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Huang Y, Liu W, Zhao C, Shi X, Zhao Q, Jia J, Wang A. Targeting cyclin-dependent kinases: From pocket specificity to drug selectivity. Eur J Med Chem 2024; 275:116547. [PMID: 38852339 DOI: 10.1016/j.ejmech.2024.116547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/11/2024]
Abstract
The development of selective modulators of cyclin-dependent kinases (CDKs), a kinase family with numerous members and functional variations, is a significant preclinical challenge. Recent advancements in crystallography have revealed subtle differences in the highly conserved CDK pockets. Exploiting these differences has proven to be an effective strategy for achieving excellent drug selectivity. While previous reports briefly discussed the structural features that lead to selectivity in individual CDK members, attaining inhibitor selectivity requires consideration of not only the specific structures of the target CDK but also the features of off-target members. In this review, we summarize the structure-activity relationships (SARs) that influence selectivity in CDK drug development and analyze the pocket features that lead to selectivity using molecular-protein binding models. In addition, in recent years, novel CDK modulators have been developed, providing more avenues for achieving selectivity. These cases were also included. We hope that these efforts will assist in the development of novel CDK drugs.
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Affiliation(s)
- Yaoguang Huang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Wenwu Liu
- School of Pharmaceutical Sciences, Tsinghua University, Haidian Dist., Beijing, 100084, People's Republic of China
| | - Changhao Zhao
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China
| | - Xiaoyu Shi
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Qingchun Zhao
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China; Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China.
| | - Jingming Jia
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
| | - Anhua Wang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
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Self assembly of a novel Cu(II) complex, (C6H9N2)2[CuCl4]: experimental, computational, and molecular docking survey. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2021. [DOI: 10.1007/s13738-021-02195-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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3
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Malami I, Bunza AM, Alhassan AM, Muhammad A, Abubakar IB, Yunusa A, Waziri PM, Etti IC. Dihydroartemisinin as a potential drug candidate for cancer therapy: a structural-based virtual screening for multitarget profiling. J Biomol Struct Dyn 2020; 40:1347-1362. [PMID: 32964804 DOI: 10.1080/07391102.2020.1824811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cancer is a rapidly growing non-communicable disease worldwide that is responsible for high mortality rates, which account for 9.6 million death in 2018. Dihydroartemisinin (DHA) is an active metabolite of artemisinin, an active principle present in the Chinese medicinal plant Artemisia annua used for malaria treatment. Dihydroartemisinin possesses remarkable and selective anticancer properties however the underlying mechanism of the antitumor effects of DHA from the structural point of view is still not yet elucidated. In the present study, we employed molecular docking simulation techniques using Autodock suits to access the binding properties of dihydroartemisinin to multiple protein targets implicated in cancer pathogenesis. Its potential targets with comprehensive pharmacophore were predicted using a PharmMapper database. The co-crystallised structures of the protein were obtained from a Protein Data Bank and prepared for molecular docking simulation. Out of the 24 selected protein targets, DHA has shown about 29% excellent binding to the targets compared to their co-crystallised ligand. Additionally, 75% of the targets identified for dihydroartemisinin binding are protein kinases, and 25% are non-protein kinases. Hydroxyl functional group of dihydroartemisinin contributed to 58.5% of the total hydrogen interactions, while pyran (12.2%), endoperoxide (9.8%), and oxepane (19.5%) contributed to the remaining hydrogen bonding. The present findings have elucidated the possible antitumor properties of dihydroartemisinin through the structural-based virtual studies, which provides a lead to a safe and effective anticancer agent useful for cancer therapy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ibrahim Malami
- Department of Pharmacognosy and Ethnopharmacy, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria.,Centre for Advanced Medical Research and Training (CAMRET), Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Aisha Muktar Bunza
- Department of Pharmacognosy and Ethnopharmacy, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Alhassan Muhammad Alhassan
- Department of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Aliyu Muhammad
- Department of Biochemistry, Faculty of life Sciences, Ahmadu Bello University, Zaria, Nigeria
| | | | - Abdulmajeed Yunusa
- Department of Pharmacology and Therapeutics, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Peter M Waziri
- Department of Biochemistry, Kaduna State University, Kaduna, Nigeria
| | - Imaobong C Etti
- Department of Pharmacology and Toxicology, University of Uyo, Uyo, Nigeria
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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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Chen EP, Song RS, Chen X. Mathematical model of hypoxia and tumor signaling interplay reveals the importance of hypoxia and cell-to-cell variability in tumor growth inhibition. BMC Bioinformatics 2019; 20:507. [PMID: 31638911 PMCID: PMC6802183 DOI: 10.1186/s12859-019-3098-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 09/13/2019] [Indexed: 01/10/2023] Open
Abstract
Background Human tumor is a complex tissue with multiple heterogeneous hypoxic regions and significant cell-to-cell variability. Due to the complexity of the disease, the explanation of why anticancer therapies fail cannot be attributed to intrinsic or acquired drug resistance alone. Furthermore, there are inconsistent reports of hypoxia-induced kinase activities in different cancer cell-lines, where increase, decreases, or no change has been observed. Thus, we asked, why are there widely contrasting results in kinase activity under hypoxia in different cancer cell-lines and how does hypoxia play a role in anti-cancer drug sensitivity? Results We took a modeling approach to address these questions by analyzing the model simulation to explain why hypoxia driven signals can have dissimilar impact on tumor growth and alter the efficacy of anti-cancer drugs. Repeated simulations with varying concentrations of biomolecules followed by decision tree analysis reveal that the highly differential effects among heterogeneous subpopulation of tumor cells could be governed by varying concentrations of just a few key biomolecules. These biomolecules include activated serine/threonine-specific protein kinases (pRAF), mitogen-activated protein kinase kinase (pMEK), protein kinase B (pAkt), or phosphoinositide-4,5-bisphosphate 3-kinase (pPI3K). Additionally, the ratio of activated extracellular signal-regulated kinases (pERK) or pAkt to its respective total was a key factor in determining the sensitivity of pERK or pAkt to hypoxia. Conclusion This work offers a mechanistic insight into how hypoxia can affect the efficacy of anti-cancer drug that targets tumor signaling and provides a framework to identify the types of tumor cells that are either sensitive or resistant to anti-cancer therapy.
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Affiliation(s)
- Emile P Chen
- Computational Sciences, GlaxoSmithKline, Collegeville, PA, 19426, USA.
| | - Roy S Song
- Computational Sciences, GlaxoSmithKline, Collegeville, PA, 19426, USA
| | - Xueer Chen
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, 15206-3701, USA
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Wood DJ, Endicott JA. Structural insights into the functional diversity of the CDK-cyclin family. Open Biol 2019; 8:rsob.180112. [PMID: 30185601 PMCID: PMC6170502 DOI: 10.1098/rsob.180112] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 08/10/2018] [Indexed: 12/17/2022] Open
Abstract
Since their characterization as conserved modules that regulate progression through the eukaryotic cell cycle, cyclin-dependent protein kinases (CDKs) in higher eukaryotic cells are now also emerging as significant regulators of transcription, metabolism and cell differentiation. The cyclins, though originally characterized as CDK partners, also have CDK-independent roles that include the regulation of DNA damage repair and transcriptional programmes that direct cell differentiation, apoptosis and metabolic flux. This review compares the structures of the members of the CDK and cyclin families determined by X-ray crystallography, and considers what mechanistic insights they provide to guide functional studies and distinguish CDK- and cyclin-specific activities. Aberrant CDK activity is a hallmark of a number of diseases, and structural studies can provide important insights to identify novel routes to therapy.
