An isocratic separation of underivatized gentamicin components, 1H NMR assignment and protonation pattern

High-pH mobile phase in reversed-phase liquid chromatography-tandem mass spectrometry to improve the separation efficiency of aminoglycoside isomers

In chromatography, the use of extreme conditions can often lead to unique separation selectivity. In this study, a highly basic mobile phase (pH > 11), which is not typically employed for reversed-phase liquid chromatography (RPLC), was utilized in RPLC-tandem mass spectrometry (MS/MS) to achieve effective separation between electrically neutral bases of aminoglycosides (AGs). A mixture of AGs was simultaneously analyzed using 500 mmol L-1 ammonia aqueous solution (pH 11.8) as the mobile phase. A total of 11 AGs, including 2 stereoisomers of neomycin (B and C) and 5 structurally similar components of gentamicin (C1, C1a, C2, C2a, and C2b), were completely separated for the first time. The high separation performance for AGs was mainly due to two factors: First, slight differences in hydrophobicity among the AGs were significantly enhanced at a high pH by the complete acid dissociation of amines. Second, the high pH of the mobile phase minimized any electrostatic interactions between the AGs and residual silanol groups in the stationary phase, resulting in extremely sharp peaks for the AGs. The sensitivity of spectinomycin decreased by more than 20% when using the highly basic mobile phase (pH 11.8) due to its degradation, therefore, a mixture of 10 AGs was analyzed with 250 mmol L-1 ammonia aqueous solution (pH 11.5) with less degradation as the optimum condition. The developed analytical method could be used to determine the concentrations of trace AGs in milk with high accuracy and precision. Thus, RPLC-MS/MS using a high-pH mobile phase has great potential for the efficient separation of basic compounds containing amino sugars such as AGs.

Synthesis of Gentamicins C1, C2, and C2a and Antiribosomal and Antibacterial Activity of Gentamicins B1, C1, C1a, C2, C2a, C2b, and X2

Complementing our earlier syntheses of the gentamicins B1, C1a, C2b, and X2, we describe the synthesis of gentamicins C1, C2, and C2a characterized by methyl substitution at the 6'-position, and so present an alternative access to previous chromatographic methods for accessing these sought-after compounds. We describe the antiribosomal activity of our full set of synthetic gentamicin congeners against bacterial ribosomes and hybrid ribosomes carrying the decoding A site of the human mitochondrial, A1555G mutant mitochondrial, and cytoplasmic ribosomes and establish structure-activity relationships with the substitution pattern around ring I to antiribosomal activity, antibacterial resistance due to the presence of aminoglycoside acetyl transferases acting on the 6'-position in ring I, and literature cochlear toxicity data.

AB-DB: Force-Field parameters, MD trajectories, QM-based data, and Descriptors of Antimicrobials

Antibiotic resistance is a major threat to public health. The development of chemo-informatic tools to guide medicinal chemistry campaigns in the efficint design of antibacterial libraries is urgently needed. We present AB-DB, an open database of all-atom force-field parameters, molecular dynamics trajectories, quantum-mechanical properties, and curated physico-chemical descriptors of antimicrobial compounds. We considered more than 300 molecules belonging to 25 families that include the most relevant antibiotic classes in clinical use, such as β-lactams and (fluoro)quinolones, as well as inhibitors of key bacterial proteins. We provide traditional descriptors together with properties obtained with Density Functional Theory calculations. Noteworthy, AB-DB contains less conventional descriptors extracted from μs-long molecular dynamics simulations in explicit solvent. In addition, for each compound we make available force-field parameters for the major micro-species at physiological pH. With the rise of multi-drug-resistant pathogens and the consequent need for novel antibiotics, inhibitors, and drug re-purposing strategies, curated databases containing reliable and not straightforward properties facilitate the integration of data mining and statistics into the discovery of new antimicrobials.

Antibacterial activity of apramycin at acidic pH warrants wide therapeutic window in the treatment of complicated urinary tract infections and acute pyelonephritis

Background

The clinical-stage drug candidate EBL-1003 (apramycin) represents a distinct new subclass of aminoglycoside antibiotics for the treatment of drug-resistant infections. It has demonstrated best-in-class coverage of resistant isolates, and preclinical efficacy in lung infection models. However, preclinical evidence for its utility in other disease indications has yet to be provided. Here we studied the therapeutic potential of EBL-1003 in the treatment of complicated urinary tract infection and acute pyelonephritis (cUTI/AP).

