1
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Saha D, Jana B. Identifying the Template for Oligomer to Fibril Conversion for Amyloid-β (1-42) Oligomers using Hamiltonian Replica Exchange Molecular Dynamics. Chemphyschem 2022; 23:e202200393. [PMID: 36052514 DOI: 10.1002/cphc.202200393] [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: 06/09/2022] [Revised: 08/26/2022] [Indexed: 01/04/2023]
Abstract
The toxicity of amyloid-β (Aβ) oligomers has been known to be higher compared to mature fibrils. Yet the presence of plaques in Alzheimer's disease patients indicates the significance of oligomer to fibril conversion for Aβ aggregates. In this study, we investigate Aβ13-42 oligomers having two to five peptide chains using extensive all-atom molecular dynamics simulations to identify the on- or off-pathway intermediates in fibril formation pathway. Hamiltonian replica exchange method through solute tempering (REST2) has been employed to explore the different structures attained by these aggregates. Using intra-chain and inter-chain contacts as reaction coordinates, we obtain the free energy surface for the Aβ13-42 oligomers. Consequently, their stable conformations and structural features have been identified. The found conformations belonging to most probable structures possess both parallel and anti-parallel β-sheets, characteristic of on- and off-pathway intermediates, respectively. Further, we have measured the tendency to form fibril like interactions among the β-sheet forming residues. Our analysis finds that residues 30-36 possess higher tendency to form fibril like contacts among all the residues. While we find stronger interaction among residues 30-36, these amino acids are also found to be more shielded from water compared to others. With previous experimental studies finding these residues to be more crucial for the stability of Aβ42 oligomers, we propose that interactions within this patch could trigger seed formation that leads to conversion of on-pathway oligomers into disease relevant fibrils.
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Affiliation(s)
- Debasis Saha
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Biman Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, Jadavpur, Kolkata, 700032, West Bengal, India
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2
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Sorout N, Chandra A. Interactions of the Aβ(1-42) Peptide with Boron Nitride Nanoparticles of Varying Curvature in an Aqueous Medium: Different Pathways to Inhibit β-Sheet Formation. J Phys Chem B 2021; 125:11159-11178. [PMID: 34605235 DOI: 10.1021/acs.jpcb.1c05805] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The aggregation of amyloid β (Aβ) peptide triggered by its conformational changes leads to the commonly known neurodegenerative disease of Alzheimer's. It is believed that the formation of β sheets of the peptide plays a key role in its aggregation and subsequent fibrillization. In the current study, we have investigated the interactions of the Aβ(1-42) peptide with boron nitride nanoparticles and the effects of the latter on conformational transitions of the peptide through a series of molecular dynamics simulations. In particular, the effects of curvature of the nanoparticle surface are studied by considering boron nitride nanotubes (BNNTs) of varying diameter and also a planar boron nitride nanosheet (BNNS). Altogether, the current study involves the generation and analysis of 9.5 μs of dynamical trajectories of peptide-BNNT/BNNS pairs in an aqueous medium. It is found that BN nanoparticles of different curvatures that are studied in the present work inhibit the conformational transition of the peptide to its β-sheet form. However, such an inhibition effect follows different pathways for BN nanoparticles of different curvatures. For the BNNT with the highest surface curvature, i.e., (3,3) BNNT, the nanoparticle is found to inhibit β-sheet formation by stabilizing the helical structure of the peptide, whereas for planar BNNS, the β-sheet formation is prevented by making more favorable pathways available for transitions of the peptide to conformations of random coils and turns. The BNNTs with intermediate curvatures are found to exhibit diverse pathways of their interactions with the peptide, but in all cases, essentially no formation of the β sheet is found whereas substantial β-sheet formation is observed for Aβ(1-42) in water in the absence of any nanoparticle. The current study shows that BN nanoparticles have the potential to act as effective tools to prevent amyloid formation from Aβ peptides.
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Affiliation(s)
- Nidhi Sorout
- Department of Chemistry, Indian Institute of Technology Kanpur, Uttar Pradesh, India 208016
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Uttar Pradesh, India 208016
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3
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Wang K, Na L, Duan M. The Pathogenesis Mechanism, Structure Properties, Potential Drugs and Therapeutic Nanoparticles against the Small Oligomers of Amyloid-β. Curr Top Med Chem 2021; 21:151-167. [PMID: 32938351 DOI: 10.2174/1568026620666200916123000] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/02/2020] [Accepted: 08/13/2020] [Indexed: 12/27/2022]
Abstract
Alzheimer's Disease (AD) is a devastating neurodegenerative disease that affects millions of people in the world. The abnormal aggregation of amyloid β protein (Aβ) is regarded as the key event in AD onset. Meanwhile, the Aβ oligomers are believed to be the most toxic species of Aβ. Recent studies show that the Aβ dimers, which are the smallest form of Aβ oligomers, also have the neurotoxicity in the absence of other oligomers in physiological conditions. In this review, we focus on the pathogenesis, structure and potential therapeutic molecules against small Aβ oligomers, as well as the nanoparticles (NPs) in the treatment of AD. In this review, we firstly focus on the pathogenic mechanism of Aβ oligomers, especially the Aβ dimers. The toxicity of Aβ dimer or oligomers, which attributes to the interactions with various receptors and the disruption of membrane or intracellular environments, were introduced. Then the structure properties of Aβ dimers and oligomers are summarized. Although some structural information such as the secondary structure content is characterized by experimental technologies, detailed structures are still absent. Following that, the small molecules targeting Aβ dimers or oligomers are collected; nevertheless, all of these ligands have failed to come into the market due to the rising controversy of the Aβ-related "amyloid cascade hypothesis". At last, the recent progress about the nanoparticles as the potential drugs or the drug delivery for the Aβ oligomers are present.
