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Shamsa Sharifi, Mehrnoosh Khaleghian. Study of the Adsorption Antioxidant Compound Malva on the BNNT(9,9-9): An Investigation based on DFT Method. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2022. [DOI: 10.1134/s1990793122010146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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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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Marvi PK, Amjad-Iranagh S, Halladj R. Molecular Dynamics Assessment of Doxorubicin Adsorption on Surface-Modified Boron Nitride Nanotubes (BNNTs). J Phys Chem B 2021; 125:13168-13180. [PMID: 34813340 DOI: 10.1021/acs.jpcb.1c07052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Loading therapeutic agents on nanocarriers in order to protect them during drug delivery and exclusively targeting damaged tissues has gained substantial significance in biology realms in the past decade. Boron nitride nanotubes have given a new lease on designing nano delivery systems by virtue of their unique properties. The studies are still ongoing to thoroughly identify their chemical characteristics. In this study, we probed into the efficacy of boron nitride nanotubes and the impact of their surface modification by hydroxyl and amine functional groups in interaction with an anticancer drug model, i.e., doxorubicin. Defining the altered electronic properties of the nanotubes as well as the distribution of partial charges were carried out through density functional theory calculations, following the simulation of the drug loading process via molecular dynamics algorithms. The primary outcomes are inferred from systematical energies, van der Waals and electrostatic interactions, radial distribution functions, the number of hydrogen bonds, mean square displacement, diffusion coefficients, and binding free energies. Negative values of van der Waals energies imply a rapid, exothermic adsorption process whereby the contribution of these driving forces is more dominant than electrostatic ones. Ultimately, the values of overall diffusion coefficients of drugs and binding free energies, performed by the MM/PBSA approach, corroborate that the hydroxyl and amine-functionalized nanotubes reinforce the binding strength of the complexes to an approximate extent.
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Affiliation(s)
- Parham Khoshbakht Marvi
- Department of Chemical Engineering, Amirkabir University of Technology, Tehran 15875-4413, Iran
| | - Sepideh Amjad-Iranagh
- Department of Materials and Metallurgical Engineering, Amirkabir University of Technology, Tehran 15875-4413, Iran
| | - Rouein Halladj
- Department of Chemical Engineering, Amirkabir University of Technology, Tehran 15875-4413, Iran
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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
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Cao Y, Khan A, Balakheyli H, Lup ANK, Ramezani Taghartapeh M, Mirzaei H, Reza Khandoozi S, Soltani A, Aghaei M, Heidari F, Sarkar SM, Albadarin AB. Penicillamine functionalized B12N12 and B12CaN12 nanocages act as potential inhibitors of proinflammatory cytokines: A combined DFT analysis, ADMET and molecular docking study. ARAB J CHEM 2021. [DOI: 10.1016/j.arabjc.2021.103200] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Mollazadeh S, Sahebkar A, Shahlaei M, Moradi S. Nano drug delivery systems: Molecular dynamic simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115823] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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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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Sohrabi S, Khedri M, Maleki R, Keshavarz Moraveji M. Molecular engineering of the last-generation CNTs in smart cancer therapy by grafting PEG-PLGA-riboflavin. RSC Adv 2020; 10:40637-40648. [PMID: 35519185 PMCID: PMC9057702 DOI: 10.1039/d0ra07500k] [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: 09/01/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
In this work, the effect of environment and additives on the self-assembly and delivery of doxorubicin (DOX) have been studied. A microfluidic system with better control over molecular interactions and high surface to volume ratio has superior performance in comparison to the bulk system. Moreover, carbon nanotube (CNT) and CNT-doped structures have a high surface area to incorporate the DOX molecules into a polymer and the presence of functional groups can influence the polymer-drug interactions. In this work, the interactions of DOX with both the polymeric complex and the nanotube structure have been investigated. For quantification of the interactions, H-bonding, gyration radius, root-mean-square deviation (RMSD), Gibbs free energy, radial distribution function (RDF), energy, and Solvent Accessible Surface Area (SASA) analyses have been performed. The most stable micelle-DOX interaction is attributed to the presence of BCN in the microfluidic system according to the gyration radius and RMSD. Meanwhile, for DOX-doped CNT interaction the phosphorus-doped CNT in the microfluidic system is more stable. The highest electrostatic interaction can be seen between polymeric micelles and DOX in the presence of BCN. For nanotube-drug interaction, phosphorus-doped carbon nanotubes in the microfluidic system have the largest electrostatic interaction with the DOX. RDF results show that in the microfluidic system, nanotube-DOX affinity is larger than that of nanotube-micelle.
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Affiliation(s)
- Somayeh Sohrabi
- Department of Chemical Engineering, Amirkabir University of Technology (Tehran Polytechnic) 424 Hafez Avenue Tehran 1591634311 Iran
| | - Mohammad Khedri
- Department of Chemical Engineering, Amirkabir University of Technology (Tehran Polytechnic) 424 Hafez Avenue Tehran 1591634311 Iran
| | - Reza Maleki
- Computational Biology and Chemistry Group (CBCG), Universal Scientific Education and Research Network (USERN) Tehran Iran
| | - Mostafa Keshavarz Moraveji
- Department of Chemical Engineering, Amirkabir University of Technology (Tehran Polytechnic) 424 Hafez Avenue Tehran 1591634311 Iran
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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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Khodabandeh R, Mohammadpour F, Zolghadr AR, Klein A. Zn capped Al2O3 and TiO2 nanoporous arrays as pH sensitive drug delivery systems: a combined experimental and simulation study. NEW J CHEM 2020. [DOI: 10.1039/d0nj02840a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
pH sensitive nanotube arrays based on Zn capped Al2O3 and TiO2 were reported for the release of vitamin C in an experimental/theoretical study using MD simulations.
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Affiliation(s)
| | | | | | - Axel Klein
- Department of Chemistry
- Shiraz University
- Shiraz
- Iran
- Department für Chemie
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