U.S. patent application number 17/369768 was filed with the patent office on 2021-10-28 for kits for using bispyridines to improve labeling of nucleophiles.
This patent application is currently assigned to Agilent Technologies, Inc.. The applicant listed for this patent is Agilent Technologies, Inc.. Invention is credited to Francis T. Haxo, Michael J. Kimzey.
Application Number | 20210333269 17/369768 |
Document ID | / |
Family ID | 1000005698878 |
Filed Date | 2021-10-28 |
United States Patent
Application |
20210333269 |
Kind Code |
A1 |
Haxo; Francis T. ; et
al. |
October 28, 2021 |
Kits for Using Bispyridines to Improve Labeling of Nucleophiles
Abstract
Bispyridines improve the labeling of nucleophiles, including
amines and thiols and are particularly useful for improving
labeling with acidic and basic labels. Use of bispyridines with
such labels dramatically increases labeling compared to protocols
without a bispyridine. The labeled nucleophile can then be
subjected to standard analytical methods.
Inventors: |
Haxo; Francis T.; (Santa
Clara, CA) ; Kimzey; Michael J.; (Laguna Hills,
CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Agilent Technologies, Inc. |
Santa Clara |
CA |
US |
|
|
Assignee: |
Agilent Technologies, Inc.
Santa Clara
CA
|
Family ID: |
1000005698878 |
Appl. No.: |
17/369768 |
Filed: |
July 7, 2021 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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16072816 |
Jul 25, 2018 |
11092595 |
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PCT/US2017/019346 |
Feb 24, 2017 |
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17369768 |
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62300609 |
Feb 26, 2016 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C07H 1/00 20130101; G01N
2560/00 20130101; C07D 207/46 20130101; G01N 33/533 20130101; C07D
213/24 20130101; C12Q 1/6806 20130101 |
International
Class: |
G01N 33/533 20060101
G01N033/533; C07D 207/46 20060101 C07D207/46; C07D 213/24 20060101
C07D213/24; C12Q 1/6806 20060101 C12Q001/6806; C07H 1/00 20060101
C07H001/00 |
Claims
1-25. (canceled)
26. A kit for labeling a nucleophile of interest, wherein said
nucleophile is an amine, a glycosylamine, a thiol, a guanidine or
an imidazole group on a protein or peptide, or an exocyclic amine
on a nucleic acid, said kit comprising, (a) a bispyridine, (b) a
label reactive with said nucleophile of interest, and (c)
instructions on labeling said nucleophile with said label.
27. The kit of claim 26, wherein said nucleophile is a
glycosylamine.
28. The kit of claim 26, wherein said label is an amine-reactive
dye.
29. The kit of claim 26, wherein said bispyridine is pyridine,
4,4'-(1,3-propanediyl)bis- or pyridine,
4,4'-(1,2-ethanediyl)bis-.
30. The kit of claim 26, wherein said label is dry
2-(diethylamino)ethyl
4-[(2,5-dioxopyrrolidin-1-yl)oxycarbonylamino]benzoate and said
bispyridine is pyridine, 4,4'-(1,3-propanediyl)bis- or pyridine,
4,4'-(1,2-ethanediyl)bis-.
31. The kit of claim 26, further wherein said bispyridine is in a
solvent.
32. The kit of claim 31, wherein said solvent is
dimethylformamide.
33. The kit of claim 26, wherein said nucleophile is an amine.
34. The kit of claim 28, wherein said amine-reactive dye is
2-(diethylamino)ethyl
4-[(2,5-dioxopyrrolidin-1-yl)oxycarbonylamino]benzoate,
8-[(2,5-dioxopyrrolidin-1-yl)oxycarbonylamino]naphthalene-1,3,5-trisulfon-
ic acid, or 4-[(2,5-dioxopyrrolidin-1-yl)oxycarbonylamino]benzoic
acid.
35. The kit of claim 28, wherein said amine-reactive dye is
2-(diethylamino)ethyl
4-[(2,5-dioxopyrrolidin-1-yl)oxycarbonylamino]benzoate,
2,5-Pyrrolidinedione,
1-[[(2',7'-difluoro-3',6'-dihydroxy-3-oxospiro[isobenzofuran-1(3H),9'-[9H-
]xanthen]-5-yl)carbonyl]oxy], 5(6)-CR 6G, SE
(5-(and-6)-Carboxyrhodamine 6G, Succinimidyl Ester),
7-diethylaminocoumarin-3-carboxylic acid,
8-[(2,5-dioxopyrrolidin-1-yl)oxycarbonylamino]naphthalene-1,3,5-trisulfon-
ic acid, or 4-[(2,5-dioxopyrrolidin-1-yl)oxycarbonylamino]benzoic
acid.
36. The kit of claim 28, wherein said amine-reactive dye is
2-(diethylamino)ethyl
4-[(2,5-dioxopyrrolidin-1-yl)oxycarbonylamino]benzoate.
