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Vrabec R, Blunden G, Cahlíková L. Natural Alkaloids as Multi-Target Compounds towards Factors Implicated in Alzheimer's Disease. Int J Mol Sci 2023; 24:ijms24054399. [PMID: 36901826 PMCID: PMC10003045 DOI: 10.3390/ijms24054399] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
Alzheimer's disease (AD) is the most common cause of dementia in elderly people; currently, there is no efficient treatment. Considering the increase in life expectancy worldwide AD rates are predicted to increase enormously, and thus the search for new AD drugs is urgently needed. A great amount of experimental and clinical evidence indicated that AD is a complex disorder characterized by widespread neurodegeneration of the CNS, with major involvement of the cholinergic system, causing progressive cognitive decline and dementia. The current treatment, based on the cholinergic hypothesis, is only symptomatic and mainly involves the restoration of acetylcholine (ACh) levels through the inhibition of acetylcholinesterase (AChE). Since the introduction of the Amaryllidaceae alkaloid galanthamine as an antidementia drug in 2001, alkaloids have been one of the most attractive groups for searching for new AD drugs. The present review aims to comprehensively summarize alkaloids of various origins as multi-target compounds for AD. From this point of view, the most promising compounds seem to be the β-carboline alkaloid harmine and several isoquinoline alkaloids since they can simultaneously inhibit several key enzymes of AD's pathophysiology. However, this topic remains open for further research on detailed mechanisms of action and the synthesis of potentially better semi-synthetic analogues.
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Affiliation(s)
- Rudolf Vrabec
- Secondary Metabolites of Plants as Potential Drugs Research Group, Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmacy, Charles University, Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Gerald Blunden
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, UK
| | - Lucie Cahlíková
- Secondary Metabolites of Plants as Potential Drugs Research Group, Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmacy, Charles University, Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
- Correspondence:
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2
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Taoka BM, Wu WL, Hao J, Dolmaski M, Wang H, Levorse D, Orth P, Hyde LA, Smith B, Michener MS, Kennedy ME, Parker EM, Cumming JN. Design and discovery of C2-fluoroalkyl iminothiazine dioxides as BACE inhibitors. Bioorg Med Chem Lett 2022; 56:128463. [PMID: 34838652 DOI: 10.1016/j.bmcl.2021.128463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 11/25/2022]
Abstract
This paper describes the structure-activity-relationships of novel fluoroalkyl substituents at the C2 position of iminothiazine dioxide beta secretase inhibitors. Key discoveries include reduced amidine basicity and its effect on Pgp, cell potency, and efficacy in various preclinical in vivo efficacy animal models. Findings from these structure-activity-relationships are discussed.
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Affiliation(s)
- Brandon M Taoka
- Department of Discovery Chemistry, MRL, Merck & Co. Inc., 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Wen-Lian Wu
- Department of Discovery Chemistry, MRL, Merck & Co. Inc., 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Jinsong Hao
- Department of Discovery Chemistry, MRL, Merck & Co. Inc., 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Martin Dolmaski
- Department of Discovery Chemistry, MRL, Merck & Co. Inc., 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Hongwu Wang
- Department of Computational and Structural Chemistry, MRL, Merck & Co. Inc., 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Dorthy Levorse
- Department of Preclinical Development, MRL, Merck & Co. Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Peter Orth
- Department of Computational and Structural Chemistry, MRL, Merck & Co. Inc., 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Lynn A Hyde
- Department of Neuroscience, Safety and Laboratory Animal Research, MRL, Merck & Co. Inc., 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Brad Smith
- Department of Safety and Laboratory Animal Research MRL, Merck & Co. Inc., 770 Sumneytown Pike, West Point, PA 19486, USA
| | - Maria S Michener
- Department of Safety and Laboratory Animal Research MRL, Merck & Co. Inc., 770 Sumneytown Pike, West Point, PA 19486, USA
| | - Matthew E Kennedy
- Department of Neuroscience, Safety and Laboratory Animal Research, MRL, Merck & Co. Inc., 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Eric M Parker
- Department of Neuroscience, Safety and Laboratory Animal Research, MRL, Merck & Co. Inc., 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Jared N Cumming
- Department of Discovery Chemistry, MRL, Merck & Co. Inc., 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
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3
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Peschiulli A, Oehlrich D, Rombouts F, Vos A, Gijsen HJM. 3,3-Difluoro-3,4,5,6-tetrahydropyridin-2-amines: Potent and permeable BACE-1 inhibitors. Bioorg Med Chem Lett 2020; 30:126999. [DOI: 10.1016/j.bmcl.2020.126999] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/19/2020] [Accepted: 01/24/2020] [Indexed: 11/17/2022]
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4
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Vitale RM, Rispoli V, Desiderio D, Sgammato R, Thellung S, Canale C, Vassalli M, Carbone M, Ciavatta ML, Mollo E, Felicità V, Arcone R, Gavagnin Capoggiani M, Masullo M, Florio T, Amodeo P. In Silico Identification and Experimental Validation of Novel Anti-Alzheimer's Multitargeted Ligands from a Marine Source Featuring a "2-Aminoimidazole plus Aromatic Group" Scaffold. ACS Chem Neurosci 2018; 9:1290-1303. [PMID: 29473731 DOI: 10.1021/acschemneuro.7b00416] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Multitargeting or polypharmacological approaches, looking for single chemical entities retaining the ability to bind two or more molecular targets, are a potentially powerful strategy to fight complex, multifactorial pathologies. Unfortunately, the search for multiligand agents is challenging because only a small subset of molecules contained in molecular databases are bioactive and even fewer are active on a preselected set of multiple targets. However, collections of natural compounds feature a significantly higher fraction of bioactive molecules than synthetic ones. In this view, we searched our library of 1175 natural compounds from marine sources for molecules including a 2-aminoimidazole+aromatic group motif, found in known compounds active on single relevant targets for Alzheimer's disease (AD). This identified two molecules, a pseudozoanthoxanthin (1) and a bromo-pyrrole alkaloid (2), which were predicted by a computational approach to possess interesting multitarget profiles on AD target proteins. Biochemical assays experimentally confirmed their biological activities. The two compounds inhibit acetylcholinesterase, butyrylcholinesterase, and β-secretase enzymes in high- to sub-micromolar range. They are also able to prevent and revert β-amyloid (Aβ) aggregation of both Aβ1-40 and Aβ1-42 peptides, with 1 being more active than 2. Preliminary in vivo studies suggest that compound 1 is able to restore cholinergic cortico-hippocampal functional connectivity.
