Computational simulations of the interactions between acetyl-coenzyme-A carboxylase and clodinafop: Resistance mechanism due to active and nonactive site mutations

Journal of Chemical Information and Modeling

Volumn 49, Issue 8, 2009, Pages 1936-1943

  Zhu, Xiao Lei ^a   Hao, Ge Fei ^a   Zhna, Chang Guo ^b   Yang, Guang Fu ^a  

^a CENTRAL CHINA NORMAL UNIVERSITY   (China)

^b UNIVERSITY OF KENTUCKY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AGRICULTURAL ROBOTS; BINDING ENERGY; COMPUTATIONAL CHEMISTRY; HERBICIDES; HYDROGEN; MOLECULAR DYNAMICS; WEED CONTROL;

ACETYL-COA CARBOXYLASE; COMPUTATIONAL SIMULATION; CONFORMATIONAL CHANGE; HYDROGEN BONDING INTERACTIONS; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR MECHANISM; POISSON BOLTZMANN SURFACE AREAS (PBSA); RESISTANCE MECHANISMS;

HYDROGEN BONDS;

ACETYL COENZYME A CARBOXYLASE; CLODINAFOP; HERBICIDE; PROPIONIC ACID DERIVATIVE; PYRIDINE DERIVATIVE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; DRUG ANTAGONISM; ENZYMOLOGY; GENETICS; METABOLISM; POACEAE; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN MULTIMERIZATION; SITE DIRECTED MUTAGENESIS; THERMODYNAMICS;

ACETYL-COA CARBOXYLASE; COMPUTER SIMULATION; HERBICIDES; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED; POACEAE; PROPIONATES; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN MULTIMERIZATION; PYRIDINES; THERMODYNAMICS;

EID: 69549086564     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci900174d     Document Type: Article

References (48)

