In Silico Analysis of Bioactive Peptides Produced from Underutilized Sea Cucumber By-Products—A Bioinformatics Approach

Abstract

Bioinformatic tools are widely used in predicting potent bioactive peptides from food derived materials. This study was focused on utilizing sea cucumber processing by-products for generating antioxidant and ACE inhibitory peptides by application of a range of in silico techniques. Identified peptides using LC−MS/MS were virtually screened by PepRank technique followed by in silico proteolysis simulation with representative digestive enzymes using BIOPEP-UWMTM data base tool. The resultant peptides after simulated digestion were evaluated for their toxicity using ToxinPred software. All digestive resistance peptides were found to be non-toxic and displayed favorable functional properties indicating their potential for use in a wide range of food applications, including hydrophobic and hydrophilic systems. Identified peptides were further assessed for their medicinal characteristics by employing SwissADME web-based application. Our findings provide an insight on potential use of undervalued sea cucumber processing discards for functional food product development and natural pharmaceutical ingredients attributed to the oral drug discovery process.

Identification of Antioxidative Peptides Derived from Arthrospira maxima in the Biorefinery Process after Extraction of C-Phycocyanin and Lipids

“…This may be related to the lack of information in databases related to the antioxidant bioactivities of peptides [ 48 ]. Another study also reported the same results, and a few antioxidant peptides lost their bioactivity after digestion by gastrointestinal proteases [ 49 ]. According to the predictions, ACE and dipeptidyl peptidase IV inhibitory peptides were found from their original sequences.…”

“…The higher A E values represent a higher number of peptides with specific activity. RALGFDFRR showed the highest A E values (0.33) in all peptide sequences, implying that more bioactive peptides can be derived from this peptide ( Table 5 ) [ 49 ], while W values are related to the number of specific catalytic sites in each enzyme [ 50 ]. Most of the bioactive fragments with ACE inhibitory activities contained phenylalanine (F), glycine (G), leucine (L), and arginine (R) after in silico simulated digestion ( Table 5 ).…”

Potential Active Marine Peptides as Anti-Aging Drugs or Drug Candidates

“…Interestingly, the in silico analysis of the peptide profile data of active peptides produced by the enzymatic digestion of isolated proteins from sea cucumber by-products, such as flowers and offal, which are often disposed of as waste, revealed that sea cucumber-derived peptides may have the potential to inhibit lipid peroxidation processes and exert anti-oxidant activity [ 170 ].…”

In Silico Methodologies to Improve Antioxidants’ Characterization from Marine Organisms

“…Beyond that, there is Peptide Ranker (PepRank) ( ; accessed on 21 February 2023) ( Table 1 ), which predicts whether a peptide is bioactive. For a list of peptides, PepRank evaluates the probabilities to find bioactive ones and rank them from 0 to 1 [ 98 ]. Thus, the listed peptides are considered active based on the selected threshold, generally referred to as 0.5 [ 113 ].…”