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Alraawi Z, Banerjee N, Mohanty S, Kumar TKS. Amyloidogenesis: What Do We Know So Far? Int J Mol Sci 2022; 23:ijms232213970. [PMID: 36430450 PMCID: PMC9695042 DOI: 10.3390/ijms232213970] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/01/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
The study of protein aggregation, and amyloidosis in particular, has gained considerable interest in recent times. Several neurodegenerative diseases, such as Alzheimer's (AD) and Parkinson's (PD) show a characteristic buildup of proteinaceous aggregates in several organs, especially the brain. Despite the enormous upsurge in research articles in this arena, it would not be incorrect to say that we still lack a crystal-clear idea surrounding these notorious aggregates. In this review, we attempt to present a holistic picture on protein aggregation and amyloids in particular. Using a chronological order of discoveries, we present the case of amyloids right from the onset of their discovery, various biophysical techniques, including analysis of the structure, the mechanisms and kinetics of the formation of amyloids. We have discussed important questions on whether aggregation and amyloidosis are restricted to a subset of specific proteins or more broadly influenced by the biophysiochemical and cellular environment. The therapeutic strategies and the significant failure rate of drugs in clinical trials pertaining to these neurodegenerative diseases have been also discussed at length. At a time when the COVID-19 pandemic has hit the globe hard, the review also discusses the plausibility of the far-reaching consequences posed by the virus, such as triggering early onset of amyloidosis. Finally, the application(s) of amyloids as useful biomaterials has also been discussed briefly in this review.
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Affiliation(s)
- Zeina Alraawi
- Department of Chemistry and Biochemistry, Fulbright College of Art and Science, University of Arkansas, Fayetteville, AR 72701, USA
| | - Nayan Banerjee
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Srujana Mohanty
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata 741246, India
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2
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Zhang J, Yao P, You S, Qi W, Su R, He Z. Study on the Kinetics and Mechanism of Ferrocene-Tripeptide Inhibiting Insulin Aggregation. J Mater Chem B 2022; 10:7780-7788. [DOI: 10.1039/d2tb01085b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptides are gaining popularity as neurodegenerative disease-targeted drugs due to their medicinal value and the simplicity in the biomedicine and pharmaceutical industry field. In this study, based on previously studied...
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3
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Bhattacharya S, Xu L, Thompson D. Characterization of Amyloidogenic Peptide Aggregability in Helical Subspace. Methods Mol Biol 2022; 2340:401-448. [PMID: 35167084 DOI: 10.1007/978-1-0716-1546-1_18] [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: 06/14/2023]
Abstract
Prototypical amyloidogenic peptides amyloid-β (Aβ) and α-synuclein (αS) can undergo helix-helix associations via partially folded helical conformers, which may influence pathological progression to Alzheimer's (AD) and Parkinson's disease (PD), respectively. At the other extreme, stable folded helical conformers have been reported to resist self-assembly and amyloid formation. Experimental characterisation of such disparities in aggregation profiles due to subtle differences in peptide stabilities is precluded by the conformational heterogeneity of helical subspace. The diverse physical models used in molecular simulations allow sampling distinct regions of the phase space and are extensive in capturing the ensemble of rich helical subspace. Robust and powerful computational predictive methods utilizing network theory and free energy mapping can model the origin of helical population shifts in amyloidogenic peptides, which highlight their inherent aggregability. In this chapter, we discuss computational models, methods, design rules, and strategies to identify the driving force behind helical self-assembly and the molecular origin of aggregation resistance in helical intermediates of Aβ42 and αS. By extensive multiscale mapping of intrapeptide interactions, we show that the computational models can capture features that are otherwise imperceptible to experiments. Our models predict that targeting terminal residues may allow modulation and control of initial pathogenic aggregability of amyloidogenic peptides.
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Affiliation(s)
- Shayon Bhattacharya
- Department of Physics, Bernal Institute, University of Limerick, Limerick, Ireland
| | - Liang Xu
- Department of Physics, Bernal Institute, University of Limerick, Limerick, Ireland
| | - Damien Thompson
- Department of Physics, Bernal Institute, University of Limerick, Limerick, Ireland.