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Affiliation(s)
- Daniel J Wood
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Jane A Endicott
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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Jorda R, Hendrychová D, Voller J, Řezníčková E, Gucký T, Kryštof V. How Selective Are Pharmacological Inhibitors of Cell-Cycle-Regulating Cyclin-Dependent Kinases? J Med Chem 2018; 61:9105-9120. [PMID: 30234987 DOI: 10.1021/acs.jmedchem.8b00049] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cyclin-dependent kinases (CDKs) are an important and emerging class of drug targets for which many small-molecule inhibitors have been developed. However, there is often insufficient data available on the selectivity of CDK inhibitors (CDKi) to attribute the effects on the presumed target CDK to these inhibitors. Here, we highlight discrepancies between the kinase selectivity of CDKi and the phenotype exhibited; we evaluated 31 CDKi (claimed to target CDK1-4) for activity toward CDKs 1, 2, 4, 5, 7, 9 and for effects on the cell cycle. Our results suggest that most CDKi should be reclassified as pan-selective and should not be used as a tool. In addition, some compounds did not even inhibit CDKs as their primary cellular targets; for example, NU6140 showed potent inhibition of Aurora kinases. We also established an online database of commercially available CDKi for critical evaluation of their utility as molecular probes. Our results should help researchers select the most relevant chemical tools for their specific applications.
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Affiliation(s)
- Radek Jorda
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
| | - Denisa Hendrychová
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
| | - Jiří Voller
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
| | - Eva Řezníčková
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
| | - Tomáš Gucký
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
| | - Vladimír Kryštof
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
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Hashmi MZ, Zhang J, Li B, Su X, Tariq M, Ahmad N, Malik RN, Ullah K, Chen C, Shen C. Effects of structurally different noncoplanar and coplanar PCBs on HELF cell proliferation, cell cycle, and potential molecular mechanisms. ENVIRONMENTAL TOXICOLOGY 2017; 32:1183-1190. [PMID: 27463516 DOI: 10.1002/tox.22315] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 06/23/2016] [Accepted: 07/02/2016] [Indexed: 05/20/2023]
Abstract
Polychlorinated biphenyls (PCBs) are a group of chemicals that persist in the environment, indoors, and humans. Lung exposure to airborne and food contaminants, such as PCBs, may cause possible lung disorders, such as cancer. In the present study, we investigated the effects of structurally different lower chlorinated (≤4Cl), noncoplanar PCB40, and coplanar PCB77 on human lung fibroblast cell line (HELF) cell proliferation, cell cycle progression, and possible molecular mechanisms. Noncoplanar PCB40 and coplanar PCB77 exhibited concentration- and time-dependent biphasic dose-response effects on HELF cell proliferation. Noncoplanar PCB40 and coplanar PCB77 induced 23 and 45% cytotoxicity at higher concentrations than the control. The flow cytometry analysis showed that exposure to PCB40 caused a significant increase in time spent in the G1 phase but decreased length of the S phase in a concentration- and time-dependent manner, whereas PCB77 exposure decreased time spent in the G1 and S phases but increased time spent in the G2 phase. Western blot analysis indicated that PCB77 increased the expression of cyclin E, CDK2, p21, and caspase-9, while PCB40 decreased the expression of these proteins (except CDK2 and p21). An increase in CDK expression after exposure to PCB77 suggests that it may cause carcinogenic effects on HELF cells at higher doses. Our results also demonstrate that the different cytotoxic effects induced by coplanar and nonplanar PCBs were correlated with their structural characteristics; the coplanar congener was more cytotoxic than the nonplanar congener. The study elaborates threshold levels for these chemicals and suggests that the cytotoxicity mechanisms by which PCB congeners act on HELF cells depend on their planarity and chemical structures. Furthermore, the study will be important for developing antidotes to the adverse effects and risk assessment practices for PCBs. © 2016 Wiley Periodicals, Inc. Environ Toxicol 32: 1183-1190, 2017.
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Affiliation(s)
- Muhammad Zaffar Hashmi
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Department of Meteorology, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Jingyu Zhang
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Binglu Li
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Xiaomei Su
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, People's Republic of China
| | - Muhammad Tariq
- Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Najid Ahmad
- School of Economics, Dongbei University of Finance and Economics, Dalian, People's Republic of China
| | - Riffat Naseem Malik
- Environmental Biology and Ecotoxicology Laboratory, Department of Environmental Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Kalim Ullah
- Department of Meteorology, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Chen Chen
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Chaofeng Shen
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
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Chohan TA, Chen JJ, Qian HY, Pan YL, Chen JZ. Molecular modeling studies to characterize N-phenylpyrimidin-2-amine selectivity for CDK2 and CDK4 through 3D-QSAR and molecular dynamics simulations. MOLECULAR BIOSYSTEMS 2016; 12:1250-68. [PMID: 26883408 DOI: 10.1039/c5mb00860c] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular modeling simulations were carried out to understand the structure–activity and selectivity correlation of N-phenylpyrimidin-2-amines binding to CDK2 and CDK4.
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Affiliation(s)
- Tahir Ali Chohan
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Jiong-Jiong Chen
- The Children's Hospital
- School of Medicine
- Zhejiang University
- Hangzhou
- China
| | - Hai-Yan Qian
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - You-Lu Pan
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Jian-Zhong Chen
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
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10
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Chohan TA, Qian HY, Pan YL, Chen JZ. Molecular simulation studies on the binding selectivity of 2-anilino-4-(thiazol-5-yl)-pyrimidines in complexes with CDK2 and CDK7. MOLECULAR BIOSYSTEMS 2016; 12:145-61. [DOI: 10.1039/c5mb00630a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular modeling simulations were performed to explore the selectivity mechanism of inhibitors binding to CDK2 and CDK7.