Methods

A combination of data-base mining, antimicrobial susceptibility testing, time-kill experiments, and four murine infection models was used in a comprehensive assessment of the microbiological coverage and efficacy of EBL-1003 against Gram-negative uropathogens. The pharmacokinetics and renal toxicology of EBL-1003 in rats was studied to assess the therapeutic window of EBL-1003 in the treatment of cUTI/AP.

Findings

EBL-1003 demonstrated broad-spectrum activity and rapid multi-log CFU reduction against a phenotypic variety of bacterial uropathogens including aminoglycoside-resistant clinical isolates. The basicity of amines in the apramycin molecule suggested a higher increase in positive charge at urinary pH when compared to gentamicin or amikacin, resulting in sustained drug uptake and bactericidal activity, and consequently in potent efficacy in mouse infection models. Renal pharmacokinetics, biomarkers for toxicity, and kidney histopathology in adult rats all indicated a significantly lower nephrotoxicity of EBL-1003 than of gentamicin.

Interpretation

This study provides preclinical proof-of-concept for the efficacy of EBL-1003 in cUTI/AP. Similar efficacy but lower nephrotoxicity of EBL-1003 in comparison to gentamicin may thus translate into a higher safety margin and a wider therapeutic window in the treatment of cUTI/API.

Funding

A full list of funding bodies that contributed to this study can be found in the Acknowledgements section.

Periodic charge matching driven immobilization of gentamicin in nanoclays for stable and long-term antibacterial coating

Matching of charge periodicity between a guest and a host enabled effective immobilization of highly water-soluble antibiotic drug, gentamicin C, in a bentonite clay by cation exchange. X-ray diffraction, infrared spectroscopy and CHNS analysis revealed the immobilization manner of gentamicin C, which was immobilized between bentonite layers via periodic charge-charge interaction with tilted arrangement, as a trication. Both gentamicin alone and a gentamicin/bentonite hybrid were coated onto a polyurethane substrate using water-borne polyurethane binder. The antibiotic character of both films was investigated as prepared or after immersion in phosphate-buffered saline till 5 days against E. coli and B. subtilis bacteria. It was clearly shown that the gentamicin/bentonite hybrid-coated film showed sustained antibacterial efficacy even after exposure to phosphate-buffered saline, while gentamicin only-coated film gradually lost its performance under the same condition.

Nanoparticles highly loaded with gentamicin sulfate by a combination of polyhydroxylated macromonomers and ROMP for the synthesis of bioactive biomaterials

Nanoparticles highly loaded with gentamicin sulfate were synthesized by ring-opening metathesis copolymerization in a dispersion of norbornene with modified polyhydroxylated macromonomers.

Influence of the Molecular Weight and Charge of Antibiotics on Their Release Kinetics From Gelatin Nanospheres

In this study, we investigated the fundamental relationship between the physicochemical characteristics of antibiotics and the kinetics of their release from gelatin nanospheres. We observed that antibiotics of high molecular weight (colistin and vancomycin) were released in a sustained manner from oppositely charged gelatin carriers for more than 14 d, as opposed to antibiotics of low molecular weight (gentamicin and moxifloxacin) which were released in a burst-like manner. The release kinetics of positively charged colistin strongly correlated with the rate of the enzymatic degradation of gelatin. To elucidate the differences among release kinetics of antibiotics, we explored the mechanism of interactions between antibiotics and gelatin nanospheres by monitoring the kinetics of release of antibiotics as a function of pH, ionic strength, and detergent concentrations. These studies revealed that the interactions between antibiotics and gelatin nanospheres were mainly dominated by (i) strong electrostatic forces for colistin; (ii) strong hydrophobic and electrostatic forces for vancomycin; (iii) weak electrostatic and hydrophobic forces for gentamicin; and (iv) weak hydrophobic forces for moxifloxacin. These results confirm that release of antibiotics from gelatin nanospheres strongly depends on the physicochemical characteristics of the antibiotics.

