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Ni SF, Huang G, Chen Y, Wright JS, Li M, Dang L. Recent advances in γ-C(sp3)–H bond activation of amides, aliphatic amines, sulfanilamides and amino acids. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214255] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Zhu H, Dronamraju V, Xie W, More SS. Sulfur-containing therapeutics in the treatment of Alzheimer's disease. Med Chem Res 2021; 30:305-352. [PMID: 33613018 PMCID: PMC7889054 DOI: 10.1007/s00044-020-02687-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 12/06/2020] [Indexed: 12/12/2022]
Abstract
Sulfur is widely existent in natural products and synthetic organic compounds as organosulfur, which are often associated with a multitude of biological activities. OBenzothiazole, in which benzene ring is fused to the 4,5-positions of the thiazolerganosulfur compounds continue to garner increasing amounts of attention in the field of medicinal chemistry, especially in the development of therapeutic agents for Alzheimer's disease (AD). AD is a fatal neurodegenerative disease and the primary cause of age-related dementia posing severe societal and economic burdens. Unfortunately, there is no cure for AD. A lot of research has been conducted on sulfur-containing compounds in the context of AD due to their innate antioxidant potential and some are currently being evaluated in clinical trials. In this review, we have described emerging trends in the field, particularly the concept of multi-targeting and formulation of disease-modifying strategies. SAR, pharmacological targets, in vitro/vivo ADMET, efficacy in AD animal models, and applications in clinical trials of such sulfur compounds have also been discussed. This article provides a comprehensive review of organosulfur-based AD therapeutic agents and provides insights into their future development.
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Affiliation(s)
- Haizhou Zhu
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Venkateshwara Dronamraju
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Wei Xie
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Swati S. More
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
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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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Shao Q, Wu QF, He J, Yu JQ. Enantioselective γ-C(sp 3)-H Activation of Alkyl Amines via Pd(II)/Pd(0) Catalysis. J Am Chem Soc 2018; 140:5322-5325. [PMID: 29629766 DOI: 10.1021/jacs.8b01094] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Pd(II)-catalyzed enantioselective γ-C(sp3)-H cross-coupling of alkyl amines via desymmetrization and kinetic resolution has been realized for the first time using chiral acetyl-protected aminomethyl oxazoline ligands (APAO). A diverse range of aryl- and vinyl-boron reagents can be used as coupling partners. The chiral γ-arylated alkylamine products are further transformed into chiral 2-substituted 1,2,3,4-tetra-hydroquinolines and spiro-pyrrolidines as important structural motifs in natural products and biologically active molecules.
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Affiliation(s)
- Qian Shao
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Qing-Feng Wu
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Jian He
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Jin-Quan Yu
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
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Wagner V, Jantz L, Briem H, Sommer K, Rarey M, Christ CD. Computational Macrocyclization: From de novo Macrocycle Generation to Binding Affinity Estimation. ChemMedChem 2017; 12:1866-1872. [PMID: 28977738 PMCID: PMC5725703 DOI: 10.1002/cmdc.201700478] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 09/26/2017] [Indexed: 12/21/2022]
Abstract
Macrocycles play an increasing role in drug discovery, but their synthesis is often demanding. Computational tools that suggest macrocyclization based on a known binding mode and that estimate the binding affinity of these macrocycles could have a substantial impact on the medicinal chemistry design process. For both tasks, we established a workflow with high practical value. For five diverse pharmaceutical targets we show that the effect of macrocyclization on binding can be calculated robustly and accurately. Applying this method to macrocycles designed by LigMac, a search tool for de novo macrocyclization, our results suggest that we have a robust protocol in hand to design macrocycles and prioritize them prior to synthesis.
