Fluoro‐Carba‐Sugars are Glycomimetic Activators of the glmS Ribozyme

Abstract

The glmS ribozyme is a bacterial gene-regulating riboswitch that controls cell wall synthesis, depending on glucosamine-6-phosphate as a cofactor. Due to the presence of this ribozyme in several human pathogen bacteria (e.g., MRSA, VRSA), the glmS ribozyme represents an attractive target for the development of artificial cofactors. The substitution of the ring oxygen in carbohydrates by functionalized methylene groups leads to a new generation of glycomimetics that exploits distinct interaction possibilities with their target structure in biological systems. Herein, we describe the synthesis of mono-fluoro-modified carba variants of α-d-glucosamine and β-l-idosamine. (5aR)-Fluoro-carba-α-d-glucosamine-6-phosphate is a synthetic mimic of the natural ligand of the glmS ribozyme and is capable of effectively addressing its unique self-cleavage mechanism. However, in contrast to what was expected, the activity is significantly decreased compared to its non-fluorinated analog. By combining self-cleavage assays with the Bacillus subtilis and Staphylococcus aureus glmS ribozyme and molecular docking studies, we provide a structure-activity relationship for fluorinated carba-sugars.

Recent Development of Glucosamine‐6‐phosphate Derivatives as Potential Antibacterial Agents

“…The observed rate constant ( k obs ) of GlcN was 0.65±0.01 min −1 , approximately 1/150 of the rate of GlcN6P under the same condition . Until now, no truly active compound derived from GlcN that can be the activator has been validated …”

“…Compound 10 , which is named fluoro‐carba‐α‐D‐glucosamine‐6‐phosphate, was obtained by replacing the oxygen atom at the pyranose of compound 9 by a carbon atom and introducing a fluorine atom at the carbon atom . A series of analyses were carried on compound 10 .…”

“…The EC 50 value for compound 10 activating the S. aureus glmS ribozyme self‐cleavage was 312±32 μM, while the EC 50 values of compound 9 and GlcN6P at the same condition were 6.24±0.66 and 3.61±0.39 μM, respectively. These assays indicate that the fluorinated carba‐GlcN6P (compound 10) induces self‐cleavage of the glmS riboswitch 50‐ to 100‐fold less when compared to its precursor, compound 9 . As mentioned above, since the ring oxygen of GlcN6P is required to stabilize its interaction with the glmS riboswitch, replacement of the oxygen atom on the pyranose ring with carbon should not cause a large decrease in self‐cleavage activity.…”

“…Additionally, it is assumed that modification at the 5‐carba position (e. g., with a fluorine atom) results in steric strain with the back of the binding pocket. It is believed that the results of these in vitro studies provide a promising future for the application of carba‐sugar derivatives as glmS riboswitch activators …”

Design and synthesis of glycomimetics: Recent advances

“…In a recent example, Ferrier rearrangement was used for the synthesis of fluoro‐carba analogues of glucosamine‐6‐phosphate (GlcN6P) ( 19a ; Figure A), the natural glmS ribozyme ligand . GlmS ribozyme is a gene‐regulating riboswitch that controls cell wall synthesis and is present in several human pathogenic bacteria .…”