1
|
Subbaiah MAM, Meanwell NA. Bioisosteres of the Phenyl Ring: Recent Strategic Applications in Lead Optimization and Drug Design. J Med Chem 2021; 64:14046-14128. [PMID: 34591488 DOI: 10.1021/acs.jmedchem.1c01215] [Citation(s) in RCA: 168] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The benzene moiety is the most prevalent ring system in marketed drugs, underscoring its historic popularity in drug design either as a pharmacophore or as a scaffold that projects pharmacophoric elements. However, introspective analyses of medicinal chemistry practices at the beginning of the 21st century highlighted the indiscriminate deployment of phenyl rings as an important contributor to the poor physicochemical properties of advanced molecules, which limited their prospects of being developed into effective drugs. This Perspective deliberates on the design and applications of bioisosteric replacements for a phenyl ring that have provided practical solutions to a range of developability problems frequently encountered in lead optimization campaigns. While the effect of phenyl ring replacements on compound properties is contextual in nature, bioisosteric substitution can lead to enhanced potency, solubility, and metabolic stability while reducing lipophilicity, plasma protein binding, phospholipidosis potential, and inhibition of cytochrome P450 enzymes and the hERG channel.
Collapse
Affiliation(s)
- Murugaiah A M Subbaiah
- Department of Medicinal Chemistry, Biocon-Bristol Myers Squibb Research and Development Centre, Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bangalore, Karnataka 560099, India
| | - Nicholas A Meanwell
- Department of Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| |
Collapse
|
2
|
Shen WX, Zeng X, Zhu F, Wang YL, Qin C, Tan Y, Jiang YY, Chen YZ. Out-of-the-box deep learning prediction of pharmaceutical properties by broadly learned knowledge-based molecular representations. NAT MACH INTELL 2021. [DOI: 10.1038/s42256-021-00301-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
3
|
Wiedmer L, Schärer C, Spiliotopoulos D, Hürzeler M, Śledź P, Caflisch A. Ligand retargeting by binding site analogy. Eur J Med Chem 2019; 175:107-113. [DOI: 10.1016/j.ejmech.2019.04.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/11/2019] [Accepted: 04/13/2019] [Indexed: 12/27/2022]
|
4
|
Hu H, Chen Z, Xu X, Xu Y. Structure-Based Survey of the Binding Modes of BACE1 Inhibitors. ACS Chem Neurosci 2019; 10:880-889. [PMID: 30540177 DOI: 10.1021/acschemneuro.8b00420] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACE1 is a key aspartic protease that cleaves the amyloid precursor protein to generate of the amyloid peptide that is believed to be responsible for the Alzheimer's disease amyloid cascade. It is thus recognized as a promising therapeutic target for Alzheimer's disease treatment, and large efforts have been made in the discovery of novel BACE1 inhibitors. This Review presents a systematic mining of BACE1 inhibitors based on 354 crystal structures of the BACE1 catalytic domain in complex with ligands in the Protein Data Bank. A thorough exploration on the frequency as well as the patterns of residue-ligand interactions enables us to subdivide the ligand binding pocket into 10 subsites and then identify favorable substructures of ligands for each subsite. In addition, it is found that the assembly of subsites with an 8-like shape is responsible to bind all inhibitors and four major ligand binding modes are revealed. Thus, such a systematic survey deepens our understanding of the structural requirements for establishment of BACE1-ligand interactions that determine the affinity of a ligand to BACE1, which is pivotal for structure-based lead optimization and design of novel inhibitors.
Collapse
Affiliation(s)
- Hangchen Hu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaoqiang Chen
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiang Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yechun Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
5
|
Nematpour M, Abedi E, Abedi E. A Novel One-pot Protocol for the Cu-Catalyzed Synthesis of Nine 2-Aminobenzimidazole Derivatives from o-Phenylenediamine and Trichloroacetonitrile. LETT ORG CHEM 2019. [DOI: 10.2174/1570178615666180914114010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The synthesis of a variety of 2-aminobenzimidazoles via a one pot reaction of ophenylenediamine
and trichloroacetonitrile catalyzed by copper (II) acetate in THF at room temperature,
with good yields is described. Use of simple and readily available starting materials, good to high
yields, free ligand, and no column chromatography are important features of this protocol.
