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Bondock S, Alabbad N, Hossan A, Abdou MM, Shati AA, Alfaifi MY, Elbehairi SEI, Mohamed NM. Design, synthesis, and anticancer evaluation of novel coumarin/thiazole congeners as potential CDK2 inhibitors with molecular dynamics. RSC Adv 2024; 14:18838-18855. [PMID: 38873551 PMCID: PMC11167341 DOI: 10.1039/d4ra02456g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/28/2024] [Indexed: 06/15/2024] Open
Abstract
A series of novel coumarin-thiazoles was designed and synthesized as a possible CDK2 inhibitor with anticancer activity with low toxicity. The design relied on having hydrazine thiazole or its open-form thioamide to form H-bonds with the ATP binding site while coumarin maintained the crucial hydrophobic interactions for proper fitting. The biological evaluation revealed that the hydroxycoumarin-thiazole derivative 6c demonstrated the best inhibition with HepG2 and HCT116 IC50 2.6 and 3.5 μM, respectively. Similarly, its open thioamide chain congener 5c exhibited potent inhibition on MCF-7 and HepG2 with IC50 of 4.5 and 5.4 μM, respectively. Molecular docking simulations supported the assumption of inhibiting CDK2 by preserving the crucial interaction pattern with the hinge ATP site and the surrounding hydrophobic (HPO) side chains. Furthermore, molecular dynamics simulations of 5c and 6c established satisfactory stability and affinity within the CDK2 active site.
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Affiliation(s)
- Samir Bondock
- Chemistry Department, Faculty of Science, King Khalid University 9004 Abha Saudi Arabia
| | - Nada Alabbad
- Chemistry Department, Faculty of Science, King Khalid University 9004 Abha Saudi Arabia
| | - Aisha Hossan
- Chemistry Department, Faculty of Science, King Khalid University 9004 Abha Saudi Arabia
| | - Moaz M Abdou
- Egyptian Petroleum Research Institute Nasr City 11727 Cairo Egypt
| | - Ali A Shati
- Biology Department, Faculty of Science, King Khalid University 9004 Abha Saudi Arabia
| | - Mohammad Y Alfaifi
- Biology Department, Faculty of Science, King Khalid University 9004 Abha Saudi Arabia
| | - Serag E I Elbehairi
- Biology Department, Faculty of Science, King Khalid University 9004 Abha Saudi Arabia
| | - Nada M Mohamed
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Modern University for Technology and Information, MTI Cairo Egypt
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2
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Chen S, Li M, Xue C, Zhou X, Wei J, Zheng L, Duan Y, Deng H, Tang F, Xiong W, Xiang B, Zhou M. Validation of Core Ingredients and Molecular Mechanism of Cinobufotalin Injection Against Liver Cancer. Drug Des Devel Ther 2024; 18:1321-1338. [PMID: 38681206 PMCID: PMC11055549 DOI: 10.2147/dddt.s443305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 04/10/2024] [Indexed: 05/01/2024] Open
Abstract
Purpose Cinobufotalin injection has obvious curative effects on liver cancer patients with less toxicity and fewer side effects than other therapeutic approaches. However, the core ingredients and mechanism underlying these anti-liver cancer effects have not been fully clarified due to its complex composition. Methods Multidimensional network analysis was used to screen the core ingredients, key targets and pathways underlying the therapeutic effects of cinobufotalin injection on liver cancer, and in vitro and in vivo experiments were performed to confirm the findings. Results By construction of ingredient networks and integrated analysis, eight core ingredients and ten key targets were finally identified in cinobufotalin injection, and all of the core ingredients are tightly linked with the key targets, and these key targets are highly associated with the cell cycle-related pathways, supporting that both cinobufotalin injection and its core ingredients exert anti-liver cancer roles by blocking cell cycle-related pathways. Moreover, in vitro and in vivo experiments confirmed that either cinobufotalin injection or one of its core ingredients, cinobufagin, significantly inhibited cell proliferation, colony formation, cell cycle progression and xenograft tumor growth, and the key target molecules involved in the cell cycle pathway such as CDK1, CDK4, CCNB1, CHEK1 and CCNE1, exhibit consistent changes in expression after treatment with cinobufotalin injection or cinobufagin. Interestingly, some key targets CDK1, CDK4, PLK1, CHEK1, TTK were predicted to bind with multiple of core ingredients of cinobufotalin injection, and the affinity between one of the critical ingredients cinobufagin and key target CDK1 was further confirmed by SPR assay. Conclusion Cinobufotalin injection was confirmed to includes eight core ingredients, and they play therapeutic effects in liver cancer by blocking cell cycle-related pathways, which provides important insights for the mechanism of cinobufotalin injection antagonizing liver cancer and the development of novel small molecule anti-cancer drugs.
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MESH Headings
- Bufanolides/pharmacology
- Bufanolides/chemistry
- Bufanolides/administration & dosage
- Humans
- Animals
- Liver Neoplasms/drug therapy
- Liver Neoplasms/pathology
- Liver Neoplasms/metabolism
- Cell Proliferation/drug effects
- Mice
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/chemistry
- Drug Screening Assays, Antitumor
- Liver Neoplasms, Experimental/drug therapy
- Liver Neoplasms, Experimental/pathology
- Liver Neoplasms, Experimental/metabolism
- Mice, Inbred BALB C
- Cell Cycle/drug effects
- Mice, Nude
- Dose-Response Relationship, Drug
- Neoplasms, Experimental/drug therapy
- Neoplasms, Experimental/pathology
- Neoplasms, Experimental/metabolism
- Tumor Cells, Cultured
- Structure-Activity Relationship
- Molecular Structure
- Injections
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Affiliation(s)
- Shipeng Chen
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, People’s Republic of China
- Cancer Research Institute, Central South University, Changsha, 410078, People’s Republic of China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, People’s Republic of China
| | - Mengna Li
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, People’s Republic of China
- Cancer Research Institute, Central South University, Changsha, 410078, People’s Republic of China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, People’s Republic of China
| | - Changning Xue
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, People’s Republic of China
- Cancer Research Institute, Central South University, Changsha, 410078, People’s Republic of China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, People’s Republic of China
| | - Xiangting Zhou
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, People’s Republic of China
- Cancer Research Institute, Central South University, Changsha, 410078, People’s Republic of China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, People’s Republic of China
| | - Jianxia Wei
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, People’s Republic of China
- Cancer Research Institute, Central South University, Changsha, 410078, People’s Republic of China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, People’s Republic of China
| | - Lemei Zheng
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, People’s Republic of China
- Cancer Research Institute, Central South University, Changsha, 410078, People’s Republic of China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, People’s Republic of China
| | - Yumei Duan
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, People’s Republic of China
- Cancer Research Institute, Central South University, Changsha, 410078, People’s Republic of China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, People’s Republic of China
| | - Hongyu Deng
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, People’s Republic of China
| | - Faqing Tang
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, People’s Republic of China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, People’s Republic of China
- Cancer Research Institute, Central South University, Changsha, 410078, People’s Republic of China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, People’s Republic of China
| | - Bo Xiang
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, People’s Republic of China
- Cancer Research Institute, Central South University, Changsha, 410078, People’s Republic of China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, People’s Republic of China
| | - Ming Zhou
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, People’s Republic of China
- Cancer Research Institute, Central South University, Changsha, 410078, People’s Republic of China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, People’s Republic of China
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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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4
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Zaki WA, El-Sayed SM, Alswah M, El-Morsy A, Bayoumi AH, Mayhoub AS, Moustafa WH, Awaji AA, Roh EJ, Hassan AH, Mahmoud K. Design, Synthesis, In Vitro, and In Silico Studies of New N5-Substituted-pyrazolo[3,4- d]pyrimidinone Derivatives as Anticancer CDK2 Inhibitors. Pharmaceuticals (Basel) 2023; 16:1593. [PMID: 38004458 PMCID: PMC10674233 DOI: 10.3390/ph16111593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
CDK2 is a key player in cell cycle processes. It has a crucial role in the progression of various cancers. Hepatocellular carcinoma (HCC) and colorectal cancer (CRC) are two common cancers that affect humans worldwide. The available therapeutic options suffer from many drawbacks including high toxicity and decreased specificity. Therefore, there is a need for more effective and safer therapeutic agents. A series of new pyrazolo[3,4-d]pyrimidine analogs was designed, synthesized, and evaluated as anticancer agents against the CRC and HCC cells, HCT116, and HepG2, respectively. Pyrazolo[3,4-d]pyrimidinone derivatives bearing N5-2-(4-halophenyl) acetamide substituents were identified as the most potent amongst evaluated compounds. Further evaluation of CDK2 kinase inhibition of two potential cytotoxic compounds 4a and 4b confirmed their CDK2 inhibitory activity. Compound 4a was more potent than the reference roscovitine regarding the CDK2 inhibitory activity (IC50 values: 0.21 and 0.25 µM, respectively). In silico molecular docking provided insights into the molecular interactions of compounds 4a and 4b with important amino acids within the ATP-binding site of CDK2 (Ile10, Leu83, and Leu134). Overall, compounds 4a and 4b were identified as interesting CDK2 inhibitors eliciting antiproliferative activity against the CRC and HCC cells, HCT116 and HepG2, respectively, for future further investigations and development.
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Affiliation(s)
- Waheed A. Zaki
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Cairo 11884, Egypt
| | - Selwan M. El-Sayed
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Mohamed Alswah
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Cairo 11884, Egypt
| | - Ahmed El-Morsy
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Cairo 11884, Egypt
- Pharmaceutical Chemistry Department, College of Pharmacy, The Islamic University, Najaf 54001, Iraq
| | - Ashraf H. Bayoumi
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Cairo 11884, Egypt
| | - Abrahman S. Mayhoub
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Cairo 11884, Egypt
- Nanoscience Program, University of Science and Technology, Zewail City of Science and Technology, October Gardens, 6th of October, Giza 12578, Egypt
| | - Walaa H. Moustafa
- Microbiology and Immunology Department, Faculty of Pharmacy, Helwan University, Cairo 19448, Egypt
| | - Aeshah A. Awaji
- Department of Biology, Faculty of Science, University College of Taymaa, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Eun Joo Roh
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Division of Bio-Medical Science & Technology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Ahmed H.E. Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Kazem Mahmoud
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City 11829, Egypt
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5
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James A, Akash K, Sharma A, Bhattacharyya S, Sriamornsak P, Nagraik R, Kumar D. Himalayan flora: targeting various molecular pathways in lung cancer. Med Oncol 2023; 40:314. [PMID: 37787816 DOI: 10.1007/s12032-023-02171-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/21/2023] [Indexed: 10/04/2023]
Abstract
The fatal amplification of lung cancer across the globe and the limitations of current treatment strategies emphasize the necessity for substitute therapeutics. The incorporation of phyto-derived components in chemo treatment holds promise in addressing those challenges. Despite the significant progressions in lung cancer therapeutics, the complexities of molecular mechanism and pathways underlying this disease remain inadequately understood, necessitating novel biomarker targeting. The Himalayas, abundant in diverse plant varieties with established chemotherapeutic potential, presents a promising avenue for investigating potential cures for lung carcinoma. The vast diversity of phytocompounds herein can be explored for targeting the disease. This review delves into the multifaceted targets of lung cancer and explores the established phytochemicals with their specific molecular targets. It emphasizes comprehending the intricate pathways that govern effective therapeutic interventions for lung cancer. Through this exploration of Himalayan flora, this review seeks to illuminate potential breakthroughs in lung cancer management using natural compounds. The amalgamation of Himalayan plant-derived compounds with cautiously designed combined therapeutic approaches such as nanocarrier-mediated drug delivery and synergistic therapy offers an opportunity to redefine the boundaries of lung cancer treatment by reducing the drug resistance and side effects and enabling an effective targeted delivery of drugs. Furthermore, additional studies are obligatory to understand the possible derivation of natural compounds used in current lung cancer treatment from plant species within the Himalayan region.
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Affiliation(s)
- Abija James
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - K Akash
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Avinash Sharma
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Sanjib Bhattacharyya
- Department of Pharmaceutical Sciences and Chinese Traditional Medicine, Southwest University, Beibei, 400715, Chongqing, People's Republic of China
- Department of Sciences, Nirma University, Ahmedabad, Gujarat, 382481, India
| | | | - Rupak Nagraik
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India.
| | - Deepak Kumar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, 173229, India.
