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - S Udhaya Kumar
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - R Gnanasambandan
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India.
| | - C George Priya Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India.
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13
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Synthesis, Cytotoxic Evaluation, and Structure-Activity Relationship of Substituted Quinazolinones as Cyclin-Dependent Kinase 9 Inhibitors. Molecules 2022; 28:molecules28010120. [PMID: 36615314 PMCID: PMC9822073 DOI: 10.3390/molecules28010120] [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: 11/10/2022] [Revised: 12/04/2022] [Accepted: 12/06/2022] [Indexed: 12/28/2022] Open
Abstract
Cyclin-dependent kinase 9 (CDK9) plays a critical role in transcriptional elongation, through which short-lived antiapoptotic proteins are overexpressed and make cancer cells resistant to apoptosis. Therefore, CDK9 inhibition depletes antiapoptotic proteins, which in turn leads to the reinstatement of apoptosis in cancer cells. Twenty-seven compounds were synthesized, and their CDK9 inhibitory and cytotoxic activities were evaluated. Compounds 7, 9, and 25 were the most potent CDK9 inhibitors, with IC50 values of 0.115, 0.131, and 0.142 μM, respectively. The binding modes of these molecules were studied via molecular docking, which shows that they occupy the adenosine triphosphate binding site of CDK9. Of these three molecules, compound 25 shows good drug-like properties, as it does not violate Lipinski's rule of five. In addition, this molecule shows promising ligand and lipophilic efficiency values and is an ideal candidate for further optimization.
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14
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Design, synthesis and anticancer evaluation of selective 2,4-disubstituted pyrimidine CDK9 inhibitors. Eur J Med Chem 2022; 244:114875. [DOI: 10.1016/j.ejmech.2022.114875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/16/2022] [Accepted: 10/20/2022] [Indexed: 11/30/2022]
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15
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Islam S, Teo T, Kumarasiri M, Slater M, Martin JH, Wang S, Head R. Combined In Silico and In Vitro Evidence Supporting an Aurora A Kinase Inhibitory Role of the Anti-Viral Drug Rilpivirine and an Anti-Proliferative Influence on Cancer Cells. Pharmaceuticals (Basel) 2022; 15:ph15101186. [PMID: 36297298 PMCID: PMC9607353 DOI: 10.3390/ph15101186] [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: 07/11/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 11/20/2022] Open
Abstract
The global burden of cancer necessitates rapid and ongoing development of effective cancer therapies. One promising approach in this context is the repurposing of existing non-cancer drugs for cancer indications. A key to this approach is selecting the cellular targets against which to identify novel repurposed drugs for pre-clinical analysis. Protein kinases are highly sought-after anticancer drug targets since dysregulation of kinases is the hallmark of cancer. To identify potential kinase-targeted drug candidates from the existing portfolio of non-cancer therapeutics, we used combined in silico and in vitro approaches, including ligand-based 3D screening followed by biochemical and cellular assessments. This strategy revealed that the anti-viral drug rilpivirine is an Aurora A kinase inhibitor. In view of previous findings implicating Aurora A kinase in abnormal cell cycle regulation, we also examined the influence of rilpivirine on the growth of T47D breast cancer cells. Herein, we detail the identification of rilpivirine as an Aurora A kinase inhibitor, its molecular basis of inhibitory activity towards this kinase, and its Aurora A-mediated anticancer mechanisms in T47D cells. Our results illustrate the value of integrated in silico and in vitro screening strategies in identifying repurposed drug candidates and provide a scientific basis for further exploring the potential anticancer properties of the anti-viral drug rilpivirine.
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Affiliation(s)
- Saiful Islam
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
| | - Theodosia Teo
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
| | - Malika Kumarasiri
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
| | - Martin Slater
- Cresset Discovery, New Cambridge House, Litlington, Royston SG8 0SS, UK
| | - Jennifer H. Martin
- Centre for Human Drug Repurposing and Medicines Research, University of Newcastle, Newcastle, NSW 2305, Australia
| | - Shudong Wang
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
| | - Richard Head
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
- Correspondence:
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16
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Fedinchyk A, Herasymchuk M, Smirnov VO, Melnykov KP, Yarmoliuk DV, Kyrylchuk AA, Grygorenko OO. Fluorine‐containing sp³‐Enriched Building Blocks for the Multigram Synthesis of Fluorinated Pyrazoles and Pyrimidines with (Hetero)aliphatic Substituents. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | | | | | - Kostiantyn P. Melnykov
- Taras Shevchenko National University of Kyiv: Kiivs'kij nacional'nij universitet imeni Tarasa Sevcenka Chemical Faculty UKRAINE
| | | | - Andrii A. Kyrylchuk
- Institute of Organic Chemistry National Academy of Sciences of Ukraine: Institut organicnoi himii Nacional'na akademia nauk Ukraini Department of Physico-Chemical Methods of Investigation UKRAINE
| | - Oleksandr O Grygorenko
- Taras Shevchenko National University of Kyiv: Kiivs'kij nacional'nij universitet imeni Tarasa Sevcenka Chemical Faculty UKRAINE
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17
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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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18
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Ettl T, Schulz D, Bauer RJ. The Renaissance of Cyclin Dependent Kinase Inhibitors. Cancers (Basel) 2022; 14:293. [PMID: 35053461 PMCID: PMC8773807 DOI: 10.3390/cancers14020293] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/29/2021] [Accepted: 01/04/2022] [Indexed: 12/14/2022] Open
Abstract
Cyclin-dependent kinases (CDK) regulate cell cycle progression. During tumor development, altered expression and availability of CDKs strongly contribute to impaired cell proliferation, a hallmark of cancer. In recent years, targeted inhibition of CDKs has shown considerable therapeutic benefit in a variety of tumor entities. Their success is reflected in clinical approvals of specific CDK4/6 inhibitors for breast cancer. This review provides a detailed insight into the molecular mechanisms of CDKs as well as a general overview of CDK inhibition. It also summarizes the latest research approaches and current advances in the treatment of head and neck cancer with CDK inhibitors. Instead of monotherapies, combination therapies with CDK inhibitors may especially provide promising results in tumor therapy. Indeed, recent studies have shown a synergistic effect of CDK inhibition together with chemo- and radio- and immunotherapy in cancer treatment to overcome tumor evasion, which may lead to a renaissance of CDK inhibitors.
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Affiliation(s)
- Tobias Ettl
- Department of Oral and Maxillofacial Surgery, University Hospital Regensburg, 93053 Regensburg, Germany;
| | - Daniela Schulz
- Department of Oral and Maxillofacial Surgery, University Hospital Regensburg, 93053 Regensburg, Germany;
- Center for Medical Biotechnology, Department of Oral and Maxillofacial Surgery, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Richard Josef Bauer
- Department of Oral and Maxillofacial Surgery, University Hospital Regensburg, 93053 Regensburg, Germany;
- Center for Medical Biotechnology, Department of Oral and Maxillofacial Surgery, University Hospital Regensburg, 93053 Regensburg, Germany
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19
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Huang Z, Wang T, Wang C, Fan Y. CDK9 Inhibitors in Cancer Research. RSC Med Chem 2022; 13:688-710. [PMID: 35814933 PMCID: PMC9215160 DOI: 10.1039/d2md00040g] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/16/2022] [Indexed: 11/21/2022] Open
Abstract
Cyclin dependent kinase 9 (CDK9) played an essential role in regulating transcriptional elongation. Aberrations in CDK9 activity have been observed in various cancers, which made CDK9 was an attractive therapeutic...