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Affiliation(s)
- Rosa Maria Vitale
- Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Comprensorio Olivetti, Ed.70, Via Campi Flegrei, 34, I-80078 Pozzuoli (NA), Italy
| | - Vincenzo Rispoli
- Department of Health Sciences, University Magna Græcia of Catanzaro, Building of Biosciences, University Campus “Salvatore Venuta”, Viale Europa, I-88100 Catanzaro (CZ), Italy
| | - Doriana Desiderio
- Department of Movement Sciences and Wellness, University of Naples “Parthenope”, Via Medina 40, I-80133 Naples (NA), Italy
| | - Roberta Sgammato
- Department of Movement Sciences and Wellness, University of Naples “Parthenope”, Via Medina 40, I-80133 Naples (NA), Italy
| | - Stefano Thellung
- Section of Pharmacology, Department of Internal Medicine and Center of Excellence for Biomedical Research (CEBR), University of Genova, Viale Benedetto XV 2, I-16132 Genoa (GE), Italy
| | - Claudio Canale
- Department of Physics, University of Genova, Via Dodecaneso 33, I-16146 Genoa (GE), Italy
| | - Massimo Vassalli
- Institute of Biophysics, National Research Council, Via De Marini, 10, I-16149 Genoa (GE), Italy
| | - Marianna Carbone
- Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Comprensorio Olivetti, Ed.70, Via Campi Flegrei, 34, I-80078 Pozzuoli (NA), Italy
| | - Maria Letizia Ciavatta
- Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Comprensorio Olivetti, Ed.70, Via Campi Flegrei, 34, I-80078 Pozzuoli (NA), Italy
| | - Ernesto Mollo
- Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Comprensorio Olivetti, Ed.70, Via Campi Flegrei, 34, I-80078 Pozzuoli (NA), Italy
| | - Vera Felicità
- Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Comprensorio Olivetti, Ed.70, Via Campi Flegrei, 34, I-80078 Pozzuoli (NA), Italy
- Department of Health Sciences, University Magna Græcia of Catanzaro, Building of Biosciences, University Campus “Salvatore Venuta”, Viale Europa, I-88100 Catanzaro (CZ), Italy
| | - Rosaria Arcone
- Department of Movement Sciences and Wellness, University of Naples “Parthenope”, Via Medina 40, I-80133 Naples (NA), Italy
- CEINGE - Advanced Biotechnologies s.c.a r.l., Via Gaetano Salvatore, 486, I-80145 Naples (NA), Italy
| | - Margherita Gavagnin Capoggiani
- Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Comprensorio Olivetti, Ed.70, Via Campi Flegrei, 34, I-80078 Pozzuoli (NA), Italy
| | - Mariorosario Masullo
- Department of Movement Sciences and Wellness, University of Naples “Parthenope”, Via Medina 40, I-80133 Naples (NA), Italy
- CEINGE - Advanced Biotechnologies s.c.a r.l., Via Gaetano Salvatore, 486, I-80145 Naples (NA), Italy
| | - Tullio Florio
- Section of Pharmacology, Department of Internal Medicine and Center of Excellence for Biomedical Research (CEBR), University of Genova, Viale Benedetto XV 2, I-16132 Genoa (GE), Italy
| | - Pietro Amodeo
- Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Comprensorio Olivetti, Ed.70, Via Campi Flegrei, 34, I-80078 Pozzuoli (NA), Italy
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5
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Gutiérrez LJ, Parravicini O, Sánchez E, Rodríguez R, Cobo J, Enriz RD. New substituted aminopyrimidine derivatives as BACE1 inhibitors: in silico design, synthesis and biological assays. J Biomol Struct Dyn 2018; 37:229-246. [DOI: 10.1080/07391102.2018.1424036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Lucas J. Gutiérrez
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 915, 5700 San Luis, Argentina
- IMIBIO-CONICET, UNSL, Chacabuco 915, 5700 San Luis, Argentina
| | - Oscar Parravicini
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 915, 5700 San Luis, Argentina
- IMIBIO-CONICET, UNSL, Chacabuco 915, 5700 San Luis, Argentina
| | - Emilse Sánchez
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 915, 5700 San Luis, Argentina
- IMIBIO-CONICET, UNSL, Chacabuco 915, 5700 San Luis, Argentina
| | - Ricaurte Rodríguez
- Departamento de Química, Universidad Nacional de Colombia, Ciudad Universitaria, Carrera 30, No. 45-03, Bogotá, Colombia
| | - Justo Cobo
- Departamento de Química Inorgánica y Orgánica, Universidad de Jaén, Campus Las Lagunillas s/n, 23071 Jaén, Spain
| | - Ricardo D. Enriz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 915, 5700 San Luis, Argentina
- IMIBIO-CONICET, UNSL, Chacabuco 915, 5700 San Luis, Argentina
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6
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Low JD, Bartberger MD, Chen K, Cheng Y, Fielden MR, Gore V, Hickman D, Liu Q, Allen Sickmier E, Vargas HM, Werner J, White RD, Whittington DA, Wood S, Minatti AE. Development of 2-aminooxazoline 3-azaxanthene β-amyloid cleaving enzyme (BACE) inhibitors with improved selectivity against Cathepsin D. MEDCHEMCOMM 2017; 8:1196-1206. [PMID: 30108829 PMCID: PMC6072065 DOI: 10.1039/c7md00106a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/20/2017] [Indexed: 12/20/2022]
Abstract
As part of an ongoing effort at Amgen to develop a disease-modifying therapy for Alzheimer's disease, we have previously used the aminooxazoline xanthene (AOX) scaffold to generate potent and orally efficacious BACE1 inhibitors. While AOX-BACE1 inhibitors demonstrated acceptable cardiovascular safety margins, a retinal pathological finding in rat toxicological studies demanded further investigation. It has been widely postulated that such retinal toxicity might be related to off-target inhibition of Cathepsin D (CatD), a closely related aspartyl protease. We report the development of AOX-BACE1 inhibitors with improved selectivity against CatD by following a structure- and property-based approach. Our efforts culminated in the discovery of a picolinamide-substituted 3-aza-AOX-BACE1 inhibitor absent of retinal effects in an early screening rat toxicology study.
