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Monteiro KLC, Dos Santos Alcântara MG, Freire NML, Brandão EM, do Nascimento VL, Dos Santos Viana LM, de Aquino TM, da Silva-Júnior EF. BACE-1 Inhibitors Targeting Alzheimer's Disease. Curr Alzheimer Res 2023; 20:131-148. [PMID: 37309767 DOI: 10.2174/1567205020666230612155953] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 04/27/2023] [Accepted: 05/25/2023] [Indexed: 06/14/2023]
Abstract
The accumulation of amyloid-β (Aβ) is the main event related to Alzheimer's disease (AD) progression. Over the years, several disease-modulating approaches have been reported, but without clinical success. The amyloid cascade hypothesis evolved and proposed essential targets such as tau protein aggregation and modulation of β-secretase (β-site amyloid precursor protein cleaving enzyme 1 - BACE-1) and γ-secretase proteases. BACE-1 cuts the amyloid precursor protein (APP) to release the C99 fragment, giving rise to several Aβ peptide species during the subsequent γ-secretase cleavage. In this way, BACE-1 has emerged as a clinically validated and attractive target in medicinal chemistry, as it plays a crucial role in the rate of Aβ generation. In this review, we report the main results of candidates in clinical trials such as E2609, MK8931, and AZD-3293, in addition to highlighting the pharmacokinetic and pharmacodynamic-related effects of the inhibitors already reported. The current status of developing new peptidomimetic, non-peptidomimetic, naturally occurring, and other class inhibitors are demonstrated, considering their main limitations and lessons learned. The goal is to provide a broad and complete approach to the subject, exploring new chemical classes and perspectives.
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Affiliation(s)
- Kadja Luana Chagas Monteiro
- Research Group on Therapeutic Strategies - GPET, Laboratory of Synthesis and Research in Medicinal Chemistry - LSPMED, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970, Maceió, Alagoas, Brazil
| | - Marcone Gomes Dos Santos Alcântara
- Research Group on Therapeutic Strategies - GPET, Laboratory of Synthesis and Research in Medicinal Chemistry - LSPMED, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970, Maceió, Alagoas, Brazil
| | - Nathalia Monteiro Lins Freire
- Research Group on Therapeutic Strategies - GPET, Laboratory of Synthesis and Research in Medicinal Chemistry - LSPMED, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970, Maceió, Alagoas, Brazil
| | - Esaú Marques Brandão
- Research Group on Therapeutic Strategies - GPET, Laboratory of Synthesis and Research in Medicinal Chemistry - LSPMED, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970, Maceió, Alagoas, Brazil
| | - Vanessa Lima do Nascimento
- Research Group on Therapeutic Strategies - GPET, Laboratory of Synthesis and Research in Medicinal Chemistry - LSPMED, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970, Maceió, Alagoas, Brazil
| | - Líbni Maísa Dos Santos Viana
- Research Group on Therapeutic Strategies - GPET, Laboratory of Synthesis and Research in Medicinal Chemistry - LSPMED, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970, Maceió, Alagoas, Brazil
| | - Thiago Mendonça de Aquino
- Research Group on Therapeutic Strategies - GPET, Laboratory of Synthesis and Research in Medicinal Chemistry - LSPMED, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970, Maceió, Alagoas, Brazil
| | - Edeildo Ferreira da Silva-Júnior
- Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970, Maceió, Alagoas, Brazil
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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: 14] [Impact Index Per Article: 4.7] [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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Mermelstein DJ, McCammon JA, Walker RC. pH-dependent conformational dynamics of beta-secretase 1: A molecular dynamics study. J Mol Recognit 2018; 32:e2765. [PMID: 30264484 DOI: 10.1002/jmr.2765] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/25/2018] [Accepted: 08/26/2018] [Indexed: 01/19/2023]
Abstract
Beta-secretase 1 (BACE-1) is an aspartyl protease implicated in the overproduction of β-amyloid fibrils responsible for Alzheimer disease. The process of β-amyloid genesis is known to be pH dependent, with an activity peak between solution pH of 3.5 and 5.5. We have studied the pH-dependent dynamics of BACE-1 to better understand the pH dependent mechanism. We have implemented support for graphics processor unit (GPU) accelerated constant pH molecular dynamics within the AMBER molecular dynamics software package and employed this to determine the relative population of different aspartyl dyad protonation states in the pH range of greatest β-amyloid production, followed by conventional molecular dynamics to explore the differences among the various aspartyl dyad protonation states. We observed a difference in dynamics between double-protonated, mono-protonated, and double-deprotonated states over the known pH range of higher activity. These differences include Tyr 71-aspartyl dyad proximity and active water lifetime. This work indicates that Tyr 71 stabilizes catalytic water in the aspartyl dyad active site, enabling BACE-1 activity.
