Binding Of Gentamicin Research Articles

Binding and displacement study of gentamicin, 5-fluorouracil, oxytetracycline and rolitetracycline with (BSA: Drug2) complex using spectroscopic and calorimetric techniques: Biophysical approach

Understanding of energetics of interactions between drug and protein is essential in pharmacokinetics and pharmacodynamics study. The binding affinity (K) helps in investigating how tightly or loosely drug is bound to protein. The binding, displacement, conformational change and stability study of drugs- gentamicin (GM), 5-fluorouracil (5FU), oxytetracycline (OTC) and rolitetracycline (RTC) with bovine serum albumin (BSA) has been carried out in presence of each other drug by fluorescence, UV–visible spectroscopy, molecular docking, circular dichroism techniques and thermal denaturation method. The site marker study and docking methods have confirmed that 5FU and GM are able to bind at site 1 and OTC and RTC at site II of BSA. The order of their binding affinities with BSA for the binary system were as GM <5FU < OTC < RTC with the order of 102 < 103 < 105 < 105–6 M−1. The displacement study has shown that higher affinity drug decreases the equilibrium constant of another drug already in bound state with BSA if both these drugs are having the same binding site. Therefore 5FU, GM (binding site 1) drugs were not able to displace OTC and RTC (binding site 2) and vice-versa as they are binding at two different sites. The binding constant values were found to be decreasing with increasing temperature for all the systems involved which suggests static or mixed type of quenching, however can only confirmed with the help of TCSPC technique. The ΔG0 (binding energy) obtained from docking method were in accordance with the ITC method. From molecular docking we have determined the amino acid residues involved in binding process for binary and ternary systems by considering first rank minimum binding energy confirmation. From CD it has been observed that RTC causes most conformational change in secondary and tertiary structure of BSA due to the presence of pyrrole ring. OTC-RTC with higher affinity showed highest melting temperature Tm values while low affinity drugs in (5FU-GM) combination showed lowest Tm value. 5FU showed large endothermic denaturation enthalpy ΔHd0 due to the presence of highly electronegative fluorine atom in the pyridine analogue.

Antibacterial activity of avocado extract (Persea americana Mill.) against aminoglycoside-resistant Klebsiella pneumoniae strains

Klebsiella pneumoniae is an important etiological agent of nosocomial infections. This study focuses on the antibacterial activity of Persea Americana extract against K. pneumoniae strains containing aminoglycoside genes. Broth microdilution technique was used to examine the antibacterial activity of P. americana extract on K. pneumoniae isolates. The phenolic components of its leaves were analysed by the HPLC-DAD system. The binding potential of the major phytochemical component of the extract, chlorogenic acid, to the KsgA was investigated by molecular docking. The stability of the resulting enzyme-ligand complexes was also assessed through molecular dynamics simulation. The result obtained showed that P. americana extract had antibacterial activity on aminoglycoside resistant strains. The binding potential of chlorogenic acid (main phenolic compound) to KsgA was found to be higher than the binding of gentamicin. Since chlorogenic acid had lower binding energy and formed higher number of H-bonding as well as other interactions in the docking analysis. The higher binding potential of the major component with the enzyme that was involved in resistance development against aminoglycoside indicated its possible role in overturning the condition. Moreover, the molecular dynamics simulation study revealed that chlorogenic acid formed a complex with relatively higher stability. The higher binding potential of the major component with higher stability implied that the computational results confirmed the experimental findings.

Poly(levodopa)-modified β-glucan as a candidate for wound dressings

Levodopa (biological precursor of dopamine) is sometimes used instead of dopamine for synthesis of highly adhesive polycatecholamine coatings on different materials. However, in comparison of polydopamine, little is known about biological safety of poly(levodopa) coatings and their efficacy in binding of therapeutically active substances. Therefore, thermally polymerized curdlan hydrogel was modified via two different modes using levodopa instead of commonly used dopamine and then coupled with gentamicin – aminoglycoside antibiotic. Physicochemical properties, biological safety and antibacterial potential of the hydrogels were evaluated. Poly(levodopa) deposited on curdlan exhibited high stability in wide pH range and blood or plasma, were nontoxic in zebrafish model and favored blood clot formation. Simultaneously, one of hydrogel modification modes allowed to observe high gentamicin binding capacity, antibacterial activity, relatively high nontoxicity for fibroblasts and was unfavorable for fibroblasts adhesion. Such modified poly(levodopa)-modified curdlan showed therefore high potential as wound dressing biomaterial.