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Affiliation(s)
- Zhi Huang
- Department of Medicinal Chemistry, School of Medicine, Nankai University 94 Weijin Road Tianjin 300071 China
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences Hefei 230031 China
| | - Tianqi Wang
- Department of Medicinal Chemistry, School of Medicine, Nankai University 94 Weijin Road Tianjin 300071 China
| | - Cheng Wang
- Department of Medicinal Chemistry, School of Medicine, Nankai University 94 Weijin Road Tianjin 300071 China
| | - Yan Fan
- Department of Medicinal Chemistry, School of Medicine, Nankai University 94 Weijin Road Tianjin 300071 China
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20
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Bangade VM, Dadmal TL, Popatkar BB, Mali PR, Meshram HM. One Pot Catalyst‐free Synthesis of Substituted Di‐amino N‐tosyl Benzoyl Thiazoles byRegioselective C−N Bond Cleavage and Its Anticancer Activity. ASIAN J ORG CHEM 2021. [DOI: 10.1002/ajoc.202100675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Vikas M. Bangade
- Department of Chemistry The Institute of Science, Mumbai Dr.HomiBhabha State University Mumbai 15, Madame Cama Road Mumbai-32 400 032 India
- Medicinal Chemistry and Pharmacology Division CSIR-Indian Institute of Chemical Technology, Hyderabad Uppal Road, Tarnaka Hyderabad Telangana 500007 India
| | - Tulshiram L. Dadmal
- Department of Chemistry Government Vidarbha Institute of Science and Humanities Amravati Maharashtra 444604 India
| | - Bhushan B. Popatkar
- Department of Chemistry University of Mumbai Vidyanagari, Kalina, Santacruz (E) Mumbai Maharashtra 400 098 India
| | - Prakash R. Mali
- Medicinal Chemistry and Pharmacology Division CSIR-Indian Institute of Chemical Technology, Hyderabad Uppal Road, Tarnaka Hyderabad Telangana 500007 India
| | - Harshadas M. Meshram
- Medicinal Chemistry and Pharmacology Division CSIR-Indian Institute of Chemical Technology, Hyderabad Uppal Road, Tarnaka Hyderabad Telangana 500007 India
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21
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Mehranpour A, Sheikhi E, Jahromi EB, Samani ZR. Synthesis of novel Schiff bases as stable enol‐imine‐containing diazene bonds and pyrimidines using trimethinium salts. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | - Elham Sheikhi
- Department of Chemistry, Faculty of Sciences Persian Gulf University Bushehr Iran
| | | | - Ziba Rafiee Samani
- Department of Chemistry, Faculty of Sciences Persian Gulf University Bushehr Iran
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22
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Han X, Song N, Saidahmatov A, Wang P, Wang Y, Hu X, Kan W, Zhu W, Gao L, Zeng M, Wang Y, Li C, Li J, Liu H, Zhou Y, Wang J. Rational Design and Development of Novel CDK9 Inhibitors for the Treatment of Acute Myeloid Leukemia. J Med Chem 2021; 64:14647-14663. [PMID: 34477384 DOI: 10.1021/acs.jmedchem.1c01148] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
CDK9 is an essential drug target correlated to the development of acute myeloid leukemia (AML). Starting from the hit compound 10, which was discovered through a screening of our in-house compound library, the structural modifications were carried out based on the bioisosterism and scaffold hopping strategies. Consequently, compound 37 displayed the optimal CDK9 inhibitory activity with an IC50 value of 5.41 nM, which was nearly 1500-fold higher than compound 10. In addition, compound 37 exhibited significant antiproliferative activity in broad cancer cell lines. Further investigation of in vivo properties demonstrated that compound 37 could be orally administrated with an acceptable bioavailability (F = 33.7%). In MV-4-11 subcutaneous xenograft mouse model, compound 37 (7.5 mg/kg) could significantly suppress the tumor progression with a T/C value of 27.80%. Compound 37 represents a promising lead compound for the development of a novel class of CDK9 inhibitors for the treatment of acute myeloid leukemia.
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Affiliation(s)
- Xu Han
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Ning Song
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.,School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Abdusaid Saidahmatov
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Peipei Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Yong Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Xiaobei Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.,Zhongshan Institute of Drug Discovery, Institution for Drug Discovery Innovation, Chinese Academy of Science, Zhongshan 528400, China
| | - Weijuan Kan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Wei Zhu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Lixin Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Mingjie Zeng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Yujie Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Chunpu Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.,School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China.,Zhongshan Institute of Drug Discovery, Institution for Drug Discovery Innovation, Chinese Academy of Science, Zhongshan 528400, China
| | - Hong Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.,School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Yubo Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.,Zhongshan Institute of Drug Discovery, Institution for Drug Discovery Innovation, Chinese Academy of Science, Zhongshan 528400, China
| | - Jiang Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
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23
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Mahapatra A, Prasad T, Sharma T. Pyrimidine: a review on anticancer activity with key emphasis on SAR. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2021. [DOI: 10.1186/s43094-021-00274-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Abstract
Background
Cancer is a global health challenge, it impacts the quality of life and its treatment is associated with several side effects. Resistance of the cancer cells to the existing drugs has led to search for novel anticancer agents. Pyrimidine, a privileged scaffold, is part of living organisms and plays vital role in various biological procedures as well as in cancer pathogenesis. Due to resemblance in structure with the nucleotide base pair of DNA and RNA, it is recognized as valuable compound in the treatment of cancer.
Main text
Many novel pyrimidine derivatives have been designed and developed for their anticancer activity in the last few years. The present review aims to focus on the structure activity relationship (SAR) of pyrimidine derivatives as anticancer agent from the last decade.
Conclusion
This review intends to assist in the development of more potent and efficacious anticancer drugs with pyrimidine scaffold.
Graphical abstract
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24
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Lee JB, Zang X, Zgair A, Ooi TQ, Foley DW, Voronin G, Kagan L, Soukarieh F, Gao R, Shao H, Soh WT, Kim TH, Kim MG, Yun HY, Wilson AJ, Fischer PM, Gershkovich P. Administration in fed state but not controlled release in the colon increases oral bioavailability of DF030263, a promising drug candidate for chronic lymphocytic leukemia. Eur J Pharm Biopharm 2021; 165:106-112. [PMID: 33991611 DOI: 10.1016/j.ejpb.2021.05.006] [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: 04/05/2021] [Accepted: 05/04/2021] [Indexed: 11/17/2022]
Abstract
For treatment of chronic cancers, the oral administration route is preferred as it provides numerous advantages over other delivery routes. However, these benefits of oral chemotherapy can be limited due to unfavorable pharmacokinetics. Accordingly, pharmacokinetic development of chemotherapeutic agents is crucial to the improvement of cancer treatment. In this study, assessment and optimization of biopharmaceutical properties of a promising drug candidate for cyclin-dependent kinase 9 (CDK9) inhibitor (DF030263) was performed to promote oral delivery. Oral bioavailability of DF030263 in fasted rats was 23.8%, and a distinct double-peak phenomenon was observed. A two-site absorption windows mechanism was proposed as a possible explanation to the phenomenon. The two-site absorption window hypothesis was supported by in vitro solubility assays in biorelevant fluids with different pH levels, as well as by in silico simulation by GastroPlus™. Controlled release to the colon was conducted in rats in order to exploit the colonic absorption window but did not improve the oral bioavailability. On the other hand, oral administration at postprandial conditions in rats (performed based on the high in vitro solubility in fed state simulated fluid and reduced pH-dependency) resulted in an almost 3-fold increase in bioavailability to 63.6%. In conclusion, this study demonstrates an efficient in vitro-in vivo-in silico drug development approach for improving the oral bioavailability of DF030263, a promising candidate for the treatment of chronic lymphocytic leukemia.
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Affiliation(s)
- Jong Bong Lee
- School of Pharmacy & Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
| | - Xiaowei Zang
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Atheer Zgair
- School of Pharmacy & Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK; College of Pharmacy, University of Anbar, Anbar, Iraq
| | - Ting Qian Ooi
- School of Pharmacy & Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
| | - David W Foley
- School of Pharmacy & Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
| | - Gregory Voronin
- Comparative Medicine Resources, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Leonid Kagan
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Fadi Soukarieh
- School of Pharmacy & Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
| | - Rui Gao
- School of Pharmacy & Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
| | - Hao Shao
- School of Pharmacy & Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK; Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wan Tying Soh
- School of Pharmacy & Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
| | - Tae Hwan Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Min Gi Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Hwi-Yeol Yun
- College of Pharmacy, Chungnam National University, Daejeon, Republic of Korea
| | - Anthony J Wilson
- School of Pharmacy & Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
| | - Peter M Fischer
- School of Pharmacy & Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
| | - Pavel Gershkovich
- School of Pharmacy & Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK.