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Affiliation(s)
- Jonathan D Low
- Department of Medicinal Chemistry , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA . ; Tel: +1 805 447 4721
| | - Michael D Bartberger
- Department of Molecular Engineering , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA
| | - Kui Chen
- Department Discovery Technologies , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA
| | - Yuan Cheng
- Department of Medicinal Chemistry , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA . ; Tel: +1 805 447 4721
| | - Mark R Fielden
- Comparative Biology and Safety Sciences , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA
| | - Vijay Gore
- Department of Medicinal Chemistry , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA . ; Tel: +1 805 447 4721
| | - Dean Hickman
- Department of Pharmacokinetics and Drug Metabolism , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA
| | - Qingyian Liu
- Department of Medicinal Chemistry , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA . ; Tel: +1 805 447 4721
| | - E Allen Sickmier
- Department of Molecular Engineering , Amgen Inc. , 360 Binney Street , Cambridge , MA 02142 , USA
| | - Hugo M Vargas
- Comparative Biology and Safety Sciences , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA
| | - Jonathan Werner
- Comparative Biology and Safety Sciences , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA
| | - Ryan D White
- Department of Medicinal Chemistry , Amgen Inc. , 360 Binney Street , Cambridge , MA 02142 , USA
| | - Douglas A Whittington
- Department of Molecular Engineering , Amgen Inc. , 360 Binney Street , Cambridge , MA 02142 , USA
| | - Stephen Wood
- Department of Neuroscience , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA
| | - Ana E Minatti
- Department of Medicinal Chemistry , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA . ; Tel: +1 805 447 4721
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7
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Current pharmacotherapy and putative disease-modifying therapy for Alzheimer's disease. Neurol Sci 2016; 37:1403-35. [PMID: 27250365 DOI: 10.1007/s10072-016-2625-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/24/2016] [Indexed: 12/14/2022]
Abstract
Alzheimer's disease (AD) is an age-related neurodegenerative disease of the central nervous system correlated with the progressive loss of cognition and memory. β-Amyloid plaques, neurofibrillary tangles and the deficiency in cholinergic neurotransmission constitute the major hallmarks of the AD. Two major hypotheses have been implicated in the pathogenesis of AD namely the cholinergic hypothesis which ascribed the clinical features of dementia to the deficit cholinergic neurotransmission and the amyloid cascade hypothesis which emphasized on the deposition of insoluble peptides formed due to the faulty cleavage of the amyloid precursor protein. Current pharmacotherapy includes mainly the acetylcholinesterase inhibitors and N-methyl-D-aspartate receptor agonist which offer symptomatic therapy and does not address the underlying cause of the disease. The disease-modifying therapy has garnered a lot of research interest for the development of effective pharmacotherapy for AD. β and γ-Secretase constitute attractive targets that are focussed in the disease-modifying approach. Potentiation of α-secretase also seems to be a promising approach towards the development of an effective anti-Alzheimer therapy. Additionally, the ameliorative agents that prevent aggregation of amyloid peptide and also the ones that modulate inflammation and oxidative damage associated with the disease are focussed upon. Development in the area of the vaccines is in progress to combat the characteristic hallmarks of the disease. Use of cholesterol-lowering agents also is a fruitful strategy for the alleviation of the disease as a close association between the cholesterol and AD has been cited. The present review underlines the major therapeutic strategies for AD with focus on the new developments that are on their way to amend the current therapeutic scenario of the disease.
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8
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Ellis CR, Tsai CC, Hou X, Shen J. Constant pH Molecular Dynamics Reveals pH-Modulated Binding of Two Small-Molecule BACE1 Inhibitors. J Phys Chem Lett 2016; 7:944-9. [PMID: 26905811 PMCID: PMC5713896 DOI: 10.1021/acs.jpclett.6b00137] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Targeting β-secretase (BACE1) with small-molecule inhibitors offers a promising route for treatment of Alzheimer's disease. However, the intricate pH dependence of BACE1 function and inhibitor efficacy has posed major challenges for structure-based drug design. Here we investigate two structurally similar BACE1 inhibitors that have dramatically different inhibitory activity using continuous constant pH molecular dynamics (CpHMD). At high pH, both inhibitors are stably bound to BACE1; however, within the enzyme active pH range, only the iminopyrimidinone-based inhibitor remains bound, while the aminothiazine-based inhibitor becomes partially dissociated following the loss of hydrogen bonding with the active site and change of the 10s loop conformation. The drastically lower activity of the second inhibitor is due to the protonation of a catalytic aspartate and the lack of a propyne tail. This work demonstrates that CpHMD can be used for screening pH-dependent binding profiles of small-molecule inhibitors, providing a new tool for structure-based drug design and optimization.
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Affiliation(s)
- Christopher R. Ellis
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD
| | - Cheng-Chieh Tsai
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD
| | - Xinjun Hou
- Neuroscience Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, Cambridge, MA
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD
- Corresponding Author:
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9
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Dražić T, Vazdar K, Vazdar M, Đaković M, Mikecin AM, Kralj M, Malnar M, Hećimović S, Habuš I. Synthesis of new 2-aminoimidazolones with antiproliferative activity via base promoted amino-β-lactam rearrangement. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.10.048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Boy KM, Guernon JM, Wu YJ, Zhang Y, Shi J, Zhai W, Zhu S, Gerritz SW, Toyn JH, Meredith JE, Barten DM, Burton CR, Albright CF, Good AC, Grace JE, Lentz KA, Olson RE, Macor JE, Thompson LA. Macrocyclic prolinyl acyl guanidines as inhibitors of β-secretase (BACE). Bioorg Med Chem Lett 2015; 25:5040-7. [DOI: 10.1016/j.bmcl.2015.10.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/08/2015] [Accepted: 10/12/2015] [Indexed: 02/02/2023]
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11
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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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12
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Egbertson M, McGaughey GB, Pitzenberger SM, Stauffer SR, Coburn CA, Stachel SJ, Yang W, Barrow JC, Neilson LA, McWherter M, Perlow D, Fahr B, Munshi S, Allison TJ, Holloway K, Selnick HG, Yang Z, Swestock J, Simon AJ, Sankaranarayanan S, Colussi D, Tugusheva K, Lai MT, Pietrak B, Haugabook S, Jin L, Chen IW, Holahan M, Stranieri-Michener M, Cook JJ, Vacca J, Graham SL. Methyl-substitution of an iminohydantoin spiropiperidine β-secretase (BACE-1) inhibitor has a profound effect on its potency. Bioorg Med Chem Lett 2015. [PMID: 26195137 DOI: 10.1016/j.bmcl.2015.06.082] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The IC50 of a beta-secretase (BACE-1) lead compound was improved ∼200-fold from 11 μM to 55 nM through the addition of a single methyl group. Computational chemistry, small molecule NMR, and protein crystallography capabilities were used to compare the solution conformation of the ligand under varying pH conditions to its conformation when bound in the active site. Chemical modification then explored available binding pockets adjacent to the ligand. A strategically placed methyl group not only maintained the required pKa of the piperidine nitrogen and filled a small hydrophobic pocket, but more importantly, stabilized the conformation best suited for optimized binding to the receptor.
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Affiliation(s)
- Melissa Egbertson
- Medicinal Chemistry Department, WP14-2 Merck and Co., West Point, PA 19486, USA.
| | | | - Steven M Pitzenberger
- NMR Structure Elucidation, Process and Analytical Chemistry, WP14-1 Merck and Co., West Point, PA 19486, USA
| | - Shaun R Stauffer
- Medicinal Chemistry Department, WP14-2 Merck and Co., West Point, PA 19486, USA
| | - Craig A Coburn
- Medicinal Chemistry Department, WP14-2 Merck and Co., West Point, PA 19486, USA
| | - Shawn J Stachel
- Medicinal Chemistry Department, WP14-2 Merck and Co., West Point, PA 19486, USA
| | - Wenjin Yang
- Sunesis Pharmaceuticals, 395 Oyster Point Blvd. Ste. 400, South San Francisco, CA 94080, USA
| | - James C Barrow
- Medicinal Chemistry Department, WP14-2 Merck and Co., West Point, PA 19486, USA
| | - Lou Anne Neilson
- Medicinal Chemistry Department, WP14-2 Merck and Co., West Point, PA 19486, USA
| | - Melody McWherter
- Medicinal Chemistry Department, WP14-2 Merck and Co., West Point, PA 19486, USA
| | - Debra Perlow
- Medicinal Chemistry Department, WP14-2 Merck and Co., West Point, PA 19486, USA
| | - Bruce Fahr
- Sunesis Pharmaceuticals, 395 Oyster Point Blvd. Ste. 400, South San Francisco, CA 94080, USA
| | - Sanjeev Munshi
- Structural Biology, WP 14-2 Merck and Co., West Point, PA 19486, USA
| | - Timothy J Allison
- Structural Biology, WP 14-2 Merck and Co., West Point, PA 19486, USA.
