Substrate specificities and structure-activity relationships for acylation of antibiotics catalyzed by kanamycin acetyltransferase

Antibiotic resistance caused by the presence of the plasmid pMH67 is mediated by the aminoglycoside acetyltransferase AAC(6')-4, also known as kanamycin acetyltransferase. Bacteria harboring the plasmid are resistant to the kanomycins plus a broad range of other deoxystreptamine-containing aminoglycosides but not to the gentamicins XK62-2 and C1 which are substituted at the 6'-position. Substrate specificity studies on the purified enzyme, however, now show that the enzyme acetylates an even broader range of aminoglycosides, including the gentamicins XK62-2 and C1. The enzyme also accepts several acyl-CoA esters, which differ in nucleotide as well as in acyl chain length. Application of the method of analysis of structure-activity data developed earlier for gentamicin acetyltransferase [Williams, J. W., & Northrop, D. B. (1978) J. Biol. Chem. 253, 5908-5914] to the kinetic data obtained for AAC(6')-4 shows that the turnover of the acylation reaction is limited by catalysis and not by the rate of release of either the acetylated antibiotic or CoA. Most structural changes in aminoglycosides cause changes in rates of release, and only drastic changes, near the 6'-amino group, affect catalysis. The structural requirements on aminoglycosides for enzymatic activity run parallel to the structural requirements for antibacterial activity.     

Determination of the rate-limiting segment of aminoglycoside nucleotidyltransferase 2'-I by pH and viscosity-dependent kinetics

Aminoglycoside nucleotidyltransferase 2'-I follows a Theorell-Chance kinetic mechanism in which turnover is controlled by the rate-limiting release of the final product (Q), a nucleotidylated aminoglycoside [Gates, C. A., & Northrop, D. B. (1988) Biochemistry (second of three papers in this issue)]. The effects of viscosity on the kinetic constants of netilmicin, gentamicin C1, and sisomicin aminoglycoside substrates are as follows: no change in the substrate inhibition constants of all three antibiotics, a small but significant and highly unusual increase in Vmax/Km for netilmicin but large, normal decreases for gentamicin C1 and sisomicin, and marked decreases in the maximal velocities for all three. The lack of effect on substrate inhibition provides essential control experiments, signifying that glycerol does not interfere with binding of aminoglycosides to EQ and that the steady-state distribution of EQ does not increase as the release of Q is slowed by a viscosogen. The decrease in the Vmax/Km of better substrates indicates dominance by a diffusion-controlled component in the catalytic segment, attributed to the release of pyrophosphate. The presence of an increase in the Vmax/Km of the poor substrate, however, is inexplicable in terms of either single or multiple diffusion-controlled steps. Instead, it is here attributed to an equilibrium between conformers of the enzyme-nucleotide complex in which glycerol favors the conformation necessary for binding of aminoglycosides. The decrease in Vmax is consistent with the diffusion-controlled release of the final product determining enzymatic turnover.(ABSTRACT TRUNCATED AT 250 WORDS)     

Alternative substrate and inhibition kinetics of aminoglycoside nucleotidyltransferase 2'-I in support of a Theorell-Chance kinetic mechanism

Aminoglycoside nucleotidyltransferase 2'-I conveys multiple antibiotic resistance to Gram-negative bacteria because the enzyme adenylylates a broad range of aminoglycoside antibiotics as substrates [Gates, C. A., & Northrop, D. B. (1988) Biochemistry (preceding paper in this issue)]. The enzyme also catalyzes the transfer of a variety of nucleotides [Van Pelt, J. E., & Northrop, D. B. (1984) Arch. Biochem. Biophys. 230, 250-263]. This doubly broad substrate specificity makes it an excellent candidate for application of the alternative substrate diagnostic [Radika, K., & Northrop, D. B. (1984) Anal. Biochem. 141, 413-417] as a means to determine its kinetic mechanism. The kinetic patterns presented here are composed of one set of intersecting lines and one coincident line and are consistent with a Theorell-Chance kinetic mechanism in which nucleotide binding precedes aminoglycosides, pyrophosphate is released prior to the nucleotidylated aminoglycoside (Q), and turnover is controlled by the rate-limiting release of the final product. Substrate inhibition by tobramycin (B) is partial and uncompetitive versus Mg-ATP, indicating that B binds to the EQ complex, but not in the usual dead-end fashion common to an ordered sequential release of products; instead, Q may escape from the abortive EQB complex at a finite rate. Dead-end inhibition by neomycin C (I) is also partial and uncompetitive versus Mg-ATP but is slope-linear, intercept-hyperbolic, partial noncompetitive versus gentamicin A; both kinetic patterns signify the formation of a partial abortive EQI complex.(ABSTRACT TRUNCATED AT 250 WORDS)     

