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Sharma P, Srivastava P, Seth A, Tripathi PN, Banerjee AG, Shrivastava SK. Comprehensive review of mechanisms of pathogenesis involved in Alzheimer's disease and potential therapeutic strategies. Prog Neurobiol 2018; 174:53-89. [PMID: 30599179 DOI: 10.1016/j.pneurobio.2018.12.006] [Citation(s) in RCA: 200] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 12/04/2018] [Accepted: 12/28/2018] [Indexed: 12/14/2022]
Abstract
AD is a progressive neurodegenerative disorder and a leading cause of dementia in an aging population worldwide. The enormous challenge which AD possesses to global healthcare makes it as urgent as ever for the researchers to develop innovative treatment strategies to fight this disease. An in-depth analysis of the extensive available data associated with the AD is needed for a more comprehensive understanding of underlying molecular mechanisms and pathophysiological pathways associated with the onset and progression of the AD. The currently understood pathological and biochemical manifestations include cholinergic, Aβ, tau, excitotoxicity, oxidative stress, ApoE, CREB signaling pathways, insulin resistance, etc. However, these hypotheses have been criticized with several conflicting reports for their involvement in the disease progression. Several issues need to be addressed such as benefits to cost ratio with cholinesterase therapy, the dilemma of AChE selectivity over BChE, BBB permeability of peptidic BACE-1 inhibitors, hurdles related to the implementation of vaccination and immunization therapy, and clinical failure of candidates related to newly available targets. The present review provides an insight to the different molecular mechanisms involved in the development and progression of the AD and potential therapeutic strategies, enlightening perceptions into structural information of conventional and novel targets along with the successful applications of computational approaches for the design of target-specific inhibitors.
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Affiliation(s)
- Piyoosh Sharma
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Pavan Srivastava
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Ankit Seth
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Prabhash Nath Tripathi
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Anupam G Banerjee
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Sushant K Shrivastava
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India.
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Youn K, Park JH, Lee J, Jeong WS, Ho CT, Jun M. The Identification of Biochanin A as a Potent and Selective β-Site App-Cleaving Enzyme 1 (Bace1) Inhibitor. Nutrients 2016; 8:nu8100637. [PMID: 27754406 PMCID: PMC5084024 DOI: 10.3390/nu8100637] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Revised: 10/01/2016] [Accepted: 10/10/2016] [Indexed: 02/02/2023] Open
Abstract
Beta-site amyloid precursor protein cleaving enzyme 1 (BACE1) is the enzyme involved in the abnormal production of the amyloidogenic peptide Aβ, one of the major causes of histological hallmarks of Alzheimer’s disease (AD). Thus, BACE1 represents a key target protein in the development of new potential target for the prevention and treatment of AD. In this study, in vitro anti-AD activity of biochanin A, a dietary isoflavone found in legumes and most notably red clover, were evaluated via human recombinant BACE1 inhibition assay, as well as enzyme kinetic and molecular docking predictions. Enzyme-based assays revealed that biochanin A exhibited a non-competitive inhibitory effect on BACE1 with an IC50 value of 28 μM and a Ki of 43 μM. In addition, docking simulation results demonstrated that ASN37, SER35, SER36, TRP76, and ARG128 residues of BACE1 interacted with biochanin A. Moreover, the binding energy of biochanin A was negative (−8.4 kcal/mol), indicating that it might potentiate a strong binding between the compound and the allosteric site of BACE1, resulting in further effective BACE1 inhibition. The present novel findings raise the possibility that biochanin A may be used as a preventative, developed into a therapeutic agent for AD, or both.
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Affiliation(s)
- Kumju Youn
- Department of Food Science and Nutrition, Dong-A University, Busan 604-714, Korea.
| | - Ji-Hyun Park
- Department of Food Science and Nutrition, Dong-A University, Busan 604-714, Korea.
| | - Jinhyuk Lee
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea.
- Department of Bioinformatics, University of Sciences and Technology, Daejeon 305-350, Korea.
| | - Woo-Sik Jeong
- Department of Food & Life Science, College of Biomedical Science & Engineering, Inje University, Gimhae 621-749, Korea.
| | - Chi-Tang Ho
- Department of Food Science, Rutgers University, New Brunswick, NJ 08901, USA.
| | - Mira Jun
- Department of Food Science and Nutrition, Dong-A University, Busan 604-714, Korea.
