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Liu M, Yang J, He Y, Cao F, Li W, Han W. VmmScore: An umami peptide prediction and receptor matching program based on a deep learning approach. Comput Biol Med 2024; 179:108814. [PMID: 38944902 DOI: 10.1016/j.compbiomed.2024.108814] [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: 03/05/2024] [Revised: 05/17/2024] [Accepted: 06/24/2024] [Indexed: 07/02/2024]
Abstract
Peptides, with recognized physiological and medical implications, such as the ability to lower blood pressure and lipid levels, are central to our research on umami taste perception. This study introduces a computational strategy to tackle the challenge of identifying optimal umami receptors for these peptides. Our VmmScore algorithm includes two integral components: Mlp4Umami, a predictive module that evaluates the umami taste potential of peptides, and mm-Score, which enhances the receptor matching process through a machine learning-optimized molecular docking and scoring system. This system encompasses the optimization of docking structures, clustering of umami peptides, and a comparative analysis of docking energies across peptide clusters, streamlining the receptor identification process. Employing machine learning, our method offers a strategic approach to the intricate task of umami receptor determination. We undertook virtual screening of peptides derived from Lateolabrax japonicus, experimentally verifying the umami taste of three identified peptides and determining their corresponding receptors. This work not only advances our understanding of the mechanisms behind umami taste perception but also provides a rapid and cost-effective method for peptide screening. The source code is publicly accessible at https://github.com/heyigacu/mlp4umami/, encouraging further scientific exploration and collaborative efforts within the research community.
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Affiliation(s)
- Minghao Liu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, 130012, China.
| | - Jiuliang Yang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, 130012, China.
| | - Yi He
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, 130012, China.
| | - Fuyan Cao
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, 130012, China.
| | - Wannan Li
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, 130012, China.
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, 130012, China.
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Sun H, Xiao D, Liu W, Li X, Lin Z, Li Y, Ding Y. Well-known polypeptides of deer antler velvet with key actives: modern pharmacological advances. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:15-31. [PMID: 37555852 DOI: 10.1007/s00210-023-02642-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 07/20/2023] [Indexed: 08/10/2023]
Abstract
Deer antler velvet, with kidney tonifying, promoting the production of essence and blood, strengthening tendons and bones, not only has a thousand-year medicinal history but also its modern pharmacology mainly focuses on its active polypeptides on motor, nerve, and immune systems. The purpose of this report is to fill the gap in the comprehensive, systematic, and detailed review of polypeptides during the recent 30 years (1992-2023). The research method was to review 53 pharmacological articles from the Public Medicine, Web of science, ACS, and Science Direct database sources by searching the keywords "pilose antler," "deer velvet," "Pilose Antler Peptide (PAP) and Velvet Antler Polypeptide (VAP)." The results showed that deer antler polypeptides (DAPs), by regulating EGF, EGFR, MAPK, P38, ERK, NF-κB, Wnt, PI3K, Akt, MMP, AMPK, Stir1, NLRP3, HO-1, Nrf, Rho, TLR, TGF-β, Smad, Ang II, etc., revealed their effects on seven system-related diseases and their mechanisms, including osteoarthritis, intervertebral disc degeneration, osteoporosis, Alzheimer's, Parkinson's, triple-negative breast cancer, liver injury, liver fibrosis, cardiovascular disease, acute lung injury, and late-onset hypogonadism. In conclusion, DAPs have good effects on motor and other system-related diseases, but the secondary and tertiary structures of DAPs (0.5-1800 KDa) need to be further elucidated, and the structure-activity relationship study is still unavailable and needs to be covered. It is expected that this review may provide the necessary literature support for further research. The activities and mechanisms of polypeptides from the past 30 years (1992-2023) are summarized covering seven systems, related diseases, and its regulatory genes and proteins.
