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Premkumar T, Sajitha Lulu S. Targeting key players in Alzheimer's disease: bioactive compounds from Moringa oleifera, Desmodium gangeticum, and Centella asiatica as potential therapeutics. J Biomol Struct Dyn 2024:1-23. [PMID: 38887054 DOI: 10.1080/07391102.2024.2335300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 03/20/2024] [Indexed: 06/20/2024]
Abstract
Alzheimer's Disease (AD) is one of the critical reasons for dementia around the world, with a huge number of cases being reported every year. The breakdown of Amyloid Precursor Protein (APP) plays a crucial role in AD development. The Beta-site APP Cleaving Enzyme 1 (BACE1) is a highly significant proteolytic enzyme found to be critically involved in the APP breakdown process and generates beta-amyloid plaques in the extracellular neuronal membrane. In this study, we have used natural compounds with cognitive and neuroprotective activities from three plants, Centella asiatica, Moringa oleifera, and Desmodium gangeticum to inhibit the activity of BACE1. We have identified nine compounds out of 73 compounds filtered out from the three plants showing high affinity with the catalytic dyad region of BACE1 through molecular docking studies. Interestingly, the 200 ns molecular dynamics simulation study further confirmed the stability of the complexes formed between 9 compounds and the BACE1 protein. Furthermore, the free energy calculations also revealed these complexes possess favorable energies. Astilbin, Delphinidin 3-glucoside, and kaempferol 7-O-glucoside showed good binding affinity and structural stability when compared to other compounds and the control CNP520. Following a preliminary screening, the Astilbin compound was chosen based on the grounds of binding affinity, ADMET Properties, Hbond formation, Molecular Dynamic simulation, and MM-PBSA studies. A subsequent 1microsecond molecular dynamics simulation was conducted for the Astilbin complex. Through microsecond simulation, it was found that Astilbin alters BACE1's behavior and induces conformational rearrangements. Thus, this study opens a gateway to inhibit the activity of BACE1 protein through Astilbin thereby disclosing the possibility of managing Alzheimer's Disease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- T Premkumar
- Integrative Multiomics Laboratory, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - S Sajitha Lulu
- Integrative Multiomics Laboratory, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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2
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Tutuş B, Kaya AZ, Baz Y, Evren AE, Sağlik Özkan BN, Yurttaş L. Synthesis of new N-(5,6-methylenedioxybenzothiazole-2-yl)-2-[(substituted)thio/piperazine]acetamide/propanamide derivatives and evaluation of their AChE, BChE, and BACE-1 inhibitory activities. Drug Dev Res 2024; 85:e22214. [PMID: 38816986 DOI: 10.1002/ddr.22214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/07/2024] [Accepted: 05/12/2024] [Indexed: 06/01/2024]
Abstract
In this study, the synthesis of N-(5,6-methylenedioxybenzothiazole-2-yl)-2-[(substituted)thio/piperazine]acetamide/propanamide derivatives (3a-3k) and to investigate their acetylcholinesterase (AChE), butyrylcholinesterase (BChE) and β-secretase 1 (BACE-1) inhibition activity were aimed. Mass, 1H NMR, and 13C NMR spectra were utilized to determine the structure of the synthesized compounds. Compounds 3b, 3c, 3f, and 3j showed AChE inhibitory activity which compound 3c (IC50 = 0.030 ± 0.001 µM) showed AChE inhibitory activity as high as the reference drug donepezil (IC50 = 0.0201 ± 0.0010 µM). Conversely, none of the compounds showed BChE activity. Compounds 3c and 3j showed the highest BACE-1 inhibitory activity and IC50 value was found as 0.119 ± 0.004 µM for compound 3j whereas IC50 value was 0.110 ± 0.005 µM for donepezil, which is one of the reference substance. Molecular docking studies have been carried out using the data retrieved from the server of the Protein Data Bank (PDBID: 4EY7 and 2ZJM). Using in silico approach behavior active compounds (3c and 3j) and their binding modes clarified.
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Affiliation(s)
- Beyzanur Tutuş
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
- Kırıkhan Vocational School, Department of Pharmacy Services, Hatay Mustafa Kemal University, Hatay, Turkey
- Institute of Graduate Education, Department of Pharmaceutical Chemistry, Anadolu University, Eskişehir, Turkey
| | - Aybüke Züleyha Kaya
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
- Institute of Graduate Education, Department of Pharmaceutical Chemistry, Anadolu University, Eskişehir, Turkey
| | - Yonca Baz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
- Institute of Graduate Education, Department of Pharmaceutical Chemistry, Anadolu University, Eskişehir, Turkey
| | - Asaf Evrim Evren
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
- Vocational School of Health Services, Department of Pharmacy Services, Bilecik Seyh Edebali University, Bilecik, Turkey
| | | | - Leyla Yurttaş
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
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3
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Zhang Y, Miao D, Liu S, Hao X. Revealing the binding mechanism of BACE1 inhibitors through molecular dynamics simulations. J Biomol Struct Dyn 2024:1-13. [PMID: 38375603 DOI: 10.1080/07391102.2024.2319676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 02/11/2024] [Indexed: 02/21/2024]
Abstract
Alzheimer's disease is a debilitating neurodegenerative disorder, and the Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1) is a key therapeutic target in its treatment. This study employs molecular dynamics simulations and binding energy analysis to investigate the binding interactions between BACE1 and four selected small molecules: CNP520, D9W, NB641, and NB360. The binding model analysis indicates that the binding of BACE1 with four molecules are stable, except the loop regions show significant fluctuation. The binding free energy analyses reveal that NB360 exhibits the highest binding affinity with BACE1, surpassing other molecules (CNP520, D9W, and NB641). Detailed energy component assessments highlight the critical roles of electrostatic interactions and van der Waals forces in the binding process. Furthermore, residue contribution analysis identifies key amino acids influencing the binding process across all systems. Hydrogen bond analysis reveals a limited number of bonds between BACE1 and each small molecule, highlighting the importance of structural modifications to enable more stable hydrogen bonds. This research provides valuable insights into the molecular mechanisms of potential Alzheimer's disease therapeutics, guiding the way for improved drug design and the development of effective treatments targeting BACE1.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yanjun Zhang
- School of Mathematics & Physics, Hebei University of Engineering, Handan, China
| | - Dongqiang Miao
- School of Mathematics & Physics, Hebei University of Engineering, Handan, China
| | - Senchen Liu
- School of Mathematics & Physics, Hebei University of Engineering, Handan, China
| | - Xiafei Hao
- Medical College, Hebei University of Engineering, Handan, China
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Barbosa DB, do Bomfim MR, de Oliveira TA, da Silva AM, Taranto AG, Cruz JN, de Carvalho PB, Campos JM, Santos CBR, Leite FHA. Development of Potential Multi-Target Inhibitors for Human Cholinesterases and Beta-Secretase 1: A Computational Approach. Pharmaceuticals (Basel) 2023; 16:1657. [PMID: 38139784 PMCID: PMC10748024 DOI: 10.3390/ph16121657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/04/2023] [Accepted: 11/13/2023] [Indexed: 12/24/2023] Open
Abstract
Alzheimer's disease causes chronic neurodegeneration and is the leading cause of dementia in the world. The causes of this disease are not fully understood but seem to involve two essential cerebral pathways: cholinergic and amyloid. The simultaneous inhibition of AChE, BuChE, and BACE-1, essential enzymes involved in those pathways, is a promising therapeutic approach to treat the symptoms and, hopefully, also halt the disease progression. This study sought to identify triple enzymatic inhibitors based on stereo-electronic requirements deduced from molecular modeling of AChE, BuChE, and BACE-1 active sites. A pharmacophore model was built, displaying four hydrophobic centers, three hydrogen bond acceptors, and one positively charged nitrogen, and used to prioritize molecules found in virtual libraries. Compounds showing adequate overlapping rates with the pharmacophore were subjected to molecular docking against the three enzymes and those with an adequate docking score (n = 12) were evaluated for physicochemical and toxicological parameters and commercial availability. The structure exhibiting the greatest inhibitory potential against all three enzymes was subjected to molecular dynamics simulations (100 ns) to assess the stability of the inhibitor-enzyme systems. The results of this in silico approach indicate ZINC1733 can be a potential multi-target inhibitor of AChE, BuChE, and BACE-1, and future enzymatic assays are planned to validate those results.
