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El Bakri Y, Karthikeyan S, Lai CH, Bakhite EA, Ahmad I, Abdel-Rahman AE, Abuelhassan S, Marae IS, Mohamed SK, Mague JT. New tetrahydroisoquinoline-4-carbonitrile derivatives as potent agents against cyclin-dependent kinases, crystal structures, and computational studies. J Biomol Struct Dyn 2024; 42:5053-5071. [PMID: 38764131 DOI: 10.1080/07391102.2023.2224899] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/07/2023] [Indexed: 05/21/2024]
Abstract
The synthesis of two new hexahydroisoquinoline-4-carbonitrile derivatives (3a and 3b) is reported along with spectroscopic data and their crystal structures. In compound 3a, the intramolecular O-H···O hydrogen bond constraints the acetyl and hydroxyl groups to be syn. In the crystal, inversion dimers are generated by C-H···O hydrogen bonds and are connected into layers parallel to (10-1) by additional C-H···O hydrogen bonds. The layers are stacked with Cl···S contacts 0.17 Å less than the sum of the respective van der Waals radii. The conformation of the compound 3b is partially determined by the intramolecular O-H···O hydrogen bond. A puckering analysis of the tetrahydroisoquinoline unit was performed. In the crystal, O-H···O and C-H···O hydrogen bonds together with C-H···π(ring) interactions form layers parallel to (01-1) which pack with normal van der Waals interactions. To understand the binding efficiency and stability of the title molecules, molecular docking, and 100 ns dynamic simulation analyses were performed with CDK5A1. To rationalize their structure-activity relationship(s), a DFT study at the B3LYP/6-311++G** theoretical level was also done. The 3D Hirshfled surfaces were also taken to investigate the crystal packings of both compounds. In addition, their ADMET properties were explored.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russia
| | - Subramani Karthikeyan
- Division of Physics, school of advanced science, Vellore Institute of Technology, Chennai Campus, Chennai, Tamil Nadu, India
| | - Chin-Hung Lai
- Department of Medical Applied Chemistry, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Education, Chung Shan Medical University Hospital, Taichung, Taiwan
| | | | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, Prof. Ravindra Nikam College of Pharmacy, Gondur, Maharashtra, India
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | | | | | - Islam S Marae
- Department of Chemistry, Assiut University, Assiut, Egypt
| | - Shaaban K Mohamed
- Chemistry and Environmental Division, Manchester Metropolitan University, Manchester, England
- Chemistry Department, Minia University, El-Minia, Egypt
| | - Joel T Mague
- Department of Chemistry, Tulane University, New Orleans, Los Angeles, USA
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2
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Faydalı N, Arpacı ÖT. Benzimidazole and Benzoxazole Derivatives Against Alzheimer's Disease. Chem Biodivers 2024; 21:e202400123. [PMID: 38494443 DOI: 10.1002/cbdv.202400123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 03/19/2024]
Abstract
Benzimidazole and benzoxazole derivatives are included in the category of medical drugs in a wide range of areas such as anticancer, anticoagulant, antihypertensive, anti- inflammatory, antimicrobial, antiparasitic, antiviral, antioxidant, immunomodulators, proton pump inhibitors, hormone modulators, etc. Many researchers have focused on synthesizing more effective benzimidazole and benzoxazole derivatives for screening various biological activities. In addition, there are benzimidazole and benzoxazole rings as bioisosteres of aromatic rings found in drugs used in the treatment of Alzheimer's disease. Because of the diverse activity of the benzimidazole and benzoxazole rings and bioisosteres marketed as drugs for Alzheimer Diseases, designed compounds containing these rings are likely to be effective against Alzheimer's disease. In this study, the effectiveness of compounds containing benzimidazole and benzoxazole rings against Alzheimer's disease will be examined.
