The aminoglycoside 6′-N-acetyltransferase type Ib [AAC(6′)-Ib] is a common cause of resistance to amikacin and other aminoglycosides in Gram-negatives. Utilization of mixture-based combinatorial libraries and application of the positional scanning strategy identified an inhibitor of AAC(6′)-Ib. This inhibitor’s chemical structure consists of a pyrrolidine pentamine scaffold substituted at four locations (R1, R3, R4, and R5). The substituents are two S-phenyl (R1 and R4), an S-hydroxymethyl (R3), and a 3-phenylbutyl (R5) groups. Another location, R2, does not have a substitution, but it is named because its stereochemistry was modified in some compounds utilized in this study. Structure-activity relationship (SAR) analysis using derivatives with different functionalities, modified stereochemistry, and truncations were carried out by assessing the effect of the addition of each compound at 8 µM to 16 µg/ml amikacin-containing media and performing checkerboard assays varying the concentrations of the inhibitor analogs and the antibiotic. The results showed that: 1) the aromatic functionalities at R1 and R4 are essential, but the stereochemistry is essential only at R4, 2) the stereochemical conformation at R2 is critical, 3) the hydroxyl moiety at R3 as well as stereoconformation are required for full inhibitory activity, 4) the phenyl functionality at R5 is not essential and can be replaced by aliphatic groups, 5) the location of the phenyl group on the butyl carbon chain at R5 is not essential, 6) the length of the aliphatic chain at R5 is not critical, 7) all truncations of the scaffold resulted in inactive compounds. Molecular docking revealed that all compounds preferentially bind to the kanamycin C binding cavity, and binding affinity correlates with the experimental data for most of the compounds evaluated. The SAR results in this study will serve as the basis for the design of new analogs in an effort to improve their ability to induce phenotypic conversion to susceptibility in amikacin-resistant pathogens.

Multidrug resistant bacteria pose a significant threat to global health, particularly in healthcare settings. This study aimed to explore the potential of aminoglycoside consumption and resistance data to correlate with multidrug resistance in Acinetobacter baumannii and Klebsiella pneumoniae. Data on aminoglycoside consumption and antibiotic resistance indices (ARI) were collected from 2010 to 2023. Descriptive statistics and Pearson correlation analyzes were performed to examine both immediate and delayed (one-year delay) correlations between aminoglycoside use (amikacin, tobramycin, gentamicin) and resistance patterns. The results indicated that the consumption of amikacin was consistently high and correlated with resistance in both bacterial species. Tobramycin and gentamicin showed variable resistance patterns, with negative correlations in some cases. Delayed effect analysis revealed that amikacin and tobramycin consumption had a slight delayed positive impact on multidrug resistance in A. baumannii, while gentamicin use was associated with a delayed reduction in resistance. In K. pneumoniae, gentamicin showed a strong delayed positive correlation with multidrug resistance, while amikacin and tobramycin had weaker associations. These findings highlight the complex and species-specific relationships between aminoglycoside consumption and resistance development, emphasizing the need for customized antibiotic management strategies that account for the immediate and delayed effects of antibiotic use.

Plazomicin is a recently U.S. Food and Drug Administration (FDA)-approved semisynthetic aminoglycoside. Its structure consists of a sisomicin scaffold modified by adding a 2(S)-hydroxy aminobutyryl group at the N1 position and a hydroxyethyl substituent at the 6′ position. These substitutions produced a molecule refractory to most aminoglycoside-modifying enzymes. The main enzyme within this group that recognizes plazomicin as substrate is the aminoglycoside 2′-N-acetyltransferase type Ia [AAC(2′)-Ia], which reduces the antibiotic’s potency. Designing formulations that combine an antimicrobial with an inhibitor of resistance is a recognized strategy to extend the useful life of existing antibiotics. We have recently found that several metal ions inhibit acetylation of numerous aminoglycosides catalyzed by the aminoglycoside 6′-N-acetyltransferase type Ib [AAC(6′)-Ib]. In particular, Ag1+, which also enhances the effect of aminoglycosides by other mechanisms, is very effective in interfering with AAC(6′)-Ib-mediated resistance to amikacin. Here we report that silver acetate is a potent inhibitor of AAC(2′)-Ia-mediated acetylation of plazomicin in vitro, and it reduces resistance levels of Escherichia coli carrying aac(2′)-Ia. The resistance reversion assays produced equivalent results when the structural gene was expressed under the control of the natural or the blaTEM-1 promoters. The antibiotic effect of plazomicin in combination with silver was bactericidal, and the mix did not show significant toxicity to human embryonic kidney 293 (HEK293) cells.

