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Natural Protein Kinase Inhibitors, Staurosporine, and Chelerythrine Suppress Wheat Blast Disease Caused by Magnaporthe oryzae Triticum. Microorganisms 2022; 10:microorganisms10061186. [PMID: 35744705 PMCID: PMC9230996 DOI: 10.3390/microorganisms10061186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/02/2022] [Accepted: 06/07/2022] [Indexed: 01/01/2023] Open
Abstract
Protein kinases (PKs), being key regulatory enzymes of a wide range of signaling pathways, are potential targets for antifungal agents. Wheat blast disease, caused by Magnaporthe oryzae Triticum (MoT), is an existential threat to world food security. During the screening process of natural metabolites against MoT fungus, we find that two protein kinase inhibitors, staurosporine and chelerythrine chloride, remarkably inhibit MoT hyphal growth. This study further investigates the effects of staurosporine and chelerythrine chloride on MoT hyphal growth, conidia production, and development as well as wheat blast inhibition in comparison to a commercial fungicide, Nativo®75WG. The growth of MoT mycelia is significantly inhibited by these compounds in a dose-dependent manner. These natural compounds greatly reduce conidia production in MoT mycelia along with suppression of conidial germination and triggered lysis, resulting in deformed germ tubes and appressoria. These metabolites greatly suppress blast development in artificially inoculated wheat plants in the field. This is the first report of the antagonistic effect of these two natural PKC inhibitory alkaloids on MoT fungal developmental processes in vitro and suppression of wheat blast disease on both leaves and spikes in vivo. Further research is needed to identify their precise mechanism of action to consider them as biopesticides or lead compounds for controlling wheat blast.
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Veit-Acosta M, de Azevedo Junior WF. Computational Prediction of Binding Affinity for CDK2-ligand Complexes. A Protein Target for Cancer Drug Discovery. Curr Med Chem 2021; 29:2438-2455. [PMID: 34365938 DOI: 10.2174/0929867328666210806105810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/15/2021] [Accepted: 06/22/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND CDK2 participates in the control of eukaryotic cell-cycle progression. Due to the great interest in CDK2 for drug development and the relative easiness in crystallizing this enzyme, we have over 400 structural studies focused on this protein target. This structural data is the basis for the development of computational models to estimate CDK2-ligand binding affinity. OBJECTIVE This work focuses on the recent developments in the application of supervised machine learning modeling to develop scoring functions to predict the binding affinity of CDK2. METHOD We employed the structures available at the protein data bank and the ligand information accessed from the BindingDB, Binding MOAD, and PDBbind to evaluate the predictive performance of machine learning techniques combined with physical modeling used to calculate binding affinity. We compared this hybrid methodology with classical scoring functions available in docking programs. RESULTS Our comparative analysis of previously published models indicated that a model created using a combination of a mass-spring system and cross-validated Elastic Net to predict the binding affinity of CDK2-inhibitor complexes outperformed classical scoring functions available in AutoDock4 and AutoDock Vina. CONCLUSION All studies reviewed here suggest that targeted machine learning models are superior to classical scoring functions to calculate binding affinities. Specifically for CDK2, we see that the combination of physical modeling with supervised machine learning techniques exhibits improved predictive performance to calculate the protein-ligand binding affinity. These results find theoretical support in the application of the concept of scoring function space.
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Affiliation(s)
- Martina Veit-Acosta
- Western Michigan University, 1903 Western, Michigan Ave, Kalamazoo, MI 49008. United States
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Bitencourt-Ferreira G, Duarte da Silva A, Filgueira de Azevedo W. Application of Machine Learning Techniques to Predict Binding Affinity for Drug Targets: A Study of Cyclin-Dependent Kinase 2. Curr Med Chem 2021; 28:253-265. [PMID: 31729287 DOI: 10.2174/2213275912666191102162959] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/22/2019] [Accepted: 09/24/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND The elucidation of the structure of cyclin-dependent kinase 2 (CDK2) made it possible to develop targeted scoring functions for virtual screening aimed to identify new inhibitors for this enzyme. CDK2 is a protein target for the development of drugs intended to modulate cellcycle progression and control. Such drugs have potential anticancer activities. OBJECTIVE Our goal here is to review recent applications of machine learning methods to predict ligand- binding affinity for protein targets. To assess the predictive performance of classical scoring functions and targeted scoring functions, we focused our analysis on CDK2 structures. METHODS We have experimental structural data for hundreds of binary complexes of CDK2 with different ligands, many of them with inhibition constant information. We investigate here computational methods to calculate the binding affinity of CDK2 through classical scoring functions and machine- learning models. RESULTS Analysis of the predictive performance of classical scoring functions available in docking programs such as Molegro Virtual Docker, AutoDock4, and Autodock Vina indicated that these methods failed to predict binding affinity with significant correlation with experimental data. Targeted scoring functions developed through supervised machine learning techniques showed a significant correlation with experimental data. CONCLUSION Here, we described the application of supervised machine learning techniques to generate a scoring function to predict binding affinity. Machine learning models showed superior predictive performance when compared with classical scoring functions. Analysis of the computational models obtained through machine learning could capture essential structural features responsible for binding affinity against CDK2.