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Affiliation(s)
- Nagihan Faydalı
- Department of Pharmaceutical Chemistry, Selcuk University, 42250, Konya, Turkey
- Graduate School of Health Sciences, Ankara University, 06110, Ankara, Turkey
| | - Özlem Temiz Arpacı
- Department of Pharmaceutical Chemistry, Ankara University, 06560, Ankara, Turkey
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Sahiba N, Teli P, Meena P, Agarwal S. Exploring the Synthetic and Antioxidant Potential of 1,2-Disubstituted Benzimidazoles Using [Et 3NH][HSO 4] Ionic Liquid Catalyst. Chem Biodivers 2024; 21:e202301159. [PMID: 37718514 DOI: 10.1002/cbdv.202301159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/13/2023] [Accepted: 09/17/2023] [Indexed: 09/19/2023]
Abstract
An [Et3NH][HSO4] ionic-liquid catalyzed, intermolecular C-N bond formation for 1,2-disubstituted benzimidazole synthesis was achieved by the reaction of OPD and substituted aldehydes at ambient reaction conditions. Operational simplicity, use of easily available substrate and reagents, good yields (74-95 %) in short reaction time (4-18 min), simple work-up, and column chromatographic free synthesis are the remarkable features of this new protocol. The applicability of [Et3NH][HSO4] ionic-liquid as a green and inexpensive catalyst with good recyclability and compatibility with a broad range of functional group having heteroatom, electron-withdrawing, and electron-releasing groups manifested the sustainability, eco-friendliness, and efficiency of the present methodology. Moreover, the antioxidant studies of the synthesized compounds using DPPH and ABTS assays were appealing and several synthesized compounds showed significant antioxidant activity.
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Affiliation(s)
- Nusrat Sahiba
- Synthetic Organic Chemistry Lab, Department of Chemistry, MLSU, Udaipur, 313001, Rajasthan, India
| | - Pankaj Teli
- Synthetic Organic Chemistry Lab, Department of Chemistry, MLSU, Udaipur, 313001, Rajasthan, India
| | - Priyadarshi Meena
- Cancer Biology Lab, Department of Zoology, University of Rajasthan, Jaipur, 302004, Rajasthan, India
| | - Shikha Agarwal
- Synthetic Organic Chemistry Lab, Department of Chemistry, MLSU, Udaipur, 313001, Rajasthan, India
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Cdk5-p25 as a key element linking amyloid and tau pathologies in Alzheimer's disease: Mechanisms and possible therapeutic interventions. Life Sci 2022; 308:120986. [PMID: 36152679 DOI: 10.1016/j.lfs.2022.120986] [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: 08/08/2022] [Revised: 09/15/2022] [Accepted: 09/19/2022] [Indexed: 11/24/2022]
Abstract
Despite the fact that the small atypical serine/threonine cyclin-dependent kinase 5 (Cdk5) is expressed in a number of tissues, its activity is restricted to the central nervous system due to the neuron-only localization of its activators p35 and p39. Although its importance for the proper development and function of the brain and its role as a switch between neuronal survival and death are unmistakable and unquestionable, Cdk5 is nevertheless increasingly emerging, as supported by a large number of publications on the subject, as a therapeutic target of choice in the fight against Alzheimer's disease. Thus, its aberrant over activation via the calpain-dependent conversion of p35 into p25 is observed during the pathogenesis of the disease where it leads to the hyperphosphorylation of the β-amyloid precursor protein and tau. The present review highlights the pivotal roles of the hyperactive Cdk5-p25 complex activity in contributing to the development of Alzheimer's disease pathogenesis, with a particular emphasis on the linking function between Aβ and tau that this kinase fulfils and on the fact that Cdk5-p25 is part of a deleterious feed forward loop giving rise to a molecular machinery runaway leading to AD pathogenesis. Additionally, we discuss the advances and challenges related to the possible strategies aimed at specifically inhibiting Cdk5-p25 activity and which could lead to promising anti-AD therapeutics.
