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Pirzada RH, Ahmad B, Qayyum N, Choi S. Modeling structure-activity relationships with machine learning to identify GSK3-targeted small molecules as potential COVID-19 therapeutics. Front Endocrinol (Lausanne) 2023; 14:1084327. [PMID: 36950681 PMCID: PMC10025526 DOI: 10.3389/fendo.2023.1084327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 02/20/2023] [Indexed: 03/08/2023] Open
Abstract
Coronaviruses induce severe upper respiratory tract infections, which can spread to the lungs. The nucleocapsid protein (N protein) plays an important role in genome replication, transcription, and virion assembly in SARS-CoV-2, the virus causing COVID-19, and in other coronaviruses. Glycogen synthase kinase 3 (GSK3) activation phosphorylates the viral N protein. To combat COVID-19 and future coronavirus outbreaks, interference with the dependence of N protein on GSK3 may be a viable strategy. Toward this end, this study aimed to construct robust machine learning models to identify GSK3 inhibitors from Food and Drug Administration-approved and investigational drug libraries using the quantitative structure-activity relationship approach. A non-redundant dataset consisting of 495 and 3070 compounds for GSK3α and GSK3β, respectively, was acquired from the ChEMBL database. Twelve sets of molecular descriptors were used to define these inhibitors, and machine learning algorithms were selected using the LazyPredict package. Histogram-based gradient boosting and light gradient boosting machine algorithms were used to develop predictive models that were evaluated based on the root mean square error and R-squared value. Finally, the top two drugs (selinexor and ruboxistaurin) were selected for molecular dynamics simulation based on the highest predicted activity (negative log of the half-maximal inhibitory concentration, pIC50 value) to further investigate the structural stability of the protein-ligand complexes. This artificial intelligence-based virtual high-throughput screening approach is an effective strategy for accelerating drug discovery and finding novel pharmacological targets while reducing the cost and time.
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Affiliation(s)
- Rameez Hassan Pirzada
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
- S&K Therapeutics, Ajou University Campus Plaza, Suwon, Republic of Korea
| | - Bilal Ahmad
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Naila Qayyum
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
- S&K Therapeutics, Ajou University Campus Plaza, Suwon, Republic of Korea
- *Correspondence: Sangdun Choi,
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2
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Puhl AC, Gao ZG, Jacobson KA, Ekins S. Machine Learning for Discovery of New ADORA Modulators. Front Pharmacol 2022; 13:920643. [PMID: 35814244 PMCID: PMC9257522 DOI: 10.3389/fphar.2022.920643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/30/2022] [Indexed: 01/12/2023] Open
Abstract
Adenosine (ADO) is an extracellular signaling molecule generated locally under conditions that produce ischemia, hypoxia, or inflammation. It is involved in modulating a range of physiological functions throughout the brain and periphery through the membrane-bound G protein-coupled receptors, called adenosine receptors (ARs) A1AR, A2AAR, A2BAR, and A3AR. These are therefore important targets for neurological, cardiovascular, inflammatory, and autoimmune diseases and are the subject of drug development directed toward the cyclic adenosine monophosphate and other signaling pathways. Initially using public data for A1AR agonists we generated and validated a Bayesian machine learning model (Receiver Operator Characteristic of 0.87) that we used to identify molecules for testing. Three selected molecules, crisaborole, febuxostat and paroxetine, showed initial activity in vitro using the HEK293 A1AR Nomad cell line. However, radioligand binding, β-arrestin assay and calcium influx assay did not confirm this A1AR activity. Nevertheless, several other AR activities were identified. Febuxostat and paroxetine both inhibited orthosteric radioligand binding in the µM range for A2AAR and A3AR. In HEK293 cells expressing the human A2AAR, stimulation of cAMP was observed for crisaborole (EC50 2.8 µM) and paroxetine (EC50 14 µM), but not for febuxostat. Crisaborole also increased cAMP accumulation in A2BAR-expressing HEK293 cells, but it was weaker than at the A2AAR. At the human A3AR, paroxetine did not show any agonist activity at 100 µM, although it displayed binding with a Ki value of 14.5 µM, suggesting antagonist activity. We have now identified novel modulators of A2AAR, A2BAR and A3AR subtypes that are clinically used for other therapeutic indications, and which are structurally distinct from previously reported tool compounds or drugs.
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Affiliation(s)
- Ana C. Puhl
- Collaborations Pharmaceuticals, Inc., Raleigh, NC, United States,*Correspondence: Ana C. Puhl, ; Sean Ekins,
| | - Zhan-Guo Gao
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Kenneth A. Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., Raleigh, NC, United States,*Correspondence: Ana C. Puhl, ; Sean Ekins,
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3
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The brain-derived neurotrophic factor prompts platelet aggregation and secretion. Blood Adv 2021; 5:3568-3580. [PMID: 34546355 DOI: 10.1182/bloodadvances.2020004098] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 06/08/2021] [Indexed: 12/19/2022] Open
Abstract
Brain-derived neurotrophic factor (BDNF) has both autocrine and paracrine roles in neurons, and its release and signaling mechanisms have been extensively studied in the central nervous system. Large quantities of BDNF have been reported in circulation, essentially stored in platelets with concentrations reaching 100- to 1000-fold those of neurons. Despite this abundance, the function of BDNF in platelet biology has not been explored. At low concentrations, BDNF primed platelets, acting synergistically with classical agonists. At high concentrations, BDNF induced complete biphasic platelet aggregation that in part relied on amplification from secondary mediators. Neurotrophin-4, but not nerve growth factor, and an activating antibody against the canonical BDNF receptor tropomyosin-related kinase B (TrkB) induced similar platelet responses to BDNF, suggesting TrkB could be the mediator. Platelets expressed, both at their surface and in their intracellular compartment, a truncated form of TrkB lacking its tyrosine kinase domain. BDNF-induced platelet aggregation was prevented by inhibitors of Ras-related C3 botulinum toxin substrate 1 (Rac1), protein kinase C, and phosphoinositide 3-kinase. BDNF-stimulated platelets secreted a panel of angiogenic and inflammatory cytokines, which may play a role in maintaining vascular homeostasis. Two families with autism spectrum disorder were found to carry rare missense variants in the BDNF gene. Platelet studies revealed defects in platelet aggregation to low concentrations of collagen, as well as reduced adenosine triphosphate secretion in response to adenosine diphosphate. In summary, circulating BDNF levels appear to regulate platelet activation, aggregation, and secretion through activation of a truncated TrkB receptor and downstream kinase-dependent signaling.
