食品与发酵工业 >

2024 , Vol. 50 >Issue 20: 104 - 112

DOI: https://doi.org/10.13995/j.cnki.11-1802/ts.037870

研究报告

多肽组学联合分子对接筛选玉足海参抗血栓肽

  • 李汉琪 ,
  • 王治军 ,
  • 郑清瑶 ,
  • 宋春勇 ,
  • 陈忠琴 ,
  • 谭明堂 ,
  • 林海生 ,
  • 曹文红
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  • 1(广东海洋大学 食品科技学院,国家贝类加工技术研发分中心(湛江),广东省水产品加工与安全重点实验室,广东省海洋食品工程技术研究中心,广东省海洋生物制品工程实验室,广东 湛江,524088)
    2(海洋食品精深加工关键技术省部共建协同创新中心,大连工业大学,辽宁 大连,116034)
第一作者:硕士研究生(曹文红教授为通信作者,E-mail:cwenhong@gdou.edu.cn)

收稿日期: 2023-11-06

  修回日期: 2023-12-06

  网络出版日期: 2024-11-01

基金资助

“十三五”国家重点研发计划重点专项(2020YFD0901104);湛江市农业技术攻关项目(2021A05187)

收起

Peptidomics combined with molecular docking screening for antithrombotic peptides from sea cucumber (Holothuria leucospilota)

  • LI Hanqi ,
  • WANG Zhijun ,
  • ZHENG Qingyao ,
  • SONG Chunyong ,
  • CHEN Zhongqin ,
  • TAN Mingtang ,
  • LIN Haisheng ,
  • CAO Wenhong
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  • 1(College of Food Science and Technology, Guangdong Ocean University, National Research and Development Branch Center for Shellfish Processing (Zhanjiang), Guangdong Provincial Key Laboratory of Aquatic Products Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, Zhanjiang 524088, China)
    2(Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China)

Received date: 2023-11-06

  Revised date: 2023-12-06

  Online published: 2024-11-01

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摘要

基于多肽组学联合分子对接技术筛选玉足海参来源的具有抗血栓作用的活性肽。采用LC-MS/MS技术表征玉足海参酶解液全肽谱,通过简易分离纯化建立小规模的候选肽库,同时借助生物信息学软件对多肽库进行理化性质分析,评估抗血栓活性筛选方法的可行性;利用Discovery Studio 软件以重组水蛭素片段(HIRV2)与凝血酶的结合模式,进行分子对接筛选潜在抗血栓肽序列,以部分凝血活酶时间、凝血酶原时间、凝血酶时间及凝血酶抑制率4项指标评估人工合成肽的抗血栓活性。结果表明,玉足海参酶解液含有1 795条肽序列。选取相对分子质量为1~3 kDa的116条肽序列建立候选肽库,分子对接筛选出 6种潜在的抗血栓活性肽(CDOCKER ENERGY均高于HIRV2)。其中 SCp-1和SCp-2分别与凝血酶的10个氨基酸残基位点紧密结合,表明它们是潜在的抗血栓活性肽。体外活性表明,SCp-1和SCp-2均呈剂量依赖趋势的内源性抗凝活性以及共同通路的抗凝活性(P＜0.05),二者相较下SCp-1在内源性通路抗凝能力较强,SCp-2则在共同通路表现出更好的抗凝活性。综上,通过多肽组学联合分子对接成功从玉足海参酶解产物中筛选获得2种新型食源性抗血栓肽。

关键词： 玉足海参; 多肽组学; 生物信息学; 分子对接; 抗血栓肽

本文引用格式

李汉琪 , 王治军 , 郑清瑶 , 宋春勇 , 陈忠琴 , 谭明堂 , 林海生 , 曹文红 . 多肽组学联合分子对接筛选玉足海参抗血栓肽[J]. 食品与发酵工业, 2024 , 50(20) : 104 -112 . DOI: 10.13995/j.cnki.11-1802/ts.037870

