Discovery of anti-hypertensive oligopeptides from adlay based on in silico proteolysis and virtual screening

International Journal of Molecular Sciences

Volumn 17, Issue 12, 2016, Pages

  Qiao, Liansheng ^a   Li, Bin ^a   Chen, Yankun ^a   Li, Lingling ^a   Chen, Xi ^a   Wang, Lingzhi ^a   Lu, Fang ^a   Luo, Ganggang ^a   Li, Gongyu ^a   Zhang, Yanling ^a  

^a University of Chinese Medicine   (China)

Author keywords

Adlay; Angiotensin I converting enzyme (ACE); Hypertension; In silico proteolysis; Molecular dynamics (MD); Oligopeptides

Indexed keywords

ANTIHYPERTENSIVE AGENT; DIPEPTIDYL CARBOXYPEPTIDASE; DIPEPTIDYL CARBOXYPEPTIDASE INHIBITOR; HIS383 PEPTIDE; HIS387 PEPTIDE; HIS513 PEPTIDE; LISINOPRIL; OLIGOPEPTIDE; UNCLASSIFIED DRUG; VAL518 PEPTIDE; ZINC ION; PEPTIDE LIBRARY;

AMINO ACID SEQUENCE; ANTIHYPERTENSIVE ACTIVITY; ARTICLE; CHEMICAL ANALYSIS; COIX; COIX LARCHRYMA JOBI; COMPUTER MODEL; CONTROLLED STUDY; CRYSTAL STRUCTURE; DRUG DESIGN; ENZYME INHIBITION; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR DOCKING; MOLECULAR DYNAMICS; NONHUMAN; PEPTIDE LIBRARY; PHARMACOPHORE; PROTEIN DEGRADATION; PROTEIN INTERACTION; REVERSED PHASE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; SCREENING; CHEMISTRY; COMPUTER INTERFACE; COMPUTER SIMULATION; DRUG DEVELOPMENT; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; PRECLINICAL STUDY; PROTEIN DATABASE; REVERSED PHASE LIQUID CHROMATOGRAPHY; TIME FACTOR; X RAY CRYSTALLOGRAPHY;

ANGIOTENSIN-CONVERTING ENZYME INHIBITORS; ANTIHYPERTENSIVE AGENTS; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; CHROMATOGRAPHY, REVERSE-PHASE; COIX; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; DRUG DISCOVERY; DRUG EVALUATION, PRECLINICAL; MOLECULAR DOCKING SIMULATION; OLIGOPEPTIDES; PEPTIDE LIBRARY; PROTEOLYSIS; TIME FACTORS; USER-COMPUTER INTERFACE;

EID: 85006836492     PISSN: 16616596     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms17122099     Document Type: Article

References (53)

