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Lee CH, Hamdan N, Nyakuma BB, Wong SL, Wong KY, Tan H, Jamaluddin H, Lee TH. Purification, identification and molecular docking studies of antioxidant and anti-inflammatory peptides from Edible Bird's Nest. Food Chem 2024; 454:139797. [PMID: 38797099 DOI: 10.1016/j.foodchem.2024.139797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/27/2024] [Accepted: 05/20/2024] [Indexed: 05/29/2024]
Abstract
This study investigated antioxidant and anti-inflammatory peptides from Edible Bird's Nest (EBN). The prepared EBN peptides were sequentially separated, purified, and successively identified by ultrafiltration, gel filtration and mass spectrometry techniques. Four potential antioxidant and anti-inflammatory peptides were identified as Peptide 1 (LFWSPSVYLK), Peptide 2 (GWPHLEDNYLDW), Peptide 3 (NPPADLHK) and Peptide 4 (GDLAYLDQGHR). Molecular docking analysis revealed that Peptide 1 and Peptide 2 can competitively interrupt the formation of Keap1-Nrf2 due to the presence of hydrophobic and antioxidant amino acids in their peptide sequences. Peptide 3 and Peptide 4 have a strong effect on interacting with the binding site of IKK-β due to the interaction of anti-inflammatory amino acids and C-terminal arginine/lysine. The four peptides were synthesised and validated for their antioxidant and anti-inflammatory activities. The results suggest that the four peptides may serve as promising bioactive peptides for preventing oxidative stress and inflammation-related diseases.
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Affiliation(s)
- Chia Hau Lee
- Faculty of Chemical & Energy Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Norfadilah Hamdan
- Faculty of Chemical & Energy Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Bemgba Bevan Nyakuma
- Department of Chemical Sciences, Faculty of Science & Computing, North-Eastern University, 0198 Gombe, Gombe State, Nigeria
| | - Syie Luing Wong
- Department of Chemical Engineering & Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the Netherlands
| | - Keng Yinn Wong
- Faculty of Mechanical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Huiyi Tan
- Faculty of Chemical & Energy Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Haryati Jamaluddin
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Ting Hun Lee
- Faculty of Chemical & Energy Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia.
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Abdul-Khalek N, Wimmer R, Overgaard MT, Gregersen Echers S. Insight on physicochemical properties governing peptide MS1 response in HPLC-ESI-MS/MS: A deep learning approach. Comput Struct Biotechnol J 2023; 21:3715-3727. [PMID: 37560124 PMCID: PMC10407266 DOI: 10.1016/j.csbj.2023.07.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 08/11/2023] Open
Abstract
Accurate and absolute quantification of peptides in complex mixtures using quantitative mass spectrometry (MS)-based methods requires foreground knowledge and isotopically labeled standards, thereby increasing analytical expenses, time consumption, and labor, thus limiting the number of peptides that can be accurately quantified. This originates from differential ionization efficiency between peptides and thus, understanding the physicochemical properties that influence the ionization and response in MS analysis is essential for developing less restrictive label-free quantitative methods. Here, we used equimolar peptide pool repository data to develop a deep learning model capable of identifying amino acids influencing the MS1 response. By using an encoder-decoder with an attention mechanism and correlating attention weights with amino acid physicochemical properties, we obtain insight on properties governing the peptide-level MS1 response within the datasets. While the problem cannot be described by one single set of amino acids and properties, distinct patterns were reproducibly obtained. Properties are grouped in three main categories related to peptide hydrophobicity, charge, and structural propensities. Moreover, our model can predict MS1 intensity output under defined conditions based solely on peptide sequence input. Using a refined training dataset, the model predicted log-transformed peptide MS1 intensities with an average error of 9.7 ± 0.5% based on 5-fold cross validation, and outperformed random forest and ridge regression models on both log-transformed and real scale data. This work demonstrates how deep learning can facilitate identification of physicochemical properties influencing peptide MS1 responses, but also illustrates how sequence-based response prediction and label-free peptide-level quantification may impact future workflows within quantitative proteomics.