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Affiliation(s)
- Vincent Wagner
- Bayer AG, Drug Discovery, Medicinal Chemistry13353BerlinGermany
| | - Linda Jantz
- Universität HamburgZBH-Center for Bioinformatics20146HamburgGermany
| | - Hans Briem
- Bayer AG, Drug Discovery, Medicinal Chemistry13353BerlinGermany
| | - Kai Sommer
- Universität HamburgZBH-Center for Bioinformatics20146HamburgGermany
| | - Matthias Rarey
- Universität HamburgZBH-Center for Bioinformatics20146HamburgGermany
| | - Clara D. Christ
- Bayer AG, Drug Discovery, Medicinal Chemistry13353BerlinGermany
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The "Sticky Patch" Model of Crystallization and Modification of Proteins for Enhanced Crystallizability. Methods Mol Biol 2017; 1607:77-115. [PMID: 28573570 DOI: 10.1007/978-1-4939-7000-1_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Crystallization of macromolecules has long been perceived as a stochastic process, which cannot be predicted or controlled. This is consistent with another popular notion that the interactions of molecules within the crystal, i.e., crystal contacts, are essentially random and devoid of specific physicochemical features. In contrast, functionally relevant surfaces, such as oligomerization interfaces and specific protein-protein interaction sites, are under evolutionary pressures so their amino acid composition, structure, and topology are distinct. However, current theoretical and experimental studies are significantly changing our understanding of the nature of crystallization. The increasingly popular "sticky patch" model, derived from soft matter physics, describes crystallization as a process driven by interactions between select, specific surface patches, with properties thermodynamically favorable for cohesive interactions. Independent support for this model comes from various sources including structural studies and bioinformatics. Proteins that are recalcitrant to crystallization can be modified for enhanced crystallizability through chemical or mutational modification of their surface to effectively engineer "sticky patches" which would drive crystallization. Here, we discuss the current state of knowledge of the relationship between the microscopic properties of the target macromolecule and its crystallizability, focusing on the "sticky patch" model. We discuss state-of-the-art in silico methods that evaluate the propensity of a given target protein to form crystals based on these relationships, with the objective to design variants with modified molecular surface properties and enhanced crystallization propensity. We illustrate this discussion with specific cases where these approaches allowed to generate crystals suitable for structural analysis.
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Hamada Y, Kiso Y. New directions for protease inhibitors directed drug discovery. Biopolymers 2016; 106:563-79. [PMID: 26584340 PMCID: PMC7161749 DOI: 10.1002/bip.22780] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/25/2015] [Accepted: 11/02/2015] [Indexed: 12/29/2022]
Abstract
Proteases play crucial roles in various biological processes, and their activities are essential for all living organisms-from viruses to humans. Since their functions are closely associated with many pathogenic mechanisms, their inhibitors or activators are important molecular targets for developing treatments for various diseases. Here, we describe drugs/drug candidates that target proteases, such as malarial plasmepsins, β-secretase, virus proteases, and dipeptidyl peptidase-4. Previously, we reported inhibitors of aspartic proteases, such as renin, human immunodeficiency virus type 1 protease, human T-lymphotropic virus type I protease, plasmepsins, and β-secretase, as drug candidates for hypertension, adult T-cell leukaemia, human T-lymphotropic virus type I-associated myelopathy, malaria, and Alzheimer's disease. Our inhibitors are also described in this review article as examples of drugs that target proteases. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 563-579, 2016.
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Affiliation(s)
- Yoshio Hamada
- Medicinal Chemistry LaboratoryKobe Pharmaceutical University, MotoyamakitaHigashinada‐kuKobe658‐8558Japan
| | - Yoshiaki Kiso
- Laboratory of Peptide Science, Nagahama Institute of Bio‐Science and TechnologyTamura‐choNagahama526‐0829Japan
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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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9
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Chen F, Liu FM. Synthesis of New Macrocyclic Schiff Bases Containing Pyrazole and Triazole as Subcyclic Units. J Heterocycl Chem 2015. [DOI: 10.1002/jhet.1968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- F. Chen
- College of Chemistry and Chemical Engineering; Xinjiang University; Urumqi 830046 People's Republic of China
| | - F-M. Liu