A liposomal fluorescence assay to study permeation kinetics of drug-like weak bases across the lipid bilayer

Lipid bilayer permeation is considered the major route for in vivo barrier passage of drugs. Despite this fact, no technique is currently available to measure the kinetics of permeation across a single lipid bilayer of structurally unrelated drug-like solutes. We developed a liposomal fluorescence assay capable to determine permeation kinetics of basic drug-like solutes across lipid bilayers. The assay is based on the hypothesis that permeation of a weak base along a concentration gradient results in net proton release at the cis-side and net proton capture at the trans-side of the bilayer. The resulting pH changes were monitored with pH-sensitive fluorophores: Test compounds were incubated with liposomes containing a pH-sensitive fluorophore at the bilayer surfaces or in the aqueous lumen and fluorescence changes were monitored with a stopped-flow apparatus in solution or by total internal reflection fluorescence microscopy with surface-captured liposomes on a microfluidic platform. Incubation with lipophilic basic drugs resulted in the expected fluorescence changes while incubation with compounds without basic functionality or high polarity did not affect fluorescence. Kinetics of fluorescence changes followed bi-exponential functions. Logarithmic permeation coefficients (logPermapp) determined in solution and by microfluidics technology showed a good correlation (r(2)=0.94, n=7) and logPermapp increased with increasing lipophilicity. Neither diffusion in the aqueous phase nor partitioning into the bilayer was rate-limiting. PEGylation of 2% of the liposomal lipids reduced Permapp by a factor ~300. In conclusion, the presented liposomal fluorescence assay is capable to determine permeation kinetics of weak basic drug-like solutes across lipid bilayers. The method is adaptable to microfluidics technology for high-throughput measurements and can potentially be modified to work for weak acid solutes.

Gentamicin binds to the megalin receptor as a competitive inhibitor using the common ligand binding motif of complement type repeats: insight from the nmr structure of the 10th complement type repeat domain alone and in complex with gentamicin

Gentamicin is an aminoglycoside widely used in treatments of, in particular, enterococcal, mycobacterial, and severe Gram-negative bacterial infections. Large doses of gentamicin cause nephrotoxicity and ototoxicity, entering the cell via the receptor megalin. Until now, no structural information has been available to describe the interaction with gentamicin in atomic detail, and neither have any three-dimensional structures of domains from the human megalin receptor been solved. To address this gap in our knowledge, we have solved the NMR structure of the 10th complement type repeat of human megalin and investigated its interaction with gentamicin. Using NMR titration data in HADDOCK, we have generated a three-dimensional model describing the complex between megalin and gentamicin. Gentamicin binds to megalin with low affinity and exploits the common ligand binding motif previously described (Jensen, G. A., Andersen, O. M., Bonvin, A. M., Bjerrum-Bohr, I., Etzerodt, M., Thogersen, H. C., O'Shea, C., Poulsen, F. M., and Kragelund, B. B. (2006) J. Mol. Biol. 362, 700-716) utilizing the indole side chain of Trp-1126 and the negatively charged residues Asp-1129, Asp-1131, and Asp-1133. Binding to megalin is highly similar to gentamicin binding to calreticulin. We discuss the impact of this novel insight for the future structure-based design of gentamicin antagonists.

Gentamicin-loaded strontium-containing hydroxyapatite bioactive bone cement--an efficient bioactive antibiotic drug delivery system

Modified strontium-containing hydroxyapatite (Sr-HA) bone cement was loaded with gentamicin sulfate to generate an efficient bioactive antibiotic drug delivery system for treatment of bone defects. Gentamicin release and its antibacterial property were determined by fluorometric method and inhibition of Staphylococcus aureus (S. aureus) growth. Gentamicin was released from Sr-HA bone cement during the entire period of study and reached around 38% (w/w) cumulatively after 30 days. Antibacterial activity of the gentamicin loaded in the cements is clearly confirmed by the growth inhibition of S. aureus. The results of the amount and duration of gentamicin release suggest a better drug delivery efficiency in Sr-HA bone cement over polymethylmethacrylate bone cement. Bioactivity of the gentamicin-loaded Sr-HA bone cement was confirmed with the formation of apatite layer with 1.836 ± 0.037 μm thick on day 1 and 5.177 ± 1.355 μm thick on day 7 after immersion in simulated body fluid. Compressive strengths of the gentamicin-loaded Sr-HA cement reached 132.60 ± 10.08 MPa, with a slight decrease from the unloaded groups by 4-9%. Bending moduli of Sr-HA cements with and without gentamicin were 1.782 ± 0.072 GPa and 1.681 ± 0.208 GPa, respectively. On the contrary, unloaded Sr-HA cement obtained slightly larger bending strength of 35.48 ± 2.63 MPa comparing with 33.00 ± 1.65 MPa for loaded cement. No statistical difference was found on the bending strengths and modulus of gentamicin-loaded and -unloaded Sr-HA cements. Sr-HA bone cement loaded with gentamicin was proven to be an efficient drug delivery system with uncompromised mechanical properties and bioactivity.

