CLEAVABLE SURFACTANTS
First Claim
1. A compound of formula I:
- wherein;
Q is (C1-C6)alkyl, (C6-C10)aryl, (C5-C10)heteroaryl, or (C6-C10)aryl-NH(C1-C6)alkyl;
Y is O, S, NH, —
X—
C(═
O)—
, —
C═
N—
, carbonyl, or —
O—
C(=Z)-X—
;
Z is O or S;
A is aryl, aryl(C1-C6)alkyl, heteroaryl, or a direct bond;
X is O, NH, or S;
V is C or N;
M is H, an alkali metal, or tetra(C1-C20)alkylammonium;
L is —
X—
C(=Z)-X—
or a direct bond;
R1 is (C4-C20)alkyl, (C2-C20)alkenyl, (C6-C16)aryl, (C5-C10)heteroaryl, (C1-C20)alkoxy(C1-C20)alkyl, (C1-C12)alkyl(C6-C20)polyalkoxy, or (C6-C20)(alkylthio)-(C1-C6)alkyl, or absent when V is N;
R2 and R3 are each independently H or (C1-C20)alkyl;
orR2 and R3 together form a 3-8 membered carbocycle ring, or a 3-8 membered heterocyclic ring comprising 1, 2, or 3 N(Rx), S, or O;
or—
V(R2)(R3)-L-R′
is optionally —
O—
R1 when A is aryl;
wherein any alkyl, alkenyl, aryl, or heteroaryl, carbocyclic ring, or heterocyclic ring, is optionally substituted with one or more (e.g., 1, 2, 3, 4, or
5) (C1-C20)alkyl, (C2-C20)alkenyl, (C2-C10)alkynyl, (C3-C10)cycloalkyl, (C1-C20)alkoxy, (C1-C20)alkylcarbonyl, (C1-C20)alkylcarboxyl, halo, hydroxyl, —
CO2Rx, —
SO2Rx, —
SO3Rx, nitro, amino, N(Rx)2, mercapto, (C1-C20)alkylthio, (C6-C16)aryl, (C6-C30)arylthio, trifluoromethyl, ═
O, heteroaryl, or heterocycle groups;
provided that Q is not substituted with CO2H; and
each Rx is independently H, (C1-C6)alkyl, (C6-C16)aryl, or (C1-C6)alkyl-(C6-C16)aryl;
or a salt thereof.
3 Assignments
0 Petitions
Accused Products
Abstract
The invention provides surfactant compounds of formulas I-IX, which can be used in methods for aiding the solubilization, digestion, preparation, analysis, and/or characterization of biological material, for example, proteins or cell membranes. The compounds can also aid in the recovery of peptides generated during protein digestion, particularly for in-gel digestion protocol. Additionally, the compounds can improve enzymatic protein deglycosylation without interfering with downstream sample preparation steps and mass spectrometric analysis. The compounds can be specifically useful as digestion aids that can be decomposed by an acid, by heat, or a combination thereof. Decomposition of the surfactants allows for facile separation from isolated samples, and/or allows for analysis of the sample without interfering with the sensitivity of various analytical techniques.
12 Citations
31 Claims
-
1. A compound of formula I:
-
wherein; Q is (C1-C6)alkyl, (C6-C10)aryl, (C5-C10)heteroaryl, or (C6-C10)aryl-NH(C1-C6)alkyl; Y is O, S, NH, —
X—
C(═
O)—
, —
C═
N—
, carbonyl, or —
O—
C(=Z)-X—
;Z is O or S; A is aryl, aryl(C1-C6)alkyl, heteroaryl, or a direct bond; X is O, NH, or S; V is C or N; M is H, an alkali metal, or tetra(C1-C20)alkylammonium; L is —
X—
C(=Z)-X—
or a direct bond;R1 is (C4-C20)alkyl, (C2-C20)alkenyl, (C6-C16)aryl, (C5-C10)heteroaryl, (C1-C20)alkoxy(C1-C20)alkyl, (C1-C12)alkyl(C6-C20)polyalkoxy, or (C6-C20)(alkylthio)-(C1-C6)alkyl, or absent when V is N; R2 and R3 are each independently H or (C1-C20)alkyl;
orR2 and R3 together form a 3-8 membered carbocycle ring, or a 3-8 membered heterocyclic ring comprising 1, 2, or 3 N(Rx), S, or O;
or—
V(R2)(R3)-L-R′
is optionally —
O—
R1 when A is aryl;wherein any alkyl, alkenyl, aryl, or heteroaryl, carbocyclic ring, or heterocyclic ring, is optionally substituted with one or more (e.g., 1, 2, 3, 4, or
5) (C1-C20)alkyl, (C2-C20)alkenyl, (C2-C10)alkynyl, (C3-C10)cycloalkyl, (C1-C20)alkoxy, (C1-C20)alkylcarbonyl, (C1-C20)alkylcarboxyl, halo, hydroxyl, —
CO2Rx, —
SO2Rx, —
SO3Rx, nitro, amino, N(Rx)2, mercapto, (C1-C20)alkylthio, (C6-C16)aryl, (C6-C30)arylthio, trifluoromethyl, ═
O, heteroaryl, or heterocycle groups;
provided that Q is not substituted with CO2H; andeach Rx is independently H, (C1-C6)alkyl, (C6-C16)aryl, or (C1-C6)alkyl-(C6-C16)aryl; or a salt thereof. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31)
or a salt thereof. -
11. A method for protein digestion comprising contacting a gel, a solid support, or a solution comprising a biomaterial that includes at least one protein, with a digestion reagent and a compound of claim 1, to provide a sample comprising at least one digested protein.
