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The X-ray crystal structures for the complexes of three designer antibiotics, compounds 1, 2, and 3, bound to two models for the ribosomal aminoacyl-tRNA site (A site) at 2.5-3.0 Angstroms resolution and that of neamine at 2.8 Angstroms resolution are described. Furthermore, the complex of antibiotic 1 bound to the A site in the entire 30S ribosomal subunit of Thermus thermophilus is reported at 3.8 Angstroms resolution. Molecular dynamics simulations revealed that the designer compounds provide additional stability to bases A1492 and A1493 in their extrahelical forms. Snapshots from the simulations were used for free energy calculations, which revealed that van der Waals and hydrophobic effects were the driving forces behind the binding of designer antibiotic 3 when compared to the parental neamine.

The structure of neamine bound to the A site of the bacterial ribosomal RNA was used in the design of novel aminoglycosides. The design took into account stereo and electronic contributions to interactions between RNA and aminoglycosides, as well as a random search of 273 000 compounds from the Cambridge structural database and the National Cancer Institute 3-D database that would fit in the ribosomal aminoglycoside-binding pocket. A total of seven compounds were designed and subsequently synthesized, with the expectation that they would bind to the A-site RNA. Indeed, all synthetic compounds were found to bind to the target RNA comparably to the parent antibiotic neamine, with dissociation constants in the lower micromolar range. The synthetic compounds were evaluated for antibacterial activity against a set of important pathogenic bacteria. These designer antibiotics showed considerably enhanced antibacterial activities against these pathogens, including organisms that hyperexpressed resistance enzymes to aminoglycosides. Furthermore, analyses of four of the synthetic compounds with two important purified resistance enzymes for aminoglycosides indicated that the compounds were very poor substrates; hence the activity of these synthetic antibiotics does not appear to be compromised by the existing resistance mechanisms, as supported by both in vivo and in vitro experiments. The design principles disclosed herein hold the promise of the generation of a large series of designer antibiotics uncompromised by the existing mechanisms of resistance.

Aminoglycoside 3'-phosphotransferases [APH(3')s] phosphorylate aminoglycoside antibiotics, a reaction that inactivates the antibiotics. These enzymes are the primary cause of resistance to aminoglycosides in bacteria. APH(3')-Ia operates by a random-equilibrium BiBi mechanism, whereas APH(3')-IIIa catalyzes its reaction by the Theorell-Chance mechanism, a form of ordered BiBi mechanism. Hence, both substrates have to be present in the active site prior to the transfer of phosphate by both mechanisms. Four bisubstrate analogues, compounds 1-4, were designed and synthesized as inhibitors for APH(3')s. These compounds are made of adenosine linked covalently to the 3'-hydroxyl of neamine (an aminoglycoside) via all-methylene tethers of 5-8 carbons. The K(i) values measured for these compounds indicated that affinities of APH(3')-Ia and APH(3')-IIa for compounds 2 and 3 (six- and seven-carbon tethers, respectively) were the best, and the inhibition constants for the two were comparable.

Room-temperature acid-catalyzed methanolysis of 7-formamido-, 7-acetamido-, or 7-isobutyramido-2-methylquinoline-5,8-diones (3, 4, 5) gives good to excellent yields of 7-amino-2-methylquinoline-5,8-dione (6). Simple methods for the synthesis of novel 7-amino-6-chloro-2-methylquinoline-5,8-dione (7), 7-alkoxy-2-methylquinoline-5,8-diones (9−11), and quinoline quinols (12, 13) are described, and the corresponding mechanisms are discussed. The replacement of an amino group on a quinone ring by alkoxy groups to produce 9−11 is reported for the first time and offers easy routes for the syntheses of these alkoxy derivatives. Also, the 1,2-addition of an ethyl group (rather than the expected 1,4-addition of a cyano group) of the reagent diethylaluminum cyanide to a quinolinedione is another novel reaction for the efficient preparation of quinoline quinols 12 and 13. An easy transformation of amino compound 6 to its acetamido derivative 4 is also described.

Novel 1-(t-butyldimethylsilyloxy)-1-aza-1,3-butadienes 1 and 2 are prepared by the reaction of O-(t-butyldimethylsilyloxy)hydroxylamine with methyl vinyl ketone and methacrolein, respectively. Azadienes 1 and 2 through sharing of oxygen nonbonding electrons are activated and thus their Diels-Alder reactions with a number of halobenzoquinones, napthoquinones and N-phenylmaleimide regiospecifically give low to good yields of various pyridine heterocycles.

