U.S. patent application number 10/466552 was filed with the patent office on 2004-12-02 for methods and means for detecting enzymatic cleavage and linkage reactions.
Invention is credited to Fries, Joachim, Jungmann, Joern, Lopez-Calle, Eloisa.
Application Number | 20040241782 10/466552 |
Document ID | / |
Family ID | 8176313 |
Filed Date | 2004-12-02 |
United States Patent
Application |
20040241782 |
Kind Code |
A1 |
Lopez-Calle, Eloisa ; et
al. |
December 2, 2004 |
Methods and means for detecting enzymatic cleavage and linkage
reactions
Abstract
The invention relates to methods and means for the detection of
enzyme-catalyzed cleavage and linking reactions. Modular chemical
compounds which serve as substrates for the enzymes involved are
provided. The detection of the reaction products is effected by
means of molecular-weight-sensitive methods.
Inventors: |
Lopez-Calle, Eloisa;
(Hamburg, DE) ; Fries, Joachim; (Tornesch, DE)
; Jungmann, Joern; (Hamburg, DE) |
Correspondence
Address: |
JACOBSON HOLMAN PLLC
400 SEVENTH STREET N.W.
SUITE 600
WASHINGTON
DC
20004
US
|
Family ID: |
8176313 |
Appl. No.: |
10/466552 |
Filed: |
January 7, 2004 |
PCT Filed: |
January 28, 2002 |
PCT NO: |
PCT/EP02/00845 |
Current U.S.
Class: |
435/23 |
Current CPC
Class: |
C12Q 1/527 20130101;
C12Q 1/25 20130101; C12Q 1/48 20130101; G01N 33/573 20130101; C12Q
1/34 20130101 |
Class at
Publication: |
435/023 |
International
Class: |
C12Q 001/37 |
Foreign Application Data
Date |
Code |
Application Number |
Jan 26, 2001 |
EP |
01 101 869.4 |
Claims
1. A method for the detection of enzyme-catalyzed cleavage
reactions, comprising the following steps: a) providing a modular
chemical compound containing the following sequence motif: Z-X--Y
or Y--X-Z wherein Z comprises a module with a selectable molecular
weight which is inert with respect to said enzymatic cleavage
reaction; X comprises a module with n cleavage sites S.sub.1 to
S.sub.n which can be cleaved by said enzyme-catalyzed cleavage
reaction into at least two cleavage products containing X.sub.1 and
X.sub.n+1, respectively, and having defined molecular weights, n
being an integer of .gtoreq.1; and Y comprises a reporter module;
as a substrate for said enzyme(s) catalyzing said cleavage
reaction(s); b) incubating the compound with said enzyme(s)
catalyzing said cleavage reaction(s) to form at least two cleavage
products which contain Z-X.sub.1 and X.sub.n+1--Y or Y--X.sub.1 and
X.sub.n+1-Z wherein the molecular weight of the cleavage product
containing Z-X.sub.1 or X.sub.n+1-Z is at least fifty percent of
the total molecular weight of the substrate; c) detecting the
enzymatic activity or activities by determining the cleavage
product containing the reporter module Y by means of a
molecular-weight-sensitive method.
2. The method according to claim 1, characterized in that X
comprises a module with one cleavage site S.sub.1 which can be
cleaved by the enzyme-catalyzed cleavage reaction into two cleavage
products containing X.sub.1 and X.sub.2, respectively, and having
defined molecular weights.
3. The method according to claim 1, characterized in that X
comprises a module with several cleavage sites S.sub.1 to S.sub.n
with n>1 which can be cleaved by enzymatic cleavage reactions
into n+1 cleavage products having defined molecular weights.
4. A method for the detection of enzyme-catalyzed linking
reactions, comprising the following steps: a) providing the
following chemical compounds: Z-X.sub.1 and X.sub.n+1--Y and
optionally X.sub.2 to X.sub.n; or Y--X.sub.1 and X.sub.n+1-Z and
optionally X.sub.2 to X.sub.n; wherein Z comprises a module with a
selectable molecular weight which is inert with respect to said
enzymatic linking reaction; X.sub.1 comprises a modular building
block which can be linked by said enzyme-catalyzed linking
reaction(s) directly with X.sub.n+1 in the case where n=1, or
optionally indirectly through at least one modular building block
selected from X.sub.2 to X.sub.n in the case where n>1;
X.sub.n+1 comprises a modular building block which can be linked by
said enzyme-catalyzed linking reaction(s) directly with X.sub.1 in
the case where n=1, or optionally indirectly through at least one
modular building block selected from X.sub.2 to X.sub.n in the case
where n>1; Y comprises a reporter module; n is an integer of
.gtoreq.1; and the molecular weight of X.sub.n+1--Y or Y--X.sub.1
is at most fifty percent of the total molecular weight of the
linked product formed; as a substrate for said enzyme(s) catalyzing
said cleavage reaction; b) incubating the compound with said
enzyme(s) catalyzing said linking reaction(s) to form linked
products Z-X--Y or Y--X-Z wherein X comprises the modular building
blocks X.sub.1 and X.sub.n+1 and optionally at least one modular
building block selected from X.sub.2 to X.sub.n; c) detecting the
enzymatic activity or activities by determining the linked product
containing the reporter module Y by means of a
molecular-weight-sensitive method.
5. The method according to claim 4, characterized in that X
consists of two modular building blocks X.sub.1 and X.sub.2 which
have been directly linked with each other by said enzyme-catalyzed
reaction.
6. The method according to claim 4, characterized in that X.sub.1
and X.sub.n+1 are indirectly linked with one another through at
least one, preferably by a plurality, of modular building blocks
selected from X.sub.2 to X.sub.n with enzyme catalysis.
7. The method according to any of claims 1 to 3, characterized in
that the molecular weight of Z-X.sub.1 and X.sub.n+1-Z in the
cleavage assay is at least about sixty percent, especially at least
about seventy percent, preferably at least about eighty percent,
more preferably at least about ninety percent, of the molecular
weight of compound Z-X--Y or Y--X-Z.
8. The method according to any of claims 4 to 6, characterized in
that the molecular weight of Y--X.sub.1 and X.sub.n+1--Y in the
linking assay is at most about forty percent, especially at most
about thirty percent, preferably at most about twenty percent, more
preferably at most about ten percent, of the molecular weight of
compound Z-X--Y or Y--X-Z.
9. The method according to any of claims 1 to 8, characterized in
that Z comprises a polymer constituted of monomer building
blocks.
10. The method according to any of claims 1 to 9, characterized in
that the components of compound Z-X--Y or Y--X-Z are or become
covalently linked with each other, and/or the components of the
individual substrates of the enzymatic linking reaction(s) are
covalently linked with each other.
11. The method according to any of claims 1 to 10, characterized in
that X and Z belong to different classes of substances.
12. The method according to any of claims 1 to 11, characterized in
that X and/or Z belong to the following classes of substances:
synthetic polymers, dendrimers, natural substances, nucleic acids,
peptide nucleic acids (PNA), peptides, proteins, lipids,
carbohydrates or derivatives of the above mentioned substances.
13. The method according to any of claims 1 to 12, characterized in
that Z comprises a double-stranded nucleic acid or a
double-stranded nucleic acid derivative.
14. The method according to any of claims 1 to 3 and 7 to 13,
characterized in that an enzyme catalyzing the reaction is a
hydrolase, especially a lipase, phosphatase, amylase, glycosidase,
nuclease, peptidase, protease, amidase, pyrophosphatase, ATPase,
sulfatase or phosphoamidase.
15. The method according to any of claims 1 to 3 and 7 to 14,
characterized in that said enzyme catalyzing the reaction is a
lyase, especially a C--C, C--O, C--N or C--S lyase.
16. The method according to claim 15, characterized in that said
lyase is a (de)carboxylase, aldolase, dehydratase, ammonia-lyase,
arginosuccinase or cysteine desulfhydrase.
17. The method according to any of claims 4 to 13, characterized in
that said enzyme catalyzing the reaction is a ligase, especially a
C--O, C--S, C--N or C--C ligase.
18. The method according to claim 17, characterized in that said
ligase is an amino-acid activating ligase, acyl-CoA synthetase,
glutamine synthetase or pyruvate carboxylase.
19. The method according to any of claims 4 to 13, characterized in
that said enzyme catalyzing the reaction is a transferase,
especially a DNA or RNA polymerase.
20. The method according to any of claims 1 to 19, characterized in
that said enzyme-catalyzed cleavage or linking reactions are
performed in the presence of cosubstrates and/or cofactors.
21. The method according to any of claims 1 to 20, characterized in
that said reporter module Y is luminescent, especially
fluorescent.
22. The method according to any of claims 1 to 21, characterized in
that the detection method determines a measure of the rotational or
translational diffusion rate of the cleavage or linked product
containing said reporter module Y.
23. The method according to claims 21 or 22, characterized in that
the detection method is based on fluorescence spectroscopy,
especially confocal fluorescence spectroscopy.
24. The method according to any of claims 21 to 23, characterized
in that the detection method is based on fluorescence correlation
spectroscopy (FCS), fluorescence polarization determination and/or
fluorescence anisotropy determination.