Collapse
Affiliation(s)
- Manijeh Nematpour
- Young Researchers and Elites Club, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Elham Abedi
- Pathology Department, Shiraz University of Medical Siences, Shiraz, Iran
| | - Elahe Abedi
- Department of Food Sciences and Technology, Fasa University, Fasa, Iran
| |
Collapse
|
6
|
Sharma P, Srivastava P, Seth A, Tripathi PN, Banerjee AG, Shrivastava SK. Comprehensive review of mechanisms of pathogenesis involved in Alzheimer's disease and potential therapeutic strategies. Prog Neurobiol 2018; 174:53-89. [PMID: 30599179 DOI: 10.1016/j.pneurobio.2018.12.006] [Citation(s) in RCA: 202] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 12/04/2018] [Accepted: 12/28/2018] [Indexed: 12/14/2022]
Abstract
AD is a progressive neurodegenerative disorder and a leading cause of dementia in an aging population worldwide. The enormous challenge which AD possesses to global healthcare makes it as urgent as ever for the researchers to develop innovative treatment strategies to fight this disease. An in-depth analysis of the extensive available data associated with the AD is needed for a more comprehensive understanding of underlying molecular mechanisms and pathophysiological pathways associated with the onset and progression of the AD. The currently understood pathological and biochemical manifestations include cholinergic, Aβ, tau, excitotoxicity, oxidative stress, ApoE, CREB signaling pathways, insulin resistance, etc. However, these hypotheses have been criticized with several conflicting reports for their involvement in the disease progression. Several issues need to be addressed such as benefits to cost ratio with cholinesterase therapy, the dilemma of AChE selectivity over BChE, BBB permeability of peptidic BACE-1 inhibitors, hurdles related to the implementation of vaccination and immunization therapy, and clinical failure of candidates related to newly available targets. The present review provides an insight to the different molecular mechanisms involved in the development and progression of the AD and potential therapeutic strategies, enlightening perceptions into structural information of conventional and novel targets along with the successful applications of computational approaches for the design of target-specific inhibitors.
Collapse
Affiliation(s)
- Piyoosh Sharma
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Pavan Srivastava
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Ankit Seth
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Prabhash Nath Tripathi
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Anupam G Banerjee
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Sushant K Shrivastava
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India.
| |
Collapse
|
7
|
Novel multi-target compounds in the quest for new chemotherapies against Alzheimer’s disease: An experimental and theoretical study. Bioorg Med Chem 2018; 26:4823-4840. [DOI: 10.1016/j.bmc.2018.08.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 08/14/2018] [Indexed: 01/05/2023]
|
8
|
Gutiérrez LJ, Parravicini O, Sánchez E, Rodríguez R, Cobo J, Enriz RD. New substituted aminopyrimidine derivatives as BACE1 inhibitors: in silico design, synthesis and biological assays. J Biomol Struct Dyn 2018; 37:229-246. [DOI: 10.1080/07391102.2018.1424036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Lucas J. Gutiérrez
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 915, 5700 San Luis, Argentina
- IMIBIO-CONICET, UNSL, Chacabuco 915, 5700 San Luis, Argentina
| | - Oscar Parravicini
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 915, 5700 San Luis, Argentina
- IMIBIO-CONICET, UNSL, Chacabuco 915, 5700 San Luis, Argentina
| | - Emilse Sánchez
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 915, 5700 San Luis, Argentina
- IMIBIO-CONICET, UNSL, Chacabuco 915, 5700 San Luis, Argentina
| | - Ricaurte Rodríguez
- Departamento de Química, Universidad Nacional de Colombia, Ciudad Universitaria, Carrera 30, No. 45-03, Bogotá, Colombia
| | - Justo Cobo
- Departamento de Química Inorgánica y Orgánica, Universidad de Jaén, Campus Las Lagunillas s/n, 23071 Jaén, Spain
| | - Ricardo D. Enriz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 915, 5700 San Luis, Argentina
- IMIBIO-CONICET, UNSL, Chacabuco 915, 5700 San Luis, Argentina
| |
Collapse
|
9
|
Wang H, Yu L, Xie M, Wu J, Qu G, Ding K, Guo H. Regio- and Enantioselective Allylic Amination of Aliphatic MBH Adducts with N-Heteroaromatics. Chemistry 2017; 24:1425-1430. [DOI: 10.1002/chem.201704772] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Indexed: 01/23/2023]
Affiliation(s)
- Haixia Wang