- College of Chemistry and Chemical Engineering; Xinjiang University; Urumqi 830046 People's Republic of China
- College of Materials and Chemical Engineering; Hangzhou Normal University; Hang Zhou 310036 People's Republic of China
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Fadda AA, El-Mekabaty A, Mousa IA, Elattar KM. Chemistry of 3-(1H-Indol-3-yl)-3-oxopropanenitrile. SYNTHETIC COMMUN 2014. [DOI: 10.1080/00397911.2013.861915] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Zou Y, Xu L, Chen W, Zhu Y, Chen T, Fu Y, Li L, Ma L, Xiong B, Wang X, Li J, He J, Zhang H, Xu Y, Li J, Shen J. Discovery of pyrazole as C-terminus of selective BACE1 inhibitors. Eur J Med Chem 2013; 68:270-83. [DOI: 10.1016/j.ejmech.2013.06.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 04/26/2013] [Accepted: 06/06/2013] [Indexed: 02/08/2023]
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Pennington LD, Whittington DA, Bartberger MD, Jordan SR, Monenschein H, Nguyen TT, Yang BH, Xue QM, Vounatsos F, Wahl RC, Chen K, Wood S, Citron M, Patel VF, Hitchcock SA, Zhong W. Hydroxyethylamine-based inhibitors of BACE1: P1–P3 macrocyclization can improve potency, selectivity, and cell activity. Bioorg Med Chem Lett 2013; 23:4459-64. [DOI: 10.1016/j.bmcl.2013.05.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 05/01/2013] [Accepted: 05/07/2013] [Indexed: 10/26/2022]
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Abstract
INTRODUCTION Alzheimer's disease (AD), which is characterized by progressive intellectual deterioration, is the most common cause of dementia. β-Secretase (or BACE1) expression is a trigger for amyloid β peptide formation, a cause of AD, and thus is a molecular target for the development of drugs against AD. Many BACE1 inhibitors have been identified by academic and pharmaceutical research groups and a number of advanced technologies in drug discovery have been applied to the drug discovery. AREAS COVERED The purpose of this review is to present and discuss the methodologies used for BACE1 inhibitor drug discovery via substrate- and structure-based design, high-throughput screening and fragment-based drug design. The authors also review the advantages and disadvantages of these methodologies. EXPERT OPINION Many BACE1 inhibitors have been designed using X-ray crystal structure-based drug design as well as through in silico screening. Nevertheless, there are serious problems with regards to deciding the best X-ray crystal structure for designing BACE1 inhibitors through computational approaches. There are two prominent configurations of BACE1 but there is still room for improvement. Future developments may make it possible to identify BACE1 inhibitors as potential drug candidates.
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Affiliation(s)
- Yoshio Hamada
- Kobe Gakuin University, Faculty of Pharmaceutical Sciences, Minatojima, Chuo-ku, Kobe 650-8586, Japan
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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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Butini S, Brogi S, Novellino E, Campiani G, Ghosh AK, Brindisi M, Gemma S. The structural evolution of β-secretase inhibitors: a focus on the development of small-molecule inhibitors. Curr Top Med Chem 2013; 13:1787-807. [PMID: 23931442 PMCID: PMC6034716 DOI: 10.2174/15680266113139990137] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 05/11/2013] [Indexed: 12/12/2022]
Abstract
Effective treatment of Alzheimer's disease (AD) remains a critical unmet need in medicine. The lack of useful treatment for AD led to an intense search for novel therapies based on the amyloid hypothesis, which states that amyloid β-42 (Aβ42) plays an early and crucial role in all cases of AD. β-Secretase (also known as BACE-1 β-site APP-cleaving enzyme, Asp-2 or memapsin-2) is an aspartyl protease representing the rate limiting step in the generation of Aβ peptide fragments, therefore it could represent an important target in the steady hunt for a disease-modifying treatment. Generally, β-secretase inhibitors are grouped into two families: peptidomimetic and nonpeptidomimetic inhibitors. However, irrespective of the class, serious challenges with respect to blood-brain barrier (BBB) penetration and selectivity still remain. Discovering a small molecule inhibitor of β-secretase represents an unnerving challenge but, due to its significant potential as a therapeutic target, growing efforts in this task are evident from both academic and industrial laboratories. In this frame, the rising availability of crystal structures of β-secretase-inhibitor complexes represents an invaluable opportunity for optimization. Nevertheless, beyond the inhibitory activity, the major issue of the current research approaches is about problems associated with BBB penetration and pharmacokinetic properties. This review follows the structural evolution of the early β-secretase inhibitors and gives a snap-shot of the hottest chemical templates in the literature of the last five years, showing research progress in this field.
