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Wrasidlo W, Crews LA, Tsigelny IF, Stocking E, Kouznetsova VL, Price D, Paulino A, Gonzales T, Overk CR, Patrick C, Rockenstein E, Masliah E. Neuroprotective effects of the anti-cancer drug sunitinib in models of HIV neurotoxicity suggests potential for the treatment of neurodegenerative disorders. Br J Pharmacol 2015; 171:5757-73. [PMID: 25117211 DOI: 10.1111/bph.12875] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/30/2014] [Accepted: 08/03/2014] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND AND PURPOSE Anti-retrovirals have improved and extended the life expectancy of patients with HIV. However, as this population ages, the prevalence of cognitive changes is increasing. Aberrant activation of kinases, such as receptor tyrosine kinases (RTKs) and cyclin-dependent kinase 5 (CDK5), play a role in the mechanisms of HIV neurotoxicity. Inhibitors of CDK5, such as roscovitine, have neuroprotective effects; however, CNS penetration is low. Interestingly, tyrosine kinase inhibitors (TKIs) display some CDK inhibitory activity and ability to cross the blood-brain barrier. EXPERIMENTAL APPROACH We screened a small group of known TKIs for a candidate with additional CDK5 inhibitory activity and tested the efficacy of the candidate in in vitro and in vivo models of HIV-gp120 neurotoxicity. KEY RESULTS Among 12 different compounds, sunitinib inhibited CDK5 with an IC50 of 4.2 μM. In silico analysis revealed that, similarly to roscovitine, sunitinib fitted 6 of 10 features of the CDK5 pharmacophore. In a cell-based model, sunitinib reduced CDK5 phosphorylation (pCDK5), calpain-dependent p35/p25 conversion and protected neuronal cells from the toxic effects of gp120. In glial fibrillary acidic protein-gp120 transgenic (tg) mice, sunitinib reduced levels of pCDK5, p35/p25 and phosphorylated tau protein, along with amelioration of the neurodegenerative pathology. CONCLUSIONS AND IMPLICATIONS Compounds such as sunitinib with dual kinase inhibitory activity could ameliorate the cognitive impairment associated with chronic HIV infection of the CNS. Moreover, repositioning existing low MW compounds holds promise for the treatment of patients with neurodegenerative disorders.
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Affiliation(s)
- Wolf Wrasidlo
- Department of Neurosciences, University of California, San Diego, CA, USA
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Cicenas J, Kalyan K, Sorokinas A, Stankunas E, Levy J, Meskinyte I, Stankevicius V, Kaupinis A, Valius M. Roscovitine in cancer and other diseases. ANNALS OF TRANSLATIONAL MEDICINE 2015. [PMID: 26207228 DOI: 10.3978/j.issn.2305-5839.2015.03.61] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Roscovitine [CY-202, (R)-Roscovitine, Seliciclib] is a small molecule that inhibits cyclin-dependent kinases (CDKs) through direct competition at the ATP-binding site. It is a broad-range purine inhibitor, which inhibits CDK1, CDK2, CDK5 and CDK7, but is a poor inhibitor for CDK4 and CDK6. Roscovitine is widely used as a biological tool in cell cycle, cancer, apoptosis and neurobiology studies. Moreover, it is currently evaluated as a potential drug to treat cancers, neurodegenerative diseases, inflammation, viral infections, polycystic kidney disease and glomerulonephritis. This review focuses on the use of roscovitine in the disease model as well as clinical model research.
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Affiliation(s)
- Jonas Cicenas
- 1 CALIPHO Group, Swiss Institute of Bioinformatics, Geneva, Switzerland ; 2 MAP Kinase Resource, Bern, Switzerland ; 3 Proteomics Centre, Vilnius University Institute of Biochemistry, Vilnius, Lithuania ; 4 Systems Biomedicine Division and Department of Virology and Immunology, Haffkine Institute for Training Research and Testing, Mumbai, India ; 5 Department of Biochemistry, Vilnius University, Vilnius, Lithuania ; 6 RTI International, Research Triangle Park, NC, USA ; 7 Lithuanian Centre of Non-Formal Youth Education Vilnius, Lithuania ; 8 National Cancer Institute, Vilnius, Lithuania ; 9 Vilnius University, Vilnius, Lithuania
| | - Karthik Kalyan
- 1 CALIPHO Group, Swiss Institute of Bioinformatics, Geneva, Switzerland ; 2 MAP Kinase Resource, Bern, Switzerland ; 3 Proteomics Centre, Vilnius University Institute of Biochemistry, Vilnius, Lithuania ; 4 Systems Biomedicine Division and Department of Virology and Immunology, Haffkine Institute for Training Research and Testing, Mumbai, India ; 5 Department of Biochemistry, Vilnius University, Vilnius, Lithuania ; 6 RTI International, Research Triangle Park, NC, USA ; 7 Lithuanian Centre of Non-Formal Youth Education Vilnius, Lithuania ; 8 National Cancer Institute, Vilnius, Lithuania ; 9 Vilnius University, Vilnius, Lithuania
| | - Aleksandras Sorokinas
- 1 CALIPHO Group, Swiss Institute of Bioinformatics, Geneva, Switzerland ; 2 MAP Kinase Resource, Bern, Switzerland ; 3 Proteomics Centre, Vilnius University Institute of Biochemistry, Vilnius, Lithuania ; 4 Systems Biomedicine Division and Department of Virology and Immunology, Haffkine Institute for Training Research and Testing, Mumbai, India ; 5 Department of Biochemistry, Vilnius University, Vilnius, Lithuania ; 6 RTI International, Research Triangle Park, NC, USA ; 7 Lithuanian Centre of Non-Formal Youth Education Vilnius, Lithuania ; 8 National Cancer Institute, Vilnius, Lithuania ; 9 Vilnius University, Vilnius, Lithuania
| | - Edvinas Stankunas
- 1 CALIPHO Group, Swiss Institute of Bioinformatics, Geneva, Switzerland ; 2 MAP Kinase Resource, Bern, Switzerland ; 3 Proteomics Centre, Vilnius University Institute of Biochemistry, Vilnius, Lithuania ; 4 Systems Biomedicine Division and Department of Virology and Immunology, Haffkine Institute for Training Research and Testing, Mumbai, India ; 5 Department of Biochemistry, Vilnius University, Vilnius, Lithuania ; 6 RTI International, Research Triangle Park, NC, USA ; 7 Lithuanian Centre of Non-Formal Youth Education Vilnius, Lithuania ; 8 National Cancer Institute, Vilnius, Lithuania ; 9 Vilnius University, Vilnius, Lithuania
| | - Josh Levy
- 1 CALIPHO Group, Swiss Institute of Bioinformatics, Geneva, Switzerland ; 2 MAP Kinase Resource, Bern, Switzerland ; 3 Proteomics Centre, Vilnius University Institute of Biochemistry, Vilnius, Lithuania ; 4 Systems Biomedicine Division and Department of Virology and Immunology, Haffkine Institute for Training Research and Testing, Mumbai, India ; 5 Department of Biochemistry, Vilnius University, Vilnius, Lithuania ; 6 RTI International, Research Triangle Park, NC, USA ; 7 Lithuanian Centre of Non-Formal Youth Education Vilnius, Lithuania ; 8 National Cancer Institute, Vilnius, Lithuania ; 9 Vilnius University, Vilnius, Lithuania
| | - Ingrida Meskinyte
- 1 CALIPHO Group, Swiss Institute of Bioinformatics, Geneva, Switzerland ; 2 MAP Kinase Resource, Bern, Switzerland ; 3 Proteomics Centre, Vilnius University Institute of Biochemistry, Vilnius, Lithuania ; 4 Systems Biomedicine Division and Department of Virology and Immunology, Haffkine Institute for Training Research and Testing, Mumbai, India ; 5 Department of Biochemistry, Vilnius University, Vilnius, Lithuania ; 6 RTI International, Research Triangle Park, NC, USA ; 7 Lithuanian Centre of Non-Formal Youth Education Vilnius, Lithuania ; 8 National Cancer Institute, Vilnius, Lithuania ; 9 Vilnius University, Vilnius, Lithuania
| | - Vaidotas Stankevicius
- 1 CALIPHO Group, Swiss Institute of Bioinformatics, Geneva, Switzerland ; 2 MAP Kinase Resource, Bern, Switzerland ; 3 Proteomics Centre, Vilnius University Institute of Biochemistry, Vilnius, Lithuania ; 4 Systems Biomedicine Division and Department of Virology and Immunology, Haffkine Institute for Training Research and Testing, Mumbai, India ; 5 Department of Biochemistry, Vilnius University, Vilnius, Lithuania ; 6 RTI International, Research Triangle Park, NC, USA ; 7 Lithuanian Centre of Non-Formal Youth Education Vilnius, Lithuania ; 8 National Cancer Institute, Vilnius, Lithuania ; 9 Vilnius University, Vilnius, Lithuania
| | - Algirdas Kaupinis