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Jain AK, Gupta A, Karthikeyan C, Trivedi P, Konar AD. Substituent Orchestration in Dimethylquinoxaline Derivatives: A Tool for Fishing Out Appropriate CDK5 Inhibitors as Potential Therapeutics for Alzheimer's. Chem Biodivers 2022; 19:e202200116. [PMID: 35983935 DOI: 10.1002/cbdv.202200116] [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: 02/07/2022] [Accepted: 07/12/2022] [Indexed: 11/12/2022]
Abstract
A set of new heterocyclic analogs (Compounds I-IX), comprising of 6,7 dimethyl Quinoxalines were found to be active against the receptor GSK3β (Compounds IV-V) (Chem. Biodiversity 2021, 18, e2100364). In an effort to modulate effective CDK5 inhibitors herein our hypothesis underpinned to fish out an appropriate derivative from the same quinoxaline series, as these two targets GSK3β and CDK5 shared structural resemblance with each other. Aligned to the goal we have synthesized Compounds I-IX, characterized them using a combination of spectroscopic techniques and evaluated their activities against CDK5. Our analysis reflected that the adjacently located alkoxy/hydroxy functionality derivatives namely Compounds III and VI, to be the most potent (micromolar) amongst others in the series, backed by Density Functional Theory (DFT) calculations and molecular modelling studies. Also, the efficacy of the Compounds I-IX, were monitored in few other members of the CMGC family namely DYRK1A, CLK1and CK1δ that have been known to be directly involved in hyperphosphorylation of Tau. But unfortunately in none of the targets, our quinoxaline series were active. In a nut shell further optimisation of these intelligent nucleus, would not only lead to the discovery of novel pharmacophores, but also marked selectivity against a pool of kinases, thereby implementing a distinct roadmap towards the design of potential therapeutics against Alzheimer's.
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Affiliation(s)
- Arvind Kumar Jain
- School of Pharmaceutical Sciences, Rajiv Gandhi Technological University, Bhopal, 462033, Madhya Pradesh, India
| | - Arindam Gupta
- Department of Chemistry, IISER Bhopal, Bhopal, 462066, Madhya Pradesh, India
| | - C Karthikeyan
- Department of Pharmacy, Indira Gandhi National Tribal University, Amarkantak (MP), 484887, India
| | - Piyush Trivedi
- School of Pharmaceutical Sciences, Rajiv Gandhi Technological University, Bhopal, 462033, Madhya Pradesh, India.,Center of Innovation & Translational Research, Bharati Vidyapeeth, Pune, 411038, Maharashtra, India
| | - Anita Dutt Konar
- School of Pharmaceutical Sciences, Rajiv Gandhi Technological University, Bhopal, 462033, Madhya Pradesh, India.,Dept. of Chemistry, Rajiv Gandhi Technological University, Bhopal, 462033, Madhya Pradesh, India.,University Grants Commission, New Delhi, 110002, New Delhi, India
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Ganeshpurkar A, Swetha R, Kumar D, Gangaram GP, Singh R, Gutti G, Jana S, Kumar D, Kumar A, Singh SK. Protein-Protein Interactions and Aggregation Inhibitors in Alzheimer's Disease. Curr Top Med Chem 2019; 19:501-533. [PMID: 30836921 DOI: 10.2174/1568026619666190304153353] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 10/31/2018] [Accepted: 11/20/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Alzheimer's Disease (AD), a multifaceted disorder, involves complex pathophysiology and plethora of protein-protein interactions. Thus such interactions can be exploited to develop anti-AD drugs. OBJECTIVE The interaction of dynamin-related protein 1, cellular prion protein, phosphoprotein phosphatase 2A and Mint 2 with amyloid β, etc., studied recently, may have critical role in progression of the disease. Our objective has been to review such studies and their implications in design and development of drugs against the Alzheimer's disease. METHODS Such studies have been reviewed and critically assessed. RESULTS Review has led to show how such studies are useful to develop anti-AD drugs. CONCLUSION There are several PPIs which are current topics of research including Drp1, Aβ interactions with various targets including PrPC, Fyn kinase, NMDAR and mGluR5 and interaction of Mint2 with PDZ domain, etc., and thus have potential role in neurodegeneration and AD. Finally, the multi-targeted approach in AD may be fruitful and opens a new vista for identification and targeting of PPIs in various cellular pathways to find a cure for the disease.
