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Guanidine-based β amyloid precursor protein cleavage enzyme 1 (BACE-1) inhibitors for the Alzheimer's disease (AD): A review. Bioorg Med Chem 2022; 74:117047. [DOI: 10.1016/j.bmc.2022.117047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/16/2022] [Accepted: 10/04/2022] [Indexed: 11/02/2022]
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Allostery Inhibition of BACE1 by Psychotic and Meroterpenoid Drugs in Alzheimer's Disease Therapy. Molecules 2022; 27:molecules27144372. [PMID: 35889246 PMCID: PMC9320338 DOI: 10.3390/molecules27144372] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/06/2022] [Accepted: 01/17/2022] [Indexed: 02/04/2023] Open
Abstract
In over a century since its discovery, Alzheimer’s disease (AD) has continued to be a global health concern due to its incurable nature and overwhelming increase among older people. In this paper, we give an overview of the efforts of researchers towards identifying potent BACE1 exosite-binding antibodies and allosteric inhibitors. Herein, we apply computer-aided drug design (CADD) methods to unravel the interactions of some proposed psychotic and meroterpenoid BACE1 allosteric site inhibitors. This study is aimed at validating the allosteric potentials of these selected compounds targeted at BACE1 inhibition. Molecular docking, molecular dynamic (MD) simulations, and post-MD analyses are carried out on these selected compounds, which have been experimentally proven to exhibit allosteric inhibition on BACE1. The SwissDock software enabled us to identify more than five druggable pockets on the BACE1 structural surface using docking. Besides the active site region, a melatonin derivative (compound 1) previously proposed as a BACE1 allostery inhibitor showed appreciable stability at eight different subsites on BACE1. Refinement with molecular dynamic (MD) simulations shows that the identified non-catalytic sites are potential allostery sites for compound 1. The allostery and binding mechanism of the selected potent inhibitors show that the smaller the molecule, the easier the attachment to several enzyme regions. This finding hereby establishes that most of these selected compounds failed to exhibit strong allosteric binding with BACE1 except for compound 1. We hereby suggest that further studies and additional identification/validation of other BACE1 allosteric compounds be done. Furthermore, this additional allosteric site investigation will help in reducing the associated challenges with designing BACE1 inhibitors while exploring the opportunities in the design of allosteric BACE1 inhibitors.
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Carret S, Poisson JF, Berthiol F, Achuenu C. 1,2-Additions on Chiral N-Sulfinylketimines: An Easy Access to Chiral α-Tertiary Amines. SYNTHESIS-STUTTGART 2022. [DOI: 10.1055/s-0041-1737563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
AbstractChiral α-tertiary amines, a motif present in α,α-disubstituted α-amino acids, in a wide range of natural products, and many drugs and drug candidates, are important targets in organic chemistry. Among the possible strategies, 1,2-addition to chiral N-sulfinylketimines is one of the best routes to form chiral α-tertiary amines with a high level of stereoselectivity. In this review, we focus first on the addition of organometallic reagents or other nucleophiles as enols or ylides to chiral N-sulfinylketimines. Then secondly we cover a selection of applications of these additions in the synthesis of valuable biologically active compounds.1 Introduction2 1,2-Addition Reaction Methodologies2.1 Organolithium Reagent Additions2.2 Grignard Additions2.3 Organozinc Reagent Additions2.4 Organoindium Reagent Additions2.5 Organoboron Reagent Additions2.6 Strecker Reactions2.7 Palladium-Catalyzed Reactions2.8 Enols, Enolates, and Other Deprotonated Reagent Additions2.9 Ylide Additions2.10 Heteroatom Nucleophiles2.11 Miscellaneous Reactions3 Applications to the Synthesis of Biologically Active Molecules4 Conclusions
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Ugbaja SC, Lawal M, Kumalo H. An Overview of β-Amyloid Cleaving Enzyme 1 (Bace1) in Alzheimer's Disease Therapy Elucidating its Exosite-Binding Antibody and Allosteric Inhibitor. Curr Med Chem 2021; 29:114-135. [PMID: 34102967 DOI: 10.2174/0929867328666210608145357] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 11/22/2022]
Abstract
Over decades of its identification, numerous past and ongoing researches have focused on the therapeutic roles of β-amyloid cleaving enzyme 1 (BACE1) as a target in treating Alzheimer's disease (AD). Although the initial BACE1 inhibitors at phase-3 clinical trials tremendously reduced β-amyloid-associated plaques in patients with AD, the researchers eventually discontinued the tests due to the lack of potency. This discontinuation has resulted in limited drug development and discovery targeted at BACE1, despite the high demand for dementia and AD therapies. It is, therefore, imperative to describe the detailed underlying biological basis of the BACE1 therapeutic option in neurological diseases. Herein, we highlight BACE1 bioactivity, genetic properties, and role in neurodegenerative therapy. We review research contributions to BACE1 exosite-binding antibody and allosteric inhibitor development as AD therapies. The review also covers BACE1 biological function, the disease-associated mechanisms, and the enzyme conditions for amyloid precursor protein sites splitting. Based on the present review, we suggest further studies on anti-BACE1 exosite antibodies and BACE1 allosteric inhibitors. Non-active site inhibition might be the way forward to BACE1 therapy in Alzheimer's neurological disorder.
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Affiliation(s)
- Samuel C Ugbaja
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Monsurat Lawal
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Hezekiel Kumalo
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4001, South Africa
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Rueeger H, Lueoend R, Machauer R, Veenstra SJ, Holzer P, Hurth K, Voegtle M, Frederiksen M, Rondeau JM, Tintelnot-Blomley M, Jacobson LH, Staufenbiel M, Laue G, Neumann U. Synthesis of the Potent, Selective, and Efficacious β-Secretase (BACE1) Inhibitor NB-360. J Med Chem 2021; 64:4677-4696. [PMID: 33844524 DOI: 10.1021/acs.jmedchem.0c02143] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Starting from lead compound 4, the 1,4-oxazine headgroup was optimized to improve potency and brain penetration. Focusing at the 6-position of the 5-amino-1,4-oxazine, the insertion of a Me and a CF3 group delivered an excellent pharmacological profile with a pKa of 7.1 and a very low P-gp efflux ratio enabling high central nervous system (CNS) penetration and exposure. Various synthetic routes to access BACE1 inhibitors bearing a 5-amino-6-methyl-6-(trifluoromethyl)-1,4-oxazine headgroup were investigated. Subsequent optimization of the P3 fragment provided the highly potent N-(3-((3R,6R)-5-amino-3,6-dimethyl-6-(trifluoromethyl)-3,6-dihydro-2H-1,4-oxazin-3-yl)-4-fluorophenyl)-5-cyano-3-methylpicolinamide 54 (NB-360), able to reduce significantly Aβ levels in mice, rats, and dogs in acute and chronic treatment regimens.