Quantum Mechanical Study of Carbon Nanotubes Functionalized with Drug Gemcitabin

In this work, using quantum mechanics, the noncovalent interactions and two mechanisms of covalent functionalization of drug gentamicin with (5,5) COOH and COCl functionalized carbon nanotubes are studied. All of the calculations are performed using a hybrid density functional method (UB3LYP) in the solution phase. Quantum molecular descriptors for four possible modes of the noncovalent interaction are investigated. It is found that the binding of gentamicin with COOH (NCOOH) and COCl (NCOCl) functionalized carbon nanotubes is thermodynamically favorable. Among NCOOH and NCOCl, the first one has higher binding energy and can act as a suitable system for the drug gentamicin delivery within biological systems (noncovalent). COOH and COCl functionalized carbon nanotubes can bond to gentamicin via OH (COOH mechanism) and Cl (COCl mechanism) groups, respectively. The activation energies of four pathways in two mechanisms are calculated and compared with each other. It is specified that the COOH mechanism has an energy barrier higher than that of the COCl mechanism, being the reason for the suitability of the COCl mechanism for covalent functionalization.

A structural basis for the antibiotic resistance conferred by an N1-methylation of A1408 in 16S rRNA.

The aminoglycoside resistance conferred by an N1-methylation of A1408 in 16S rRNA by a novel plasmid-mediated methyltransferase NpmA can be a future health threat. In the present study, we have determined crystal structures of the bacterial ribosomal decoding A site with an A1408m1A antibiotic-resistance mutation both in the presence and absence of aminoglycosides. G418 and paromomycin both possessing a 6′-OH group specifically bind to the mutant A site and disturb its function as a molecular switch in the decoding process. On the other hand, binding of gentamicin with a 6′-NH3+ group to the mutant A site could not be observed in the present crystal structure. These observations agree with the minimum inhibitory concentration of aminoglycosides against Escherichia coli. In addition, one of our crystal structures suggests a possible conformational change of A1408 during the N1-methylation reaction by NpmA. The structural information obtained explains how bacteria acquire resistance against aminoglycosides along with a minimum of fitness cost by the N1-methylation of A1408 and provides novel information for designing the next-generation aminoglycoside.

Quantum mechanical study of carbon nanotubes functionalized with drug gentamicin

In this work, using quantum mechanics, the noncovalent interactions and two mechanisms of covalent functionalization of drug gentamicin with (5,5) COOH and COCl functionalized carbon nanotubes are studied. All of the calculations are performed using a hybrid density functional method (UB3LYP) in the solution phase. Quantum molecular descriptors for four possible modes of the noncovalent interaction are investigated. It is found that the binding of gentamicin with COOH (NCOOH) and COCl (NCOCl) functionalized carbon nanotubes is thermodynamically favorable. Among NCOOH and NCOCl, the first one has higher binding energy and can act as a suitable system for the drug gentamicin delivery within biological systems (noncovalent). COOH and COCl functionalized carbon nanotubes can bond to gentamicin via OH (COOH mechanism) and Cl (COCl mechanism) groups, respectively. The activation energies of four pathways in two mechanisms are calculated and compared with each other. It is specified that the COOH mechanism has an energy barrier higher than that of the COCl mechanism, being the reason for the suitability of the COCl mechanism for covalent functionalization.

