Gelatin degradation assay reveals MMP-9 inhibitors and function of O-glycosylated domain

Abstract

To establish a novel, sensitive and high-throughput gelatinolytic assay to define new inhibitors and compare domain deletion mutants of gelatinase B/matrix metalloproteinase (MMP)-9.
Fluorogenic Dye-quenched (DQ)™-gelatin was used as a substrate and biochemical parameters (substrate and enzyme concentrations, DMSO solvent concentrations) were optimized to establish a high-throughput assay system. Various small-sized libraries (ChemDiv, InterBioScreen and ChemBridge) of heterocyclic, drug-like substances were tested and compared with prototypic inhibitors.
First, we designed a test system with gelatin as a natural substrate. Second, the assay was validated by selecting a novel pyrimidine-2,4,6-trione (barbiturate) inhibitor. Third, and in line with present structural data on collagenolysis, it was found that deletion of the O-glycosylated region significantly decreased gelatinolytic activity (k(cat)/k(M) ± 40% less than full-length MMP-9).
The DQ™-gelatin assay is useful in high-throughput drug screening and exosite targeting. We demonstrate that flexibility between the catalytic and hemopexin domain is functionally critical for gelatinolysis.

Full text

Gelatin degradation assay reveals MMP-9 inhibitors and
function of O-glycosylated domain
Jennifer Vandooren, Nathalie Geurts, Erik Martens, Philippe E Van den Steen, Steven De Jonghe, Piet Herdewijn,
Ghislain Opdenakker
Jennifer Vandooren, Nathalie Geurts, Erik Martens, Philippe
E Van den Steen, Ghislain Opdenakker, Laboratory of Im-
munobiology, Rega Institute for Medical Research, University
of Leuven, Minderbroederstraat 10, Leuven B-3000, Belgium
Steven De Jonghe, Piet Herdewijn, Medicinal Chemistry,
Rega Institute for Medical Research, University of Leuven,
Minderbroederstraat 10, Leuven B-3000, Belgium
Author contributions: Vandooren J performed the majority
of the experiments and wrote the majority of the manuscript;
Geurts N, Martens E and Van den Steen PE performed the ex-
periments and assisted in writing the manuscript; De Jonghe
S and Herdewijn P provided the ChemBridge, ChemDiv and
InterBioScreen compound library and were involved in study
design; Opdenakker G co-ordinated the study and was involved
in study design and writing and editing the manuscript.
Supported by A postdoctoral fellow of the Belgian Fund for
Scientic Research (F.W.O. Vlaanderen) (Van den Steen PE); A
research assistant of the F.W.O. Vlaanderen (Geurts N)
Correspondence to: Ghislain Opdenakker, MD, PhD, Profes-
sor, Laboratory of Immunobiology, Rega Institute for Medical
Research, University of Leuven, Minderbroederstraat 10, Leuven
B-3000, Belgium. ghislain.opdenakker@rega.kuleuven.be
Telephone: +32-16-337341 Fax: +32-16-337340
Received: September 17, 2010 Revised: November 18, 2010
Accepted: November 25, 2010
Published online: January 26, 2011
Abstract
AIM: To establish a novel, sensitive and high-through-
put gelatinolytic assay to dene new inhibitors and com-
pare domain deletion mutants of gelatinase B/matrix
metalloproteinase (MMP)-9.
METHODS: Quenched Dye-quenched (DQ)™-gelatin
was used as a substrate and biochemical parameters
(substrate and enzyme concentrations, DMSO solvent
concentrations) were optimized to establish a high-
throughput assay system. Various small-sized libraries
(ChemDiv, InterBioScreen and ChemBridge) of hetero-
cyclic, drug-like substances were tested and compared
with prototypic inhibitors.
RESULTS: First, we designed a test system with gelatin
as a natural substrate. Second, the assay was validated
by selecting a novel pyrimidine-2,4,6-trione (barbitu-
rate) inhibitor. Third, and in line with present structural
data on collagenolysis, it was found that deletion of the
O-glycosylated region significantly decreased gelatino-
lytic activity (kcat/kM ± 40% less than full-length MMP-9).