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Affiliation(s)
- Daniel J Mermelstein
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, Department of Pharmacology, University of California San Diego, La Jolla, California
| | - Ross C Walker
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California.,Department of Scientific Research Computing and Analytics, GlaxoSmithKline PLC, Collegeville, Pennsylvania
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Yu HS, Deng Y, Wu Y, Sindhikara D, Rask AR, Kimura T, Abel R, Wang L. Accurate and Reliable Prediction of the Binding Affinities of Macrocycles to Their Protein Targets. J Chem Theory Comput 2017; 13:6290-6300. [PMID: 29120625 DOI: 10.1021/acs.jctc.7b00885] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Macrocycles have been emerging as a very important drug class in the past few decades largely due to their expanded chemical diversity benefiting from advances in synthetic methods. Macrocyclization has been recognized as an effective way to restrict the conformational space of acyclic small molecule inhibitors with the hope of improving potency, selectivity, and metabolic stability. Because of their relatively larger size as compared to typical small molecule drugs and the complexity of the structures, efficient sampling of the accessible macrocycle conformational space and accurate prediction of their binding affinities to their target protein receptors poses a great challenge of central importance in computational macrocycle drug design. In this article, we present a novel method for relative binding free energy calculations between macrocycles with different ring sizes and between the macrocycles and their corresponding acyclic counterparts. We have applied the method to seven pharmaceutically interesting data sets taken from recent drug discovery projects including 33 macrocyclic ligands covering a diverse chemical space. The predicted binding free energies are in good agreement with experimental data with an overall root-mean-square error (RMSE) of 0.94 kcal/mol. This is to our knowledge the first time where the free energy of the macrocyclization of linear molecules has been directly calculated with rigorous physics-based free energy calculation methods, and we anticipate the outstanding accuracy demonstrated here across a broad range of target classes may have significant implications for macrocycle drug discovery.
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Affiliation(s)
- Haoyu S Yu
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Yuqing Deng
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Yujie Wu
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Dan Sindhikara
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Amy R Rask
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Takayuki Kimura
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Robert Abel
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Lingle Wang
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
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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: 8] [Impact Index Per Article: 1.1] [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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Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria. PLoS Comput Biol 2015; 11:e1004341. [PMID: 26506513 PMCID: PMC4623973 DOI: 10.1371/journal.pcbi.1004341] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/17/2015] [Indexed: 11/19/2022] Open
Abstract
BACE-1 is the β-secretase responsible for the initial amyloidogenesis in Alzheimer’s disease, catalyzing hydrolytic cleavage of substrate in a pH-sensitive manner. The catalytic mechanism of BACE-1 requires water-mediated proton transfer from aspartyl dyad to the substrate, as well as structural flexibility in the flap region. Thus, the coupling of protonation and conformational equilibria is essential to a full in silico characterization of BACE-1. In this work, we perform constant pH replica exchange molecular dynamics simulations on both apo BACE-1 and five BACE-1-inhibitor complexes to examine the effect of pH on dynamics and inhibitor binding properties of BACE-1. In our simulations, we find that solution pH controls the conformational flexibility of apo BACE-1, whereas bound inhibitors largely limit the motions of the holo enzyme at all levels of pH. The microscopic pKa values of titratable residues in BACE-1 including its aspartyl dyad are computed and compared between apo and inhibitor-bound states. Changes in protonation between the apo and holo forms suggest a thermodynamic linkage between binding of inhibitors and protons localized at the dyad. Utilizing our recently developed computational protocol applying the binding polynomial formalism to the constant pH molecular dynamics (CpHMD) framework, we are able to obtain the pH-dependent binding free energy profiles for various BACE-1-inhibitor complexes. Our results highlight the importance of correctly addressing the binding-induced protonation changes in protein-ligand systems where binding accompanies a net proton transfer. This work comprises the first application of our CpHMD-based free energy computational method to protein-ligand complexes and illustrates the value of CpHMD as an all-purpose tool for obtaining pH-dependent dynamics and binding free energies of biological systems. Formation of insoluble amyloid plaques in the vascular and hippocampal areas of the brain characterizes Alzheimer’s disease, a devastating neurodegenerative disorder causing dementia. Site-specific hydrolytic catalysis of β-secretase, or BACE-1, is responsible for production of oligomerative amyloid β-peptide. As the catalytic activity of BACE-1 is pH-dependent and its structural dynamics are intrinsic to the catalysis, we examine the dependence of dynamics of BACE-1 on solution pH and its implications on the catalytic mechanism of BACE-1. Also, we highlight the importance of accurate description of protonation states of the titratable groups in computer-aided drug discovery targeting BACE-1. We hope the understanding of pH dependence of the dynamics and inhibitor binding properties of BACE-1 will aid the structure-based inhibitor design efforts against Alzheimer’s disease.
