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Sharma V, Chander Sharma P, Reang J, Yadav V, Kumar Tonk R, Majeed J, Sharma K. Impact of GSK-3β and CK-1δ on Wnt signaling pathway in alzheimer disease: A dual target approach. Bioorg Chem 2024; 147:107378. [PMID: 38643562 DOI: 10.1016/j.bioorg.2024.107378] [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: 12/02/2023] [Revised: 04/02/2024] [Accepted: 04/14/2024] [Indexed: 04/23/2024]
Abstract
Alzheimer's disease (AD) is an enigmatic neurological illness that offers few treatment options. Recent exploration has highlighted the crucial connection of the Wnt signaling pathway in AD pathogenesis, shedding light on potential therapeutic targets. The present study focuses on the dual targeting of glycogen synthase kinase-3β (GSK-3β) and casein kinase-1δ (CK-1δ) within the framework of the Wnt signaling pathway as a possible technique for AD intervention. GSK-3β and CK-1δ are multifunctional kinases known for their roles in tau hyperphosphorylation, amyloid processing, and synaptic dysfunction, all of which are major hallmarks of Alzheimer's disease. They are intricately linked to Wnt signaling, which plays a pivotal part in sustaining neuronal function and synaptic plasticity. Dysregulation of the Wnt pathway in AD contributes to cognitive decline and neurodegeneration. This review delves into the molecular mechanisms by which GSK-3β and CK-1δ impact the Wnt signaling pathway, elucidating their roles in AD pathogenesis. We discuss the potential of small-molecule inhibitors along with their SAR studies along with the multi-targetd approach targeting GSK-3β and CK-1δ to modulate Wnt signaling and mitigate AD-related pathology. In summary, the dual targeting of GSK-3β and CK-1δ within the framework of the Wnt signaling pathway presents an innovative and promising avenue for future AD therapies, offering new hope for patients and caregivers in the quest to combat this challenging condition.
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Affiliation(s)
- Vinita Sharma
- Department of Pharmaceutical Chemistry, SPS, DPSRU, New Delhi, 110017, India
| | | | - Jurnal Reang
- Department of Pharmaceutical Chemistry, SPS, DPSRU, New Delhi, 110017, India
| | - Vivek Yadav
- Department of Pharmaceutical Chemistry, SPS, DPSRU, New Delhi, 110017, India
| | - Rajiv Kumar Tonk
- Department of Pharmaceutical Chemistry, SPS, DPSRU, New Delhi, 110017, India
| | - Jaseela Majeed
- School of Allied Health Sciences and Management, Delhi Pharmaceutical Sciences and Research University, New Delhi, 110017, India.
| | - Kalicharan Sharma
- Department of Pharmaceutical Chemistry, SPS, DPSRU, New Delhi, 110017, India; Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, Punjab, 142001, India.
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Gupta MK, Gouda G, Sultana S, Punekar SM, Vadde R, Ravikiran T. Structure-related relationship: Plant-derived antidiabetic compounds. STUDIES IN NATURAL PRODUCTS CHEMISTRY 2023:241-295. [DOI: 10.1016/b978-0-323-91294-5.00008-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
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Xu X, Zhang Y. Regulation of Oxidative Stress by Long Non-coding RNAs in Central Nervous System Disorders. Front Mol Neurosci 2022; 15:931704. [PMID: 35782387 PMCID: PMC9241987 DOI: 10.3389/fnmol.2022.931704] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
Central nervous system (CNS) disorders, such as ischemic stroke, Alzheimer’s disease, Parkinson’s disease, spinal cord injury, glioma, and epilepsy, involve oxidative stress and neuronal apoptosis, often leading to long-term disability or death. Emerging studies suggest that oxidative stress may induce epigenetic modifications that contribute to CNS disorders. Non-coding RNAs are epigenetic regulators involved in CNS disorders and have attracted extensive attention. Long non-coding RNAs (lncRNAs) are non-coding RNAs more than 200 nucleotides long and have no protein-coding function. However, these molecules exert regulatory functions at the transcriptional, post-transcriptional, and epigenetic levels. However, the major role of lncRNAs in the pathophysiology of CNS disorders, especially related to oxidative stress, remains unclear. Here, we review the molecular functions of lncRNAs in oxidative stress and highlight lncRNAs that exert positive or negative roles in oxidation/antioxidant systems. This review provides novel insights into the therapeutic potential of lncRNAs that mediate oxidative stress in CNS disorders.