- Henan Key Laboratory of Organic Functional Molecules and Drugs Innovation; School of Chemistry and Chemical Engineering; Henan Normal University; Xinxiang 453007 China
| | - Lulu Yu
- Henan Key Laboratory of Organic Functional Molecules and Drugs Innovation; School of Chemistry and Chemical Engineering; Henan Normal University; Xinxiang 453007 China
| | - Mingsheng Xie
- Henan Key Laboratory of Organic Functional Molecules and Drugs Innovation; School of Chemistry and Chemical Engineering; Henan Normal University; Xinxiang 453007 China
| | - Jiang Wu
- State Key Laboratory of Organometallic Chemistry; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Lu Shanghai 200032 China
| | - Guirong Qu
- Henan Key Laboratory of Organic Functional Molecules and Drugs Innovation; School of Chemistry and Chemical Engineering; Henan Normal University; Xinxiang 453007 China
| | - Kuiling Ding
- State Key Laboratory of Organometallic Chemistry; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Lu Shanghai 200032 China
| | - Haiming Guo
- Henan Key Laboratory of Organic Functional Molecules and Drugs Innovation; School of Chemistry and Chemical Engineering; Henan Normal University; Xinxiang 453007 China
| |
Collapse
|
10
|
Zheng Y, Wang Q, Yang X, Li Z, Gao L, Zhang H, Nie W, Geng X, Wang K. Investigation of the interactions between aptamer and misfolded proteins: From monomer and oligomer to fibril by single-molecule force spectroscopy. J Mol Recognit 2017; 31. [PMID: 29143447 DOI: 10.1002/jmr.2686] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 10/10/2017] [Accepted: 10/19/2017] [Indexed: 12/13/2022]
Abstract
Increasing knowledge on the understanding interactions of aptamer with misfolded proteins (including monomer, oligomer, and amyloid fibril) is crucial for development of aggregation inhibitors and diagnosis of amyloid diseases. Herein, the interactions of lysozyme monomer-, oligomer-, and amyloid fibril-aptamer were investigated using single-molecule force spectroscopy. The results revealed that the aptamer screened against lysozyme monomer could also bind to oligomer and amyloid fibril, in spite of the recognition at a lower binding probability. It may be attributed to the inherent structural differences of misfolded proteins and the flexible conformation of aptamer. In addition, dynamic force spectra showed that there were similar dissociation paths in the dissociation process of lysozyme monomer-, oligomer-, and amyloid fibril-aptamer complexes. It showed that the dissociation only passed 1 energy barrier from the binding state to the detachment. However, the dynamic parameters suggested that the oligomer- and amyloid fibril-aptamer were more stable than lysozyme monomer-aptamer. The phenomena may result from the exposure of aptamer-recognized sequences on the surface and the electrostatic interactions. This work demonstrated that single-molecule force spectroscopy could be a powerful tool to study the binding behavior of the aptamer with misfolded proteins at single-molecule level, providing abundant information for researches and comprehensive applications of aptamer probes in diagnosis of amyloid diseases.
Collapse
Affiliation(s)
- Yan Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Qing Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Zhiping Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Lei Gao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Hua Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Wenyan Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Xiuhua Geng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| |
Collapse
|
11
|
Abstract
This viewpoint describes the results obtained from matched molecular pair analyses and quantum mechanics calculations that show unsaturated rings found in drug-like molecules may be replaced with their saturated counterparts without losing potency even if they are engaged in stacking interactions with the side chains of aromatic residues.
Collapse
Affiliation(s)
- Hakan Gunaydin
- Department of Structural Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Michael D. Bartberger
- Department of Molecular Engineering, Therapeutic Discovery, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| |
Collapse
|
12
|
Wyss DF, Cumming JN, Strickland CO, Stamford AW. BACE Inhibitors. FRAGMENT-BASED DRUG DISCOVERY LESSONS AND OUTLOOK 2016. [DOI: 10.1002/9783527683604.ch14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
13
|
Hossain T, Mukherjee A, Saha A. Chemometric design to explore pharmacophore features of BACE inhibitors for controlling Alzheimer's disease. MOLECULAR BIOSYSTEMS 2015; 11:549-57. [DOI: 10.1039/c4mb00540f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Pharmacophoric features of potent BACE inhibitors derived from multi-chemometric studies.