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Zhu H, Dronamraju V, Xie W, More SS. Sulfur-containing therapeutics in the treatment of Alzheimer's disease. Med Chem Res 2021; 30:305-352. [PMID: 33613018 PMCID: PMC7889054 DOI: 10.1007/s00044-020-02687-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 12/06/2020] [Indexed: 12/12/2022]
Abstract
Sulfur is widely existent in natural products and synthetic organic compounds as organosulfur, which are often associated with a multitude of biological activities. OBenzothiazole, in which benzene ring is fused to the 4,5-positions of the thiazolerganosulfur compounds continue to garner increasing amounts of attention in the field of medicinal chemistry, especially in the development of therapeutic agents for Alzheimer's disease (AD). AD is a fatal neurodegenerative disease and the primary cause of age-related dementia posing severe societal and economic burdens. Unfortunately, there is no cure for AD. A lot of research has been conducted on sulfur-containing compounds in the context of AD due to their innate antioxidant potential and some are currently being evaluated in clinical trials. In this review, we have described emerging trends in the field, particularly the concept of multi-targeting and formulation of disease-modifying strategies. SAR, pharmacological targets, in vitro/vivo ADMET, efficacy in AD animal models, and applications in clinical trials of such sulfur compounds have also been discussed. This article provides a comprehensive review of organosulfur-based AD therapeutic agents and provides insights into their future development.
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Affiliation(s)
- Haizhou Zhu
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Venkateshwara Dronamraju
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Wei Xie
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Swati S. More
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
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Richardson J, Lindsay-Scott PJ, Larichev V, Pocock E. Efficient Method for the Synthesis of Amino-1,3-Oxazines from Thioureas. Org Process Res Dev 2020. [DOI: 10.1021/acs.oprd.0c00369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jeffery Richardson
- Discovery Chemistry Research and Technologies, Eli Lilly and Company, Erl Wood Manor, Sunninghill Road, Windlesham, Surrey GU20 6PH, U.K
| | - Peter J. Lindsay-Scott
- Discovery Chemistry Research and Technologies, Eli Lilly and Company, Erl Wood Manor, Sunninghill Road, Windlesham, Surrey GU20 6PH, U.K
| | - Vladimir Larichev
- AMRI UK Ltd., Erl Wood Manor, Sunninghill Road, Windlesham, Surrey GU20 6PH, U.K
| | - Emily Pocock
- Discovery Chemistry Research and Technologies, Eli Lilly and Company, Erl Wood Manor, Sunninghill Road, Windlesham, Surrey GU20 6PH, U.K
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Rombouts F, Kusakabe KI, Hsiao CC, Gijsen HJM. Small-molecule BACE1 inhibitors: a patent literature review (2011 to 2020). Expert Opin Ther Pat 2020; 31:25-52. [PMID: 33006491 DOI: 10.1080/13543776.2021.1832463] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Inhibition of β-site amyloid precursor protein cleaving enzyme 1 (BACE1) has been extensively pursued as potential disease-modifying treatment for Alzheimer's disease (AD). Clinical failures with BACE inhibitors have progressively raised the bar forever cleaner candidates with reduced cardiovascular liability, toxicity risk, and increased selectivity over cathepsin D (CatD) and BACE2. AREAS COVERED This review provides an overview of patented BACE1 inhibitors between 2011 and 2020 per pharmaceutical company or research group and highlights the progress that was made in dialing out toxicity liabilities. EXPERT OPINION Despite an increasingly crowded IP situation, significant progress was made using highly complex chemistry in avoiding toxicity liabilities, with BACE1/BACE2 selectivity being the most remarkable achievement. However, clinical trial data suggest on-target toxicity is likely a contributing factor, which implies the only potential future of BACE1 inhibitors lies in careful titration of highly selective compounds in early populations where the amyloid burden is still minimal as prophylactic therapy, or as an affordable oral maintenance therapy following amyloid-clearing therapies.
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Affiliation(s)
- Frederik Rombouts
- Medicinal Chemistry, Janssen Research & Development , Beerse, Belgium
| | - Ken-Ichi Kusakabe
- Laboratory for Medicinal Chemistry Research, Shionogi & Co., Ltd ., Toyonaka, Osaka, Japan
| | - Chien-Chi Hsiao
- Medicinal Chemistry, Janssen Research & Development , Beerse, Belgium
| | - Harrie J M Gijsen
- Medicinal Chemistry, Janssen Research & Development , Beerse, Belgium
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Biological evaluation and interaction mechanism of beta-site APP cleaving enzyme 1 inhibitory pentapeptide from egg albumin. FOOD SCIENCE AND HUMAN WELLNESS 2020. [DOI: 10.1016/j.fshw.2020.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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11
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Docking studies suggest the important role of interactions among the catalytic dyad and inhibitors for designing Bace1 specific inhibitors. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.127893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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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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13
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Caron S. Where Does the Fluorine Come From? A Review on the Challenges Associated with the Synthesis of Organofluorine Compounds. Org Process Res Dev 2020. [DOI: 10.1021/acs.oprd.0c00030] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Stéphane Caron
- Chemical Research & Development, Pfizer Worldwide Research & Development, MS 8220-2432, Eastern Point Rd, Groton, Connecticut 06340, United States
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Iraji A, Khoshneviszadeh M, Firuzi O, Khoshneviszadeh M, Edraki N. Novel small molecule therapeutic agents for Alzheimer disease: Focusing on BACE1 and multi-target directed ligands. Bioorg Chem 2020; 97:103649. [PMID: 32101780 DOI: 10.1016/j.bioorg.2020.103649] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 01/05/2020] [Accepted: 02/03/2020] [Indexed: 12/17/2022]
Abstract
Alzheimer's Disease (AD) is a progressive neurodegenerative disorder that effects 50 million people worldwide. In this review, AD pathology and the development of novel therapeutic agents targeting AD were fully discussed. In particular, common approaches to prevent Aβ production and/or accumulation in the brain including α-secretase activators, specific γ-secretase modulators and small molecules BACE1 inhibitors were reviewed. Additionally, natural-origin bioactive compounds that provide AD therapeutic advances have been introduced. Considering AD is a multifactorial disease, the therapeutic potential of diverse multi target-directed ligands (MTDLs) that combine the efficacy of cholinesterase (ChE) inhibitors, MAO (monoamine oxidase) inhibitors, BACE1 inhibitors, phosphodiesterase 4D (PDE4D) inhibitors, for the treatment of AD are also reviewed. This article also highlights descriptions on the regulator of serotonin receptor (5-HT), metal chelators, anti-aggregants, antioxidants and neuroprotective agents targeting AD. Finally, current computational methods for evaluating the structure-activity relationships (SAR) and virtual screening (VS) of AD drugs are discussed and evaluated.