- 1 CALIPHO Group, Swiss Institute of Bioinformatics, Geneva, Switzerland ; 2 MAP Kinase Resource, Bern, Switzerland ; 3 Proteomics Centre, Vilnius University Institute of Biochemistry, Vilnius, Lithuania ; 4 Systems Biomedicine Division and Department of Virology and Immunology, Haffkine Institute for Training Research and Testing, Mumbai, India ; 5 Department of Biochemistry, Vilnius University, Vilnius, Lithuania ; 6 RTI International, Research Triangle Park, NC, USA ; 7 Lithuanian Centre of Non-Formal Youth Education Vilnius, Lithuania ; 8 National Cancer Institute, Vilnius, Lithuania ; 9 Vilnius University, Vilnius, Lithuania
| | - Mindaugas Valius
- 1 CALIPHO Group, Swiss Institute of Bioinformatics, Geneva, Switzerland ; 2 MAP Kinase Resource, Bern, Switzerland ; 3 Proteomics Centre, Vilnius University Institute of Biochemistry, Vilnius, Lithuania ; 4 Systems Biomedicine Division and Department of Virology and Immunology, Haffkine Institute for Training Research and Testing, Mumbai, India ; 5 Department of Biochemistry, Vilnius University, Vilnius, Lithuania ; 6 RTI International, Research Triangle Park, NC, USA ; 7 Lithuanian Centre of Non-Formal Youth Education Vilnius, Lithuania ; 8 National Cancer Institute, Vilnius, Lithuania ; 9 Vilnius University, Vilnius, Lithuania
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Boulahjar R, Ouach A, Bourg S, Bonnet P, Lozach O, Meijer L, Guguen-Guillouzo C, Le Guevel R, Lazar S, Akssira M, Troin Y, Guillaumet G, Routier S. Advances in tetrahydropyrido[1,2-a]isoindolone (valmerins) series: Potent glycogen synthase kinase 3 and cyclin dependent kinase 5 inhibitors. Eur J Med Chem 2015; 101:274-87. [PMID: 26142492 DOI: 10.1016/j.ejmech.2015.06.046] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 06/10/2015] [Accepted: 06/22/2015] [Indexed: 12/29/2022]
Abstract
An efficient synthetic strategy was developed to modulate the structure of the tetrahydropyridine isoindolone (Valmerin) skeleton. A library of more than 30 novel final structures was generated. Biological activities on CDK5 and GSK3 as well as cellular effects on cancer cell lines were measured for each novel compound. Additionally docking studies were performed to support medicinal chemistry efforts. A strong GSK3/CDK5 dual inhibitor (38, IC50 GSK3/CDK5 32/84 nM) was obtained. A set of highly selective GSK3 inhibitors was synthesized by fine-tuning structural modifications (29 IC50 GSK3/CDK5 32/320 nM). Antiproliferative effects on cells were correlated with the in vitro kinase activities and the best effects were obtained with lung and colon cell lines.
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Affiliation(s)
- Rajâa Boulahjar
- Univ Orleans, CNRS UMR 7311, Institut de Chimie Organique et Analytique, rue de Chartres, BP 6759, 45067 Orléans Cedex 2, France
| | - Aziz Ouach
- Univ Orleans, CNRS UMR 7311, Institut de Chimie Organique et Analytique, rue de Chartres, BP 6759, 45067 Orléans Cedex 2, France
| | - Stéphane Bourg
- Univ Orleans, CNRS UMR 7311, Institut de Chimie Organique et Analytique, rue de Chartres, BP 6759, 45067 Orléans Cedex 2, France
| | - Pascal Bonnet
- Univ Orleans, CNRS UMR 7311, Institut de Chimie Organique et Analytique, rue de Chartres, BP 6759, 45067 Orléans Cedex 2, France
| | - Olivier Lozach
- C.N.R.S., 'Protein Phosphorylation & Human Disease' Group, USR3151, Station Biologique, BP 74, 29682 Roscoff Cedex, France
| | - Laurent Meijer
- C.N.R.S., 'Protein Phosphorylation & Human Disease' Group, USR3151, Station Biologique, BP 74, 29682 Roscoff Cedex, France
| | - Christiane Guguen-Guillouzo
- Plateforme ImPACcell-SFR BIOSIT UMS-CNRS3480 UMS-INSERM018, Université de Rennes1, 35043 Rennes Cedex, France
| | - Rémy Le Guevel
- Plateforme ImPACcell-SFR BIOSIT UMS-CNRS3480 UMS-INSERM018, Université de Rennes1, 35043 Rennes Cedex, France
| | - Saïd Lazar
- Laboratoire de Chimie, Bioorganique et Analytique, URAC 22 pôle Répam, Université Hassan II Mohammedia-Casablanca, BP 146, 28800 Mohammedia, Morocco
| | - Mohamed Akssira
- Laboratoire de Chimie, Bioorganique et Analytique, URAC 22 pôle Répam, Université Hassan II Mohammedia-Casablanca, BP 146, 28800 Mohammedia, Morocco
| | - Yves Troin
- Clermont Université, ENSCCF, Laboratoire de Chimie des Hétérocycles et des Glucides, BP 10448, 63000 Clermont-Ferrand, France
| | - Gérald Guillaumet
- Univ Orleans, CNRS UMR 7311, Institut de Chimie Organique et Analytique, rue de Chartres, BP 6759, 45067 Orléans Cedex 2, France.
| | - Sylvain Routier
- Univ Orleans, CNRS UMR 7311, Institut de Chimie Organique et Analytique, rue de Chartres, BP 6759, 45067 Orléans Cedex 2, France.
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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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55
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Geschwindner S, Ulander J, Johansson P. Ligand Binding Thermodynamics in Drug Discovery: Still a Hot Tip? J Med Chem 2015; 58:6321-35. [DOI: 10.1021/jm501511f] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
| | - Johan Ulander
- CVMD Innovative Medicines, AstraZeneca R&D Mölndal, S-43183 Mölndal, Sweden
| | - Patrik Johansson
- Discovery Sciences, AstraZeneca R&D Mölndal, S-43183 Mölndal, Sweden
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56
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Bakherad M, Keivanloo A, Omidian M, Samangooei S. Synthesis of Pyrrolo[2,3-b]pyrazines Through Sonogashira Coupling Reaction of 5,6-dichloropyrazine-2,3-dicarbonitrile with Hydrazine, Phenylacetylene and Various Aldehydes. JOURNAL OF CHEMICAL RESEARCH 2014. [DOI: 10.3184/174751914x14180425794376] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The Pd–Cu catalysed one-pot multicomponent reaction of 5,6-dichloropyrazine-2,3-dicarbonitrile with hydrazine, phenylacetylene, and a variety of aldehydes provides an efficient and direct method for the preparation of 5-(arylideneamino)-6-phenyl-5H-pyrrolo[2,3- b]pyrazine-2,3-dicarbonitriles.
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Affiliation(s)
- Mohammad Bakherad
- School of Chemistry, Shahrood University of Technology, Shahrood, Iran
| | - Ali Keivanloo
- School of Chemistry, Shahrood University of Technology, Shahrood, Iran
| | - Mina Omidian
- School of Chemistry, Shahrood University of Technology, Shahrood, Iran
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57
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Chatterjee A, Cutler SJ, Doerksen RJ, Khan IA, Williamson JS. Discovery of thienoquinolone derivatives as selective and ATP non-competitive CDK5/p25 inhibitors by structure-based virtual screening. Bioorg Med Chem 2014; 22:6409-21. [PMID: 25438765 PMCID: PMC4254530 DOI: 10.1016/j.bmc.2014.09.043] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 09/15/2014] [Accepted: 09/20/2014] [Indexed: 01/17/2023]
Abstract
Calpain mediated cleavage of CDK5 natural precursor p35 causes a stable complex formation of CDK5/p25, which leads to hyperphosphorylation of tau. Thus inhibition of this complex is a viable target for numerous acute and chronic neurodegenerative diseases involving tau protein, including Alzheimer's disease. Since CDK5 has the highest sequence homology with its mitotic counterpart CDK2, our primary goal was to design selective CDK5/p25 inhibitors targeting neurodegeneration. A novel structure-based virtual screening protocol comprised of e-pharmacophore models and virtual screening workflow was used to identify nine compounds from a commercial database containing 2.84 million compounds. An ATP non-competitive and selective thieno[3,2-c]quinolin-4(5H)-one inhibitor (10) with ligand efficiency (LE) of 0.3 was identified as the lead molecule. Further SAR optimization led to the discovery of several low micromolar inhibitors with good selectivity. The research represents a new class of potent ATP non-competitive CDK5/p25 inhibitors with good CDK2/E selectivity.
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Affiliation(s)
- Arindam Chatterjee
- Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi, MS 38677, United States
| | - Stephen J Cutler
- Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi, MS 38677, United States.
| | - Robert J Doerksen
- Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi, MS 38677, United States
| | - Ikhlas A Khan
- National Center for Natural Products Research, University of Mississippi, MS 38677, United States
| | - John S Williamson
- Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi, MS 38677, United States.