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Affiliation(s)
- Xiaoman Xu
- Department of Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yi Zhang
- Department of Gerontology and Geriatrics, Shengjing Hospital of China Medical University, Shenyang, China
- *Correspondence: Yi Zhang,
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Mouchlis VD, Melagraki G, Zacharia LC, Afantitis A. Computer-Aided Drug Design of β-Secretase, γ-Secretase and Anti-Tau Inhibitors for the Discovery of Novel Alzheimer's Therapeutics. Int J Mol Sci 2020; 21:E703. [PMID: 31973122 PMCID: PMC7038192 DOI: 10.3390/ijms21030703] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 12/14/2022] Open
Abstract
Aging-associated neurodegenerative diseases, which are characterized by progressive neuronal death and synapses loss in human brain, are rapidly growing affecting millions of people globally. Alzheimer's is the most common neurodegenerative disease and it can be caused by genetic and environmental risk factors. This review describes the amyloid-β and Tau hypotheses leading to amyloid plaques and neurofibrillary tangles, respectively which are the predominant pathways for the development of anti-Alzheimer's small molecule inhibitors. The function and structure of the druggable targets of these two pathways including β-secretase, γ-secretase, and Tau are discussed in this review article. Computer-Aided Drug Design including computational structure-based design and ligand-based design have been employed successfully to develop inhibitors for biomolecular targets involved in Alzheimer's. The application of computational molecular modeling for the discovery of small molecule inhibitors and modulators for β-secretase and γ-secretase is summarized. Examples of computational approaches employed for the development of anti-amyloid aggregation and anti-Tau phosphorylation, proteolysis and aggregation inhibitors are also reported.
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Affiliation(s)
| | - Georgia Melagraki
- Division of Physical Sciences & Applications, Hellenic Military Academy, Vari 16672, Greece;
| | - Lefteris C. Zacharia
- Department of Life and Health Sciences, University of Nicosia, Nicosia 1700, Cyprus;
| | - Antreas Afantitis
- Department of ChemoInformatics, NovaMechanics Ltd., Nicosia 1046, Cyprus
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Insights into the EGFR SAR of N-phenylquinazolin-4-amine-derivatives using quantum mechanical pairwise-interaction energies. J Comput Aided Mol Des 2019; 33:745-757. [PMID: 31494804 DOI: 10.1007/s10822-019-00221-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 08/21/2019] [Indexed: 10/26/2022]
Abstract
Protein kinases are an important class of enzymes that play an essential role in virtually all major disease areas. In addition, they account for approximately 50% of the current targets pursued in drug discovery research. In this work, we explore the generation of structure-based quantum mechanical (QM) quantitative structure-activity relationship models (QSAR) as a means to facilitate structure-guided optimization of protein kinase inhibitors. We explore whether more accurate, interpretable QSAR models can be generated for a series of 76 N-phenylquinazolin-4-amine inhibitors of epidermal growth factor receptor (EGFR) kinase by comparing and contrasting them to other standard QSAR methodologies. The QM-based method involved molecular docking of inhibitors followed by their QM optimization within a ~ 300 atom cluster model of the EGFR active site at the M062X/6-31G(d,p) level. Pairwise computations of the interaction energies with each active site residue were performed. QSAR models were generated by splitting the datasets 75:25 into a training and test set followed by modelling using partial least squares (PLS). Additional QSAR models were generated using alignment dependent CoMFA and CoMSIA methods as well as alignment independent physicochemical, e-state indices and fingerprint descriptors. The structure-based QM-QSAR model displayed good performance on the training and test sets (r2 ~ 0.7) and was demonstrably more predictive than the QSAR models built using other methods. The descriptor coefficients from the QM-QSAR models allowed for a detailed rationalization of the active site SAR, which has implications for subsequent design iterations.
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Sciú ML, Sebastián-Pérez V, Martinez-Gonzalez L, Benitez R, Perez DI, Pérez C, Campillo NE, Martinez A, Moyano EL. Computer-aided molecular design of pyrazolotriazines targeting glycogen synthase kinase 3. J Enzyme Inhib Med Chem 2018; 34:87-96. [PMID: 30362380 PMCID: PMC6211276 DOI: 10.1080/14756366.2018.1530223] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Numerous studies have highlighted the implications of the glycogen synthase kinase 3 (GSK-3) in several processes associated with Alzheimer's disease (AD). Therefore, GSK-3 has become a crucial therapeutic target for the treatment of this neurodegenerative disorder. Hereby, we report the design and multistep synthesis of ethyl 4-oxo-pyrazolo[4,3-d][1-3]triazine-7-carboxylates and their biological evaluation as GSK-3 inhibitors. Molecular modelling studies allow us to develop this new scaffold optimising the chemical structure. Potential binding mode determination in the enzyme and the analysis of the key features in the catalytic site are also described. Furthermore, the ability of pyrazolotriazinones to cross the blood-brain barrier (BBB) was evaluated by passive diffusion and those who showed great GSK-3 inhibition and permeation to the central nervous system (CNS) showed neuroprotective properties against tau hyperphosphorylation in a cell-based model. These new brain permeable pyrazolotriazinones may be used for key in vivo studies and may be considered as new leads for further optimisation for the treatment of AD.