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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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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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McIntire LBJ, Landman N, Kang MS, Finan GM, Hwang JC, Moore AZ, Park LS, Lin CS, Kim TW. Phenotypic assays for β-amyloid in mouse embryonic stem cell-derived neurons. ACTA ACUST UNITED AC 2014; 20:956-67. [PMID: 23890013 DOI: 10.1016/j.chembiol.2013.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 06/07/2013] [Accepted: 06/13/2013] [Indexed: 10/26/2022]
Abstract
Given the complex nature of Alzheimer's disease (AD), a cell-based model that recapitulates the physiological properties of the target neuronal population would be extremely valuable for discovering improved drug candidates and chemical probes to uncover disease mechanisms. We established phenotypic neuronal assays for the biogenesis and synaptic action of amyloid β peptide (Aβ) based on embryonic stem cell-derived neurons (ESNs). ESNs enriched with pyramidal neurons were robust, scalable, and amenable to a small-molecule screening assay, overcoming the apparent limitations of neuronal models derived from human pluripotent cells. Small-molecule screening of clinical compounds identified four compounds capable of reducing Aβ levels in ESNs derived from the Tg2576 mouse model of AD. Our approach is therefore highly suitable for phenotypic screening in AD drug discovery and has the potential to identify therapeutic candidates with improved efficacy and safety potential.
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Affiliation(s)
- Laura Beth J McIntire
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
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(11)C-Labeling of a potent hydroxyethylamine BACE-1 inhibitor and evaluation in vitro and in vivo. Nucl Med Biol 2014; 41:536-43. [PMID: 24857866 DOI: 10.1016/j.nucmedbio.2014.03.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 03/13/2014] [Accepted: 03/27/2014] [Indexed: 02/01/2023]
Abstract
INTRODUCTION The enzyme β-secretase 1 (BACE-1) is associated with the catalytic cleavage of amyloid precursor protein (APP) which leads to the production of amyloid-β, an amyloidogenic peptide that forms insoluble fibrils and is linked to neurodegeneration and Alzheimer's disease (AD). A PET-radioligand for the quantification of BACE-1 would be useful for the understanding of AD. In this report, we describe the synthesis and carbon-11 radiolabeling of a potent hydroxyethylamine BACE-1 enzyme inhibitor (BSI-IV) and its evaluation in vitro and in vivo. METHODS (11)[C]-N(1)-((2S,3R)-4-(cyclopropylamino)-3-hydroxy-1-phenylbutan-2-yl)-5-(N-methylmethyl-sulfonamido)-N(3)-((R)-1-phenylethyl)isophthalamide, a β-secretase inhibitor, denoted here as [(11)C]BSI-IV was synthesized through a palladium-mediated aminocarbonylation with an aryl halide precursor (I or Br) and [(11)C]CO. The effect of different palladium/ligand-complexes on radiochemical yield in the carbonylative reaction was investigated. The binding of the labeled compound to BACE-1 enzyme was studied in vitro by frozen section autoradiography from brains of healthy rats. Dynamic small animal PET-CT studies and ex vivo biodistribution were performed in male rats. RESULTS The halide precursors were synthesized in six steps starting from methyl-3-nitrobenzoate with an overall yield of 21-26%. [(11)C]BSI-IV was obtained in 29±12% decay corrected radiochemical yield (n=12) with a specific activity of 790±155GBq/μmol at the end of synthesis with a radiochemical purity of >99%. The preclinical studies showed that [(11)C]BSI-IV has a rapid metabolism in rat with excretion to the small intestines. CONCLUSION (11)[C]BSI-IV was obtained in sufficient amount and purity to enable preclinical investigation. The preclinical studies showed low specific binding in vitro and fast clearance in vivo and a low uptake in the brain. These findings suggests that [(11)C]BSI-IV has limited use as a PET-ligand for the study of BACE-1 or AD.
