In Silico Analysis of Peptide Potential Biological Functions

Kalmykova, Svetlana; Арапиди, Г. П.; Urban, Anatoly S.; Osetrova, Maria; Gordeeva, Veronika; Иванов, В. Т.; Govorun, Vadim M.

doi:10.1134/s106816201804009x

Cited by 11 publications

(4 citation statements)

References 201 publications

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“…Recently, bioinformatic databases and software represent basic tools in the research on biologically active peptides, e.g., those derived from food. Their role was described in several reviews [1,2,3,4,5,6,7]. The BIOPEP-UWM™ (formerly BIOPEP) database of bioactive peptides is one of these tools.…”

Section: Introductionmentioning

confidence: 99%

BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities

Minkiewicz

Iwaniak

Darewicz

2019

IJMS

579

397

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The BIOPEP-UWM™ database of bioactive peptides (formerly BIOPEP) has recently become a popular tool in the research on bioactive peptides, especially on these derived from foods and being constituents of diets that prevent development of chronic diseases. The database is continuously updated and modified. The addition of new peptides and the introduction of new information about the existing ones (e.g., chemical codes and references to other databases) is in progress. New opportunities include the possibility of annotating peptides containing D-enantiomers of amino acids, batch processing option, converting amino acid sequences into SMILES code, new quantitative parameters characterizing the presence of bioactive fragments in protein sequences, and finding proteinases that release particular peptides.

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Section: Introductionmentioning

confidence: 99%

BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities

Minkiewicz

Iwaniak

Darewicz

2019

IJMS

579

397

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show abstract

“…In this regard, bioinformatic studies, such as docking techniques, present an economical, reliable, and straightforward approach to identify candidate ligands against key proteins involved in the process of adipogenesis. Databases of BAPs are reported, providing information necessary to construct new algorithms for predicting biological functions [ 22 , 23 ]. This article provides molecular evidence for the potential ligand bioactivity of peptides derived from the in silico hydrolysis of rice proteins, specifically glutelin and prolamin fractions, that showed high affinity for the antiadipogenic areas of the PPARγ receptor.…”

Section: Introductionmentioning

confidence: 99%

In Silico Identification of Peptides with PPARγ Antagonism in Protein Hydrolysate from Rice (Oryza sativa)

et al. 2023

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At least half the population in industrialized countries suffers from obesity due to excessive accumulation of adipose tissue. Recently, rice (Oryza sativa) proteins have been considered valuable sources of bioactive peptides with antiadipogenic potential. In this study, the digestibility and bioaccessibility in vitro of a novel protein concentrate (NPC) from rice were determined through INFOGEST protocols. Furthermore, the presence of prolamin and glutelin was evaluated via SDS-PAGE, and their potential digestibility and the bioactivity of ligands against peroxisome proliferator-activated receptor gamma (PPARγ) were explored by BIOPEP UWM and HPEPDOCK. For the top candidates, molecular simulations were conducted using Autodock Vina to evaluate their binding affinity against the antiadipogenic region of PPARγ and their pharmacokinetics and drug-likeness using SwissADME. Simulating gastrointestinal digestion showed a recovery of 43.07% and 35.92% bioaccessibility. The protein banding patterns showed the presence of prolamin (57 kDa) and glutelin (12 kDa) as the predominant proteins in the NPC. The in silico hydrolysis predicts the presence of three and two peptide ligands in glutelin and prolamin fraction, respectively, with high affinity for PPARγ (≤160). Finally, the docking studies suggest that the prolamin-derived peptides QSPVF and QPY (−6.38 & −5.61 kcal/mol, respectively) have expected affinity and pharmacokinetic properties to act as potential PPARγ antagonists. Hence, according to our results, bioactive peptides resulting from NPC rice consumption might have an antiadipogenic effect via PPARγ interactions, but further experimentation and validation in suitable biological model systems are necessary to gain more insight and to provide evidence to support our in silico findings.

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“…For example, Peptide Ranker is used for evaluating the peptide bioactivity, which scores the peptide bioactivity based on amino acids (AA) composition and rankings. Scores >0.5 indicate potential bioactivities, when higher scores manifested higher probability and lower false positive (Kalmykova et al ., 2018).…”

Section: Introductionmentioning

confidence: 99%

Identification of peptides from protease‐fermented milk protein and immunomodulatory effect in vivo against lipopolysaccharide‐induced inflammation

Xie

Zhang

2022

Int J of Food Sci Tech

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Food-derived peptides exhibit potential immunomodulatory effects and become popular functional ingredients in food industry. However, the in vivo effect varies from in vitro while the optimal utilisation content remains unclear. This study aimed to identify novel peptides from protease-facilitated fermentation, to evaluate their immunomodulatory effect and effect-dose relationship in vivo. Totally 2045 peptides were screened by liquid chromatography mass spectrometry (LC-MS/MS), and in silico methods were applied to predict the potential bioactivity through Peptide Ranker, GRAVY Calculator and PepDraw. In vivo assay indicated that 200 mg kg −1 milk-derived peptides showed the optimal regulation on lipopolysaccharide-induced inflammation by enhancing the immune function of spleen and regulating immunoglobulin and cytokine production. These peptides contributed to the prevention of inflammation through the oral route and could be further applied in functional food development.

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In Silico Analysis of Peptide Potential Biological Functions

Cited by 11 publications

References 201 publications

BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities

BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities

In Silico Identification of Peptides with PPARγ Antagonism in Protein Hydrolysate from Rice (Oryza sativa)

Identification of peptides from protease‐fermented milk protein and immunomodulatory effect in vivo against lipopolysaccharide‐induced inflammation

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