A Mechanism for the Potent Inhibition of Eukaryotic Acetyl-Coenzyme A Carboxylase by Soraphen A, a Macrocyclic Polyketide Natural Product

Abstract

Acetyl-coenzyme A carboxylases (ACCs) have crucial roles in fatty acid metabolism. Soraphen A, a macrocyclic polyketide natural product, is a nanomolar inhibitor against the biotin carboxylase (BC) domain of human, yeast, and other eukaryotic ACCs. Here we report the crystal structures of the yeast BC domain, alone and in complex with soraphen A. Soraphen has extensive interactions with an allosteric site, about 25 A from the active site. The specificity of soraphen is explained by large structural differences between the eukaryotic and prokaryotic BC in its binding site, confirmed by our studies on the effects of single-site mutations in this binding site. Unexpectedly, our structures suggest that soraphen may bind in the BC dimer interface and inhibit the BC activity by disrupting the oligomerization of this domain. Observations from native gel electrophoresis confirm this structural insight. The structural information provides a foundation for structure-based design of new inhibitors against these enzymes.

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

“…The crystal structure of the biotin carboxylase domain of the Aquifex aeolicus pyruvate carboxylase, however, also showed the B-domain in an open conformation. 23 In contrast, crystal structures of the apo biotin carboxylase domains from yeast acetylCoA carboxylase, 24 human acetyl-CoA carboxylase 2, 25 and Bacillus thermodenitrificans pyruvate carboxylase 26 all demonstrated conformations for the Bdomains somewhere between the closed and completely open forms. Recent molecular dynamics studies of E. coli biotin carboxylase suggest that the most stable position for the B-domain may not be in the completely open state in the absence of substrate but rather in a partially closed state.…”

“…9(d)]. 24 Crystals of the yeast enzyme, in complex with soraphen A, contain three subunits in the asymmetric unit, and these subunits demonstrate neither dimeric nor trimeric associations. It is thought that soraphen A functions by inhibiting dimerization.…”

Chemical Inhibition of Acetyl-CoA Carboxylase Induces Growth Arrest and Cytotoxicity Selectively in Cancer Cells

“…It displays potent antifungal activities that have been attributed to its ability to bind to the biotin carboxylase domain dimer interface of eukaryotic ACCs, thereby disrupting the oligomerization of the enzyme and inhibiting its activity (27)(28)(29)(30)(31)(32). Soraphen A has been shown to inhibit also human ACCs in an isoform-nonselective manner (31).…”

Myxobacterial secondary metabolites: bioactivities and modes-of-action

“…In addition, identification of ACC as the protein target enabled more detailed study of soraphen's mode-of-action, including the determination of its binding site within the ACC, the catalytic BC domain. 174 Furthermore, the crystal structures of soraphen A bound to the BC domain of yeast 175 ( Fig. 1) and human ACC 176 strongly suggests that the inhibitory effect of the metabolite arises from binding in the BC dimer interface, interrupting its oligomerization -thus soraphen is a protein-protein interaction inhibitor.…”