25. The method according to any of claims 1 to 24, characterized in
that said method is performed as a homogeneous assay.
26. The method according to any of claims 1 to 25, characterized in
that one or more enzymes and/or substrates are employed
simultaneously or sequentially.
27. The method according to any of claims 1 to 26, characterized in
that the enzyme or enzymes catalyzing the cleavage or linking
reactions is detached from the reaction product containing the
reporter module Y, preferably (bio)chemically, before the enzymatic
activity is established by a molecular-weight-sensitive method.
28. The method according to any of claims 1 to 27, characterized by
being performed in the presence of modulators or potential
modulators of enzymatic activity.
29. The method according to any of claims 1 to 28, characterized by
being employed for testing enzyme and/or modulator specificities,
for testing enzyme and/or modulator activities, for the
identification of modulators and/or substrates, for the screening
for pharmacologically active substances, for diagnostic purposes,
or for the detection of contaminations in chemical or biological
samples.
30. The method according to any of claims 1 to 29, characterized in
that enzymes having substrate, group or steric specificity are
employed.
31. The method according to any of claims 1 to 30, characterized in
that Z has such a chemical structure that Z does not sterically
interact with the cleavage or linking site.
32. A generic modular substrate, especially for performing
enzyme-catalyzed cleavage reactions according to any of claims 1 to
3 and 7 to 31, containing the following sequence motif: Z-X--Y or
Y--X-Z wherein X comprises a module with n cleavage sites S.sub.1
to S.sub.n which can be cleaved by at least one enzyme-catalyzed
cleavage reaction into at least two cleavage products containing
X.sub.1 and X.sub.n+1, respectively, and having defined molecular
weights, n being an integer of .gtoreq.1; Y comprises a reporter
module; and Z comprises a module with a selectable molecular weight
which is inert with respect to said enzymatic cleavage reaction(s)
and whose molecular weight has been selected such that the
molecular weight of the cleavage product containing Z-X.sub.1 or
X.sub.n+1-Z after the enzymatic reaction has occurred is at least
fifty percent of the total molecular weight of the generic
substrate.
33. The substrate according to claim 32, characterized in that the
molecular weight of Z is selected in such a way that, after the
enzymatic reaction has occurred, the molecular weight of the
cleavage product containing Z-X.sub.1 and X.sub.n+1-Z is at least
about sixty percent, especially at least about seventy percent,
preferably at least about eighty percent, more preferably at least
about ninety percent, of the molecular weight of compound Z-X--Y or
Y--X-Z.
34. The substrate according to claim 32 or 33, characterized in
that X comprises a module with one cleavage site Si which can be
cleaved by the enzyme-catalyzed cleavage reaction into two cleavage
products containing X.sub.1 and X.sub.2, respectively, and having
defined molecular weights.
35. The substrate according to claim 32 or 33, characterized in
that X comprises a module with several cleavage sites S.sub.1 to
S.sub.n with n>1 which can be cleaved by enzymatic cleavage
reactions into n+1 cleavage products having defined molecular
weights.
36. A kit containing a substrate according to any of claims 32 to
35 and at least one enzyme for catalyzing said cleavage reaction(s)
at the cleavage sites S.sub.1 to S.sub.n, and optionally
cosubstrates, cofactors, modulators, buffers and/or reagents for
stopping said enzymatic reaction.
37. Use of a substrate according to any of claims 32 to 35 or of a
kit according to claim 36 in enzymatic cleavage reactions.
38. A kit, especially for performing enzyme-catalyzed linking
reactions according to any of claims 4 to 31, comprising the
following chemical compounds as substrates for said enzyme or
enzymes catalyzing the linking reaction(s): Z-X.sub.1 and
X.sub.n+1--Y and optionally X.sub.2 to X.sub.n; or Y--X.sub.1 and
X.sub.n+1-Z and optionally X.sub.2 to X.sub.n; wherein X.sub.1
comprises a modular building block which can be linked by said
enzyme-catalyzed linking reaction(s) directly with X.sub.n+1 in the
case where n=1, or optionally indirectly through at least one
modular building block selected from X.sub.2 to X.sub.n in the case
where n>1; X.sub.n+1 comprises a modular building block which
can be linked by said enzyme-catalyzed linking reaction(s) directly
with X.sub.1 in the case where n=1, or optionally indirectly
through at least one modular building block selected from X.sub.2
to X.sub.n in the case where n>1; Y comprises a reporter module;
n is an integer of .gtoreq.1; and Z comprises a module with a
selectable molecular weight which is inert with respect to said
enzymatic linking reaction and whose molecular weight has been
selected such that the molecular weight of X.sub.n+1--Y or
Y--X.sub.1 is at most fifty percent of the total molecular weight
of the linked product formed; and optionally at least one enzyme
catalyzing said linking reaction, cosubstrates, cofactors,
modulators, buffers and/or reagents for stopping said enzymatic
reaction.
39. A kit according to claim 38, characterized in that the
molecular weight of Z is selected in such a way that the molecular
weight of Y--X.sub.1 and X.sub.n+1--Y is at most about forty
percent, especially at most about thirty percent, preferably at
most about twenty percent, more preferably about ten percent, of
the molecular weight of the compound Z-X--Y or Y--X-Z.
40. Use of a kit according to claim 38 or 39 in enzymatic linking
reactions.
41. Use of a substrate according to any of claims 32 to 35 or of a
kit according to any of claims 36 to 39 for testing enzyme and/or
modulator specificities, for testing enzyme and/or modulator
activities, for the identification of modulators and/or substrates,
for the detection of contaminations in chemical or biological
samples, for the screening for pharmacologically active substances,
or for diagnostic purposes.
42. A method for the detection of contaminations in at least one
reagent which is to be used for performing an enzymatic cleavage
reaction in which either a modular chemical compound Z-X--Y is
cleaved into at least two cleavage products Z-X.sub.1 and
X.sub.n+1--Y, or a modular chemical compound Z-X--Y is cleaved into
at least two cleavage products Y--X.sub.1 and X.sub.n+1-Z,
comprising the following steps: a) providing a modular chemical
compound containing the following sequence motif: Z-X--Y or Y--X-Z
wherein Z comprises a module with a selectable molecular weight
which is inert with respect to said enzymatic cleavage reaction and
whose molecular weight has been selected such that the molecular
weight of the cleavage product containing Z-X.sub.1 or X.sub.n+1-Z
after the chemical reaction has occurred is at least fifty percent
of the total molecular weight of said modular chemical compound; X
comprises a module with n cleavage sites S.sub.1 to S.sub.n which
can be cleaved by said enzyme-catalyzed cleavage reaction into at
least two cleavage products containing X.sub.1 and X.sub.n+1,
respectively, and having defined molecular weights, n being an
integer of .gtoreq.1; and Y comprises a reporter module; b)
incubating said compound with said reagent; c) detecting
contaminations by determining a compound containing the reporter
module Y by means of a molecular-weight-sensitive method.
43. The method according to claim 42, characterized in that said
reagent comprises the enzyme catalyzing the cleavage reaction as
well as an inhibitor specific for this enzyme.
Description
[0001] The invention relates to methods for the detection of
enzyme-catalyzed cleavage and linking reactions and to means,
especially kits and substrates, for performing such methods.
[0002] Enzymatic cleavage reactions, such as, in particular,
proteolytic reactions, are wide-spread in biochemistry and play a
decisive role in the biological function of organisms. Therefore,
it is an important task to monitor these reactions in suitable test
methods, so-called assays. The functionality of an assay is
critically dominated by its reliability and reproducibility.
Especially to assay systems employed in the high-throughput
screening for novel pharmacologically active substances, very high
standards are to be applied in this respect, since the time which
remains for performing the assay and, in particular, for detecting
a measuring point is extremely short. The currently known assay
systems and substrates for proteolytic reactions, in particular, do
not meet these demands in many respects.
[0003] For example, known assays include assays for non-specific
proteolytic enzymes on the basis of bacterial luciferase as a
substrate (Njus et al., Analytical Biochemistry 61, 280-287, 1974);
these assays naturally fail when enzymes having a precisely defined
substrate specificity are to be examined.
[0004] In addition, the prior art describes assay systems with the
related substrates which are based on fluorogenic or chromogenic
principles using a dye for coupling to the substrate. The
fluorogenic principle is based on the synthesis of an amide from a
primary or secondary amine moiety of a dye with the carboxy group
of an amino acid. The electron-withdrawing property of the carboxy
group causes the electron density in the dye system to be reduced
(incidentally, this also holds for the chromogenic principle) and
thus the chromophorous system to be impaired, i.e., the dye loses
its dye properties. A peptide having an arbitrary sequence can now
be synthesized onto the coupled-on amino acid. At any rate, it is
critical that the cleavage site for the proteolytic reaction is the
amide bond between the dye and the first amino acid. The cleavage
of this bond restores the electronic system of the dye and thus its
dye properties (chromogenic system), and in the case of a
fluorescent dye, it is again capable of emitting light quanta upon
appropriate excitement (fluorogenic system). Such a system has been
disclosed, for example, in U.S. Pat. Nos. 4,557,862 and 4,640,893,
which describe a class of rhodamine derivatives which are not
fluorescent in the form of bisamide substitution products while the
monoamide substitution products exhibit a high degree of
fluorescence. Thus, the cleavage of a single specific amide bond by
specific proteases converts the non-fluorescent derivative into a
fluorescent derivative, which serves as a read-out parameter for
the proteolytic reaction. Applications of these techniques for
serine proteases have been described, for example, by Leytus et al.
