1
|
Dabas A, Goyal B. Structural Reorganization Mechanism of the Aβ 42 Fibril Mediated by N-Substituted Oligopyrrolamide ADH-353. ACS Chem Neurosci 2024; 15:3136-3151. [PMID: 39158263 DOI: 10.1021/acschemneuro.4c00253] [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] [Indexed: 08/20/2024] Open
Abstract
The inhibition of amyloid-β (Aβ) fibrillation and clearance of Aβ aggregates have emerged as a potential pharmacological strategy to alleviate Aβ aggregate-induced neurotoxicity in Alzheimer's disease (AD). Maity et al. shortlisted ADH-353 from a small library of positively charged N-substituted oligopyrrolamides for its notable ability to inhibit Aβ fibrillation, disintegrate intracellular cytotoxic Aβ oligomers, and alleviate Aβ-induced cytotoxicity in the SH-SY5Y and N2a cells. However, the molecular mechanism through which ADH-353 interacts with the Aβ42 fibrils, leading to their disruption and subsequent clearance, remains unclear. Thus, a detailed molecular mechanism underlying the disruption of neurotoxic Aβ42 fibrils (PDB ID 2NAO) by ADH-353 has been illuminated in this work using molecular dynamics simulations. Interestingly, conformational snapshots during simulation depicted the shortening and disappearance of β-strands and the emergence of a helix conformation, indicating a loss of the well-organized β-sheet-rich structure of the disease-relevant Aβ42 fibril on the incorporation of ADH-353. ADH-353 binds strongly to the Aβ42 fibril (ΔGbinding= -142.91 ± 1.61 kcal/mol) with a notable contribution from the electrostatic interactions between positively charged N-propylamine side chains of ADH-353 with the glutamic (Glu3, Glu11, and Glu22) and aspartic (Asp7 and Asp23) acid residues of the Aβ42 fibril. This aligns well with heteronuclear single quantum coherence NMR studies, which depict that the binding of ADH-353 with the Aβ peptide is driven by electrostatic and hydrophobic contacts. Furthermore, a noteworthy decrease in the binding affinity of Aβ42 fibril chains on the incorporation of ADH-353 indicates the weakening of interchain interactions leading to the disruption of the double-horseshoe conformation of the Aβ42 fibril. The illumination of key interactions responsible for the destabilization of the Aβ42 fibril by ADH-353 in this work will greatly aid in designing new chemical scaffolds with enhanced efficacy for the clearance of Aβ aggregates in AD.
Collapse
Affiliation(s)
- Arushi Dabas
- Department of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, Punjab 147004, India
| | - Bhupesh Goyal
- Department of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, Punjab 147004, India
| |
Collapse
|
2
|
Kaur A, Kumar A, Kumari G, Muduli R, Das M, Kundu R, Mukherjee S, Majumdar T. Rational design and computational evaluation of a multi-epitope vaccine for monkeypox virus: Insights into binding stability and immunological memory. Heliyon 2024; 10:e36154. [PMID: 39247273 PMCID: PMC11380015 DOI: 10.1016/j.heliyon.2024.e36154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Accepted: 08/11/2024] [Indexed: 09/10/2024] Open
Abstract
Multi-epitope vaccines strategically tackle rapidly mutating viruses by targeting diverse epitopes from different proteins, providing a comprehensive and adaptable immune protection approach for enhanced coverage against various viral variants. This research employs a comprehensive approach that includes the mapping of immune cells activating epitopes derived from the six structural glycoproteins (A29L, A30L, A35R, L1R, M1R, and E8L) of Monkeypox virus (Mpox). A total of 7 T-cells-specific epitopes, 13 B-cells-specific epitopes, and 5 IFN-γ activating epitopes were forecasted within these glycoproteins. The selection process focused on epitopes indicating high immunogenicity and favorable binding affinity with multiple MHC alleles. Following this, a vaccine has been formulated by incorporating the chosen epitopes, alongside adjuvants (PADRE peptide) and various linkers (EAAAK, GPGPG, and AAY). The physicochemical properties and 3D structure of the multi-epitope hybrid vaccine were analysed for characterization. MD simulations were employed to predict the binding stability between the vaccine and various pathogen recognition receptors such as TLRs (TLR1, TLR2, TLR4, and TLR6), as well as both class I and II MHC, achieved through hydrogen bonding and hydrophobic interactions. Through in silico cloning and immune simulation, it was observed that the multi-epitopes vaccine induced a robust memory immune response upon booster doses, forecasting protective immunity upon viral challenge. This protective immunity was characterized by the production of IgM + IgG antibodies, along with release of inflammatory cytokines like IFN-γ, and IL12, and the activation of various immune cells. This study offers valuable insights into the potential of a multi-epitope vaccine targeting the Mpox virus.
