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Hu H, Chen Z, Xu X, Xu Y. Structure-Based Survey of the Binding Modes of BACE1 Inhibitors. ACS Chem Neurosci 2019; 10:880-889. [PMID: 30540177 DOI: 10.1021/acschemneuro.8b00420] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACE1 is a key aspartic protease that cleaves the amyloid precursor protein to generate of the amyloid peptide that is believed to be responsible for the Alzheimer's disease amyloid cascade. It is thus recognized as a promising therapeutic target for Alzheimer's disease treatment, and large efforts have been made in the discovery of novel BACE1 inhibitors. This Review presents a systematic mining of BACE1 inhibitors based on 354 crystal structures of the BACE1 catalytic domain in complex with ligands in the Protein Data Bank. A thorough exploration on the frequency as well as the patterns of residue-ligand interactions enables us to subdivide the ligand binding pocket into 10 subsites and then identify favorable substructures of ligands for each subsite. In addition, it is found that the assembly of subsites with an 8-like shape is responsible to bind all inhibitors and four major ligand binding modes are revealed. Thus, such a systematic survey deepens our understanding of the structural requirements for establishment of BACE1-ligand interactions that determine the affinity of a ligand to BACE1, which is pivotal for structure-based lead optimization and design of novel inhibitors.
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Affiliation(s)
- Hangchen Hu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaoqiang Chen
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiang Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yechun Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
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2
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Schaduangrat N, Prachayasittikul V, Choomwattana S, Wongchitrat P, Phopin K, Suwanjang W, Malik AA, Vincent B, Nantasenamat C. Multidisciplinary approaches for targeting the secretase protein family as a therapeutic route for Alzheimer's disease. Med Res Rev 2019; 39:1730-1778. [PMID: 30628099 DOI: 10.1002/med.21563] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 11/21/2018] [Accepted: 12/24/2018] [Indexed: 12/27/2022]
Abstract
The continual increase of the aging population worldwide renders Alzheimer's disease (AD) a global prime concern. Several attempts have been focused on understanding the intricate complexity of the disease's development along with the on- andgoing search for novel therapeutic strategies. Incapability of existing AD drugs to effectively modulate the pathogenesis or to delay the progression of the disease leads to a shift in the paradigm of AD drug discovery. Efforts aimed at identifying AD drugs have mostly focused on the development of disease-modifying agents in which effects are believed to be long lasting. Of particular note, the secretase enzymes, a group of proteases responsible for the metabolism of the β-amyloid precursor protein (βAPP) and β-amyloid (Aβ) peptides production, have been underlined for their promising therapeutic potential. This review article attempts to comprehensively cover aspects related to the identification and use of drugs targeting the secretase enzymes. Particularly, the roles of secretases in the pathogenesis of AD and their therapeutic modulation are provided herein. Moreover, an overview of the drug development process and the contribution of computational (in silico) approaches for facilitating successful drug discovery are also highlighted along with examples of relevant computational works. Promising chemical scaffolds, inhibitors, and modulators against each class of secretases are also summarized herein. Additionally, multitarget secretase modulators are also taken into consideration in light of the current growing interest in the polypharmacology of complex diseases. Finally, challenging issues and future outlook relevant to the discovery of drugs targeting secretases are also discussed.