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Affiliation(s)
- Ankit Ganeshpurkar
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Rayala Swetha
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Devendra Kumar
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Gore P Gangaram
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Ravi Singh
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Gopichand Gutti
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Srabanti Jana
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Dileep Kumar
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Ashok Kumar
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Sushil K Singh
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
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7
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Shukla R, Singh TR. Virtual screening, pharmacokinetics, molecular dynamics and binding free energy analysis for small natural molecules against cyclin-dependent kinase 5 for Alzheimer's disease. J Biomol Struct Dyn 2019; 38:248-262. [PMID: 30688165 DOI: 10.1080/07391102.2019.1571947] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder and characterized by brain cell death, memory loss and is the most common form of dementia. Although AD has devastating effects, however, drugs which can treat the AD remain limited. The cyclin-dependent kinase 5 (CDK5) has been recognized as being involved in the pathological hyperphosphorylation of tau protein, which leads to the formation of neurofibrillary tangles (NFTs). We utilized the structure-based virtual screening (SBVS) approach to find the potential inhibitors against HsCDK5. The natural compound subset from the ZINC database (n = 167,741) was retrieved and screened by using SBVS method. From here, we have predicted 297 potent inhibitors. These 297 compounds were evaluated through their pharmacokinetic properties by ADMET (absorption, distribution, metabolism, elimination/excretion and toxicity) descriptors. Finally, 17 compounds were selected and used for re-docking. After the refinement by molecular docking and by using drug-likeness analysis, we have identified four potential inhibitors (ZINC85877721, ZINC96114862, ZINC96115616 and ZINC96116231). All these four ligands were employed for 100 ns MDS study. From the root mean square deviation (RMSD), root mean square fluctuation (RMSF), Rg, number of hydrogen bonds, solvent accessible surface area (SASA), principal component analysis (PCA) and binding free energy analysis we have found that out of four inhibitors ZINC85877721 and ZINC96116231 showed good binding free energy of -198.84 and -159.32 kJ.mol-1, respectively, and also good in other structural analyses. Both compounds displayed excellent pharmacological and structural properties to be the drug candidates. Collectively, these findings recommend that two compounds have great potential to be a promising agent against AD to reduce the CDK5 induced hyperphosphorylation and could be considered as therapeutic agents for the AD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rohit Shukla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, India
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, India
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8
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Dong K, Wang X, Yang X, Zhu X. Binding mechanism of CDK5 with roscovitine derivatives based on molecular dynamics simulations and MM/PBSA methods. J Mol Graph Model 2016; 68:57-67. [PMID: 27371933 DOI: 10.1016/j.jmgm.2016.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 05/21/2016] [Accepted: 06/15/2016] [Indexed: 12/11/2022]
Abstract
Roscovitine derivatives are potent inhibitors of cyclin-dependent kinase 5 (CDK5), but they exhibit different activities, which has not been understood clearly up to now. On the other hand, the task of drug design is difficult because of the fuzzy binding mechanism. In this context, the methods of molecular docking, molecular dynamics (MD) simulation, and binding free energy analysis are applied to investigate and reveal the detailed binding mechanism of four roscovitine derivatives with CDK5. The electrostatic and van der Waals interactions of the four inhibitors with CDK5 are analyzed and discussed. The calculated binding free energies in terms of MM-PBSA method are consistent with experimental ranking of inhibitor effectiveness for the four inhibitors. The hydrogen bonds of the inhibitors with Cys83 and Lys33 can stabilize the inhibitors in binding sites. The van der Waals interactions, especially the pivotal contacts with Ile10 and Leu133 have larger contributions to the binding free energy and play critical roles in distinguishing the variant bioactivity of four inhibitors. In terms of binding mechanism of the four inhibitors with CDK5 and energy contribution of fragments of each inhibitor, two new CDK5 inhibitors are designed and have stronger inhibitory potency.
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Affiliation(s)
- Keke Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, Nanjing 210009, China
| | - Xuan Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, Nanjing 210009, China
| | - Xueyu Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, Nanjing 210009, China
| | - Xiaolei Zhu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, Nanjing 210009, China.