- Institute of Convergence Bio-Health (ICBH), Dong-A University, 32, Daeshingongwon-Ro, Seo-Gu, Busan 602-715, Korea.
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3
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Zeng H, Wu X. Alzheimer's disease drug development based on Computer-Aided Drug Design. Eur J Med Chem 2015; 121:851-863. [PMID: 26415837 DOI: 10.1016/j.ejmech.2015.08.039] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 07/01/2015] [Accepted: 08/21/2015] [Indexed: 12/21/2022]
Abstract
Alzheimer's disease (AD) is a common neurodegenerative disorder characterized by the excessive deposition of amyloids in the brain. The pathological features mainly include the extracellular amyloid plaques and intracellular neurofibrillary tangles, which are the production of amyloid precursor protein (APP) processed by the α-, β- and γ-secretases. Based on the amyloid cascade hypotheses of AD, a large number of amyloid-β agents and secretase inhibitors against AD have been recently developed by using computational methods. This review article describes pathophysiology of AD and the structure of the Aβ plaques, β- and γ-secretases, and discusses the recent advances in the development of the amyloid agents for AD therapy and diagnosis by using Computer-Aided Drug Design approach.
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Affiliation(s)
- Huahui Zeng
- Science & Technology Department, Henan University of Traditional Chinese Medicine, Zhengzhou 450046, China; Department of Nuclear Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China.
| | - Xiangxiang Wu
- Science & Technology Department, Henan University of Traditional Chinese Medicine, Zhengzhou 450046, China.
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Viklund J, Kolmodin K, Nordvall G, Swahn BM, Svensson M, Gravenfors Y, Rahm F. Creation of Novel Cores for β-Secretase (BACE-1) Inhibitors: A Multiparameter Lead Generation Strategy. ACS Med Chem Lett 2014; 5:440-5. [PMID: 24900855 DOI: 10.1021/ml5000433] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 02/03/2014] [Indexed: 12/18/2022] Open
Abstract
In order to find optimal core structures as starting points for lead optimization, a multiparameter lead generation workflow was designed with the goal of finding BACE-1 inhibitors as a treatment for Alzheimer's disease. De novo design of core fragments was connected with three predictive in silico models addressing target affinity, permeability, and hERG activity, in order to guide synthesis. Taking advantage of an additive SAR, the prioritized cores were decorated with a few, well-characterized substituents from known BACE-1 inhibitors in order to allow for core-to-core comparisons. Prediction methods and analyses of how physicochemical properties of the core structures correlate to in vitro data are described. The syntheses and in vitro data of the test compounds are reported in a separate paper by Ginman et al. [J. Med. Chem. 2013, 56, 4181-4205]. The affinity predictions are described in detail by Roos et al. [J. Chem. Inf. 2014, DOI: 10.1021/ci400374z].
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Affiliation(s)
- Jenny Viklund
- Department of Medicinal Chemistry AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Karin Kolmodin
- Department of Medicinal Chemistry AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Gunnar Nordvall
- Department of Medicinal Chemistry AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Britt-Marie Swahn
- Department of Medicinal Chemistry AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Mats Svensson
- Department of Medicinal Chemistry AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Ylva Gravenfors
- Department of Medicinal Chemistry AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Fredrik Rahm
- Department of Medicinal Chemistry AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
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Mondal K, Regnstrom K, Morishige W, Barbour R, Probst G, Xu YZ, Artis DR, Yao N, Beroza P, Bova MP. Thermodynamic and kinetic characterization of hydroxyethylamine β-secretase-1 inhibitors. Biochem Biophys Res Commun 2013; 441:291-6. [PMID: 24070613 DOI: 10.1016/j.bbrc.2013.09.081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 09/16/2013] [Indexed: 10/26/2022]
Abstract
Alzheimer's disease (AD) is a devastating neurodegenerative disease affecting millions of people. β-Secretase-1 (BACE-1), an enzyme involved in the processing of the amyloid precursor protein (APP) to form Aβ, is a well validated target for AD. Herein, the authors characterize 10 randomly selected hydroxyethylamine (HEA) BACE-1 inhibitors in terms of their association and dissociation rate constants and thermodynamics of binding using surface plasmon resonance (SPR). Rate constants of association (ka) measured at 25 °C ranged from a low of 2.42×10(4) M(-1) s(-1) to the highest value of 8.3×10(5) M(-1) s(-1). Rate constants of dissociation (kd) ranged from 1.09×10(-4) s(-1) (corresponding to a residence time of close to three hours), to the fastest of 0.028 s(-1). Three compounds were selected for further thermodynamic analysis where it was shown that equilibrium binding was enthalpy driven while unfavorable entropy of binding was observed. Structural analysis revealed that upon ligand binding, the BACE-1flap folds down over the bound ligand causing an induced fit. The maximal difference between alpha carbon positions in the open and closed conformations of the flap was over 5 Å. Thus the negative entropy of binding determined using SPR analysis was consistent with an induced fit observed by structural analysis.
