1
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Zondagh LS, Malan SF, Joubert J. Edaravone N-benzyl pyridinium derivatives: BACE-1 inhibition, kinetics and in silico binding pose determination. Eur J Pharm Sci 2024; 201:106869. [PMID: 39102997 DOI: 10.1016/j.ejps.2024.106869] [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: 05/24/2024] [Revised: 07/08/2024] [Accepted: 08/02/2024] [Indexed: 08/07/2024]
Abstract
BACE-1 plays a pivotal role in the production of β-amyloid (Aβ) peptides, implicated in Alzheimer's Disease (AD) pathology. We previously described edaravone N-benzyl pyridinium derivatives (EBPDs) that exhibited multifunctional activity against multiple AD targets. In this study we explored the EBPDs BACE-1 inhibitory activity to potentially enhance the compounds therapeutic profile. The EBPDs exhibited moderate BACE-1 inhibitory activity (IC50 = 44.10 µM - 123.70 µM) and obtained IC50 values between 2.0 and 5.8-fold greater than resveratrol, a known BACE-1 inhibitor (IC50 = 253.20 µM), in this assay. Compound 3 was the most potent inhibitor with an IC50 of 44.10 µM and a Ki of 19.96 µM and a mixed-type mode of inhibition that favored binding in a competitive manner. Molecular docking identified crucial interactions with BACE-1 active site residues, supported by 100 ns MD simulations. The study highlighted the EBPDs therapeutic potential as BACE-1 inhibitors and multifunctional anti-AD therapeutic agents.
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Affiliation(s)
- L S Zondagh
- Pharmaceutical Chemistry, School of Pharmacy, University of the Western Cape, Cape Town, Western Cape 7535, South Africa
| | - S F Malan
- Pharmaceutical Chemistry, School of Pharmacy, University of the Western Cape, Cape Town, Western Cape 7535, South Africa
| | - J Joubert
- Pharmaceutical Chemistry, School of Pharmacy, University of the Western Cape, Cape Town, Western Cape 7535, South Africa.
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2
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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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3
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Kaur G, Goyal B. Deciphering the Molecular Mechanism of Inhibition of β‐Secretase (BACE1) Activity by a 2‐Amino‐imidazol‐4‐one Derivative. ChemistrySelect 2022. [DOI: 10.1002/slct.202202561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Gurmeet Kaur
- School of Chemistry & Biochemistry Thapar Institute of Engineering & Technology Patiala 147004 Punjab India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry Thapar Institute of Engineering & Technology Patiala 147004 Punjab India
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4
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Nadh AG, Revikumar A, Sudhakaran P, Nair AS. Identification of potential lead compounds against BACE1 through in-silico screening of phytochemicals of Medhya rasayana plants for Alzheimer's disease management. Comput Biol Med 2022; 145:105422. [DOI: 10.1016/j.compbiomed.2022.105422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/11/2022] [Accepted: 03/17/2022] [Indexed: 11/03/2022]
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5
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Bhakat S, Söderhjelm P. Flap Dynamics in Pepsin-Like Aspartic Proteases: A Computational Perspective Using Plasmepsin-II and BACE-1 as Model Systems. J Chem Inf Model 2022; 62:914-926. [PMID: 35138093 PMCID: PMC8889585 DOI: 10.1021/acs.jcim.1c00840] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Indexed: 11/28/2022]
Abstract
The flexibility of β hairpin structure known as the flap plays a key role in catalytic activity and substrate intake in pepsin-like aspartic proteases. Most of these enzymes share structural and sequential similarity. In this study, we have used apo Plm-II and BACE-1 as model systems. In the apo form of the proteases, a conserved tyrosine residue in the flap region remains in a dynamic equilibrium between the normal and flipped states through rotation of the χ1 and χ2 angles. Independent MD simulations of Plm-II and BACE-1 remained stuck either in the normal or flipped state. Metadynamics simulations using side-chain torsion angles (χ1 and χ2 of tyrosine) as collective variables sampled the transition between the normal and flipped states. Qualitatively, the two states were predicted to be equally populated. The normal and flipped states were stabilized by H-bond interactions to a tryptophan residue and to the catalytic aspartate, respectively. Further, mutation of tyrosine to an amino-acid with smaller side-chain, such as alanine, reduced the flexibility of the flap and resulted in a flap collapse (flap loses flexibility and remains stuck in a particular state). This is in accordance with previous experimental studies, which showed that mutation to alanine resulted in loss of activity in pepsin-like aspartic proteases. Our results suggest that the ring flipping associated with the tyrosine side-chain is the key order parameter that governs flap dynamics and opening of the binding pocket in most pepsin-like aspartic proteases.