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Affiliation(s)
- M Lourdes Sciú
- a Department of Chemical and Physical Biology , Centro de Investigaciones Biológicas (CIB, CSIC) Ramiro de Maeztu , Madrid , Spain.,b INFIQC- Department of Organic Chemistry, School of Chemical Sciences , National University of Córdoba , Córdoba , Argentine
| | - Victor Sebastián-Pérez
- a Department of Chemical and Physical Biology , Centro de Investigaciones Biológicas (CIB, CSIC) Ramiro de Maeztu , Madrid , Spain
| | - Loreto Martinez-Gonzalez
- a Department of Chemical and Physical Biology , Centro de Investigaciones Biológicas (CIB, CSIC) Ramiro de Maeztu , Madrid , Spain
| | - Rocio Benitez
- a Department of Chemical and Physical Biology , Centro de Investigaciones Biológicas (CIB, CSIC) Ramiro de Maeztu , Madrid , Spain
| | - Daniel I Perez
- a Department of Chemical and Physical Biology , Centro de Investigaciones Biológicas (CIB, CSIC) Ramiro de Maeztu , Madrid , Spain
| | | | - Nuria E Campillo
- a Department of Chemical and Physical Biology , Centro de Investigaciones Biológicas (CIB, CSIC) Ramiro de Maeztu , Madrid , Spain
| | - Ana Martinez
- a Department of Chemical and Physical Biology , Centro de Investigaciones Biológicas (CIB, CSIC) Ramiro de Maeztu , Madrid , Spain
| | - E Laura Moyano
- b INFIQC- Department of Organic Chemistry, School of Chemical Sciences , National University of Córdoba , Córdoba , Argentine
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Makhouri FR, Ghasemi JB. In Silico Studies in Drug Research Against Neurodegenerative Diseases. Curr Neuropharmacol 2018; 16:664-725. [PMID: 28831921 PMCID: PMC6080098 DOI: 10.2174/1570159x15666170823095628] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 07/24/2017] [Accepted: 08/16/2017] [Indexed: 01/14/2023] Open
Abstract
Background Neurodegenerative diseases such as Alzheimer's disease (AD), amyotrophic lateral sclerosis, Parkinson's disease (PD), spinal cerebellar ataxias, and spinal and bulbar muscular atrophy are described by slow and selective degeneration of neurons and axons in the central nervous system (CNS) and constitute one of the major challenges of modern medicine. Computer-aided or in silico drug design methods have matured into powerful tools for reducing the number of ligands that should be screened in experimental assays. Methods In the present review, the authors provide a basic background about neurodegenerative diseases and in silico techniques in the drug research. Furthermore, they review the various in silico studies reported against various targets in neurodegenerative diseases, including homology modeling, molecular docking, virtual high-throughput screening, quantitative structure activity relationship (QSAR), hologram quantitative structure activity relationship (HQSAR), 3D pharmacophore mapping, proteochemometrics modeling (PCM), fingerprints, fragment-based drug discovery, Monte Carlo simulation, molecular dynamic (MD) simulation, quantum-mechanical methods for drug design, support vector machines, and machine learning approaches. Results Detailed analysis of the recently reported case studies revealed that the majority of them use a sequential combination of ligand and structure-based virtual screening techniques, with particular focus on pharmacophore models and the docking approach. Conclusion Neurodegenerative diseases have a multifactorial pathoetiological origin, so scientists have become persuaded that a multi-target therapeutic strategy aimed at the simultaneous targeting of multiple proteins (and therefore etiologies) involved in the development of a disease is recommended in future.