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Design and synthesis of novel 3,5-bis-N-(aryl/heteroaryl) carbamoyl-4-aryl-1,4-dihydropyridines as small molecule BACE-1 inhibitors. Bioorg Med Chem 2013; 21:6893-909. [DOI: 10.1016/j.bmc.2013.09.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 09/04/2013] [Accepted: 09/12/2013] [Indexed: 11/23/2022]
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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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Ghemtio L, Muzet N. Retrospective molecular docking study of WY-25105 ligand to β-secretase and bias of the three-dimensional structure flexibility. J Mol Model 2013; 19:2971-9. [DOI: 10.1007/s00894-013-1821-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 03/10/2013] [Indexed: 01/04/2023]
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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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Abstract
INTRODUCTION When two novel aspartyl proteases were published in 1999 and 2000, beta-site APP-cleaving enzyme 1 (BACE1) was confirmed as the long sought after beta-secretase and Alzheimer's disease drug target. However, the role of its paralogue, BACE2, proved elusive until a 2011 publication implicated it as a Collectrin (TMEM27) secretase controlling pancreatic beta-cell proliferation and a new therapeutic intervention for diabetes. AREAS COVERED This review, using SureChemOpen, encompasses early validation compounds and small-molecule BACE2 inhibitors for diabetes. Since 2010, one assay patent and several chemical series have been published by Roche but these were followed by filings from Novartis and Schering in 2012. The patents from these three companies include BACE2-only filings but also some specifying both BACE1 and BACE2 inhibitors. EXPERT OPINION Roche's early collaborative target validation has given them a lead in BACE2 medicinal chemistry. However, the extensive data output for BACE1 in patents and papers over the last decade, plus liganded crystal structures for both proteases, should expedite the design of BACE2 inhibitors by other organisations. This may also shorten the development time for clinical candidates that, unlike those now entering Phase I trials for BACE1, would not need to be brain-penetrant.
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Razzaghi-Asl N, Ebadi A, Edraki N, Shahabipour S, Miri R. Ab initio modeling of a potent isophthalamide-based BACE-1 inhibitor: amino acid decomposition analysis. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0277-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Gerritz SW, Zhai W, Shi S, Zhu S, Toyn JH, Meredith JE, Iben LG, Burton CR, Albright CF, Good AC, Tebben AJ, Muckelbauer JK, Camac DM, Metzler W, Cook LS, Padmanabha R, Lentz KA, Sofia MJ, Poss MA, Macor JE, Thompson LA. Acyl Guanidine Inhibitors of β-Secretase (BACE-1): Optimization of a Micromolar Hit to a Nanomolar Lead via Iterative Solid- and Solution-Phase Library Synthesis. J Med Chem 2012; 55:9208-23. [DOI: 10.1021/jm300931y] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Samuel W. Gerritz
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Weixu Zhai
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Shuhao Shi
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Shirong Zhu
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Jeremy H. Toyn
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Jere E. Meredith
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Lawrence G. Iben
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Catherine R. Burton
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Charles F. Albright
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Andrew C. Good
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Andrew J. Tebben
- Bristol-Myers Squibb Research,
P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Jodi K. Muckelbauer
- Bristol-Myers Squibb Research,
P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Daniel M. Camac
- Bristol-Myers Squibb Research,
P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - William Metzler
- Bristol-Myers Squibb Research,
P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Lynda S. Cook
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Ramesh Padmanabha
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Kimberley A. Lentz
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Michael J. Sofia
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Michael A. Poss
- Bristol-Myers Squibb Research,
P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - John E. Macor
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Lorin A. Thompson
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
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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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20
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Small DH, Aguilar MI. Targeting pre-mRNA splicing: a BACE-ic strategy for AD drug development? J Neurochem 2012; 121:695-6. [DOI: 10.1111/j.1471-4159.2012.07679.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Niu Y, Ma C, Jin H, Xu F, Gao H, Liu P, Li Y, Wang C, Yang G, Xu P. The Discovery of Novel β-Secretase Inhibitors: Pharmacophore Modeling, Virtual Screening, and Docking Studies. Chem Biol Drug Des 2012; 79:972-80. [DOI: 10.1111/j.1747-0285.2012.01367.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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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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23
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Pérez-Nueno VI, Ritchie DW. Identifying and characterizing promiscuous targets: implications for virtual screening. Expert Opin Drug Discov 2011; 7:1-17. [PMID: 22468890 DOI: 10.1517/17460441.2011.632406] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Ligand-based shape matching approaches have become established as important and popular virtual screening (VS) techniques. However, despite their relative success, the question of how to best choose the initial query compounds and their conformations remains largely unsolved. This issue gains importance when dealing with promiscuous targets, that is, proteins that bind multiple ligand scaffold families in one or more binding site. Conventional shape matching VS approaches assume that there is only one binding mode for a given protein target. This may be true for some targets, but it is certainly not true in all cases. Several recent studies have shown that some protein targets bind to different ligands in different ways. AREAS COVERED The authors discuss the concept of promiscuity in the context of virtual drug screening, and present and analyze several examples of promiscuous targets. The article also reports on the impact of the query conformation on the performance of shape-based VS and the potential to improve VS performance by using consensus shape clustering techniques. EXPERT OPINION The notion of polypharmacology is becoming highly relevant in drug discovery. Understanding and exploiting promiscuity present challenges and opportunities for drug discovery endeavors. The examples of promiscuity presented here suggest that promiscuous targets and ligands are much more common than previously assumed, and this should be taken into account in practical VS protocols. Although some progress has been made, there is a need to develop more sophisticated computational techniques and protocols that can identify and characterize promiscuous targets on a genomic scale.