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StC. Black D, Somphol K, Kumar N. Synthesis of Some Macrocyclic Diimines from Mono-, Di-, Tri-, and Tetra-Indolyl Dialdehydes. HETEROCYCLES 2021. [DOI: 10.3987/com-21-14411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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5
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Vignaux P, Minerali E, Foil DH, Puhl AC, Ekins S. Machine Learning for Discovery of GSK3β Inhibitors. ACS OMEGA 2020; 5:26551-26561. [PMID: 33110983 PMCID: PMC7581251 DOI: 10.1021/acsomega.0c03302] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/25/2020] [Indexed: 05/08/2023]
Abstract
Alzheimer's disease (AD) is the most common cause of dementia, affecting approximately 35 million people worldwide. The current treatment options for people with AD consist of drugs designed to slow the rate of decline in memory and cognition, but these treatments are not curative, and patients eventually suffer complete cognitive injury. With the substantial amounts of published data on targets for this disease, we proposed that machine learning software could be used to find novel small-molecule treatments that can supplement the AD drugs currently on the market. In order to do this, we used publicly available data in ChEMBL to build and validate Bayesian machine learning models for AD target proteins. The first AD target that we have addressed with this method is the serine-threonine kinase glycogen synthase kinase 3 beta (GSK3β), which is a proline-directed serine-threonine kinase that phosphorylates the microtubule-stabilizing protein tau. This phosphorylation prompts tau to dissociate from the microtubule and form insoluble oligomers called paired helical filaments, which are one of the components of the neurofibrillary tangles found in AD brains. Using our Bayesian machine learning model for GSK3β consisting of 2368 molecules, this model produced a five-fold cross validation ROC of 0.905. This model was also used for virtual screening of large libraries of FDA-approved drugs and clinical candidates. Subsequent testing of selected compounds revealed a selective small-molecule inhibitor, ruboxistaurin, with activity against GSK3β (avg IC50 = 97.3 nM) and GSK3α (IC50 = 695.9 nM). Several other structurally diverse inhibitors were also identified. We are now applying this machine learning approach to additional AD targets to identify approved drugs or clinical trial candidates that can be repurposed as AD therapeutics. This represents a viable approach to accelerate drug discovery and do so at a fraction of the cost of traditional high throughput screening.
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Affiliation(s)
- Patricia
A. Vignaux
- Collaborations Pharmaceuticals,
Inc., 840 Main Campus
Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Eni Minerali
- Collaborations Pharmaceuticals,
Inc., 840 Main Campus
Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Daniel H. Foil
- Collaborations Pharmaceuticals,
Inc., 840 Main Campus
Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Ana C. Puhl
- Collaborations Pharmaceuticals,
Inc., 840 Main Campus
Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Sean Ekins
- Collaborations Pharmaceuticals,
Inc., 840 Main Campus
Drive, Lab 3510, Raleigh, North Carolina 27606, United States
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Liu Z, Chen L, Yu P, Zhang Y, Fang B, Wu C, Luo W, Chen X, Li C, Liang G. Discovery of 3-(Indol-5-yl)-indazole Derivatives as Novel Myeloid Differentiation Protein 2/Toll-like Receptor 4 Antagonists for Treatment of Acute Lung Injury. J Med Chem 2019; 62:5453-5469. [DOI: 10.1021/acs.jmedchem.9b00316] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Zhiguo Liu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Lingfeng Chen
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, China
| | - Pengtian Yu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
- Department of Pharmacy, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310000, China
| | - Yali Zhang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Bo Fang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Chao Wu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Wu Luo
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Xianxin Chen
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Chenglong Li
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Guang Liang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, China
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7
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Saraswati AP, Ali Hussaini SM, Krishna NH, Babu BN, Kamal A. Glycogen synthase kinase-3 and its inhibitors: Potential target for various therapeutic conditions. Eur J Med Chem 2017; 144:843-858. [PMID: 29306837 DOI: 10.1016/j.ejmech.2017.11.103] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 11/29/2017] [Accepted: 11/30/2017] [Indexed: 11/16/2022]
Abstract
Glycogen Synthase Kinase-3 (GSK-3) is a serine/threonine kinase which is ubiquitously expressed and is regarded as a regulator for various cellular events and signalling pathways. It exists in two isoforms, GSK-3α and GSK-3β and can phosphorylate a wide range of substrates. Aberrancy in the GSK-3 activity can lead to various diseases like Alzheimer's, diabetes, cancer, neurodegeneration etc., rendering it an attractive target to develop potent and specific inhibitors. The present review focuses on the recent developments in the area of GSK-3 inhibitors and also enlightens its therapeutic applicability in various disease conditions.
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Affiliation(s)
- A Prasanth Saraswati
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, 500 037, India
| | - S M Ali Hussaini
- Medicinal Chemistry & Pharmacology, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, India
| | - Namballa Hari Krishna
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, 500 037, India; Medicinal Chemistry & Pharmacology, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, India
| | - Bathini Nagendra Babu
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, 500 037, India
| | - Ahmed Kamal
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, 500 037, India; Medicinal Chemistry & Pharmacology, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, India; School Pharmaceutical Education and Research (SPER), Jamia Hamdard, New Delhi 110062, India.
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8
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Research advances in kinase enzymes and inhibitors for cardiovascular disease treatment. Future Sci OA 2017; 3:FSO204. [PMID: 29134113 PMCID: PMC5674217 DOI: 10.4155/fsoa-2017-0010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 03/29/2017] [Indexed: 12/13/2022] Open
Abstract
The targeting of protein kinases has great future potential for the design of new drugs against cardiovascular diseases (CVDs). Enormous efforts have been made toward achieving this aim. Unfortunately, kinase inhibitors designed to treat CVDs have suffered from numerous limitations such as poor selectivity, bad permeability and toxicity. So, where are we now in terms of discovering effective kinase targeting drugs to treat CVDs? Various drug design techniques have been approached for this purpose since the discovery of the inhibitory activity of Staurosporine against protein kinase C in 1986. This review aims to provide context for the status of several emerging classes of direct kinase modulators to treat CVDs and discuss challenges that are preventing scientists from finding new kinase drugs to treat heart disease.
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9
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Patil SA, Patil SA, Patil R. Medicinal applications of (benz)imidazole- and indole-based macrocycles. Chem Biol Drug Des 2017; 89:639-649. [DOI: 10.1111/cbdd.12802] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 06/05/2016] [Accepted: 06/07/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Siddappa A. Patil
- Centre for Nano & Material Sciences; Jain University; Bangalore Karnataka India
| | - Shivaputra A. Patil
- Pharmaceutical Sciences Department; College of Pharmacy; Rosalind Franklin University of Medicine and Science; North Chicago IL USA
| | - Renukadevi Patil
- Pharmaceutical Sciences Department; College of Pharmacy; Rosalind Franklin University of Medicine and Science; North Chicago IL USA
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10
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Kandemir H, Sengul IF, Kumar N, Black DS. Synthesis of Imine and Amine-Linked Macrocycles Containing Tris-Indoles. Aust J Chem 2017. [DOI: 10.1071/ch17264] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The synthesis of 21-membered imine- and amine-linked tris-indole macrocycles starting from 7-nitroethylindoles is described. The 7-nitroethylindoles are converted to 2,2′-diindolylmethanes and the nitro groups reduced to amino. The resulting diamines undergo reactions with indole-2,7-dicarbaldehydes to form the macrocyclic imines, which can subsequently be reduced to the macrocyclic amines.
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11
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Pandey MK, DeGrado TR. Glycogen Synthase Kinase-3 (GSK-3)-Targeted Therapy and Imaging. Am J Cancer Res 2016; 6:571-93. [PMID: 26941849 PMCID: PMC4775866 DOI: 10.7150/thno.14334] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 01/27/2016] [Indexed: 12/11/2022] Open
Abstract
Glycogen synthase kinase-3 (GSK-3) is associated with various key biological processes, including glucose regulation, apoptosis, protein synthesis, cell signaling, cellular transport, gene transcription, proliferation, and intracellular communication. Accordingly, GSK-3 has been implicated in a wide variety of diseases and specifically targeted for both therapeutic and imaging applications by a large number of academic laboratories and pharmaceutical companies. Here, we review the structure, function, expression levels, and ligand-binding properties of GSK-3 and its connection to various diseases. A selected list of highly potent GSK-3 inhibitors, with IC50 <20 nM for adenosine triphosphate (ATP)-competitive inhibitors and IC50 <5 μM for non-ATP-competitive inhibitors, were analyzed for structure activity relationships. Furthermore, ubiquitous expression of GSK-3 and its possible impact on therapy and imaging are also highlighted. Finally, a rational perspective and possible route to selective and effective GSK-3 inhibitors is discussed.