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Almansour BS, Binjubair FA, Abdel-Aziz AAM, Al-Rashood ST. Synthesis and In Vitro Anticancer Activity of Novel 4-Aryl-3-(4-methoxyphenyl)-1-phenyl-1 H-pyrazolo[3,4- b]pyridines Arrest Cell Cycle and Induce Cell Apoptosis by Inhibiting CDK2 and/or CDK9. Molecules 2023; 28:6428. [PMID: 37687256 PMCID: PMC10490123 DOI: 10.3390/molecules28176428] [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: 06/25/2023] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 09/10/2023] Open
Abstract
Two series of pyrazolo[3,4-b]pyridine derivatives, 9a-h and 14a-h, are synthesized and evaluated for their anti-cancer potency towards Hela, MCF7, and HCT-116 cancer cell lines. Compound 9a showed the highest anticancer activity with IC50 = 2.59 µM against Hela when compared with doxorubicin (IC50 = 2.35 µM). Compound 14g revealed cytotoxicity IC50 = 4.66 and 1.98 µM towards MCF7 and HCT-116 compared to doxorubicin with IC50 = 4.57 and 2.11 µM, respectively. Compound 9a exhibited cell cycle arrest at the S phase for Hela, whereas 14g revealed an arresting cell cycle for MCF7 at G2/M phase and an arresting cell cycle at S phase in HCT-116. In addition, 9a induced a significant level of early and late apoptosis in Hela when compared with the control cells, whereas 14g induced an apoptosis in MCF7 and HCT-116, respectively. Compounds 9a (IC50 = 26.44 ± 3.23 µM) and 14g (IC50 = 21.81 ± 2.96 µM) showed good safety profiles on normal cell line WI-38. Compounds 9a and 14g showed good inhibition activity towards CDK2, with IC50 = 1.630 ± 0.009 and 0.460 ± 0.024 µM, respectively, when compared with ribociclib (IC50 = 0.068 ± 0.004). Furthermore, 9a and 14g showed inhibitory activity towards CDK9 with IC50 = 0.262 ± 0.013 and 0.801 ± 0.041 µM, respectively, related to IC50 of ribociclib = 0.050 ± 0.003. Docking study for 9a and 14g exhibited good fitting in the CDK2 and CDK9 active sites.
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Affiliation(s)
- Basma S. Almansour
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia; (B.S.A.); (F.A.B.); (A.A.-M.A.-A.)
| | - Faizah A. Binjubair
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia; (B.S.A.); (F.A.B.); (A.A.-M.A.-A.)
| | - Alaa A.-M. Abdel-Aziz
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia; (B.S.A.); (F.A.B.); (A.A.-M.A.-A.)
| | - Sara T. Al-Rashood
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia; (B.S.A.); (F.A.B.); (A.A.-M.A.-A.)
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7
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Zhou BH, Ding HY, Yang JY, Chai J, Guo HW, Tian EJ. Diclazuril-induced expression of CDK-related kinase 2 in the second-generation merozoites of Eimeria tenella. Mol Biochem Parasitol 2023; 255:111575. [PMID: 37302489 DOI: 10.1016/j.molbiopara.2023.111575] [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: 03/31/2023] [Revised: 05/23/2023] [Accepted: 06/06/2023] [Indexed: 06/13/2023]
Abstract
Diclazuril is a classic anticoccidial drug. The key molecules of diclazuril in anticoccidial action allows target screening for the development of anticoccidial drugs. Cyclin-dependent kinases (CDK) are prominent target proteins in apicomplexan parasites. In this study, a diclazuril anticoccidiosis animal model was established, and the transcription and translation levels of the CDK-related kinase 2 of Eimeria tenella (EtCRK2) were detected. mRNA and protein expression levels of EtCRK2 decreased in the infected/diclazuril group compared with those in the infected/control group. In addition, immunofluorescence analysis showed that EtCRK2 was localised in the cytoplasm of the merozoites. The fluorescence intensity of EtCRK2 in the infected/diclazuril group was significantly weaker than that in the infected/control group. The anticoccidial drug diclazuril against E.tenella affects the expression pattern of EtCRK2 molecule, and EtCRK2 is a potential target for new drug development.
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Affiliation(s)
- Bian-Hua Zhou
- College of Animal Science and Technology, Henan University of Science and Technology, Kaiyuan Avenue 263, Luolong District, Luoyang 471023, Henan, People's Republic of China.
| | - Hai-Yan Ding
- College of Animal Science and Technology, Henan University of Science and Technology, Kaiyuan Avenue 263, Luolong District, Luoyang 471023, Henan, People's Republic of China
| | - Jing-Yun Yang
- College of Animal Science and Technology, Henan University of Science and Technology, Kaiyuan Avenue 263, Luolong District, Luoyang 471023, Henan, People's Republic of China
| | - Jun Chai
- School of information technology and urban construction, Luoyang Vocational and Technical College, Keji Avenue 6, Yibin District, Luoyang 471934, Henan, People's Republic of China
| | - Hong-Wei Guo
- College of Animal Science & Technology, Henan University of Animal Husbandry and Economy, Longzi Hubei Road 6, Zhengzhou 450046, Henan, People's Republic of China
| | - Er-Jie Tian
- College of Animal Science and Technology, Henan University of Science and Technology, Kaiyuan Avenue 263, Luolong District, Luoyang 471023, Henan, People's Republic of China
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8
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Farghaly TA, Abbas EMH, Al-Sheikh MA, Medrasi HY, Masaret GS, Pashameah RA, Qurban J, Harras MF. Synthesis of tricyclic and tetracyclic benzo[6,7]cycloheptane derivatives linked morpholine moiety as CDK2 inhibitors. Drug Dev Res 2023; 84:1127-1141. [PMID: 37170788 DOI: 10.1002/ddr.22074] [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: 02/07/2023] [Revised: 03/11/2023] [Accepted: 04/29/2023] [Indexed: 05/13/2023]
Abstract
With the aim of developing cyclin-dependent kinase 2 (CDK2) inhibitors with strong antibreast cancer efficacy, new tricyclic and tetracyclic benzo[6,7]cycloheptane derivatives were synthesized. The newly synthesized tri- and tetracyclic derivatives were achieved from the reaction of 4-(4-morpholin-4-yl-phenyl)-1,3,4,5,6,7-hexahydro-benzo[6,7]cyclohepta[1,2-d]pyrimidine-2-thione (5) with α-haloketone derivatives as hydrazonyl chlorides, phenacyl bromide derivatives, chloroacetone, and ethyl substituted acetate derivatives. The MCF-7 and MDA-MB-231 breast cancer cell lines were utilized to examine the anticancer properties. Compounds 5 and 8 were shown to be the most effective, with half-maximal inhibitory concentration (IC50 ) values between 5.73 and 9.11 µM, which are on the level with doxorubicin. Mechanistic studies showed that 5 and 8 caused tumor cell death by inducing apoptosis and they also produced cancer arrest in the S phase of the cell cycle. In addition, compounds 5 and 8 showed strong anti-CDK2 action (IC50 = 0.112 and 0.18 µM, respectively) comparable to roscovitine (IC50 = 0.127 µM). Moreover, the docking result demonstrated that derivatives 5 and 8 fit into the CDK2 active site in the proper orientation.
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Affiliation(s)
- Thoraya A Farghaly
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Eman M H Abbas
- Chemistry of National and Microbial Products Department, National Research Centre, Giza, Egypt
| | - Mariam A Al-Sheikh
- Department of Chemistry, Faculty of Science, University of Jeddah, AlFaisaliah, Jeddah, Saudi Arabia
| | - Hanadi Y Medrasi
- Department of Chemistry, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Ghada S Masaret
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Rami Adel Pashameah
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Jihan Qurban
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Marwa F Harras
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
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9
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Wang H, Tang X, Liu Y. SlCK2α as a novel substrate for CRL4 E3 ligase regulates fruit size through maintenance of cell division homeostasis in tomato. PLANTA 2023; 257:38. [PMID: 36645501 DOI: 10.1007/s00425-023-04070-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
This study unravels a novel regulatory module (CRL4-CK2α-CDK2) involving fruit size control by mediating cell division homeostasis (SlCK2α and SlCDK2) in tomato. Fruit size is one of the crucial agronomical traits for crop production. UV-damaged DNA binding protein 1 (DDB1), a core component of Cullin4-RING E3 ubiquitin ligase complex (CRL4), has been identified as a negative regulator of fruit size in tomato (Solanum lycopersicum). However, the underlying molecular mechanism remains largely unclear. Here, we report the identification and characterization of a SlDDB1-interacting protein putatively involving fruit size control through regulating cell proliferation in tomato. It is a tomato homolog SlCK2α, the catalytic subunit of the casein kinase 2 (CK2), identified by yeast two-hybrid (Y2H) assays. The interaction between SlDDB1 and SlCK2α was demonstrated by bimolecular fluorescence complementation (BiFC) and co-immunoprecipitation (Co-IP). RNA interference (RNAi) and CRISPR/Cas9-based mutant analyses showed that lack of SlCK2α resulted in reduction of fruit size with reduced cell number, suggesting it is a positive regulator on fruit size by promoting cell proliferation. We also showed SlDDB1 is required to ubiquitinate SlCK2α and negatively regulate its stability through 26S proteasome-mediated degradation. Furthermore, we found that a tomato homolog of cell division protein kinase 2 (SlCDK2) could interact with and specifically be phosphorylated by SlCK2α, resulting in an increase of SlCDK2 protein stability. CRISPR/Cas9-based genetic evidence showed that SlCDK2 is also a positive regulator of fruit size by influencing cell division in tomato. Taken together, our findings, thus, unravel a novel regulatory module CRL4-CK2α-CDK2 in finely modulating cell division homeostasis and the consequences on fruit size.
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Affiliation(s)
- Hongtao Wang
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Xiaofeng Tang
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China.
| | - Yongsheng Liu
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China.
- School of Horticulture and State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China.
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China.
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10
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Mandour AA, Nassar IF, Abdel Aal MT, Shahin MAE, El-Sayed WA, Hegazy M, Yehia AM, Ismail A, Hagras M, Elkaeed EB, Refaat HM, Ismail NSM. Synthesis, biological evaluation, and in silico studies of new CDK2 inhibitors based on pyrazolo[3,4- d]pyrimidine and pyrazolo[4,3- e][1,2,4]triazolo[1,5- c]pyrimidine scaffold with apoptotic activity. J Enzyme Inhib Med Chem 2022; 37:1957-1973. [PMID: 35815597 PMCID: PMC9278437 DOI: 10.1080/14756366.2022.2086866] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cyclin-dependent kinase inhibition is considered a promising target for cancer treatment for its crucial role in cell cycle regulation. Pyrazolo pyrimidine derivatives were well established for their antitumor activity via CDK2 inhibition. In this research, new series of pyrazolopyrimidine derivatives (4-15) was designed and synthesised as novel CDK2 inhibitors. The anti-proliferative activities against MCF-7, HCT-116, and HepG-2 were used to evaluate their anticancer activity as novel CDK2 inhibitors. Most of the compounds showed superior cytotoxic activity against MCF-7 and HCT-116 compared to Sorafenib. Only compounds 8, 14, and 15 showed potent activity against HepG-2. The CDK2/cyclin A2 enzyme inhibitory activity was tested for all synthesised compounds. Compound 15 showed the most significant inhibitory activity with IC50 0.061 ± 0.003 µM. It exerted remarkable alteration in Pre G1 and S phase cell cycle progression and caused apoptosis in HCT cells. In addition, the normal cell line cytotoxicity for compound 15 was assigned revealing low cytotoxic results in normal cells rather than cancer cells. Molecular docking was achieved on the designed compounds and confirmed the two essential hydrogen binding with Leu83 in CDK2 active site. In silico ADMET studies and drug-likeness showed proper pharmacokinetic properties which helped in structure requirements prediction for the observed antitumor activity.
