Prediction and analysis of antimicrobial peptides from rapeseed protein using in silico approach

Duan, Xiaojie; Zhang, Min; Chen, Fusheng

doi:10.1111/jfbc.13598

Cited by 30 publications

(30 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For instance, 93% of the hemp peptides resulting from tryptic hydrolysis was generated from the globulin-type proteins (edestin 1-3 and 7S vicilin-like protein) (Table 1). A similar trend was observed in other studies of the in silico hydrolysis of oilseed proteins [26,27]. Overall, our results suggest that the globulin-type proteins of oilseeds are prominent sources of peptides that could remain intact in the shrimp digestive tract.…”

Section: In Silico Tryptic Hydrolysis Of Oilseed Meal Proteinssupporting

confidence: 90%

Targeting PirAvp and PirBvp Toxins of Vibrio parahaemolyticus with Oilseed Peptides: An In Silico Approach

Ong

Wong

et al. 2021

Antibiotics

View full text Add to dashboard Cite

Acute hepatopancreatic necrosis disease (AHPND), caused by PirAvp- and PirBvp-releasing Vibrio parahaemolyticus strains, has resulted in massive mortality in shrimp aquaculture. Excessive use of antibiotics for AHPND management has led to antibiotic resistance, highlighting the urgency to search for alternatives. Using an in silico approach, we aimed to discover PirAvp/PirBvp-binding peptides from oilseed meals as alternatives to antibiotics. To search for peptides that remain intact in the shrimp digestive tract, and therefore would be available for toxin binding, we focused on peptides released from tryptic hydrolysis of 37 major proteins from seeds of hemp, pumpkin, rape, sesame, and sunflower. This yielded 809 peptides. Further screening led to 24 peptides predicted as being non-toxic to shrimp, fish, and humans, with thermal stability and low water solubility. Molecular docking on the 24 peptides revealed six dual-target peptides capable of binding to key regions responsible for complex formation on both PirAvp and PirBvp. The peptides (ISYVVQGMGISGR, LTFVVHGHALMGK, QSLGVPPQLGNACNLDNLDVLQPTETIK, ISTINSQTLPILSQLR, PQFLVGASSILR, and VQVVNHMGQK) are 1139–2977 Da in mass and 10–28 residues in length. Such peptides are potential candidates for the future development of peptide-based anti-AHPND agents which potentially mitigate V. parahaemolyticus pathogenesis by intercepting PirAvp/PirBvp complex formation.

show abstract

Section: In Silico Tryptic Hydrolysis Of Oilseed Meal Proteinssupporting

confidence: 90%

Targeting PirAvp and PirBvp Toxins of Vibrio parahaemolyticus with Oilseed Peptides: An In Silico Approach

Ong

Wong

et al. 2021

Antibiotics

View full text Add to dashboard Cite

show abstract

“…In comparison with toxicity prediction, 47–48% of our antioxidant peptide virtual library comprised allergenic and hemolytic peptides. In an in silico study of 26 antimicrobial peptides of rapeseed, 54% were predicted as non-allergenic and 46% allergenic [ 35 ]. This relative distribution of allergenicity and non-allergenicity resembles that observed in our virtual screening.…”

Section: Resultsmentioning

confidence: 99%

Computational Screening for the Anticancer Potential of Seed-Derived Antioxidant Peptides: A Cheminformatic Approach

et al. 2021

View full text Add to dashboard Cite

Some seed-derived antioxidant peptides are known to regulate cellular modulators of ROS production, including those proposed to be promising targets of anticancer therapy. Nevertheless, research in this direction is relatively slow owing to the inevitable time-consuming nature of wet-lab experimentations. To help expedite such explorations, we performed structure-based virtual screening on seed-derived antioxidant peptides in the literature for anticancer potential. The ability of the peptides to interact with myeloperoxidase, xanthine oxidase, Keap1, and p47phox was examined. We generated a virtual library of 677 peptides based on a database and literature search. Screening for anticancer potential, non-toxicity, non-allergenicity, non-hemolyticity narrowed down the collection to five candidates. Molecular docking found LYSPH as the most promising in targeting myeloperoxidase, xanthine oxidase, and Keap1, whereas PSYLNTPLL was the best candidate to bind stably to key residues in p47phox. Stability of the four peptide-target complexes was supported by molecular dynamics simulation. LYSPH and PSYLNTPLL were predicted to have cell- and blood-brain barrier penetrating potential, although intolerant to gastrointestinal digestion. Computational alanine scanning found tyrosine residues in both peptides as crucial to stable binding to the targets. Overall, LYSPH and PSYLNTPLL are two potential anticancer peptides that deserve deeper exploration in future.