Collapse
Affiliation(s)
| | - Amit Kumar
- National Institute of Immunology, New Delhi, India
| | | | | | - Mayami Das
- National Institute of Immunology, New Delhi, India
| | - Rakesh Kundu
- Department of Zoology, Visva-Bharati University, Santiniketan, West Bengal, India
| | - Suprabhat Mukherjee
- Department of Animal Science, Kazi Nazrul University, Asansol, West Bengal, India
| | | |
Collapse
|
3
|
Singh K, Kaur A, Goyal B, Goyal D. Harnessing the Therapeutic Potential of Peptides for Synergistic Treatment of Alzheimer's Disease by Targeting Aβ Aggregation, Metal-Mediated Aβ Aggregation, Cholinesterase, Tau Degradation, and Oxidative Stress. ACS Chem Neurosci 2024; 15:2545-2564. [PMID: 38979773 DOI: 10.1021/acschemneuro.4c00246] [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] [Indexed: 07/10/2024] Open
Abstract
Alzheimer's disease (AD) is a progressive multifaceted neurodegenerative disease and remains a formidable global health challenge. The current medication for AD gives symptomatic relief and, thus, urges us to look for alternative disease-modifying therapies based on a multitarget directed approach. Looking at the remarkable progress made in peptide drug development in the last decade and the benefits associated with peptides, they offer valuable chemotypes [multitarget directed ligands (MTDLs)] as AD therapeutics. This review recapitulates the current developments made in harnessing peptides as MTDLs in combating AD by targeting multiple key pathways involved in the disease's progression. The peptides hold immense potential and represent a convincing avenue in the pursuit of novel AD therapeutics. While hurdles remain, ongoing research offers hope that peptides may eventually provide a multifaceted approach to combat AD.
Collapse
Affiliation(s)
- Kamaljot Singh
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, 140406 Punjab, India
| | - Anupamjeet Kaur
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, 140406 Punjab, India
| | - Bhupesh Goyal
- Department of Chemistry and Biochemistry, Thapar Institute of Engineering & Technology, Patiala, 147004 Punjab, India
| | - Deepti Goyal
- Department of Chemistry, DAV College, Sector 10, Chandigarh 160011, India
| |
Collapse
|
4
|
Nie RZ, Zhang SS, Yan XK, Feng K, Lao YJ, Bao YR. Molecular insights into the structure destabilization effects of ECG and EC on the Aβ protofilament: An all-atom molecular dynamics simulation study. Int J Biol Macromol 2023; 253:127002. [PMID: 37729983 DOI: 10.1016/j.ijbiomac.2023.127002] [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: 05/04/2023] [Revised: 09/13/2023] [Accepted: 09/17/2023] [Indexed: 09/22/2023]
Abstract
The formation of Aβ into amyloid fibrils was closely connected to AD, therefore, the Aβ aggregates were the primary therapeutic targets against AD. Previous studies demonstrated that epicatechin-3-gallate (ECG), which possessed a gallate moiety, exhibited a greater ability to disrupt the preformed Aβ amyloid fibrils than epicatechin (EC), indicating that the gallate moiety was crucial. In the present study, the molecular mechanisms were investigated. Our results demonstrated that ECG had more potent disruptive impacts on the β-sheet structure and K28-A42 salt bridges than EC. We found that ECG significantly interfered the interactions between Peptide-4 and Peptide-5. However, EC could not. The disruption of K28-A42 salt bridges by ECG was mainly due to the interactions between ECG and the hydrophobic residues located at C-terminus. Interestingly, EC disrupted the K28-A42 salt bridges by the interactions with C-terminal hydrophobic residues and the cation-π interactions with K28. Moreover, our results indicated that hydrophobic interactions, H-bonds, π-π interactions and cation-π interactions between ECG and the bend of L-shaped region caused the disaggregation of interactions between Peptide-4 and Peptide-5. Significantly, gallate moiety in ECG had contributed tremendously to the disaggregation. We believed that our findings could be useful for designing prospective drug candidates targeting AD.