Molecular determinants of affinity for aminoglycoside binding to the aminoglycoside nucleotidyltransferase(2')-Ia

One of the most commonly occurring aminoglycoside resistance enzymes is aminoglycoside 2'-O-nucleotidyltransferase [ANT(2')]. In the present study molecular determinants of affinity and specificity for aminoglycoside binding to this enzyme are investigated using isothermal titration calorimetry (ITC). Binding of aminoglycosides is enthalpically driven accompanied by negative entropy changes. The presence of metal-nucleotide increases the affinity for all but one of the aminoglycosides studied but has no effect on specificity. The substituents at positions 1, 2', and 6' are important determinants of substrate specificity. An amino group at these positions leads to greater affinity. No correlation is observed between the change in affinity and enthalpy. At the 2' position greater affinity results from a more negative enthalpy for an aminoglycoside containing an amino rather than a hydroxyl at that position. At the 6' position the greater affinity for an aminoglycoside containing an amino substituent results from a less disfavorable entropic contribution. The thermodynamic basis for the change in affinity at position 1 could not be determined because of the weak binding of one of the aminoglycoside substrates, amikacin. The effect of increasing osmotic stress on affinity was used to determine that a net release of approximately four water molecules occurs when tobramycin binds to ANT(2'). No measurable net change in the number of bound water molecules is observed when neomycin binds the enzyme. Data acquired in this work provide the rationale for the ability of ANT(2') to confer resistance against kanamycins but not neomycins.     

Hairpin ribozyme cleavage catalyzed by aminoglycoside antibiotics and the polyamine spermine in the absence of metal ions.

The hairpin ribozyme is a small catalytic RNA that achieves an active configuration by docking of its two helical domains in an antiparallel fashion. Both docking and subsequent cleavage are dependent on the presence of divalent metal ions, such as magnesium, but there is no evidence to date for direct participation of such ions in the chemical cleavage step. We show that aminoglycoside antibiotics inhibit cleavage of the hairpin ribozyme in the presence of metal ions with the most effective being 5-epi-sisomicin and neomycin B. In contrast, in the absence of metal ions, a number of aminoglycoside antibiotics at 10 mM concentration promote hairpin cleavage with rates only 13-20-fold lower than the magnesium-dependent reaction. We show that neomycin B competes with metal ions by ion replacement with the postively charged amino groups of the antibiotic. In addition, we show that the polyamine spermine at 10 mM promotes efficient hairpin cleavage with rates similar to the magnesium-dependent reaction. Low concentrations of either spermine or the shorter polyamine spermidine synergize with 5 mM magnesium ions to boost cleavage rates considerably. In contrast, at 500 microM magnesium ions, 4 mM spermine, but not spermidine, boosts the cleavage rate. The results have significance both in understanding the role of ions in hairpin ribozyme cleavage and in potential therapeutic applications in mammalian cells.     

Modulation of RNA function by aminoglycoside antibiotics

One of the most important families of antibiotics are the aminoglycosides, including drugs such as neomycin B, paromomycin, gentamicin and streptomycin. With the discovery of the catalytic potential of RNA, these antibiotics became very popular due to their RNA-binding capacity. They serve for the analysis of RNA function as well as for the study of RNA as a potential therapeutic target. Improvements in RNA structure determination recently provided first insights into the decoding site of the ribosome at high resolution and how aminoglycosides might induce misreading of the genetic code. In addition to inhibiting prokaryotic translation, aminoglycosides inhibit several catalytic RNAs such as self-splicing group I introns, RNase P and small ribozymes in vitro. Furthermore, these antibiotics interfere with human immunodeficiency virus (HIV) replication by disrupting essential RNA-protein contacts. Most exciting is the potential of many RNA-binding antibiotics to stimulate RNA activities, conceiving small-molecule partners for the hypothesis of an ancient RNA world. SELEX (systematic evolution of ligands by exponential enrichment) has been used in this evolutionary game leading to small synthetic RNAs, whose NMR structures gave valuable information on how aminoglycosides interact with RNA, which could possibly be used in applied science.     

Inhibition of superoxide-dependent processes by aminoglycoside antibiotics

The ability of various antibiotics to inhibit superoxide anion(O-2)-mediated formation of adrenochrome from adrenaline and recovery of cytochrome c by xanthine oxidase was studied. In the adrenaline system (pH 10.2), aminoglycosides might be arranged, according to the inhibitory effect, in the following order: monomycin greater than gentamicin greater than kanamycin greater than lincomycin greater than streptomycin. In the xanthine oxidase system (pH 7.8), that order was the following: monomycin greater than gentamicin greater than lincomycin greater than greater than kanamycin. It was suggested that the antibiotic inhibition of the O-2-dependent processes at the essential sites of metabolism and/or the antibiotic involvement into the process of free radical oxidation initiated by O-2 in the cells might be one of the mechanisms of the drug action and toxicity with respect to the host.     