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Affiliation(s)
- Gabriela Bitencourt-Ferreira
- Laboratory of Computational Systems Biology. Pontifical Catholic University of Rio Grande do Sul (PUCRS). Av. Ipiranga, 6681 Porto Alegre/RS 90619-900 , Brazil
| | - Amauri Duarte da Silva
- Specialization Program in Bioinformatics. Pontifical Catholic University of Rio Grande do Sul (PUCRS). Av. Ipiranga, 6681 Porto Alegre/RS 90619-900, Brazil
| | - Walter Filgueira de Azevedo
- Laboratory of Computational Systems Biology. Pontifical Catholic University of Rio Grande do Sul (PUCRS). Av. Ipiranga, 6681 Porto Alegre/RS 90619-900 , Brazil
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Mou J, Chen D, Deng Y. Inhibitors of Cyclin-Dependent Kinase 1/2 for Anticancer Treatment. Med Chem 2020; 16:307-325. [PMID: 31241436 DOI: 10.2174/1573406415666190626113900] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 03/05/2019] [Accepted: 05/14/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND The cell cycle is regulated by cyclin-dependent kinases (CDKs) and their cognate cyclins, along with their endogenous inhibitors (CDKIs). CDKs act as central regulators in this process. Different CDKs play relevant roles in different phases. Among all CDKs, CDK1 is indispensible, which can drive all events that are required in the cell cycle in the absence of interphase CDKs (CDK2, CDK3, CDK4 and CDK6). So, CDK1 is an attractive target for anticancer drug development. METHODS CDK1 and CDK2 have 89.19% similar residues and 74.32% identical residues, their structures especially the ATP-binding sites are of great similarity. So, it is difficult to inhibit CDK1 and CDK2 individually. In this review, recent advances about CDK1/2 inhibitors were summarized. The chemical structures of different classes of CDK1/2 inhibitors and their structure activity are presented. RESULTS 19 kinds of CDK1/2 or CDK1 inhibitors with different scaffolds, including CDK2 allosteric inhibitors, were summarized. Some inhibitors are nature derived, for example, phenanthrene derivatives, nortopsentin derivatives, variolin B derivatives and meridians. CONCLUSION Nature products, especially marine ones are potential resources for CDK1 inhibitors development. The findings of CDK2 allosteric inhibitors open an avenue to the discovery of novel selective CDK1 or other CDKs allosteric inhibitors.
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Affiliation(s)
- Jiajia Mou
- Department of Medicinal Chemistry, School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Health Industry Park, Jinghai District, Tianjin, 301617, China
| | - Danghui Chen
- Department of Medicinal Chemistry, School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Health Industry Park, Jinghai District, Tianjin, 301617, China
| | - Yanru Deng
- Department of Medicinal Chemistry, School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Health Industry Park, Jinghai District, Tianjin, 301617, China
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Cheng C, Yun F, Ullah S, Yuan Q. Discovery of novel cyclin-dependent kinase (CDK) and histone deacetylase (HDAC) dual inhibitors with potent in vitro and in vivo anticancer activity. Eur J Med Chem 2020; 189:112073. [PMID: 31991336 DOI: 10.1016/j.ejmech.2020.112073] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/03/2020] [Accepted: 01/13/2020] [Indexed: 12/14/2022]
Abstract
In the current study, we reported a series of novel 1-H-pyrazole-3-carboxamide-based inhibitors targeting histone deacetylase (HDAC) and cyclin-dependent kinase (CDK). The representative compounds N-(4-((2-aminophenyl)carbamoyl)benzyl)-4-(2,6-dichlorobenzamido)-1H-pyrazole-3-carboxamide (7c) and N-(4-(2-((2-aminophenyl)amino)-2-oxoethyl)phenyl)-4-(2,6-dichlorobenzamido)-1H-pyrazole-3-carboxamide (14a) with potent antiproliferative activities towards five solid cancer cell lines, showed excellent inhibitory activities against HDAC2 (IC50 = 0.25 and 0.24 nM respectively) and CDK2 (IC50 = 0.30 and 0.56 nM respectively). In addition, compounds 7c and 14a significantly inhibited the migration of A375 and H460 cells. Further studies revealed that compounds 7c and 14a could arrest cell cycle in G2/M phase and promote apoptosis in A375, HCT116, H460 and Hela cells, which was associated with increasing the intracellular reactive oxygen species (ROS) levels. More importantly, compound 7c possessed favorable pharmacokinetic properties with the intraperitoneal bioavailability of 63.6% in ICR mice, and potent in vivo antitumor efficacy in the HCT116 xenograft model. Our study demonstrated that compound 7c provides a promising strategy for the treatment of malignant tumors.
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Affiliation(s)
- Chunhui Cheng
- Key Laboratory of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology), Ministry of Education, College of Life Science and Technology, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Beijing, 100029, China
| | - Fan Yun
- Key Laboratory of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology), Ministry of Education, College of Life Science and Technology, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Beijing, 100029, China
| | - Sadeeq Ullah
- Key Laboratory of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology), Ministry of Education, College of Life Science and Technology, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Beijing, 100029, China
| | - Qipeng Yuan
- Key Laboratory of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology), Ministry of Education, College of Life Science and Technology, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Beijing, 100029, China.