37. The kit of claim 26, wherein said bispyridine is pyridine,
4,4',4'',4'''-(2,3,4,5-thiophenetetrayl)tetrakis; 1,2-Ethanediol,
1,2-di-4-pyridinyl; methanone, di-4-pyridinyl; cyclohexanone,
2,6-bis(4-pyridinylmethylene-,(2E6E)-; 2H-Indol-2-one,
1,3-dihydro-1-phenyl-3,3-bis(4-pyridinylmethyl)-; 2,3-Butanediol,
2,3-di-4-pyridinyl-; 1,2-Ethanediol, 1,2-di-4-pyridinyl-,
(1R,2S)-rel-; 9(10H)-Anthracenone, 10,10-bis(4-pyridinylmethyl)-;
2,4,6(1H,3H,5H)-Pyrimidinetrione,
1-(3-methoxyphenyl)-5,5-bis[2-(4-pyridinyl)ethyl]-;
2,4,6(1H,3H,5H)-Pyrimidinetrione,
1,3-dimethyl-5,5-bis[2-(4-pyridinyl)ethyl]-; Ethanone,
1,2-di-4-pyridinyl-; Pyridine, 4.4'-(1,4-butanediyl)bis-;
2,4,6(1H,3H,5H)-Pyrimidinetrione,
1-(phenylmethyl)-5,5-bis[2-(4-pyridinyl)ethyl]-;
2,4,6(1H,3H,5H)-Pyrimidinetrione,
1-(4-ethoxyphenyl)-5,5-bis[2-(4-pyridinyl)ethyl]-;
4-Pyridinepropanenitrile, .alpha.-4-pyridinyl-; 1,2-Ethanediarnine,
N,N'-dimethyl-1,2-di-4-pyridinyl-(9Cl); pyridine,
4,4',4''-(1H-imidazole-2,4,5-triyl)tris-;
4,6(1H,5H)Pyrimidinedione,
dihydro-5,5-bis[2-(4-pyridinyl)ethyl]-2-thioxo-; or Pyridine,
4,4'-methylenebis-.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application claims the benefit of U.S. Provisional
Patent Application No. 62/300,609, filed Feb. 26, 2016, the
contents of which are incorporated herein by reference for all
purposes.
STATEMENT OF FEDERAL FUNDING
[0002] Not applicable.
BACKGROUND OF THE INVENTION
[0003] This invention relates to the field of improving labeling of
nucleophilic biomolecules by electrophilic labels, and particularly
to labeling glycosylamines.
[0004] Many of the proteins produced by eukaryotic cells are
modified after translation by the addition of covalently-linked,
linear or branched chains of carbohydrates. These
protein-carbohydrate conjugates are referred to as glycoproteins;
the point at which the carbohydrate is attached is referred to as a
glycosylation site. Attached polysaccharides or oligosaccharides
are referred to as glycans. A wide range of glycans are found on
the different glycosylation sites of particular glycoproteins. The
particular pattern of glycans on a particular glycoprotein is
determined by the specific cell line that produced the protein and
the conditions under which the cells were grown.
[0005] Since the glycans conjugated to a protein can affect
characteristics critical to its function, including
pharmacokinetics, stability, bioactivity, or immunogenicity, it is
important in many uses to determine which glycans are present.
Thus, the ability to remove some or all of the glycans from a
protein and to analyze the glycans to determine their composition
is useful for determining whether the glycoprotein will have its
desired effect. For example, the Food and Drug Administration
("FDA") requires characterization of carbohydrates attached to
biologics (such as therapeutic glycoproteins and vaccines) to show
composition of matter and consistency of manufacture, resulting in
a need for extensive characterization of the product. Analysis of
the profile of the released carbohydrates is also important for
quality control in the production of recombinant proteins, in which
a change in carbohydrate profile may indicate stress in the system,
signaling conditions that may require a commercial-scale fermenter
of expensive protein to be discarded. There is therefore
considerable interest by biochemists, clinical chemists and
pharmaceutical manufacturers in determining the distribution
profiles of glycans in biological samples, such as therapeutic
glycoproteins.
[0006] Glycans are typically attached to glycoproteins in one of
two ways. In the first, referred to as N-glycans, the glycans are
attached through an N-glycosidic bond at an asparagine residue. In
the second, referred to as O-glycans, glycans are attached to an
oxygen atom on an amino acid residue. For example,
N-acetyl-galactosamine can be enzymatically attached to an oxygen
on a serine or a threonine residue.
[0007] N-glycans can be enzymatically released from glycoproteins
by enzymatic cleavage by various enzymes, such as PNGase F
(Peptide-N4-(acetyl-.beta.-glucosaminyl)-asparagine amidase, EC
3.5.1.52). Release of glycans from a glycoconjugate, such as a
glycoprotein, by an enzyme is sometimes referred to in the art as
"enzymatic digestion." Enzymatic digestion of N-glycans, such as by
PNGase F, typically occurs in an aqueous solution, and results in
the initial release of the N-glycans as .beta.-glycosylamines, in
which the free-reducing end of the released glycan is conjugated
with ammonia (see, e.g., Tarentino, et al. TIGG 1993, 23:163-170;
Rasmussen J. R. J. Am. Chem. Soc. 1992, 114:1124-1126; Risley, et
al. J. Biol. Chem. 1985, 260:15488-15494, 1985). PNGase F-released
N-glycans are most commonly labeled by reductive amination, in
which the free-reducing end of a glycan is conjugated to the free
amino group of a label, such as a fluorescent dye or a electrical
charge. Depending on the label used, the labeled glycans can then
be analyzed by any of a variety of analytical methods, such as
high-performance liquid chromatography ("HPLC"), capillary
electrophoresis ("CE"), carbohydrate gel electrophoresis, or
microfluidic separation. Labeling of N-glycans is taught, for
example, in co-owned U.S. Pat. Nos. 8,124,792 and 8,445,292.