Inhibition of polyphosphoinositide phosphodiesterase by aminoglycoside antibiotics

The calcium-activated phosphodiesteratic hydrolysis of³²P-labeled phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 4-phosphate in prelabeled nerve ending membranes is inhibited by the aminoglycosides neomycin and gentamicin, and to a lesser extent, by streptomycin. The inhibition is overcome by increasing concentrations of Ca²⁺, indicating that the aminoglycosides exert their effect by displacing Ca²⁺ from lipid.Dedicated to Professor Yasuzo Tsukada.     

Topographical relationships among H-2 specificities controlled by theD region

In the present work, we used the differential redistribution method to study the molecular expression of several H-2 specificities controlled by theD region of theH-2 ^a haplotype. We observed that: capping of the private specificity H-2.4 induced capping of the public specificities H-2.3, H-2.35, and H-2.36, and vice versa; capping of any one of these specificities did not induce capping of the public specificity H-2.28, controlled by the same region. By contrast, capping of the H-2.28 specificity induced capping of these specificities; redistribution of H-2K and H-2D private specificities or redistribution of H-2D private specificity and Ia specificities did not induce capping of the H-2.28 specificity. These data indicate that a part of a molecule carrying the H-2.28 specificity is linked to a molecule carrying H-2.4, H-2.3, H-2.35, and H-2.36 specificities and that a part of a polypeptide chain bearing the H-2.28 specificity is independent from that bearing other specificities controlled either by theD region (i.e., H-2.4, H-2.3, H-2.35, and H-2.36) or by theK andI regions. These results further strengthened the hypothesis of the existence of at least two genes controlling theD-region H-2 antigenic specificities.     

A comparison of the chitin synthase-inhibitory and antifungal efficacy of nucleoside-peptide antibiotics: structure-activity relationships

Abstract Using Mucor rouxii , the chitin synthase (ChS)-inhibitory and antifungal activity was determined of 6 nucleoside-peptide antibiotics (NPAs) representing pairs of structural analogues, each consisting of a dipeptide (DP) and a corresponding tripeptide (TP). These were the nikkomycins X and I (X, I), the nikkomycins Z and J (Z, J), and the polyoxins D and A (D, A). Although all were very good ChS-inhibitors (X and A being best, with K _i approx. 0.5 μM), only X and Z elicited a strong response in vivo as determined by the degree of inhibition exerted on N -acetylglucosamine (GlcNAc) incorporation into the chitin fraction, the survival rate, and the minimum inhibitory concentration (MIC). The MIC values were about 2 μM (for X and Z) and 100 μM (for I, J, D and A). Certain DPs and TPs reduced the antifungal activity of X, the effect being much more pronounced with DPs. It is suggested that uptake of NPAs involves the transpeptidase reaction of the γ-glutamyl cycle, the observed antagonism thus resulting from competition for a common carrier.     

Inhibition of ribosomal translocation by aminoglycoside antibiotics.

The translocation of AcPhe-tRNA in a purified system and that of peptidyl-tRNA in a crude, complete polypeptide synthesizing system containing endogenous $\text{E. coli}$ polysomes are inhibited by antibiotics of the neomycin, kanamycin and gentamicin groups. The extent of inhibition varies with the different antibiotics, but it correlates well with the capacity of each antibiotic to inhibit polypeptide chain elongation. Thus, the inhibition of translocation by these antibiotics is clearly significant for their inhibitory effect on polypeptide synthesis.     

Inhibition of initiation of DNA synthesis by aminoglycoside antibiotics

In a $\text{dna}\text{C}{}^{\mathrm{ts}}$ mutant of $\text{E. coli}$, the reinitiation of DNA synthesis, which occurred by the shift of the culture from a restrictive temperature to a permissive temperature, was markedly prevented by habakacin, dibekacin, kanamycin, and gentamicin. On the contrary, chloramphenicol did not inhibit the reinitiation synthesis for 30 min. In a parallel experiment, leucine uptake into protein was profoundly blocked by chloramphenicol, but only slightly by habekacin. Habekacin did not significantly affect DNA elongation of the cells at a restrictive temperature. We propose that inhibition of initiation of replication by aminoglycoside antibiotics is related to their lethality.     