CONCLUSION: The DQ™-gelatin assay is useful in
high-throughput drug screening and exosite targeting.
We demonstrate that exibility between the catalytic and
hemopexin domain is functionally critical for gelatinolysis.
© 2011 Baishideng. All rights reserved.
Key words: Exosite inhibitors; Fluorogenic substrate;
Gelatin; High-throughput screening assays; Matrix me-
talloproteinase-9; Substrate specicity
Peer reviewers: Caroline A Owen, MD, PhD, FRCP Edin, As-
sistant Professor of Medicine, Division of Pulmonary and Criti-
cal Care Medicine, Brigham and Women’s Hospital, 75 Francis
Street, 905 Thorn Building, Boston, MA 02115, United States;
Yan Huang, MD, PhD, Associate Professor, Department of
Medicine, Medical University of South Carolina, 114 Doughty
Street, Room 531, Charleston, SC 29403, United States
Vandooren J, Geurts N, Martens E, Van den Steen PE, De
Jonghe S, Herdewijn P, Opdenakker G. Gelatin degradation as-
say reveals MMP-9 inhibitors and function of O-glycosylated
domain. World J Biol Chem 2011; 2(1): 14-24 Available from:
URL: http://www.wjgnet.com/1949-8454/full/v2/i1/14.htm
DOI: http://dx.doi.org/10.4331/wjbc.v2.i1.14
INTRODUCTION
Matrix metalloproteinases (MMPs) constitute a family of
ORIGINAL ARTICLE
World J Biol Chem 2011 January 26; 2(1): 14-24
ISSN 1949-8454 (online)
© 2011 Baishideng. All rights reserved.
Online Submissions: http://www.wjgnet.com/1949-8454ofce
wjbc@wjgnet.com
doi:10.4331/wjbc.v2.i1.14
World Journal of
Biological Chemistry
W J B C
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Vandooren J
et al
. Gelatinase test for structure-function analysis
more than 25 soluble or membrane bound Zn2+-depen-
dent proteases involved in remodeling of the extracellular
matrix, and in regulation of the function of bioactive
molecules. MMPs are secreted as latent pro-enzymes and
become activated after disruption of the coordination
between the cysteine of the propeptide and the catalytic
zinc (Zn2+) in the active site, for example by proteolysis[1].
This process is described as the cysteine switch model[2].
During normal physiological processes, such as embryo-
genesis, vasculogenesis, wound healing and stem cell mo-
bilization, MMP activities are regulated by transcriptional
regulation, activation and by endogenous inhibitors, such
as the tissue inhibitors of metalloproteinases. Disturbance
of this essential balance between proteinases and natural
inhibitors leads to uncontrolled MMP activities which re-
sults in pathological conditions such as tumor progression
and metastasis, inammation, neurodegenerative, cardio-
vascular and autoimmune diseases[3-6].
MMP inhibitors (MMPIs) have been considered as po-
tential therapeutics for diseases in which excess MMP ac-
tivity is detrimental. The MMPIs, all sharing a zinc binding
group, are categorized into various classes[6], such as the
hydroxamate based MMPIs[7] (e.g. batimastat), the non-hy-
droxamate based MMPIs[8] (e.g. SB-3CT), novel MMPIs[6]
(barbiturates), synthetic peptides and pseudopeptides[9]
(e.g. Regasepin 1) and biotechnological and macromo-
lecular inhibitors of MMPs[10] (e.g. REGA-3G12). Bio-
availability and MMP-specicity are major bottlenecks in
designing MMPIs. The limited success of broad spectrum
inhibitors in clinical trials stimulated research towards the
development of highly sensitive assay methods to screen
for specic MMP activities and to search for selective in-
hibitors[6,11,12].