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Affiliation(s)
- Asmaa A Mandour
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Future University in Egypt (FUE), Cairo, Egypt
| | - Ibrahim F Nassar
- Faculty of Specific Education, Ain Shams University (ASU), Cairo, Egypt
| | - Mohammed T Abdel Aal
- Chemistry Department, Faculty of Science, Menoufia University, Shebin El-Kom, Egypt
| | - Mahmoud A E Shahin
- Chemistry Department, Faculty of Science, Menoufia University, Shebin El-Kom, Egypt
| | - Wael A El-Sayed
- Chemistry Department, College of Science, Qassim University, Qassim, Saudi Arabia.,Photochemistry Department, National Research Centre, Cairo, Egypt
| | - Maghawry Hegazy
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Amr Mohamed Yehia
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Ahmed Ismail
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Mohamed Hagras
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Eslam B Elkaeed
- Department of Pharmaceutical Science, College of Pharmacy, Al Maarefa University, Riyadh, Saudi Arabia
| | - Hanan M Refaat
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Future University in Egypt (FUE), Cairo, Egypt
| | - Nasser S M Ismail
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Future University in Egypt (FUE), Cairo, Egypt
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11
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FMR1NB Involved in Glioma Tumorigenesis Is a Promising Target for Prognosis and Therapy. Curr Med Sci 2022; 42:803-816. [DOI: 10.1007/s11596-022-2586-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 11/12/2021] [Indexed: 11/03/2022]
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12
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Farghaly TA, Al-Hasani WA, Ibrahim MH, Abdellattif MH, Abdallah ZA. Design, Synthesis, Anticancer Activity and Docking Studies of Thiazole Linked Phenylsulfone Moiety as Cyclin-Dependent Kinase 2 (CDK2) Inhibitors. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2097715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Thoraya A. Farghaly
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Wedian A. Al-Hasani
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mona H. Ibrahim
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Magda H. Abdellattif
- Department of Chemistry, College of Science, Taif University, Taif, Saudi Arabia
| | - Zeinab A. Abdallah
- Department of Chemistry, Faculty of Science, Cairo University, Giza, Egypt
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13
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Synthesis and Evaluation of Some New 4H-Pyran Derivatives as Antioxidant, Antibacterial and Anti-HCT-116 Cells of CRC, with Molecular Docking, Antiproliferative, Apoptotic and ADME Investigations. Pharmaceuticals (Basel) 2022; 15:ph15070891. [PMID: 35890189 PMCID: PMC9317316 DOI: 10.3390/ph15070891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/24/2022] [Accepted: 07/02/2022] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer oncogenesis is linked to dysbiosis, oxidative stress and overexpression of CDK2. The 4H-pyran scaffold is considered an antitumoral, antibacterial and antioxidant lead as well as a CDK2 inhibitor. Herein, certain 4H-pyran derivatives were evaluated as antibacterial, antioxidant and cytotoxic agents against HCT-116 cells. Derivatives 4g and 4j inhibited all the tested Gram-positive isolates, except for B. cereus (ATCC 14579), with lower IC50 values (µM) than ampicillin. In addition, 4g and 4j demonstrated the strongest DPPH scavenging and reducing potencies, with 4j being more efficient than BHT. In cell viability assays, 4d and 4k suppressed the proliferation of HCT-116 cells, with the lowest IC50 values being 75.1 and 85.88 µM, respectively. The results of molecular docking simulations of 4d and 4k, inhibitory kinase assays against CDK2, along with determination of CDK2 protein concentration and the expression level of CDK2 gene in the lysates of HCT-116 treated cells, suggested that these analogues blocked the proliferation of HCT-116 cells by inhibiting kinase activity and downregulating expression levels of CDK2 protein and gene. Moreover, 4d and 4k were found to induce apoptosis in HCT-116 cells via activation of the caspase-3 gene. Lastly, compounds 4g, 4j, 4d and 4k were predicted to comply with Lipinski’s rule of five, and they are expected to possess excellent physiochemical and pharmacokinetic properties suitable for in vivo bioavailability, as predicted by the SwissADME web tool.
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14
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Zhang J, Gan Y, Li H, Yin J, He X, Lin L, Xu S, Fang Z, Kim BW, Gao L, Ding L, Zhang E, Ma X, Li J, Li L, Xu Y, Horne D, Xu R, Yu H, Gu Y, Huang W. Inhibition of the CDK2 and Cyclin A complex leads to autophagic degradation of CDK2 in cancer cells. Nat Commun 2022; 13:2835. [PMID: 35595767 PMCID: PMC9122913 DOI: 10.1038/s41467-022-30264-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 04/23/2022] [Indexed: 12/20/2022] Open
Abstract
Cyclin-dependent kinase 2 (CDK2) complex is significantly over-activated in many cancers. While it makes CDK2 an attractive target for cancer therapy, most inhibitors against CDK2 are ATP competitors that are either nonspecific or highly toxic, and typically fail clinical trials. One alternative approach is to develop non-ATP competitive inhibitors; they disrupt interactions between CDK2 and either its partners or substrates, resulting in specific inhibition of CDK2 activities. In this report, we identify two potential druggable pockets located in the protein-protein interaction interface (PPI) between CDK2 and Cyclin A. To target the potential druggable pockets, we perform a LIVS in silico screening of a library containing 1925 FDA approved drugs. Using this approach, homoharringtonine (HHT) shows high affinity to the PPI and strongly disrupts the interaction between CDK2 and cyclins. Further, we demonstrate that HHT induces autophagic degradation of the CDK2 protein via tripartite motif 21 (Trim21) in cancer cells, which is confirmed in a leukemia mouse model and in human primary leukemia cells. These results thus identify an autophagic degradation mechanism of CDK2 protein and provide a potential avenue towards treating CDK2-dependent cancers. CDK2 can drive the proliferation of cancer cells. Here, the authors screened for a non-ATP competitive inhibitor of the CDK2/cylinA complex and find that Homoharringtonine can disrupt the complex and promote the degradation of CDK2.
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Affiliation(s)
- Jiawei Zhang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), Second Affiliated Hospital, School of Medicine, Zhejiang University, 310009, Hangzhou, China.,Molecular and Cellular Biology of Cancer Program & Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Yichao Gan
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), Second Affiliated Hospital, School of Medicine, Zhejiang University, 310009, Hangzhou, China.,Institute of Genetics, Zhejiang University and Department of Human Genetics, Zhejiang University School of Medicine, 310058, Hangzhou, Zhejiang, China
| | - Hongzhi Li
- Department of Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Jie Yin
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), Second Affiliated Hospital, School of Medicine, Zhejiang University, 310009, Hangzhou, China.,Institute of Genetics, Zhejiang University and Department of Human Genetics, Zhejiang University School of Medicine, 310058, Hangzhou, Zhejiang, China
| | - Xin He
- Division of Hematopoietic Stem Cell & Leukemia Research, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Liming Lin
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), Second Affiliated Hospital, School of Medicine, Zhejiang University, 310009, Hangzhou, China.,Department of Hematology, Second Affiliated Hospital, School of Medicine, Zhejiang University, 310009, Hangzhou, China
| | - Senlin Xu
- Molecular and Cellular Biology of Cancer Program & Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA.,Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Zhipeng Fang
- Molecular and Cellular Biology of Cancer Program & Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Byung-Wook Kim
- Molecular and Cellular Biology of Cancer Program & Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Lina Gao
- Molecular and Cellular Biology of Cancer Program & Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Lili Ding
- Molecular and Cellular Biology of Cancer Program & Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Eryun Zhang
- Molecular and Cellular Biology of Cancer Program & Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Xiaoxiao Ma
- Molecular and Cellular Biology of Cancer Program & Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Junfeng Li
- Department of Translational Research & Cellular Therapeutics, Beckman Research Institute of the City of Hope, Duarte, CA, 91010, USA
| | - Ling Li
- Division of Hematopoietic Stem Cell & Leukemia Research, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Yang Xu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), Second Affiliated Hospital, School of Medicine, Zhejiang University, 310009, Hangzhou, China.,Department of Hematology, Second Affiliated Hospital, School of Medicine, Zhejiang University, 310009, Hangzhou, China
| | - David Horne
- Department of Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Rongzhen Xu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), Second Affiliated Hospital, School of Medicine, Zhejiang University, 310009, Hangzhou, China.,Department of Hematology, Second Affiliated Hospital, School of Medicine, Zhejiang University, 310009, Hangzhou, China
| | - Hua Yu
- Department of Immuno-Oncology, Beckman Research Institute of the City of Hope, Duarte, CA, 91010, USA
| | - Ying Gu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), Second Affiliated Hospital, School of Medicine, Zhejiang University, 310009, Hangzhou, China. .,Institute of Genetics, Zhejiang University and Department of Human Genetics, Zhejiang University School of Medicine, 310058, Hangzhou, Zhejiang, China. .,Zhejiang Provincial Key Lab of Genetic and Developmental Disorder, 310058, Hangzhou, Zhejiang, China. .,Liangzhu Laboratory, Zhejiang University Medical Center, 311121, Hangzhou, Zhejiang, China.
| | - Wendong Huang
- Molecular and Cellular Biology of Cancer Program & Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA. .,Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA.
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15
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Said MA, Abdelrahman MA, Abourehab MAS, Fares M, Eldehna WM. A patent review of anticancer CDK2 inhibitors (2017-present). Expert Opin Ther Pat 2022; 32:885-898. [PMID: 35583393 DOI: 10.1080/13543776.2022.2078193] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION : The success of the CDK4/6 inhibitor Ibrance™ (Palbociclib) as an anticancer agent inspired and directed more efforts towards the discovery of selective cyclin-dependent kinase (CDKs) inhibitors. CDK2 is a member of the CDKs family that plays an important role in regulating the progression of cells into both S- and M-phases of the cell cycle. Studies suggest that overexpression of CDK2 may be implicated in tumor growth in cancer. AREAS COVERED : This review covers the patent literature of CDK2 inhibitors published between 2017 and 2021. We searched the online databases of the European Patent Office, American Chemical Society, and Google patents. EXPERT OPINION Developing selective CDK2 inhibitors is challenging due to the absence of a previously approved selective CDK2 inhibitor. However, ongoing efforts by Incyte Corporation and Pfizer Inc., which are reported herein, may stand out as a new starting point and bring novel information critical for the medicinal chemistry and drug design scientists in the field of CDK2 inhibitors development.
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Affiliation(s)
- Mohamed A Said
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo, 11829, Egypt
| | - Mohamed A Abdelrahman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo, 11829, Egypt
| | - Mohammed A S Abourehab
- Department of Pharmaceutics, Faculty of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia.,Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Minia University, Minia 61519, Egypt
| | - Mohamed Fares
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo, 11829, Egypt.,School of Chemistry, The University of Sydney, NSW 2006, Australia
| | - Wagdy M Eldehna
- School of Biotechnology, Badr University in Cairo, Badr City, Cairo 11829, Egypt.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt
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16
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Novel Azine Linked Hybrids of 2-indolinone and Thiazolodinone Scaffolds as CDK2 inhibitors with potential anticancer activity: In Silico Design, Synthesis, Biological, Molecular Dynamics and Binding Free Energy Studies. Bioorg Chem 2022; 126:105884. [PMID: 35623140 DOI: 10.1016/j.bioorg.2022.105884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/28/2022] [Accepted: 05/17/2022] [Indexed: 11/23/2022]
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17
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Badaoui M, Buigues PJ, Berta D, Mandana GM, Gu H, Földes T, Dickson CJ, Hornak V, Kato M, Molteni C, Parsons S, Rosta E. Combined Free-Energy Calculation and Machine Learning Methods for Understanding Ligand Unbinding Kinetics. J Chem Theory Comput 2022; 18:2543-2555. [PMID: 35195418 PMCID: PMC9097281 DOI: 10.1021/acs.jctc.1c00924] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
The
determination of drug residence times, which define the time
an inhibitor is in complex with its target, is a fundamental part
of the drug discovery process. Synthesis and experimental measurements
of kinetic rate constants are, however, expensive and time consuming.
In this work, we aimed to obtain drug residence times computationally.
Furthermore, we propose a novel algorithm to identify molecular design
objectives based on ligand unbinding kinetics. We designed an enhanced
sampling technique to accurately predict the free-energy profiles
of the ligand unbinding process, focusing on the free-energy barrier
for unbinding. Our method first identifies unbinding paths determining
a corresponding set of internal coordinates (ICs) that form contacts
between the protein and the ligand; it then iteratively updates these
interactions during a series of biased molecular dynamics (MD) simulations
to reveal the ICs that are important for the whole of the unbinding
process. Subsequently, we performed finite-temperature string simulations
to obtain the free-energy barrier for unbinding using the set of ICs
as a complex reaction coordinate. Importantly, we also aimed to enable
the further design of drugs focusing on improved residence times.
To this end, we developed a supervised machine learning (ML) approach
with inputs from unbiased “downhill” trajectories initiated
near the transition state (TS) ensemble of the string unbinding path.
We demonstrate that our ML method can identify key ligand–protein
interactions driving the system through the TS. Some of the most important
drugs for cancer treatment are kinase inhibitors. One of these kinase
targets is cyclin-dependent kinase 2 (CDK2), an appealing target for
anticancer drug development. Here, we tested our method using two
different CDK2 inhibitors for the potential further development of
these compounds. We compared the free-energy barriers obtained from
our calculations with those observed in available experimental data.
We highlighted important interactions at the distal ends of the ligands
that can be targeted for improved residence times. Our method provides
a new tool to determine unbinding rates and to identify key structural
features of the inhibitors that can be used as starting points for
novel design strategies in drug discovery.