Controlling release kinetics of gentamicin from silica nano-carriers

Antibiotic release from a carrier can be employed to reduce the frequency of administration or prolong efficacy. In this work, we prepared silica nanoparticles loaded with gentamicin through different synthetis routes (entrapment, adsorption, covalent bonding and Layer-by-Layer (LbL)). The nanocarriers physical-chemical properties were characterised and antibiotic release from the nanocarriers was monitored. The nanoparticles prepared entrapping gentamicin gave the highest drug load but completed the release over a period of 4 h. No significant differences in antibiotic load were noticed between absorption or binding of gentamicin onto the silica nanoparticles surface; moreover the release of the drug occurred over 2 days in both cases. The nanoparticles coated with gentamicin through LbL technique released the antibiotic for 3 weeks. This work demonstrates that silica nanoparticles can be employed as antibiotic carriers providing a continuous release of antibiotic over a period that can be tuned through the choice of preparation method.

Structural Analysis of the Tobramycin and Gentamicin Clinical Resistome Reveals Limitations for Next-generation Aminoglycoside Design.

Widespread use and misuse of antibiotics has allowed for the selection of resistant bacteria capable of avoiding the effects of antibiotics. The primary mechanism for resistance to aminoglycosides, a broad-spectrum class of antibiotics, is through covalent enzymatic modification of the drug, waning their bactericidal effect. Tobramycin and gentamicin are two medically important aminoglycosides targeted by several different resistance factors, including aminoglycoside 2″-nucleotidyltransferase [ANT(2″)], the primary cause of aminoglycoside resistance in North America. We describe here two crystal structures of ANT(2″), each in complex with AMPCPP, Mn(2+), and either tobramycin or gentamicin. Together these structures outline ANT(2″)'s specificity for clinically used substrates. Importantly, these structures complete our structural knowledge for the set of enzymes that most frequently confer clinically observed resistance to tobramycin and gentamicin. Comparison of tobramycin and gentamicin binding to enzymes in this resistome, as well as to the intended target, the bacterial ribosome, reveals surprising diversity in observed drug-target interactions. Analysis of the diverse binding modes informs that there are limited opportunities for developing aminoglycoside analogs capable of evading resistance.

Evidence That Antibiotics Bind to Human Mitochondrial Ribosomal RNA Has Implications for Aminoglycoside Toxicity

Aminoglycosides are a well known antibiotic family used to treat bacterial infections in humans and animals, but which can be toxic. By binding to the decoding site of helix44 of the small subunit RNA of the bacterial ribosome, the aminoglycoside antibiotics inhibit protein synthesis, cause misreading, or obstruct peptidyl-tRNA translocation. Although aminoglycosides bind helix69 of the bacterial large subunit RNA as well, little is known about their interaction with the homologous human helix69. To probe the role this binding event plays in toxicity, changes to thermal stability, base stacking, and conformation upon aminoglycoside binding to the human cytoplasmic helix69 were compared with those of the human mitochondrial and Escherichia coli helix69. Surprisingly, binding of gentamicin and kanamycin A to the chemically synthesized terminal hairpins of the human cytoplasmic, human mitochondrial, and E. coli helix69 revealed similar dissociation constants (1.3-1.7 and 4.0-5.4 μM, respectively). In addition, aminoglycoside binding enhanced conformational stability of the human mitochondrial helix69 by increasing base stacking. Proton one-dimensional and two-dimensional NMR suggested significant and specific conformational changes of human mitochondrial and E. coli helix69 upon aminoglycoside binding, as compared with human cytoplasmic helix69. The conformational changes and similar aminoglycoside binding affinities observed for human mitochondrial helix69 and E. coli helix69, as well as the increase in structural stability shown for the former, suggest that this binding event is important to understanding aminoglycoside toxicity.