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Affiliation(s)
- Deyse B. Barbosa
- Laboratório de Modelagem Molecular, Departamento de Saúde, Universidade Estadual de Feira de Santana, Feira de Santana 44036-900, BA, Brazil; (D.B.B.); (M.R.d.B.); (F.H.A.L.)
| | - Mayra R. do Bomfim
- Laboratório de Modelagem Molecular, Departamento de Saúde, Universidade Estadual de Feira de Santana, Feira de Santana 44036-900, BA, Brazil; (D.B.B.); (M.R.d.B.); (F.H.A.L.)
| | - Tiago A. de Oliveira
- Departamento de Informática, Gestão e Desenho, Centro Federal de Educação Tecnológica de Minas Gerais, Divinópolis 30575-180, MG, Brazil;
| | - Alisson M. da Silva
- Laboratório de Bioinformática e Desenho de Fármacos, Universidade Federal de São João del-Rei, São João del-Rei 36307-352, MG, Brazil; (A.M.d.S.); (A.G.T.)
| | - Alex G. Taranto
- Laboratório de Bioinformática e Desenho de Fármacos, Universidade Federal de São João del-Rei, São João del-Rei 36307-352, MG, Brazil; (A.M.d.S.); (A.G.T.)
| | - Jorddy N. Cruz
- Laboratório de Modelagem e Química Computacional, Departamento de Ciências Biológicas e de Saúde, Universidade Federal do Amapá, Macapá 68903-419, AP, Brazil;
| | - Paulo B. de Carvalho
- Feik School of Pharmacy, University of the Incarnate Word, San Antonio, TX 78209, USA;
| | - Joaquín M. Campos
- Departamento de Química Orgánica Farmacéutica, Facultad de Farmacia, Campus de la Cartuja, Universidad de Granada, 18012 Granada, Spain;
| | - Cleydson B. R. Santos
- Laboratório de Modelagem e Química Computacional, Departamento de Ciências Biológicas e de Saúde, Universidade Federal do Amapá, Macapá 68903-419, AP, Brazil;
- Programa de Pós-Graduação em Biodiversidade e Biotecnologia—Rede BIONORTE, Universidade Federal do Amapá, Macapá 68903-419, AP, Brazil
| | - Franco H. A. Leite
- Laboratório de Modelagem Molecular, Departamento de Saúde, Universidade Estadual de Feira de Santana, Feira de Santana 44036-900, BA, Brazil; (D.B.B.); (M.R.d.B.); (F.H.A.L.)
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5
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Wang Y, Yang F, Yan D, Zeng Y, Wei B, Chen J, He W. Identification Mechanism of BACE1 on Inhibitors Probed by Using Multiple Separate Molecular Dynamics Simulations and Comparative Calculations of Binding Free Energies. Molecules 2023; 28:4773. [PMID: 37375328 DOI: 10.3390/molecules28124773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
β-amyloid cleaving enzyme 1 (BACE1) is regarded as an important target of drug design toward the treatment of Alzheimer's disease (AD). In this study, three separate molecular dynamics (MD) simulations and calculations of binding free energies were carried out to comparatively determine the identification mechanism of BACE1 for three inhibitors, 60W, 954 and 60X. The analyses of MD trajectories indicated that the presence of three inhibitors influences the structural stability, flexibility and internal dynamics of BACE1. Binding free energies calculated by using solvated interaction energy (SIE) and molecular mechanics generalized Born surface area (MM-GBSA) methods reveal that the hydrophobic interactions provide decisive forces for inhibitor-BACE1 binding. The calculations of residue-based free energy decomposition suggest that the sidechains of residues L91, D93, S96, V130, Q134, W137, F169 and I179 play key roles in inhibitor-BACE1 binding, which provides a direction for future drug design toward the treatment of AD.
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Affiliation(s)
- Yiwen Wang
- School of Information Science and Electrical Engineering, Shandong Jiaotong University, Jinan 250357, China
- School of Aeronautics, Shandong Jiaotong University, Jinan 250357, China
| | - Fen Yang
- School of Information Science and Electrical Engineering, Shandong Jiaotong University, Jinan 250357, China
| | - Dongliang Yan
- School of Information Science and Electrical Engineering, Shandong Jiaotong University, Jinan 250357, China
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Yalin Zeng
- School of Information Science and Electrical Engineering, Shandong Jiaotong University, Jinan 250357, China
| | - Benzheng Wei
- Center for Medical Artificial Intelligence, Shandong University of Traditional Chinese Medicine, Qingdao 266112, China
| | - Jianzhong Chen
- School of Information Science and Electrical Engineering, Shandong Jiaotong University, Jinan 250357, China
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Weikai He
- School of Information Science and Electrical Engineering, Shandong Jiaotong University, Jinan 250357, China
- School of Aeronautics, Shandong Jiaotong University, Jinan 250357, China
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6
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O'Day DH. Phytochemical Interactions with Calmodulin and Critical Calmodulin Binding Proteins Involved in Amyloidogenesis in Alzheimer's Disease. Biomolecules 2023; 13:biom13040678. [PMID: 37189425 DOI: 10.3390/biom13040678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/03/2023] [Accepted: 04/13/2023] [Indexed: 05/17/2023] Open
Abstract
An increasing number of plant-based herbal treatments, dietary supplements, medical foods and nutraceuticals and their component phytochemicals are used as alternative treatments to prevent or slow the onset and progression of Alzheimer's disease. Their appeal stems from the fact that no current pharmaceutical or medical treatment can accomplish this. While a handful of pharmaceuticals are approved to treat Alzheimer's, none has been shown to prevent, significantly slow or stop the disease. As a result, many see the appeal of alternative plant-based treatments as an option. Here, we show that many phytochemicals proposed or used as Alzheimer's treatments share a common theme: they work via a calmodulin-mediated mode of action. Some phytochemicals bind to and inhibit calmodulin directly while others bind to and regulate calmodulin-binding proteins, including Aβ monomers and BACE1. Phytochemical binding to Aβ monomers can prevent the formation of Aβ oligomers. A limited number of phytochemicals are also known to stimulate calmodulin gene expression. The significance of these interactions to amyloidogenesis in Alzheimer's disease is reviewed.
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Affiliation(s)
- Danton H O'Day
- Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
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Kaur R, Narang SS, Singh P, Goyal B. Structural and molecular insights into tacrine-benzofuran hybrid induced inhibition of amyloid-β peptide aggregation and BACE1 activity. J Biomol Struct Dyn 2023; 41:13211-13227. [PMID: 37013977 DOI: 10.1080/07391102.2023.2191722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 01/16/2023] [Indexed: 04/05/2023]
Abstract
Amyloid-β (Aβ) aggregation and β-amyloid precursor protein cleaving enzyme 1 (BACE1) are the potential therapeutic drug targets for Alzheimer's disease (AD). A recent study highlighted that tacrine-benzofuran hybrid C1 displayed anti-aggregation activity against Aβ42 peptide and inhibit BACE1 activity. However, the inhibition mechanism of C1 against Aβ42 aggregation and BACE1 activity remains unclear. Thus, molecular dynamics (MD) simulations of Aβ42 monomer and BACE1 with and without C1 were performed to inspect the inhibitory mechanism of C1 against Aβ42 aggregation and BACE1 activity. In addition, a ligand-based virtual screening followed by MD simulations was employed to explore potent new small-molecule dual inhibitors of Aβ42 aggregation and BACE1 activity. MD simulations highlighted that C1 promotes the non aggregating helical conformation in Aβ42 and destabilizes D23-K28 salt bridge that plays a vital role in the self-aggregation of Aβ42. C1 displays a favourable binding free energy (-50.7 ± 7.3 kcal/mol) with Aβ42 monomer and preferentially binds to the central hydrophobic core (CHC) residues. MD simulations highlighted that C1 strongly interacted with the BACE1 active site (Asp32 and Asp228) and active pockets. The scrutiny of interatomic distances among key residues of BACE1 highlighted the close flap (non-active) position in BACE1 on the incorporation of C1. The MD simulations explain the observed high inhibitory activity of C1 against Aβ aggregation and BACE1 in the in vitro studies. The ligand-based virtual screening followed by MD simulations identified CHEMBL2019027 (C2) as a promising dual inhibitor of Aβ42 aggregation and BACE1 activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rajdeep Kaur
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Simranjeet Singh Narang
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Pritpal Singh
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
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Monteiro KLC, Dos Santos Alcântara MG, Freire NML, Brandão EM, do Nascimento VL, Dos Santos Viana LM, de Aquino TM, da Silva-Júnior EF. BACE-1 Inhibitors Targeting Alzheimer's Disease. Curr Alzheimer Res 2023; 20:131-148. [PMID: 37309767 DOI: 10.2174/1567205020666230612155953] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 04/27/2023] [Accepted: 05/25/2023] [Indexed: 06/14/2023]
Abstract
The accumulation of amyloid-β (Aβ) is the main event related to Alzheimer's disease (AD) progression. Over the years, several disease-modulating approaches have been reported, but without clinical success. The amyloid cascade hypothesis evolved and proposed essential targets such as tau protein aggregation and modulation of β-secretase (β-site amyloid precursor protein cleaving enzyme 1 - BACE-1) and γ-secretase proteases. BACE-1 cuts the amyloid precursor protein (APP) to release the C99 fragment, giving rise to several Aβ peptide species during the subsequent γ-secretase cleavage. In this way, BACE-1 has emerged as a clinically validated and attractive target in medicinal chemistry, as it plays a crucial role in the rate of Aβ generation. In this review, we report the main results of candidates in clinical trials such as E2609, MK8931, and AZD-3293, in addition to highlighting the pharmacokinetic and pharmacodynamic-related effects of the inhibitors already reported. The current status of developing new peptidomimetic, non-peptidomimetic, naturally occurring, and other class inhibitors are demonstrated, considering their main limitations and lessons learned. The goal is to provide a broad and complete approach to the subject, exploring new chemical classes and perspectives.