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Affiliation(s)
- Nalini Schaduangrat
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
| | - Veda Prachayasittikul
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
| | - Saowapak Choomwattana
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
| | - Prapimpun Wongchitrat
- Faculty of Medical Technology, Center for Research and Innovation, Mahidol University, Bangkok, Thailand
| | - Kamonrat Phopin
- Faculty of Medical Technology, Center for Research and Innovation, Mahidol University, Bangkok, Thailand
| | - Wilasinee Suwanjang
- Faculty of Medical Technology, Center for Research and Innovation, Mahidol University, Bangkok, Thailand
| | - Aijaz Ahmad Malik
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
| | - Bruno Vincent
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand.,Centre National de la Recherche Scientifique, Paris, France
| | - Chanin Nantasenamat
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
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3
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Koukoulitsa C, Villalonga-Barber C, Csonka R, Alexi X, Leonis G, Dellis D, Hamelink E, Belda O, Steele BR, Micha-Screttas M, Alexis MN, Papadopoulos MG, Mavromoustakos T. Biological and computational evaluation of resveratrol inhibitors against Alzheimer's disease. J Enzyme Inhib Med Chem 2015; 31:67-77. [PMID: 26147348 DOI: 10.3109/14756366.2014.1003928] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
It has been reported that beta amyloid induces production of radical oxygen species and oxidative stress in neuronal cells, which in turn upregulates β-secretase (BACE-1) expression and beta amyloid levels, thereby propagating oxidative stress and increasing neuronal injury. A series of resveratrol derivatives, known to be inhibitors of oxidative stress-induced neuronal cell death (oxytosis) were biologically evaluated against BACE-1 using homogeneous time-resolved fluorescence (TRF) assay. Correlation between oxytosis inhibitory and BACE-1 inhibitory activity of resveratrol derivatives was statistically significant, supporting the notion that BACE-1 may act as pivotal mediator of neuronal cell oxytosis. Four of the biologically evaluated resveratrol analogs demonstrated considerably higher activity than resveratrol in either assay. The discovery of some "hits" led us to initiate detailed docking studies associated with Molecular Dynamics in order to provide a plausible explanation for the experimental results and understand their molecular basis of action.
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Affiliation(s)
| | - Caroline Villalonga-Barber
- b Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation , Athens , Greece
| | - Robert Csonka
- b Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation , Athens , Greece
| | - Xanthippi Alexi
- b Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation , Athens , Greece
| | - Georgios Leonis
- b Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation , Athens , Greece
| | - Dimitris Dellis
- c Institute of Accelerating Systems and Applications , Panepistimiopolis Zografou , Athens , Greece , and
| | | | | | - Barry R Steele
- b Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation , Athens , Greece
| | - Maria Micha-Screttas
- b Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation , Athens , Greece
| | - Michael N Alexis
- b Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation , Athens , Greece
| | - Manthos G Papadopoulos
- b Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation , Athens , Greece
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4
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Ghosh AK, Osswald HL. BACE1 (β-secretase) inhibitors for the treatment of Alzheimer's disease. Chem Soc Rev 2015; 43:6765-813. [PMID: 24691405 DOI: 10.1039/c3cs60460h] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
BACE1 (β-secretase, memapsin 2, Asp2) has emerged as a promising target for the treatment of Alzheimer's disease. BACE1 is an aspartic protease which functions in the first step of the pathway leading to the production and deposition of amyloid-β peptide (Aβ). Its gene deletion showed only mild phenotypes. BACE1 inhibition has direct implications in the Alzheimer's disease pathology without largely affecting viability. However, inhibiting BACE1 selectively in vivo has presented many challenges to medicinal chemists. Since its identification in 2000, inhibitors covering many different structural classes have been designed and developed. These inhibitors can be largely classified as either peptidomimetic or non-peptidic inhibitors. Progress in these fields resulted in inhibitors that contain many targeted drug-like characteristics. In this review, we describe structure-based design strategies and evolution of a wide range of BACE1 inhibitors including compounds that have been shown to reduce brain Aβ, rescue the cognitive decline in transgenic AD mice and inhibitor drug candidates that are currently in clinical trials.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
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5
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Sandgren V, Belda O, Kvarnström I, Lindberg J, Samuelsson B, Dahlgren A. Design and Synthesis of Novel Arylketo-containing P1-P3 Linked Macro-cyclic BACE-1 Inhibitors. THE OPEN MEDICINAL CHEMISTRY JOURNAL 2015; 9:13-26. [PMID: 25937848 PMCID: PMC4412958 DOI: 10.2174/1874104501509010013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/06/2015] [Accepted: 01/22/2015] [Indexed: 11/22/2022]
Abstract
A series of arylketo-containing P1-P3 linked macrocyclic BACE-1 inhibitors were designed, synthesized, and compared with compounds with a previously known and extensively studied corresponding P2 isophthalamide moiety with the aim to improve on permeability whilst retaining the enzyme- and cell-based activities. Several inhibitors displayed substantial increases in Caco-2 cell-based permeability compared to earlier synthesized inhibitors and notably also with retained activities, showing that this approach might yield BACE-1 inhibitors with improved properties.