Sensitization of Staphylococcus aureus to Methicillin and Other Antibiotics In Vitro and In Vivo in the Presence of HAMLET

HAMLET (human alpha-lactalbumin made lethal to tumor cells) is a protein-lipid complex from human milk with both tumoricidal and bactericidal activities. HAMLET exerts a rather specific bactericidal activity against some respiratory pathogens, with highest activity against Streptococcus pneumoniae, but lacks activity against most other bacterial pathogens, including Staphylococci. Still, ion transport associated with death in S. pneumoniae is also detected to a lower degree in insensitive organisms. In this study we demonstrate that HAMLET acts as an antimicrobial adjuvant that can increase the activity of a broad spectrum of antibiotics (methicillin, vancomycin, gentamicin and erythromycin) against multi-drug resistant Staphylococcus aureus, to a degree where they become sensitive to those same antibiotics, both in antimicrobial assays against planktonic and biofilm bacteria and in an in vivo model of nasopharyngeal colonization. We show that HAMLET exerts these effects specifically by dissipating the proton gradient and inducing a sodium-dependent calcium influx that partially depolarizes the plasma membrane, the same mechanism induced during pneumococcal death. These effects results in an increased cell associated binding and/or uptake of penicillin, gentamicin and vancomycin, especially in resistant stains. Finally, HAMLET inhibits the increased resistance of methicillin seen under antibiotic pressure and the bacteria do not become resistant to the adjuvant, which is a major advantageous feature of the molecule. These results highlight HAMLET as a novel antimicrobial adjuvant with the potential to increase the clinical usefulness of antibiotics against drug resistant strains of S. aureus.

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.

Simulations of the Bacterial Ribosomal Decoding Switch

Gentamicin is a potent antibiotic often used in therapy for methicillin-resistant Staphylococcusaureus. Gentamicin works by flipping a conformational switch on the ribosome, disrupting the reading head (i.e., 16S ribosomal decoding bases A1492-A1493 used for decoding messenger RNA. We use explicit solvent all-atom molecular simulation to study the thermodynamics of the ribosomal decoding site and its interaction with gentamicin. The replica exchange molecular dynamics simulations allow enhanced sampling of the unbinding free-energy landscape, including a rigorous treatment of enthalpic and entropic effects. The decoding bases flip on a timescale faster than that of gentamicin binding, supporting a stochastic gating mechanism for antibiotic binding, rather than an induced-fit model where the bases only flip in the presence of a ligand. The study also allows us to explore the nonspecific binding landscape near the binding site and reveals that, rather than a two-state bound/unbound scenario, drug dissociation entails shuttling between many metastable local minima in the free-energy landscape. Additional simulations address the effect of mutation/modification of the A-site on the free energy landscapes. In particular, mutations of base A1408 known to confer high-level resistance in “superbug” bacteria to common antibiotic therapies are investigated. Special care is dedicated to validation of the obtained results, both by direct comparison to experiment and by estimation of simulation convergence.

Effect of PEGylation of N-WASP181-200 on the Inhibitory Potency for Renal Aminoglycoside Accumulation

We previously showed that a 20-residue basic peptide, N-WASP181-200 (NISHTKEKKKGKAKKKRLTK), inhibits renal accumulation of aminoglycoside antibiotics such as gentamicin and arbekacin. The aim of this study is to determine whether PEGylation of N-WASP181-200 enhances its inhibitory potency for renal accumulation of aminoglycosides. N-terminally PEGylated peptide (PEG1k-N-W) was synthesized by conjugating N-WASP181-200 with PEG of approximately 1 kDa using the Fmoc protection/deprotection method. PEG1k-N-W decreased gentamicin binding to isolated rat renal brush-border membrane in a concentration-dependent manner, but the in vitro inhibitory potency of PEG1k-N-W was weaker than that of N-WAP181-200. On the other hand, under in vivo conditions, PEG1k-N-W decreased the renal accumulation of arbekacin more potently than N-WASP181-200. When injected intravenously, PEG1k-N-W showed a 1.7-fold longer plasma half-life relative to N-WASP181-200. In addition, the stability of N-WASP181-200 in renal brush-borer membrane suspension was found to be increased by PEGylation. Our findings suggest that PEGylation of N-WASP181-200 is a useful strategy for reducing dosage of the concomitant with which to decrease renal accumulation in the kidney, leading to prevention of aminoglycoside-induced nephrotoxicity.