One of the most studied and structurally most com-
plex members of the MMP family is MMP-9 or gelatinase
B. In contrast to the constitutively expressed MMP-2 or
gelatinase A, MMP-9 expression is induced by various
agonists. After neutrophil activation, MMP-9 is released
from preformed granules[13]. Since many disease states, e.g.
acute inammation, autoimmunity and invasive cancer, are
associated with excess gelatinase B activation, this enzyme
is an interesting and important target for inhibition[6,13,14].
Here we describe a novel, fast and highly sensitive
method for the screening of MMP-9 inhibitors. Dye-
quenched (DQ)™-gelatin consists of quenched FITC-
labeled gelatin which, upon gelatinolytic activity, is con-
verted into bright fluorescent peptides. This reaction is
conveniently used for in situ zymography techniques[15] and
the substrate conversion was parametrically studied in this
work. In contrast to all other MMPs, only gelatinases have
a gelatin-binding fibronectin domain[16]. Hence, compared
to the small uorogenic peptide (FP) (7-methoxycoumarin-
4yl)Acetyl-Pro-Leu-Gly-Leu-[3-(2,4-dinitrophenyl)-L-2,3
diaminopropionyl]-Ala-Arg-NH2 described by Knight
et al[17], DQ™-gelatin mimics the natural substrate to mea-
sure (MMP-9/MMP-2) gelatinolytic activity with high
sensitivity. We studied the catalytic parameters of DQ™-
gelatin conversion by human MMP-9, on the basis of which
a high-throughput assay for rapid screening of MMP-9
inhibitors was established. With this assay we screened li-
braries (ChemDiv, InterBioScreen, ChemBridge) of small
molecules for MMP-9 inhibition. Out of 1612 compounds,
5 inhibited MMP-9 by more than 50% at concentrations be-
low 40 μmol/L. The best selected novel MMP-9 inhibitor
was structurally analogous to an already described MMPI,
RO-28-2653, which belongs to the class of pyrimidine-
2,4,6-triones (barbiturates)[18]. Finally, it was demonstrated
that this assay is useful for MMP exosite studies, because de-
letion of the O-glycosylated domain resulted in signicantly
reduced catalysis of DQ™-gelatin, in comparison with the
activities of the intact MMP-9/gelatinase B.
MATERIALS AND METHODS
Proteins and reagents
Recombinant human full-length proMMP-9 (MMP-9 FL,
92 kDa) as well as mutants lacking the O-glycosylated do-
main (MMP-9∆OG), or the hemopexin domain (MMP-9∆
Hem), or both the O-glycosylated and hemopexin domain
(MMP-9∆OGHem) and a mutant with a point mutation
in the active site (the catalytic Glu402 is mutated into Ala,
rendering the enzyme inactive) and a point mutation in the
OG domain (Cys468 is mutated into Ala) (MMP-9 MutEC)
were expressed in Sf9 insect cells and puried by gelatin-
Sepharose chromatography. Subsequently, the enzymes
were activated by incubation with the catalytic domain of
stromelysin-1/MMP-3. These techniques were performed
as described previously[13,19,20]. The enzymes were always
used in the assays at a concentration of 0.1 nmol/L unless
mentioned otherwise.
For the fluorogenic gelatin assay, DQ™-gelatin was
purchased from Invitrogen (Carlsbad, CA, USA) and dis-
solved in water at 1 mg/mL. For this assay, all solutions
and dilutions were prepared in assay-buffer (50 mmol/L
Tris-HCl pH 7.6, 150 mmol/L NaCl, 5 mmol/L CaCl2
and 0.01% Tween 20). In all experiments, DQ™-gelatin
was used at a concentration of 2.5 μg/mL, unless men-
tioned otherwise.
The uorogenic DQ
™
-gelatin assay
The following general protocol was used for the setup
of a uorogenic DQ™- gelatin assay. To a 96-well plate
(Macro-assay plate (chimney, 96-well, black, clear bottom,
Greiner Bio-one, Frickenhausen, Germany), 0.1 nmol/L
(for a nal volume of 100 μL) of the enzyme was added.
For inhibitor tests, the required amount of inhibitor was
added and the plate was incubated for 30 min at 37℃
(note that in this case the actual concentrations of enzyme
and inhibitor were 1.7 times higher during this incubation
period than in the interval used for substrate conversion).
