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Ji S, Wu J, An F, Lou M, Zhang T, Guo J, Wu P, Zhu Y, Wu R. Umami-gcForest: Construction of a predictive model for umami peptides based on deep forest. Food Chem 2025; 464:141826. [PMID: 39522377 DOI: 10.1016/j.foodchem.2024.141826] [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: 06/20/2024] [Revised: 10/07/2024] [Accepted: 10/27/2024] [Indexed: 11/16/2024]
Abstract
Umami peptides have recently gained attention for their ability to enhance umami flavor, reduce salt content, and provide nutritional benefits. However, traditional wet laboratory methods to identify them are time-consuming, laborious, and costly. Therefore, we developed the Umami-gcForest model using the deep forest algorithm. It constructs amino acid feature matrices using ProtBERT, amino acid composition, composition-transition-distribution, and pseudo amino acid composition, applying mutual information for feature selection to optimize dimensions. Compared to other machine learning baseline, umami peptide prediction, and composite models, the validation results of Umami-gcForest on different test sets demonstrated outstanding predictive accuracy. Using SHapley Additive exPlanations to calculate feature contributions, we found that the key features of Umami-gcForest were hydrophobicity, charge, and polarity. Based on this, an online platform was developed to facilitate its user application. In conclusion, Umami-gcForest serves as a powerful tool, providing a solid foundation for the efficient and accurate screening of umami peptides.
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Affiliation(s)
- Shuaiqi Ji
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China; Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang 110866, PR China
| | - Junrui Wu
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China; Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang 110866, PR China
| | - Feiyu An
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China; Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang 110866, PR China
| | - Mengxue Lou
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China; Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang 110866, PR China
| | - Taowei Zhang
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China; Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang 110866, PR China
| | - Jiawei Guo
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China; Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang 110866, PR China
| | - Penggong Wu
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China; Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang 110866, PR China
| | - Yi Zhu
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China; Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang 110866, PR China
| | - Rina Wu
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China; Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang 110866, PR China.
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Barreiro-Sisto U, Fernández-Fariña S, González-Noya AM, Pedrido R, Maneiro M. Enemies or Allies? Hormetic and Apparent Non-Dose-Dependent Effects of Natural Bioactive Antioxidants in the Treatment of Inflammation. Int J Mol Sci 2024; 25:1892. [PMID: 38339170 PMCID: PMC10855620 DOI: 10.3390/ijms25031892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
This review aims to analyze the emerging number of studies on biological media that describe the unexpected effects of different natural bioactive antioxidants. Hormetic effects, with a biphasic response depending on the dose, or activities that are apparently non-dose-dependent, have been described for compounds such as resveratrol, curcumin, ferulic acid or linoleic acid, among others. The analysis of the reported studies confirms the incidence of these types of effects, which should be taken into account by researchers, discarding initial interpretations of imprecise methodologies or measurements. The incidence of these types of effects should enhance research into the different mechanisms of action, particularly those studied in the field of basic research, that will help us understand the causes of these unusual behaviors, depending on the dose, such as the inactivation of the signaling pathways of the immune defense system. Antioxidative and anti-inflammatory activities in biological media should be addressed in ways that go beyond a mere statistical approach. In this work, some of the research pathways that may explain the understanding of these activities are revised, paying special attention to the ability of the selected bioactive compounds (curcumin, resveratrol, ferulic acid and linoleic acid) to form metal complexes and the activity of these complexes in biological media.
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Affiliation(s)
- Uxía Barreiro-Sisto
- Departamento de Química Inorgánica, Facultade de Ciencias, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain; (U.B.-S.); (S.F.-F.)
| | - Sandra Fernández-Fariña
- Departamento de Química Inorgánica, Facultade de Ciencias, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain; (U.B.-S.); (S.F.-F.)
| | - Ana M. González-Noya
- Departamento de Química Inorgánica, Facultade de Química, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | - Rosa Pedrido
- Departamento de Química Inorgánica, Facultade de Química, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | - Marcelino Maneiro
- Departamento de Química Inorgánica, Facultade de Ciencias, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain; (U.B.-S.); (S.F.-F.)