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Affiliation(s)
- Kadja Luana Chagas Monteiro
- Research Group on Therapeutic Strategies - GPET, Laboratory of Synthesis and Research in Medicinal Chemistry - LSPMED, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970, Maceió, Alagoas, Brazil
| | - Marcone Gomes Dos Santos Alcântara
- Research Group on Therapeutic Strategies - GPET, Laboratory of Synthesis and Research in Medicinal Chemistry - LSPMED, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970, Maceió, Alagoas, Brazil
| | - Nathalia Monteiro Lins Freire
- Research Group on Therapeutic Strategies - GPET, Laboratory of Synthesis and Research in Medicinal Chemistry - LSPMED, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970, Maceió, Alagoas, Brazil
| | - Esaú Marques Brandão
- Research Group on Therapeutic Strategies - GPET, Laboratory of Synthesis and Research in Medicinal Chemistry - LSPMED, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970, Maceió, Alagoas, Brazil
| | - Vanessa Lima do Nascimento
- Research Group on Therapeutic Strategies - GPET, Laboratory of Synthesis and Research in Medicinal Chemistry - LSPMED, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970, Maceió, Alagoas, Brazil
| | - Líbni Maísa Dos Santos Viana
- Research Group on Therapeutic Strategies - GPET, Laboratory of Synthesis and Research in Medicinal Chemistry - LSPMED, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970, Maceió, Alagoas, Brazil
| | - Thiago Mendonça de Aquino
- Research Group on Therapeutic Strategies - GPET, Laboratory of Synthesis and Research in Medicinal Chemistry - LSPMED, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970, Maceió, Alagoas, Brazil
| | - Edeildo Ferreira da Silva-Júnior
- Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970, Maceió, Alagoas, Brazil
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Daoud I, Mesli F, Melkemi N, Ghalem S, Salah T. Discovery of potential SARS-CoV 3CL protease inhibitors from approved antiviral drugs using: virtual screening, molecular docking, pharmacophore mapping evaluation and dynamics simulation. J Biomol Struct Dyn 2022; 40:12574-12591. [PMID: 34541995 PMCID: PMC8459931 DOI: 10.1080/07391102.2021.1973563] [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] [Indexed: 12/27/2022]
Abstract
The spread of corona-virus disease 2019 (COVID-19) has been faster than any other corona-viruses that have succeeded in crossing the animal-human barrier. This disease, caused by the severe acute respiratory syndrome corona-virus 2 (SARS-CoV-2/2019-nCoV) posing a serious threat to global public health and local economies. There are three responsible for this disease; SARS-CoV-2, SARS-CoV and MERS-CoV. Whereas our goal is to test the affinity for a new class of compounds obtained from a hybridization of Chloroquine, Amodiaquine and Mefloquine with three targets SARS-CoV-2, SARS-CoV and MERS-CoV, in order to find new compounds as new inhibitors against Covid-19. In this work, we first used: the molecular docking/dynamics methods and ADME properties to study interaction and affinity between eight new compounds against three targets involved in the Covid-19. The results of the docking simulations and dynamics revealed that inhibitor of the malaria (Ligand 87) has an affinity to interact with SARS-CoV-2, SARS-CoV and MERS-CoV targets and they can be good inhibitors for treatment of Covid-19. Moreover, they give best affinity compared to the Remdesivir and Chloroquine and other clinical tests. The Pharmacokinetics was justified by means of lipophilicity and high coefficient of skin permeability. The in silico evaluation of ADME and drug-likeness revealed that L87 has higher absorption in the intestines with good bioavailability. However, an additional in vitro and/or in vivo experimental study should make it possible to verify the theoretical results obtained in silico.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ismail Daoud
- Department of Matter Sciences, University Mohamed Khider, Biskra, Algeria,Faculty of Science, Laboratory of Natural and Bio-Actives Substances, Tlemcen University, Tlemcen, Algeria,Ismail Daoud Faculty of Science, Laboratory of Natural and Bio-Actives Substances, Tlemcen University, Tlemcen, Algeria
| | - Fouzia Mesli
- Faculty of Science, Laboratory of Natural and Bio-Actives Substances, Tlemcen University, Tlemcen, Algeria,CONTACT Fouzia Mesli ;
| | - Nadjib Melkemi
- Group of Computational and Pharmaceutical Chemistry LMCE Laboratory, University of Biskra, Algeria
| | - Said Ghalem
- Faculty of Science, Laboratory of Natural and Bio-Actives Substances, Tlemcen University, Tlemcen, Algeria
| | - Toufik Salah
- Group of Computational and Pharmaceutical Chemistry LMCE Laboratory, University of Biskra, Algeria
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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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11
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Mohamed Yusof NIS, Abdullah ZL, Othman N, Mohd Fauzi F. Structure–Activity Relationship Analysis of Flavonoids and Its Inhibitory Activity Against BACE1 Enzyme Toward a Better Therapy for Alzheimer’s Disease. Front Chem 2022; 10:874615. [PMID: 35832462 PMCID: PMC9271896 DOI: 10.3389/fchem.2022.874615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 05/16/2022] [Indexed: 11/18/2022] Open
Abstract
Drug development in Alzheimer’s disease (AD) suffers from a high attrition rate. In 2021, 117 agents tested in phases I and II and 36 agents tested in phase III were discontinued. Natural product compounds may be good lead compounds for AD as they contain functional groups that are important for binding against key AD targets such as β-secretase enzyme (BACE1). Hence, in this study, 64 flavonoids collected from rigorous literature search and screening that have been tested from 2010 to 2022 against BACE1, which interferes in the formation of amyloid plaque, were analyzed. The 64 unique flavonoids can be further classified into five core fragments. The flavonoids were subjected to clustering analysis based on its structure, and each representative of the clusters was subjected to molecular docking. There were 12 clusters formed, where only 1 cluster contained compounds from two different core fragments. Several observations can be made where 1) flavanones with sugar moieties showed higher inhibitory activity compared to flavanones without sugar moieties. The number of sugar moieties and position of glycosidic linkage may also affect the inhibitory activity. 2) Non-piperazine-substituted chalcones when substituted with functional groups with decreasing electronegativity at the para position of both rings result in a decrease in inhibitory activity. Molecular docking indicates that ring A is involved in hydrogen bond, whereas ring B is involved in van der Waals interaction with BACE1. 3) Hydrogen bond is an important interaction with the catalytic sites of BACE1, which are Asp32 and Asp228. As flavonoids contain favorable structures and properties, this makes them an interesting lead compound for BACE1. However, to date, no flavonoids have made it through clinical trials. Hence, these findings may aid in the design of highly potent and specific BACE1 inhibitors, which could delay the progression of AD.