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12
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Natarajan P, Priyadarshini V, Pradhan D, Manne M, Swargam S, Kanipakam H, Bhuma V, Amineni U. E-pharmacophore-based virtual screening to identify GSK-3β inhibitors. J Recept Signal Transduct Res 2015; 36:445-58. [PMID: 27305963 DOI: 10.3109/10799893.2015.1122043] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Glycogen synthase kinase-3β (GSK-3β) is a serine/threonine kinase which has attracted significant attention during recent years in drug design studies. The deregulation of GSK-3β increased the loss of hippocampal neurons by triggering apoptosis-mediating production of neurofibrillary tangles and alleviates memory deficits in Alzheimer's disease (AD). Given its role in the formation of neurofibrillary tangles leading to AD, it has been a major therapeutic target for intervention in AD, hence was targeted in the present study. Twenty crystal structures were refined to generate pharmacophore models based on energy involvement in binding co-crystal ligands. Four common e-pharmacophore models were optimized from the 20 pharmacophore models. Shape-based screening of four e-pharmacophore models against nine established small molecule databases using Phase v3.9 had resulted in 1800 compounds having similar pharmacophore features. Rigid receptor docking (RRD) was performed for 1800 compounds and 20 co-crystal ligands with GSK-3β to generate dock complexes. Interactions of the best scoring lead obtained through RRD were further studied with quantum polarized ligand docking (QPLD), induced fit docking (IFD) and molecular mechanics/generalized Born surface area. Comparing the obtained leads to 20 co-crystal ligands resulted in 18 leads among them, lead1 had the lowest docking score, lower binding free energy and better binding orientation toward GSK-3β. The 50 ns MD simulations run confirmed the stable nature of GSK-3β-lead1 docking complex. The results from RRD, QPLD, IFD and MD simulations confirmed that lead1 might be used as a potent antagonist for GSK-3β.
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Affiliation(s)
- Pradeep Natarajan
- a Bioinformatics Centre, Department of Bioinformatics, SVIMS University , Tirupati , India and
| | - Vani Priyadarshini
- a Bioinformatics Centre, Department of Bioinformatics, SVIMS University , Tirupati , India and
| | - Dibyabhaba Pradhan
- a Bioinformatics Centre, Department of Bioinformatics, SVIMS University , Tirupati , India and
| | - Munikumar Manne
- a Bioinformatics Centre, Department of Bioinformatics, SVIMS University , Tirupati , India and
| | - Sandeep Swargam
- a Bioinformatics Centre, Department of Bioinformatics, SVIMS University , Tirupati , India and
| | - Hema Kanipakam
- a Bioinformatics Centre, Department of Bioinformatics, SVIMS University , Tirupati , India and
| | - Vengamma Bhuma
- b Department of Neurology , SVIMS University , Tirupati , India
| | - Umamaheswari Amineni
- a Bioinformatics Centre, Department of Bioinformatics, SVIMS University , Tirupati , India and
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Quesada-Romero L, Mena-Ulecia K, Tiznado W, Caballero J. Insights into the interactions between maleimide derivates and GSK3β combining molecular docking and QSAR. PLoS One 2014; 9:e102212. [PMID: 25010341 PMCID: PMC4092126 DOI: 10.1371/journal.pone.0102212] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 06/16/2014] [Indexed: 11/25/2022] Open
Abstract
Many protein kinase (PK) inhibitors have been reported in recent years, but only a few have been approved for clinical use. The understanding of the available molecular information using computational tools is an alternative to contribute to this process. With this in mind, we studied the binding modes of 77 maleimide derivates inside the PK glycogen synthase kinase 3 beta (GSK3β) using docking experiments. We found that the orientations that these compounds adopt inside GSK3β binding site prioritize the formation of hydrogen bond (HB) interactions between the maleimide group and the residues at the hinge region (residues Val135 and Asp133), and adopt propeller-like conformations (where the maleimide is the propeller axis and the heterocyclic substituents are two slanted blades). In addition, quantitative structure–activity relationship (QSAR) models using CoMSIA methodology were constructed to explain the trend of the GSK3β inhibitory activities for the studied compounds. We found a model to explain the structure–activity relationship of non-cyclic maleimide (NCM) derivatives (54 compounds). The best CoMSIA model (training set included 44 compounds) included steric, hydrophobic, and HB donor fields and had a good Q2 value of 0.539. It also predicted adequately the most active compounds contained in the test set. Furthermore, the analysis of the plots of the steric CoMSIA field describes the elements involved in the differential potency of the inhibitors that can be considered for the selection of suitable inhibitors.
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Affiliation(s)
- Luisa Quesada-Romero
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, Talca, Chile
| | - Karel Mena-Ulecia
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Santiago de Chile, Chile
| | - William Tiznado
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Santiago de Chile, Chile
| | - Julio Caballero
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, Talca, Chile
- * E-mail:
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15
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Design, synthesis and evaluation of 7-azaindazolyl-indolyl-maleimides as glycogen synthase kinase-3β (GSK-3β) inhibitors. Eur J Med Chem 2013; 68:361-71. [PMID: 23994329 DOI: 10.1016/j.ejmech.2013.07.046] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 07/05/2013] [Accepted: 07/12/2013] [Indexed: 11/23/2022]
Abstract
A series of 7-azaindazolyl-indolyl-maleimides were designed, synthesized and evaluated for their GSK-3β inhibitory activity. Most compounds exhibited potent activity against GSK-3β. Among them, compounds 17a, 17b, 17g, 17i, 29a and 30 significantly reduced Aβ-induced Tau hyperphosphorylation, showin;g the inhibition of GSK-3β at the cell level. Preliminary structure-activity relationships were discussed based on the experimental data obtained.
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16
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Ye Q, Li M, Zhou Y, Pang T, Xu L, Cao J, Han L, Li Y, Wang W, Gao J, Li J. Synthesis and biological evaluation of 3-benzisoxazolyl-4-indolylmaleimides as potent, selective inhibitors of glycogen synthase kinase-3β. Molecules 2013; 18:5498-516. [PMID: 23669633 PMCID: PMC6270165 DOI: 10.3390/molecules18055498] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 05/02/2013] [Accepted: 05/07/2013] [Indexed: 01/01/2023] Open
Abstract
A series of novel 3-benzisoxazolyl-4-indolyl-maleimides were synthesized and evaluated for their GSK-3β inhibitory activity. Most compounds exhibited high inhibitory potency towards GSK-3β. Among them, compound 7j with an IC₅₀ value of 0.73 nM was the most promising GSK-3β inhibitor. Preliminary structure-activity relationships were examined and showed that different substituents on the indole ring and N¹-position of the indole ring had varying degrees of influence on the GSK-3β inhibitory potency. Compounds 7c, 7f, 7j-l and 7o-q could obviously reduce Aβ-induced Tau hyperphosphorylation by inhibiting GSK-3β in a cell-based functional assay.
