This project aims to develop a revolutionary screening platform that will allow for the rapid isolation of hundreds of high affinity and specificity synthetic ligands for proteins in a highly parallel fashion. The central feature of the proposal is to label dozens to hundreds of mechanistically related proteins simultaneously using reagents developed for Activity-Based Protein Profiling (ABPP). This mixture of labeled proteins will then be screened en masse against a several million member combinatorial library of peptoids displayed on beads. Peptoid-displaying beads that retain labeled protein will be collected by fluorescence-activated flow sorting. Mass spectrometry-based techniques will then be employed to identify the protein captured on the bead as well as the sequence of the peptoid. These peptoids can be employed as capture agents in the creation of protein-detecting microarrays. They will also be modified for use as high potency, photo-triggered pharmacological inhibitors of their target proteins. This will involve appendage of a Ru(II)-containing complex to the peptoid. When irradiated with visible light, the ruthenium complex generates singlet oxygen, which is capable of destroying proteins in the immediate vicinity. These novel reagents will be used to probe the roles of the target proteins in biological assays. If successful, this effort will revolutionize the discovery of specific protein ligands, a goal identified by the NIH as a strategic priority. Because the ligands will be peptoids, which can be easily synthesized in large quantities even by laboratories lacking specialized organic chemistry skills, these ligands will be far more widely accessible to the research community than would be the case for most other classes of protein binding-molecules. Therefore, we believe that this project is transformative in its potential scope and impact.

Public Health Relevance

The identification of large numbers of protein ligands has been identified by the NIH as a high priority for biomedical research. Such ligands could be employed as reagents to construct tools for the discovery of diagnostically useful disease biomarkers. The synthetic compounds that we plan to identify could also serve as drug leads for a variety of therapeutically interesting targets.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1-BCMB-A (51))
Program Officer
Fabian, Miles
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Scripps Research Institute
La Jolla
United States
Zip Code
Doran, Todd M; Kodadek, Thomas (2014) A liquid array platform for the multiplexed analysis of synthetic molecule-protein interactions. ACS Chem Biol 9:339-46
Niphakis, Micah J; Cravatt, Benjamin F (2014) Enzyme inhibitor discovery by activity-based protein profiling. Annu Rev Biochem 83:341-77
Zuhl, Andrea M; Mohr, Justin T; Bachovchin, Daniel A et al. (2012) Competitive activity-based protein profiling identifies aza-?-lactams as a versatile chemotype for serine hydrolase inhibition. J Am Chem Soc 134:5068-71
Bachovchin, Daniel A; Cravatt, Benjamin F (2012) The pharmacological landscape and therapeutic potential of serine hydrolases. Nat Rev Drug Discov 11:52-68
Aditya, Animesh; Kodadek, Thomas (2012) Incorporation of heterocycles into the backbone of peptoids to generate diverse peptoid-inspired one bead one compound libraries. ACS Comb Sci 14:164-9
Adibekian, Alexander; Martin, Brent R; Wang, Chu et al. (2011) Click-generated triazole ureas as ultrapotent in vivo-active serine hydrolase inhibitors. Nat Chem Biol 7:469-78
Bachovchin, Daniel A; Ji, Tianyang; Li, Weiwei et al. (2010) Superfamily-wide portrait of serine hydrolase inhibition achieved by library-versus-library screening. Proc Natl Acad Sci U S A 107:20941-6
Johnson, Douglas S; Weerapana, Eranthie; Cravatt, Benjamin F (2010) Strategies for discovering and derisking covalent, irreversible enzyme inhibitors. Future Med Chem 2:949-64
Weerapana, Eranthie; Wang, Chu; Simon, Gabriel M et al. (2010) Quantitative reactivity profiling predicts functional cysteines in proteomes. Nature 468:790-5