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Affiliation(s)
- Stefania Butini
- European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, Italy
| | - Simone Brogi
- European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, Italy
| | - Ettore Novellino
- European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, Italy
- Dipartimento di Farmacia, University of Naples Federico II, Italy
| | - Giuseppe Campiani
- European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, Italy
| | - Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Margherita Brindisi
- European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, Italy
| | - Sandra Gemma
- European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, Italy
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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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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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Probst G, Xu YZ. Small-molecule BACE1 inhibitors: a patent literature review (2006 - 2011). Expert Opin Ther Pat 2012; 22:511-40. [PMID: 22512789 DOI: 10.1517/13543776.2012.681302] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Alzheimer's disease is a devastating neurodegenerative disorder for which no disease-modifying therapy exists. The amyloid hypothesis, which implicates Aβ as the toxin initiating a biological cascade leading to neurodegeneration, is the most prominent theory concerning the underlying cause of the disease. BACE1 is one of two aspartyl proteinases that generate Aβ, thus inhibition of BACE1 has the potential to ameliorate the progression of Alzheimer's disease by abating the production of Aβ. AREAS COVERED This review chronicles small-molecule BACE1 inhibitors as described in the patent literature between 2006 and 2011 and their potential use as disease-modifying treatments for Alzheimer's disease. Over the past half a dozen years, numerous BACE1 inhibitors have been published in the patent applications, but often these contain a paltry amount of pertinent biological data (e.g. potency, selectivity, and efficacy). Fortunately, numerous relevant publications containing important data have appeared in the journal literature during this period. The goal in this effort was to create an amalgam of the two records to add value to this review. EXPERT OPINION The pharmaceutical industry has made tremendous progress in the development of small-molecule BACE1 inhibitors that lower Aβ in the central nervous system. Assuming the amyloid hypothesis is veracious, we anticipate a disease-modifying therapy to combat Alzheimer's disease is near.
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Affiliation(s)
- Gary Probst
- Elan Pharmaceuticals, Molecular Design, 180 Oyster Point Boulevard, South San Francisco, CA 94080, USA.
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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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Ghosh AK, Brindisi M, Tang J. Developing β-secretase inhibitors for treatment of Alzheimer's disease. J Neurochem 2011; 120 Suppl 1:71-83. [PMID: 22122681 DOI: 10.1111/j.1471-4159.2011.07476.x] [Citation(s) in RCA: 204] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
β-Secretase (memapsin 2; BACE-1) is the first protease in the processing of amyloid precursor protein leading to the production of amyloid-β (Aβ) in the brain. It is believed that high levels of brain Aβ are responsible for the pathogenesis of Alzheimer's disease (AD). Therefore, β-secretase is a major therapeutic target for the development of inhibitor drugs. During the past decade, steady progress has been made in the evolution of β-secretase inhibitors toward better drug properties. Recent inhibitors are potent, selective and have been shown to penetrate the blood-brain barrier to inhibit Aβ levels in the brains of experimental animals. Moreover, continuous administration of a β-secretase inhibitor was shown to rescue age-related cognitive decline in transgenic AD mice. A small number of β-secretase inhibitors have also entered early phase clinical trials. These developments offer some optimism for the clinical development of a disease-modifying drug for AD.
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Affiliation(s)
- Arun K Ghosh
- Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, Indiana, USA
| | - Margherita Brindisi
- Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, Indiana, USA
| | - Jordan Tang
- Protein Studies Program, Oklahoma Medical Research Foundation, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma, USA
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21
