Structural and energetic comparison of the complexes of aminoglycosides with the model of the ribosomal A-site

Abstract

Understanding the interactions which govern aminoglycoside antibiotic binding to ribosomal RNA is essential to propose modifications of these antibiotics. We have investigated the hydrogen bond patterns, solvent accessibility, and stacking energies of the nucleobases in twelve different aminoglycoside-RNA crystal complexes. These analyses pointed to some antibiotic-induced RNA structural differences that depend on the type of bound aminoglycoside. The largest differences were in the hydrogen bonding pattern in the vicinity of the U1406 and U1495 base pairs, especially in the complexes with geneticin and modified paromomycin. The complexes that stand out were the ones with neamine and kanamycin. We found that the solvent-accessible surface area buried upon aminoglycoside binding to RNA increases with the number of aminoglycoside rings but its correlation with the net charge of the antibiotic or experimental binding free energies was weak. We also investigated the dependence of other aminoglycoside characterizing descriptors, such as the number of rings and total charge, on the experimentally determined Gibbs energies. The correlation of ΔG with the total charge had the coefficient of determination R 2 over 0.8–0.9, depending on experimental data set, and was the highest of all descriptors.