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58
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Li L, Zhang C, Zi X, Tu Q, Guo K. Epigenetic modulation of Cdk5 contributes to memory deficiency induced by amyloid fibrils. Exp Brain Res 2014; 233:165-73. [PMID: 25234403 DOI: 10.1007/s00221-014-4100-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/05/2014] [Indexed: 12/31/2022]
Abstract
Alzheimer's disease (AD) is a frequent neurodegenerative disorder with progressive neuroinflammation, loss of synaptic plasticity in central neurons and memory deficiency. Numerous studies demonstrated the epigenetic modification of the expression of specific genes involved in the pathogenesis of amyloid-associated memory deficiency. It was also reported that dysregulation of cyclin-dependent kinase 5 (Cdk5) activity critically contributed to the synaptic dysfunction and memory deficiency in the rodent model of AD. The present study aims to study the epigenetic mechanism underlying the altered Cdk5 activity and its functional significance in the rats with hippocampal infusion of amyloid fibrils. Significantly increased mRNA and expression of Cdk5 were observed in the hippocampal CA1 in the rats injected with amyloid fibrils. Increased acetylation of histone H3 was detected in the Cdk5 promoter region in hippocampal CA1 in these rats. Further chromatin immunoprecipitation and bisulfite sequencing studies illustrated the decreased cytosine methylation in the Cdk5 promoter region in hippocampal CA1 in the modeled rats. Administration with Cdk5 inhibitor roscovitine significantly attenuated the phosphorylation of tau, recovered the synaptic dysfunction of hippocampal CA1 neurons, and improved the behavioral performance in the Morris water maze test and novel object recognition test in the rats injected with amyloid fibrils. These results elucidate the potential epigenetic mechanism underlying the upregulated expression of Cdk5 induced by amyloid fibrils and provided novel insights into the pathogenic mechanism of Alzheimer's disease.
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Affiliation(s)
- Liuhong Li
- Department of Neurology, The Third Xiangya Hospital of Central South University, 138 Tongzipo Rd, Changsha, 410013, Hunan, China
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Identification and in vitro evaluation of new leads as selective and competitive glycogen synthase kinase-3β inhibitors through ligand and structure based drug design. J Mol Graph Model 2014; 53:31-47. [DOI: 10.1016/j.jmgm.2014.06.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 06/26/2014] [Accepted: 06/28/2014] [Indexed: 01/08/2023]
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60
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Li X, Wang X, Tian Z, Zhao H, Liang D, Li W, Qiu Y, Lu S. Structural basis of valmerins as dual inhibitors of GSK3β/CDK5. J Mol Model 2014; 20:2407. [PMID: 25142337 DOI: 10.1007/s00894-014-2407-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 07/29/2014] [Indexed: 11/24/2022]
Abstract
Development of multi-target drugs is becoming increasingly attractive in the repertoire of protein kinase inhibitors discovery. In this study, we carried out molecular docking, molecular dynamics simulations, molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) binding free energy calculations, principal component analysis (PCA), and dynamical cross-correlation matrices (DCCM) to dissect the molecular mechanism for the valmerin-19 acting as a dual inhibitor for glycogen synthase kinase 3β (GSK3β) and cyclin-dependent kinase 5 (CDK5). Detailed MM-PBSA calculations revealed that the binding free energies of the valmerin-19 to GSK3β/CDK5 were calculated to be -12.60 ± 2.28 kcal mol(-1) and -11.85 ± 2.54 kcal mol(-1), respectively, indicating that valmerin-19 has the potential to act as a dual inhibitor of GSK3β/CDK5. The analyses of PCA and DCCM results unraveled that binding of the valmerin-19 reduced the conformational dynamics of GSK3β/CDK5 and the valmerin-19 bound to GSK3β/CDK5 might occur mostly through a conformational selection mechanism. This study may be helpful for the future design of novel and potent dual GSK3β/CDK5 inhibitors.
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Affiliation(s)
- Xiaolong Li
- Depatment of Spinal Surgery, Affiliated Hospital of Weifang Medical University, Weifang, 261000, China
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Synthesis and biological evaluation of tetrahydro[1,4]diazepino[1,2-a]indol-1-ones as cyclin-dependent kinase inhibitors. Eur J Med Chem 2014; 83:617-29. [DOI: 10.1016/j.ejmech.2014.06.063] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 06/04/2014] [Accepted: 06/27/2014] [Indexed: 11/21/2022]
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Investigation of the flexibility of protein kinases implicated in the pathology of Alzheimer's disease. Molecules 2014; 19:9134-59. [PMID: 24983862 PMCID: PMC6270768 DOI: 10.3390/molecules19079134] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 06/16/2014] [Accepted: 06/19/2014] [Indexed: 12/22/2022] Open
Abstract
The pathological characteristics of Alzheimer’s Disease (AD) have been linked to the activity of three particular kinases—Glycogen Synthase Kinase 3β (GSK3β), Cyclin-Dependent Kinase 5 (CDK5) and Extracellular-signal Regulated Kinase 2 (ERK2). As a consequence, the design of selective, potent and drug-like inhibitors of these kinases is of particular interest. Structure-based design methods are well-established in the development of kinase inhibitors. However, progress in this field is limited by the difficulty in obtaining X-ray crystal structures suitable for drug design and by the inability of this method to resolve highly flexible regions of the protein that are crucial for ligand binding. To address this issue, we have undertaken a study of human protein kinases CDK5/p25, CDK5, ERK2 and GSK3β using both conventional molecular dynamics (MD) and the new Active Site Pressurisation (ASP) methodology, to look for kinase-specific patterns of flexibility that could be leveraged for the design of selective inhibitors. ASP was used to examine the intrinsic flexibility of the ATP-binding pocket for CDK5/p25, CDK5 and GSK3β where it is shown to be capable of inducing significant conformational changes when compared with X-ray crystal structures. The results from these experiments were used to quantify the dynamics of each protein, which supported the observations made from the conventional MD simulations. Additional information was also derived from the ASP simulations, including the shape of the ATP-binding site and the rigidity of the ATP-binding pocket. These observations may be exploited in the design of selective inhibitors of GSK3β, CDK5 and ERK2.
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63
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Dehbi O, Tikad A, Bourg S, Bonnet P, Lozach O, Meijer L, Aadil M, Akssira M, Guillaumet G, Routier S. Synthesis and optimization of an original V-shaped collection of 4-7-disubstituted pyrido[3,2-d]pyrimidines as CDK5 and DYRK1A inhibitors. Eur J Med Chem 2014; 80:352-63. [PMID: 24793883 DOI: 10.1016/j.ejmech.2014.04.055] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 04/17/2014] [Accepted: 04/19/2014] [Indexed: 11/26/2022]
Abstract
We here report the synthesis and biological evaluation of an original collection of 4,7-disubstituted pyrido[3,2-d]pyrimidines designed as potential kinase inhibitors. The collection was generated from a single starting material, 4,7-dichloropyrido[3,2-d]pyrimidine, which afforded the final compounds after two steps: a sequential or one-pot sequence including selective cross coupling reactions in C-4, followed by the second cross-coupling in C-7. In position C-4, a Suzuki-Miyaura type reaction led to monosubstituted derivatives whereas in position C-7, synthesis was achieved via a Suzuki or a Buchwald type reaction using commercially available or undescribed boron derivatives. The biological activity of the V-shaped family was measured in protein kinase assays. The structure activity relationship (SAR) revealed that some compounds selectively inhibited DYRK1A and CDK5 without affecting GSK3. Docking studies furnished possible explanations that correlate with the SAR data. The most active compound on the two biological targets was 27 which exhibited the following IC50: 110 nM for CDK5, 24 nM for DYRK1A and only 1.2 μM for GSK3. In the C-7 amino subfamily, the best derivative was indubitably compound 48 which led to a near selective action on DYRK1A and a remarkable IC50 of 60 nM.
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Affiliation(s)
- Oussama Dehbi
- Institut de Chimie Organique et Analytique, CNRS UMR 7311, B.P. 6759, 45067 Orléans Cedex 2, France; Equipe de Chimie Bioorganique & Analytique, URAC 22, Université Hassan II Mohammedia-Casablanca, BP 146, 28800 Mohammedia, Morocco
| | - Abdellatif Tikad
- Institut de Chimie Organique et Analytique, CNRS UMR 7311, B.P. 6759, 45067 Orléans Cedex 2, France; Equipe de Chimie Bioorganique & Analytique, URAC 22, Université Hassan II Mohammedia-Casablanca, BP 146, 28800 Mohammedia, Morocco
| | - Stéphane Bourg
- Institut de Chimie Organique et Analytique, CNRS UMR 7311, B.P. 6759, 45067 Orléans Cedex 2, France
| | - Pascal Bonnet
- Institut de Chimie Organique et Analytique, CNRS UMR 7311, B.P. 6759, 45067 Orléans Cedex 2, France
| | - Olivier Lozach
- C.N.R.S., Protein Phosphorylation & Human Disease, USR3151, Station Biologique, B.P. 74, 29682 Roscoff Cedex, France
| | - Laurent Meijer
- C.N.R.S., Protein Phosphorylation & Human Disease, USR3151, Station Biologique, B.P. 74, 29682 Roscoff Cedex, France
| | - Mina Aadil
- Equipe de Chimie Bioorganique & Analytique, URAC 22, Université Hassan II Mohammedia-Casablanca, BP 146, 28800 Mohammedia, Morocco
| | - Mohammed Akssira
- Equipe de Chimie Bioorganique & Analytique, URAC 22, Université Hassan II Mohammedia-Casablanca, BP 146, 28800 Mohammedia, Morocco
| | - Gérald Guillaumet
- Institut de Chimie Organique et Analytique, CNRS UMR 7311, B.P. 6759, 45067 Orléans Cedex 2, France.
| | - Sylvain Routier
- Institut de Chimie Organique et Analytique, CNRS UMR 7311, B.P. 6759, 45067 Orléans Cedex 2, France.