1. Wu, H.; Ren, C.; Yang, F.; Qin, Y.; Zhang, Y.; Liu, J. Extraction and identification of collagen-derived peptides with hematopoietic activity from Colla Corii Asini. J. Ethnopharmacol. 2016, 182, 129-136.
2. Liu, R.; Wang, M.; Duan, J.A.; Guo, J.M.; Tang, Y.P. Purification and identification of three novel antioxidant peptides from Cornu Bubali (water buffalo horn). Peptides 2010, 31, 786-793.
3. Wu, Q.; Du, J.; Jia, J.; Cong, K. Production of ace inhibitory peptides from sweet sorghum grain protein using alcalase: Hydrolysis kinetic, purification and molecular docking study. Food Chem. 2016, 199, 140-149.
4. Agrawal, H.; Joshi, R.; Gupta, M. Isolation, purification and characterization of antioxidative peptide of pearl millet (Pennisetum glaucum) protein hydrolysate. Food Chem. 2016, 204, 365-372.
5. Kuo, C.C.; Chen, H.H.; Chiang, W. Adlay (yi yi; “soft-shelled job’s tears”; the seeds of coix lachryma-jobi l. Var. Ma-yuen stapf) is a potential cancer chemopreventive agent toward multistage carcinogenesis processes. J. Tradit. Complement. Med. 2012, 2, 267-275.
6. Lin, L.J.; Hsiao, E.S.L.; Tseng, H.S. Molecular cloning, mass spectrometric identification, and nutritional evaluation of 10 coixins in adlay (Coix lachryma-jobi L.). J. Agric. Food Chem. 2009, 57, 10916-10921.
7. Watanabe, M.; Kato, M.; Ayugase, J. Anti-diabetic effects of adlay protein in type 2 diabetic db/db mice. Food Sci. Technol. Res. 2012, 18, 383-390.
8. Kim, S.O.; Yun, S.J.; Jung, B.; Lee, E.H.; Hahm, D.H.; Shim, I.; Lee, H.J. Hypolipidemic effects of crude extract of adlay seed (Coix lachrymajobi var. Mayuen) in obesity rat fed high fat diet: Relations of TNF-α and leptin mRNA expressions and serum lipid levels. Life Sci. 2004, 75, 1391-1404.
9. Yuan, J.; Liang, Y.; Cui, S.; Zhang, X.; Wang, L.; Qiao, Y. Angiotensin I converting enzyme inhibitory and antioxidant activity of adlay (Coix lacryma-jobi l. Var. Ma-yuen stapf) glutelin hydrolysate. Ital. J. Food Sci. 2014, 26, 282.
10. Minkiewicz, P.; Dziuba, J.; Iwaniak, A.; Dziuba, M.; Darewicz, M. Biopep database and other programs for processing bioactive peptide sequences. J. Aoac Int. 2008, 91, 965-980. [PubMed]
11. Gasteiger, E.; Hoogland, C.; Gattiker, A.; Duvaud, S.E.; Wilkins, M.R.; Appel, R.D.; Bairoch, A. Protein identification and analysis tools on the expasy server. Prot. Protoc. Handb. 2005, 112, 571-607.
12. Lau, C.C.; Abdullah, N.; Shuib, A.S. Novel angiotensin i-converting enzyme inhibitory peptides derived from an edible mushroom, pleurotus cystidiosus O.K. Miller identified by LC-MS/MS. BMC Complement. Altern. Med. 2013, 13, 1-10.
13. Otte, J.; Shalaby, S.M.; Zakora, M.; Pripp, A.H.; El-Shabrawy, S.A. Angiotensin-converting enzyme inhibitory activity of milk protein hydrolysates: Effect of substrate, enzyme and time of hydrolysis. Int. Dairy J. 2007, 17, 488-503.
14. Puchalska, P.; García, M.C.; Marina, M.L. Identification of native angiotensin-I converting enzyme inhibitory peptides in commercial soybean based infant formulas using HPLC-Q-TOF-MS. Food Chem. 2014, 157, 62-69.
15. Chang, Y.W.; Hunag, B.B.; Lin, H.C. Analysis of proteins and potential bioactive peptides from tilapia (oreochromis spp.) processing co-products using proteomic techniques coupled with biopep database. J. Funct. Foods 2015, 19, 629-640.
16. Dziuba, B.; Dziuba, M. New milk protein-derived peptides with potential antimicrobial activity: An approach based on bioinformatic studies. Int. J. Mol. Sci. 2014, 15, 14531-14545.
17. Lafarga, T.; O’Connor, P.; Hayes, M. Identification of novel dipeptidyl peptidase-IV and angiotensin-I-converting enzyme inhibitory peptides from meat proteins using in silico analysis. Peptides 2014, 59, 53-62.
18. Ghanbari, R.; Zarei, M.; Ebrahimpour, A.; Abdulhamid, A.; Ismail, A.; Saari, N. Angiotensin-I converting enzyme (ACE) inhibitory and anti-oxidant activities of sea cucumber (Actinopyga lecanora) hydrolysates. Int. J. Mol. Sci. 2015, 16, 28870-28885.