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Affiliation(s)
- Ke Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Liu Na
- School of Biological and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Mojie Duan
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
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4
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Ngo ST, Tam NM, Pham MQ, Nguyen TH. Benchmark of Popular Free Energy Approaches Revealing the Inhibitors Binding to SARS-CoV-2 Mpro. J Chem Inf Model 2021; 61:2302-2312. [PMID: 33829781 PMCID: PMC8043216 DOI: 10.1021/acs.jcim.1c00159] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Indexed: 12/13/2022]
Abstract
The COVID-19 pandemic has killed millions of people worldwide since its outbreak in December 2019. The pandemic is caused by the SARS-CoV-2 virus whose main protease (Mpro) is a promising drug target since it plays a key role in viral proliferation and replication. Currently, developing an effective therapy is an urgent task, which requires accurately estimating the ligand-binding free energy to SARS-CoV-2 Mpro. However, it should be noted that the accuracy of a free energy method probably depends on the protein target. A highly accurate approach for some targets may fail to produce a reasonable correlation with the experiment when a novel enzyme is considered as a drug target. Therefore, in this context, the ligand-binding affinity to SARS-CoV-2 Mpro was calculated via various approaches. The molecular docking approach was manipulated using Autodock Vina (Vina) and Autodock4 (AD4) protocols to preliminarily investigate the ligand-binding affinity and pose to SARS-CoV-2 Mpro. The binding free energy was then refined using the fast pulling of ligand (FPL), linear interaction energy (LIE), molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA), and free energy perturbation (FEP) methods. The benchmark results indicated that for docking calculations, Vina is more accurate than AD4, and for free energy methods, FEP is the most accurate method, followed by LIE, FPL, and MM-PBSA (FEP > LIE ≈ FPL > MM-PBSA). Moreover, atomistic simulations revealed that the van der Waals interaction is the dominant factor. The residues Thr26, His41, Ser46, Asn142, Gly143, Cys145, His164, Glu166, and Gln189 are essential elements affecting the binding process. Our benchmark provides guidelines for further investigations using computational approaches.
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Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical and Computational
Biophysics, Ton Duc Thang University, Ho Chi Minh City 700000,
Vietnam
- Faculty of Applied Sciences, Ton Duc
Thang University, Ho Chi Minh City 700000,
Vietnam
| | - Nguyen Minh Tam
- Faculty of Applied Sciences, Ton Duc
Thang University, Ho Chi Minh City 700000,
Vietnam
- Computional Chemistry Research Group, Ton
Duc Thang University, Ho Chi Minh City 700000,
Vietnam
| | - Minh Quan Pham
- Graduate University of Science and Technology,
Vietnam Academy of Science and Technology, Hanoi 100000,
Vietnam
- Institute of Natural Products Chemistry,
Vietnam Academy of Science and Technology, Hanoi 100000,
Vietnam
| | - Trung Hai Nguyen
- Laboratory of Theoretical and Computational
Biophysics, Ton Duc Thang University, Ho Chi Minh City 700000,
Vietnam
- Faculty of Applied Sciences, Ton Duc
Thang University, Ho Chi Minh City 700000,
Vietnam
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5
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Tran TT, Pan F, Tran L, Roland C, Sagui C. The F19W mutation reduces the binding affinity of the transmembrane Aβ 11-40 trimer to the membrane bilayer. RSC Adv 2021; 11:2664-2676. [PMID: 35424222 PMCID: PMC8693879 DOI: 10.1039/d0ra08837d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/28/2020] [Indexed: 12/23/2022] Open
Abstract
Alzheimer's disease is linked to the aggregation of the amyloid-β protein (Aβ) of 40 or 42 amino acids. Lipid membranes are known to modulate the rate and mechanisms of the Aβ aggregation. Point mutations in Aβ can alter these rates and mechanisms. In particular, experiments show that F19 mutations influence the aggregation rate, but maintain the fibril structures. Here, we used molecular dynamics simulations to examine the effect of the F19W mutation in the 3Aβ11-40 trimer immersed in DPPC lipid bilayers submerged in aqueous solution. Substituting Phe by its closest (non-polar) aromatic amino acid Trp has a dramatic reduction in binding affinity to the phospholipid membrane (measured with respect to the solvated protein) compared to the wild type: the binding free energy of the protein-DPPC lipid bilayer increases by 40-50 kcal mol-1 over the wild-type. This is accompanied by conformational changes and loss of salt bridges, as well as a more complex free energy surface, all indicative of a more flexible and less stable mutated trimer. These results suggest that the impact of mutations can be assessed, at least partially, by evaluating the interaction of the mutated peptides with the lipid membranes.
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Affiliation(s)
- Thanh Thuy Tran
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University Ho Chi Minh City Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University Ho Chi Minh City Vietnam
| | - Feng Pan
- Department of Statistics, Florida State University Tallahassee Florida USA
| | - Linh Tran
- Institute of Fundamental and Applied Sciences, Duy Tan University Ho Chi Minh City 700000 Vietnam
- Faculty of Natural Sciences, Duy Tan University Da Nang City 550000 Vietnam
| | - Christopher Roland
- Department of Physics, North Carolina State University Raleigh North Carolina USA
| | - Celeste Sagui
- Department of Physics, North Carolina State University Raleigh North Carolina USA
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6
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Ngo ST, Nguyen TH, Pham DH, Tung NT, Nam PC. Thermodynamics and kinetics in antibody resistance of the 501Y.V2 SARS-CoV-2 variant. RSC Adv 2021; 11:33438-33446. [PMID: 35497518 PMCID: PMC9042284 DOI: 10.1039/d1ra04134g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 10/06/2021] [Indexed: 02/01/2023] Open
Abstract
Understanding the thermodynamics and kinetics of the binding process of an antibody to the SARS-CoV-2 receptor-binding domain (RBD) of the spike protein is very important for the development of COVID-19 vaccines. In particular, it is essential to understand how the binding mechanism may change under the effects of RBD mutations. In this context, we have demonstrated that the South African variant (B1.351 or 501Y.V2) can resist the neutralizing antibody (NAb). Three substitutions in the RBD including K417N, E484K, and N501Y alter the free energy landscape, binding pose, binding free energy, binding kinetics, hydrogen bonding, nonbonded contacts, and unbinding pathway of RBD + NAb complexes. The low binding affinity of NAb to 501Y.V2 RBD confirms the antibody resistance of the South African variant. Moreover, the fragment of NAb + RBD can be used as an affordable model to investigate changes in the binding process between the mutated RBD and antibodies. Increasing FEL minima of 501Y.V2 RBD + antibody in comparison with the WT RBD systems imply that the complex 501Y.V2 RBD + antibody is more unstable than the WT one.![]()
