Increased awareness of the multiple roles of RNA molecules has led to the realization that, in addition to their structural and functional roles, RNAs can be drug targets for small molecular therapy. The aim of this study was to identify multivalent amikacin specific RNA aptamers that can be a new target sites for aminoglycoside antibiotics, including amikacin using the systemic evolution of ligands by exponential enrichment (SELEX) method. Amikacin, a member of the aminoglycoside group of antibiotics, binds to specific sites in bacterial 16S ribosomal RNAs (rRNAs) and interferes with protein synthesis, leading to cell death. Here, we used the SELEX method to isolate high affinity RNA fragments (aptamers) that bind to amikacin. After five rounds of SELEX selection, in which a linear N25 DNA template was used for the first selection cycle, the resulting RNA was cloned and sequenced. Among the 38 clones generated, five groups of sequences (groups A through E) containing nine conserved motifs were identified. The sequences of groups A and B were almost identical, indicating that the selected RNA was enriched. Subsequently, the Basic Local Alignment Search Tool program was used to search for the conserved motifs in bacterial 16S rRNA sequences. Strikingly, no sequence homology was observed, suggesting that the conserved sequences (motifs) identified in this study may be novel target sites for amikacin.

Clinical resistance to amikacin and other aminoglycosides is usually due to enzymatic acetylation of the antimicrobial molecule. A ubiquitous resistance enzyme among Gram-negatives is the aminoglycoside 6'-N-acetyltransferase type Ib [AAC(6')-Ib], which catalyzes acetylation using acetyl-CoA as donor substrate. Therapies that combine the antibiotic and an inhibitor of the inactivation reaction could be an alternative to treat infections caused by resistant bacteria. We had previously observed that metal ions such as Zn2+ or Cu2+ in complex with ionophores interfere with the AAC(6')-Ib-mediated inactivation of aminoglycosides and reduced resistance to susceptibility levels. Ag1+ recently attracted attention as a potentiator of aminoglycosides' action by mechanisms still in discussion. We found that silver acetate is also a robust inhibitor of the enzymatic acetylation mediated by AAC(6')-Ib in vitro. This action seems to be independent of other mechanisms, like increased production of reactive oxygen species and enhanced membrane permeability, proposed to explain the potentiation of the antibiotic effect by silver ions. The addition of this compound to aac(6')-Ib harboring Acinetobacter baumannii and Escherichia coli cultures resulted in a dramatic reduction of the resistance levels. Time-kill assays showed that the combination of silver acetate and amikacin was bactericidal and exhibited low cytotoxicity to HEK293 cells.

Background: Disentangling adverse drug reactions from confounders remains a major challenge to assess causality and severity in neonates. Vancomycin and amikacin are perceived as nephrotoxic and often prescribed in neonates. We selected these compounds to assess their impact on creatinine dynamics as sensitive tool to detect a renal impairment signal. Methods: A recently developed dynamical model that characterized serum creatinine concentrations of 217 ELBW neonates (4036 serum creatinine observations) was enhanced with data on individual administration of vancomycin and/or amikacin to identify a potential effect of antibiotic exposure by nonlinear mixed-effects modelling analysis. Results: Of our ELBW patients, 77% were exposed to either vancomycin or amikacin. Antibiotic exposure resulted in transient lower overall creatinine clearance and a modest increase in serum creatinine. Dependency on gestational age was observed in the difference in serum creatinine when exposed to antibiotics during the third week after birth (difference in creatinine for a neonate at 24 weeks gestation decreased with 56% for a 32-week-old neonate). Conclusions: A previously described model on creatinine dynamics was used to explore and quantify the impact amikacin or vancomycin exposure on creatinine dynamics. Such tools can be used to explore minor changes, or compare minor differences between treatment modalities.