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4
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Choi B, Kim NH, Jin GY, Kim YS, Kim YH, Eom K. Sequence-dependent aggregation-prone conformations of islet amyloid polypeptide. Phys Chem Chem Phys 2021; 23:22532-22542. [PMID: 34590645 DOI: 10.1039/d1cp01061a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Amyloid proteins, which aggregate to form highly ordered structures, play a crucial role in various disease pathologies. Despite many previous studies on amyloid fibrils, which are an end product of protein aggregation, the structural characteristics of amyloid proteins in the early stage of aggregation and their related aggregation mechanism still remain elusive. The role of the amino acid sequence in the aggregation-prone structures of amyloid proteins at such a stage is not understood. Here, we have studied the sequence-dependent structural characteristics of islet amyloid polypeptide based on atomistic simulations and spectroscopic experiments. We show that the amino acid sequence determines non-bonded interactions that play a leading role in the formation of aggregation-prone conformations. Specifically, a single point mutation critically changes the population of aggregation-prone conformations, resulting in a change of the aggregation mechanism. Our simulation results were supported by experimental results suggesting that mutation affects the kinetics of aggregation and the structural characteristics of amyloid aggregates. Our study provides an insight into the role of sequence-dependent aggregation-prone conformations in the underlying mechanisms of amyloid aggregation.
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Affiliation(s)
- Bumjoon Choi
- Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea.
| | - Nam Hyeong Kim
- SKKU Advanced Institute of Nano Technology (SAINT), Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea.
| | - Geun Young Jin
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Yung Sam Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Yong Ho Kim
- SKKU Advanced Institute of Nano Technology (SAINT), Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea. .,Department of Nano Engineering, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea.,Center for Neuroscience Imaging Research, Institute for Basic Science (IBS), Suwon 16419, Republic of Korea
| | - Kilho Eom
- Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea.
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5
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Molecular insight into the early stage of amyloid-β(1-42) Homodimers aggregation influenced by histidine tautomerism. Int J Biol Macromol 2021; 184:887-897. [PMID: 34153362 DOI: 10.1016/j.ijbiomac.2021.06.078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 05/23/2021] [Accepted: 06/10/2021] [Indexed: 11/20/2022]
Abstract
Aggregated amyloid β-peptide (Aβ) in small oligomeric forms inside the brain causes synaptic function disruption and the development of Alzheimer's disease (AD). Histidine is an important amino acid that may lead to structural changes. Aβ42 monomer chain includes 3 histidine residues that considering two ε and δ tautomers 8 isomers, including (εεε) and (εδδ) could be formed. Molecular dynamics simulation on homodimerization of (εεε) (the most common type of tautomers) and (εδδ) tautomers with different initial configurations using monomer chains from our previous work were performed to uncover the tautomeric behavior of histidine on Aβ42 aggregation in a physiological pH which is still largely unknown and impossible to observe experimentally. We found a higher propensity of forming β-sheet in (εδδ) homodimers and specifically in a greater amount from Aβ42 than from Aβ40. A smaller amount of β-sheet formation was observed for (εεε) homodimers compared with (εδδ). Additionally, interactions in (εδδ) homodimers may indicate the importance of the hydrophobic core and C-/N-terminals during oligomerization. Our findings indicate the important role of the tautomeric effect of histidine and (εδδ) homodimers at the early stage of Aβ aggregation.
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6
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Elmezayen AD, Kemal Y. Structure-based virtual screening for novel potential selective inhibitors of class IIa histone deacetylases for cancer treatment. Comput Biol Chem 2021; 92:107491. [PMID: 33930743 DOI: 10.1016/j.compbiolchem.2021.107491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 10/21/2022]
Abstract
The fundamental cause of human cancer is strongly influenced by down- or up-regulations of epigenetic factors. Upregulated histone deacetylases (HDAC) have been shown to be effectively neutralized by the action of HDACs inhibitors (HDACi). However, cytotoxicity has been reported in normal cells because of non-specificity of several available HDACis that are in clinical use or at different phases of clinical trials. Because of the high amino acid sequence and structural similarity among HDAC enzymes, it is believed to be a challenging task to obtain isoform-selectivity. The essential aim of the present research work was to identify isoform-selective inhibitors against class IIa HDACs via structure-based drug design. Based on the highest binding affinity and isoform-selectivity, the top-ranked inhibitors were in silico tested for their absorption, distribution, metabolism, elimination, and toxicity (ADMET) properties, which were classified as drug-like compounds. Later, molecular dynamics simulation (MD) was carried out for all compound-protein complexes to evaluate the structural stability and the biding mode of the inhibitors, which showed high stability throughout the 100 ns simulation. Free binding energy predictions by MM-PBSA method showed the high binding affinity of the identified compounds toward their respective targets. Hence, these inhibitors could be used as drug candidates or as lead compounds for more in silico or in vitro optimization to design safe isoform-selective HDACs inhibitors.