Studies of structure-activity relationships of human interleukin-2

Human interleukin-2 (IL-2) has 3 cysteine residues; cysteines 58 and 105 form an intramolecular disulfide bridge, whereas cysteine 125 has a free sulfhydryl group. In this study, site-specific mutagenesis has been used to modify the cysteine residues of recombinant Escherichia coli-derived IL-2 (rIL-2) to evaluate the functional structure of IL-2. Substitution or deletion of cysteine 105 disrupted the disulfide bridge and yielded a mutant protein which was 8-10 times less active than wild type rIL-2. A similar modification at position 58, however, reduced the activity of rIL-2 by more than 250-fold. Although substitution of serine for cysteine 125 did not affect IL-2 activity, deletion of cysteine 125 or deletion of amino acids in the vicinity of this cysteine yielded mutant proteins with little, if any, activity. These results indicate that the protein structure in the vicinity of both positions 58 and 125 is more critical than that close to position 105. These findings may provide a clue to the understanding of the functional structure of human IL-2.     

Substrate specificities in hydrolysis of polyhydroxyalkanoates by microbial esterases

Summary Enzymatic degradations of 5 different polyhydroxyalkanoates (PHA) were investigated at 37°C in the aqueous solutions (pH 7.4) containing different microbial enzymes of 16 lipases and 5 PHA depolymerases. The substrate specificities of microbial PHA depolymerases on hydrolysis of polyhydroxyalkanoates were distinguished from those of microbial lipases.     

Mg2+ mimicry in the promotion of group I ribozyme activities by aminoglycoside antibiotics

Aminoglycoside antibiotics inhibit several types of ribozymes, including group I introns, by displacing critical Mg2+ ions. However, they stimulate activity of the small hairpin ribozyme. We show here that aminoglycosides promote self-splicing of the Cr.psbA2 group I intron at subthreshold Mg2+ concentrations. Neomycin is the most effective of the aminoglycosides tested; it stimulates splicing of Cr.psbA2 at micromolar concentrations, and, in this respect, is >100-fold more effective than spermidine. At optimal Mg2+ for Cr.psbA2 splicing, these drugs, especially kanamycin B and tobramycin, promote GTP attack at the 3' splice-site. Kinetic analysis suggests that this is due to an alternatively folded state of the ribozyme that is induced, or stabilized, by aminoglycosides. A similar effect is observed at high Mg2+ concentrations. Comparing the effects of structurally related aminoglycosides indicates that splicing promotion is more sensitive to drug structure than misfolding and occurs at lower drug concentrations. These data show that aminoglycosides can promote biochemical activities of a large ribozyme by acting as a Mg2+ mimic. The results also underscore the functional diversity of group I introns in nature.     

Quantitative structure-activity relationships for the pre-steady state acetylcholinesterase inhibition by carbamates

4-Nitrophenyl-N-substituted carbamates (1) are characterized as pseudosubstrate inhibitors of acetylcholinesterase. The first step is formation of the enzyme-inhibitor tetrahedral intermediate with the inhibition constant (Ki), the second step is formation of the carbamyl enzyme with the carbamylation constant (kc), and the third step is hydrolysis of the carbamyl enzyme with decarbamylation constant (kd). According to pre-steady state kinetics the Ki step is divided further into two steps: (1) formation of the enzyme-inhibitor complex with the dissociation constant (KS) and (2) formation of the enzyme-inhibitor tetrahedral intermediate from the complex with the equilibrium constant (k2/k-2). Since the inhibitors are protonated in pH 7.0 buffer solution, the virtual dissociation constant (KS') of the enzyme-protonated inhibitor complex can be calculated from the equation, -log KS'=-log KS-pKa + 14. The -logKS, -log KS', log k2, and log k-2 values are multiply linearly correlated with the Jave equation (log(k/k0)=rho*sigma* + deltaEs + psi pi). For -log KS'-sigma*-Es)pi-correlation, the rho* value of -0.4 indicates that the enzyme-protonated inhibitor complexes have more positive charges than the protonated inhibitors, the delta value of 0.44 suggests that the bulkily substituted inhibitors lessen the reaction due to the difficulty of the inhibitors to enter the narrow enzyme active site gorge, and the psi value of 0.27 implies that the inhibitors with hydrophobic substituents accelerate the inhibitors entering the active site gorge of the enzyme. For log k2/k-2,-sigma*-Es-pi-correlation, the rho* value of 1.1 indicates that the enzyme-protonated inhibitor tetrahedral intermediates have more negative charges than the enzyme-protonated inhibitor complexes, the delta value of 0.15 suggests that the bulkily substituted inhibitors are difficult to bind into a small acyl binding site of the enzyme, and the psi value of -0.3 implies that the inhibitors with hydrophobic substituents resist binding to the hydrophilic acyl binding site of the enzyme.