Collapse
Affiliation(s)
- Rong-Zu Nie
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China; Henan Key Laboratory of Cold Chain Food Quality and Safety Control, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Shan-Shuo Zhang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Xiao-Ke Yan
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Kun Feng
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China; Henan Key Laboratory of Cold Chain Food Quality and Safety Control, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Yan-Jing Lao
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Ya-Ru Bao
- Science and Technology Division, Zhengzhou University of Light Industry, Zhengzhou 450002, China.
| |
Collapse
|
5
|
Chen C, Yan ZS, Ma YQ, Ding HM. Effect of Terahertz Waves on the Structure of the Aβ42 Monomer, Dimer, and Protofibril: Insights from Molecular Dynamics Simulations. ACS Chem Neurosci 2023; 14:4128-4138. [PMID: 37983764 DOI: 10.1021/acschemneuro.3c00485] [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] [Indexed: 11/22/2023] Open
Abstract
Amyloid-β (Aβ) and its assemblies play important roles in the pathogenesis of Alzheimer's disease (AD). Recent studies conducted by experimental and computational researchers have extensively explored the structure, assembly, and influence of biomolecules and cell membranes on Aβ. However, the impact of terahertz waves on the structures of Aβ monomers and aggregates remains largely unexplored. In this study, we systematically investigate the molecular mechanisms by which terahertz waves affect the structure of the Aβ42 monomer, dimer, and tetramer through all-atom molecular dynamics (MD) simulations. Our findings indicate that terahertz waves at a specific frequency (42.55 THz) can enhance intramolecular and intermolecular interactions in the Aβ42 monomer and dimer, respectively, by resonating with the symmetric stretching mode of the -COO- groups and the symmetric bending/stretching mode of -CH3 groups. Consequently, the β-structure content of the Aβ42 monomer is greatly increased, and the binding energy between the monomers in the Aβ42 dimer is significantly enhanced. Additionally, our observations suggest that terahertz waves can mildly stabilize the structure of tetrameric protofibrils by enhancing the interactions among peripheral peptides. Furthermore, we also investigated the effect of the frequency of terahertz waves on the structure of Aβ42. The present study contributes to a better understanding of the impact of external fields on the biobehavior of Aβ42 peptides and may shed some light on the potential risks associated with electromagnetic field radiation.
Collapse
Affiliation(s)
- Chen Chen
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Zeng-Shuai Yan
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Yu-Qiang Ma
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Hong-Ming Ding
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
| |
Collapse
|
6
|
Wu Z, Ye L, Yuan N, Che Ajuyo NM, Xiao Z, Liu L, Chen Z, Pei Y, Min Y, Wang D. A Molecular Integrative Study on the Inhibitory Effects of WRR and ERW on Amyloid β Peptide (1-42) Polymerization and Cell Toxicity. Polymers (Basel) 2023; 15:4356. [PMID: 38006082 PMCID: PMC10674201 DOI: 10.3390/polym15224356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease and the main pathological characteristic of AD is the deposition of Aβ42 in the brain. Inhibition of Aβ42 polymerization is one of the important research directions. Due to the pathological complexity of Alzheimer's disease, studies on Aβ42 polymerization inhibitors have not made significant progress worldwide. Using an independently constructed structure database of oligopeptides, in this study, molecular docking, umbrella sampling analysis of free energy, ThT fluorescence detection of Aβ42 polymerization, transmission electron microscopy, and flow cytometry detection of reactive oxygen species (ROS) and apoptosis were performed to screen tripeptides and pentapeptides that inhibit polymerization. It was found that two tripeptides, i.e., WRR and ERW, bind stably to the core of Aβ42 polymerization in the molecular dynamics analysis, and they significantly inhibited the aggregation of Aβ42 and reduced their cell toxicity in vitro.