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Videla-Richardson GA, Furmento VA, Garcia CP, Morris-Hanon O, Sevlever GE, Romorini L, Scassa ME. Human embryonic stem cells display a pronounced sensitivity to the cyclin dependent kinase inhibitor Roscovitine. BMC Mol Cell Biol 2019; 20:40. [PMID: 31462218 PMCID: PMC6712821 DOI: 10.1186/s12860-019-0222-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 08/19/2019] [Indexed: 12/14/2022] Open
Abstract
Background The essentially unlimited expansion potential and the pluripotency of human embryonic stem cells (hESCs) make them attractive for cell-based therapeutic purposes. Although hESCs can indefinitely proliferate in culture, unlike transformed cancer cells, they are endowed with a cell-intrinsic property termed mitochondrial priming that renders them highly sensitive to apoptotic stimuli. Thus, all attempts to broaden the insights into hESCs apoptosis may be helpful for establishing pro-survival strategies valuable for its in vitro culture and further use in clinical applications. Cyclin-dependent kinases (CDKs), a family of serine/threonine protein kinases originally identified as regulators of the eukaryotic cell cycle, can also regulate transcription and differentiation. Moreover, there are compelling data suggesting that its activities are involved in certain apoptotic programs in different cell types. Currently, it is not completely determined whether CDKs regulate apoptotic processes in rapidly proliferating and apoptosis-prone hESCs. In this study, to elucidate the effect of CDKs inhibition in hESCs we used Roscovitine (ROSC), a purine analogue that selectively inhibits the activities of these kinases. Results Inhibition of CDKs by ROSC triggers programmed cell death in hESCs but not in proliferating somatic cells (human fibroblasts). The apoptotic process encompasses caspase-9 and -3 activation followed by PARP cleavage. ROSC treatment also leads to p53 stabilization, which coincides with site-specific phosphorylation at serine 46 and decreased levels of Mdm2. Additionally, we observed a transcriptional induction of p53AIP1, a repression of pro-survival factor Mcl-1 and an up-regulation of pro-apoptotic BH3-only proteins NOXA and PUMA. Importantly, we found that the role of CDK2 inhibition appears to be at best accessory as an active CDK2 is not required to ensure hESCs survival. Conclusion Our experimental data reveal that hESCs, contrary to fibroblasts, exhibit a pronounced sensitivity to ROSC.
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Affiliation(s)
- Guillermo A Videla-Richardson
- Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (FLENI), Belén de Escobar, Provincia de Buenos Aires, Argentina
| | - Verónica A Furmento
- Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (FLENI), Belén de Escobar, Provincia de Buenos Aires, Argentina
| | - Carolina P Garcia
- Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (FLENI), Belén de Escobar, Provincia de Buenos Aires, Argentina
| | - Olivia Morris-Hanon
- Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (FLENI), Belén de Escobar, Provincia de Buenos Aires, Argentina
| | - Gustavo E Sevlever
- Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (FLENI), Belén de Escobar, Provincia de Buenos Aires, Argentina
| | - Leonardo Romorini
- Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (FLENI), Belén de Escobar, Provincia de Buenos Aires, Argentina
| | - María E Scassa
- Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (FLENI), Belén de Escobar, Provincia de Buenos Aires, Argentina.
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Abstract
Since the early 1980s, we have witnessed considerable progress in the development and application of docking programs to assess protein-ligand interactions. Most of these applications had as a goal the identification of potential new binders to protein targets. Another remarkable progress is taking place in the determination of the structures of protein-ligand complexes, mostly using X-ray diffraction crystallography. Considering these developments, we have a favorable scenario for the creation of a computational tool that integrates into one workflow all steps involved in molecular docking simulations. We had these goals in mind when we developed the program SAnDReS. This program allows the integration of all computational features related to modern docking studies into one workflow. SAnDReS not only carries out docking simulations but also evaluates several docking protocols allowing the selection of the best approach for a given protein system. SAnDReS is a free and open-source (GNU General Public License) computational environment for running docking simulations. Here, we describe the combination of SAnDReS and AutoDock4 for protein-ligand docking simulations. AutoDock4 is a free program that has been applied to over a thousand receptor-ligand docking simulations. The dataset described in this chapter is available for downloading at https://github.com/azevedolab/sandres.
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Affiliation(s)
- Gabriela Bitencourt-Ferreira
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Walter Filgueira de Azevedo
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil.
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Bitencourt-Ferreira G, Veit-Acosta M, de Azevedo WF. Van der Waals Potential in Protein Complexes. Methods Mol Biol 2019; 2053:79-91. [PMID: 31452100 DOI: 10.1007/978-1-4939-9752-7_6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Van der Waals forces are determinants of the formation of protein-ligand complexes. Physical models based on the Lennard-Jones potential can estimate van der Waals interactions with considerable accuracy and with a computational complexity that allows its application to molecular docking simulations and virtual screening of large databases of small organic molecules. Several empirical scoring functions used to evaluate protein-ligand interactions approximate van der Waals interactions with the Lennard-Jones potential. In this chapter, we present the main concepts necessary to understand van der Waals interactions relevant to molecular recognition of a ligand by the binding pocket of a protein target. We describe the Lennard-Jones potential and its application to calculate potential energy for an ensemble of structures to highlight the main features related to the importance of this interaction for binding affinity.