Collapse
Affiliation(s)
- Tabassum Hossain
- Department of Chemical Technology
- University of Calcutta
- Kolkata-700009
- India
| | - Arup Mukherjee
- Department of Chemical Technology
- University of Calcutta
- Kolkata-700009
- India
| | - Achintya Saha
- Department of Chemical Technology
- University of Calcutta
- Kolkata-700009
- India
| |
Collapse
|
14
|
Synthesis and antiproliferative activity in vitro of new 2-aminobenzimidazole derivatives. Reaction of 2-arylideneaminobenzimidazole with selected nitriles containing active methylene group. OPEN CHEM 2014. [DOI: 10.2478/s11532-014-0533-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractA series of pyrimido[1,2-a]benzimidazole and α-cyanocinnamic acid derivatives have been synthesized in the reactions of Schiff bases 2–7 with selected nitriles containing an active methylene group: malononitrile 8–12, cyanoacetamide 13–16, benzyl cyanide 17–21, benzoylacetonitrile 22–24, cyanoacetate methyl ester 25–28 and benzylacetamide 29. The structures 8–29 were confirmed by the results of elementary analysis and their IR, 1H-, 13C-NMR and MS spectra. The products 8–29 of various chemical structure pyrimido[1,2-a] benzimidazole 8–12, 14–16, 17–21, 23–24, 26 and α-cyanocinnamic acid derivatives 13, 22, 25, 27, 28 were obtained, which are of interest for biological studies or which can be substrates for further synthesis. The selected compounds 10, 13, 14, 17, 19, 21, 23–25 and 28 were screened for their antiproliferative activity in vitro against neoplastic and normal cell lines. The most active two compounds were: 2-(o-bromophenylene)-3-cyano-4-phenyl-1,2-dihydropyrimido[1,2-a]benzimidazole (24) and 3-cyano-4-phenyl-2-(2,4-dimethoxyphenyl)-1,2-dihydropyrimido[1,2-a]benzimidazole (23). However, similarly like cisplatin used as the control, they showed no selectivity towards cancer cells, by inhibiting proliferation of normal mouse fibroblasts in similar manner.
Collapse
|
15
|
Viklund J, Kolmodin K, Nordvall G, Swahn BM, Svensson M, Gravenfors Y, Rahm F. Creation of Novel Cores for β-Secretase (BACE-1) Inhibitors: A Multiparameter Lead Generation Strategy. ACS Med Chem Lett 2014; 5:440-5. [PMID: 24900855 DOI: 10.1021/ml5000433] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 02/03/2014] [Indexed: 12/18/2022] Open
Abstract
In order to find optimal core structures as starting points for lead optimization, a multiparameter lead generation workflow was designed with the goal of finding BACE-1 inhibitors as a treatment for Alzheimer's disease. De novo design of core fragments was connected with three predictive in silico models addressing target affinity, permeability, and hERG activity, in order to guide synthesis. Taking advantage of an additive SAR, the prioritized cores were decorated with a few, well-characterized substituents from known BACE-1 inhibitors in order to allow for core-to-core comparisons. Prediction methods and analyses of how physicochemical properties of the core structures correlate to in vitro data are described. The syntheses and in vitro data of the test compounds are reported in a separate paper by Ginman et al. [J. Med. Chem. 2013, 56, 4181-4205]. The affinity predictions are described in detail by Roos et al. [J. Chem. Inf. 2014, DOI: 10.1021/ci400374z].