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Affiliation(s)
- Qing Ye
- State Key Laboratory Breeding Base of Green Chemistry-Synthesis Technology, Zhejiang University of Technology, Hangzhou 310032, Zhejiang, China; E-Mails: (Q.Y.); (M.L.); (L.H.); (Y.L.)
| | - Meng Li
- State Key Laboratory Breeding Base of Green Chemistry-Synthesis Technology, Zhejiang University of Technology, Hangzhou 310032, Zhejiang, China; E-Mails: (Q.Y.); (M.L.); (L.H.); (Y.L.)
| | - Yubo Zhou
- The National Center for Drug Screening, Shanghai 201203, China; E-Mails: (Y.Z.); (T.P.); (L.X.); (J.C.)
| | - Tao Pang
- The National Center for Drug Screening, Shanghai 201203, China; E-Mails: (Y.Z.); (T.P.); (L.X.); (J.C.)
| | - Lei Xu
- The National Center for Drug Screening, Shanghai 201203, China; E-Mails: (Y.Z.); (T.P.); (L.X.); (J.C.)
| | - Jiayi Cao
- The National Center for Drug Screening, Shanghai 201203, China; E-Mails: (Y.Z.); (T.P.); (L.X.); (J.C.)
| | - Liang Han
- State Key Laboratory Breeding Base of Green Chemistry-Synthesis Technology, Zhejiang University of Technology, Hangzhou 310032, Zhejiang, China; E-Mails: (Q.Y.); (M.L.); (L.H.); (Y.L.)
| | - Yujin Li
- State Key Laboratory Breeding Base of Green Chemistry-Synthesis Technology, Zhejiang University of Technology, Hangzhou 310032, Zhejiang, China; E-Mails: (Q.Y.); (M.L.); (L.H.); (Y.L.)
| | - Weisi Wang
- ZJU-ENS Joint Laboratory of Medicinal Chemistry, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China, E-Mail:
| | - Jianrong Gao
- State Key Laboratory Breeding Base of Green Chemistry-Synthesis Technology, Zhejiang University of Technology, Hangzhou 310032, Zhejiang, China; E-Mails: (Q.Y.); (M.L.); (L.H.); (Y.L.)
| | - Jia Li
- The National Center for Drug Screening, Shanghai 201203, China; E-Mails: (Y.Z.); (T.P.); (L.X.); (J.C.)
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Ye Q, Li M, Zhou YB, Cao JY, Xu L, Li YJ, Han L, Gao JR, Hu YZ, Li J. Design, Synthesis, and Evaluation of 3-Aryl-4-pyrrolyl-maleimides as Glycogen Synthase Kinase-3β Inhibitors. Arch Pharm (Weinheim) 2013; 346:349-58. [DOI: 10.1002/ardp.201300008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 02/26/2013] [Accepted: 03/01/2013] [Indexed: 11/06/2022]
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Small-Molecule Inhibitors of GSK-3: Structural Insights and Their Application to Alzheimer's Disease Models. Int J Alzheimers Dis 2012; 2012:381029. [PMID: 22888461 PMCID: PMC3408674 DOI: 10.1155/2012/381029] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 01/31/2012] [Indexed: 11/17/2022] Open
Abstract
The world health organization (WHO) estimated that 18 million people are struck by Alzheimer's disease (AD). The USA, France, Germany, and other countries launched major programmes targeting the identification of risk factors, the improvement of caretaking, and fundamental research aiming to postpone the onset of AD. The glycogen synthase kinase 3 (GSK-3) is implicated in multiple cellular processes and has been linked to the pathogenesis of several diseases including diabetes mellitus, cancer, and AD. Inhibition of GSK-3 leads to neuroprotective effects, decreased β-amyloid production, and a reduction in tau hyperphosphorylation, which are all associated with AD. Various classes of small molecule GSK-3 inhibitors have been published in patents and original publications. Herein, we present a comprehensive summary of small molecules reported to interact with GSK-3. We illustrate the interactions of the inhibitors with the active site. Furthermore, we refer to the biological characterisation in terms of activity and selectivity for GSK-3, elucidate in vivo studies and pre-/clinical trials.
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Sobhia ME, Grewal BK, Bhat J, Rohit S, Punia V. Protein kinase C βII in diabetic complications: survey of structural, biological and computational studies. Expert Opin Ther Targets 2012; 16:325-44. [PMID: 22404224 DOI: 10.1517/14728222.2012.667804] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION PKC-βII is a conventional isoform of PKC. It is overexpressed in hyperglycemic conditions and is known to trigger various diabetic complications, mainly cardiovascular complications and to a certain extent nephropathy, neuropathy, retinopathy etc. Selective inhibition of this enzyme will be one of the favorable approaches to treat diabetes-mellitus-related complications. Due to high sequence similarities among PKC isoforms, selective inhibition of PKC-βII is difficult and yet to be achieved successfully. AREAS COVERED This review discusses the studies carried out in various aspects of PKC-βII. The biological aspects, crystal structure data, structure–activity relationship study (SAR) and in silico studies related to PKC-βII such as homology modeling, molecular docking, molecular dynamics, quantitative structure–activity relationship (QSAR) studies and pharmacophore modeling etc. are summarized. EXPERT OPINION PKC-βII is a potential target for treating diabetes-related complications. Selective inhibitors of this enzyme are under clinical trials but to date, success has not been achieved. Thus, extensive research is essential in this direction; the contribution of in silico tools in designing and optimizing selective inhibitors of PKC-βII is valuable.
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Affiliation(s)
- M Elizabeth Sobhia
- National Institute of Pharmaceutical Education and Research, Department of Pharmacoinformatics, Punjab, India.