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Affiliation(s)
- Magd Badaoui
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom.,Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Pedro J Buigues
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Dénes Berta
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Gaurav M Mandana
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom
| | - Hankang Gu
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Tamás Földes
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Callum J Dickson
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Viktor Hornak
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Mitsunori Kato
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Carla Molteni
- Department of Physics, King's College London, London WC2R 2LS, United Kingdom
| | - Simon Parsons
- School of Computer Science, University of Lincoln, Lincoln LN6 7TS, United Kingdom
| | - Edina Rosta
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom.,Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
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18
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Nassar IF, Abdel Aal MT, El-Sayed WA, A. E Shahin M, Elsakka EGE, Mokhtar MM, Hegazy M, Hagras M, Mandour AA, Ismail NSM. Discovery of pyrazolo[3,4- d]pyrimidine and pyrazolo[4,3- e][1,2,4]triazolo[1,5- c]pyrimidine derivatives as novel CDK2 inhibitors: synthesis, biological and molecular modeling investigations. RSC Adv 2022; 12:14865-14882. [PMID: 35702208 PMCID: PMC9112407 DOI: 10.1039/d2ra01968j] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 04/28/2022] [Indexed: 12/30/2022] Open
Abstract
CDK2 inhibition is an appealing target for cancer treatment that targets tumor cells in a selective manner. A new set of small molecules featuring the privileged pyrazolo[3,4-d]pyrimidine and pyrazolo[4,3-e][1,2,4]triazolo[1,5-c]pyrimidine scaffolds (4–13) as well as the thioglycoside derivatives (14, 15) were designed, and synthesized as novel CDK2 targeting compounds. The growth of the three examined cell lines was significantly inhibited by most of the prepared compounds. Results revealed that most of the compounds showed superior cytotoxic activities against MCF-7 and HCT-116 with IC50 range (45–97 nM) and (6–99 nM), respectively, and moderate activity against HepG-2 with IC50 range of (48–90 nM) compared to sorafenib (IC50: 144, 176 and 19 nM, respectively). Of these compounds, 14 & 15 showed the best cytotoxic activities against the three cell lines with IC50 values of 45, 6, and 48 nM and 46, 7, and 48 nM against MCF-7, HCT-116 and HepG-2, respectively. Enzymatic inhibitory activity against CDK2/cyclin A2 was achieved for the most potent anti-proliferative compounds. Compounds 14, 13 and 15 revealed the most significant inhibitory activity with IC50 values of 0.057 ± 0.003, 0.081 ± 0.004 and 0.119 ± 0.007 μM, respectively compared to sorafenib (0.184 ± 0.01 μM). Compound 14 displayed potent dual activity against the examined cell lines and CDK2, and was thus selected for further investigations. It exerted a significance alteration in cell cycle progression, in addition to apoptosis induction within HCT cells. Molecular docking simulation of the designed compounds confirmed the good fit into the CDK2 active site through the essential hydrogen bonding with Leu83. In silico ADMET studies and drug-likeness studies using a Boiled Egg chart showed suitable pharmacokinetic properties which helped in structure requirement prediction for the observed antitumor activity. A new set of pyrazolo[3,4-d]pyrimidine and pyrazolo[4,3-e][1,2,4]triazolo[1,5-c]pyrimidine scaffolds (4–13) as well as the thioglycoside derivatives (14, 15) were designed, and synthesized as novel CDK2 targeting compounds.![]()
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Affiliation(s)
- Ibrahim F. Nassar
- Faculty of Specific Education, Ain Shams University (ASU), 365 Ramsis Street, Abassia, Cairo, Egypt
| | | | - Wael A. El-Sayed
- Department of Chemistry, College of Science, Qassim University, Kingdom of Saudi Arabia
- Photochemistry Department, National Research Centre, El-Behouth St., Dokki, Cairo, Egypt
| | - Mahmoud A. E Shahin
- Chemistry Department, Faculty of Science, Menoufia University, Shebin El-Kom, Egypt
| | - Elsayed G. E. Elsakka
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Mahmoud Mohamed Mokhtar
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Maghawry Hegazy
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Mohamed Hagras
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Asmaa A. Mandour
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Future University in Egypt (FUE), Cairo 11835, Egypt
| | - Nasser S. M. Ismail
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Future University in Egypt (FUE), Cairo 11835, Egypt
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19
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Abd El-wahab HA, Mansour HS, Ali AM, El-Awady R, Aboul-Fadl T. New Cell Cycle Checkpoint Pathways Regulators with 2-Oxo-indoline Scaffold as Potential Anticancer Agents: Design, Synthesis, Biological Activities and In Silico Studies. Bioorg Chem 2022; 120:105622. [DOI: 10.1016/j.bioorg.2022.105622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 12/18/2021] [Accepted: 01/11/2022] [Indexed: 12/11/2022]
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Liu X, Liu S, Piao C, Zhang Z, Zhang X, Jiang Y, Kong C. Non-metabolic function of MTHFD2 activates CDK2 in bladder cancer. Cancer Sci 2021; 112:4909-4919. [PMID: 34632667 PMCID: PMC8645701 DOI: 10.1111/cas.15159] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/30/2021] [Accepted: 10/03/2021] [Indexed: 12/24/2022] Open
Abstract
Bladder cancer is a common tumor with a high recurrence rate and high fatality rate, and its mechanism of occurrence and development remains unclear. Many proteins and metabolites reprogram at different stages of tumor development to support tumor cell growth. The moonlighting effect happens when a protein performs multiple functions simultaneously in a cell. In this study, we identified a metabolic protein, MTHFD2, which participates in the cell cycle by binding to CDK2 in bladder cancer. MTHFD2 has been shown to affect bladder cancer cell growth, which is independent of its metabolic function. We found that MTHFD2 was involved in cell cycle regulation and could encourage cell cycle progression by activating CDK2 and sequentially affecting E2F1 activation. In addition, moonlighting MTHFD2 might be regulated by the dynamics of the mitochondria. In conclusion, MTHFD2 localizes in the nucleus to perform a distinct function of catalyzing metabolic reactions. Moreover, the nuclear MTHFD2 activates CDK2 and promotes bladder cancer cell growth by modulating the cell cycle.
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Affiliation(s)
- Xi Liu
- Department of UrologyThe First Hospital of China Medical UniversityShenyangChina
| | - Shuangjie Liu
- Department of UrologyThe First Hospital of China Medical UniversityShenyangChina
| | - Chiyuan Piao
- Department of UrologyThe First Hospital of China Medical UniversityShenyangChina
| | - Zhe Zhang
- Department of UrologyThe First Hospital of China Medical UniversityShenyangChina
| | - Xiaotong Zhang
- Department of UrologyThe First Hospital of China Medical UniversityShenyangChina
| | - Yuanjun Jiang
- Department of UrologyThe First Hospital of China Medical UniversityShenyangChina
| | - Chuize Kong
- Department of UrologyThe First Hospital of China Medical UniversityShenyangChina
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21
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Synthesis of Novel 2-Thiouracil-5-Sulfonamide Derivatives as Potent Inducers of Cell Cycle Arrest and CDK2A Inhibition Supported by Molecular Docking. Int J Mol Sci 2021; 22:ijms222111957. [PMID: 34769385 PMCID: PMC8584424 DOI: 10.3390/ijms222111957] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/19/2021] [Accepted: 10/29/2021] [Indexed: 01/16/2023] Open
Abstract
In an effort to discover potent anticancer agents, 2-thiouracil-5-sulfonamides derivatives were designed and synthesized. The cytotoxic activity of all synthesized compounds was investigated against four human cancer cell lines viz A-2780 (ovarian), HT-29 (colon), MCF-7 (breast), and HepG2 (liver). Compounds 6b,d-g, and 7b showed promising anticancer activity and significant inhibition of CDK2A. Moreover, they were all safe when tested on WI38 normal cells with high selectivity index for cancer cells. Flow cytometric analysis for the most active compound 6e displayed induction of cell growth arrest at G1/S phase (A-2780 cells), S phase (HT-29 and MCF-7 cells), and G2/M phase (HepG2 cells) and stimulated the apoptotic death of all cancer cells. Moreover, 6e was able to cause cycle arrest indirectly through enhanced expression of cell cycle inhibitors p21 and p27. Finally, molecular docking of compound 6e endorsed its proper binding to CDK2A, which clarifies its potent anticancer activity.
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22
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Almehmadi SJ, Alsaedi AMR, Harras MF, Farghaly TA. Synthesis of a new series of pyrazolo[1,5-a]pyrimidines as CDK2 inhibitors and anti-leukemia. Bioorg Chem 2021; 117:105431. [PMID: 34688130 DOI: 10.1016/j.bioorg.2021.105431] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 09/21/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022]
Abstract
Based on the structural study of previously known CDK2 inhibitors, a new series of pyrazolo[1,5-a]pyrimidine derivatives was designed and synthesized. The target compounds were biologically assessed as potent CDK2 inhibitors and promising anti-leukemia hits. The 7-(4-Bromo-phenyl)-3-(3-chloro/2-chloro-phenylazo)-pyrazolo[1,5-a]pyrimidin-2-ylamines 5 h and 5i revealed the best CDK2 inhibitory activity with comparable potency (IC50 = 22 and 24 nM, respectively) to that of dinaciclib (IC50 = 18 nM). Additionally, both analogues showed potent activities against CDK1, CDK5 and CDK9 at nanomolar concentrations (IC50 = 28-80 nM). The anti-leukemia screening of the target compounds showed strong to moderate cytotoxicity against the used leukemia cell lines (MOLT-4 and HL-60). Compound 5 h inhibited MOLT-4 and HL-60 by 1.4 and 2.3 folds (IC50 = 0.93 and 0.80 µM), respectively, compared to dinaciclib (IC50 = 1.30 and 1.84 µM). Furthermore, compound 5i was comparable to dinaciclib against MOLT-4 and exhibited twice its activity against HL-60. Besides, the cytotoxicity of the promising analogues on normal human blood cells indicated the safety of 5h and 5i as compared to the reference dinaciclib. The pharmacokinetic properties of 5h and 5i were predicted using ADME calculations revealing good oral bioavailability and high GI absorption. The molecular docking simulations indicated, as expected, that the dinaciclib analogues can well-accommodate the CDK2 binding site, forming a variety of interactions.
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Affiliation(s)
- Samar J Almehmadi
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah Almukaramah 21514, Saudi Arabia
| | - Amani M R Alsaedi
- Department of Chemistry, Collage of Science, Taif University, P. O. Box 11099, Taif 21944, Saudi Arabia
| | - Marwa F Harras
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt.
| | - Thoraya A Farghaly
- Department of Chemistry, Faculty of Science, Cairo University, Giza 12613, Egypt.
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23
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Shawky AM, Ibrahim NA, Abdalla AN, Abourehab MAS, Gouda AM. Novel pyrrolizines bearing 3,4,5-trimethoxyphenyl moiety: design, synthesis, molecular docking, and biological evaluation as potential multi-target cytotoxic agents. J Enzyme Inhib Med Chem 2021; 36:1313-1333. [PMID: 34154478 PMCID: PMC8221158 DOI: 10.1080/14756366.2021.1937618] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
In the present study, two new series of pyrrolizines bearing 3,4,5-trimethoxyphenyl moiety were designed, synthesised, and evaluated for their cytotoxic activity. The benzamide derivatives 16a-e showed higher cytotoxicity than their corresponding Schiff bases 15a-e. Compounds 16a,b,d also inhibited the growth of MCF-7/ADR cells with IC50 in the range of 0.52-6.26 μM. Interestingly, the new compounds were less cytotoxic against normal MRC-5 cells (IC50=0.155-17.08 μM). Mechanistic studies revealed the ability of compounds 16a,b,d to inhibit tubulin polymerisation and multiple oncogenic kinases. Moreover, compounds 16a,b,d induced preG1 and G2/M cell cycle arrest and early apoptosis in MCF-7 cells. The molecular docking analyses of compounds 16a,b,d into the active site in tubulin, CDK-2, and EGFR proteins revealed higher binding affinities compared to the co-crystallised ligands. These preliminary results suggested that compounds 16a,b,d could serve as promising lead compounds for the future development of new potent anticancer agents.HighlightsTwo new series of pyrrolizines bearing 3,4,5-trimethoxyphenyl moieties were synthesized.Compounds 16a,b,d displayed the highest cytotoxicity against the three cancer cell lines.Kinase profiling test revealed inhibition of multiple oncogenic kinases by compounds 16a,b,d.Compounds 16a,b,d exhibited weak to moderate inhibition of tubulin-polymerization.Compounds 16a,b,d induced preG1 and G2/M cell cycle arrest and early apoptosis in MCF-7 cells.Docking studies revealed high binding affinities for compounds 16a,b towards tubulin and CDK-2.