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25
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Bangade VM, Mali PR, Meshram HM. Synthesis of Potent Anticancer Substituted 5-Benzimidazol-2-amino Thiazoles Controlled by Bifunctional Hydrogen Bonding under Microwave Irradiations. J Org Chem 2021; 86:6056-6065. [PMID: 33872008 DOI: 10.1021/acs.joc.0c02542] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Benzimidazol-amino thiazoles are synthesized under microwave irradiations using benzimidazole phenyl thiourea and 2-bromoacetophenone. Bifunctional hydrogen bonding plays an important role in chemical conversion. The reaction was carried out by C-C bond formation, followed by C-N bond cleavage and simultaneous migration of the benzimidazole ring. This reaction is novel and efficient for the synthesis of benzimidazol-amino thiazoles in which microwaves were used as driving forces. Synthesis of the product was controlled by double hydrogen bonding which is practically confirmed by the synthesis of routine imino-thiazole as an alternative product in the simple acidic condition. The simple acidic condition is neither responsible nor sufficient for optimum conversion of the benzimidazole migrated product. The synthesized products benzimidazole amino thiazoles D4 (IC50 = 4.207 μM) and D8 (IC50 = 2.398 μM) show interesting anticancer activities for human lung cancer with reference to doxorubicin (IC50 = 1.750 μM).
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Affiliation(s)
- Vikas M Bangade
- Medicinal Chemistry and Pharmacology Division, Indian Institute of Chemical Technology, Hyderabad, 500 607, India.,Department of Chemistry, The Institute of Science, Mumbai, Dr. Homi Bhabha State University, Mumbai, 15, Madame Cama Road, Mumbai, 32, India
| | - Prakash R Mali
- Medicinal Chemistry and Pharmacology Division, Indian Institute of Chemical Technology, Hyderabad, 500 607, India
| | - Harshadas M Meshram
- Medicinal Chemistry and Pharmacology Division, Indian Institute of Chemical Technology, Hyderabad, 500 607, India
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26
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Bhagat DS, Chawla PA, Gurnule WB, Shejul SK, Bumbrah GS. An Insight into Synthesis and Anticancer Potential of Thiazole and 4-thiazolidinone Containing Motifs. CURR ORG CHEM 2021. [DOI: 10.2174/1385272825999210101234704] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Over the years, the branch of oncology has reached a mature stage, and substantial
development and advancement have been achieved in this dimension of medical science. The
synthesis and isolation of numerous novel anticancer agents of natural and synthetic origins
have been reported. Thiazole and 4-thiazolidinone containing heterocyclic compounds, having
a broad spectrum of pharmaceutical activities, represent a significant class of medicinal
chemistry. Thiazole and 4-thiazolidinone are five-membered unique heterocyclic motifs containing
S and N atoms as an essential core scaffold and have commendable medicinal significance.
Thiazoles and 4-thiazolidinones containing heterocyclic compounds are used as building
blocks for the next generation of pharmaceuticals. Thiazole precursors have been frequently
used due to their capabilities to bind to numerous cancer-specific protein targets.
Suitably, thiazole motifs have a biological suit via inhibition of different signaling pathways involved in cancer
causes. The scientific community has always tried to synthesize novel thiazole-based heterocycles by carrying out
different replacements of functional groups or skeleton around thiazole moiety. Herein, we report the current trend of
research and development in anticancer activities of thiazoles and 4-thiazolidinones containing scaffolds. In the current
study, we have also highlighted some other significant biological properties of thiazole, novel protocols of synthesis
for the synthesis of the new candidates, along with a significant broad spectrum of the anticancer activities of
thiazole containing scaffolds. This study facilitates the development of novel thiazole and 4-thiazolidinone containing
candidates with potent, efficient anticancer activity and less cytotoxic property.
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Affiliation(s)
- Devidas S. Bhagat
- Department of Forensic Chemistry and Toxicology, Government Institute of Forensic Science, Aurangabad 431 004, (MS), India
| | - Pooja A. Chawla
- Department of Pharmaceutical Chemistry and Analysis, ISF College of Pharmacy, Moga 142001, Punjab, India
| | - Wasudeo B. Gurnule
- Department of Chemistry, Kamla Nehru Mahavidyalaya, Nagpur-440024, (MS), India
| | - Sampada K. Shejul
- Department of Life Science, Vivekanand Arts, Sardar Dalipsingh Commerce and Science College, Aurangabad 431 001, (MS), India
| | - Gurvinder S. Bumbrah
- Department of Chemistry, Biochemistry and Forensic Science, Amity School of Applied Sciences, Amity University, 122413, Haryana, India
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27
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Discovery of a potent, highly selective, and orally bioavailable inhibitor of CDK8 through a structure-based optimisation. Eur J Med Chem 2021; 218:113391. [PMID: 33823391 DOI: 10.1016/j.ejmech.2021.113391] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 12/24/2022]
Abstract
CDK8 is deregulated in multiple types of human cancer and is viewed as a therapeutic target for the treatment of the disease. Accordingly, the search for small-molecule inhibitors of CDK8 is being intensified. Capitalising on our initial discovery of AU1-100, a potent CDK8 inhibitor yet with a limited degree of kinase selectivity, a structure-based optimisation was carried out, with a series of new multi-substituted pyridines rationally designed, chemically prepared and biologically evaluated. Such endeavour has culminated in the identification of 42, a more potent CDK8 inhibitor with superior kinomic selectivity and oral bioavailability. The mechanism underlying the anti-proliferative effect of 42 on MV4-11 cells was studied, revealing that the compound arrested the G1 cell cycle and triggered apoptosis. The low risk of hepato- and cardio-toxicity of 42 was estimated. These findings merit further investigation of 42 as a targeted cancer therapeutic.
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28
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Broni E, Kwofie SK, Asiedu SO, Miller WA, Wilson MD. A Molecular Modeling Approach to Identify Potential Antileishmanial Compounds Against the Cell Division Cycle (cdc)-2-Related Kinase 12 (CRK12) Receptor of Leishmania donovani. Biomolecules 2021; 11:458. [PMID: 33803906 PMCID: PMC8003136 DOI: 10.3390/biom11030458] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/12/2021] [Accepted: 03/14/2021] [Indexed: 12/11/2022] Open
Abstract
The huge burden of leishmaniasis caused by the trypanosomatid protozoan parasite Leishmania is well known. This illness was included in the list of neglected tropical diseases targeted for elimination by the World Health Organization. However, the increasing evidence of resistance to existing antimonial drugs has made the eradication of the disease difficult to achieve, thus warranting the search for new drug targets. We report here studies that used computational methods to identify inhibitors of receptors from natural products. The cell division cycle-2-related kinase 12 (CRK12) receptor is a plausible drug target against Leishmania donovani. This study modelled the 3D molecular structure of the L. donovani CRK12 (LdCRK12) and screened for small molecules with potential inhibitory activity from African flora. An integrated library of 7722 African natural product-derived compounds and known inhibitors were screened against the LdCRK12 using AutoDock Vina after performing energy minimization with GROMACS 2018. Four natural products, namely sesamin (NANPDB1649), methyl ellagic acid (NANPDB1406), stylopine (NANPDB2581), and sennecicannabine (NANPDB6446) were found to be potential LdCRK12 inhibitory molecules. The molecular docking studies revealed two compounds NANPDB1406 and NANPDB2581 with binding affinities of -9.5 and -9.2 kcal/mol, respectively, against LdCRK12 which were higher than those of the known inhibitors and drugs, including GSK3186899, amphotericin B, miltefosine, and paromomycin. All the four compounds were predicted to have inhibitory constant (Ki) values ranging from 0.108 to 0.587 μM. NANPDB2581, NANPDB1649 and NANPDB1406 were also predicted as antileishmanial with Pa and Pi values of 0.415 and 0.043, 0.391 and 0.052, and 0.351 and 0.071, respectively. Molecular dynamics simulations coupled with molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) computations reinforced their good binding mechanisms. Most compounds were observed to bind in the ATP binding pocket of the kinase domain. Lys488 was predicted as a key residue critical for ligand binding in the ATP binding pocket of the LdCRK12. The molecules were pharmacologically profiled as druglike with inconsequential toxicity. The identified molecules have scaffolds that could form the backbone for fragment-based drug design of novel leishmanicides but warrant further studies to evaluate their therapeutic potential.
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Affiliation(s)
- Emmanuel Broni
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana;
| | - Samuel K. Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana;
- West African Center for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 54, Ghana
| | - Seth O. Asiedu
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana; (S.O.A.); (M.D.W.)
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153, USA;
- Department of Molecular Pharmacology and Neuroscience, Loyola University Medical Center, Maywood, IL 60153, USA
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, IL 19104, USA
| | - Michael D. Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana; (S.O.A.); (M.D.W.)
