Food and Fermentation Industries >

2023 , Vol. 49 >Issue 13: 144 - 151

DOI: https://doi.org/10.13995/j.cnki.11-1802/ts.035099

Screening of anti-inflammatory peptides from Ruditapes philippinarum by molecular docking

  • JIANG Yu ,
  • LIN Haisheng ,
  • QIN Xiaoming ,
  • GAO Jialong ,
  • CAO Wenhong ,
  • CHEN Zhongqin ,
  • ZHENG Huina ,
  • WU Bin
Expand
  • 1(College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China)
    2(Guangdong Key Laboratory of Aquatic Products Processing and Safety, Key Laboratory of Aquatic Products Deep Processing of Guangdong Universities, National Research and Development Branch Center for Shellfish Processing Technology (Zhanjiang), South China Sea Biological Resources Development and Utilization Collaborative Innovation Center, Zhanjiang 524088, China)

Received date: 2023-02-11

  Revised date: 2023-03-14

  Online published: 2023-08-07

Fold

Abstract

Screening of active peptides with anti-inflammatory effects of Ruditapes philippinarum based on molecular docking. In this study, the proteins of R. philippinarum were extracted by trichloroacetic acid-acetone precipitation and identified by 2-DE and LC-MS/MS. The main protein was enzymolized by BIOPEP-UWM and the PeptideRanker and ToxinPred programs were used to evaluate and predict the physicochemical properties of peptides. Molecular docking was performed using Discovery studio 2019 and AutoDock Vina to screen potential anti-inflammatory peptide fragments, the improvement of LPS-induced inflammation in RAW264.7 cells was verified by synthetic anti-inflammatory peptides. The results showed that tropomyosin and histone were the main proteins of muscle tissue. Eight potential unreported active peptides were screened to use tropomyosin as substrate by virtual enzymolysis. DQTF had seven amino acid residues and eight amino acid residues binding sites with TLR2 and TLR4 respectively, while GYTR was closely combined with ten amino acid residues in TLR2 molecule and seven amino acid residues in TLR4 molecule , with the binding energy lower than -5 kcal/mol, indicating that it was a potential anti-inflammatory peptide. The activity verification results showed that the two synthetic oligopeptides could significantly enhance the cell viability (P<0.001) and reduce the ability of NO production(P<0.05), showing great anti-inflammatory activity. In conclusion, virtual enzymolysis and molecular docking methods can be used to screen anti-inflammatory peptides derived from R. philippinarum.

Key words： Ruditapes philippinarum; tropomyosin; virtual enzymatic hydrolysis; molecular docking; RAW 264.7 cells; anti-inflammatory oligopeptides

Cite this article

JIANG Yu , LIN Haisheng , QIN Xiaoming , GAO Jialong , CAO Wenhong , CHEN Zhongqin , ZHENG Huina , WU Bin . Screening of anti-inflammatory peptides from Ruditapes philippinarum by molecular docking[J]. Food and Fermentation Industries, 2023 , 49(13) : 144 -151 . DOI: 10.13995/j.cnki.11-1802/ts.035099