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Affiliation(s)
- Ammar D Elmezayen
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083, Cibali, Istanbul, Turkey
| | - Yelekçi Kemal
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083, Cibali, Istanbul, Turkey.
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7
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Mahmoudinobar F, Nilsson BL, Dias CL. Effects of Ions and Small Compounds on the Structure of Aβ 42 Monomers. J Phys Chem B 2021; 125:1085-1097. [PMID: 33481611 DOI: 10.1021/acs.jpcb.0c09617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aggregation of amyloid-β (Aβ) proteins in the brain is a hallmark of Alzheimer's disease. This phenomenon can be promoted or inhibited by adding small molecules to the solution where Aβ is embedded. These molecules affect the ensemble of conformations sampled by Aβ monomers even before aggregation starts. Here, we perform extensive all-atom replica exchange molecular dynamics (REMD) simulations to provide a comparative study of the ensemble of conformations sampled by Aβ42 monomers in solutions that promote (i.e., aqueous solution containing NaCl) and inhibit (i.e., aqueous solutions containing scyllo-inositol or 4-aminophenol) aggregation. Simulations performed in pure water are used as our reference. We find that secondary-structure content is only affected in an antagonistic manner by promoters and inhibitors at the C-terminus and the central hydrophilic core. Moreover, the end of the C-terminus binds more favorably to the central hydrophobic core region of Aβ42 in NaCl adopting a type of strand-loop-strand structure that is disfavored by inhibitors. Nonpolar residues that form the dry core of larger aggregates of Aβ42 (e.g., PDB ID 2BEG) are found at close proximity in these strand-loop-strand structures, suggesting that their formation could play an important role in initiating nucleation. In the presence of inhibitors, the C-terminus binds the central hydrophilic core with a higher probability than in our reference simulation. This sensitivity of the C-terminus, which is affected in an antagonistic manner by inhibitors and promoters, provides evidence for its critical role in accounting for aggregation.
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Affiliation(s)
- Farbod Mahmoudinobar
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Cristiano L Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
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8
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Noor A, Zafar S, Zerr I. Neurodegenerative Proteinopathies in the Proteoform Spectrum-Tools and Challenges. Int J Mol Sci 2021; 22:1085. [PMID: 33499319 PMCID: PMC7865347 DOI: 10.3390/ijms22031085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/11/2022] Open
Abstract
Proteinopathy refers to a group of disorders defined by depositions of amyloids within living tissue. Neurodegenerative proteinopathies, including Alzheimer's disease, Parkinson's disease, Creutzfeldt-Jakob disease, and others, constitute a large fraction of these disorders. Amyloids are highly insoluble, ordered, stable, beta-sheet rich proteins. The emerging theory about the pathophysiology of neurodegenerative proteinopathies suggests that the primary amyloid-forming proteins, also known as the prion-like proteins, may exist as multiple proteoforms that contribute differentially towards the disease prognosis. It is therefore necessary to resolve these disorders on the level of proteoforms rather than the proteome. The transient and hydrophobic nature of amyloid-forming proteins and the minor post-translational alterations that lead to the formation of proteoforms require the use of highly sensitive and specialized techniques. Several conventional techniques, like gel electrophoresis and conventional mass spectrometry, have been modified to accommodate the proteoform theory and prion-like proteins. Several new ones, like imaging mass spectrometry, have also emerged. This review aims to discuss the proteoform theory of neurodegenerative disorders along with the utility of these proteomic techniques for the study of highly insoluble proteins and their associated proteoforms.
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Affiliation(s)
- Aneeqa Noor
- Department of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany; (A.N.); (I.Z.)
- German Center for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany
| | - Saima Zafar
- Department of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany; (A.N.); (I.Z.)
- German Center for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany
- Biomedical Engineering and Sciences Department, School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Bolan Road, H-12, 44000 Islamabad, Pakistan
| | - Inga Zerr
- Department of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany; (A.N.); (I.Z.)