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Affiliation(s)
- Naim Abdul-Khalek
- Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark
| | - Reinhard Wimmer
- Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark
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Gregersen Echers S, Abdul-Khalek N, Mikkelsen RK, Holdt SL, Jacobsen C, Hansen EB, Olsen TH, Sejberg JJ, Overgaard MT. Is Gigartina a potential source of food protein and functional peptide-based ingredients? Evaluating an industrial, pilot-scale extract by proteomics and bioinformatics. FUTURE FOODS 2022. [DOI: 10.1016/j.fufo.2022.100189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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4
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Targeted hydrolysis of native potato protein: A novel workflow for obtaining hydrolysates with improved interfacial properties. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.108299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Gregersen S, Kongsted ASH, Nielsen RB, Hansen SS, Lau FA, Rasmussen JB, Holdt SL, Jacobsen C. Enzymatic extraction improves intracellular protein recovery from the industrial carrageenan seaweed Eucheuma denticulatum revealed by quantitative, subcellular protein profiling: A high potential source of functional food ingredients. Food Chem X 2021; 12:100137. [PMID: 34746746 PMCID: PMC8554166 DOI: 10.1016/j.fochx.2021.100137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/27/2021] [Accepted: 10/01/2021] [Indexed: 01/13/2023] Open
Abstract
Seaweeds are regarded as a sustainable source of food protein, but protein extraction is severely impaired by the complex extracellular matrix. In this work, we investigated the protein-level effects of enzymatic extraction upstream of carrageenan extraction for the industrial red seaweed Eucheuma denticulatum. Combination of quantitative proteomics and bioinformatic prediction of subcellular localization was shown to have immense potential for process evaluation; even in the case of poorly annotated species such as E. denticulatum. Applying cell wall degrading enzymes markedly improved the relative recovery of intracellular proteins compared to treatment with proteolytic enzymes or no enzymatic treatment. Moreover, results suggest that proteomics data may prove useful for characterizing amino acid composition and that length-normalization is a viable approach for relative protein quantification in non-specific analysis. Importantly, the extracts were abundant in proteins, which contained both previously verified and novel, potential bioactive peptides, highlighting their potential for application as functional food ingredients.
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Affiliation(s)
- Simon Gregersen
- Department of Chemistry and Bioscience, Aalborg University, Denmark
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6
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Yesiltas B, Gregersen S, Lægsgaard L, Brinch ML, Olsen TH, Marcatili P, Overgaard MT, Hansen EB, Jacobsen C, García-Moreno PJ. Emulsifier peptides derived from seaweed, methanotrophic bacteria, and potato proteins identified by quantitative proteomics and bioinformatics. Food Chem 2021; 362:130217. [PMID: 34098440 DOI: 10.1016/j.foodchem.2021.130217] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/16/2021] [Accepted: 05/17/2021] [Indexed: 10/21/2022]
Abstract
Global focus on sustainability has accelerated research into alternative non-animal sources of food protein and functional food ingredients. Amphiphilic peptides represent a class of promising biomolecules to replace chemical emulsifiers in food emulsions. In contrast to traditional trial-and-error enzymatic hydrolysis, this study utilizes a bottom-up approach combining quantitative proteomics, bioinformatics prediction, and functional validation to identify novel emulsifier peptides from seaweed, methanotrophic bacteria, and potatoes. In vitro functional validation reveal that all protein sources contained embedded novel emulsifier peptides comparable to or better than sodium caseinate (CAS). Thus, peptides efficiently reduced oil-water interfacial tension and generated physically stable emulsions with higher net zeta potential and smaller droplet sizes than CAS. In silico structure modelling provided further insight on peptide structure and the link to emulsifying potential. This study clearly demonstrates the potential and broad applicability of the bottom-up approach for identification of abundant and potent emulsifier peptides.