Enterococcus faecalis is a bacterium that can develop a multidrug resistance profile associated with the community as well as nosocomial-acquired infections. Among the treatment options for these infections are aminoglycosides combined with bacterial cell wall inhibitors such as beta-lactams, since E. faecalis is intrinsically resistant to aminoglycosides. One of its most representative resistance mechanisms is the expression of aminoglycoside-modifying enzymes, such as the aminoglycoside phosphotransferase type IIIa of E. faecalis (EfAPH(3')-IIIa). This enzyme acts by phosphorylating aminoglycosides in an ATP-dependent reaction, modifying the 3' position of hydroxyl groups of these antibiotics. Considering this scenario, 3,092 natural products obtained from the ZINC22 database were analyzed to select molecules with the highest affinity for the nucleotide-binding pocket of EfAPH(3')-IIIa, which could be potential aminoglycoside adjuvants. The molecules that showed the best-score results obtained from ensemble docking-based virtual screening were ZINC000000952700 (BS-1), ZINC000014793040 (BS-2) and ZINC000015498603 (BS-3). The most promising results were for BS-2, a flavone derivative, due to its improved stability profile in molecular dynamics simulation (average values of RMSD of 0.23 nm, and Rg of 1.94 nm), binding free energy calculations (average ΔG total of -35.3 nm), as well as better toxicological profile (lower probability of hepatotoxicity, carcinogenic, immunotoxicity, mutagenicity, and cytotoxicity effects), compared to BS-1 and BS-3. These results allow us to propose that a flavone derivative may act as an adjuvant to aminoglycosides in the treatment of E. faecalis infections, acting as an inhibitor in the nucleotide-binding pocket of EfAPH(3')-IIIa.

Neurodegenerative protein conformational diseases are characterized by misfolding and aggregation of metastable proteins encoded within the host genome. The host is also home to thousands of proteins encoded within exogenous genomes harbored by bacteria, fungi, and viruses. Yet, their contributions to host protein-folding homeostasis, or proteostasis, remain elusive. Recent studies, including our previous work, suggest that bacterial products contribute to toxic aggregation of endogenous host proteins. We refer to these products as bacteria-derived protein aggregates (BDPAs). Furthermore, antibiotics were recently associated with increased risk for neurodegenerative diseases, including Parkinson’s disease and amyotrophic lateral sclerosis  possibly by virtue of altering the composition of the human gut microbiota. Other studies have shown a negative correlation between disease progression and antibiotic administration, supporting their protective effect against neurodegenerative diseases. These contradicting studies emphasize the complexity of the human gut microbiota, the gut-brain axis, and the effect of antibiotics. Here, we further our understanding of bacteria’s effect on host protein folding using the model Caenorhabditis elegans. We employed genetic and chemical methods to demonstrate that the proteotoxic effect of bacteria on host protein folding correlates with the presence of BDPAs. Furthermore, the abundance and proteotoxicity of BDPAs are influenced by gentamicin, an aminoglycoside antibiotic that induces protein misfolding, and by butyrate, a short-chain fatty acid that we previously found to affect host protein aggregation and the associated toxicity. Collectively, these results increase our understanding of host-bacteria interactions in the context of protein conformational diseases.