- German Center for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany
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9
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Nakajima K, Yamazaki T, Kimura Y, So M, Goto Y, Ogi H. Time-Resolved Observation of Evolution of Amyloid-β Oligomer with Temporary Salt Crystals. J Phys Chem Lett 2020; 11:6176-6184. [PMID: 32687370 DOI: 10.1021/acs.jpclett.0c01487] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The aggregation behavior of amyloid-β (Aβ) peptides remains unclarified despite the fact that it is closely related to the pathogenic mechanism of Alzheimer's disease. Aβ peptides form diverse oligomers with various diameters before nucleation, making clarification of the mechanism involved a complex problem with conventional macroscopic analysis methods. Time-resolved single-molecule level analysis in bulk solution is thus required to fully understand their early stage aggregation behavior. Here, we perform time-resolved observation of the aggregation dynamics of Aβ oligomers in bulk solution using liquid-state transmission electron microscopy. Our observations reveal previously unknown behaviors. The most important discovery is that a salt crystal can precipitate even with a concentration much lower than its solubility, and it then dissolves in a short time, during which the aggregation reaction of Aβ peptides is significantly accelerated. These findings will provide new insights in the evolution of the Aβ oligomer.
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Affiliation(s)
- Kichitaro Nakajima
- Global Center for Medical Engineering and Informatics, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tomoya Yamazaki
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-8638, Japan
| | - Yuki Kimura
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-8638, Japan
| | - Masatomo So
- Institute of Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yuji Goto
- Institute of Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hirotsugu Ogi
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
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10
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Bhattacharya S, Xu L, Thompson D. Long-range Regulation of Partially Folded Amyloidogenic Peptides. Sci Rep 2020; 10:7597. [PMID: 32371882 PMCID: PMC7200734 DOI: 10.1038/s41598-020-64303-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 04/15/2020] [Indexed: 01/20/2023] Open
Abstract
Neurodegeneration involves abnormal aggregation of intrinsically disordered amyloidogenic peptides (IDPs), usually mediated by hydrophobic protein-protein interactions. There is mounting evidence that formation of α-helical intermediates is an early event during self-assembly of amyloid-β42 (Aβ42) and α-synuclein (αS) IDPs in Alzheimer’s and Parkinson’s disease pathogenesis, respectively. However, the driving force behind on-pathway molecular assembly of partially folded helical monomers into helical oligomers assembly remains unknown. Here, we employ extensive molecular dynamics simulations to sample the helical conformational sub-spaces of monomeric peptides of both Aβ42 and αS. Our computed free energies, population shifts, and dynamic cross-correlation network analyses reveal a common feature of long-range intra-peptide modulation of partial helical folds of the amyloidogenic central hydrophobic domains via concerted coupling with their charged terminal tails (N-terminus of Aβ42 and C-terminus of αS). The absence of such inter-domain fluctuations in both fully helical and completely unfolded (disordered) states suggests that long-range coupling regulates the dynamicity of partially folded helices, in both Aβ42 and αS peptides. The inter-domain coupling suggests a form of intra-molecular allosteric regulation of the aggregation trigger in partially folded helical monomers. This approach could be applied to study the broad range of amyloidogenic peptides, which could provide a new path to curbing pathogenic aggregation of partially folded conformers into oligomers, by inhibition of sites far from the hydrophobic core.
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Affiliation(s)
- Shayon Bhattacharya
- Department of Physics, Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Liang Xu
- Department of Physics, Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Damien Thompson
- Department of Physics, Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland.
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11
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Exploring the Multi-Target Performance of Mitochondriotropic Antioxidants against the Pivotal Alzheimer's Disease Pathophysiological Hallmarks. Molecules 2020; 25:molecules25020276. [PMID: 31936622 PMCID: PMC7024345 DOI: 10.3390/molecules25020276] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/05/2020] [Accepted: 01/07/2020] [Indexed: 12/19/2022] Open
Abstract
Alzheimer disease (AD) is the most common neurodegenerative disease featuring progressive and degenerative neurological impairments resulting in memory loss and cognitive decline. The specific mechanisms underlying AD are still poorly understood, but it is suggested that a deficiency in the brain neurotransmitter acetylcholine, the deposition of insoluble aggregates of fibrillar β-amyloid 1–42 (Aβ42), and iron and glutamate accumulation play an important role in the disease progress. Despite the existence of approved cholinergic drugs, none of them demonstrated effectiveness in modifying disease progression. Accordingly, the development of new chemical entities acting on more than one target is attracting progressively more attention as they can tackle intricate network targets and modulate their effects. Within this endeavor, a series of mitochondriotropic antioxidants inspired on hydroxycinnamic (HCA’s) scaffold were synthesized, screened toward cholinesterases and evaluated as neuroprotectors in a differentiated human SH-SY5Y cell line. From the series, compounds 7 and 11 with a 10-carbon chain can be viewed as multi-target leads for the treatment of AD, as they act as dual and bifunctional cholinesterase inhibitors and prevent the neuronal damage caused by diverse aggressors related to protein misfolding and aggregation, iron accumulation and excitotoxicity.