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Affiliation(s)
- He Sun
- School of Pharmaceutical Sciences, Changchun University of Chinese Medicine, Changchun, 130117, Jilin, China
| | - Dandan Xiao
- School of Pharmaceutical Sciences, Changchun University of Chinese Medicine, Changchun, 130117, Jilin, China
| | - Wei Liu
- School of Pharmaceutical Sciences, Changchun University of Chinese Medicine, Changchun, 130117, Jilin, China
| | - Xue Li
- School of Pharmaceutical Sciences, Changchun University of Chinese Medicine, Changchun, 130117, Jilin, China
| | - Zhe Lin
- School of Pharmaceutical Sciences, Changchun University of Chinese Medicine, Changchun, 130117, Jilin, China
| | - Yong Li
- School of Pharmaceutical Sciences, Changchun University of Chinese Medicine, Changchun, 130117, Jilin, China.
| | - Yuling Ding
- School of Pharmaceutical Sciences, Changchun University of Chinese Medicine, Changchun, 130117, Jilin, China.
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Ye J, Tian X, Wang Q, Zheng J, Yang Y, Xu B, Zhang S, Yuan F, Yang Z. Monkfish Peptides Mitigate High Fat Diet-Induced Hepatic Steatosis in Mice. Mar Drugs 2022; 20:md20050312. [PMID: 35621963 PMCID: PMC9147042 DOI: 10.3390/md20050312] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/01/2022] [Accepted: 05/02/2022] [Indexed: 02/05/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a hepatic metabolic syndrome usually accompanied by fatty degeneration and functional impairment. The aim of the study was to determine whether monkfish peptides (LPs) could ameliorate high-fat diet (HFD)-induced NAFLD and its underlying mechanisms. NAFLD was induced in mice by giving them an HFD for eight weeks, after which LPs were administered in various dosages. In comparison to the HFD control group: body weight in the LP-treated groups decreased by 23–28%; triacylglycerol levels in the blood decreased by 16–35%; and low-density lipoproteins levels in the blood decreased by 23–51%. Additionally, we found that LPs elevated the activity of hepatic antioxidant enzymes and reduced the inflammatory reactions within fatty liver tissue. Investigating the effect on metabolic pathways, we found that in LP-treated mice: the levels of phospho-AMP-activated protein kinase (p-AMPK), and phospho-acetyl CoA carboxylase (p-ACC) in the AMP-activated protein kinase (AMPK) pathway were up-regulated and the levels of downstream sterol regulatory element-binding transcription factor 1 (SREBP-1) were down-regulated; lipid oxidation increased and free fatty acid (FFA) accumulation decreased (revealed by the increased carnitine palmitoyltransferase-1 (CPT-1) and the decreased fatty acid synthase (FASN) expression, respectively); the nuclear factor erythroid-2-related factor 2 (Nrf2) antioxidant pathway was activated; and the levels of heme oxygenase-1 (HO-1) and nicotinamide quinone oxidoreductase 1 (NQO1) were increased. Overall, all these findings demonstrated that LPs can improve the antioxidant capacity of liver to alleviate NAFLD progression mainly through modulating the AMPK and Nrf2 pathways, and thus it could be considered as an effective candidate in the treatment of human NAFLD.
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Affiliation(s)
- Jiena Ye
- Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China; (J.Y.); (X.T.); (J.Z.); (Y.Y.); (B.X.); (S.Z.)
| | - Xiaoxiao Tian
- Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China; (J.Y.); (X.T.); (J.Z.); (Y.Y.); (B.X.); (S.Z.)
| | - Qiongfen Wang
- Zhoushan Institute for Food and Drug Control, Zhoushan 316000, China;
| | - Jiawen Zheng
- Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China; (J.Y.); (X.T.); (J.Z.); (Y.Y.); (B.X.); (S.Z.)
| | - Yanzhuo Yang
- Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China; (J.Y.); (X.T.); (J.Z.); (Y.Y.); (B.X.); (S.Z.)
| | - Baogui Xu
- Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China; (J.Y.); (X.T.); (J.Z.); (Y.Y.); (B.X.); (S.Z.)
| | - Shuai Zhang
- Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China; (J.Y.); (X.T.); (J.Z.); (Y.Y.); (B.X.); (S.Z.)
| | - Falei Yuan
- Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China; (J.Y.); (X.T.); (J.Z.); (Y.Y.); (B.X.); (S.Z.)