Abstract

Based on peptidomics combined with molecular docking technology, active peptides with antithrombotic effects were screened from Holothuria leucospilota. LC-MS/MS technology was used to characterize the full peptide spectrum of the enzymatic hydrolysate of sea cucumber, and a small-scale candidate peptide library was established through simple separation and purification.At the same time, bioinformatics software was used to analyze the physicochemical properties of the peptide library and evaluate the feasibility of the anti-thrombotic activity screening method.Using Discovery Studio software to screen potential antithrombotic peptide sequences by molecular docking based on the binding mode of recombinant hirudin fragment (HIRV2) and thrombin, the antithrombotic activity of artificially synthesized peptides was evaluated using four indicators, including activated partial thromboplatin time, prothrombin time, thrombin time, and thrombin inhibition rate.Results showed that the enzymatic hydrolysate of sea cucumber contained 1 795 peptide sequences.116 peptide sequences with a relative molecular weight of 1-3 kDa were selected to establish a candidate peptide library.Six potential antithrombotic active peptides (CDOCKER ENERGY was higher than HIRV2) were screened through molecular docking.SCp-1 and SCp-2 were closely bound to the 10 amino acid residues of thrombin, indicating that they were potential antithrombotic peptides.In vitro activity showed that both SCp-1 and SCp-2 exhibited (P＜0.05) a dose-dependent endogenous anticoagulant activity and a common pathway anticoagulant activity.Compared to the two, SCp-1 exhibited stronger anticoagulant activity in the endogenous pathway, while SCp-2 exhibited better anticoagulant activity in the common pathway.In summary, two novel foodborne antithrombotic peptides were successfully screened from the enzymatic hydrolysis products of sea cucumber through peptide omics combined with molecular docking.

Key words： sea cucumber (Holothuria leucospilota); peptidomics; bioinformatics; molecular docking; antithrombotic peptide