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Affiliation(s)
- Ahmed M Shawky
- Science and Technology Unit (STU), Umm Al-Qura University, Makkah, Saudi Arabia.,Central Laboratory for Micro-analysis, Minia University, Minia, Egypt
| | - Nashwa A Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia.,Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia.,Department of Pharmacology and Toxicology, Medicinal and Aromatic Plants Research Institute, National Center for Research, Khartoum, Sudan
| | - Mohammed A S Abourehab
- Department of Pharmaceutics, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia.,Department of Pharmaceutics, Faculty of Pharmacy, Minia University, Minia, Egypt
| | - Ahmed M Gouda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia.,Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
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24
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Eldehna WM, El Hassab MA, Abo-Ashour MF, Al-Warhi T, Elaasser MM, Safwat NA, Suliman H, Ahmed MF, Al-Rashood ST, Abdel-Aziz HA, El-Haggar R. Development of isatin-thiazolo[3,2-a]benzimidazole hybrids as novel CDK2 inhibitors with potent in vitro apoptotic anti-proliferative activity: Synthesis, biological and molecular dynamics investigations. Bioorg Chem 2021; 110:104748. [PMID: 33684714 DOI: 10.1016/j.bioorg.2021.104748] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/09/2020] [Accepted: 02/13/2021] [Indexed: 12/14/2022]
Abstract
In the current medical era, human health is experiencing numerous challenges, particularly the human malignancies. Therefore, the therapeutic arsenal for these malignancies is to be inexorably enhanced with new treatments that target tumor cells in a selective manner. In this regard, the present work aims at developing a new set of small molecules featuring the privileged isatin scaffold conjugated with a thiazolo[3,2-a]benzimidazole (TBI) motif through a cleavable hydrazide linker (7a-e and 10a-i) as potential anticancer CDK2 inhibitors. The large tricyclic TBI motif is anticipated to achieve a plethora of hydrophobic interactions within the CDK2 binding site. The growth of the two examined cell lines was significantly inhibited by most the prepared hybrids with IC50 ranges; (2.60 ± 1.47-20.90 ± 1.17 µM, against MDA-MB-231) and (1.27 ± 0.06-16.83 ± 0.95 µM, against MCF-7). In particular, hybrids 7a, 7d and 10a displayed potent dual activity against the examined cell lines, and thus selected for further investigations. They exerted a significance alteration in the cell cycle progression, in addition to an apoptosis induction within both MDA-MB-231 and MCF-7 cells. Furthermore, 7a, 7d and 10a displayed potent CDK2 inhibitory action (IC50 = 96.46 ± 5.3, 26.24 ± 1.4 and 42.95 ± 2.3 nM, respectively). The docking simulations unveiled, as expected, the ability of the TBI ring to well-accommodate and establish several hydrophobic interactions within a hydrophobic pocket in the CDK2 binding site. Also, the docking simulations highlighted the significance of incorporation of the hydrazide linker and isatin unsubstituted (NH) functionality in the H-bonding interactions. Interestingly, the most potent CDK2 inhibitor 7d achieved the best binding score (-11.2 Kcal/mole) and formed the most stable complex with CDK2 enzyme (RMSD = 1.24 Å) in a 100 ns MD simulation. In addition, the MM-PBSA calculations ascribed the lowest binding free energy to the 7d-CDK2 complex (-323.69 ± 15.17 kJ/mol). This could be attributed to an incorporation of the 5-OCH3 group that was engaged in an extra hydrogen bonding with key THR14 amino acid residue. Finally, these results suggested hybrid 7d as a good candidate for further optimization as promising breast cancer antitumor agent and CDK2 inhibitor.
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Affiliation(s)
- Wagdy M Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh P.O. Box 33516, Egypt.
| | - Mahmoud A El Hassab
- Department of Pharmaceutical Chemistry, School of Pharmacy, Badr University in Cairo, Badr City 11829, Cairo, Egypt
| | - Mahmoud F Abo-Ashour
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo, Egypt
| | - Tarfah Al-Warhi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Mahmoud M Elaasser
- The Regional Center for Mycology and Biotechnology, Al-Azhar University, Cairo, Egypt
| | - Nesreen A Safwat
- The Regional Center for Mycology and Biotechnology, Al-Azhar University, Cairo, Egypt
| | - Howayda Suliman
- Department of Medical Biochemistry, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Marwa F Ahmed
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Helwan University, 11795 Cairo, Egypt; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Taif University, Taif 21974, Saudi Arabia
| | - Sara T Al-Rashood
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Hatem A Abdel-Aziz
- Department of Applied Organic Chemistry, National Research Center, Dokki, Giza P.O. Box 12622, Egypt
| | - Radwan El-Haggar
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Helwan University, 11795 Cairo, Egypt
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25
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Vettori A, Paolacci S, Maltese PE, Herbst KL, Cestari M, Michelini S, Michelini S, Samaja M, Bertelli M. Genetic Determinants of the Effects of Training on Muscle and Adipose Tissue Homeostasis in Obesity Associated with Lymphedema. Lymphat Res Biol 2020; 19:322-333. [PMID: 33373545 DOI: 10.1089/lrb.2020.0057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
It is widely accepted that metabolic changes associated with training are influenced by a person's genetic background. In this review, we explore the polymorphisms underlying interindividual variability in response to training of weight loss and muscle mass increase in obese individuals, with or without lymphedema, and in normal-weight subjects. We searched PubMed for articles in English published up to May 2019 using the following keywords: (((physical training[Title/Abstract] OR sport activity[Title/Abstract]) AND predisposition[Title/Abstract]) AND polymorphism [Title/Abstract]). We identified 38 single-nucleotide polymorphisms that may modulate the genetic adaptive response to training. The identification of genetic marker(s) that improve the beneficial effects of training may in perspective make it possible to assess training programs, which in combination with dietary intervention can optimize body weight reduction in obese subjects, with or without lymphedema. This is particularly important for patients with lymphedema because obesity can worsen the clinical status, and therefore, a personalized approach that could reduce obesity would be fundamental in the clinical management of lymphedema.
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Affiliation(s)
- Andrea Vettori
- Department of Biotechnology, University of Verona, Verona, Italy
| | | | | | - Karen L Herbst
- Department of Medicine, University of Arizona, Tucson, Arizona, USA.,Department of Pharmacy, University of Arizona, Tucson, Arizona, USA.,Department of Medical Imaging, University of Arizona, Tucson, Arizona, USA.,Department of Surgery, University of Arizona, Tucson, Arizona, USA
| | - Marina Cestari
- Study Centre Pianeta Linfedema, Terni, Italy.,Lymphology Sector of the Rehabilitation Service, USLUmbria2, Terni, Italy
| | - Sandro Michelini
- Department of Vascular Rehabilitation, San Giovanni Battista Hospital, Rome, Italy
| | - Serena Michelini
- Unit of Physical Medicine and Rehabilitation, Sant'Andrea Hospital, "Sapienza" University of Rome, Rome, Italy
| | - Michele Samaja
- Department of Health Science, University of Milan-San Paolo Hospital, Milan, Italy
| | - Matteo Bertelli
- MAGI'S Lab, Rovereto, Italy.,MAGI Euregio, Bolzano, Italy.,EBTNA-LAB, Rovereto, Italy
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26
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Zhang Y, Duan S, Jang A, Mao L, Liu X, Huang G. JQ1, a selective inhibitor of BRD4, suppresses retinoblastoma cell growth by inducing cell cycle arrest and apoptosis. Exp Eye Res 2020; 202:108304. [PMID: 33080301 DOI: 10.1016/j.exer.2020.108304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 10/02/2020] [Accepted: 10/13/2020] [Indexed: 12/11/2022]
Abstract
Retinoblastoma (RB) is the most common intraocular cancer in children, and chemotherapy has been the first-line treatment. However, due to the side effects of chemotherapy drugs, novel treatments must be developed. JQ1, a selective inhibitor of BRD4, suppresses cell growth in several cancers in which BRD4 is overexpressed. In the present study, BRD4 was overexpressed in retinoblastoma, and JQ1 effectively inhibited RB cell proliferation and colony formation by inducing cell cycle arrest and promoting apoptosis. Furthermore, the Myc-P21-CDK2 and Myc-cyclinD3/CDK6 pathways were activated in RB cells treated with JQ1, and an animal experiment suggested that JQ1 significantly inhibited tumour growth in vivo. In conclusion, JQ1 may be a potential drug treatment for retinoblastoma.
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Affiliation(s)
- Yanyan Zhang
- Department of Ophthalmology, The Third Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China; Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, The Third Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China; Medical Department of Graduate School, Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Sujuan Duan
- Department of Ophthalmology, The Third Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China; Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, The Third Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Alan Jang
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, The Third Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Longbing Mao
- Medical Department of Graduate School, Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Xing Liu
- Medical Department of Graduate School, Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Guofu Huang
- Department of Ophthalmology, The Third Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China; Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, The Third Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China.
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Marak BN, Dowarah J, Khiangte L, Singh VP. A comprehensive insight on the recent development of Cyclic Dependent Kinase inhibitors as anticancer agents. Eur J Med Chem 2020; 203:112571. [DOI: 10.1016/j.ejmech.2020.112571] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 12/19/2022]
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28
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Bhowmick S, AlFaris NA, ALTamimi JZ, ALOthman ZA, Aldayel TS, Wabaidur SM, Islam MA. Screening and analysis of bioactive food compounds for modulating the CDK2 protein for cell cycle arrest: Multi-cheminformatics approaches for anticancer therapeutics. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128316] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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29
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Identification of a Growth-Associated Single Nucleotide Polymorphism (SNP) in Cyclin C of the Giant Tiger Shrimp Penaeus monodon. Biochem Genet 2020; 59:114-133. [PMID: 32780225 DOI: 10.1007/s10528-020-09993-8] [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: 09/29/2019] [Accepted: 07/31/2020] [Indexed: 10/23/2022]
Abstract
The full-length cDNA of cyclin C of the giant tiger shrimp Penaeus monodon (PmCyC) was isolated by RACE-PCR. It was 1443 bp in length containing an open reading frame (ORF) of 804 bp and 267 deduced amino acids. Tissue distribution analysis indicated that PmCyC was more abundantly expressed in ovaries and testes than other tissues of female and male juveniles (P < 0.05). A pair of primers was designed, and an amplification product of 403 bp containing an intron of 123 bp was obtained. Polymorphism of amplified PmCyC gene segments of the 5th (3-month-old G5, N = 30) and 7th (5-month-old G7, N = 18) generations of domesticated juveniles was analyzed. Four conserved SNPs (T>C134, T>C188, G>A379, and T>C382) were found within the examined sequences. A TaqMan genotyping assay was developed for detection of a T>C134 SNP. Association analysis indicated that this SNP displayed significant association with body weight (P < 4.2e-10) and total length (P < 2e-09) of the examined G7 P. monodon (N = 419) with an allele substitution effect of 5.02 ± 0.78 g and 1.41 ± 0.19 cm, respectively. Juveniles with C/C134 (22.80 ± 2.51 g and 12.97 ± 0.53 cm, N = 19) and T/C134 (20.41 ± 0.93 g and 12.77 ± 0.21 cm, N = 129) genotypes exhibited a significantly greater average body weight and total length than those with a T/T134 genotype (14.72 ± 0.53 g and 11.37 ± 0.13 cm, N = 271) (P < 0.05).
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30
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Talapati SR, Nataraj V, Pothuganti M, Gore S, Ramachandra M, Antony T, More SS, Krishnamurthy NR. Structure of cyclin-dependent kinase 2 (CDK2) in complex with the specific and potent inhibitor CVT-313. Acta Crystallogr F Struct Biol Commun 2020; 76:350-356. [PMID: 32744246 PMCID: PMC7397463 DOI: 10.1107/s2053230x20009243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 07/07/2020] [Indexed: 01/18/2023] Open
Abstract
CVT-313 is a potent CDK2 inhibitor that was identified by screening a purine-analogue library and is currently in preclinical studies. Since this molecule has the potential to be developed as a CDK2 inhibitor for cancer therapy, the potency of CVT-313 to bind and stabilize CDK2 was evaluated, together with its ability to inhibit aberrant cell proliferation. CVT-313 increased the melting temperature of CDK2 by 7°C in thermal stabilization studies, thus indicating its protein-stabilizing effect. CVT-313 inhibited the growth of human lung carcinoma cell line A549 in a dose-dependent manner, with an IC50 of 1.2 µM, which is in line with the reported biochemical potency of 0.5 µM. To support the further chemical modification of CVT-313 and to improve its biochemical and cellular potency, a crystal structure was elucidated in order to understand the molecular interaction of CVT-313 and CDK2. The crystal structure of CDK2 bound to CVT-313 was determined to a resolution of 1.74 Å and clearly demonstrated that CVT-313 binds in the ATP-binding pocket, interacting with Leu83, Asp86 and Asp145 directly, and the binding was further stabilized by a water-mediated interaction with Asn132. Based on the crystal structure, further modifications of CVT-313 are proposed to provide additional interactions with CDK2 in the active site, which may significantly increase the biochemical and cellular potency of CVT-313.
