2-Deoxystreptamine (2-DOS)
aminoglycosides are a family of structurally related broad-spectrum
antibiotics that are used widely in the treatment of
infections caused by aerobic Gram-negative bacilli. Their
antibiotic activities are ascribed to their abilities to bind a highly conserved A site in the 16 S rRNA of the 30 S ribosomal subunit and interfere with
protein synthesis. The abilities of the 2-DOS
aminoglycosides to recognize a specific subdomain of a large
RNA molecule make these compounds archetypical models for
RNA-targeting drugs. This article presents a series of calorimetric, spectroscopic, osmotic stress, and computational studies designed to evaluate the thermodynamics (DeltaG, DeltaH, DeltaS, DeltaCp) of
aminoglycoside-rRNA interactions, as well as the hydration changes that accompany these interactions. In conjunction with the current structural database, the results of these studies provide important insights into the molecular forces that dictate and control the rRNA binding affinities and specificities of the
aminoglycosides. Significantly, identification of these molecular driving forces [which include binding-linked
drug protonation reactions,
polyelectrolyte contributions from counterion release, conformational changes, hydration effects, and molecular interactions (e.g., hydrogen bonds and van der Waals interactions)], as well as the relative magnitudes of their contributions to the binding free energy, could not be achieved by consideration of structural data alone, highlighting the importance of acquiring both thermodynamic and structural information for developing a complete understanding of the
drug-
RNA binding process. The results presented here begin to establish a database that can be used to predict, over a range of conditions, the relative affinity of a given
aminoglycoside or
aminoglycoside mimetic for a targeted
RNA site vs binding to potential competing secondary sites. This type of predictive capability is essential for establishment of a rational design approach to the development of new
RNA-targeted drugs.