[0008] The stability of glycosylamines is dependent on the pH: a
lower pH favors rapid hydrolysis of glycosylamines to glycans with
free-reducing ends and ammonium, while a more elevated pH slows
glycosylamine hydrolysis, which allows glycans released as
glycosylamines to be labeled with reagents reactive toward the
amino groups instead of the free-reducing ends. Thus, the released
glycosylamines are both more stable and more reactive with labeling
reagents within a pH range of about pH 7.5 to about pH 9.
Unfortunately, many of the amine-reactive dyes compatible with
different analytical techniques are either acidic or basic and are
more stable at pHs lower than 6. This dichotomy between the
conditions most favorable for stability of the glycosylamines and
those most favorable for stability of a basic or an acidic dye can
cause incomplete labeling of glycans released from glycoproteins by
enzymatic digestion.
[0009] There remains a need in the art for compositions and methods
that improve labeling of glycosylamines and other nucleophiles.
Surprisingly, the present invention meets these and other
needs.
BRIEF SUMMARY OF THE INVENTION
[0010] In some embodiments, the invention provides methods of
labeling a nucleophile of interest in vitro. The methods comprise
the step of incubating the nucleophile with a solution comprising
(a) a solvent, (b) an electrophilic label reactive with the
nucleophile, and (c) a bispyridine soluble in the solvent, thereby
labeling the nucleophile. In some embodiments, the nucleophile is
an amine. In some embodiments, the amine is a glycosylamine. In
some embodiments, the glycosylamine is released from a glycoprotein
prior to the incubation step. In some embodiments, the release of
the glycosylamines from the glycoprotein is by enzymatic digestion.
In some embodiments, the enzymatic digestion of said glycoprotein
comprises digestion by the enzyme PNGase F. In some embodiments,
the nucleophile is a thiol. In some embodiments, the nucleophile is
a guanidine or an imidazole group on a protein or peptide. In some
embodiments, the nucleophile is an exocyclic amine on a nucleic
acid. In some embodiments, the bispyridine is pyridine,
4,4'-(1,3-propanediyl)bis- or pyridine, 4,4'-(1,2-ethanediyl)bis-.
In some embodiments, the solvent is dimethylformamide or dimethyl
sulfoxide. In some embodiments, the electrophilic label is acidic
in aqueous solution. In some embodiments, the electrophilic label
is basic in aqueous solution.
[0011] In some embodiments, the invention further provides methods
for labeling N-glycans released from a glycoprotein of interest.
The methods comprise (a) incubating the glycoprotein with an enzyme
that releases the N-glycans from the glycoprotein as
glycosylamines, and (b) contacting the glycosylamines with a
solution comprising a solvent, an amine-reactive label, and a
bispyridine, under conditions allowing labeling of the
glycosylamines by the amine-reactive label, thereby labeling the
N-glycans released from the glycoprotein. In some embodiments, the
glycoprotein is an antibody. In some embodiments, the glycoprotein
is immobilized on a solid support before step (b). In some
embodiments, the deglycosylation enzyme is an endoglycosidase. In
some embodiments, the deglycosylation enzyme is an amidase. In some
embodiments, the amidase is PNG F. In some embodiments, the solvent
is dimethylformamide or dimethyl sulfoxide. In some embodiments,
the bispyridine is pyridine, 4,4'-(1,3-propanediyl)bis- or
pyridine, 4,4'-(1,2-ethanediyl)bis-. In some embodiments, the
labeled glycosylamines are analyzed by an analytical means. In some
embodiments, the analytical means is selected from the group
consisting of high-pressure liquid chromatography, capillary
electrophoresis, microfluidic separation, and mass
spectrometry.
[0012] In some embodiments, the invention further provides kits for
labeling a nucleophile of interest. The kits comprise (a) a
bispyridine, (b) a label reactive with the nucleophile of interest,
and (c) instructions on labeling the nucleophile. In some
embodiments, the nucleophile is a glycosylamine. In some
embodiments, the label is an amine-reactive dye. In some
embodiments, the bispyridine is pyridine,
4,4'-(1,3-propanediyl)bis- or pyridine, 4,4'-(1,2-ethanediyl)bis-.
In some embodiments, the label is dry 2-(diethylamino)ethyl
4-[(2,5-dioxopyrrolidin-1-yl)oxycarbonylamino]benzoate and said
bispyridine is pyridine, 4,4'-(1,3-propanediyl)bis- or pyridine,
4,4'-(1,2-ethanediyl)bis-. In some embodiments, the bispyridine is
in a solvent. In some embodiments, the solvent is
dimethylformamide.
