1
|
Wang Y, Dix MM, Bianco G, Remsberg JR, Lee HY, Kalocsay M, Gygi SP, Forli S, Vite G, Lawrence RM, Parker CG, Cravatt BF. Expedited mapping of the ligandable proteome using fully functionalized enantiomeric probe pairs. Nat Chem 2019; 11:1113-1123. [PMID: 31659311 PMCID: PMC6874898 DOI: 10.1038/s41557-019-0351-5] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 09/10/2019] [Indexed: 11/29/2022]
Abstract
A fundamental challenge in chemical biology and medicine is to understand and expand the fraction of the human proteome that can be targeted by small molecules. We recently described a strategy that integrates fragment-based ligand discovery with chemical proteomics to furnish global portraits of reversible small-molecule/protein interactions in human cells. Excavating clear structure-activity relationships from these 'ligandability' maps, however, was confounded by the distinct physicochemical properties and corresponding overall protein-binding potential of individual fragments. Here, we describe a compelling solution to this problem by introducing a next-generation set of fully functionalized fragments differing only in absolute stereochemistry. Using these enantiomeric probe pairs, or 'enantioprobes', we identify numerous stereoselective protein-fragment interactions in cells and show that these interactions occur at functional sites on proteins from diverse classes. Our findings thus indicate that incorporating chirality into fully functionalized fragment libraries provides a robust and streamlined method to discover ligandable proteins in cells.
Collapse
Affiliation(s)
- Yujia Wang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Melissa M Dix
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Giulia Bianco
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jarrett R Remsberg
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Hsin-Yu Lee
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Marian Kalocsay
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Gregory Vite
- Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - R Michael Lawrence
- Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Christopher G Parker
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA.
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
| |
Collapse
|
2
|
Savino R, Paduano S, Preianò M, Terracciano R. The proteomics big challenge for biomarkers and new drug-targets discovery. Int J Mol Sci 2012. [PMID: 23203042 PMCID: PMC3509558 DOI: 10.3390/ijms131113926] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
In the modern process of drug discovery, clinical, functional and chemical proteomics can converge and integrate synergies. Functional proteomics explores and elucidates the components of pathways and their interactions which, when deregulated, lead to a disease condition. This knowledge allows the design of strategies to target multiple pathways with combinations of pathway-specific drugs, which might increase chances of success and reduce the occurrence of drug resistance. Chemical proteomics, by analyzing the drug interactome, strongly contributes to accelerate the process of new druggable targets discovery. In the research area of clinical proteomics, proteome and peptidome mass spectrometry-profiling of human bodily fluid (plasma, serum, urine and so on), as well as of tissue and of cells, represents a promising tool for novel biomarker and eventually new druggable targets discovery. In the present review we provide a survey of current strategies of functional, chemical and clinical proteomics. Major issues will be presented for proteomic technologies used for the discovery of biomarkers for early disease diagnosis and identification of new drug targets.
Collapse
Affiliation(s)
- Rocco Savino
- Department of Health Sciences, Laboratory of Mass Spectrometry and Proteomics, University "Magna Græcia", Catanzaro, University Campus, Europa Avenue, 88100 Catanzaro, Italy.
| | | | | | | |
Collapse
|