1
|
Roldán-Martín L, Sodupe M, Maréchal JD. Computational Study of Amyloidβ 42 Familial Mutations and Metal Interaction: Impact on Monomers and Aggregates Dynamical Behaviors. Inorg Chem 2024; 63:4725-4737. [PMID: 38408469 PMCID: PMC10934806 DOI: 10.1021/acs.inorgchem.3c04555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/02/2024] [Accepted: 02/02/2024] [Indexed: 02/28/2024]
Abstract
One of the main hallmarks of Alzheimer's Disease is the formation of β-amyloid plaques, whose formation may be enhanced by metal binding or the appearance of familial mutations. In the present study, the simultaneous effect of familial mutations (E22Q, E22G, E22K, and D23N) and binding to metal ions (Cu(II) or Al(III)) is studied at the Aβ42 monomeric and fibrillar levels. With the application of GaMD and MD simulations, it is observed that the effects of metal binding and mutations differ in the monomeric and fibrillar forms. In the monomeric structures, without metal binding, all mutations reduce the amount of α-helix and increase, in some cases, the β-sheet content. In the presence of Cu(II) and Al(III) metal ions, the peptide becomes less flexible, and the β-sheet content decreases in favor of forming α-helix motifs that stabilize the system through interhelical contacts. Regarding the fibrillar structures, mutations decrease the opening of the fiber in the vertical axis, thereby stabilizing the S-shaped structure of the fiber. This effect is, in general, enhanced upon metal binding. These results may explain the different Aβ42 aggregation patterns observed in familial mutations.
Collapse
Affiliation(s)
- Lorena Roldán-Martín
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Vallès, Spain
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Vallès, Spain
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Vallès, Spain
| |
Collapse
|
2
|
Roldán-Martín L, Sodupe M, Maréchal JD. Computational assessment of the impact of Cu(II) and Al(III) on β-amyloid 42 fibrils: Binding sites, structural stability, and possible physiological implications. Front Neurosci 2023; 17:1110311. [PMID: 36814794 PMCID: PMC9940836 DOI: 10.3389/fnins.2023.1110311] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/10/2023] [Indexed: 02/09/2023] Open
Abstract
One of Alzheimer's disease major hallmarks is the aggregation of β-amyloid peptide, a process in which metal ions play an important role. In the present work, an integrative computational study has been performed to identify the metal-binding regions and determine the conformational impact of Cu(II) and Al(III) ion binding to the β-amyloid (Aβ42) fibrillary structure. Through classical and Gaussian accelerated molecular dynamics, it has been observed that the metal-free fiber shows a hinge fan-like motion of the S-shaped structure, maintaining the general conformation. Upon metal coordination, distinctive patterns are observed depending on the metal. Cu(II) binds to the flexible N-terminal region and induces structural changes that could ultimately disrupt the fibrillary structure. In contrast, Al(III) binding takes place with the residues Glu22 and Asp23, and its binding reinforces the core stability of the system. These results give clues on the molecular impact of the interaction of metal ions with the aggregates and sustain their non-innocent roles in the evolution of the illness.
Collapse
|
3
|
Workman AS. Comparative analyses and molecular videography of MD simulations on WT human SOD1. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
4
|
Zia Q, Rehman MT, Hashmi MA, Siddiqui S, Bin Dukhyil A, Ahmed MZ, Jamal A, Banawas S, Almalki SG, Owais M, Aldhafeeri HQ, Ibrahim IM, Alturaiki W, AlAjmi MF, Alsieni M, Alqurashi YE. Effect of Date Palm ( Phoenix dactylifera) Phytochemicals on Aβ 1-40 Amyloid Formation: An in-silico Analysis. Front Neurosci 2022; 16:915122. [PMID: 35958986 PMCID: PMC9359633 DOI: 10.3389/fnins.2022.915122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease and the most prevalent form of dementia. The generation of oxygen free radicals and oxidative damage is believed to be involved in the pathogenesis of AD. It has been suggested that date palm, a plant rich in phenolic compounds and flavonoids, can provide an alternative treatment to fight memory loss and cognitive dysfunction due to its potent antioxidant activity. Thus, we studied the effect of flavonoids present in date palm on Aβ1-40 amyloid formation using molecular docking and molecular dynamics simulation. AutoDock. Myricetin was used as a positive control drug. The flavonoids Diosmetin, Luteolin, and Rutin were found to be potent inhibitors of aggregation (docking energies ≤ -8.05 kcal mol-1) targeting Aβ1-40 fibrils (both 2LMO and 6TI5), simultaneously. Further screening by physicochemical properties and drug-likeness analysis suggested that all flavonoids except Rutin followed Lipinski's rule of five. Rutin was, thus, taken as a negative control (due to its violation of Lipinski's rule) to compare its dynamics with Diosmetin. Diosmetin exhibited the highest positive scores for drug likeness. Since Luteolin exhibited moderate drug-likeness and better absorption properties, it was also included in molecular dynamics simulation. Molecular dynamics of shortlisted compounds (Rutin, Diosmetin, and Luteolin) were performed for 200 ns, and the results were analyzed by monitoring root mean square deviations (RMSD), root mean square fluctuation (RMSF) analysis, the radius of gyration (Rg), and solvent accessible surface area (SASA). The results proved the formation of a stable protein-compound complex. Based on binding energies and non-bonded interactions, Rutin and Luteolin emerged as better lead molecules than Diosmetin. However, high MW (610.5), lowest absorption rate (16.04%), and more than one violation of Lipinski's rule make Rutin a less likely candidate as an anti-amyloidogenic agent. Moreover, among non-violators of Lipinski's rule, Diosmetin exhibited a greater absorption rate than Luteolin as well as the highest positive scores for drug-likeness. Thus, we can conclude that Diosmetin and Luteolin may serve as a scaffold for the design of better inhibitors with higher affinities toward the target proteins. However, these results warrant in-vitro and in-vivo validation before practical use.