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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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Liang C, Savinov SN, Fejzo J, Eyles SJ, Chen J. Modulation of Amyloid-β42 Conformation by Small Molecules Through Nonspecific Binding. J Chem Theory Comput 2019; 15:5169-5174. [PMID: 31476124 DOI: 10.1021/acs.jctc.9b00599] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Aggregation of amyloid-β (Aβ) peptides is a crucial step in the progression of Alzheimer's disease (AD). Identifying aggregation inhibitors against AD has been a great challenge. We report an atomistic simulation study of the inhibition mechanism of two small molecules, homotaurine and scyllo-inositol, which are AD drug candidates currently under investigation. We show that both small molecules promote a conformational change of the Aβ42 monomer toward a more collapsed phase through a nonspecific binding mechanism. This finding provides atomistic-level insights into designing potential drug candidates for future AD treatments.
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Affiliation(s)
- Chungwen Liang
- Computational Modeling Core Facility, Institute for Applied Life Sciences (IALS) , University of Massachusetts Amherst , Amherst , Massachusetts 01003 , United States
| | - Sergey N Savinov
- Computational Modeling Core Facility, Institute for Applied Life Sciences (IALS) , University of Massachusetts Amherst , Amherst , Massachusetts 01003 , United States.,Department of Biochemistry and Molecular Biology , University of Massachusetts Amherst , Amherst , Massachusetts 01003 , United States
| | - Jasna Fejzo
- Biomolecular NMR Core Facility, Institute for Applied Life Sciences (IALS) , University of Massachusetts Amherst , Amherst , Massachusetts 01003 , United States
| | - Stephen J Eyles
- Mass Spectrometry Core Facility, Institute for Applied Life Sciences (IALS) , University of Massachusetts Amherst , Amherst , Massachusetts 01003 , United States
| | - Jianhan Chen
- Department of Biochemistry and Molecular Biology , University of Massachusetts Amherst , Amherst , Massachusetts 01003 , United States.,Department of Chemistry , University of Massachusetts Amherst , Amherst , Massachusetts 01003 , United States
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14
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Bhattacharya S, Xu L, Thompson D. Molecular Simulations Reveal Terminal Group Mediated Stabilization of Helical Conformers in Both Amyloid-β42 and α-Synuclein. ACS Chem Neurosci 2019; 10:2830-2842. [PMID: 30917651 DOI: 10.1021/acschemneuro.9b00053] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The presence of partially structured helices in natively unfolded amyloid-β42 (Aβ42) and α-synuclein (αS) has been shown to accelerate fibrillation in the onset of Alzheimer's and Parkinson's disease, respectively. At the other extreme, folded stable helical conformers have also been reported to resist amyloid formation. Recent studies indicate that amyloidogenic aggregation can be impeded using small molecules that stabilize the α-helical monomers and switch off the neurotoxic pathway. We predict a common intrapeptide route to stabilization based on the plasticity of helical conformations of Aβ42 and αS as assessed through extensive atomistic molecular dynamics (MD) computer simulations (∼36 μs) across ten distinct protein force field and water model combinations. Computed free energies and interaction maps (not obtainable from experiments alone) show that flexible terminal groups (N-terminus of Aβ42 and C-terminus of αS) show a tendency to stabilize folded helical conformations in both peptides via primary hydrophobic interactions with central hydrophobic domains, and secondary salt bridges with other domains. These interactions confer aggregation resistance by decreasing the population of partially structured helices and are absent in control simulations of complete unfolding. Computed helical stability is also significantly reduced in terminal-deleted variants. The models suggest new strategies to tackle neurodegeneration by rationally re-engineering terminal groups to optimize their predicted ability to deactivate helical monomers.