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Affiliation(s)
- Soumendranath Bhakat
- Division
of Biophysical Chemistry, Center for Molecular Protein Science, Department
of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
- Department
of Biochemistry and Molecular Biophysics, Washington University, School of Medicine, St. Louis, Missouri 63110, United States
| | - Pär Söderhjelm
- Division
of Biophysical Chemistry, Center for Molecular Protein Science, Department
of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
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6
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Nozal V, García‐Rubia A, Cuevas EP, Pérez C, Tosat‐Bitrián C, Bartolomé F, Carro E, Ramírez D, Palomo V, Martínez A. From Kinase Inhibitors to Multitarget Ligands as Powerful Drug Leads for Alzheimer's Disease using Protein-Templated Synthesis. Angew Chem Int Ed Engl 2021; 60:19344-19354. [PMID: 34169618 PMCID: PMC8457121 DOI: 10.1002/anie.202106295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/24/2021] [Indexed: 11/24/2022]
Abstract
Multitarget directed ligands (MTDLs) are arising as promising tools to tackle complex diseases. The main goal of this work is to create powerful modulating agents for neurodegenerative disorders. To achieve this aim, we have combined fragments that inhibit key protein kinases involved in the main pathomolecular pathways of Alzheimer's disease (AD) such as tau aggregation, neuroinflammation and decreased neurogenesis, whilst looking for a third action in beta-secretase (BACE1), responsible of β-amyloid production. We obtained well-balanced MTDLs with in vitro activity in three different relevant targets and efficacy in two cellular models of AD. Furthermore, computational studies confirmed how these compounds accommodate adequately into the long and rather narrow BACE1 catalytic site. Finally, we employed in situ click chemistry using BACE1 as protein template as a versatile synthetic tool that allowed us to obtain further MTDLs.
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Affiliation(s)
- Vanesa Nozal
- Structural and Chemical Biology DepartmentCentro de Investigaciones Biológicas-CSICRamiro de Maeztu 928040MadridSpain
| | - Alfonso García‐Rubia
- Structural and Chemical Biology DepartmentCentro de Investigaciones Biológicas-CSICRamiro de Maeztu 928040MadridSpain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED)Instituto de Salud Carlos III28031MadridSpain
| | - Eva P. Cuevas
- Structural and Chemical Biology DepartmentCentro de Investigaciones Biológicas-CSICRamiro de Maeztu 928040MadridSpain
| | - Concepción Pérez
- Instituto de Química Médica-CSIC)Juan de la Cierva 328006MadridSpain
| | - Carlota Tosat‐Bitrián
- Structural and Chemical Biology DepartmentCentro de Investigaciones Biológicas-CSICRamiro de Maeztu 928040MadridSpain
| | - Fernando Bartolomé
- Hospital Universitario 12 de Octubre Research Institute (imas12)Group of Neurodegenerative DiseasesJuan de la Cierva 328006MadridSpain
| | - Eva Carro
- Hospital Universitario 12 de Octubre Research Institute (imas12)Group of Neurodegenerative DiseasesJuan de la Cierva 328006MadridSpain
| | - David Ramírez
- Instituto de Ciencias BiomédicasUniversidad Autónoma de ChileLlano Subercaseaux2801—piso 6SantiagoChile
| | - Valle Palomo
- Structural and Chemical Biology DepartmentCentro de Investigaciones Biológicas-CSICRamiro de Maeztu 928040MadridSpain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED)Instituto de Salud Carlos III28031MadridSpain
| | - Ana Martínez
- Structural and Chemical Biology DepartmentCentro de Investigaciones Biológicas-CSICRamiro de Maeztu 928040MadridSpain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED)Instituto de Salud Carlos III28031MadridSpain
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7
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Nozal V, García‐Rubia A, Cuevas EP, Pérez C, Tosat‐Bitrián C, Bartolomé F, Carro E, Ramírez D, Palomo V, Martínez A. From Kinase Inhibitors to Multitarget Ligands as Powerful Drug Leads for Alzheimer's Disease using Protein‐Templated Synthesis. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Vanesa Nozal
- Structural and Chemical Biology Department Centro de Investigaciones Biológicas-CSIC Ramiro de Maeztu 9 28040 Madrid Spain
