First X-ray Cocrystal Structure of a Bacterial FabH Condensing Enzyme and a Small Molecule Inhibitor Achieved Using Rational Design and Homology Modeling

Daines, R. A.; Pendrak, Israil; Sham, Kelvin; Aller, Glenn S. Van; Konstantinidis, Alex K.; Lonsdale, John T.; Janson, Cheryl A.; Qiu, Xiayang; Brandt, Martín; Khandekar, Sanjay S.; Silverman, Carol; Head, Martha S.

doi:10.1021/jm025571b

Cited by 71 publications

(76 citation statements)

References 8 publications

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“…Phomallenic acids, along with other FabH and FabF/B inhibitors (5,14,22,24), provide additional opportunities for development of new antibiotics with novel modes of action to overcome the threat posed by emerging resistant pathogens.…”

Section: Discussionmentioning

confidence: 99%

Discovery of FabH/FabF Inhibitors from Natural Products

Young

Jayasuriya

Ondeyka

et al. 2006

Antimicrob Agents Chemother

192

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Condensing enzymes are essential in type II fatty acid synthesis and are promising targets for antibacterial drug discovery. Recently, a new approach using a xylose-inducible plasmid to express antisense RNA in Staphylococcus aureus has been described; however, the actual mechanism was not delineated. In this paper, the mechanism of decreased target protein production by expression of antisense RNA was investigated using Northern blotting. This revealed that the antisense RNA acts posttranscriptionally by targeting mRNA, leading to 5 mRNA degradation. Using this technology, a two-plate assay was developed in order to identify FabF/ FabH target-specific cell-permeable inhibitors by screening of natural product extracts. Over 250,000 natural product fermentation broths were screened and then confirmed in biochemical assays, yielding a hit rate of 0.1%. All known natural product FabH and FabF inhibitors, including cerulenin, thiolactomycin, thiotetromycin, and Tü3010, were discovered using this whole-cell mechanism-based screening approach. Phomallenic acids, which are new inhibitors of FabF, were also discovered. These new inhibitors exhibited target selectivity in the gel elongation assay and in the whole-cell-based two-plate assay. Phomallenic acid C showed good antibacterial activity, about 20-fold better than that of thiolactomycin and cerulenin, against S. aureus. It exhibited a spectrum of antibacterial activity against clinically important pathogens including methicillinresistant Staphylococcus aureus, Bacillus subtilis, and Haemophilus influenzae.Hundreds of essential proteins have been identified in bacteria as potential drug targets (1,16,18,23). Of these, only a few are targets of therapeutically useful drugs. These include penicillin binding proteins, D-Ala-D-Ala ligase, MurA, undecaprenyl pyrophosphate, and alanine racemase for cell wall; 30S and 50S ribosomal subunits, elongation factor G, and IletRNA synthetase for protein synthesis; RNA polymerase for RNA synthesis; InhA (FabI) for fatty acid synthesis; dihydrofolate reductase (FolA) and p-aminobenzoic acid synthase (FolP) for metabolism; and DNA gyrase and topoisomerase IV for DNA synthesis. In past decades, extensive chemical modification of existing antibiotics has afforded improved activity against their targets. This strategy served well to develop new and effective antibiotics; however, such modification is becoming increasingly difficult and identification of new classes of compounds with different modes of action is critical to combat emerging resistance and meet clinical needs.

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Section: Discussionmentioning

confidence: 99%

Discovery of FabH/FabF Inhibitors from Natural Products

Young

Jayasuriya

Ondeyka

et al. 2006

Antimicrob Agents Chemother

192

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“…Presumably, the repressible construct for fabHB allows sufficient residual expression to allow growth. FabHA and FabHB are therefore isologous, and biochemical data (15,20) suggest that they are 3-oxoacyl-[acyl carrier protein] synthases involved in fatty acid biosynthesis. They are duplicated in P. aeruginosa.…”

Section: Vol 189 2007mentioning

confidence: 99%

“…They are conserved as single enzymes in E. coli, S. aureus, S. pneumoniae, E. faecalis, and H. influenzae and absent from humans, so this enzyme is a good antibacterial target. Indeed, there are reports of antibacterial discovery programs directed at the single enzyme in E. coli (20).…”

Section: Vol 189 2007mentioning

confidence: 99%

Essential Bacterial Functions Encoded by Gene Pairs

et al. 2007

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To address the need for new antibacterials, a number of bacterial genomes have been systematically disrupted to identify essential genes. Such programs have focused on the disruption of single genes and may have missed functions encoded by gene pairs or multiple genes. In this work, we hypothesized that we could predict the identity of pairs of proteins within one organism that have the same function. We identified 135 putative protein pairs in Bacillus subtilis and attempted to disrupt the genes forming these, singly and then in pairs. The single gene disruptions revealed new genes that could not be disrupted individually and other genes required for growth in minimal medium or for sporulation. The pairwise disruptions revealed seven pairs of proteins that are likely to have the same function, as the presence of one protein can compensate for the absence of the other. Six of these pairs are essential for bacterial viability and in four cases show a pattern of species conservation appropriate for potential antibacterial development. This work highlights the importance of combinatorial studies in understanding gene duplication and identifying functional redundancy.

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“…In a control experiment, when a known FabH inhibitor (Fig. 3D) (30) was tested in this assay it blocked FabH activity, leading to loss of accumulation of acetoacetyl-ACP [IC 50 ϭ 2 g/ml (3.96 M) for FabH] (Fig. 3B and data not shown).…”

mentioning

confidence: 99%

Discovery of platencin, a dual FabF and FabH inhibitor with in vivo antibiotic properties

Wang

Kodali²,

Lee³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

367

366

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Emergence of bacterial resistance is a major issue for all classes of antibiotics; therefore, the identification of new classes is critically needed. Recently we reported the discovery of platensimycin by screening natural product extracts using a target-based whole-cell strategy with antisense silencing technology in concert with cell free biochemical validations. Continued screening efforts led to the discovery of platencin, a novel natural product that is chemically and biologically related but different from platensimycin. Platencin exhibits a broad-spectrum Gram-positive antibacterial activity through inhibition of fatty acid biosynthesis. It does not exhibit cross-resistance to key antibiotic resistant strains tested, including methicillin-resistant Staphylococcus aureus, vancomycin-intermediate S. aureus, and vancomycin-resistant Enterococci. Platencin shows potent in vivo efficacy without any observed toxicity. It targets two essential proteins, ␤-ketoacyl-[acyl carrier protein (ACP)] synthase II (FabF) and III (FabH) with IC 50 values of 1.95 and 3.91 g/ml, respectively, whereas platensimycin targets only FabF (IC 50 ‫؍‬ 0.13 g/ml) in S. aureus, emphasizing the fact that more antibiotics with novel structures and new modes of action can be discovered by using this antisense differential sensitivity wholecell screening paradigm.platensimycin ͉ natural product ͉ thiolactomycin ͉ antisense ͉ fatty acid synthesis

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First X-ray Cocrystal Structure of a Bacterial FabH Condensing Enzyme and a Small Molecule Inhibitor Achieved Using Rational Design and Homology Modeling

Cited by 71 publications

References 8 publications

Discovery of FabH/FabF Inhibitors from Natural Products

Discovery of FabH/FabF Inhibitors from Natural Products

Essential Bacterial Functions Encoded by Gene Pairs

Discovery of platencin, a dual FabF and FabH inhibitor with in vivo antibiotic properties

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