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Affiliation(s)
- Tahir Ali Chohan
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Hai-Yan Qian
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - You-Lu Pan
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Jian-Zhong Chen
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
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Mottin M, Souza PCT, Skaf MS. Molecular Recognition of PPARγ by Kinase Cdk5/p25: Insights from a Combination of Protein–Protein Docking and Adaptive Biasing Force Simulations. J Phys Chem B 2015; 119:8330-9. [DOI: 10.1021/acs.jpcb.5b04269] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Melina Mottin
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, Campinas, São Paulo 13082-864, Brazil
| | - Paulo C. T. Souza
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, Campinas, São Paulo 13082-864, Brazil
| | - Munir S. Skaf
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, Campinas, São Paulo 13082-864, Brazil
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12
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Jayaraman A, Jamil K. Drug targets for cell cycle dysregulators in leukemogenesis: in silico docking studies. PLoS One 2014; 9:e86310. [PMID: 24454966 PMCID: PMC3893288 DOI: 10.1371/journal.pone.0086310] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 12/09/2013] [Indexed: 01/10/2023] Open
Abstract
Alterations in cell cycle regulating proteins are a key characteristic in neoplastic proliferation of lymphoblast cells in patients with Acute Lymphoblastic Leukemia (ALL). The aim of our study was to investigate whether the routinely administered ALL chemotherapeutic agents would be able to bind and inhibit the key deregulated cell cycle proteins such as - Cyclins E1, D1, D3, A1 and Cyclin Dependent Kinases (CDK) 2 and 6. We used Schrödinger Glide docking protocol to dock the chemotherapeutic drugs such as Doxorubicin and Daunorubicin and others which are not very common including Clofarabine, Nelarabine and Flavopiridol, to the crystal structures of these proteins. We observed that the drugs were able to bind and interact with cyclins E1 and A1 and CDKs 2 and 6 while their docking to cyclins D1 and D3 were not successful. This binding proved favorable to interact with the G1/S cell cycle phase proteins that were examined in this study and may lead to the interruption of the growth of leukemic cells. Our observations therefore suggest that these drugs could be explored for use as inhibitors for these cell cycle proteins. Further, we have also highlighted residues which could be important in the designing of pharmacophores against these cell cycle proteins. This is the first report in understanding the mechanism of action of the drugs targeting these cell cycle proteins in leukemia through the visualization of drug-target binding and molecular docking using computational methods.
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Affiliation(s)
- Archana Jayaraman
- Centre for Biotechnology and Bioinformatics, School of Life Sciences, Jawaharlal Nehru Institute of Advanced Studies, Secunderabad, Andhra Pradesh, India
| | - Kaiser Jamil
- Centre for Biotechnology and Bioinformatics, School of Life Sciences, Jawaharlal Nehru Institute of Advanced Studies, Secunderabad, Andhra Pradesh, India
- * E-mail:
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Kim S, Lee J, Jang BC, Kwon TK, Park JW. BAI, a novel cyclin-dependent kinase inhibitor induces apoptosis in A549 cells through activation of caspases and inactivation of Akt. J Cell Biochem 2013; 114:282-93. [PMID: 22887215 DOI: 10.1002/jcb.24314] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 07/30/2012] [Indexed: 11/06/2022]
Abstract
Previously, we have synthesized a novel cyclin-dependent kinase (CDK) inhibitor, 2-[1,1'biphenyl]-4-yl-N-[5-(1,1-dioxo-1λ(6) -isothiazolidin-2-yl)-1H-indazol-3-yl]acetamide (BAI) and reported its anti-cancer activity in head and neck cancer cells. In this study, we further evaluated the effect of BAI on growth of various human cancer cell lines, including A549 (nonsmall cell lung cancer), HCT116 (colon), and Caki (kidney). Profoundly, results of XTT and clonogenic assays demonstrated that BAI at nanomolar concentrations (20-60 nM) inhibited growth of A549, HCT116, and Caki cells, suggesting the anti-cancer potency. We show that BAI induced a dose-dependent apoptotic cell death in these human cancer cells, as measured by fluorescence-activated cell sorting (FACS). Interestingly, further biochemical analysis showed that treatment with BAI at 20 nM induced apoptosis in A549 cells in association with activation of caspases, cleavage of phospholipase C-γ1 (PLC-γ1), and inhibition of Akt in A549 cells. Importantly, pharmacological inhibition study revealed that pretreatment with z-VAD-fmk, a pan caspase inhibitor strongly blocked the BAI-induced apoptosis in A549 cells. Transfection analysis with Akt cDNA encoding constitutively active Akt further addressed the significance of Akt inhibition in the BAI-induced apoptosis in A549 cells. Notably, disruption of the PI3K/Akt pathway by LY294002, a PI3K/Akt inhibitor potentiated apoptosis in A549 cells by BAI at a subcytotoxic concentration. These findings collectively suggest that BAI potently inhibits growth of A549, HCT116, and Caki cells, and that the BAI-induced apoptosis in A549 cells is associated with activation of caspases, and inhibition of Akt.
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Affiliation(s)
- Shin Kim
- Department of Immunology, School of Medicine, Keimyung University, 1095 Dalgubeoldaero, Dalseo-Gu, Daegu 704-701, South Korea
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Tripathi SK, Muttineni R, Singh SK. Extra precision docking, free energy calculation and molecular dynamics simulation studies of CDK2 inhibitors. J Theor Biol 2013; 334:87-100. [PMID: 23727278 DOI: 10.1016/j.jtbi.2013.05.014] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 05/17/2013] [Accepted: 05/20/2013] [Indexed: 12/22/2022]
Abstract
Molecular docking, free energy calculation and molecular dynamics (MD) simulation studies have been performed, to explore the putative binding modes of 3,5-diaminoindazoles, imidazo(1,2-b)pyridazines and triazolo(1,5-a) pyridazines series of Cyclin-dependent kinase (CDK2) inhibitors. To evaluate the effectiveness of docking protocol in flexible docking, we have selected crystallographic bound compound to validate our docking procedure as evident from root mean square deviations (RMSDs). We found different binding sites namely catalytic, inhibitory phosphorylation, cyclin binding and CKS-binding site of the CDK2 contributing towards the binding of these compounds. Moreover, correlation between free energy of binding and biological activity yielded a statistically significant correlation coefficient. Finally, three representative protein-ligand complexes were subjected to molecular dynamics simulation to determine the stability of the predicted conformations. The low value of the RMSDs between the initial complex structure and the energy minimized final average complex structure suggests that the derived docked complexes are close to equilibrium. We suggest that the phenylacetyl type of substituents and cyclohexyl moiety make the favorable interactions with a number of residues in the active site, and show better inhibitory activity to improve the pharmacokinetic profile of compounds against CDK2. The structure-based drug design strategy described in this study will be highly useful for the development of new inhibitors with high potency and selectivity.
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Affiliation(s)
- Sunil Kumar Tripathi
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
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The CDK9 tail determines the reaction pathway of positive transcription elongation factor b. Structure 2012; 20:1788-95. [PMID: 22959624 PMCID: PMC3469819 DOI: 10.1016/j.str.2012.08.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 07/04/2012] [Accepted: 08/10/2012] [Indexed: 11/22/2022]
Abstract
CDK9, the kinase of positive transcription elongation factor b (P-TEFb), stimulates transcription elongation by phosphorylating RNA polymerase II and transcription elongation factors. Using kinetic analysis of a human P-TEFb complex consisting of CDK9 and cyclin T, we show that the CDK9 C-terminal tail sequence is important for the catalytic mechanism and imposes an ordered binding of substrates and release of products. Crystallographic analysis of a CDK9/cyclin T complex in which the C-terminal tail partially blocks the ATP binding site reveals a possible reaction intermediate. Biochemical characterization of CDK9 mutants supports a model in which the CDK9 tail cycles through different conformational states. We propose that this mechanism is critical for the pattern of CTD Ser2 phosphorylation on actively transcribed genes.