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Affiliation(s)
- Aida Iraji
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahsima Khoshneviszadeh
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Omidreza Firuzi
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehdi Khoshneviszadeh
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Medicinal Chemistry, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Najmeh Edraki
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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Anan K, Iso Y, Oguma T, Nakahara K, Suzuki S, Yamamoto T, Matsuoka E, Ito H, Sakaguchi G, Ando S, Morimoto K, Kanegawa N, Kido Y, Kawachi T, Fukushima T, Teisman A, Urmaliya V, Dhuyvetter D, Borghys H, Austin N, Van Den Bergh A, Verboven P, Bischoff F, Gijsen HJM, Yamano Y, Kusakabe KI. Trifluoromethyl Dihydrothiazine‐Based β‐Secretase (BACE1) Inhibitors with Robust Central β‐Amyloid Reduction and Minimal Covalent Binding Burden. ChemMedChem 2019; 14:1894-1910. [DOI: 10.1002/cmdc.201900478] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 09/19/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Kosuke Anan
- Discovery Research Laboratory for Core Therapeutic AreasShionogi Pharmaceutical Research Center 1-1 Futaba-cho 3-chome, Toyonaka Osaka 561-0825 Japan
| | - Yasuyoshi Iso
- Discovery Research Laboratory for Core Therapeutic AreasShionogi Pharmaceutical Research Center 1-1 Futaba-cho 3-chome, Toyonaka Osaka 561-0825 Japan
| | - Takuya Oguma
- Discovery Research Laboratory for Core Therapeutic AreasShionogi Pharmaceutical Research Center 1-1 Futaba-cho 3-chome, Toyonaka Osaka 561-0825 Japan
| | - Kenji Nakahara
- Discovery Research Laboratory for Core Therapeutic AreasShionogi Pharmaceutical Research Center 1-1 Futaba-cho 3-chome, Toyonaka Osaka 561-0825 Japan
| | - Shinji Suzuki
- Discovery Research Laboratory for Core Therapeutic AreasShionogi Pharmaceutical Research Center 1-1 Futaba-cho 3-chome, Toyonaka Osaka 561-0825 Japan
| | - Takahiko Yamamoto
- Discovery Research Laboratory for Core Therapeutic AreasShionogi Pharmaceutical Research Center 1-1 Futaba-cho 3-chome, Toyonaka Osaka 561-0825 Japan
- Current address: API Process Development Department (Biotechnology)Pharmaceutical Technology Division, Chugai Pharmaceutical Co., Ltd. 5–1, Ukima 5-chome, Kita-ku Tokyo 115-8543 Japan
| | - Eriko Matsuoka
- Discovery Research Laboratory for Core Therapeutic AreasShionogi Pharmaceutical Research Center 1-1 Futaba-cho 3-chome, Toyonaka Osaka 561-0825 Japan
| | - Hisanori Ito
- Discovery Research Laboratory for Core Therapeutic AreasShionogi Pharmaceutical Research Center 1-1 Futaba-cho 3-chome, Toyonaka Osaka 561-0825 Japan
| | - Gaku Sakaguchi
- Discovery Research Laboratory for Core Therapeutic AreasShionogi Pharmaceutical Research Center 1-1 Futaba-cho 3-chome, Toyonaka Osaka 561-0825 Japan
| | - Shigeru Ando
- Research Laboratory for DevelopmentShionogi Pharmaceutical Research Center 1-1 Futaba-cho 3-chome, Toyonaka Osaka 561-0825 Japan
| | - Kenji Morimoto
- Research Laboratory for DevelopmentShionogi Pharmaceutical Research Center 1-1 Futaba-cho 3-chome, Toyonaka Osaka 561-0825 Japan
| | - Naoki Kanegawa
- Research Laboratory for DevelopmentShionogi Pharmaceutical Research Center 1-1 Futaba-cho 3-chome, Toyonaka Osaka 561-0825 Japan
| | - Yasuto Kido
- Research Laboratory for DevelopmentShionogi Pharmaceutical Research Center 1-1 Futaba-cho 3-chome, Toyonaka Osaka 561-0825 Japan
| | - Tomoyuki Kawachi
- Research Laboratory for DevelopmentShionogi Pharmaceutical Research Center 1-1 Futaba-cho 3-chome, Toyonaka Osaka 561-0825 Japan
| | - Tamio Fukushima
- Research Laboratory for DevelopmentShionogi Pharmaceutical Research Center 1-1 Futaba-cho 3-chome, Toyonaka Osaka 561-0825 Japan
| | - Ard Teisman
- Non-Clinical SafetyJanssen Research & Development Turnhoutseweg 30 2340 Beerse Belgium
| | - Vijay Urmaliya
- Non-Clinical SafetyJanssen Research & Development Turnhoutseweg 30 2340 Beerse Belgium
| | - Deborah Dhuyvetter
- Non-Clinical SafetyJanssen Research & Development Turnhoutseweg 30 2340 Beerse Belgium
| | - Herman Borghys
- Non-Clinical SafetyJanssen Research & Development Turnhoutseweg 30 2340 Beerse Belgium
| | - Nigel Austin
- Discovery SciencesJanssen Research & Development Turnhoutseweg 30 2340 Beerse Belgium
- Current address: Sosei HeptaresSteinmetz Building, Granta Park, Great Abington Cambridge CB21 6DG UK
| | - An Van Den Bergh
- Discovery SciencesJanssen Research & Development Turnhoutseweg 30 2340 Beerse Belgium
| | - Peter Verboven
- Discovery SciencesJanssen Research & Development Turnhoutseweg 30 2340 Beerse Belgium
| | - Francois Bischoff
- Discovery SciencesJanssen Research & Development Turnhoutseweg 30 2340 Beerse Belgium
| | - Harrie J. M. Gijsen
- Discovery SciencesJanssen Research & Development Turnhoutseweg 30 2340 Beerse Belgium
| | - Yoshinori Yamano
- Discovery Research Laboratory for Core Therapeutic AreasShionogi Pharmaceutical Research Center 1-1 Futaba-cho 3-chome, Toyonaka Osaka 561-0825 Japan
| | - Ken-ichi Kusakabe
- Discovery Research Laboratory for Core Therapeutic AreasShionogi Pharmaceutical Research Center 1-1 Futaba-cho 3-chome, Toyonaka Osaka 561-0825 Japan
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New evolutions in the BACE1 inhibitor field from 2014 to 2018. Bioorg Med Chem Lett 2019; 29:761-777. [DOI: 10.1016/j.bmcl.2018.12.049] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/18/2018] [Accepted: 12/21/2018] [Indexed: 11/24/2022]
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Henderson JA, Harris RC, Tsai CC, Shen J. How Ligand Protonation State Controls Water in Protein-Ligand Binding. J Phys Chem Lett 2018; 9:5440-5444. [PMID: 30188715 PMCID: PMC6467052 DOI: 10.1021/acs.jpclett.8b02440] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The role of water in protein-ligand binding has been an intensely studied topic in recent years; however, how ligand protonation state change perturbs water has not been considered. Here we show that water dynamics and interactions can be controlled by the protonation state of ligand using continuous constant pH molecular dynamics simulations of two closely related model systems, β-secretase 1 and 2 (BACE1 and BACE2), in complex with a small-molecule inhibitor. Simulations revealed that, upon binding, the inhibitor pyrimidine ring remains deprotonated in BACE1 but becomes protonated in BACE2. Pyrimidine protonation results in water displacement, rigidification of the binding pocket, and shift in the ligand binding mode from water-mediated to direct hydrogen bonding. These findings not only support but also rationalize the most recent structure-selectivity data in BACE1 drug design. Binding-induced protonation state changes are likely common; our work offers a glimpse at how modeling protein-ligand binding while allowing ligand titration can further advance the understanding of water and structure-based drug design.
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Affiliation(s)
- Jack A Henderson
- Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , Baltimore , Maryland 21201 , United States
| | - Robert C Harris
- Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , Baltimore , Maryland 21201 , United States
| | - Cheng-Chieh Tsai
- Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , Baltimore , Maryland 21201 , United States
| | - Jana Shen
- Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , Baltimore , Maryland 21201 , United States
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Singh A, Srivastava A, Singh MS. Metal-Free One-Pot Four-Component Cascade Annulation in Ionic Liquids at Room Temperature: Convergent Access to Thiazoloquinolinone Derivatives. J Org Chem 2018; 83:7950-7961. [PMID: 29978705 DOI: 10.1021/acs.joc.8b00814] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
An efficient, eco-friendly, and highly convergent one-pot route to privileged thiazoloquinolinone derivatives has been developed via four-component cascade coupling (4CCC) of α-enolic dithioesters, cysteamine/2-aminothiophenols, aldehydes, and cyclic 1,3-diketones in recyclable [EMIM][EtSO4] ionic liquid at room temperature for the first time. The reaction proceeds via a N,S-acetal formation, Knoevenagel condensation, aza-ene reaction, imine-enamine/keto-enol tautomerization, and intramolecular N-cyclization cascade sequence. The merit of the protocol is highlighted by its efficacy of forming consecutive five new bonds (two C-C, two C-N, and one C-S) and two rings with all reactants being efficiently utilized. The operational simplicity, sustainability, mild conditions, excellent yields, tolerance of wide functional groups, and avoidance of expensive/toxic reagents are additional attributes to this domino four-component protocol. Notably, the products were easily separated from the ionic liquid, and thus the ionic liquid obtained was reused four times without considerable loss of any activity.