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Affiliation(s)
| | - Jahan B Ghasemi
- Chemistry Department, Faculty of Sciences, University of Tehran, Tehran, Iran
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López-Lira C, Alzate-Morales JH, Paulino M, Mella-Raipán J, Salas CO, Tapia RA, Soto-Delgado J. Combined molecular modelling and 3D-QSAR study for understanding the inhibition of NQO1 by heterocyclic quinone derivatives. Chem Biol Drug Des 2017. [PMID: 28643389 DOI: 10.1111/cbdd.13051] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A combination of three-dimensional quantitative structure-activity relationship (3D-QSAR), and molecular modelling methods were used to understand the potent inhibitory NAD(P)H:quinone oxidoreductase 1 (NQO1) activity of a set of 52 heterocyclic quinones. Molecular docking results indicated that some favourable interactions of key amino acid residues at the binding site of NQO1 with these quinones would be responsible for an improvement of the NQO1 activity of these compounds. The main interactions involved are hydrogen bond of the amino group of residue Tyr128, π-stacking interactions with Phe106 and Phe178, and electrostatic interactions with flavin adenine dinucleotide (FADH) cofactor. Three models were prepared by 3D-QSAR analysis. The models derived from Model I and Model III, shown leave-one-out cross-validation correlation coefficients (q2LOO ) of .75 and .73 as well as conventional correlation coefficients (R2 ) of .93 and .95, respectively. In addition, the external predictive abilities of these models were evaluated using a test set, producing the predicted correlation coefficients (r2pred ) of .76 and .74, respectively. The good concordance between the docking results and 3D-QSAR contour maps provides helpful information about a rational modification of new molecules based in quinone scaffold, in order to design more potent NQO1 inhibitors, which would exhibit highly potent antitumor activity.
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Affiliation(s)
- Claudia López-Lira
- Departamento de Química Orgánica, Facultad de Química, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jans H Alzate-Morales
- Facultad de Ingeniería, Centro de Bioinformática y Simulación Molecular, Universidad de Talca, Talca, Chile
| | - Margot Paulino
- Facultad de Química, Centro de Bioinformática Estructural-DETEMA, Universidad de la República, Montevideo, Uruguay
| | - Jaime Mella-Raipán
- Facultad de Ciencias, Instituto de Química y Bioquímica, Universidad de Valparaíso, Valparaíso, Casilla, Chile
| | - Cristian O Salas
- Departamento de Química Orgánica, Facultad de Química, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ricardo A Tapia
- Departamento de Química Orgánica, Facultad de Química, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jorge Soto-Delgado
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andrés Bello, Viña del Mar, Chile
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Arafa RK, Elghazawy NH. Personalized Medicine and Resurrected Hopes for the Management of Alzheimer's Disease: A Modular Approach Based on GSK-3β Inhibitors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1007:199-224. [PMID: 28840559 DOI: 10.1007/978-3-319-60733-7_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Alzheimer's disease (AD) is one of the most common neurological disorders with vast reaching worldwide prevalence. Research attempts to decipher what's happening to the human mind have shown that pathogenesis of AD is associated with misfolded protein intermediates displaying tertiary structure conformational changes eventually leading to forming large polymers of unwanted aggregates. The two hallmarks of AD pathological protein aggregates are extraneuronal β-amyloid (Aβ) based senile plaques and intraneuronal neurofibrillary tangles (NFTs). As such, AD is categorized as a protein misfolding neurodegenerative disease (PMND) . Therapeutic interventions interfering with the formation of these protein aggregates have been widely explored as potential pathways for thwarting AD progression. One such tactic is modulating the function of enzymes involved in the metabolic pathways leading to formation of these misfolded protein aggregates. Much evidence has shown that glycogen synthase kinase-3β (GSK-3β) plays a key role in hyperphosphorylation of tau protein leading eventually to its aggregation to form NFTs. Data presented hereby will display a plethora of information as to how to interfere with progression of AD through the route of GSK-3β activity control.
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Affiliation(s)
- Reem K Arafa
- Zewail City of Science and Technology, Cairo, 12588, Egypt.
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Ebrahimpour Z, Shiri A, Bakavoli M, Seyedi SM, Bahreini M, Oroojalian F. Microwave-assisted synthesis and antibacterial evaluation of new derivatives of 1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one. HETEROCYCL COMMUN 2016. [DOI: 10.1515/hc-2015-0145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractSynthesis of new 1,2-dihydro-3H-pyrazolo[3,4-d] pyrimidin-3-ones4–6starting with ethyl 4-hydroxy-2-methylthio-pyrimidine-5-carboxylate (1) under classical heating and microwave-induced conditions is reported. The antibacterial activities of the synthesized compounds were evaluated using chloramphenicol and streptomycin as reference drugs.