Subsequently, DQ™-gelatin at a final concentration of
2.5 μg/mL was added. Immediately thereafter, the plate
was placed in the uorescence reader (FL600 Microplate
uorescence reader, Biotek, Highland Park, IL, USA) and
uorescence was measured every 10 min for 2 h at 37℃
(ex. 485 nm/em. 530 nm). In each experiment, both posi-
tive (no inhibitor) and negative (no enzyme) controls were
included. All data were corrected by subtraction of their
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respective negative controls. Graphs and calculations were
obtained with Prism 5 (GraphPad Software, Inc.). For the
calculation of substrate molarities we used an approxi-
mate molecular weight of 100 000 g/mol.
Optimization of the uorogenic gelatin assay
Concentration ranges of both the full length enzyme (MMP-9
FL) and substrate (DQ™-gelatin) were tested. MMP-9 FL
was serially diluted 1/3 starting with a concentration of
4 nmol/L. The substrate was diluted by 1/2, starting with
40 μg/mL (0.4 μmol/L) DQ™-gelatin. As a negative con-
trol, each substrate dilution, without enzyme and in assay
buffer, was always included as a control for spontaneous
substrate conversion.
Analysis of enzyme kinetics of MMP-9 FL and MMP-9
mutants using DQ
™
-gelatin
MMP-9 FL, MMP-9 ∆Hem, MMP-9 ∆OG, MMP-9 ∆
OGHem and MMP-9 mutEC were used at a concentra-
tion of 1 nmol/L. Each enzyme form was tested at a range
of substrate concentrations (40 μg/mL to 0.075 μg/mL
in a 1/2 dilution series). For each enzyme variant, the cor-
responding kinetic parameters and kinetic graphs were
calculated.
Assay validation with a range of known protease
inhibitors
A random set of available protease inhibitors was tested for
their potential MMP-9 FL inhibition in our uorescent gela-
tin assay. Details of the used inhibitors are summarized in
Table 1. A rst screening was carried out with all compounds
at a concentration of 20 μmol/L. After the initial screening,
the active compounds were tested in a 1/2 dilution series
starting at the highest concentration of 20 μmol/L.
The inuence of DMSO on the uorogenic gelatin assay
In view of the fact that hydrophobic compounds are often
dissolved in DMSO, and 10% DMSO disrupts the interac-
tion between gelatin and MMP-9[13], we evaluated the high-
est concentration of DMSO that may be used without in-
terfering with the test system. Prior to the enzymatic tests,
a series of DMSO dilutions were added to the 96-well
plate containing MMP-9 FL and DQ™-gelatin. Negative
controls were included, containing the used DMSO con-
centration and 2.5 μg/mL DQ™-gelatin.
High-throughput screening for MMP-9 inhibition with the
use of the uorogenic gelatin assay
The compound library: The compound library con-
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Table 1 Set of used protease inhibitors in control experiments
Inhibitor (%
inhibition)
Alternative name MW
(g/mol)
Target Mechanism Ref.