show abstract

“…In BIOPEP-UWM, six goat milk proteins were hydrolyzed using in silico gastrointestinal simulations using pepsin (pH 1. or trypsin alone, according to a comparable in silico study. Using the cocktail of enzymes produced the most valid peptides (269) (Duan et al, 2021).…”

Section: In Silico Gastrointestinal Enzymatic Hydrolysis By Goat Milk...mentioning

confidence: 99%

“…Rapseed and milk proteins, were predicted to have potential antibacterial activity identified by in silico methods (Duan et al, 2021;Dziuba & Dziuba, 2014;Rahman et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…The bioinformatics technique has been used to discover valuable and effective antioxidant peptides, angiotensin converting enzyme (ACE) inhibitory peptides and dipeptidyl peptidase‐IV (DPP‐IV) inhibitory peptides (Han et al, 2019; Tejano et al, 2019; Yu et al, 2018). AMPs have also been predicted from a number of protein sources, including tuber storage proteins (Ibrahim et al, 2019), rapeseed ( Brassica napus ) proteins (Duan et al, 2021), and milk proteins (Dziuba & Dziuba, 2014), using an in silico technique.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Antimicrobial bioactive peptides from goat Milk proteins: In silico prediction and analysis

Sansi

Iram

Zanab

et al. 2022

Journal of Food Biochemistry

View full text Add to dashboard Cite

The main goal of this study was to assess the potential proteins of goat milk (i.e. α‐s1‐casein, α‐s2‐casein, β‐casein, κ‐casein, α‐lactoglobulin and β‐lactalbumin) as precursors of antimicrobial peptides (AMPs). Bioinformatics tools such as BIOPEP‐UWM (enzyme action) were used for the in silico gastrointestinal digestion via a cocktail of pepsin, trypsin, and chymotrypsin A. The antimicrobial activity of peptides was predicted by using four algorithms, including Random Forest, Support Vector Machines, Artificial Neural Network and Discriminant Analysis on CAMPR3 online server, which works on Hidden Markov Models. Different online tools predicted the physiochemical properties, allergenicity, and toxicity of peptides as well. In silico gastrointestinal digestion simulation of proteins by enzymes cocktail yielded a total of 83 potential AMPs, with thirteen peptides being confident by all four algorithms. More AMPs were released from β‐casein (21) than from β‐lactoglobulin (16), α‐s1‐casein (15), α‐s2‐casein (12), κ‐casein (11) and α‐lactalbumin (9). A total of 17 peptides were cationic, and the majority of the peptides were extended AMPs. These peptides were released from α‐s1‐casein (SGK, IQK), α‐s2‐casein (SIR, AIH, TQPK), β‐casein (GPVR, AVPQR, AIAR, GVPK, SQPK, PVPQK, IH, VPK), k‐casein (AIPPK, QQR, IAK, TVPAK). All of the AMPs were anticipated to be non‐toxic, and 54 of the 83 peptides were confirmed to be non‐allergic, with the remaining 29 suspected of being allergenic and 31 to be predicted to have good water solubility. Further the molecular docking was used to evaluate the potent dihydropteroate synthase (DHPS) inhibitors. On the basis of ligand binding energy, 17 predicted AMPs were selected and then analyzed by AutoDock tools. Among the 17 AMPs, 3 AMPs were predicted as high‐potent antimicrobial. Based on these findings, in silico investigations reveal that proteins of goat milk are a potential source of AMPs. These peptides can be synthesized and improved for use in the food sector. Practical applications Goat milk is regarded as a high‐quality milk protein source. According to this study, goat milk protein is a possible source of AMPs, and therefore, most important AMPs can be synthesized and developed for use in the food sector.

show abstract

Prediction and analysis of antimicrobial peptides from rapeseed protein using in silico approach

Cited by 30 publications

References 39 publications

Targeting PirAvp and PirBvp Toxins of Vibrio parahaemolyticus with Oilseed Peptides: An In Silico Approach

Targeting PirAvp and PirBvp Toxins of Vibrio parahaemolyticus with Oilseed Peptides: An In Silico Approach

Computational Screening for the Anticancer Potential of Seed-Derived Antioxidant Peptides: A Cheminformatic Approach

Antimicrobial bioactive peptides from goat Milk proteins: In silico prediction and analysis

Contact Info

Product

Resources

About