Collapse
Affiliation(s)
- Jenny Viklund
- Department of Medicinal Chemistry AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Karin Kolmodin
- Department of Medicinal Chemistry AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Gunnar Nordvall
- Department of Medicinal Chemistry AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Britt-Marie Swahn
- Department of Medicinal Chemistry AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Mats Svensson
- Department of Medicinal Chemistry AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Ylva Gravenfors
- Department of Medicinal Chemistry AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Fredrik Rahm
- Department of Medicinal Chemistry AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| |
Collapse
|
16
|
Kalászi A, Szisz D, Imre G, Polgár T. Screen3D: A Novel Fully Flexible High-Throughput Shape-Similarity Search Method. J Chem Inf Model 2014; 54:1036-49. [DOI: 10.1021/ci400620f] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Adrián Kalászi
- ChemAxon Ltd., Graphisoft park, Zahony
u. 7, Budapest, Hungary, 1037
| | - Dániel Szisz
- ChemAxon Ltd., Graphisoft park, Zahony
u. 7, Budapest, Hungary, 1037
| | - Gábor Imre
- ChemAxon Ltd., Graphisoft park, Zahony
u. 7, Budapest, Hungary, 1037
| | - Tímea Polgár
- ChemAxon Ltd., Graphisoft park, Zahony
u. 7, Budapest, Hungary, 1037
| |
Collapse
|
17
|
Pérez-Ruiz E, Kemper M, Spasic D, Gils A, van Ijzendoorn LJ, Lammertyn J, Prins MWJ. Probing the force-induced dissociation of aptamer-protein complexes. Anal Chem 2014; 86:3084-91. [PMID: 24579568 DOI: 10.1021/ac404107s] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Aptamers are emerging as powerful synthetic bioreceptors for fundamental research, diagnostics, and therapeutics. For further advances, it is important to gain a better understanding of how aptamers interact with their targets. In this work, we have used magnetic force-induced dissociation experiments to study the dissociation process of two different aptamer-protein complexes, namely for hIgE and Ara h 1. The measurements show that both complexes exhibit dissociation with two distinct regimes: the dissociation rate depends weakly on the applied force at high forces but depends stronger on force at low forces. We attribute these observations to the existence of at least one intermediate state and at least two energy barriers in the aptamer-protein interaction. The measured spontaneous dissociation rate constants were validated with SPR using both Biacore and fiber optic technology. This work demonstrates the potential of the magnetic force-induced dissociation approach for an in-depth study of the dissociation kinetics of aptamer-protein bonds, which is not possible with SPR technologies. The results will help in the development and expansion of aptamers as bioaffinity probes.
Collapse
Affiliation(s)
- Elena Pérez-Ruiz
- Department of Biosystems - MeBioS, KU Leuven-University of Leuven , Leuven, Belgium
| | | | | | | | | | | | | |
Collapse
|
18
|
Ginman T, Viklund J, Malmström J, Blid J, Emond R, Forsblom R, Johansson A, Kers A, Lake F, Sehgelmeble F, Sterky KJ, Bergh M, Lindgren A, Johansson P, Jeppsson F, Fälting J, Gravenfors Y, Rahm F. Core refinement toward permeable β-secretase (BACE-1) inhibitors with low hERG activity. J Med Chem 2013; 56:4181-205. [PMID: 23126626 DOI: 10.1021/jm3011349] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
By use of iterative design aided by predictive models for target affinity, brain permeability, and hERG activity, novel and diverse compounds based on cyclic amidine and guanidine cores were synthesized with the goal of finding BACE-1 inhibitors as a treatment for Alzheimer's disease. Since synthesis feasibility had low priority in the design of the cores, an extensive synthesis effort was needed to make the relevant compounds. Syntheses of these compounds are reported, together with physicochemical properties and structure-activity relationships based on in vitro data. Four crystal structures of diverse amidines binding in the active site are deposited and discussed. Inhibitors of BACE-1 with 3 μM to 32 nM potencies in cells are shown, together with data on in vivo brain exposure levels for four compounds. The results presented show the importance of the core structure for the profile of the final compounds.
Collapse
Affiliation(s)
- Tobias Ginman
- Department of Medicinal Chemistry, AstraZeneca R&D Södertälje, SE-151 85, Södertälje, Sweden
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Stamford A, Strickland C. Inhibitors of BACE for treating Alzheimer's disease: a fragment-based drug discovery story. Curr Opin Chem Biol 2013; 17:320-8. [PMID: 23683349 DOI: 10.1016/j.cbpa.2013.04.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 04/02/2013] [Accepted: 04/15/2013] [Indexed: 11/27/2022]
Abstract
Several fragment-based methods have been applied to the discovery of new lead sources for inhibitors of BACE1, an important therapeutic target for Alzheimer's disease. Among the most common fragment hits were various amidine-containing molecules in which the amidine engaged in discrete H-bond donor-acceptor interaction with the BACE1 catalytic dyad. Structure and medicinal chemistry knowledge-based optimization with emphasis on ligand efficiency resulted in identification of a key pharmacophore comprising a non-planar cyclic amidine scaffold directly attached to a phenyl group projecting into S1. This key pharmacophore is a common feature of known clinical candidates and has dominated the recent patent literature. A structural comparison of the non-planar cyclic amidine motif with other BACE1 pharmacophores highlights its uniqueness and distinct advantages.