(Biochem. J. 209, 299-307, 1983; Biochem. J. 215, 253-260, 1983).
The techniques have also been employed for cysteine protease
assays, for example, for the detection of the caspase enzyme class,
which is relevant to the detection of apoptotic processes, see, for
example, Hug et al. (Biochemistry 38, 13906-13911, 1999), Weber et
al. (WO 99/18856), Xiang et al. (Proc. Natl. Acad. Sci. USA, 93,
14559-14563, 1996), and Talanian et al. (The Journal of Biological
Chemistry, 272, 9677-9682, 1997).
[0005] The disadvantages of these techniques reside in the very
limited selection of dyes which can be linked with amino acids in
the way described and can thus reversibly lose their dye
properties. The few known examples are rhodamine 110 and
7-aminomethylcoumarin. The synthesis of these molecules is very
difficult in part. In addition, the amide bond between the dye and
the amino acid is not a peptidic bond as in real biological
substrates of a proteinase. This results in a dramatic
deterioration of molecular recognition by the enzyme. Therefore, it
is necessary here to work in a concentration range which is not
tolerable for single-molecule techniques, for example, on confocal
basis. The read-out parameter is fluorescence intensity, which is
difficult to standardize, so that the parameters of the proteolytic
reaction to be examined can be derived therefrom only with high
difficulty. A high amount of background fluorescence as encountered
with these substrates also leads to a reduction of the usefulness
of such a system. Due to the impaired electronic system of the dye
prior to the occurrence of an enzymatic reaction, there is no
emission, and thus it cannot be checked how much substrate has been
charged.
[0006] Further, the prior art describes assays using substrates
which are labeled with two dye molecules. Proteolytic assays of
this kind contain a peptide sequence which preferably bears a
specific cleavage sequence and is labeled with two dye markers on
both ends of the peptide chain. The proteolytic reaction decomposes
the peptide chain into two (when there is one cleavage site) or
more fragments and spatially separates the two dye markers. In the
case of heterogenic labeling, this is a pair of dyes which is
capable of performing fluorescence resonance energy transfer
(FRET). The proteolytic reaction destroys this FRET effect, and the
two spectrally separated dyes exhibit their respective
characteristic fluorescence properties, which had previously been
interacting in the uncleaved peptide chain. FRET measurements have
been performed, for example, on fluorogenic substrates for
interleukin-1.beta. converting enzyme (ICE) (Pennington et al.,
Peptide Research, 7, 72-76, 1994). The FRET effect is based on the
mutual spatial orientation of the two partners involved, so that
fluctuations in their distance, as occur in a peptide chain which
is not spatially fixed, also lead to fluctuations in the signal,
which prevents an accurate detection. Another disadvantage is the
fact that the cleavage site must be between the two dyes of the
FRET pair. Due to this spatial proximity, interference with the
enzymatic bond may occur. In homogeneous labeling, two identical
dye molecules are employed, for example tetramethylrhodamine, as
described by Packard et al. (J. Phys. Chem. B 102, 1820-1827, 1998;
J. Phys. Chem. B 102, 752-758, 1998; Biophysical Chemistry, 67,
167-176, 1997). In an aqueous environment, tetramethylrhodamine
tends to undergo hydrophobic interactions which lead to
dimerization of the dye and to a loss of its fluorescence
properties. This means that the two dye molecules dimerize
intramolecularly in common on one peptide and that this
intramolecular dimerization is reverted only after the cleavage of
the peptide chain. Although intermolecular dimerization after the
occurrence of the cleavage is still possible, it is little relevant
due to the concentration conditions in which the assay is effected.
However, the dimerization of the dyes in the uncleaved condition is
not complete either, so that a detectable background signal
remains. Further, naturally, only dyes having hydrophobic
properties can be used, because only these exhibit a tendency to
dimerize, which results in substantial problems in the design of an
assay which has to be employed in a biologically compatible and
thus aqueous environment.
[0007] The prior art further describes proteolytic assays on the
basis of fluorescence anisotropy. These work according to the
principle that small fragments labeled with fluorescent dyes have a
higher mobility after the proteolytic reaction and thus exhibit a
faster rotation than that of a whole molecule prior to the
reaction. On the one hand, the whole molecule can be a large
protein which is randomly labeled with a high degree of labeling
and which does not have a specific cleavage sequence for a
particular protease. The protein is cleaved into fragments of which
some fraction bears fluorescence markers. Such an assay which is
based on the determination of fluorescence polarization as the
detection method of choice as well as suitable substrates have been
described, for example, by Maeda (Analytical Chemistry 92, 222-227,
1979). On the other hand, it may be a peptide having a, preferably
specific, cleavage sequence and bearing a dye on one side and a
biotin molecule on the other side. Through a biotin/(strept)avidin
interaction, a very large complex having a high anisotropy is
formed. The specific cleavage sequence which has been incorporated
into the peptide is cleaved by the proteolytic reaction to form a
small dye-bearing peptide fragment (see, for example, Bolger et
al., BioTechniques 17, 586-589, 1994; Levine et al., Analytical
Biochemistry 247, 83-88, 1997). However, depending on the protease
employed, the (strept)avidin protein may also be attacked, so that
there is no specificity since a proteolytic reaction which is not
specific for the incorporated cleavage sequence may also mimic a
corresponding reaction by the cleavage of the (strept)avidin. Even
by the later addition of (strept)avidin, this disadvantage cannot
be removed, so that this system may be useless, depending on
circumstances. Anyway, when (strept)avidin is added later, only an
end-point determination can be performed, and it is not possible to
monitor the course of the reaction. Such a biotinylated substrate
which is treated with (strept)avidin only after the enzymatic
reaction has occurred in order to enable detection is not suitable
for kinetic experiments because the reaction also tends to be
stopped upon the addition of (strept)avidin. Thus, different
reaction times could be realized only by a corresponding number of
reactions. But even the mentioned stopping effect cannot be
calculated, as shown in our own experiments with caspase-3 in which
an enzymatic conversion of the caspase-3 substrate to which
(strept)avidin had been added took place against expectations.
Thus, to conclude, such assay systems do not meet the demands with
respect to reliability of the results obtained and robustness in
performance.
[0008] Therefore, it is the object of the present invention to
provide universally useful methods for the detection of enzymatic
cleavage and linking reactions as well as corresponding means which
do not have the above mentioned drawbacks and are suitable, in
particular, for use in high-throughput methods for the screening of
pharmacologically active modulators of enzymatic reaction(s).
[0009] These objects are achieved by substrates, kits and assay
methods according to the independent claims.
[0010] Thus, in a first aspect, the invention relates to a method
for the detection of enzyme-catalyzed cleavage reactions,
comprising the following steps:
[0011] a) providing a modular chemical compound containing the
following sequence motif:
Z-X--Y or Y--X-Z
[0012] wherein Z comprises a module with a selectable molecular
weight which is inert with respect to said enzymatic cleavage
reaction;
[0013] X comprises a module with n cleavage sites S.sub.1 to
S.sub.n which can be cleaved by said enzyme-catalyzed cleavage
reaction into at least two cleavage products containing X.sub.1 and
X.sub.n+1, respectively, and having defined molecular weights, n
being an integer of .gtoreq.1; and
[0014] Y comprises a reporter module;
[0015] as a substrate for said enzyme(s) catalyzing said cleavage
reaction(s);
[0016] b) incubating the compound with said enzyme(s) catalyzing
said cleavage reaction(s) to form at least two cleavage products
which contain
Z-X.sub.1 and X.sub.n+1--Y
or
Y--X.sub.1 and X.sub.n+1-Z
[0017] wherein the molecular weight of the cleavage product
containing Z-X.sub.1 or X.sub.n+1-Z is at least fifty percent of
the total molecular weight of the substrate;
[0018] c) detecting the enzymatic activity or activities by
determining the cleavage product containing the reporter module Y
by means of a molecular-weight-sensitive method.
[0019] Further, according to the invention, a generic modular
substrate is provided which contains the following sequence
motif:
Z-X--Y or Y--X-Z
[0020] wherein X comprises a module with n cleavage sites S.sub.1
to S.sub.n which can be cleaved by at least one enzyme-catalyzed
cleavage reaction into at least two cleavage products containing
X.sub.1 and X.sub.n+1, respectively, and having defined molecular
weights;
[0021] Y comprises a reporter module; and
[0022] Z comprises a module with a selectable molecular weight
which is inert with respect to said enzymatic cleavage reaction(s)
and whose molecular weight has been selected such that the
molecular weight of the cleavage product containing Z-X.sub.1 or
X.sub.n+1-Z after the enzymatic reaction has occurred is at least
fifty percent of the total molecular weight of the generic
substrate.