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Affiliation(s)
| | | | - Norodiyah Othman
- Faculty of Pharmacy, Universiti Teknologi MARA Selangor, Selangor, Malaysia
- Haematology Unit, Cancer Research Centre, Institute for Medical Research, National Institutes of Health Complex, Selangor, Malaysia
| | - Fazlin Mohd Fauzi
- Faculty of Pharmacy, Universiti Teknologi MARA Selangor, Selangor, Malaysia
- Collaborative Drug Discovery Research, Faculty of Pharmacy, Universiti Teknologi MARA Selangor, Selangor, Malaysia
- *Correspondence: Fazlin Mohd Fauzi,
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García Marín ID, Camarillo López RH, Martínez OA, Padilla-Martínez II, Correa-Basurto J, Rosales-Hernández MC. New compounds from heterocyclic amines scaffold with multitarget inhibitory activity on Aβ aggregation, AChE, and BACE1 in the Alzheimer disease. PLoS One 2022; 17:e0269129. [PMID: 35657793 PMCID: PMC9165844 DOI: 10.1371/journal.pone.0269129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 05/15/2022] [Indexed: 11/25/2022] Open
Abstract
The preset neurodegenerations in Alzheimer disease (AD) are due to several mechanisms such as amyloidogenic proteolysis, neuroinflammation, mitochondrial dysfunction, neurofibrillary tangles, cholinergic dysfunction, among others. The aim of this work was to develop multitarget molecules for the treatment of AD. Therefore, a family of 64 molecules was designed based on ligand structure pharmacophores able to inhibit the activity of beta secretase (BACE1) and acetylcholinesterase (AChE) as well as to avoid amyloid beta (Aβ1–42) oligomerization. The backbone of designed molecules consisted of a trisubstituted aromatic ring, one of the substituents was a heterocyclic amine (piperidine, morpholine, pyrrolidine or N-methyl pyrrolidine) separated from the aromatic system by three carbon atoms. The set of compounds was screened in silico employing molecular docking calculations and chemoinformatic analyses. Based on Gibbs free energy of binding, binding mode and in silico predicted toxicity results, three of the best candidates were selected, synthesized, and evaluated in vitro; F3S4-m, F2S4-m, and F2S4-p. All three compounds prevented Aβ1–42 aggregation (F3S4-m in 30.5%, F2S4-p in 42.1%, and F2S4-m in 60.9%). Additionally, inhibitory activity against AChE (ki 0.40 μM and 0.19 μM) and BACE1 (IC50 15.97 μM and 8.38 μM) was also observed for compounds F2S4-m and F3S4-m, respectively. Despite the BACE IC50 results demonstrated that all compounds are very less potent respect to peptidomimetic inhibitor (PI-IV IC50 3.20 nM), we can still say that F3S4-m is capable to inhibit AChE and BACE1.
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Affiliation(s)
- Iohanan Daniel García Marín
- Laboratorio de Biofísica y Biocatálisis, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
| | - Raúl Horacio Camarillo López
- Laboratorio de Biofísica y Biocatálisis, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
- Dirección Académica de Ingenierías Civil, Mecánica, Química, Ambiental y Sustentabilidad, Universidad Tecnológica de México, Campus Sur, Ciudad de México, México
| | - Oscar Aurelio Martínez
- Laboratorio de Biofísica y Biocatálisis, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
| | - Itzia Irene Padilla-Martínez
- Laboratorio de Investigación en Química Orgánica y Supramolecular, Unidad Profesional Interdisciplinaria de Biotecnología del Instituto Politécnico Nacional, Ciudad de México, México
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
| | - Martha Cecilia Rosales-Hernández
- Laboratorio de Biofísica y Biocatálisis, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
- * E-mail:
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do Bomfim MR, Barbosa DB, de Carvalho PB, da Silva AM, de Oliveira TA, Taranto AG, Leite FHA. Identification of potential human beta-secretase 1 inhibitors by hierarchical virtual screening and molecular dynamics. J Biomol Struct Dyn 2022:1-15. [DOI: 10.1080/07391102.2022.2069155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Mayra Ramos do Bomfim
- Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | - Deyse Brito Barbosa
- Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | | | - Alisson Marques da Silva
- Departamento de Informática, Gestão e Design, Centro Federal de Educação Tecnológica de Minas Gerais, Divinópolis, Brazil
| | - Tiago Alves de Oliveira
- Departamento de Informática, Gestão e Design, Centro Federal de Educação Tecnológica de Minas Gerais, Divinópolis, Brazil
- Departamento de Bioengenharia, Universidade Federal de São João del-Rei, São João del-Rei, Brazil
| | - Alex Gutterres Taranto
- Departamento de Bioengenharia, Universidade Federal de São João del-Rei, São João del-Rei, Brazil
- Faculty of Computing, University of Latvia (UL), Riga, Latvia
| | - Franco Henrique Andrade Leite
- Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
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In Vitro and Computational Studies of Perezone and Perezone Angelate as Potential Anti-Glioblastoma Multiforme Agents. Molecules 2022; 27:molecules27051565. [PMID: 35268667 PMCID: PMC8911992 DOI: 10.3390/molecules27051565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 02/01/2023] Open
Abstract
Glioblastoma multiforme (GBM) represents the most malignant type of astrocytoma, with a life expectancy of two years. It has been shown that Poly (ADP-ribose) polymerase 1 (PARP-1) protein is over-expressed in GBM cells, while its expression in healthy tissue is low. In addition, perezone, a phyto-compound, is a PARP-1 inhibitor with anti-neoplastic activity. As a consequence, in the present study, both in vitro and computational evaluations of perezone and its chemically related compound, perezone angelate, as anti-GBM agents were performed. Hence, the anti-proliferative assay showed that perezone angelate induces higher cytotoxicity in the GBM cell line (U373 IC50 = 6.44 μM) than perezone (U373 IC50 = 51.20 μM) by induction of apoptosis. In addition, perezone angelate showed low cytotoxic activity in rat glial cells (IC50 = 173.66 μM). PARP-1 inhibitory activity (IC50 = 5.25 μM) and oxidative stress induction by perezone angelate were corroborated employing in vitro studies. In the other hand, the performed docking studies allowed explaining the PARP-1 inhibitory activity of perezone angelate, and ADMET studies showed its probability to permeate cell membranes and the blood–brain barrier, which is an essential characteristic of drugs to treat neurological diseases. Finally, it is essential to highlight that the results confirm perezone angelate as a potential anti-GBM agent.
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Ugbaja S, Lawal I, Kumalo H, Lawal M. Alzheimer's Disease and β-Secretase Inhibition: An Update With a Focus on Computer-Aided Inhibitor Design. Curr Drug Targets 2021; 23:266-285. [PMID: 34370634 DOI: 10.2174/1389450122666210809100050] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 11/22/2022]
Abstract
INTRODUCTION Alzheimer's disease (AD) is an intensifying neurodegenerative illness due to its irreversible nature. Identification of β-site amyloid precursor protein (APP) cleaving enzyme1 (BACE1) has been a significant medicinal focus towards AD treatment, and this has opened ground for several investigations. Despite the numerous works in this direction, no BACE1 inhibitor has made it to the final approval stage as an anti-AD drug. METHOD We provide an introductory background of the subject with a general overview of the pathogenesis of AD. The review features BACE1 inhibitor design and development with a focus on some clinical trials and discontinued drugs. Using the topical keywords BACE1, inhibitor design, and computational/theoretical study in the Web of Science and Scopus database, we retrieved over 49 relevant articles. The search years are from 2010 and 2020, with analysis conducted from May 2020 to March 2021. RESULTS AND DISCUSSION Researchers have employed computational methodologies to unravel potential BACE1 inhibitors with a significant outcome. The most used computer-aided approach in BACE1 inhibitor design and binding/interaction studies are pharmacophore development, quantitative structure-activity relationship (QSAR), virtual screening, docking, and molecular dynamics (MD) simulations. These methods, plus more advanced ones including quantum mechanics/molecular mechanics (QM/MM) and QM, have proven substantial in the computational framework for BACE1 inhibitor design. Computational chemists have embraced the incorporation of in vitro assay to provide insight into the inhibition performance of identified molecules with potential inhibition towards BACE1. Significant IC50 values up to 50 nM, better than clinical trial compounds, are available in the literature. CONCLUSION The continuous failure of potent BACE1 inhibitors at clinical trials is attracting many queries prompting researchers to investigate newer concepts necessary for effective inhibitor design. The considered properties for efficient BACE1 inhibitor design seem enormous and require thorough scrutiny. Lately, researchers noticed that besides appreciable binding affinity and blood-brain barrier (BBB) permeation, BACE1 inhibitor must show low or no affinity for permeability-glycoprotein. Computational modeling methods have profound applications in drug discovery strategy. With the volume of recent in silico studies on BACE1 inhibition, the prospect of identifying potent molecules that would reach the approved level is feasible. Investigators should try pushing many of the identified BACE1 compounds with significant anti-AD properties to preclinical and clinical trial stages. We also advise computational research on allosteric inhibitor design, exosite modeling, and multisite inhibition of BACE1. These alternatives might be a solution to BACE1 drug discovery in AD therapy.