19. Khaket, T.P.; Singh, J. Potential of plant’s dipeptidyl peptidase I & II homologs in generation of ace inhibitory peptides. Int. J. Pept. Res. Ther. 2016, 1-10.
20. Miyoshi, S.; Ishikawa, H.; Kaneko, T.; Fukui, F.; Tanaka, H.; Maruyama, S. Structures and activity of angiotensin-converting enzyme inhibitors in an α-zein hydrolysate. Agric. Biol. Chem. 1991, 55, 1313-1318.
21. Yokomizo, A.; Takenaka, Y.; Takenaka, T. Antioxidative activity of peptides prepared from OKARA protein. Food Sci. Technol. Res. 2002, 8, 357-359.
22. Morifuji, M.; Koga, J.; Kawanaka, K.; Higuchi, M. Branched-chain amino acid-containing dipeptides, identified from whey protein hydrolysates, stimulate glucose uptake rate in l6 myotubes and isolated skeletal muscles. J. Nutr. Sci. Vitaminol. 2009, 55, 81-86.
23. Liu, X.; Ouyang, S.; Yu, B.; Liu, Y.; Huang, K.; Gong, J.; Zheng, S.; Li, Z.; Li, H.; Jiang, H. Pharmmapper server: A web server for potential drug target identification using pharmacophore mapping approach. Nucleic Acids Res. 2010, 38, 609-614.
24. Wang, X.; Pan, C.; Gong, J.; Liu, X.; Li, H. Enhancing the enrichment of pharmacophore-based target prediction for the polypharmacological profiles of drugs. J. Chem. Inf. Model. 2016, 56, 1175-1183.
25. Shao, Y.; Qiao, L.; Wu, L.; Sun, X.; Zhu, D.; Yang, G.; Zhang, X.; Mao, X.; Chen, W.; Liang, W.; et al. Structure identification and anti-cancer pharmacological prediction of triterpenes from ganoderma lucidum. Molecules 2016, 21, 678.
26. Sakkiah, S.; Thangapandian, S.; John, S.; Yong, J.K.; Lee, K.W. 3D QSAR pharmacophore based virtual screening and molecular docking for identification of potential HSP90 inhibitors. Eur. J. Med. Chem. 2010, 45, 2132-2140.
27. He, X.Y.; Lu, L.; Qiu, J.; Zou, P.; Yu, F.; Jiang, X.K.; Li, L.; Jiang, S.; Liu, S.; Xie, L. Small molecule fusion inhibitors: Design, synthesis and biological evaluation of (Z)-3-(5-(3-benzyl-4-oxo-2-thioxothiazolidinylidene)methyl)-N-(3-carboxy-4-hydroxy)phenyl-2,5-dimethylpyrroles and related derivatives targeting HIV-1 gp41. Bioorg. Med. Chem. 2013, 21, 7539-7548.
28. Zhou, X.; Yu, S.; Su, J.; Sun, L. Computational study on new natural compound inhibitors of pyruvate dehydrogenase kinases. Int. J. Mol. Sci. 2016, 17, 340.
29. Ramanathan, N.; Schwager, S.L.U.; Sturrock, E.D.; Ravi, A. Crystal structure of the human angiotensin-converting enzyme-lisinopril complex. Nature 2003, 421, 551-554.
30. Kang, N.; Lee, J.H.; Lee, W.W.; Ko, J.Y.; Kim, E.A.; Kim, J.S.; Heu, M.S.; Kim, G.H.; Jeon, Y.J. Gallic acid isolated from spirogyra sp. Improves cardiovascular disease through a vasorelaxant and antihypertensive effect. Environ. Toxicol. Pharmacol. 2015, 39, 764-772.
31. Muhammad, S.A.; Fatima, N. In silico analysis and molecular docking studies of potential angiotensin-converting enzyme inhibitor using quercetin glycosides. Pharmacogn. Mag. 2015, 11, 123-126.
32. Geoffrey, M.; Mohd, A.; Bertrand, C.; Fabrice, B.; Schwager, S.L.U.; Sturrock, E.D.; R Elwyn, I.; Vincent, D.; Ravi, A. Crystal structures of highly specific phosphinic tripeptide enantiomers in complex with the angiotensin-I converting enzyme. FEBS J. 2014, 281, 956.
33. Kramer, G.J.; Mohd, A.; Schwager, S.L.; Masuyer, G.; Acharya, K.R.; Sturrock, E.D.; Bachmann, B.O. Interkingdom pharmacology of angiotensin-I converting enzyme inhibitor phosphonates produced by actinomycetes. ACS Med. Chem. Lett. 2014, 5, 346-351.
34. Zhang, Y.; Skolnick, J. TM-align: A protein structure alignment algorithm based on the TM-score. Nucleic Acids Res. 2005, 33, 2302-2309.
35. Duan, Y.T.; Yao, Y.F.; Huang, W.; Makawana, J.A.; Teraiya, S.B.; Thumar, N.J.; Tang, D.J.; Tao, X.X.; Wang, Z.C.; Jiang, A.Q. Synthesis, biological evaluation, and molecular docking studies of novel 2-styryl-5-nitroimidazole derivatives containing 1,4-benzodioxan moiety as Fak inhibitors with anticancer activity. Bioorg. Med. Chem. 2014, 22, 2947-2954.
