Exploration of Pomalidomide for Heterobifunctional Protein Degraders:  From Chemistry to Application

Brownsey, Duncan Keith

Exploration of Pomalidomide for Heterobifunctional Protein Degraders: From Chemistry to Application

dc.contributor.advisor	Derksen, Darren J.
dc.contributor.author	Brownsey, Duncan Keith
dc.contributor.committeemember	Van Humbeck, Jeffrey F.
dc.contributor.committeemember	Back, Thomas G.
dc.contributor.committeemember	Ling, Chang-Chun
dc.contributor.committeemember	Williams, Florence J.
dc.date	2023-06
dc.date.accessioned	2023-04-26T19:51:32Z
dc.date.available	2023-04-26T19:51:32Z
dc.date.issued	2023-04-04
dc.description.abstract	Targeted protein degradation (TPD) has recently come to the forefront of chemical biology and medicinal chemistry as a means to disrupt protein function by selective degradation. Proteolysis targeting chimeras (PROTACs) are heterobifunctional molecules that exemplify TPD technology. One of the most widely used E3 ligase ligands in PROTAC development is pomalidomide which make up 46% of all CRBN-targeting PROTACs. This work explores the chemistry of pomalidomide: first by improving the synthesis of pomalidomide derivatives, second by application in new protein degraders of p300, and then third by characterizing the fluorescent properties of pomalidomide. The improved synthesis of pomalidomide derivatives via an SNAr pathway was began by identification and avoidance of the formation of dimethyl pomalidomide, an undesired byproduct. This led to greatly enhanced yields of compounds that can be used to build new pomalidomide containing PROTACs. As well, differences in the reactivity of amines used to create pomalidomide derivatives were exploited to produce PROTACs in one-pot reactions, which in some instances, exceeded the yields of multistep syntheses used in the literature. Secondly, new degraders of the protein target p300 were prepared using a known p300 ligand A-485, outlining a new strategy to create PROTACs. To verify that linker attachment onto A-485 was amenable to PROTAC function, biotin conjugates were installed and verified using immunoprecipitation blots. A library of A-485-pomalidomide conjugates were then prepared and tested for their p300 degradation capability, which showed a general trend that the PROTACs with longer linkers were more effective degraders. Finally, the fluorescent properties of pomalidomide derivatives were explored. In aqueous solutions, pomalidomide emits visible light with a maximum at ~530 nm upon excitation at 420 nm. This emission was characterized and a library of pomalidomide PROTACs were synthesized and tested in vitro with osteosarcoma cells. In vitro fluorescence microscopy imaging of the pomalidomide library showed trends with linker structure. Relationships between fluorescence, target degradation and calculated partition coefficients were then explored.
dc.identifier.citation	Brownsey, D. K. (2023). Exploration of pomalidomide for heterobifunctional protein degraders: from chemistry to application (Doctoral thesis, University of Calgary, Calgary, Canada). Retrieved from https://prism.ucalgary.ca.
dc.identifier.uri	http://hdl.handle.net/1880/116110
dc.identifier.uri	https://dx.doi.org/10.11575/PRISM/dspace/40956
dc.language.iso	en
dc.publisher.faculty	Graduate Studies
dc.publisher.institution	University of Calgary
dc.rights	University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission.
dc.subject	PROTAC
dc.subject	Pomalidomide
dc.subject	Target Protein Degradation
dc.subject.classification	Chemistry--Organic
dc.subject.classification	Chemistry--Pharmaceutical
dc.title	Exploration of Pomalidomide for Heterobifunctional Protein Degraders: From Chemistry to Application
dc.type	doctoral thesis
thesis.degree.discipline	Chemistry
thesis.degree.grantor	University of Calgary
thesis.degree.name	Doctor of Philosophy (PhD)
ucalgary.thesis.accesssetbystudent	I require a thesis withhold – I need to delay the release of my thesis due to a patent application, and other reasons outlined in the link above. I have/will need to submit a thesis withhold application.