Bacterial fatty acid metabolism in modern antibiotic discovery

Abstract

Bacterial fatty acid synthesis is essential for many pathogens and different from the mammalian counterpart. These features make bacterial fatty acid synthesis a desirable target for antibiotic discovery. The structural divergence of the conserved enzymes and the presence of different isozymes catalyzing the same reactions in the pathway make bacterial fatty acid synthesis a narrow spectrum target rather than the traditional broad spectrum target. Furthermore, bacterial fatty acid synthesis inhibitors are single-targeting, rather than multi-targeting like traditional monotherapeutic, broad-spectrum antibiotics. The single-targeting nature of bacterial fatty acid synthesis inhibitors makes overcoming fast-developing, target-based resistance a necessary consideration for antibiotic development. Target-based resistance can be overcome through multi-targeting inhibitors, a cocktail of single-targeting inhibitors, or by making the single targeting inhibitor sufficiently high affinity through a pathogen selective approach such that target-based mutants are still susceptible to therapeutic concentrations of drug. Many of the pathogens requiring new antibiotic treatment options encode for essential bacterial fatty acid synthesis enzymes. This review will evaluate the most promising targets in bacterial fatty acid metabolism for antibiotic therapeutics development and review the potential and challenges in advancing each of these targets to the clinic and circumventing target-based resistance. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.

Keywords: Antibiotic discovery; Bacterial fatty acid synthesis; Resistance.

Fig. 1

The conserved, core enzymes in bacterial FASII. The first committed step of fatty acid synthesis is the irreversible carboxylation of acetyl-CoA by the acetyl-CoA carboxylase enzyme complex to make malonyl-CoA, the building block of fatty acids. Next, malonyl-CoA is converted into malonyl-ACP by FabD. FabH initiates fatty acid synthesis by catalyzing the Claisen condensation of acetyl-CoA with malonyl-ACP to make acetoacetyl-ACP. From here, the acyl-ACP is elongated 2 carbons per cycle by the elongation enzymes. First, the β-ketoacyl-ACP (including acetoacetyl-ACP) is reduced by FabG to make β-hydroxyacyl-ACP. Next, β-hydroxyacyl-ACP is dehydrated by FabZ to make trans-2-enoyl-ACP. trans-2-Enoyl-ACP is reduced by enoyl-ACP reductase to make acyl-ACP. Acyl-ACP is elongated by the Claisen condensation reaction with a malonyl-ACP by FabF to increase the acyl chain by another 2 carbons and start another round of elongation. Acyl-ACP of sufficient length is used by the acyltransferase system to make phosphatidic acid from glycerol-3-phosphate. Certain bacteria make branched-chain anteiso fatty acids. The FabH of these bacteria use 2-methylbutyryl-CoA instead of acetyl-CoA in the first Claisen condensation reaction. The rate-limiting enzymatic steps that would make good drug targets are in a green box. The equilibrium enzymatic steps that would make poor drug targets are in a red box.

Fig. 2

Structures of validated FASII inhibitors. The validated molecular targets in FASII are the acetyl-CoA carboxylase, the condensing enzymes (FabH and FabF), and the enoyl-ACP reductase FabI.

Fig. 3

The advantage and disadvantage of side-chain interactions in single-target antibiotic design. In this example of a single-target antibiotic, AFN-1252 and NADPH bind to the active site of Staphylococcus aureus FabI (PDBID: 4FS3). The FabI protein structure is depicted as a wheat colored cartoon diagram. NADPH is depicted as sticks, and the Met-99 and Tyr-147 side-chains (light blue) contact the AFN-1252 (green). Tyr-147 interacts with the 3-methylbenzofuran portion of AFN-1252 and is involved in catalysis. Although the mutation of Tyr-147 residue to histidine imparts resistance, it also results in a severe catalytic defect and a slower growth rate. The variable Met-99 interacts with the oxotetrahydronaphthyridine portion of AFN-1252. Mutation of the Met-99 to threonine caused a 128 fold increase in resistance with minimal effects on the strain fitness, meaning that this missense mutation could lead to rapid development of clinical resistance. The Met-99 is only found in Staphylococcus FabI and is responsible for the high-affinity, pathogen-selective property of AFN-1252.