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Affiliation(s)
- Samuel Ugbaja
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4001, Saudi Arabia
| | - Isiaka Lawal
- Chemistry Department, Faculty of Applied and Computer Science, Vaal University of Technology, Vanderbijlpark Campus, Boulevard, 1900, Vanderbijlpark, Saudi Arabia
| | - Hezekiel Kumalo
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4001, Saudi Arabia
| | - Monsurat Lawal
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4001, Saudi Arabia
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Chen J, Zhang S, Wang W, Sun H, Zhang Q, Liu X. Binding of Inhibitors to BACE1 Affected by pH-Dependent Protonation: An Exploration from Multiple Replica Gaussian Accelerated Molecular Dynamics and MM-GBSA Calculations. ACS Chem Neurosci 2021; 12:2591-2607. [PMID: 34185514 DOI: 10.1021/acschemneuro.0c00813] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
To date, inhibiting the activity of β-amyloid cleaving enzyme 1 (BACE1) has been considered an efficient approach for treating Alzheimer's disease (AD). In the current work, multiple replica Gaussian accelerated molecular dynamics (MR-GaMD) simulations and the molecular mechanics general Born surface area (MM-GBSA) method were combined to investigate the effect of pH-dependent protonation on the binding of the inhibitors CS9, C6U, and 6WE to BACE1. Dynamic analyses based on the MR-GaMD trajectory show that pH-dependent protonation strongly affects the structural flexibility, correlated motions, and dynamic behavior of inhibitor-bound BACE1. According to the constructed free energy profiles, in the protonated state at low pH, inhibitor-bound BACE1 tends to populate at more conformations than in high pH. The binding free energies calculated by MM-GBSA suggest that inhibitors possess stronger binding abilities under the protonation conditions at high pH than under the protonation conditions at low pH. Moreover, pH-dependent protonation exerts a significant effect on the hydrogen bonding interactions of CS9, C6U, and 6WE to BACE1, which correspondingly alters the binding abilities of the three inhibitors to BACE1. Furthermore, in different protonated environments, three inhibitors share common interaction clusters and similar binding sites in BACE1, which are reliably used as efficient targets for the design of potent inhibitors of BACE1.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China
| | - Wei Wang
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Haibo Sun
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China
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Chen J, Yin B, Wang W, Sun H. Effects of Disulfide Bonds on Binding of Inhibitors to β-Amyloid Cleaving Enzyme 1 Decoded by Multiple Replica Accelerated Molecular Dynamics Simulations. ACS Chem Neurosci 2020; 11:1811-1826. [PMID: 32459964 DOI: 10.1021/acschemneuro.0c00234] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The β-amyloid cleaving enzyme 1 (BACE1) has been thought to be an efficient target for treatment of Alzheimer's disease (AD). Deep insight into inhibitor-BACE1 binding mechanism is of significance for design of potent drugs toward BACE1. In this work, multiple replica accelerated molecular dynamics (MR-aMD) simulations, principal component (PC) analysis, and free energy landscapes were integrated to decode the effect of disulfide bonds (SSBs) in BACE1 on bindings of three inhibitors 3KO, 3KT, and 779 to BACE1. The results from cross-correlation analysis suggest that the breaking of SSBs exerts significant influence on structural flexibility and internal dynamics of inhibitor-bound BACE1. PC analysis and free energy landscapes reveal that the breaking of SSBs not only evidently induces the conformational rearrangement of BACE1 but also highly changes binding poses of three inhibitors in BACE1 and leads to more disordered binding of three inhibitors to BACE1, which is further supported by the increase in binding entropy of inhibitors to BACE1 due to the breaking of SSBs. Residue-based free energy decomposition method was utilized to evaluate contributions of separate residues to inhibitor-BACE1 binding. The results suggest that although the breaking of SSBs in BACE1 does not destroy the interaction network of inhibitors with BACE1 it changes interaction strength of some residues with inhibitors. Meanwhile, the information from residue-based free energy decomposition indicates that residues L91, S96, V130, Y132, Q134, W137, F169, I171, and I179 can be used as efficient targets of drug design toward BACE1.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Baohua Yin
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Wei Wang
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Haibo Sun
- School of Science, Shandong Jiaotong University, Jinan 250357, China
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18
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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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Mouchlis VD, Melagraki G, Zacharia LC, Afantitis A. Computer-Aided Drug Design of β-Secretase, γ-Secretase and Anti-Tau Inhibitors for the Discovery of Novel Alzheimer's Therapeutics. Int J Mol Sci 2020; 21:E703. [PMID: 31973122 PMCID: PMC7038192 DOI: 10.3390/ijms21030703] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 12/14/2022] Open
Abstract
Aging-associated neurodegenerative diseases, which are characterized by progressive neuronal death and synapses loss in human brain, are rapidly growing affecting millions of people globally. Alzheimer's is the most common neurodegenerative disease and it can be caused by genetic and environmental risk factors. This review describes the amyloid-β and Tau hypotheses leading to amyloid plaques and neurofibrillary tangles, respectively which are the predominant pathways for the development of anti-Alzheimer's small molecule inhibitors. The function and structure of the druggable targets of these two pathways including β-secretase, γ-secretase, and Tau are discussed in this review article. Computer-Aided Drug Design including computational structure-based design and ligand-based design have been employed successfully to develop inhibitors for biomolecular targets involved in Alzheimer's. The application of computational molecular modeling for the discovery of small molecule inhibitors and modulators for β-secretase and γ-secretase is summarized. Examples of computational approaches employed for the development of anti-amyloid aggregation and anti-Tau phosphorylation, proteolysis and aggregation inhibitors are also reported.
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Affiliation(s)
| | - Georgia Melagraki
- Division of Physical Sciences & Applications, Hellenic Military Academy, Vari 16672, Greece;
| | - Lefteris C. Zacharia
- Department of Life and Health Sciences, University of Nicosia, Nicosia 1700, Cyprus;
| | - Antreas Afantitis
- Department of ChemoInformatics, NovaMechanics Ltd., Nicosia 1046, Cyprus
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Shadrack DM, Swai HS, Hassanali A. A computational study on the role of water and conformational fluctuations in Hsp90 in response to inhibitors. J Mol Graph Model 2019; 96:107510. [PMID: 31877402 DOI: 10.1016/j.jmgm.2019.107510] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 12/04/2019] [Accepted: 12/11/2019] [Indexed: 10/25/2022]
Abstract
Molecular chaperone Heat Shock Protein 90 (Hsp90) represents an interesting chemotherapeutic target for cancer treatments as it plays a role in cancer proliferation. Thus, continued effort to identify novel inhibitors of this target is an important task. Drug design using computational approach has gained significant attention in recent years. This work aims to propose docking protocols to re-purpose FDA-approved drugs targeting Hsp90. Sensitivity of results to different docking protocols such apo, holo and receptor ensembles (relaxed complex) structures, the role of water and conformational changes of Hsp90, are described. We show that the protein conformation and water have effects on drug binding. Holo relaxed complex receptors ensembles improves the binding energy of ligands to the protein. We also compare and contrast structural stability of three drugs namely: ezetimibe, pitavastatin and vilazodon in the Hsp90 protein. The results obtained serves as a possible basis towards developing Hsp90 inhibitors.
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Affiliation(s)
- Daniel M Shadrack
- Department of Health and Biomedical Sciences, School of Life Science and Bioengieering, The Nelson Mandela African Institution of Science and Technology, P.O.Box 447, Arusha, Tanzania; International Centre for Theoretical Physics, Strada Costiera, 11, 34151, Trieste, Italy; Department of Chemistry, FaNAS, St John's University of Tanzania, P.O.Box 47, Dodoma, Tanzania.
| | - Hulda S Swai
- Department of Health and Biomedical Sciences, School of Life Science and Bioengieering, The Nelson Mandela African Institution of Science and Technology, P.O.Box 447, Arusha, Tanzania
| | - Ali Hassanali
- International Centre for Theoretical Physics, Strada Costiera, 11, 34151, Trieste, Italy.
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21
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Joseph E, Villalobos-Acosta DMÁ, Torres-Ramos MA, Farfán-García ED, Gómez-López M, Miliar-García Á, Fragoso-Vázquez MJ, García-Marín ID, Correa-Basurto J, Rosales-Hernández MC. Neuroprotective Effects of Apocynin and Galantamine During the Chronic Administration of Scopolamine in an Alzheimer's Disease Model. J Mol Neurosci 2019; 70:180-193. [PMID: 31768942 DOI: 10.1007/s12031-019-01426-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/31/2019] [Indexed: 12/20/2022]
Abstract
Alzheimer's disease (AD) is one of the most complicated neurodegenerative diseases, and several hypotheses have been associated with its development and progression, such as those involving glucose hypometabolism, the cholinergic system, calcium imbalance, inflammation, oxidative imbalance, microtubule instability, and the amyloid cascade, several of which are related to oxidative stress (free radical generation), which contributes to neuronal death. Therefore, several efforts have been made to establish a sporadic AD model that takes into account these hypotheses. One model that replicates the increase in amyloid beta (Aβ) and oxidative stress in vivo is the scopolamine model. In the present work, the chronic administration (6 weeks) of scopolamine was used to analyze the neuroprotective effects of apocynin and galantamine. The results showed that scopolamine induced cognitive impairment, which was evaluated 24 h after the final dose was administered. In addition, after scopolamine administration, the Aβ and superoxide anion levels were increased, and NADPH oxidase 2 (NOX2), nuclear factor erythroid 2-related factor 2 (Nrf2), and nuclear factor kappa B (NFkB) genes were overexpressed. These effects were not observed when either apocynin or galantamine was administered during the last 3 weeks of scopolamine treatment, and although the results from both molecules were related to lower Aβ production and, consequently, lower superoxide anion production, they were likely realized through different pathways. That is, both apocynin and galantamine diminished NADPH oxidase expression, but their effects on transcription factor expression differed. Moreover, experiments in silico showed that galantamine did not interact with the active site of beta secretase, whereas diapocynin, an apocynin metabolite, interacted with the beta-site APP-cleaving enzyme (BACE1) at the catalytic site.