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Affiliation(s)
- Betül Yesiltas
- National Food Institute, Technical University of Denmark, Denmark.
| | - Simon Gregersen
- Department of Chemistry and Bioscience, Aalborg University, Denmark.
| | - Linea Lægsgaard
- National Food Institute, Technical University of Denmark, Denmark
| | - Maja L Brinch
- National Food Institute, Technical University of Denmark, Denmark
| | - Tobias H Olsen
- Department of Bio and Health Informatics, Technical University of Denmark, Denmark
| | - Paolo Marcatili
- Department of Bio and Health Informatics, Technical University of Denmark, Denmark
| | | | - Egon B Hansen
- National Food Institute, Technical University of Denmark, Denmark
| | | | - Pedro J García-Moreno
- National Food Institute, Technical University of Denmark, Denmark; Department of Chemical Engineering, University of Granada, Spain.
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Food-Derived Bioactive Peptides with Antioxidative Capacity, Xanthine Oxidase and Tyrosinase Inhibitory Activity. Processes (Basel) 2021. [DOI: 10.3390/pr9050747] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bioactive peptides (BPs) released by proteases from different food protein sources are often served as antioxidants in food applications. This study aims to investigate 11 BPs derived from fish and egg white as potential natural antioxidants by antioxidant activity assays. The kinetic activity of the BPs against xanthine oxidase (XOD) and tyrosinase was also analyzed. The antioxidative capacity of the BPs indicated that VWWW (VW4, mackerel meat), followed by IRW (IW3, egg white) and VKAGFAWTANQQLS (VS14, tuna backbone protein), possessed the highest antioxidant activity in 1,1-diphenyl-2-picrylhydrazyl radical (DPPH), 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) and reducing power (RP) assays. Both the free-radical scavenging score predicted from the AnOxPePred algorithm and the DPPH, ABTS and RP results indicated that VW4 was the best antioxidant. Furthermore, the XOD and tyrosinase inhibition by three selected peptides exhibited competitive patterns of effective inhibition. The half maximal inhibitory concentrations (IC50) of the peptides for XOD inhibition were 5.310, 3.935, and 1.804 mM for VW4, IW3, and VS14, respectively, and they could serve as competitive natural XOD inhibitors. The IC50 of the peptides for tyrosinase inhibition were 1.254, 2.895, and 0.595 mM for VW4, IW3, and VS14, respectively. Overall, VW4, IW3, and VS14 are potential antioxidants and natural XOD inhibitors for preventing milk-fat oxidation, and anti-browning sources for inhibiting food-derived tyrosinase oxidation.
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Messina CM, Manuguerra S, Arena R, Renda G, Ficano G, Randazzo M, Fricano S, Sadok S, Santulli A. In Vitro Bioactivity of Astaxanthin and Peptides from Hydrolisates of Shrimp ( Parapenaeus longirostris) By-Products: From the Extraction Process to Biological Effect Evaluation, as Pilot Actions for the Strategy "From Waste to Profit". Mar Drugs 2021; 19:md19040216. [PMID: 33924455 PMCID: PMC8070669 DOI: 10.3390/md19040216] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 12/14/2022] Open
Abstract
Non-edible parts of crustaceans could be a rich source of valuable bioactive compounds such as the carotenoid astaxanthin and peptides, which have well-recognized beneficial effects. These compounds are widely used in nutraceuticals and pharmaceuticals, and their market is rapidly growing, suggesting the need to find alternative sources. The aim of this work was to set up a pilot-scale protocol for the reutilization of by-products of processed shrimp, in order to address the utilization of this valuable biomass for nutraceutical and pharmaceuticals application, through the extraction of astaxanthin-enriched oil and antioxidant-rich protein hydrolysates. Astaxanthin (AST) was obtained using “green extraction methods,” such as using fish oil and different fatty acid ethyl esters as solvents and through supercritical fluid extraction (SFE), whereas bioactive peptides were obtained by protease hydrolysis. Both astaxanthin and bioactive peptides exhibited bioactive properties in vitro in cellular model systems, such as antioxidant and angiotensin I converting enzyme (ACE) inhibitory activities (IA). The results show higher astaxanthin yields in ethyl esters fatty acids (TFA) extraction and significant enrichment by short-path distillation (SPD) up to 114.80 ± 1.23 µg/mL. Peptide fractions of <3 kDa and 3–5 kDa exhibited greater antioxidant activity while the fraction 5–10 kDa exhibited a better ACE-IA. Lower-molecular-weight bioactive peptides and astaxanthin extracted using supercritical fluids showed protective effects against oxidative damage in 142BR and in 3T3 cell lines. These results suggest that “green” extraction methods allow us to obtain high-quality bioactive compounds from large volumes of shrimp waste for nutraceutical and pharmaceutical applications.
