Critical c-Met-inhibitor interactions resolved from molecular dynamics simulations of different c-Met complexes

Damghani, Tahereh; Sedghamiz, Tahereh; Sharifi, Shahrzad; Pirhadi, Somayeh

doi:10.1016/j.molstruc.2019.127456

Cited by 21 publications

(10 citation statements)

References 30 publications

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“…Thus, the best conformation was selected on the basis of bonding energy (vdW and electrostatic interaction energy) or binding affinity between three interacting systems. The total binding free energy is an average of vdW and electrostatic interaction energies [ 40 , 41 ].…”

Section: Resultsmentioning

confidence: 99%

Atomistic insight into 2D COFs as antiviral agents against SARS-CoV-2

Jahromi

Solhjoo

Ghasemi

et al. 2022

Materials Chemistry and Physics

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Section: Resultsmentioning

confidence: 99%

Atomistic insight into 2D COFs as antiviral agents against SARS-CoV-2

Jahromi

Solhjoo

Ghasemi

et al. 2022

Materials Chemistry and Physics

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“…Energy in molecular dynamics simulations may help in investigating and analyzing the van der Waals and electrostatic bonds. The greater (i.e., more negative) the absolute energy of the van der Waals and the electrostatic bonds, the stronger the interactions in a given reaction simulation. − The total energy of the van der Waals and electrostatic bonding is also an indicator of the urea adsorption intensity. Strong interactions between the adsorbent and urea may hence be associated with higher capabilities in urea adsorption.…”

Section: Results and Discussionmentioning

confidence: 99%

“…Strong interactions between the adsorbent and urea may hence be associated with higher capabilities in urea adsorption. Here, the energy analysis was carried out by the mmpbsa software. − The van der Waals and electrostatic energies were calculated for N2, N5, N8, N15, N10, PC, and pristine graphene. The sum of the energies was also averaged during the simulation period.…”

Section: Results and Discussionmentioning

confidence: 99%

Optimization of the Urea Removal in a Wearable Dialysis Device Using Nitrogen-Doped and Phosphorus-Doped Graphene

Karimi

Rahsepar

2022

ACS Omega

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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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“…The energies from the electrostatic bonds and vdW bonds in the simulations for Fullerene-N5, Fullerene-N8, Fullerene-N10, Fullerene-N15, Fullerene-N25, Fullerene-P, and Fullerene are calculated by the mmpbsa [57,58] software. The sum of the energies resulting from the intermolecular bonds is a good indicator for the intensity of urea adsorption in the simulations performed in this paper [59][60][61].…”

Section: Intermolecular Bonds By Energy Analysismentioning

confidence: 94%

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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Critical c-Met-inhibitor interactions resolved from molecular dynamics simulations of different c-Met complexes

Cited by 21 publications

References 30 publications

Atomistic insight into 2D COFs as antiviral agents against SARS-CoV-2

Atomistic insight into 2D COFs as antiviral agents against SARS-CoV-2

Optimization of the Urea Removal in a Wearable Dialysis Device Using Nitrogen-Doped and Phosphorus-Doped Graphene

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

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