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Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Trung Hai Nguyen
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Duc-Hung Pham
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati 45229, OH, USA
| | - Nguyen Thanh Tung
- Institute of Materials Science, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Pham Cam Nam
- Department of Chemical Engineering, The University of Da Nang, University of Science and Technology, Da Nang City, Vietnam
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7
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Assessing the role of osmolytes on the conformational harmony of islet amyloid polypeptide. Int J Biol Macromol 2020; 164:2569-2582. [DOI: 10.1016/j.ijbiomac.2020.08.104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 08/05/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023]
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8
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Nguyen H, Linh HQ, Matteini P, La Penna G, Li MS. Emergence of Barrel Motif in Amyloid-β Trimer: A Computational Study. J Phys Chem B 2020; 124:10617-10631. [PMID: 33180492 PMCID: PMC7735726 DOI: 10.1021/acs.jpcb.0c05508] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 10/29/2020] [Indexed: 12/20/2022]
Abstract
Amyloid-β (Aβ) peptides form assemblies that are pathological hallmarks of Alzheimer's disease. Aβ oligomers are soluble, mobile, and toxic forms of the peptide that act in the extracellular space before assembling into protofibrils and fibrils. Therefore, oligomers play an important role in the mechanism of Alzheimer's disease. Since it is difficult to determine by experiment the atomic structures of oligomers, which accumulate fast and are polymorphic, computer simulation is a useful tool to investigate elusive oligomers' structures. In this work, we report extended all-atom molecular dynamics simulations, both canonical and replica exchange, of Aβ(1-42) trimer starting from two different initial conformations: (i) the pose produced by the best docking of a monomer aside of a dimer (simulation 1), representing oligomers freshly formed by assembling monomers, and (ii) a configuration extracted from an experimental mature fibril structure (simulation 2), representing settled oligomers in equilibrium with extended fibrils. We showed that in simulation 1, regions with small β-barrels are populated, indicating the chance of spontaneous formation of domains resembling channel-like structures. These structural domains are alternative to those more representative of mature fibrils (simulation 2), the latter showing a stable bundle of C-termini that is not sampled in simulation 1. Moreover, trimer of Aβ(1-42) can form internal pores that are large enough to be accessed by water molecules and Ca2+ ions.
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Affiliation(s)
- Hoang
Linh Nguyen
- Institute
for Computational Science and Technology, SBI Building, Quang Trung Software
City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Ho
Chi Minh City University of Technology (HCMUT), Ho Chi Minh City 700000, Vietnam
- Vietnam
National University, Ho Chi Minh
City 700000, Vietnam
| | - Huynh Quang Linh
- Ho
Chi Minh City University of Technology (HCMUT), Ho Chi Minh City 700000, Vietnam
- Vietnam
National University, Ho Chi Minh
City 700000, Vietnam
| | - Paolo Matteini
- Institute
of Applied Physics “Nello Carrara”, National Research Council, Via Madonna Del Piano 10, I-50019 Sesto Fiorentino, Italy
| | - Giovanni La Penna
- National
Research Council of Italy (CNR), Institute
for Chemistry of Organometallic Compounds (ICCOM), 50019 Florence, Italy
- National Institute for Nuclear Physics
(INFN), Section of Roma-Tor
Vergata Institute of Physics, Polish Academy of
Sciences, Al. Lotnikow
32/46, 02-668 Warsaw, Poland
| | - Mai Suan Li
- National Institute for Nuclear Physics
(INFN), Section of Roma-Tor
Vergata Institute of Physics, Polish Academy of
Sciences, Al. Lotnikow
32/46, 02-668 Warsaw, Poland
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9
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Saravanan KM, Zhang H, Zhang H, Xi W, Wei Y. On the Conformational Dynamics of β-Amyloid Forming Peptides: A Computational Perspective. Front Bioeng Biotechnol 2020; 8:532. [PMID: 32656188 PMCID: PMC7325929 DOI: 10.3389/fbioe.2020.00532] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/04/2020] [Indexed: 12/12/2022] Open
Abstract
Understanding the conformational dynamics of proteins and peptides involved in important functions is still a difficult task in computational structural biology. Because such conformational transitions in β-amyloid (Aβ) forming peptides play a crucial role in many neurological disorders, researchers from different scientific fields have been trying to address issues related to the folding of Aβ forming peptides together. Many theoretical models have been proposed in the recent years for studying Aβ peptides using mathematical, physicochemical, and molecular dynamics simulation, and machine learning approaches. In this article, we have comprehensively reviewed the developmental advances in the theoretical models for Aβ peptide folding and interactions, particularly in the context of neurological disorders. Furthermore, we have extensively reviewed the advances in molecular dynamics simulation as a tool used for studying the conversions between polymorphic amyloid forms and applications of using machine learning approaches in predicting Aβ peptides and aggregation-prone regions in proteins. We have also provided details on the theoretical advances in the study of Aβ peptides, which would enhance our understanding of these peptides at the molecular level and eventually lead to the development of targeted therapies for certain acute neurological disorders such as Alzheimer's disease in the future.
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Affiliation(s)
| | | | | | - Wenhui Xi
- Center for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yanjie Wei
- Center for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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10
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Minh Hung H, Nguyen MT, Tran PT, Truong VK, Chapman J, Quynh Anh LH, Derreumaux P, Vu VV, Ngo ST. Impact of the Astaxanthin, Betanin, and EGCG Compounds on Small Oligomers of Amyloid Aβ 40 Peptide. J Chem Inf Model 2020; 60:1399-1408. [PMID: 32105466 DOI: 10.1021/acs.jcim.9b01074] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
There is experimental evidence that the astaxanthin, betanin, and epigallocatechin-3-gallate (EGCG) compounds slow down the aggregation kinetics and the toxicity of the amyloid-β (Aβ) peptide. How these inhibitors affect the self-assembly at the atomic level remains elusive. To address this issue, we have performed for each ligand atomistic replica exchange molecular dynamic (REMD) simulations in an explicit solvent of the Aβ11-40 trimer from the U-shape conformation and MD simulations starting from Aβ1-40 dimer and tetramer structures characterized by different intra- and interpeptide conformations. We find that the three ligands have similar binding free energies on small Aβ40 oligomers but very distinct transient binding sites that will affect the aggregation of larger assemblies and fibril elongation of the Aβ40 peptide.