Collapse
Affiliation(s)
- Qamar Zia
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Md Amiruddin Hashmi
- Interdisciplinary Biotechnology Unit, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Sahabjada Siddiqui
- Department of Biotechnology, Era's Lucknow Medical College and Hospital, Era University, Lucknow, India
| | - Abdulaziz Bin Dukhyil
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
| | - Mohammad Z. Ahmed
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Azfar Jamal
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah, Saudi Arabia
- Department of Biology, College of Science Al-Zulfi, Majmaah University, Majmaah, Saudi Arabia
| | - Saeed Banawas
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah, Saudi Arabia
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR, United States
| | - Sami G. Almalki
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
| | - Mohammad Owais
- Interdisciplinary Biotechnology Unit, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Hamad Qasem Aldhafeeri
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
| | - Ibrahim M. Ibrahim
- Department of Pharmacology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wael Alturaiki
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
| | - Mohamed F. AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Alsieni
- Department of Pharmacology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Yaser E. Alqurashi
- Department of Biology, College of Science Al-Zulfi, Majmaah University, Majmaah, Saudi Arabia
| |
Collapse
|
5
|
Mohan A, Shaji S, Padmanabhan S, Naisam S, Sreekumar N. The potentials of Calotropis procera against filarial elephantiasis: an in-silico approach. J Parasit Dis 2022; 46:384-394. [PMID: 35692472 PMCID: PMC9177934 DOI: 10.1007/s12639-021-01456-0] [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: 04/12/2021] [Accepted: 09/17/2021] [Indexed: 10/20/2022] Open
Abstract
Lymphatic filariasis is one of the major diseases that belong to the category of neglected tropical illness. Filarial nematodes are the cause of the disease and are transmitted to humans via blood-feeding arthropod vectors. Drugs such as Albendazole, Ivermectin and diethylcarbamazine are administered either individually or in combination to overcome the progress of the lymphatic filariasis. These drugs have some minor side effects like temporary hair loss, dizziness, nausea etc. The filarial parasites have multifunctional proteins including the Glutathione-s-transferase (GST) enzyme. This study aims at the identification of a natural molecule that has the potential to bind with the GST enzyme, which plays a major role in detoxification of endogenous electrophilic compounds. Thus the binding interrupts the detoxification process within the filarial parasite, Brugia malayi. A medicinal plant Calotropis procera, owing to its anthelmintic properties was searched for the presence of potential phytocompounds. The phytocompounds were docked against the homology modeled GST enzyme using the MOE software. The results were screened and analyzed based on the Lipinski rule of 5. N-octanoate was the phytocompound obtained based on molecular docking, subjected to molecular dynamics. These results require further in vitro and in vivo validation to consider n-octanoate as a potential drug candidate for lymphatic filariasis treatment.