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Affiliation(s)
- Zahra Ebrahimpour
- 1Faculty of Science, Department of Chemistry, Ferdowsi University of Mashhad, 91775-1436 Mashhad, Iran (Islamic Republic of)
| | - Ali Shiri
- 1Faculty of Science, Department of Chemistry, Ferdowsi University of Mashhad, 91775-1436 Mashhad, Iran (Islamic Republic of)
| | - Mehdi Bakavoli
- 1Faculty of Science, Department of Chemistry, Ferdowsi University of Mashhad, 91775-1436 Mashhad, Iran (Islamic Republic of)
| | - Seyed Mohammad Seyedi
- 1Faculty of Science, Department of Chemistry, Ferdowsi University of Mashhad, 91775-1436 Mashhad, Iran (Islamic Republic of)
| | - Masoumeh Bahreini
- 2Faculty of Science, Department of Biology, Ferdowsi University of Mashhad, Mashhad, Iran (Islamic Republic of)
| | - Fatemeh Oroojalian
- 3Faculty of New Sciences and Technologies, Department of Life Science Engineering, University of Tehran, 14395-1561 Tehran, Iran (Islamic Republic of)
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Abuhammad A, Taha MO. QSAR studies in the discovery of novel type-II diabetic therapies. Expert Opin Drug Discov 2015; 11:197-214. [PMID: 26558613 DOI: 10.1517/17460441.2016.1118046] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Type-II diabetes mellitus (T2DM) is a complex chronic disease that represents a major therapeutic challenge. Despite extensive efforts in T2DM drug development, therapies remain unsatisfactory. Currently, there are many novel and important antidiabetic drug targets under investigation by many research groups worldwide. One of the main challenges to develop effective orally active hypoglycemic agents is off-target effects. Computational tools have impacted drug discovery at many levels. One of the earliest methods is quantitative structure-activity relationship (QSAR) studies. QSAR strategies help medicinal chemists understand the relationship between hypoglycemic activity and molecular properties. Hence, QSAR may hold promise in guiding the synthesis of specifically designed novel ligands that demonstrate high potency and target selectivity. AREAS COVERED This review aims to provide an overview of the QSAR strategies used to model antidiabetic agents. In particular, this review focuses on drug targets that raised recent scientific interest and/or led to successful antidiabetic agents in the market. Special emphasis has been made on studies that led to the identification of novel antidiabetic scaffolds. EXPERT OPINION Computer-aided molecular design and discovery techniques like QSAR have a great potential in designing leads against complex diseases such as T2DM. Combined with other in silico techniques, QSAR can provide more useful and rational insights to facilitate the discovery of novel compounds. However, since T2DM is a complex disease that includes several faulty biological targets, multi-target QSAR studies are recommended in the future to achieve efficient antidiabetic therapies.
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Affiliation(s)
- Areej Abuhammad
- a Department of Pharmaceutical Sciences, Faculty of Pharmacy , The University of Jordan , Amman 11942 , Jordan
| | - Mutasem O Taha
- a Department of Pharmaceutical Sciences, Faculty of Pharmacy , The University of Jordan , Amman 11942 , Jordan
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Ambure P, Roy K. Advances in quantitative structure–activity relationship models of anti-Alzheimer’s agents. Expert Opin Drug Discov 2014; 9:697-723. [DOI: 10.1517/17460441.2014.909404] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Wang J, Li F, Li Y, Yang Y, Zhang S, Yang L. Structural features of falcipain-3 inhibitors: an in silico study. MOLECULAR BIOSYSTEMS 2014; 9:2296-310. [PMID: 23765034 DOI: 10.1039/c3mb70105k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Falcipain-3, the major cysteine hemoglobinase from the human malaria parasite Plasmodium falciparum, is critical for parasite development and is considered as a promising chemotherapeutic target. In order to understand the structure-activity correlation of falcipain-3 inhibitors, a set of ligand- and receptor-based 3D-QSAR models were developed in the present work employing comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) for 247 2-pyrimidinecarbonitrile derivatives. An optimum ligand-based CoMSIA model yielded a cross validation Q(2) = 0.501, non-cross validation Rncv(2) = 0.821 and predictive Rpred(2) = 0.750. In addition, docking analysis and molecular dynamics simulation were applied to elucidate the probable binding modes of the ligand in the falcipain-3 binding pocket. Graphic representation of the results, as contoured 3D coefficient plots, also provides a clue to the reasonable modification of molecules. (1) Bulky substituents at the 3-position, and rings B and D increase the biological activity; (2) electrostatic groups at rings B, C and D are likely helpful to increase the falcipain-3 inhibition; (3) hydrophobic groups at rings B and D are favored; (4) Gly92, Ile94 and Thr95 which formed several H-bonds and a water-bridged H-bond are crucial for falcipain-3 inhibitors. This model, we hope, will be of help in designing and predicting novel falcipain-3 inhibitors.
