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

Abstract

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.diabetes ͉ fatty acid metabolism ͉ herbicides ͉ structure-based drug design A cetyl-CoA carboxylases (ACCs) catalyze the production of malonyl-CoA from acetyl-CoA and CO 2 in two steps (1-3). The biotin carboxylase (BC) activity catalyzes the ATPdependent carboxylation of a biotin cofactor, and then the carboxyltransferase (CT) activity catalyzes the transfer of this activated carboxyl group to the acceptor acetyl-CoA. In bacteria, the BC and CT activities reside in separate subunits of the ACC holoenzyme. In comparison, ACCs are large, multidomain enzymes in most eukaryotes, with highly conserved BC and CT domains.ACCs are crucial enzymes for the metabolism of fatty acids. Two isoforms of ACCs are present in mammals, and mice lacking ACC2 have elevated fatty acid oxidation and reduced body fat and body weight (4). ACCs are attractive targets for the discovery of anti-diabetes and anti-obesity agents (5, 6), and currently there is significant interest in understanding their catalysis, regulation, and mechanism of inhibition.The relevance of ACCs for drug discovery is also underscored by the fact that two distinct classes of compounds, as illustrated by haloxyfop (FOPs) and tepraloxydim (DIMs) (Fig. 1A), are potent inhibitors of ACCs from sensitive plants and are in wide use as herbicides (7-12). These compounds inhibit the CT activity, as does a potent inhibitor of mammalian ACCs, CP-640186 (13), suggesting that the CT domain may be a suitable target for discovering small-molecule inhibitors against ACCs.We have reported the crystal structures of the CT domain of yeast ACC and its complex with CoA (14), haloxyfop (15), and CP-640186 (16). In comparison, the human CT domain has been ...

The enzymes of biotin dependent CO2 metabolism: What structures reveal about their reaction mechanisms

“…All of the herbicides bind in the active site at the interface between the N-terminal domain of one subunit and the C-terminal domain of a neighboring monomer, and all block the acetyl-CoA binding site. [79][80][81] Obstructing the acetyl-CoA binding site is consistent with the observed competitive inhibition versus the product malonyl-CoA. 72 Earlier kinetic analyses with the aryloxyphenoxypropionates and the cyclohexandiones showed noncompetitive inhibition with respect to acetyl-CoA.…”

Mechanism for the inhibition of the carboxyltransferase domain of acetyl-coenzyme A carboxylase by pinoxaden

“…The binding mode of pinoxaden is similar to that of tepraloxydim (12) (Fig. 3A), even though the two compounds are rather distinct from each other chemically (Fig.…”

“…The position of this oxygen atom is also occupied by one of the carboxylate oxygen atoms of haloxyfop (Fig. 3B) (12), suggesting that it is an oxyanion in all three inhibitors (enolate in tepraloxydim and pinoxaden, Fig. 1A).…”

“…We have reported the crystal structures of the CT domain of yeast ACC and its complex with CoA (10), haloxyfop (11), and tepraloxydim (12). We have also reported the structure of the CT domain in complex with CP-640186 (13), a structurally distinct class of compounds that were identified as potent inhibitors of mammalian ACCs (14).…”

“…Despite their chemical diversity (Fig. 1A), haloxyfop and tepraloxydim share two common points of contact (or anchoring points) with the CT domain (12), which are crucial for the inhibitory activity of these two classes of herbicides.…”