BRIEF DESCRIPTION OF THE DRAWINGS
[0013] FIG. 1 is a graph showing the total glycan signal of
glycosylamines released by PNGase F from an exemplar glycoprotein,
porcine gamma globulin, and labeled by an acidic dye,
8-[(2,5-dioxopyrrolidin-1-yl)oxycarbonylamino]naphthalene-1,3,5-trisulfon-
ic acid, in the presence of 1 M pyridine ("PYR", represented by
squares), 1 M Pyridine, 4,4'-(1,2-ethanediyl)bis-("BPE",
represented by diamonds), or 1 M Pyridine,
4,4'-(1,3-propanediyl)bis-("TMD", represented by triangles). Each
of these chemicals was dissolved in anhydrous dimethyl sulfoxide
("DMSO") as the solvent. The control, represented by circles, was
the DMSO solvent without pyridine or a bispyridine. Vertical axis:
total glycan signal, in relative fluorescence units ("RFUs"),
measured at 430 nm. Horizontal axis: number of microliters of the
dye ("ANTS") present in the assay. The amounts of dye used were:
0.1 .mu.l, 1 .mu.l, 2.5 .mu.l, and 5 .mu.l.
[0014] FIG. 2 is a graph showing the total glycan signal of labeled
glycosylamines released by PNGase F from an exemplar glycoprotein,
porcine gamma globulin, labeled by a different acidic dye,
4-[(2,5-dioxopyrrolidin-1-yl)oxycarbonylamino]benzoic acid, in the
presence of either 1 M Pyridine, 4,4'-(1,3-propanediyl)bis-("TMD")
dissolved in anhydrous dimethylformamide ("DMF"), 4 M TMD in DMF,
or DMF without TMD ("control"). Vertical axis: total glycan signal,
in RFUs, measured at 430 nm. Horizontal axis: The bars show the
average value of RFUs in the presence of the control or stated
concentration of TMD, with the numeric value of the average stated
above the bar for ready comparison. The error bars show one
standard deviation.
[0015] FIG. 3 is a graph showing a ranging study of the effect of
the concentration of TMD on total glycan signal. Glycosylamines
released by PNGase F from porcine gamma globulin were labeled with
a basic dye, InstantPC.TM., dissolved in anhydrous DMSO, and
analyzed by HPLC, with total fluorescent signal measured at 345 nm.
Vertical axis: circles show the glycan signal, in RFUs for each
concentration of TMD tested. Horizontal axis: Molar concentrations
of TMD tested.
DETAILED DESCRIPTION
[0016] As set forth in the Background, analysis of the glycans
attached to glycoproteins has become important for meeting various
regulatory requirements, including showing composition of matter
and consistency of manufacture of therapeutic glycoproteins and for
providing quality control during the production of recombinant
glycoproteins. As further described in the Background, N-glycans
are typically analyzed by releasing them by enzymatic digestion and
then labeling the resulting glycosylamines with an amine-reactive
dye. Unfortunately, while the glycosylamines released from
glycoproteins are both more stable and more reactive with labeling
reagents within a pH range of about pH 7.5 to about pH 9, many of
the amine-reactive dyes used for labeling glycosylamines are either
acidic or basic and are more stable at pHs lower than 6. At higher
pHs, such as above pH 9, the glycosylamines are stable but the
nucleophile-reactive tags hydrolyze rapidly, especially if water is
the primary solvent. Therefore, it is advantageous to neutralize
the amine-reactive dyes prior to addition to the glycosylamines.
This dichotomy between the conditions most favorable for stability
of the glycosylamines and those most favorable for stability of a
basic or an acidic dye reduces the ability to get complete labeling
of glycans released from glycoproteins by enzymatic digestion.
[0017] Despite this dichotomy, buffers are currently not typically
added to the organic solvent portion in labeling protocols. Typical
protocols recommend the buffering of the aqueous solution only,
i.e. with a buffer such as sodium carbonate pH 7-9. These protocols
generally apply to stable nucleophiles such as primary amines and
do not factor in the transient nature of glycosylamines, which are
rapidly hydrolyzed at low pH. This may be because common laboratory
buffers, such as phosphate buffered saline, are aqueous solutions
which themselves hydrolyze amine reactive dyes and other labels. If
aqueous-solution buffers were to be used, therefore, they would
have to be added to the amine reactive label or dye immediately
before or after the label or dye is added to the solution
containing the glycans. As any delay in buffering could result in
some of the glycosylamines being hydrolyzed before they can be
labeled, the timing of adding such a buffer itself could introduce
undesirable variation in the measurement of the glycans present in
the solution. It is preferred to buffer the electrophilic label
prior to labeling the aqueous nucleophile. Further, a number of
amine-reactive dyes or other labels are sold as powders, which are
resolubilized by the user and then stored until use, either as is
or, when additional storage life is desired, in a freezer. It is
therefore more convenient for the user if the buffer can be added
at the time the dye is first resolubilized thereby avoiding an
additional time-critical step during the labeling protocol.
Aqueous-solution buffers are incompatible with being added to
resolubilized amine reactive dyes in advance of use for the reasons
noted above.