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64
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Kobayashi H, Saito T, Sato K, Furusawa K, Hosokawa T, Tsutsumi K, Asada A, Kamada S, Ohshima T, Hisanaga SI. Phosphorylation of cyclin-dependent kinase 5 (Cdk5) at Tyr-15 is inhibited by Cdk5 activators and does not contribute to the activation of Cdk5. J Biol Chem 2014; 289:19627-36. [PMID: 24872417 DOI: 10.1074/jbc.m113.501148] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cdk5 is a member of the cyclin-dependent kinase (Cdk) family. In contrast to other Cdks that promote cell proliferation, Cdk5 plays a role in regulating various neuronal functions, including neuronal migration, synaptic activity, and neuron death. Cdks responsible for cell proliferation need phosphorylation in the activation loop for activation in addition to binding a regulatory subunit cyclin. Cdk5, however, is activated only by binding to its activator, p35 or p39. Furthermore, in contrast to Cdk1 and Cdk2, which are inhibited by phosphorylation at Tyr-15, the kinase activity of Cdk5 is reported to be stimulated when phosphorylated at Tyr-15 by Src family kinases or receptor-type tyrosine kinases. We investigated the activation mechanism of Cdk5 by phosphorylation at Tyr-15. Unexpectedly, however, it was found that Tyr-15 phosphorylation occurred only on monomeric Cdk5, and the coexpression of activators, p35/p25, p39, or Cyclin I, inhibited the phosphorylation. In neuron cultures, too, the activation of Fyn tyrosine kinase did not increase Tyr-15 phosphorylation of Cdk5. Further, phospho-Cdk5 at Tyr-15 was not detected in the p35-bound Cdk5. In contrast, expression of active Fyn increased p35 in neurons. These results indicate that phosphorylation at Tyr-15 is not an activation mechanism of Cdk5 but, rather, indicate that tyrosine kinases could activate Cdk5 by increasing the protein amount of p35. These results call for reinvestigation of how Cdk5 is regulated downstream of Src family kinases or receptor tyrosine kinases in neurons, which is an important signaling cascade in a variety of neuronal activities.
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Affiliation(s)
- Hiroyuki Kobayashi
- From the Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Taro Saito
- From the Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Ko Sato
- From the Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Kotaro Furusawa
- From the Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Tomohisa Hosokawa
- From the Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Koji Tsutsumi
- From the Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Akiko Asada
- From the Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Shinji Kamada
- the Biosignal Research Center, Kobe University, 1-1 Rokkodaicho, Nada, Kobe, 657-8501, and
| | - Toshio Ohshima
- the Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu, Shinjuku, Tokyo 162-8480, Japan
| | - Shin-ichi Hisanaga
- From the Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan,
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65
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Patel JS, Berteotti A, Ronsisvalle S, Rocchia W, Cavalli A. Steered molecular dynamics simulations for studying protein-ligand interaction in cyclin-dependent kinase 5. J Chem Inf Model 2014; 54:470-80. [PMID: 24437446 DOI: 10.1021/ci4003574] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In this study, we applied steered molecular dynamics (SMD) simulations to investigate the unbinding mechanism of nine inhibitors of the enzyme cyclin-dependent kinase 5 (CDK5). The study had two major objectives: (i) to create a correlation between the unbinding force profiles and the inhibition activities of these compounds expressed as IC50 values; (ii) to investigate the unbinding mechanism and to reveal atomistic insights, which could help identify accessory binding sites and transient interactions. Overall, we carried out 1.35 μs of cumulative SMD simulations. We showed that SMD could qualitatively discriminate binders from nonbinders, while it failed to properly rank series of inhibitors, particularly when IC50 values were too similar. From a mechanistic standpoint, SMD provided useful insights related to transient and dynamical interactions, which could complement static description obtained by X-ray crystallography experiments. In conclusion, the present study represents a further step toward a systematic exploitation of SMD and other dynamical approaches in structure-based drug design and computational medicinal chemistry.
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Affiliation(s)
- Jagdish Suresh Patel
- Department of Drug Discovery and Development, Istituto Italiano di Tecnologia , Via Morego 30, I-16163 Genova, Italy
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66
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Erben F, Michalik D, Feist H, Kleeblatt D, Hein M, Matin A, Iqbal J, Langer P. Synthesis and antiproliferative activity of (Z)-1-glycosyl-3-(5-oxo-2-thioxoimidazolidin-4-ylidene)indolin-2-ones and (Z)-3-(2-glycosylsulfanyl-4-oxo-4,5-dihydro-thiazol-5-ylidene)indolin-2-ones. RSC Adv 2014. [DOI: 10.1039/c3ra44362k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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67
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Echols N, Moriarty NW, Klei HE, Afonine PV, Bunkóczi G, Headd JJ, McCoy AJ, Oeffner RD, Read RJ, Terwilliger TC, Adams PD. Automating crystallographic structure solution and refinement of protein-ligand complexes. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:144-54. [PMID: 24419387 PMCID: PMC3919266 DOI: 10.1107/s139900471302748x] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 10/07/2013] [Indexed: 11/29/2022]
Abstract
High-throughput drug-discovery and mechanistic studies often require the determination of multiple related crystal structures that only differ in the bound ligands, point mutations in the protein sequence and minor conformational changes. If performed manually, solution and refinement requires extensive repetition of the same tasks for each structure. To accelerate this process and minimize manual effort, a pipeline encompassing all stages of ligand building and refinement, starting from integrated and scaled diffraction intensities, has been implemented in Phenix. The resulting system is able to successfully solve and refine large collections of structures in parallel without extensive user intervention prior to the final stages of model completion and validation.
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Affiliation(s)
- Nathaniel Echols
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Nigel W. Moriarty
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Herbert E. Klei
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Pavel V. Afonine
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Gábor Bunkóczi
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | - Jeffrey J. Headd
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Airlie J. McCoy
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | - Robert D. Oeffner
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | - Randy J. Read
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | | | - Paul D. Adams
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
- Department of Bioengineering, University of California at Berkeley, Berkeley, CA 94720-1762, USA
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68
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Kleeblatt D, Cordes CA, Lebrenz P, Hein M, Feist H, Matin A, Raza R, Iqbal J, Munshi O, Rahman Q, Villinger A, Langer P. Synthesis and antiproliferative activity of N-glycosyl-3,3-diaryloxindoles. RSC Adv 2014. [DOI: 10.1039/c4ra02627f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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69
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Ambure P, Roy K. Exploring structural requirements of leads for improving activity and selectivity against CDK5/p25 in Alzheimer's disease: an in silico approach. RSC Adv 2014. [DOI: 10.1039/c3ra46861e] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A congeneric series of 224 cyclin-dependant kinase 5/p25 (CDK5/p25) inhibitors was exploited to understand the structural requirements for improving activity against CDK5/p25 and selectivity over CDK2.
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Affiliation(s)
- Pravin Ambure
- Drug Theoretics and Cheminformatics Laboratory
- Department of Pharmaceutical Technology
- Jadavpur University
- Kolkata 700032, India
| | - Kunal Roy
- Drug Theoretics and Cheminformatics Laboratory
- Department of Pharmaceutical Technology
- Jadavpur University
- Kolkata 700032, India
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70
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Saito T, Yano M, Kawai Y, Asada A, Wada M, Doi H, Hisanaga SI. Structural basis for the different stability and activity between the Cdk5 complexes with p35 and p39 activators. J Biol Chem 2013; 288:32433-32439. [PMID: 24085300 DOI: 10.1074/jbc.m113.512293] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cyclin-dependent kinase 5 (Cdk5) is a brain-specific membrane-bound protein kinase that is activated by binding to the p35 or p39 activator. Previous studies have focused on p35-Cdk5, and little is known regarding p39-Cdk5. The lack of functional understanding of p39-Cdk5 is due, in part, to the labile property of p39-Cdk5, which dissociates and loses kinase activity in nonionic detergent conditions. Here we investigated the structural basis for the instability of p39-Cdk5. p39 and p35 contain N-terminal p10 regions and C-terminal Cdk5 activation domains (AD). Although p35 and p39 show higher homology in the C-terminal AD than the N-terminal region, the difference in stability is derived from the C-terminal AD. Based on the crystal structures of the p25 (p35 C-terminal region including AD)-Cdk5 complex, we simulated the three-dimensional structure of the p39 AD-Cdk5 complex and found differences in the hydrogen bond network between Cdk5 and its activators. Three amino acids of p35, Asp-259, Asn-266, and Ser-270, which are involved in hydrogen bond formation with Cdk5, are changed to Gln, Gln, and Pro in p39. Because these three amino acids in p39 do not participate in hydrogen bond formation, we predicted that the number of hydrogen bonds between p39 and Cdk5 was reduced compared with p35 and Cdk5. Using substitution mutants, we experimentally validated that the difference in the hydrogen bond network contributes to the different properties between Cdk5 and its activators.
