1
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Abd El-Hameed RH, Mohamed MS, Awad SM, Hassan BB, Khodair MAEF, Mansour YE. Novel benzo chromene derivatives: design, synthesis, molecular docking, cell cycle arrest, and apoptosis induction in human acute myeloid leukemia HL-60 cells. J Enzyme Inhib Med Chem 2023; 38:405-422. [DOI: 10.1080/14756366.2022.2151592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Affiliation(s)
- Rania H. Abd El-Hameed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Mosaad S. Mohamed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Samir M. Awad
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Bardes B. Hassan
- Department of Pathology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | | | - Yara E. Mansour
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Cairo, Egypt
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2
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Joshi H, Tuli HS, Ranjan A, Chauhan A, Haque S, Ramniwas S, Bhatia GK, Kandari D. The Pharmacological Implications of Flavopiridol: An Updated Overview. Molecules 2023; 28:7530. [PMID: 38005250 PMCID: PMC10673037 DOI: 10.3390/molecules28227530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 11/06/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Flavopiridol is a flavone synthesized from the natural product rohitukine, which is derived from an Indian medicinal plant, namely Dysoxylum binectariferum Hiern. A deeper understanding of the biological mechanisms by which such molecules act may allow scientists to develop effective therapeutic strategies against a variety of life-threatening diseases, such as cancer, viruses, fungal infections, parasites, and neurodegenerative diseases. Mechanistic insight of flavopiridol reveals its potential for kinase inhibitory activity of CDKs (cyclin-dependent kinases) and other kinases, leading to the inhibition of various processes, including cell cycle progression, apoptosis, tumor proliferation, angiogenesis, tumor metastasis, and the inflammation process. The synthetic derivatives of flavopiridol have overcome a few demerits of its parent compound. Moreover, these derivatives have much improved CDK-inhibitory activity and therapeutic abilities for treating severe human diseases. It appears that flavopiridol has potential as a candidate for the formulation of an integrated strategy to combat and alleviate human diseases. This review article aims to unravel the potential therapeutic effectiveness of flavopiridol and its possible mechanism of action.
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Affiliation(s)
- Hemant Joshi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India;
| | - Hardeep Singh Tuli
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar Engineering College, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala 133207, India;
| | - Anuj Ranjan
- Academy of Biology and Biotechnology, Southern Federal University, Stachki 194/1, Rostov-on-Don 344090, Russia;
| | - Abhishek Chauhan
- Amity Institute of Environmental Toxicology Safety and Management, Amity University, Sector 125, Noida 201301, India;
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia;
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut 11022801, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman 13306, United Arab Emirates
| | - Seema Ramniwas
- University Centre for Research and Development, University Institute of Pharmaceutical Sciences, Chandigarh University, Gharuan, Mohali 140413, India;
| | - Gurpreet Kaur Bhatia
- Department of Physics, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala 133207, India;
| | - Divya Kandari
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India;
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3
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Belal A, Abdel Gawad NM, Mehany ABM, Abourehab MAS, Elkady H, Al-Karmalawy AA, Ismael AS. Design, synthesis and molecular docking of new fused 1 H-pyrroles, pyrrolo[3,2- d]pyrimidines and pyrrolo[3,2- e][1, 4]diazepine derivatives as potent EGFR/CDK2 inhibitors. J Enzyme Inhib Med Chem 2022; 37:1884-1902. [PMID: 35801486 PMCID: PMC9272933 DOI: 10.1080/14756366.2022.2096019] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A new series of 1H-pyrrole (6a-c, 8a-c), pyrrolo[3,2-d]pyrimidines (9a-c) and pyrrolo[3,2-e][1, 4]diazepines (11a-c) were designed and synthesised. These compounds were designed to have the essential pharmacophoric features of EGFR Inhibitors, they have shown anticancer activities against HCT116, MCF-7 and Hep3B cancer cells with IC50 values ranging from 0.009 to 2.195 µM. IC50 value of doxorubicin is 0.008 µM, compounds 9a and 9c showed IC50 values of 0.011 and 0.009 µM respectively against HCT-116 cells. Compound 8b exerted broad-spectrum activity against all tested cell lines with an IC50 value less than 0.05 µM. Compound 8b was evaluated against a panel of kinases. This compound potently inhibited CDK2/Cyclin A1, DYRK3 and GSK3 alpha kinases with 10-23% compared to imatinib (1-10%). It has also arrested the cell cycle of MCF-7 cells at the S phase. Its antiproliferative activity was further augmented by molecular docking into the active sites of EGFR and CDK2 cyclin A1.