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Albert JS. Progress in the development of beta-secretase inhibitors for Alzheimer's disease. PROGRESS IN MEDICINAL CHEMISTRY 2011; 48:133-61. [PMID: 21544959 DOI: 10.1016/s0079-6468(09)04804-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Since the original identification of BACE in 1999 and until quite recently, BACE was often regarded as a "difficult" drug target, much as renin has proven to be. The reasons for this include the following. First, the long and shallow nature of the substrate binding pocket suggested that it would not be possible to identify small molecule drugs that could have adequate binding affinity. Second, functional groups that typically interact with the active site aspartates are usually highly polarized and, therefore, contribute to reduced CNS localization. Early BACE inhibitors were all designed using knowledge of the peptide substrates and usually contained some variation of a few well-known transition-state isosteres. While these had great impact on fundamental understanding of the enzyme structure and key interaction regions, they were very large, very polar, and had essentially no CNS availability. Continued progress by reducing the peptidic nature of these compounds resulted in incremental advances and has provided compounds that meet, or nearly meet, typical CNS drug-like criteria. The challenges associated with peptidic starting points inspired innovative new approaches to search for different starting points. Several groups employed high concentration screening (ligand concentration 100 microM and higher) to find weak hits after conventional screening (typically at 10 microM) failed to find more potent ones. Fragment-based methods have also been developed to identify even weaker hits (IC50 1 mM and greater). This was accomplished through the evolution and refinement of several detection methodologies including calorimetry, surface plasmon resonance, NMR, and crystallography. Coupled with detailed structural understanding of ligand-enzyme interactions and focus on maintaining ligand efficiency, these developments have resulted in several examples where potency was improved by 10,000-fold to afford compounds with IC50 values < 10 nM and promising drug-like characteristics. Together, all these efforts have afforded a diverse array of chemotypes as BACE inhibitors. Early work focused on improving BACE potency in isolated enzyme assays. However, most of these compounds showed potency reductions in cellular assays. Continued improvements in drug properties and in understanding of the physiologically relevant conditions have resulted in many compounds that show strong potency in both isolated and cellular assays. Several compounds have shown reduction of Abeta using rodent in-vivo models both peripherally and in the brain. Recently, one compound has demonstrated reduction of brain Abeta levels in a non-human primate. Phase I clinical trials were initiated on BACE inhibitor CTS-21166 from CoMentis in July of 2007. This compound derives from the earliest described peptidic inhibitors such as OM99-2 [58] but no details have been reported. In addition to strategies involving small molecule inhibitors of BACE and gamma-secretase to reduce Abeta levels, the application of biological agents has been under investigation since the identification of Abeta. The earliest efforts in this area failed. Despite encouraging results in preclinical models, immunization against Abeta by administration of AN-1792 from Elan led to development of aseptic meningoencephalitis in 6% of the patients receiving the drug. Nevertheless, continued efforts with other biological approaches appear encouraging. Most advanced in clinical trials is bapineuzumab from Elan, which is in Phase III clinical trials. This is a humanized monoclonal antibody against Abeta plaques. A recent monograph is devoted to progress in these areas. Taken together, considerable progress has been made in developing CNS-penetrant agents that reduce AP levels and in providing validation that such agents will be therapeutically beneficial for the treatment of Alzheimer's disease.
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Affiliation(s)
- Jeffrey S Albert
- CNS Discovery Research, AstraZeneca Pharmaceuticals, 1800 Concord Pike, P O Box 15437, Wilmington, DE 19850-5437, USA
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22
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Developing consensus 3D-QSAR and pharmacophore models for several beta-secretase, farnesyl transferase and histone deacetylase inhibitors. J Mol Model 2011; 18:675-92. [DOI: 10.1007/s00894-011-1094-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Accepted: 04/14/2011] [Indexed: 12/20/2022]
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23
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Monceaux CJ, Hirata-Fukae C, Lam PCH, Totrov MM, Matsuoka Y, Carlier PR. Triazole-linked reduced amide isosteres: an approach for the fragment-based drug discovery of anti-Alzheimer's BACE1 inhibitors. Bioorg Med Chem Lett 2011; 21:3992-6. [PMID: 21621412 DOI: 10.1016/j.bmcl.2011.05.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 04/28/2011] [Accepted: 05/02/2011] [Indexed: 11/19/2022]
Abstract
In the course of a β-site APP-cleaving enzyme 1 (BACE1) inhibitor discovery project an in situ synthesis/screening protocol was employed to prepare 120 triazole-linked reduced amide isostere inhibitors. Among these compounds, four showed modest (single digit micromolar) BACE1 inhibition. Our ligand design was based on a potent reduced amide isostere 1, wherein the P(2) amide moiety was replaced with an anti-1,2,3-triazole unit. Unfortunately, this replacement resulted in a 1000-fold decrease in potency. Docking studies of triazole-linked reduced amide isostere A3Z10 and potent oxadiazole-linked tertiary carbinamine 2a with BACE1 suggests that the docking poses of A3Z10 and 2a in the active sites are quite similar, with one exception. In the docked structures the placement of the protonated amine that engages D228 differs considerably between 2a and A3Z10. This difference could account for the lower BACE1 inhibition potency of A3Z10 and related compounds relative to 2a.