| | | | - Harold G Selnick
- Medicinal Chemistry Department, WP14-2 Merck and Co., West Point, PA 19486, USA.
| | - ZhiQiang Yang
- Medicinal Chemistry Department, WP14-2 Merck and Co., West Point, PA 19486, USA
| | - John Swestock
- Process Chemistry, WP 14-1 Merck and Co., West Point, PA 19486, USA
| | - Adam J Simon
- Pharmacology, WP 26-1 Merck and Co., West Point, PA 19486, USA
| | | | - Dennis Colussi
- Pharmacology, WP 26-1 Merck and Co., West Point, PA 19486, USA
| | | | - Ming-Tain Lai
- Pharmacology, WP 26-1 Merck and Co., West Point, PA 19486, USA
| | - Beth Pietrak
- Pharmacology, WP 26-1 Merck and Co., West Point, PA 19486, USA
| | - Shari Haugabook
- Pharmacology, WP 26-1 Merck and Co., West Point, PA 19486, USA
| | - Lixia Jin
- Drug Metabolism, WP 75-B Merck and Co., West Point, PA 19486, USA
| | - I-W Chen
- Drug Metabolism, WP 75-B Merck and Co., West Point, PA 19486, USA
| | - Marie Holahan
- Imaging Research, WP 44c Merck and Co., West Point, PA 19486, USA
| | | | | | - Joseph Vacca
- Medicinal Chemistry Department, WP14-2 Merck and Co., West Point, PA 19486, USA
| | - Samuel L Graham
- Medicinal Chemistry Department, WP14-2 Merck and Co., West Point, PA 19486, USA
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13
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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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14
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Epstein O, Bryan MC, Cheng AC, Derakhchan K, Dineen TA, Hickman D, Hua Z, Human JB, Kreiman C, Marx IE, Weiss MM, Wahl RC, Wen PH, Whittington DA, Wood S, Zheng XM, Fremeau RT, White RD, Patel VF. Lead optimization and modulation of hERG activity in a series of aminooxazoline xanthene β-site amyloid precursor protein cleaving enzyme (BACE1) inhibitors. J Med Chem 2014; 57:9796-810. [PMID: 25389560 DOI: 10.1021/jm501266w] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The optimization of a series of aminooxazoline xanthene inhibitors of β-site amyloid precursor protein cleaving enzyme 1 (BACE1) is described. An early lead compound showed robust Aβ lowering activity in a rat pharmacodynamic model, but advancement was precluded by a low therapeutic window to QTc prolongation in cardiovascular models consistent with in vitro activity on the hERG ion channel. While the introduction of polar groups was effective in reducing hERG binding affinity, this came at the expense of higher than desired Pgp-mediated efflux. A balance of low Pgp efflux and hERG activity was achieved by lowering the polar surface area of the P3 substituent while retaining polarity in the P2' side chain. The introduction of a fluorine in position 4 of the xanthene ring improved BACE1 potency (5-10-fold). The combination of these optimized fragments resulted in identification of compound 40, which showed robust Aβ reduction in a rat pharmacodynamic model (78% Aβ reduction in CSF at 10 mg/kg po) and also showed acceptable cardiovascular safety in vivo.
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Affiliation(s)
- Oleg Epstein
- Departments of Therapeutic Discovery, ‡Neuroscience, §Molecular Structure and Characterization, ∥Pharmacokinetics and Drug Metabolism, and ⊥Comparative Biology and Safety Sciences, Amgen Inc. , 360 Binney Street, Cambridge, Massachusetts 02142, One Amgen Center Drive, Thousand Oaks, California 91320, and 1120 Veterans Boulevard, South San Francisco, California 94080, United States
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15
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Oehlrich D, Prokopcova H, Gijsen HJ. The evolution of amidine-based brain penetrant BACE1 inhibitors. Bioorg Med Chem Lett 2014; 24:2033-45. [DOI: 10.1016/j.bmcl.2014.03.025] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/06/2014] [Accepted: 03/07/2014] [Indexed: 01/18/2023]
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16
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Viklund J, Kolmodin K, Nordvall G, Swahn BM, Svensson M, Gravenfors Y, Rahm F. Creation of Novel Cores for β-Secretase (BACE-1) Inhibitors: A Multiparameter Lead Generation Strategy. ACS Med Chem Lett 2014; 5:440-5. [PMID: 24900855 DOI: 10.1021/ml5000433] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 02/03/2014] [Indexed: 12/18/2022] Open
Abstract
In order to find optimal core structures as starting points for lead optimization, a multiparameter lead generation workflow was designed with the goal of finding BACE-1 inhibitors as a treatment for Alzheimer's disease. De novo design of core fragments was connected with three predictive in silico models addressing target affinity, permeability, and hERG activity, in order to guide synthesis. Taking advantage of an additive SAR, the prioritized cores were decorated with a few, well-characterized substituents from known BACE-1 inhibitors in order to allow for core-to-core comparisons. Prediction methods and analyses of how physicochemical properties of the core structures correlate to in vitro data are described. The syntheses and in vitro data of the test compounds are reported in a separate paper by Ginman et al. [J. Med. Chem. 2013, 56, 4181-4205]. The affinity predictions are described in detail by Roos et al. [J. Chem. Inf. 2014, DOI: 10.1021/ci400374z].
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Affiliation(s)
- Jenny Viklund
- Department of Medicinal Chemistry AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Karin Kolmodin
- Department of Medicinal Chemistry AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Gunnar Nordvall
- Department of Medicinal Chemistry AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Britt-Marie Swahn
- Department of Medicinal Chemistry AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Mats Svensson
- Department of Medicinal Chemistry AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Ylva Gravenfors
- Department of Medicinal Chemistry AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Fredrik Rahm
- Department of Medicinal Chemistry AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
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17
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Ginman T, Viklund J, Malmström J, Blid J, Emond R, Forsblom R, Johansson A, Kers A, Lake F, Sehgelmeble F, Sterky KJ, Bergh M, Lindgren A, Johansson P, Jeppsson F, Fälting J, Gravenfors Y, Rahm F. Core refinement toward permeable β-secretase (BACE-1) inhibitors with low hERG activity. J Med Chem 2013; 56:4181-205. [PMID: 23126626 DOI: 10.1021/jm3011349] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
By use of iterative design aided by predictive models for target affinity, brain permeability, and hERG activity, novel and diverse compounds based on cyclic amidine and guanidine cores were synthesized with the goal of finding BACE-1 inhibitors as a treatment for Alzheimer's disease. Since synthesis feasibility had low priority in the design of the cores, an extensive synthesis effort was needed to make the relevant compounds. Syntheses of these compounds are reported, together with physicochemical properties and structure-activity relationships based on in vitro data. Four crystal structures of diverse amidines binding in the active site are deposited and discussed. Inhibitors of BACE-1 with 3 μM to 32 nM potencies in cells are shown, together with data on in vivo brain exposure levels for four compounds. The results presented show the importance of the core structure for the profile of the final compounds.