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Affiliation(s)
- Anshu Singh
- Department of Chemistry , Institute of Science, Banaras Hindu University , Varanasi 221005 , India
| | - Abhijeet Srivastava
- Department of Chemistry , Institute of Science, Banaras Hindu University , Varanasi 221005 , India
| | - Maya Shankar Singh
- Department of Chemistry , Institute of Science, Banaras Hindu University , Varanasi 221005 , India
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Veenstra SJ, Rueeger H, Voegtle M, Lueoend R, Holzer P, Hurth K, Tintelnot-Blomley M, Frederiksen M, Rondeau JM, Jacobson L, Staufenbiel M, Neumann U, Machauer R. Discovery of amino-1,4-oxazines as potent BACE-1 inhibitors. Bioorg Med Chem Lett 2018; 28:2195-2200. [DOI: 10.1016/j.bmcl.2018.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/27/2018] [Accepted: 05/02/2018] [Indexed: 12/13/2022]
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20
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Coimbra JRM, Marques DFF, Baptista SJ, Pereira CMF, Moreira PI, Dinis TCP, Santos AE, Salvador JAR. Highlights in BACE1 Inhibitors for Alzheimer's Disease Treatment. Front Chem 2018; 6:178. [PMID: 29881722 PMCID: PMC5977085 DOI: 10.3389/fchem.2018.00178] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/04/2018] [Indexed: 12/22/2022] Open
Abstract
Alzheimer's disease (AD) is a severe neurodegenerative disorder and the most common type of dementia in the elderly. The clinical symptoms of AD include a progressive loss of memory and impairment of cognitive functions interfering with daily life activities. The main neuropathological features consist in extracellular amyloid-β (Aβ) plaque deposition and intracellular Neurofibrillary tangles (NFTs) of hyperphosphorylated Tau. Understanding the pathophysiological mechanisms that underlie neurodegeneration in AD is essential for rational design of neuroprotective agents able to prevent disease progression. According to the "Amyloid Cascade Hypothesis" the critical molecular event in the pathogenesis of AD is the accumulation of Aβ neurotoxic oligomers. Since the proteolytic processing of Amyloid Precursor Protein (APP) by β-secretase (beta-site APP cleaving enzyme 1, BACE1) is the rate-limiting step in the production of Aβ, this enzyme is considered a major therapeutic target and BACE1 inhibitors have the potential to be disease-modifying drugs for AD treatment. Therefore, intensive efforts to discover and develop inhibitors that can reach the brain and effectively inhibit BACE1 have been pursued by several groups worldwide. The aim of this review is to highlight the progress in the discovery of potent and selective small molecule BACE1 inhibitors over the past decade.
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Affiliation(s)
- Judite R. M. Coimbra
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of CoimbraCoimbra, Portugal
- Center for Neuroscience and Cell Biology, University of CoimbraCoimbra, Portugal
| | - Daniela F. F. Marques
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of CoimbraCoimbra, Portugal
- Center for Neuroscience and Cell Biology, University of CoimbraCoimbra, Portugal
| | - Salete J. Baptista
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of CoimbraCoimbra, Portugal
- Center for Neuroscience and Cell Biology, University of CoimbraCoimbra, Portugal
- Chem4Pharma, Edifício IPN IncubadoraCoimbra, Portugal
| | - Cláudia M. F. Pereira
- Center for Neuroscience and Cell Biology, University of CoimbraCoimbra, Portugal
- Faculty of Medicine, University of CoimbraCoimbra, Portugal
| | - Paula I. Moreira
- Center for Neuroscience and Cell Biology, University of CoimbraCoimbra, Portugal
- Laboratory of Physiology, Faculty of Medicine, University of CoimbraCoimbra, Portugal
| | - Teresa C. P. Dinis
- Center for Neuroscience and Cell Biology, University of CoimbraCoimbra, Portugal
- Laboratory of Biochemistry, Faculty of Pharmacy, University of CoimbraCoimbra, Portugal
| | - Armanda E. Santos
- Center for Neuroscience and Cell Biology, University of CoimbraCoimbra, Portugal
- Laboratory of Biochemistry, Faculty of Pharmacy, University of CoimbraCoimbra, Portugal
| | - Jorge A. R. Salvador
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of CoimbraCoimbra, Portugal
- Center for Neuroscience and Cell Biology, University of CoimbraCoimbra, Portugal
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21
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Taylor AP, Robinson RP, Fobian YM, Blakemore DC, Jones LH, Fadeyi O. Modern advances in heterocyclic chemistry in drug discovery. Org Biomol Chem 2018; 14:6611-37. [PMID: 27282396 DOI: 10.1039/c6ob00936k] [Citation(s) in RCA: 434] [Impact Index Per Article: 72.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
New advances in synthetic methodologies that allow rapid access to a wide variety of functionalized heterocyclic compounds are of critical importance to the medicinal chemist as it provides the ability to expand the available drug-like chemical space and drive more efficient delivery of drug discovery programs. Furthermore, the development of robust synthetic routes that can readily generate bulk quantities of a desired compound help to accelerate the drug development process. While established synthetic methodologies are commonly utilized during the course of a drug discovery program, the development of innovative heterocyclic syntheses that allow for different bond forming strategies are having a significant impact in the pharmaceutical industry. This review will focus on recent applications of new methodologies in C-H activation, photoredox chemistry, borrowing hydrogen catalysis, multicomponent reactions, regio- and stereoselective syntheses, as well as other new, innovative general syntheses for the formation and functionalization of heterocycles that have helped drive project delivery. Additionally, the importance and value of collaborations between industry and academia in shaping the development of innovative synthetic approaches to functionalized heterocycles that are of greatest interest to the pharmaceutical industry will be highlighted.
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Affiliation(s)
- Alexandria P Taylor
- Worldwide Medicinal Chemistry, Pfizer, Eastern Point Road, Groton, CT 06340, USA.
| | - Ralph P Robinson
- Worldwide Medicinal Chemistry, Pfizer, Eastern Point Road, Groton, CT 06340, USA.
| | - Yvette M Fobian
- Worldwide Medicinal Chemistry, Pfizer, Eastern Point Road, Groton, CT 06340, USA.
| | - David C Blakemore
- Worldwide Medicinal Chemistry, Pfizer, Eastern Point Road, Groton, CT 06340, USA.
| | - Lyn H Jones
- Worldwide Medicinal Chemistry, Pfizer, 610 Main Street, Cambridge, MA 02139, USA
| | - Olugbeminiyi Fadeyi
- Worldwide Medicinal Chemistry, Pfizer, Eastern Point Road, Groton, CT 06340, USA.