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Affiliation(s)
- Huynh Minh Hung
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Minh Tho Nguyen
- Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
| | - Phuong-Thao Tran
- Department of Pharmaceutical Chemistry, Hanoi University of Pharmacy, Hanoi 100000, Vietnam
| | - Vi Khanh Truong
- School of Science, RMIT University, GPO Box 2476, Melbourne 3001, Australia
| | - James Chapman
- School of Science, RMIT University, GPO Box 2476, Melbourne 3001, Australia
| | - Le Huu Quynh Anh
- Department of Climate Change and Renewable Energy, Ho Chi Minh City University of Natural Resources and Environment, Ho Chi Minh City 700000, Vietnam
| | - Philippe Derreumaux
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam.,Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam.,Laboratoire de Biochimie Théorique, UPR9080, CNRS, Université de Paris, 13 rue Pierre et Marie Curie, F-75005 Paris, France.,Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, 75005 Paris, France
| | - Van V Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam.,Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
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11
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Xing X, Liu C, Yang H, Nouman MF, Ai H. Folding dynamics of Aβ42 monomer at pH 4.0–7.5 with and without physiological salt conditions – does the β1 or β2 region fold first? NEW J CHEM 2020. [DOI: 10.1039/d0nj01090a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The seeding region of Aβ42 monomer is jointly affected by the solution acidity, ionic distribution of the salt, and charged residues.
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Affiliation(s)
- Xiaofeng Xing
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan
- China
| | - Chengqiang Liu
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan
- China
| | - Huijuan Yang
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan
- China
| | | | - Hongqi Ai
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan
- China
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12
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Ngo ST, Hong ND, Quynh Anh LH, Hiep DM, Tung NT. Effective estimation of the inhibitor affinity of HIV-1 protease via a modified LIE approach. RSC Adv 2020; 10:7732-7739. [PMID: 35492181 PMCID: PMC9049864 DOI: 10.1039/c9ra09583g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 02/06/2020] [Indexed: 01/07/2023] Open
Abstract
The inhibition of the Human Immunodeficiency Virus Type 1 Protease (HIV-1 PR) can prevent the synthesis of new viruses. Computer-aided drug design (CADD) would enhance the discovery of new therapies, through which the estimation of ligand-binding affinity is critical to predict the most efficient inhibitor. A time-consuming binding free energy method would reduce the usefulness of CADD. The modified linear interaction energy (LIE) approach emerges as an appropriate protocol that performs this task. In particular, the polar interaction free energy, which is obtained via numerically resolving the linear Poisson–Boltzmann equation, plays as an important role in driving the binding mechanism of the HIV-1 PR + inhibitor complex. The electrostatic interaction energy contributes to the attraction between two molecules, but the vdW interaction acts as a repulsive factor between the ligand and the HIV-1 PR. Moreover, the ligands were found to adopt a very strong hydrophobic interaction with the HIV-1 PR. Furthermore, the results obtained corroborate the high accuracy and precision of computational studies with a large correlation coefficient value R = 0.83 and a small RMSE δRMSE = 1.25 kcal mol−1. This method is less time-consuming than the other end-point methods, such as the molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) and free energy perturbation (FEP) approaches. Overall, the modified LIE approach would provide ligand-binding affinity with HIV-1 PR accurately, precisely, and rapidly, resulting in a more efficient design of new inhibitors. The inhibition of the Human Immunodeficiency Virus Type 1 Protease (HIV-1 PR) can prevent the synthesis of new viruses.![]()
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Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics
- Ton Duc Thang University
- Ho Chi Minh City
- Vietnam
- Faculty of Applied Sciences
| | - Nam Dao Hong
- University of Medicine and Pharmacy at Ho Chi Minh City
- Ho Chi Minh City
- Vietnam
| | - Le Huu Quynh Anh
- Department of Climate Change and Renewable Energy
- Ho Chi Minh City University of Natural Resources and Environment
- Ho Chi Minh City
- Vietnam
| | | | - Nguyen Thanh Tung
- Institute of Materials Science & Graduate University of Science and Technology
- Vietnam Academy of Science and Technology
- Hanoi
- Vietnam
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13
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Ngo ST, Nguyen TH, Tung NT, Nam PC, Vu KB, Vu VV. Oversampling Free Energy Perturbation Simulation in Determination of the Ligand‐Binding Free Energy. J Comput Chem 2019; 41:611-618. [DOI: 10.1002/jcc.26130] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 12/01/2019] [Accepted: 12/02/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical and Computational BiophysicsTon Duc Thang University Ho Chi Minh City Vietnam
- Faculty of Applied SciencesTon Duc Thang University Ho Chi Minh City Vietnam
| | - Trung Hai Nguyen
- Laboratory of Theoretical and Computational BiophysicsTon Duc Thang University Ho Chi Minh City Vietnam
- Faculty of Applied SciencesTon Duc Thang University Ho Chi Minh City Vietnam
| | - Nguyen Thanh Tung
- Institute of Materials Science & Graduate University of Science and Technology, Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Pham Cam Nam
- Department of Chemical EngineeringThe University of Da Nang, University of Science and Technology Da Nang City Vietnam
| | - Khanh B. Vu
- NTT Hi‐Tech Institute, Nguyen Tat Thanh University Ho Chi Minh City Vietnam
| | - Van V. Vu
- NTT Hi‐Tech Institute, Nguyen Tat Thanh University Ho Chi Minh City Vietnam
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14
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Tung N, Derreumaux P, Vu VV, Nam PC, Ngo ST. C-Terminal Plays as the Possible Nucleation of the Self-Aggregation of the S-Shape Aβ 11-42 Tetramer in Solution: Intensive MD Study. ACS OMEGA 2019; 4:11066-11073. [PMID: 31460204 PMCID: PMC6648102 DOI: 10.1021/acsomega.9b00992] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/27/2019] [Indexed: 06/10/2023]
Abstract
Amyloid beta (Aβ) peptides are characterized as the major factors associated with neuron death in Alzheimer's disease, which is listed as the most common form of neurodegeneration. Disordered Aβ peptides are released from proteolysis of the amyloid precursor protein. The Aβ self-assembly process roughly takes place via five steps: disordered forms → oligomers → photofibrils → mature fibrils → plaques. Although Aβ fibrils are often observed in patient brains, oligomers were recently indicated to be major neurotoxic elements. In this work, the neurotoxic compound S-shape Aβ11-42 tetramer (S4Aβ11-42) was investigated over 10 μs of unbiased MD simulations. In particular, the S4Aβ11-42 oligomer adopted a high dynamics structure, resulting in unsuccessful determination of their structures in experiments. The C-terminal was suggested as the possible nucleation of the Aβ42 aggregation. The sequences 27-35 and 39-40 formed rich β-content, whereas other residues mostly adopted coil structures. The mean value of the β-content over the equilibrium interval is ∼42 ± 3%. Furthermore, the dissociation free energy of the S4Aβ11-42 peptide was predicted using a biased sampling method. The obtained free energy is ΔG US = -58.44 kcal/mol which is roughly the same level as the corresponding value of the U-shape Aβ17-42 peptide. We anticipate that the obtained S4Aβ11-42 structures could be used as targets for AD inhibitor screening over the in silico study.