The novel 7-(N-formyl-, 7-(N-acetyl-, and 7-(N-isobutyrylamino)-2-methylquinoline-5,8-diones were synthesized in excellent overall yields in three steps via the nitration of the commercially available 8-hydroxy-2-methylquinoline followed by a reduction-acylation step and then oxidation. Acid hydrolysis of 7-(N-acetylamino)-2-methylquinoline-5,8-dione (14a) afforded the novel 7-aminoquinoline-5,8-dione 7 in excellent yields. Due to our efficient preparation of dione 14a, we now report a short and practical method for the total synthesis of the potent antitumor agent lavendamycin methyl ester (1b) with an excellent overall yield.

The novel 7-(N-formyl-, 7-(N-acetyl-, and 7-(N-isobutyrylamino)-2-methylquinoline-5,8-diones were synthesized in excellent overall yields in three steps via the nitration of the commercially available 8-hydroxy-2-methylquinoline followed by a reduction−acylation step and then oxidation. Acid hydrolysis of 7-(N-acetylamino)-2-methylquinoline-5,8-dione (14a) afforded the novel 7-aminoquinoline-5,8-dione 7 in excellent yields. Due to our efficient preparation of dione 14a, we now report a short and practical method for the total synthesis of the potent antitumor agent lavendamycin methyl ester (1b) with an excellent overall yield.

Novel 1-(t-butyldimethylsilyloxy)-1-aza-1,3-butadienes 1 and 2 are prepared by the reaction of O-(t-butyldimethylsilyloxy)hydroxylamine with methyl vinyl ketone and methacrolein, respectively. Azadienes 1 and 2 through sharing of oxygen nonbonding electrons are activated and thus their Diels-Alder reactions with a number of halobenzoquinones, napthoquinones and N-phenylmaleimide regiospecifically give low to good yields of various pyridine heterocycles.

Aminoglycoside 3'-phosphotransferases [APH(3')s] are important bacterial resistance enzymes for aminoglycoside antibiotics. These enzymes phosphorylate the 3'-hydroxyl of these antibiotics, a reaction that inactivates the drug. A series of experiments were carried out to shed light on the details of the turnover chemistry by these enzymes. Quench-flow pre-steady-state kinetic analyses of the reactions of Gram-negative APH(3') types Ia and IIa with kanamycin A, neamine, and their respective difluorinated analogues 4'-deoxy-4',4'-difluorokanamycin A and 4'-deoxy-4',4'-difluoroneamine were carried out, in conjunction with measurements of thio effect and viscosity studies. The fluorinated analogues were shown to be severely impaired as substrates for these enzymes. The magnitude of the effect of the impairment of the fluorinated substrates was in the same range as when the D198A mutant APH(3')-Ia was studied with nonfluorinated substrates. Residue 198 is the proposed active site base that promotes the aminoglycoside hydroxyl for phosphorylation. These findings collectively argue that the Gram-negative APH(3')s show significant nucleophilic participation in the transition state for the phosphate transfer reaction.

The ribosome is an important target for aminoglycoside antibiotics; however, the clinical effectiveness of aminoglycosides has diminished due to bacterial resistance mechanisms. Here we report the X-ray structure of a novel synthetic aminoglycoside bound to the A site of the ribosome, its target for manifestation of activity. The structure validates the in silico design paradigms for the antibiotic and reveals the molecular interactions made by this novel antibiotic in prokaryotes.

Publisher Summary This chapter describes antibacterials as wonder drugs and discusses how their effectiveness is being compromised. Treatment of infections by bacterial pathogens became possible only in the twentieth century. Virtually all classes of antibacterials that are in clinical use presently were discovered and developed in the span of a mere 30 years or so. The advent of antibiotics, along with immunization, has had profound consequences on the quality of life. Life expectancy increased in the United States by 30 years from the beginning to the end of the twentieth century, as a direct consequence of these developments. The use of aminoglycoside antibiotics has facilitated evolution of a number of enzymes that structurally modify the antibiotics, whereby the affinity for binding to the bacterial ribosome is lost. This is a very common mechanism for resistance to these antibacterials. The most common mechanism for resistance to these antibiotics is by the activity of aminoglycoside 3’-phosphotransferases [APH(3’)s].

Aminoglycosides are among the most commonly used broad-spectrum antibiotics in the anti-infective armamentarium. The vast majority of aminoglycosides are bactericidal, they have predictable pharmacokinetics, and they often act in synergy with other antibiotics, properties that make them valuable as

The structures of six new C20 quassinoids and one new C19 quassinoid, all isolated from the twigs and thorns of Castela polyandra, were established by a combination of spectroscopic and single-crystal X-ray analysis. Five known quassinoids and one known sterol were also identified.