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20
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Lee H, Hamilton JR. Physiology, pharmacology, and therapeutic potential of protease-activated receptors in vascular disease. Pharmacol Ther 2012; 134:246-59. [DOI: 10.1016/j.pharmthera.2012.01.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 01/17/2012] [Indexed: 01/09/2023]
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21
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Kumar H, Kumar R, Grewal BK, Sobhia ME. Insights into the Structural Requirements of PKCβII Inhibitors Based on HQSAR and CoMSIA Analyses. Chem Biol Drug Des 2011; 78:283-8. [DOI: 10.1111/j.1747-0285.2011.01144.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Li H, Hong Y, Nukui S, Lou J, Johnson S, Scales S, Botrous I, Tompkins E, Yin C, Zhou R, He M, Jensen J, Bouzida D, Alton G, Lafontaine J, Grant S. Identification of novel pyrrolopyrazoles as protein kinase C β II inhibitors. Bioorg Med Chem Lett 2011; 21:584-7. [DOI: 10.1016/j.bmcl.2010.10.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 10/05/2010] [Accepted: 10/06/2010] [Indexed: 10/19/2022]
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23
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2D and 3D QSAR analyses to predict favorable substitution sites in anilino-monoindolylmaleimides acting as PKCβII selective inhibitors. Med Chem Res 2010. [DOI: 10.1007/s00044-010-9439-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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24
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Ma XH, Wang R, Tan CY, Jiang YY, Lu T, Rao HB, Li XY, Go ML, Low BC, Chen YZ. Virtual screening of selective multitarget kinase inhibitors by combinatorial support vector machines. Mol Pharm 2010; 7:1545-60. [PMID: 20712327 DOI: 10.1021/mp100179t] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Multitarget agents have been increasingly explored for enhancing efficacy and reducing countertarget activities and toxicities. Efficient virtual screening (VS) tools for searching selective multitarget agents are desired. Combinatorial support vector machines (C-SVM) were tested as VS tools for searching dual-inhibitors of 11 combinations of 9 anticancer kinase targets (EGFR, VEGFR, PDGFR, Src, FGFR, Lck, CDK1, CDK2, GSK3). C-SVM trained on 233-1,316 non-dual-inhibitors correctly identified 26.8%-57.3% (majority >36%) of the 56-230 intra-kinase-group dual-inhibitors (equivalent to the 50-70% yields of two independent individual target VS tools), and 12.2% of the 41 inter-kinase-group dual-inhibitors. C-SVM were fairly selective in misidentifying as dual-inhibitors 3.7%-48.1% (majority <20%) of the 233-1,316 non-dual-inhibitors of the same kinase pairs and 0.98%-4.77% of the 3,971-5,180 inhibitors of other kinases. C-SVM produced low false-hit rates in misidentifying as dual-inhibitors 1,746-4,817 (0.013%-0.036%) of the 13.56 M PubChem compounds, 12-175 (0.007%-0.104%) of the 168 K MDDR compounds, and 0-84 (0.0%-2.9%) of the 19,495-38,483 MDDR compounds similar to the known dual-inhibitors. C-SVM was compared to other VS methods Surflex-Dock, DOCK Blaster, kNN and PNN against the same sets of kinase inhibitors and the full set or subset of the 1.02 M Zinc clean-leads data set. C-SVM produced comparable dual-inhibitor yields, slightly better false-hit rates for kinase inhibitors, and significantly lower false-hit rates for the Zinc clean-leads data set. Combinatorial SVM showed promising potential for searching selective multitarget agents against intra-kinase-group kinases without explicit knowledge of multitarget agents.
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Affiliation(s)
- X H Ma
- Bioinformatics and Drug Design Group, Department of Pharmacy, Centre for Computational Science and Engineering, National University of Singapore, Blk S16, Level 8, 3 Science Drive 2, Singapore 117543
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Prateeptongkum S, Driller KM, Jackstell R, Beller M. Iron-Catalyzed Carbonylation as a Key Step in the Short and Efficient Syntheses of Himanimide A and B. Chem Asian J 2010; 5:2173-6. [DOI: 10.1002/asia.201000384] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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26
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Prateeptongkum S, Driller K, Jackstell R, Spannenberg A, Beller M. Efficient Synthesis of Biologically Interesting 3,4-Diaryl-Substituted Succinimides and Maleimides: Application of Iron-Catalyzed Carbonylations. Chemistry 2010; 16:9606-15. [DOI: 10.1002/chem.201000369] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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Laronze-Cochard M, Cochard F, Daras E, Lansiaux A, Brassart B, Vanquelef E, Prost E, Nuzillard JM, Baldeyrou B, Goosens JF, Lozach O, Meijer L, Riou JF, Henon E, Sapi J. Synthesis and biological evaluation of new penta- and heptacyclic indolo- and quinolinocarbazole ring systems obtained via Pd0 catalysed reductive N-heteroannulation. Org Biomol Chem 2010; 8:4625-36. [DOI: 10.1039/c0ob00149j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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28
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Grant S, Tran P, Zhang Q, Zou A, Dinh D, Jensen J, Zhou S, Kang X, Zachwieja J, Lippincott J, Liu K, Johnson SL, Scales S, Yin C, Nukui S, Stoner C, Prasanna G, Lafontaine J, Wells P, Li H. Discovery of a novel class of targeted kinase inhibitors that blocks protein kinase C signaling and ameliorates retinal vascular leakage in a diabetic rat model. Eur J Pharmacol 2009; 627:16-25. [PMID: 19850035 DOI: 10.1016/j.ejphar.2009.10.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Revised: 09/18/2009] [Accepted: 10/06/2009] [Indexed: 01/21/2023]
Abstract
Protein kinase C (PKC) family members such as PKCbetaII may become activated in the hyperglycemic state associated with diabetes. Preclinical and clinical data implicate aberrant PKC activity in the development of diabetic microvasculature abnormalities. Based on this potential etiological role for PKC in diabetic complications, several therapeutic PKC inhibitors have been investigated in clinical trials for the treatment of diabetic patients. In this report, we present the discovery and preclinical evaluation of a novel class of 3-amino-pyrrolo[3,4-c]pyrazole derivatives as inhibitors of PKC that are structurally distinct from the prototypical indolocarbazole and bisindolylmaleimide PKC inhibitors. From this pyrrolo-pyrazole series, several compounds were identified from biochemical assays as potent, ATP-competitive inhibitors of PKC activity with high specificity for PKC over other protein kinases. These compounds were also found to block PKC signaling activity in multiple cellular functional assays. PF-04577806, a representative from this series, inhibited PKC activity in retinal lysates from diabetic rats stimulated with phorbol myristate acetate. When orally administered, PF-04577806 showed good exposure in the retina of diabetic Long-Evans rats and ameliorated retinal vascular leakage in a streptozotocin-induced diabetic rat model. These novel PKC inhibitors represent a promising new class of targeted protein kinase inhibitors with potential as therapeutic agents for the treatment of patients with diabetic microvascular complications.
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Affiliation(s)
- Stephan Grant
- Department of Biochemistry and Primary Screening, Pfizer Global Research & Development, Pfizer La Jolla Laboratories, San Diego, CA 92121, United States.
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Ye Q, Xu G, Lv D, Cheng Z, Li J, Hu Y. Synthesis and biological evaluation of novel 4-azaindolyl-indolyl-maleimides as glycogen synthase kinase-3beta (GSK-3beta) inhibitors. Bioorg Med Chem 2009; 17:4302-12. [PMID: 19481464 DOI: 10.1016/j.bmc.2009.05.031] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Revised: 05/08/2009] [Accepted: 05/12/2009] [Indexed: 10/20/2022]
Abstract
A series of novel 4-azaindolyl-indolyl-maleimides were synthesized and evaluated for their GSK-3beta inhibitory activity. Most compounds exhibited high potency to GSK-3beta. Among them, compound 7c was the most promising GSK-3beta inhibitor. Preliminary structure-activity relationships were discussed based on the experimental data obtained and showed that different substituents on the indole ring and side chains at 1-position of indole had varying degrees of influence on the GSK-3beta inhibitory potency. In a cell-based functional assay, compounds 7c and 15a significantly reduced Abeta-induced Tau hyperphosphorylation by inhibiting GSK-3beta.