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Affiliation(s)
- Concetta Maria Messina
- Dipartimento di Scienze della terra e del Mare DiSTeM, Laboratorio di Biochimica Marina ed Ecotossicologia, Università degli Studi di Palermo, Via G. Barlotta 4, 91100 Trapani, Italy; (S.M.); (R.A.); (G.R.); (G.F.); (A.S.)
- Correspondence:
| | - Simona Manuguerra
- Dipartimento di Scienze della terra e del Mare DiSTeM, Laboratorio di Biochimica Marina ed Ecotossicologia, Università degli Studi di Palermo, Via G. Barlotta 4, 91100 Trapani, Italy; (S.M.); (R.A.); (G.R.); (G.F.); (A.S.)
| | - Rosaria Arena
- Dipartimento di Scienze della terra e del Mare DiSTeM, Laboratorio di Biochimica Marina ed Ecotossicologia, Università degli Studi di Palermo, Via G. Barlotta 4, 91100 Trapani, Italy; (S.M.); (R.A.); (G.R.); (G.F.); (A.S.)
| | - Giuseppe Renda
- Dipartimento di Scienze della terra e del Mare DiSTeM, Laboratorio di Biochimica Marina ed Ecotossicologia, Università degli Studi di Palermo, Via G. Barlotta 4, 91100 Trapani, Italy; (S.M.); (R.A.); (G.R.); (G.F.); (A.S.)
| | - Giovanna Ficano
- Dipartimento di Scienze della terra e del Mare DiSTeM, Laboratorio di Biochimica Marina ed Ecotossicologia, Università degli Studi di Palermo, Via G. Barlotta 4, 91100 Trapani, Italy; (S.M.); (R.A.); (G.R.); (G.F.); (A.S.)
| | - Mariano Randazzo
- Istituto di Biologia Marina, Consorzio Universitario della Provincia di Trapani, Via G. Barlotta 4, 91100 Trapani, Italy;
| | - Stefano Fricano
- Dipartimento di Science Economiche, Aziendali e Statistiche, DSEAS, Università degli Studi di Palermo, Viale delle Scienze, Edificio 13, 90100 Palermo, Italy;
| | - Saloua Sadok
- Laboratory of Blue Biotechnology & Aquatic Bioproducts (B3Aqua), Institut National des Sciences et Technologies de la Mer (INSTM), Annexe La Goulette Port de Pêche, La Goulette 2060, Tunisia;
| | - Andrea Santulli
- Dipartimento di Scienze della terra e del Mare DiSTeM, Laboratorio di Biochimica Marina ed Ecotossicologia, Università degli Studi di Palermo, Via G. Barlotta 4, 91100 Trapani, Italy; (S.M.); (R.A.); (G.R.); (G.F.); (A.S.)
- Istituto di Biologia Marina, Consorzio Universitario della Provincia di Trapani, Via G. Barlotta 4, 91100 Trapani, Italy;
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