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Affiliation(s)
- Taro Saito
- From the Department of Biological Sciences, Tokyo Metropolitan University, Minami-osawa, Hachioji, Tokyo 192-0397
| | - Masashi Yano
- From the Department of Biological Sciences, Tokyo Metropolitan University, Minami-osawa, Hachioji, Tokyo 192-0397
| | - Yusei Kawai
- From the Department of Biological Sciences, Tokyo Metropolitan University, Minami-osawa, Hachioji, Tokyo 192-0397
| | - Akiko Asada
- From the Department of Biological Sciences, Tokyo Metropolitan University, Minami-osawa, Hachioji, Tokyo 192-0397
| | - Mitsuhito Wada
- Celestar Lexico-Sciences, Inc., Nakase, Mihama-ku, Chiba 261-8501
| | - Hirofumi Doi
- Celestar Lexico-Sciences, Inc., Nakase, Mihama-ku, Chiba 261-8501; the Research Center for Advanced Science and Technology, The University of Tokyo, Komaba, Meguro, Tokyo 153-8914, Japan
| | - Shin-Ichi Hisanaga
- From the Department of Biological Sciences, Tokyo Metropolitan University, Minami-osawa, Hachioji, Tokyo 192-0397,.
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71
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Molecular basis of differential selectivity of cyclobutyl-substituted imidazole inhibitors against CDKs: insights for rational drug design. PLoS One 2013; 8:e73836. [PMID: 24058495 PMCID: PMC3772847 DOI: 10.1371/journal.pone.0073836] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 07/25/2013] [Indexed: 11/19/2022] Open
Abstract
Cyclin-dependent kinases (CDKs) belong to the CMGC subfamily of protein kinases and play crucial roles in eukaryotic cell division cycle. At least seven different CDKs have been reported to be implicated in the cell cycle regulation in vertebrates. These CDKs are highly homologous and contain a conserved catalytic core. This makes the design of inhibitors specific for a particular CDK difficult. There is, however, growing need for CDK5 specific inhibitors to treat various neurodegenerative diseases. Recently, cis-substituted cyclobutyl-4-aminoimidazole inhibitors have been identified as potent CDK5 inhibitors that gave up to 30-fold selectivity over CDK2. Available IC50 values also indicate a higher potency of this class of inhibitors over commercially available drugs, such as roscovitine. To understand the molecular basis of higher potency and selectivity of these inhibitors, here, we present molecular dynamics simulation results of CDK5/p25 and CDK2/CyclinE complexed with a series of cyclobutyl-substituted imidazole inhibitors and roscovitine. The atomic details of the stereospecificity and selectivity of these inhibitors are obtained from energetics and binding characteristics to the CDK binding pocket. The study not only complements the experimental findings, but also provides a wealth of detailed information that could help the structure-based drug designing processes.
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72
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Bruyère C, Meijer L. Targeting cyclin-dependent kinases in anti-neoplastic therapy. Curr Opin Cell Biol 2013; 25:772-9. [PMID: 24011867 DOI: 10.1016/j.ceb.2013.08.004] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 08/15/2013] [Accepted: 08/15/2013] [Indexed: 12/12/2022]
Abstract
Cell cycle progression is controlled by sequential activation of cyclin-dependent kinases (CDKs), which are often deregulated in cancer. Consequently numerous pharmacological inhibitors of CDKs have been developed with the aim of treating cancers. The article briefly reviews CDK inhibitors and their use to treat cancers, with specific focus on the use of biomarkers and drugs combination to improve their therapeutic efficacy.
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Affiliation(s)
- Céline Bruyère
- ManRos Therapeutics, Centre de Perharidy, 29680 Roscoff, France
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73
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Robbins TJ, Wang Y, Yao QZ, Wang ZH, Cheng J, Li YS. Vibrational spectra, DFT calculations, and conformations of 5′-chloro-1-isopropyl-7-azaindirubin-3′-oxime. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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74
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Shrestha S, Natarajan S, Park JH, Lee DY, Cho JG, Kim GS, Jeon YJ, Yeon SW, Yang DC, Baek NI. Potential neuroprotective flavonoid-based inhibitors of CDK5/p25 from Rhus parviflora. Bioorg Med Chem Lett 2013; 23:5150-4. [PMID: 23927974 DOI: 10.1016/j.bmcl.2013.07.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 06/24/2013] [Accepted: 07/12/2013] [Indexed: 12/18/2022]
Abstract
Rhus parviflora (Anacardiaceae) is an indigenous medicinal shrub found in South Asia with flavonoid rich edible fruit. This study examined flavonoid derivatives of R. parviflora fruit with CDK5/p25 inhibition activity. Evaluation by in vitro assay and docking simulations for CDK5/p25 revealed that the aurones, sulfuretin (1) and aureusidin (2), the aurone glycoside, aureusidin-6-O-β-D-glucopyranoside (3) and hovetrichoside C (4), the flavonoid glycoside, quercetin-3-O-β-D-galactopyranoside (5), and the biflavonoid, cupressuflavone (6), had the potential to inhibit CDK5/p25, which could be useful in the treatment of neurodegenerative disorders such as Alzheimer's disease. Compound2 showed the significant in vitro inhibition capacity (IC50 value of 4.81 μM) as well as binding affinity with docking energy of -8.73 (kcal/mol) for active sites CYS83 and GLN130 of CDK5/p25 enzyme in comparison to reference compound R-roscovitine.
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Affiliation(s)
- Sabina Shrestha
- Graduate School of Biotechnology, Institute of Life Sciences and Resources, Kyung Hee University, Yongin 446-701, Republic of Korea
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75
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Wang W, Cao X, Zhu X, Gu Y. Molecular dynamic simulations give insight into the mechanism of binding between 2-aminothiazole inhibitors and CDK5. J Mol Model 2013; 19:2635-45. [PMID: 23525963 DOI: 10.1007/s00894-013-1815-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Accepted: 03/04/2013] [Indexed: 12/20/2022]
Abstract
Molecular docking, molecular dynamics (MD) simulations, and binding free energy analysis were performed to reveal differences in the binding affinities between five 2-aminothiazole inhibitors and CDK5. The hydrogen bonding and hydrophobic interactions between inhibitors and adjacent residues are analyzed and discussed. The rank of calculated binding free energies using the MM-PBSA method is consistent with experimental result. The results illustrate that hydrogen bonds with Cys83 favor inhibitor binding. The van der Waals interactions, especially the important contact with Ile10, dominate in the binding free energy and play a crucial role in distinguishing the different bioactivity of the five inhibitors.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemistry and Chemical Engineering, Nanjing University of Technology, Nanjing 210009, China
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76
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Wu Q, Kang H, Tian C, Huang Q, Zhu R. Binding Mechanism of Inhibitors to CDK5/p25 Complex: Free Energy Calculation and Ranking Aggregation Analysis. Mol Inform 2013; 32:251-60. [DOI: 10.1002/minf.201200139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Accepted: 01/17/2013] [Indexed: 11/11/2022]
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77
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Kim HM, Kim YC, Kim JI, Choi YS, Kim YG. DEVELOPMENT OF A LIQUID CHROMATOGRAPHY-TANDEM MASS SPECTROMETRY METHOD FOR THE DETERMINATION OF INDIRUBIN-5-NITRO-3′-MONOXIME, A NOVEL CDK INHIBITOR, IN RAT PLASMA. J LIQ CHROMATOGR R T 2012. [DOI: 10.1080/10826076.2011.629389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Hyun Mi Kim
- a Department of Pharmacology , College of Medicine, Dankook University , Cheonan , Republic of Korea
| | - Yong-Chul Kim
- b Department of Life Science , Gwangju Institute of Science and Technology , Gwangju , Republic of Korea
| | - Jae Il Kim
- b Department of Life Science , Gwangju Institute of Science and Technology , Gwangju , Republic of Korea
| | - Yong Seok Choi
- c College of Pharmacy, Dankook University , Cheonan , Republic of Korea
| | - Yoon Gyoon Kim
- c College of Pharmacy, Dankook University , Cheonan , Republic of Korea
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78
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Malmström J, Viklund J, Slivo C, Costa A, Maudet M, Sandelin C, Hiller G, Olsson LL, Aagaard A, Geschwindner S, Xue Y, Vasänge M. Synthesis and structure-activity relationship of 4-(1,3-benzothiazol-2-yl)-thiophene-2-sulfonamides as cyclin-dependent kinase 5 (cdk5)/p25 inhibitors. Bioorg Med Chem Lett 2012; 22:5919-23. [DOI: 10.1016/j.bmcl.2012.07.068] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 07/17/2012] [Accepted: 07/18/2012] [Indexed: 01/17/2023]
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79
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Boutajangout A, Sigurdsson EM, Krishnamurthy PK. Tau as a therapeutic target for Alzheimer's disease. Curr Alzheimer Res 2012; 8:666-77. [PMID: 21679154 DOI: 10.2174/156720511796717195] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2010] [Revised: 04/10/2011] [Accepted: 04/15/2011] [Indexed: 01/02/2023]
Abstract
Neurofibrillary tangles (NFTs) are one of the pathological hallmarks of Alzheimer's disease (AD) and are primarily composed of aggregates of hyperphosphorylated forms of the microtubule associated protein tau. It is likely that an imbalance of kinase and phosphatase activities leads to the abnormal phosphorylation of tau and subsequent aggregation. The wide ranging therapeutic approaches that are being developed include to inhibit tau kinases, to enhance phosphatase activity, to promote microtubule stability, and to reduce tau aggregate formation and/or enhance their clearance with small molecule drugs or by immunotherapeutic means. Most of these promising approaches are still in preclinical development whilst some have progressed to Phase II clinical trials. By pursuing these lines of study, a viable therapy for AD and related tauopathies may be obtained.
