Toxicity Modulation, Resistance Enzyme Evasion, and A-Site X-ray Structure of Broad-Spectrum Antibacterial Neomycin Analogs

Abstract

Aminoglycoside antibiotics are pseudosaccharides decorated with ammonium groups that are critical for their potent broad-spectrum antibacterial activity. Despite over three decades of speculation whether or not modulation of pKa is a viable strategy to curtail aminoglycoside kidney toxicity, there is a lack of methods to systematically probe amine-RNA interactions and resultant cytotoxicity trends. This study reports the first series of potent aminoglycoside antibiotics harboring fluorinated N1-hydroxyaminobutyryl acyl (HABA) appendages for which fluorine-RNA contacts are revealed through an X-ray cocrystal structure within the RNA A-site. Cytotoxicity in kidney-derived cells was significantly reduced for the derivative featuring our novel β,β-difluoro-HABA group, which masks one net charge by lowering the pKa without compromising antibacterial potency. This novel side-chain assists in evasion of aminoglycoside-modifying enzymes, and it can be easily transferred to impart these properties onto any number of novel analogs.

Applications of Fluorine in Medicinal Chemistry

“…59 The modified aminoglycoside antibiotic 3′,4′,-3‴,4‴-tetradeoxyneomycin (105) and its N1-(S)-hydroxyaminobutyric amide derivative 106 exhibit improved antibacterial activity compared to the hydroxylated progenitor. This benefit is due to an absence of hydroxyl substituents which, as part of resistance pathways discussed above, are targeted by modifying enzymes for acetylation.…”

“…This benefit is due to an absence of hydroxyl substituents which, as part of resistance pathways discussed above, are targeted by modifying enzymes for acetylation. 59 The introduction of electronwithdrawing substituents proximal to the hydroxylated butyramide provided an opportunity to modulate the pK a of the terminal amine in an effort to achieve a balance between antibacterial activity and avoidance of renal toxicity. Hydroxylated analog 107, monofluoro analog 108, and difluoro analog 109 provided a successive reduction of the amine pK a of up to 3 log 10 .…”

In Vivo Efficacy of Anuran Trypsin Inhibitory Peptides against Staphylococcal Skin Infection and the Impact of Peptide Cyclization

“…The negativecontrol group of mice (untreated group) was given PBS instead of antimicrobial agent, whereas the positive-control group was treated with neomycin sulfate antibiotic at 10 mg · kg Ϫ1 (antibiotic-treated group). Neomycin sulfate is an antibiotic from the aminogylcoside family that is used in topical ointments, and this has been used to study S. aureus infections (47,48). The bacterial recoveries for the antibiotic-treated group and the untreated group were found to be 4.1 Ϯ 1.0 and 10.9 Ϯ 0.3 log 10 CFU/g of tissue, respectively.…”

Influence of Linker Length and Composition on Enzymatic Activity and Ribosomal Binding of Neomycin Dimers

“…To elicit their antibacterial response, AGs bind to a highly conserved set of nucleotides on helix 44 (h44) of the bacterial 16S rRNA (3)(4)(5). To a lesser extent, AGs have also been shown to bind to the mammalian ribosomes, and efforts have been devoted to achieve higher selectivity of these drugs toward their bacterial target (6)(7)(8). Three main groups of AGs have been structurally defined based on the substitution pattern of their common 2-deoxystreptamine (2-DOS) ring: (i) the monosubstituted 2-DOS AGs (e.g., apramycin and hygromycin), (ii) the 4,5-disubstituted 2-DOS AGs (e.g., butirosin, neomycin B [NEO], paromomycin, and ribostamycin), and (iii) the 4,6-disubstituted 2-DOS AGs (e.g., amikacin, kanamycin, tobramycin, etc.).…”

“…1), a potent antibacterial, is mainly sold for topical use due to its significant ototoxicity. A number of purified AMEs, such as AAC(6=)-Ie/APH(2Љ)-Ia (11), AAC(3)-IV (12), ANT(4=)-Ia (13), and APH(3=)-IIIa (14,15), among others, have been found to modify NEO in vitro and to limit its effectiveness in vivo (7,16). NEO dimers have been previously reported to bind the bacterial A site with differing affinities and showed large differences in bacterial inhibition (17).…”