Date of Award

May 2021

Document Type


Degree Name

Doctor of Philosophy (PhD)



Committee Member

Kristi Whitehead

Committee Member

Dev Arya

Committee Member

Julia Brumaghim

Committee Member

Brian Dominy


Recent discoveries regarding the connection between changes to the human gut microbiome (GM) and the onset of various illnesses, especially those mediated by an autoimmune response, has led to interest in novel therapeutic methods to address such alterations. Targeted small molecule therapeutics could pave the way for phylum, genus, or even species-level population control of the GM in order to prevent undesirable changes that might promote disease onset. In pursuit of such treatments, the work presented in this dissertation demonstrates to use of small molecule amylase inhibitors to disrupt the starch utilization system (Sus) found in Bacteroides species, a common GM member belonging to the Bacteroidetes phylum, in a selective yet non-lethal manner.

While a variety of small molecule amylase inhibitors were probed, acarbose showed consistent and drastic inhibition against multiple Bacteroides spp., including multiple strains of the clinically relevant species Bacteroides dorei. Inhibition was mediated through the disruption of Sus, depriving these bacteria of their primary metabolic energy source. Additionally, no serious adverse effects were noted against other common GM constituents. These factors highlight acarbose as a potent, selective, and non-lethal inhibitor of Sus-containing members of the GM.

A mouse study was conducted with non-obese diabetic (NOD) mice treated with either a 10 µg/mL or 5 µg/mL dose of acarbose from 9 weeks to 28 weeks after birth to ascertain if the compound had any effects on the GM of a living organism. This mouse cohort is also a model for type 1 diabetes (T1D), an illness whose onset has been linked to shifts in GM members, so it was of interest if acarbose treatment would delay onset of the disease. Both shifts in GM composition and a small delays in the onset of diabetic symptoms were noticed in the 10 µg/mL dose cohort.

In attempts to identify new small molecule inhibitors, synthetic alterations to the flavonoid quercetin were investigated. Quercetin has demonstrated a range of biological activities, including human amylase inhibition. Unfortunately its insolubility in water impedes use in many biological assays. To circumvent this, synthetic modifications were performed that successfully increased its solubility, and assays were performed against model GM organisms, though no Sus inhibitory properties were discovered.

While the mechanism behind Sus mediated inhibition by acarbose is still under investigation and new small molecule inhibitors are being sought, the work presented here forms the basis for the use small molecule amylase inhibitors as therapeutics for dysbiosis mediated illnesses.



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