The Korean Journal of Pesticide Science (농약과학회지)

The Korean Society of Pesticide Science (한국농약과학회)
권호 표지

Molecular Docking to Acetyl-CoA Carboxylase of 2-(4-(6-chloro-2-benzoxazolyl)oxy)phenoxy-N-phenylpropionamide Analogues and Their Herbicidal Activity

Acetyl-CoA Carboxylase에 대한 2-(4-(6-chloro-2-benzoxazolyl)oxy)phenoxy-N-phenylpropionamide 유도체들의 분자 도킹과 제초활성

  • Choi, Won-Seok (Department of Applied Biology & Chemistry, College of Agriculture and Life Sciences, Chungnam National University) ;
  • Sung, Nack-Do (Department of Applied Biology & Chemistry, College of Agriculture and Life Sciences, Chungnam National University)
  • 최원석 (충남대학교 농업생명과학대학 응용생물화학과) ;
  • 성낙도 (충남대학교 농업생명과학대학 응용생물화학과)
  • Received : 2010.08.12
  • Accepted : 2010.08.20
  • Published : 2010.09.30
Download PDF
⟨ Previous Next ⟩

Abstract

To search the new potent herbicidal agents by receptor-based approach, the interactions between receptor and substrate molecules from molecular docking to acetyl-CoA carboxylase(PDB code: 3K8X) of 2-(4-(6-chloro-2-benzoxazolyl)oxy)phenoxy-N-phenylpropionamide analogues (1-38) as substrate molecules were performed and discussed quantitatively. The most of the substrate molecules were formated 2 H-bonds between carbonyl oxygen atom of the substrate molecules and the amino acid residues (Ala1627 and Ile1735) in binding site of acetyl-CoA carboxylase (ACCase). But, the substrate molecules such as $R_l$=Acetyl substituents (6 & P9) were formated 3 H-bonds between H-bond acceptors in the substrate molecules and the H-bond donors in three amino acid residues including the rest residue (Gly 1998). Therefore, the inhibitory activity factors of the substrate molecules against ACCase are due to the H-bonding characters that will be able to apply to the optimization of herbicidal agents.

수용체 접근 방법으로 새로운 제초성 물질을 탐색하기 위하여 acetyl-CoA carboxylase(PDB code: 3K8X)에 대한 2-(4-(6-chloro-2-benzoxazolyl)oxy)phenoxy-N-phenylpropionamide 유도체(1-38)의 분자도킹으로부터 기질분자와 수용체 사이의 상호작용을 정량적으로 검토하였다. 대부분의 기질분자들은 ACCase의 반응점내 아미노산 잔기들(Ala1627 및 Ile1735) 사이에 2개의 수소결합이 생성되었다. 그러나 $R_1$=Acetyl 지환체(6 및 P9)와 같은 기질분자들은 나머지 잔기(Gly1998)를 포함하는 3개의 아미노산 잔기내 수소결합 주게들과 기질분자의 수소결합 받게들 사이에 3개의 수소결합이 생성되었다. 그러므로 수소결합 특성들에 기인한 기질분자들의 ACCase에 대한 저해활성 요소들은 제초성 물질을 최적화하는데 적용될 수 있을것이다.