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153, USA;
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29
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Ammazzalorso A, Agamennone M, De Filippis B, Fantacuzzi M. Development of CDK4/6 Inhibitors: A Five Years Update. Molecules 2021; 26:molecules26051488. [PMID: 33803309 PMCID: PMC7967197 DOI: 10.3390/molecules26051488] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 03/02/2021] [Accepted: 03/06/2021] [Indexed: 12/24/2022] Open
Abstract
The inhibition of cyclin dependent kinases 4 and 6 plays a role in aromatase inhibitor resistant metastatic breast cancer. Three dual CDK4/6 inhibitors have been approved for the breast cancer treatment that, in combination with the endocrine therapy, dramatically improved the survival outcomes both in first and later line settings. The developments of the last five years in the search for new selective CDK4/6 inhibitors with increased selectivity, treatment efficacy, and reduced adverse effects are reviewed, considering the small-molecule inhibitors and proteolysis-targeting chimeras (PROTACs) approaches, mainly pointing at structure-activity relationships, selectivity against different kinases and antiproliferative activity.
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30
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Yu M, Teo T, Yang Y, Li M, Long Y, Philip S, Noll B, Heinemann GK, Diab S, Eldi P, Mekonnen L, Anshabo AT, Rahaman MH, Milne R, Hayball JD, Wang S. Potent and orally bioavailable CDK8 inhibitors: Design, synthesis, structure-activity relationship analysis and biological evaluation. Eur J Med Chem 2021; 214:113248. [PMID: 33571827 DOI: 10.1016/j.ejmech.2021.113248] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/23/2021] [Accepted: 01/24/2021] [Indexed: 12/23/2022]
Abstract
CDK8 regulates transcription either by phosphorylation of transcription factors or, as part of a four-subunit kinase module, through a reversible association of the kinase module with the Mediator complex, a highly conserved transcriptional coactivator. Deregulation of CDK8 has been found in various types of human cancer, while the role of CDK8 in supressing anti-cancer response of natural killer cells is being understood. Currently, CDK8-targeting cancer drugs are highly sought-after. Herein we detail the discovery of a series of novel pyridine-derived CDK8 inhibitors. Medicinal chemistry optimisation gave rise to 38 (AU1-100), a potent CDK8 inhibitor with oral bioavailability. The compound inhibited the proliferation of MV4-11 acute myeloid leukaemia cells with the kinase activity of cellular CDK8 dampened. No systemic toxicology was observed in the mice treated with 38. These results warrant further pre-clinical studies of 38 as an anti-cancer agent.
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Affiliation(s)
- Mingfeng Yu
- Drug Discovery and Development, Cancer Research Institute, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Theodosia Teo
- Drug Discovery and Development, Cancer Research Institute, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Yuchao Yang
- Drug Discovery and Development, Cancer Research Institute, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Manjun Li
- Drug Discovery and Development, Cancer Research Institute, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Yi Long
- Drug Discovery and Development, Cancer Research Institute, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Stephen Philip
- Drug Discovery and Development, Cancer Research Institute, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Benjamin Noll
- Drug Discovery and Development, Cancer Research Institute, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Gary K Heinemann
- Drug Discovery and Development, Cancer Research Institute, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Sarah Diab
- Drug Discovery and Development, Cancer Research Institute, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Preethi Eldi
- Experimental Therapeutics, Cancer Research Institute, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Laychiluh Mekonnen
- Drug Discovery and Development, Cancer Research Institute, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Abel T Anshabo
- Drug Discovery and Development, Cancer Research Institute, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Muhammed H Rahaman
- Drug Discovery and Development, Cancer Research Institute, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Robert Milne
- Drug Discovery and Development, Cancer Research Institute, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia
| | - John D Hayball
- Experimental Therapeutics, Cancer Research Institute, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Shudong Wang
- Drug Discovery and Development, Cancer Research Institute, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia.
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31
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Shao H, Foley DW, Huang S, Abbas AY, Lam F, Gershkovich P, Bradshaw TD, Pepper C, Fischer PM, Wang S. Structure-based design of highly selective 2,4,5-trisubstituted pyrimidine CDK9 inhibitors as anti-cancer agents. Eur J Med Chem 2021; 214:113244. [PMID: 33581551 DOI: 10.1016/j.ejmech.2021.113244] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/25/2021] [Accepted: 01/25/2021] [Indexed: 11/17/2022]
Abstract
Cyclin-dependent kinases (CDKs) are a family of Ser/Thr kinases involved in cell cycle and transcriptional regulation. CDK9 regulates transcriptional elongation and this unique property has made it a potential target for several diseases. Due to the conserved ATP binding site, designing selective CDK9 inhibitors has been challenging. Here we report our continued efforts in the optimization of 2,4,5-tri-substituted pyrimidine compounds as potent and selective CDK9 inhibitors. The most selective compound 30m was >100-fold selective for CDK9 over CDK1 and CDK2. These compounds showed broad anti-proliferative activities in various solid tumour cell lines and patient-derived chronic lymphocytic leukaemia (CLL) cells. Decreased phosphorylation of the carboxyl terminal domain (CTD) of RNAPII at Ser-2 and down-regulation of anti-apoptotic protein Mcl-1 were confirmed in both the ovarian cancer model A2780 and patient-derived CLL cells.
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Affiliation(s)
- Hao Shao
- School of Pharmacy and Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - David W Foley
- School of Pharmacy and Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Shiliang Huang
- School of Pharmacy and Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Abdullahi Y Abbas
- School of Pharmacy and Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Frankie Lam
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5001, Australia
| | - Pavel Gershkovich
- School of Pharmacy and Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Tracey D Bradshaw
- School of Pharmacy and Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Chris Pepper
- Brighton and Sussex Medical School, University of Sussex, Brighton, East Sussex, BN1 9PX, UK
| | - Peter M Fischer
- School of Pharmacy and Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - Shudong Wang
- School of Pharmacy and Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK; Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5001, Australia.
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32
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Long Y, Yu M, Ochnik AM, Karanjia JD, Basnet SK, Kebede AA, Kou L, Wang S. Discovery of novel 4-azaaryl-N-phenylpyrimidin-2-amine derivatives as potent and selective FLT3 inhibitors for acute myeloid leukaemia with FLT3 mutations. Eur J Med Chem 2021; 213:113215. [PMID: 33516985 DOI: 10.1016/j.ejmech.2021.113215] [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: 12/06/2020] [Revised: 01/15/2021] [Accepted: 01/15/2021] [Indexed: 01/12/2023]
Abstract
Feline McDonough sarcoma (FMS)-like tyrosine kinase 3 (FLT3) is one of the most pursued targets in the treatment of acute myeloid leukaemia (AML) as its gene amplification and mutations, particularly internal tandem duplication (ITD), contribute to the pathogenesis of AML and the resistance to known FLT3 inhibitors. To conquer this challenge, there is a quest for structurally novel FLT3 inhibitors. Herein, we report the discovery of a new series of 4-azaaryl-N-phenylpyrimidin-2-amine derivatives as potent and selective FLT3 inhibitors. Compounds 12b and 12r were capable of suppressing a wide range of mutated FLT3 kinases including ITD and D835Y mutants; the latter isoform is closely associated with acquired drug resistance. In addition, both compounds displayed an anti-proliferative specificity for FLT3-ITD-harbouring cell lines (i.e., MV4-11 and MOLM-13 cells) over those with expression of the wild-type kinase or even without FLT3 expression. In mechanistic studies using MV4-11 cells, 12b was found to diminish the phosphorylation of key downstream effectors of FLT3 and induce apoptosis, supporting an FLT3-ITD-targeted mechanism of its anti-proliferative action.
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Affiliation(s)
- Yi Long
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5001, Australia
| | - Mingfeng Yu
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5001, Australia
| | - Aleksandra M Ochnik
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5001, Australia
| | - Jasmine D Karanjia
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5001, Australia
| | - Sunita Kc Basnet
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5001, Australia
| | - Alemwork A Kebede
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5001, Australia
| | - Lianmeng Kou
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5001, Australia
| | - Shudong Wang
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5001, Australia.