Collapse
Affiliation(s)
- Aswin Mohan
- Dept. of Computational Biology and Bioinformatics, Kariavattom Campus, University of Kerala, Trivandrum, Kerala India
| | - Shanitha Shaji
- Dept. of Computational Biology and Bioinformatics, Kariavattom Campus, University of Kerala, Trivandrum, Kerala India
| | - Sunitha Padmanabhan
- Dept. of Computational Biology and Bioinformatics, Kariavattom Campus, University of Kerala, Trivandrum, Kerala India
| | - Shahanas Naisam
- Accubits Invent Pvt. Ltd, The Pirates Square, Trivandrum, Kerala India
| | - Nidhin Sreekumar
- Accubits Invent Pvt. Ltd, The Pirates Square, Trivandrum, Kerala India
| |
Collapse
|
6
|
Petersingham G, Zaman MS, Johnson AJ, Reddy N, Torres AM, Wu MJ. Molecular details of aluminium-amyloid β peptide interaction by nuclear magnetic resonance. Biometals 2022; 35:759-769. [PMID: 35639270 DOI: 10.1007/s10534-022-00399-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 05/16/2022] [Indexed: 11/24/2022]
Abstract
Alzheimer's disease (AD) is a devastating neurodegenerative condition that poses major challenges to human health. Both amyloid β (Aβ) and metal ions such as aluminium are implicated in the development of AD. By the means of NMR, the interactions of Al3+ with Aβ1-28 peptide as well as the Aβ1-28 analogues were studied, and the key binding sites of Al3+ in Aβ determined. NMR data showed Al3+ interacts with Aβ1-28 at the NH and αH of numerous residues by exhibiting upfield shifts. Using Aβ analogues where His6, His13 and His14 were individually replaced by alanine residue(s), including Aβ H6A, Aβ H13A, Aβ H14A, and Aβ H6,13,14A, the results demonstrated that the histidine residues (His6, His13 and His14) and N-terminal Asp1 were involved in the Al3+ coordination. These findings provide, for the first time, the details of the molecular interaction between Al3+ and Aβ, which points to the potential role of Al3+ in Aβ aggregation, hence in AD development.
Collapse
Affiliation(s)
- Gayani Petersingham
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Mohammad S Zaman
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Adam J Johnson
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Narsimha Reddy
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Allan M Torres
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia.,Nanoscale Organisation and Dynamics Group, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Ming J Wu
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia.
| |
Collapse
|
7
|
Chen H, Siu SWI, Wong CTT, Qiu J, Cheung AKK, Lee SMY. Anti-epileptic Kunitz-like peptides discovered in the branching coral Acropora digitifera through transcriptomic analysis. Arch Toxicol 2022; 96:2589-2608. [PMID: 35604417 DOI: 10.1007/s00204-022-03311-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/27/2022] [Indexed: 11/29/2022]
Abstract
Approximately 50 million people are suffering from epilepsy worldwide. Corals have been used for treating epilepsy in traditional Chinese medicine, but the mechanism of this treatment is unknown. In this study, we analyzed the transcriptome of the branching coral Acropora digitifera and obtained its Kyoto Encyclopedia of Genes and Genomes (KEGG), EuKaryotic Orthologous Groups (KOG) and Gene Ontology (GO) annotation. Combined with multiple sequence alignment and phylogenetic analysis, we discovered three polypeptides, we named them AdKuz1, AdKuz2 and AdKuz3, from A. digitifera that showed a close relationship to Kunitz-type peptides. Molecular docking and molecular dynamics simulation indicated that AdKuz1 to 3 could interact with GABAA receptor but AdKuz2-GABAA remained more stable than others. The biological experiments showed that AdKuz1 and AdKuz2 exhibited an anti-inflammatory effect by decreasing the aberrant level of nitric oxide (NO), IL-6, TNF-α and IL-1β induced by LPS in BV-2 cells. In addition, the pentylenetetrazol (PTZ)-induced epileptic effect on zebrafish was remarkably suppressed by AdKuz1 and AdKuz2. AdKuz2 particularly showed superior anti-epileptic effects compared to the other two peptides. Furthermore, AdKuz2 significantly decreased the expression of c-fos and npas4a, which were up-regulated by PTZ treatment. In addition, AdKuz2 reduced the synthesis of glutamate and enhanced the biosynthesis of gamma-aminobutyric acid (GABA). In conclusion, the results indicated that AdKuz2 may affect the synthesis of glutamate and GABA and enhance the activity of the GABAA receptor to inhibit the symptoms of epilepsy. We believe, AdKuz2 could be a promising anti-epileptic agent and its mechanism of action should be further investigated.