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Affiliation(s)
- Amany Belal
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt.,Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Nagwa M Abdel Gawad
- Medicinal Chemistry Department, Faculty of Pharmacy, Cairo University, Giza, Egypt
| | - Ahmed B M Mehany
- Department of Zoology, Faculty of Science, Al-Azhar University, Nasr City, Egypt
| | - Mohammed A S Abourehab
- Department of Pharmaceutics, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia.,Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Minia University, Minia, Egypt
| | - Hazem Elkady
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Ahmed A Al-Karmalawy
- Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy, Horus University- Egypt, New Damietta, Egypt
| | - Ahmed S Ismael
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
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4
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Novel benzylidene benzofuranone analogues as potential anticancer agents: design, synthesis and in vitro evaluation based on CDK2 inhibition assays. 3 Biotech 2022; 12:256. [PMID: 36065423 PMCID: PMC9440176 DOI: 10.1007/s13205-022-03312-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 08/15/2022] [Indexed: 11/26/2022] Open
Abstract
The classical anticancer agents do not have their efficacy on inhibiting the G2 phase of the cell cycle. There are a very few reports available on drugs that work at G2 phase. Flavopiridol is one such drug candidate. In the current study, we sought to make analogues of flavopiridol. Still, the conditions used during their synthesis were unfavourable for the formation of flavopiridol and led to the generation of benzofuranones. In the present work, a new series of benzylidene benzofuranones were designed, synthesized and evaluated for their antioxidant, anti-colorectal cancer activity. Molecular docking, MMGBSA and molecular dynamics studies were conducted to assess their binding affinity at the active site of CDK2. Based on the cytotoxicity exhibited by test compounds, the compound NISOA4 (from isopropyl series) was further selected for mechanistic anticancer studies on HCT 116 cell lines. The compound selected was evaluated by comet assay, DNA fragmentation assay, cell cycle analysis, apoptosis detection by annexin FITC, semi-quantitative RTPCR based gene expression studies and FRET assay on the target CDK2/Cyclin A. Compound NISOA4 exhibited marked olive moments in comet assay studies. The apoptotic DNA fragmentation for compound NISOA4 demonstrated a marked change in the DNA fragmentation. The compound exhibited cell cycle arrest at G2/M phase at both the test concentrations. Apoptosis induction was observed at both the test concentrations and the compound was found to be a potent proapoptotic agent. It exhibited marked inhibition for the CDK2 gene expression and did not show any effect on CyclinA gene expression. However, the compound NISOA4 along with other analogues showed appreciable inhibition for the CDK2/Cyclin A target enzyme.
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5
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Mou J, Qiu S, Chen D, Deng Y, Tekleab T. Design, synthesis, and primary activity assays of baicalein derivatives as cyclin-dependent kinase 1 inhibitors. Chem Biol Drug Des 2021; 98:639-654. [PMID: 34233076 DOI: 10.1111/cbdd.13917] [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: 10/28/2020] [Revised: 04/27/2021] [Accepted: 07/03/2021] [Indexed: 12/01/2022]
Abstract
Malignant tumor is a disease with high mortality. Traditional treatment methods have many disadvantages, such as side-effects, drug resistance. Because cyclin-dependent kinase 1 (CDK1) plays an indispensable role in cell cycle regulation, it became an attractive target in rational anti-cancer drug discovery. Herein, we reported a series of baicalein derivatives, which remarkably repressed the proliferation of MCF-7 tumor cells and the activity of CDK1/cyclin B kinase. Among them, compound 4a displayed better inhibition rate than flavopiridol against MCF-7 proliferation at the concentration of 50 μg/ml, comparable to compound CGP74514A, while compound 3o possessed the best activity against CDK1/cyclin B kinase (IC50 = 1.26 μM). The inhibitory activities toward the kinase well correlated with anti-proliferative activities. Molecular docking results suggested that compound 3o can interact with the key amino acid residues, E81, L83, and D146, of CDK1 through hydrogen bond just like flavopiridol does. And it can also form an extra hydrogen bond with D146 by its introduced 7-acrylate group, which flavopiridol does not have. These findings proved that baicalein derivatives can be used as CDK1 inhibitors fighting against cancer.