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Affiliation(s)
- Gabriela Bitencourt-Ferreira
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Martina Veit-Acosta
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Walter Filgueira de Azevedo
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil.
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9
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Abstract
Homology modeling is a computational approach to generate three-dimensional structures of protein targets when experimental data about similar proteins are available. Although experimental methods such as X-ray crystallography and nuclear magnetic resonance spectroscopy successfully solved the structures of nearly 150,000 macromolecules, there is still a gap in our structural knowledge. We can fulfill this gap with computational methodologies. Our goal in this chapter is to explain how to perform homology modeling of protein targets for drug development. We choose as a homology modeling tool the program MODELLER. To illustrate its use, we describe how to model the structure of human cyclin-dependent kinase 3 using MODELLER. We explain the modeling procedure of CDK3 apoenzyme and the structure of this enzyme in complex with roscovitine.
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Affiliation(s)
- Gabriela Bitencourt-Ferreira
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Walter Filgueira de Azevedo
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil.
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10
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Abstract
Fast and reliable evaluation of the hydrogen bond potential energy has a significant impact in the drug design and development since it allows the assessment of large databases of organic molecules in virtual screening projects focused on a protein of interest. Semi-empirical force fields implemented in molecular docking programs make it possible the evaluation of protein-ligand binding affinity where the hydrogen bond potential is a common term used in the calculation. In this chapter, we describe the concepts behind the programs used to predict hydrogen bond potential energy employing semi-empirical force fields as the ones available in the programs AMBER, AutoDock4, TreeDock, and ReplicOpter. We described here the 12-10 potential and applied it to evaluate the binding affinity for an ensemble of crystallographic structures for which experimental data about binding affinity are available.
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Affiliation(s)
- Gabriela Bitencourt-Ferreira
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Martina Veit-Acosta
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Walter Filgueira de Azevedo
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil.
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Deep A, Marwaha RK, Marwaha MG, Jyoti J, Nandal R, Sharma AK. Flavopiridol as cyclin dependent kinase (CDK) inhibitor: a review. NEW J CHEM 2018. [DOI: 10.1039/c8nj04306j] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Flavopiridol (alvocidib) is a synthetic flavonoid based on the extract from an Indian plant developed for potential treatment of cancer whose first clinical trials were initiated in 1994 as a frontline combination therapy for leukaemia.
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Affiliation(s)
- Aakash Deep
- Department of Pharmaceutical Sciences
- Chaudhary Bansi Lal University
- Bhiwani-127021
- India
| | - Rakesh Kumar Marwaha
- Department of Pharmaceutical Sciences
- Maharshi Dayanand University
- Rohtak-124001
- India
| | | | - Jyoti Jyoti
- Department of Pharmaceutical Sciences
- Maharshi Dayanand University
- Rohtak-124001
- India
| | - Rimmy Nandal
- Department of Pharmaceutical Sciences
- Chaudhary Bansi Lal University
- Bhiwani-127021
- India
| | - Arun Kumar Sharma
- Department of Pharmacology
- Amity Institute of Pharmacy
- Amity University
- Gurugram
- India
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12
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de Ávila MB, Xavier MM, Pintro VO, de Azevedo WF. Supervised machine learning techniques to predict binding affinity. A study for cyclin-dependent kinase 2. Biochem Biophys Res Commun 2017; 494:305-310. [DOI: 10.1016/j.bbrc.2017.10.035] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 10/06/2017] [Indexed: 02/01/2023]
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Pharmacophore identification, docking and “in silico” screening for novel CDK1 inhibitors. J Mol Graph Model 2012; 37:77-86. [DOI: 10.1016/j.jmgm.2012.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 04/04/2012] [Accepted: 04/17/2012] [Indexed: 11/19/2022]
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14
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Saraiva LA, Veloso MP, Camps I, da Silveira NJF. Structural Bioinformatics Approach of Cyclin-Dependent Kinases 1 and 3 Complexed with Inhibitors. Mol Inform 2011; 30:219-31. [PMID: 27466775 DOI: 10.1002/minf.201000143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2010] [Accepted: 01/17/2011] [Indexed: 11/06/2022]
Abstract
The cyclin-dependent kinases or CDKs participate in the regulation of both the cell progression cycle and the RNA polymerase-II transcription cycle. In several human tumours deregulation of CDK-related mechanisms have been detected, e.g., overexpression of cyclins or deletion of genes encoding for CKIs. Regarding these observations, CDKs came up to be interesting targets for elaboration of novel antitumour drugs. Based on the importance of the CDKs, this research aimed to describe, to characterize and to compare the molecular models of CDK1 and CDK3. Since the structures of human CDK1 and CDK3 are unavailable in the Protein Data Bank -PDB, homology models were created based on the CDK2 as the template, once they share a substantial identity. The structural studies of the CDK1 and CDK3 biding sites were conducted by molecular docking with 15 different CDK inhibitors previously identified to CDK2. This study allowed the understanding of the structure of the complexes between CDK1/ CDK3 with inhibitors. The knowledge of their structural features mainly the biding sites might be useful to discovery and rationalization of drug design process.
