Structure-based inhibitor design of AccD5, an essential acyl-CoA carboxylase carboxyltransferase domain of Mycobacterium tuberculosis

Abstract

Mycolic acids and multimethyl-branched fatty acids are found uniquely in the cell envelope of pathogenic mycobacteria. These unusually long fatty acids are essential for the survival, virulence, and antibiotic resistance of Mycobacterium tuberculosis. Acyl-CoA carboxylases (ACCases) commit acyl-CoAs to the biosynthesis of these unique fatty acids. Unlike other organisms such as Escherichia coli or humans that have only one or two ACCases, M. tuberculosis contains six ACCase carboxyltransferase domains, AccD1-6, whose specific roles in the pathogen are not well defined. Previous studies indicate that AccD4, AccD5, and AccD6 are important for cell envelope lipid biosynthesis and that its disruption leads to pathogen death. We have determined the 2.9-Å crystal structure of AccD5, whose sequence, structure, and active site are highly conserved with respect to the carboxyltransferase domain of the Streptomyces coelicolor propionyl-CoA carboxylase. Contrary to the previous proposal that AccD4 -5 accept long-chain acyl-CoAs as their substrates, both crystal structure and kinetic assay indicate that AccD5 prefers propionyl-CoA as its substrate and produces methylmalonyl-CoA, the substrate for the biosyntheses of multimethyl-branched fatty acids such as mycocerosic, phthioceranic, hydroxyphthioceranic, mycosanoic, and mycolipenic acids. Extensive in silico screening of National Cancer Institute compounds and the University of California, Irvine, ChemDB database resulted in the identification of one inhibitor with a K i of 13.1 M. Our results pave the way toward understanding the biological roles of key ACCases that commit acyl-CoAs to the biosynthesis of cell envelope fatty acids, in addition to providing a target for structure-based development of antituberculosis therapeutics.cell wall lipid ͉ multimethyl-branched fatty acid ͉ mycolic acid ͉ tuberculosis ͉ mycocerosic acid

Lipidomics reveals control of Mycobacterium tuberculosis virulence lipids via metabolic coupling

“…In the case of propionate addition, propionate is most likely converted directly from propionyl CoA to MMCoA via a propionyl CoA carboxylase. Several propionyl CoA carboxylase homologs exist in M. tuberculosis and one of these has recently been characterized (27). PDIM and SL-1 production are specifically affected while the rest of the lipid mass-spectrum observed in MutAB overexpressing cells was similar to wild-type (data not shown).…”

Antibacterial targets in fatty acid biosynthesis

“…Lead inhibitors of AccD5 were sought through in silico screens of the NCI diversity set and the ChemDB database at the University of California, Irvine [26]. A compound (NCI 65828) with a competitive K i = 13.1 μM was identified in the NCI set (Fig.…”

AccD6, a Key Carboxyltransferase Essential for Mycolic Acid Synthesis in Mycobacterium tuberculosis, Is Dispensable in a Nonpathogenic Strain

“…To date, the roles of accD4 and accD5 in mycolic acid biosynthesis have been studied (see Fig. S1 in the supplemental material) (21,28,38,51,58), and the expression profiles of all accD family members in M. tuberculosis are known (18).…”