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Affiliation(s)
- Jiajia Mou
- Department of Medicinal Chemistry, School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shuang Qiu
- Department of Medicinal Chemistry, School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Danghui Chen
- Department of Medicinal Chemistry, School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yanru Deng
- Department of Medicinal Chemistry, School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Teka Tekleab
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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6
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Qiu X, Li Y, Yu B, Ren J, Huang H, Wang M, Ding H, Li Z, Wang J, Bian J. Discovery of selective CDK9 degraders with enhancing antiproliferative activity through PROTAC conversion. Eur J Med Chem 2021; 211:113091. [PMID: 33338869 DOI: 10.1016/j.ejmech.2020.113091] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/05/2020] [Accepted: 12/05/2020] [Indexed: 10/22/2022]
Abstract
Cyclin-dependent kinase 9 (CDK9) is an increasingly important potential cancer treatment target. Nowadays, developing selective CDK9 inhibitors has been extremely challenging as its ATP-binding sites are similar with other CDKs. Here, we report that the CDK9 inhibitor BAY-1143572 is converted into a series of proteolysis targeting chimeras (PROTACs) which leads to several compounds inducing the degradation of CDK9 in acute myeloid leukemia cells at a low nanomolar concentration. In addition, the most potent PROTAC molecule B03 could inhibit cell growth more effectively than warhead alone, with little inhibition of other kinases. This enhanced antiproliferative activity is mediated by a slight increase in kinase inhibitory activity and an increase in the level of apoptosis induction. Moreover, B03 could induce the degradation of CDK9 in vivo. Our work provides evidence that B03 represents a lead for further development and that CDK9 degradation is a potential valuable therapeutic strategy in acute myeloid leukemia.
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Affiliation(s)
- Xiaqiu Qiu
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Yuanqing Li
- State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Bin Yu
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Jie Ren
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Huidan Huang
- School of Pharmacy, Wannan Medical College, Wuhu, 241002, PR China.
| | - Min Wang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Hong Ding
- State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Zhiyu Li
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Jubo Wang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Jinlei Bian
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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7
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Shankar EPS, Bahulayan D. Chemistry, chemical biology and photophysics of certain new chromene–triazole–coumarin triads as fluorescent inhibitors of CDK2 and CDK4 induced cancers. NEW J CHEM 2019. [DOI: 10.1039/c9nj02924a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The chromene–triazole–coumarin triads synthesized through the MCR-Click strategy possess intense solution state fluorescence, intense solid-state fluorescence and CDK2/CDK4 targeted cytotoxic activity against human cervical cancer cells (HeLa).
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8
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Uivarosi V, Munteanu AC, Nițulescu GM. An Overview of Synthetic and Semisynthetic Flavonoid Derivatives and Analogues: Perspectives in Drug Discovery. STUDIES IN NATURAL PRODUCTS CHEMISTRY 2019. [DOI: 10.1016/b978-0-444-64181-6.00002-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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9
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El Qaidi S, Zhu C, McDonald P, Roy A, Maity PK, Rane D, Perera C, Hardwidge PR. High-Throughput Screening for Bacterial Glycosyltransferase Inhibitors. Front Cell Infect Microbiol 2018; 8:435. [PMID: 30619781 PMCID: PMC6305410 DOI: 10.3389/fcimb.2018.00435] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/05/2018] [Indexed: 11/25/2022] Open
Abstract
The enteropathogenic and enterohemorrhagic Escherichia coli NleB proteins as well as the Salmonella enterica SseK proteins are type III secretion system effectors that function as glycosyltransferase enzymes to post-translationally modify host substrates on arginine residues. This modification is unusual because it occurs on the guanidinium groups of arginines, which are poor nucleophiles, and is distinct from the activity of the mammalian O-linked N-acetylglucosaminyltransferase. We conducted high-throughput screening assays to identify small molecules that inhibit NleB/SseK activity. Two compounds, 100066N and 102644N, both significantly inhibited NleB1, SseK1, and SseK2 activities. Addition of these compounds to cultured mammalian cells was sufficient to inhibit NleB1 glycosylation of the tumor necrosis factor receptor type 1-associated DEATH domain protein. These compounds were also capable of inhibiting Salmonella enterica strain ATCC 14028 replication in mouse macrophage-like cells. Neither inhibitor was significantly toxic to mammalian cells, nor showed in vitro cross-reactivity with the mammalian O-linked N-acetylglucosaminyltransferase. These compounds or derivatives generated from medicinal chemistry refinements may have utility as a potential alternative therapeutic strategy to antibiotics or as reagents to further the study of bacterial glycosyltransferases.