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22
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Zhang L, Chen L, Dutra JK, Beck EM, Nag S, Takano A, Amini N, Arakawa R, Brodney MA, Buzon LM, Doran SD, Lanyon LF, McCarthy TJ, Bales KR, Nolan CE, O’Neill BT, Schildknegt K, Halldin C, Villalobos A. Identification of a Novel Positron Emission Tomography (PET) Ligand for Imaging β-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE-1) in Brain. J Med Chem 2018; 61:3296-3308. [DOI: 10.1021/acs.jmedchem.7b01769] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Lei Zhang
- Medicine Design, Medicinal Chemistry, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Laigao Chen
- Clinical & Translational Imaging, Early Clinical Development, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Jason K. Dutra
- Medicine Design, Medicinal Chemistry, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Elizabeth M. Beck
- Medicine Design, Medicinal Chemistry, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Sangram Nag
- Department of Clinical Neuroscience, Center for Psychiatry Research, Karolinska Institutet and Stockholm County Council, SE-17176 Stockholm, Sweden
| | - Akihiro Takano
- Department of Clinical Neuroscience, Center for Psychiatry Research, Karolinska Institutet and Stockholm County Council, SE-17176 Stockholm, Sweden
| | - Nahid Amini
- Department of Clinical Neuroscience, Center for Psychiatry Research, Karolinska Institutet and Stockholm County Council, SE-17176 Stockholm, Sweden
| | - Ryosuke Arakawa
- Department of Clinical Neuroscience, Center for Psychiatry Research, Karolinska Institutet and Stockholm County Council, SE-17176 Stockholm, Sweden
| | - Michael A. Brodney
- Medicine Design, Medicinal Chemistry, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Leanne M. Buzon
- Medicine Design, Medicinal Chemistry, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Shawn D. Doran
- Medicine Design, Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Lorraine F. Lanyon
- Medicine Design, Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Timothy J. McCarthy
- Clinical & Translational Imaging, Early Clinical Development, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Kelly R. Bales
- Internal Medicine, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Charles E. Nolan
- Internal Medicine, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Brian T. O’Neill
- Medicine Design, Medicinal Chemistry, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Klaas Schildknegt
- Pharmaceutical Sciences, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Christer Halldin
- Department of Clinical Neuroscience, Center for Psychiatry Research, Karolinska Institutet and Stockholm County Council, SE-17176 Stockholm, Sweden
| | - Anabella Villalobos
- Medicinal Synthesis Technologies, Pfizer Inc., Groton, Connecticut 06340, United States
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23
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Martinez-Alsina LA, Murray JC, Buzon LM, Bundesmann MW, Young JM, O'Neill BT. Spiropiperidine Sultam and Lactam Templates: Diastereoselective Overman Rearrangement and Metathesis followed by NH Arylation. J Org Chem 2017; 82:12246-12256. [PMID: 29096057 DOI: 10.1021/acs.joc.7b02096] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We report the diastereoselective synthesis of novel spiropiperidine templates for use in SAR studies of β-secretase (BACE) inhibitors and also as versatile ligands for other receptor types. The overall synthetic approach stems from chiral starting material benzyl (S)-2-methyl-4-oxopiperidine-1-carboxylate and employs an Overman rearrangement to control the stereochemistry at the quaternary center. This process is followed by a Grubbs metathesis to close a five-membered "top" ring to form an α,β-unsaturated lactam or an α,β-unsaturated sultam. We also demonstrate that this chemistry can accommodate additional substituents on the lactam/sultam ring and allows late stage sequential functionalization of the amine and amide nitrogens to rapidly produce diverse analogues.
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Affiliation(s)
- Luis A Martinez-Alsina
- Medicine Design, Medicinal Chemistry, Pfizer Worldwide Research and Development , 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - John C Murray
- Medicine Design, Medicinal Chemistry, Pfizer Worldwide Research and Development , 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Leanne M Buzon
- Medicine Design, Medicinal Chemistry, Pfizer Worldwide Research and Development , 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Mark W Bundesmann
- Medicine Design, Medicinal Chemistry, Pfizer Worldwide Research and Development , 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Joseph M Young
- Novartis Institute for BioMedical Research , 5300 Chiron Way, Emeryville, California 94608-2916, United States
| | - Brian T O'Neill
- Medicine Design, Medicinal Chemistry, Pfizer Worldwide Research and Development , 445 Eastern Point Road, Groton, Connecticut 06340, United States
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24
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Harris RC, Tsai CC, Ellis CR, Shen J. Proton-Coupled Conformational Allostery Modulates the Inhibitor Selectivity for β-Secretase. J Phys Chem Lett 2017; 8:4832-4837. [PMID: 28927275 PMCID: PMC5713904 DOI: 10.1021/acs.jpclett.7b02309] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Many important pharmaceutical targets, such as aspartyl proteases and kinases, exhibit pH-dependent dynamics, functions and inhibition. Accurate prediction of their binding free energies is challenging because current computational techniques neglect the effects of pH. Here we combine free energy perturbation calculations with continuous constant pH molecular dynamics to explore the selectivity of a small-molecule inhibitor for β-secretase (BACE1), an important drug target for Alzheimer's disease. The calculations predicted identical affinity for BACE1 and the closely related cathepsin D at high pH; however, at pH 4.6 the inhibitor is selective for BACE1 by 1.3 kcal/mol, in excellent agreement with experiment. Surprisingly, the pH-dependent selectivity can be attributed to the protonation of His45, which allosterically modulates a loop-inhibitor interaction. Allosteric regulation induced by proton binding is likely common in biology; considering such allosteric sites could lead to exciting new opportunities in drug design.
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Affiliation(s)
- Robert C Harris
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , Baltimore, Maryland 21201, United States
| | - Cheng-Chieh Tsai
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , Baltimore, Maryland 21201, United States
| | - Christopher R Ellis
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , Baltimore, Maryland 21201, United States
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , Baltimore, Maryland 21201, United States
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25
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Prati F, Bottegoni G, Bolognesi ML, Cavalli A. BACE-1 Inhibitors: From Recent Single-Target Molecules to Multitarget Compounds for Alzheimer’s Disease. J Med Chem 2017; 61:619-637. [DOI: 10.1021/acs.jmedchem.7b00393] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Federica Prati
- Drug Discovery Unit,
Division of Biological Chemistry and Drug Discovery, College of Life
Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, U.K
| | - Giovanni Bottegoni
- CompuNet, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
- Heptares Therapeutics Ltd., BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, U.K
| | - Maria Laura Bolognesi
- Department
of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Andrea Cavalli
- CompuNet, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
- Department
of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
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26
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Jang H, Romiti F, Torker S, Hoveyda AH. Catalytic diastereo- and enantioselective additions of versatile allyl groups to N-H ketimines. Nat Chem 2017; 9:1269-1275. [PMID: 29168479 DOI: 10.1038/nchem.2816] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 06/01/2017] [Indexed: 01/25/2023]
Abstract
There are many biologically active organic molecules that contain one or more nitrogen-containing moieties, and broadly applicable and efficient catalytic transformations that deliver them diastereoselectively and/or enantioselectively are much sought after. Various methods for enantioselective synthesis of α-secondary amines are available (for example, from additions to protected/activated aldimines), but those involving ketimines are much less common. There are no reported additions of carbon-based nucleophiles to unprotected/unactivated (or N-H) ketimines. Here, we report a catalytic, diastereo- and enantioselective three-component strategy for merging an N-H ketimine, a monosubstituted allene and B2(pin)2, affording products in up to 95% yield, >98% diastereoselectivity and >99:1 enantiomeric ratio. The utility of the approach is highlighted by synthesis of the tricyclic core of a class of compounds that have been shown to possess anti-Alzheimer activity. Stereochemical models developed with the aid of density functional theory calculations, which account for the observed trends and levels of enantioselectivity, are presented.