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Affiliation(s)
- Eliezer Joseph
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, 11340, México City, México
| | - Daniel Miguel Ángel Villalobos-Acosta
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, 11340, México City, México
| | - Mónica Adriana Torres-Ramos
- Unidad Periférica de Neurociencias, Facultad de Medicina UNAM, Instituto Nacional de Neurología y Neurocirugía, MVS-SSA, Insurgentes sur 3877, La Fama, Tlalpan, 14269, México City, México
| | - Eunice Dalet Farfán-García
- Departamento de Fisiología y Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Modesto Gómez-López
- Laboratorio de biología molecular, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, México
| | - Ángel Miliar-García
- Laboratorio de biología molecular, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, México
| | - Manuel Jonathan Fragoso-Vázquez
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, México City, México
| | - Iohanan Daniel García-Marín
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, 11340, México City, México
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, 11340, México City, México
| | - Martha Cecilia Rosales-Hernández
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, 11340, México City, México.
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Dhakal S, Kushairi N, Phan CW, Adhikari B, Sabaratnam V, Macreadie I. Dietary Polyphenols: A Multifactorial Strategy to Target Alzheimer's Disease. Int J Mol Sci 2019; 20:E5090. [PMID: 31615073 PMCID: PMC6834216 DOI: 10.3390/ijms20205090] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/11/2019] [Accepted: 10/11/2019] [Indexed: 02/06/2023] Open
Abstract
Ageing is an inevitable fundamental process for people and is their greatest risk factor for neurodegenerative disease. The ageing processes bring changes in cells that can drive the organisms to experience loss of nutrient sensing, disrupted cellular functions, increased oxidative stress, loss of cellular homeostasis, genomic instability, accumulation of misfolded protein, impaired cellular defenses and telomere shortening. Perturbation of these vital cellular processes in neuronal cells can lead to life threatening neurological disorders like Alzheimer's Disease, Parkinson's Disease, Huntington's Disease, Lewy body dementia, etc. Alzheimer's Disease is the most frequent cause of deaths in the elderly population. Various therapeutic molecules have been designed to overcome the social, economic and health care burden caused by Alzheimer's Disease. Almost all the chemical compounds in clinical practice have been found to treat symptoms only limiting them to palliative care. The reason behind such imperfect drugs may result from the inefficiencies of the current drugs to target the cause of the disease. Here, we review the potential role of antioxidant polyphenolic compounds that could possibly be the most effective preventative strategy against Alzheimer's Disease.
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Affiliation(s)
- Sudip Dhakal
- School of Science, RMIT University, Bundoora, Victoria 3083, Australia.
| | - Naufal Kushairi
- Mushroom Research Centre, University of Malaya, 50603 Kuala Lumpur, Malaysia.
- Department of Anatomy, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Chia Wei Phan
- Mushroom Research Centre, University of Malaya, 50603 Kuala Lumpur, Malaysia.
- Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Benu Adhikari
- School of Science, RMIT University, Bundoora, Victoria 3083, Australia.
| | - Vikineswary Sabaratnam
- Mushroom Research Centre, University of Malaya, 50603 Kuala Lumpur, Malaysia.
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Ian Macreadie
- School of Science, RMIT University, Bundoora, Victoria 3083, Australia.
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Influence of functional moiety in lupane-type triterpenoids in BACE1 inhibition. Comput Biol Chem 2019; 83:107101. [PMID: 31442708 DOI: 10.1016/j.compbiolchem.2019.107101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/05/2019] [Accepted: 08/08/2019] [Indexed: 11/21/2022]
Abstract
Lupane-type triterpenoids have shown a potential effect against neurodegenerative disorders. Alzheimer's disease, one of the common neurodegenerative disease, is evident by the accumulation of amyloid-beta (Aβ) plaque in the extracellular regions of the brain. β-site amyloid precursor protein cleaving enzyme 1 (BACE1) is a key enzyme for the Aβ formation viathe cleavage of amyloid precursor protein (APP). Therefore, to find the potent BACE1 inhibitors and furthermore to explore the role of the functional group responsible for the strong BACE1 inhibitory activity, we synthesized a series of triterpenoids with lupane skeleton starting from the natural compounds calenduladiol and lupeol. Compound 1 revealed a potent competitive BACE1 inhibitory activity (IC50 = 16.77 ± 1.16 μM; Ki = 19.38). Furthermore, the molecular docking simulation revealed the importance of Tyr198 residue along with the other hydrophobic interactions for the strong affinity of 1‒BACE1 complex. To sum up, our results demonstrated the importance of carbonyl moiety at 3 and 16 position of lupane-type triterpenoid over the hydroxyl group at the same position.
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Moussa-Pacha NM, Abdin SM, Omar HA, Alniss H, Al-Tel TH. BACE1 inhibitors: Current status and future directions in treating Alzheimer's disease. Med Res Rev 2019; 40:339-384. [PMID: 31347728 DOI: 10.1002/med.21622] [Citation(s) in RCA: 160] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/22/2019] [Accepted: 06/13/2019] [Indexed: 12/28/2022]
Abstract
Alzheimer's disease (AD) is an irreversible, progressive neurodegenerative brain disorder with no current cure. One of the important therapeutic approaches of AD is the inhibition of β-site APP cleaving enzyme-1 (BACE1), which is involved in the rate-limiting step of the cleavage process of the amyloid precursor protein (APP) leading to the generation of the neurotoxic amyloid β (Aβ) protein after the γ-secretase completes its function. The produced insoluble Aβ aggregates lead to plaques deposition and neurodegeneration. BACE1 is, therefore, one of the attractive targets for the treatment of AD. This approach led to the development of potent BACE1 inhibitors, many of which were advanced to late stages in clinical trials. Nonetheless, the high failure rate of lead drug candidates targeting BACE1 brought to the forefront the need for finding new targets to uncover the mystery behind AD. In this review, we aim to discuss the most promising classes of BACE1 inhibitors with a description and analysis of their pharmacodynamic and pharmacokinetic parameters, with more focus on the lead drug candidates that reached late stages of clinical trials, such as MK8931, AZD-3293, JNJ-54861911, E2609, and CNP520. In addition, the manuscript discusses the safety concerns and insignificant physiological effects, which were highlighted for the most successful BACE1 inhibitors. Furthermore, the review demonstrates with increasing evidence that despite tremendous efforts and promising results conceived with BACE1 inhibitors, the latest studies suggest that their clinical use for treating Alzheimer's disease should be reconsidered. Finally, the review sheds light on alternative therapeutic options for targeting AD.
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Affiliation(s)
- Nour M Moussa-Pacha
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Shifaa M Abdin
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Hany A Omar
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,College of Pharmacy and College of Medicine, University of Sharjah, Sharjah, United Arab Emirates.,Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Hasan Alniss
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,College of Pharmacy and College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Taleb H Al-Tel
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,College of Pharmacy and College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
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25
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Maia MA, Sousa E. BACE-1 and γ-Secretase as Therapeutic Targets for Alzheimer's Disease. Pharmaceuticals (Basel) 2019; 12:ph12010041. [PMID: 30893882 PMCID: PMC6469197 DOI: 10.3390/ph12010041] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/13/2019] [Accepted: 03/15/2019] [Indexed: 12/16/2022] Open
Abstract
Alzheimer’s disease (AD) is a growing global health concern with a massive impact on affected individuals and society. Despite the considerable advances achieved in the understanding of AD pathogenesis, researchers have not been successful in fully identifying the mechanisms involved in disease progression. The amyloid hypothesis, currently the prevalent theory for AD, defends the deposition of β-amyloid protein (Aβ) aggregates as the trigger of a series of events leading to neuronal dysfunction and dementia. Hence, several research and development (R&D) programs have been led by the pharmaceutical industry in an effort to discover effective and safety anti-amyloid agents as disease modifying agents for AD. Among 19 drug candidates identified in the AD pipeline, nine have their mechanism of action centered in the activity of β or γ-secretase proteases, covering almost 50% of the identified agents. These drug candidates must fulfill the general rigid prerequisites for a drug aimed for central nervous system (CNS) penetration and selectivity toward different aspartyl proteases. This review presents the classes of γ-secretase and beta-site APP cleaving enzyme 1 (BACE-1) inhibitors under development, highlighting their structure-activity relationship, among other physical-chemistry aspects important for the successful development of new anti-AD pharmacological agents.