[0018] Surprisingly, it has now been found that bispyridines,
commonly used in polymer chemistry, dramatically improve the
labeling of glycosylamines with acidic or basic dyes compared to
current labeling protocols. As shown below and in the Examples,
studies using two different bispyridines, two different acidic
amine-reactive dyes and a basic amine-reactive dye, and two
different solvents, showed that the presence of bispyridines during
the labeling procedure resulted in a surprisingly more complete
labeling of glycosylamines than did the standard labeling procedure
without a bispyridine being present.
[0019] FIG. 1 presents the results of studies were performed using
an acidic amine-reactive dye to label glycosylamines released from
an exemplar glycoprotein in the presence of (a) the bispyridine
Pyridine, 4,4'-(1,2-ethanediyl)bis-("BPE," compound 1 in the list
of bispyridines below) prepared in anhydrous DMSO, (b) the
bispyridine 4,4'-(1,3-propanediyl)bis-pyridine ("TMD," compound 2
in the list of structures in the section on bispyridines below),
prepared in anhydrous DMSO, (c) pyridine ("PYR") in DMSO, or (d)
DMSO without pyridine or a bispyridine ("control"). As shown in
FIG. 1, the use of pyridine in DMSO resulted in glycan labeling
approximately the same as that of the DMSO-only control. In
contrast, once enough label (2.5 .mu.l) was present to provide
relatively adequate labeling, the presence of TMD resulted almost
doubled the amount of glycosylamines labeled compared to the
control and pyridine solutions, while when 5 .mu.l of dye was used,
the presence of either TMD or BPE resulted in labeling over twice
as much glycan compared to mixtures containing either pyridine or
the DMSO control.
[0020] Without wishing to be bound by theory, it is believed that
the presence of the bispyridine buffers the solution and stabilizes
the glycosylamines, the amine-reactive dye, or both, allowing a
larger amount of the glycosylamines to be labeled before they or
the dye were hydrolyzed. The results may not, however, be
explainable by a buffering action alone, as the glycosylamines were
released from the glycoprotein by enzymatic digestion with the
enzyme PNGase F in a solution containing the buffer HEPES at pH8,
and that buffer was already present in each of the samples then
subjected to labeling with the dye.
[0021] Based on the studies underlying embodiments of the present
invention, it is believed that bispyridines can be used to improve
the labeling by electrophilic labels of nucleophiles, including
amines and thiols, as well as guanidine and imidazole groups on
proteins and peptides and exocyclic amines on nucleic acids. In
some embodiments, the labeling is of amines with amine-reactive
dyes, In some embodiments, the labeling is of thiols with
thiol-reactive dyes. In some embodiments, the nucleophile is an
amine. In some embodiments, the nucleophile is a thiol. The label
can be one that can be detected optically, such as a fluorescent
dye, or that can add a fixed charge that is detectable by MS or
that can facilitate separation and detection of the labeled moiety
by electrokinetic separation techniques such as capillary
electrophoresis.
[0022] Further studies underlying embodiments of the present
invention revealed some differences exist between the ability of
different bispyridines in different solvents or to undergo freezing
in a solvent. In preferred embodiments, the bispyridine selected is
soluble at room temperature in the solvent in which the dye is
soluble. Since, as noted above, water hydrolyzes amine-reactive
dyes, for uses in which storage of the dye-bispyridine mixture is
desired, the solvent is preferably not water.
[0023] Studies found, for example, that the exemplar bispyridines
TMD and BPE discussed above are both soluble in DMSO, and that TMD
is also soluble in the solvent dimethylformamide ("DMF"). Another
bispyridine studied, 4,4'-methylenebis-pyridine (compound 21 in the
list set forth below), was not soluble in DMF, but is expected to
be soluble in other organic solvents usable in some labeling
procedures, such as dimethyl sulfoxide. The bispyridine BPE, which,
as discussed above dramatically increases labeling of glycans over
a like mixture not containing a bispyridine, was soluble in an
aqueous solution. This bispyridine, however, came out of solution
when frozen and did not go back into solution when the
dye-bispyridine mixture was thawed. This bispyridine is therefore
very useful for embodiments in which the practitioner does not need
to store the mixture by freezing it, but less preferred for
embodiments in which the user wishes to extend the storage life by
freezing the mixture.
[0024] Bispyridines can also be used to label glycosylamines
released from O-glycans by, for example, .beta.-elimination.
Further, bispyridines can be used in protocols to label thiols,
such as the cysteines present in proteins or peptides. They may
also be used to improve labeling of nucleophilic groups on
proteins, such as the N-terminus (which can have a primary amine
available for labeling), or lysine, arginine, or histidine, each of
which nucleophilic groups available for labeling. Similarly, they
may also be used to improve labeling of nucleophilic groups on
nucleic acid bases such as the exocyclic amines of adenine and
guanine. Finally, they may also be used to improve stability of
electrophilic labels during storage while in solution. Persons of
skill will appreciate that nucleophiles such as amines and thiols
on proteins, peptides or nucleic acids can be labeled using the
same protocols as discussed in the Examples using glycosylamines as
an exemplar nucleophile to be labeled.