The Crystal Structures of Substrate and Nucleotide Complexes of Enterococcus faecium Aminoglycoside-2′′-Phosphotransferase-IIa [APH(2′′)-IIa] Provide Insights into Substrate Selectivity in the APH(2′′) Subfamily

Aminoglycoside-2''-phosphotransferase-IIa [APH(2'')-IIa] is one of a number of homologous bacterial enzymes responsible for the deactivation of the aminoglycoside family of antibiotics and is thus a major component in bacterial resistance to these compounds. APH(2'')-IIa produces resistance to several clinically important aminoglycosides (including kanamycin and gentamicin) in both gram-positive and gram-negative bacteria, most notably in Enterococcus species. We have determined the structures of two complexes of APH(2'')-IIa, the binary gentamicin complex and a ternary complex containing adenosine-5'-(beta,gamma-methylene)triphosphate (AMPPCP) and streptomycin. This is the first crystal structure of a member of the APH(2'') family of aminoglycoside phosphotransferases. The structure of the gentamicin-APH(2'')-IIa complex was solved by multiwavelength anomalous diffraction methods from a single selenomethionine-substituted crystal and was refined to a crystallographic R factor of 0.210 (R(free), 0.271) at a resolution of 2.5 A. The structure of the AMPPCP-streptomycin complex was solved by molecular replacement using the gentamicin-APH(2'')-IIa complex as the starting model. The enzyme has a two-domain structure with the substrate binding site located in a cleft in the C-terminal domain. Gentamicin binding is facilitated by a number of conserved acidic residues lining the binding cleft, with the A and B rings of the substrate forming the majority of the interactions. The inhibitor streptomycin, although binding in the same pocket as gentamicin, is orientated such that no potential phosphorylation sites are adjacent to the catalytic aspartate residue. The binding of gentamicin and streptomycin provides structural insights into the substrate selectivity of the APH(2'') subfamily of aminoglycoside phosphotransferases, specifically, the selectivity between the 4,6-disubstituted and the 4,5-disubstituted aminoglycosides.

Stochastic Gating and Drug–Ribosome Interactions

Gentamicin is a potent antibiotic that is used in combination therapy for inhalation anthrax disease. The drug is also often used in therapy for methicillin-resistant Staphylococcus aureus. Gentamicin works by flipping a conformational switch on the ribosome, disrupting the reading head (i.e., 16S ribosomal decoding bases 1492–1493) used for decoding messenger RNA. We use explicit solvent all-atom molecular simulation to study the thermodynamics of the ribosomal decoding site and its interaction with gentamicin. The replica exchange molecular dynamics simulations used an aggregate sampling of 15 μs when summed over all replicas, allowing us to explicitly calculate the free-energy landscape, including a rigorous treatment of enthalpic and entropic effects. Here, we show that the decoding bases flip on a timescale faster than that of gentamicin binding, supporting a stochastic gating mechanism for antibiotic binding, rather than an induced-fit model where the bases only flip in the presence of a ligand. The study also allows us to explore the nonspecific binding landscape near the binding site and reveals that, rather than a two-state bound/unbound scenario, drug dissociation entails shuttling between many metastable local minima in the free-energy landscape. Special care is dedicated to validation of the obtained results, both by direct comparison to experiment and by estimation of simulation convergence.

Comparative Pharmacokinetics of Gentamicin after Intravenous, Intramuscular, Subcutaneous and Oral Administration in Broiler Chickens