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Affiliation(s)
- Sumalatha Rani Talapati
- Aurigene Discovery Technologies Ltd, 39-40 KIADB Industrial Area, Electronic City Phase II, Hosur Road, Bangalore 560 100, India
| | - Vijayashankar Nataraj
- Aurigene Discovery Technologies Ltd, 39-40 KIADB Industrial Area, Electronic City Phase II, Hosur Road, Bangalore 560 100, India
| | - Manoj Pothuganti
- Aurigene Discovery Technologies Ltd, 39-40 KIADB Industrial Area, Electronic City Phase II, Hosur Road, Bangalore 560 100, India
| | - Suraj Gore
- Aurigene Discovery Technologies Ltd, 39-40 KIADB Industrial Area, Electronic City Phase II, Hosur Road, Bangalore 560 100, India
| | - Murali Ramachandra
- Aurigene Discovery Technologies Ltd, 39-40 KIADB Industrial Area, Electronic City Phase II, Hosur Road, Bangalore 560 100, India
| | - Thomas Antony
- Aurigene Discovery Technologies Ltd, 39-40 KIADB Industrial Area, Electronic City Phase II, Hosur Road, Bangalore 560 100, India
| | - Sunil Shivaji More
- School of Basic and Applied Sciences, Dayananada Sagar University, Shavige Malleshawara Hills, Kumaraswamy Layout, Bangalore 560 078, India
| | - Narasimha Rao Krishnamurthy
- Aurigene Discovery Technologies Ltd, 39-40 KIADB Industrial Area, Electronic City Phase II, Hosur Road, Bangalore 560 100, India
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31
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ANS Interacts with the Ca 2+-ATPase Nucleotide Binding Site. J Fluoresc 2020; 30:483-496. [PMID: 32146650 DOI: 10.1007/s10895-020-02518-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 02/14/2020] [Indexed: 10/24/2022]
Abstract
The binding of 8-anilino-1-naphthalene sulfonate (ANS) to the nucleotide binding domain (N-domain) of the sarcoplasmic reticulum Ca2+-ATPase (SERCA) was studied. Molecular docking predicted two ANS binding modes (BMI and BMII) in the nucleotide binding site. The molecular interaction was confirmed as the fluorescence intensity of ANS was dramatically increased when in the presence of an engineered recombinant N-domain. Molecular dynamics simulation showed BMI (which occupies the ATP binding site) as the mode that is stable in solution. The above was confirmed by the absence of ANS fluorescence in the presence of a fluorescein isothiocyanate (FITC)-labeled N-domain. Further, the labeling of the N-domain with FITC was hindered by the presence of ANS, i.e., ANS was bound to the ATP binding site. Importantly, ANS displayed a higher affinity than ATP. In addition, ANS binding led to quenching the N-domain intrinsic fluorescence displaying a FRET pattern, which suggested the existence of a Trp-ANS FRET couple. Nonetheless, the chemical modification of the sole Trp residue with N-bromosuccinimide (NBS) discarded the existence of FRET and instead indicated structural rearrangements in the nucleotide binding site during ANS binding. Finally, Ca2+-ATPase kinetics in the presence of ANS showed a partial mixed-type inhibition. The Dixon plot showed the ANS-Ca2+-ATPase complex as catalytically active, hence supporting the existence of a functional dimeric Ca2+-ATPase in sarcoplasmic reticulum vesicles. ANS may be used as a molecular platform for the development of more effective inhibitors of Ca2+-ATPase and appears to be a new fluorescent probe for the nucleotide binding site. Graphical Abstract Molecular docking of ANS to the nucleotide binding site of Ca2+-ATPase. ANS fluorescence increase reveals molecular interaction.
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32
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Cyclin-dependent kinase inhibition: an opportunity to target protein-protein interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 121:115-141. [PMID: 32312419 DOI: 10.1016/bs.apcsb.2019.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Cyclin-dependent kinases (CDKs) play an integral part in cellular activities. To date, most of the activities have been evaluated in the cell cycle and transcription. Several diseases are affected by abnormalities in CDKs, related-pathways, or proteins that regulate CDK activity. CDKs are primarily dependent on activation by binding other proteins, namely Cyclins. In addition, phosphorylation of key CDK residues also plays a major part in CDK activity. To date, the most successful drugs have been developed against CDK4 and CDK6 and are FDA approved for use in advanced breast cancer. However, this is likely only a small fraction of the potential for targeting CDKs as a strategy against cancer and other diseases. Based on the extensive protein-protein interactions made by CDKs with other proteins (Cyclins and others), there are numerous possibilities for targeting strategies against protein-protein interactions. Here we describe the predominant roles of CDKs in the cell, key interacting proteins, significant 3-dimensional structural characteristics, and summarize the work-to-date in inhibition of CDKs.
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García-Gutiérrez L, Bretones G, Molina E, Arechaga I, Symonds C, Acosta JC, Blanco R, Fernández A, Alonso L, Sicinski P, Barbacid M, Santamaría D, León J. Myc stimulates cell cycle progression through the activation of Cdk1 and phosphorylation of p27. Sci Rep 2019; 9:18693. [PMID: 31822694 PMCID: PMC6904551 DOI: 10.1038/s41598-019-54917-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/14/2019] [Indexed: 12/24/2022] Open
Abstract
Cell cycle stimulation is a major transforming mechanism of Myc oncoprotein. This is achieved through at least three concomitant mechanisms: upregulation of cyclins and Cdks, downregulation of the Cdk inhibitors p15 and p21 and the degradation of p27. The Myc-p27 antagonism has been shown to be relevant in human cancer. To be degraded, p27 must be phosphorylated at Thr-187 to be recognized by Skp2, a component of the ubiquitination complex. We previously described that Myc induces Skp2 expression. Here we show that not only Cdk2 but Cdk1 phosphorylates p27 at the Thr-187. Moreover, Myc induced p27 degradation in murine fibroblasts through Cdk1 activation, which was achieved by Myc-dependent cyclin A and B induction. In the absence of Cdk2, p27 phosphorylation at Thr-187 was mainly carried out by cyclin A2-Cdk1 and cyclin B1-Cdk1. We also show that Cdk1 inhibition was enough for the synthetic lethal interaction with Myc. This result is relevant because Cdk1 is the only Cdk strictly required for cell cycle and the reported synthetic lethal interaction between Cdk1 and Myc.
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Affiliation(s)
- Lucía García-Gutiérrez
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, and Departmento de Biología Molecular, Universidad de Cantabria, Santander, Spain.,Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Gabriel Bretones
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, and Departmento de Biología Molecular, Universidad de Cantabria, Santander, Spain.,Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología-IUOPA, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Ester Molina
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, and Departmento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Ignacio Arechaga
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, and Departmento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Catherine Symonds
- Experimental Oncology, Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain.,Global Oncology Franchise, EMD Serono, Rockland, Massachusetts, USA
| | - Juan C Acosta
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Rosa Blanco
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, and Departmento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Adrián Fernández
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, and Departmento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Leticia Alonso
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, and Departmento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | - Mariano Barbacid
- Experimental Oncology, Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - David Santamaría
- University of Bordeaux, INSERM U1218, ACTION Laboratory, IECB, Pessac, France
| | - Javier León
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, and Departmento de Biología Molecular, Universidad de Cantabria, Santander, Spain.
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Progress in Research on the Role of Flavonoids in Lung Cancer. Int J Mol Sci 2019; 20:ijms20174291. [PMID: 31480720 PMCID: PMC6747533 DOI: 10.3390/ijms20174291] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 08/30/2019] [Indexed: 12/24/2022] Open
Abstract
Lung cancer is the leading cause of cancer deaths worldwide. Therefore, for the prevention, diagnosis, prognosis and treatment of lung cancer, efficient preventive strategies and new therapeutic strategies are needed to face these challenges. Natural bioactive compounds and particular flavonoids compounds have been proven to have an important role in lung cancer prevention and of particular interest is the dose used for these studies, to underline the molecular effects and mechanisms at a physiological concentration. The purpose of this review was to summarize the current state of knowledge regarding relevant molecular mechanisms involved in the pharmacological effects, with a special focus on the anti-cancer role, by regulating the coding and non-coding genes. Furthermore, this review focused on the most commonly altered and most clinically relevant oncogenes and tumor suppressor genes and microRNAs in lung cancer. Particular attention was given to the biological effect in tandem with conventional therapy, emphasizing the role in the regulation of drug resistance related mechanisms.
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Schaller D, Pach S, Wolber G. PyRod: Tracing Water Molecules in Molecular Dynamics Simulations. J Chem Inf Model 2019; 59:2818-2829. [PMID: 31117512 DOI: 10.1021/acs.jcim.9b00281] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Ligands entering a protein binding pocket essentially compete with water molecules for binding to the protein. Hence, the location and thermodynamic properties of water molecules in protein structures have gained increased attention in the drug design community. Including corresponding data into 3D pharmacophore modeling is essential for efficient high throughput virtual screening. Here, we present PyRod, a free and open-source Python software that allows for visualization of pharmacophoric binding pocket characteristics, identification of hot spots for ligand binding, and subsequent generation of pharmacophore features for virtual screening. The implemented routines analyze the protein environment of water molecules in molecular dynamics (MD) simulations and can differentiate between hydrogen bonded waters as well as waters in a protein environment of hydrophobic, charged, or aromatic atom groups. The gathered information is further processed to generate dynamic molecular interaction fields (dMIFs) for visualization and pharmacophoric features for virtual screening. The described software was applied to 5 therapeutically relevant drug targets, and generated pharmacophores were evaluated using DUD-E benchmarking sets. The best performing pharmacophore was found for the HIV1 protease with an early enrichment factor of 54.6. PyRod adds a new perspective to structure-based screening campaigns by providing easy-to-interpret dMIFs and purely protein-based pharmacophores that are solely based on tracing water molecules in MD simulations. Since structural information about cocrystallized ligands is not needed, screening campaigns can be followed, for which less or no ligand information is available. PyRod is freely available at https://github.com/schallerdavid/pyrod .
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Affiliation(s)
- David Schaller
- Pharmaceutical and Medicinal Chemistry , Freie Universität Berlin , Königin-Luise-Strasse 2+4 , 14195 Berlin , Germany
| | - Szymon Pach
- Pharmaceutical and Medicinal Chemistry , Freie Universität Berlin , Königin-Luise-Strasse 2+4 , 14195 Berlin , Germany
| | - Gerhard Wolber
- Pharmaceutical and Medicinal Chemistry , Freie Universität Berlin , Königin-Luise-Strasse 2+4 , 14195 Berlin , Germany
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Rozpędek W, Pytel D, Nowak-Zduńczyk A, Lewko D, Wojtczak R, Diehl JA, Majsterek I. Breaking the DNA Damage Response via Serine/Threonine Kinase Inhibitors to Improve Cancer Treatment. Curr Med Chem 2019; 26:1425-1445. [PMID: 29345572 DOI: 10.2174/0929867325666180117102233] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/13/2017] [Accepted: 11/24/2017] [Indexed: 12/22/2022]
Abstract
Multiple, both endogenous and exogenous, sources may induce DNA damage and DNA replication stress. Cells have developed DNA damage response (DDR) signaling pathways to maintain genomic stability and effectively detect and repair DNA lesions. Serine/ threonine kinases such as Ataxia-telangiectasia mutated (ATM) and Ataxia-telangiectasia and Rad3-Related (ATR) are the major regulators of DDR, since after sensing stalled DNA replication forks, DNA double- or single-strand breaks, may directly phosphorylate and activate their downstream targets, that play a key role in DNA repair, cell cycle arrest and apoptotic cell death. Interestingly, key components of DDR signaling networks may constitute an attractive target for anti-cancer therapy through two distinct potential approaches: as chemoand radiosensitizers to enhance the effectiveness of currently used genotoxic treatment or as single agents to exploit defects in DDR in cancer cells via synthetic lethal approach. Moreover, the newest data reported that serine/threonine protein kinase R (PKR)-like endoplasmic reticulum kinase (PERK) is also closely associated with cancer development and progression. Thereby, utilization of small-molecule, serine/threonine kinase inhibitors may provide a novel, groundbreaking, anti-cancer treatment strategy. Currently, a range of potent, highlyselective toward ATM, ATR and PERK inhibitors has been discovered, but after foregoing study, additional investigations are necessary for their future clinical use.