Collapse
Affiliation(s)
- Andrew Stamford
- Merck Research Laboratories, 126 East Lincoln Avenue, Rahway, NJ 07065, United States.
| | | |
Collapse
|
20
|
Effect of pH and ligand charge state on BACE-1 fragment docking performance. J Comput Aided Mol Des 2013; 27:403-17. [DOI: 10.1007/s10822-013-9653-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 04/24/2013] [Indexed: 10/26/2022]
|
21
|
Abstract
INTRODUCTION Alzheimer's disease (AD), which is characterized by progressive intellectual deterioration, is the most common cause of dementia. β-Secretase (or BACE1) expression is a trigger for amyloid β peptide formation, a cause of AD, and thus is a molecular target for the development of drugs against AD. Many BACE1 inhibitors have been identified by academic and pharmaceutical research groups and a number of advanced technologies in drug discovery have been applied to the drug discovery. AREAS COVERED The purpose of this review is to present and discuss the methodologies used for BACE1 inhibitor drug discovery via substrate- and structure-based design, high-throughput screening and fragment-based drug design. The authors also review the advantages and disadvantages of these methodologies. EXPERT OPINION Many BACE1 inhibitors have been designed using X-ray crystal structure-based drug design as well as through in silico screening. Nevertheless, there are serious problems with regards to deciding the best X-ray crystal structure for designing BACE1 inhibitors through computational approaches. There are two prominent configurations of BACE1 but there is still room for improvement. Future developments may make it possible to identify BACE1 inhibitors as potential drug candidates.
Collapse
Affiliation(s)
- Yoshio Hamada
- Kobe Gakuin University, Faculty of Pharmaceutical Sciences, Minatojima, Chuo-ku, Kobe 650-8586, Japan
| | | |
Collapse
|
22
|
Yuan J, Venkatraman S, Zheng Y, McKeever BM, Dillard LW, Singh SB. Structure-based design of β-site APP cleaving enzyme 1 (BACE1) inhibitors for the treatment of Alzheimer's disease. J Med Chem 2013; 56:4156-80. [PMID: 23509904 DOI: 10.1021/jm301659n] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The amyloid hypothesis asserts that excess production or reduced clearance of the amyloid-β (Aβ) peptides in the brain initiates a sequence of events that ultimately lead to Alzheimer's disease and dementia. The Aβ hypothesis has identified BACE1 as a therapeutic target to treat Alzheimer's and led to medicinal chemistry efforts to design its inhibitors both in the pharmaceutical industry and in academia. This review summarizes two distinct categories of inhibitors designed based on conformational states of "closed" and "open" forms of the enzyme. In each category the inhibitors are classified based on the core catalytic interaction group or the aspartyl binding motif (ABM). This review covers the description of inhibitors in each ABM class with X-ray crystal structures of key compounds, their binding modes, related structure-activity data highlighting potency advances, and additional properties such as selectivity profile, P-gp efflux, pharmacokinetic, and pharmacodynamic data.
Collapse
Affiliation(s)
- Jing Yuan
- Vitae Pharmaceuticals, 502 W. Office Center Drive, Fort Washington, Pennsylvania 19034, USA
| | | | | | | | | | | |
Collapse
|
23
|
Razzaghi-Asl N, Ebadi A, Edraki N, Shahabipour S, Miri R. Ab initio modeling of a potent isophthalamide-based BACE-1 inhibitor: amino acid decomposition analysis. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0277-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
24
|
Yonezawa S, Yamamoto T, Yamakawa H, Muto C, Hosono M, Hattori K, Higashino K, Yutsudo T, Iwamoto H, Kondo Y, Sakagami M, Togame H, Tanaka Y, Nakano T, Takemoto H, Arisawa M, Shuto S. Conformational Restriction Approach to β-Secretase (BACE1) Inhibitors: Effect of a Cyclopropane Ring To Induce an Alternative Binding Mode. J Med Chem 2012; 55:8838-58. [PMID: 22998419 DOI: 10.1021/jm3011405] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Shuji Yonezawa
- Shionogi Innovation Center for Drug Discovery, Shionogi & Co., Ltd., Kita-21 Nishi-11 Kita-ku, Sapporo 001-0021, Japan
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo
060-0812, Japan
| | - Takahiko Yamamoto