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Affiliation(s)
- Samir El Qaidi
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Congrui Zhu
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Peter McDonald
- High Throughput Screening Laboratory, University of Kansas, Lawrence, KS, United States
| | - Anuradha Roy
- High Throughput Screening Laboratory, University of Kansas, Lawrence, KS, United States
| | - Pradip Kumar Maity
- Synthetic Chemical Biology Core Laboratory, University of Kansas, Lawrence, KS, United States
| | - Digamber Rane
- Synthetic Chemical Biology Core Laboratory, University of Kansas, Lawrence, KS, United States
| | - Chamani Perera
- Synthetic Chemical Biology Core Laboratory, University of Kansas, Lawrence, KS, United States
| | - Philip R Hardwidge
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
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10
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Bharate SB, Kumar V, Jain SK, Mintoo MJ, Guru SK, Nuthakki VK, Sharma M, Bharate SS, Gandhi SG, Mondhe DM, Bhushan S, Vishwakarma RA. Discovery and Preclinical Development of IIIM-290, an Orally Active Potent Cyclin-Dependent Kinase Inhibitor. J Med Chem 2018; 61:1664-1687. [PMID: 29370702 DOI: 10.1021/acs.jmedchem.7b01765] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Rohitukine (1), a chromone alkaloid isolated from Indian medicinal plant Dysoxylum binectariferum, has inspired the discovery of flavopiridol and riviciclib, both of which are bioavailable only via intravenous route. With the objective to address the oral bioavailability issue of this scaffold, four series of rohitukine derivatives were prepared and screened for Cdk inhibition and cellular antiproliferative activity. The 2,6-dichloro-styryl derivative IIIM-290 (11d) showed strong inhibition of Cdk-9/T1 (IC50 1.9 nM) kinase and Molt-4/MIAPaCa-2 cell growth (GI50 < 1.0 μM) and was found to be highly selective for cancer cells over normal fibroblast cells. It inhibited the cell growth of MIAPaCa-2 cells via caspase-dependent apoptosis. It achieved 71% oral bioavailability with in vivo efficacy in pancreatic, colon, and leukemia xenografts at 50 mg/kg, po. It did not have CYP/efflux-pump liability, was not mutagenic/genotoxic or cardiotoxic, and was metabolically stable. The preclinical data presented herein indicates the potential of 11d for advancement in clinical studies.
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Affiliation(s)
- Sandip B Bharate
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu-180001, India.,Academy of Scientific & Innovative Research, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu-180001, India
| | - Vikas Kumar
- Academy of Scientific & Innovative Research, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu-180001, India.,Preformulation Laboratory, PK-PD Toxicology & Formulation Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu-180001, India
| | - Shreyans K Jain
- Natural Products Chemistry Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu-180001, India
| | - Mubashir J Mintoo
- Academy of Scientific & Innovative Research, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu-180001, India.,Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu-180001, India
| | - Santosh K Guru
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu-180001, India
| | - Vijay K Nuthakki
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu-180001, India
| | - Mohit Sharma
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu-180001, India
| | - Sonali S Bharate
- Preformulation Laboratory, PK-PD Toxicology & Formulation Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu-180001, India
| | - Sumit G Gandhi
- Academy of Scientific & Innovative Research, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu-180001, India.,Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu-180001, India
| | - Dilip M Mondhe
- Academy of Scientific & Innovative Research, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu-180001, India.,Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu-180001, India
| | - Shashi Bhushan
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu-180001, India.,Indian Pharmacopeia Commission , Sec-23, Raj Nagar, Ghaziabad-201002, India
| | - Ram A Vishwakarma
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu-180001, India.,Academy of Scientific & Innovative Research, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu-180001, India
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11
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Ilkei V, Hazai L, Antus S, Bölcskei H. Flavonoid Alkaloids: Isolation, Bioactivity, and Synthesis. STUDIES IN NATURAL PRODUCTS CHEMISTRY 2018. [DOI: 10.1016/b978-0-444-64058-1.00008-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