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Affiliation(s)
- Wioletta Rozpędek
- Department of Clinical Chemistry and Biochemistry, Military-Medical Faculty, Medical University of Lodz, Lodz, Poland
| | - Dariusz Pytel
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, United States
| | - Alicja Nowak-Zduńczyk
- Department of Clinical Chemistry and Biochemistry, Military-Medical Faculty, Medical University of Lodz, Lodz, Poland
| | - Dawid Lewko
- Department of Clinical Chemistry and Biochemistry, Military-Medical Faculty, Medical University of Lodz, Lodz, Poland
| | - Radosław Wojtczak
- Department of Clinical Chemistry and Biochemistry, Military-Medical Faculty, Medical University of Lodz, Lodz, Poland
| | - J Alan Diehl
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, United States
| | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Military-Medical Faculty, Medical University of Lodz, Lodz, Poland
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Gao S, Wang J, Tian S, Luo J. miR‑9 depletion suppresses the proliferation of osteosarcoma cells by targeting p16. Int J Oncol 2019; 54:1921-1932. [PMID: 31081054 PMCID: PMC6521929 DOI: 10.3892/ijo.2019.4783] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 10/13/2019] [Indexed: 12/21/2022] Open
Abstract
Osteosarcoma (OS) is a common primary malignancy in adolescents and children. MicroRNAs (miRNAs or miRs) can regulate the progression of OS. Herein, we explored the target genes and effects of miR-9 in OS. Cell growth, colony formation and cell cycle were respectively examined using a cell counting kit-8 (CCK-8), crystal violet staining and flow cytometry. The target gene of miR-9 was predicted according to the MicroRNA.org website. Luciferase activity was examined using a dual luciferase reporter gene assay kit. The corresponding factors levels were analyzed by carrying out reverse transcription-quantitative PCR (RT-qPCR) and western blot analysis. A mouse model of OS was also established and the volume and weight of the tumors of the mice with OS were measured. The levels of p16 in the mice with OS were detected by immunohistochemistry (IHC). The data revealed a high expression of miR-9 and a low expression of p16 in the OS tissue. p16 was found to be the target gene for miR-9 in OS. miR-9 depletion decreased the proliferation and colony formation of Saos-2 cells by arresting the cells at the G1 phase, accompanied by the downregulation of cyclin A, cyclin D1 and c-Myc expression levels. Moreover, miR-9 depletion inhibited the phosphorylation of p38, c-Jun N-terminal kinase (JNK) and extracellular signal-regulated kinase (ERK). In vivo, miR-9 depletion decreased the tumor volume and weight and increased p16 expression in the mouse tumor tissues. Nevertheless, p16 silencing reversed the suppressive effects of miR-9 inhibitors on OS cells. On the whole, the findings of this study substantiate that miR-9 depletion suppresses cell proliferation by targeting p16 in OS and by mediating the activation of the ERK/p38/JNK pathway.
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Affiliation(s)
- Song Gao
- Department of Orthopedics, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Jianchao Wang
- Department of Orthopedics, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Shujian Tian
- Department of Orthopedics, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Jianping Luo
- Department of Orthopedics, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
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Nuñez-Hernandez DM, Camacho-Jiménez L, González-Ruiz R, Mata-Haro V, Ezquerra-Brauer JM, Yepiz-Plascencia G. Cyclin-dependent kinase 2 (Cdk-2) from the White shrimp Litopenaeus vannamei: Molecular characterization and tissue-specific expression during hypoxia and reoxygenation. Comp Biochem Physiol A Mol Integr Physiol 2018; 230:56-63. [PMID: 30594527 DOI: 10.1016/j.cbpa.2018.12.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/18/2018] [Accepted: 12/19/2018] [Indexed: 01/01/2023]
Abstract
The cell cycle comprises a series of steps necessary for cell growth until cell division. The participation of proteins responsible for cell cycle regulation, known as cyclin dependent kinases or Cdks, is necessary for cycle progression. Cyclin dependent kinase 2 (Cdk-2) is one of the most studied Cdks. This kinase regulates the passage through the G1/S phase and is involved in DNA replication in the S phase. Cdks have been extensively studied in mammals, but there is little information about these proteins in crustaceans. In the present work, the nucleotide and amino acid sequence of Cdk-2 from the white shrimp (Cdk-2) and its expression during hypoxia and reoxygenation are reported. Cdk-2 is a highly conserved protein and contains the serine/threonine catalytic domain, an ATP binding site and the PSTAIRE sequence. The predicted Cdk-2 structure showed the two-lobed structure characteristic of kinases. Expression of Cdk-2 was detected in hepatopancreas, gills and muscle, with hepatopancreas having the highest expression during normoxic conditions. Cdk-2 expression was significantly induced after hypoxia for 24 h in muscle cells, but in hypoxia exposure for 24 followed by 1 h of reoxygenation, the expression levels returned to the levels found in normoxic conditions, suggesting induction of cell cycle progression in muscular cells during hypoxia. No significant changes in expression of Cdk-2 were detected in these conditions in hepatopancreas and gills.
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Affiliation(s)
- Dahlia M Nuñez-Hernandez
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C. Carretera Gustavo Enrique Astiazarán Rosa No. 46, Col La Victoria, CP 83304 Hermosillo, Sonora, Mexico
| | - Laura Camacho-Jiménez
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C. Carretera Gustavo Enrique Astiazarán Rosa No. 46, Col La Victoria, CP 83304 Hermosillo, Sonora, Mexico
| | - Ricardo González-Ruiz
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C. Carretera Gustavo Enrique Astiazarán Rosa No. 46, Col La Victoria, CP 83304 Hermosillo, Sonora, Mexico
| | - Verónica Mata-Haro
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C. Carretera Gustavo Enrique Astiazarán Rosa No. 46, Col La Victoria, CP 83304 Hermosillo, Sonora, Mexico
| | | | - Gloria Yepiz-Plascencia
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C. Carretera Gustavo Enrique Astiazarán Rosa No. 46, Col La Victoria, CP 83304 Hermosillo, Sonora, Mexico.
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Zhang J, Zhang L, Xu Y, Jiang S, Shao Y. Deciphering the binding behavior of flavonoids to the cyclin dependent kinase 6/cyclin D complex. PLoS One 2018; 13:e0196651. [PMID: 29715320 PMCID: PMC5929560 DOI: 10.1371/journal.pone.0196651] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/17/2018] [Indexed: 12/17/2022] Open
Abstract
Flavonoids, a class of natural compounds with variable phenolic structures, have been found to possess anti-cancer activities by modulating different enzymes and receptors like CDK6. To understand the binding behavior of flavonoids that inhibit the active CDK6, molecular dynamics (MD) simulations were performed on six inhibitors, chrysin (M01), fisetin (M03), galangin (M04), genistein (M05), quercetin (M06) and kaempferol (M07), complexed with CDK6/cyclin D. For all six flavonoids, the 3'-OH and 4'-OH of B-ring were found to be favorable for hydrogen bond formation, but the 3-OH on the C-ring and 5-OH on the A-ring were unfavorable, which were confirmed by the MD simulation results of the test molecule, 3', 4', 7-trihydroxyflavone (M15). The binding efficiencies of flavonoids against the CDK6/cyclin D complex were mainly through the electrostatic (especially the H-bond force) and vdW interactions with residues ILE19, VAL27, ALA41, GLU61, PHE98, GLN103, ASP163 and LEU152. The order of binding affinities of these flavonoids toward the CDK6/cyclin D was M03 > M01 > M07 > M15 > M06 > M05 > M04. It is anticipated that the binding features of flavonoid inhibitors studied in the present work may provide valuable insights for the development of CDK6 inhibitors.
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Affiliation(s)
- Jingxiao Zhang
- College of Chemistry and Environmental Engineering, Hubei University for Nationalities, Enshi, Hubei, China
- College of Chemistry and Chemical Engineering, Luoyang Normal University, Luoyang, Henan, China
| | - Lilei Zhang
- College of Chemistry and Environmental Engineering, Hubei University for Nationalities, Enshi, Hubei, China
- College of Chemistry and Chemical Engineering, Luoyang Normal University, Luoyang, Henan, China
| | - Yangcheng Xu
- College of Chemistry and Environmental Engineering, Hubei University for Nationalities, Enshi, Hubei, China
| | - Shanshan Jiang
- College of Chemistry and Environmental Engineering, Hubei University for Nationalities, Enshi, Hubei, China
| | - Yueyue Shao
- College of Chemistry and Environmental Engineering, Hubei University for Nationalities, Enshi, Hubei, China
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Wu YZ, Ying HZ, Xu L, Cheng G, Chen J, Hu YZ, Liu T, Dong XW. Design, synthesis, and molecular docking study of 3H
-imidazole[4,5-c
]pyridine derivatives as CDK2 inhibitors. Arch Pharm (Weinheim) 2018; 351:e1700381. [DOI: 10.1002/ardp.201700381] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 04/04/2018] [Accepted: 04/05/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Yi-Zhe Wu
- ZJU-ENS Joint Laboratory of Medicinal Chemistry; Zhejiang Province Key Laboratory of Anti-Cancer Drug Research; Hangzhou Institute of Innovative Medicine; College of Pharmaceutical Sciences; Zhejiang University; Hangzhou P. R. China
| | - Hua-Zhou Ying
- ZJU-ENS Joint Laboratory of Medicinal Chemistry; Zhejiang Province Key Laboratory of Anti-Cancer Drug Research; Hangzhou Institute of Innovative Medicine; College of Pharmaceutical Sciences; Zhejiang University; Hangzhou P. R. China
| | - Lei Xu
- School of Life Science and Technology; ShanghaiTech University; Shanghai P. R. China
- State Key Laboratory of Drug Research; Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai P. R. China
| | - Gang Cheng
- College of Pharmaceutical Science; Zhejiang Chinese Medical University; Hangzhou P. R. China
| | - Jing Chen
- College of Pharmaceutical Science; Zhejiang Chinese Medical University; Hangzhou P. R. China
| | - Yong-Zhou Hu
- ZJU-ENS Joint Laboratory of Medicinal Chemistry; Zhejiang Province Key Laboratory of Anti-Cancer Drug Research; Hangzhou Institute of Innovative Medicine; College of Pharmaceutical Sciences; Zhejiang University; Hangzhou P. R. China
| | - Tao Liu
- ZJU-ENS Joint Laboratory of Medicinal Chemistry; Zhejiang Province Key Laboratory of Anti-Cancer Drug Research; Hangzhou Institute of Innovative Medicine; College of Pharmaceutical Sciences; Zhejiang University; Hangzhou P. R. China
| | - Xiao-Wu Dong
- ZJU-ENS Joint Laboratory of Medicinal Chemistry; Zhejiang Province Key Laboratory of Anti-Cancer Drug Research; Hangzhou Institute of Innovative Medicine; College of Pharmaceutical Sciences; Zhejiang University; Hangzhou P. R. China
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Rampogu S, Baek A, Zeb A, Lee KW. Exploration for novel inhibitors showing back-to-front approach against VEGFR-2 kinase domain (4AG8) employing molecular docking mechanism and molecular dynamics simulations. BMC Cancer 2018. [PMID: 29514608 PMCID: PMC5842552 DOI: 10.1186/s12885-018-4050-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background Angiogenesis is a process of formation of new blood vessels and is an important criteria demonstrated by cancer cells. Over a period of time, these cancer cells infect the other parts of the healthy body by a process called progression. The objective of the present article is to identify a drug molecule that inhibits angiogenesis and progression. Methods In this pursuit, ligand based pharmacophore virtual screening was employed, generating a pharmacophore model, Hypo1 consisting of four features. Furthermore, this Hypo1 was validated recruiting, Fischer’s randomization, test set method and decoy set method. Later, Hypo1 was allowed to screen databases such as Maybridge, Chembridge, Asinex and NCI and were further filtered by ADMET filters and Lipinski’s Rule of Five. A total of 699 molecules that passed the above criteria, were challenged against 4AG8, an angiogenic drug target employing GOLD v5.2.2. Results The results rendered by molecular docking, DFT and the MD simulations showed only one molecule (Hit) obeyed the back-to-front approach. This molecule displayed a dock score of 89.77, involving the amino acids, Glu885 and Cys919, Asp1046, respectively and additionally formed several important hydrophobic interactions. Furthermore, the identified lead molecule showed interactions with key residues when challenged with CDK2 protein, 1URW. Conclusion The lead candidate showed several interactions with the crucial residues of both the targets. Furthermore, we speculate that the residues Cys919 and Leu83 are important in the development of dual inhibitor. Therefore, the identified lead molecule can act as a potential inhibitor for angiogenesis and progression. Electronic supplementary material The online version of this article (10.1186/s12885-018-4050-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shailima Rampogu
- Division of Applied Life Science (BK21 Plus Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Ayoung Baek
- Division of Applied Life Science (BK21 Plus Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Amir Zeb
- Division of Applied Life Science (BK21 Plus Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Keun Woo Lee
- Division of Applied Life Science (BK21 Plus Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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A compendium of physical exercise-related human genes: an 'omic scale analysis. Biol Sport 2017; 35:3-11. [PMID: 30237656 PMCID: PMC6135974 DOI: 10.5114/biolsport.2018.70746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/11/2016] [Accepted: 06/05/2017] [Indexed: 12/14/2022] Open
Abstract
Regular exercise is an exogenous factor of gene regulation with numerous health benefits. The study aimed to evaluate human genes linked to physical exercise in an ‘omic scale, addressing biological questions to the generated database. Three literature databases were searched with the terms ‘exercise’, ‘fitness’, ‘physical activity’, ‘genetics’ and ‘gene expression’. For additional references, papers were scrutinized and a text-mining tool was used. Papers linking genes to exercise in humans through microarray, RNA-Seq, RT-PCR and genotyping studies were included. Genes were extracted from the collected literature, together with information on exercise protocol, experimental design, gender, age, number of individuals, analytical method, fold change and statistical data. The ‘omic scale dataset was characterized and evaluated with bioinformatics tools searching for gene expression patterns, functional meaning and gene clusters. As a result, a physical exercise-related human gene compendium was created, with data from 58 scientific papers and 5.147 genes functionally correlated with 17 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. While 50.9% of the gene set was up-regulated, 41.9% was down-regulated. 743 up- and 530 down-regulated clusters were found, some connected by regulatory networks. To summarize, up- and down-regulation was encountered, with a wide genomic distribution of the gene set and up- and down-regulated clusters possibly assembled by functional gene evolution. Physical exercise elicits a widespread response in gene expression.