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Affiliation(s)
- Lucas A Saraiva
- Faculty of Pharmaceutical Science, Rua Gabriel Monteiro da Silva, 700 Centro - Alfenas/MG Postal Code: 37130000, Brazil. tel: +553133322556.
| | - Marcia P Veloso
- Faculty of Pharmaceutical Science, Rua Gabriel Monteiro da Silva, 700 Centro - Alfenas/MG Postal Code: 37130000, Brazil. tel: +553133322556
| | - I Camps
- Institute of Exacts Science, Rua Gabriel Monteiro da Silva, 700 Centro - Alfenas/MG Postal Code: 37130000, Brazil
| | - Nelson J F da Silveira
- Institute of Exacts Science, Rua Gabriel Monteiro da Silva, 700 Centro - Alfenas/MG Postal Code: 37130000, Brazil
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Idowu MA. Cyclin-Dependent Kinases as Drug Targets for Cell Growth and Proliferation Disorders. A Role for Systems Biology Approach in Drug Development. Part I—Cyclin-Dependent Kinases as Drug Targets in Cancer. BIOTECHNOL BIOTEC EQ 2011. [DOI: 10.5504/bbeq.2011.0107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Węsierska-Gądek J, Kryštof V. Selective Cyclin-Dependent Kinase Inhibitors Discriminating between Cell Cycle and Transcriptional Kinases. Ann N Y Acad Sci 2009; 1171:228-41. [DOI: 10.1111/j.1749-6632.2009.04726.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Pauli I, Macedo Timmers LFS, Andrade Caceres R, Augusto Basso L, Santiago Santos D, Filgueira de Azevedo Jr. W. Molecular modeling and dynamics studies of purine nucleoside phosphorylase from Bacteroides fragilis. J Mol Model 2009; 15:913-22. [DOI: 10.1007/s00894-008-0445-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Accepted: 12/08/2008] [Indexed: 10/21/2022]
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18
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Raffa D, Maggio B, Cascioferro S, Raimondi MV, Daidone G, Plescia S, Schillaci D, Cusimano MG, Titone L, Colomba C, Tolomeo M. N-(Indazolyl)benzamido Derivatives as CDK1 Inhibitors: Design, Synthesis, Biological Activity, and Molecular Docking Studies. Arch Pharm (Weinheim) 2009; 342:265-73. [DOI: 10.1002/ardp.200800159] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Timmers LFSM, Caceres RA, Dias R, Basso LA, Santos DS, de Azevedo WF. Molecular modeling, dynamics and docking studies of purine nucleoside phosphorylase from Streptococcus pyogenes. Biophys Chem 2009; 142:7-16. [PMID: 19282092 DOI: 10.1016/j.bpc.2009.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Revised: 02/17/2009] [Accepted: 02/17/2009] [Indexed: 11/19/2022]
Abstract
Purine Nucleoside Phosphorylase (PNP) catalyzes the reversible phosphorolysis of N-glycosidic bonds of purine nucleosides and deoxynucleosides, except for adenosine, to generate ribose 1-phosphate and the purine base. PNP has been submitted to intensive structural studies. This work describes for the first time a structural model of PNP from Streptococcus pyogenes (SpPNP). We modeled the complexes of SpPNP with six different ligands in order to determine the structural basis for specificity of these ligands against SpPNP. Molecular dynamics (MD) simulations were performed in order to evaluate the overall stability of SpPNP model. The analysis of the MD simulation was assessed mainly by principal component analysis (PCA) to explore the trimeric structure behavior. Structural comparison, between SpPNP and human PNP, was able to identify the main features responsible for differences in ligand-binding affinities, such as mutation in the purine-binding site and in the second phosphate-binding site. The PCA analysis suggests a different behavior for each subunit in the trimer structure.
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Affiliation(s)
- Luis Fernando Saraiva Macedo Timmers
- Faculdade de Biociências, Laboratório de Bioquímica Estrutural, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre-RS, Brazil.
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20
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Perez PC, Caceres RA, Canduri F, de Azevedo WF. Molecular modeling and dynamics simulation of human cyclin-dependent kinase 3 complexed with inhibitors. Comput Biol Med 2009; 39:130-40. [PMID: 19152876 DOI: 10.1016/j.compbiomed.2008.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Revised: 08/15/2008] [Accepted: 11/20/2008] [Indexed: 11/27/2022]
Abstract
The complex CDK3-cyclin is involved in the control of the progression of G0. While the mechanisms governing early and late G1 progression are well understood, very little is known about the G0-G1 transition. Human CDK3 is closely related to cyclin-dependent kinase 2 (CDK2). Since there is no crystallographic structure of human CDK3, this work describes for the first time a molecular model of human CDK3 complexed with several inhibitors. Comparison of the binary complexes with different inhibitors strongly indicates that those inhibitors should inhibit CDK3 as well as CDK2.