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Affiliation(s)
- Hwanjong Jang
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, USA
| | - Filippo Romiti
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, USA
| | - Sebastian Torker
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, USA
| | - Amir H Hoveyda
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, USA
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27
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Ellis CR, Tsai CC, Lin FY, Shen J. Conformational dynamics of cathepsin D and binding to a small-molecule BACE1 inhibitor. J Comput Chem 2017; 38:1260-1269. [PMID: 28370344 PMCID: PMC5403572 DOI: 10.1002/jcc.24719] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 11/21/2016] [Accepted: 12/06/2016] [Indexed: 02/06/2023]
Abstract
BACE1 is a major therapeutic target for prevention and treatment of Alzheimer's disease. Developing inhibitors that can selectively target BACE1 in favor of other proteases, especially cathepsin D (CatD), has presented significant challenges. Here, we investigate the conformational dynamics and protonation states of BACE1 and CatD using continuous constant pH molecular dynamics with pH replica-exchange sampling protocol. Despite similar structure, BACE1 and CatD exhibit markedly different active site dynamics. BACE1 displays pH-dependent flap dynamics that controls substrate accessibility, while the CatD flap is relatively rigid and remains open in the pH range 2.5-6. Interestingly, although each protease hydrolyzes peptide bonds, the protonation states of the catalytic dyads are different within the active pH range. The acidic and basic components of the BACE1 catalytic dyad are clear, while either aspartic acid of the CatD catalytic dyad could play the role of acid or base. Finally, we investigate binding of the inhibitor LY2811376 developed by Eli Lilly to BACE1 and CatD. Surprisingly, in the enzyme active pH range, LY2811376 forms a stronger salt bridge with the catalytic dyad in CatD than in BACE1, which might explain the retinal toxicity of the inhibitor related to off-target inhibition of CatD. This work highlights the complexity and challenge in structure-based drug design where receptor-ligand binding induces protonation state change in both the protein and the inhibitor. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Christopher R. Ellis
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Cheng-Chieh Tsai
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Fang-Yu Lin
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
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28
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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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29
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Butler CR, Ogilvie K, Martinez-Alsina L, Barreiro G, Beck EM, Nolan CE, Atchison K, Benvenuti E, Buzon L, Doran S, Gonzales C, Helal CJ, Hou X, Hsu MH, Johnson EF, Lapham K, Lanyon L, Parris K, O'Neill BT, Riddell D, Robshaw A, Vajdos F, Brodney MA. Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging Gly230 without an Anilide Functionality. J Med Chem 2016; 60:386-402. [PMID: 27997172 PMCID: PMC5461923 DOI: 10.1021/acs.jmedchem.6b01451] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
![]()
A growing subset of β-secretase
(BACE1) inhibitors for the
treatment of Alzheimer’s disease (AD) utilizes an anilide chemotype
that engages a key residue (Gly230) in the BACE1 binding site. Although
the anilide moiety affords excellent potency, it simultaneously introduces
a third hydrogen bond donor that limits brain availability and provides
a potential metabolic site leading to the formation of an aniline,
a structural motif of prospective safety concern. We report herein
an alternative aminomethyl linker that delivers similar potency and
improved brain penetration relative to the amide moiety. Optimization
of this series identified analogues with an excellent balance of ADME
properties and potency; however, potential drug–drug interactions
(DDI) were predicted based on CYP 2D6 affinities. Generation and analysis
of key BACE1 and CYP 2D6 crystal structures identified strategies
to obviate the DDI liability, leading to compound 16,
which exhibits robust in vivo efficacy as a BACE1 inhibitor.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Mei-Hui Hsu
- Molecular and Experimental Medicine, The Scripps Research Institute , 10550 Torrey Pines Road, La Jolla, California 92024, United States
| | - Eric F Johnson
- Molecular and Experimental Medicine, The Scripps Research Institute , 10550 Torrey Pines Road, La Jolla, California 92024, United States
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30
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Eketjäll S, Janson J, Kaspersson K, Bogstedt A, Jeppsson F, Fälting J, Haeberlein SB, Kugler AR, Alexander RC, Cebers G. AZD3293: A Novel, Orally Active BACE1 Inhibitor with High Potency and Permeability and Markedly Slow Off-Rate Kinetics. J Alzheimers Dis 2016; 50:1109-23. [PMID: 26890753 PMCID: PMC4927864 DOI: 10.3233/jad-150834] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A growing body of pathological, biomarker, genetic, and mechanistic data suggests that amyloid accumulation, as a result of changes in production, processing, and/or clearance of brain amyloid-β peptide (Aβ) concentrations, plays a key role in the pathogenesis of Alzheimer’s disease (AD). Beta-secretase 1 (BACE1) mediates the first step in the processing of amyloid-β protein precursor (AβPP) to Aβ peptides, with the soluble N terminal fragment of AβPP (sAβPPβ) as a direct product, and BACE1 inhibition is an attractive target for therapeutic intervention to reduce the production of Aβ. Here, we report the in vitro and in vivo pharmacological profile of AZD3293, a potent, highly permeable, orally active, blood-brain barrier (BBB) penetrating, BACE1 inhibitor with unique slow off-rate kinetics. The in vitro potency of AZD3293 was demonstrated in several cellular models, including primary cortical neurons. In vivo in mice, guinea pigs, and dogs, AZD3293 displayed significant dose- and time-dependent reductions in plasma, cerebrospinal fluid, and brain concentrations of Aβ40, Aβ42, and sAβPPβ. The in vitro potency of AZD3293 in mouse and guinea pig primary cortical neuronal cells was correlated to the in vivo potency expressed as free AZD3293 concentrations in mouse and guinea pig brains. In mice and dogs, the slow off-rate from BACE1 may have translated into a prolongation of the observed effect beyond the turnover rate of Aβ. The preclinical data strongly support the clinical development of AZD3293, and patients with AD are currently being recruited into a combined Phase 2/3 study to test the disease-modifying properties of AZD3293.