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Affiliation(s)
- Miguel A Maia
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
| | - Emília Sousa
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal.
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26
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Mermelstein DJ, McCammon JA, Walker RC. pH-dependent conformational dynamics of beta-secretase 1: A molecular dynamics study. J Mol Recognit 2019; 32:e2765. [PMID: 30264484 PMCID: PMC6476308 DOI: 10.1002/jmr.2765] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/25/2018] [Accepted: 08/26/2018] [Indexed: 01/19/2023]
Abstract
Beta-secretase 1 (BACE-1) is an aspartyl protease implicated in the overproduction of β-amyloid fibrils responsible for Alzheimer disease. The process of β-amyloid genesis is known to be pH dependent, with an activity peak between solution pH of 3.5 and 5.5. We have studied the pH-dependent dynamics of BACE-1 to better understand the pH dependent mechanism. We have implemented support for graphics processor unit (GPU) accelerated constant pH molecular dynamics within the AMBER molecular dynamics software package and employed this to determine the relative population of different aspartyl dyad protonation states in the pH range of greatest β-amyloid production, followed by conventional molecular dynamics to explore the differences among the various aspartyl dyad protonation states. We observed a difference in dynamics between double-protonated, mono-protonated, and double-deprotonated states over the known pH range of higher activity. These differences include Tyr 71-aspartyl dyad proximity and active water lifetime. This work indicates that Tyr 71 stabilizes catalytic water in the aspartyl dyad active site, enabling BACE-1 activity.
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Affiliation(s)
- Daniel J. Mermelstein
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - J. Andrew McCammon
- Department of Chemistry & Biochemistry, Center for Theoretical Biological Physics, Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Ross C. Walker
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- GlaxoSmithKline PLC, 1250 S. Collegeville Rd, Collegeville, PA, 19426, USA
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Xu X, Lü P, Wang J, Xu F, Liang L, Wang C, Niu Y, Xu P. Design, synthesis, and biological evaluation of 4‐aminopyrimidine or 4,6‐diaminopyrimidine derivatives as beta amyloid cleaving enzyme‐1 inhibitors. Chem Biol Drug Des 2019; 93:926-933. [DOI: 10.1111/cbdd.13489] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 12/14/2018] [Accepted: 01/09/2019] [Indexed: 02/02/2023]
Affiliation(s)
- Xiufeng Xu
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Peng Lü
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Junjie Wang
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Fengrong Xu
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Lei Liang
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Chao Wang
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Yan Niu
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Ping Xu
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
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28
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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.
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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.
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Hassan M, Shahzadi S, Seo SY, Alashwal H, Zaki N, Moustafa AA. Molecular Docking and Dynamic Simulation of AZD3293 and Solanezumab Effects Against BACE1 to Treat Alzheimer's Disease. Front Comput Neurosci 2018; 12:34. [PMID: 29910719 PMCID: PMC5992503 DOI: 10.3389/fncom.2018.00034] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 05/11/2018] [Indexed: 12/21/2022] Open
Abstract
The design of novel inhibitors to target BACE1 with reduced cytotoxicity effects is a promising approach to treat Alzheimer's disease (AD). Multiple clinical drugs and antibodies such as AZD3293 and Solanezumab are being tested to investigate their therapeutical potential against AD. The current study explores the binding pattern of AZD3293 and Solanezumab against their target proteins such as β-secretase (BACE1) and mid-region amyloid-beta (Aβ) (PDBIDs: 2ZHV & 4XXD), respectively using molecular docking and dynamic simulation (MD) approaches. The molecular docking results show that AZD3293 binds within the active region of BACE1 by forming hydrogen bonds against Asp32 and Lys107 with distances 2.95 and 2.68 Å, respectively. However, the heavy chain of Solanezumab interacts with Lys16 and Asp23 of amyloid beta having bond length 2.82, 2.78, and 3.00 Å, respectively. The dynamic cross correlations and normal mode analyses show that BACE1 depicted good residual correlated motions and fluctuations, as compared to Solanezumab. Using MD, the Root Mean Square Deviation and Fluctuation (RMSD/F) graphs show that AZD3293 residual fluctuations and RMSD value (0.2 nm) was much better compared to Solanezumab (0.7 nm). Moreover, the radius of gyration (Rg) results also depicts the significance of AZD3293 docked complex compared to Solanezumab through residual compactness. Our comparative results show that AZD3293 is a better therapeutic agent for treating AD than Solanezumab.
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Affiliation(s)
- Mubashir Hassan
- College of Natural Science, Department of Biological Sciences, Kongju National University, Gongju, South Korea
| | - Saba Shahzadi
- Institute of Molecular Science and Bioinformatics, Lahore, Pakistan.,Department of Bioinformatics, Virtual University Davis Road, Lahore, Pakistan
| | - Sung Y Seo
- College of Natural Science, Department of Biological Sciences, Kongju National University, Gongju, South Korea
| | - Hany Alashwal
- College of Information Technology, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Nazar Zaki
- College of Information Technology, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Ahmed A Moustafa
- School of Social Sciences and Psychology, MARCS Institute for Brain and Behaviour, Western Sydney University, Sydney, NSW, Australia
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Combined QSAR, molecular docking and molecular dynamics study on new Acetylcholinesterase and Butyrylcholinesterase inhibitors. Comput Biol Chem 2018; 74:304-326. [DOI: 10.1016/j.compbiolchem.2018.03.021] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 03/01/2018] [Accepted: 03/17/2018] [Indexed: 12/25/2022]
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31
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Yu T, Paudel P, Seong SH, Kim JA, Jung HA, Choi JS. Computational insights into β-site amyloid precursor protein enzyme 1 (BACE1) inhibition by tanshinones and salvianolic acids from Salvia miltiorrhiza via molecular docking simulations. Comput Biol Chem 2018; 74:273-285. [PMID: 29679864 DOI: 10.1016/j.compbiolchem.2018.04.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 04/11/2018] [Accepted: 04/12/2018] [Indexed: 12/13/2022]
Abstract
The rhizome of Salvia miltiorrhiza has emerged as a rich source of natural therapeutic agents, and its several compounds are supposed to exhibit favorable effects on Alzheimer's disease (AD). The present work investigate the anti-AD potentials of 12 tanshinones, three salvianolic acids and three caffeic acid derivatives from S. miltiorrhiza via the inhibition of β-site amyloid precursor protein cleaving enzyme 1 (BACE1). Among the tested compounds, deoxyneocryptotanshinone (1), salvianolic acid A (13) and salvianolic acid C (15) displayed good inhibitory effect on BACE1 with IC50 values of 11.53 ± 1.13, 13.01 ± 0.32 and 9.18 ± 0.03 μM, respectively. Besides this, enzyme kinetic analysis on BACE1 revealed 13, a competitive type inhibitor while 1 and 15 showed mixed-type inhibition. Furthermore, molecular docking simulation displayed negative binding energies (AutoDock 4.2.6 = -10.0 to -7.1 kcal/mol) of 1, 13, and 15 for BACE1, indicating these compounds bound tightly to the active site of the enzyme with low energy and high affinity. The results of the present study clearly demonstrate that S. miltiorrhiza and its constituents have potential anti-AD activity and can be used as a therapeutic agent for the treatment of AD.
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Affiliation(s)
- Ting Yu
- Department of Food and Life Science, Pukyong National University, Busan, 48513, Republic of Korea
| | - Pradeep Paudel
- Department of Food and Life Science, Pukyong National University, Busan, 48513, Republic of Korea
| | - Su Hui Seong
- Department of Food and Life Science, Pukyong National University, Busan, 48513, Republic of Korea
| | - Jeong Ah Kim
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Hyun Ah Jung
- Department of Food Science and Human Nutrition, Chonbuk National University, Jeonju, 54896, Republic of Korea.
| | - Jae Sue Choi
- Department of Food and Life Science, Pukyong National University, Busan, 48513, Republic of Korea.