Collapse
Affiliation(s)
- Zhongyun Wu
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Lianmeng Ye
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Nan Yuan
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Nuela Manka’a Che Ajuyo
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Zhengpan Xiao
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Liangwang Liu
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Zuqian Chen
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Yechun Pei
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
- Department of Biotechnology, School of Life Sciences, Hainan University, Haikou 570228, China
- One Health Cooperative Innovation Center, Hainan University, Haikou 570228, China
| | - Yi Min
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
- Department of Biotechnology, School of Life Sciences, Hainan University, Haikou 570228, China
| | - Dayong Wang
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
- One Health Cooperative Innovation Center, Hainan University, Haikou 570228, China
- Key Laboratory of Tropical Biological Resources of the Ministry of Education of China, Hainan University, Haikou 570228, China
| |
Collapse
|
7
|
Mohammed AA, Barale SS, Kamble SA, Paymal SB, Sonawane KD. Molecular insights into the inhibition of early stage of Aβ peptide aggregation and destabilization of Alzheimer's Aβ protofibril by dipeptide D-Trp-Aib: A molecular modelling approach. Int J Biol Macromol 2023; 242:124880. [PMID: 37217059 DOI: 10.1016/j.ijbiomac.2023.124880] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/24/2023]
Abstract
Amyloid beta (Aβ) peptide aggregates rapidly into the soluble oligomers, protofibrils and fibrils to form senile plaques, a neurotoxic component and pathological hallmark of Alzheimer's disease (AD). Experimentally, it has been demonstrated the inhibition of an early stages of Aβ aggregation by a dipeptide D-Trp-Aib inhibitor, but its molecular mechanism is still unclear. Hence, in the present study, we used molecular docking and molecular dynamics (MD) simulations to explore the molecular mechanism of inhibition of an early oligomerization and destabilization of preformed Aβ protofibril by D-Trp-Aib. Molecular docking study showed that the D-Trp-Aib binds at the aromatic (Phe19, Phe20) region of Aβ monomer, Aβ fibril and hydrophobic core of Aβ protofibril. MD simulations revealed the binding of D-Trp-Aib at the aggregation prone region (Lys16-Glu22) resulted in the stabilization of Aβ monomer by π-π stacking interactions between Tyr10 and indol ring of D-Trp-Aib, which decreases the β-sheet content and increases the α-helices. The interaction between Lys28 of Aβ monomer to D-Trp-Aib could be responsible to block the initial nucleation and may impede the fibril growth and elongation. The loss of hydrophobic contacts between two β-sheets of Aβ protofibril upon binding of D-Trp-Aib at the hydrophobic cavity resulted in the partial opening of β-sheets. This also disrupts a salt bridge (Asp23-Lys28) leading to the destabilization of Aβ protofibril. Binding energy calculations revealed that van der Waals and electrostatic interactions maximally favours the binding of D-Trp-Aib to Aβ monomer and Aβ protofibril respectively. The residues Tyr10, Phe19, Phe20, Ala21, Glu22, Lys28 of Aβ monomer, whereas Leu17, Val18, Phe19, Val40, Ala42 of protofibril contributing for the interactions with D-Trp-Aib. Thus, the present study provides structural insights into the inhibition of an early oligomerization of Aβ peptides and destabilization of Aβ protofibril, which could be useful to design novel inhibitors for the treatment of AD.