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Affiliation(s)
- Susanna Eketjäll
- AstraZeneca Translational Sciences Centre, Science for Life Laboratory, Personal Healthcare and Biomarkers, AstraZeneca, Solna, Sweden.,Department of Clinical Neuroscience, Karolinska Institutet, Solna, Sweden
| | - Juliette Janson
- AstraZeneca Translational Sciences Centre, Science for Life Laboratory, Personal Healthcare and Biomarkers, AstraZeneca, Solna, Sweden.,Department of Clinical Neuroscience, Karolinska Institutet, Solna, Sweden
| | | | - Anna Bogstedt
- AstraZeneca Translational Sciences Centre, Science for Life Laboratory, Personal Healthcare and Biomarkers, AstraZeneca, Solna, Sweden.,Department of Clinical Neuroscience, Karolinska Institutet, Solna, Sweden
| | - Fredrik Jeppsson
- CNS and Pain iMed, AstraZeneca, Södertälje, Sweden.,Operations Global Quality, AstraZeneca, Södertälje, Sweden
| | | | | | - Alan R Kugler
- Neuroscience iMed, IMED Biotech Unit, AstraZeneca, Cambridge, MA, USA
| | | | - Gvido Cebers
- Neuroscience iMed, IMED Biotech Unit, AstraZeneca, Cambridge, MA, USA
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31
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Scott JD, Li SW, Brunskill APJ, Chen X, Cox K, Cumming JN, Forman M, Gilbert EJ, Hodgson RA, Hyde LA, Jiang Q, Iserloh U, Kazakevich I, Kuvelkar R, Mei H, Meredith J, Misiaszek J, Orth P, Rossiter LM, Slater M, Stone J, Strickland CO, Voigt JH, Wang G, Wang H, Wu Y, Greenlee WJ, Parker EM, Kennedy ME, Stamford AW. Discovery of the 3-Imino-1,2,4-thiadiazinane 1,1-Dioxide Derivative Verubecestat (MK-8931)-A β-Site Amyloid Precursor Protein Cleaving Enzyme 1 Inhibitor for the Treatment of Alzheimer's Disease. J Med Chem 2016; 59:10435-10450. [PMID: 27933948 DOI: 10.1021/acs.jmedchem.6b00307] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Verubecestat 3 (MK-8931), a diaryl amide-substituted 3-imino-1,2,4-thiadiazinane 1,1-dioxide derivative, is a high-affinity β-site amyloid precursor protein cleaving enzyme 1 (BACE1) inhibitor currently undergoing Phase 3 clinical evaluation for the treatment of mild to moderate and prodromal Alzheimer's disease. Although not selective over the closely related aspartyl protease BACE2, verubecestat has high selectivity for BACE1 over other key aspartyl proteases, notably cathepsin D, and profoundly lowers CSF and brain Aβ levels in rats and nonhuman primates and CSF Aβ levels in humans. In this annotation, we describe the discovery of 3, including design, validation, and selected SAR around the novel iminothiadiazinane dioxide core as well as aspects of its preclinical and Phase 1 clinical characterization.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Qin Jiang
- Albany Molecular Research Inc. , 26 Corporate Circle, Albany, New York 12203, United States
| | | | | | | | | | | | | | | | - Lana M Rossiter
- Albany Molecular Research Inc. , 26 Corporate Circle, Albany, New York 12203, United States
| | - Meagan Slater
- Albany Molecular Research Inc. , 26 Corporate Circle, Albany, New York 12203, United States
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32
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Radeva N, Schiebel J, Wang X, Krimmer SG, Fu K, Stieler M, Ehrmann FR, Metz A, Rickmeyer T, Betz M, Winquist J, Park AY, Huschmann FU, Weiss MS, Mueller U, Heine A, Klebe G. Active Site Mapping of an Aspartic Protease by Multiple Fragment Crystal Structures: Versatile Warheads To Address a Catalytic Dyad. J Med Chem 2016; 59:9743-9759. [PMID: 27726357 DOI: 10.1021/acs.jmedchem.6b01195] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Crystallography is frequently used as follow-up method to validate hits identified by biophysical screening cascades. The capacity of crystallography to directly screen fragment libraries is often underestimated, due to its supposed low-throughput and need for high-quality crystals. We applied crystallographic fragment screening to map the protein-binding site of the aspartic protease endothiapepsin by individual soaking experiments. Here, we report on 41 fragments binding to the catalytic dyad and adjacent specificity pockets. The analysis identifies already known warheads but also reveals hydrazide, pyrazole, or carboxylic acid fragments as novel functional groups binding to the dyad. A remarkable swapping of the S1 and S1' pocket between structurally related fragments is explained by either steric demand, required displacement of a well-bound water molecule, or changes of trigonal-planar to tetrahedral geometry of an oxygen functional group in a side chain. Some warheads simultaneously occupying both S1 and S1' are promising starting points for fragment-growing strategies.
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Affiliation(s)
- Nedyalka Radeva
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Johannes Schiebel
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Xiaojie Wang
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Stefan G Krimmer
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Kan Fu
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Martin Stieler
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Frederik R Ehrmann
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Alexander Metz
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Thomas Rickmeyer
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Michael Betz
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Johan Winquist
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Ah Young Park
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Franziska U Huschmann
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany.,Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography (HZB-MX), Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Manfred S Weiss
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography (HZB-MX), Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Uwe Mueller
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography (HZB-MX), Albert-Einstein-Strasse 15, 12489 Berlin, Germany.,MAX IV Laboratory, Lund University , Fotongatan 2, 225 94 Lund, Sweden
| | - Andreas Heine
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Gerhard Klebe
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
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33
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Zuhl AM, Nolan CE, Brodney MA, Niessen S, Atchison K, Houle C, Karanian DA, Ambroise C, Brulet JW, Beck EM, Doran SD, O'Neill BT, Am Ende CW, Chang C, Geoghegan KF, West GM, Judkins JC, Hou X, Riddell DR, Johnson DS. Chemoproteomic profiling reveals that cathepsin D off-target activity drives ocular toxicity of β-secretase inhibitors. Nat Commun 2016; 7:13042. [PMID: 27727204 PMCID: PMC5062570 DOI: 10.1038/ncomms13042] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 08/26/2016] [Indexed: 01/18/2023] Open
Abstract
Inhibition of β-secretase BACE1 is considered one of the most promising approaches for treating Alzheimer's disease. Several structurally distinct BACE1 inhibitors have been withdrawn from development after inducing ocular toxicity in animal models, but the target mediating this toxicity has not been identified. Here we use a clickable photoaffinity probe to identify cathepsin D (CatD) as a principal off-target of BACE1 inhibitors in human cells. We find that several BACE1 inhibitors blocked CatD activity in cells with much greater potency than that displayed in cell-free assays with purified protein. Through a series of exploratory toxicology studies, we show that quantifying CatD target engagement in cells with the probe is predictive of ocular toxicity in vivo. Taken together, our findings designate off-target inhibition of CatD as a principal driver of ocular toxicity for BACE1 inhibitors and more generally underscore the power of chemical proteomics for discerning mechanisms of drug action. Several β-secretase (BACE) inhibitors exhibit unexplained ocular toxicity in preclinical studies. Here the authors generate a clickable photoaffinity probe to interrogate off-targets in cells and animals, and identify inhibition of cathepsin D as a driver of ocular toxicity.