| | - Alfonso García‐Rubia
- Structural and Chemical Biology Department Centro de Investigaciones Biológicas-CSIC Ramiro de Maeztu 9 28040 Madrid Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) Instituto de Salud Carlos III 28031 Madrid Spain
| | - Eva P. Cuevas
- Structural and Chemical Biology Department Centro de Investigaciones Biológicas-CSIC Ramiro de Maeztu 9 28040 Madrid Spain
| | - Concepción Pérez
- Instituto de Química Médica-CSIC) Juan de la Cierva 3 28006 Madrid Spain
| | - Carlota Tosat‐Bitrián
- Structural and Chemical Biology Department Centro de Investigaciones Biológicas-CSIC Ramiro de Maeztu 9 28040 Madrid Spain
| | - Fernando Bartolomé
- Hospital Universitario 12 de Octubre Research Institute (imas12) Group of Neurodegenerative Diseases Juan de la Cierva 3 28006 Madrid Spain
| | - Eva Carro
- Hospital Universitario 12 de Octubre Research Institute (imas12) Group of Neurodegenerative Diseases Juan de la Cierva 3 28006 Madrid Spain
| | - David Ramírez
- Instituto de Ciencias Biomédicas Universidad Autónoma de Chile Llano Subercaseaux 2801—piso 6 Santiago Chile
| | - Valle Palomo
- Structural and Chemical Biology Department Centro de Investigaciones Biológicas-CSIC Ramiro de Maeztu 9 28040 Madrid Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) Instituto de Salud Carlos III 28031 Madrid Spain
| | - Ana Martínez
- Structural and Chemical Biology Department Centro de Investigaciones Biológicas-CSIC Ramiro de Maeztu 9 28040 Madrid Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) Instituto de Salud Carlos III 28031 Madrid Spain
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8
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Bhakat S. Pepsin-like aspartic proteases (PAPs) as model systems for combining biomolecular simulation with biophysical experiments. RSC Adv 2021; 11:11026-11047. [PMID: 35423571 PMCID: PMC8695779 DOI: 10.1039/d0ra10359d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/21/2021] [Indexed: 01/26/2023] Open
Abstract
Pepsin-like aspartic proteases (PAPs) are a class of aspartic proteases which shares tremendous structural similarity with human pepsin. One of the key structural features of PAPs is the presence of a β-hairpin motif otherwise known as flap. The biological function of the PAPs is highly dependent on the conformational dynamics of the flap region. In apo PAPs, the conformational dynamics of the flap is dominated by the rotational degrees of freedom associated with χ1 and χ2 angles of conserved Tyr (or Phe in some cases). However it is plausible that dihedral order parameters associated with several other residues might play crucial roles in the conformational dynamics of apo PAPs. Due to their size, complexities associated with conformational dynamics and clinical significance (drug targets for malaria, Alzheimer's disease etc.), PAPs provide a challenging testing ground for computational and experimental methods focusing on understanding conformational dynamics and molecular recognition in biomolecules. The opening of the flap region is necessary to accommodate substrate/ligand in the active site of the PAPs. The BIG challenge is to gain atomistic details into how reversible ligand binding/unbinding (molecular recognition) affects the conformational dynamics. Recent reports of kinetics (K i, K d) and thermodynamic parameters (ΔH, TΔS, and ΔG) associated with macro-cyclic ligands bound to BACE1 (belongs to PAP family) provide a perfect challenge (how to deal with big ligands with multiple torsional angles and select optimum order parameters to study reversible ligand binding/unbinding) for computational methods to predict binding free energies and kinetics beyond typical test systems e.g. benzamide-trypsin. In this work, i reviewed several order parameters which were proposed to capture the conformational dynamics and molecular recognition in PAPs. I further highlighted how machine learning methods can be used as order parameters in the context of PAPs. I then proposed some open ideas and challenges in the context of molecular simulation and put forward my case on how biophysical experiments e.g. NMR, time-resolved FRET etc. can be used in conjunction with biomolecular simulation to gain complete atomistic insights into the conformational dynamics of PAPs.