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Affiliation(s)
- Jinghui Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Dalian University of Technology, Dalian, Liaoning 116024, PR China.
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Kumar R, Malla P, Verma A, Kumar M. Design of potent human steroid 5α-reductase inhibitors: 3D-QSAR CoMFA, CoMSIA and docking studies. Med Chem Res 2013. [DOI: 10.1007/s00044-012-0456-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Kandeel MM, Mohamed LW, Abd El Hamid MK, Negmeldin AT. Design, Synthesis, and Antitumor Evaluation of Novel Pyrazolo[3,4-d]pyrimidine Derivatives. Sci Pharm 2012; 80:531-45. [PMID: 23008804 PMCID: PMC3447607 DOI: 10.3797/scipharm.1204-23] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 06/25/2012] [Indexed: 11/22/2022] Open
Abstract
A new series of pyrazolo[3,4-d]pyrimidines has been synthesized. The new compounds were tested for their antitumor activity on 60 different cell lines, and some of the compounds were found to have potent antitumor activity. In particular, 2-hydroxybenzaldehyde [1-(4-chlorophenyl)-3-methyl-1H-pyrazolo-[3,4-d]pyrimidin-4-yl]hydrazone (VIIa) was found to be the most effective among the other derivatives, showing IC50 values of 0.326 to 4.31 μM on 57 different cell lines.
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Affiliation(s)
- Manal M Kandeel
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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Akhtar M, Bharatam PV. 3D-QSAR and molecular docking studies on 3-anilino-4-arylmaleimide derivatives as glycogen synthase kinase-3β inhibitors. Chem Biol Drug Des 2012; 79:560-71. [PMID: 22168279 DOI: 10.1111/j.1747-0285.2011.01291.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Glycogen synthase kinase-3, a serine/threonine kinase, is a fascinating enzyme with diverse biological actions in intracellular signaling systems, making it an emerging target for diseases such as diabetes mellitus, cancer, chronic inflammation, bipolar disorders, and Alzheimer's disease. It is important to inhibit glycogen synthase kinase-3 selectively, and the net effect of the glycogen synthase kinase-3 inhibitors thus should be target specific, over other phylogenetically related kinases such as CDK-2. In the present work, we have carried out three-dimensional quantitative structure-activity relationship studies on novel class of 3-anilino-4-arylmaleimide derivatives to have improved cellular activity. Docked conformation of the most active molecule in the series, which shows desirable interactions in the receptor, was taken as template for the alignment of the molecules. Statistically significant CoMSIA (r2(cv)=0.614, r2(ncv)=0.948) and comparative molecular field analysis (r2(cv) =0.652, r2(ncv)=0.958) models were generated using 57 molecules in training set. The predictive ability of CoMSIA and comparative molecular field analysis models was determined using a test set of 17 molecules, which gave predictive correlation coefficients (r2(pred)) of 0.87 and 0.82, respectively, indicating good predictive power. Based on the information derived from CoMSIA and comparative molecular field analysis contour maps, we have identified some key features that explain the observed variance in the activity and have been used to design new anilinoarylmaleimide derivatives. The designed molecules showed better binding affinity in terms of estimated docking scores with respect to the already reported systems, hence suggesting that newly designed molecules can be more potent and selective toward glycogen synthase kinase-3β inhibition.
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Affiliation(s)
- Mymoona Akhtar
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Jamia Hamdard, Hamdard University, New Delhi 110062, India.
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Hassan GS, Kadry HH, Abou-Seri SM, Ali MM, Mahmoud AEED. Synthesis and in vitro cytotoxic activity of novel pyrazolo[3,4-d]pyrimidines and related pyrazole hydrazones toward breast adenocarcinoma MCF-7 cell line. Bioorg Med Chem 2011; 19:6808-17. [PMID: 22000322 DOI: 10.1016/j.bmc.2011.09.036] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 09/12/2011] [Accepted: 09/20/2011] [Indexed: 01/07/2023]
Abstract
New series of pyrazolo[3,4-d]pyrimidines (7a-e and 13a-d) and pyrazole hydrazones 17a-d were synthesized and evaluated for their antiproliferative activity against human breast adenocarcinoma MCF-7 cell line. Most of the tested compounds exploited potent to moderate growth inhibitory activity, in particular compound 7e exhibited superior potency to the reference drug cisplatin (IC(50)=7.60 and 13.29 μM, respectively). The antitumor activity of the new compounds was accompanied by significant increase in the activity of superoxide dismutase with concomitant decrease in the activities of catalase and glutathione peroxidase and reduced glutathione level. Accordingly, the overproduction of hydrogen peroxide, nitric oxide and other free radicals allowed reactive oxygen species (ROS)-mediated tumor cells death, as monitored by reduction in the synthesis of protein and nucleic acids.