Collapse
Affiliation(s)
- Hanbin Chen
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macao, China.,Department of Rehabilitation Sciences, The Hong Kong Polytechnic University, Hong Kong, China
| | - Shirley Weng In Siu
- Institute of Science and Environment, University of Saint Joseph, Macao, China
| | - Clarence Tsun Ting Wong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Jianwen Qiu
- Department of Biology and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong Baptist University, Hong Kong, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Alex Kwok-Kuen Cheung
- Department of Rehabilitation Sciences, The Hong Kong Polytechnic University, Hong Kong, China.
| | - Simon Ming Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macao, China. .,Department of Pharmaceutical Sciences, Faculty of Health Sciences, University of Macau, Macao, China.
| |
Collapse
|
8
|
Abstract
Amyloids are protein aggregates bearing a highly ordered cross β structural motif, which may be functional but are mostly pathogenic. Their formation, deposition in tissues and consequent organ dysfunction is the central event in amyloidogenic diseases. Such protein aggregation may be brought about by conformational changes, and much attention has been directed toward factors like metal binding, post-translational modifications, mutations of protein etc., which eventually affect the reactivity and cytotoxicity of the associated proteins. Over the past decade, a global effort from different groups working on these misfolded/unfolded proteins/peptides has revealed that the amino acid residues in the second coordination sphere of the active sites of amyloidogenic proteins/peptides cause changes in H-bonding pattern or protein-protein interactions, which dramatically alter the structure and reactivity of these proteins/peptides. These second sphere effects not only determine the binding of transition metals and cofactors, which define the pathology of some of these diseases, but also change the mechanism of redox reactions catalyzed by these proteins/peptides and form the basis of oxidative damage associated with these amyloidogenic diseases. The present review seeks to discuss such second sphere modifications and their ramifications in the etiopathology of some representative amyloidogenic diseases like Alzheimer's disease (AD), type 2 diabetes mellitus (T2Dm), Parkinson's disease (PD), Huntington's disease (HD), and prion diseases.
Collapse
Affiliation(s)
- Madhuparna Roy
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Arnab Kumar Nath
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Ishita Pal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Somdatta Ghosh Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| |
Collapse
|
9
|
Combined Modeling Study of the Binding Characteristics of Natural Compounds, Derived from Psoralea Fruits, to β-Amyloid Peptide Monomer. Int J Mol Sci 2022; 23:ijms23073546. [PMID: 35408917 PMCID: PMC8998326 DOI: 10.3390/ijms23073546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 11/16/2022] Open
Abstract
A dysfunctional protein aggregation in the nervous system can lead to several neurodegenerative disorders that result in intracellular inclusions or extracellular aggregates. An early critical event within the pathogenesis of Alzheimer’s disease is the accumulation of amyloid beta peptide within the brain. Natural compounds isolated from Psoralea Fructus (PF) have significant anti-Alzheimer effects as strong inhibitors of Aβ42 aggregation. Computer simulations provide a powerful means of linking experimental findings to nanoscale molecular events. As part of this research four prenylated compounds, the active ingredients of Psoralea Fructus (PF), were studied as Aβ42 accumulation inhibitors using molecular simulations modeling. In order to resolve the binding modes of the ligands and identify the main interactions of Aβ42 residues, we performed a 100 ns molecular dynamics simulation and binding free energy calculations starting from the model of the compounds obtained from the docking study. This study was able to pinpoint the key amino acid residues in the Aβ42 active site and provide useful information that could benefit the development of new Aβ42 accumulation inhibitors.
Collapse
|
10
|
Jahromi AM, Solhjoo A, Ghasemi M, Khedri M, Maleki R, Tayebi L. Atomistic insight into 2D COFs as antiviral agents against SARS-CoV-2. MATERIALS CHEMISTRY AND PHYSICS 2022; 276:125382. [PMID: 34725529 PMCID: PMC8550915 DOI: 10.1016/j.matchemphys.2021.125382] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 10/23/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
The recent pandemic of COVID-19 has raised global health concerns. Preventing severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) activity in the body is a very promising method to overcome the COVID-19 pandemic. One of the prevention methods is constraining the binding process among the human cell receptor-ACE2 and coronavirus spike protein. In the research done, the effect of deformation of the spike protein structure, due to the covalent organic frameworks (COFs), in reducing the interactions of ACE2 and the spike protein by the computational method was investigated. In this regard, atomic analysis of the interactions of ACE2 and the spike protein is provided using a molecular dynamics simulation. First, we investigated the interactions of the three different COFs, including COF-78, DAAQ-TFP, and COF-OEt, with the spike protein by analyzing the bond energies, as well as structural changes of the spike protein. Then, intermolecular interactions of the deformed spike protein along with ACE2 were assessed to clarify the protein's fusion after the deformation. As indicated by the results, although all introduced COFs deformed the spike protein in an effective way, COF-78 showed the best performance in the prevention of spike protein-ACE2 interactions by changing the molecular structure of the protein. Indeed, the interaction analysis of the deformed spike protein by COF-78 with the ACE2 showed that their interactions had the lowest absolute value of energy, along with the least amount of hydrogen bonds, in which the compaction of the protein was lower compared to the other deformed proteins. Moreover, having a high contact area with an aqueous media as well as severe fluctuations during the simulation time confirmed the positive performance of COF-78. In the current study, we aimed to introduce novel materials and COVID-19 prevention methodology that can be used in face masks and for surface disinfection.