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Affiliation(s)
- Veronica Sandgren
- Department of Chemistry, Linköping University, S-581 83 Linköping, Sweden
| | - Oscar Belda
- Medivir AB, Lunastigen 7, S-141 44 Huddinge, Sweden
| | - Ingemar Kvarnström
- Department of Chemistry, Linköping University, S-581 83 Linköping, Sweden
| | | | | | - Anders Dahlgren
- Department of Chemistry, Linköping University, S-581 83 Linköping, Sweden
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6
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Ahmed W, Mainkar PS, Pabbaraja S, Chandrasekhar S. Total synthesis of a thromboxane receptor antagonist, terutroban. Org Biomol Chem 2015; 13:2951-7. [DOI: 10.1039/c4ob02302a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthesis of terutroban (2) is achieved following a non-Diels–Alder approach using cost-effective chemicals.
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Affiliation(s)
- Wasim Ahmed
- Division of Natural Products Chemistry
- CSIR-Indian Institute of Chemical Technology
- Hyderabad
- India 500 007
- Academy of Scientific and Innovative Research
| | - Prathama S. Mainkar
- Division of Natural Products Chemistry
- CSIR-Indian Institute of Chemical Technology
- Hyderabad
- India 500 007
| | - Srihari Pabbaraja
- Division of Natural Products Chemistry
- CSIR-Indian Institute of Chemical Technology
- Hyderabad
- India 500 007
| | - Srivari Chandrasekhar
- Division of Natural Products Chemistry
- CSIR-Indian Institute of Chemical Technology
- Hyderabad
- India 500 007
- Academy of Scientific and Innovative Research
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7
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Zou Y, Li L, Chen W, Chen T, Ma L, Wang X, Xiong B, Xu Y, Shen J. Virtual screening and structure-based discovery of indole acylguanidines as potent β-secretase (BACE1) inhibitors. Molecules 2013; 18:5706-22. [PMID: 23681056 PMCID: PMC6270065 DOI: 10.3390/molecules18055706] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 04/09/2013] [Accepted: 05/09/2013] [Indexed: 11/19/2022] Open
Abstract
Proteolytic cleavage of amyloid precursor protein by β-secretase (BACE1) is a key step in generating the N-terminal of β-amyloid (Aβ), which further forms into amyloid plaques that are considered as the hallmark of Alzheimer’s disease. Inhibitors of BACE1 can reduce the levels of Aβ and thus have a therapeutic potential for treating the disease. We report here the identification of a series of small molecules bearing an indole acylguanidine core structure as potent BACE1 inhibitors. The initial weak fragment was discovered by virtual screening, and followed with a hit-to-lead optimization. With the aid of co-crystal structures of two discovered inhibitors (compounds 19 and 25) with BACE1, we explored the SAR around the indole and aryl groups, and obtained several BACE1 inhibitors about 1,000-fold more potent than the initial fragment hit. Accompanying the lead optimization, a previously under-explored sub-site opposite the flap loop was redefined as a potential binding site for later BACE1 inhibitor design.