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Affiliation(s)
- Ghaneya Sayed Hassan
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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Fang J, Huang D, Zhao W, Ge H, Luo HB, Xu J. A new protocol for predicting novel GSK-3β ATP competitive inhibitors. J Chem Inf Model 2011; 51:1431-8. [PMID: 21615159 DOI: 10.1021/ci2001154] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Glycogen synthase kinase 3β (GSK-3β) is a potential therapeutic target for cancer, type-2 diabetes, and Alzheimer's disease. This paper proposes a new lead identification protocol that predicts new GSK-3β ATP competitive inhibitors with topologically diverse scaffolds. First, three-dimensional quantitative structure-activity relationship (3D QSAR) models were built and validated. These models are based upon known GSK-3β inhibitors, benzofuran-3-yl-(indol-3-yl) maleimides, by means of comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). Second, 28 826 maleimide derivatives were selected from the PubChem database. After filtration via Lipinski's rules, 10 429 maleimide derivatives were left. Third, the FlexX-dock program was employed to virtually screen the 10 429 compounds against GSK-3β. This resulted in 617 virtual hits. Fourth, the 3D QSAR models predicted that from the 617 virtual hits, 93 compounds would have GSK-3β inhibition values of less than 15 nM. Finally, from the 93 predicted active hits, 23 compounds were confirmed as GSK-3β inhibitors from literatures; their GSK-3β inhibition ranged from 1.3 to 480 nM. Therefore, the hits rate of our virtual screening protocol is greater than 25%. The protocol combines ligand- and structure-based approaches and therefore validates both approaches and is capable of identifying new hits with topologically diverse scaffolds.
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Affiliation(s)
- Jiansong Fang
- Research Center for Drug Discovery and Institute of Human Virology, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China
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19
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A combined molecular modeling study on a series of pyrazole/isoxazole based human Hsp90α inhibitors. J Mol Model 2011; 17:3241-50. [DOI: 10.1007/s00894-011-1011-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 02/06/2011] [Indexed: 12/13/2022]
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Khanfar MA, Asal BA, Mudit M, Kaddoumi A, El Sayed KA. The marine natural-derived inhibitors of glycogen synthase kinase-3beta phenylmethylene hydantoins: In vitro and in vivo activities and pharmacophore modeling. Bioorg Med Chem 2009; 17:6032-9. [PMID: 19616957 PMCID: PMC2743475 DOI: 10.1016/j.bmc.2009.06.054] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 06/22/2009] [Accepted: 06/23/2009] [Indexed: 12/22/2022]
Abstract
The Red Sea sponge Hemimycale arabica afforded the known (Z)-5-(4-hydroxybenzylidene)-hydantoin (1). This natural phenylmethylene hydantoin (PMH) 1 and the synthetic (Z)-5-(4-(ethylthio)benzylidene)-hydantoin (2) showed potent in vitro and in vivo anti-growth and anti-invasive properties against PC-3M prostate cancer cells in MTT, spheroid disaggregation, and in mice models. To explore a possible molecular target of PMHs, the most potent synthetic analogue 2 has been virtually screened against various protein kinases. Molecular modeling study has shown that 2 can be successfully docked within the binding pocket of glycogen synthase kinase-3beta (GSK-3beta) similar to the well-known GSK-3beta inhibitor I-5. Several PMHs showed potent in vitro GSK-3beta inhibitory activity with an IC(50) range of 4-20microM. The most potent analogue 3 showed a significant increase in liver glycogen level at the 5, 15, and 25mg/kg dose levels, in vivo. Pharmacophore model was built and validated using in-house database of active and inactive GSK-3beta inhibitors. The GSK-3beta inhibitory activity of PMHs entitles them to be potential leads for the treatment of cancer, Alzheimer's disease, bipolar disorders, stroke, different tau pathologies, and type-2 diabetes.
