Reproductive and Developmental Biology

The Korean Society of Animal Reproduction (한국동물번식학회)
권호 표지

Molecular Docking of Tetrahydrofuran-2-yl Analogues to Porcine Odorant Binding Proteins (pOBP & pPBP) and Binding Interactions

돼지 냄새물질 결합 단백질 (pOBP 및 pPBP)에 대한 Tetrahydrofuran-2-yl 유도체의 분자도킹과 결합 상호작용

  • Cho, Yun-Gi (Department of Applied Biolog & Environmental Chemistry, Chung-Nam National University) ;
  • Park, Chang-Sik (Research Center for Transgenic Cloned Pigs, Chung-Nam National University) ;
  • Sung, Nack-Do (Department of Applied Biolog & Environmental Chemistry, Chung-Nam National University)
  • 조윤기 (충남대학교 농업생명과학대학 응용생물환경화학과) ;
  • 박창식 (충남대학교 형질전환복제돼지연구센터) ;
  • 성낙도 (충남대학교 농업생명과학대학 응용생물환경화학과)
  • Received : 2010.01.28
  • Accepted : 2010.03.23
  • Published : 2010.03.31
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Abstract

The binding affinity constants ($p(Od)_{50}$) and molecular docking scores (OS) between porcine odorant binding proteins pOBP (1HQP) and pPBP (1GM6) as receptor and a series of tetrahydrofuran-2-yl (A & B) analogues as substrate, and their interactions were discussed quantitatively using three-dimensional quantitative structure-activity relationship (30-QSAR) models. The statistical qualities of the optimized CoMF A models for pOBP were better than those of the CoMSIA models. The binding affinity constants and OS between substrate and receptor molecules were dependent upon steric and hydrophobic interaction. The DS constants of the substrates into the binding site of OBP (1HQP) were bigger than those of PBP (1GM6). The resulting contour maps produced by the optimized CoMFA model were used to identify the structural features relevant to the binding affinity in binding site of pOBP.