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Smith GK, Ke Z, Guo H, Hengge AC. Insights into the phosphoryl transfer mechanism of cyclin-dependent protein kinases from ab initio QM/MM free-energy studies. J Phys Chem B 2011; 115:13713-22. [PMID: 21999515 DOI: 10.1021/jp207532s] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Phosphorylation reactions catalyzed by kinases and phosphatases play an indispensible role in cellular signaling, and their malfunctioning is implicated in many diseases. A better understanding of the catalytic mechanism will help design novel and effective mechanism-based inhibitors of these enzymes. In this work, ab initio quantum mechanical/molecular mechanical studies are reported for the phosphoryl transfer reaction catalyzed by a cyclin-dependent kinase, CDK2. Our results suggest that an active-site Asp residue, rather than ATP as previously proposed, serves as the general base to activate the Ser nucleophile. The corresponding transition state features a dissociative, metaphosphate-like structure, stabilized by the Mg(2+) ion and several hydrogen bonds. The calculated free-energy barrier is consistent with experimental values. Implications of our results in this and other protein kinases are discussed.
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Affiliation(s)
- Gregory K Smith
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
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17
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The interaction graph structure of mass-action reaction networks. J Math Biol 2011; 65:375-402. [PMID: 21858686 DOI: 10.1007/s00285-011-0462-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Revised: 07/15/2011] [Indexed: 10/17/2022]
Abstract
Behaviour of chemical networks that are described by systems of ordinary differential equations can be analysed via the associated graph structures. This paper deals with observations based on the interaction graph which is defined by the signs of the Jacobian matrix entries. Some of the important graph structures linked to network dynamics are signed circuits and the nucleus (or Hamiltonian hooping). We use mass-action chemical reaction networks as an example to showcase interesting observations about the aforementioned interaction graph structures. We show that positive circuits and specific nucleus structures (associated to multistationarity) are always present in a great generic class of mass-action chemical and biological networks. The theory of negative circuits remains poorly understood, but there is some evidence that they are indicators of stable periodicity. Here we introduce the concept of non-isolated circuits which indicate the presence of a negative circuit.
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18
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Li QZ, Luo LF, Zhang LR. Study on the Model for Regulation of the Allosteric Enzyme Activity. CHINESE J CHEM 2010. [DOI: 10.1002/cjoc.20020201209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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19
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Nisius B, Rester U. Fragment Shuffling: An Automated Workflow for Three-Dimensional Fragment-Based Ligand Design. J Chem Inf Model 2009; 49:1211-22. [DOI: 10.1021/ci8004572] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Britta Nisius
- Bayer HealthCare AG, Global Drug Discovery, Lead Generation and Optimization, Aprather Weg 18a, D-42096 Elberfeld, Germany
| | - Ulrich Rester
- Bayer HealthCare AG, Global Drug Discovery, Lead Generation and Optimization, Aprather Weg 18a, D-42096 Elberfeld, Germany
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20
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Crystal structure of human CDK4 in complex with a D-type cyclin. Proc Natl Acad Sci U S A 2009; 106:4166-70. [PMID: 19237565 DOI: 10.1073/pnas.0809645106] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The cyclin D1-cyclin-dependent kinase 4 (CDK4) complex is a key regulator of the transition through the G(1) phase of the cell cycle. Among the cyclin/CDKs, CDK4 and cyclin D1 are the most frequently activated by somatic genetic alterations in multiple tumor types. Thus, aberrant regulation of the CDK4/cyclin D1 pathway plays an essential role in oncogenesis; hence, CDK4 is a genetically validated therapeutic target. Although X-ray crystallographic structures have been determined for various CDK/cyclin complexes, CDK4/cyclin D1 has remained highly refractory to structure determination. Here, we report the crystal structure of CDK4 in complex with cyclin D1 at a resolution of 2.3 A. Although CDK4 is bound to cyclin D1 and has a phosphorylated T-loop, CDK4 is in an inactive conformation and the conformation of the heterodimer diverges from the previously known CDK/cyclin binary complexes, which suggests a unique mechanism for the process of CDK4 regulation and activation.
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21
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Liu M, Choi S, Cuny GD, Ding K, Dobson BC, Glicksman MA, Auerbach K, Stein RL. Kinetic Studies of Cdk5/p25 Kinase: Phosphorylation of Tau and Complex Inhibition by Two Prototype Inhibitors. Biochemistry 2008; 47:8367-77. [DOI: 10.1021/bi800732v] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Min Liu
- Laboratory for Drug Discovery in Neurodegeneration, Harvard NeuroDiscovery Center, 65 Landsdowne Street, Fourth Floor, Cambridge, Massachusetts 02139
| | - Sungwoon Choi
- Laboratory for Drug Discovery in Neurodegeneration, Harvard NeuroDiscovery Center, 65 Landsdowne Street, Fourth Floor, Cambridge, Massachusetts 02139
| | - Gregory D. Cuny
- Laboratory for Drug Discovery in Neurodegeneration, Harvard NeuroDiscovery Center, 65 Landsdowne Street, Fourth Floor, Cambridge, Massachusetts 02139
| | - Kai Ding
- Laboratory for Drug Discovery in Neurodegeneration, Harvard NeuroDiscovery Center, 65 Landsdowne Street, Fourth Floor, Cambridge, Massachusetts 02139
| | - Brittany C. Dobson
- Laboratory for Drug Discovery in Neurodegeneration, Harvard NeuroDiscovery Center, 65 Landsdowne Street, Fourth Floor, Cambridge, Massachusetts 02139
| | - Marcie A. Glicksman
- Laboratory for Drug Discovery in Neurodegeneration, Harvard NeuroDiscovery Center, 65 Landsdowne Street, Fourth Floor, Cambridge, Massachusetts 02139
| | - Ken Auerbach
- Laboratory for Drug Discovery in Neurodegeneration, Harvard NeuroDiscovery Center, 65 Landsdowne Street, Fourth Floor, Cambridge, Massachusetts 02139
| | - Ross L. Stein
- Laboratory for Drug Discovery in Neurodegeneration, Harvard NeuroDiscovery Center, 65 Landsdowne Street, Fourth Floor, Cambridge, Massachusetts 02139
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22
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May A, Zacharias M. Protein−Ligand Docking Accounting for Receptor Side Chain and Global Flexibility in Normal Modes: Evaluation on Kinase Inhibitor Cross Docking. J Med Chem 2008; 51:3499-506. [DOI: 10.1021/jm800071v] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andreas May
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 6, D-28759 Bremen, Germany
| | - Martin Zacharias
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 6, D-28759 Bremen, Germany
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23
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Mazanetz MP, Fischer PM. Untangling tau hyperphosphorylation in drug design for neurodegenerative diseases. Nat Rev Drug Discov 2007; 6:464-79. [PMID: 17541419 DOI: 10.1038/nrd2111] [Citation(s) in RCA: 311] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Aggregation of hyperphosphorylated tau is one of the characteristic neuropathological lesions of Alzheimer's disease and other neurodegenerative disorders. Pharmacological modulation of tau hyperphosphorylation might represent a valid and feasible therapeutic strategy for such disorders. Here, we consider recent evidence supporting the validity of the three most relevant kinases affecting tau hyperphosphorylation - GSK3beta, CDK5 and ERK2 - as drug targets and describe progress in the design of inhibitors for these kinases.