[0025] Any particular bispyridine can be readily tested to
determine if it is soluble in a selected solvent at room
temperature by simply mixing it with the selected solvent in a test
tube and observing whether it goes into solution. Similarly, any
particular bispyridine can be readily tested to determine if it is
suitable for use in applications in which the user will freeze for
later use a solution containing a selected dye in a selected
solvent by placing the bispyridine in the selected solvent,
freezing the resulting mixture, thawing it, and observing whether
the bispyridine stays in solution upon freezing or, if it
precipitates, whether it resolubilizes in the mixture upon being
thawed. Further, any particular bispyridine can be readily tested
to see if it improves storage of any particular electrophilic label
in solution by (a) storing parallel aliquots of the label with and
without the bispyridine (b) then testing them by adding excess of
any of the nucleophiles mentioned above to each aliquot, (c)
measuring the amount of labeled nucleophile, and (d) determining
whether of the resulting amount of labeled nucleophile is greater
or lesser in the aliquot with the bispyridine compared to the
aliquot without the bispyridine.
[0026] The studies reported herein show that bispyridines are
particularly useful when using labels that are acidic or basic in
aqueous solutions. Labels that are neutral in aqueous solutions may
act in ways that are not well characterized when dissolved in
organic solvents, in which only trace amounts of water may be
present. Any particular neutral label can be readily tested to
determine whether it will label a nucleophile of interest better if
a particular bispyridine is present than in its absence by testing
parallel aliquots of the neutral label with and without the
bispyridine, as described in the preceding paragraph.
Bispyridines
[0027] As suggested by the name, bispyridines are a class of
compounds comprising two pyridine rings. As characterized by
Wikipedia, pyridine rings are heterocyclic rings similar to
benzene, but with one methane group replaced by a nitrogen. The
compound pyridine has an unpleasant, fish-like odor and is
hazardous. In contrast, bispyridines do not have unpleasant odors
and are not flammable, making them significantly safer and more
pleasant to work with than pyridine. As shown by FIG. 1,
bispyridines are surprisingly better reagents in protocols for
labeling glycosylamines (and by extension, other amines and
nucleophiles) than pyridine is, with substantial improvements in
labeling the glycosylamines with the amine reactive dye used in
that study once adequate amounts of label were present.
[0028] Bispyridines are commonly used in polymer chemistry. A
search of the SciFinder.RTM. database maintained by Chemical
Abstract Services ("CAS") came up with over 100 commercially
available bispyridines from 3 or more suppliers. The following 21
bispyridines were those listed as being available from the largest
number of providers. Each one is identified by its CAS registry
number, its structure, its chemical composition and its scientific
name. It will be appreciated that the list below is intended merely
to be exemplary of bispyridines that can be used in the inventive
methods and is not intended to be limiting.
##STR00001## ##STR00002## ##STR00003## ##STR00004##
##STR00005##
Nucleophile-Reactive Labels
[0029] A number of amine-reactive labels are known in the art. The
website of Thermo Fisher Scientific (Waltham, Mass.), for example,
lists 152 reagents under the label "Amine-Reactive Fluorophores,
Biotins, Quantum Dots, & Other Labels," including:
1-pyrenebutanoic acid, succinimidyl ester,
2',7'-Difluorofluorescein (Oregon Green.RTM. 488), 5(6)-CR 6G, SE
(5-(and-6)-Carboxyrhodamine 6G, Succinimidyl Ester), mixed isomers,
and 7-Diethylaminocoumarin-3-Carboxylic Acid. ProZyme, Inc.
(Hayward, Calif.) sells a variety of amine-reactive labels,
including a basic dye, InstantPC.TM. (2-(diethylamino)ethyl
4-[(2,5-dioxopyrrolidin-1-yl)oxycarbonylamino]benzoate). Two acid
labels disclosed in co-owned U.S. Pat. No. 8,124,792,
8-[(2,5-dioxopyrrolidin-1-yl)oxycarbonylamino]naphthalene-1,3,5-trisulfon-
ic acid ("InstantANTS.TM.") and
4-[(2,5-dioxopyrrolidin-1-yl)oxycarbonylamino]benzoic acid
("InstantAA.TM."), were used in the Examples reported below.
InstantANTS.TM. adds 3 negative charges and a fluorophore to the
glycans, which facilitates their separation by capillary
electrophoresis and detection. And, Waters Corporation (Milford,
Mass.), sells "RapiFluor-MS.TM." for labeling glycosylamines. It is
anticipated that bispyridines can be used to improve labeling with
each of these amine-reactive labels.
[0030] Similarly, a large number of thiol-reactive labels are known
in the art. The website of Thermo Fisher Scientific, for example,
lists 94 reagents under the title "Thiol-Reactive Fluorophores,
Biotins & Other Labels", including: BODIPY.RTM. 507/545 IA
(N-(4,4-Difluoro-1,3,5,7-Tetramethyl-4-Bora-3a,4a-Diaza-s-Indacene-2-yl)
Iodoacetamide, 5-(Bromomethyl)Fluorescein, Alexa Fluor.RTM. 350 C5
Maleimide, and DACM,
N-(7-Dimethylamino-4-Methylcoumarin-3-yl))Maleimide. It is
anticipated that bispyridines can be used to improve labeling with
each of these thiol-reactive labels.