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Affiliation(s)
- Andrea M Zuhl
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, USA.,Worldwide Medicinal Chemistry
| | - Charles E Nolan
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, USA.,Neuroscience Research Unit
| | - Michael A Brodney
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, USA.,Worldwide Medicinal Chemistry
| | - Sherry Niessen
- Worldwide Medicinal Chemistry.,Pfizer Worldwide Research and Development, San Diego, California 92121, USA
| | - Kevin Atchison
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, USA.,Neuroscience Research Unit
| | - Christopher Houle
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, USA.,Drug Safety Research and Development
| | - David A Karanian
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, USA.,Drug Safety Research and Development
| | - Claude Ambroise
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, USA.,Neuroscience Research Unit
| | - Jeffrey W Brulet
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, USA.,Worldwide Medicinal Chemistry
| | - Elizabeth M Beck
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, USA.,Worldwide Medicinal Chemistry
| | - Shawn D Doran
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, USA.,Pharmacokinetics, Dynamics and Metabolism
| | - Brian T O'Neill
- Worldwide Medicinal Chemistry.,Pfizer Worldwide Research and Development, Groton, Connecticut 06340, USA
| | - Christopher W Am Ende
- Worldwide Medicinal Chemistry.,Pfizer Worldwide Research and Development, Groton, Connecticut 06340, USA
| | - Cheng Chang
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, USA.,Pharmacokinetics, Dynamics and Metabolism
| | - Kieran F Geoghegan
- Worldwide Medicinal Chemistry.,Pfizer Worldwide Research and Development, Groton, Connecticut 06340, USA.,Structural Biology and Biophysics Group
| | - Graham M West
- Worldwide Medicinal Chemistry.,Pfizer Worldwide Research and Development, Groton, Connecticut 06340, USA.,Structural Biology and Biophysics Group
| | - Joshua C Judkins
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, USA.,Worldwide Medicinal Chemistry
| | - Xinjun Hou
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, USA.,Worldwide Medicinal Chemistry
| | - David R Riddell
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, USA.,Neuroscience Research Unit
| | - Douglas S Johnson
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, USA.,Worldwide Medicinal Chemistry
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34
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Wu YJ, Guernon J, Shi J, Marcin L, Higgins M, Rajamani R, Muckelbauer J, Lewis H, Chang C, Camac D, Toyn JH, Ahlijanian MK, Albright CF, Macor JE, Thompson LA. Discovery of S3-Truncated, C-6 Heteroaryl Substituted Aminothiazine β-Site APP Cleaving Enzyme-1 (BACE1) Inhibitors. J Med Chem 2016; 59:8593-600. [DOI: 10.1021/acs.jmedchem.6b01012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Yong-Jin Wu
- Research
and Development, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford, Connecticut 06492-7660, United States
| | - Jason Guernon
- Research
and Development, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford, Connecticut 06492-7660, United States
| | - Jianliang Shi
- Research
and Development, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford, Connecticut 06492-7660, United States
| | - Lawrence Marcin
- Research
and Development, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford, Connecticut 06492-7660, United States
| | - Mendi Higgins
- Research
and Development, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford, Connecticut 06492-7660, United States
| | - Ramkumar Rajamani
- Research
and Development, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford, Connecticut 06492-7660, United States
| | - Jodi Muckelbauer
- Research
and Development, Bristol-Myers Squibb Company, PO Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Hal Lewis
- Research
and Development, Bristol-Myers Squibb Company, PO Box 4000, Princeton, New Jersey 08543-4000, United States
| | - ChiehYing Chang
- Research
and Development, Bristol-Myers Squibb Company, PO Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Dan Camac
- Research
and Development, Bristol-Myers Squibb Company, PO Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Jeremy H. Toyn
- Research
and Development, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford, Connecticut 06492-7660, United States
| | - Michael K. Ahlijanian
- Research
and Development, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford, Connecticut 06492-7660, United States
| | - Charles F. Albright
- Research
and Development, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford, Connecticut 06492-7660, United States
| | - John E. Macor
- Research
and Development, Bristol-Myers Squibb Company, PO Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Lorin A. Thompson
- Research
and Development, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford, Connecticut 06492-7660, United States
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35
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Mandal M, Wu Y, Misiaszek J, Li G, Buevich A, Caldwell JP, Liu X, Mazzola RD, Orth P, Strickland C, Voigt J, Wang H, Zhu Z, Chen X, Grzelak M, Hyde LA, Kuvelkar R, Leach PT, Terracina G, Zhang L, Zhang Q, Michener MS, Smith B, Cox K, Grotz D, Favreau L, Mitra K, Kazakevich I, McKittrick BA, Greenlee W, Kennedy ME, Parker EM, Cumming JN, Stamford AW. Structure-Based Design of an Iminoheterocyclic β-Site Amyloid Precursor Protein Cleaving Enzyme (BACE) Inhibitor that Lowers Central Aβ in Nonhuman Primates. J Med Chem 2016; 59:3231-48. [DOI: 10.1021/acs.jmedchem.5b01995] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Mihirbaran Mandal
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Yusheng Wu
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Jeffrey Misiaszek
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Guoqing Li
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Alexei Buevich
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - John P. Caldwell
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Xiaoxiang Liu
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Robert D. Mazzola
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Peter Orth
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Corey Strickland
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Johannes Voigt
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Hongwu Wang
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Zhaoning Zhu
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Xia Chen
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Michael Grzelak
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Lynn A. Hyde
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Reshma Kuvelkar
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Prescott T. Leach
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Giuseppe Terracina
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Lili Zhang
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Qi Zhang
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Maria S. Michener
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Brad Smith
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Kathleen Cox
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Diane Grotz
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Leonard Favreau
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Kaushik Mitra
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Irina Kazakevich
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Brian A. McKittrick
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - William Greenlee
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Matthew E. Kennedy
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Eric M. Parker
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Jared N. Cumming
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Andrew W. Stamford
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
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36
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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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37
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Chambers RK, Khan TA, Olsen DB, Sleebs BE. Synthesis of amino heterocycle aspartyl protease inhibitors. Org Biomol Chem 2016; 14:4970-85. [DOI: 10.1039/c5ob01842k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthetic strategies to access 2-amino heterocycle head groups that inhibit aspartyl proteases, are reviewed.
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Affiliation(s)
- Rachel K. Chambers
- The Walter and Eliza Hall Institute for Medical Research
- Parkville
- Australia
| | | | | | - Brad E. Sleebs
- The Walter and Eliza Hall Institute for Medical Research
- Parkville
- Australia
- The University of Melbourne
- Parkville
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Brodney MA, Beck EM, Butler CR, Barreiro G, Johnson EF, Riddell D, Parris K, Nolan CE, Fan Y, Atchison K, Gonzales C, Robshaw AE, Doran SD, Bundesmann MW, Buzon L, Dutra J, Henegar K, LaChapelle E, Hou X, Rogers BN, Pandit J, Lira R, Martinez-Alsina L, Mikochik P, Murray JC, Ogilvie K, Price L, Sakya SM, Yu A, Zhang Y, O'Neill BT. Utilizing structures of CYP2D6 and BACE1 complexes to reduce risk of drug-drug interactions with a novel series of centrally efficacious BACE1 inhibitors. J Med Chem 2015; 58:3223-52. [PMID: 25781223 PMCID: PMC4415909 DOI: 10.1021/acs.jmedchem.5b00191] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
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In recent years, the first generation
of β-secretase (BACE1)
inhibitors advanced into clinical development for the treatment of
Alzheimer’s disease (AD). However, the alignment of drug-like
properties and selectivity remains a major challenge. Herein, we describe
the discovery of a novel class of potent, low clearance, CNS penetrant
BACE1 inhibitors represented by thioamidine 5. Further
profiling suggested that a high fraction of the metabolism (>95%)
was due to CYP2D6, increasing the potential risk for victim-based
drug–drug interactions (DDI) and variable exposure in the clinic
due to the polymorphic nature of this enzyme. To guide future design,
we solved crystal structures of CYP2D6 complexes with substrate 5 and its corresponding metabolic product pyrazole 6, which provided insight into the binding mode and movements between
substrate/inhibitor complexes. Guided by the BACE1 and CYP2D6 crystal
structures, we designed and synthesized analogues with reduced risk
for DDI, central efficacy, and improved hERG therapeutic margins.
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Affiliation(s)
| | | | | | | | - Eric F Johnson
- #The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92024, United States
| | | | | | | | - Ying Fan
- #The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92024, United States
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Aijia Yu
- ∇WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Yong Zhang
- ∇WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
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