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Affiliation(s)
- Yiquan Zou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China; E-Mails: (Y.Z.); (L.M.); (X.W.)
| | - Li Li
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China; E-Mails: (L.L.); (W.C.); (T.C.)
| | - Wuyan Chen
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China; E-Mails: (L.L.); (W.C.); (T.C.)
| | - Tiantian Chen
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China; E-Mails: (L.L.); (W.C.); (T.C.)
| | - Lanping Ma
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China; E-Mails: (Y.Z.); (L.M.); (X.W.)
| | - Xin Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China; E-Mails: (Y.Z.); (L.M.); (X.W.)
| | - Bing Xiong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China; E-Mails: (Y.Z.); (L.M.); (X.W.)
- Authors to whom correspondence should be addressed; E-Mail: (B.X.); (Y.X.); (J.S.); Tel.: +86-21-5080-6600 (ext. 5412) (B.X.); Fax: +86-21-5080-7088 (B.X.)
| | - Yechun Xu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China; E-Mails: (L.L.); (W.C.); (T.C.)
- Authors to whom correspondence should be addressed; E-Mail: (B.X.); (Y.X.); (J.S.); Tel.: +86-21-5080-6600 (ext. 5412) (B.X.); Fax: +86-21-5080-7088 (B.X.)
| | - Jingkang Shen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China; E-Mails: (Y.Z.); (L.M.); (X.W.)
- Authors to whom correspondence should be addressed; E-Mail: (B.X.); (Y.X.); (J.S.); Tel.: +86-21-5080-6600 (ext. 5412) (B.X.); Fax: +86-21-5080-7088 (B.X.)
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8
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Yuan J, Venkatraman S, Zheng Y, McKeever BM, Dillard LW, Singh SB. Structure-based design of β-site APP cleaving enzyme 1 (BACE1) inhibitors for the treatment of Alzheimer's disease. J Med Chem 2013; 56:4156-80. [PMID: 23509904 DOI: 10.1021/jm301659n] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The amyloid hypothesis asserts that excess production or reduced clearance of the amyloid-β (Aβ) peptides in the brain initiates a sequence of events that ultimately lead to Alzheimer's disease and dementia. The Aβ hypothesis has identified BACE1 as a therapeutic target to treat Alzheimer's and led to medicinal chemistry efforts to design its inhibitors both in the pharmaceutical industry and in academia. This review summarizes two distinct categories of inhibitors designed based on conformational states of "closed" and "open" forms of the enzyme. In each category the inhibitors are classified based on the core catalytic interaction group or the aspartyl binding motif (ABM). This review covers the description of inhibitors in each ABM class with X-ray crystal structures of key compounds, their binding modes, related structure-activity data highlighting potency advances, and additional properties such as selectivity profile, P-gp efflux, pharmacokinetic, and pharmacodynamic data.
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Affiliation(s)
- Jing Yuan
- Vitae Pharmaceuticals, 502 W. Office Center Drive, Fort Washington, Pennsylvania 19034, USA
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9
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Sandgren V, Bäck M, Kvarnström I, Dahlgren A. Design and Synthesis of Hydroxyethylene-Based BACE-1 Inhibitors Incorporating Extended P1 Substituents. THE OPEN MEDICINAL CHEMISTRY JOURNAL 2013; 7:1-15. [PMID: 23585822 PMCID: PMC3617544 DOI: 10.2174/1874104501307010001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 11/18/2012] [Accepted: 11/26/2012] [Indexed: 01/14/2023]
Abstract
Novel BACE-1 inhibitors with a hydroxyethylene central core have been developed. Modified P1´ and extended P1 substituents were incorporated with the aim to explore potential interactions with the S1´ and the S1-S3 pocket, respectively, of BACE-1. Inhibitors were identified displaying IC50 values in the nanomolar range, i.e. 69 nM for the most potent compound. Possible inhibitor interactions with the enzyme are also discussed.