-
12. The method of claim 11 wherein the biomaterial is in a gel or is bound to a solid support.
-
13. The method of claim 11 wherein the biomaterial is in an aqueous solution.
-
14. The method claim 11 wherein the digestion reagent comprises one or more of a protease, CNBr, or hydroxylamine.
-
15. The method of claim 14 wherein the protease is a serine protease.
-
16. The method of claim 15 wherein the serine protease is trypsin or chymotrypsin.
-
17. The method of claim 11 further comprising decomposing the surfactant after protein digestion, wherein the degrading optionally comprises contacting the surfactant with an acidic solution, heating the surfactant, or a combination thereof.
-
18. The method of claim 11 wherein the compound self-hydrolyses in solution after protein digestion.
-
19. The method of claim 11 further comprising isolating the one or more digested proteins.
-
20. The method of claim 11 further comprising analyzing the digested proteins, wherein the digested proteins are analyzed by mass spectrometry, liquid chromatography, gel electrophoresis, or a combination thereof.
-
21. A method to stabilize or enhance the activity of a protease comprising contacting a composition comprising a protease with an effective amount of a compound of claim 1.
-
22. The method of claim 21 wherein the composition further comprises a gel, a solid support, or a solution comprising the protein.
-
23. A method for analyzing a sample comprising providing a mixture comprising a sample, a compound of claim 1, and a digestion reagent;
- and analyzing the mixture using gel electrophoresis, high performance liquid chromatography, mass spectrometry, liquid chromatography, or a combination thereof; and
wherein the digestion reagent comprises a protease, CNBr, or hydroxylamine.
- and analyzing the mixture using gel electrophoresis, high performance liquid chromatography, mass spectrometry, liquid chromatography, or a combination thereof; and
-
24. A composition comprising a gel and a compound of claim 1.
-
25. A method of solubilizing a sample comprising contacting a sample and a compound claim 1 in a solvent system.
-
26. The method of claim 25 wherein the sample comprises a protein, a peptide, or a cell membrane.
-
27. The method of claim 25 wherein the sample is solubilized by reducing, preventing, or reversing the adsorption of the sample to a surface, wherein the surface is glass or the surface comprises an organic polymer.
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28. A method to extract a peptide from a gel that contains one or more peptides, comprising contacting the gel with a compound claim 1 and an aqueous solution to form a mixture comprising a liquid and the gel, and separating the liquid from the gel, thereby providing a gel-extracted peptide in an aqueous solution.
-
29. A method to combine in-gel protein digestion and peptide extraction into a single step comprising contacting a protein-containing gel with an aqueous solution that contains a protease and a compound of claim 1, whereby a protein in the gel solubilizes and unfolds to allow for digestion by the protease in the aqueous solution, and separating the aqueous solution that contains digested peptides extracted from the gel.
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30. A method of reducing, preventing, or reversing the adsorbtion of a peptide to a surface, comprising contacting a composition that includes a peptide with a compound of claim 1, wherein the surface comprises glass or the surface comprises an organic polymer.
-
31. A method for deglycosylating a glycoprotein comprising contacting a sample comprising at least one glycoprotein with a glycosidase and a compound of claim 1.
-
Specification