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Affiliation(s)
- Qing Ye
- ZJU-ENS Joint Laboratory of Medicinal Chemistry, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
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30
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Rayasam GV, Tulasi VK, Sodhi R, Davis JA, Ray A. Glycogen synthase kinase 3: more than a namesake. Br J Pharmacol 2009; 156:885-98. [PMID: 19366350 DOI: 10.1111/j.1476-5381.2008.00085.x] [Citation(s) in RCA: 359] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Glycogen synthase kinase 3 (GSK3), a constitutively acting multi-functional serine threonine kinase is involved in diverse physiological pathways ranging from metabolism, cell cycle, gene expression, development and oncogenesis to neuroprotection. These diverse multiple functions attributed to GSK3 can be explained by variety of substrates like glycogen synthase, tau protein and beta catenin that are phosphorylated leading to their inactivation. GSK3 has been implicated in various diseases such as diabetes, inflammation, cancer, Alzheimer's and bipolar disorder. GSK3 negatively regulates insulin-mediated glycogen synthesis and glucose homeostasis, and increased expression and activity of GSK3 has been reported in type II diabetics and obese animal models. Consequently, inhibitors of GSK3 have been demonstrated to have anti-diabetic effects in vitro and in animal models. However, inhibition of GSK3 poses a challenge as achieving selectivity of an over achieving kinase involved in various pathways with multiple substrates may lead to side effects and toxicity. The primary concern is developing inhibitors of GSK3 that are anti-diabetic but do not lead to up-regulation of oncogenes. The focus of this review is the recent advances and the challenges surrounding GSK3 as an anti-diabetic therapeutic target.
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Affiliation(s)
- Geetha Vani Rayasam
- Department of Pharmacology, Research & Development (R&D III), Ranbaxy Research Labs, Gurgaon, Haryana, India.
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31
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Brennführer A, Neumann H, Pews-Davtyan A, Beller M. Catalytic and Stoichiometric Synthesis of Novel 3-Aminocarbonyl-, 3-Alkoxycarbonyl-, and 3-Amino-4-indolylmaleimides. European J Org Chem 2008. [DOI: 10.1002/ejoc.200800964] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Abstract
Bisindolylmaleimide derivatives were originally described as protein kinase C inhibitors. However, several studies have shown that bisindolylmaleimides target several other signaling molecules. The review presents bisindolylmaleimide-mediated PKC-dependent and PKC-independent biological effects, such as reversal of MDR and modulation of Wnt signaling through GSK-3b and b-catenin. Importantly, the potent proapoptotic properties of bisindolylmaleimides are also described. Bis-IX appears as the most efficient activator of intrinsic apoptotic pathway and additionally, facilitates extrinsic apoptosis. Presented molecular mechanisms indicate that bisindolylmaleimides could be useful agents in anticancer therapy. They repress uncontrolled proliferation and restore the sensitivity to chemotherapy which allows eradication of cancer cells.
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Dessalew N, Bharatam PV. 3D-QSAR and molecular docking study on bisarylmaleimide series as glycogen synthase kinase 3, cyclin dependent kinase 2 and cyclin dependent kinase 4 inhibitors: An insight into the criteria for selectivity. Eur J Med Chem 2007; 42:1014-27. [PMID: 17335939 DOI: 10.1016/j.ejmech.2007.01.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2006] [Revised: 12/28/2006] [Accepted: 01/09/2007] [Indexed: 11/16/2022]
Abstract
Selective glycogen synthase kinase 3 (GSK3) inhibition over cyclin dependent kinases such as cyclin dependent kinase 2 (CDK2) and cyclin dependent kinase 4 (CDK4) is an important requirement for improved therapeutic profile of GSK3 inhibitors. The concepts of selectivity and additivity fields have been employed in developing selective CoMFA models for these related kinases. Initially, sets of three individual CoMFA models were developed, using 36 compounds of bisarylmaleimide series to correlate with the GSK3, CDK2 and CDK4 inhibitory potencies. These models showed a satisfactory statistical significance: CoMFA-GSK3 (r(2)(con), r(2)(cv): 0.931, 0.519), CoMFA-CDK2 (0.937, 0.563), and CoMFA-CDK4 (0.892, 0.725). Three different selective CoMFA models were then developed using differences in pIC(50) values. These three models showed a superior statistical significance: (i) CoMFA-Selective1 (r(2)(con), r(2)(cv): 0.969, 0.768), (ii) CoMFA-Selective 2 (0.974, 0.835) and (iii) CoMFA-Selective3 (0.963, 0.776). The selective models were found to outperform the individual models in terms of the quality of correlation and were found to be more informative in pinpointing the structural basis for the observed quantitative differences of kinase inhibition. An in-depth comparative investigation was carried out between the individual and selective models to gain an insight into the selectivity criterion. To further validate this approach, a set of new compounds were designed which show selectivity and were docked into the active site of GSK3, using FlexX based incremental construction algorithm.
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Affiliation(s)
- Nigus Dessalew
- Department of Pharmaceutical Chemistry, School of Pharmacy, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia.
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Dessalew N, Bharatam PV. Identification of potential glycogen kinase-3 inhibitors by structure based virtual screening. Biophys Chem 2007; 128:165-75. [PMID: 17482749 DOI: 10.1016/j.bpc.2007.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2007] [Revised: 04/01/2007] [Accepted: 04/05/2007] [Indexed: 11/28/2022]
Abstract
Glycogen synthase kinase-3 (GSK3) is a serine/threonine kinase that has attracted much drug discovery attention in recent years. Structural crystallography of the kinase has produced several high resolution inhibitor-GSK3 complexes and this is offering valuable information about the important pharmacophoric features present in the inhibitor, the protein target and the bioactive conformation. The availability of several GSK3-inhibitor co-crystals was successfully exploited to derive a pharmacophore query which retains the all important inhibitor-GSK3 interaction chemistry. A hypothesis containing three features: two hydrogen bond donors and one hydrogen acceptor was found to explain much of the inhibitor-GSK3 interaction. Subsequently, the query has been submitted to three databases for electronic screening. The hits obtained were docked into glycogen synthase kinase-3beta active site. A total of 21 novel potential leads were proposed after thorough examination by a combination of methods: (i) visual examination of how well they dock into the glycogen synthase kinase-3beta binding site, (ii) detailed analysis of their FlexX, G_Score, PMF_Score, ChemScore and D_Score values, (iii) comparative investigation of the docking scores of the hits with that of the thus far reported inhibitors (iv) determination of the binding mode and examination of how the hits retain interactions with the important amino acid residues of the kinase binding site. The hydrophobic heterocycles identified in this investigation are expected to be important additions to the armamentarium of GSK3 hyperactivity antagonism. Further more, the present work may further our current knowledge of the molecular basis of activation, inhibition and regulation of this pharmaceutically important kinase.
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Affiliation(s)
- Nigus Dessalew
- Department of Pharmaceutical Chemistry, School of Pharmacy, Addis Ababa University, Addis Ababa, Ethiopia.
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35
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Zhang HC, Boñaga LVR, Ye H, Derian CK, Damiano BP, Maryanoff BE. Novel bis(indolyl)maleimide pyridinophanes that are potent, selective inhibitors of glycogen synthase kinase-3. Bioorg Med Chem Lett 2007; 17:2863-8. [PMID: 17350261 DOI: 10.1016/j.bmcl.2007.02.059] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2007] [Revised: 02/21/2007] [Accepted: 02/21/2007] [Indexed: 10/23/2022]
Abstract
Novel bis(indolyl)maleimide pyridinophanes 3, 9a, 9b, 10a, 10b, and 11 were prepared by cobalt-mediated [2+2+2] cycloaddition of an appropriate alpha,omega-diyne with an N,N-dialkylcyanamide. These macrocyclic heterophanes were found to be potent, selective inhibitors of glycogen synthase kinase-3beta. An X-ray structure of a co-crystal of GSK-3beta and 3 (IC(50)=3nM) depicts the hydrogen bonding and hydrophobic interactions in the ATP-binding pocket of this serine/threonine protein kinase.
