Composition and surface chemistry engineering of graphene grafting chitosan for stimuli-responsive cancer therapy: An in-silico study

Dahri, Mohammad; Abolmaali, Samira Sadat; Abedanzadeh, Mozhgan; Salmanpour, Mohsen; Maleki, Reza

doi:10.1016/j.imu.2021.100627

Cited by 3 publications

(2 citation statements)

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“…Simulation boxes for these systems were 20 × 20 × 20 nm. For docking simulations, rst, the AutoDock Tool-1.5.6 and the gasteiger charge were added to the spike protein PDB le, and polar hydrogen was added to the ACE2 PDB le 42 .…”

Section: Methodsmentioning

confidence: 99%

Metal-Organic Frameworks (MOFs); A Promising Approach to Combat SARS-CoV-2

Dahri

Sadeghi

Abolmaali

2022

Preprint

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The COVID-19 causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has a critical surface protein called spike protein (S protein), which is the target of many vaccines and drugs developments. Among non-structural proteins of SARS-CoV-2, main protease (Mpro) has drawn much attention to itself for designing antiviral drugs since it is very crucial for the virus replication in host cells. In the first part of the present study, the application of metal-organic frameworks (MOFs), one of the developing nanomaterials in the deformation and consequently inhibition of S protein binding to the receptor, angiotensin-converting enzyme 2 (ACE 2), is investigated. In this line, various S protein inhibitors were designed virtually, including ZIF, UIO, and IRMOF that their interactions with S protein and were investigated using molecular dynamics (MD) simulation. The results revealed that ZIF is the best candidate among the investigated MOFs with the least amount of energy interference with S protein. In the second part, the interaction of three-dimensional (3D) MOFs (such as ZIF, IRMOF, and HKUST) with SARS-CoV-2 Mpro was investigated. HKUST had the most potent interaction with Mpro and showed more promise in deforming this protein's secondary structure among all materials tested. Furthermore, we investigated the interaction of HKUST-OH with Mpro to determine the effect of functionalization. The findings of this study could be used in future studies to introduce bioconjugates of MOFs and biological molecules (e.g., antibody or nanobody) or to use MOFs as carriers for antiviral drug delivery.

show abstract

Section: Methodsmentioning

confidence: 99%

Metal-Organic Frameworks (MOFs); A Promising Approach to Combat SARS-CoV-2

Dahri

Sadeghi

Abolmaali

2022

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Simulation boxes for these systems were 20 × 20 × 20 nm. For docking simulations, first, the AutoDock Tool-1.5.6 and the gasteiger charge were added to the spike protein PDB file, and polar hydrogen was added to the ACE2 PDB file 40 . Then the files were saved in pdbqt format.…”

Section: Methodsmentioning

confidence: 99%

A computational study of metal–organic frameworks (MOFs) as potential nanostructures to combat SARS-CoV-2

Dahri

Sadeghi

Abolmaali

2022

Sci Rep

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The COVID-19 causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has a critical surface protein called spike protein (S protein), which is the target of many vaccines and drugs developments. Among non-structural proteins of SARS-CoV-2, main protease (Mpro) has drawn much attention to itself for designing antiviral drugs since it is very crucial for the virus replication in host cells. In the first part of the present study, the application of metal–organic frameworks (MOFs), one of the developing nanomaterials in the deformation and consequently inhibition of S protein binding to the receptor, angiotensin-converting enzyme 2 (ACE 2), is investigated. In this line, various S protein inhibitors were designed virtually, including ZIF, UIO, and IRMOF that their interactions with S protein and were investigated using molecular dynamics (MD) simulation. The results revealed that ZIF is the best candidate among the investigated MOFs with the least amount of energy interference with S protein. In the second part, the interaction of three-dimensional (3D) MOFs (such as ZIF, IRMOF, and HKUST) with SARS-CoV-2 Mpro was investigated. HKUST had the most potent interaction with Mpro and showed more promise in deforming this protein's secondary structure among all materials tested. Furthermore, we investigated the interaction of HKUST-OH with Mpro to determine the effect of functionalization. The findings of this study could be used in future studies to introduce bioconjugates of MOFs and biological molecules (e.g., antibody or nanobody) or to use MOFs as carriers for antiviral drug delivery.

show abstract