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33
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Yuan K, Wang X, Dong H, Min W, Hao H, Yang P. Selective inhibition of CDK4/6: A safe and effective strategy for developing anticancer drugs. Acta Pharm Sin B 2021; 11:30-54. [PMID: 33532179 PMCID: PMC7838032 DOI: 10.1016/j.apsb.2020.05.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/27/2020] [Accepted: 05/04/2020] [Indexed: 01/02/2023] Open
Abstract
The sustained cell proliferation resulting from dysregulation of the cell cycle and activation of cyclin-dependent kinases (CDKs) is a hallmark of cancer. The inhibition of CDKs is a highly promising and attractive strategy for the development of anticancer drugs. In particular, third-generation CDK inhibitors can selectively inhibit CDK4/6 and regulate the cell cycle by suppressing the G1 to S phase transition, exhibiting a perfect balance between anticancer efficacy and general toxicity. To date, three selective CDK4/6 inhibitors have received approval from the U.S. Food and Drug Administration (FDA), and 15 CDK4/6 inhibitors are in clinical trials for the treatment of cancers. In this perspective, we discuss the crucial roles of CDK4/6 in regulating the cell cycle and cancer cells, analyze the rationale for selectively inhibiting CDK4/6 for cancer treatment, review the latest advances in highly selective CDK4/6 inhibitors with different chemical scaffolds, explain the mechanisms associated with CDK4/6 inhibitor resistance and describe solutions to overcome this issue, and briefly introduce proteolysis targeting chimera (PROTAC), a new and revolutionary technique used to degrade CDK4/6.
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Key Words
- AKT, protein kinase B
- AML, acute myeloid leukemia
- CDK4/6
- CDKs, cyclin-dependent kinases
- CIP/KIP, cyclin-dependent kinase inhibitor 1/kinase inhibitory protein
- CKIs, cyclin-dependent kinase inhibitors
- CPU, China Pharmaceutical University
- CRPC, castration-resistant prostate cancer
- Cancer
- Cell cycle
- Drug resistance
- ER, estrogen receptor
- ERK, extracellular regulated protein kinases
- FDA, U.S. Food and Drug Administration
- FLT, fms-like tyrosine kinase
- HER2, human epidermal growth factor receptor 2
- INK4, inhibitors of CDK4
- JAK, janus kinase
- MCL, mantle cell lymphoma
- MM, multiple myeloma
- NSCLC, non-small cell lung cancer
- ORR, overall response rates
- PDK1, 3-phosphoinositide-dependent protein kinase 1
- PFS, progression-free survival
- PI3K, phosphatidylinositol 3-hydroxy kinase
- PR, progesterone receptor
- PROTAC
- PROTAC, proteolysis targeting chimera
- RB, retinoblastoma protein
- SPH, Shanghai Pharmaceuticals Holding Co., Ltd.
- STATs, signal transducers and activators of transcription
- Selectivity
- UNISA, University of South Australia
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Affiliation(s)
- Kai Yuan
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xiao Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Haojie Dong
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Wenjian Min
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Haiping Hao
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Peng Yang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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Albanese SK, Chodera JD, Volkamer A, Keng S, Abel R, Wang L. Is Structure-Based Drug Design Ready for Selectivity Optimization? J Chem Inf Model 2020; 60:6211-6227. [PMID: 33119284 PMCID: PMC8310368 DOI: 10.1021/acs.jcim.0c00815] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Alchemical free-energy calculations are now widely used to drive or maintain potency in small-molecule lead optimization with a roughly 1 kcal/mol accuracy. Despite this, the potential to use free-energy calculations to drive optimization of compound selectivity among two similar targets has been relatively unexplored in published studies. In the most optimistic scenario, the similarity of binding sites might lead to a fortuitous cancellation of errors and allow selectivity to be predicted more accurately than affinity. Here, we assess the accuracy with which selectivity can be predicted in the context of small-molecule kinase inhibitors, considering the very similar binding sites of human kinases CDK2 and CDK9 as well as another series of ligands attempting to achieve selectivity between the more distantly related kinases CDK2 and ERK2. Using a Bayesian analysis approach, we separate systematic from statistical errors and quantify the correlation in systematic errors between selectivity targets. We find that, in the CDK2/CDK9 case, a high correlation in systematic errors suggests that free-energy calculations can have significant impact in aiding chemists in achieving selectivity, while in more distantly related kinases (CDK2/ERK2), the correlation in systematic error suggests that fortuitous cancellation may even occur between systems that are not as closely related. In both cases, the correlation in systematic error suggests that longer simulations are beneficial to properly balance statistical error with systematic error to take full advantage of the increase in apparent free-energy calculation accuracy in selectivity prediction.
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Affiliation(s)
- Steven K. Albanese
- Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - John D. Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Andrea Volkamer
- Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin
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Deshmukh SU, Toche RB, Takate SJ, Salve SP, Sabnis RW. Synthesis of novel thiazol‐5‐ylpyrimidine derivatives and their antimicrobial evaluation. J Heterocycl Chem 2020. [DOI: 10.1002/jhet.4116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sanjay U. Deshmukh
- Department of Chemistry KRT Arts, BH Commerce & AM Science College Nashik India
| | - Raghunath B. Toche
- Department of Chemistry Dadasheb Bidkar Arts, Science & Commerce College Peth, Nashik‐422208 India
| | - Sushama J. Takate
- Department of Chemistry New Art, Commerce and Science College Ahmednagar India
| | - Supriya P. Salve
- Department of Chemistry New Art, Commerce and Science College Ahmednagar India
| | - Ram W. Sabnis
- Patent Law Department Georgia‐Pacific LLC Atlanta Georgia USA
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Ibis O, Zora M. A facile synthesis of 6-chloro-2-methylene-2,3-dihydro-1,4-oxazepines from N-propargylic β-enaminones. Tetrahedron 2020. [DOI: 10.1016/j.tet.2020.131650] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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El-Azab AS, Abdel-Aziz AAM, AlSaif NA, Alkahtani HM, Alanazi MM, Obaidullah AJ, Eskandrani RO, Alharbi A. Antitumor activity, multitarget mechanisms, and molecular docking studies of quinazoline derivatives based on a benzenesulfonamide scaffold: Cell cycle analysis. Bioorg Chem 2020; 104:104345. [PMID: 33142413 DOI: 10.1016/j.bioorg.2020.104345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/27/2020] [Accepted: 10/01/2020] [Indexed: 12/19/2022]
Abstract
The in vitro cytotoxicity of some substituted quinazolinones, 1-15, was evaluated using NCI (10 µM) in a full NCI 59-cell line panel assay. Relative to the reference drug, imatinib (PCE = 20/59), compounds 3, 4, 7, 9, and 10 exhibited remarkable antitumor activity against the tested cell lines, with positive cytotoxic effects (PCE) of 29/59, 18/59, 17/59, 44/59, and 24/59 respectively. Enzymatic inhibitory assay conducted on 3, 4, 9, and 10 as the most potent antitumor agents against EGFR, HER2 and CDK9 kinases, and COX-2 enzyme. Compound 3 possessed good COX-2 inhibitory activity (IC50 = 0.775 μM) compared to the reference drug, celecoxib (IC50 = 0.153 μM). Compounds 4 and 9 were closely potent to the reference compounds against EGFR and (HER2) tyrosine kinases, with IC50 values of 90.17 (and 131.39 for HER2) for 4 and 145.35 (and 129.07 for HER2) nM for 9; the reference drugs in this case, namely, gefitinib and erlotinib, exhibited IC50 values of 55.58 (90) and 110 (79.28) nM against the EGFR and (HER2) tyrosine kinases, respectively. Compound 4 was approximately similar potent against CDK9 kinase (IC50 = 67.04 nM) like the reference compound, dinaciclib (IC50 = 53.12 nM). Compound 9 induced cytotoxicity in the MCF-7 cell line (GI % at 10.0 μM = 47%) through pre-G1 apoptosis, thereby inhibiting cell growth at the G2/M phase. Molecular docking models of 3 and 4 with COX-2, EGFR, and CDK9 were conducted to determine their binding mode within the putative binding pockets.