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Affiliation(s)
- Soumendranath Bhakat
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University P. O. Box 124 SE-22100 Lund Sweden +46-769608418
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9
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Molecular insights into the inhibitory mechanism of bi-functional bis-tryptoline triazole against β-secretase (BACE1) enzyme. Amino Acids 2019; 51:1593-1607. [PMID: 31654211 DOI: 10.1007/s00726-019-02797-0] [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: 03/15/2019] [Accepted: 10/04/2019] [Indexed: 02/07/2023]
Abstract
The β-site amyloid precursor protein-cleaving enzyme 1 (β-secretase, BACE1) is involved in the formation of amyloid-β (Aβ) peptide that aggregates into soluble oligomers, amyloid fibrils, and plaques responsible for the neurodegeneration in Alzheimer disease (AD). BACE1 is one of the prime therapeutic targets for the design of inhibitors against AD as BACE1 participate in the rate-limiting step in Aβ production. Jiaranaikulwanitch et al. reported bis-tryptoline triazole (BTT) compound as a potent inhibitor against BACE1, Aβ aggregation as well as possessing metal chelation and antioxidant activity. However, the molecular mechanism of BACE1 inhibition by BTT remains unclear. Thus, molecular docking and molecular dynamics (MD) simulations were performed to elucidate the inhibitory mechanism of BTT against BACE1. MD simulations highlight that BTT interact with catalytic aspartic dyad residues (Asp32 and Asp228) and active pocket residues of BACE1. The hydrogen-bond interactions, hydrophobic contacts, and π-π stacking interactions of BTT with flap residues (Val67-Asp77) of BACE1 confine the movement of the flap and help to achieve closed (non-active) conformation. The PCA analysis highlights lower conformational fluctuations for BACE1-BTT complex, which suggests enhanced conformational stability in comparison to apo-BACE1. The results of the present study provide key insights into the underlying inhibitory mechanism of BTT against BACE1 and will be helpful for the rational design of novel inhibitors with enhanced potency against BACE1.
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10
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Mycroft-West CJ, Cooper LC, Devlin AJ, Procter P, Guimond SE, Guerrini M, Fernig DG, Lima MA, Yates EA, Skidmore MA. A Glycosaminoglycan Extract from Portunus pelagicus Inhibits BACE1, the β Secretase Implicated in Alzheimer's Disease. Mar Drugs 2019; 17:E293. [PMID: 31100859 PMCID: PMC6562973 DOI: 10.3390/md17050293] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 12/23/2022] Open
Abstract
Therapeutic options for Alzheimer's disease, the most common form of dementia, are currently restricted to palliative treatments. The glycosaminoglycan heparin, widely used as a clinical anticoagulant, has previously been shown to inhibit the Alzheimer's disease-relevant β-secretase 1 (BACE1). Despite this, the deployment of pharmaceutical heparin for the treatment of Alzheimer's disease is largely precluded by its potent anticoagulant activity. Furthermore, ongoing concerns regarding the use of mammalian-sourced heparins, primarily due to prion diseases and religious beliefs hinder the deployment of alternative heparin-based therapeutics. A marine-derived, heparan sulphate-containing glycosaminoglycan extract, isolated from the crab Portunus pelagicus, was identified to inhibit human BACE1 with comparable bioactivity to that of mammalian heparin (IC50 = 1.85 μg mL-1 (R2 = 0.94) and 2.43 μg mL-1 (R2 = 0.93), respectively), while possessing highly attenuated anticoagulant activities. The results from several structural techniques suggest that the interactions between BACE1 and the extract from P. pelagicus are complex and distinct from those of heparin.
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Affiliation(s)
- Courtney J Mycroft-West
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK.
| | - Lynsay C Cooper
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK.
| | - Anthony J Devlin
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK.
- Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni, Via G. Colombo 81, 20133 Milan, Italy.
| | - Patricia Procter
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK.
| | - Scott E Guimond
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK.
- Institute for Science and Technology in Medicine, Keele University, Keele, Staffordshire ST5 5BG, UK.
| | - Marco Guerrini
- Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni, Via G. Colombo 81, 20133 Milan, Italy.
| | - David G Fernig
- School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK.
| | - Marcelo A Lima
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK.
| | - Edwin A Yates
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK.
- School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK.
| | - Mark A Skidmore
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK.
- Institute for Science and Technology in Medicine, Keele University, Keele, Staffordshire ST5 5BG, UK.
- School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK.