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Pérez-Nueno VI, Ritchie DW. Using Consensus-Shape Clustering To Identify Promiscuous Ligands and Protein Targets and To Choose the Right Query for Shape-Based Virtual Screening. J Chem Inf Model 2011; 51:1233-48. [DOI: 10.1021/ci100492r] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
| | - David W. Ritchie
- INRIA Nancy, LORIA, 615 rue du Jardin Botanique, 54600 Villers-lès-Nancy, France
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25
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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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26
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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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27
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28
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29
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Sund C, Belda O, Wiktelius D, Sahlberg C, Vrang L, Sedig S, Hamelink E, Henderson I, Agback T, Jansson K, Borkakoti N, Derbyshire D, Eneroth A, Samuelsson B. Design and synthesis of potent macrocyclic renin inhibitors. Bioorg Med Chem Lett 2011; 21:358-62. [DOI: 10.1016/j.bmcl.2010.10.140] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Revised: 10/29/2010] [Accepted: 10/31/2010] [Indexed: 02/02/2023]
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30
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Nicholls A, McGaughey GB, Sheridan RP, Good AC, Warren G, Mathieu M, Muchmore SW, Brown SP, Grant JA, Haigh JA, Nevins N, Jain AN, Kelley B. Molecular shape and medicinal chemistry: a perspective. J Med Chem 2010; 53:3862-86. [PMID: 20158188 PMCID: PMC2874267 DOI: 10.1021/jm900818s] [Citation(s) in RCA: 235] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The eight contributions here provide ample evidence that shape as a volume or as a surface is a vibrant and useful concept when applied to drug discovery. It provides a reliable scaffold for "decoration" with chemical intuition (or bias) for virtual screening and lead optimization but also has its unadorned uses, as in library design, ligand fitting, pose prediction, or active site description. Computing power has facilitated this evolution by allowing shape to be handled precisely without the need to reduce down to point descriptors or approximate metrics, and the diversity of resultant applications argues for this being an important step forward. Certainly, it is encouraging that as computation has enabled our intuition, molecular shape has consistently surprised us in its usefulness and adaptability. The first Aurelius question, "What is the essence of a thing?", seems well answered, however, the third, "What do molecules do?", only partly so. Are the topics covered here exhaustive, or is there more to come? To date, there has been little published on the use of the volumetric definition of shape described here as a QSAR variable, for instance, in the prediction or classification of activity, although other shape definitions have been successful applied, for instance, as embodied in the Compass program described above in "Shape from Surfaces". Crystal packing is a phenomenon much desired to be understood. Although powerful models have been applied to the problem, to what degree is this dominated purely by the shape of a molecule? The shape comparison described here is typically of a global nature, and yet some importance must surely be placed on partial shape matching, just as the substructure matching of chemical graphs has proved useful. The approach of using surfaces, as described here, offers some flavor of this, as does the use of metrics that penalize volume mismatch less than the Tanimoto, e.g., Tversky measures. As yet, there is little to go on as to how useful a paradigm this will be because there is less software and fewer concrete results.Finally, the distance between molecular shapes, or between any shapes defined as volumes or surfaces, is a metric property in the mathematical sense of the word. As yet, there has been little, if any, application of this observation. We cannot know what new application to the design and discovery of pharmaceuticals may yet arise from the simple concept of molecular shape, but it is fair to say that the progress so far is impressive.
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Affiliation(s)
- Anthony Nicholls
- OpenEye Scientific Software, Inc., Santa Fe, New Mexico 87508, USA.
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31
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Choi SJ, Cho JH, Im I, Lee SD, Jang JY, Oh YM, Jung YK, Jeon ES, Kim YC. Design and synthesis of 1,4-dihydropyridine derivatives as BACE-1 inhibitors. Eur J Med Chem 2010; 45:2578-90. [DOI: 10.1016/j.ejmech.2010.02.046] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Revised: 02/17/2010] [Accepted: 02/19/2010] [Indexed: 12/31/2022]
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32
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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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33
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Godemann R, Madden J, Krämer J, Smith M, Fritz U, Hesterkamp T, Barker J, Höppner S, Hallett D, Cesura A, Ebneth A, Kemp J. Fragment-based discovery of BACE1 inhibitors using functional assays. Biochemistry 2009; 48:10743-51. [PMID: 19799414 DOI: 10.1021/bi901061a] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Novel nonpeptidic inhibitors of beta-secretase (BACE1) have been discovered by employing a fragment-based biochemical screening approach. A diverse library of 20000 low-molecular weight compounds were screened and yielded 26 novel hits that were confirmed by biochemical and surface plasmon resonance secondary assays. We describe here fragment inhibitors cocrystallized with BACE1 in a flap open and flap closed conformation as determined by X-ray crystallography.
