Defining the basis for the specificity of aminoglycoside-rRNA recognition: a comparative study of drug binding to the A sites of Escherichia coli and human rRNA

Survey of the year 2005: literature on applications of isothermal titration calorimetry

Isothermal titration calorimetry (ITC) can provide a full thermodynamic characterization of an interaction. Its usage does not suffer from constraints of molecular size, shape or chemical constitution. Neither is there any need for chemical modification or attachment to solid support. This ease of use has made it an invaluable instrumental resource and led to its appearance in many laboratories. Despite this, the value of the thermodynamic parameterization has, only quite recently, become widely appreciated. Although our understanding of the correlation between thermodynamic data and structural details continues to be somewhat naïve, a large number of publications have begun to improve the situation. In this overview of the literature for 2005, we have attempted to highlight works of interest and novelty. Furthermore, we draw attention to those works which we feel have provided a route to better analysis and increased our ability to understand the meaning of thermodynamic change on binding.

Redesign of aminoglycosides for treatment of human genetic diseases caused by premature stop mutations

A series of new derivatives of the clinically used aminoglycoside antibiotic paromomycin were designed, synthesized, and their ability to read-through premature stop codon mutations was examined in both in vitro translation system and ex vivo mammalian cultured cells. One of these structures, a pseudo-trisaccharide derivative, showed notably higher stop codon read-through activity in cultured cells compared to those of paromomycin and gentamicin.

Biochemical and Thermodynamic Characterization of Compounds That Bind to RNA Hairpin Loops: Toward an Understanding of Selectivity

Elucidation of the molecular forces governing small molecule-RNA binding is paramount to the progress of rational design strategies. The extensive characterization of the aminoglycoside-16S rRNA A-site interaction has deepened our understanding of how aminoglycosides bind to their target and exert their antimicrobial effects. However, to date no other RNA binding compounds have undergone such rigorous evaluation, and in general the origins of small molecule-RNA binding remain a mystery. We recently reported the identification of small molecules, dimers of 2-deoxystreptamine, which are able to bind selectively to RNA tetraloops and octaloops, respectively [Thomas, Liu, and Hergenrother (2005) J. Am. Chem. Soc. 127, 12434-12435]. Described herein is the biochemical and biophysical characterization of the RNA binding properties of the most selective compound, B-12, as well as closely related analogues. These studies further substantiate that B-12 is indeed selective for RNA octaloop sequences and indicate that the origin of this selectivity may lie in B-12's unusual binding mode, in which entropic factors are major contributors to the overall binding energy. In fact, isothermal titration calorimetry (ITC) experiments indicate that the binding of B-12 and most of its analogues is associated with a strong entropic contribution to the total binding energy. This is in stark contrast to the aminoglycosides, for which favorable enthalpy typically provides the driving force for binding. These studies are the first to examine small molecule-RNA hairpin loop binding in detail and are a necessary step toward the design of compounds that are specific binders for a given RNA sequence.

Binding of neomycin-class aminoglycoside antibiotics to mutant ribosomes with alterations in the A site of 16S rRNA

Aminoglycoside antibiotics that bind to the aminoacyl-tRNA site (A site) of the ribosome are composed of a common neamine core in which a glycopyranosyl ring is attached to position 4 of a 2-deoxystreptamine moiety. The core is further substituted by one (ribostamycin), two (neomycin and paromomycin), or three (lividomycin A) additional sugars attached to position 5 of the 2-deoxystreptamine. To study the role of rings III, IV, and V in aminoglycoside binding, we used isogenic Mycobacterium smegmatis DeltarrnB mutants carrying homogeneous populations of mutant ribosomes with alterations in the 16S rRNA A site. MICs were determined to investigate drug-ribosome interactions, and the results were compared with that of the previously published crystal structure of paromomycin bound to the ribosomal A site. Our analysis demonstrates that the stacking interaction between ring I and G1491 is largely sequence independent, that rings III and IV each increase the strength of drug binding to the ribosome, that ring IV of the 6'-NH3+ aminoglycosides compensates for loss of interactions between ring II and U1495 and between ring III and G1491, that the aminoglycosides rely on pseudo-base pairing between ring I and A1408 for binding independently of the number of sugar rings attached to the neamine core, that addition of ring V to the 6'-OH 4,5-aminoglycoside paromomycin does not alter the mode of binding, and that alteration of the U1406.U1495 wobble base pair to the Watson-Crick interaction pair 1406C-1495G yields ribosomal drug susceptibilities to 4,5-aminoglycosides comparable to those seen with the wild-type A site.

Aminoglycoside-induced reduction in nucleotide mobility at the ribosomal RNA A-site as a potentially key determinant of antibacterial activity

Steady-state and time-resolved fluorescence techniques have been used to characterize the energetics and dynamics associated with the interaction of an E. coli 16 S rRNA A-site model oligonucleotide and four aminoglycoside antibiotics that exhibit a broad range of antibacterial activity. The results of these characterizations suggest that aminoglycoside-induced reduction in the mobility of an adenine residue at position 1492 of the rRNA A-site is a more important determinant of antibacterial activity than drug affinity for the A-site. This observation is consistent with a recently proposed model for the mechanism of protein synthesis inhibition by aminoglycosides that invokes a drug-induced alteration in the conformational equilibrium of the rRNA A-site (centered around the conserved adenine residues at positions 1492 and 1493), which, in turn, promotes an enhanced interaction between the rRNA and the minihelix formed by the tRNA anticodon and the mRNA codon, even when the anticodon is noncognate. Regarded as a whole, the results reported here indicate that the rational design of antibiotics that target the 16 S rRNA A-site requires consideration of not only the structure and energetics of the drug-RNA complex but also the dynamics associated with that complex.

Molecular understanding of aminoglycoside action and resistance

Aminoglycosides are potent bactericidal antibiotics targeting the bacterial ribosome, where they bind to the A-site and disrupt protein synthesis. They are particularly active against aerobic, Gram-negative bacteria and act synergistically against certain Gram-positive organisms. Aminoglycosides are used in the treatment of severe infections of the abdomen and urinary tract, bacteremia, and endocarditis. They are also used for prophylaxis, especially against endocarditis. Bacterial resistance to aminoglycosides continues to escalate and is widely recognized as a serious health threat. This might be the reason for the interest in understanding the mechanisms of resistance. It is now clear that the resistance occurs by different mechanisms such as prevention of drug entry, active extrusion of drugs, alteration of the drug target (mutational modification of 16S rRNA and mutational modification of ribosomal proteins), and enzymatic inactivation through the expression of enzymes, which covalently modify these antibiotics. Enzymatic inactivation is normally due to acetyltransferases, nucleotidyltransferases, and phosphotransferases. In this review, we focus on the recent concept of molecular understanding of aminoglycoside action and resistance.

Interactions of Designer Antibiotics and the Bacterial Ribosomal Aminoacyl-tRNA Site

The X-ray crystal structures for the complexes of three designer antibiotics, compounds 1, 2, and 3, bound to two models for the ribosomal aminoacyl-tRNA site (A site) at 2.5-3.0 Angstroms resolution and that of neamine at 2.8 Angstroms resolution are described. Furthermore, the complex of antibiotic 1 bound to the A site in the entire 30S ribosomal subunit of Thermus thermophilus is reported at 3.8 Angstroms resolution. Molecular dynamics simulations revealed that the designer compounds provide additional stability to bases A1492 and A1493 in their extrahelical forms. Snapshots from the simulations were used for free energy calculations, which revealed that van der Waals and hydrophobic effects were the driving forces behind the binding of designer antibiotic 3 when compared to the parental neamine.