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Affiliation(s)
- Veronica Sandgren
- Department of Chemistry, Linköping University, S-581 83 Linköping, Sweden
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10
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Niu Y, Gao H, Xu F, Wang C, Liu P, Yang G, Sun Q, Xu P. Synthesis,in vitroBiological Evaluation and Molecular Docking Studies of Benzimidamides as Potential BACE1 Inhibitors. Chem Biol Drug Des 2012; 80:775-80. [DOI: 10.1111/cbdd.12016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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11
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Sund C, Belda O, Borkakoti N, Lindberg J, Derbyshire D, Vrang L, Hamelink E, Åhgren C, Woestenenk E, Wikström K, Eneroth A, Lindström E, Kalayanov G. Design and synthesis of potent hydroxyethylamine (HEA) BACE-1 inhibitors carrying prime side 4,5,6,7-tetrahydrobenzazole and 4,5,6,7-tetrahydropyridinoazole templates. Bioorg Med Chem Lett 2012; 22:6721-7. [PMID: 23010268 DOI: 10.1016/j.bmcl.2012.08.097] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 08/22/2012] [Accepted: 08/24/2012] [Indexed: 01/05/2023]
Abstract
A set of low molecular weight compounds containing a hydroxyethylamine (HEA) core structure with different prime side alkyl substituted 4,5,6,7-tetrahydrobenzazoles and one 4,5,6,7-tetrahydropyridinoazole was synthesized. Striking differences were observed on potencies in the BACE-1 enzymatic and cellular assays depending on the nature of the heteroatoms in the bicyclic ring, from the low active compound 4 to inhibitor 6, displaying BACE-1 IC(50) values of 44 nM (enzyme assay) and 65 nM (cell-based assay).
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12
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Liu S, Fu R, Cheng X, Chen SP, Zhou LH. Exploring the binding of BACE-1 inhibitors using comparative binding energy analysis (COMBINE). BMC STRUCTURAL BIOLOGY 2012; 12:21. [PMID: 22925713 PMCID: PMC3533579 DOI: 10.1186/1472-6807-12-21] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2011] [Accepted: 08/03/2012] [Indexed: 01/14/2023]
Abstract
BACKGROUND The inhibition of the activity of β-secretase (BACE-1) is a potentially important approach for the treatment of Alzheimer disease. To explore the mechanism of inhibition, we describe the use of 46 X-ray crystallographic BACE-1/inhibitor complexes to derive quantitative structure-activity relationship (QSAR) models. The inhibitors were aligned by superimposing 46 X-ray crystallographic BACE-1/inhibitor complexes, and gCOMBINE software was used to perform COMparative BINding Energy (COMBINE) analysis on these 46 minimized BACE-1/inhibitor complexes. The major advantage of the COMBINE analysis is that it can quantitatively extract key residues involved in binding the ligand and identify the nature of the interactions between the ligand and receptor. RESULTS By considering the contributions of the protein residues to the electrostatic and van der Waals intermolecular interaction energies, two predictive and robust COMBINE models were developed: (i) the 3-PC distance-dependent dielectric constant model (built from a single X-ray crystal structure) with a q2 value of 0.74 and an SDEC value of 0.521; and (ii) the 5-PC sigmoidal electrostatic model (built from the actual complexes present in the Brookhaven Protein Data Bank) with a q2 value of 0.79 and an SDEC value of 0.41. CONCLUSIONS These QSAR models and the information describing the inhibition provide useful insights into the design of novel inhibitors via the optimization of the interactions between ligands and those key residues of BACE-1.
