Molecular Docking as a Promising Predictive Model for Silver Nanoparticle-Mediated Inhibition of Cytochrome P450 Enzymes

Wasukan, Nootcharin; Kuno, Mayuso; Maniratanachote, Rawiwan

doi:10.1021/acs.jcim.9b00572

Cited by 27 publications

(17 citation statements)

References 57 publications

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“…Molecular docking study showed that SSd displayed a high binding energy of −11.3 kcal/mol. It has been reported that the amino acid residues of Phe57, Phe108, Ile120, Leu211, Phe241, Ile301, Phe304, Ile369, Leu373, Arg105, Leu364, Arg365, Leu366, Phe367, Pro368, Ala370, Met371, Arg372 and Glu374 in CYP3A4 played a key role in ligand binding 38‐44 . Another study suggested that Phe57, Arg105, Arg106, Phe108, Phe215, Met371, Arg372, Leu373, Glu374 and Arg375 were involved in interaction between sauchinone and CYP3A4 protein 45 .…”

Section: Discussionmentioning

confidence: 98%

Effects of saikosaponin‐d on CYP3A4 in HepaRG cell and protein‐ligand docking study

Tang

Wei

et al. 2021

Basic Clin Pharma Tox

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Saikosaponin‐d (SSd) is a major bioactive triterpenoid saponin extracted from Bupleurum, which has anti‐inflammatory, anticancer, antioxidative and anti‐hepatic fibrosis effects. Due to the effects of Bupleurum‐related formulations on cytochrome P450 (CYPs) expression still remain unclear, the combination therapies involved formulations containing Bupleurum may sometimes lead to unexpected drug‐drug interactions in clinical practice. These interactions can limit the clinical applications of related formulations. In this study, we tried to explore the effects of SSd on CYP3A4 mRNA, protein expression and the enzyme activity in HepaRG cells by real‐time quantitative reverse transcription polymerase chain reaction (RT‐qPCR), Western blot (WB) and HPLC method, respectively. The interaction between SSd and CYP3A4 was analysed by molecular docking. HepaRG cells were cultured with different concentrations of SSd (0.5, 1, 5 and 10 μmol/L) for 72 hours. It is revealed that SSd can inhibit CYP3A4 mRNA and its protein expression, and also the enzyme activity. Molecular docking study demonstrated that SSd can bind to several key active sites of amino acid residues of CYP3A4 protein with hydrogen bonds and hydrophobic interactions. Thus, drug‐drug interactions resulted by SSd inhibiting CYP3A4 need attention when formulations containing SSd or Bupleurum are co‐administrated with drugs metabolized by CYP3A4.

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Section: Discussionmentioning

confidence: 98%

Effects of saikosaponin‐d on CYP3A4 in HepaRG cell and protein‐ligand docking study

Tang

Wei

et al. 2021

Basic Clin Pharma Tox

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“…For instance, cytochrome P450 (CYP) is an important enzyme system for drug metabolism. Hence, molecular docking approaches can be applied to NP and CYP enzymes in order to estimate the molecular interactions of the proteinligand complex on the basis of its 3D structure [76]. Inhibition of the CYP enzyme by co-administered drugs is clinically significant in terms of drug−drug interactions, which may reduce drug efficacy or increase toxicity [77][78][79].…”

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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“…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%

“…2]. The proteinligand complex was obtained by Chimera v.1.6.2 14 and PyMOL v.1.3 15 for visual analyses. Ligplot v.1.4.5 program showed the ligand interaction plots of protein-ligand complexes.…”

Section: In Silico Studiesmentioning

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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Molecular Docking as a Promising Predictive Model for Silver Nanoparticle-Mediated Inhibition of Cytochrome P450 Enzymes

Cited by 27 publications

References 57 publications

Effects of saikosaponin‐d on CYP3A4 in HepaRG cell and protein‐ligand docking study

Effects of saikosaponin‐d on CYP3A4 in HepaRG cell and protein‐ligand docking study

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

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

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