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Affiliation(s)
- Michael P Mazanetz
- Centre for Biomolecular Sciences and School of Pharmacy, University of Nottingham, University Park, Nottingham NG7 2RD, UK
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24
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Chignola R, Del Fabbro A, Pellegrina CD, Milotti E. Ab initio phenomenological simulation of the growth of large tumor cell populations. Phys Biol 2007; 4:114-33. [PMID: 17664656 DOI: 10.1088/1478-3975/4/2/005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In a previous paper we have introduced a phenomenological model of cell metabolism and of the cell cycle to simulate the behavior of large tumor cell populations (Chignola and Milotti 2005 Phys. Biol. 2 8). Here we describe a refined and extended version of the model that includes some of the complex interactions between cells and their surrounding environment. The present version takes into consideration several additional energy-consuming biochemical pathways such as protein and DNA synthesis, the tuning of extracellular pH and of the cell membrane potential. The control of the cell cycle, which was previously modeled by means of ad hoc thresholds, has been directly addressed here by considering checkpoints from proteins that act as targets for phosphorylation on multiple sites. As simulated cells grow, they can now modify the chemical composition of the surrounding environment which in turn acts as a feedback mechanism to tune cell metabolism and hence cell proliferation: in this way we obtain growth curves that match quite well those observed in vitro with human leukemia cell lines. The model is strongly constrained and returns results that can be directly compared with actual experiments, because it uses parameter values in narrow ranges estimated from experimental data, and in perspective we hope to utilize it to develop in silico studies of the growth of very large tumor cell populations (10(6) cells or more) and to support experimental research. In particular, the program is used here to make predictions on the behavior of cells grown in a glucose-poor medium: these predictions are confirmed by experimental observation.
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Affiliation(s)
- Roberto Chignola
- Dipartimento Scientifico e Tecnologico, Università di Verona, Verona, Italy.
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25
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Subramanian J, Sharma S, B-Rao C. A novel computational analysis of ligand-induced conformational changes in the ATP binding sites of cyclin dependent kinases. J Med Chem 2006; 49:5434-41. [PMID: 16942017 DOI: 10.1021/jm060172s] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein kinases in general are known to be very flexible macromolecules. In this article, the conformational plasticity of the ATP binding site in cyclin dependent kinases is analyzed. Movement of the two lysine residues lining the ATP binding site are shown to play a major role in the conformational variability of the site. Linear models are developed to identify and quantify ligand properties that maximally influence the lysine side chain conformations. A few simple properties of the ligands are shown to account for more than 70% of the variation in the lysine conformations. The results are validated using test data and molecular simulation studies. Illustrative applications of the results of this analysis to finding the appropriate crystal structure for molecular docking and binding mode predictions of novel ligands are provided. This work provides a new approach to quantify ligand-induced conformational changes in the active sites of flexible proteins and to find the appropriate crystal structure for docking novel ligands.
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Affiliation(s)
- Jyothi Subramanian
- Cheminformatics, Nicholas Piramal Research Centre, 1 Nirlon Complex, Off Western Express Highway, Goregaon(E), Mumbai-400063, India
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26
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Craciun G, Tang Y, Feinberg M. Understanding bistability in complex enzyme-driven reaction networks. Proc Natl Acad Sci U S A 2006; 103:8697-702. [PMID: 16735474 PMCID: PMC1592242 DOI: 10.1073/pnas.0602767103] [Citation(s) in RCA: 218] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Indexed: 11/18/2022] Open
Abstract
Much attention has been paid recently to bistability and switch-like behavior that might be resident in important biochemical reaction networks. There is, in fact, a great deal of subtlety in the relationship between the structure of a reaction network and its capacity to engender bistability. In common physicochemical settings, large classes of extremely complex networks, taken with mass action kinetics, cannot give rise to bistability no matter what values the rate constants take. On the other hand, bistable behavior can be induced in those same settings by certain very simple and classical mass action mechanisms for enzyme catalysis of a single overall reaction. We present a theorem that distinguishes between those mass action networks that might support bistable behavior and those that cannot. Moreover, we indicate how switch-like behavior results from a well-studied mechanism for the action of human dihydrofolate reductase, an important anti-cancer target.
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Affiliation(s)
- Gheorghe Craciun
- *Mathematical Biosciences Institute, 231 West 18th Avenue, and
- Departments of Mathematics and Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706
| | | | - Martin Feinberg
- Departments of Chemical Engineering and
- Mathematics, 140 West 19th Avenue, Ohio State University, Columbus, OH 43210; and
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27
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Thomas MP, McInnes C, Fischer PM. Protein structures in virtual screening: a case study with CDK2. J Med Chem 2006; 49:92-104. [PMID: 16392795 DOI: 10.1021/jm050554i] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The influence of protein structure on the successful reproduction of known ligand poses by high-throughput docking programs is rarely discussed. Two commonly used programs, Glide and GOLD, were used to dock a set of CDK2 inhibitors of known bound pose into 20 different CDK2 structures. The numbers of docked poses that reproduced the known pose are reported. Depending on the program and protein structure, 0.3%-96.2% of the ligands docked with the correct pose. Although it is not possible to say that any one structure is "the best" for virtual screening, there are some structures that are clearly better than others. The main determinants of this are the volume of the binding site into which the ligands are docked and the exact orientation of the residues forming the binding site.
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Affiliation(s)
- Mark P Thomas
- Cyclacel Ltd., James Lindsay Place, Dundee, DD1 5JJ, UK.
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28
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Chassagnole C, Jackson RC, Hussain N, Bashir L, Derow C, Savin J, Fell DA. Using a mammalian cell cycle simulation to interpret differential kinase inhibition in anti-tumour pharmaceutical development. Biosystems 2006; 83:91-7. [PMID: 16236428 DOI: 10.1016/j.biosystems.2005.04.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2005] [Revised: 03/24/2005] [Accepted: 04/04/2005] [Indexed: 11/19/2022]
Abstract
Systems biology needs to show practical relevance to commercial biological challenges such as those of pharmaceutical development. The aim of this work is to design and validate some applications in anti-cancer therapeutic development. The test system was a group of novel cyclin-dependent kinase (CDK) inhibitors synthesised by Cyclacel Ltd. The measured in vitro IC50s of each compound were used as input data to a proprietary cell cycle model developed by Physiomics plc. The model was able to predict over three orders of magnitude the cytotoxicity of each compound without model adaptation to specific cancer cell types. This pattern matched the experimentally determined data. One class of compounds was predicted to cause an increase of the cell cycle length with a non-linear dose-response curve. Further work will use apoptosis and DNA replication simulations to look at overall cell effects.
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Affiliation(s)
- C Chassagnole
- Physiomics plc, Magdalen Centre, Oxford Science Park, Oxford OX4 4GA, UK.
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29
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Vulpetti A, Casale E, Roletto F, Amici R, Villa M, Pevarello P. Structure-based drug design to the discovery of new 2-aminothiazole CDK2 inhibitors. J Mol Graph Model 2005; 24:341-8. [PMID: 16260160 DOI: 10.1016/j.jmgm.2005.09.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2004] [Revised: 06/10/2005] [Accepted: 09/29/2005] [Indexed: 11/27/2022]
Abstract
N-(5-Bromo-1,3-thiazol-2-yl)butanamide (compound 1) was found active (IC50=808 nM) in a high throughput screening (HTS) for CDK2 inhibitors. By exploiting crystal structures of several complexes between CDK2 and inhibitors and applying structure-based drug design (SBDD), we rapidly discovered a very potent and selective CDK2 inhibitor 4-[(5-isopropyl-1,3-thiazol-2-yl)amino] benzenesulfonamide (compound 4, IC50=20 nM). The syntheses, structure-based analog design, kinases inhibition data and X-ray crystallographic structures of CDK2/inhibitor complexes are reported.