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34
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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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35
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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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36
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Silvestri R. Boom in the development of non-peptidic β-secretase (BACE1) inhibitors for the treatment of Alzheimer's disease. Med Res Rev 2009; 29:295-338. [DOI: 10.1002/med.20132] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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37
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La Regina G, Piscitelli F, Silvestri R. Synthetic strategies of nonpeptidic β-secretase (BACE1) inhibitors. J Heterocycl Chem 2009. [DOI: 10.1002/jhet.24] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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38
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Hamze A, Veau D, Provot O, Brion JD, Alami M. Palladium-Catalyzed Markovnikov Terminal Arylalkynes Hydrostannation: Application to the Synthesis of 1,1-Diarylethylenes. J Org Chem 2008; 74:1337-40. [DOI: 10.1021/jo802460z] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Abdallah Hamze
- Laboratoire de Chimie Thérapeutique, Faculté de Pharmacie, Universite Paris-Sud, CNRS, BioCIS, UMR 8076, rue J. B. Clément, Châtenay-Malabry, F-92296, France
| | - Damien Veau
- Laboratoire de Chimie Thérapeutique, Faculté de Pharmacie, Universite Paris-Sud, CNRS, BioCIS, UMR 8076, rue J. B. Clément, Châtenay-Malabry, F-92296, France
| | - Olivier Provot
- Laboratoire de Chimie Thérapeutique, Faculté de Pharmacie, Universite Paris-Sud, CNRS, BioCIS, UMR 8076, rue J. B. Clément, Châtenay-Malabry, F-92296, France
| | - Jean-Daniel Brion
- Laboratoire de Chimie Thérapeutique, Faculté de Pharmacie, Universite Paris-Sud, CNRS, BioCIS, UMR 8076, rue J. B. Clément, Châtenay-Malabry, F-92296, France
| | - Mouâd Alami
- Laboratoire de Chimie Thérapeutique, Faculté de Pharmacie, Universite Paris-Sud, CNRS, BioCIS, UMR 8076, rue J. B. Clément, Châtenay-Malabry, F-92296, France
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39
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Chirapu SR, Pachaiyappan B, Nural HF, Cheng X, Yuan H, Lankin DC, Abdul-Hay SO, Thatcher GRJ, Shen Y, Kozikowski AP, Petukhov PA. Molecular modeling, synthesis, and activity studies of novel biaryl and fused-ring BACE1 inhibitors. Bioorg Med Chem Lett 2008; 19:264-74. [PMID: 19013792 DOI: 10.1016/j.bmcl.2008.10.096] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Revised: 10/15/2008] [Accepted: 10/17/2008] [Indexed: 10/21/2022]
Abstract
A series of transition state analogues of beta-secretases 1 and 2 (BACE1, 2) inhibitors containing fused-ring or biaryl moieties were designed computationally to probe the S2 pocket, synthesized, and tested for BACE1 and BACE2 inhibitory activity. It has been shown that unlike the biaryl analogs, the fused-ring moiety is successfully accommodated in the BACE1 binding site resulting in the ligands with excellent inhibitory activity. Ligand 5b reduced 65% of Abeta40 production in N2a cells stably transfected with Swedish human APP.
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Affiliation(s)
- Srinivas Reddy Chirapu
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
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40
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Limongelli V, Marinelli L, Cosconati S, Braun HA, Schmidt B, Novellino E. Ensemble-docking approach on BACE-1: pharmacophore perception and guidelines for drug design. ChemMedChem 2008; 2:667-78. [PMID: 17407105 DOI: 10.1002/cmdc.200600314] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Beta-secretase (BACE-1), a key enzyme in the etiopathogenesis and progression of Alzheimer disease, is the focus of medicinal chemistry efforts both in the pharmaceutical industry and in academia. Despite the availability of diverse peptidomimetic BACE-1 inhibitors, nonpeptidic compounds suitable for oral delivery and transport across the blood brain barrier are in great demand. Herein, a number of active and structurally diverse inhibitors were selected and subjected to an ensemble-docking process into five BACE-1 X-ray structures. The calculated bioactive conformations of these inhibitors allowed us to build an exhaustive pharmacophore model, which captures both the common geometric and electronic features essential for enzyme inhibition. The model is intended to aid the rational design of new BACE-1 inhibitors. Furthermore, a comparison of BACE/cathepsin D X-ray structures was made to provide guidelines for the design of BACE-selective inhibitors.