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Affiliation(s)
- Shu Liu
- Guangdong Province Key Laboratory of Functional Molecules in Oceanic Microorganism, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
- Department of Anatomy, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
| | - Rao Fu
- Department of Anatomy, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
| | - Xiao Cheng
- Department of Anatomy, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
| | - Sheng-Ping Chen
- Guangdong Province Key Laboratory of Functional Molecules in Oceanic Microorganism, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
| | - Li-Hua Zhou
- Department of Anatomy, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
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13
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Sandgren V, Agback T, Johansson PO, Lindberg J, Kvarnström I, Samuelsson B, Belda O, Dahlgren A. Highly potent macrocyclic BACE-1 inhibitors incorporating a hydroxyethylamine core: design, synthesis and X-ray crystal structures of enzyme inhibitor complexes. Bioorg Med Chem 2012; 20:4377-89. [PMID: 22698785 DOI: 10.1016/j.bmc.2012.05.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 04/17/2012] [Accepted: 05/16/2012] [Indexed: 11/30/2022]
Abstract
A series of P1-P3 linked macrocyclic BACE-1 inhibitors containing a hydroxyethylamine (HEA) isostere scaffold has been synthesized. All inhibitors comprise a toluene or N-phenylmethanesulfonamide P2 moiety. Excellent BACE-1 potencies, both in enzymatic and cell-based assays, were observed in this series of target compounds, with the best candidates displaying cell-based IC(50) values in the low nanomolar range. As an attempt to improve potency, a phenyl substituent aiming at the S3 subpocket was introduced in the macrocyclic ring. X-ray analyzes were performed on selected compounds, and enzyme-inhibitor interactions are discussed.
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Affiliation(s)
- Veronica Sandgren
- Department of Chemistry, Linköping University, S-581 83 Linköping, Sweden
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14
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Xu Y, Li MJ, Greenblatt H, Chen W, Paz A, Dym O, Peleg Y, Chen T, Shen X, He J, Jiang H, Silman I, Sussman JL. Flexibility of the flap in the active site of BACE1 as revealed by crystal structures and molecular dynamics simulations. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2011; 68:13-25. [DOI: 10.1107/s0907444911047251] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2011] [Accepted: 11/08/2011] [Indexed: 11/10/2022]
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16
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Domínguez JL, Christopeit T, Villaverde MC, Gossas T, Otero JM, Nyström S, Baraznenok V, Lindström E, Danielson UH, Sussman F. Effect of the Protonation State of the Titratable Residues on the Inhibitor Affinity to BACE-1. Biochemistry 2010; 49:7255-63. [DOI: 10.1021/bi100637n] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- José L. Domínguez
- Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Tony Christopeit
- Department of Biochemistry and Organic Chemistry, Uppsala University, Uppsala, Sweden
| | - M. Carmen Villaverde
- Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Thomas Gossas
- Department of Biochemistry and Organic Chemistry, Uppsala University, Uppsala, Sweden
| | - José M. Otero
- Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | | | | | | | - U. Helena Danielson
- Department of Biochemistry and Organic Chemistry, Uppsala University, Uppsala, Sweden
| | - Fredy Sussman
- Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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17
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Synthesis of potent BACE-1 inhibitors incorporating a hydroxyethylene isostere as central core. Eur J Med Chem 2010; 45:870-82. [DOI: 10.1016/j.ejmech.2009.11.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Revised: 10/28/2009] [Accepted: 11/05/2009] [Indexed: 11/18/2022]
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18
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Björklund C, Oscarson S, Benkestock K, Borkakoti N, Jansson K, Lindberg J, Vrang L, Hallberg A, Rosenquist Å, Samuelsson B. Design and Synthesis of Potent and Selective BACE-1 Inhibitors. J Med Chem 2010; 53:1458-64. [DOI: 10.1021/jm901168f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Catarina Björklund
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Stefan Oscarson
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
- School of Chemistry and Chemical Biology, UCD, Dublin 4, Ireland
| | | | | | | | | | - Lotta Vrang
- Medivir AB, P.O. Box 1086, SE-141 22 Huddinge, Sweden
| | - Anders Hallberg
- Department of Medicinal Chemistry, BMC, Uppsala University, Box 574, SE-751 23 Uppsala, Sweden
| | | | - Bertil Samuelsson
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
- Medivir AB, P.O. Box 1086, SE-141 22 Huddinge, Sweden
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19