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Bisht S, Nolting J, Schütte U, Haarmann J, Jain P, Shah D, Brossart P, Flaherty P, Feldmann G. Cyclin-Dependent Kinase 5 (CDK5) Controls Melanoma Cell Motility, Invasiveness, and Metastatic Spread-Identification of a Promising Novel therapeutic target. Transl Oncol 2015; 8:295-307. [PMID: 26310376 PMCID: PMC4562979 DOI: 10.1016/j.tranon.2015.06.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 06/16/2015] [Accepted: 06/23/2015] [Indexed: 01/03/2023] Open
Abstract
Despite considerable progress in recent years, the overall prognosis of metastatic malignant melanoma remains poor, and curative therapeutic options are lacking. Therefore, better understanding of molecular mechanisms underlying melanoma progression and metastasis, as well as identification of novel therapeutic targets that allow inhibition of metastatic spread, are urgently required. The current study provides evidence for aberrant cyclin-dependent kinase 5 (CDK5) activation in primary and metastatic melanoma lesions by overexpression of its activator protein CDK5R1/p35. Moreover, using melanoma in vitro model systems, shRNA-mediated inducible knockdown of CDK5 was found to cause marked inhibition of cell motility, invasiveness, and anchorage-independent growth, while at the same time net cell growth was not affected. In vivo, CDK5 knockdown inhibited growth of orthotopic xenografts as well as formation of lung and liver colonies in xenogenic injection models mimicking systemic metastases. Inhibition of lung metastasis was further validated in a syngenic murine melanoma model. CDK5 knockdown was accompanied by dephosphorylation and overexpression of caldesmon, and concomitant caldesmon knockdown rescued cell motility and proinvasive phenotype. Finally, it was found that pharmacological inhibition of CDK5 activity by means of roscovitine as well as by a novel small molecule CDK5-inhibitor, N-(5-isopropylthiazol-2-yl)-3-phenylpropanamide, similarly caused marked inhibition of invasion/migration, colony formation, and anchorage-independent growth of melanoma cells. Thus, experimental data presented here provide strong evidence for a crucial role of aberrantly activated CDK5 in melanoma progression and metastasis and establish CDK5 as promising target for therapeutic intervention.
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Affiliation(s)
- Savita Bisht
- Department of Internal Medicine 3, Center of Integrated Oncology (CIO) Cologne-Bonn, University Hospital of Bonn, Germany
| | - Jens Nolting
- Department of Internal Medicine 3, Center of Integrated Oncology (CIO) Cologne-Bonn, University Hospital of Bonn, Germany
| | - Ute Schütte
- Department of Internal Medicine 3, Center of Integrated Oncology (CIO) Cologne-Bonn, University Hospital of Bonn, Germany
| | - Jens Haarmann
- Department of Internal Medicine 3, Center of Integrated Oncology (CIO) Cologne-Bonn, University Hospital of Bonn, Germany
| | - Prashi Jain
- Mylan School of Pharmacy, Medicinal Chemistry, Duquesne University, Pittsburgh, PA
| | - Dhruv Shah
- Mylan School of Pharmacy, Medicinal Chemistry, Duquesne University, Pittsburgh, PA
| | - Peter Brossart
- Department of Internal Medicine 3, Center of Integrated Oncology (CIO) Cologne-Bonn, University Hospital of Bonn, Germany
| | - Patrick Flaherty
- Mylan School of Pharmacy, Medicinal Chemistry, Duquesne University, Pittsburgh, PA
| | - Georg Feldmann
- Department of Internal Medicine 3, Center of Integrated Oncology (CIO) Cologne-Bonn, University Hospital of Bonn, Germany.
