Inhibitors of FabI, an Enzyme Drug Target in the Bacterial Fatty Acid Biosynthesis Pathway

Abstract

The modern age of drug discovery, which had been slowly gathering momentum during the early part of the twentieth century, exploded into life in the 1940s with the isolation of penicillin and streptomycin. The immense success of these early drug discovery efforts prompted the general view that many infectious diseases would now be effectively controlled and even eradicated. However this initial optimism was misplaced, and pathogens such as multidrug-resistant Mycobacterium tuberculosis and methicillin-resistant Staphylococcus aureus present a major current threat to human health. Drug resistance arises through the unrelenting pressure of natural selection, and there is thus a continuing need to identify novel drug targets and develop chemotherapeutics that circumvent existing drug resistance mechanisms. In this Account, we summarize current progress in developing inhibitors of FabI, the NADH-dependent enoyl reductase from the type II bacterial fatty acid biosynthesis pathway (FAS-II), a validated but currently underexploited target for drug discovery. The FabI inhibitors have been divided into two groups, based on whether they form a covalent adduct with the NAD (+) cofactor. Inhibitors that form a covalent adduct include the diazaborines, as well as the front-line tuberculosis drug isoniazid. The NAD adducts formed with these compounds are formally bisubstrate enzyme inhibitors, and we summarize progress in developing novel leads based on these pharmacophores. Inhibitors that do not form covalent adducts form a much larger group, although generally these compounds also require the cofactor to be bound to the enzyme. Using structure-based approaches, we have developed a series of alkyl diphenyl ethers that are nanomolar inhibitors of InhA, the FabI from M. tuberculosis, and that are active against INH-resistant strains of M. tuberculosis. This rational approach to inhibitor development is based on the proposal that high-affinity inhibition of the FabI enzymes is coupled to the ordering of a loop of amino acids close to the active site. Compounds that promote loop ordering are slow onset FabI inhibitors with increased residence time on the enzyme. The diphenyl ether skeleton has also been used as a framework by us and others to develop potent inhibitors of the FabI enzymes from other pathogens such as Escherichia coli, S. aureus, and Plasmodium falciparum. Meanwhile chemical optimization of compounds identified in high-throughput screening programs has resulted in the identification of several classes of heteroaromatic FabI inhibitors with potent activity both in vitro and in vivo. Finally, screening of natural product libraries may provide useful chemical entities for the development of novel agents with low toxicity. While the discovery that not all pathogens contain FabI homologues has led to reduced industrial interest in FabI as a broad spectrum target, there is substantial optimism that FabI inhibitors can be developed for disease-specific applications. In addition, the availability of genome sequencing data...

Dynamics of Plasmodium falciparum enoyl‐ACP reductase and implications on drug discovery

“…2 Second, though fatty acids are essential for bacterial growth, they cannot be scavenged from the host and must be synthesized de novo. 3 Third, the pathway in most pathogenic prokaryotes is different from that in humans; consequently, drugs targeting the prokaryotic FAS pathway would be less likely to cause side effects by interacting with homologous human proteins. A detailed understanding of the structures and processes involved in type II FAS may therefore offer insight that will be helpful in future drug-discovery projects.…”

Slow Onset Inhibition of Bacterial β-Ketoacyl-acyl Carrier Protein Synthases by Thiolactomycin

“…Although many antibiotics, such as the ␤-lactams and vancomycin, target peptidoglycan biosynthesis, there is growing evidence that fatty acid biosynthesis is a promising target for drug discovery (6,7). This is particularly true for mycobacteria, where the frontline tuberculosis drug isoniazid compromises cell wall integrity by inhibiting the biosynthesis of mycolic acids, very long chain lipids that provide protection and allow the bacteria to persist in the human macrophage (8).…”

Structural Insights into the Acyl Intermediates of the Plasmodium falciparum Fatty Acid Synthesis Pathway

“…A number of enzymes involved in the process viz. ␤-ketoacyl acyl carrier protein (ACP) 5 synthase III, ␤-hydroxy acyl-ACP hydratase, and enoyl-ACP reductase are targets for drug design (1,2). An indispensable component, crucial for each step of the pathway, is a small acidic protein, the ACP.…”