Keywords

References

  1. Bakkali, Y., Ruiz-Santaella, J. P., Osuna, M. D., Wagner, J., Fischer, A. J. and Prado, R. D. (2007) Late watergrass (Echinochloa phyllopogon): Mechanisms involved in the resistance to fenoxaprop-pethyl. J. Agric. Food Chem. 55: 4052-4058. https://doi.org/10.1021/jf0624749
  2. Chonan, T., Tanaka, H., Yamamoto, D., Yashiro, M., Oi, T., Wakasugi, D., Ohoka-Sugita, A., Io, F., Koretsune, H. and Hiratate, A. (2010) Design and synthesis of disubstituted (4-piperidinyl)piperazine derivatives as potent acetyl-CoA carboxylase inhibitors. Bioorg. Med. Chem. Lett. 20:3965-3968. https://doi.org/10.1016/j.bmcl.2010.04.134
  3. Cronan Jr, J. E. and Waldrop, G. L. (2002) Multi-subunit acetyl-CoA carboxylases. Prog. Lipid Res. 41:407-435. https://doi.org/10.1016/S0163-7827(02)00007-3
  4. Delye, C., Zhang, X. -Q., Chalopin, C., Michel, S., Powles, S. B. (2003) An isoleucine residue within the carboxyl-transferase domain of multidomain acetyl-coenzyme A carboxylase is a major determinant of sensitivity to aryloxyphenoxypropionate but not to cyclohexanedione inhibitors. Plant Physiol. 132: 1716-1723. https://doi.org/10.1104/pp.103.021139
  5. Etter, M. C. (1990) Encoding and decoding hydrogen-bond patterns of organic compounds. Acc. Chem. Res. 23: 120-126. https://doi.org/10.1021/ar00172a005
  6. Gronwald, J. W. (1991) Lipid biosynthesis inhibitiors. Weed Sci. 39:435-449.
  7. Holt, P. A., Chaires, J. B. and Trent, J. O. (2008) Molecular Docking of Interactions and Groove-Binders to Nucleic Acids Using Autodock and Surflex. J. Chem. Inf. Model. 48:1602-1615. https://doi.org/10.1021/ci800063v
  8. HRAC (2002) Publications, Classification of Herbicides according to Mode of Action, Herbicide Resistance Action Committe, Plant Protection. Org/HRAC.
  9. Incledon, B. J. and Hall, J. C. (1997) Acetyl-CoA carboxylase: Quaternary structure and inhibition by graminicidal herbicides. Pestic. Biochem. Physiol. 57:255-271. https://doi.org/10.1006/pest.1997.2279
  10. Jain, A. N. (2003) Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. J Med Chem. 46:499-511. https://doi.org/10.1021/jm020406h
  11. Jain, A. J. (1996) Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities. J. Comp.-Aided Mol. Des. 10:427-440. https://doi.org/10.1007/BF00124474
  12. Kashani, F. B., Alizade, H. M. and Zand, E. (2007) Investigation the resistance of wild oat (avena ludoviciana Durieu.) to fenoxaprop-p-ethyl by whole plant bioassay and seed bioassay. Pakistan J. Biol. Sci. 10:72-77. https://doi.org/10.3923/pjbs.2007.72.77
  13. Levert, K., Waldrop, G. and Stephens, J. (2002) A biotin analog inhibits acetyl-CoA carboxylase activity and adipogenesis. J. Biol. Chem. 277:16347-16350. https://doi.org/10.1074/jbc.C200113200
  14. Lin, J., Chen, J., Wang, Y., Cai., X., Wei, X. and Qiao, X. (2008) More toxic and photoresistant products from photodegradation of fenoxaprop-p-ethyl. J. Agric. Food Chem. 56:8226-8230. https://doi.org/10.1021/jf801341s
  15. Patrick, A. H., Jonathan, B. C. and John, O. T. (2008) Molecular docking of interactions and groove-binders to nucleic acids using autodock and Surflex. J. Chem. Inf. Model. 48: 1602-1615. https://doi.org/10.1021/ci800063v
  16. Pornprom, T., Mahatamnuchoke, P. and Usui, K. (2006) The role of altered acetyl-CoA carboxylase in conferring resistance to fenoxaprop-P-ethyl in Chinese sprangletop (Leptochloa chinensis (L.) Nees). Pest Management Sci. 62:1109-1115. https://doi.org/10.1002/ps.1287