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Affiliation(s)
- Anna Vulpetti
- Department of Chemistry, Nerviano Medical Sciences, Discovery Research Oncology, Viale Pasteur 10, 20014 Nerviano (MI), Italy.
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30
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Ahn JS, Radhakrishnan ML, Mapelli M, Choi S, Tidor B, Cuny GD, Musacchio A, Yeh LA, Kosik KS. Defining Cdk5 ligand chemical space with small molecule inhibitors of tau phosphorylation. ACTA ACUST UNITED AC 2005; 12:811-23. [PMID: 16039528 DOI: 10.1016/j.chembiol.2005.05.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2005] [Revised: 04/13/2005] [Accepted: 05/11/2005] [Indexed: 11/20/2022]
Abstract
Cyclin-dependent kinase 5 (Cdk5) is widely viewed as a possible target for a wide variety of neurological disorders. One pathological role attributed to Cdk5 is the abnormal phosphorylation of tau that may lead to the neuronal inclusions known as neurofibrillary tangles. A high through-put screen for inhibitors of Cdk5-mediated phosphorylation of tau resulted in three compounds with distinct mechanisms of action. One compound is competitive with ATP and has a high affinity for the Cdk5 ATP binding pocket. The second compound also competes with ATP, is noncompetitive with tau, and (uniquely among this class of inhibitors) displaces adjacent amino acid residues to make room for the nitrophenyl group. A third compound did not compete with ATP, but did compete with tau at low concentrations of tau. The SAR and charge optimization derived from cocrystals of the two ATP competitors along with cocrystals of three other ATP competitors map out the importance of filling and properly charging different regions of the ATP binding pocket. Taken together, this analysis shows how the structure of Cdk5 constrains the space of potential inhibitors and reveals a pocket unfilled in all of the structures. These leads could be a starting point for structure-based drug design of more potent and selective inhibitors.
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Affiliation(s)
- Jae Suk Ahn
- Department of Neurology and Laboratory for Drug Discovery in Neurodegeneration, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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31
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Srinivasan J, Cload ST, Hamaguchi N, Kurz J, Keene S, Kurz M, Boomer RM, Blanchard J, Epstein D, Wilson C, Diener JL. ADP-specific sensors enable universal assay of protein kinase activity. ACTA ACUST UNITED AC 2004; 11:499-508. [PMID: 15123244 DOI: 10.1016/j.chembiol.2004.03.014] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2003] [Revised: 01/09/2004] [Accepted: 01/12/2004] [Indexed: 11/18/2022]
Abstract
Two molecular sensors that specifically recognize ADP in a background of over 100-fold molar excess of ATP are described. These sensors are nucleic-acid based and comprise a general method for monitoring protein kinase activity. The ADP-aptamer scintillation proximity assay is configured in a single-step, homogeneous format while the allosteric ribozyme (RiboReporter) sensor generates a fluorescent signal upon ADP-dependent ribozyme self-cleavage. Both systems perform well when configured for high-throughput screening and have been used to rediscover a known protein kinase inhibitor in a high-throughput screening format.
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32
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Liu SJ, Zhang JY, Li HL, Fang ZY, Wang Q, Deng HM, Gong CX, Grundke-Iqbal I, Iqbal K, Wang JZ. Tau Becomes a More Favorable Substrate for GSK-3 When It Is Prephosphorylated by PKA in Rat Brain. J Biol Chem 2004; 279:50078-88. [PMID: 15375165 DOI: 10.1074/jbc.m406109200] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Microtubule-associated protein tau is abnormally hyperphosphorylated in Alzheimer's disease (AD) and other tauopathies and is believed to lead to neurodegeneration in this family of diseases. Here we show that infusion of forskolin, a specific cAMP-dependent protein kinase A (PKA) activator, into the lateral ventricle of brain in adult rats induced activation of PKA by severalfold and concurrently enhanced the phosphorylation of tau at Ser-214, Ser-198, Ser-199, and or Ser-202 (Tau-1 site) and Ser-396 and or Ser-404 (PHF-1 site), which are among the major abnormally hyperphosphorylated sites seen in AD. PKA activation positively correlated to the extent of tau phosphorylation at these sites. Infusion of forskolin together with PKA inhibitor or glycogen synthase kinase-3 (GSK-3) inhibitor revealed that the phosphorylation of tau at Ser-214 was catalyzed by PKA and that the phosphorylation at both the Tau-1 and the PHF-1 sites is induced by basal level of GSK-3, because forskolin activated PKA and not GSK-3 and inhibition of the latter inhibited the phosphorylation at Tau-1 and PHF-1 sites. Inhibition of cdc2, cdk5, or MAPK had no significant effect on the forskolin-induced hyperphosphorylation of tau. Forskolin inhibited spatial memory in a dose-dependent manner in the absence but not in the presence of R(p)-adenosine 3',5'-cyclic monophosphorothioate triethyl ammonium salt, a PKA inhibitor. These results demonstrate for the first time that phosphorylation of tau by PKA primes it for phosphorylation by GSK-3 at the Tau-1 and the PHF-1 sites and that an associated loss in spatial memory is inhibited by inhibition of the hyperphosphorylation of tau. These data provide a novel mechanism of the hyperphosphorylation of tau and identify both PKA and GSK-3 as promising therapeutic targets for AD and other tauopathies.
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Affiliation(s)
- Shi Jie Liu
- Pathophysiology Department, Neuroscience Institute, Tongji Medical College, Hua-Zhong University of Science and Technology, Wuhan 430030, People's Republic of China
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33
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Monaco EA, Beaman-Hall CM, Mathur A, Vallano ML. Roscovitine, olomoucine, purvalanol: inducers of apoptosis in maturing cerebellar granule neurons. Biochem Pharmacol 2004; 67:1947-64. [PMID: 15130771 DOI: 10.1016/j.bcp.2004.02.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2003] [Accepted: 02/02/2004] [Indexed: 12/21/2022]
Abstract
Cyclin-dependent kinases (CDKs) mediate proliferation and neuronal development, while aberrant CDK activity is associated with cancer and neurodegeneration. Consequently, pharmacologic inhibitors, such as 2,6,9-trisubstituted purines, which potently inhibit CDKs 1, 2, and 5, were developed to combat these pathologies. One agent, R-roscovitine (CYC202), has advanced to clinical trials as a potential cancer therapy. In primary neuronal cultures, these agents have been used to delineate the physiologic and pathologic functions of CDKs, and associated signaling pathways. Herein we demonstrate that three 2,6,9-trisubstituted purines: olomoucine, roscovitine, and purvalanol, used at concentrations ascribed by others to potently inhibit CDKs 1, 2, and 5, are powerful triggers of death in maturing cerebellar granule neurons, assessed by loss of mitochondrial reductive capacity and differential staining with fluorescent indicators of living/dead neurons. Based on several criteria, including delayed time course and establishment of an irreversible commitment point of death, pyknotic cell and nuclear morphology, and caspase-3 cleavage, the death process is apoptotic. However, pharmacological and biochemical data indicate that apoptosis is independent of CDK 1, 2, or 5 inhibition. This is based on the pattern of changes in c-jun mRNA, c-Jun protein, and Ca(2+)/cAMP response element binding protein (CREB) phosphorylation, and also, the ineffectiveness of structurally distinct CDK 1, 2, and 5 inhibitors butyrolactone-1 and PNU112445A to induce apoptosis. Collectively, our results, and those of others, indicate that the CDK regulation of transcription (CDKs 7 and 9) should be examined as a target of these agents, and as an indirect mediator of neuronal fate.