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11
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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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12
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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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13
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Ellis CR, Tsai CC, Lin FY, Shen J. Conformational dynamics of cathepsin D and binding to a small-molecule BACE1 inhibitor. J Comput Chem 2017; 38:1260-1269. [PMID: 28370344 PMCID: PMC5403572 DOI: 10.1002/jcc.24719] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 11/21/2016] [Accepted: 12/06/2016] [Indexed: 02/06/2023]
Abstract
BACE1 is a major therapeutic target for prevention and treatment of Alzheimer's disease. Developing inhibitors that can selectively target BACE1 in favor of other proteases, especially cathepsin D (CatD), has presented significant challenges. Here, we investigate the conformational dynamics and protonation states of BACE1 and CatD using continuous constant pH molecular dynamics with pH replica-exchange sampling protocol. Despite similar structure, BACE1 and CatD exhibit markedly different active site dynamics. BACE1 displays pH-dependent flap dynamics that controls substrate accessibility, while the CatD flap is relatively rigid and remains open in the pH range 2.5-6. Interestingly, although each protease hydrolyzes peptide bonds, the protonation states of the catalytic dyads are different within the active pH range. The acidic and basic components of the BACE1 catalytic dyad are clear, while either aspartic acid of the CatD catalytic dyad could play the role of acid or base. Finally, we investigate binding of the inhibitor LY2811376 developed by Eli Lilly to BACE1 and CatD. Surprisingly, in the enzyme active pH range, LY2811376 forms a stronger salt bridge with the catalytic dyad in CatD than in BACE1, which might explain the retinal toxicity of the inhibitor related to off-target inhibition of CatD. This work highlights the complexity and challenge in structure-based drug design where receptor-ligand binding induces protonation state change in both the protein and the inhibitor. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Christopher R. Ellis
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Cheng-Chieh Tsai
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Fang-Yu Lin
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
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Mohamed T, Shakeri A, Rao PP. Amyloid cascade in Alzheimer's disease: Recent advances in medicinal chemistry. Eur J Med Chem 2016; 113:258-72. [DOI: 10.1016/j.ejmech.2016.02.049] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 02/16/2016] [Accepted: 02/18/2016] [Indexed: 12/21/2022]
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15
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Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria. PLoS Comput Biol 2015; 11:e1004341. [PMID: 26506513 PMCID: PMC4623973 DOI: 10.1371/journal.pcbi.1004341] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/17/2015] [Indexed: 11/19/2022] Open
Abstract
BACE-1 is the β-secretase responsible for the initial amyloidogenesis in Alzheimer’s disease, catalyzing hydrolytic cleavage of substrate in a pH-sensitive manner. The catalytic mechanism of BACE-1 requires water-mediated proton transfer from aspartyl dyad to the substrate, as well as structural flexibility in the flap region. Thus, the coupling of protonation and conformational equilibria is essential to a full in silico characterization of BACE-1. In this work, we perform constant pH replica exchange molecular dynamics simulations on both apo BACE-1 and five BACE-1-inhibitor complexes to examine the effect of pH on dynamics and inhibitor binding properties of BACE-1. In our simulations, we find that solution pH controls the conformational flexibility of apo BACE-1, whereas bound inhibitors largely limit the motions of the holo enzyme at all levels of pH. The microscopic pKa values of titratable residues in BACE-1 including its aspartyl dyad are computed and compared between apo and inhibitor-bound states. Changes in protonation between the apo and holo forms suggest a thermodynamic linkage between binding of inhibitors and protons localized at the dyad. Utilizing our recently developed computational protocol applying the binding polynomial formalism to the constant pH molecular dynamics (CpHMD) framework, we are able to obtain the pH-dependent binding free energy profiles for various BACE-1-inhibitor complexes. Our results highlight the importance of correctly addressing the binding-induced protonation changes in protein-ligand systems where binding accompanies a net proton transfer. This work comprises the first application of our CpHMD-based free energy computational method to protein-ligand complexes and illustrates the value of CpHMD as an all-purpose tool for obtaining pH-dependent dynamics and binding free energies of biological systems. Formation of insoluble amyloid plaques in the vascular and hippocampal areas of the brain characterizes Alzheimer’s disease, a devastating neurodegenerative disorder causing dementia. Site-specific hydrolytic catalysis of β-secretase, or BACE-1, is responsible for production of oligomerative amyloid β-peptide. As the catalytic activity of BACE-1 is pH-dependent and its structural dynamics are intrinsic to the catalysis, we examine the dependence of dynamics of BACE-1 on solution pH and its implications on the catalytic mechanism of BACE-1. Also, we highlight the importance of accurate description of protonation states of the titratable groups in computer-aided drug discovery targeting BACE-1. We hope the understanding of pH dependence of the dynamics and inhibitor binding properties of BACE-1 will aid the structure-based inhibitor design efforts against Alzheimer’s disease.