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Affiliation(s)
- Patrícia Cardoso Perez
- Faculdade de Biociências-Laboratório de Bioquímica Estrutural-PUCRS, Porto Alegre, RS, Brazil
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21
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Tomii R, Kurome M, Wako N, Ochiai T, Matsunari H, Kano K, Nagashima H. Production of cloned pigs by nuclear transfer of preadipocytes following cell cycle synchronization by differentiation induction. J Reprod Dev 2008; 55:121-7. [PMID: 19106484 DOI: 10.1262/jrd.20126] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Four methods of cell cycle synchronization of porcine preadipocytes for use as nuclear donors in somatic cell cloning were compared: serum starvation, differentiation induction, contact inhibition and roscovitine treatment. After three days of differentiation induction, the percentage of nuclear donor cells synchronized at the G0/G1 phase reached a peak value of 91.8%, which was significantly higher (P<0.05) than the percentage attained by serum starvation (84.9-89.8%), contact inhibition (78.3-83.7%) or roscovitine treatment (67.8-80.3%). Cell cycle synchronization by serum starvation, contact inhibition and roscovitine treatment all increased the percentage of apoptotic cells, while no increase was observed when the donor-cell cycle was synchronized by differentiation induction (Annexin V-positive: 15.7% to 19.3% vs. 7.7%, P<0.05; TUNEL-positive: 12.8% to 14.0% vs. 8.3%, P<0.05). Additionally, comparison of the in vitro development of nuclear transfer (NT) embryos formed from the nuclei of differentiation-induced or serum-starved preadipocytes revealed that, in both cases, a high proportion of embryos developed to the blastocyst stage (39.0 and 33.7%, respectively). In this study, NT embryos reconstructed with preadipocytes synchronized by differentiation induction were transferred to four recipient pigs, three of which gave birth to a total of 17 piglets (4.2%, 17/403). These results demonstrate that donor-cell cycle synchronization by differentiation induction enables effective production of cloned pigs. The findings also indicate that differentiation induction of multipotent cells is an excellent method of cell cycle synchronization that permits highly efficient synchronization of cells at the G0/G1 phase.
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Affiliation(s)
- Ryo Tomii
- Laboratory of Developmental Engineering, Department of Life Science, School of Agriculture, Meiji University, Kawasaki, Japan.
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22
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Hinrichsen R, Hansen AH, Haunsø S, Busk PK. Phosphorylation of pRb by cyclin D kinase is necessary for development of cardiac hypertrophy. Cell Prolif 2008; 41:813-29. [PMID: 18700867 DOI: 10.1111/j.1365-2184.2008.00549.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
OBJECTIVES A number of stimuli induce cardiac hypertrophy and may lead to cardiomyopathy and heart failure. It is believed that cardiomyocytes withdraw from the cell cycle shortly after birth and become terminally differentiated. However, cell cycle regulatory proteins take part in the development of hypertrophy, and it is important to elucidate the mechanisms of how these proteins are involved in the hypertrophic response in cardiomyocytes. MATERIALS AND METHODS, AND RESULTS In the present study, by immunohistochemistry with a phosphorylation-specific antibody, we found that cyclin D-cdk4/6-phosphorylated retinoblastoma protein (pRb) during hypertrophy and expression of an unphosphorylatable pRb mutant impaired hypertrophic growth in cardiomyocytes. Transcription factor E2F was activated by hypertrophic elicitors but activation was impaired by pharmacological inhibition of cyclin D-cdk4/6. Inhibition of cyclin E-cdk2 complex only partly impaired E2F activity and did not prevent hypertrophic growth, but diminished endoreplication during hypertrophy. CONCLUSIONS These results indicate that cyclin D-cdk4/6-dependent phosphorylation of pRb and activation of E2F is necessary for hypertrophic growth in cardiomyocytes, whereas cyclin E-cdk2 kinase is not necessary for hypertrophy but regulates endoreplication in these cells. The data support the notion that hypertrophic growth of cardiomyocytes involves a partial progression through the G1 phase of the cell cycle
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Affiliation(s)
- R Hinrichsen
- Risø National Laboratory, Biosystems Department, Cell Biology Programme, Roskilde, Denmark.
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23
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Pauli I, Caceres RA, de Azevedo WF. Molecular modeling and dynamics studies of Shikimate Kinase from Bacillus anthracis. Bioorg Med Chem 2008; 16:8098-108. [PMID: 18706819 DOI: 10.1016/j.bmc.2008.07.051] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Revised: 07/17/2008] [Accepted: 07/19/2008] [Indexed: 11/16/2022]
Abstract
Bacillus anthracis has been used as weapon in bioterrorist activities, with high mortality, despite anti-microbial treatment, which strongly indicates a need of new drugs to treat anthrax. Shikimate Pathway is a seven-step biosynthetic route which generates chorismic acid. The shikimate pathway is essential for many pathological organisms, whereas it is absent in mammals. Therefore, these enzymes are potential targets for the development of non-toxic anti-microbial agents and herbicides and have been submitted to intensive structural studies. Shikimate Kinase is the fifth enzyme of shikimate pathway and catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimate using ATP as a co-substrate, resulting in shikimate-3-phosphate and ADP. The present work describes for the first time a structural model for the Shikimate Kinase from B. anthracis using molecular modeling approach and molecular dynamics simulations. This study was able to identify the main residues of the ATP-binding and the shikimate pockets responsible for ligand affinities. Analysis of the molecular dynamics simulations indicates the structural features responsible for the stability of the structure. This study may help in the identification of new inhibitors for this enzyme.