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Affiliation(s)
- Edward A Monaco
- Department of Neuroscience & Physiology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
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34
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Pierce AC, Rao G, Bemis GW. BREED: Generating Novel Inhibitors through Hybridization of Known Ligands. Application to CDK2, P38, and HIV Protease. J Med Chem 2004; 47:2768-75. [PMID: 15139755 DOI: 10.1021/jm030543u] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work we describe BREED, a method for the generation of novel inhibitors from structures of known ligands bound to a common target. The method is essentially an automation of the common medicinal chemistry practice of joining fragments of two known ligands to generate a new inhibitor. The ligand-bound target structures are overlaid, all overlapping bonds in all pairs of ligands are found, and the fragments on each side of each matching bond are swapped to generate the new molecules. Since the method is automated, it can be applied recursively to generate all possible combinations of known ligands. In an application of this method to HIV protease inhibitors and protein kinase inhibitors, hundreds of new molecular structures were generated. These included known inhibitor scaffolds not included in the initial set, entirely novel scaffolds, and novel substituents on known scaffolds. The method is fast, and since all of the ligand functional groups are known to bind the target in the precise position and orientation present in the novel ligand, the success rate of this method should be superior to more traditional de novo design techniques. In an era of increasingly high-throughput structural biology, such methods for high-throughput utilization of structural information will become increasingly valuable.
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Affiliation(s)
- Albert C Pierce
- Vertex Pharmaceuticals, 130 Waverly Street, Cambridge, Massachusetts 02139.
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35
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Bramson HN. In vitro enzymatic assays for Ser/Thr-selective protein kinases. CURRENT PROTOCOLS IN PHARMACOLOGY 2003; Chapter 3:Unit 3.11. [PMID: 22294084 DOI: 10.1002/0471141755.ph0311s19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Medium and high throughput methods for measuring the activities of Ser/Thr-selective protein kinases are described. These methods utilize radiochemical detection, fluorescence polarization, and ultraviolet spectroscopy to monitor transfer of the gamma-phosphoryl group of ATP to protein or peptide substrates. These assays have utility in characterizing protein kinase inhibitors and in mechanistic studies.
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Affiliation(s)
- H Neal Bramson
- GlaxoSmithKline, Research Triangle Park, North Carolina, USA
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36
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Mesguiche V, Parsons RJ, Arris CE, Bentley J, Boyle FT, Curtin NJ, Davies TG, Endicott JA, Gibson AE, Golding BT, Griffin RJ, Jewsbury P, Johnson LN, Newell DR, Noble MEM, Wang LZ, Hardcastle IR. 4-Alkoxy-2,6-diaminopyrimidine derivatives: inhibitors of cyclin dependent kinases 1 and 2. Bioorg Med Chem Lett 2003; 13:217-22. [PMID: 12482427 DOI: 10.1016/s0960-894x(02)00884-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The cyclin dependent kinase (cdk) inhibitor NU6027, 4-cyclohexylmethoxy-5-nitroso-pyrimidine-2,6-diamine (IC(50) vs cdk1/cyclinB1=2.9+/-0.1 microM and IC(50) vs cdk2/cyclinA3=2.2+/-0.6 microM), was used as the basis for the design of a series of 4-alkoxy-2,6-diamino-5-nitrosopyrimidine derivatives. The synthesis and evaluation of 21 compounds as potential inhibitors of cyclin-dependent kinases 1 and 2 is described and the structure-activity relationships relating to NU6027 have been probed. Simple alkoxy- or cycloalkoxy-groups at the O(4)-position were tolerated, with the 4-(2-methylbutoxy)-derivative (IC(50) vs cdk1/cyclinB1=12+/-2 microM and cdk2/cyclinA3=13+/-4 microM) retaining significant activity. Substitutions at the N(6) position were not tolerated. Replacement of the 5-nitroso substituent with ketone, oxime and semicarbazone groups essentially abolished activity. However, the derivative bearing an isosteric 5-formyl group, 2,6-diamino-4-cyclohexylmethoxy-pyrimidine-5-carbaldehyde, showed modest activity (IC(50) vs cdk1/cyclinB1=35+/-3 microM and cdk2/cyclinA3=43+/-3 microM). The X-ray crystal structure of the 5-formyl compound bound to cdk2 has been determined to 2.3A resolution. The intramolecular H-bond deduced from the structure with NU6027 bound to cdk2 is not evident in the structure with the corresponding formyl compound. Thus the parent compound, 4-cyclohexylmethoxy-5-nitrosopyrimidine-2,6-diamine (NU6027), remains the optimal basis for future structure-activity studies for cyclin-dependent kinase inhibitors in this series.
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Affiliation(s)
- Veronique Mesguiche
- Northern Institute of Cancer Research and Department of Chemistry, Bedson Building, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
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37
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Mettey Y, Gompel M, Thomas V, Garnier M, Leost M, Ceballos-Picot I, Noble M, Endicott J, Vierfond JM, Meijer L. Aloisines, a new family of CDK/GSK-3 inhibitors. SAR study, crystal structure in complex with CDK2, enzyme selectivity, and cellular effects. J Med Chem 2003; 46:222-36. [PMID: 12519061 DOI: 10.1021/jm020319p] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyclin-dependent kinases (CDKs) regulate the cell cycle, apoptosis, neuronal functions, transcription, and exocytosis. The observation of CDK deregulations in various pathological situations suggests that CDK inhibitors may have a therapeutic value. In this article, we report on the identification of 6-phenyl[5H]pyrrolo[2,3-b]pyrazines (aloisines) as a novel potent CDK inhibitory scaffold. A selectivity study performed on 26 kinases shows that aloisine A is highly selective for CDK1/cyclin B, CDK2/cyclin A-E, CDK5/p25, and GSK-3 alpha/beta; the two latter enzymes have been implicated in Alzheimer's disease. Kinetic studies, as well as the resolution of a CDK2-aloisine cocrystal structure, demonstrate that aloisines act by competitive inhibition of ATP binding to the catalytic subunit of the kinase. As observed with all inhibitors reported so far, aloisine interacts with the ATP-binding pocket through two hydrogen bonds with backbone nitrogen and oxygen atoms of Leu 83. Aloisine inhibits cell proliferation by arresting cells in both G1 and G2.