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Ellis CR, Shen J. pH-Dependent Population Shift Regulates BACE1 Activity and Inhibition. J Am Chem Soc 2015; 137:9543-6. [PMID: 26186663 DOI: 10.1021/jacs.5b05891] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACE1, a major therapeutic target for treatment of Alzheimer's disease, functions within a narrow pH range. Despite tremendous effort and progress in the development of BACE1 inhibitors, details of the underlying pH-dependent regulatory mechanism remain unclear. Here we elucidate the pH-dependent conformational mechanism that regulates BACE1 activity using continuous constant-pH molecular dynamics (MD). The simulations reveal that BACE1 mainly occupies three conformational states and that the relative populations of the states shift according to pH. At intermediate pH, when the catalytic dyad is monoprotonated, a binding-competent state is highly populated, while at low and high pH a Tyr-inhibited state is dominant. Our data provide strong evidence supporting conformational selection as a major mechanism for substrate and peptide-inhibitor binding. These new insights, while consistent with experiment, greatly extend the knowledge of BACE1 and have implications for further optimization of inhibitors and understanding potential side effects of targeting BACE1. Finally, the work highlights the importance of properly modeling protonation states in MD simulations.
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Affiliation(s)
- Christopher R Ellis
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Jana Shen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
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17
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Ghemtio L, Muzet N. Retrospective molecular docking study of WY-25105 ligand to β-secretase and bias of the three-dimensional structure flexibility. J Mol Model 2013; 19:2971-9. [DOI: 10.1007/s00894-013-1821-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 03/10/2013] [Indexed: 01/04/2023]
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18
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Yuan J, Venkatraman S, Zheng Y, McKeever BM, Dillard LW, Singh SB. Structure-based design of β-site APP cleaving enzyme 1 (BACE1) inhibitors for the treatment of Alzheimer's disease. J Med Chem 2013; 56:4156-80. [PMID: 23509904 DOI: 10.1021/jm301659n] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The amyloid hypothesis asserts that excess production or reduced clearance of the amyloid-β (Aβ) peptides in the brain initiates a sequence of events that ultimately lead to Alzheimer's disease and dementia. The Aβ hypothesis has identified BACE1 as a therapeutic target to treat Alzheimer's and led to medicinal chemistry efforts to design its inhibitors both in the pharmaceutical industry and in academia. This review summarizes two distinct categories of inhibitors designed based on conformational states of "closed" and "open" forms of the enzyme. In each category the inhibitors are classified based on the core catalytic interaction group or the aspartyl binding motif (ABM). This review covers the description of inhibitors in each ABM class with X-ray crystal structures of key compounds, their binding modes, related structure-activity data highlighting potency advances, and additional properties such as selectivity profile, P-gp efflux, pharmacokinetic, and pharmacodynamic data.
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Affiliation(s)
- Jing Yuan
- Vitae Pharmaceuticals, 502 W. Office Center Drive, Fort Washington, Pennsylvania 19034, USA
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19
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Wang H, Li R, Shen Y. β-Secretase: its biology as a therapeutic target in diseases. Trends Pharmacol Sci 2013; 34:215-25. [PMID: 23452816 DOI: 10.1016/j.tips.2013.01.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 01/21/2013] [Accepted: 01/29/2013] [Indexed: 11/24/2022]
Abstract
β-Secretase (BACE1, β-site APP cleaving enzyme 1) is an aspartic proteinase that has multiple functions in various physiological processes, such as cell differentiation, immunoregulation, and cell death. There is increasing evidence that changes in BACE1 activity are involved in many diseases, such as Alzheimer's disease (AD), schizophrenia, epileptic behavior, and others. However, a deeper understanding of the molecular biology of BACE1 is necessary for further exploration of cell development, immunological regulation, and disease pathogenesis. Here, we review the molecular and cellular biology of BACE1, including its enzymatic properties, structure, biosynthesis, and physiological functions to provide a new perspective and rational assessment of drugability. Lastly, we discuss proposed strategies to control BACE1 activity for possible therapeutic application.
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Affiliation(s)
- Haibo Wang
- Center for Advanced Therapeutic Strategies for Brain Disorders, Roskamp Institute, Sarasota, FL 34203, USA
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