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Affiliation(s)
- Vittorio Limongelli
- Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
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41
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Fujimoto T, Matsushita Y, Gouda H, Yamaotsu N, Hirono S. In silico multi-filter screening approaches for developing novel β-secretase inhibitors. Bioorg Med Chem Lett 2008; 18:2771-5. [DOI: 10.1016/j.bmcl.2008.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2007] [Revised: 03/11/2008] [Accepted: 04/07/2008] [Indexed: 11/26/2022]
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42
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Park H, Min K, Kwak HS, Koo KD, Lim D, Seo SW, Choi JU, Platt B, Choi DY. Synthesis, SAR, and X-ray structure of human BACE-1 inhibitors with cyclic urea derivatives. Bioorg Med Chem Lett 2008; 18:2900-4. [DOI: 10.1016/j.bmcl.2008.03.081] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2007] [Revised: 03/28/2008] [Accepted: 03/29/2008] [Indexed: 10/22/2022]
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43
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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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44
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Polgár T, Magyar C, Simon I, Keserü GM. Impact of Ligand Protonation on Virtual Screening against β-Secretase (BACE1). J Chem Inf Model 2007; 47:2366-73. [DOI: 10.1021/ci700223p] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tímea Polgár
- Gedeon Richter Plc, P.O. Box 27, H-1475 Budapest, Hungary, and Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, P.O. Box 7, H-1518 Budapest, Hungary
| | - Csaba Magyar
- Gedeon Richter Plc, P.O. Box 27, H-1475 Budapest, Hungary, and Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, P.O. Box 7, H-1518 Budapest, Hungary
| | - István Simon
- Gedeon Richter Plc, P.O. Box 27, H-1475 Budapest, Hungary, and Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, P.O. Box 7, H-1518 Budapest, Hungary
| | - György M. Keserü
- Gedeon Richter Plc, P.O. Box 27, H-1475 Budapest, Hungary, and Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, P.O. Box 7, H-1518 Budapest, Hungary
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45
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McGaughey GB, Holloway MK. Structure-guided design of β-secretase (BACE-1) inhibitors. Expert Opin Drug Discov 2007; 2:1129-38. [PMID: 23484877 DOI: 10.1517/17460441.2.8.1129] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Georgia B McGaughey
- Merck Research Laboratories, Molecular Systems, WP53F-301, West Point, PA 19486, USA ;
| | - M Katharine Holloway
- Merck Research Laboratories, Molecular Systems, WP53F-301, West Point, PA 19486, USA ;
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46
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Stanton MG, Stauffer SR, Gregro AR, Steinbeiser M, Nantermet P, Sankaranarayanan S, Price EA, Wu G, Crouthamel MC, Ellis J, Lai MT, Espeseth AS, Shi XP, Jin L, Colussi D, Pietrak B, Huang Q, Xu M, Simon AJ, Graham SL, Vacca JP, Selnick H. Discovery of Isonicotinamide Derived β-Secretase Inhibitors: In Vivo Reduction of β-Amyloid. J Med Chem 2007; 50:3431-3. [PMID: 17583334 DOI: 10.1021/jm070272d] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
beta-Secretase inhibition offers an exciting opportunity for therapeutic intervention in the progression of Alzheimer's disease. A series of isonicotinamides derived from traditional aspartyl protease transition state isostere inhibitors has been optimized to yield low nanomolar inhibitors with sufficient penetration across the blood-brain barrier to demonstrate beta-amyloid lowering in a murine model.
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47
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Kortum SW, Benson TE, Bienkowski MJ, Emmons TL, Prince DB, Paddock DJ, Tomasselli AG, Moon JB, LaBorde A, TenBrink RE. Potent and selective isophthalamide S2 hydroxyethylamine inhibitors of BACE1. Bioorg Med Chem Lett 2007; 17:3378-83. [PMID: 17434734 DOI: 10.1016/j.bmcl.2007.03.096] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2007] [Revised: 03/23/2007] [Accepted: 03/29/2007] [Indexed: 11/16/2022]
Abstract
The design and synthesis of a novel series of potent BACE1 hydroxyethylamine inhibitors. These inhibitors feature hydrogen bonding substituents at the C-5 position of the isophthalamide ring with improved selectivity over cathepsin D.