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Affiliation(s)
- Kalyani Mondal
- Elan Pharmaceutical, 180 Oyster Point Blvd., South San Francisco, CA 94080, USA
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Honarparvar B, Govender T, Maguire GEM, Soliman MES, Kruger HG. Integrated Approach to Structure-Based Enzymatic Drug Design: Molecular Modeling, Spectroscopy, and Experimental Bioactivity. Chem Rev 2013; 114:493-537. [DOI: 10.1021/cr300314q] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Bahareh Honarparvar
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Thavendran Govender
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Glenn E. M. Maguire
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Mahmoud E. S. Soliman
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Hendrik G. Kruger
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
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7
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Ghemtio L, Muzet N. Retrospective molecular docking study of WY-25105 ligand to β-secretase and bias of the three-dimensional structure flexibility. J Mol Model 2013; 19:2971-9. [DOI: 10.1007/s00894-013-1821-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 03/10/2013] [Indexed: 01/04/2023]
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8
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Peuchmaur M, Lacour MA, Sévalle J, Lisowski V, Touati-Jallabe Y, Rodier F, Martinez J, Checler F, Hernandez JF. Further characterization of a putative serine protease contributing to the γ-secretase cleavage of β-amyloid precursor protein. Bioorg Med Chem 2013; 21:1018-29. [DOI: 10.1016/j.bmc.2012.11.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 11/05/2012] [Accepted: 11/15/2012] [Indexed: 12/11/2022]
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9
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Wang C, Yang A, Li X, Li D, Zhang M, Du H, Li C, Guo Y, Mao X, Dong M, Besenbacher F, Yang Y, Wang C. Observation of molecular inhibition and binding structures of amyloid peptides. NANOSCALE 2012; 4:1895-909. [PMID: 22334382 DOI: 10.1039/c2nr11508e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Unveiling interactions between labeling molecules and amyloid fibrils is essential to develop new detection methods for studying amyloid structures under various conditions. This review endeavours to reflect the progress in studying interactions between molecular inhibitors and amyloid peptides using a series of experimental approaches, such as X-ray diffraction, nuclear magnetic resonance, scanning probe microscopy, and electron microscopy. The revealed binding mechanisms of anti-amyloid drugs and target proteins could benefit the rational design of drugs for prevention or treatment of amyloidal diseases.
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Affiliation(s)
- Chenxuan Wang
- National Center for Nanoscience and Technology, Beijing, 100190, PR China
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10
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Sheean P, Rout MK, Head RJ, Bennett LE. Modulation of in vitro activity of zymogenic and mature recombinant human β-secretase by dietary plants. FEBS J 2012; 279:1291-305. [DOI: 10.1111/j.1742-4658.2012.08524.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Chiriano G, De Simone A, Mancini F, Perez DI, Cavalli A, Bolognesi ML, Legname G, Martinez A, Andrisano V, Carloni P, Roberti M. A small chemical library of 2-aminoimidazole derivatives as BACE-1 inhibitors: Structure-based design, synthesis, and biological evaluation. Eur J Med Chem 2012; 48:206-13. [DOI: 10.1016/j.ejmech.2011.12.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 11/03/2011] [Accepted: 12/09/2011] [Indexed: 10/14/2022]
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12
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Secretase Inhibitors and Modulators as a Disease-Modifying Approach Against Alzheimer's Disease. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2012. [DOI: 10.1016/b978-0-12-396492-2.00005-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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13
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Chiriano G, Sartini A, Mancini F, Andrisano V, Bolognesi ML, Roberti M, Recanatini M, Carloni P, Cavalli A. Sequential virtual screening approach to the identification of small organic molecules as potential BACE-1 inhibitors. Chem Biol Drug Des 2011; 77:268-71. [PMID: 21244641 DOI: 10.1111/j.1747-0285.2011.01087.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In this letter, we report on the sequential application of two different in silico screening approaches combined with bioassays aimed at the identification of small organic molecules as potential BACE-1 inhibitors. Two hits endowed of micromolar inhibitory potency were selected, and the binding mode of the most potent compound was further characterized through docking simulations.