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Affiliation(s)
- Tobias Ginman
- Department of Medicinal Chemistry, AstraZeneca R&D Södertälje, SE-151 85, Södertälje, Sweden
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18
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Effect of pH and ligand charge state on BACE-1 fragment docking performance. J Comput Aided Mol Des 2013; 27:403-17. [DOI: 10.1007/s10822-013-9653-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 04/24/2013] [Indexed: 10/26/2022]
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19
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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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20
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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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21
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Design, synthesis and evaluation of 3-(2-aminoheterocycle)-4-benzyloxyphenylbenzamide derivatives as BACE-1 inhibitors. Molecules 2013; 18:3577-94. [PMID: 23519200 PMCID: PMC6269915 DOI: 10.3390/molecules18033577] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Revised: 03/15/2013] [Accepted: 03/18/2013] [Indexed: 11/16/2022] Open
Abstract
Three series of 3-(2-aminoheterocycle)-4-benzyloxyphenylbenzamide derivatives, 2-aminooxazoles, 2-aminothiazoles, and 2-amino-6H-1,3,4-thiadizines were designed, synthesized and evaluated as β-secretase (BACE-1) inhibitors. Preliminary structure-activity relationships revealed that the existence of a 2-amino-6H-1,3,4-thiadizine moiety and α-naphthyl group were favorable for BACE-1 inhibition. Among the synthesized compounds, 5e exhibited the most potent BACE-1 inhibitory activity, with an IC50 value of 9.9 μΜ and it exhibited high brain uptake potential in Madin-Darby anine kidney cell lines (MDCK) and a Madin-Darby canine kidney-multidrug resistance 1 (MDCK-MDR1) model.
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22
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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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23
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Folk DS, Torosian JC, Hwang S, McCafferty DG, Franz KJ. Monitoring β-secretase activity in living cells with a membrane-anchored FRET probe. Angew Chem Int Ed Engl 2012; 51:10795-9. [PMID: 23023944 PMCID: PMC3495557 DOI: 10.1002/anie.201206673] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Indexed: 11/09/2022]
Affiliation(s)
| | | | | | | | - Katherine J. Franz
- Department of Chemistry, Duke University 124 Science Dr., Durham, NC 27708, USA
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24
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Yonezawa S, Yamamoto T, Yamakawa H, Muto C, Hosono M, Hattori K, Higashino K, Yutsudo T, Iwamoto H, Kondo Y, Sakagami M, Togame H, Tanaka Y, Nakano T, Takemoto H, Arisawa M, Shuto S. Conformational Restriction Approach to β-Secretase (BACE1) Inhibitors: Effect of a Cyclopropane Ring To Induce an Alternative Binding Mode. J Med Chem 2012; 55:8838-58. [PMID: 22998419 DOI: 10.1021/jm3011405] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Shuji Yonezawa
- Shionogi Innovation Center for Drug Discovery, Shionogi & Co., Ltd., Kita-21 Nishi-11 Kita-ku, Sapporo 001-0021, Japan
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo
060-0812, Japan
| | - Takahiko Yamamoto
- Pharmaceutical Research Division, Medicinal Research Laboratories, and Innovative Drug Discovery Research Laboratories, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Hidekuni Yamakawa
- Pharmaceutical Research Division, Medicinal Research Laboratories, and Innovative Drug Discovery Research Laboratories, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Chie Muto
- Pharmaceutical Research Division, Medicinal Research Laboratories, and Innovative Drug Discovery Research Laboratories, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Motoko Hosono
- Pharmaceutical Research Division, Medicinal Research Laboratories, and Innovative Drug Discovery Research Laboratories, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Kazunari Hattori
- Pharmaceutical Research Division, Medicinal Research Laboratories, and Innovative Drug Discovery Research Laboratories, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Kenichi Higashino
- Shionogi Innovation Center for Drug Discovery, Shionogi & Co., Ltd., Kita-21 Nishi-11 Kita-ku, Sapporo 001-0021, Japan
| | - Takashi Yutsudo
- Pharmaceutical Research Division, Medicinal Research Laboratories, and Innovative Drug Discovery Research Laboratories, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Hideo Iwamoto
- Shionogi Techno Advance Research
Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Yutaka Kondo
- Shionogi Techno Advance Research
Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Masahiro Sakagami
- Pharmaceutical Research Division, Medicinal Research Laboratories, and Innovative Drug Discovery Research Laboratories, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Hiroko Togame
- Quality, Safety and Regulatory Affairs Management Division, Shionogi & Co., Ltd., 1-8, Doshomachi 3-chome, Chuo-ku, Osaka 541-0045, Japan
| | - Yoshikazu Tanaka
- Shionogi Innovation Center for Drug Discovery, Shionogi & Co., Ltd., Kita-21 Nishi-11 Kita-ku, Sapporo 001-0021, Japan
| | - Toru Nakano
- Shionogi Innovation Center for Drug Discovery, Shionogi & Co., Ltd., Kita-21 Nishi-11 Kita-ku, Sapporo 001-0021, Japan
| | - Hiroshi Takemoto
- Pharmaceutical Research Division, Medicinal Research Laboratories, and Innovative Drug Discovery Research Laboratories, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Mitsuhiro Arisawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo
060-0812, Japan
| | - Satoshi Shuto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo
060-0812, Japan
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25
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Brodney MA, Barreiro G, Ogilvie K, Hajos-Korcsok E, Murray J, Vajdos F, Ambroise C, Christoffersen C, Fisher K, Lanyon L, Liu J, Nolan CE, Withka JM, Borzilleri KA, Efremov I, Oborski CE, Varghese A, O'Neill BT. Spirocyclic sulfamides as β-secretase 1 (BACE-1) inhibitors for the treatment of Alzheimer's disease: utilization of structure based drug design, WaterMap, and CNS penetration studies to identify centrally efficacious inhibitors. J Med Chem 2012; 55:9224-39. [PMID: 22984865 DOI: 10.1021/jm3009426] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
β-Secretase 1 (BACE-1) is an attractive therapeutic target for the treatment and prevention of Alzheimer's disease (AD). Herein, we describe the discovery of a novel class of BACE-1 inhibitors represented by sulfamide 14g, using a medicinal chemistry strategy to optimize central nervous system (CNS) penetration by minimizing hydrogen bond donors (HBDs) and reducing P-glycoprotein (P-gp) mediated efflux. We have also taken advantage of the combination of structure based drug design (SBDD) to guide the optimization of the sulfamide analogues and the in silico tool WaterMap to explain the observed SAR. Compound 14g is a potent inhibitor of BACE-1 with excellent permeability and a moderate P-gp liability. Administration of 14g to mice produced a significant, dose-dependent reduction in central Aβ(X-40) levels at a free drug exposure equivalent to the whole cell IC(50) (100 nM). Furthermore, studies of the P-gp knockout mouse provided evidence that efflux transporters affected the amount of Aβ lowering versus that observed in wild-type (WT) mouse at an equivalent dose.
