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)
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Special Emphasis Panel (ZRG1-BCMB-A (51))
Program Officer
Fabian, Miles
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Scripps Research Institute
La Jolla
United States
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Sarma, Bani Kanta; Liu, Xiaodan; Kodadek, Thomas (2016) Identification of selective covalent inhibitors of platelet activating factor acetylhydrolase 1B2 from the screening of an oxadiazolone-capped peptoid-azapeptoid hybrid library. Bioorg Med Chem 24:3953-3963
Backus, Keriann M; Correia, Bruno E; Lum, Kenneth M et al. (2016) Proteome-wide covalent ligand discovery in native biological systems. Nature 534:570-4
Sarma, Bani Kanta; Liu, Xiaodan; Wu, Hao et al. (2015) Solid phase synthesis of 1,3,4-oxadiazin-5 (6R)-one and 1,3,4-oxadiazol-2-one scaffolds from acyl hydrazides. Org Biomol Chem 13:59-63
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Simpson, Levi S; Kodadek, Thomas (2012) A Cleavable Scaffold Strategy for the Synthesis of One-Bead One-Compound Cyclic Peptoid Libraries That Can Be Sequenced By Tandem Mass Spectrometry. Tetrahedron Lett 53:2341-2344
Bachovchin, Daniel A; Cravatt, Benjamin F (2012) The pharmacological landscape and therapeutic potential of serine hydrolases. Nat Rev Drug Discov 11:52-68
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
Cisar, Justin S; Cravatt, Benjamin F (2012) Fully functionalized small-molecule probes for integrated phenotypic screening and target identification. J Am Chem Soc 134:10385-8

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