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12
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New chalcones bearing isatin scaffold: synthesis, molecular modeling and biological evaluation as anticancer agents. RESEARCH ON CHEMICAL INTERMEDIATES 2017. [DOI: 10.1007/s11164-017-3019-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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13
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Tutone M, Almerico AM. Recent advances on CDK inhibitors: An insight by means of in silico methods. Eur J Med Chem 2017; 142:300-315. [PMID: 28802482 DOI: 10.1016/j.ejmech.2017.07.067] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 07/19/2017] [Accepted: 07/28/2017] [Indexed: 02/06/2023]
Abstract
The cyclin dependent kinases (CDKs) are a small family of serine/threonine protein kinases that can act as a potential therapeutic target in several proliferative diseases, including cancer. This short review is a survey on the more recent research progresses in the field achieved by using in silico methods. All the "armamentarium" available to the medicinal chemists (docking protocols and molecular dynamics, fragment-based, de novo design, virtual screening, and QSAR) has been employed to the discovery of new, potent, and selective inhibitors of cyclin dependent kinases. The results cited herein can be useful to understand the nature of the inhibitor-target interactions, and furnish an insight on the structural/molecular requirements necessary to achieve the required selectivity against cyclin dependent kinases over other types of kinases.
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Affiliation(s)
- Marco Tutone
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Anna Maria Almerico
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Via Archirafi 32, 90123 Palermo, Italy.
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14
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Pajtás D, Kónya K, Kiss-Szikszai A, Džubák P, Pethő Z, Varga Z, Panyi G, Patonay T. Optimization of the Synthesis of Flavone–Amino Acid and Flavone–Dipeptide Hybrids via Buchwald–Hartwig Reaction. J Org Chem 2017; 82:4578-4587. [DOI: 10.1021/acs.joc.7b00124] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dávid Pajtás
- Department
of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Krisztina Kónya
- Department
of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Attila Kiss-Szikszai
- Department
of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Petr Džubák
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hnevotinska 5, 779
00 Olomouc, Czech Republic
| | - Zoltán Pethő
- Department
of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, H-4032 Debrecen, Hungary
| | - Zoltán Varga
- Department
of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, H-4032 Debrecen, Hungary
| | - György Panyi
- Department
of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, H-4032 Debrecen, Hungary
| | - Tamás Patonay
- Department
of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
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15
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Arba M, Ihsan S, Ramadhan LOAN, Tjahjono DH. In silico study of porphyrin-anthraquinone hybrids as CDK2 inhibitor. Comput Biol Chem 2016; 67:9-14. [PMID: 28024230 DOI: 10.1016/j.compbiolchem.2016.12.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 11/17/2016] [Accepted: 12/15/2016] [Indexed: 10/20/2022]
Abstract
Cyclin-Dependent Kinases (CDKs) are known to play crucial roles in controlling cell cycle progression of eukaryotic cell and inhibition of their activity has long been considered as potential strategy in anti-cancer drug research. In the present work, a series of porphyrin-anthraquinone hybrids bearing meso-substituents, i.e. either pyridine or pyrazole rings were designed and computationally evaluated for their Cyclin Dependent Kinase-2 (CDK2) inhibitory activity using molecular docking, molecular dynamics simulation, and binding free energy calculation. The molecular docking simulation revealed that all six porphyrin hybrids were able to bind to ATP-binding site of CDK2 and interacted with key residues constituted the active cavity of CDK2, while molecular dynamics simulation indicated that all porphyrins bound to CDK2 were stable for 6ns. The binding free energies predicted by MM-PBSA method showed that most compounds exhibited higher affinity than that of native ligand (4-anilinoquinazoline, DTQ) and the affinity of mono-H2PyP-AQ was about three times better than that of DTQ, indicating its potential to be advanced as a new CDK2 inhibitor.
