Chemistry, Department of


Date of this Version



this publication should be cited as a Ph.D. dissertation


A DISSERTATION Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Doctor of Philosophy, Major: Chemistry, Under the Supervision of Professor David B. Berkowitz. Lincoln, Nebraska: November, 2014

Copyright (c) 2014 Xiang Fei


The glmS riboswitch undergoes self-cleavage upon binding its metabolic product GlcN6P, thereby providing a negative feedback mechanism limiting translation of the glmS protein when GlcN6P is abundant. As a first step toward the development of novel antimicrobials, we have synthesized a series of GlcN6P analogues bearing phosphatase-inert surrogates in place of the natural phosphate ester functionality. The self-cleavage assay identified two such compounds that display significant riboswitch actuator activity; namely those bearing a 6-phosphonomethyl group or a 6-O-malonyl ether. These two analogues exhibit a 22-fold and a 27-fold higher catalytic efficiency, respectively, than does glucosamine. Docking experiments were conducted to provide insight into the structural basis for SAR (Structure/Activity Relationship) seen across this battery of GlcN6P analogues and directions for future design of such small molecule actuators.

M6P/IGF2R regulates intracellular sorting of lysosomal enzymes, as well as endocytosis of extracellular ligands. To explore the possibility of multivalent receptor-ligand interactions, we have utilized novel chemistries to synthesize “tailored” bivalent ligands. A “linker diversification” approach has been recently developed. It emanates from a monomer with a terminal azide. Five different chemistries were exploited to connect two monomers together, leading to five structurally and functionally distinct linkages. The assay showed that when the angles between two linking bonds are acute rather than obtuse, the corresponding ligands present higher binding affinity, suggesting the three dimensional shape of the ligand is crucial for achieving multivalency.

The ISES technique has proven to be a useful technique for catalyst screening. In this procedure, an organic reaction product or byproduct diffuses into an aqueous layer, wherein an enzymatic transformation leads to signal that can be monitored by UV/vis spectroscopy. Herein, we describe proof of principle of a miniaturized ISES assay, in which volumes are significantly reduced by utilizing a quartz micromulticell. This miniaturized ISES platform is used to examine a 4*4 combinatorial library of salen ligands, that is derived from both oxa- and carbacyclic D-fructopyranosyl-1,2-diamines. The Co(III)-salen derived from 3’,5’-diiodo-salicylaldehyde and beta-D-carbafructopyranosyl-1,2-diamine shows the highest chiral bias. X-ray crystallographic analysis reveals important structural differences between the more selective carbofructopyranosyl-1,2-diamine-derived salens and their oxacyclic counterparts.

Advisor: David. B. Berkowitz