Date of Completion


Embargo Period



2-nitroimidazole; activity-based; affinity tagging; albumin; chemical probe; chemical proteomics; compound-centric; covalent drug; covalent inhibitor; covalent probe; glutathione; hypoxia; interaction; lactone; mass spectrometry; methylene; orlistat; parthenolide; protein profiling; proteomics; reactivity; selectivity; small molecule; tumor; warhead

Major Advisor

Xudong Yao, Ph.D.

Associate Advisor

Alfredo Angeles-Boza, Ph.D.

Associate Advisor

Christian Brückner, Ph.D.

Associate Advisor

Mark W. Peczuh, Ph.D.

Associate Advisor

Fatma Selampinar, Ph.D.

Field of Study



Doctor of Philosophy

Open Access

Open Access


The biomedical and pharmaceutical communities are experiencing a growing demand for new druggable targets. On the other hand, many marketed drugs are being repurposed for their newly uncovered pharmacological activities. In fact, off-target drug effects can either lead to adverse events or new marketable indications. As the healthcare industry moves closer toward systems biology and precision medicine, comprehensive profiling of small molecule-protein interactions has become increasingly crucial. Chemical proteomics is a powerful set of bioanalytical approaches that utilize small molecule chemical probes and affinity capture mass spectrometry to study proteome-wide actions of reactive small molecules like drugs, toxins, and metabolites.

This dissertation discusses multiple technical and methodological aspects of chemical proteomics as a multidisciplinary subject. It presents two projects that exemplify the development of chemical probes and implementation of chemical proteomics in two distinct directions known as compound-centric and activity-based. Within both studies, the modification-specific data processing principle has provoked awareness and thoughts on tailoring bioinformatics tools for chemical proteomics.

The 2-nitroimidazole-indocyanine green (2-nitro-ICG) project features the deployment of a novel compound-centric chemical probe that answers how 2-nitroimidazole targets tumor hypoxia. This study concludes that 2-nitro-ICG and its reduced fragments modify mouse albumin as the primary target, but at two distinct sites via two different mechanisms. The development and application of 2-nitro-ICG also demonstrate various analytical benefits, challenges, and pitfalls in the compound-centric direction of chemical proteomics.

The α-methylene-β-lactone (MeLac) project presents an innovative activity-based probe with multiple electrophilic sites. This study explores the significance of broad probe reactivity in activity-based chemical proteomics. It concludes that MeLac is reactive to amino, hydroxyl, and thiol groups on proteins. Moreover, the discovery of MeLac-alkyne glutathione adduct reveals a potential shortcut for customizing compound-centric probes. Therefore, the multi-electrophilic MeLac moiety creates both a versatile activity-based probe and a scaffold for assembling compound-centric probes.

Overall, chemical proteomics has established its irreplaceable position in chemical biology. Researchers exert efforts to make chemical proteomics technologies more applicable. The chemical tools, analytical workflows, and bioinformatics support continue to improve. The field of chemical proteomics will expand faster as more innovations emerge at its cutting edge.

Appendix.xlsx (664 kB)

Available for download on Sunday, February 28, 2021