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Affiliation(s)
- Muhammad Arba
- Faculty of Pharmacy, Universitas Halu Oleo, Kendari, 93231, Indonesia.
| | - Sunandar Ihsan
- Faculty of Pharmacy, Universitas Halu Oleo, Kendari, 93231, Indonesia
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Abdel Latif NA, Batran RZ, Khedr MA, Abdalla MM. 3-Substituted-4-hydroxycoumarin as a new scaffold with potent CDK inhibition and promising anticancer effect: Synthesis, molecular modeling and QSAR studies. Bioorg Chem 2016; 67:116-29. [DOI: 10.1016/j.bioorg.2016.06.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/17/2016] [Accepted: 06/23/2016] [Indexed: 01/04/2023]
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Nadirov RK, Nadirov KS, Bimbetova GZ, Nadirova ZK. Synthesis and Cytotoxic Activity of New Flavopiridol Analogs. Chem Nat Compd 2016. [DOI: 10.1007/s10600-016-1686-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Kónya K, Pajtás D, Kiss-Szikszai A, Patonay T. Buchwald-Hartwig Reactions of Monohaloflavones. European J Org Chem 2014. [DOI: 10.1002/ejoc.201403108] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Haque A, Koide N, Iftakhar-E-Khuda I, Noman ASM, Odkhuu E, Badamtseren B, Naiki Y, Komatsu T, Yoshida T, Yokochi T. Flavopiridol inhibits lipopolysaccharide-induced TNF-α production through inactivation of nuclear factor-κB and mitogen-activated protein kinases in the MyD88-dependent pathway. Microbiol Immunol 2011; 55:160-7. [PMID: 21204955 DOI: 10.1111/j.1348-0421.2010.00304.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Flavopiridol is a cyclin-dependent kinase inhibitor and inhibits the growth of various cancer cells. The effect of flavopiridol on lipopolysaccharide (LPS)-induced proinflammatory mediator production was examined in RAW 264.7 macrophage-like cells. Flavopiridol significantly reduced the production of tumor necrosis factor-α and, to a lesser extent, nitric oxide in LPS-stimulated cells. Flavopiridol inhibited the activation of nuclear factor-κB and IκB kinase in response to LPS. Flavopiridol also inhibited the activation of a series of mitogen-activated protein kinases, such as p38, stress-activated protein kinase/c-Jun N-terminal kinase and extracellular signal-regulated kinase 1/2 in response to LPS. However, flavopiridol did not alter the expression of tumor necrosis factor receptor-associated factor 6, myeloid differentiation factor 88 (MyD88) or CD14/toll-like receptor (TLR) 4. Flavopiridol inhibited nitric oxide production induced by a MyD88-dependent TLR2 ligand, but not a MyD88-independent TLR3 ligand. Further, flavopiridol did not alter the phosphorylation of interferon regulatory factor 3 in the MyD88-independent pathway. Therefore, it was suggested that flavopiridol exclusively inhibited the activation of nuclear factor-κB and mitogen-activated protein kinases in the MyD88-dependent pathway. Flavopiridol might be useful for the prevention of LPS-induced inflammatory response.
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Affiliation(s)
- Abedul Haque
- Department of Microbiology and Immunology, Aichi Medical University School of Medicine, Nagakute, Aichi, Japan
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Wang F, Ma Z, Li Y, Zhu S, Xiao Z, Zhang H, Wang Y. Development of in silico models for pyrazoles and pyrimidine derivatives as cyclin-dependent kinase 2 inhibitors. J Mol Graph Model 2011; 30:67-81. [PMID: 21763166 DOI: 10.1016/j.jmgm.2011.06.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 06/03/2011] [Accepted: 06/14/2011] [Indexed: 11/30/2022]
Affiliation(s)
- Fangfang Wang
- Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi 712100,China
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3D-QSAR and docking studies on pyrazolo[4,3-h]qinazoline-3-carboxamides as cyclin-dependent kinase 2 (CDK2) inhibitors. Bioorg Med Chem Lett 2010; 20:6764-72. [PMID: 20869873 DOI: 10.1016/j.bmcl.2010.08.131] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 08/13/2010] [Accepted: 08/27/2010] [Indexed: 02/02/2023]