Collapse
Affiliation(s)
- Ali Abdulmawjood Mohammed
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur 416004, Maharashtra, (M.S.), India
| | - Sagar S Barale
- Department of Microbiology, Shivaji University, Kolhapur 416004, Maharashtra (MS), India
| | - Subodh Ashok Kamble
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur 416004, Maharashtra, (M.S.), India
| | - Sneha B Paymal
- Department of Microbiology, Shivaji University, Kolhapur 416004, Maharashtra (MS), India
| | - Kailas D Sonawane
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur 416004, Maharashtra, (M.S.), India; Department of Chemistry, Shivaji University, Kolhapur 416004, Maharashtra (M.S.), India.
| |
Collapse
|
8
|
Maghsoodi F, Martin TD, Chi EY. Partial Destabilization of Amyloid-β Protofibril by Methionine Photo-Oxidation: A Molecular Dynamic Simulation Study. ACS OMEGA 2023; 8:10148-10159. [PMID: 36969430 PMCID: PMC10035002 DOI: 10.1021/acsomega.2c07468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Selective photosensitized oxidation of amyloid protein aggregates is being investigated as a possible therapeutic strategy for treating Alzheimer's disease (AD). Photo-oxidation has been shown to degrade amyloid-β (Aβ) aggregates and ameliorate aggregate toxicity in vitro and reduce aggregate levels in the brains of AD animal models. To shed light on the mechanism by which photo-oxidation induces fibril destabilization, we carried out an all-atom molecular dynamics (MD) simulation to examine the effect of methionine (Met35) oxidation on the conformation and stability of a β-sheet-rich Aβ9-40 protofibril. Analyses of up to 1 μs simulations showed that the oxidation of the Met35 residues, which resulted in the addition of hydrophilic oxygens in the fibril core, reduced the overall conformational stability of the protofibril. Specifically, Met35 disrupted the hydrophobic interface that stabilizes the stacking of the two hexamers that comprise the protofibril. The oxidized protofibril is more solvent exposed and exhibits more backbone flexibility. However, the protofibril retained the underlying U-shaped architecture of each peptide upon oxidation, and although some loss of β-sheets occurred, a significant portion remained. Our simulation results are thus consistent with our experimental observation that photo-oxidation of Aβ40 fibril resulted in the dis-agglomeration and fragmentation of Aβ fibrils but did not cause complete disruption of the fibrillar morphology or β-sheet structures. The partial destabilization of Aβ aggregates supports the further development of photosensitized platforms for the targeting and clearing of Aβ aggregates as a therapeutic strategy for treating AD.
Collapse
Affiliation(s)
- Fahimeh Maghsoodi
- Nanoscience
and Microsystems Engineering Graduate Program, University of New Mexico, Albuquerque, New Mexico 87131, United States
- Center
for Biomedical Engineering, University of
New Mexico, Albuquerque, New Mexico 87131, United States
| | - Tye D. Martin
- Center
for Biomedical Engineering, University of
New Mexico, Albuquerque, New Mexico 87131, United States
| | - Eva Y. Chi
- Center
for Biomedical Engineering, University of
New Mexico, Albuquerque, New Mexico 87131, United States
- Department
of Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States
| |
Collapse
|
9
|
Ghosh S, Ali R, Verma S. Aβ-oligomers: A potential therapeutic target for Alzheimer's disease. Int J Biol Macromol 2023; 239:124231. [PMID: 36996958 DOI: 10.1016/j.ijbiomac.2023.124231] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/22/2023] [Accepted: 03/25/2023] [Indexed: 03/30/2023]
Abstract
The cascade of amyloid formation relates to multiple complex events at the molecular level. Previous research has established amyloid plaque deposition as the leading cause of Alzheimer's disease (AD) pathogenesis, detected mainly in aged population. The primary components of the plaques are two alloforms of amyloid-beta (Aβ), Aβ1-42 and Aβ1-40 peptides. Recent studies have provided considerable evidence contrary to the previous claim indicating that amyloid-beta oligomers (AβOs) as the main culprit responsible for AD-associated neurotoxicity and pathogenesis. In this review, we have discussed the primary features of AβOs, such as assembly formation, the kinetics of oligomer formation, interactions with various membranes/membrane receptors, the origin of toxicity, and oligomer-specific detection methods. Recently, the discovery of rationally designed antibodies has opened a gateway for using synthesized peptides as a grafting component in the complementarity determining region (CDR) of antibodies. Thus, the Aβ sequence motif or the complementary peptide sequence in the opposite strand of the β-sheet (extracted from the Protein Data Bank: PDB) helps design oligomer-specific inhibitors. The microscopic event responsible for oligomer formation can be targeted, and thus prevention of the overall macroscopic behaviour of the aggregation or the associated toxicity can be achieved. We have carefully reviewed the oligomer formation kinetics and associated parameters. Besides, we have depicted a thorough understanding of how the synthesized peptide inhibitors can impede the early aggregates (oligomers), mature fibrils, monomers, or a mixture of the species. The oligomer-specific inhibitors (peptides or peptide fragments) lack in-depth chemical kinetics and optimization control-based screening. In the present review, we have proposed a hypothesis for effectively screening oligomer-specific inhibitors using the chemical kinetics (determining the kinetic parameters) and optimization control strategy (cost-dependent analysis). Further, it may be possible to implement the structure-kinetic-activity-relationship (SKAR) strategy instead of structure-activity-relationship (SAR) to improve the inhibitor's activity. The controlled optimization of the kinetic parameters and dose usage will be beneficial for narrowing the search window for the inhibitors.