Aprotinin
(5%)
Bovine pancreatic trypsin inhibitor Approxi-
mately
6500
Serine proteases including plasmin,
tissue plasminogen activator,
kallikrein and thrombin
Nonspecic protease inhibitor [33,34]
Batimastat
(94%)
BB-94; [4-(N-hydroxyamino)-2R-isobutyl-
3S-(thiopen-2-ylthiomethyl)succinyl]-L-
phenylalanine-N-methylamide
478 MMP-1, -2, -3, -7 and -9 Peptide backbone similar to
the cleavage site in collagen (=
peptidomimetic inhibitor)
[6,9,35-37]
TACE (MMP IC50 = 10-30 nmol/L)
Benzamidine
(0%)
- 120 Trypsin, plasmin and thrombin Competitive inhibitor [36]
Bestatin (0%) [(2S,3R)-3-amino-2-hydroxy-4-
phenylbutanoyl]-L-leucine, Ubenimex
308 Aminopeptidase N Slow-binding competitive inhibitor [38-40]
Chymostatin
(0%)
- 608 Proteinases including Serine, thiol,
and carboxyl endopeptidases serine
proteinases, chymotrypsin and
Streptomyces griseus proteinase A,
and several cysteine proteinases
Tetrapeptide analogue, formation of a
hemiacetal or hemithioacetal adduct
with the nucleophilic hydroxy or
thiol group of the serine and cysteine
proteinases
[41,42]
E-64d (0%) Aloxistatin, EST, [2S,3S-trans-
(Ethoxycarbonyloxirane-2-carbonyl)-L
leucine-(3-methylbutyl) amide]
342 Specic thiol protease inhibitor such
as papain and cathepsin B
Interaction with active thiol group [43]
EGCG (33%) Epigallocatechin-3-gallate 458 Multiple targets including MMP-2 and
MMP-9 (MMP IC50 = 8-50 μmol/L)
Blocking the activation mechanism of
MMP-2 induced by concanavalin A
[44-47]
Other exact molecular targets remain
unknown
Pefabloc (0%) AEBSF; 4-(2-Aminoethyl)
benzenesulfonyl uoride hydrochloride
239 Serine protease inhibitor Irreversible inhibition by covalent
interaction with the active-site serine
[48,49]
Pepstatin
(0%)
Isovaleryl-L-valyl-L-valyl-4-amino-3-
hydroxy-6-methylheptanoyl-L- alanyl-4-
amino-3-hydroxy-6-methylheptanoic acid
686 Pepsin and gastricsin (acid proteinase
activity)
-[50]
PMSF (0%) Phenylmethylsulfonyl uoride 174 Serine protease/carboxylesterase
inhibitor
Covalent binding to the serine
residue of the catalytic Ser-His-Asp
triad
[51]
SB-3CT (91%) - 306 MMP-2 and MMP-9 (MMP IC50 =
185-290 nmol/L)
Competitive, mechanism-based,
thiirane-opening mechanism
[8,52]
The chemical compounds were drawn with ACD/ChemSketch Freeware Software and the structure of Aprotinin was obtained from the Protein Data Bank
(PDB ID: 3LDI). The inhibition percentages are shown below the compound names, as obtained in the initial screen with the compounds at 20 μmol/L.
MMP: Matrix metalloproteinase.
Vandooren J
et al
. Gelatinase test for structure-function analysis

tained in total 1612 small-molecule compounds (MW ap-
proximately 300 g/mol). 555 were purchased from Chem-
Div (San Diego, CA, USA), 360 from InterBioScreen Ltd.
(Moscow, RUS) and 697 from ChemBridge Corporation
(San Diego, CA, USA). All compounds were first dis-
solved in DMSO (concentration of 10 mmol/L). The
compounds were prediluted in assay buffer.
Initial screening: All compounds were tested at a nal
concentration of 20 μmol/L. For each compound a nega-
tive control was included (the enzyme was replaced by
assay buffer). For each plate a positive enzyme control
was included (no inhibitor but an equivalent amount of
DMSO; 0.2%). The data for each compound were cor-
rected with its negative control and compared with the
positive control, giving a percentage decrease in uores-
cence. The compounds which showed more than 20%
inhibitory activity were tested twice more for corrobora-
tions. Inhibition percentages were calculated based on the
uorescence measurement after 2 h.
Dose response: All active compounds were tested again
but at multiple concentrations (1/2 dilution starting at a
concentration of 40 μmol/L and ending at a concentra-
tion of 0.312 μmol/L). For each compound the IC50 was
calculated and a dose response plot was drawn.
FP assay
If necessary, extra information on catalysis by MMP-9
was obtained by using a second FP substrate; {DNP-
Pro-Cha-Gly-Cys(Me)-His-Ala-Lys(N-Me-Abz)-NH2 (ex.