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Affiliation(s)
- Steven W Kortum
- Pfizer Global Research and Development, Pfizer Inc., St. Louis Laboratories, 700 Chesterfield Parkway West, Chesterfield, MO 63017, USA.
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48
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Hussain I, Hawkins J, Harrison D, Hille C, Wayne G, Cutler L, Buck T, Walter D, Demont E, Howes C, Naylor A, Jeffrey P, Gonzalez MI, Dingwall C, Michel A, Redshaw S, Davis JB. Oral administration of a potent and selective non-peptidic BACE-1 inhibitor decreases beta-cleavage of amyloid precursor protein and amyloid-beta production in vivo. J Neurochem 2007; 100:802-9. [PMID: 17156133 DOI: 10.1111/j.1471-4159.2006.04260.x] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Generation and deposition of the amyloid beta (Abeta) peptide following proteolytic processing of the amyloid precursor protein (APP) by BACE-1 and gamma-secretase is central to the aetiology of Alzheimer's disease. Consequently, inhibition of BACE-1, a rate-limiting enzyme in the production of Abeta, is an attractive therapeutic approach for the treatment of Alzheimer's disease. We have designed a selective non-peptidic BACE-1 inhibitor, GSK188909, that potently inhibits beta-cleavage of APP and reduces levels of secreted and intracellular Abeta in SHSY5Y cells expressing APP. In addition, we demonstrate that this compound can effectively lower brain Abeta in vivo. In APP transgenic mice, acute oral administration of GSK188909 in the presence of a p-glycoprotein inhibitor to markedly enhance the exposure of GSK188909 in the brain decreases beta-cleavage of APP and results in a significant reduction in the level of Abeta40 and Abeta42 in the brain. Encouragingly, subchronic dosing of GSK188909 in the absence of a p-glycoprotein inhibitor also lowers brain Abeta. This pivotal first report of central Abeta lowering, following oral administration of a BACE-1 inhibitor, supports the development of BACE-1 inhibitors for the treatment of Alzheimer's disease.
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Affiliation(s)
- Ishrut Hussain
- Neurology and GastroIntestinal Centre of Excellence for Drug Discovery, GlaxoSmithKline Research & Development Ltd, Harlow, Essex, UK.
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49
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Stauffer SR, Stanton MG, Gregro AR, Steinbeiser MA, Shaffer JR, Nantermet PG, Barrow JC, Rittle KE, Collusi D, Espeseth AS, Lai MT, Pietrak BL, Holloway MK, McGaughey GB, Munshi SK, Hochman JH, Simon AJ, Selnick HG, Graham SL, Vacca JP. Discovery and SAR of isonicotinamide BACE-1 inhibitors that bind β-secretase in a N-terminal 10s-loop down conformation. Bioorg Med Chem Lett 2007; 17:1788-92. [PMID: 17257835 DOI: 10.1016/j.bmcl.2006.12.051] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2006] [Revised: 12/12/2006] [Accepted: 12/13/2006] [Indexed: 11/18/2022]
Abstract
A series of low-molecular weight 2,6-diamino-isonicotinamide BACE-1 inhibitors containing an amine transition-state isostere were synthesized and shown to be highly potent in both enzymatic and cell-based assays. These inhibitors contain a trans-S,S-methyl cyclopropane P(3) which bind BACE-1 in a 10s-loop down conformation giving rise to highly potent compounds with favorable molecular weight and moderate to high susceptibility to P-glycoprotein (P-gp) efflux.
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Affiliation(s)
- Shaun R Stauffer
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA.
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50
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McGaughey GB, Colussi D, Graham SL, Lai MT, Munshi SK, Nantermet PG, Pietrak B, Rajapakse HA, Selnick HG, Stauffer SR, Holloway MK. β-Secretase (BACE-1) inhibitors: Accounting for 10s loop flexibility using rigid active sites. Bioorg Med Chem Lett 2007; 17:1117-21. [PMID: 17112725 DOI: 10.1016/j.bmcl.2006.11.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2006] [Revised: 11/01/2006] [Accepted: 11/01/2006] [Indexed: 10/23/2022]
Abstract
BACE-1 is a flexible enzyme with experimentally determined motion in the flap region, the catalytic aspartates, and the 10s loop. Four in-house crystallographically determined complexes of tertiary carbinamine inhibitors revealed 10s loop motion in the S(3) pocket. These X-ray structures were used to correlate K(i) values, which span over five orders of magnitude, with the calculated interaction energy, using the Merck Molecular Force Field for a series of 19 tertiary carbinamine inhibitors.
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Affiliation(s)
- Georgia B McGaughey
- Department of Molecular Systems, Merck Research Laboratories, PO Box 4, West Point, PA 19486, USA.
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