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Affiliation(s)
- Adel S El-Azab
- Department of Pharmaceutical Chemistry, College of Pharmacy, P.O. Box 2457, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Alaa A-M Abdel-Aziz
- Department of Pharmaceutical Chemistry, College of Pharmacy, P.O. Box 2457, King Saud University, Riyadh 11451, Saudi Arabia
| | - Nawaf A AlSaif
- Department of Pharmaceutical Chemistry, College of Pharmacy, P.O. Box 2457, King Saud University, Riyadh 11451, Saudi Arabia
| | - Hamad M Alkahtani
- Department of Pharmaceutical Chemistry, College of Pharmacy, P.O. Box 2457, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohammed M Alanazi
- Department of Pharmaceutical Chemistry, College of Pharmacy, P.O. Box 2457, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ahmad J Obaidullah
- Department of Pharmaceutical Chemistry, College of Pharmacy, P.O. Box 2457, King Saud University, Riyadh 11451, Saudi Arabia
| | - Razan O Eskandrani
- Department of Pharmaceutical Chemistry, College of Pharmacy, P.O. Box 2457, King Saud University, Riyadh 11451, Saudi Arabia
| | - Amal Alharbi
- Department of Pharmaceutical Chemistry, College of Pharmacy, P.O. Box 2457, King Saud University, Riyadh 11451, Saudi Arabia
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Nainwal LM, Shaququzzaman M, Akhter M, Husain A, Parvez S, Khan F, Naematullah M, Alam MM. Synthesis, ADMET prediction and reverse screening study of 3,4,5-trimethoxy phenyl ring pendant sulfur-containing cyanopyrimidine derivatives as promising apoptosis inducing anticancer agents. Bioorg Chem 2020; 104:104282. [PMID: 33010624 DOI: 10.1016/j.bioorg.2020.104282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/03/2020] [Accepted: 09/12/2020] [Indexed: 02/09/2023]
Abstract
Cancer remains considered as one of the leading global health problems either due to meagre and suboptimal therapeutic response of chemotherapeutic agents or due to the emergence of spontaneous complex multidrug resistance in cancer cells. This created a persistent need for the development of new anticancer agents. Enthralled by the high success rate for natural product-based drug discovery and current research scenario, we synthesized a new series of 3,4,5-trimethoxy phenyl ring pendant sulfur-containingcyanopyrimidine derivatives clubbed with different amines intending to search an anticancer lead compound. To probe the anti-proliferative spectrum of the synthesized derivatives, an in-vitro evaluation was piloted against a panel of 60 cancer cell lines at the National Cancer Institute (NCI) representing major types of cancer diseases. Most of the derivatives showed good to moderate anti-proliferative activity. The results revealed that compound 4e displayed the most promising broad-spectrum anticancer activity with high growth inhibition of various cell lines representing multiple cancers diseases. Mechanistic investigation of compound 4e in human breast cancer MDA-MB-231 cells showed that compound 4e triggers cell death through the induction of apoptosis. ADMET studies and reverse screening were also performed to identify the potential targets of designed molecules. It was concluded that 3,4,5-trimethoxy phenyl ring pendant sulfur-containingcyanopyrimidine derivative 4e could act as a promising hit molecule for further development of novel anticancer therapeutics.
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Affiliation(s)
- Lalit Mohan Nainwal
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India
| | - Mohammad Shaququzzaman
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India
| | - Mymoona Akhter
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India
| | - Asif Husain
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India
| | - Suhel Parvez
- Department of Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Farah Khan
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Md Naematullah
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Mohammad Mumtaz Alam
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India.
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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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40
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Akhtar W, Nainwal LM, Khan MF, Verma G, Chashoo G, Bakht A, Iqbal M, Akhtar M, Shaquiquzzaman M, Alam MM. Synthesis, COX-2 inhibition and metabolic stability studies of 6-(4-fluorophenyl)-pyrimidine-5-carbonitrile derivatives as anticancer and anti-inflammatory agents. J Fluor Chem 2020. [DOI: 10.1016/j.jfluchem.2020.109579] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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41
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Haoran W, Akhtar W, Nainwal LM, Kaushik SK, Akhter M, Shaquiquzzaman M, Alam MM. Synthesis and biological evaluation of benzimidazole pendant cyanopyrimidine derivatives as anticancer agents. J Heterocycl Chem 2020. [DOI: 10.1002/jhet.4052] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Wang Haoran
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and ResearchJamia Hamdard New Delhi India
| | - Wasim Akhtar
- Department of Pharmaceutical ChemistryAlwar College of Pharmacy Alwar India
| | - Lalit Mohan Nainwal
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and ResearchJamia Hamdard New Delhi India
| | - Sumit Kumar Kaushik
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and ResearchJamia Hamdard New Delhi India
| | - Mymoona Akhter
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and ResearchJamia Hamdard New Delhi India
| | - Mohammad Shaquiquzzaman
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and ResearchJamia Hamdard New Delhi India
| | - Mohammad Mumtaz Alam
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and ResearchJamia Hamdard New Delhi India
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Xu J, Li H, Wang X, Huang J, Li S, Liu C, Dong R, Zhu G, Duan C, Jiang F, Zhang Y, Zhu Y, Zhang T, Chen Y, Tang W, Lu T. Discovery of coumarin derivatives as potent and selective cyclin-dependent kinase 9 (CDK9) inhibitors with high antitumour activity. Eur J Med Chem 2020; 200:112424. [PMID: 32447197 DOI: 10.1016/j.ejmech.2020.112424] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/24/2020] [Accepted: 05/04/2020] [Indexed: 02/07/2023]
Abstract
Specific inhibition of CDK9 is considered a promising strategy for developing effective anticancer therapeutics. However, most of the reported CDK9 inhibitors are still at an early stage of development and lack selectivity against other CDKs. Herein, we discovered coumarin derivative 30i as a potent CDK9 inhibitor with high selectivity (8300-fold over CDK7). Binding mode analysis illustrated that the substituent coumarin moiety is a critical group for CDK9 selectivity by occupying a flexible hinge/αD region, which is sterically hindered in other CDKs. Compound 30i showed excellent cellular antiproliferative activity, moderate pharmacokinetic property and low hERG inhibition. Moreover, 30i significantly induced tumour growth inhibition in a dose-dependent manner without causing an obvious loss of body weight in an MV4-11 xenograft mice model. Altogether, these results suggest that 30i may serve as a potential acute myeloid leukaemia (AML) therapeutics by selectively targeting CDK9.
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Affiliation(s)
- Junyu Xu
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China; Hainan province Key Laboratory for Research and Development of Tropical Herbs, Hainan Medical University, Haikou, 571199, China
| | - Hongmei Li
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Xinren Wang
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Jianhang Huang
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Shuwen Li
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Chenhe Liu
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Ruinan Dong
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Gaoyuan Zhu
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Chunqi Duan
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Fei Jiang
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Yanmin Zhang
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China; Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Yuqin Zhu
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Tianyi Zhang
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Yadong Chen
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China; Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China.
| | - Weifang Tang
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China.
| | - Tao Lu
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China; Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China.
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Therapeutic Targeting of the General RNA Polymerase II Transcription Machinery. Int J Mol Sci 2020; 21:ijms21093354. [PMID: 32397434 PMCID: PMC7246882 DOI: 10.3390/ijms21093354] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 12/27/2022] Open
Abstract
Inhibitors targeting the general RNA polymerase II (RNAPII) transcription machinery are candidate therapeutics in cancer and other complex diseases. Here, we review the molecular targets and mechanisms of action of these compounds, framing them within the steps of RNAPII transcription. We discuss the effects of transcription inhibitors in vitro and in cellular models (with an emphasis on cancer), as well as their efficacy in preclinical and clinical studies. We also discuss the rationale for inhibiting broadly acting transcriptional regulators or RNAPII itself in complex diseases.
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Diab S, Yu M, Wang S. CDK7 Inhibitors in Cancer Therapy: The Sweet Smell of Success? J Med Chem 2020; 63:7458-7474. [DOI: 10.1021/acs.jmedchem.9b01985] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Sarah Diab
- School of Pharmacy, Lebanese American University, P.O. Box 36, Byblos, Lebanon
| | - Mingfeng Yu
- Drug Discovery and Development, University of South Australia Cancer Research Institute, Adelaide, SA 5000, Australia
| | - Shudong Wang
- Drug Discovery and Development, University of South Australia Cancer Research Institute, Adelaide, SA 5000, Australia
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Sorvina A, Shandala T, Wang S, Sharkey DJ, Parkinson-Lawrence E, Selemidis S, Brooks DA. CDKI-73 is a Novel Pharmacological Inhibitor of Rab11 Cargo Delivery and Innate Immune Secretion. Cells 2020; 9:cells9020372. [PMID: 32033486 PMCID: PMC7072129 DOI: 10.3390/cells9020372] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 12/22/2022] Open
Abstract
Innate immunity is critical for host defence against pathogen and environmental challenge and this involves the production and secretion of immune mediators, such as antimicrobial peptides and pro-inflammatory cytokines. However, when dysregulated, innate immunity can contribute to multifactorial diseases, including inflammatory rheumatic disorders, type 2 diabetes, cancer, neurodegenerative and cardiovascular diseases and even septic shock. During an innate immune response, antimicrobial peptides and cytokines are trafficked via Rab11 multivesicular endosomes, and then sorted into Rab11 vesicles for traffic to the plasma membrane and secretion. In this study, a cyclin-dependent kinase inhibitor CDKI-73 was used to determine its effect on the innate immune response, based on previously identified targets for this compound. Our results showed that CDKI-73 inhibited the delivery of Rab11 vesicles to the plasma membrane, resulting in the accumulation of large multivesicular Rab11 endosomes near the cell periphery. In addition to the effect on endosome delivery, CDKI-73 down-regulated the amount of innate immune cargo, including the antimicrobial peptide Drosomycin and pro-inflammatory cytokines interleukin-6 (IL-6) and tumour necrosis factor alpha (TNFα). We concluded that CDKI-73 has the potential to regulate the delivery and secretion of certain innate immune cargo, which could be used to control inflammation.