References

[1] LIU W L, CHEN X W, LI H, et al.Anti-inflammatory function of plant-derived bioactive peptides:A review[J].Foods (Basel, Switzerland), 2022, 11(15):2361.
[2] XU J Z, YI M Q, DING L J, et al.A review of anti-inflammatory compounds from marine fungi, 2000—2018[J].Marine Drugs, 2019, 17(11):636.
[3] HOTAMISLIGIL G S.Inflammation, metaflammation and immunometabolic disorders[J].Nature, 2017, 542(7640):177-185.
[4] 饶梦微, 章超桦, 林海生, 等.菲律宾蛤仔肉不同提取物呈味特性[J].广东海洋大学学报, 2022, 42(1):90-97.
RAO M W, ZHANG C H, LIN H S, et al.Sensory characteristic of different extracts from Ruditapes philippinarum[J].Journal of Guangdong Ocean University, 2022, 42(1):90-97.
[5] 杨金兰, 李刘冬, 黄珂, 等.菲律宾蛤仔全脏器的营养成分分析与评价[J].中国渔业质量与标准, 2014, 4(2):26-31.
YANG J L, LI L D, HUANG K, et al.Analysis and evaluation on nutrients in whole viscera of Ruditapes philippinarum[J].Chinese Fishery Quality and Standards, 2014, 4(2):26-31.
[6] YU Y, FAN F J, WU D, et al.Antioxidant and ACE inhibitory activity of enzymatic hydrolysates from Ruditapes philippinarum[J].Molecules (Basel, Switzerland), 2018, 23(5):1 189.
[7] ZHANG Y, PAN D D, YANG Z C, et al.Angiotensin I-Converting enzyme (ACE) inhibitory and dipeptidyl Peptidase-4 (DPP-Ⅳ) inhibitory activity of umami peptides from Ruditapes philippinarum[J].LWT, 2021, 144:111265.
[8] WANG Q, LIU F J, WANG X M, et al.Preparation and hepatoprotective activities of peptides derived from mussels (Mytilus edulis) and clams (Ruditapes philippinarum)[J].Marine Drugs, 2022, 20(11):719.
[9] SONG Y H, CAI Q L, WANG S L, et al.The ameliorative effect and mechanisms of Ruditapes philippinarum bioactive peptides on obesity and hyperlipidemia induced by a high-fat diet in mice[J].Nutrients, 2022, 14(23):5066.
[10] JO C, KHAN F F, KHAN M I, et al.Marine bioactive peptides:Types, structures, and physiological functions[J].Food Reviews International, 2017, 33(1):44-61.
[11] 赵贵琴, 李婷婷, 宋敏杰, 等.分子对接技术筛选鲈鱼肌球蛋白中黄嘌呤氧化酶抑制肽[J].中国食品学报, 2021, 21(6):81-91.
ZHAO G Q, LI T T, SONG M J, et al.Screening of xanthine oxidase inhibitory peptide from bass myosin by molecular docking[J].Journal of Chinese Institute of Food Science and Technology, 2021, 21(6):81-91.
[12] 田文慧, 孙丽平, 张翠, 等.白啤中二肽基肽酶-IV抑制肽的虚拟筛选及活性分析[J].食品科学, 2022, 43(10):81-87.
TIAN W H, SUN L P, ZHANG C, et al.Virtual screening of activity evaluation of dipeptidyl peptidase-IV inhibitory peptides in white beer[J].Food Science, 2022, 43(10):81-87.
[13] LUO L X, ZHONG A, WANG Q, et al.Structure-based pharmacophore modeling, virtual screening, molecular docking, ADMET, and molecular dynamics (MD) simulation of potential inhibitors of PD-L1 from the library of marine natural products[J].Marine Drugs, 2021, 20(1):29.
[14] ZI J, ZHANG J Y, WANG Q H, et al.Proteomics study of rice embryogenesis:Discovery of the embryogenesis-dependent globulins[J].Electrophoresis, 2012, 33(7):1129-1138.
[15] UDONSOM R, REAMTONG O, ADISAKWATTANA P, et al.Immunoproteomics to identify species-specific antigens in Neospora caninum recognised by infected bovine sera[J].Parasite (Paris, France), 2022, 29:60.
[16] MINKIEWICZ P, DZIUBA J, IWANIAK A, et al.BIOPEP database and other programs for processing bioactive peptide sequences[J].Journal of AOAC International, 2008, 91(4):965-980.