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Affiliation(s)
- Ivani Pauli
- Faculdade de Biociências, Laboratório de Bioquímica Estrutural, Pontifícia Universidade Católica do Rio Grande do Sul, Av. Ipiranga, 6681, Porto Alegre, 90619-900 Rio Grande do Sul, CEP, Brazil
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Xin X, Wang Y, Ma XM, Rompolas P, Keutmann HT, Mains RE, Eipper BA. Regulation of Kalirin by Cdk5. J Cell Sci 2008; 121:2601-11. [PMID: 18628310 DOI: 10.1242/jcs.016089] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Kalirin, one of the few Rho guanine nucleotide exchange factors (GEFs) that contains spectrin-like repeats, plays a critical role in axon extension and maintenance of dendritic spines. PC12 cells were used to determine whether Cdk5, a critical participant in both processes, regulates the action of Kalirin. Expression of Kalirin-7 in nondifferentiated PC12 cells caused GEF-activity-dependent extension of broad cytoplasmic protrusions; coexpression of dominant-negative Cdk5 largely eliminated this response. The spectrin-like repeat region of Kalirin plays an essential role in this response, which is not mimicked by the GEF domain alone. Thr1590, which follows the first GEF domain of Kalirin, is the only Cdk5 phosphorylation site in Kalirin-7. Although mutant Kalirin-7 with Ala1590 retains GEF activity, it is unable to cause extension of protrusions. Kalirin-7 with an Asp1590 mutation has slightly increased GEF activity and dominant-negative Cdk5 fails to block its ability to cause extension of protrusions. Phosphorylation of Thr1590 causes a slight increase in GEF activity and Kalirin-7 solubility. Dendritic spines formed by cortical neurons in response to the expression of Kalirin-7 with Ala1590 differ in shape from those formed in response to wild-type Kalirin-7 or Kalirin-7 containing Asp1590. The presence of Thr1590 in each major Kalirin isoform would allow Cdk5 to regulate Kalirin function throughout development.
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Affiliation(s)
- Xiaonan Xin
- Department of Neuroscience, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030-3401, USA
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Caceres RA, Saraiva Timmers LF, Dias R, Basso LA, Santos DS, de Azevedo WF. Molecular modeling and dynamics simulations of PNP from Streptococcus agalactiae. Bioorg Med Chem 2008; 16:4984-93. [DOI: 10.1016/j.bmc.2008.03.044] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Revised: 03/12/2008] [Accepted: 03/14/2008] [Indexed: 11/15/2022]
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Zharskaya OO, Barsukova AS, Zatsepina OV. Effect of roscovitine, a selective cyclin B-dependent kinase 1 inhibitor, on assembly of the nucleolus in mitosis. BIOCHEMISTRY. BIOKHIMIIA 2008; 73:411-9. [PMID: 18457570 DOI: 10.1134/s0006297908040056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
It is well known that at the beginning of mitosis the nucleolus disassembles but then reassembles at the end of mitosis. However, the mechanisms of these processes are still unclear. In the present work, we show for the first time that selective inhibition of cyclin B-dependent kinase 1 (CDK1) by roscovitine induces premature assembly of the nucleolus in mammalian cells in metaphase. Treatment of metaphase cells with roscovitine induces formation of structures in their cytoplasm that contain major proteins of the mature nucleolus participating in rRNA processing, such as B23/nucleophosmin, C23/nucleolin, fibrillarin, Nop52, as well as partially processed (immature) 46-45S pre-rRNA. This effect is reproducible in cells of various types; this indicates that general mechanisms regulate early stages of the nucleolus reassembly with CDK1 participation in mammalian cells. Based on our and literature data, we suggest that inactivation of the CDK1-cyclin B complex at the end of mitosis results in dephosphorylation of B23/nucleophosmin and C23/nucleolin; this facilitates their interaction with pre-rRNA and leads to formation of insoluble supramolecular complexes--nucleolus-derived foci.
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Affiliation(s)
- O O Zharskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
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27
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Molecular modeling and dynamics studies of cytidylate kinase from Mycobacterium tuberculosis H37Rv. J Mol Model 2008; 14:427-34. [PMID: 18343960 DOI: 10.1007/s00894-008-0291-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Accepted: 02/12/2008] [Indexed: 10/22/2022]
Abstract
Bacterial cytidylate kinase or cytidine monophosphate kinase (CMP kinase) catalyses the phosphoryl transfer from ATP to CMP and dCMP, resulting in the formation nucleoside diphosphates. In eukaryotes, CMP/UMP kinase catalyses the conversion of UMP and CMP to, respectively, UDP and CDP with high efficiency. This work describes for the first time a model of bacterial cytidylate kinase or cytidine monophosphate kinase (CMP kinase) from mycobacterium tuberculosis (MtCMPK). We modeled MtPCMPK in apo form and in complex with cytidine 5'-monophosphate (CMP) to try to determine the structural basis for specificity. Comparative analysis of the model of MtCMPK allowed identification of structural features responsible for ligand affinities. Analysis of the molecular dynamics simulations of these two systems indicates the structural features responsible for the stability of the structure, and may help in the identification of new inhibitors for this enzyme.