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Affiliation(s)
- Michael A Brodney
- Department of Neuroscience, Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States.
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26
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Gravenfors Y, Viklund J, Blid J, Ginman T, Karlström S, Kihlström J, Kolmodin K, Lindström J, von Berg S, von Kieseritzky F, Bogar K, Slivo C, Swahn BM, Olsson LL, Johansson P, Eketjäll S, Fälting J, Jeppsson F, Strömberg K, Janson J, Rahm F. New aminoimidazoles as β-secretase (BACE-1) inhibitors showing amyloid-β (Aβ) lowering in brain. J Med Chem 2012; 55:9297-311. [PMID: 23017051 DOI: 10.1021/jm300991n] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amino-2H-imidazoles are described as a new class of BACE-1 inhibitors for the treatment of Alzheimer's disease. Synthetic methods, crystal structures, and structure-activity relationships for target activity, permeability, and hERG activity are reported and discussed. Compound (S)-1m was one of the most promising compounds in this report, with high potency in the cellular assay and a good overall profile. When guinea pigs were treated with compound (S)-1m, a concentration and time dependent decrease in Aβ40 and Aβ42 levels in plasma, brain, and CSF was observed. The maximum reduction of brain Aβ was 40-50%, 1.5 h after oral dosing (100 μmol/kg). The results presented highlight the potential of this new class of BACE-1 inhibitors with good target potency and with low effect on hERG, in combination with a fair CNS exposure in vivo.
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Affiliation(s)
- Ylva Gravenfors
- Department of Medicinal Chemistry, AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden.
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27
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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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Folk DS, Torosian JC, Hwang S, McCafferty DG, Franz KJ. Monitoring β-Secretase Activity in Living Cells with a Membrane-Anchored FRET Probe. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206673] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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29
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Swahn BM, Kolmodin K, Karlström S, von Berg S, Söderman P, Holenz J, Berg S, Lindström J, Sundström M, Turek D, Kihlström J, Slivo C, Andersson L, Pyring D, Rotticci D, Öhberg L, Kers A, Bogar K, von Kieseritzky F, Bergh M, Olsson LL, Janson J, Eketjäll S, Georgievska B, Jeppsson F, Fälting J. Design and Synthesis of β-Site Amyloid Precursor Protein Cleaving Enzyme (BACE1) Inhibitors with in Vivo Brain Reduction of β-Amyloid Peptides. J Med Chem 2012; 55:9346-61. [DOI: 10.1021/jm3009025] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Lise-Lotte Olsson
- Discovery Sciences, AstraZeneca R&D Mölndal, SE-43183 Mölndal, Sweden
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30
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Huang H, La DS, Cheng AC, Whittington DA, Patel VF, Chen K, Dineen TA, Epstein O, Graceffa R, Hickman D, Kiang YH, Louie S, Luo Y, Wahl RC, Wen PH, Wood S, Fremeau RT. Structure- and Property-Based Design of Aminooxazoline Xanthenes as Selective, Orally Efficacious, and CNS Penetrable BACE Inhibitors for the Treatment of Alzheimer’s Disease. J Med Chem 2012; 55:9156-69. [DOI: 10.1021/jm300598e] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hongbing Huang
- Department
of Medicinal Chemistry and ‡Department of Molecular Structure, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts
02142, United States
- Department
of Neuroscience, ∥Department of Pharmacokinetics and Drug Metabolism, ⊥Department of HTS and Molecular
Pharmacology, and #Department of Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United
States
| | - Daniel S. La
- Department
of Medicinal Chemistry and ‡Department of Molecular Structure, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts
02142, United States
- Department
of Neuroscience, ∥Department of Pharmacokinetics and Drug Metabolism, ⊥Department of HTS and Molecular
Pharmacology, and #Department of Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United
States
| | - Alan C. Cheng
- Department
of Medicinal Chemistry and ‡Department of Molecular Structure, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts
02142, United States
- Department
of Neuroscience, ∥Department of Pharmacokinetics and Drug Metabolism, ⊥Department of HTS and Molecular
Pharmacology, and #Department of Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United
States
| | - Douglas A. Whittington
- Department
of Medicinal Chemistry and ‡Department of Molecular Structure, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts
02142, United States
- Department
of Neuroscience, ∥Department of Pharmacokinetics and Drug Metabolism, ⊥Department of HTS and Molecular
Pharmacology, and #Department of Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United
States
| | - Vinod F. Patel
- Department
of Medicinal Chemistry and ‡Department of Molecular Structure, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts
02142, United States
- Department
of Neuroscience, ∥Department of Pharmacokinetics and Drug Metabolism, ⊥Department of HTS and Molecular
Pharmacology, and #Department of Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United
States
| | - Kui Chen
- Department
of Medicinal Chemistry and ‡Department of Molecular Structure, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts
02142, United States
- Department
of Neuroscience, ∥Department of Pharmacokinetics and Drug Metabolism, ⊥Department of HTS and Molecular
Pharmacology, and #Department of Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United
States
| | - Thomas A. Dineen
- Department
of Medicinal Chemistry and ‡Department of Molecular Structure, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts
02142, United States
- Department
of Neuroscience, ∥Department of Pharmacokinetics and Drug Metabolism, ⊥Department of HTS and Molecular
Pharmacology, and #Department of Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United
States
| | - Oleg Epstein
- Department
of Medicinal Chemistry and ‡Department of Molecular Structure, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts
02142, United States
- Department
of Neuroscience, ∥Department of Pharmacokinetics and Drug Metabolism, ⊥Department of HTS and Molecular
Pharmacology, and #Department of Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United
States
| | - Russell Graceffa
- Department
of Medicinal Chemistry and ‡Department of Molecular Structure, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts
02142, United States
- Department
of Neuroscience, ∥Department of Pharmacokinetics and Drug Metabolism, ⊥Department of HTS and Molecular
Pharmacology, and #Department of Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United
States
| | - Dean Hickman
- Department
of Medicinal Chemistry and ‡Department of Molecular Structure, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts
02142, United States
- Department
of Neuroscience, ∥Department of Pharmacokinetics and Drug Metabolism, ⊥Department of HTS and Molecular
Pharmacology, and #Department of Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United
States
| | - Y.-H. Kiang
- Department
of Medicinal Chemistry and ‡Department of Molecular Structure, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts
02142, United States
- Department
of Neuroscience, ∥Department of Pharmacokinetics and Drug Metabolism, ⊥Department of HTS and Molecular
Pharmacology, and #Department of Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United
States
| | - Steven Louie
- Department
of Medicinal Chemistry and ‡Department of Molecular Structure, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts
02142, United States
- Department
of Neuroscience, ∥Department of Pharmacokinetics and Drug Metabolism, ⊥Department of HTS and Molecular
Pharmacology, and #Department of Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United
States
| | - Yi Luo
- Department
of Medicinal Chemistry and ‡Department of Molecular Structure, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts
02142, United States
- Department
of Neuroscience, ∥Department of Pharmacokinetics and Drug Metabolism, ⊥Department of HTS and Molecular
Pharmacology, and #Department of Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United
States
| | - Robert C. Wahl
- Department
of Medicinal Chemistry and ‡Department of Molecular Structure, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts
02142, United States
- Department
of Neuroscience, ∥Department of Pharmacokinetics and Drug Metabolism, ⊥Department of HTS and Molecular
Pharmacology, and #Department of Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United
States
| | - Paul H. Wen
- Department
of Medicinal Chemistry and ‡Department of Molecular Structure, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts
02142, United States
- Department
of Neuroscience, ∥Department of Pharmacokinetics and Drug Metabolism, ⊥Department of HTS and Molecular
Pharmacology, and #Department of Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United
States
| | - Stephen Wood
- Department
of Medicinal Chemistry and ‡Department of Molecular Structure, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts
02142, United States
- Department
of Neuroscience, ∥Department of Pharmacokinetics and Drug Metabolism, ⊥Department of HTS and Molecular
Pharmacology, and #Department of Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United
States
| | - Robert T. Fremeau
- Department
of Medicinal Chemistry and ‡Department of Molecular Structure, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts
02142, United States
- Department
of Neuroscience, ∥Department of Pharmacokinetics and Drug Metabolism, ⊥Department of HTS and Molecular
Pharmacology, and #Department of Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United
States
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Wood S, Wen PH, Zhang J, Zhu L, Luo Y, Babu-Khan S, Chen K, Pham R, Esmay J, Dineen TA, Kaller MR, Weiss MM, Hitchcock SA, Citron M, Zhong W, Hickman D, Williamson T. Establishing the Relationship between In Vitro Potency, Pharmacokinetic, and Pharmacodynamic Parameters in a Series of Orally Available, Hydroxyethylamine-Derived β-Secretase Inhibitors. J Pharmacol Exp Ther 2012; 343:460-7. [DOI: 10.1124/jpet.112.197954] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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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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33
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Heterocycles in peptidomimetics and pseudopeptides: design and synthesis. Pharmaceuticals (Basel) 2012; 5:297-316. [PMID: 24281380 PMCID: PMC3763636 DOI: 10.3390/ph5030297] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 02/22/2012] [Accepted: 02/28/2012] [Indexed: 11/17/2022] Open
Abstract
This minireview provides a brief outline of the peculiar aspects of the preparation of peptidomimetic and pseudopeptidic structures containing heterocycles. In particular novel tricyclic structures are investigated as potential drugs.
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Chiriano G, De Simone A, Mancini F, Perez DI, Cavalli A, Bolognesi ML, Legname G, Martinez A, Andrisano V, Carloni P, Roberti M. A small chemical library of 2-aminoimidazole derivatives as BACE-1 inhibitors: Structure-based design, synthesis, and biological evaluation. Eur J Med Chem 2012; 48:206-13. [DOI: 10.1016/j.ejmech.2011.12.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 11/03/2011] [Accepted: 12/09/2011] [Indexed: 10/14/2022]
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35
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Aminoimidazoles as BACE-1 inhibitors: the challenge to achieve in vivo brain efficacy. Bioorg Med Chem Lett 2012; 22:1854-9. [PMID: 22325942 DOI: 10.1016/j.bmcl.2012.01.079] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 01/20/2012] [Accepted: 01/21/2012] [Indexed: 10/14/2022]
Abstract
The evaluation of a series of bicyclic aminoimidazoles as potent BACE-1 inhibitors is described. The crystal structures of compounds 14 and 23 in complex with BACE-1 reveal hydrogen bond interactions with the protein important for achieving potent inhibition. The optimization of permeability and efflux properties of the compounds is discussed as well as the importance of these properties for attaining in vivo brain efficacy. Compound (R)-25 was selected for evaluation in vivo in wild type mice and 1.5h after oral co-administration of 300μmol/kg (R)-25 and efflux inhibitor GF120918 the brain Aβ40 level was reduced by 17% and the plasma Aβ40 level by 76%.
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36
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Discovery of pyrrolidine-based β-secretase inhibitors: Lead advancement through conformational design for maintenance of ligand binding efficiency. Bioorg Med Chem Lett 2012; 22:240-4. [DOI: 10.1016/j.bmcl.2011.11.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2011] [Revised: 11/04/2011] [Accepted: 11/07/2011] [Indexed: 11/23/2022]
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37
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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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38
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Rational design and synthesis of aminopiperazinones as β-secretase (BACE) inhibitors. Bioorg Med Chem Lett 2011; 21:7255-60. [DOI: 10.1016/j.bmcl.2011.10.050] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 10/13/2011] [Accepted: 10/14/2011] [Indexed: 11/23/2022]
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39
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Köster H, Craan T, Brass S, Herhaus C, Zentgraf M, Neumann L, Heine A, Klebe G. A small nonrule of 3 compatible fragment library provides high hit rate of endothiapepsin crystal structures with various fragment chemotypes. J Med Chem 2011; 54:7784-96. [PMID: 21972967 DOI: 10.1021/jm200642w] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Druglike molecules are defined by Lipinski's rule of 5, to characterize fragment thresholds, they have been reduced from 5 to 3 (Astex's rule of 3). They are applied to assemble fragment libraries, and providers use them to select fragments for commercial offer. We question whether these rules are too stringent to compose fragment libraries with candidates exhibiting sufficient room for chemical subsequent growing and merging modifications as appropriate functional groups for chemical transformations are required. Usually these groups exhibit properties as hydrogen bond donors/acceptors and provide entry points for optimization chemistry. We therefore designed a fragment library (364 entries) without strictly applying the rule of 3. For initial screening for endothiapepsin binding, we performed a biochemical cleavage assay of a fluorogenic substrate at 1 mM. "Hits" were defined to inhibit the enzyme by at least 40%. Fifty-five hits were suggested and subsequently soaked into endothiapepsin crystals. Eleven crystal structures could be determined covering fragments with diverse binding modes: (i) direct binding to the catalytic dyad aspartates, (ii) water-mediated binding to the aspartates, (iii) no direct interaction with the dyad. They occupy different specificity pockets. Only 4 of the 11 fragments are consistent with the rule of 3. Restriction to this rule would have limited the fragment hits to a strongly reduced variety of chemotypes.