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Affiliation(s)
- A Boutajangout
- Departments of Physiology and Neuroscience, New York University School of Medicine, New York, NY 10016, USA.
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80
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Keivanloo A, Bakherad M, Nasr-Isfahani H, Esmaily S. Highly efficient synthesis of 5,6-disubstituted-5H-pyrrolo[2,3-b]pyrazine-2,3-dicarbonitriles through a one-pot palladium-catalyzed coupling reaction/cyclization in water. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.04.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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81
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Plisson F, Conte M, Khalil Z, Huang XC, Piggott AM, Capon RJ. Kinase Inhibitor Scaffolds against Neurodegenerative Diseases from a Southern Australian Ascidian,Didemnumsp. ChemMedChem 2012; 7:983-90. [DOI: 10.1002/cmdc.201200169] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Indexed: 11/06/2022]
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82
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Nguyen TB, Lozach O, Surpateanu G, Wang Q, Retailleau P, Iorga BI, Meijer L, Guéritte F. Synthesis, Biological Evaluation, and Molecular Modeling of Natural and Unnatural Flavonoidal Alkaloids, Inhibitors of Kinases. J Med Chem 2012; 55:2811-9. [DOI: 10.1021/jm201727w] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thanh Binh Nguyen
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles (ICSN), CNRS, 91198 Gif-sur-Yvette Cedex,
France
| | - Olivier Lozach
- “Protein Phosphorylation & Human Disease”, CNRS, Station Biologique, Place G. Teissier, 29682 Roscoff Cedex, France
| | - Georgiana Surpateanu
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles (ICSN), CNRS, 91198 Gif-sur-Yvette Cedex,
France
| | - Qian Wang
- Institute of Chemical Sciences
and Engineering, Ecole Polytechnique Fédérale de Lausanne, EPFL-SB-ISIC-LSPN, 1015 Lausanne, Switzerland
| | - Pascal Retailleau
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles (ICSN), CNRS, 91198 Gif-sur-Yvette Cedex,
France
| | - Bogdan I. Iorga
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles (ICSN), CNRS, 91198 Gif-sur-Yvette Cedex,
France
| | - Laurent Meijer
- “Protein Phosphorylation & Human Disease”, CNRS, Station Biologique, Place G. Teissier, 29682 Roscoff Cedex, France
- ManRos Therapeutics, Centre de Perharidy, 29680 Roscoff, France
| | - Françoise Guéritte
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles (ICSN), CNRS, 91198 Gif-sur-Yvette Cedex,
France
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83
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Cyclin-dependent kinases: bridging their structure and function through computations. Future Med Chem 2011; 3:1551-9. [PMID: 21882947 DOI: 10.4155/fmc.11.113] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Cyclin-dependent kinases (CDKs) are one of the most promising target families for drug discovery for several diseases, such as cancer and neurodegenerative disorders. Over the years, structural insights on CDKs have demonstrated high protein plasticity, with several cases where two or more structures of the same protein adopt different conformations. This has generated a great deal of interest in understanding the relationship between CDK structure and function. Here, we highlight how computer simulations have recently contributed in characterizing some key rare and transient events in CDKs, such as the reaction transition state and activation loop movement. Although not yet fully defined, we can now portray the enzymatic mechanism and plasticity of CDKs at high spatial and temporal resolution. These theoretical studies bridge with experiments and highlight structural determinants that could help in designing specific CDK inhibitors.
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84
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Pitchuanchom S, Boonyarat C, Forli S, Olson AJ, Yenjai C. Cyclin-dependent kinases 5 template: useful for virtual screening. Comput Biol Med 2011; 42:106-11. [PMID: 22079569 DOI: 10.1016/j.compbiomed.2011.10.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 10/09/2011] [Accepted: 10/27/2011] [Indexed: 11/16/2022]
Abstract
The present study reports the development of a template for the active binding site of Cdk5 for structure-based drug design. The developed template of Cdk5 was validated by redocking with ligands I (PBD code 1UNG), II (PBD code 1UNL) and III (PBD code 1UNH). The results demonstrate a good match of the docked and the crystallographic binding orientations with RMSD less than 2.0Å. The validation results show that the constructed Cdk5 template is a good model system for predicting ligand binding orientations and binding affinities. Furthermore, the developed template was applied to predict binding mode and binding affinity of thirty-six known Cdk5 inhibitors. The results showed that the binding energy of almost Cdk5 inhibitors related to their biological evaluation.
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Affiliation(s)
- Siripit Pitchuanchom
- Natural Products Research Unit, Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
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85
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Patel JS, Branduardi D, Masetti M, Rocchia W, Cavalli A. Insights into Ligand-Protein Binding from Local Mechanical Response. J Chem Theory Comput 2011; 7:3368-3378. [PMID: 22003321 PMCID: PMC3191767 DOI: 10.1021/ct200324j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Indexed: 11/28/2022]
Abstract
Computational studies of ligand–protein binding are crucial for properly designing novel compounds of potential pharmacological interest. In this respect, researchers are increasingly interested in steered molecular dynamics for ligand–protein binding and unbinding studies. In particular, it has been suggested that analyzing the work profiles along the ligand–protein undocking paths could be fruitful. Here, we propose that small portions of work profiles, termed “local mechanical responses” of the system to a steering force, could serve as a universal measure for capturing relevant information about the system under investigation. Specifically, we first collected a high number of steering trajectories using two biological systems of increasing complexity (i.e., alanine dipeptide and (R)-roscovitine/CDK5 complex). Then, we devised a novel postprocessing tool to be applied to the local mechanical responses, to extract structural information related to the biological processes under investigation. Despite the out-of-equilibrium character of the trajectories, the analysis carried out on the work profiles provided pivotal information about the investigated biological processes. This could eventually be applied to drug design.
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86
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Nair N, Kudo W, Smith MA, Abrol R, Goddard WA, Reddy VP. Novel purine-based fluoroaryl-1,2,3-triazoles as neuroprotecting agents: Synthesis, neuronal cell culture investigations, and CDK5 docking studies. Bioorg Med Chem Lett 2011; 21:3957-61. [PMID: 21641213 DOI: 10.1016/j.bmcl.2011.05.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2011] [Revised: 05/05/2011] [Accepted: 05/06/2011] [Indexed: 01/27/2023]
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87
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Zhang B, Corbel C, Guéritte F, Couturier C, Bach S, Tan VBC. An in silico approach for the discovery of CDK5/p25 interaction inhibitors. Biotechnol J 2011; 6:871-81. [PMID: 21681969 DOI: 10.1002/biot.201100139] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 05/11/2011] [Accepted: 05/20/2011] [Indexed: 11/11/2022]
Abstract
The lack of selectivity of all existing ATP competitive inhibitors for a single cyclin-dependent kinase (CDK) has led us to redirect the structure-based molecule design from targeting the classic ATP-binding pocket in CDK5 toward the CDK5/p25 interface. The aim was to seek novel inhibition mechanisms to interrupt protein-protein interactions. A combined strategy of alanine-scanning calculations for locating binding sites, virtual screening for small molecules, molecular dynamics simulations for examining the binding stability of virtual screening hits and bio-assays for testing the level of inhibition was set up and used to explore novel inhibitors capable of interrupting the interactions between the proteins, and consequently of inhibiting the kinase activity. Two compounds were shown to inhibit the complex formation between CDK5 and p25 through p25 binding. They could open avenues for the discovery of new types of structures that prevent interactions between CDK5 and p25 or other CDK and activator proteins, and, more importantly, provide leads in the development of selective inhibitors among CDKs.