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Affiliation(s)
- Han-Cheng Zhang
- Vascular Research Team, Johnson & Johnson Pharmaceutical Research & Development, Spring House, PA 19477-0776, USA.
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36
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Dessalew N, Bharatam PV. Investigation of Potential Glycogen Synthase Kinase 3 Inhibitors Using Pharmacophore Mapping and Virtual Screening. Chem Biol Drug Des 2006; 68:154-65. [PMID: 17062013 DOI: 10.1111/j.1747-0285.2006.00430.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glycogen synthase kinase-3 is a serine/threonine kinase that has attracted significant drug discovery attention in recent years. To investigate the identification of new potential glycogen synthase kinase-3 inhibitors, a pharmacophore mapping study was carried out using a set of 21 structurally diverse glycogen synthase kinase-3 inhibitors. A hypothesis containing four features: two hydrophobic, one hydrogen bond donor and another hydrogen bond acceptor was found to be the best from the 10 common feature hypotheses produced by HipHop module of Catalyst. The best hypothesis has a high cost of 156.592 and higher best fit values were obtained for the 21 inhibitors using this best hypothesis than the other HipHop hypotheses. The best hypothesis was then used to screen electronically the NCI2000 database. The hits obtained were docked into glycogen synthase kinase-3beta active site. A total of five novel potential leads were proposed after: (i) visual examination of how well they dock into the glycogen synthase kinase-3beta-binding site, (ii) comparative analysis of their FlexX, G-Score, PMF-Score, ChemScore and D-Scores values, (iii) comparison of their best fit value with the known inhibitors and (iv) examination of the how the hits retain interactions with the important amino acid residues of glycogen synthase kinase-3beta-binding site.
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Affiliation(s)
- Nigus Dessalew
- Department of Pharmaceutical Chemistry, School of Pharmacy, Addis Ababa University, PO Box 1176, Addis Ababa, Ethiopia.
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Tanaka M, Sagawa S, Hoshi JI, Shimoma F, Yasue K, Ubukata M, Ikemoto T, Hase Y, Takahashi M, Sasase T, Ueda N, Matsushita M, Inaba T. Synthesis, SAR studies, and pharmacological evaluation of 3-anilino-4-(3-indolyl) maleimides with conformationally restricted structure as orally bioavailable PKCbeta-selective inhibitors. Bioorg Med Chem 2006; 14:5781-94. [PMID: 16762554 DOI: 10.1016/j.bmc.2006.05.033] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2006] [Revised: 05/15/2006] [Accepted: 05/16/2006] [Indexed: 11/22/2022]
Abstract
Conformationally restricted 3-anilino-4-(3-indolyl)maleimide derivatives were designed and synthesized aiming at discovery of novel protein kinase Cbeta (PKCbeta)-selective inhibitors possessing oral bioavailability. Among them, compounds having a fused five-membered ring at the indole 1,2-position inhibited PKCbeta2 with IC50 of nM-order and showed good oral bioavailability. One of the most potent compounds was found to be PKCbeta-selective over other 6 isozymes and exhibited ameliorative effects in a rat diabetic retinopathy model via oral route.
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Affiliation(s)
- Masahiro Tanaka
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., Takatsuki Osaka 569-1125, Japan
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Kypta RM. GSK-3 inhibitors and their potential in the treatment of Alzheimer’s disease. Expert Opin Ther Pat 2005. [DOI: 10.1517/13543776.15.10.1315] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Engler TA, Malhotra S, Burkholder TP, Henry JR, Mendel D, Porter WJ, Furness K, Diefenbacher C, Marquart A, Reel JK, Li Y, Clayton J, Cunningham B, McLean J, O'toole JC, Brozinick J, Hawkins E, Misener E, Briere D, Brier RA, Wagner JR, Campbell RM, Anderson BD, Vaughn R, Bennett DB, Meier TI, Cook JA. The development of potent and selective bisarylmaleimide GSK3 inhibitors. Bioorg Med Chem Lett 2005; 15:899-903. [PMID: 15686883 DOI: 10.1016/j.bmcl.2004.12.063] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2004] [Revised: 12/18/2004] [Accepted: 12/21/2004] [Indexed: 01/13/2023]
Abstract
Many 3-aryl-4-(1,2,3,4-tetrahydro[1,4]diazepino[6,7,1-hi]indol-7-yl)maleimides exhibit potent GSK3 inhibitory activity (<100 nM IC(50)), although few show significant selectivity (>100x) versus CDK2, CDK4, or PKCbetaII. However, combining 3-(imidazo[1,2-a]pyridin-3-yl), 3-(pyrazolo[1,5-a]pyridin-3-yl) or aza-analogs with a 4-(2-acyl-(1,2,3,4-tetrahydro[1,4]diazepino[6,7,1-hi]indol-7-yl)) group on the maleimide resulted in very potent inhibitors of GSK3 (</=5 nM) with >160 to >10,000-fold selectivity versus CDK2/4 and PKCbetaII. These compounds also inhibited tau phosphorylation in cells and were effective in lowering plasma glucose in a rat model of type 2 diabetes (ZDF rat).
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Affiliation(s)
- Thomas A Engler
- Lilly Research Laboratories, A Division of Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA.
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40
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Tanaka M, Sagawa S, Hoshi JI, Shimoma F, Matsuda I, Sakoda K, Sasase T, Shindo M, Inaba T. Synthesis of anilino-monoindolylmaleimides as potent and selective PKCbeta inhibitors. Bioorg Med Chem Lett 2005; 14:5171-4. [PMID: 15380221 DOI: 10.1016/j.bmcl.2004.07.061] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2004] [Revised: 07/26/2004] [Accepted: 07/26/2004] [Indexed: 10/26/2022]
Abstract
We report herein synthesis of PKCbeta-selective inhibitors possessing the novel pharmacophore of anilino-monoindolylmaleimide. Several compounds of this series exhibited IC50's as low as 50 nM against human PKCbeta2. One of the most potent compounds, 6l, inhibited PKCbeta1 and PKCbeta2 with IC50 of 21 and 5 nM, respectively, and exhibited selectivity of more than 60-fold in favor of PKCbeta2 relative to other PKC isozymes (PKCalpha, PKCgamma, and PKCepsilon).
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Affiliation(s)
- Masahiro Tanaka
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
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41
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Laronze M, Boisbrun M, Léonce S, Pfeiffer B, Renard P, Lozach O, Meijer L, Lansiaux A, Bailly C, Sapi J, Laronze JY. Synthesis and anticancer activity of new pyrrolocarbazoles and pyrrolo-β-carbolines. Bioorg Med Chem 2005; 13:2263-83. [PMID: 15830466 DOI: 10.1016/j.bmc.2004.12.045] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
'Bended' 1, 3 or 'linear' 2 pyrrolidino-fused (aza)carbazoles were prepared and screened towards a few cancer-related targets. Whereas 'bended' derivatives 1 and 3 proved to be weakly toxic, several members of the 'linear' family strongly interact with DNA, especially derivative 28a.
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Affiliation(s)
- M Laronze
- CNRS FRE 2715 'Isolement, Structure, Transformations et Synthèse de Produits Naturels', IFR 53, Faculté de Pharmacie, 51 Rue Cognacq Jay, 51096 Reims cedex, France.
