Interaction of nanoparticles with biological macromolecules: a review of molecular docking studies

Abdelsattar, Abdallah S.; Dawoud, Alyaa; Helal, Mohamed A.

doi:10.1080/17435390.2020.1842537

Cited by 59 publications

(48 citation statements)

References 235 publications

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“…Additionally, these models can be used in collaboration with in vitro experiments for estimating toxicological properties in the development of novel nanomaterials. As another example, molecular docking has also been used to determine the potential toxicity of different types of NPs with biological macromolecules, including CuO, TiO 2 , Fe 3 O 4 , Au, Ag, ZnO, Mn 2 O 3 , and Fe 3 O 4 [80]. Hence, docking analysis between NPs and biological molecules has gained increased attention in the field of nanotoxicology as an alternative method that is able to predict potential toxicity [81].…”

Section: Molecular Dockingmentioning

confidence: 99%

Current Strategies in Assessment of Nanotoxicity: Alternatives to In Vivo Animal Testing

Huang

Lee

Hsu

et al. 2021

IJMS

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Millions of experimental animals are widely used in the assessment of toxicological or biological effects of manufactured nanomaterials in medical technology. However, the animal consciousness has increased and become an issue for debate in recent years. Currently, the principle of the 3Rs (i.e., reduction, refinement, and replacement) is applied to ensure the more ethical application of humane animal research. In order to avoid unethical procedures, the strategy of alternatives to animal testing has been employed to overcome the drawbacks of animal experiments. This article provides current alternative strategies to replace or reduce the use of experimental animals in the assessment of nanotoxicity. The currently available alternative methods include in vitro and in silico approaches, which can be used as cost-effective approaches to meet the principle of the 3Rs. These methods are regarded as non-animal approaches and have been implemented in many countries for scientific purposes. The in vitro experiments related to nanotoxicity assays involve cell culture testing and tissue engineering, while the in silico methods refer to prediction using molecular docking, molecular dynamics simulations, and quantitative structure–activity relationship (QSAR) modeling. The commonly used novel cell-based methods and computational approaches have the potential to help minimize the use of experimental animals for nanomaterial toxicity assessments.

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Section: Molecular Dockingmentioning

confidence: 99%

Current Strategies in Assessment of Nanotoxicity: Alternatives to In Vivo Animal Testing

Huang

Lee

Hsu

et al. 2021

IJMS

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“…4IUG was used for crystal structure of β-galactosidase. Dock v.6.5 software 13 confirmed the probe and the region around 10 A° of galactose [Fig. 2].…”

Section: In Silico Studiesmentioning

confidence: 97%

“…ChEBI (Chemical Entities of Biological Interest (https://www.ebi.ac.uk/chebi/) was used to obtain the 3-D structure of MgO-NPs with ChEBI ID 36973. Dock v.6.5 was used for docking [13][14][15] .…”

Section: In Silico Interaction Of Aspergillus Oryzae β-Galactosidase With Mgo-npsmentioning

confidence: 99%

Future Clinical Application of β-galactosidase Stabilized by Magnesium oxide Nanoparticles

Alshanberi

Ansari

2021

Orient. J. Chem

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The present study demonstrates the application of freshly prepared neem leaf extract as a reducing agent for synthesizing magnesium oxide nanoparticles (MgO-NPs). In silico interaction of Aspergillus oryzae β-galactosidase with MgO-NPs was observed by using molecular docking program Dock v.6.5 while the visual analyses and illustration of protein–ligand complex were investigated by utilizing chimera v.1.6.2 and PyMOL v.1.3 softwares. The prepared nanomatrix provided 83% immobilization yield, and broadened the biocatalytic activity of immobilized β-galactosidase at higher pH and temperature ranges. Immobilized β-galactosidase exhibited greater activity even at 5.0% galactose concentration as compared to the soluble enzyme under similar experimental conditions. Hence, the use of green nanotechnology makes the process inexpensive, and therefore, immobilization of these enzymes on such nanoparticles can help to recover the enzyme, which ultimately decreases the cost of process.

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“…112 Molecular modelling techniques, density functional theory calculations, kinetic mean field models and molecular dynamic simulations have been employed to achieve an understanding of the dynamics and interaction of nanoparticles within biological systems. 113 Recently, Mishra et al utilized molecular docking to analyse the interactions between silver nanoparticles and the digestive enzymes of termites and gut-associated microbes. The study revealed the potential prospects of fabricated nanopesticides for pest management in the agricultural and forestry sectors.…”

Section: Additional Benefits Provided By the Computational Modeling Of Nanopesticidesmentioning

confidence: 99%

The framework of nanopesticides: a paradigm in biodiversity

et al. 2021

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Interaction of nanoparticles with biological macromolecules: a review of molecular docking studies

Cited by 59 publications

References 235 publications

Current Strategies in Assessment of Nanotoxicity: Alternatives to In Vivo Animal Testing

Current Strategies in Assessment of Nanotoxicity: Alternatives to In Vivo Animal Testing

Future Clinical Application of β-galactosidase Stabilized by Magnesium oxide Nanoparticles

The framework of nanopesticides: a paradigm in biodiversity

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