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Affiliation(s)
- Mohammad A Khanfar
- Department of Basic Pharmaceutical Sciences, University of Louisiana at Monroe, LA 71201, United States
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21
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Kim KH, Gaisina I, Gallier F, Holzle D, Blond SY, Mesecar A, Kozikowski AP. Use of molecular modeling, docking, and 3D-QSAR studies for the determination of the binding mode of benzofuran-3-yl-(indol-3-yl)maleimides as GSK-3beta inhibitors. J Mol Model 2009; 15:1463-79. [PMID: 19440740 DOI: 10.1007/s00894-009-0498-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Accepted: 04/16/2009] [Indexed: 01/18/2023]
Abstract
Molecular modeling and docking studies along with three-dimensional quantitative structure relationships (3D-QSAR) studies have been used to determine the correct binding mode of glycogen synthase kinase 3beta (GSK-3beta) inhibitors. The approaches of comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) are used for the 3D-QSAR of 51 substituted benzofuran-3-yl-(indol-3-yl)maleimides as GSK-3beta inhibitors. Two binding modes of the inhibitors to the binding site of GSK-3beta are investigated. The binding mode 1 yielded better 3D-QSAR correlations using both CoMFA and CoMSIA methodologies. The three-component CoMFA model from the steric and electrostatic fields for the experimentally determined pIC(50) values has the following statistics: R(2)(cv) = 0.386 nd SE(cv) = 0.854 for the cross-validation, and R(2) = 0.811 and SE = 0.474 for the fitted correlation. F (3,47) = 67.034, and probability of R(2) = 0 (3,47) = 0.000. The binding mode suggested by the results of this study is consistent with the preliminary results of X-ray crystal structures of inhibitor-bound GSK-3beta. The 3D-QSAR models were used for the estimation of the inhibitory potency of two additional compounds.
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Affiliation(s)
- Ki Hwan Kim
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 60612, USA.
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22
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Investigation of the structural requirement for inhibiting HIV integrase: QSAR study. ACTA PHARMACEUTICA (ZAGREB, CROATIA) 2009; 59:31-43. [PMID: 19304556 DOI: 10.2478/v10007-009-0006-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
HIV integrase has emerged as a promising target for discovery of agents against the acquired immunodeficiency syndrome (AIDS) pandemic. With the purpose of designing new chemotypes with enhanced potencies against the HIV integrase enzyme, the QSAR study carried out on 37 novel phthalimide derivatives is presented. The developed QSAR model was validated by standard statistical parameters and through a detailed structural study of how it reproduces and explains the quantitative differences seen in experimentally known pharmacological data. The model showed a good correlative and predictive ability having a cross-validated correlation coefficient (r2 cv) of 0.709 and a conventional correlation coefficient (r2) of 0.949. The predictive correlation coefficient (r2 pred) was found to be 0.512. The study revealed that the antiretroviral activity is predominantly explained by the substituent size, shape and polarity and provided insights into how modulation of the steric bulkiness and polarities of the substituents could be made to optimize the integrase-inhibitor interaction chemistry. A detailed investigation was made of the structural basis for the antiretroviral activity and the findings from the study could be usefully employed to design antagonists with a much more enhanced potency and selectivity.
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Prasanna S, Daga PR, Xie A, Doerksen RJ. Glycogen synthase kinase-3 inhibition by 3-anilino-4-phenylmaleimides: insights from 3D-QSAR and docking. J Comput Aided Mol Des 2008; 23:113-27. [DOI: 10.1007/s10822-008-9244-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Accepted: 09/06/2008] [Indexed: 10/21/2022]
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Dessalew N. QSAR Study on Piperidinecarboxamides as Antiretroviral Agents: An Insight Into the Structural Basis for HIV Coreceptor Antagonist Activity. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/qsar.200760177] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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25
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Lather V, Kristam R, Saini J, Kristam R, Karthikeyan N, Balaji V. QSAR Models for Prediction of Glycogen Synthase Kinase‐3β Inhibitory Activity of Indirubin Derivatives. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/qsar.200730052] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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26
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Dessalew N. QSAR Study on Dual 5-HT1Aand 5-HT1BAntagonists: An Insight into the Structural Requirement for Antidepressant Activity. Arch Pharm (Weinheim) 2008; 341:314-22. [DOI: 10.1002/ardp.200700224] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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27
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Dessalew N. QSAR study on aminophenylbenzamides and acrylamides as histone deacetylase inhibitors: An insight into the structural basis of antiproliferative activity. Med Chem Res 2008. [DOI: 10.1007/s00044-007-9085-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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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: 1.7] [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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29
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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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