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Affiliation(s)
- Nguyen
Thanh Tung
- Institute
of Materials Science, Vietnam Academy of
Science and Technology, Hanoi 10307, Vietnam
| | - Philippe Derreumaux
- Laboratory of Theoretical and Chemistry, Ton Duc Thang University, Ho Chi Minh City 758307, Vietnam
- Faculty
of Pharmacy, Ton Duc Thang University, Ho Chi Minh City 758307, Vietnam
- Laboratoire
de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Paris 7, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Van V. Vu
- NTT
Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 70000, Vietnam
| | - Pham Cam Nam
- Department
of Chemical Engineering, The University
of Da Nang—University of Science and Technology, Da Nang City 550000, Vietnam
| | - Son Tung Ngo
- Laboratory
of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City 758307, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang
University, Ho Chi
Minh City 758307, Vietnam
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15
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Liu C, Zhao W, Xing X, Shi H, Kang B, Liu H, Li P, Ai H. An Original Monomer Sampling from a Ready‐Made Aβ
42
NMR Fibril Suggests a Turn‐β‐Strand Synergetic Seeding Mechanism. Chemphyschem 2019; 20:1649-1660. [DOI: 10.1002/cphc.201801137] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Indexed: 01/15/2023]
Affiliation(s)
- Chengqiang Liu
- School of Chemistry and Chemical EngineeringUniversity of Jinan Jinan 250022 China
| | - Wei Zhao
- School of Chemistry and Chemical EngineeringUniversity of Jinan Jinan 250022 China
| | - Xiaofeng Xing
- School of Chemistry and Chemical EngineeringUniversity of Jinan Jinan 250022 China
| | - Hu Shi
- School of Chemistry and Chemical EngineeringShanxi University Taiyuan 030006 China
| | - Baotao Kang
- School of Chemistry and Chemical EngineeringUniversity of Jinan Jinan 250022 China
| | - Haiying Liu
- School of PhysicsUniversity of Jinan Jinan 250022 China
| | - Ping Li
- Key Laboratory of Life-Organic Analysis, School of Chemistry and Chemical EngineeringQufu Normal University Qufu 273165 China
| | - Hongqi Ai
- School of Chemistry and Chemical EngineeringUniversity of Jinan Jinan 250022 China
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16
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Ngo ST, Mai BK, Derreumaux P, Vu VV. Adequate prediction for inhibitor affinity of Aβ 40 protofibril using the linear interaction energy method. RSC Adv 2019; 9:12455-12461. [PMID: 35515829 PMCID: PMC9063661 DOI: 10.1039/c9ra01177c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/11/2019] [Indexed: 11/21/2022] Open
Abstract
The search for efficient inhibitors targeting Aβ oligomers and fibrils is an important issue in Alzheimer's disease treatment. As a consequence, an accurate and computationally cheap approach to estimate the binding affinity for many ligands interacting with Aβ peptides is very important. Here, the calculated binding free energies of 30 ligands interacting with 12Aβ11-40 peptides using the linear interaction energy (LIE) approach are found to be in good correlation with experimental data (R = 0.79). The binding affinities of these complexes are also calculated by using free energy perturbation (FEP) and molecular mechanic/Poisson-Boltzmann surface area (MM/PBSA) methods. The time-consuming FEP method provides results with similar correlation (R = 0.72), whereas MM/PBSA calculations show very low correlation with experimental data (R = 0.27). In all complexes, van der Waals interactions contribute much more than electrostatic interactions. The LIE model, which is much less time-consuming than both the FEP and MM/PBSA methods, opens the door to accurate and rapid affinity prediction of ligands with Aβ peptides and the design of new ligands.