36. Wu, G.; Robertson, D.H.; Iii, C.L.B.; Vieth, M. Detailed analysis of grid-based molecular docking: A case study of cdocker—A charmm-based MD docking algorithm. J. Comput. Chem. 2003, 24, 1549-1562.
37. Qiao, L.; He, Y.; Huo, X.; Jiang, L.; Chen, Y.; Chen, X.; Zhang, Y.; Li, G. Construction and evaluation of merged pharmacophore based on peroxisome proliferator receptor-α agonists. Chin. J. Chem. Phys. 2016, 29, 508-516.
38. Ni, H.; Li, L.; Liu, G.; Hu, S.Q. Inhibition mechanism and model of an angiotensin I-converting enzyme (ACE)-inhibitory hexapeptide from yeast (Saccharomyces cerevisiae). PLoS ONE 2012, 7, 1529-1536.
39. Watermeyer, J.M.; Kröger, W.L.; O’Neill, H.G.; Sewell, B.T.; Sturrock, E.D. Probing the basis of domain-dependent inhibition using novel ketone inhibitors of angiotensin-converting enzyme. Biochemistry 2008, 47, 5942-5950.
40. Wu, Q.; Jia, J.; Yan, H.; Du, J.; Gui, Z. A novel angiotensin-i converting enzyme (ACE) inhibitory peptide from gastrointestinal protease hydrolysate of silkworm pupa (Bombyx mori) protein: Biochemical characterization and molecular docking study. Peptides 2014, 68, 17-24.
41. Jimsheena, V.K.; Gowda, L.R. Arachin derived peptides as selective angiotensin i-converting enzyme (ACE) inhibitors: Structure-activity relationship. Peptides 2010, 31, 1165-1176.
42. Ebrahimi, M.; Mani-Varnosfaderani, A.; Khayamian, T.; Gharaghani, S. An in silico approach to design peptide mimetics based on docking and molecular dynamics simulation of EGFR–matuzumab complex. J. Iran. Chem. Soc. 2016, 13, 1-13.
43. Huang, H.J.; Jian, Y.R.; Chen, Y.C. Traditional chinese medicine application in HIV: An in silico study. J. Biomol. Struct. Dyn. 2014, 32, 1-12.
44. Kapil, J.; Dara, A.; Elizabeth, S.M. Targeting PKC-β II and PKB connection: Design of dual inhibitors. Mol. Inform. 2011, 30, 329-344.
45. Meslamani, J.; Li, J.; Sutter, J.; Stevens, A.; Bertrand, H.O.; Rognan, D. Protein-ligand-based pharmacophores: Generation and utility assessment in computational ligand profiling. J. Chem. Inform. Model. 2012, 52, 943-955.
46. Jain, U.K.; Bhatia, R.K.; Rao, A.R.; Singh, R.; Saxena, A.K.; Sehar, I. Design and development of halogenated chalcone derivatives as potential anticancer agents. Trop. J. Pharm. Res. 2014, 13, 73-80.
47. Sakkiah, S.; Thangapandian, S.; Lee, K.W. Pharmacophore modeling, molecular docking, and molecular dynamics simulation approaches for identifying new lead compounds for inhibiting aldose reductase 2. J. Mol. Model. 2012, 18, 3267-3282.
48. Wu, Y.; Chong, H.; Yang, G.; Shan, H.; Ying, L.; Lai, L. Dynamic modeling of human 5-lipoxygenase-inhibitor interactions helps to discover novel inhibitors. J. Med. Chem. 2012, 55, 2597-2605.
49. Schüttelkopf, A.W.; van Aalten, D.M.F. PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr. Sect. D 2004, 60, 1355-1363.
50. Nandy, S.K.; Bhuyan, R.; Seal, A. Modelling family 2 cystatins and their interaction with papain. J. Biomol. Struct. Dyn. 2013, 31, 649-664.
51. Borah, P.K.; Chakraborty, S.; Jha, A.N.; Rajkhowa, S.; Duary, R.K. In silico approaches and proportional odds model towards identifying selective adam17 inhibitors from anti-inflammatory natural molecules. J. Mol. Gr. Model. 2016, 70, 129-139.
52. Menchon, G.; Bombarde, O.; Trivedi, M.; Négrel, A.; Inard, C.; Giudetti, B.; Baltas, M.; Milon, A.; Modesti, M.; Czaplicki, G. Structure-based virtual ligand screening on the XRCC4/DNA ligase iv interface. Sci. Rep. 2016, 6, 1-13.
53. Jiang, L.; Zhang, X.; Chen, X.; He, Y.; Qiao, L.; Zhang, Y.; Li, G.; Xiang, Y. Virtual screening and molecular dynamics study of potential negative allosteric modulators of mGluR1 from Chinese herbs. Molecules 2015, 20, 12769-12786.