Collapse
Affiliation(s)
- Ahmad Miri Jahromi
- Computational Biology and Chemistry Group (CBCG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Aida Solhjoo
- Computational Biology and Chemistry Group (CBCG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehdi Ghasemi
- Computational Biology and Chemistry Group (CBCG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Department of Petroleum Engineering, Amirkabir University of Technology, Tehran, Iran
| | - Mohammad Khedri
- Computational Biology and Chemistry Group (CBCG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Reza Maleki
- Computational Biology and Chemistry Group (CBCG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Lobat Tayebi
- Marquette University School of Dentistry, Milwaukee, WI, 53233, USA
| |
Collapse
|
11
|
Closset M, Cailliau K, Slaby S, Marin M. Effects of Aluminium Contamination on the Nervous System of Freshwater Aquatic Vertebrates: A Review. Int J Mol Sci 2021; 23:ijms23010031. [PMID: 35008450 PMCID: PMC8744726 DOI: 10.3390/ijms23010031] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 12/18/2022] Open
Abstract
Aluminium (Al) is the most common natural metallic element in the Earth’s crust. It is released into the environment through natural processes and human activities and accumulates in aquatic environments. This review compiles scientific data on the neurotoxicity of aluminium contamination on the nervous system of aquatic organisms. More precisely, it helps identify biomarkers of aluminium exposure for aquatic environment biomonitoring in freshwater aquatic vertebrates. Al is neurotoxic and accumulates in the nervous system of aquatic vertebrates, which is why it could be responsible for oxidative stress. In addition, it activates and inhibits antioxidant enzymes and leads to changes in acetylcholinesterase activity, neurotransmitter levels, and in the expression of several neural genes and nerve cell components. It also causes histological changes in nerve tissue, modifications of organism behaviour, and cognitive deficit. However, impacts of aluminium exposure on the early stages of aquatic vertebrate development are poorly described. Lastly, this review also poses the question of how accurate aquatic vertebrates (fishes and amphibians) could be used as model organisms to complement biological data relating to the developmental aspect. This “challenge” is very relevant since freshwater pollution with heavy metals has increased in the last few decades.
Collapse
Affiliation(s)
- Marie Closset
- University Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France; (M.C.); (K.C.)
| | - Katia Cailliau
- University Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France; (M.C.); (K.C.)
| | - Sylvain Slaby
- Normandie University, UNILEHAVRE, CNRS, UMR 3730 SCALE, Environmental Stress and Aquatic Biomonitoring (SEBIO), F-76600 Le Havre, France;
| | - Matthieu Marin
- University Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France; (M.C.); (K.C.)
- Correspondence:
| |
Collapse
|
12
|
Boopathi S, Poma AB, Garduño-Juárez R. An Overview of Several Inhibitors for Alzheimer's Disease: Characterization and Failure. Int J Mol Sci 2021; 22:10798. [PMID: 34639140 PMCID: PMC8509255 DOI: 10.3390/ijms221910798] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 10/01/2021] [Accepted: 10/03/2021] [Indexed: 01/04/2023] Open
Abstract
Amyloid beta (Aβ) oligomers are the most neurotoxic aggregates causing neuronal death and cognitive damage. A detailed elucidation of the aggregation pathways from oligomers to fibril formation is crucial to develop therapeutic strategies for Alzheimer's disease (AD). Although experimental techniques rely on the measure of time- and space-average properties, they face severe difficulties in the investigation of Aβ peptide aggregation due to their intrinsically disorder character. Computer simulation is a tool that allows tracing the molecular motion of molecules; hence it complements Aβ experiments, as it allows to explore the binding mechanism between metal ions and Aβ oligomers close to the cellular membrane at the atomic resolution. In this context, integrated studies of experiments and computer simulations can assist in mapping the complete pathways of aggregation and toxicity of Aβ peptides. Aβ oligomers are disordered proteins, and due to a rapid exploration of their intrinsic conformational space in real-time, they are challenging therapeutic targets. Therefore, no good drug candidate could have been identified for clinical use. Our previous investigations identified two small molecules, M30 (2-Octahydroisoquinolin-2(1H)-ylethanamine) and Gabapentin, capable of Aβ binding and inhibiting molecular aggregation, synaptotoxicity, intracellular calcium signaling, cellular toxicity and memory losses induced by Aβ. Thus, we recommend these molecules as novel candidates to assist anti-AD drug discovery in the near future. This review discusses the most recent research investigations about the Aβ dynamics in water, close contact with cell membranes, and several therapeutic strategies to remove plaque formation.
