Shedding Light on Miniaturized Dialysis Using MXene 2D Materials: A Computational Chemistry Approach

Zandi, Pegah; Ghasemy, Ebrahim; Khedri, Mohammad; Rashidi, Alimorad; Maleki, Reza; Jahromi, Ahmad Miri

doi:10.1021/acsomega.0c06118

Cited by 21 publications

(24 citation statements)

References 41 publications

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“…Snapshots are provided in Figures 1A and S3.A at the initial (0 ns) and the final stage (50 ns) of the simulation to deliver a visual perception of the study. First, to assess the stability of the molecular systems, the root mean square deviations (RMSD) as criteria of the system's stability has been analyzed [51,52] . RMSD evaluates the average distance of atoms and their fluctuations in organic molecular systems (Figure S3.B).…”

Section: Resultsmentioning

confidence: 99%

β‐Amyloid Targeting with Two‐Dimensional Covalent Organic Frameworks: Multi‐Scale In‐Silico Dissection of Nano‐Biointerface

et al. 2021

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Cytotoxic aggregation of misfolded β‐amyloid (Aβ) proteins is the main culprit suspected to be behind the development of Alzheimer's disease (AD). In this study, Aβ interactions with the novel two‐dimensional (2D) covalent organic frameworks (COFs) as therapeutic options for avoiding β‐amyloid aggregation have been investigated. The results from multi‐scale atomistic simulations suggest that amine‐functionalized COFs with a large surface area (more than 1000 m2/gr) have the potential to prevent Aβ aggregation. Gibb's free energy analysis confirmed that COFs could prevent protofibril self‐assembly in addition to inhibiting β‐amyloid aggregation. Additionally, it was observed that the amine functional group and high contact area could improve the inhibitory effect of COFs on Aβ aggregation and enhance the diffusivity of COFs through the blood‐brain barrier (BBB). In addition, microsecond coarse‐grained (CG) simulations with three hundred amyloids reveal that the presence of COFs creates instability in the structure of amyloids and consequently prevents the fibrillation. These results suggest promising applications of engineered COFs in the treatment of AD and provide a new perspective on future experimental research.

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Section: Resultsmentioning

confidence: 99%

β‐Amyloid Targeting with Two‐Dimensional Covalent Organic Frameworks: Multi‐Scale In‐Silico Dissection of Nano‐Biointerface

et al. 2021

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“…OPLSA force eld [72][73][74] was used in all-atom simulations. To perform these simulations, spike proteins and 2D structures were placed in 10×10×10 nm 3 boxes.…”

Section: Methodsmentioning

confidence: 99%

Engineering of 2D Materials To Trap And Kill SARS-CoV-2: A New Insight From Multi-Microsecond Atomistic Simulations

Khedri

Maleki

Dahri

et al. 2021

Preprint

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In late 2019, coronavirus disease 2019 (COVID-19) caused severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Spike protein is one of the surface proteins of SARS-CoV-2 that is essential for its infectious function. Therefore, it received lots of attention for the preparation of antiviral drugs, vaccines, and diagnostic tools. Herein, we use computational methods of chemistry and biology to study the interaction between spike protein and its receptor in the body, angiotensin-I-converting enzyme-2 (ACE2). Additionally, the possible interaction of two-dimensional (2D) structures, including graphene, bismuthene, phosphorene, p-doped graphene, and functionalized p-doped graphene, with spike protein is investigated. The functionalized p-doped graphene nanosheets were found to interfere with spike protein better than the other tested nanomaterials. In addition, the interaction of the proposed nanosheets with the main protease (Mpro) of SARS-CoV-2 was studied. Functionalized p-doped graphene nanosheets showed more capacity to prevent the activity of Mpro. This 2D structure efficiently reduce the transmissibility and infectivity of SARS-CoV-2 by both the deformation of the spike protein and inhibiting the Mpro. The results suggest the potential use of 2D materials in a variety of prophylactic approaches, such as masks or surface coatings, and would deserve further studies in the coming years.

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“…On the other hand, the minimum value for energy value belongs to fullerene with an average value of −37.923 for the total energy. Compared to the Ti 3 C 2 OH, which is an efficient MXene developed for WAK [29], the fullerene-N8 is predicted to be better.…”

Section: Intermolecular Bonds By Energy Analysismentioning

confidence: 99%

“…and MXenes [28,29]. However, all of the used adsorbents had a low adsorption affinity and capacity, such that they could not be effective in eliminating the high urea content in the urine.…”

Section: Introductionmentioning

confidence: 99%

Molecular insight into optimizing the N- and P-doped fullerenes for urea removal in wearable artificial kidneys

Jahromi

Zandi

Khedri

et al. 2021

J Mater Sci: Mater Med

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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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Shedding Light on Miniaturized Dialysis Using MXene 2D Materials: A Computational Chemistry Approach

Cited by 21 publications

References 41 publications

β‐Amyloid Targeting with Two‐Dimensional Covalent Organic Frameworks: Multi‐Scale In‐Silico Dissection of Nano‐Biointerface

β‐Amyloid Targeting with Two‐Dimensional Covalent Organic Frameworks: Multi‐Scale In‐Silico Dissection of Nano‐Biointerface

Engineering of 2D Materials To Trap And Kill SARS-CoV-2: A New Insight From Multi-Microsecond Atomistic Simulations

Molecular insight into optimizing the N- and P-doped fullerenes for urea removal in wearable artificial kidneys

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