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Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University Ho Chi Minh City Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University Ho Chi Minh City Vietnam
| | - Binh Khanh Mai
- Institute for Computational Science and Technology (ICST), Quang Trung Software City Ho Chi Minh City Vietnam
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, IBPC, Université Paris Diderot 13 rue Pierre et Marie Curie 75005 Paris France
- Laboratory of Theoretical Chemistry, Ton Duc Thang University Ho Chi Minh City Vietnam
- Faculty of Pharmacy, Ton Duc Thang University Ho Chi Minh City Vietnam
| | - Van V Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University Ho Chi Minh City Vietnam
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17
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Ngo ST, Derreumaux P, Vu VV. Probable Transmembrane Amyloid α-Helix Bundles Capable of Conducting Ca2+ Ions. J Phys Chem B 2019; 123:2645-2653. [DOI: 10.1021/acs.jpcb.8b10792] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Son Tung Ngo
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Philippe Derreumaux
- Laboratoire de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Paris, 7, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Van V. Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
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18
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Tran PT, Hoang VH, Lee J, Hien TTT, Tung NT, Ngo ST. In vitroandin silicodetermination of glutaminyl cyclase inhibitors. RSC Adv 2019; 9:29619-29627. [PMID: 35531555 PMCID: PMC9071946 DOI: 10.1039/c9ra05763c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 09/13/2019] [Indexed: 12/12/2022] Open
Abstract
Alzheimer's disease (AD) is the most common form of neurodegenerative disease currently. It is widely accepted that AD is characterized by the self-assembly of amyloid beta (Aβ) peptides. The human glutaminyl cyclase (hQC) enzyme is characterized by association with Aβ peptide generation. The development of hQC inhibitors could prevent the self-aggregation of Aβ peptides, resulting in impeding AD. Utilizing structural knowledge of the hQC substrates and known hQC inhibitors, new heterocyclic and peptidomimetic derivatives were synthesized and were able to inhibit the hQC enzyme. The inhibiting abilities of these compounds were evaluated using a fluorometric assay. The binding mechanism at the atomic level was estimated using molecular docking, free energy perturbation, and quantum chemical calculation methods. The predicted log(BBB) and human intestinal absorption values indicated that these compounds are able to permeate the blood–brain barrier and be well-absorbed through the gastrointestinal tract. Overall, 5,6-dimethoxy-N-(3-(5-methyl-1H-imidazol-1-yl)propyl)-1H-benzo[d]imidazol-2-amine (1_2) was indicated as a potential drug for AD treatment. Rational design of new hQC inhibitors.![]()
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Affiliation(s)
- Phuong-Thao Tran
- Department of Pharmaceutical Chemistry
- Hanoi University of Pharmacy
- Hanoi
- Vietnam
| | - Van-Hai Hoang
- Institute of Research and Development
- Duy Tan University
- Da Nang 550000
- Vietnam
| | - Jeewoo Lee
- Laboratory of Medicinal Chemistry
- College of Pharmacy
- Seoul National University
- Seoul
- Korea
| | | | - Nguyen Thanh Tung
- Institute of Materials Science
- Vietnam Academy of Science and Technology
- Hanoi
- Vietnam
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics
- Ton Duc Thang University
- Ho Chi Minh City
- Vietnam
- Faculty of Applied Sciences
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19
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Ngo ST, Tran-Le PD, Ho GT, Le LQ, Bui LM, Vu BK, Thu Phung HT, Nguyen HD, Vo TS, Vu VV. Interaction of carbohydrate binding module 20 with starch substrates. RSC Adv 2019; 9:24833-24842. [PMID: 35528656 PMCID: PMC9069913 DOI: 10.1039/c9ra01981b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/23/2019] [Indexed: 12/03/2022] Open
Abstract
CBM20s are starch-binding domains found in many amylolytic enzymes, including glucoamylase, alpha-amylase, beta-amylases, and a new family of starch-active polysaccharide monooxygenases (AA13 PMOs). Previous studies of CBM20–substrate interaction only concerned relatively small or soluble amylose molecules, while amylolytic enzymes often work on extended chains of insoluble starch molecules. In this study, we utilized molecular simulation techniques to gain further insights into the interaction of CBM20 with substrates of various sizes via its two separate binding sites, termed as BdS1 and BdS2. Results show that substrate binding at BdS1 involving two conserved tryptophan residues is about 2–4 kcal mol−1 stronger than that at BdS2. CBM20 exhibits about two-fold higher affinity for helical substrates than for the amylose random coils. The affinity for amylose individual double helices does not depend on the helices' length. At least three parallel double helices are required for optimal binding. The binding affinity for a substrate containing 3 or more double helices is ∼−15 kcal mol−1, which is 2–3 kcal mol−1 larger than that for individual double helices. 100 ns molecular dynamics simulations were carried out for the binding of CBM20 to an extended substrate containing 3 layers of 9 60-unit double helices (A3L). A stable conformation of CBM20–A3L was found at BdS1. However, when CBM20 binds A3L viaBdS2, it moves across the surface of the substrate and does not form a stable complex. MD simulations show that small amylose helices are quickly disrupted upon binding to CBM20. Our results provide some important molecular insights into the interactions of CBM20 with starch substrates, which will serve as the basis for further studies of CBM20-containing enzymes, including AA13 PMOs. CBM20 quickly disrupts small helical amylose substrates and exhibits optimal binding affinity when the substrate has three or more parallel double helices.![]()
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Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics
- Ton Duc Thang University
- Ho Chi Minh City
- Vietnam
- Faculty of Applied Sciences
| | | | - Giap T. Ho
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
| | - Loan Q. Le
- Institute of Tropical Biology
- Vietnam Academy of Science and Technology
- Ho Chi Minh City
- Vietnam
| | - Le Minh Bui
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
| | - Bao Khanh Vu
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
| | | | - Hoang-Dung Nguyen
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
- Institute of Tropical Biology
| | - Thanh-Sang Vo
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
| | - Van V. Vu
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
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20
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Etersalate prevents the formations of 6Aβ16-22 oligomer: An in silico study. PLoS One 2018; 13:e0204026. [PMID: 30226897 PMCID: PMC6143259 DOI: 10.1371/journal.pone.0204026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 09/01/2018] [Indexed: 11/19/2022] Open
Abstract
Oligomerization of amyloid beta (Aβ) peptides has been considered as the crucially causative agent in the development of Alzheimer's disease. Etersalate, a nonsteroidal anti-inflammatory oral drug (United State Food and Drug Administration—Unique Ingredient Identifier: 653GN04T2G) was previously suggested to bind well to proto-fibrils of Aβ peptides in silico. Here, the effect of etersalate on the oligomerization of soluble Aβ16–22 hexamer (6Aβ16–22) were extensively investigated using temperature replica exchange molecular dynamics (REMD) simulations over ~16.8 μs in total for 48 replicas (350 ns per replica). The results reveal that etersalate can enter the inner space or bind on the surface of 6Aβ16–22 conformations, which destabilizes the hexamer. Etersalate was predicted to able to cross the blood brain barrier using prediction of absorption, distribution, metabolism, and excretion—toxicity (preADMET) tools. Overall, although the investigation was performed with the low concentration of trial inhibitor, the obtained results indicate that etersalate is a potential drug candidate for AD through inhibiting formation of Aβ oligomers with the average binding free energy of -11.7 kcal/mol.