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Affiliation(s)
- Shayon Bhattacharya
- Department of Physics, Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland
| | - Liang Xu
- Department of Physics, Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland
| | - Damien Thompson
- Department of Physics, Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland
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15
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Shuaib S, Narang SS, Goyal D, Goyal B. Computational design and evaluation of β‐sheet breaker peptides for destabilizing Alzheimer's amyloid‐β
42
protofibrils. J Cell Biochem 2019; 120:17935-17950. [DOI: 10.1002/jcb.29061] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 04/20/2019] [Accepted: 04/29/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Suniba Shuaib
- Department of Chemistry, Faculty of Basic and Applied Sciences Sri Guru Granth Sahib World University Fatehgarh Sahib India
| | - Simranjeet Singh Narang
- Department of Chemistry, Faculty of Basic and Applied Sciences Sri Guru Granth Sahib World University Fatehgarh Sahib India
| | - Deepti Goyal
- Department of Chemistry, Faculty of Basic and Applied Sciences Sri Guru Granth Sahib World University Fatehgarh Sahib India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry Thapar Institute of Engineering & Technology Patiala India
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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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Recent Advances in Computational Protocols Addressing Intrinsically Disordered Proteins. Biomolecules 2019; 9:biom9040146. [PMID: 30979035 PMCID: PMC6523529 DOI: 10.3390/biom9040146] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 01/09/2023] Open
Abstract
Intrinsically disordered proteins (IDP) are abundant in the human genome and have recently emerged as major therapeutic targets for various diseases. Unlike traditional proteins that adopt a definitive structure, IDPs in free solution are disordered and exist as an ensemble of conformations. This enables the IDPs to signal through multiple signaling pathways and serve as scaffolds for multi-protein complexes. The challenge in studying IDPs experimentally stems from their disordered nature. Nuclear magnetic resonance (NMR), circular dichroism, small angle X-ray scattering, and single molecule Förster resonance energy transfer (FRET) can give the local structural information and overall dimension of IDPs, but seldom provide a unified picture of the whole protein. To understand the conformational dynamics of IDPs and how their structural ensembles recognize multiple binding partners and small molecule inhibitors, knowledge-based and physics-based sampling techniques are utilized in-silico, guided by experimental structural data. However, efficient sampling of the IDP conformational ensemble requires traversing the numerous degrees of freedom in the IDP energy landscape, as well as force-fields that accurately model the protein and solvent interactions. In this review, we have provided an overview of the current state of computational methods for studying IDP structure and dynamics and discussed the major challenges faced in this field.
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18
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Shuaib S, Saini RK, Goyal D, Goyal B. Impact of K16A and K28A mutation on the structure and dynamics of amyloid-β42 peptide in Alzheimer’s disease: key insights from molecular dynamics simulations. J Biomol Struct Dyn 2019; 38:708-721. [DOI: 10.1080/07391102.2019.1586587] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Suniba Shuaib
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Rajneet Kaur Saini
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Deepti Goyal
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
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19
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Computer Simulation of Protein Materials at Multiple Length Scales: From Single Proteins to Protein Assemblies. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s42493-018-00009-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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20
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Das P, Matysiak S, Mittal J. Looking at the Disordered Proteins through the Computational Microscope. ACS CENTRAL SCIENCE 2018; 4:534-542. [PMID: 29805999 PMCID: PMC5968442 DOI: 10.1021/acscentsci.7b00626] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Indexed: 05/04/2023]
Abstract
Intrinsically disordered proteins (IDPs) have attracted wide interest over the past decade due to their surprising prevalence in the proteome and versatile roles in cell physiology and pathology. A large selection of IDPs has been identified as potential targets for therapeutic intervention. Characterizing the structure-function relationship of disordered proteins is therefore an essential but daunting task, as these proteins can adapt transient structure, necessitating a new paradigm for connecting structural disorder to function. Molecular simulation has emerged as a natural complement to experiments for atomic-level characterizations and mechanistic investigations of this intriguing class of proteins. The diverse range of length and time scales involved in IDP function requires performing simulations at multiple levels of resolution. In this Outlook, we focus on summarizing available simulation methods, along with a few interesting example applications. We also provide an outlook on how these simulation methods can be further improved in order to provide a more accurate description of IDP structure, binding, and assembly.
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Affiliation(s)
- Payel Das
- IBM Thomas J.
Watson Research Center, Yorktown Heights, New York 10598, United States
- E-mail:
| | - Silvina Matysiak
- Fischell
Department of Bioengineering, University
of Maryland, College Park, Maryland 20742, United States
| | - Jeetain Mittal
- Department
of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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