参考文献

[1] World Heart Report 2023:Confronting the World′s Number One Killer[R].World Heart Federation.Geneva, Switzerland.2023.
[2] UCEDA-MARTIN M, LAMBERT A, MIREMONT G, et al.Bullous haemorrhagic dermatitis induced by heparins and other anticoagulants:94 cases from French pharmacovigilance centres and a literature review[J].Annales de Dermatologie et de Vénéréologie, 2022, 149(1):45-50.
[3] VERMA K, REAVEY-CANTWELL J, CAMERON B M.Apixaban-associated spontaneous thoracic intramedullary hemorrhage[J].Clinical Neurology and Neurosurgery, 2021, 202:106512.
[4] TIGLIOGLU M, AKYOL P, SAGLAM B, et al.Thrombocytopenia due to rivaroxaban:A rare adverse effect[J].Transfusion and Apheresis Science, 2020, 59(6):102883.
[5] TU M L, XU S Q, XU Z, et al.Identification of dual-function bovine lactoferrin peptides released using simulated gastrointestinal digestion[J].Food Bioscience, 2021, 39:100806.
[6] CHENG S Z, TU M L, LIU H X, et al.A novel heptapeptide derived from Crassostrea gigas shows anticoagulant activity by targeting for thrombin active domain[J].Food Chemistry, 2021, 334:127507.
[7] 李汉琪, 王治军, 郑清瑶, 等.食源性抗血栓活性肽的研究进展[J].食品科学, 2023, 44(17):268-277.
LI H Q, WANG Z J, ZHENG Q Y, et al.Research progress on foodborne antithrombotic peptides[J] Food Science, 2023, 44(17):268-277.
[8] 杨隆恩, 张永平, 张才, 等.海参酶解液对角叉菜胶所致小鼠血栓形成的抑制作用[J].广东海洋大学学报, 2018, 38(4):57-62.
YANG L E, ZHANG Y P, ZHANG C, et al.Inhibitory effect of sea cucumber enzymatic hydrolysate on carrageenan-induced thrombus formation in mice[J].Journal of Guangdong Ocean University, 2018, 38(4):57-62.
[9] 李亚娟, 王佳佳, 张才, 等.海参酶解液对斑马鱼糖尿病并发抑郁样行为的改善作用[J].广东海洋大学学报, 2019, 39(1):84-89.
LI Y J, WANG J J, ZHANG C, et al.Effect of sea cucumber hydrolysis extract on depression-like behavior of zebrafish induced by diabete[J] Journal of Guangdong Ocean University, 2019, 39(1):84-89.
[10] WANG Q Q, SHI J Y, ZHONG H, et al.High-degree hydrolysis sea cucumber peptides improve exercise performance and exert antifatigue effect via activating the NRF2 and AMPK signaling pathways in mice[J].Journal of Functional Foods, 2021, 86:104677.
[11] ZHANG J, LIU X, WANG Y K, et al.Transcriptome and metabolome analyses reveal gender-specific expression genes in sea cucumber (Holothuria leucospilota)[J].Comparative Biochemistry and Physiology Part D:Genomics and Proteomics, 2023, 47:101117.
[12] WEN J P, BO M, YANG L,et al. Developing artificial mixed diets for larval culture of sea cucumber, Holthuria leucospilota, and their effects on the internal microbiota. Aquaculture Reports,2023,33:101868.
[13] 郗亚凡, 林海生, 曹文红, 等.三种南海礁栖海参体壁营养成分分析[J].广东海洋大学学报, 2023, 43(2):113-119.
XI Y F, LIN H S, CAO W H,et al.Analysis of nutrient composition in the body wall of three south china sea reef dwelling sea cucumbers[J] Journal of Guangdong Ocean University, 2023, 43(2):113-119.
[14] CAI L, WU S W, JIA C G, et al.Active peptides with hypoglycemic effect obtained from hemp (Cannabis sativa L.) protein through identification, molecular docking, and virtual screening[J].Food Chemistry, 2023, 429:136912.
[15] CUI F C, XI L Q, ZHAO G Q, et al.Screening of xanthine oxidase inhibitory peptides by ligand fishing and molecular docking technology[J].Food Bioscience, 2022, 50:102152.
[16] MAO Z J, JIANG H, SUN J N, et al.Virtual screening and structure optimization of xanthine oxidase inhibitory peptides from whole protein sequences of Pacific white shrimp via molecular docking[J].Food Chemistry, 2023, 429:136837.
[17] ZHU J Y, SUN D, LI X T, et al.Developing new PI3Kγ inhibitors by combining pharmacophore modeling, molecular dynamic simulation, molecular docking, fragment-based drug design, and virtual screening[J].Computational Biology and Chemistry, 2023, 104:107879.
[18] CHENG S Z, WANG Y W, CHEN H, et al.Anticoagulant dodecapeptide suppresses thrombosis in vivo by inhibiting the thrombin exosite-I binding site[J].Journal of Agricultural and Food Chemistry, 2021.63(37):10920-10931
[19] RIVERO-PINO F, MILLAN-LINARES M C, MONTSERRAT-DE-LA-PAZ S.Strengths and limitations of in silico tools to assess physicochemical properties, bioactivity, and bioavailability of food-derived peptides[J].Trends in Food Science & Technology, 2023, 138:433-440.
[20] MATTHEWS J H, KRISHNAN R, COSTANZO M J, et al.Crystal structures of thrombin with thiazole-containing inhibitors:Probes of the S1′ binding site[J].Biophysical Journal, 1996, 71(5):2830-2839.
[21] TABERNO L, CHANG C Y, OHRINGER S L, et al.Structure of a retro-binding peptide inhibitor complexed with human α-thrombin[J].Journal of Molecular Biology, 1995, 246(1):14-20.
[22] DWIVEDI R, POMIN V H.Marine antithrombotics[J].Marine Drugs, 2020, 18(10):514.
[23] JACQUES S L, LEMASURIER M, SHERIDAN P J, et al.Substrate-assisted catalysis of the PAR1 thrombin receptor:Enhancement of macromolecular association and cleavage[J].Journal of Biological Chemistry, 2000, 275(52):40671-40678.
[24] LIU L W, VU T K, ESMON C T, et al.The region of the thrombin receptor resembling hirudin binds to thrombin and alters enzyme specificity[J].Journal of Biological Chemistry, 1991, 266(26):16977-16980.
[25] CHENG S Z, TU M L, LIU H X, et al.Food-derived antithrombotic peptides:Preparation, identification, and interactions with thrombin[J].Critical Reviews in Food Science and Nutrition, 2019, 59:S81-S95.
[26] BOURDON P, JABLONSKI J-A, CHAO B H, et al.Structure-function relationships of hirulog peptide interactions with thrombin[J].FEBS Letters, 1991, 294(3):163-166.
[27] CHEN F Y, HUANG G R.Mechanism and inhibition kinetics of peptide P13 as thrombin inhibitor[J].International Journal of Biological Macromolecules, 2020, 150:1046-1052.
[28] BODE W.Structure and interaction modes of thrombin[J].Blood Cells, Molecules, and Diseases, 2006, 36(2):122-130.
[29] XU R, HUANG Y B, HOU Y, et al.Isolation and identification of thrombin-inhibiting peptides derived from soybean protein[J].Food Biotechnology, 2022, 36(2):154-172.
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