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Affiliation(s)
- Yvette Mettey
- Faculté de Médecine et de Pharmacie, 34 rue du Jardin des Plantes, B.P. 199, 86005 Poitiers Cedex, France
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Canduri F, Silveira NJFD, Camera Jr JC, Azevedo Jr WFD. Structural bioinformatics study of cyclin-dependent kinases complexed with inhibitors. ECLÉTICA QUÍMICA 2003. [DOI: 10.1590/s0100-46702003000100006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The present work describes molecular models for the binary complexes CDK9, CDK5 and CDK1 complexed with Flavopiridol and Roscovitine. These structural models indicate that the inhibitors strongly bind to the ATP-binding pocket of CDKs and the structural comparison with the complexes CDK2:Flavopiridol and CDK2:Roscovitine correlates the structural differences with differences in inhibition of these CDKs by the inhibitors. These structures open the possibility of testing new inhibitor families, in addition to new substituents for the already known lead structures such as flavones and adenine derivatives.
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Filgueira de Azevedo W, Gaspar RT, Canduri F, Camera JC, Freitas da Silveira NJ. Molecular model of cyclin-dependent kinase 5 complexed with roscovitine. Biochem Biophys Res Commun 2002; 297:1154-8. [PMID: 12372407 DOI: 10.1016/s0006-291x(02)02352-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Here is described a structural model for the binary complex CDK5-roscovitine. Roscovitine has been shown to potently inhibit cyclin-dependent kinases 1, 2 and 5 (CDK1, 2, and 5), and the structure of CDK2 complexed with roscovitine has been reported; however, no structural data are available for complexes of CDK5 with inhibitors. The structural model indicates that roscovitine strongly binds to the ATP-binding pocket of CDK5 and structural comparison of the CDK2-roscovitine complex correlates the structural differences with differences in inhibition of these CDKs by this inhibitor. This structure opens the possibility of testing new inhibitor families, in addition to new substituents for the already known lead structures of adenine derivatives.
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Knockaert M, Lenormand P, Gray N, Schultz P, Pouysségur J, Meijer L. p42/p44 MAPKs are intracellular targets of the CDK inhibitor purvalanol. Oncogene 2002; 21:6413-24. [PMID: 12226745 DOI: 10.1038/sj.onc.1205908] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2001] [Revised: 07/01/2002] [Accepted: 07/24/2002] [Indexed: 11/09/2022]
Abstract
Chemical inhibitors of cyclin-dependent kinases (CDKs) have a great therapeutic potential against various proliferative and neurodegenerative disorders. Intensive screening of a combinatorial chemistry library of 2,6,9-trisubstituted purines has led to the identification of purvalanol, one of the most potent and selective CDK inhibitors to date. In preliminary studies, this compound demonstrates definite anti-mitotic properties, consistent with its nanomolar range efficiency towards purified CDK1 and CDK2. However, the actual intracellular targets of purvalanol remain to be identified, and a method for the determination of its in vivo selectivity was developed. In this technique, cell extracts were screened for purvalanol-interacting proteins by affinity chromatography on immobilized inhibitor. In addition to CDK1, p42/p44 MAPK were found to be two major purvalanol-interacting proteins in five different mammalian cell lines (CCL39, PC12, HBL100, MCF-7 and Jurkat cells), suggesting the generality of the purvalanol/p42/p44 MAPK interaction. The Chinese hamster lung fibroblast cell line CCL39 was used as a model to investigate the anti-proliferative properties of purvalanol. The compound inhibited cell growth with a GI(50) value of 2.5 microM and induced a G2/M block when added to exponentially growing cells. It did not appear to trigger massive activation of caspase. We next tested whether CDKs and p42/p44 MAPK were actually targeted by the compound in vivo. p42/p44 MAPK activity was visualized using an Elk-Gal4 luciferase reporter system and CDK1 activity was detected by the phosphonucleolin level. When cells were treated with purvalanol, p42/p44 MAPK and CDK1 activities were inhibited in a dose-dependent manner. Furthermore, purvalanol inhibited the nuclear accumulation of p42/p44 MAPK, an event dependent on the catalytic activity of these kinases. We conclude that the anti-proliferative properties of purvalanol are mediated by inhibition of both p42/p44 MAPK and CDKs. These observations highlight the potency of moderate selectivity compounds and encourage the search for new therapeutics which simultaneously target distinct but relevant pathways of cell proliferation.
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Affiliation(s)
- Marie Knockaert
- Station Biologique de Roscoff, CNRS, B.P.74, 29682 Roscoff Cedex, Bretagne, France
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41
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Abstract
Cyclin-dependent kinases (CDKs) regulate the cell division cycle, apoptosis, transcription and differentiation in addition to functions in the nervous system. Deregulation of CDKs in various diseases has stimulated an intensive search for selective pharmacological inhibitors of these kinases. More than 50 inhibitors have been identified, among which >20 have been co-crystallized with CDK2. These inhibitors all target the ATP-binding pocket of the catalytic site of the kinase. The actual selectivity of most known CDK inhibitors, and thus the underlying mechanism of their cellular effects, is poorly known. Pharmacological inhibitors of CDKs are currently being evaluated for therapeutic use against cancer, alopecia, neurodegenerative disorders (e.g. Alzheimer's disease, amyotrophic lateral sclerosis and stroke), cardiovascular disorders (e.g. atherosclerosis and restenosis), glomerulonephritis, viral infections (e.g. HCMV, HIV and HSV) and parasitic protozoa (Plasmodium sp. and Leishmania sp.).
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Affiliation(s)
- Marie Knockaert
- Station Biologique de Roscoff, CNRS, BP 74, 29682 Roscoff Cedex, Bretagne, France
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Schindler JF, Godbey A, Hood WF, Bolten SL, Broadus RM, Kasten TP, Cassely AJ, Hirsch JL, Merwood MA, Nagy MA, Fok KF, Saabye MJ, Morgan HM, Compton RP, Mourey RJ, Wittwer AJ, Monahan JB. Examination of the kinetic mechanism of mitogen-activated protein kinase activated protein kinase-2. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1598:88-97. [PMID: 12147348 DOI: 10.1016/s0167-4838(02)00340-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The kinetic mechanism of mitogen-activated protein kinase activated protein kinase-2 (MAPKAPK2) was investigated using a peptide (LKRSLSEM) based on the phosphorylation site found in serum response factor (SRF). Initial velocity studies yielded a family of double-reciprocal lines that appear parallel and indicative of a ping-pong mechanism. The use of dead-end inhibition studies did not provide a definitive assignment of a reaction mechanism. However, product inhibition studies suggested that MAPKAPK2 follows an ordered bi-bi kinetic mechanism, where ATP must bind to the enzyme prior to the SRF-peptide and the phosphorylated product is released first, followed by ADP. In agreement with these latter results, surface plasmon resonance measurements demonstrate that the binding of the inhibitor peptide to MAPKAPK2 requires the presence of ATP. Furthermore, competitive inhibitors of ATP, adenosine 5'-(beta,gamma-imino)triphosphate (AMPPNP) and a staurosporine analog (K252a), can inhibit this ATP-dependent binding providing further evidence that the peptide substrate binds preferably to the E:ATP complex.
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Affiliation(s)
- John F Schindler
- Signal Transduction and Enzymology Group, Pharmacia Corporation, Chesterfield Parkway North, St. Louis, MO 63198, USA.
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