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21
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Ngo ST, Hung HM, Hong ND, Tung NT. The influences of E22Q mutant on solvated 3Aβ 11-40 peptide: A REMD study. J Mol Graph Model 2018; 83:122-128. [PMID: 29902674 DOI: 10.1016/j.jmgm.2018.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/03/2018] [Accepted: 06/01/2018] [Indexed: 10/14/2022]
Abstract
The residue E22 plays a critical role in the aggregation process of Amyloid beta (Aβ) peptides. The effect of E22Q mutant on the shapes of the solvated Aβ11-40 trimer is clarified using a replica exchange molecular dynamics (REMD) simulation employing ∼20.6 μs of MD simulations with 48 disparate replicas. The increase of intramolecular polar contacts and salt bridge between the residue D23 to residues (24-29) was observed. The residual secondary structure of the mutated trimer is shifted in a similar way to the picture observed in previous investigations of F19W mutant. The free energy surface (FES) of the mutated E22Q system has a fewer number of minima in comparison with the wild-type trimer. The optimized shapes of the mutated E22Q form a significant increase in beta structure (47%) and serious decrease in coil content (46%) compared with the wild-type (of 36 and 56%, respectively). The binding affinity of constituting chains to the rest is of -43.7 ± 6.5 kcal/mol, implying that the representative structure of E22Q is more stable than the wild-type one. Furthermore, the E22Q mutant increases the size of stable structures due to larger collision cross section (CCS) and solvent accessible area (SASA). The observed results may enhance the Aβ inhibition throughout the contribution to the knowledge of the Aβ oligomerization/aggregation.
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Affiliation(s)
- Son Tung Ngo
- Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam; Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
| | - Huynh Minh Hung
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001, Leuven, Belgium
| | - Nam Dao Hong
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | - Nguyen Thanh Tung
- Institute of Materials Science and Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
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22
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Zhao W, Ai H. Effect of pH on Aβ 42 Monomer and Fibril-like Oligomers-Decoding in Silico of the Roles of pK Values of Charged Residues. Chemphyschem 2018; 19:1103-1116. [PMID: 29380494 DOI: 10.1002/cphc.201701384] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Indexed: 01/10/2023]
Abstract
Amyloid beta-peptide (Aβ) is the key to developing Alzheimer's disease. Experiments have confirmed that different acidity influences directly not only the structural morphology and population of Aβ oligomers, but also the toxicity. The atomic-level association between the pH, charged residues, and Aβ properties remains obscure. Herein, conformational changes of Aβ42 monomer, fibril-like trimer, and pentamer in the medium pH range of 4.0-7.5 are studied. The results reveal that, as the pH changes from 7.5 to the isoelectric pH, His6, His13, and His14 are protonated in turn, successively approach the center of mass of folded Aβ monomer, trigger ionic interactions and changes of neighboring turns (Asp7-Ser8, His14-Lys16) and even a distant one (Leu34-Met35), as well as concomitant changes of secondary structure, and promote the conformation transition from unfolded to folded. This observation discloses that protonation can convert these charged residues from originally hydrophilic to "hydrophobic-like". For fibril-like oligomers, the pH susceptibility essentially stems from the pK values of charged residues in the context of the Aβ fibril, and in turn one can predict the dynamic behavior of these residues in the processes of dissociation or stabilization of a fibril by comparing the pK values of residues involved in salt bridges in the normal state with those in the current context. This idea is justified by two fibril models and appears to be applicable to other peptides and their fibril systems.
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Affiliation(s)
- Wei Zhao
- Shandong Provincial Key Laboratory, of Fluorine Chemistry and Chemical Materials, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, P. R. China
| | - Hongqi Ai
- Shandong Provincial Key Laboratory, of Fluorine Chemistry and Chemical Materials, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, P. R. China
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23
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24
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Grasso G, Rebella M, Muscat S, Morbiducci U, Tuszynski J, Danani A, Deriu MA. Conformational Dynamics and Stability of U-Shaped and S-Shaped Amyloid β Assemblies. Int J Mol Sci 2018; 19:ijms19020571. [PMID: 29443891 PMCID: PMC5855793 DOI: 10.3390/ijms19020571] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/04/2018] [Accepted: 02/10/2018] [Indexed: 11/16/2022] Open
Abstract
Alzheimer’s disease is the most fatal neurodegenerative disorder characterized by the aggregation and deposition of Amyloid β (Aβ) oligomers in the brain of patients. Two principal variants of Aβ exist in humans: Aβ1–40 and Aβ1–42. The former is the most abundant in the plaques, while the latter is the most toxic species and forms fibrils more rapidly. Interestingly, fibrils of Aβ1–40 peptides can only assume U-shaped conformations while Aβ1–42 can also arrange as S-shaped three-stranded chains, as recently discovered. As alterations in protein conformational arrangement correlate with cell toxicity and speed of disease progression, it is important to characterize, at molecular level, the conformational dynamics of amyloid fibrils. In this work, Replica Exchange Molecular Dynamics simulations were carried out to compare the conformational dynamics of U-shaped and S-shaped Aβ17–42 small fibrils. Our computational results provide support for the stability of the recently proposed S-shaped model due to the maximized interactions involving the C-terminal residues. On the other hand, the U-shaped motif is characterized by significant distortions resulting in a more disordered assembly. Outcomes of our work suggest that the molecular architecture of the protein aggregates might play a pivotal role in formation and conformational stability of the resulting fibrils.
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Affiliation(s)
- Gianvito Grasso
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Università della Svizzera Italiana (USI), Centro Galleria 2, CH-6928 Manno, Switzerland.
| | - Martina Rebella
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128 Torino, Italy.
| | - Stefano Muscat
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128 Torino, Italy.
| | - Umberto Morbiducci
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128 Torino, Italy.
| | - Jack Tuszynski
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128 Torino, Italy.
- Department of Physics, University of Alberta, Edmonton, AB T6G 2R3, Canada.
| | - Andrea Danani
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Università della Svizzera Italiana (USI), Centro Galleria 2, CH-6928 Manno, Switzerland.
| | - Marco A Deriu
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Università della Svizzera Italiana (USI), Centro Galleria 2, CH-6928 Manno, Switzerland.