[0023] For example, the substrate can be provided in the form of a
kit. In addition to a substrate or several different substrates
according to the invention, such a kit may optionally also comprise
at least one enzyme for catalyzing said cleavage reaction(s) at the
cleavage sites S.sub.1 to S.sub.n as well as cosubstrates,
cofactors, modulators, buffers and/or reagents for stopping said
enzymatic reaction.
[0024] Of particular importance to the method according to the
invention and for the substrate is, on the one hand, the use of a
module Z which is inert with respect to the enzymatic cleavage
reaction. Thus, when a non-inert module Z were used, cases could
occur, for example, in which reaction products are formed which are
but slightly distinct with respect to their molecular weights and
could not be read out by molecular-weight-sensitive methods, or
only so with a high inaccuracy. If the module Z were cleaved at
several sites by the enzymatic activity, a large number of reaction
products with different molecular weights would be produced,
resulting in a "smeared" detection signal. On the other hand, it is
further of particular importance to ensure a sufficiently high
difference between the molecular weight of the substrate and that
of the cleavage product containing the reporter module Y in order
to enable a high detection accuracy. Especially in High-throughput
screening (HTS) methods for pharmacologically effective modulators
of the enzymatic reaction, the detection time is often limited to
only a few seconds per modulator, so that a more than average
detection accuracy is indispensable. According to the invention,
these requirements are ensured by the fact that the molecular
weight of the module Z is to be selected such that the molecular
weight of the cleavage product containing Z-X.sub.1 or X.sub.n+1-Z
after the enzymatic reaction has occurred is at least fifty percent
of the total molecular weight of the generic substrate.
[0025] Due to the modular composition of the substrate according to
the invention, it is possible to adapt it in a simple and
inexpensive way to the enzyme(s) to be tested and to the detection
method employed. The identities of Z and Y are subject to some
flexibility, in principle, which can be utilized for designing an
optimum assay. Due to the modular concept, substrates can be
assembled for any desired cleavage reactions having a defined
cleavage sequence/cleavage region. The assay designer can have
different modules Z and Y on stock, so to speak, in order to be
able to quickly incorporate any desired cleavage regions which can
then be tested in enzymatic reactions.
[0026] In a particularly advantageous way, the components of the
substrate are covalently linked to each other. The particular
importance of the covalent linkage between the substrate components
is impressively seen in a comparison with the (strept)avidin/biotin
system of the prior art. For example, in a substance library which
is to be tested in high-throughput screening, substances could
exist which affect the binding of (strept)avidin to biotin. In a
screening for enzyme inhibitors or enzyme activators, such
substances would appear as false negative or false positive hits.
However, in view of the immense costs of the further optimization
of hits, an elimination of false-positive hits is of utmost
commercial importance to the pharmaceutical industry.
[0027] In a preferred embodiment, X comprises a module with one
cleavage site S.sub.1 which can be cleaved by the enzyme-catalyzed
cleavage reaction into two cleavage products containing X.sub.1 and
X.sub.2, respectively, and having defined molecular weights.
However, in a further embodiment, there are also provided a
substrate and a corresponding detection method in which X is a
module having several cleavage sites S.sub.1 to S.sub.n, wherein
n>1. Thus, n+1 cleavage products having defined molecular
weights are produced by the enzymatic cleavage reactions. Thus, the
substrate may contain, for example, two cleavage sequences S.sub.1
and S.sub.2 which can be cleaved by the enzymes E.sub.1 and
E.sub.2. The same substrate can be used for respective incubations
with either of the enzymes E.sub.1 or E.sub.2. The formation of the
respective products, Z-X.sub.1 and X.sub.2X.sub.3--Y or
Z-X.sub.1X.sub.2 and X.sub.3--Y, can be detected by a
molecular-weight-sensitive method. This embodiment of the substrate
with several, especially two, cleavage sites enables, firstly, to
perform several drug discovery programs (search for modulators of
enzyme E.sub.1 or enzyme E.sub.2) with only one substrate and,
secondly, to determine the selectivity of modulators. In this
latter case, it is examined whether a modulator of enzyme E.sub.1
is also a modulator of enzyme E.sub.2, or whether a modulator of
enzyme E.sub.2 is also a modulator of enzyme E.sub.1. This is an
important issue in the development of pharmaceutical products,
since any undesirable side-effects of a modulator of E.sub.1 on
further enzymes, such as E.sub.2, can be detected.
[0028] In a preferred embodiment, the substrate has such a design
that the molecular weight of Z is selected such that the molecular
weight of Z-X.sub.1 and that of X.sub.n+1-Z are at least about 60%
of the total molecular weight of the substrate Z-X--Y or Y--X-Z.
However, it is often preferred that the molecular weight of
Z-X.sub.1 and that of X.sub.n+1-Z are at least about 70%,
especially at least about 80%, more preferably at least about 90%,
of the total molecular weight of the substrate. Thus, depending on
the detection efficiency of the molecular-weight-sensitive
detection method employed, the optimum molecular weight difference
or molecular volume difference between the educt and products
formed after the enzymatic cleavage reaction can be adjusted. Thus,
for example, particularly suitable detection methods are those
which are based on fluorescence polarization or fluorescence
anisotropy determinations, or fluorescence correlation
spectroscopy. The detection can preferably by performed by using a
confocal optical design, by which any background signals can be
clearly reduced due to the very small measuring volumes (down to
the femtoliter range). With the substrate according to the
invention, which thus preferably comprises a fluorescence marker as
the reporter module Y, a number of molecular parameters can be read
out directly or indirectly. The correlation time, i.e., the
characteristic time required for a molecule to perform some defined
movement, is directly related to the volume of the molecule. The
rotational correlation time .phi. is given according to the
following relationship:
.phi.=.eta.V/RT
[0029] where .eta.: viscosity
[0030] V: volume of the molecule
[0031] R: general gas constant
[0032] T: temperature in K
[0033] This shows that the following holds under typical assay
conditions at a fixed temperature in a solvent having a fixed
viscosity: .phi.=.eta. times constant.
[0034] The parameter r, the anisotropy of the fluorescence light,
which is readily available experimentally, is related to the
rotational correlation time .phi. according to the Perrin
equation:
r=r.sub.0/[1+(.tau./.phi.)]
[0035] where: r.sub.0: anisotropy at the time t=0
[0036] .tau.: fluorescence lifetime of the dye.
[0037] In the method according to the invention, a change of the
volume or molecular weight of the chemical compound comprising the
dye-bearing reporter module Y is caused by the cleavage reaction
(e.g., proteolytic reaction). It is to be noted, in particular,
that the anisotropy can not only be read out as a sum signal, but
can also be analyzed on the level of individual molecules. This
means that the absolute concentration of the substrate cleaved, for
example, by proteolysis, and having a high rotational correlation
time (fast rotation) and the absolute concentration of (as yet)
unreacted substrate having a low correlation time (slow rotation)
can be determined directly from the sample. External calibration
can be omitted, since the ratio of the two species can be
determined directly and thus the conversion can be calculated in a
simple way. An analogous consideration applies to the behavior of
the substrate according to the invention when detection systems are
used which establish a translational diffusion correlation time.
Thus, fluorescence correlation spectroscopy (FCS) can be used to
establish the diffusion constant of the fluorescent molecule, which
directly depends on the mass of the molecule and by means of which
an absolute concentration of the two species can also be
detected.
[0038] In order to achieve the inert character of the preferably
polymeric fraction Z in the total substrate, it is suggested
according to the invention to select Z and X from different classes
of substances. Thus, for example, a proteolytic enzyme reaction
could be examined by means of molecular-weight-sensitive optical
methods in which X is an amino acid sequence with suitable cleavage
sites for the enzyme employed, and Z belongs to a different class
of substances, i.e., is not a peptide or protein. In this case, it
is particularly advantageous to construct Z from nucleotides, a
double-stranded nucleic acid being particularly preferred. Such a
substrate is shown illustratively in FIG. 1. However, any other,
preferably hydrophilic, polymer is also suitable as the Z module.
Hydrophilic Z modules are particularly preferred if the assay is to
be performed in aqueous solution in order to take biological
conditions into account.
[0039] In contrast to previously known systems, the substrate
according to the invention and its application in the cleavage
assay according to the invention exhibits the following
advantages:
[0040] 1. Clearly defined cleavage products after the cleavage
reaction, such as a proteolytic reaction: Only those cleavage
products which are clearly defined by the structure of the
substrate and which have unambiguous molecular weights are
formed.
[0041] 2. Homogeneous signal distribution due to a defined
molecular structure: Since clearly defined fragments are present
after the cleavage reaction, such as a proteolytic reaction, one
unambiguous rotational or diffusion correlation time is to be
expected for the fragment bearing the dye. A polydispersity of the
products with an associated "smearing" of the detected signal as
often observed in the prior art is avoided.
[0042] 3. Modular structure: The substrate according to the
invention has a modular structure and can be adapted in many ways
to the problem to be examined:
[0043] Reporter module: When optical detection is used, the dye
which is suitable in terms of the detection technology and in
chemical and photophysical terms can be selected from a wide
variety of dyes capable of coupling (amine-reactive, thio-reactive,
carboxylic-acid-reactive etc.). Thus, there may be used, for
example, coumarins, fluoresceins, rhodamines, xanthenes, oxazines,
cyanines and the like as well as their derivatives.