  17. Quian, L., Brian, M., Smith, K. and Smith, J. (2007) Tagged fragment method for evolution structure-based De Novo Lead generation and optimization. J. Med. Chem. 50:5392-5402. https://doi.org/10.1021/jm070750k
  18. Ramsay, R. R., Gandour, R. D., Van der Leij, F. R. (2001) Molecular enzymology of carnitine transfer and transport. Biochim. Biophys. Acta. 1546:21-43. https://doi.org/10.1016/S0167-4838(01)00147-9
  19. Rendia, A. R., Craig-Kennard, A. C., Beaudoin, J. D. and Breen, M. K. (1990) Inhibition of the acetyl-coenzyme A carboxylase by two class of grass-selective herbicides. J. Agric. Food Chem. 38:1282-1287. https://doi.org/10.1021/jf00095a029
  20. Sinilnikova, O. M., Ginolhac, S. M., Magnard, C., Leone, M., Anczukow, O., Hughes, D., Moreau, K., Thompson, D., Coutanson, C., Hall, J., Romestaing, P., Gerard, J. P., Bonadona, V., Lasset, C., Goldgar, D. E., Joulin, V., Venezia, N. D. and Lenoir, G. M. (2004) Acetyl-CoA carboxylase a gene and breast cancer susceptibility. Carcinogenesis. 25:2417-2424. https://doi.org/10.1093/carcin/bgh273
  21. Takahashi, A. S. and Tanaka, K. (2002) Mechanism of herbicidal activity of a new cyclohexane-1,3-dione, tepraloxydim to Poa annua L. Weed Biol. Management. 2:84-91. https://doi.org/10.1046/j.1445-6664.1999.00044.x
  22. Tanaka, S., Takahashi, M., Funaki, Y., Izumi, K., Takano, H. and Miyakado, M. (1995) Hydrophobicity and systematic activities of fungicidal triazoles and blaching herbicidal compounds, Ch. 8. pp. 108-119. In Classical and three-dimensional QSAR in Agrochemistry (Ed. Hansch, C. and Fujita, T.). ACS Symposium series No. 606, American Chemical society. Washington, DC. USA.
  23. Tripos L. P. (2009) A Certara-Company. 1699 S. Hanley Rd., St. Louis, MO 63144-2319, USA.
  24. Xiang, S., Callaghan, M. M., Watson, K. G. and Tong, L. (2009) A different mechanism for the inhibition of the carboxyltransferase domain of acetyl-coenzyme A carboxylase by tepraloxydim, Proc. Natl. Acad. Sci. USA. 106:20723-20727. https://doi.org/10.1073/pnas.0908431106
  25. Yusuf, D., Davis, A. M., Kleywegt, G. J. and Schmitt, S. (2008) An alternative method for the evaluation of docking performance: RSR vs. RMSD. J. Chem. Infor. Modeling. 48:1411-1422. https://doi.org/10.1021/ci800084x
  26. Zhang, H., Yang, Z., Shen, Y. and Tong, L. (2003) Crystal structure of the carboxyl-transferase domain of acetyl-coenzyme A carboxylase. Science. 299:2064-2067. https://doi.org/10.1126/science.1081366
  27. Zhang, H., Tweel, B. and ong, L. (2004) Molecular basis for the inhibition of the carboxyltransferase domain of acetyl coenzyme-A carboxylase by haloxyfop and diclofop, Proc. Natl. Acad. Sci. USA. 101:5910-5915. https://doi.org/10.1073/pnas.0400891101
  28. 성낙도, 이상호, 장해성, 김대황, 김진석 (1999) 2-(4-(6-chloro-2-benzoxazolyl)oxy)phenoxy-N-phenylpropionamide 유도체 중 N-phenyl 치환제들에 의한 벼와 피의 선택적 제초활성에 미치는 구조-활성관계. 한국농약과학회지. 3:11-19.
  29. 성낙도, 이상호, 고영관, 이경모, 김대황, 김태준 (2000a) 수답에서 2-(4-(6-chloro-2-benzxazolyl)oxy)phenoxy-N-phenylpropionamide 유도체중 N-phenyl 치환체들의 제초활성. 한국농약과학회지 4:21-28.
  30. 성낙도, 이상호, 류재욱, 우재춘, 구동완, 김대황 (2000b) 발아전 후 벼의 약해에 미치는 2-(4-(6-chloro-2-benzoxazolyl)oxy)phenoxy-N-phenylpropionamide 유도체중 N-phenyl 치환기의 효과. 한국농화학회지. 43:52-56.
  31. 성낙도, 송선섭 (2003) 제초제의 활성성분에 대한 물리-화학 파라미터의 범위. 한국농약과학회지, 7:58-65.
  32. 성낙도, 정훈성 (2005a) 새로운 2-(4-(6-chloro-2-benzoxazolyl)oxy)phenoxy-N-phenylpropionamide 유도체들의 제초활성에 관한 3차원적인 정량적 구조와 활성과의 관계. 한국응용생명화학회지. 48:252-257.
  33. 성낙도, 김대황, 정훈성 (2005b) 새로운 2-(4-(6-chloro-2-benzoxazolyl)oxy)phenoxy-N-phenylpropionamide 유도체들의 제초활성에 관한 HQSAR 모델과 높은 활성 화합물의 예측. 한국농약과학회지, 9:279-286.