Synthesis and structure–activity relationships of thiotetronic acid analogues of thiolactomycin

Sakya, Subas M.; Suarez-Contreras, Melani; Dirlam, John P.; O’Connell, Thomas N.; Hayashi, Shigeru; Santoro, Sheryl L.; Kamicker, Barbara J.; George, D. M.; Ziegler, Carl B.

doi:10.1016/s0960-894x(01)00567-4

Cited by 40 publications

(31 citation statements)

References 15 publications

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“…Since its discovery in 1982 as an antibacterial agent with low toxicity due to bacterial target selectivity, thiolactomycin has been proposed as a promising antibacterial lead and significant chemical modifications have been made (7,10,19,20,25,29,38,40,41). 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

193

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

193

192

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“…We examined the TLM-FabB cocrystal structure (52) and used it in conjunction with data from analyses of TLM analogs (23,30,58) and our own preliminary TLM-FabH docking study to…”

Section: Identification Of 12-dithiole-3-ones As Fabh Inhibitorsmentioning

confidence: 99%

“…1), a unique thiolactone antibiotic, is selective for the type II FAS and mimics MACP binding in the condensing enzymes (29,47,52). The low toxicity of TLM and its promising antibacterial and antiparasitic activities have led to numerous synthetic approaches for the generation of novel TLM analogues with improved activities (23,37,45,58).…”

mentioning

confidence: 99%

1,2-Dithiole-3-Ones as Potent Inhibitors of the Bacterial 3-Ketoacyl Acyl Carrier Protein Synthase III (FabH)

Reeve

Desai

et al. 2004

Antimicrob Agents Chemother

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The enzyme FabH catalyzes the initial step of fatty acid biosynthesis via a type II dissociated fatty acid synthase. The pivotal role of this essential enzyme, combined with its unique structural features and ubiquitous occurrence in bacteria, has made it an attractive new target for the development of antibacterial and antiparasitic compounds. We have searched the National Cancer Institute database for compounds bearing structural similarities to thiolactomycin, a natural product which exhibits a weak activity against FabH. This search has yielded several substituted 1,2-dithiole-3-ones that are potent inhibitors of FabH from both Escherichia coli (ecFabH) and Staphylococcus aureus (saFabH). The most potent inhibitor was 4,5-dichloro-1,2-dithiole-3-one, which had 50% inhibitory concentration (IC 50 ) values of 2 M (ecFabH) and 0.16 M (saFabH). The corresponding 3-thione analog exhibited comparable activities. Analogs in which the 4-chloro substituent was replaced with a phenyl group were also potent inhibitors, albeit somewhat less effectively (IC 50 values of 5.7 and 0.98 M for ecFabH and saFabH, respectively). All of the 5-chlorinated inhibitors were most effective when they were preincubated with FabH in the absence of substrates. The resulting enzyme-inhibitor complex did not readily regain activity after excess inhibitor was removed, suggesting that a slow dissociation occurs. In stark contrast, a series of inhibitors in which the 5-chloro substituent was replaced with the isosteric and isoelectronic trifluoromethyl group were poorer inhibitors (IC 50 values typically ranging from 25 to >100 M for both ecFabH and saFabH), did not require a preincubation period for maximal activity, and generated an enzymeinhibitor complex which readily dissociated. Possible modes of binding of 5-chloro-1,2-dithiole-3-ones and 5-chloro-1,2-dithiole-3-thiones with FabH which account for the role of the 5-chloro substituent were considered.Fatty acid biosynthesis, an essential process for all organisms, is catalyzed in plants and bacteria by a series of discrete dissociable enzymes and a central acyl carrier protein (ACP) (43). This set of enzymes is known collectively as a type II fatty acid synthase (FAS) and differs significantly from the type I FAS of metazoans, in which all of the enzymatic activities are contained on one or two polypeptides (12,31,67). The structural and mechanistic differences between the two FAS systems, in conjunction with the fact that the type I FAS is down regulated in well-nourished mammals (38, 39), have led to significant interest in components of the type II FAS as targets for the development of new antibacterial agents. Such agents may also have promise as novel antimalarials because protozoan parasites of the genus Plasmodium have been shown recently to contain a type II FAS in their apicoplast (53,62,63).Significant efforts and progress have been made in the understanding of small-molecule inhibition of two different components of the type II FAS. FabI (InhA), the enoyl ACP reductase that c...