Collapse
Affiliation(s)
- Subramanian Boopathi
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico;
| | - Adolfo B. Poma
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research Polish Academy of Science, Pawińskiego 5B, 02-106 Warsaw, Poland
- International Center for Research on Innovative Biobased Materials (ICRI-BioM)—International Research Agenda, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland;
| | - Ramón Garduño-Juárez
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico;
| |
Collapse
|
13
|
Alimohammadi E, Nikzad A, Khedri M, Shafiee S, Miri Jahromi A, Maleki R, Rezaei N. Molecular Tuning of the Nano–Bio Interface: Alpha-Synuclein’s Surface Targeting with Doped Carbon Nanostructures. ACS APPLIED BIO MATERIALS 2021; 4:6073-6083. [DOI: 10.1021/acsabm.1c00421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ehsan Alimohammadi
- Department of Neurosurgery, Kermanshah University of Medical Sciences, Imam Reza Hospital, 67158-47141 Kermanshah, Iran
| | - Arash Nikzad
- Department of Mechanical Engineering, University of British Columbia, 2054-6250 Applied
Science Lane, Vancouver, British Columbia V6T1Z4, Canada
| | - Mohammad Khedri
- Computational Biology and Chemistry Group (CBCG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Sepehr Shafiee
- School of Medicine, Shahid Beheshti University of Medical Sciences, 19839-63113 Tehran, Iran
| | - Ahmad Miri Jahromi
- Computational Biology and Chemistry Group (CBCG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Reza Maleki
- Computational Biology and Chemistry Group (CBCG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children’s Medical Center, Tehran University of Medical Sciences, 14167-53955 Tehran, Iran
- Network of Immunity in Infection, Malignancy, and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran 1419733141, Iran
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, 14167-53955 Tehran, Iran
| |
Collapse
|
14
|
Molecular mechanisms of aluminum neurotoxicity: Update on adverse effects and therapeutic strategies. ADVANCES IN NEUROTOXICOLOGY 2021; 5:1-34. [PMID: 34263089 DOI: 10.1016/bs.ant.2020.12.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
15
|
Mocanu CS, Jureschi M, Drochioiu G. Aluminium Binding to Modified Amyloid-β Peptides: Implications for Alzheimer's Disease. Molecules 2020; 25:molecules25194536. [PMID: 33022965 PMCID: PMC7582331 DOI: 10.3390/molecules25194536] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/22/2020] [Accepted: 10/02/2020] [Indexed: 12/13/2022] Open
Abstract
Aluminium (Al) is clearly neurotoxic and considerable evidence exists that Al may play a role in the aetiology or pathogenesis of Alzheimer’s disease (AD). Nevertheless, the link between AD pathology and Al is still open to debate. Therefore, we investigated here the interaction of aluminium ions with two Aβ peptide fragments and their analogues. First, we synthesised by the Fmoc/tBu solid-phase peptide synthesis (SPPS) strategy using an automated peptide synthesiser two new peptides starting from the Aβ(1–16) native peptide fragment. For this purpose, the three histidine residues (H6, H13, and H14) of the Aβ(1–16) peptide were replaced by three alanine and three serine residues to form the modified peptides Aβ(1–16)A36,13,14 and Aβ(1–16)S36,13,14 (primary structures: H-1DAEFRADSGYEVAAQK16-NH2 and H-1DAEFRSDSGYEVSSQK16-NH2). In addition, the Aβ(9–16) peptide fragment (H-9GYEVHHQK16-NH2) and its glycine analogues, namely Aβ(9–16)G110, (H-9GGEVHHQK16-NH2), Aβ(9–16)G213,14 (H-9GYEVGGQK16-NH2), and Aβ(9–16)G310,13,14 (H-9GGEVGGQK16-NH2), were manually synthesised in order to study Al binding to more specific amino acid residues. Both the peptides and the corresponding complexes with aluminium were comparatively investigated by mass spectrometry (MS), circular dichroism spectroscopy (CD), atomic force microscopy (AFM), scanning electron microscopy (SEM), and Fourier transform infrared spectroscopy (FT-IR). Al–peptide molecular ions and Al-fragment ions were unambiguously identified in the MS and MS/MS spectra. AFM images showed dramatic changes in the film morphology of peptides upon Al binding. Our findings from the investigation of N-terminal 1-16 and even 9-16 normal and modified sequences of Aβ peptides suggest that they have the capability to be involved in aluminium ion binding associated with AD.