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Affiliation(s)
- Bing Zhang
- Thermal Physics Center, School of Renewable Energy, North China Electric Power University, Beijing, China
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88
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Smyth LA, Matthews TP, Collins I. Design and evaluation of 3-aminopyrazolopyridinone kinase inhibitors inspired by the natural product indirubin. Bioorg Med Chem 2011; 19:3569-78. [DOI: 10.1016/j.bmc.2011.03.069] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Revised: 03/28/2011] [Accepted: 03/31/2011] [Indexed: 01/09/2023]
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89
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Laha JK, Zhang X, Qiao L, Liu M, Chatterjee S, Robinson S, Kosik KS, Cuny GD. Structure-activity relationship study of 2,4-diaminothiazoles as Cdk5/p25 kinase inhibitors. Bioorg Med Chem Lett 2011; 21:2098-101. [PMID: 21353545 DOI: 10.1016/j.bmcl.2011.01.140] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 01/27/2011] [Accepted: 01/31/2011] [Indexed: 11/30/2022]
Abstract
Cdk5/p25 has emerged as a principle therapeutic target for numerous acute and chronic neurodegenerative diseases, including Alzheimer's disease. A structure-activity relationship study of 2,4-diaminothiazole inhibitors revealed that increased Cdk5/p25 inhibitory activity could be accomplished by incorporating pyridines on the 2-amino group and addition of substituents to the 2- or 3-position of the phenyl ketone moiety. Interpretation of the SAR results for many of the analogs was aided through in silico docking with Cdk5/p25 and calculating protein hydrations sites using WaterMap. Finally, improved in vitro mouse microsomal stability was also achieved.
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Affiliation(s)
- Joydev K Laha
- Laboratory for Drug Discovery in Neurodegeneration, Harvard NeuroDiscovery Center, Brigham & Women's Hospital and Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA
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90
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Ravichandran K, Pal A, Ravichandran R. Effect of indirubin-3-monoxime against lung cancer as evaluated by histological and transmission electron microscopic studies. Microsc Res Tech 2011; 73:1053-8. [PMID: 20169620 DOI: 10.1002/jemt.20832] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The aim of this study is to evaluate the antitumor effect of indirubin-3-monoxime and its mode of action in benzo(α)pyrene [B(α)P] induced lung cancer in A/J mice. Light microscopic examination of lung sections of [B(α)P] induced lung cancer mice revealed the presence of adenocarcinoma characterized by extensive proliferation of alveolar epithelium and loss of alveolar spaces. The control lung tissue showed a normal architecture with clear alveolar spaces. Interestingly the indirubin-3-monoxime treated groups showed the reduced adenocarcinoma with appearance of alveolar spaces. Transmission Electron Microscopic (TEM) studies of lung sections of [B(α)P] induced lung cancer mice showed the presence of phaemorphic cells with dense granules and increased mitochondria. The lung sections of mice treated with indirubin-3-monoxime showed the presence of shrunken, fragmented, and condensed nuclei implying apoptosis. The effects were dose dependent and prominent in 10 mg/kg/5 d/week groups suggesting the therapeutic role of indirubin analogue against this deadly human malignancy. Here, our results indicate that indirubin-3-monoxime brings antitumor effect against [B(α)P] induced lung cancer by its apoptotic action in A/J mice.
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Affiliation(s)
- Kameswaran Ravichandran
- Department of Zoology, Unit of Biomonitoring and Management, University of Madras, Guindy Campus, Chennai 600025, India
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91
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Lowman XH, McDonnell MA, Kosloske A, Odumade OA, Jenness C, Karim CB, Jemmerson R, Kelekar A. The proapoptotic function of Noxa in human leukemia cells is regulated by the kinase Cdk5 and by glucose. Mol Cell 2011; 40:823-33. [PMID: 21145489 DOI: 10.1016/j.molcel.2010.11.035] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Revised: 08/20/2010] [Accepted: 10/05/2010] [Indexed: 01/11/2023]
Abstract
The BH3-only protein, Noxa, is induced in response to apoptotic stimuli, such as DNA damage, hypoxia, and proteasome inhibition in most human cells. Noxa is constitutively expressed in proliferating cells of hematopoietic lineage and required for apoptosis in response to glucose stress. We show that Noxa is phosphorylated on a serine residue (S(13)) in the presence of glucose. Phosphorylation promotes its cytosolic sequestration and suppresses its apoptotic function. We identify Cdk5 as the Noxa kinase and show that Cdk5 knockdown or expression of a Noxa S(13) to A mutant increases sensitivity to glucose starvation, confirming that the phosphorylation is protective. Both glucose deprivation and Cdk5 inhibition promote apoptosis by dephosphorylating Noxa. Paradoxically, Noxa stimulates glucose consumption and may enhance glucose turnover via the pentose phosphate pathway rather than through glycolysis. We propose that Noxa plays both growth-promoting and proapoptotic roles in hematopoietic cancers with phospho-S(13) as the glucose-sensitive toggle switch controlling these opposing functions.
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Affiliation(s)
- Xazmin H Lowman
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
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92
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Zhang N, Zhong R, Yan H, Jiang Y. Structural Features Underlying Selective Inhibition of GSK3β by Dibromocantharelline: Implications for Rational Drug Design. Chem Biol Drug Des 2011; 77:199-205. [DOI: 10.1111/j.1747-0285.2010.01069.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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93
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Roscovitine inhibits EBNA1 serine 393 phosphorylation, nuclear localization, transcription, and episome maintenance. J Virol 2011; 85:2859-68. [PMID: 21209116 DOI: 10.1128/jvi.01628-10] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Latent Epstein-Barr virus (EBV) infection causes human lymphomas and carcinomas. EBV usually persists as an episome in malignant cells. EBV episome persistence, replication, and gene expression are dependent on EBNA1 binding to multiple cognate sites in oriP. To search for inhibitors of EBNA1- and oriP-dependent episome maintenance or transcription, a library of 40,550 small molecules was screened for compounds that inhibit EBNA1- and oriP-dependent transcription and do not inhibit EBNA1- and oriP-independent transcription. This screening identified roscovitine, a selective inhibitor of cyclin-dependent kinase 1 (CDK1), CDK2, CDK5, and CDK7. Based on motif predictions of EBNA1 serine 393 as a CDK phosphorylation site and (486)RALL(489) and (580)KDLVM(584) as potential cyclin binding domains, we hypothesized that cyclin binding to EBNA1 may enable CDK1, -2, -5, or -7 to phosphorylate serine 393. We found that Escherichia coli-expressed EBNA1 amino acids 387 to 641 were phosphorylated in vitro by CDK1-, -2-, -5-, and -7/cyclin complexes and serine 393 phosphorylation was roscovitine inhibited. Further, S393A mutation abrogated phosphorylation. S393A mutant EBNA1 was deficient in supporting EBNA1- and oriP-dependent transcription and episome persistence, and roscovitine had little further effect on the diminished S393A mutant EBNA1-mediated transcription or episome persistence. Immunoprecipitated FLAG-EBNA1 was phosphorylated in vitro, and roscovitine inhibited this phosphorylation. Moreover, roscovitine decreased nuclear EBNA1 and often increased cytoplasmic EBNA1, whereas S393A mutant EBNA1 was localized equally in the nucleus and cytoplasm and was unaffected by roscovitine treatment. These data indicate that roscovitine effects are serine 393 specific and that serine 393 is important in EBNA1- and oriPCp-dependent transcription and episome persistence.
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94
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Patel RY, Doerksen RJ. Protein kinase-inhibitor database: structural variability of and inhibitor interactions with the protein kinase P-loop. J Proteome Res 2011; 9:4433-42. [PMID: 20681595 DOI: 10.1021/pr100662s] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Structure-based drug design of protein-kinase inhibitors has been facilitated by availability of an enormous number of structures in the Protein Databank (PDB), systematic analyses of which can provide insight into the factors that govern ligand-protein kinase interactions and into the conformational variability of the protein kinases. In this study, a nonredundant database containing 755 unique, curated, and annotated PDB protein kinase-inhibitor complexes (each consisting of a single protein kinase chain, a ligand, and water molecules around the ligand) was created. With this dataset, analyses were performed of protein conformational variability and interactions of ligands with 11 P-loop residues. Analysis of ligand-protein interactions included ligand atom preference, ligand-protein hydrogen bonds, and the number and position of crystallographic water molecules around important P-loop residues. Analysis of variability in the conformation of the P-loop considered backbone and side-chain dihedral angles, and solvent accessible surface area (SASA). A distorted conformation of the P-loop was observed for some of the protein kinase structures. Lower SASA was observed for the hydrophobic residue in beta1 of several members of the AGC family of protein kinases. Our systematic studies were performed amino acid-by-amino acid, which is unusual for analyses of protein kinase-inhibitor complexes.