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Affiliation(s)
- Helene Köster
- Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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40
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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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41
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Spronk SA, Carlson HA. The role of tyrosine 71 in modulating the flap conformations of BACE1. Proteins 2011; 79:2247-59. [PMID: 21590744 DOI: 10.1002/prot.23050] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 03/03/2011] [Accepted: 03/22/2011] [Indexed: 11/09/2022]
Abstract
β-Site amyloid precursor protein cleaving enzyme 1 (BACE1) is a potential target for treating Alzheimer's disease. BACE1's binding site is partially covered by a flexible loop on its N-terminal domain, known as the "flap," which has been found in several conformations in crystal structures of BACE1 and other aspartyl proteases. The side chain of the invariant residue Tyr71 on the flap adopts several rotameric orientations, leading to our hypothesis that the orientation of this residue dictates the movement and conformations available to the flap. We investigated this hypothesis by performing 220 ns of molecular dynamics simulations of bound and unbound wild-type BACE1 as well as the unbound Y71A mutant. Our findings indicate that the flap exhibits various degrees of mobility and adopts different conformations depending on the Tyr71 orientation. Surprisingly, the "self-inhibited" form is stable in our simulations, making it a reasonable target for drug design. The alanine mutant, lacking a large side chain at position 71, displays significant differences in flap dynamics from wild type, freely sampling very open and closed conformations. Our simulations show that Tyr71, in addition to its previously determined functions in catalysis and substrate binding, has the important role of modulating flap conformations in BACE1.
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Affiliation(s)
- Steven A Spronk
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA.
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42
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Cole DC, Bursavich MG. Nonpeptide BACE1 Inhibitors: Design and Synthesis. ASPARTIC ACID PROTEASES AS THERAPEUTIC TARGETS 2011. [DOI: 10.1002/9783527630943.ch17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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43
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Rueeger H, Rondeau JM, McCarthy C, Möbitz H, Tintelnot-Blomley M, Neumann U, Desrayaud S. Structure based design, synthesis and SAR of cyclic hydroxyethylamine (HEA) BACE-1 inhibitors. Bioorg Med Chem Lett 2011; 21:1942-7. [DOI: 10.1016/j.bmcl.2011.02.038] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2010] [Revised: 02/09/2011] [Accepted: 02/10/2011] [Indexed: 01/16/2023]
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44
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Christopeit T, Stenberg G, Gossas T, Nyström S, Baraznenok V, Lindström E, Danielson UH. A surface plasmon resonance-based biosensor with full-length BACE1 in a reconstituted membrane. Anal Biochem 2011; 414:14-22. [PMID: 21382336 DOI: 10.1016/j.ab.2011.02.041] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 02/17/2011] [Accepted: 02/27/2011] [Indexed: 10/18/2022]
Abstract
A surface plasmon resonance (SPR) biosensor-based assay for membrane-embedded full-length BACE1 (β-site amyloid precursor protein cleaving enzyme 1), a drug target for Alzheimer's disease, has been developed. It allows the analysis of interactions with the protein in its natural lipid membrane environment. The enzyme was captured via an antibody recognizing a C-terminal His6 tag, after which a lipid membrane was reconstituted on the chip using a brain lipid extract. The interaction between the enzyme and several inhibitors confirmed that the surface was functional. It had slightly different interaction characteristics as compared with a reference surface with immobilized ectodomain BACE1 but had the same inhibitor characteristic pH effect. The possibility of studying interactions with BACE1 under more physiological conditions than assays using truncated enzyme or conditions dictated by high enzyme activity is expected to increase our understanding of the role of BACE1 in Alzheimer's disease and contribute to the discovery of clinically efficient BACE1 inhibitors. The strategy exploited in the current study can be adapted to other membrane-bound drug targets by selecting suitable capture antibodies and lipid mixtures for membrane reconstitution.
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Affiliation(s)
- Tony Christopeit
- Department of Biochemistry and Organic Chemistry, Uppsala University, Sweden
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45
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Domínguez JL, Christopeit T, Villaverde MC, Gossas T, Otero JM, Nyström S, Baraznenok V, Lindström E, Danielson UH, Sussman F. Effect of the Protonation State of the Titratable Residues on the Inhibitor Affinity to BACE-1. Biochemistry 2010; 49:7255-63. [DOI: 10.1021/bi100637n] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- José L. Domínguez
- Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Tony Christopeit
- Department of Biochemistry and Organic Chemistry, Uppsala University, Uppsala, Sweden
| | - M. Carmen Villaverde
- Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Thomas Gossas
- Department of Biochemistry and Organic Chemistry, Uppsala University, Uppsala, Sweden
| | - José M. Otero
- Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | | | | | | | - U. Helena Danielson
- Department of Biochemistry and Organic Chemistry, Uppsala University, Uppsala, Sweden
| | - Fredy Sussman
- Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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46
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Murray CW, Blundell TL. Structural biology in fragment-based drug design. Curr Opin Struct Biol 2010; 20:497-507. [DOI: 10.1016/j.sbi.2010.04.003] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Revised: 03/26/2010] [Accepted: 04/14/2010] [Indexed: 10/19/2022]
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47
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Novel pyrrolyl 2-aminopyridines as potent and selective human β-secretase (BACE1) inhibitors. Bioorg Med Chem Lett 2010; 20:2068-73. [DOI: 10.1016/j.bmcl.2010.02.075] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 02/14/2010] [Accepted: 02/18/2010] [Indexed: 11/21/2022]
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48
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Rapid P1 SAR of brain penetrant tertiary carbinamine derived BACE inhibitors. Bioorg Med Chem Lett 2010; 20:1779-82. [DOI: 10.1016/j.bmcl.2010.01.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Revised: 12/30/2009] [Accepted: 01/04/2010] [Indexed: 11/21/2022]
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49
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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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50
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Wang YS, Strickland C, Voigt JH, Kennedy ME, Beyer BM, Senior MM, Smith EM, Nechuta TL, Madison VS, Czarniecki M, McKittrick BA, Stamford AW, Parker EM, Hunter JC, Greenlee WJ, Wyss DF. Application of Fragment-Based NMR Screening, X-ray Crystallography, Structure-Based Design, and Focused Chemical Library Design to Identify Novel μM Leads for the Development of nM BACE-1 (β-Site APP Cleaving Enzyme 1) Inhibitors. J Med Chem 2009; 53:942-50. [DOI: 10.1021/jm901472u] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu-Sen Wang
- Schering-Plough Research Institute, 320 Bent Street, Cambridge, Massachusetts 02141
| | - Corey Strickland
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Johannes H. Voigt
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Matthew E. Kennedy
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Brian M. Beyer
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Mary M. Senior
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Elizabeth M. Smith
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Terry L. Nechuta
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Vincent S. Madison
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Michael Czarniecki
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Brian A. McKittrick
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Andrew W. Stamford
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Eric M. Parker
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - John C. Hunter
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - William J. Greenlee
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Daniel F. Wyss
- Schering-Plough Research Institute, 320 Bent Street, Cambridge, Massachusetts 02141
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