Collapse
|
16
|
Alimohammadi E, Khedri M, Miri Jahromi A, Maleki R, Rezaian M. Graphene-Based Nanoparticles as Potential Treatment Options for Parkinson's Disease: A Molecular Dynamics Study. Int J Nanomedicine 2020; 15:6887-6903. [PMID: 32982240 PMCID: PMC7509323 DOI: 10.2147/ijn.s265140] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/08/2020] [Indexed: 12/20/2022] Open
Abstract
INTRODUCTION The study of abnormal aggregation of proteins in different tissues of the body has recently earned great attention from researchers in various fields of science. Concerning neurological diseases, for instance, the accumulation of amyloid fibrils can contribute to Parkinson's disease, a progressively severe neurodegenerative disorder. The most prominent features of this disease are the degeneration of neurons in the substantia nigra and accumulation of α-synuclein aggregates, especially in the brainstem, spinal cord, and cortical areas. Dopamine replacement therapies and other medications have reduced motor impairment and had positive consequences on patients' quality of life. However, if these medications are stopped, symptoms of the disease will recur even more severely. Therefore, the improvement of therapies targeting more basic mechanisms like prevention of amyloid formation seems to be critical. It has been shown that the interactions between monolayers like graphene and amyloids could prevent their fibrillation. METHODS For the first time, the impact of four types of last-generation graphene-based nanostructures on the prevention of α-synuclein amyloid fibrillation was investigated in this study by using molecular dynamics simulation tools. RESULTS Although all monolayers were shown to prevent amyloid fibrillation, nitrogen-doped graphene (N-Graphene) caused the most instability in the secondary structure of α-synuclein amyloids. Moreover, among the four monolayers, N-Graphene was shown to present the highest absolute value of interaction energy, the lowest contact level of amyloid particles, the highest number of hydrogen bonds between water and amyloid molecules, the highest instability caused in α-synuclein particles, and the most significant decrease in the compactness of α-synuclein protein. DISCUSSION Ultimately, it was concluded that N-Graphene could be the most effective monolayer to disrupt amyloid fibrillation, and consequently, prevent the progression of Parkinson's disease.
Collapse
Affiliation(s)
- Ehsan Alimohammadi
- Neurosurgery Department, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohammad Khedri
- Department of Chemical Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran1591634311, Iran
| | - Ahmad Miri Jahromi
- Department of Petroleum Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran1591634311, Iran
| | - Reza Maleki
- Department of Chemical Engineering, Sharif University of Technology, Tehran, Iran
| | - Milad Rezaian
- Department of Pharmacology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran19839-63113, Iran
| |
Collapse
|
17
|
Radwan A, Mahrous GM. Docking studies and molecular dynamics simulations of the binding characteristics of waldiomycin and its methyl ester analog to Staphylococcus aureus histidine kinase. PLoS One 2020; 15:e0234215. [PMID: 32502195 PMCID: PMC7274439 DOI: 10.1371/journal.pone.0234215] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 05/20/2020] [Indexed: 12/13/2022] Open
Abstract
Bacterial histidine kinases (HKs) are considered attractive drug targets because of their ability to govern adaptive responses coupled with their ubiquity. There are several classes of HK inhibitors; however, they suffer from drug resistance, poor bioavailability, and a lack of selectivity. The 3D structure of Staphylococcus aureus HK was not isolated in high-resolution coordinates, precluding further disclosure of structure-dependent binding to the specific antibiotics. To elucidate structure-dependent binding, the 3D structure of the catalytic domain WalK of S. aureus HK was constructed using homology modeling to investigate the WalK-ligand binding mechanisms through molecular docking studies and molecular dynamics simulations. The binding free energies of the waldiomycin and its methyl ester analog were calculated using molecular mechanics/generalized born surface area scoring. The key residues for protein-ligand binding were postulated. The structural divergence responsible for the 7.4-fold higher potency of waldiomycin than that of its ester analog was clearly observed. The optimized 3D macromolecule-ligand binding modes shed light on the S. aureus HK/WalK-ligand interactions that afford a means to assess binding affinity to design new HK/WalK inhibitors.