[0044] Module X with cleavage site: Any cleavage site, which
preferably can be synthetically produced, can be incorporated,
i.e., any enzyme, such as a protease with a known recognition or
cleavage sequence, can be specifically and selectively examined.
Thus, it is possible to specifically offer a substrate for a
selected protease in a mixture of different proteases and to
specifically study the reaction of this protease.
[0045] The module Z (for example, a polymer, especially an
oligonucleotide) can be freely selected, and its length/mass can be
adjusted according to requirements in terms of detection
technology. Also, hybridizations to DNA sequences in the assay can
be used, if desired. Each and every module can contain different
classes of substances, for example, the module Z can comprise a
nucleic acid and a cyclohexanoic acid derivative (see
Examples).
[0046] 4. Linear or rigid structure of the substrate: Due to the
stretched structure of a substrate as described, for example, in
FIG. 1, especially when a DNA double strand is used, it is ensured
that no influencing of the enzymatic, especially proteolytic,
reaction occurs from a molecular interaction in the form of spatial
contacts between the Z and X modules (e.g., the oligonucleotide and
peptide portions in FIG. 1).
[0047] 5. The water-solubility can be selectively adjusted. Thus, a
high water-solubility can be achieved, in particular, by using a
polyanionic oligomer moiety as the Z module. For biological assay
systems in an aqueous environment, a high water-solubility of the
substrate is naturally necessary and advantageous.
[0048] 6. Direct monitoring of the reaction course: The substrate
offers the possibility of observing the enzymatic cleavage reaction
during the course of the reaction and thus to perform kinetics
studies.
[0049] 7. The substrate can be detected per se (cf. prior art with
fluorogenic/chromogenic principles).
[0050] 8. The module Z can be designed in such a way that it may
also serve as (i) a recognition site for enzyme binding (e.g.,
binding of particular restriction endonucleases) or (ii) a binding
site for factors influencing the enzyme binding or activity.
[0051] 9. The reporter module Y can be spatially separated from the
cleavage region (cf. prior art with fluorogenic/chromogenic
principle; FRET).
[0052] Further, in another aspect, the invention relates to a
method for the detection of enzyme-catalyzed linking reactions,
comprising the following steps:
[0053] a) providing the following chemical compounds:
Z-X.sub.1 and X.sub.n+1--Y and optionally X.sub.2 to X.sub.n;
or
Y--X.sub.1 and X.sub.n+1-Z and optionally X.sub.2 to X.sub.n;
[0054] wherein Z comprises a module with a selectable molecular
weight which is inert with respect to said enzymatic linking
reaction;
[0055] X.sub.1 comprises a modular building block which can be
linked by said enzyme-catalyzed linking reaction(s) directly with
X.sub.n+1 in the case where n=1, or optionally indirectly through
at least one modular building block selected from X.sub.2 to
X.sub.n in the case where n>1;
[0056] X.sub.n+1 comprises a modular building block which can be
linked by said enzyme-catalyzed linking reaction(s) directly with
X.sub.1 in the case where n=1, or optionally indirectly through at
least one modular building block selected from X.sub.2 to X.sub.n
in the case where n>1;
[0057] Y comprises a reporter module;
[0058] n is an integer of .gtoreq.1; and
[0059] the molecular weight of X.sub.n+1--Y or Y--X.sub.1 is at
most fifty percent of the total molecular weight of the linked
product formed;
[0060] as a substrate for said enzyme(s) catalyzing said cleavage
reaction;
[0061] b) incubating the compound with said enzyme(s) catalyzing
said linking reaction(s) to form linked products
Z-X--Y
or
Y--X-Z
[0062] wherein X comprises the modular building blocks X.sub.1 and
X.sub.n+1 and optionally at least one modular building block
selected from X.sub.2 to X.sub.n;
[0063] c) detecting the enzymatic activity or activities by
determining the linked product containing the reporter module Y by
means of a molecular-weight-sensitive method.
[0064] In a preferred embodiment of this method, two modular
building blocks X.sub.1 and X.sub.2 are directly linked with each
other by said enzyme-catalyzed reaction. However, it is also
possible to indirectly link X.sub.1 and X.sub.n+1 with each other
through a modular building block X.sub.2. A further embodiment of
the method according to the invention consists in the indirect
linking of X.sub.1 and X.sub.n+1 with each other through a
plurality of modular building blocks. These building blocks are
selected from the building blocks X.sub.2 to X.sub.n.
[0065] According to the invention, a kit of the following chemical
compounds for the enzyme(s) catalyzing the linking reaction(s) is
also provided for performing enzyme-catalyzed linking
reactions:
Z-X.sub.1 and X.sub.n+1--Y and optionally X.sub.2 to X.sub.n;
or
Y--X.sub.1 and X.sub.n+1-Z and optionally X.sub.2 to X.sub.n;
[0066] wherein
[0067] X.sub.1 comprises a modular building block which can be
linked by said enzyme-catalyzed linking reaction(s) directly with
X.sub.n+1 in the case where n=1, or optionally indirectly through
at least one modular building block selected from X.sub.2 to
X.sub.n in the case where n>1;
[0068] X.sub.n+1 comprises a modular building block which can be
linked by said enzyme-catalyzed linking reaction(s) directly with
X.sub.1 in the case where n=1, or optionally indirectly through at
least one modular building block selected from X.sub.2 to X.sub.n
in the case where n>1;
[0069] Y comprises a reporter module;
[0070] n is an integer of .gtoreq.1; and
[0071] Z comprises a module with a selectable molecular weight
which is inert with respect to said enzymatic linking reaction and
whose molecular weight has been selected such that the molecular
weight of X.sub.n+1--Y or Y--X.sub.1 is at most fifty percent of
the total molecular weight of the linked product formed;
[0072] and optionally at least one enzyme catalyzing said linking
reaction, cosubstrates, cofactors, modulators, buffers and/or
reagents for stopping said enzymatic reaction.
[0073] Preferably, both with respect to the above mentioned method
for the detection of linking reactions and to the description of
the kit, the molecular weight of Z is selected such that the
molecular weight of Y--X.sub.1 or X.sub.n+1--Y is at most about
forty percent, especially at most about thirty percent, preferably
at most about twenty percent, more preferably about ten percent, of
the molecular weight of the compound Z-X--Y or Y--X-Z. Thus, by
analogy with the description of the method according to the
invention for the detection of cleavage reactions, a substrate
choice which is optimally adapted to the detection method can also
be enabled in linking reactions.
[0074] As already discussed in the description of the substrate
according to the invention for cleaving reactions, it is also
preferred for these substrates for linking reactions that X and Z
belong to different classes of substances. Thus, for example, they
may respectively belong to the following classes of substances:
nucleic acids, peptide nucleic acids (PNA), peptides, proteins,
lipids, carbohydrates or derivatives of the above mentioned
substances. In particular, these may be synthetic polymers.
[0075] It may be noted generally that all the stated substrates,
kits and assays are particularly suitable for testing enzyme and/or
modulator specificities, for testing enzyme and/or modulator
activities, for the identification of modulators and/or substrates,
for the detection of contaminations in chemical or biological
samples, for the screening for pharmacologically active substances,
or for diagnostic purposes. These applications can also be seen, in
particular, from the Figures shown below and the related Figure
descriptions.
[0076] Further, it is also generally desirable to select the module
Z to have such a chemical structure as does not sterically interact
with the cleavage or linking site. This can be enabled, in
particular, by a rigid structure of Z, e.g., a linear structure,
such as that of a polyanion. As already mentioned somewhere, it is
particularly preferred to use a double-stranded nucleic acid or a
derivative thereof.
[0077] In one embodiment, the enzyme catalyzing the reaction may be
a hydrolase, especially a lipase, phosphatase, amylase,
glycosidase, nucleosidase, peptidase, protease, amidase,
pyrophosphatase, ATPase or phosphoamidase. The enzyme catalyzing
the reaction may also be a lyase, especially a C--C, C--O, C--N or
C--S lyase. In particular, it may be a (de)carboxylase, aldolase,
dehydratase, ammonia-lyase, arginosuccinase or cysteine
desulfhydrase. Further, the enzyme catalyzing the reaction may be,
for example, a ligase, especially a C--O, C--S, C--N or C--C
ligase. Illustratively, there may be mentioned an amino-acid
activating ligase, acyl-CoA synthetase, glutamine synthetase or
pyruvate carboxylase. In addition, transferases such as DNA or RNA
polymerases may also be employed. Generally, it may be preferred to
employ enzymes having substrate, group or steric specificity. As
set forth in the Examples, the enzyme may also be, in particular, a
caspase, such as caspase 3 or caspase 8. The substrate according to
the invention then comprises a cleaving sequence specific for the
respective caspase in its module designated with X, while the
module designated with Z preferably belongs to a different class of
substances, such as oligonucleotides.
[0078] In particular, the enzyme-catalyzed cleaving or linking
reaction may be performed in the presence of one or more
cosubstrates or cofactors. Also, one or more enzymes and/or
substrates may be employed simultaneously or sequentially. In
particular, the linking or cleaving reactions may be performed in
the presence of modulators or potential modulators of enzymatic
activity.
