Integration of Molecular Docking Analysis and Molecular Dynamics Simulations for Studying Food Proteins and Bioactive Peptides

Vidal-Limón, Abraham; Aguilar-Toalá, José E.; Liceaga, Andrea M.

doi:10.1021/acs.jafc.1c06110

Cited by 148 publications

(65 citation statements)

References 94 publications

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“…The procedure of molecular docking was based on the method adopted by Vidal-Limon et al ( 29 ), with a slight modification. The crystal structures of EPCR (PDB ID: 1LQV) ( 30 ), CBR2 (PDB ID: 6PT0) ( 31 ), and ERα (PDB ID: 1X7R) ( 32 ) were obtained from the Protein Data Bank (PDB).…”

Section: Methodsmentioning

confidence: 99%

Identification of Di/Tripeptide(s) With Osteoblasts Proliferation Stimulation Abilities of Yak Bone Collagen by in silico Screening and Molecular Docking

Chen

Guo²,

Liu³

et al. 2022

Front. Nutr.

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Endothelial protein C receptor (EPCR), cannabinoid receptor 2 (CBR2), and estrogen receptor α (ERα) play vital roles in osteoblasts proliferation. Also, collagen peptides have osteoblasts proliferation stimulation abilities, and di/tri-peptides could be absorbed by the intestine more easily. This study obtained three di/tripeptides with potential osteoblasts proliferation stimulation abilities of yak bone collagen, namely, MGF, CF, and MF, by in silico screening. Results suggested that these three peptides exhibited good absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties. They also had strong affinities with EPCR, CBR2, and ERα, and the total -CDOCKER energy (-CE) values were 150.9469, 113.1835, and 115.3714 kcal/mol, respectively. However, further Cell Counting Kit-8 (CCK-8) assays indicated that only MGF could significantly (P < 0.05) stimulate osteoblasts proliferation at 0.3 mg/ml. At the same time, the proliferating index (PI) of the osteoblasts treated with MGF increased significantly (P < 0.05), and the alkaline phosphatase (ALP) activity decreased highly significantly (P < 0.01). In summary, MGF exhibited the potential to be an effective treatment for osteoporosis.

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Section: Methodsmentioning

confidence: 99%

Identification of Di/Tripeptide(s) With Osteoblasts Proliferation Stimulation Abilities of Yak Bone Collagen by in silico Screening and Molecular Docking

Chen

Guo²,

Liu³

et al. 2022

Front. Nutr.

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“…In recent years, there has been an increased interest in finding bioactive peptides that can prevent the risk of chronic diseases and/or boost the immune system. The advancement of peptidomics and bioinformatics in food science has enabled integrated studies to be carried out for the rapid development of food-derived bioactive peptides [1]. Moreover, the application of an integrated approach in the study of bioactive peptides allows for their production to be optimized, leads to the discovery of peptides of specific interest, and contributes to the understanding of the mechanism of action between bioactive peptides and human target receptors [2].…”

Section: Introductionmentioning

confidence: 99%

Multifunctional Analysis of Chia Seed (Salvia hispanica L.) Bioactive Peptides Using Peptidomics and Molecular Dynamics Simulations Approaches

Aguilar-Toalá

Vidal-Limón

Liceaga

2022

IJMS

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Chia seed peptides (CSP) can be a source of multifunctional biopeptides to treat non-communicable diseases. However, interactions and binding affinity involved in targeting specific receptors remains unexplored. In this study, molecular simulation techniques were used as virtual screening of CSP to determine drug-like candidates using a multi-target-directed ligand approach. CSP fraction with the best bioactivities in vitro was sequenced. Then, a prediction model was built using physicochemical descriptors (hydrophobicity, hydrophilicity, intestinal stability, antiangiogenic, antihypertensive, and anti-inflammatory) to calculate potential scores and rank possible biopeptides. Furthermore, molecular dynamics simulations (MDS) and ensemble molecular docking analysis were carried out using four human protein targets (ACE, angiotensin converting enzyme; VEGF, vascular endothelial growth factor; GLUC, glucocorticoid and MINC, mineralocorticoid receptors). Five known-sequence peptides (NNVFYPF, FNIVFPG, SRPWPIDY, QLQRWFR, GSRFDWTR) and five de novo peptides (DFKF, DLRF, FKAF, FRSF, QFRF) had the lowest energy score and higher affinity for ACE and VEGF. The therapeutic effects of these selected peptides can be related to the inhibition of the enzymes involved in angiogenesis and hypertension, due to formation of stable complexes with VEGF and ACE binding sites, respectively. The application of MDS is a good resource for identifying bioactive peptides for future experimental validation.

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“…Recently, the importance of the computational approach has been highlighted in, for example, the search for anti-SARS-CoV2 peptides [4][5][6]. The in silico approach includes molecular docking studies of peptides, which appear to be an emerging tool for predicting the bioactivity of food peptides [4,[6][7][8][9]. Its application for educational purposes has been recently described by Khan and coworkers [10].…”

Section: Introductionmentioning

confidence: 99%

BIOPEP-UWM Virtual—A Novel Database of Food-Derived Peptides with In Silico-Predicted Biological Activity

2022

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The novel BIOPEP-UWM Virtual database is designed as a repository of peptide sequences whose bioactivity or taste information was the result of in silico predictions. It is a tool complementary to the existing BIOPEP-UWM database summarizing the results of experimental data on bioactive peptides. The layout and organization of the new database are identical to those of the existing BIOPEP-UWM database of bioactive peptides. The peptide data record includes the following information: name; sequence and function information (understood as information about the predicted target biomacromolecule); bibliographic data with the reference paper describing the peptide; additional information, including the peptide structure, annotated using chemical codes as well as the specification of the method used for bioactivity prediction; information about other activities discovered experimentally or predicted using computational methods; peptide taste (if available); and a database reference tab providing information about compound annotations in other databases (if available).

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Integration of Molecular Docking Analysis and Molecular Dynamics Simulations for Studying Food Proteins and Bioactive Peptides

Cited by 148 publications

References 94 publications

Identification of Di/Tripeptide(s) With Osteoblasts Proliferation Stimulation Abilities of Yak Bone Collagen by in silico Screening and Molecular Docking

Identification of Di/Tripeptide(s) With Osteoblasts Proliferation Stimulation Abilities of Yak Bone Collagen by in silico Screening and Molecular Docking

Multifunctional Analysis of Chia Seed (Salvia hispanica L.) Bioactive Peptides Using Peptidomics and Molecular Dynamics Simulations Approaches

BIOPEP-UWM Virtual—A Novel Database of Food-Derived Peptides with In Silico-Predicted Biological Activity

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