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Peng B, Xu S, Liang Y, Dong X, Sun Y. Effect of Bacterial Amyloid Protein Phenol-Soluble Modulin Alpha 3 on the Aggregation of Amyloid Beta Protein Associated with Alzheimer's Disease. Biomimetics (Basel) 2023; 8:459. [PMID: 37887589 PMCID: PMC10604207 DOI: 10.3390/biomimetics8060459] [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: 08/20/2023] [Revised: 09/24/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
Since the proposal of the brainstem axis theory, increasing research attention has been paid to the interactions between bacterial amyloids produced by intestinal flora and the amyloid β-protein (Aβ) related to Alzheimer's disease (AD), and it has been considered as the possible cause of AD. Therefore, phenol-soluble modulin (PSM) α3, the most virulent protein secreted by Staphylococcus aureus, has attracted much attention. In this work, the effect of PSMα3 with a unique cross-α fibril architecture on the aggregation of pathogenic Aβ40 of AD was studied by extensive biophysical characterizations. The results proposed that the PSMα3 monomer inhibited the aggregation of Aβ40 in a concentration-dependent manner and changed the aggregation pathway to form granular aggregates. However, PSMα3 oligomers promoted the generation of the β-sheet structure, thus shortening the lag phase of Aβ40 aggregation. Moreover, the higher the cross-α content of PSMα3, the stronger the effect of the promotion, indicating that the cross-α structure of PSMα3 plays a crucial role in the aggregation of Aβ40. Further molecular dynamics (MD) simulations have shown that the Met1-Gly20 region in the PSMα3 monomer can be combined with the Asp1-Ala2 and His13-Val36 regions in the Aβ40 monomer by hydrophobic and electrostatic interactions, which prevents the conformational conversion of Aβ40 from the α-helix to β-sheet structure. By contrast, PSMα3 oligomers mainly combined with the central hydrophobic core (CHC) and the C-terminal region of the Aβ40 monomer by weak H-bonding and hydrophobic interactions, which could not inhibit the transition to the β-sheet structure in the aggregation pathway. Thus, the research has unraveled molecular interactions between Aβ40 and PSMα3 of different structures and provided a deeper understanding of the complex interactions between bacterial amyloids and AD-related pathogenic Aβ.
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Affiliation(s)
| | | | | | - Xiaoyan Dong
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China; (B.P.); (S.X.); (Y.L.)
| | - Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China; (B.P.); (S.X.); (Y.L.)
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Miri-Jahromi A, Mohammady Maklavany D, Rouzitalab Z, Ghaemi Khiavi S, Ghasemy E, Khedri M, Rezvantalab S, Sharafinia S, Rashidi A, Maleki R. Engineering of two-dimensional monolayers to phenolic compounds removal from wastewater: An experimental and computational insight. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Karimi K, Rahsepar M. Optimization of the Urea Removal in a Wearable Dialysis Device Using Nitrogen-Doped and Phosphorus-Doped Graphene. ACS OMEGA 2022; 7:4083-4094. [PMID: 35155902 PMCID: PMC8829914 DOI: 10.1021/acsomega.1c05495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/12/2022] [Indexed: 05/31/2023]
Abstract
Dialysis has been recognized as an essential treatment for end-stage renal disease (ESRD). This therapy, however, suffers from several limitations leading to numerous complications in the patients. As dialysis cannot completely substitute healthy kidney functions, the health condition of an ESRD patient is ultimately affected. Wearable artificial kidney (WAK) can resolve the restrictions of blood purification by the dialysis method. However, absorbing large amounts of urea produced in the body is one of the main challenges of these WAK and overcoming this is necessary to improve both functionality and footprint of the device. This study investigates the adsorption capabilities of N- and P-doped graphene nanosorbents for the first time by using molecular dynamic simulation. Urea removal on carbon nanosheets was simulated with different percentages of phosphorus and nitrogen dopants along with the pristine graphene. Specifically, the effects of interaction energy, adsorption percentage, gyration radius, hydrogen bonding, and other molecular dynamic analyses on urea removal were also investigated. The results from this study match well with the existing research, demonstrating the accuracy of the model. The results further suggest that graphene nanosheets doped by 10% nitrogen are likely the most effective in removing urea given that it is associated with the maximum radial distribution function (RDF), the maximum reduction in gyration radius, a high number of hydrogen bonds, and the most negative adsorption energy. This molecular study offers attractive suggestions for the novel adsorbents of artificial kidney devices and paves the way for the development of novel and enhanced urea adsorbents.
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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.
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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
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Miri Jahromi A, Zandi P, Khedri M, Ghasemy E, Maleki R, Tayebi L. Molecular insight into optimizing the N- and P-doped fullerenes for urea removal in wearable artificial kidneys. JOURNAL OF MATERIALS SCIENCE. MATERIALS IN MEDICINE 2021; 32:49. [PMID: 33891249 PMCID: PMC8065003 DOI: 10.1007/s10856-021-06525-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 04/01/2021] [Indexed: 06/12/2023]
Abstract
Urea is the result of the breakdown of proteins in the liver, the excess of which circulates in the blood and is adsorbed by the kidneys. However, in the case of kidney diseases, some products, specifically urea, cannot be removed from the blood by the kidneys and causes serious health problems. The end-stage renal disease (ESRD) patients are not able to purify their blood, which endangers their life. ESRD patients require dialysis, a costly and difficult method of urea removal from the blood. Wearable artificial kidneys (WAKs) are consequently designed to remove the waste from blood. Regarding the great amount of daily urea production in the body, WAKs should contain strong and selective urea adsorbents. Fullerenes-which possess fascinating chemical properties-have been considered herein to develop novel urea removal adsorbents. Molecular dynamics (MD) has enabled researchers to study the interaction of different materials and can pave the way toward facilitating the development of wearable devices. In this study, urea adsorption by N-doped fullerenes and P-doped fullerenes were assessed through MD simulations. The urea adsorption was simulated by five samples of fullerenes, with phosphorous and different nitrogen dopant contents. For comparing the urea adsorption capacity in the performed simulations, detailed characteristics-including the energy analysis, radius of gyration, radial distribution function (RDF), root-mean-square fluctuation (RMSD), and H-bond analyses were investigated. It had been determined that the fullerene containing 8% nitrogen-with the highest reduction in the radius of gyration, the maximum RDF, a high adsorption energy, and a high number of hydrogen bonds-adsorbs urea more efficiently.
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Affiliation(s)
- Ahmad Miri Jahromi
- Computational Biology and Chemistry Group (CBCG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Pegah Zandi
- School of Metallurgy and Materials Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Mohammad Khedri
- Computational Biology and Chemistry Group (CBCG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Ebrahim Ghasemy
- Nanotechnology Department, School of New Technologies, Iran University of Science and Technology, 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.
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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.
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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
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