- Pharmaceutical Research Division, Medicinal Research Laboratories, and Innovative Drug Discovery Research Laboratories, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Hidekuni Yamakawa
- Pharmaceutical Research Division, Medicinal Research Laboratories, and Innovative Drug Discovery Research Laboratories, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Chie Muto
- Pharmaceutical Research Division, Medicinal Research Laboratories, and Innovative Drug Discovery Research Laboratories, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Motoko Hosono
- Pharmaceutical Research Division, Medicinal Research Laboratories, and Innovative Drug Discovery Research Laboratories, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Kazunari Hattori
- Pharmaceutical Research Division, Medicinal Research Laboratories, and Innovative Drug Discovery Research Laboratories, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Kenichi Higashino
- Shionogi Innovation Center for Drug Discovery, Shionogi & Co., Ltd., Kita-21 Nishi-11 Kita-ku, Sapporo 001-0021, Japan
| | - Takashi Yutsudo
- Pharmaceutical Research Division, Medicinal Research Laboratories, and Innovative Drug Discovery Research Laboratories, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Hideo Iwamoto
- Shionogi Techno Advance Research
Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Yutaka Kondo
- Shionogi Techno Advance Research
Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Masahiro Sakagami
- Pharmaceutical Research Division, Medicinal Research Laboratories, and Innovative Drug Discovery Research Laboratories, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Hiroko Togame
- Quality, Safety and Regulatory Affairs Management Division, Shionogi & Co., Ltd., 1-8, Doshomachi 3-chome, Chuo-ku, Osaka 541-0045, Japan
| | - Yoshikazu Tanaka
- Shionogi Innovation Center for Drug Discovery, Shionogi & Co., Ltd., Kita-21 Nishi-11 Kita-ku, Sapporo 001-0021, Japan
| | - Toru Nakano
- Shionogi Innovation Center for Drug Discovery, Shionogi & Co., Ltd., Kita-21 Nishi-11 Kita-ku, Sapporo 001-0021, Japan
| | - Hiroshi Takemoto
- Pharmaceutical Research Division, Medicinal Research Laboratories, and Innovative Drug Discovery Research Laboratories, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Mitsuhiro Arisawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo
060-0812, Japan
| | - Satoshi Shuto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo
060-0812, Japan
| |
Collapse
|
25
|
Scott DE, Coyne AG, Hudson SA, Abell C. Fragment-Based Approaches in Drug Discovery and Chemical Biology. Biochemistry 2012; 51:4990-5003. [DOI: 10.1021/bi3005126] [Citation(s) in RCA: 324] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Duncan E. Scott
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Anthony G. Coyne
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Sean A. Hudson
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Chris Abell
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| |
Collapse
|
26
|
Iminoheterocycle as a druggable motif: BACE1 inhibitors and beyond. Trends Pharmacol Sci 2012; 33:233-40. [DOI: 10.1016/j.tips.2012.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 02/01/2012] [Accepted: 02/21/2012] [Indexed: 11/20/2022]
|
27
|
Rueeger H, Lueoend R, Rogel O, Rondeau JM, Möbitz H, Machauer R, Jacobson L, Staufenbiel M, Desrayaud S, Neumann U. Discovery of Cyclic Sulfone Hydroxyethylamines as Potent and Selective β-Site APP-Cleaving Enzyme 1 (BACE1) Inhibitors: Structure-Based Design and in Vivo Reduction of Amyloid β-Peptides. J Med Chem 2012; 55:3364-86. [DOI: 10.1021/jm300069y] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Heinrich Rueeger
- Department
of Global Discovery Chemistry, ‡Structural Biology Platform, §Department of Neuroscience, and ∥Metabolism and
Pharmacokinetics, Institutes for BioMedical Research, Novartis Pharma AG, CH-4057 Basel, Switzerland
| | - Rainer Lueoend
- Department
of Global Discovery Chemistry, ‡Structural Biology Platform, §Department of Neuroscience, and ∥Metabolism and
Pharmacokinetics, Institutes for BioMedical Research, Novartis Pharma AG, CH-4057 Basel, Switzerland
| | - Olivier Rogel
- Department
of Global Discovery Chemistry, ‡Structural Biology Platform, §Department of Neuroscience, and ∥Metabolism and
Pharmacokinetics, Institutes for BioMedical Research, Novartis Pharma AG, CH-4057 Basel, Switzerland
| | - Jean-Michel Rondeau
- Department