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24
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25
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Xia J, Zhuo C, You S. Synthesis of Cyclopropane-containing Building Blocks via Ir-Catalyzed Enantioselective Allylic Substitution Reaction. CHINESE J CHEM 2010. [DOI: 10.1002/cjoc.201090259] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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26
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Rajapakse HA, Nantermet PG, Selnick HG, Barrow JC, McGaughey GB, Munshi S, Lindsley SR, Young MB, Ngo PL, Katherine Holloway M, Lai MT, Espeseth AS, Shi XP, Colussi D, Pietrak B, Crouthamel MC, Tugusheva K, Huang Q, Xu M, Simon AJ, Kuo L, Hazuda DJ, Graham S, Vacca JP. SAR of tertiary carbinamine derived BACE1 inhibitors: Role of aspartate ligand amine pKa in enzyme inhibition. Bioorg Med Chem Lett 2010; 20:1885-9. [DOI: 10.1016/j.bmcl.2010.01.137] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 01/27/2010] [Accepted: 01/28/2010] [Indexed: 11/30/2022]
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Abstract
Treatment for Alzheimer's disease is entering a new and exciting phase, with several new drugs beginning clinical trials. Many of these new therapies are based on our best current understanding of the pathogenesis of Alzheimer's disease, and are designed to try to either slow or halt the progression of the disease. There are several different theories underlying the current efforts, and these are briefly reviewed. Therapies directed against some aspect of β-amyloid formation, against neurofibrillary tangle formation and against the inflammatory response are all considered, as are the problems associated with each area. It is as yet unclear which, if any, of these approaches will be successful, but the high level of activity in each of these three fields provides some hope that an effective treatment for Alzheimer's disease is on the horizon.
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Affiliation(s)
- Peter Davies
- Litwin-Zucker Center for Research on Alzheimer's Disease, Feinstein Institute for Medical Research, Manhasset, NY 11030, USA.
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28
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Hamada Y, Kiso Y. Recent progress in the drug discovery of non-peptidic BACE1 inhibitors. Expert Opin Drug Discov 2009; 4:391-416. [DOI: 10.1517/17460440902806377] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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29
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Pandey A, Mungalpara J, Mohan CG. Comparative molecular field analysis and comparative molecular similarity indices analysis of hydroxyethylamine derivatives as selective human BACE-1 inhibitor. Mol Divers 2009; 14:39-49. [PMID: 19330459 DOI: 10.1007/s11030-009-9139-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2008] [Accepted: 03/27/2009] [Indexed: 10/21/2022]
Abstract
Three-dimensional quantitative structure-activity relationship (3D-QSAR) models were developed based on comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA), on a series of 43 hydroxyethylamine derivatives, acting as potent inhibitors of beta-site amyloid precursor protein (APP) cleavage enzyme (BACE-1). The crystal structure of the BACE-1 enzyme (PDB ID: 2HM1) with one of the most active compound 28 was available, and we assumed it to be the bioactive conformation of the studied series, for 3D-QSAR analysis. Statistically significant 3D-QSAR model was established on a training set of 34 compounds, which were validated by a test set of 9 compounds. For the best CoMFA model, the statistics are, r2 = 0.998, r2 cv =0.810, n = 34 for the training set and r2 pred = 0.934, n = 9 for the test set. For the best CoMSIA model (combined steric, electrostatic, hydrophobic, and hydrogen bond donor fields), the statistics are r2 = 0.978, r2 cv = 0.754, n = 34 for the training set and r2 pred = 0.750, n = 9 for the test set. The resulting contour maps, produced by the best CoMFA and CoMSIA models, were used to identify the structural features relevant to the biological activity in this series of analogs. The data generated from the present study will further help to design novel, potent, and selective BACE-1 inhibitors.
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Affiliation(s)
- Ashish Pandey
- Centre for Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Mohali, Punjab, 160 062, India
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30
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Structure-based design and synthesis of macrocyclic peptidomimetic β-secretase (BACE-1) inhibitors. Bioorg Med Chem Lett 2009; 19:1361-5. [DOI: 10.1016/j.bmcl.2009.01.036] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Revised: 01/09/2009] [Accepted: 01/14/2009] [Indexed: 11/22/2022]
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31
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Macrocyclic peptidomimetic β-secretase (BACE-1) inhibitors with activity in vivo. Bioorg Med Chem Lett 2009; 19:1366-70. [DOI: 10.1016/j.bmcl.2009.01.055] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Revised: 01/14/2009] [Accepted: 01/15/2009] [Indexed: 11/20/2022]