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Affiliation(s)
- Alexandra Sorvina
- Cell Biology and Disease Research Group, Cancer Research Institute, University of South Australia, Adelaide, SA 5000, Australia (E.P.-L.)
- Correspondence: (A.S.); (D.A.B.)
| | - Tetyana Shandala
- Cell Biology and Disease Research Group, Cancer Research Institute, University of South Australia, Adelaide, SA 5000, Australia (E.P.-L.)
| | - Shudong Wang
- Centre for Drug Discovery and Development, Cancer Research Institute, University of South Australia, Adelaide, SA 5000, Australia;
| | - David J. Sharkey
- Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia;
| | - Emma Parkinson-Lawrence
- Cell Biology and Disease Research Group, Cancer Research Institute, University of South Australia, Adelaide, SA 5000, Australia (E.P.-L.)
| | - Stavros Selemidis
- School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC 3083, Australia;
| | - Douglas A. Brooks
- Cell Biology and Disease Research Group, Cancer Research Institute, University of South Australia, Adelaide, SA 5000, Australia (E.P.-L.)
- Correspondence: (A.S.); (D.A.B.)
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Synthesis, cytotoxic activity and quantum chemical calculations of new 7-thioxopyrazolo[1,5-f]pyrimidin-2-one derivatives. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127261] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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47
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H.S. Richter G, Hensel T, Schmidt O, Saratov V, von Heyking K, Becker-Dettling F, Prexler C, Yen HY, Steiger K, Fulda S, Dirksen U, Weichert W, Wang S, Burdach S, Schäfer BW. Combined Inhibition of Epigenetic Readers and Transcription Initiation Targets the EWS-ETS Transcriptional Program in Ewing Sarcoma. Cancers (Basel) 2020; 12:cancers12020304. [PMID: 32012890 PMCID: PMC7072515 DOI: 10.3390/cancers12020304] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/17/2020] [Accepted: 01/24/2020] [Indexed: 12/17/2022] Open
Abstract
Background: Previously, we used inhibitors blocking BET bromodomain binding proteins (BRDs) in Ewing sarcoma (EwS) and observed that long term treatment resulted in the development of resistance. Here, we analyze the possible interaction of BRD4 with cyclin-dependent kinase (CDK) 9. Methods: Co-immunoprecipitation experiments (CoIP) to characterize BRD4 interaction and functional consequences of inhibiting transcriptional elongation were assessed using drugs targeting of BRD4 or CDK9, either alone or in combination. Results: CoIP revealed an interaction of BRD4 with EWS-FLI1 and CDK9 in EwS. Treatment of EwS cells with CDKI-73, a specific CDK9 inhibitor (CDK9i), induced a rapid downregulation of EWS-FLI1 expression and block of contact-dependent growth. CDKI-73 induced apoptosis in EwS, as depicted by cleavage of Caspase 7 (CASP7), PARP and increased CASP3 activity, similar to JQ1. Microarray analysis following CDKI-73 treatment uncovered a transcriptional program that was only partially comparable to BRD inhibition. Strikingly, combined treatment of EwS with BRD- and CDK9-inhibitors re-sensitized cells, and was overall more effective than individual drugs not only in vitro but also in a preclinical mouse model in vivo. Conclusion: Treatment with BRD inhibitors in combination with CDK9i offers a new treatment option that significantly blocks the pathognomonic EWS-ETS transcriptional program and malignant phenotype of EwS.
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Affiliation(s)
- Günther H.S. Richter
- Children’s Cancer Research Centre and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, 80804 München, Germany; (T.H.); (O.S.); (K.v.H.); (F.B.-D.); (C.P.); (S.B.)
- German Cancer Research Center (DKFZ), partner site Munich, 81377 Munich, Germany; (H.-Y.Y.); (W.W.)
- Division of Oncology and Hematology, Department of Pediatrics, Charité - Universitätsmedizin Berlin, 13353 Berlin, Germany
- Correspondence:
| | - Tim Hensel
- Children’s Cancer Research Centre and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, 80804 München, Germany; (T.H.); (O.S.); (K.v.H.); (F.B.-D.); (C.P.); (S.B.)
- German Cancer Research Center (DKFZ), partner site Munich, 81377 Munich, Germany; (H.-Y.Y.); (W.W.)
| | - Oxana Schmidt
- Children’s Cancer Research Centre and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, 80804 München, Germany; (T.H.); (O.S.); (K.v.H.); (F.B.-D.); (C.P.); (S.B.)
- German Cancer Research Center (DKFZ), partner site Munich, 81377 Munich, Germany; (H.-Y.Y.); (W.W.)
| | - Vadim Saratov
- Department of Oncology and Children’s Research Center, University Children’s Hospital, 8032 Zurich, Switzerland; (V.S.); (B.W.S.)
| | - Kristina von Heyking
- Children’s Cancer Research Centre and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, 80804 München, Germany; (T.H.); (O.S.); (K.v.H.); (F.B.-D.); (C.P.); (S.B.)
- German Cancer Research Center (DKFZ), partner site Munich, 81377 Munich, Germany; (H.-Y.Y.); (W.W.)
| | - Fiona Becker-Dettling
- Children’s Cancer Research Centre and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, 80804 München, Germany; (T.H.); (O.S.); (K.v.H.); (F.B.-D.); (C.P.); (S.B.)
| | - Carolin Prexler
- Children’s Cancer Research Centre and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, 80804 München, Germany; (T.H.); (O.S.); (K.v.H.); (F.B.-D.); (C.P.); (S.B.)
- German Cancer Research Center (DKFZ), partner site Munich, 81377 Munich, Germany; (H.-Y.Y.); (W.W.)
| | - Hsi-Yu Yen
- German Cancer Research Center (DKFZ), partner site Munich, 81377 Munich, Germany; (H.-Y.Y.); (W.W.)
- Institute of Pathology, Technical University of Munich and Comparative Experimental Pathology (CEP), Technical University of Munich, 81675 Munich, Germany;
| | - Katja Steiger
- Institute of Pathology, Technical University of Munich and Comparative Experimental Pathology (CEP), Technical University of Munich, 81675 Munich, Germany;
| | - Simone Fulda
- Institute for Experimental Cancer Research in Paediatrics, Goethe-University Frankfurt, 60528 Frankfurt/Main, Germany;
| | - Uta Dirksen
- Pediatrics III, West German Cancer Centre, University Hospital of Essen, 45147 Essen, Germany;
- German Cancer Research Center (DKFZ), partner site Essen, 45147 Essen, Germany
| | - Wilko Weichert
- German Cancer Research Center (DKFZ), partner site Munich, 81377 Munich, Germany; (H.-Y.Y.); (W.W.)
- Institute of Pathology, Technical University of Munich and Comparative Experimental Pathology (CEP), Technical University of Munich, 81675 Munich, Germany;
| | - Shudong Wang
- Centre for Drug Discovery and Development and School of Pharmacy and Medical Sciences, University of South Australia Cancer Research Institute, Adelaide, South Australia 5001, Australia;
| | - Stefan Burdach
- Children’s Cancer Research Centre and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, 80804 München, Germany; (T.H.); (O.S.); (K.v.H.); (F.B.-D.); (C.P.); (S.B.)