Keywords

Acknowledgement

Supported by : 한국연구재단

References

  1. Beynon RJ, Hurst R (2004): Urinary proteins and the modulation of chemical scents in mice and rats. Peptides 23:1553-1563.
  2. Brennan PA (2001): The vomeronasal system. Cell Mol Life Sci 58:546-555. https://doi.org/10.1007/PL00000880
  3. Chen G, Luo X, Zhu W, Luo C, Liu H, Puah CM, Chen K, Jiang H (2004): Elucidating inhibitory models of the inhibitors of epidermal growth factor receptor by docking an 3D-QSAR. Eur J Med Chem 12:2409-2417.
  4. Dal Monte M, Centini M, Anselmi C, Pelosi P (1993): Binding of selected odorants to bovine and porcine odorant-binding proteins. Chem Sences 18:713-721. https://doi.org/10.1093/chemse/18.6.713
  5. Gerritsen R, Lnagendijk P, Soede NM, Kemp B (2005): Effeet of (artifical) boar stimuli on uterine activity in estrous sows. Theriogenology 64:1518-1525. https://doi.org/10.1016/j.theriogenology.2005.03.014
  6. Gohlke H, Klebe G (2002): Approaches to the description and prediction of the binding affinity of small-mollecule ligands to macromolecular receptors. Angew Chem Int 41:2644-2676. https://doi.org/10.1002/1521-3773(20020802)41:15<2644::AID-ANIE2644>3.0.CO;2-O
  7. Jain AN (2003): Sulflex: Fully automatic flexible molecular docking using a molecular similarity-based search engine. J Med Chem 46:499-511. https://doi.org/10.1021/jm020406h
  8. Krzymowski T, Grzegorzewski W, Stefanczyk, Krzymowska S, Skipor J, Wasowska B (1999): Humoral pathway for transfer of the boar pheromone, androstenol from the nasal mucosa to the brain and hypophysis of gilts. Theriogenology 52:1225-1240. https://doi.org/10.1016/S0093-691X(99)00200-9
  9. Lee SH, Yang SH, Lee KT, Kwon YJ, Cho WJ (2009): Molecular design, synthesis and docking study of benz[b] oxepines and 12-oxobenzo[c] phenan-thridinones as topoisomerase 1 inhibitors. Bioorganic & Medical Chemisry Letters 19:2444-2447. https://doi.org/10.1016/j.bmcl.2009.03.058
  10. Lindber W, Persson JA, Wold S (1988): Partial lesast- squares method for spectrofluorimetric analysis of mixture of humic acid and ligninsulfonate. Anal Chem 55:643-648.
  11. Lnagendijk P, Bouwman BG, Schams D, Soede NM, Kemp B (2003): Effeets of different sexual stimuli on oxytocin release, uterine activity and receptive behaviour in oestrous sows. Theriogenology 59:849-861. https://doi.org/10.1016/S0093-691X(02)01157-3
  12. Massimiliano P, Filippo M, Romina DG, Hugo LM (2001): Crystal structure of a truncated form of porcine odorant-binding protein. Proteins: Structure Function and Genetics 42:201-209. https://doi.org/10.1002/1097-0134(20010201)42:2<201::AID-PROT70>3.0.CO;2-7
  13. Pelosi P (1994): Odorant-binding proteins. Crit Rev Biochem Mol Biol 29:199-228. https://doi.org/10.3109/10409239409086801
  14. Pelosi P (1996): Perireceptor events in olfaction. J Neurobiol 30:3-19. https://doi.org/10.1002/(SICI)1097-4695(199605)30:1<3::AID-NEU2>3.0.CO;2-A
  15. Pelosi P (2001): The role of the perireceptor events in vertebrates olfaction. Cell Mol Life sci 58:503-509. https://doi.org/10.1007/PL00000875
  16. Peng H, Wang T, Xie Pe, Chen T, He HW, Wan J (2007): Molecular docking and three-dimensional quantitative structure-activity relationship studies on the binding modes of herbicidal 1-(substituted phenacetoxy)-alkylphosphonates to the E1 component of pyruvate dehydrogenase. J Agric Food Chem 55:1871-1880. https://doi.org/10.1021/jf062730h
  17. Quian L, Brian M, Karl S, Julian S (2007): Tagged fragment method for evolutionary structure-based de novo lead generation and optimization. J Med Chem 50:5392-5402. https://doi.org/10.1021/jm070750k
  18. Rekwo PI, Ogwu D, Oyedipe EO, Sekoni VO (2001): The role of pheromones and biostimulation in animal reproduction. Animal Reproduction Science 65:157-170. https://doi.org/10.1016/S0378-4320(00)00223-2
  19. Sankar R, Archunan G (2004): Flehmen response in bull: role of vaginal mucus and other body fluids of bovine with special reference to estrus. Behav Processes 67:81-86. https://doi.org/10.1016/j.beproc.2004.02.007
  20. Schneider G, Baringhaus, KH (2008); Molecular Design: Concepts and Applications. Wiley-VCH Verlag GmbH & Co. LGaA, Weinheim 149-192.
  21. Spinelli S, Vincent F, Pelosi P, Tegoni M, Cambillau (2002): Boar salivary lipocalin; Three-dimensional X-ray structure and androstenol/androstenone docking simulations. Eur J Biochem 269:2449-2456. https://doi.org/10.1046/j.1432-1033.2002.02901.x
  22. Sybyl, Version 8.1; Tripos Inc. St. Louis, USA 2009.
  23. Vincent F, Spinelli S, Ramoni R, Grolli S, Pelosi P, Cambillau C, Tegon M (2000): Complexes of porcine odorant binding protein with odorant molecules belonging to different chemical classes. J Mol Biol 300:127-139. https://doi.org/10.1006/jmbi.2000.3820
  24. Yi P, Qiu M (2008): 3D-QSAR and docking studies of aminopyridine carboxamide inhibitor of c-Jun N-terminal kinase-1. Eur J Med Chem 43:604-613. https://doi.org/10.1016/j.ejmech.2007.04.020
  25. 박창식, 최양석, 성낙도 (2007): 생물학적 자극통제 수단으로 활용하기 위한 돼지 페로몬 성 냄새물질의 탐 색: 2-(cyclohexyloxy)tetrahydrofurane 유도체 구조와 porcine odorant binding protein 사이의 결합 친화력에 관한 2D-Q5AR 모델. 동물번식학회지 31:15-20.
  26. 박창식, 송석오, 임재삼, 성민규, 성낙도 (2009): 생물학적 자극통제 수단으로 활용하기 위한 돼지 냄새물질의 탐색 $N^{1}$-allyl-$N^{2}$-(tetrahydrofuran-2 -ylmethyl)-oxalamide 분자의 합성과 돼지발정 유도 효과. 동물번식학회지 33:1-5.
  27. 성낙도, 박창식, 정훈성, 성민규 (2006): 생물학적 자극 통제 수단으로 활용하기 위한 돼지 페로몬성 냄새물질의 탐색: 2-(cyclohexyloxy)tetrahydrofurane 유도체 구조와 돼지 냄새물질 결합 단백질 사이의 결합 친화력에 관한 비교 분자장 분석(CoMFA). 동불번식학회지 30:13-19.
  28. 조윤기 (2009): 2-(Cyclohexyloxy)tetrahydrofurane 유도체의 Lipocalin에 대한 분자도킹과 높은 결합 친화력 화합물의 예측. 충남대학교 대학원 석사학위논문.