[17] MOONEY C, HASLAM N J, POLLASTRI G, et al.Towards the improved discovery and design of functional peptides:Common features of diverse classes permit generalized prediction of bioactivity[J].PLoS One, 2012, 7(10):e45012.
[18] GUPTA S, KAPOOR P, CHAUDHARY K, et al.In silico approach for predicting toxicity of peptides and proteins[J].PLoS One, 2013, 8(9):e73957.
[19] JI C F, ZHANG Z Y, CHEN J R, et al.Immune-enhancing effects of a novel glucan from purple sweet potato Ipomoea batatas (L.) lam on RAW264.7 macrophage cells via TLR2-and TLR4-mediated pathways[J].Journal of Agricultural and Food Chemistry, 2021, 69(32):9313-9325.
[20] 黄平, 洪静霞, 米杰, 等.羊栖菜多酚通过核转录因子-κB/丝裂原活化蛋白激酶通路缓解脂多糖诱导的RAW264.7细胞炎症反应[J].食品科学, 2022, 43(23):141-148.
HUANG P, HONG J X, MI J, et al.Polyphenols from Sargassum fusiforme alleviate lipopolysaccharide-induced inflammatory reaction in RAW264.7 cells through nuclear transcription factor-κB/mitogen-activated protein kinase pathway[J].Food Science, 2022, 43(23):141-148.
[21] 章超桦,薛长湖.水产食品学[M].北京:中国农业出版社,2010.
ZHANG C H,XUE C H.Aquatic Food Science[M].Beijing:China Agricultural Press,2010.
[22] 陈艳楠, 邱智军, 刘学强, 等.紫贻贝(Mytilus edulis)蛋白计算机模拟消化物活性的生物信息学分析[J].食品与发酵工业, 2022, 48(15):185-192.
CHEN Y N, QIU Z J, LIU X Q, et al.Bioinformatics analysis of the bioactivities of in silico digest from Mytilus edulis proteins[J].Food and Fermentation Industries, 2022, 48(15):185-192.
[23] 孙洁, 李燕, 郑昌亮, 等.中国毛虾二肽基肽酶-IV抑制肽的分离纯化与结构鉴定[J].食品与发酵工业, 2023, 49(1):160-167.
SUN J, LI Y, ZHENG C L, et al.Isolation, purification and structural identification of dipeptidyl peptidase-IV inhibitory peptide from China shrimp[J].Food and Fermentation Industries, 2023, 49(1):160-167.
[24] GUHA S, MAJUMDER K.Structural-features of food-derived bioactive peptides with anti-inflammatory activity:A brief review[J].Journal of Food Biochemistry, 2019, 43(1):e12531.
[25] GONZÁLEZ-MONTOYA M, HERNÁNDEZ-LEDESMA B, SILVÁN J M, et al.Peptides derived from in vitro gastrointestinal digestion of germinated soybean proteins inhibit human colon cancer cells proliferation and inflammation[J].Food Chemistry, 2018, 242:75-82.
[26] TAO X, HUANG Y K, WANG C, et al.Recent developments in molecular docking technology applied in food science:A review[J].International Journal of Food Science & Technology, 2020, 55(1):33-45.
[27] SU L J, WANG Y, WANG J M, et al.Structural basis of TLR2/TLR1 activation by the synthetic agonist diprovocim[J].Journal of Medicinal Chemistry, 2019, 62(6):2938-2949.
[28] 朱丹丹, 江世贵, 黄建华, 等.斑节对虾性腺组织、细胞的原代培养条件优化[J].水产科学, 2019, 38(2):163-172.
ZHU D D, JIANG S G, HUANG J H, et al.Optimization of tissue and primary cell culture of tiger shrimp Penaeus monodon[J].Fisheries Science, 2019, 38(2):163-172.
[29] 储倩. 醇溶性鲟鱼软骨多肽的制备及抗炎活性研究[D].镇江:江苏大学, 2021.
CHU Q.Preparation of ethanol-soluble polypeptide from sturgeon cartilage and anti-inflammatory activity[D].Zhenjiang:Jiangsu University,2021.
[30] LEE S J, KIM E K, KIM Y S, et al.Purification and characterization of a nitric oxide inhibitory peptide from Ruditapes philippinarum[J].Food and Chemical Toxicology, 2012, 50(5):1660-1666.
Options
Outlines

/

〈 〉

Powered by Beijing Magtech Co. Ltd,.