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25
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Ngo ST, Thu Phung HT, Vu KB, Vu VV. Atomistic investigation of an Iowa Amyloid-β trimer in aqueous solution. RSC Adv 2018; 8:41705-41712. [PMID: 35558787 PMCID: PMC9091969 DOI: 10.1039/c8ra07615d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/04/2018] [Indexed: 11/21/2022] Open
Abstract
The self-assembly of Amyloid beta (Aβ) peptides are widely accepted to associate with Alzheimer's disease (AD) via several proposed mechanisms. Because Aβ oligomers exist in a complicated environment consisting of various forms of Aβ, including oligomers, protofibrils, and fibrils, their structure has not been well understood. The negatively charged residue D23 is one of the critical residues of the Aβ peptide as it is located in the central hydrophobic domain of the Aβ N-terminal and forms a salt-bridge D23-K28, which helps stabilize the loop domain. In the familial Iowa (D23N) mutant, the total net charge of Aβ oligomers decreases, resulting in the decrease of electrostatic repulsion between D23N Aβ monomers and thus the increase in their self-aggregation rate. In this work, the impact of the D23N mutation on 3Aβ11–40 trimer was characterized utilizing temperature replica exchange molecular dynamics (REMD) simulations. Our simulation reveals that D23N mutation significantly enhances the affinity between the constituting chains in the trimer, increases the β-content (especially in the sequence 21–23), and shifts the β-strand hydrophobic core from crossing arrangement to parallel arrangement, which is consistent with the increase in self-aggregation rate. Molecular docking indicates that the Aβ fibril-binding ligands bind to the D23N and WT forms at different poses. These compounds prefer to bind to the N-terminal β-strand of the D23N mutant trimer, while they mostly bind to the N-terminal loop region of the WT. It is important to take into account the difference in the binding of ligands to mutant and wild type Aβ peptides in designing efficient inhibitors for various types of AD. Amyloid beta peptide oligomers are believed to play key roles in Alzheimer's disease pathogenesis. D23N mutation significantly changes their structure and how they bind potential inhibitors.![]()
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Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics
- Ton Duc Thang University
- Ho Chi Minh City
- Vietnam
- Faculty of Applied Sciences
| | | | - Khanh B. Vu
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
| | - Van V. Vu
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
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26
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Ngo ST, Nguyen MT, Nguyen NT, Vu VV. The Effects of A21G Mutation on Transmembrane Amyloid Beta (11–40) Trimer: An In Silico Study. J Phys Chem B 2017; 121:8467-8474. [DOI: 10.1021/acs.jpcb.7b05906] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Son Tung Ngo
- Computational
Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty
of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Minh Tung Nguyen
- Binh Duong University, Thu Dau Mot City, Binh Duong Province, Vietnam
| | - Nguyen Thanh Nguyen
- Department
of Theoretical Physics, University of Science, Ho Chi Minh City, Vietnam
| | - Van V. Vu
- NTT
Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
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27
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Evaluation of the absolute affinity of neuraminidase inhibitor using steered molecular dynamics simulations. J Mol Graph Model 2017; 77:137-142. [PMID: 28854402 DOI: 10.1016/j.jmgm.2017.08.018] [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] [Received: 05/04/2017] [Revised: 08/18/2017] [Accepted: 08/21/2017] [Indexed: 11/20/2022]
Abstract
The absolute free energy difference of binding (ΔG) between neuraminidase and its inhibitor was evaluated using fast pulling of ligand (FPL) method over steered molecular dynamics (SMD) simulations. The metric was computed through linear interaction approximation. Binding nature was described by free energy differences of electrostatic and van der Waals (vdW) interactions. The finding indicates that vdW metric is dominant over electrostatics in binding process. The computed values are in good agreement with experimental data with a correlation coefficient of R=0.82 and error of σΔGexp=2.2kcal/mol. The results were observed using Amber99SB-ILDN force field in comparison with CHARMM27 and GROMOS96 43a1 force fields. Obtained results may stimulate the search for an Influenza therapy.
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28
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EGCG inhibits the oligomerization of amyloid beta (16-22) hexamer: Theoretical studies. J Mol Graph Model 2017; 76:1-10. [PMID: 28658644 DOI: 10.1016/j.jmgm.2017.06.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 06/16/2017] [Accepted: 06/19/2017] [Indexed: 11/21/2022]
Abstract
An extensive replica exchange molecular dynamics (REMD) simulation was performed to investigate the progress patterns of the inhibition of (-)-epigallocatechin-3-gallate (EGCG) on the Aβ16-22 hexamer. Structural variations of the oligomers without and with EGCG were monitored and analyzed in detail. It has been found that EGCG prevents the formation of Aβ oligomer through two different ways by either accelerating the Aβ oligomerization or reducing the β-content of the hexamer. It also decreases the potential "highly toxic" conformations of Aβ oligomer, which is related to the conformations having high order β-sheet sizes. Both electrostatic and van der Waals interaction energies are found to be involved to the binding process. Computed results using quantum chemical methods show that the π-π stacking is a critical factor of the interaction between EGCG and the peptides. As a result, the binding free energy of the EGCG to the Aβ peptides is slightly larger than that of the curcumin.
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Ngo ST, Nguyen MT, Nguyen MT. Determination of the absolute binding free energies of HIV-1 protease inhibitors using non-equilibrium molecular dynamics simulations. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.03.034] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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30
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Ngo ST, Hung HM, Tran KN, Nguyen MT. Replica exchange molecular dynamics study of the amyloid beta (11–40) trimer penetrating a membrane. RSC Adv 2017. [DOI: 10.1039/c6ra26461a] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The transmembrane Aβ11–40 trimer is investigated for the first time using REMD and FEP.
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Affiliation(s)
- Son Tung Ngo
- Computational Chemistry Research Group
- Ton Duc Thang University
- Ho Chi Minh City
- Vietnam
- Faculty of Applied Sciences
| | | | - Khoa Nhat Tran
- Department of Biological Sciences
- University of Maryland Baltimore County
- 21250 Baltimore
- USA
| | - Minh Tho Nguyen
- Computational Chemistry Research Group
- Ton Duc Thang University
- Ho Chi Minh City
- Vietnam
- Faculty of Applied Sciences
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31
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Ngo ST, Luu XC, Nguyen MT, Le CN, Vu VV. In silico studies of solvated F19W amyloid β (11–40) trimer. RSC Adv 2017. [DOI: 10.1039/c7ra07187f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
REMD studies shows that F19W mutation does not change in the overall structure of Aβ11–40 trimer significantly but increases it flexibility, consistent with the observed formation of the same fibril structures at slower rates.
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Affiliation(s)
- Son Tung Ngo
- Computational Chemistry Research Group
- Ton Duc Thang University
- Ho Chi Minh City
- Vietnam
- Faculty of Applied Sciences
| | - Xuan-Cuong Luu
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
| | | | - Chinh N. Le
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
| | - Van V. Vu
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
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