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Discovery of potent BACE-1 inhibitors containing a new hydroxyethylene (HE) Scaffold: Exploration of P1′ alkoxy residues and an aminoethylene (AE) central core. Bioorg Med Chem 2010; 18:1711-23. [DOI: 10.1016/j.bmc.2009.12.051] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Revised: 11/23/2009] [Accepted: 12/20/2009] [Indexed: 11/23/2022]
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20
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Meredith JA, Björklund C, Adolfsson H, Jansson K, Hallberg A, Rosenquist Å, Samuelsson B. P2′-truncated BACE-1 inhibitors with a novel hydroxethylene-like core. Eur J Med Chem 2010; 45:542-54. [DOI: 10.1016/j.ejmech.2009.10.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Revised: 09/27/2009] [Accepted: 10/22/2009] [Indexed: 10/20/2022]
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21
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Wang YS, Strickland C, Voigt JH, Kennedy ME, Beyer BM, Senior MM, Smith EM, Nechuta TL, Madison VS, Czarniecki M, McKittrick BA, Stamford AW, Parker EM, Hunter JC, Greenlee WJ, Wyss DF. Application of Fragment-Based NMR Screening, X-ray Crystallography, Structure-Based Design, and Focused Chemical Library Design to Identify Novel μM Leads for the Development of nM BACE-1 (β-Site APP Cleaving Enzyme 1) Inhibitors. J Med Chem 2009; 53:942-50. [DOI: 10.1021/jm901472u] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu-Sen Wang
- Schering-Plough Research Institute, 320 Bent Street, Cambridge, Massachusetts 02141
| | - Corey Strickland
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Johannes H. Voigt
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Matthew E. Kennedy
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Brian M. Beyer
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Mary M. Senior
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Elizabeth M. Smith
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Terry L. Nechuta
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Vincent S. Madison
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Michael Czarniecki
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Brian A. McKittrick
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Andrew W. Stamford
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Eric M. Parker
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - John C. Hunter
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - William J. Greenlee
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Daniel F. Wyss
- Schering-Plough Research Institute, 320 Bent Street, Cambridge, Massachusetts 02141
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22
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Russo F, Wångsell F, Sävmarker J, Jacobsson M, Larhed M. Synthesis and evaluation of a new class of tertiary alcohol based BACE-1 inhibitors. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.09.106] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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23
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Wångsell F, Russo F, Sävmarker J, Rosenquist Å, Samuelsson B, Larhed M. Design and synthesis of BACE-1 inhibitors utilizing a tertiary hydroxyl motif as the transition state mimic. Bioorg Med Chem Lett 2009; 19:4711-4. [DOI: 10.1016/j.bmcl.2009.06.065] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Revised: 06/16/2009] [Accepted: 06/16/2009] [Indexed: 10/20/2022]
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24
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Orrling KM, Marzahn MR, Gutiérrez-de-Terán H, Åqvist J, Dunn BM, Larhed M. α-Substituted norstatines as the transition-state mimic in inhibitors of multiple digestive vacuole malaria aspartic proteases. Bioorg Med Chem 2009; 17:5933-49. [DOI: 10.1016/j.bmc.2009.06.065] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Revised: 06/24/2009] [Accepted: 06/28/2009] [Indexed: 11/16/2022]
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25
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Ghosh AK, Shurrush K, Kulkarni S. Asymmetric synthesis of anti-aldol segments via a nonaldol route: synthetic applications to statines and (-)-tetrahydrolipstatin. J Org Chem 2009; 74:4508-18. [PMID: 19438217 PMCID: PMC6055226 DOI: 10.1021/jo900642f] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An asymmetric synthesis of anti-aldol segments via a nonaldol route is described. The strategy involves a highly diastereoselective synthesis of functionalized tetrahydrofuran derivatives from optically active 4-phenylbutyrolactone. Treatment of the tetrahydrofuran derivatives with a Lewis acid and acetic anhydride provided the corresponding ring-opened styrene derivatives. Oxidative cleavage of the styrene derivatives provided access to the anti-aldol segments. The utility of this methodology was demonstrated by the synthesis of statine derivatives and pancreatic lipase inhibitor, (-)-tetrahydrolipstatin.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
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