[0031] Although the compounds discussed above are electrophiles
that have been designated by the suppliers to be "amine-reactive"
or "thiol-reactive," persons of skill will appreciate that many of
the compounds will also label other moieties on nucleophiles of
interest, such as guanidine or imidazole groups on proteins or
peptides, as well as exocyclic amines on nucleic acids, and can be
used to label these nucleophiles. Any particular label can be
readily tested to see if it adequately labels any given nucleophile
or nucleophilic moiety of interest by running parallel aliquots of
the nucleophile, with the label being studied in a first aliquot
and a label known to label the nucleophile in a second aliquot, and
then analyzing the two aliquots and determining whether the label
being studied labels the nucleophile at least as well as the label
known to label that nucleophile.
Concentrations
[0032] Typically, the bispyridine will be used in a concentration
of about 0.5 M to about 2.5 M, in some embodiments, will be used at
concentrations of about 0.5 M to about 2.25 M, in some embodiments,
will be used at concentrations of about 0.75 M to about 2.0 M, in
some embodiments, will be used at concentrations of about 0.8 M to
about 1.75 M, more preferably at concentrations of about 1 M to
1.75 M, in some embodiments, will be used at concentrations of
about 1 M to about 1.5 M, and in some embodiments, will be used at
concentrations of about 0.8 M to about 1.25 M, and still more
preferably at concentrations of about 1 M, where the term "about"
means plus or minus 0.2 M.
Removal of the Bispyridine
[0033] In some embodiments, it may be desirable to remove the
bispyridine before subjecting the labeled compound to analytical
techniques, such as mass spectrometry. The bispyridine can be
removed by any convenient means known in the art. In preferred
embodiments, the bispyridine is removed by using a solid phase
cartridge or other solid phase extraction device used in the art to
remove undesired components from a solution. The labeled glycans
are typically loaded onto a selected cleanup cartridge, washed to
remove most non-glycan contaminants, and then eluted. Cleanup
procedures for labeled glycans are routinely used in the art and it
is expected that they are well known to practitioners in the art of
glycan labeling and analysis.
EXAMPLES
Example 1
[0034] This Example sets forth abbreviations for some of the
reagents used in exemplar workflows of deglycosylation and labeling
procedures performed using exemplar bispyridines in some of the
Examples below. [0035] "HEPES":
4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid [0036] "DMF":
dimethylformamide [0037] "DMSO": dimethyl sulfoxide [0038] "TMD":
Pyridine, 4,4'-(1,3-propanediyl)bis- [0039] "BPE": Pyridine,
4,4'-(1,2-ethanediyl)bis- [0040] "PNGase F mix": a 1:1 mix of
PNGase F (.about.1 mg/ml) and 750 mM HEPES pH 8.0 buffer.
Example 2
[0041] This Example sets forth an exemplar workflow for
deglycosylating and labeling an amine-reactive compound using an
exemplar bispyridine.
Denaturation Step
[0042] Twenty .mu.l of 2 mg/ml glycoprotein is added to the bottom
of a PCR plate. Two .mu.l of a detergent, such as sodium lauroyl
sarcosinate, is added. Optionally, a reductant, such as
bis(2-mercaptoethyl) sulfone, can be added. The mixture is
incubated for 3 minutes at 90.degree. C.
Enzymatic Digestion Step
[0043] Two .mu.l of PNGase F mix is added. The resulting mixture is
incubated for 5 mins at 50.degree. C.
Labeling Step
[0044] The released glycosylamines are labeled with a dye of
choice. The dye is typically a fluorescent dye and in some
embodiments is also compatible with mass spectrometry. As an
example, the dye can be activated procaine, sold as InstantPC
(ProZyme, Inc., Hayward, Calif.). For example, glycans released
from a glycoprotein by the action of PNGase F are initially
released as glycosamines, which can be labeled by, for example,
adding 5 .mu.l of a freshly prepared 1:1 mixture of 0.2 M
2-diethylaminoethyl
4-[(2,5-dioxopyrrolidin-1-yl)oxycarbonylamino]benzoate in DMSO: 1 M
TMD. The labeling is allowed to proceed for 2 minutes.
Cleanup Step:
[0045] If desired, the labeled glycans can be cleaned up before
analysis by subjecting them to solid phase extraction, for example,
by loading them onto a cartridge, prior to analyzing them by one or
more analytic techniques. For example, the cartridge can be washed
with 200 .mu.l of a 1:3:96 formic acid:water:acetonitrile solution
for 3 minutes at 300.times.g and the samples eluted with 50 .mu.l
of a solution of 200 mM ammonium formate, pH 7, containing 20%
DMSO.
Analysis Step
[0046] Following elution, glycans released by the PNGase F can be
analyzed. For example, 1 .mu.l of eluted sample can be injected for
high performance liquid chromatography (HPLC) analysis.
Example 3
[0047] This Example reports the effect of studies on the use of
bispyridines on labeling of glycosylamines.