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Fang J, Yang R, Gao L, Yang S, Pang X, Li C, He Y, Liu AL, Du GH. Consensus models for CDK5 inhibitors in silico and their application to inhibitor discovery. Mol Divers 2014; 19:149-62. [DOI: 10.1007/s11030-014-9561-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Accepted: 11/25/2014] [Indexed: 02/07/2023]
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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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12
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Huber RJ. The cyclin-dependent kinase family in the social amoebozoan Dictyostelium discoideum. Cell Mol Life Sci 2014; 71:629-39. [PMID: 23974243 PMCID: PMC11113532 DOI: 10.1007/s00018-013-1449-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 07/24/2013] [Accepted: 08/05/2013] [Indexed: 10/26/2022]
Abstract
Cyclin-dependent kinases (Cdk) are a family of serine/threonine protein kinases that regulate eukaryotic cell cycle progression. Their ability to modulate the cell cycle has made them an attractive target for anti-cancer therapies. Cdk protein function has been studied in a variety of Eukaryotes ranging from yeast to humans. In the social amoebozoan Dictyostelium discoideum, several homologues of mammalian Cdks have been identified and characterized. The life cycle of this model organism is comprised of a feeding stage where single cells grow and divide mitotically as they feed on their bacterial food source and a multicellular developmental stage that is induced by starvation. Thus it is a valuable system for studying a variety of cellular and developmental processes. In this review I summarize the current knowledge of the Cdk protein family in Dictyostelium by highlighting the research efforts focused on the characterization of Cdk1, Cdk5, and Cdk8 in this model Eukaryote. Accumulated evidence indicates that each protein performs distinct functions during the Dictyostelium life cycle with Cdk1 being required for growth and Cdk5 and Cdk8 being required for processes that occur during development. Recent studies have shown that Dictyostelium Cdk5 shares attributes with mammalian Cdk5 and that the mammalian Cdk inhibitor roscovitine can be used to inhibit Cdk5 activity in Dictyostelium. Together, these results show that Dictyostelium can be used as a model system for studying Cdk protein function.
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Affiliation(s)
- Robert J Huber
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Richard B. Simches Research Center, 185 Cambridge Street, Boston, MA, 02114, USA,
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13
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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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Fei F, Zhou Z. New substituted benzimidazole derivatives: a patent review (2010 – 2012). Expert Opin Ther Pat 2013; 23:1157-79. [DOI: 10.1517/13543776.2013.800857] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Jain P, Yi S, Flaherty PT. Suzuki-Miyaura Cross-Coupling of Potassium Organoborates with 6-Sulfonate Benzimidazoles Using Microwave Irradiation. J Heterocycl Chem 2013. [DOI: 10.1002/jhet.1109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Prashi Jain
- School of Pharmacy, Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences; Duquesne University; Pittsburgh; Pennsylvania; United States
| | - Shuyan Yi
- School of Pharmacy, Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences; Duquesne University; Pittsburgh; Pennsylvania; United States
| | - Patrick Thomas Flaherty
- School of Pharmacy, Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences; Duquesne University; Pittsburgh; Pennsylvania; United States
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16
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Design, synthesis and anticancer activity of 1-acyl-3-amino-1,4,5,6-tetrahydropyrrolo[3,4-c]pyrazole derivatives. Bioorg Med Chem Lett 2012; 22:6947-51. [DOI: 10.1016/j.bmcl.2012.08.117] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Revised: 08/28/2012] [Accepted: 08/30/2012] [Indexed: 11/18/2022]
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17
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Huber RJ, O'Day DH. The cyclin-dependent kinase inhibitor roscovitine inhibits kinase activity, cell proliferation, multicellular development, and Cdk5 nuclear translocation in Dictyostelium discoideum. J Cell Biochem 2012; 113:868-76. [PMID: 22234985 DOI: 10.1002/jcb.23417] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Roscovitine, a cyclin-dependent kinase (Cdk) inhibitor, inhibited kinase activity and the axenic growth of Dictyostelium discoideum at micromolar concentrations. Growth was almost fully rescued in 50 µM and ≈ 50% rescued in 100 µM roscovitine-treated cultures by the over-expression of Cdk5-GFP. This supports the importance of Cdk5 function during cell proliferation in Dictyostelium and indicates that Cdk5 is a primary target of the drug. Roscovitine did not affect the expression of Cdk5 protein during axenic growth but did inhibit its nuclear translocation. This novel result suggests that the effects of roscovitine could be due in part to altering Cdk5 translocation in other systems as well. Kinase activity was inhibited by roscovitine in assays using AX3 whole cell lysates, but not in assays using lysates from Cdk5-GFP over-expressing cells. At higher concentrations, roscovitine impaired slug and fruiting body formation. Fruiting bodies that did form were small and produced relatively fewer spores many of which were round. However, roscovitine did not affect stalk cell differentiation. Together with previous findings, these data reveal that roscovitine inhibits Cdk5 during growth and as yet undefined Cdks during mid-late development.
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Affiliation(s)
- Robert J Huber
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, Canada
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18
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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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