Collapse
Affiliation(s)
- Awwad Radwan
- Kayyali Chair, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Assiut University, Assiut, Egypt
| | - Gamal M. Mahrous
- Kayyali Chair, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| |
Collapse
|
18
|
Exley C, Mold MJ. Imaging of aluminium and amyloid β in neurodegenerative disease. Heliyon 2020; 6:e03839. [PMID: 32368656 PMCID: PMC7184253 DOI: 10.1016/j.heliyon.2020.e03839] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/16/2020] [Accepted: 04/21/2020] [Indexed: 12/28/2022] Open
Abstract
Objectives Recent research has confirmed the presence of aluminium in human brain tissue. Quantitative analyses suggest increased brain aluminium content in a number of neurodegenerative diseases including familial Alzheimer's disease, congophilic amyloid angiopathy, epilepsy and autism. Complementary aluminium-specific fluorescence microscopy identifies the location of aluminium in human brain tissue and demonstrates significant differences in distribution between diseases. Herein we combine these approaches in investigating associations between aluminium in human brain tissue and specific disease-associated neuropathologies. Methods We have used aluminium-specific fluorescence microscopy, Congo red staining using light and polarised light and thioflavin S fluorescence microscopy on serial sections of brain tissues to identify co-localisation of aluminium and amyloid β and tau neuropathology. Results A combination of light, polarised and fluorescence microscopy demonstrates an intimate relationship between aluminium and amyloid β in familial Alzheimer's disease but not in other conditions and diseases, such as congophilic amyloid angiopathy and autism. We demonstrate preliminary evidence of amyloid β pathology, including associations with vasculature and parenchymal tissues, in autism in tissues heavily loaded with aluminium. Conclusion We suggest that complementary aluminium-specific fluorescence microscopy may reveal important information about the putative toxicity of aluminium in neurodegenerative and neurodevelopmental disorders.
Collapse
Affiliation(s)
- Christopher Exley
- The Birchall Centre, Lennard-Jones Laboratories, Keele University, Staffordshire, United Kingdom
| | - Matthew J Mold
- The Birchall Centre, Lennard-Jones Laboratories, Keele University, Staffordshire, United Kingdom
| |
Collapse
|
19
|
Saini RK, Thakur H, Goyal B. Effect of Piedmont mutation (L34V) on the structure, dynamics, and aggregation of Alzheimer's Aβ 40 peptide. J Mol Graph Model 2020; 97:107571. [PMID: 32143150 DOI: 10.1016/j.jmgm.2020.107571] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 01/26/2020] [Accepted: 02/19/2020] [Indexed: 12/22/2022]
Abstract
The amyloid-β (Aβ) aggregation in the brain has been associated with the development of Alzheimer's disease (AD). The previous studies have reported that Piedmont mutation (L34V) increases the rate of Aβ40 aggregation. However, the underlying molecular mechanism of the effect of L34V mutation on Aβ40 structure, dynamics, and aggregation remains largely unclear. In the present study, molecular dynamics (MD) simulations were performed to elucidate the effect of L34V mutation on the structural changes and conformational dynamics of Aβ40. The secondary structure analysis highlight that L34V mutation enhances Aβ40 self-assembly due to the formation of aggregation-prone β-sheet structure at the C-terminus of Aβ40 monomeric structure. The higher probability of Asp23-Lys28 salt bridge interaction in Aβ40(L34V) leads to aggregation prone β-sheet conformations, which has the potential to increase the fibril formation rate. The free energy landscape (FEL) analysis depict a sampling of coil conformation in the free energy minima of Aβ40, whereas the aggregation-prone β-sheet conformation was observed at the C-terminal region of Aβ40(L34V) in the minimum energy conformations extracted from FEL of Aβ40(L34V). MD simulations, in agreement with experiment, highlight that L34V mutation increases Aβ40 aggregation as the sampling of the aggregation-prone β-sheet conformation substantially increased. Overall, MD simulations provided atomic level details into the increased fibril formation tendency upon L34V mutation and physical insights into the L34V-mediated conformational as well as structural changes in Aβ40.
Collapse
Affiliation(s)
- Rajneet Kaur Saini
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, 140406, Punjab, India
| | - Hema Thakur
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, 147004, Punjab, India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, 147004, Punjab, India.
| |
Collapse
|
20
|
Platts JA. Quantum chemical molecular dynamics and metadynamics simulation of aluminium binding to amyloid-β and related peptides. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191562. [PMID: 32257321 PMCID: PMC7062105 DOI: 10.1098/rsos.191562] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 12/10/2019] [Indexed: 06/11/2023]
Abstract
We report semi-empirical tight-binding simulations of the interaction between Al(III) and biologically relevant peptides. The GFN2-XTB method is shown to accurately reproduce previously reported and density functional theory (DFT)-calculated geometries of model systems. Molecular dynamics simulations based on this method are able to sample peptide flexibility over timescales of up to nanoseconds, but these timescales are insufficient to explore potential changes in metal-peptide binding modes. To achieve this, metadynamics simulations using root mean square deviation as a collective variable were employed. With suitably chosen biasing potentials, these are able to efficiently explore diverse coordination modes, for instance, through Glu and/or Asp residues in a model peptide. Using these methods, we find that Al(III) binding to the N-terminal sequence of amyloid-β is highly fluxional, with all acidic sidechains and several backbone oxygens participating in coordination. We also show that such simulations could provide a means to predict a priori possible binding modes as a precursor to longer, atomistic simulations.
Collapse
|