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32
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Holloway MK, Hunt P, McGaughey GB. Structure and modeling in the design of β- and γ-secretase inhibitors. Drug Dev Res 2009. [DOI: 10.1002/ddr.20291] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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33
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Sankaranarayanan S, Holahan MA, Colussi D, Crouthamel MC, Devanarayan V, Ellis J, Espeseth A, Gates AT, Graham SL, Gregro AR, Hazuda D, Hochman JH, Holloway K, Jin L, Kahana J, Lai MT, Lineberger J, McGaughey G, Moore KP, Nantermet P, Pietrak B, Price EA, Rajapakse H, Stauffer S, Steinbeiser MA, Seabrook G, Selnick HG, Shi XP, Stanton MG, Swestock J, Tugusheva K, Tyler KX, Vacca JP, Wong J, Wu G, Xu M, Cook JJ, Simon AJ. First Demonstration of Cerebrospinal Fluid and Plasma Aβ Lowering with Oral Administration of a β-Site Amyloid Precursor Protein-Cleaving Enzyme 1 Inhibitor in Nonhuman Primates. J Pharmacol Exp Ther 2008; 328:131-40. [DOI: 10.1124/jpet.108.143628] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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34
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Girgis AS. Facile synthesis of dithiatetraaza-macrocycles of potential anti-inflammatory activity. Eur J Med Chem 2008; 43:2116-21. [DOI: 10.1016/j.ejmech.2007.12.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2007] [Revised: 11/05/2007] [Accepted: 12/06/2007] [Indexed: 11/15/2022]
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35
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Abstract
beta-Secretase (memapsin 2, BACE1) is an attractive target for the development of inhibitor drugs to treat Alzheimer's disease (AD). Not only does this protease function at the first step in the pathway leading to the production of amyloid-beta (Abeta), its gene deletion produces only mild phenotypes. In addition, beta-secretase is an aspartic protease whose mechanism and inhibition are well known. The development of beta-secretase inhibitors, actively pursued over the last seven years, has been slow, due to the difficulty in combining the required properties in a single inhibitor molecule. Steady progress in this field, however, has brought about inhibitors that contain many targeted characteristics. In this review, we describe the strategy of structure-based inhibitor evolution in the development of beta-secretase inhibitor drug. The current status of the field offers grounds for some optimism, in that beta-secretase inhibitors have been shown to reduce brain Abeta and to rescue the cognitive decline in transgenic AD mice, and an orally available beta-secretase inhibitor drug candidate is in clinical trial. With this knowledge base, it seems reasonable to expect that more drug candidates will be tested in human, and then successful disease-modifying drugs may ultimately emerge from this target.
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Affiliation(s)
- Arun K. Ghosh
- grid.169077.e0000000419372197Departments of Chemistry and Medicinal Chemistry, Purdue University, 47907 West Lafayette, Indiana
| | - Sandra Gemma
- grid.169077.e0000000419372197Departments of Chemistry and Medicinal Chemistry, Purdue University, 47907 West Lafayette, Indiana
| | - Jordan Tang
- grid.266902.90000000121793618Oklahoma Medical Research Foundation, University of Oklahoma Health Science Center, 73104 Oklahoma City, Oklahoma
- grid.266902.90000000121793618Department of Biochemistry and Molecular Biology, University of Oklahoma Health Science Center, 73104 Oklahoma City, Oklahoma
- grid.274264.10000000085276890Protein Studies Research Program, MS 28, Oklahoma Medical Research Foundation, 825 N.E. 13th Street, 73104 Oklahoma City, OK
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36
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Barazza A, Götz M, Cadamuro SA, Goettig P, Willem M, Steuber H, Kohler T, Jestel A, Reinemer P, Renner C, Bode W, Moroder L. Macrocyclic Statine-Based Inhibitors of BACE-1. Chembiochem 2007; 8:2078-91. [DOI: 10.1002/cbic.200700383] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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37
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Moore KP, Zhu H, Rajapakse HA, McGaughey GB, Colussi D, Price EA, Sankaranarayanan S, Simon AJ, Pudvah NT, Hochman JH, Allison T, Munshi SK, Graham SL, Vacca JP, Nantermet PG. Strategies toward improving the brain penetration of macrocyclic tertiary carbinamine BACE-1 inhibitors. Bioorg Med Chem Lett 2007; 17:5831-5. [PMID: 17827011 DOI: 10.1016/j.bmcl.2007.08.040] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Revised: 08/17/2007] [Accepted: 08/17/2007] [Indexed: 11/23/2022]
Abstract
This letter describes replacements for the P3 amide moiety present in previously reported tertiary carbinamine macrolactones. Although P-gp efflux issues associated with these amide-macrolactones were solved and full brain penetration was measured in one case, potency was compromised in the process.
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Affiliation(s)
- Keith P Moore
- Department of Medicinal Chemistry, Merck Research Laboratories, PO Box 4, West Point, PA 19486, USA.
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