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“…Indeed, triclosan (17,28) and isoniazid (2) are two commonly used antibacterial agents that are known to target fatty acid synthesis. The fungal antibiotic thiolactomycin (TLM) specifically targets bacterial condensing enzymes (49), and the search is intensifying for TLM derivatives that specifically target these enzymes from major pathogens (11,44). To complement these efforts, we have completed the structure of FabF from Streptococcus pneumoniae (spFabF) at 1.3-Å resolution, the highest resolution for any member of the superfamily.…”

mentioning

confidence: 99%

The 1.3-Angstrom-Resolution Crystal Structure of β-Ketoacyl-Acyl Carrier Protein Synthase II fromStreptococcus pneumoniae

Price¹,

Rock

White

2003

J Bacteriol

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The ␤-ketoacyl-acyl carrier protein synthases are members of the thiolase superfamily and are key regulators of bacterial fatty acid synthesis. As essential components of the bacterial lipid metabolic pathway, they are an attractive target for antibacterial drug discovery. We have determined the 1.3 Å resolution crystal structure of the ␤-ketoacyl-acyl carrier protein synthase II (FabF) from the pathogenic organism Streptococcus pneumoniae. The protein adopts a duplicated ␤␣␤␣␤␣␤␤ fold, which is characteristic of the thiolase superfamily. The two-fold pseudosymmetry is broken by the presence of distinct insertions in the two halves of the protein. These insertions have evolved to bind the specific substrates of this particular member of the thiolase superfamily. Docking of the pantetheine moiety of the substrate identifies the loop regions involved in substrate binding and indicates roles for specific, conserved residues in the substrate binding tunnel. The active site triad of this superfamily is present in spFabF as His 303, His 337, and Cys 164. Near the active site is an ion pair, Glu 346 and Lys 332, that is conserved in the condensing enzymes but is unusual in our structure in being stabilized by an Mg 2؉ ion which interacts with Glu 346. The active site histidines interact asymmetrically with Lys 332, whose positive charge is closer to His 303, and we propose a specific role for the lysine in polarizing the imidazole ring of this histidine. This asymmetry suggests that the two histidines have unequal roles in catalysis and provides new insights into the catalytic mechanisms of these enzymes.The ␤-ketoacyl-acyl carrier protein synthases catalyze the addition of two-carbon units onto the growing acyl chain during the elongation phase of fatty acid synthesis. This enzymatic activity involves what is an irreversible chemical event in biosynthetic pathways, the formation of a carbon-carbon bond via a Claisen-like condensation reaction (15). These condensing enzymes are members of a superfamily of enzymes whose members all catalyze essentially the same reaction. Included in the superfamily are the thiolases involved in fatty acid degradation (␤-oxidation) (46), or sterol biosynthesis (25), and the related enzymes that synthesize polyketides in plants and bacteria (18). Structural studies on this superfamily of enzymes have revealed that they share a common ␤␣␤␣␤␣␤␤ topology which is duplicated by an internal pseudodyad that may have arisen by gene duplication (26). Members of the superfamily that have been structurally characterized include the peroxisomal 3-ketoacyl-coenzyme A (3-ketoacyl-CoA) thiolases from a variety of organisms (26), an array of bacterial fatty acidcondensing enzymes (8,19,31,36,38,40,41,45), and the polyketide chalcone synthase (13). Based on the structural and functional differences between the enzymes, the superfamily is subdivided into three classes (31). The thiolases form one group, the fatty acid elongation-condensing enzymes form a second group, and those involved in polyketide synt...

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Synthesis and structure–activity relationships of thiotetronic acid analogues of thiolactomycin

Cited by 40 publications

References 15 publications

Discovery of FabH/FabF Inhibitors from Natural Products

Discovery of FabH/FabF Inhibitors from Natural Products

1,2-Dithiole-3-Ones as Potent Inhibitors of the Bacterial 3-Ketoacyl Acyl Carrier Protein Synthase III (FabH)

The 1.3-Angstrom-Resolution Crystal Structure of β-Ketoacyl-Acyl Carrier Protein Synthase II fromStreptococcus pneumoniae

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