[0048] An exemplar glycoprotein, porcine gamma globulin, was
subjected to enzymatic digestion by an exemplar deglycosylation
enzyme, PNGase F. Glycosylamines released from the glycoprotein,
containing the buffer HEPES, at pH 8, were labeled using four
different amounts, 0.1 .mu.l, 1 .mu.l, 2.5 .mu.l or 5 .mu.l, of an
acidic dye,
8-[(2,5-dioxopyrrolidin-1-yl)oxycarbonylamino]naphthalene-1,3,5-trisulfon-
ic acid, at a concentration of 0.2 M, using anhydrous dimethyl
sulfoxide ("DMSO") as a solvent, in the presence of 2.5 .mu.l of
the following, each of which were also prepared in anhydrous DMSO:
(a) 1 M Pyridine, 4,4'-(1,3-propanediyl)bis-("TMD"), (b) 1 M
Pyridine, 4,4'-(1,2-ethanediyl)bis-("BPE"), or (c) 1 M pyridine
("PYR"). As a control, glycosylamines were also labeled using the
same amounts of the dye, but with only the DMSO solvent
("control"). The labeled glycans were analyzed by HPLC and total
fluorescent signal was measured using fluorescent wavelengths of
310 nm for excitation and 430 nm for emission.
[0049] As shown in FIG. 1, in all of the tests, the amount labeled
when pyridine was present in the mixture was very close to that
labeled when DMSO was present without pyridine. In contrast, once
dye was present in sufficient amounts to label most of the
glycosylamines present, the amount labeled in the presence of
either bispyridine was surprisingly greater than that labeled by
either the control or in the presence of pyridine. When 2.5 .mu.l
of dye was present, the presence of BPE increased the amount of
labeled glycosylamines by approximately 70% over the amount labeled
using only DMSO, while the presence of TMD increased labeled glycan
by just under 100%. When 5 .mu.l of dye was used, both BPE and TMD
resulted in more than doubling the amount of labeled glycosylamines
as shown by relative fluorescent units, or "RFUs".
Example 4
[0050] This Example reports the effect of studies to determine the
effect of different concentrations of a bispyridine on labeling
glycosylamines.
[0051] An exemplar glycoprotein, porcine gamma globulin, was
subjected to enzymatic digestion by an exemplar deglycosylation
enzyme, PNGase F. Glycosylamines released from the glycoprotein
were labeled using 2.5 .mu.l of an acidic dye,
4-[(2,5-dioxopyrrolidin-1-yl)oxycarbonylamino]benzoic acid, at a
concentration of 0.2 M, using anhydrous dimethylformamide ("DMF")
as a solvent, in the presence of (a) DMF alone, as a control, (b)
2.5 .mu.l of 4 M TMD, or (c) 1 M TMD. The labeled glycans were
analyzed by HPLC and total fluorescent signal was measured using
fluorescent wavelengths of 380 nm for excitation and 430 nm for
emission.
[0052] As shown in FIG. 2, the use of 1 M TMD resulted in just
under twice the amount of labeled glycosylamines as did the use of
the control, solvent alone. The use of 4 M TMD resulted in over a
69% increase of labeled glycosylamines, while the use of 1 M TMD
resulted over an 86% increase in labeled glycosylamines. For
convenience, the average reading of the amount of labeled
glycosylamines is shown numerically in FIG. 2 over each bar, with
the error bars showing 1 standard deviation.
Example 5
[0053] This Example reports the effect of studies to determine
optimal concentrations of a bispyridine on labeling
glycosylamines.
[0054] The exemplar glycoprotein, porcine gamma globulin, was
subjected to enzymatic digestion by the exemplar deglycosylation
enzyme, PNGase F. Glycosylamines released from the glycoprotein
were labeled using 2.5 .mu.l of the basic dye InstantPC.TM.
(ProZyme, Inc., Hayward, Calif.) at a concentration of 0.2 M in
DMF, mixed with 2.5 .mu.l of 0.5, 1, 1.5, or 2 M TMD. The labeled
glycans were then analyzed by HPLC and total fluorescent signal was
measured using fluorescent wavelengths of 285 nm for excitation and
345 nm for emission. As shown in FIG. 3, very similar amounts of
labeling were seen using 1 M. 1.5 M, and 2 M TMD with this dye.
Example 6
[0055] This Example sets forth an exemplar protocol for preparing a
solution for labeling an exemplar nucleophile, a glycosylamine,
with an exemplar basic label in a solution containing an exemplar
bispyridine.
[0056] A solution of 0.5 M TMD in anhydrous DMF is prepared. 150
.mu.l of this solution is added to 30 mg of dry InstantPC.TM.
(2-(diethylamino)ethyl
4-[(2,5-dioxopyrrolidin-1-yl)oxycarbonylamino]benzoate). Five .mu.l
of this solution (InstantPC.TM. with 0.5 M TMD in DMF) is added to
25 .mu.l of a protein digest containing glycosylamines in HEPES
buffer pH 8.
[0057] It is understood that the examples and embodiments described
herein are for illustrative purposes only and that various
modifications or changes in light thereof will be suggested to
persons skilled in the art and are to be included within the spirit
and purview of this application and scope of the appended claims.
All publications, patents, and patent applications cited herein are
hereby incorporated by reference in their entirety for all
purposes.
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