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Orba Y, Sunden Y, Suzuki T, Nagashima K, Kimura T, Tanaka S, Sawa H. Pharmacological cdk inhibitor R-Roscovitine suppresses JC virus proliferation. Virology 2007; 370:173-83. [PMID: 17919676 DOI: 10.1016/j.virol.2007.08.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Revised: 08/22/2007] [Accepted: 08/30/2007] [Indexed: 10/22/2022]
Abstract
The human Polyomavirus JC virus (JCV) utilizes cellular proteins for viral replication and transcription in the host cell nucleus. These cellular proteins represent potential targets for antiviral drugs against the JCV. In this study, we examined the antiviral effects of the pharmacological cyclin-dependent kinase (cdk) inhibitor R-Roscovitine, which has been shown to have antiviral activity against other viruses. We found that Roscovitine significantly inhibited the viral production and cytopathic effects of the JCV in a JCV-infected cell line. Roscovitine attenuated the transcriptional activity of JCV late genes, but not early genes, and also prevented viral replication via inhibiting phosphorylation of the viral early protein, large T antigen. These data suggest that the JCV requires cdks to transcribe late genes and to replicate its own DNA. That Roscovitine exhibited antiviral activity in JCV-infected cells suggests that Roscovitine might have therapeutic utility in the treatment of progressive multifocal leukoencephalopathy (PML).
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Affiliation(s)
- Yasuko Orba
- Department of Molecular Pathobiology, Hokkaido University Research Center for Zoonosis Control, N18, W9, Kita-ku, 060-0818, Sapporo, Japan
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Galons H, Bettayeb K, Meijer L. (R)-Roscovitine (CYC202, Seliciclib). ENZYME INHIBITORS SERIES 2006. [DOI: 10.1201/9781420005400.ch9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Selective small-molecule inhibitor reveals critical mitotic functions of human CDK1. Proc Natl Acad Sci U S A 2006; 103:10660-5. [PMID: 16818887 DOI: 10.1073/pnas.0600447103] [Citation(s) in RCA: 565] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
CDK1 is a nonredundant cyclin-dependent kinase (CDK) with an essential role in mitosis, but its multiple functions still are poorly understood at a molecular level. Here we identify a selective small-molecule inhibitor of CDK1 that reversibly arrests human cells at the G(2)/M border of the cell cycle and allows for effective cell synchronization in early mitosis. Inhibition of CDK1 during cell division revealed that its activity is necessary and sufficient for maintaining the mitotic state of the cells, preventing replication origin licensing and premature cytokinesis. Although CDK1 inhibition for up to 24 h is well tolerated, longer exposure to the inhibitor induces apoptosis in tumor cells, suggesting that selective CDK1 inhibitors may have utility in cancer therapy.
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31
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Leopoldino AM, Canduri F, Cabral H, Junqueira M, de Marqui ABT, Apponi LH, da Fonseca IO, Domont GB, Santos DS, Valentini S, Bonilla-Rodriguez GO, Fossey MA, de Azevedo WF, Tajara EH. Expression, purification, and circular dichroism analysis of human CDK9. Protein Expr Purif 2006; 47:614-20. [PMID: 16580843 DOI: 10.1016/j.pep.2006.02.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2005] [Revised: 02/02/2006] [Accepted: 02/14/2006] [Indexed: 11/29/2022]
Abstract
The human cyclin-dependent kinase 9 (CDK9) protein was expressed in E. coli BL21 using the pET23a vector at 30 degrees C. Several milligrams of protein were purified from soluble fraction using ionic exchange and ATP-affinity chromatography. The structural quality of recombinant CDK9 and the estimation of its secondary structure were obtained by circular dichroism. Structural models of CDK9 presented 26% of helices in agreement with the spectra by circular dichroism analysis. This is the first report on human CDK9 expression in Escherichia coli and structure analysis and provides the first step for the development of CDK9 inhibitors.
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32
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Manhani KK, Arcuri HA, da Silveira NJF, Uchôa HB, de Azevedo WF, Canduri F. Molecular models of protein kinase 6 from Plasmodium falciparum. J Mol Model 2005; 12:42-8. [PMID: 16096806 DOI: 10.1007/s00894-005-0002-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2004] [Accepted: 07/01/2005] [Indexed: 11/26/2022]
Abstract
Cyclin-dependent kinases (CDKs) have been identified as potential targets for development of drugs, mainly against cancer. These studies generated a vast library of chemical inhibitors of CDKs, and some of these molecules can also inhibit kinases identified in the Plasmodium falciparum genome. Here we describe structural models for Protein Kinase 6 from P. falciparum (PfPK6) complexed with Roscovitine and Olomoucine. These models show clear structural evidence for differences observed in the inhibition, and may help designing inhibitors for PfPK6 generating new potential drugs against malaria.
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Affiliation(s)
- Karisa Karla Manhani
- Departamento de Física, Universidade Estadual Paulista, UNESP, Rua Cristovão Colombo, 2265, 15054-000 São José do Rio Preto, São Paulo, Brasil
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