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Affiliation(s)
- Ronak Y Patel
- Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi, University, Mississippi 38677-1848, USA
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95
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Design, synthesis, and testing of an 6-O-linked series of benzimidazole based inhibitors of CDK5/p25. Bioorg Med Chem 2010; 19:359-73. [PMID: 21144757 DOI: 10.1016/j.bmc.2010.11.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 11/01/2010] [Accepted: 11/06/2010] [Indexed: 02/02/2023]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disease resulting in cognitive and behavioral impairment. The two classic pathological hallmarks of AD include extraneuronal deposition of amyloid β (Aβ) and intraneuronal formation of neurofibrillary tangles (NFTs). NFTs contain hyperphosphorylated tau. Tau is the major microtubule-associated protein in neurons and stabilizes microtubules (MTs). Cyclin dependent kinase 5 (CDK5), when activated by the regulatory binding protein p25, phosphorylates tau at a number of proline-directed serine/threonine residues, resulting in formation of phosphorylated tau as paired helical filaments (PHFs) then in subsequent deposition of PHFs as NFTs. Beginning with the structure of Roscovitine, a moderately selective CDK5 inhibitor, we sought to conduct structural modifications to increase inhibitory potency of CDK5 and increase selectivity over a similar enzyme, cyclin dependent kinase 2 (CDK2). The design, synthesis, and testing of a series of 1-isopropyl-4-aminobenzyl-6-ether-linked benzimidazoles is presented.
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96
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Hayes JM, Skamnaki VT, Archontis G, Lamprakis C, Sarrou J, Bischler N, Skaltsounis AL, Zographos SE, Oikonomakos NG. Kinetics, in silico docking, molecular dynamics, and MM-GBSA binding studies on prototype indirubins, KT5720, and staurosporine as phosphorylase kinase ATP-binding site inhibitors: the role of water molecules examined. Proteins 2010; 79:703-19. [PMID: 21287607 DOI: 10.1002/prot.22890] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 09/15/2010] [Accepted: 09/16/2010] [Indexed: 11/10/2022]
Abstract
With an aim toward glycogenolysis control in Type 2 diabetes, we have investigated via kinetic experiments and computation the potential of indirubin (IC₅₀ > 50 μM), indirubin-3'-oxime (IC₅₀ = 144 nM), KT5720 (K(i) = 18.4 nM) and staurosporine (K(i) = 0.37 nM) as phosphorylase kinase (PhKγtrnc) ATP-binding site inhibitors, with the latter two revealed as potent inhibitors in the low nM range. Because of lack of structural information, we have exploited information from homologous kinase complexes to direct in silico calculations (docking, molecular dynamics, and MMGBSA) to predict the binding characteristics of the four ligands. All inhibitors are predicted to bind in the same active site area as the ATP adenine ring, with binding dominated by hinge region hydrogen bonds to Asp104:O and Met106:O (all four ligands) and also Met106:NH (for the indirubins). The PhKγtrnc-staurosporine complex has the greatest number of receptor-ligand hydrogen bonds, while for the indirubin-3'-oxime and KT5720 complexes there is an important network of interchanging water molecules bridging inhibitor-enzyme contacts. The MM-GBSA results revealed the source of staurosporine's low nM potency to be favorable electrostatic interactions, while KT5720 has strong van der Waals contributions. KT5720 interacts with the greatest number of protein residues either by direct or 1-water bridged hydrogen bond interactions, and the potential for more selective PhK inhibition based on a KT5720 analogue has been established. Including receptor flexibility in Schrödinger induced-fit docking calculations in most cases correctly predicted the binding modes as compared with the molecular dynamics structures; the algorithm was less effective when there were key structural waters bridging receptor-ligand contacts.
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Affiliation(s)
- Joseph M Hayes
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, Athens 11635, Greece.
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97
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S-nitrosylation of cyclin-dependent kinase 5 (cdk5) regulates its kinase activity and dendrite growth during neuronal development. J Neurosci 2010; 30:14366-70. [PMID: 20980593 DOI: 10.1523/jneurosci.3899-10.2010] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Precise regulation of cyclin-dependent kinase 5 (Cdk5), a member of the cyclin-dependent kinase family, is critical for proper neuronal development and functions. Cdk5 is activated through its association with the neuron-specific activator p35 or p39. Nonetheless, how its kinase activity is regulated in neurons is not well understood. In this study, we found that Cdk5 activity is regulated by S-nitrosylation, a post-translational modification of protein that affects a plethora of neuronal functions. S-nitrosylation of Cdk5 occurs at Cys83, which is one of the critical amino acids within the ATP-binding pocket of the kinase. Upon S-nitrosylation, Cdk5 exhibits reduced kinase activity, whereas mutation of Cys83 to Ala on Cdk5 renders the kinase refractory to such inhibition. Importantly, S-nitrosylated Cdk5 can be detected in the mouse brain, and blocking the S-nitrosylation of Cdk5 in cultured hippocampal neurons enhances dendritic growth and branching. Together, our findings reveal an important role of S-nitrosylation in regulating Cdk5 kinase activity and dendrite growth in neurons during development.
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98
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Pareek TK, Lam E, Zheng X, Askew D, Kulkarni AB, Chance MR, Huang AY, Cooke KR, Letterio JJ. Cyclin-dependent kinase 5 activity is required for T cell activation and induction of experimental autoimmune encephalomyelitis. ACTA ACUST UNITED AC 2010; 207:2507-19. [PMID: 20937706 PMCID: PMC2964575 DOI: 10.1084/jem.20100876] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cyclin-dependent kinase 5 (Cdk5) is a ubiquitously expressed serine/threonine kinase. However, a requirement for Cdk5 has been demonstrated only in postmitotic neurons where there is abundant expression of its activating partners p35 and/or p39. Although hyperactivation of the Cdk5-p35 complex has been found in a variety of inflammatory neurodegenerative disorders, the potential contribution of nonneuronal Cdk5-p35 activity has not been explored in this context. We describe a previously unknown function of the Cdk5-p35 complex in T cells that is required for induction of experimental autoimmune encephalomyelitis (EAE). T cell receptor (TCR) stimulation leads to a rapid induction of Cdk5-p35 expression that is required for T lymphocyte activation. Chimeric mice lacking Cdk5 gene expression in hematopoietic tissues (Cdk5(-/-C)) are resistant to induction of EAE, and adoptive transfer of either Cdk5(-/-C) or p35(-/-) encephalitogenic lymphocytes fails to transfer disease. Moreover, our data reveal a novel mechanism involving Cdk5-mediated phosphorylation of the actin modulator coronin 1a on threonine 418. Cdk5-deficient lymphocytes lack this posttranslational modification of coronin 1a and exhibit defective TCR-induced actin polarization and reduced migration toward CCL-19. These data define a distinct role for Cdk5 in lymphocyte biology and suggest that inhibition of this kinase may be beneficial in the treatment of T cell-mediated inflammatory disorders.
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Affiliation(s)
- Tej K Pareek
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University Hospitals Case Medical Center and The Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
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99
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Krystof V, Chamrád I, Jorda R, Kohoutek J. Pharmacological targeting of CDK9 in cardiac hypertrophy. Med Res Rev 2010; 30:646-66. [PMID: 19757441 DOI: 10.1002/med.20172] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cardiac hypertrophy allows the heart to adapt to workload, but persistent or unphysiological stimulus can result in pump failure. Cardiac hypertrophy is characterized by an increase in the size of differentiated cardiac myocytes. At the molecular level, growth of cells is linked to intensive transcription and translation. Several cyclin-dependent kinases (CDKs) have been identified as principal regulators of transcription, and among these CDK9 is directly associated with cardiac hypertrophy. CDK9 phosphorylates the C-terminal domain of RNA polymerase II and thus stimulates the elongation phase of transcription. Chronic activation of CDK9 causes not only cardiac myocyte enlargement but also confers predisposition to heart failure. Due to the long interest of molecular oncologists and medicinal chemists in CDKs as potential targets of anticancer drugs, a portfolio of small-molecule inhibitors of CDK9 is available. Recent determination of CDK9's crystal structure now allows the development of selective inhibitors and their further optimization in terms of biochemical potency and selectivity. CDK9 may therefore constitute a novel target for drugs against cardiac hypertrophy.
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Affiliation(s)
- Vladimír Krystof
- Faculty of Science, Laboratory of Growth Regulators, Palacký University & Institute of Experimental Botany AS CR, Slechtitelů 11, Olomouc 783 71, Czech Republic.
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100
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Ul Haq Z, Uddin R, Wai LK, Wadood A, Lajis NH. Docking and 3D-QSAR modeling of cyclin-dependent kinase 5/p25 inhibitors. J Mol Model 2010; 17:1149-61. [PMID: 20686908 DOI: 10.1007/s00894-010-0817-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Accepted: 07/19/2010] [Indexed: 10/19/2022]
Abstract
Structure-based 3D-QSAR approaches (CoMFA and CoMSIA) were applied to understand the structural requirements of the Cyclin-dependent kinase 5/p25 inhibitors. Cyclin-dependent kinase 5 (CDK5) is believed to play an important role in the development of the central nervous system during the process of mammalian embryogenesis. Genetic algorithm based docking program (GOLD) was successfully utilized to orient the compounds inside the binding pocket of the CDK5/p25 structure. The adapted alignment method with the suitable parameters resulted in a reliable model. Furthermore, the final model was robust enough to forecast the activities of test compounds, satisfactorily. The contour maps were produced around the functional groups to understand the SAR requirements. Moreover, we also investigate the structural attributes of the inhibitors which make them selective toward CDK5/p25 over its close counterpart, i.e., CDK2. The study could be helpful to rationalize the new compounds with better inhibition and selectivity profiles against CDK5/p25.
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Affiliation(s)
- Zaheer Ul Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
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