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Alu'datt MH, Tranchant CC, Alhamad MN, Rababah T, Al-U'datt D, Gammoh S, Alrosan M, Alkandari S, Zghoul R. Impact of ultrasonication on the contents, profiles and biofunctional properties of free and bound phenolics from white desert truffle (Tirmania nivea) and its protein fractions. Food Res Int 2023; 174:113453. [PMID: 37986408 DOI: 10.1016/j.foodres.2023.113453] [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: 04/20/2023] [Revised: 08/31/2023] [Accepted: 09/10/2023] [Indexed: 11/22/2023]
Abstract
The molecular and biofunctional properties of protein and phenolic fractions in edible truffles remain largely unknown. This study examined the effect of ultrasonication on the contents, profiles, and bioactive properties of free and bound phenolics (FP and BP) from desert truffle (Tirmania nivea) and its protein fractions. Protein fractions from the Osborne extraction scheme were biochemically and structurally characterized. The albumin fraction showed the highest abundance (16.8%) and yield (35.8%). Total phenolic contents were the highest in non-sonicated samples (3.5-34.1 mg/g), particularly in the albumin fraction and in whole truffle. FP extracted at 30 °C (FP-30 °C) accounted for the largest proportion of total phenolics in all protein fractions, whereas BP-30 °C and FP-60 °C were predominant in non-sonicated and sonicated truffle, respectively. The highest antioxidant activity was obtained with FP-30 °C extracts from non-sonicated albumins, globulins and truffle (91.9, 72.7 and 30.0%), followed by BP-30 °C from non-sonicated albumins (25.4%) and FP-60 °C from sonicated glutelins-1 (24.2%). High inhibition of α-amylase was evidenced in several extracts, including FP-30 °C from non-sonicated glutelins-1 (99.2%) and FP-30 °C from sonicated globulins (72.4%). Several extracts also displayed high inhibition of angiotensin I-converting enzyme (ACE), including FP-60 °C from non-sonicated glutelins-1 (65.1%) and sonicated glutelins-1 (71.1%) and globulins (64.7%). Most extracts were rich in epicatechin, gallic acid, chlorogenic acid and catechin. Correlations between phenolic content, antioxidant activity, anti-α-amylase and anti-ACE activities were influenced by sonication. Sonication reduced the particle size of the proteins and modified their structural characteristics. These findings demonstrate that white desert truffle proteins co-occur with bioactive phenolics whose functionalities can be tailored by protein fractionation and sonication.
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Affiliation(s)
- Muhammad H Alu'datt
- Department of Nutrition and Food Technology, Faculty of Agriculture, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan; Department of Food Science & Nutrition, College of Life Sciences, Kuwait University, P.O. Box. 5969, Safat 13060, Kuwait.
| | - Carole C Tranchant
- School of Food Science, Nutrition and Family Studies, Faculty of Health Sciences and Community Services, Université de Moncton, Moncton, New Brunswick E1A 3E9, Canada.
| | - Mohammad N Alhamad
- Department of Natural Resources and Environment, Faculty of Agriculture, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan
| | - Taha Rababah
- Department of Nutrition and Food Technology, Faculty of Agriculture, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan
| | - Doa'a Al-U'datt
- Department of Physiology and Biochemistry, Faculty of Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Sana Gammoh
- Department of Nutrition and Food Technology, Faculty of Agriculture, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan
| | - Mohammad Alrosan
- Applied Science Research Center, Applied Science Private University, Amman 11937, Jordan
| | - Sharifa Alkandari
- Department of Food Science & Nutrition, College of Life Sciences, Kuwait University, P.O. Box. 5969, Safat 13060, Kuwait
| | - Roa'a Zghoul
- Department of Nutrition and Food Technology, Faculty of Agriculture, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan
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