NMR and amber analysis of the neamine pharmacophore for the design of novel aminoglycoside antibiotics

The dependence of the solution structure of neamine on pH was determined by NMR and AMBER molecular dynamics methods at pD 3.3, pD 6.5, and pD 7.4 in D(2)O at 25°C. Unlike neamine structures at pD 3.3 and 6.5, which essentially showed only one conformer, slowly exchanging primary, P-state, and secondary, S-state, neamine conformers populated on the NMR time scale at ~80% and ~20%, respectively, were detected at pD 7.4 with kinetic constants k(on(P→S))=1.9771s(-1) and k(off(S→P))=1.1319s(-1). A tertiary, T-state, neamine species populated at ~3% was also detected by NMR at pD 7.4. The pKa values determined by NMR titration experiments are pKa1 6.44±0.13 for N3 of ring-II, pKa2 7.23±0.09 for N2' of ring-I, pKa3 7.77±0.19 for N1 of ring-II, and pKa4 8.08±0.15 for N6' of ring-I. Ring-I and ring-II of the P-state neamine and ring-I of the S and T-states of neamine possess the (4)C(1) chair conformation between pD 3.3 and pD=7.4. In contrast, ring-II of the S and T-states of neamine most likely adopt the (6)rH(1) half-chair conformation. The P and S-states of neamine exhibit a negative syn-ψ glycosidic geometry. The exocyclic aminomethyl group of ring-I adopts the gt exocyclic rotamer conformation around physiological pHs while the gg exocyclic rotamer conformation predominates in acidic solutions near and below pH 4.5. Neamine exists in the P-state as a mixture of tetra-/tri-/di-protonated species between pD 4.5 and pD 7.4, while the S-state neamine exist only in a di-protonated species around physiological pDs. The existence of the S-state neamine may facilitate binding of neamine-like aminoglycosides by favorable entropy of binding to the A-site of 16S ribosomal RNA, suggesting that novel aminoglycoside compounds carrying a S-state neamine pharmacophore can be developed.

Protonation of kanamycin A: detailing of thermodynamics and protonation sites assignment

Protonation of an aminoglycoside antibiotic kanamycin A sulfate was studied by potentiometric titrations at variable ionic strength, sulfate concentration and temperature. From these results the association constants of differently protonated forms of kanamycin A with sulfate and enthalpy changes for protonation of each amino group were determined. The protonation of all amino groups of kanamycin A is exothermic, but the protonation enthalpy does not correlate with basicity as in a case of simple polyamines. The sites of stepwise protonation of kanamycin A have been assigned by analysis of (1)H-(13)C-HSQC spectra at variable pH in D(2)O. Plots of chemical shifts for each H and C atom of kanamycin A vs. pH were fitted to the theoretical equation relating them to pK(a) values of ionogenic groups and it was observed that changes in chemical shifts of all atoms in ring C were controlled by ionization of a single amino group with pK(a) 7.98, in ring B by ionization of two amino groups with pK(a) 6.61 and 8.54, but in ring A all atoms felt ionization of one group with pK(a) 9.19 and some atoms felt ionization of a second group with pK(a) 6.51, which therefore should belong to amino group at C3 in ring B positioned closer to the ring A while higher pK(a) 8.54 can be assigned to the group at C1. This resolves the previously existed uncertainty in assignment of protonation sites in rings B and C.