of Global Discovery Chemistry, ‡Structural Biology Platform, §Department of Neuroscience, and ∥Metabolism and
Pharmacokinetics, Institutes for BioMedical Research, Novartis Pharma AG, CH-4057 Basel, Switzerland
| | - Henrik Möbitz
- Department
of Global Discovery Chemistry, ‡Structural Biology Platform, §Department of Neuroscience, and ∥Metabolism and
Pharmacokinetics, Institutes for BioMedical Research, Novartis Pharma AG, CH-4057 Basel, Switzerland
| | - Rainer Machauer
- Department
of Global Discovery Chemistry, ‡Structural Biology Platform, §Department of Neuroscience, and ∥Metabolism and
Pharmacokinetics, Institutes for BioMedical Research, Novartis Pharma AG, CH-4057 Basel, Switzerland
| | - Laura Jacobson
- Department
of Global Discovery Chemistry, ‡Structural Biology Platform, §Department of Neuroscience, and ∥Metabolism and
Pharmacokinetics, Institutes for BioMedical Research, Novartis Pharma AG, CH-4057 Basel, Switzerland
| | - Matthias Staufenbiel
- Department
of Global Discovery Chemistry, ‡Structural Biology Platform, §Department of Neuroscience, and ∥Metabolism and
Pharmacokinetics, Institutes for BioMedical Research, Novartis Pharma AG, CH-4057 Basel, Switzerland
| | - Sandrine Desrayaud
- Department
of Global Discovery Chemistry, ‡Structural Biology Platform, §Department of Neuroscience, and ∥Metabolism and
Pharmacokinetics, Institutes for BioMedical Research, Novartis Pharma AG, CH-4057 Basel, Switzerland
| | - Ulf Neumann
- Department
of Global Discovery Chemistry, ‡Structural Biology Platform, §Department of Neuroscience, and ∥Metabolism and
Pharmacokinetics, Institutes for BioMedical Research, Novartis Pharma AG, CH-4057 Basel, Switzerland
| |
Collapse
|
28
|
Xu Y, Li MJ, Greenblatt H, Chen W, Paz A, Dym O, Peleg Y, Chen T, Shen X, He J, Jiang H, Silman I, Sussman JL. Flexibility of the flap in the active site of BACE1 as revealed by crystal structures and molecular dynamics simulations. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2011; 68:13-25. [DOI: 10.1107/s0907444911047251] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2011] [Accepted: 11/08/2011] [Indexed: 11/10/2022]
|
29
|
Edink E, Akdemir A, Jansen C, van Elk R, Zuiderveld O, de Kanter FJJ, van Muijlwijk-Koezen JE, Smit AB, Leurs R, de Esch IJP. Structure-based design, synthesis and structure-activity relationships of dibenzosuberyl- and benzoate-substituted tropines as ligands for acetylcholine-binding protein. Bioorg Med Chem Lett 2011; 22:1448-54. [PMID: 22243960 DOI: 10.1016/j.bmcl.2011.12.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 11/30/2011] [Accepted: 12/01/2011] [Indexed: 12/26/2022]
Abstract
Using structure-based optimization procedures on in silico hits, dibenzosuberyl- and benzoate substituted tropines were designed as ligands for acetylcholine-binding protein (AChBP). This protein is a homolog to the ligand binding domain of the nicotinic acetylcholine receptor (nAChR). Distinct SAR is observed between two AChBP species variants and between the α7 and α4β2 nAChR subtype. The AChBP species differences are indicative of a difference in accessibility of a ligand-inducible subpocket. Hereby, we have identified a region that can be scrutinized to achieve selectivity for nicotinic receptor subtypes.
Collapse
Affiliation(s)
- Ewald Edink
- Leiden/Amsterdam Center of Drug Research, Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, The Netherlands
| | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Rueeger H, Rondeau JM, McCarthy C, Möbitz H, Tintelnot-Blomley M, Neumann U, Desrayaud S. Structure based design, synthesis and SAR of cyclic hydroxyethylamine (HEA) BACE-1 inhibitors. Bioorg Med Chem Lett 2011; 21:1942-7. [DOI: 10.1016/j.bmcl.2011.02.038] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2010] [Revised: 02/09/2011] [Accepted: 02/10/2011] [Indexed: 01/16/2023]
|
31
|
Combining NMR and X-ray Crystallography in Fragment-Based Drug Discovery: Discovery of Highly Potent and Selective BACE-1 Inhibitors. Top Curr Chem (Cham) 2011; 317:83-114. [DOI: 10.1007/128_2011_183] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
32
|
Whittaker M, Law RJ, Ichihara O, Hesterkamp T, Hallett D. Fragments: past, present and future. DRUG DISCOVERY TODAY. TECHNOLOGIES 2010; 7:e147-e202. [PMID: 24103768 DOI: 10.1016/j.ddtec.2010.11.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
|