[0079] In particular, it is preferred to perform the methods
according to the invention as homogeneous assays, i.e., without
washing steps. Especially the fluorescence-spectroscopic detection
methods described in more detail above allow such an approach in
combination with the substrates according to the invention for
cleaving or linking reactions. In order not to falsify the results,
it may be desirable in special cases to detach the enzyme
catalyzing the cleaving or linking reaction from the reaction
product containing the reporter module Y, preferably
(bio)chemically. Further, it is generally often advantageous to use
a reporter module Y with a fluorescent dye.
[0080] In the following, the invention is illustrated in an
exemplary way by the Figures. Further, Examples are presented,
especially of the synthesis of the substrates according to the
invention.
[0081] FIG. 1 shows the structure of an embodiment of the substrate
according to the invention, wherein the fluorescent dye may be any
dye that can be covalently coupled with an amino acid, especially
coumarins, fluoresceins, rhodamines, xanthenes, oxazines, cyanines
and the like, or derivatives thereof. The length of the peptide
module is preferably from n=1 to n=100, more preferably to n=10.
Within the peptide sequence, at least one combination of successive
amino acids which is specific for a particular proteolytic reaction
is preferably present. The recognition sequence of the respective
protease can also be incorporated selectively and specifically
here. The fragment formed upon the proteolytic cleavage which bears
the DNA double strand is preferably such that its proportion in the
total molecular weight of the molecule is at least 80%.
[0082] By means of the Example underlying FIG. 2, it shall be
demonstrated how an embodiment of the substrate according to the
invention which bears the specific recognition sequence of the
caspase 3 protease is cleaved proteolytically. The proteolytic
cleavage is monitored by measuring the diffusion time .tau..sub.D
by means of fluorescence correlation spectroscopy (FCS). Thus, a 5
nM solution of the substrate described in Example 1 in a buffer (50
mM HEPES, pH 7.5, 100 mM NaCl, 10% saccharose, 0.1% CHAPS, 10 mM
DTT) is incubated together with 1 nM caspase, and the course of the
fluorescence correlation signal is observed as a function of time.
The fitting of the measured curve to the correlation function (2
components) was effected with the values .tau..sub.D1=313 ns
(uncleaved substrate) and .tau..sub.D2=70 .mu.s (cleaved
substrate). The reduction of the average diffusion time can already
be seen from the change of the correlation curves in time.
[0083] The exact analysis of the parameters mentioned under FIG. 2
result in the proportions of the individual diffusion times as
plotted in FIG. 3 and thus in the proportions of the individual
species of dye-bearing particles.
[0084] By means of the Example underlying FIG. 4, it shall be
demonstrated how an embodiment of the substrate according to the
invention which bears the specific recognition sequence of the
caspase 3 protease is cleaved proteolytically. The proteolytic
cleavage is monitored by measuring the fluorescence polarization.
Thus, a 1 nM solution of the substrate described in Example 1 in a
buffer (50 mM HEPES, pH 7.5, 100 mM NaCl, 10% saccharose, 0.1%
CHAPS, 10 mM DTT) is incubated together with 1 nM caspase, and the
course of the fluorescence polarization is observed as a function
of time. The graph shows how the polarization of the sample
decreases with time. The stated standard deviations respectively
result from 25 measurements. The cause of this course resides in
the cleavage of the substrate by the proteolytic activity of the
caspase.
[0085] FIG. 5 shows an embodiment of the substrate according to the
invention and its application in a caspase 3 assay. The tripartite
substrate consists of a schematically represented polymer, a
sequence to be cleaved containing the recognition sequence DEVD (in
a one-letter code) which is typical of caspase 3, and the
fluorescent dye TAMRA. A clear difference in the detected
fluorescence polarization which is associated with the cleavage can
be seen.
[0086] FIG. 6 shows the determination of the Z' factor, which is a
measure of the signal-to-noise ratio of the assay using 10 nM
substrate and applying a confocal detection set-up. The experiment
provides the assay designer with information about (i) the dynamic
region, (ii) the time window for a linear reaction, (iii) standard
deviation, CV (data statistics) and (iv) Z' factor (comparison with
inhibited reaction). These results permit the determination of the
so-called "screening window" (could this assay be used for
screening?). An excellent Z' factor of .gtoreq.0.83 is shown here
already after 40 minutes.
[0087] FIG. 7 shows the established IC.sub.50 values. The Figure
shows that an almost identical dose-response curve can be measured
in the absence/presence of DMSO. Since compounds are usually
dissolved in DMSO and a residual concentration is often unavoidable
in HTS, such a test is important.
[0088] FIG. 8 illustrates the adaptation of the assay to a final
volume of 1 .mu.l in nanotitration plates. It is found that the
so-called highs (in the presence of an inhibitor) and "lows" (in
the absence of an inhibitor) are still readily distinguished, and
the Z' factor is sufficient for employing the assay in a
high-throughput screening for modulators of enzymatic activity
which, if suitable, may be used later as pharmaceuticals.
[0089] FIG. 9 shows a comparison between the IC.sub.50 values in 60
.mu.l and 1 .mu.l assay formats with the addition of screening
additives. The assay performance in the 1 .mu.l format, which is
advantageously employed in high-throughput screening due to the low
consumption of substances, is comparable with the performance in
assay development. Thus, the assay designer can release the assay
for high-throughput screening for pharmacologically active
substances.
[0090] FIG. 10 schematically shows an embodiment of the substrate
(Z-X--Y) according to the invention and its use in the detection of
enzyme-catalyzed cleavage reactions. In this Figure, the substrate
has a single cleavage site S.sub.1. Upon cleavage by the enzyme
E.sub.1, the two cleavage products Z-X.sub.1 and X.sub.2--Y are
formed. This reaction can be detected by a
molecular-weight-sensitive method.
[0091] FIG. 11 schematically shows an embodiment of the substrate
(Z-X--Y) according to the invention and its use for the
identification of modulators (compounds "C") of enzyme-catalyzed
cleaving reactions ("drug discovery"). In this Figure, the
substrate has a single cleavage site S.sub.1. Compounds which
modulate (inhibit or activate) the enzymatic activity result in a
lower amount (in the case of inhibition) or higher amount (in the
case of activation) of products formed within a defined incubation
time. Then, a molecular-weight-sensitive method can be used for
relating the amount of products formed in the presence of a
compound (this Figure) with the amount of products formed in the
absence of a compound (see FIG. 10) in order to establish the
degree of inhibition or activation of the enzymatic reaction. In
this Figure, compound C inhibits the enzyme E1 completely, so that
no products Z-X.sub.1 and X.sub.2--Y are formed. This corresponds
to a degree of inhibition of 100%.
[0092] FIG. 12 shows another embodiment of the substrate (Z-X--Y)
according to the invention and its use in the detection of
sequentially performed enzyme-catalyzed cleavage reactions. In this
Figure, the substrate has two cleavage sequences S.sub.1 and
S.sub.2. The same substrate can be employed by incubation with one
of the enzymes E.sub.1 or E.sub.2 which cleaves the substrate at
the cleaving site S.sub.1 or S.sub.2 to form the products Z-X.sub.1
and X.sub.2X.sub.3--Y or Z-X.sub.1X.sub.2 and X.sub.3--Y; the
reaction can be detected by a molecular-weight-sensitive method.
This embodiment of the substrate with several cleaving sites
enables, firstly, to perform several drug discovery programs
(search for modulators of enzyme E.sub.1 or enzyme E.sub.2) with
only one substrate and, secondly, to determine the selectivity of
modulators (Question: Is a modulator of enzyme E.sub.1 also a
modulator of enzyme E.sub.2, or is a modulator of enzyme E.sub.2
also a modulator of enzyme E.sub.1?).
[0093] FIG. 13 shows an embodiment of the substrate (Z-X--Y)
according to the invention and another use thereof in the detection
of simultaneously performed enzyme-catalyzed cleavage reactions. In
this Figure, the substrate has two cleavage sequences S.sub.1 and
S.sub.2; however, the assay can also be performed with more than
two cleavage sequences and a corresponding number of enzymes. The
substrate can be cleaved into the cleavage products Z-X.sub.1,
X.sub.2 and X.sub.3--Y by simultaneous incubation with the two
enzymes E.sub.1 and E.sub.2. This assay can be employed for
identifying modulators of a whole class of enzymes (e.g.,
modulators of caspases) in a drug discovery campaign, for example,
for developing a broad-range medicament
[0094] FIG. 14 shows an embodiment of the substrate (Z-X--Y)
according to the invention and its use for the detection of
contaminations K which result in the cleavage of the module X. In
this Figure, the substrate has a single cleavage sequence S.sub.1
which would be cleaved upon incubation with enzyme E.sub.1.