TRPV1 regulators mediate gentamicin penetration of cultured kidney cells

Transient receptor potential (TRP) receptors are, typically, calcium-permeant cation channels that transduce environmental stimuli. Both kidney epithelial and inner ear sensory cells express TRPV1, are mechanosensors and accumulate the aminoglycoside antibiotic gentamicin. Recently, we showed that Texas Red-conjugated gentamicin (GTTR) enters kidney cells via an endosome-independent pathway. Here, we used GTTR to investigate this non-endocytotic mechanism of gentamicin uptake. In serum-free buffers, GTTR penetrated MDCK cells within 30 s and uptake was modulated by extracellular, multivalent cations (Ca2+, La3+, Gd3+) or protons. We verified the La3+ modulation of GTTR uptake using immunocytochemical detection of unconjugated gentamicin. Membrane depolarization, induced by high extracellular K+ or valinomycin, also reduced GTTR uptake, suggesting electrophoretic permeation through ion channels. GTTR uptake was enhanced by the TRPV1 agonists, resiniferatoxin and anandamide, in Ca2+-free media. Competitive antagonists of the TRPV1 cation current, iodo-resiniferatoxin and SB366791, also enhanced GTTR uptake independently of Ca2+, reinforcing these antagonists' potential as latent agonists in specific situations. Ruthenium Red blocked GTTR uptake in the presence or absence of these TRPV1-agonists and antagonists. In addition, GTTR uptake was blocked by RTX in the presence of more physiological levels (2 mM) of Ca2+. Thus gentamicin enters cells via cation channels, and gentamicin uptake can be modulated by regulators of the TRPV1 channel.

Complete thermodynamic characterization of the multiple protonation equilibria of the aminoglycoside antibiotic paromomycin: a calorimetric and natural abundance 15N NMR study

The binding of aminoglycoside antibiotics to a broad range of macromolecular targets is coupled to protonation of one or more of the amino groups that typify this class of drugs. Determining how and to what extent this linkage influences the energetics of the aminoglycoside-macromolecule binding reaction requires a detailed understanding of the thermodynamics associated with the protonation equilibria of the aminoglycoside amino groups. In recognition of this need, a calorimetric- and NMR-based approach for obtaining the requisite thermodynamic information is presented using paromomycin as the model aminoglycoside. Temperature- and pH-dependent 15N NMR studies provide pK(a) values for the five paromomycin amino groups, as well as the temperature dependence of these pK(a) values. These studies also indicate that the observed pK(a) values associated with the free base form of paromomycin are lower in magnitude than the corresponding values associated with the sulfate salt form of the drug. This difference in pK(a) is due to drug interactions with the sulfate counterions at the high drug concentrations (> or = 812 mM) used in the 15N NMR studies. Isothermal titration calorimetry studies conducted at drug concentrations < or = 45 microM reveal that the extent of paromomycin protonation linked to the binding of the drug to its pharmacologically relevant target, the 16 S rRNA A-site, is consistent with the pK(a) values of the free base and not the sulfate salt form of the drug. Temperature- and pH-dependent isothermal titration calorimetry studies yield exothermic enthalpy changes (deltaH) for protonation of the five paromomycin amino groups, as well as positive heat capacity changes (deltaC(p)) for three of the five amino groups. Regarded as a whole, the results presented here represent an important first step toward establishing a thermodynamic database that can be used to predict how aminoglycoside-macromolecule binding energetics will be influenced by conditions such as temperature, pH, and ionic strength. Such a predictive capability is a critical component of any drug design strategy.

Direct determination of gentamicin components by capillary electrophoresis with potential gradient detection

A simple and fast method was developed to determine non-UV active compounds directly without derivatization. The usefulness of the method was demonstrated by detecting the major components in aminoglycoside antibiotic mixtures using capillary zone electrophoresis with potential gradient detection. Under optimized separation conditions (0.2 mM cetyltrimethylammonium bromide (CTAB), 1 mM ammonium citrate, pH 3.5), gentamicin was separated into three major peaks (C1, C1a, and C2+C2a) within 15 min. This method showed better sensitivity than other capillary electrophoresis (CE) methods for determining underivatized gentamicin. The linear range was from 10 to 500 ppm. Because of its good repeatability and simplicity, this new method could be a good alternative for the current assays given by US Pharmacopoeia and European Pharmacopoeia.