Fragment-based drug discovery of glycan sulfatase inhibitors and chemical probes for investigating gut symbionts in inflammatory bowel disease

• Applicant: Dr. Conor Joseph Crawford, Ph.D.
• Subject Area: Biological and Biomimetic Chemistry ; Biochemistry ; Pharmacy
• Term: since 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 570219261

Utilizing fragment-based drug discovery, I aim to develop first-in-class small molecule inhibitors of BT16363S-Gal, a keystone glycan sulfatase from Bacteroides thetaiotaomicron. This enzyme enables the digestion of mucin O-glycans and microbial gut colonization. In dysbiosis, elevated BT16363S-Gal is associated with worsened outcomes in inflammatory bowel disease (IBD) and colon cancer. Current IBD current treatments lack specificity and often cause broad immune suppression. I hypothesize that selective inhibition of BT16363S-Gal will impair mucin O-glycan degradation, reduce microbial colonization, and alleviate intestinal inflammation in IBD. This is a novel approach aimed at modulating the gut microbiota. To date, there are no known small molecule inhibitors of BT1636 3S-Gal or any glycan sulfatase. A preliminary fragment screening of 2,780 fragments, identified a common core scaffold that reduces BT16363S-Gal activity by ~85%, with a lead fragment exhibiting a Kᵢ of 33 μM. In this fellowship, I will optimize these fragments through structure-based design and chemical synthesis to develop potent, selective inhibitors. These small molecules are chemical tools to decipher the function of BT16363S-Gal in gut health and disease. Alongside inhibitor development, I will create specific activity-based probes to enable basic research into the function of BT16363S-Gal and the wider S1_20 glycan sulfatase subfamily. These probes will utilize classic sulfamate warheads and novel sulfonyl hydrazides to selectively label the catalytic formyl glycine residue of sulfatases, which will be characterized by mass spectrometry and x-ray structural analyses. Additionally, fluorescent imaging tools will enable spatiotemporal resolution of our leading inhibitors in B. thetaiotaomicron in microbial communities, which will allow early diagnostics, but also, for example characterization of potential off-target effects on the microbiota. Together, this work will provide the first small molecule inhibitors and the chemical probes for glycan sulfatases. These compounds will make a significant contribution to our fundamental understanding of the biological function and therapeutic potential of sulfatases. In the long term, this will pave the way for the development of novel therapies for the treatment of IBD through selective inhibition of a bacterial sulfatase. This precision approach aims to restore the gut health of millions of patients without broad disruption of the microbiome.

• DFG Programme: WBP Position