The pattern of distribution of amino groups modulates the structure and dynamics of natural aminoglycosides: implications for RNA recognition.

Aminoglycosides are clinically relevant antibiotics that participate in a large variety of molecular recognition processes involving different RNA and protein receptors. The 3-D structures of these policationic oligosaccharides play a key role in RNA binding and therefore determine their biological activity. Herein, we show that the particular NH2/NH3(+)/OH distribution within the antibiotic scaffold modulates the oligosaccharide conformation and flexibility. In particular, those polar groups flanking the glycosidic linkages have a significant influence on the antibiotic structure. A careful NMR/theoretical analysis of different natural aminoglycosides, their fragments, and synthetic derivatives proves that both hydrogen bonding and charge-charge repulsive interactions are at the origin of this effect. Current strategies to obtain new aminoglycoside derivatives are mainly focused on the optimization of the direct ligand/receptor contacts. Our results strongly suggest that the particular location of the NH2/NH3(+)/OH groups within the antibiotics can also modulate their RNA binding properties by affecting the conformational preferences and inherent flexibility of these drugs. This fact should also be carefully considered in the design of new antibiotics with improved activity.

A simple NMR analysis of the protonation equilibrium that accompanies aminoglycoside recognition: dramatic alterations in the neomycin-B protonation state upon binding to a 23-mer RNA aptamer.

A complete characterisation of the protonation equilibrium that accompanies the molecular recognition of neomycin-B by a specific RNA receptor has been achieved by employing simple NMR measurements.

Molecular recognition of aminoglycoside antibiotics by bacterial defence proteins: NMR study of the structural and conformational features of streptomycin inactivation by Bacillus subtilis aminoglycoside-6-adenyl transferase.

The molecular recognition of streptomycin by Bacillus subtilis aminoglycoside-6-adenyl transferase has been analysed by a combination of NMR techniques and molecular dynamic simulations. This protein inactivates streptomycin by transferring an adenyl group to position six of the streptidine moiety. Our combined approach provides valuable information about the bioactive conformation for both the antibiotic and ATP and shows that the molecular recognition process for streptomycin involves a conformational selection phenomenon. The binding epitope for both ligands has also been analysed by 1D-STD experiments. Finally, the specificity of the recognition process with respect to the aminoglycoside and to the nucleotide has been studied.

Experimental evidence for the existence of non-exo-anomeric conformations in branched oligosaccharides: the neomycin-B case.

For the first time in natural O-glycosides, a large amount of non-exo-anomeric conformation is experimentally detected, in solution.

Experimental evidence for the existence of non-exo-anomeric conformations in branched oligosaccharides: NMR analysis of the structure and dynamics of aminoglycosides of the neomycin family.

It is commonly known that the exo-anomeric effect is a major factor governing the conformational behavior of naturally occurring oligosaccharides. Conformational flexibility in these molecules mainly concerns the aglycon psi angle since phi is restricted by this stereo-electronic effect. In fact, to the best of our knowledge no case of a natural glycoside adopting a non-exo-anomeric conformation in solution has yet been reported. With respect to the flexibility among naturally occurring carbohydrates, branched type oligosaccharides including sugar residues glycosidated at contiguous positions (such as blood type carbohydrate antigens Lewis X) have been considered as the paradigm of rigid saccharides--the rigidity being enhanced by van der Waals interactions. Herein, we demonstrate unambiguously that both common beliefs are not to be generalized. For example in neomycin B, a branched oligosaccharide antibiotic, a large number of non-exo-anomeric conformations was detected in solution for the first time in naturally occurring sugars. This unusual behavior is attributed to branching. Here, polar contacts between non-vicinal sugar units lead to an enhanced flexibility of the ribose glycosidic torsion phi. The influence of sugar flexibility on RNA recognition will also be discussed.