According to the invention, the module Z is inert towards the
enzymatic reaction of E1. However, if the substrate is incubated
with an arbitrary sample rather than with enzyme E.sub.1, then it
can be detected by a molecular-weight-sensitive method whether the
substrate is nevertheless cleaved. Depending on circumstances,
there may be formed more products (non-specific contamination) as
compared to cleavage with the enzyme E.sub.1. In this Figure, the
contamination K results in the three products Z-X.sub.1, X.sub.2
and X.sub.3--Y. If inhibitors which prevent the cleavage of Z are
additionally added to the incubation, contaminations which cleave X
can be selectively identified. The molecular-weight-sensitive
method may also be used to detect specific contaminations.
[0095] FIG. 15 shows an embodiment of the substrate (Z-X--Y)
according to the invention and its use for the detection of
contaminations K which result in the cleavage of the module Z. In
this Figure, the substrate has a single cleavage sequence S.sub.1
which would be cleaved upon incubation with enzyme E.sub.1.
According to the invention, the module Z is inert towards the
enzymatic reaction of E1. However, if the substrate is incubated
with an arbitrary sample rather than with enzyme E.sub.1, then it
can be detected by a molecular-weight-sensitive method whether the
substrate is nevertheless cleaved. In this Figure, the
contamination K results in the three products Z.sub.1, Z.sub.2 and
Z.sub.3-X--Y. If inhibitors which prevent the cleavage of X are
additionally added to the incubation, contaminations which cleave Z
can be selectively identified.
[0096] FIG. 16 shows an embodiment of the substrate (Z-X--Y)
according to the invention and its use for the detection of
contaminations K of the added charge of enzyme E.sub.1 which
cleaves the substrate at the cleavage site S.sub.1. If the
substrate is incubated with enzyme E.sub.1 and additionally with an
inhibitor I.sub.1 of the enzymatic activity of the enzyme E.sub.1,
then it can be detected by a molecular-weight-sensiti- ve method
whether cleavage of the substrate nevertheless occurs. In this
Figure, the three products Z.sub.1, Z.sub.2 and Z.sub.3-X--Y are
formed.
[0097] FIG. 17 schematically shows two embodiments of the substrate
(Z-X--Y) according to the invention and its use for the
determination of the substrate specificity of enzyme E.sub.1. In
the first embodiment of the substrate (Z-X--Y) according to the
invention, the module X contains the cleavage site S.sub.1. In the
second embodiment of the substrate (Z-X--Y) according to the
invention, the module X contains the cleavage site S.sub.2. The two
substrates contain different reporter modules Y.sub.1 and Y.sub.2.
Especially, Y.sub.1 and Y.sub.2 can be different fluorescence dyes
which emit fluorescence light at distinct wavelengths. If the two
substrates are simultaneously incubated with the enzyme E1, then it
can be detected by a molecular-weight-sensitive method which can
distinguish between the two reporter modules (1) whether one of the
two substrates has been cleaved, (2) which of the two substrates
has been cleaved, and (3) whether both substrates have been
cleaved. In this Figure, E.sub.1 is specific for the substrate with
the cleavage site S.sub.1.
[0098] FIG. 18 shows the detection of the activity of an enzyme E
which links individual substrates, by determining the linked
product Z-X--Y containing the reporter module Y by means of a
molecular-weight-sensitive method. This assay can also be used for
the identification of modulators of enzyme activity. In this
Figure, Z-X.sub.1 and X.sub.3--Y are indirectly linked with each
other through X.sub.2.
[0099] FIG. 19 shows the practical use of the substrate described
in FIG. 5 for the identification of caspase-3 inhibitors in a drug
discovery campaign. The Figure gives a survey of the course and the
results of the campaign. 193,146 potential modulators (compounds)
were analyzed for their inhibitory effect on caspase-3. The
compounds were employed in concentrations of 17 .mu.M. In this
campaign, 1.5% (primary hit rate) of the compounds showed an
inhibition which exceeded a defined threshold value. These primary
hits were tested again in the same concentration (17 .mu.M) in
multiple determinations for their inhibitory effect. In this way,
the inhibitory effect of 229 compounds could be confirmed. The
potency of these 229 compounds was established through the
recording of dose-effect curves, which reflect the dependence of
the inhibitory effect of a compound from the concentration employed
of this compound. 27 compounds showed an IC.sub.50 value which is
lower than 50 .mu.M. The mean value for the Z' factor, which is a
measure of the robustness of an assay (Zhang, J.-H., et al. (1999).
J. Biomol. Screen., 4, 67-73), was 0.8 over the entire process. Z'
values of larger than 0.5 indicate that the assay is excellent.
Thus, the caspase-3 assay is very suitable for a drug discovery
campaign.
[0100] FIG. 20 illustratively shows the dose-effect curve for one
of the 27 inhibitory compounds described in the legend to FIG. 19.
The compound was examined for its inhibitors effect in 6 different
concentrations (50 .mu.M, 25 .mu.M, 12.5 .mu.M, 6.25 .mu.M, 3.13
.mu.M and 1.56 .mu.M). An IC.sub.50 value of 19.11 .mu.M was
determined.
EXAMPLE 1
Synthesis of a Caspase-3 Specific Substrate (Peptide No. 1)
[0101] The peptide with the sequence
H-Gly-Asp-Glu-Val-Asp-Gly-Lys-OH was prepared by a standard
solid-phase synthesis (Fmoc strategy). As the resin, Rink Amide
MBHA resin with a loading of 0.54 mmol/g was used. A charge size of
20 .mu.mol was selected (m.sub.resin=37.0 mg). The activation of
the amino acids was effected with 5 equivalents of HATU
([O-(7-azabenzotriazol-1-yl)-1,1,3,3-tetra-methyluronium
hexafluorophosphate]) and 10 equivalents of DIPEA
(N-ethyldiisopropylamin- e) in DMF (N,N-dimethylformamide) (100
.mu.mol HATU (38.0 mg) and 200 .mu.mol DIPEA (34.0 .mu.l)). The
volume of the solvent was 5 ml per g of resin. Five equivalents of
amino acid was employed. The reaction time was twice 1 hour (double
coupling) at room temperature. The cleavage of the Fmoc protective
group (fluorenylmethoxycarbonyl) was performed with 20% piperidine
in DMF. The cleavage time was twice 15 minutes. Each time after the
couplings, and also after the Fmoc cleavage, the resin was washed
with 3.times.DMF, 2.times.DMF/DCM (dichloromethane) [1:1],
3.times.DMF reagent grade. The Fmoc protective group on the N
terminus was not removed. Thus, after the couplings of
Fmoc-Lys(Mtt)-OH, Fmoc-Gly-OH, Fmoc-Asp(OtBu)-OH, Fmoc-Val-OH,
Fmoc-Glu(OtBu)-OH, Fmoc-Asp(OtBu)-OH and Fmoc-Gly-OH, the following
sequence results:
Fmoc-Gly-Asp(OtBu)-Glu(OtBu)-Val-Asp(OtBu)-Gly-Lys(Mtt)-resin.
[0102] Coupling of the Dye to the Peptide:
[0103] For the labeling, 5 .mu.mol of peptide-charged resin (9.3
mg) was employed. From the immobilized, completely protected
Fmoc-GDEVDGK-OH, the Mtt (4-methyl-trityl) protective group on
lysine was removed with 1 ml of 30% HFIP
(1,1,1,3,3,3-hexafluoro-2-propanol) in DMF. Thereafter, washings
were performed six times with 1 ml each of 30% HFIP in DMF. The
subsequent washing was again effected with 3.times.DMF,
2.times.DMF/DCM, 3.times.DMF reagent grade. The primary amine
formed was coupled with 1 equivalent (based on the charge
size.fwdarw.5 .mu.mol) of 5-TAMRA-NHS
(5-carboxytetramethylrhodamine succinimidyl ester) in DMF. The
reaction time was 8 hours at room temperature. After the labeling,
the resin was washed. This results in the following intermediate
product: 1
[0104] Coupling of a Linker to the Labeled Peptide:
[0105] After Fmoc cleavage with 20% piperidine in DMF, the labeled
peptide 1 was modified with a linker
(4-(N-maleimidomethyl)cyclohexane-1-carboxyl- ic acid
N-hydroxy-succinimide ester) to form the corresponding maleimide.
For the coupling of the linker, 2 .mu.mol of peptide resin (m=3.7
mg) was employed. Two equivalents of linker (based on the charge
size) in DMF was charged onto the resin. The reaction time was 8
hours at room temperature. After washing the resin with
3.times.DMF, 3.times.DMF/DCM (1:1), 3.times.DCM and
3.times.tert-butyl methyl ether, the intermediate product was
cleaved from the resin with TFA/TIPS/H.sub.2O (95%/2.5%/2.5%). The
cleaving time was 2.5 hours at room temperature. Thus, the
following intermediate product is obtained: 2
[0106] The purification of the intermediate product was effected by
HPLC. The mobile solvents employed were water+0.1% TFA (A) and
methanol (B). A column (Waters, Symmetry 100, RP-18, 5 .mu.m, 150
mm.times.19 mm) having a flow rate of 18 ml/min was used. The
purification was effected with the following gradient: 0
min.fwdarw.10% B, 5 min.fwdarw.30% B, 45 min.fwdarw.70% B, 50
min.fwdarw.100% B. The characterization of the intermediate product
was effected by LC-MS, MALDI-TOF-MS and UV/VIS spectroscopy.