The pharmacokinetics and bioavailability of gentamicin sulphate (5 mg/kg body weight) were studied in 50 female broiler chickens after single intravenous (i.v.), intramuscular (i.m.), subcutaneous (s.c.) and oral administration. Blood samples were collected at time 0 (pretreatment), and at 5, 15 and 30 min and 1, 2, 4, 6, 8, 12, 24 and 48 h after drug administration. Gentamicin concentrations were determined using a microbiological assay and Bacillus subtillis ATCC 6633 as a test organism. The limit of quantification was 0.2 microg/ml. The plasma concentration-time curves were analysed using non-compartmental methods based on statistical moment theory. Following i.v. administration, the elimination half-life (t (1/2beta)), the mean residence time (MRT), the volume of distribution at steady state (V (ss)), the volume of distribution (V (d,area)) and the total body clearance (Cl(B)) were 2.93 +/- 0.15 h, 2.08 +/- 0.12 h, 0.77 +/- 0.05 L/kg, 1.68 +/- 0.39 L/kg and 5.06 +/- 0.21 ml/min per kg, respectively. After i.m. and s.c. dosing, the mean peak plasma concentrations (C (max)) were 11.37 +/- 0.73 and 16.65 +/- 1.36 microg/ml, achieved at a post-injection times (t (max)) of 0.55 +/- 0.05 and 0.75 +/- 0.08 h, respectively. The t (1/2beta) was 2.87 +/- 0.44 and 3.48 +/- 0.37 h, respectively after i.m. and s.c. administration. The V (d,area) and Cl(B) were 1.49 +/- 0.21 L/kg and 6.18 +/- 0.31 ml/min per kg, respectively, after i.m. administration and were 1.43 +/- 0.19 L/kg and 4.7 +/- 0.33 ml/min per kg, respectively, after s.c. administration. The absolute bioavailability (F) of gentamicin after i.m. administration was lower (79%) than that after s.c. administration (100%). Substantial differences in the resultant kinetics data were obtained between i.m. and s.c. administration. The in vitro protein binding of gentamicin in chicken plasma was 6.46%.

Improved collagen type I/III ratio at the interface of gentamicin-supplemented polyvinylidenfluoride mesh materials

Formation of recurrent inguinal and incisional hernia shows an underlying defect in the wound-healing process with an insufficient quality of scar formation. Even after mesh repair an altered collagen formation and insufficient mesh integration has been found as main reason for recurrences. Therefore, the development of bioactive mesh materials to achieve a local modification of the scar formation to improve patients outcome is advisable. A polyvinylidenfluoride mesh material (PVDF) was constructed and surface modified by plasma-induced graft polymerization of acrylic acid (PVDF + PAAc). Surface supplementation was sought by binding of gentamicin to the provided active sites of the grafted mesh surfaces (PVDF+PAAc+Gentamicin). In vivo modulation of collagen formation was evaluated in a standardized animal model where an abdominal wall replacement was performed in 45 Sprague-Dawley rats. Seven, 21, and 90 days after mesh implantation, collagen/protein ratio and the collagen type I/III ratio as well as the expression of type I alpha 1 collagen mRNA (SYBR Green real-time RT-PCR) were analyzed at the perifilamentary region. Additionally, expression of matrix metalloproteinases (MMP-8/-13) has been investigated immunohistochemically. Implantation of the PVDF + PAAc + Gentamicin mesh induced a significantly decreased expression of MMP-8 and MMP-13 at the interface 21 and 90 days after implantation compared to the other groups. Whereas no significant effect was observed comparing the overall collagen/protein ratio, the quality of collagen formation expressed by the collagen type I/III ratio showed significantly higher ratios around the PVDF + PAAc + Gentamicin mesh 21 and 90 days after implantation. Correspondingly, an up to 5.3-fold expression of type I alpha 1 collagen mRNA was found. The present data confirm that a surface modification of PVDF mesh samples using plasma-induced graft polymerization of acrylic acid and supplementation of gentamicin is able to improve scar quality and mesh integration.

Aminoglycoside Resistance by ArmA-mediated Ribosomal 16 S Methylation in Human Bacterial Pathogens