Collapse
|
10
|
Xu Z, Gong Y, Zou Y, Wan J, Tang J, Zhan C, Wei G, Zhang Q. Dissecting the Inhibitory Mechanism of the αB-Crystallin Domain against Aβ 42 Aggregation and Its Effect on Aβ 42 Protofibrils: A Molecular Dynamics Simulation Study. ACS Chem Neurosci 2022; 13:2842-2851. [PMID: 36153964 DOI: 10.1021/acschemneuro.2c00224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Alzheimer's disease (AD) is related to the misfolding and aggregation of amyloid-β (Aβ) protein, and its major pathological hallmark is fibrillary β-amyloid plaques. Impeding the formation of Aβ β-structure-rich aggregates and dissociating Aβ fibrils are considered potent strategies to suppress the onset and progression of AD. As a molecular chaperone, human αB-crystallin has received extensive attention in the inhibition of protein aggregation. Previous experiments reported that the structured core region of αB-crystallin (αBC) exhibits a better preventive effect on Aβ aggregation and toxicity than the full-length protein. However, the molecular mechanism behind the effect of inhibition remains mostly unknown. Herein, we carried out six 500 ns molecular dynamics (MD) simulations to investigate the inhibitory mechanism of αBC on Aβ42 aggregation. Our simulations show that αBC greatly impedes the formation of β-structure contents. We find that the binding of αBC to the Aβ42 monomer is driven by polar, hydrophobic, and H-bonding interactions. To explore whether αBC could destabilize Aβ42 protofibrils, we also carried out MD simulations of Aβ42 protofibrils with and without αBC. The results show that αBC interacts with three binding sites of the Aβ42 protofibril, and the binding is mainly driven by polar and H-bonding interactions. The binding of αBC at these three sites has a preferred dissociation effect on the β-structure content, kink angle, and K28-A42 salt bridges. Overall, this study not only discloses the molecular mechanism of αBC against Aβ42 aggregation but also demonstrates the disruption effects of αBC on Aβ42 protofibrils, which yields an avenue for designing anti-AD drug candidates.
Collapse
Affiliation(s)
- Zhengdong Xu
- School of Physical Education, Shanghai University of Sport, 399 Chang Hai Road, Shanghai 200438, People's Republic of China
| | - Yehong Gong
- School of Physical Education, Shanghai University of Sport, 399 Chang Hai Road, Shanghai 200438, People's Republic of China.,School of Sports Science and Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, People's Republic of China
| | - Yu Zou
- Department Sport and Exercise Science, College of Education, Zhejiang University, 148 Tianmenshan Road, Hangzhou 310007, Zhejiang, People's Republic of China
| | - Jiaqian Wan
- School of Physical Education, Shanghai University of Sport, 399 Chang Hai Road, Shanghai 200438, People's Republic of China
| | - Jiaxing Tang
- School of Physical Education, Shanghai University of Sport, 399 Chang Hai Road, Shanghai 200438, People's Republic of China
| | - Chendi Zhan
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China
| | - Qingwen Zhang
- School of Physical Education, Shanghai University of Sport, 399 Chang Hai Road, Shanghai 200438, People's Republic of China
| |
Collapse
|