[0107] Coupling of the Maleimide-Peptide1-5-TAMRA to DNA:
[0108] The intermediate product formed was converted to the desired
final product using the lyophilized DNA double strand which was
5'-thiol-modified at one strand. 3
[0109] Thus, the maleimide-peptide1-5-TAMRA (42 nmol) was taken up
in 50 .mu.l of 10 mM sodium phosphate buffer, pH 7.5. The number of
equivalents of the peptide, based on the DNA, is 4. Thus, 10.4 nmol
of DNA in 10 .mu.l of H.sub.2O was employed. The reaction time was
5 hours at 25.degree. C. 4
[0110] The product was purified by HPLC over a gel column
(Phenomenex, Biosep-SEC-S 2000, 300 mm.times.4.6 mm) with a flow
rate of 0.15 ml/min at 12.degree. C. An isocratic run with 10 mM
sodium phosphate buffer, pH 7.5, was performed over 45 minutes. The
characterization of the product was effected by UV/VIS
spectroscopy, fluorescence spectroscopy, polarization and
anisotropy determinations. The purity was established by an
analytical run through the gel column.
[0111] Thus, the substrate specific for caspase 3 comprises:
Asp-Glu-Val-Asp*-Gly, where Asp-Glu-Val-Asp is the recognition
sequence of the protease and the cleavage is effected after
Asp*.
EXAMPLE 2
Synthesis of a Caspase-8 Specific Substrate (Peptide No. 2)
[0112] The peptide with the sequence
H-Gly-Ile-Glu-Thr-Asp-Gly-Lys-OH was prepared by a standard
solid-phase synthesis (Fmoc strategy). As the resin, Rink Amide
MBHA resin with a loading of 0.54 mmol/g was used. A charge size of
20 .mu.mol was selected (37.0 mg). The activation of the amino
acids was effected with 5 equivalents of HATU
([O-(7-azabenzotriazol-1-yl)-1,1,3,3-tetramethyl-uronium
hexafluorophosphate]) and 10 equivalents of DIPEA
(N-ethyldiisopropylamin- e) in DMF (N,N-dimethylformamide). This
yields the following amounts per coupling: 100 .mu.mol HATU (38.0
mg) and 200 .mu.mol DIPEA (34.0 .mu.l). The volume of the solvent
was 5 ml per g of resin. Five equivalents of amino acid was
employed. The reaction time was twice 1 hour (double coupling) at
room temperature. The cleavage of the Fmoc protective group
(fluorenylmethoxycarbonyl) was performed with 20% piperidine in
DMF. The cleavage time was twice 15 minutes. Each time after the
couplings, and also after the Fmoc cleavage, the resin was washed
with 3.times.DMF, 2.times.DMF/DCM (dichloromethane) [1:1],
3.times.DMF reagent grade. The Fmoc protective group on the N
terminus was not removed. Thus, after the couplings of
Fmoc-Lys(Mtt)-OH, Fmoc-Gly-OH, Fmoc-Asp(OtBu)-OH, Fmoc-Thr(tBu)-OH,
Fmoc-Glu(OtBu)-OH, Fmoc-Ile-OH and Fmoc-Gly-OH, the following
sequence results: Fmoc-Gly-Ile-Glu(OtBu)-Thr(tBu)-Asp(OtBu)-Gly-
-Lys(Mtt)-resin.
[0113] Coupling of the Dye to Peptide 2:
[0114] For the labeling, 5 .mu.mol of peptide-charged resin (9.3
mg) was employed. From the immobilized, completely protected
Fmoc-GIETDGK-OH, the Mtt (4-methyl-trityl) protective group on
lysine was removed with 1 ml of 30% HFIP
(1,1,1,3,3,3-hexafluoro-2-propanol) in DMF. Thereafter, washings
were performed six times with 1 ml each of 30% HFIP in DMF. The
subsequent washing was again effected with 3.times.DMF,
2.times.DMF/DCM, 3.times.DMF reagent grade. The primary amine
formed was coupled with 1 equivalent (based on the charge
size.fwdarw.5 .mu.mol) of 5-TAMRA-NHS
(5-carboxytetramethylrhodamine succinimidyl ester) in DMF. The
reaction time was about 8 hours (over night) at room temperature.
This now resulted in the following intermediate product: 5
[0115] Coupling of a Linker to the Labeled Peptide 2:
[0116] After Fmoc cleavage with 20% piperidine in DMF, the peptide
2 was modified with a linker
(4-(N-maleimidomethyl)cyclohexane-1-carboxylic acid
N-hydroxy-succinimide ester) to form the corresponding maleimide.
For the coupling of the linker, 2 .mu.mol of peptide resin (m=3.7
mg) was employed. Two equivalents of linker (based on the charge
size) in DMF was charged onto the resin. The reaction time was 8
hours at room temperature. After washing the resin with
3.times.DMF, 3.times.DMF/DCM (1:1), 3.times.DCM and 3.times.
tert-butyl methyl ether, the intermediate product was cleaved from
the resin with TFA/TIPS/H.sub.2O (95%/2.5%/2.5%). The cleaving time
was 2.5 hours at room temperature. Thus, the following intermediate
product was obtained: 6
[0117] The purification of the intermediate product was effected by
HPLC. The mobile solvents employed were water+0.1% TFA (A) and
methanol (B). A column (Waters, Symmetry 100, RP-18, 5 .mu.m, 150
mm.times.19 mm) having a flow rate of 18 ml/min was used. The
purification was effected with the following gradient: 0
min.fwdarw.10% B, 5 min.fwdarw.30% B, 45 min.fwdarw.70% B, 50
min.fwdarw.100% B. The characterization of the intermediate product
was effected by LC-MS, MALDI-TOF-MS and UV/VIS spectroscopy.
[0118] Coupling of the Maleimide-Peptide2-5-TAMRA to DNA:
[0119] The intermediate product formed was converted to the desired
final product using the lyophilized 5'-thiol-modified DNA double
strand. 7
[0120] Thus, the maleimide-peptide2-5-TAMRA (n=42 nmol) was taken
up in 50 .mu.l of 10 mM sodium phosphate buffer, pH 7.5. The number
of equivalents of the peptide, based on the DNA, is 4. Thus, 10.4
nmol of DNA in 10 .mu.l of H.sub.2O was employed. The reaction time
was 5 hours at 25.degree. C. This yielded the following final
product: 8
[0121] The product was purified by HPLC over a gel column
(Phenomenex, Biosep-SEC-S 2000, 300 mm.times.4.6 mm) with a flow
rate of 0.15 ml/min at 12.degree. C. An isocratic run with 10 mM
sodium phosphate buffer, pH 7.5, was performed over 45 minutes. The
characterization of the product was effected by UV/VIS
spectroscopy, fluorescence spectroscopy, polarization and
anisotropy determinations. The purity was established by an
analytical run through the gel column.
[0122] Thus, the substrate specific for caspase 8 comprises:
Ile-Glu-Thr-Asp*-Gly, where Ile-Glu-Thr-Asp is the recognition
sequence of the protease and the cleavage is effected after
Asp*.
EXAMPLE 3
Ultrahigh-Throughput Screening (uHTS) for Inhibitors for
Identifying Inhibitors of the Cysteine Protease Caspase-3 ("Drug
Discovery")
[0123] Apoptosis (programmed cell death, PCD) is a phenomenon which
can be observed under physiological and pathological conditions.
Apoptosis is the main form of cell death in eukaryotic organisms.
It is found, inter alia, in the development of an embryo and in
metamorphosis processes. In certain diseases (Alzheimer's, tumors,
auto-immune diseases), the apoptotic process is disturbed. Key
molecules in the apoptotic cascade are the so-called caspases.
Therefore, inhibitors or activators of the caspases would be
valuable for treating patients which suffer from a misregulation of
apoptosis.
[0124] The cysteine protease caspase-3 is a central mediator of
apoptosis in a wide variety of cells. A selective caspase-3
inhibitor could be employed for therapy, for example in strokes, in
organ transplantations, in Parkinson's disease and in amyotrophic
lateral sclerosis (ALS).
[0125] Therefore, the substrate described in Example 1 was also
successfully employed for "ultrahigh-throughput screening" (uHTS)
for inhibitors for identifying inhibitors of caspase-3 ("drug
discovery"). The execution and results of this screening campaign
are further described in the legend of FIG. 19.
EXAMPLE 4
Selectivity Determination of Caspase-3 Inhibitors Described in
Example 3
[0126] The caspase-8 substrate described in Example 2 was employed
for determining the selectivity of the caspase-3 inhibitors
identified in the ultrahigh-throughput screening (uHTS). The method
for the molecular-weight-sensitive detection of an enzyme-catalyzed
cleavage reaction as already employed for caspase-3 could be
successfully employed also in a caspase-8 assay.
Sequence CWU 1
1
3 1 7 PRT Artificial Sequence Synthesized 1 Gly Asp Glu Val Asp Gly
Lys 1 5 2 7 PRT Artificial Sequence Synthesized 2 Gly Ile Glu Thr
Asp Gly Lys 1 5 3 15 DNA Artificial Sequence Synthesized 3
ccccaccacc acccc 15
* * * * *