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US 2018/0372751 A1Published application
Lysine reactive probes and uses thereof
AssigneeThe Scripps Research Institute
InventorsBenjamin F. CRAVATT, Stephan M. HACKER, Keriann M. BACKUS
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Abstract
Disclosed herein are methods and compounds for profiling a lysine reactive protein. Also described herein are methods, compounds, and compositions for identifying a small molecule fragment ligand that interacts with a reactive lysine residue.
Claims23
A method of identifying a reactive lysine of a protein, comprising:
- a) providing a protein sample comprising isolated proteins, living cells, or a cell lysate;
- b) contacting the protein sample with a probe compound of Formula (I) at a first concentration for a time sufficient for the probe compound to react with the reactive lysine of the protein sample;
- and
- c) analyzing the proteins of the protein sample to identify the reactive lysine that bound with the probe compound at the first concentration;
- wherein the probe compound has a structure represented by Formula (I):
- wherein,
- F1 is a small molecule fragment moiety comprising an alkyne moiety, a fluorophore moiety, a labeling group, or a combination thereof;
- and
- LG is a leaving group moiety.
6 more elements
A method of identifying a reactive lysine of a protein, comprising:
- a) providing a protein sample comprising isolated proteins, living cells, or a cell lysate and separating the protein sample into a first protein sample and a second protein sample;
- b) contacting the first protein sample with a probe compound of Formula (I) at a first concentration for a time sufficient for the probe compound to react with a reactive lysine of the first protein sample, and contacting the second protein sample with the probe compound of Formula (I) at a second concentration for a sufficient time for the probe compound to react with a reactive lysine of the second protein sample;
- c) analyzing the proteins of the first protein sample and the second protein samples of step b) to identify the reactive lysines that bound with the probe compound;
- d) comparing the identity of the reactive lysines of step c) from the first protein sample at the first concentration of probe compound to the reactive lysines from the second protein sample at the second concentration of probe compound;
- and
- e) based on step d), determining a reactive lysine of a protein;
- wherein the probe compound has a structure represented by Formula (I):
- wherein,
- F1 is a small molecule fragment moiety comprising an alkyne moiety, a fluorophore moiety, a labeling group, or a combination thereof;
- and
- LG is a leaving group moiety.
8 more elements
16-41. (canceled)
A modified lysine-containing protein comprising:
- a small molecule fragment moiety, covalently bonded to a lysine residue of a lysine-containing protein, wherein a covalent bond is formed by reaction with a non-naturally occurring small molecule probe having a structure of Formula (I):
- wherein,
- F1 is a small molecule fragment moiety comprising an alkyne moiety, a fluorophore moiety, a labeling group, or a combination thereof;
- and
- LG is a leaving group moiety.
2 more elements
43-45. (canceled)
50-59. (canceled)
Dependencies are inferred from the claim text.