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Drwal MN, Jacquemard C, Perez C, Desaphy J, Kellenberger E. Do Fragments and Crystallization Additives Bind Similarly to Drug-like Ligands? J Chem Inf Model 2017; 57:1197-1209. [PMID: 28414463 DOI: 10.1021/acs.jcim.6b00769] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The success of fragment-based drug design (FBDD) hinges upon the optimization of low-molecular-weight compounds (MW < 300 Da) with weak binding affinities to lead compounds with high affinity and selectivity. Usually, structural information from fragment-protein complexes is used to develop ideas about the binding mode of similar but drug-like molecules. In this regard, crystallization additives such as cryoprotectants or buffer components, which are highly abundant in crystal structures, are frequently ignored. Thus, the aim of this study was to investigate the information present in protein complexes with fragments as well as those with additives and how they relate to the binding modes of their drug-like counterparts. We present a thorough analysis of the binding modes of crystallographic additives, fragments, and drug-like ligands bound to four diverse targets of wide interest in drug discovery and highly represented in the Protein Data Bank: cyclin-dependent kinase 2, β-secretase 1, carbonic anhydrase 2, and trypsin. We identified a total of 630 unique molecules bound to the catalytic binding sites, among them 31 additives, 222 fragments, and 377 drug-like ligands. In general, we observed that, independent of the target, protein-fragment interaction patterns are highly similar to those of drug-like ligands and mostly cover the residues crucial for binding. Crystallographic additives are also able to show conserved binding modes and recover the residues important for binding in some of the cases. Moreover, we show evidence that the information from fragments and drug-like ligands can be applied to rescore docking poses in order to improve the prediction of binding modes.
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Affiliation(s)
- Malgorzata N Drwal
- Laboratoire d'Innovation Thérapeutique UMR 7200, CNRS-Université de Strasbourg , 74 Route du Rhin, 674000 Illkirch, France
| | - Célien Jacquemard
- Laboratoire d'Innovation Thérapeutique UMR 7200, CNRS-Université de Strasbourg , 74 Route du Rhin, 674000 Illkirch, France
| | - Carlos Perez
- Eli Lilly Research Laboratories , Avenida de la Industria 30, 28108 Alcobendas, Madrid, Spain
| | - Jérémy Desaphy
- Lilly Research Laboratories, Eli Lilly and Company , Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Esther Kellenberger
- Laboratoire d'Innovation Thérapeutique UMR 7200, CNRS-Université de Strasbourg , 74 Route du Rhin, 674000 Illkirch, France
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Monzon AM, Zea DJ, Fornasari MS, Saldaño TE, Fernandez-Alberti S, Tosatto SCE, Parisi G. Conformational diversity analysis reveals three functional mechanisms in proteins. PLoS Comput Biol 2017; 13:e1005398. [PMID: 28192432 PMCID: PMC5330503 DOI: 10.1371/journal.pcbi.1005398] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 02/28/2017] [Accepted: 02/02/2017] [Indexed: 02/02/2023] Open
Abstract
Protein motions are a key feature to understand biological function. Recently, a large-scale analysis of protein conformational diversity showed a positively skewed distribution with a peak at 0.5 Å C-alpha root-mean-square-deviation (RMSD). To understand this distribution in terms of structure-function relationships, we studied a well curated and large dataset of ~5,000 proteins with experimentally determined conformational diversity. We searched for global behaviour patterns studying how structure-based features change among the available conformer population for each protein. This procedure allowed us to describe the RMSD distribution in terms of three main protein classes sharing given properties. The largest of these protein subsets (~60%), which we call "rigid" (average RMSD = 0.83 Å), has no disordered regions, shows low conformational diversity, the largest tunnels and smaller and buried cavities. The two additional subsets contain disordered regions, but with differential sequence composition and behaviour. Partially disordered proteins have on average 67% of their conformers with disordered regions, average RMSD = 1.1 Å, the highest number of hinges and the longest disordered regions. In contrast, malleable proteins have on average only 25% of disordered conformers and average RMSD = 1.3 Å, flexible cavities affected in size by the presence of disordered regions and show the highest diversity of cognate ligands. Proteins in each set are mostly non-homologous to each other, share no given fold class, nor functional similarity but do share features derived from their conformer population. These shared features could represent conformational mechanisms related with biological functions.
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Affiliation(s)
- Alexander Miguel Monzon
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes (CONICET), Bernal, Buenos Aires, Argentina
| | - Diego Javier Zea
- Bioinformatics Unit, Fundación Instituto Leloir (CONICET), Buenos Aires, Argentina
| | - María Silvina Fornasari
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes (CONICET), Bernal, Buenos Aires, Argentina
| | - Tadeo E. Saldaño
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes (CONICET), Bernal, Buenos Aires, Argentina
| | - Sebastian Fernandez-Alberti
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes (CONICET), Bernal, Buenos Aires, Argentina
| | | | - Gustavo Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes (CONICET), Bernal, Buenos Aires, Argentina
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Dong K, Yang X, Zhao T, Zhu X. An insight into the inhibitory selectivity of 4-(Pyrazol- 4-yl)-pyrimidines to CDK4 over CDK2. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1279283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Keke Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, Nanjing, P.R. China
| | - Xueyu Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, Nanjing, P.R. China
| | - Tengteng Zhao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, Nanjing, P.R. China
| | - Xiaolei Zhu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, Nanjing, P.R. China
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Proteomic Interaction Patterns between Human Cyclins, the Cyclin-Dependent Kinase Ortholog pUL97 and Additional Cytomegalovirus Proteins. Viruses 2016; 8:v8080219. [PMID: 27548200 PMCID: PMC4997581 DOI: 10.3390/v8080219] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/25/2016] [Accepted: 08/02/2016] [Indexed: 01/13/2023] Open
Abstract
The human cytomegalovirus (HCMV)-encoded cyclin-dependent kinase (CDK) ortholog pUL97 associates with human cyclin B1 and other types of cyclins. Here, the question was addressed whether cyclin interaction of pUL97 and additional viral proteins is detectable by mass spectrometry-based approaches. Proteomic data were validated by coimmunoprecipitation (CoIP), Western blot, in vitro kinase and bioinformatic analyses. Our findings suggest that: (i) pUL97 shows differential affinities to human cyclins; (ii) pUL97 inhibitor maribavir (MBV) disrupts the interaction with cyclin B1, but not with other cyclin types; (iii) cyclin H is identified as a new high-affinity interactor of pUL97 in HCMV-infected cells; (iv) even more viral phosphoproteins, including all known substrates of pUL97, are detectable in the cyclin-associated complexes; and (v) a first functional validation of pUL97-cyclin B1 interaction, analyzed by in vitro kinase assay, points to a cyclin-mediated modulation of pUL97 substrate preference. In addition, our bioinformatic analyses suggest individual, cyclin-specific binding interfaces for pUL97-cyclin interaction, which could explain the different strengths of interactions and the selective inhibitory effect of MBV on pUL97-cyclin B1 interaction. Combined, the detection of cyclin-associated proteins in HCMV-infected cells suggests a complex pattern of substrate phosphorylation and a role of cyclins in the fine-modulation of pUL97 activities.
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Molecular Dynamics Simulations and Classical Multidimensional Scaling Unveil New Metastable States in the Conformational Landscape of CDK2. PLoS One 2016; 11:e0154066. [PMID: 27100206 PMCID: PMC4839568 DOI: 10.1371/journal.pone.0154066] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/07/2016] [Indexed: 01/04/2023] Open
Abstract
Protein kinases are key regulatory nodes in cellular networks and their function has been shown to be intimately coupled with their structural flexibility. However, understanding the key structural mechanisms of large conformational transitions remains a difficult task. CDK2 is a crucial regulator of cell cycle. Its activity is finely tuned by Cyclin E/A and the catalytic segment phosphorylation, whereas its deregulation occurs in many types of cancer. ATP competitive inhibitors have failed to be approved for clinical use due to toxicity issues raised by a lack of selectivity. However, in the last few years type III allosteric inhibitors have emerged as an alternative strategy to selectively modulate CDK2 activity. In this study we have investigated the conformational variability of CDK2. A low dimensional conformational landscape of CDK2 was modeled using classical multidimensional scaling on a set of 255 crystal structures. Microsecond-scale plain and accelerated MD simulations were used to populate this landscape by using an out-of-sample extension of multidimensional scaling. CDK2 was simulated in the apo-form and in complex with the allosteric inhibitor 8-anilino-1-napthalenesulfonic acid (ANS). The apo-CDK2 landscape analysis showed a conformational equilibrium between an Src-like inactive conformation and an active-like form. These two states are separated by different metastable states that share hybrid structural features with both forms of the kinase. In contrast, the CDK2/ANS complex landscape is compatible with a conformational selection picture where the binding of ANS in proximity of the αC helix causes a population shift toward the inactive conformation. Interestingly, the new metastable states could enlarge the pool of candidate structures for the development of selective allosteric CDK2 inhibitors. The method here presented should not be limited to the CDK2 case but could be used to systematically unmask similar mechanisms throughout the human kinome.
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Yokoyama T, Kosaka Y, Mizuguchi M. Structural Insight into the Interactions between Death-Associated Protein Kinase 1 and Natural Flavonoids. J Med Chem 2015; 58:7400-8. [PMID: 26322379 DOI: 10.1021/acs.jmedchem.5b00893] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Death-associated protein kinase 1 (DAPK1) is a 160 kDa serine/threonine protein kinase that belongs to the Ca(2+)/calmodulin-dependent protein kinase subfamily. DAPK1 is a possible target for the treatment of acute ischemic stroke and endometrial adenocarcinomas. In the present study, we investigated the binding characteristics of 17 natural flavonoids to DAPK1 using a 1-anilinonaphthalene-8-sulfonic acid competitive binding assay and revealed that morin was the strongest binder among the selected compounds. The crystallographic analysis of DAPK1 and 7 selected flavonoid complexes revealed the structure-binding affinity relationship in atomic-level detail. It was suggested that the high affinity of morin could be accounted for by the ionic interaction between 2'-OH and K42 and that such an interaction would not take place with either cyclin-dependent protein kinases or PIM kinases because of their broader entrance regions. Thus, morin would be a more selective inhibitor of DAPK1 than either of these other types of kinases. In addition, we found that the binding of kaempferol to DAPK1 was associated with a chloride ion. The present study provides a better understanding of the molecular properties of the ATP site of DAPK1 and may be useful for the design of specific DAPK1 inhibitors.
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Affiliation(s)
- Takeshi Yokoyama
- Faculty of Pharmaceutical Sciences, University of Toyama , 2630 Sugitani, Toyama 930-0914, Japan
| | - Yuto Kosaka
- Faculty of Pharmaceutical Sciences, University of Toyama , 2630 Sugitani, Toyama 930-0914, Japan
| | - Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama , 2630 Sugitani, Toyama 930-0914, Japan
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