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Affiliation(s)
- Gianpaolo Chiriano
- International School for Advanced Studies (ISAS/SISSA), Via Beirut 2-4, Trieste, Italy
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14
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Gutierrez LJ, Enriz RD, Baldoni HA. Structural and Thermodynamic Characteristics of the Exosite Binding Pocket on the Human BACE1: A Molecular Modeling Approach. J Phys Chem A 2010; 114:10261-9. [DOI: 10.1021/jp104983a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Lucas J. Gutierrez
- Área de Química General e Inorgánica, Universidad Nacional de San Luis (UNSL), Chacabuco 917, 5700 San Luis, Argentina, Instituto Multidisciplinario de Investigaciones Biológicas de San Luis (UNSL, CONICET), Ejercito de Los Andes 950, 5700 San Luis, Argentina, and Instituto de Matemática Aplicada San Luis (UNSL, CONICET), Ejercito de Los Andes 950, 5700 San Luis, Argentina
| | - Ricardo D. Enriz
- Área de Química General e Inorgánica, Universidad Nacional de San Luis (UNSL), Chacabuco 917, 5700 San Luis, Argentina, Instituto Multidisciplinario de Investigaciones Biológicas de San Luis (UNSL, CONICET), Ejercito de Los Andes 950, 5700 San Luis, Argentina, and Instituto de Matemática Aplicada San Luis (UNSL, CONICET), Ejercito de Los Andes 950, 5700 San Luis, Argentina
| | - Héctor A. Baldoni
- Área de Química General e Inorgánica, Universidad Nacional de San Luis (UNSL), Chacabuco 917, 5700 San Luis, Argentina, Instituto Multidisciplinario de Investigaciones Biológicas de San Luis (UNSL, CONICET), Ejercito de Los Andes 950, 5700 San Luis, Argentina, and Instituto de Matemática Aplicada San Luis (UNSL, CONICET), Ejercito de Los Andes 950, 5700 San Luis, Argentina
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Hu N, Tu YP, Jiang K, Pan Y. Intramolecular Charge Transfer in the Gas Phase: Fragmentation of Protonated Sulfonamides in Mass Spectrometry. J Org Chem 2010; 75:4244-50. [DOI: 10.1021/jo100761k] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Nan Hu
- Department of Chemistry, Zhejiang University, 38 Zheda Road, Hangzhou, Zhejiang 310027, China
| | - Ya-Ping Tu
- Drug Metabolism and Pharmacokinetics, Infectious Diseases Center of Excellence for Drug Discovery, GlaxoSmithKline, 5 Moore Drive, Research Triangle Park, North Carolina 27709
| | - Kezhi Jiang
- Department of Chemistry, Zhejiang University, 38 Zheda Road, Hangzhou, Zhejiang 310027, China
| | - Yuanjiang Pan
- Department of Chemistry, Zhejiang University, 38 Zheda Road, Hangzhou, Zhejiang 310027, China
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Yi Mok N, Chadwick J, Kellett KAB, Hooper NM, Johnson AP, Fishwick CWG. Discovery of novel non-peptide inhibitors of BACE-1 using virtual high-throughput screening. Bioorg Med Chem Lett 2009; 19:6770-4. [PMID: 19854048 DOI: 10.1016/j.bmcl.2009.09.103] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 09/22/2009] [Accepted: 09/24/2009] [Indexed: 11/26/2022]
Abstract
A novel series of isatin-based inhibitors of beta-secretase (BACE-1) have been identified using a virtual high-throughput screening approach. Structure-activity relationship studies revealed structural features important for inhibition. Docking studies suggest these inhibitors may bind within the BACE-1 active site through H-bonding interactions involving the catalytic aspartate residues.
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Affiliation(s)
- N Yi Mok
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
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