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32
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Recent Advances in Computational Approaches for Designing Potential Anti-Alzheimer’s Agents. NEUROMETHODS 2018. [DOI: 10.1007/978-1-4939-7404-7_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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33
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Kumar A, Sharma A. Computational Modeling of Multi-target-Directed Inhibitors Against Alzheimer’s Disease. NEUROMETHODS 2018. [DOI: 10.1007/978-1-4939-7404-7_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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34
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Structure Related Inhibition of Enzyme Systems in Cholinesterases and BACE1 In Vitro by Naturally Occurring Naphthopyrone and Its Glycosides Isolated from Cassia obtusifolia. Molecules 2017; 23:molecules23010069. [PMID: 29283428 PMCID: PMC6017707 DOI: 10.3390/molecules23010069] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/26/2017] [Accepted: 12/27/2017] [Indexed: 11/23/2022] Open
Abstract
Cassia obtusifolia Linn. have been used to improve vision, inflammatory diseases, and as hepatoprotective agents and to promote urination from ancient times. In the present study, we investigated the influence of glycosylation of components of C. obtusifolia and structure-activity relationships (SARs) with respect to the inhibition of acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and β-site amyloid precursor protein (APP)-cleaving enzyme 1 (BACE1), which are related to Alzheimer’s disease (AD). All six C. obtusifolia-derived compounds, rubrofusarin (1), rubrofusarin 6-O-β-d-glucopyranoside (2), rubrofusarin 6-O-β-d-gentiobioside (3), nor-rubrofusarin 6-O-β-d-glucoside (4), isorubrofusarin 10-O-β-d-gentiobioside (5), and rubrofusarin 6-O-β-d-triglucoside (6) showed promising inhibitory activity against AChE/BACE1. Compounds 3 and 4 showed most significant inhibition against AChE and BACE1, respectively. The SARs results emphasized the importance of gentiobiosyl moiety in the rubrofusarin for AChE inhibition, whereas the presence of hydroxyl group at C-8 and the glucosyl moiety at the C-6 position in the nor-rubrofusarin appeared to largely determine BACE1 inhibition. Kinetics and docking studies showed the lowest binding energy and highest affinity for mixed-type inhibitors, 3 and 4. Hydrophobic bonds interactions and the number of hydrogen bonds determined the strength of the protein-inhibitor interaction. These results suggest that C. obtusifolia and its constituents have therapeutic potential, and that the SARs of its active components are further explored with a view towards developing a treatment for AD.
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35
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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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Gueto-Tettay C, Martinez-Consuegra A, Zuchniarz J, Gueto-Tettay LR, Drosos-Ramírez JC. A PM7 dynamic residue-ligand interactions energy landscape of the BACE1 inhibitory pathway by hydroxyethylamine compounds. Part I: The flap closure process. J Mol Graph Model 2017; 76:274-288. [PMID: 28746905 DOI: 10.1016/j.jmgm.2017.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 07/10/2017] [Accepted: 07/11/2017] [Indexed: 01/08/2023]
Abstract
BACE1 is an enzyme of scientific interest because it participates in the progression of Alzheimer's disease. Hydroxyethylamines (HEAs) are a family of compounds which exhibit inhibitory activity toward BACE1 at a nanomolar level, favorable pharmacokinetic properties and oral bioavailability. The first step in the inhibition of BACE1 by HEAs consists of their entrance into the protease active site and the resultant conformational change in the protein, from Apo to closed form. These two conformations differ in the position of an antiparallel loop (called the flap) which covers the entrance to the catalytic site. For BACE1, closure of this flap is vital to its catalytic activity and to inhibition of the enzyme due to the new interactions thereby formed with the ligand. In the present study a dynamic energy landscape of residue-ligand interaction energies (ReLIE) measured for 112 amino acids in the BACE1 active site and its immediate vicinity during the closure of the flap induced by 8 HEAs of different inhibitory power is presented. A total of 6.272 million ReLIE calculations, based on the PM7 semiempirical method, provided a deep and quantitative view of the first step in the inhibition of the aspartyl protease. The information suggests that residues Asp93, Asp289, Thr292, Thr293, Asn294 and Arg296 are anchor points for the ligand, accounting for approximately 45% of the total protein-ligand interaction. Additionally, flap closure improved the BACE1-HEA interaction by around 25%. Furthermore, the inhibitory activity of HEAs could be related to the capacity of these ligands to form said anchor point interactions and maintain them over time: the lack of some of these anchor interactions delayed flap closure or impeded it completely, or even caused the flap to reopen. The methodology employed here could be used as a tool to evaluate future structural modifications which lead to improvements in the favorability and stability of BACE1-HEA ReLIEs, aiding in the design of better inhibitors.
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Affiliation(s)
- Carlos Gueto-Tettay
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena, Colombia.
| | - Alejandro Martinez-Consuegra
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena, Colombia
| | - Joshua Zuchniarz
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena, Colombia
| | - Luis Roberto Gueto-Tettay
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena, Colombia
| | - Juan Carlos Drosos-Ramírez
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena, Colombia.
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37
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Yan G, Hao L, Niu Y, Huang W, Wang W, Xu F, Liang L, Wang C, Jin H, Xu P. 2-Substituted-thio-N-(4-substituted-thiazol/1H-imidazol-2-yl)acetamides as BACE1 inhibitors: Synthesis, biological evaluation and docking studies. Eur J Med Chem 2017. [PMID: 28624701 DOI: 10.1016/j.ejmech.2017.06.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this work, a series of 2-substituted-thio-N-(4-substituted-thiazol/1H-imidazol-2-yl)acetamide derivatives were developed as β-secretase (BACE-1) inhibitors. Supported by docking study, a small library of derivatives were designed, synthesized and biologically evaluated in vitro. In addition, the selected compounds were tested with affinity (KD) towards BACE-1, blood brain barrier (BBB) permeability and cytotoxicity. The studies revealed that the most potent analog 41 (IC50 = 4.6 μM) with high predicted BBB permeability and low cellular cytotoxicity, could serve as a good lead structure for further optimization.
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Affiliation(s)
- Gang Yan
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Lina Hao
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Yan Niu
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China.
| | - Wenjie Huang
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Wei Wang
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Fengrong Xu
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Lei Liang
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Chao Wang
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Ping Xu
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China.
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Gueto-Tettay C, Zuchniarz J, Fortich-Seca Y, Gueto-Tettay LR, Drosos-Ramirez JC. A molecular dynamics study of the BACE1 conformational change from Apo to closed form induced by hydroxyethylamine derived compounds. J Mol Graph Model 2016; 70:181-195. [PMID: 27750187 DOI: 10.1016/j.jmgm.2016.10.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/05/2016] [Accepted: 10/06/2016] [Indexed: 12/11/2022]
Abstract
BACE1 is an aspartyl protease which is a therapeutic target for Alzheimer's disease (AD) because of its participation in the rate-limiting step in the production of Aβ-peptide, the accumulation of which produces senile plaques and, in turn, the neurodegenerative effects associated with AD. The active site of this protease is composed in part by two aspartic residues (Asp93 and Asp289). Additionally, the catalytic site has been found to be covered by an antiparallel hairpin loop called the flap. The dynamics of this flap are fundamental to the catalytic function of the enzyme. When BACE1 is inactive (Apo), the flap adopts an open conformation, allowing a substrate or inhibitor to access the active site. Subsequent interaction with the ligand induces flap closure and the stabilization of the macromolecular complex. Further, the protonation state of the aspartic dyad is affected by the chemical nature of the species entering the active site, so that appropriate selection of protonation states for the ligand and the catalytic residues will permit the elucidation of the inhibitory pathway for BACE1. In the present study, comparative analysis of different combinations of protonation states for the BACE1-hydroxyethylamine (HEA) system is reported. HEAs are potent inhibitors of BACE1 with favorable pharmacological and kinetic properties, as well as oral bioavailability. The results of Molecular Dynamics (MD) simulations and population density calculations using 8 different parameters demonstrate that the LnAsp289 configuration (HEA with a neutral amine and the Asp289 residue protonated) is the only one which permits the expected conformational change in BACE1, from apo to closed form, after flap closure. Additionally, differences in their capacities to establish and maintain interactions with residues such as Asp93, Gly95, Thr133, Asp289, Gly291, and Asn294 during this step allow differentiation among the inhibitory activities of the HEAs. The results and methodology here reported will serve to elucidate the inhibitory pathway of other families of compounds that act as BACE1 inhibitors, as well as the design of better leader compounds for the treatment of AD.
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Affiliation(s)
- Carlos Gueto-Tettay
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Colombia
| | - Joshua Zuchniarz
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Colombia
| | - Yeyson Fortich-Seca
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Colombia
| | - Luis Roberto Gueto-Tettay
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Colombia
| | - Juan Carlos Drosos-Ramirez
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Colombia.
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