A different mechanism for the inhibition of the carboxyltransferase domain of acetyl-coenzyme A carboxylase by tepraloxydim

Acetyl-CoA carboxylases (ACCs) are crucial metabolic enzymes and are attractive targets for drug discovery. Haloxyfop and tepraloxydim belong to two distinct classes of commercial herbicides and kill sensitive plants by inhibiting the carboxyltransferase (CT) activity of ACC. Our earlier structural studies showed that haloxyfop is bound near the active site of the CT domain, at the interface of its dimer, and a large conformational change in the dimer interface is required for haloxyfop binding. We report here the crystal structure at 2.3 Å resolution of the CT domain of yeast ACC in complex with tepraloxydim. The compound has a different mechanism of inhibiting the CT activity compared to haloxyfop, as well as the mammalian ACC inhibitor CP-640186. Tepraloxydim probes a different region of the dimer interface and requires only small but important conformational changes in the enzyme, in contrast to haloxyfop. The binding mode of tepraloxydim explains the structure-activity relationship of these inhibitors, and provides a molecular basis for their distinct sensitivity to some of the resistance mutations, as compared to haloxyfop. Despite the chemical diversity between haloxyfop and tepraloxydim, the compounds do share two binding interactions to the enzyme, which may be important anchoring points for the development of ACC inhibitors.

[1]  Liang Tong,et al.  Acetyl‐coenzyme A carboxylases: Versatile targets for drug discovery , 2006, Journal of cellular biochemistry.

[2]  H. Sham,et al.  Phenoxy thiazole derivatives as potent and selective acetyl-CoA carboxylase 2 inhibitors: Modulation of isozyme selectivity by incorporation of phenyl ring substituents. , 2007, Bioorganic & medicinal chemistry letters.

[3]  Z. Otwinowski,et al.  Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[4]  L. Tong,et al.  Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase in complex with CP-640186. , 2004, Structure.

[5]  M. Devine,et al.  Altered target sites as a mechanism of herbicide resistance , 2000 .

[6]  Martin M. Matzuk,et al.  Continuous Fatty Acid Oxidation and Reduced Fat Storage in Mice Lacking Acetyl-CoA Carboxylase 2 , 2001, Science.

[7]  Shawn P. Williams,et al.  The human ACC2 CT-domain C-terminus is required for full functionality and has a novel twist. , 2009, Acta crystallographica. Section D, Biological crystallography.

[8]  S. Srivastava,et al.  Synthesis of spiro[chroman-2,4'-piperidin]-4-one derivatives as acetyl-CoA carboxylase inhibitors. , 2009, Bioorganic & medicinal chemistry letters.

[9]  R. Haselkorn,et al.  An isoleucine/leucine residue in the carboxyltransferase domain of acetyl-CoA carboxylase is critical for interaction with aryloxyphenoxypropionate and cyclohexanedione inhibitors , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[10]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[11]  A. Rendina,et al.  Inhibition of acetyl-coenzyme A carboxylase by two classes of grass-selective herbicides , 1990 .

[12]  Liang Tong,et al.  Molecular basis for the inhibition of the carboxyltransferase domain of acetyl-coenzyme-A carboxylase by haloxyfop and diclofop. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[13]  S. Wakil,et al.  Fatty acid synthesis and its regulation. , 1983, Annual review of biochemistry.

[14]  S. Powles,et al.  Molecular Bases for Sensitivity to Acetyl-Coenzyme A Carboxylase Inhibitors in Black-Grass1 , 2005, Plant Physiology.

[15]  Robert Haselkorn,et al.  Single-site mutations in the carboxyltransferase domain of plastid acetyl-CoA carboxylase confer resistance to grass-specific herbicides , 2007, Proceedings of the National Academy of Sciences.

[16]  S. Powles,et al.  Six amino acid substitutions in the carboxyl-transferase domain of the plastidic acetyl-CoA carboxylase gene are linked with resistance to herbicides in a Lolium rigidum population. , 2006, The New phytologist.

[17]  L. Tong,et al.  Acetyl-coenzyme A carboxylase: crucial metabolic enzyme and attractive target for drug discovery , 2005, Cellular and Molecular Life Sciences CMLS.

[18]  J. W. Gronwald.  Lipid Biosynthesis Inhibitors , 1991, Weed Science.

[19]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[20]  Mike Carson,et al.  Ribbon models of macromolecules , 1987 .

[21]  J. W. Corbett,et al.  Inhibitors of mammalian acetyl-CoA carboxylase. , 2007, Recent patents on cardiovascular drug discovery.

[22]  Katsunori Tanaka,et al.  Mechanism of herbicidal activity of a new cyclohexane-1,3-dione, tepraloxydim to Poa annua L. , 2002 .

[23]  Liang Tong,et al.  Crystal Structure of the Carboxyltransferase Domain of Acetyl-Coenzyme A Carboxylase , 2003, Science.

[24]  D. Hargrove,et al.  Isozyme-nonselective N-Substituted Bipiperidylcarboxamide Acetyl-CoA Carboxylase Inhibitors Reduce Tissue Malonyl-CoA Concentrations, Inhibit Fatty Acid Synthesis, and Increase Fatty Acid Oxidation in Cultured Cells and in Experimental Animals* , 2003, Journal of Biological Chemistry.

[25]  G. Murshudov,et al.  Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.

[26]  S. Powles,et al.  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 Inhibitors1 , 2003, Plant Physiology.

[27]  J. Zondlo,et al.  Expression, purification, and characterization of human acetyl-CoA carboxylase 2. , 2007, Protein Expression and Purification.

[28]  H. Sham,et al.  Structure-activity relationships for a novel series of thiazolyl phenyl ether derivatives exhibiting potent and selective acetyl-CoA carboxylase 2 inhibitory activity. , 2006, Bioorganic & medicinal chemistry letters.

[29]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[30]  C. Chu,et al.  Expression, purification, and characterization of human and rat acetyl coenzyme A carboxylase (ACC) isozymes. , 2007, Protein expression and purification.

[31]  K. Sharp,et al.  Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons , 1991, Proteins.

[32]  J. Corbett.  Review of recent acetyl-CoA carboxylase inhibitor patents: mid-2007 – 2008 , 2009, Expert opinion on therapeutic patents.

[33]  H. J. Harwood,et al.  Treating the metabolic syndrome: acetyl-CoA carboxylase inhibition. , 2005, Expert opinion on therapeutic targets.