- German Cancer Research Center (DKFZ), partner site Munich, 81377 Munich, Germany; (H.-Y.Y.); (W.W.)
| | - Beat W. Schäfer
- Department of Oncology and Children’s Research Center, University Children’s Hospital, 8032 Zurich, Switzerland; (V.S.); (B.W.S.)
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Wang X, Yu C, Wang C, Ma Y, Wang T, Li Y, Huang Z, Zhou M, Sun P, Zheng J, Yang S, Fan Y, Xiang R. Novel cyclin-dependent kinase 9 (CDK9) inhibitor with suppression of cancer stemness activity against non-small-cell lung cancer. Eur J Med Chem 2019; 181:111535. [DOI: 10.1016/j.ejmech.2019.07.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/08/2019] [Accepted: 07/10/2019] [Indexed: 01/16/2023]
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49
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Abdelaziz AM, Diab S, Islam S, Basnet SKC, Noll B, Li P, Mekonnen LB, Lu J, Albrecht H, Milne RW, Gerber C, Yu M, Wang S. Discovery of N-Phenyl-4-(1H-pyrrol-3-yl)pyrimidin-2-amine Derivatives as Potent Mnk2 Inhibitors: Design, Synthesis, SAR Analysis, and Evaluation of in vitro Anti-leukaemic Activity. Med Chem 2019; 15:602-623. [PMID: 30569866 DOI: 10.2174/1573406415666181219111511] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 12/03/2018] [Accepted: 12/11/2018] [Indexed: 01/25/2023]
Abstract
BACKGROUND Aberrant expression of eukaryotic translation initiation factor 4E (eIF4E) is common in many types of cancer including acute myeloid leukaemia (AML). Phosphorylation of eIF4E by MAPK-interacting kinases (Mnks) is essential for the eIF4E-mediated oncogenic activity. As such, the pharmacological inhibition of Mnks can be an effective strategy for the treatment of cancer. METHODS A series of N-phenyl-4-(1H-pyrrol-3-yl)pyrimidin-2-amine derivatives was designed and synthesised. The Mnk inhibitory activity of these derivatives as well as their anti-proliferative activity against MV4-11 AML cells was determined. RESULTS These compounds were identified as potent Mnk2 inhibitors. Most of them demonstrated potent anti-proliferative activity against MV4-11 AML cells. The cellular mechanistic studies of the representative inhibitors revealed that they reduced the level of phosphorylated eIF4E and induced apoptosis by down-regulating the anti-apoptotic protein myeloid cell leukaemia 1 (Mcl-1) and by cleaving poly(ADP-ribose)polymerase (PARP). The lead compound 7k possessed desirable pharmacokinetic properties and oral bioavailability. CONCLUSION This work proposes that exploration of the structural diversity in the context of Nphenyl- 4-(1H-pyrrol-3-yl)pyrimidin-2-amine would offer potent and selective Mnk inhibitors.
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Affiliation(s)
- Ahmed M Abdelaziz
- Centre for Drug Discovery and Development, Cancer Research Institute, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia 5001, Australia
| | - Sarah Diab
- Centre for Drug Discovery and Development, Cancer Research Institute, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia 5001, Australia
| | - Saiful Islam
- Centre for Drug Discovery and Development, Cancer Research Institute, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia 5001, Australia
| | - Sunita K C Basnet
- Centre for Drug Discovery and Development, Cancer Research Institute, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia 5001, Australia
| | - Benjamin Noll
- Centre for Drug Discovery and Development, Cancer Research Institute, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia 5001, Australia
| | - Peng Li
- Centre for Drug Discovery and Development, Cancer Research Institute, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia 5001, Australia
| | - Laychiluh B Mekonnen
- Centre for Drug Discovery and Development, Cancer Research Institute, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia 5001, Australia
| | - Jingfeng Lu
- Centre for Drug Discovery and Development, Cancer Research Institute, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia 5001, Australia
| | - Hugo Albrecht
- Centre for Drug Discovery and Development, Cancer Research Institute, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia 5001, Australia
| | - Robert W Milne
- Centre for Drug Discovery and Development, Cancer Research Institute, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia 5001, Australia
| | - Cobus Gerber
- Centre for Drug Discovery and Development, Cancer Research Institute, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia 5001, Australia
| | - Mingfeng Yu
- Centre for Drug Discovery and Development, Cancer Research Institute, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia 5001, Australia
| | - Shudong Wang
- Centre for Drug Discovery and Development, Cancer Research Institute, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia 5001, Australia
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50
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Rahaman MH, Lam F, Zhong L, Teo T, Adams J, Yu M, Milne RW, Pepper C, Lokman NA, Ricciardelli C, Oehler MK, Wang S. Targeting CDK9 for treatment of colorectal cancer. Mol Oncol 2019; 13:2178-2193. [PMID: 31398271 PMCID: PMC6763784 DOI: 10.1002/1878-0261.12559] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 07/30/2019] [Accepted: 08/07/2019] [Indexed: 12/11/2022] Open
Abstract
Colorectal cancer (CRC) remains one of the most lethal human malignancies, and pursuit of new therapeutic targets for treatment has been a major research focus. Cyclin-dependent kinase 9 (CDK9), which plays a crucial role in transcription, has emerged as a target for cancer treatment. CDKI-73, one of the most potent and pharmacologically superior CDK9 inhibitors, has demonstrated excellent anti-tumour efficacy against several types of cancers. In this study, we evaluated its therapeutic potential against CRC. CDKI-73 elicited high cytotoxicity against all colon cancer cell lines tested. Cell cycle and apoptosis analysis in HCT 116 and HT29 cells revealed that CDKI-73 induced cell death without accumulation of DNA at any phase of the cell cycle. Moreover, it caused depolarisation of mitochondrial membrane, leading to caspase-independent apoptosis. Knockdown by shRNA demonstrated the CDK9-targeted mechanism of CDKI-73, which also affected the Mnk/eIF4E signalling axis. In addition, RT-qPCR analysis showed that CDKI-73 down-regulated multiple pro-survival factors at the mRNA level. Its in vivo anti-tumour efficacy was further evaluated in Balb/c nude mice bearing HCT 116 xenograft tumours. CDKI-73 significantly inhibited tumour growth (***P < 0.001) without overt toxicity. Analysis of the tumour tissues collected from the xenografted animals confirmed that the in vivo anti-tumour efficacy was associated with CDK9 targeting of CDKI-73. Overall, this study provides compelling evidence that CDKI-73 is a promising drug candidate for treating colorectal cancer.
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Affiliation(s)
- Muhammed H Rahaman
- Centre for Drug Discovery and Development, School of Pharmacy and Medical Sciences, University of South Australia Cancer Research Institute, Adelaide, SA, Australia
| | - Frankie Lam
- Centre for Drug Discovery and Development, School of Pharmacy and Medical Sciences, University of South Australia Cancer Research Institute, Adelaide, SA, Australia
| | - Longjin Zhong
- Centre for Drug Discovery and Development, School of Pharmacy and Medical Sciences, University of South Australia Cancer Research Institute, Adelaide, SA, Australia
| | - Theodosia Teo
- Centre for Drug Discovery and Development, School of Pharmacy and Medical Sciences, University of South Australia Cancer Research Institute, Adelaide, SA, Australia
| | - Julian Adams
- Centre for Drug Discovery and Development, School of Pharmacy and Medical Sciences, University of South Australia Cancer Research Institute, Adelaide, SA, Australia
| | - Mingfeng Yu
- Centre for Drug Discovery and Development, School of Pharmacy and Medical Sciences, University of South Australia Cancer Research Institute, Adelaide, SA, Australia
| | - Robert W Milne
- Centre for Drug Discovery and Development, School of Pharmacy and Medical Sciences, University of South Australia Cancer Research Institute, Adelaide, SA, Australia
| | - Chris Pepper
- School of Medicine, Cardiff University, Health Park, UK
| | - Noor A Lokman
- Discipline of Obstetrics and Gynaecology, Adelaide Medical School, University of Adelaide, SA, Australia
| | - Carmela Ricciardelli
- Discipline of Obstetrics and Gynaecology, Adelaide Medical School, University of Adelaide, SA, Australia
| | - Martin K Oehler
- Discipline of Obstetrics and Gynaecology, Adelaide Medical School, University of Adelaide, SA, Australia
| | - Shudong Wang
- Centre for Drug Discovery and Development, School of Pharmacy and Medical Sciences, University of South Australia Cancer Research Institute, Adelaide, SA, Australia
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