Aminoglycosides are a medically important class of antibiotics used to treat serious infections. Methylation of the ribosomal target is an emerging mechanism that produces a high level of resistance to all clinically available aminoglycosides for systemic therapy except streptomycin. ArmA was the first methyltransferase using this mechanism to be discovered in a clinical isolate. We demonstrate that ArmA methylates the N7 position of nucleotide G1405 in 16S rRNA. Methylation at this position is presumed to mediate cellular resistance by blocking aminoglycoside binding by ribosomes. To test this hypothesis, we measured the binding of gentamicin by 30S subunits. Under our conditions, we did not observe binding by ribosomes methylated by ArmA. Furthermore, the ArmA methylation reaction is specific for the 30S ribosomal subunit; neither 16S rRNA alone nor the 70S ribosome is a substrate for this reaction under our experimental conditions, implicating ribosomal proteins in substrate recognition. The biochemical characteristics of ArmA place it in the Agr family of methyltransferases, whose members are predominantly anti-suicide genes from Actinomycetes aminoglycoside producers. The discrepancy between the 30% GC content of armA and the >60% GC content of Actinomycetes, however, calls into question the origin of armA. We demonstrate that surprisingly, the natural promoter of armA from gram-negative Klebsiella pneumoniae was active in gram-positive Bacillus subtilis, suggesting that armA originated from a low-GC, gram-positive aminoglycoside-producing organism.

Inhibition of gentamicin binding to rat renal brush-border membrane by megalin ligands and basic peptides

Our previous studies showed that coadministration of cytochrome c and a 20-residue basic peptide, N-WASP181–200 (NISHTKEKKKGKAKKKRLTK, p I = 10.87) inhibits renal accumulation of gentamicin. In this study, we examined effects of ligands of megalin, an endocytic receptor involved in renal uptake of gentamicin, and basic peptides including N-WASP180–200 and its mutant peptides on gentamicin binding to isolated rat renal brush-border membrane (BBM). Gentamicin binding to BBM was inhibited by megalin ligands, basic peptide fragments of cytochrome c, and N-WASP181–200 in a concentration-dependent manner. Klotz plot analysis showed that N-WASP181–200 inhibited the binding of gentamicin in a competitive manner. By substituting glycines for lysines in N-WASP181–200 at positions 9 and 15, the inhibitory effect on gentamicin binding to BBM was reduced, which may be related to a decrease in the α-helix content in the peptide. Gentamicin binding to BBM treated with trypsin, in which megalin completely disappeared, was significantly but not completely decreased compared with the native BBM. In addition, treatment of BBM with trypsin led to a decrease in the inhibitory effect of N-WASP181–200 on gentamicin binding. These observations support that megalin ligands and basic peptides including N-WASP181–200 decrease renal accumulation of gentamicin by inhibiting its binding to BBM of proximal tubule cells, partly interacting with megalin. In addition, the α-helix conformation may play an important role in the inhibitory effect of N-WASP181-200 on the binding of gentamicin to BBM.

Cytoplasmic and intra-nuclear binding of gentamicin does not require endocytosis

Understanding the cellular mechanism(s) by which the oto- and nephrotoxic aminoglycoside antibiotics penetrate cells, and the precise intracellular distribution of these molecules, will enable identification of aminoglycoside-sensitive targets, and potential uptake blockers. Clones of two kidney cell lines, OK and MDCK, were treated with the aminoglycoside gentamicin linked to the fluorophore Texas Red (GTTR). As in earlier reports, endosomal accumulation was observed in live cells, or cells fixed with formaldehyde only. However, delipidation of fixed cells revealed GTTR fluorescence in cytoplasmic and nuclear compartments. Immunolabeling of both GTTR and unconjugated gentamicin corresponded to the cytoplasmic distribution of GTTR fluorescence. Intra-nuclear GTTR binding co-localized with labeled RNA in the nucleoli and trans-nuclear tubules. Cytoplasmic and nuclear distribution of GTTR was quenched by phosphatidylinositol-bisphosphate (PIP 2), a known ligand for gentamicin. Cytoplasmic and nuclear GTTR binding increased over time (at 37 °C, or on ice to inhibit endocytosis), and was serially competed off by increasing concentrations of unconjugated gentamicin, i.e., GTTR binding is saturable. In contrast, little or no reduction of endocytotic GTTR uptake was observed when cells were co-incubated with up to 4 mg/mL unconjugated gentamicin. Thus, cytoplasmic and nuclear GTTR uptake is time-dependent, weakly temperature-dependent and saturable, suggesting that it occurs via an endosome-independent mechanism, implicating ion channels, transporters or pores in the plasma membrane as bioregulatory routes for gentamicin entry into cells.