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Phosrithong N, Ungwitayatorn J. Molecular docking study on anticancer activity of plant-derived natural products. Med Chem Res 2009. [DOI: 10.1007/s00044-009-9233-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Dolle RE, Bourdonnec BL, Goodman AJ, Morales GA, Thomas CJ, Zhang W. Comprehensive Survey of Chemical Libraries for Drug Discovery and Chemical Biology: 2007. ACTA ACUST UNITED AC 2008; 10:753-802. [PMID: 18991466 DOI: 10.1021/cc800119z] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Roland E. Dolle
- Adolor Corporation, 700 Pennsylvania Drive, Exton, Pennsylvania 19341, Semafore Pharmaceuticals Inc., 8496 Georgetown Road, Indianapolis, Indiana 46268, NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, and Department of Chemistry, University of Massachusetts, 100 Morrissey Boulevard, Boston, Massachusetts 02125
| | - Bertrand Le Bourdonnec
- Adolor Corporation, 700 Pennsylvania Drive, Exton, Pennsylvania 19341, Semafore Pharmaceuticals Inc., 8496 Georgetown Road, Indianapolis, Indiana 46268, NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, and Department of Chemistry, University of Massachusetts, 100 Morrissey Boulevard, Boston, Massachusetts 02125
| | - Allan J. Goodman
- Adolor Corporation, 700 Pennsylvania Drive, Exton, Pennsylvania 19341, Semafore Pharmaceuticals Inc., 8496 Georgetown Road, Indianapolis, Indiana 46268, NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, and Department of Chemistry, University of Massachusetts, 100 Morrissey Boulevard, Boston, Massachusetts 02125
| | - Guillermo A. Morales
- Adolor Corporation, 700 Pennsylvania Drive, Exton, Pennsylvania 19341, Semafore Pharmaceuticals Inc., 8496 Georgetown Road, Indianapolis, Indiana 46268, NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, and Department of Chemistry, University of Massachusetts, 100 Morrissey Boulevard, Boston, Massachusetts 02125
| | - Craig J. Thomas
- Adolor Corporation, 700 Pennsylvania Drive, Exton, Pennsylvania 19341, Semafore Pharmaceuticals Inc., 8496 Georgetown Road, Indianapolis, Indiana 46268, NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, and Department of Chemistry, University of Massachusetts, 100 Morrissey Boulevard, Boston, Massachusetts 02125
| | - Wei Zhang
- Adolor Corporation, 700 Pennsylvania Drive, Exton, Pennsylvania 19341, Semafore Pharmaceuticals Inc., 8496 Georgetown Road, Indianapolis, Indiana 46268, NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, and Department of Chemistry, University of Massachusetts, 100 Morrissey Boulevard, Boston, Massachusetts 02125
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Nitrogen-containing flavonoid analogues as CDK1/cyclin B inhibitors: synthesis, SAR analysis, and biological activity. Bioorg Med Chem 2008; 16:7128-33. [PMID: 18639462 DOI: 10.1016/j.bmc.2008.06.055] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Revised: 06/24/2008] [Accepted: 06/26/2008] [Indexed: 11/24/2022]
Abstract
A series of nitrogen-containing flavonoid analogues were designed and synthesized by Mannich reaction, and screened for the inhibitory activities of cyclin-dependent kinases using a FRET-based biochemical assay method. The results showed that C-8 nitrogen-containing baicalein analogues 3a-3f exhibited potent CDK1/Cyclin B inhibitory activities. 5,6,7-Trihydroxy-8-(dimethylaminomethyl)-2-phenyl-4H-chromen-4-one 3a, 5,6,7-trihydroxy-8-(pyrrolid inylmethyl)-2-phenyl-4H-chromen-4-one 3b, and 5,6,7-trihydroxy-8-(piperidinylmethyl)-2-phenyl-4H-chromen-4-one 3c (IC(50) 1.05-1.28 microM) were about sixfold more potent than baicalein 2 (IC(50) 6.53 microM). 5,6,7-Trihydroxy-8-(morpholinomethyl)-2-phenyl-4H-chromen-4-one 3d, 5,6,7-trihydroxy-8-(thiomorpholinomethy)-2-phenyl-4H-chrom en-4-one 3e, and 5,6,7-trihydroxy-8-(4-methylpiperazinylmethyl)-2-phenyl-4H-chromen-4-one 3f (IC(50) 0.27-0.38 microM) were about 20-fold more potent than baicalein, and were at the same level as flavopiridol (IC(50) 0.33 microM).
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