1. Nikolau, B. J.; Ohlrogge, J. B.; Wurtele, E. S. Plant biotin-containing carboxylases. Arch. Biochem. Biophys. 2003, 414, 211-222.
2. Egli, M. A.; Gengenbach, B. G.; Gronwald, J. W.; Somers, D. A.; Wyse, D. L. Characterization of maize acetyl-coenzyme A carboxylase. Plant. Physiol. 1993, 101, 499-506.
3. Rendina, A. R.; Craig-Kennard, A. C.; Beaudoin, J. D.; Breen, M. K. Inhibition of acetyl-coenzyme A carboxylase by two classes of grass-selective herbicides. J. Agrie Food Chem. 1990, 38, 1282-1287.
4. Burton, J. D.; Gronwald, J. W.; Keith, R. A.; Somers, D. A.; Gegenbach, B. G.; Wyse, D. L. Kinetics of inhibition of acetylcoenzyme A carboxylase by sethoxydim and haloxyfop. Pestic Biochem. Physiol. 1991, 39, 100-109.
5. Sasaki, Y.; Konishi, T.; Nagano, Y. The compartmentation of acetylcoenzyme A carboxylase in pants. Plant. Physiol. 1995, 108, 445-449.
6. Post-Beittenmiller, D. Biochemistry and molecular biology of wax production in plants. Annu. Rev. Plant. Physiol. Plant. Mol. Biol. 1996, 47, 405-430. (Pubitemid 126640362)
7. (7) Konishi, T.; Shinohara, K.; Yamada, K.; Sasaki, Y. Acetyl-CoA carboxylase in higher plants: most plants other than gramineae have both the prokaryotic and eukaryotic forms of this enzyme. Plant. Cell. Phusiol. 1996, 37, 117-122. (Pubitemid 126609626)
8. (8) Campbell, J. W.; Cronan, J. J. E. BACTERIAL FATTY ACID BIOSYNTHESIS: Targets for Antibacterial Drug Discovery. Annu. Rev. Microbiol. 2001, 55, 305-332. (Pubitemid 32978108)
9. Abu-Elheiga, L.; Matzuk, M. M.; K. Abo-Hashema, A. H.; Wakil, S. J. Continuous Fatty Acid Oxidation and Reduced Fat Storage in Mice Lacking Acetyl-CoA Carboxylase 2. Science 2001, 297, 2613-2616.
10. Lenhard, J. M.; Gottschalk, W. K. Preclinical developments in type 2 diabetes. Adv. Drug Delivery Rev. 2002, 54, 1199-1212.
11. Levert, K. L.; Waldrop, G. L.; Stephens, J. M. A Biotin Analog Inhibits Acetyl-CoA Carboxylase Activity and Adipogenesis. J. Biol. Chem. 2002, 277, 16347-16350.
12. Wakil, S. J.; Stoops, J. K.; Joshi, V. C. Fatty Acid Synthesis and its Regulation. Annu. Rev. Biochem. 1983, 52, 537-579.
13. (13) McGarry, J. D.; Brown, N. F. The Mitochondrial Carnitine Palmitoyltransferase System- From Concept to Molecular Analysis. Eur. J. Biochem. 1997, 244, 1-14. (Pubitemid 27079689)
14. Ramsay, R. R.; Gandour, R. D.; Van der Leij, F. R. Molecular enzymology of carnitine transfer and transport. Biochim. Biophys. Acta 2001, 1546, 21-43.
15. (15) Délye, C.; Zhang, X. Q.; Michel, S.; Matejicek, A.; Powles, S. B. Molecular bases for sensitivity to acetyl-coenzyme a carboxylase inhibitors in black-grass. Plant Physiol. 2005, 137, 794-806. (Pubitemid 43138151)
16. Liu, W. J.; Harrison, D. K.; Chalupska, D.; Gornicki, P.; O'Donnell, C. C.; Adkins, S. W.; Haselkorn, R.; Williams, R. R. Single-site mutations in the carboxyltransferase domain of plastid acetyl-CoA carboxylase confer resistance to grass-specific herbicides. Proc. Natl. Acad. Sci. USA. 2007, 104, 3627-3632.
17. (17) Yu, Q.; Collavo, C.; Zheng, M. Q.; Owen, M.; Sattin, M.; Powles, S. Diversity of ACCase mutations in resistant Lolium populations: Evaluation using clethodim. Plant. Physiol. 2007, 145, 547-558. (Pubitemid 47575137)
18. (18) Délye, C. Weed resistance to acetyl coenzyme A carboxylase inhibitors: an update. Weed Sci. 2005, 53, 728-746. (Pubitemid 44298129)
19. (19) Zhang, H.; Yang, Z. R.; Shen, Y.; Tong, L. Crystal structure of the carboxylase domain of acetyl coenzyme-A carboxylase. Science 2003, 299, 2064-2067. (Pubitemid 36383732)
20. (20) Zhang, H.; Tweet, B.; Tong, L. Molecular basis for the inhibiton of the carboxyltransferase domain of acetyl coenzyme-A carboxylase by haloxyfop and diclofop. Proc. Natl. Acad. Sci. USA. 2004, 107, 59105915. (Pubitemid 38520502)
21. (21) Sali, A.; Blundell, T. L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 1993, 234, 779-815. (Pubitemid 24007801)
22. Sali, A.; Overington, J. P. Derivation of rules for comparative protein modeling from a database of protein structure alignments. Protien Sei. 1994, 3, 1582-1596.
23. Laskowski, R. A.; MacArthur, M. W.; Moss, D. S.; Thornton, J. M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 1993, 26, 283-291.
24. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Verven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokumo, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, revision A. 1; Gaussian, Inc.: Pittsburgh, 2003.
25. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Kollmann, P. A. Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation. J. Am. Chem. Soc. 1993, 115, 9620-9631.
26. Zhu., X. L.; Zhang., L.; Chen., Q.; Wan,., J.; Yang., G. F. Interactions of Aryloxyphen- oxypropionic Acids with Sensitive and Resistant Acetyl-Coenzyme A Carboxylase by Homology Modeling and Molecular Dynamic Simulations. J. Chem. Inf. Model. 2006, 46, 1819-1826.
27. Gao, D. Q.; Cho, H.; Yang, W. C.; Pan, Y. M.; Yang, G. F.; Tai, H. H.; Zhan, C G. Computational design of a human butyrylcholinesterase mutant for accelerating cocaine hydrolysis based on the transition-state simulation. Angew. Chem., Int. Ed. 2006, 45, 653-657.
28. Pan, Y. M.; Gao, D. Q.; Yang, W. C.; Cho, H.; Yang, G. F.; Tai, H. H.; Zhan, C. G. Computational Redesign of Human Butyrylcholinesterase for Anti-Cocaine Medication. Proc. Natl. Acad. Sci. U.SA. 2005, 102, 16656-16661.
29. AbdulHameed, M. D. M.; Hamza, A.; Zhan, C. G. Microscopic modes and free energies of 3-phosphoinositide-dependent kinase-1 (PDKl) binding with celecoxib and other inhibitors. J. Phys. Chem. B 2006, 110, 26365-26374.
30. Hamza, A.; Cho, H.; Tai, H. H.; Zhan, C. G. Molecular dynamics simulation of cocaine binding with human butyrylcholinesterase and its mutants. J. Phys. Chem. B 2005, 109, 4776-4782.
31. (31) Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 2006, 65, 712-725. (Pubitemid 44583220)
32. Case, D. A.; Darden, T.; Cheatham, T. E., III; Simmerling, C.; Wang, J.; Duke, R. E.; Luo, R. AMBER8 Users' Manaual; University of California, 2004.
33. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983, 79, 926-935.
34. Berendsen, H. C; Postma. J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 1984, 87, 3684-3690.
35. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 1977, 23, 327-341.
36. Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: An N.log (N) method for Ewald sums in large systems. J. Chem. Phys. 1993, 98, 10089-10092.
37. Essmann, U.; Perera, L.; Berkowitz, M. L. A smooth particle mesh Ewald method. J. Chem. Phys. 1995, 103, 8577-8593.
38. Rafi, S. B.; Cui, G. L.; Song, K.; Cheng, X. L.; Tonge, P. J.; Simmerling, C Insight through Molecular Mechanics Poisson-Boltzmann Surface Area Calculations into the Binding Affinity of Triclosan and Three Analogues for FabI, the E. coli Enoyl Reductase. J. Med. Chem. 2006, 494574-494580
39. Hou, T. J.; Yu, R. Molecular Dynamics and Free Energy Studies on the Wild-type and Double Mutant HIV-1 Protease Complexed with Amprenavir and Two Amprenavir-Related Inhibitors: Mechanism for Binding and Drug Resistance. J. Med. Chem. 2007, 50, 1177-1188.
40. (40) Weis, A.; Katebzadeh, K.; Söderhjelm, P.; Nilsson, I.; Ryde, U. Ligand Affinities Predicted with the MM/PBSA Method: Dependence on the Simulation Method and the Force Field. J. Med. Chem. 2006, 49, 6596-6606. (Pubitemid 44657454)
41. Wu, E. L.; Mei, Y.; Han, K. L.; Zhang, Z. H. J. Quantum and Molecular Dynamics Study for Binding of Macrocyclic Inhibitors to Human a-Thrombin. Biophys. J. 2007, 92, 4244-4253.
42. Wu, E. L.; Han, K. L.; Zhang, Z. H. J. Selectivity of Neutral/Weakly Basic Pl Group Inhibitors of Thrombin and Trypsin by a Molecular Dynamics Study. Chem.-Eur. J. 2008, 14, 8704-8714.
43. (43) Bardi, J. S.; Luque, I.; Freire, E. Structure-based thermodynamic analysis of HIV-1 protease inhibitors. Biochemistry 1997, 36, 65886596. (Pubitemid 27242316)
44. Sitkoff, D.; Sharp, K. A.; Honig, B. Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models. J. Phys. Chem. 1994, 98, 1978-1988.
45. Connolly, M. L. Analytical molecular surface calculation. J. Appl. Crystallogr. 1983, 16, 548-558.
46. Hao, G. F.; Zhu, X. L.; Ji, F. Q.; Zhang, L.; Yang, G. G.; Zhan, C. G. Understanding the Mechanism of Drug Resistance Due to a Codon Deletion in Protoporphyrinogen Oxidase through Computational Modeling. J. Phys. Chem. B 2009, 113, 4865-4875.
47. Ji, F. Q.; Niu, C. W.; Chen, C. N.; Chen, Q.; Yang, G. F.; Xi, Z.; Zhan, C. G. Computational Design and Discovery of Conformationally Flexible Inhibitors of Acetohydroxyacid Synthase to Overcome Drug Resistance Associated with the W586L Mutation. ChemMedChem. 2008, 3, 1203-1206.
48. Pan, Y. M.; Gao, D. Q.; Zhan, C. G. Modeling the Catalysis of AntiCocaine Catalytic Antibody: Competing Reaction Pathways and Free Energy Barriers. J. Am. Chem. Soc. 2008, 130, 5140-5149.