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42
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O'Neill DJ, Shen L, Prouty C, Conway BR, Westover L, Xu JZ, Zhang HC, Maryanoff BE, Murray WV, Demarest KT, Kuo GH. Design, synthesis, and biological evaluation of novel 7-azaindolyl-heteroaryl-maleimides as potent and selective glycogen synthase kinase-3beta (GSK-3beta) inhibitors. Bioorg Med Chem 2005; 12:3167-85. [PMID: 15158785 DOI: 10.1016/j.bmc.2004.04.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2004] [Accepted: 04/06/2004] [Indexed: 01/31/2023]
Abstract
Two approaches were developed to synthesize the novel 7-azaindolyl-heteroarylmaleimides. The first approach was based upon the palladium-catalyzed Suzuki cross-coupling or Stille cross-coupling of 2-chloro-maleimide 5 with various arylboronic acids or arylstannanes. The second approach was based upon the condensation of ethyl 7-azaindolyl-3-glyoxylate 12 with various acetamides. The hydroxypropyl-substituted 7-azaindolylmaleimide template was first used to screen different heteroaryls attached to the maleimide. Replacement of hydroxypropyl with different chain lengths and different functional groups were studied next. Many compounds synthesized were demonstrated to have high potency at GSK-3beta, good GS activity in HEK293 cells and good to excellent metabolic stability in human liver microsomes. Three representative compounds (21, 33, and 34) were demonstrated to have good selectivity against a panel of 80 kinase assays. Among them, compound 33 exhibited very weak inhibitions at the other 79 kinase assays, and behaved as a highly selective GSK-3beta inhibitor.
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Affiliation(s)
- David J O'Neill
- Drug Discovery Division, Johnson and Johnson Pharmaceutical Research and Development, L.L.C., Raritan, NJ 08869-0602, USA
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43
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Shen L, Prouty C, Conway BR, Westover L, Xu JZ, Look RA, Chen X, Beavers MP, Roberts J, Murray WV, Demarest KT, Kuo GH. Synthesis and biological evaluation of novel macrocyclic bis-7-azaindolylmaleimides as potent and highly selective glycogen synthase kinase-3 beta (GSK-3 beta) inhibitors. Bioorg Med Chem 2004; 12:1239-55. [PMID: 14980636 DOI: 10.1016/j.bmc.2003.09.047] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2003] [Accepted: 09/11/2003] [Indexed: 10/26/2022]
Abstract
Palladium catalyzed cross-coupling reactions were used to synthesize two key intermediates 3 and 5 that resulted in the synthesis of novel series of macrocyclic bis-7-azaindolylmaleimides. Among the three series of macrocycles, the oxygen atom and thiophene containing linkers yielded molecules with higher inhibitory potency at GSK-3 beta (K(i)=0.011-0.079 microM) while the nitrogen atom containing linkers yielded molecules with lower potency (K(i)=0.150->1 microM). Compound 33 and 36 displayed 1-2 orders of magnitude selectivity at GSK-3 beta against CDK2, PKC beta II, Rsk3 and little or no inhibitions to the other 62 protein kinases. Compound 46 was at least 100-fold more selective towards GSK-3 beta than PKC beta II, and it had little or no activity against a panel of 65 protein kinases, almost behaved as a GSK-3 beta 'specific inhibitor'. All three compounds showed good potency in GS assay. Molecular docking studies were conducted in an attempt to rationalize the GSK-3 beta selectivity of azaindolylmaleimides. The high selectivity, inhibitory potency and cellular activities of these non-crown-ether typed molecules may provide them as a valuable pharmacological tools in elucidating the complex roles of GSK-3 beta in cell signaling pathways and the potential usage for the treatment of elevated level of GSK-3 beta involved diseases.
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Affiliation(s)
- Lan Shen
- Drug Discovery Division, Johnson and Johnson Pharmaceutical Research and Development, L.L.C., 1000 Route 202, PO Box 300, Raritan, NJ 08869, USA
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44
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Engler TA, Henry JR, Malhotra S, Cunningham B, Furness K, Brozinick J, Burkholder TP, Clay MP, Clayton J, Diefenbacher C, Hawkins E, Iversen PW, Li Y, Lindstrom TD, Marquart AL, McLean J, Mendel D, Misener E, Briere D, O'Toole JC, Porter WJ, Queener S, Reel JK, Owens RA, Brier RA, Eessalu TE, Wagner JR, Campbell RM, Vaughn R. Substituted 3-imidazo[1,2-a]pyridin-3-yl- 4-(1,2,3,4-tetrahydro-[1,4]diazepino-[6,7,1-hi]indol-7-yl)pyrrole-2,5-diones as highly selective and potent inhibitors of glycogen synthase kinase-3. J Med Chem 2004; 47:3934-7. [PMID: 15267232 DOI: 10.1021/jm049768a] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Glycogen synthase kinase-3 (GSK3) is involved in signaling from the insulin receptor. Inhibitors of GSK3 are expected to effect lowering of plasma glucose similar to insulin, making GSK3 an attractive target for the treatment of type 2 diabetes. Herein we report the discovery of a series of potent and selective GSK3 inhibitors. Compounds 7-12 show oral activity in an in vivo model of type II diabetes, and 9 and 12 have desirable PK properties.
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Affiliation(s)
- Thomas A Engler
- Lilly Research Laboratories, A Division of Eli Lilly & Company, Lilly Corporate Center, Indianapolis, Indiana 46285, USA.
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45
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Abstract
Increasingly, it is being recognised that a balanced modulation of several targets can provide a superior therapeutic effect and side effect profile compared to the action of a selective ligand. Rational approaches in which structural features from selective ligands are combined have produced designed multiple ligands that span a wide variety of targets and target classes. A key challenge in the design of multiple ligands is attaining a balanced activity at each target of interest while simultaneously achieving a wider selectivity and a suitable pharmacokinetic profile. An analysis of literature examples reveals trends and insights that might help medicinal chemists discover the next generation of these types of compounds.
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Affiliation(s)
- Richard Morphy
- Medicinal Chemistry Department, Organon Laboratories, Newhouse, Lanarkshire ML1 5SH, UK.
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46
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Zhang HC, Ye H, Conway BR, Derian CK, Addo MF, Kuo GH, Hecker LR, Croll DR, Li J, Westover L, Xu JZ, Look R, Demarest KT, Andrade-Gordon P, Damiano BP, Maryanoff BE. 3-(7-Azaindolyl)-4-arylmaleimides as potent, selective inhibitors of glycogen synthase kinase-3. Bioorg Med Chem Lett 2004; 14:3245-50. [PMID: 15149684 DOI: 10.1016/j.bmcl.2004.03.090] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2004] [Revised: 03/26/2004] [Accepted: 03/29/2004] [Indexed: 11/23/2022]
Abstract
A novel series of acyclic 3-(7-azaindolyl)-4-(aryl/heteroaryl)maleimides was synthesized and evaluated for activity against GSK-3beta and selectivity versus PKC-betaII, as well as a broad panel of protein kinases. Compounds 14 and 17c potently inhibited GSK-3beta (IC(50)=7 and 26 nM, respectively) and exhibited excellent selectivity over PKC-betaII (325 and >385-fold, respectively). Compound 17c was also highly selective against 68 other protein kinases. In a cell-based functional assay, both 14 and 17c effectively increased glycogen synthase activity by inhibiting GSK-3beta.
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Affiliation(s)
- Han-Cheng Zhang
- Drug Discovery, Johnson & Johnson Pharmaceutical Research & Development, Spring House, PA 19477-0776, USA.
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