- Correspondence: (F.Y.); (Z.Y.)
| | - Zuisu Yang
- Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China; (J.Y.); (X.T.); (J.Z.); (Y.Y.); (B.X.); (S.Z.)
- Correspondence: (F.Y.); (Z.Y.)
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Zhao M, Chen S, Ji X, Shen X, You J, Liang X, Yin H, Zhao L. Current innovations in nutraceuticals and functional foods for intervention of non-alcoholic fatty liver disease. Pharmacol Res 2021; 166:105517. [PMID: 33636349 DOI: 10.1016/j.phrs.2021.105517] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/27/2021] [Accepted: 02/21/2021] [Indexed: 02/07/2023]
Abstract
As innovations in global agricultural production and food trading systems lead to major dietary shifts, high morbidity rates from non-alcoholic fatty liver disease (NAFLD), accompanied by elevated risk of lipid metabolism-related complications, has emerged as a growing problem worldwide. Treatment and prevention of NAFLD and chronic liver disease depends on the availability of safe, effective, and diverse therapeutic agents, the development of which is urgently needed. Supported by a growing body of evidence, considerable attention is now focused on interventional approaches that combines nutraceuticals and functional foods. In this review, we summarize the pathological progression of NAFLD and discuss the beneficial effects of nutraceuticals and the active ingredients in functional foods. We also describe the underlying mechanisms of these compounds in the intervention of NAFLD, including their effects on regulation of lipid homeostasis, activation of signaling pathways, and their role in gut microbial community dynamics and the gut-liver axis. In order to identify novel targets for treatment of lipid metabolism-related diseases, this work broadly explores the molecular mechanism linking nutraceuticals and functional foods, host physiology, and gut microbiota. Additionally, the limitations in existing knowledge and promising research areas for development of active interventions and treatments against NAFLD are discussed.
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Affiliation(s)
- Mengyao Zhao
- School of Biotechnology, State Key Laboratory of Bioreactor Engineering, R&D Center of Separation and Extraction Technology in Fermentation Industry, East China University of Science and Technology, Shanghai 200237, China; Shanghai Collaborative Innovation Center for Biomanufacturing Technology (SCICBT), Shanghai 200237, China
| | - Shumin Chen
- School of Biotechnology, State Key Laboratory of Bioreactor Engineering, R&D Center of Separation and Extraction Technology in Fermentation Industry, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaoguo Ji
- School of Biotechnology, State Key Laboratory of Bioreactor Engineering, R&D Center of Separation and Extraction Technology in Fermentation Industry, East China University of Science and Technology, Shanghai 200237, China
| | - Xin Shen
- School of Biotechnology, State Key Laboratory of Bioreactor Engineering, R&D Center of Separation and Extraction Technology in Fermentation Industry, East China University of Science and Technology, Shanghai 200237, China
| | - Jiangshan You
- School of Biotechnology, State Key Laboratory of Bioreactor Engineering, R&D Center of Separation and Extraction Technology in Fermentation Industry, East China University of Science and Technology, Shanghai 200237, China
| | - Xinyi Liang
- School of Biotechnology, State Key Laboratory of Bioreactor Engineering, R&D Center of Separation and Extraction Technology in Fermentation Industry, East China University of Science and Technology, Shanghai 200237, China
| | - Hao Yin
- Organ Transplant Center, Shanghai Changzheng Hospital, Shanghai 200003, China.
| | - Liming Zhao
- School of Biotechnology, State Key Laboratory of Bioreactor Engineering, R&D Center of Separation and Extraction Technology in Fermentation Industry, East China University of Science and Technology, Shanghai 200237, China; School of Life Science, Shandong University of Technology, Zibo, Shandong 255000, China; Shanghai Collaborative Innovation Center for Biomanufacturing Technology (SCICBT), Shanghai 200237, China.
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Pilose antler polypeptides ameliorate inflammation and oxidative stress and improves gut microbiota in hypoxic-ischemic injured rats. Nutr Res 2019; 64:93-108. [DOI: 10.1016/j.nutres.2019.01.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 01/12/2019] [Accepted: 01/19/2019] [Indexed: 12/11/2022]
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