365 nm/em. 450 nm, MM: 1077.2/EMD/Calbiochem®,
Darmstadt, Germany). This substrate is cleaved to a single
cleavage product, Dnm-Pro-Cha-Gly. It can be used for
the evaluation of MMP-9 inhibitors in a uorescent plate
reader[21 ]. MMP-9 FL was used at a concentration of
1 nmol/L (vs 0.1 nmol/L in the uorogenic gelatin assay)
and the FP was used at a concentration of 10 μg/mL (vs
2.5 μg/mL in the uorogenic gelatin assay). Fluorescence
was measured every 10 min for 2 h with the uorescence
reader (FL600 Microplate fluorescence reader, Biotek,
Highland Park, IL, USA).
RESULTS
Assay optimization and validation
Development of the uorescent gelatin assay: An en-
zyme assay was developed with DQ™-gelatin as substrate.
By using different substrate/enzyme concentrations, we
determined the sensitivity of the assay and the optimal
substrate concentration. Figure 1 shows a 3D surface
representation of the signal (measured uorescence at the
respective enzyme and substrate concentration) to noise
(fluorescence measured in wells only containing DQ™-
gelatin = spontaneous degradation) ratio at variable sub-
strate and enzyme concentrations. At lower enzyme con-
centrations the signal-to-noise ratio dropped signicantly.
Based on a compromise between a good detection signal
and minimal enzyme use, we selected the concentration
of 0.1 nmol/L as the enzyme concentration for further
testing in high-throughput drug screening. The yellow line
(Figure 1A) shows this optimal enzyme concentration and
Figure 1B shows uorescence as a function of gelatinase
B concentration with a fixed substrate concentration of
2.5 μg/mL.
To determine the optimal substrate concentration, we
made similar compromises and dened 2.5 μg/mL DQ™-
gelatin as the optimal substrate concentration. This con-
centration is represented by the red line in Figure 1A and
again in Figure 1C. By using only 2.5 μg/mL substrate,
MMP-9 FL levels below 0.1 nmol/L (corresponding to
920 pg) could still be detected.
Standard: To determine the relationship between uores-
cence and product formation a standard curve was con-
structed. A 1/2 dilution series of the substrate was prepared
and ranged from 10 μg/mL DQ™-gelatin to 0.01 μg/mL
DQ™-gelatin. In one dilution series, 0.2 nmol/L of MMP-9
was added. A negative control for spontaneous degrada-
tion was included. When all substrate was converted to
product, when no more changes in uorescence were ob-
served, the uorescence was measured. By using a linear
regression analysis we determined that the fluorescence
was proportional to the converted substrate concentration
(in μmol/L) (Figure 2). 46 h later, another reading was
done, which showed that fluorescence dropped slightly
with time (less than 6%). With the use of a Wilcoxon
signed rank test we found that the difference between
both graphs was signicant (P = 0.0269).
Enzyme kinetics of MMP-9 FL and MMP-9 mutants
using DQ™-gelatin: MMP-9 FL, MMP-9 ∆Hem, MMP-9
∆OG, MMP-9 ∆OGHem and MutEC activity were tested
using the uorescent gelatin assay. The Michaelis-Men-
ten curves and Vmax and kcat/KM parameters are shown in
Figure 3 and Table 2. Deletion of the Hemopexin or the
Hemopexin and O-glycosylated domain seemed to have
least inuence on the enzyme efciency. kcat/KM was re-
duced by ± 10% (relative to the parameters obtained for
MMP-9 FL). As expected, the inactive MMP-9 MutEC did
not show any signicant activity. Interestingly, the MMP-9
∆OG was less active (kcat/KM ± 40% less efcient) than
the mutant lacking both O-glycosylated and hemopexin
domains, suggesting an important role for the linker (OG)
domain for MMP-9 gelatinolytic activity (vida infra). This
OG-domain is a highly glycosylated and proline-rich
sequence of approximately 64 amino acids. It links the
active site and hemopexin domain, but its exact function
remains elusive[19].
Assay validation with a range of known protease inhib-
itors: Initial screening at 20 μmol/L inhibitor concentration
showed that only SB-3CT, BB-94 and EGCG signicantly
lowered MMP-9 activity (for inhibition percentages, Table 1).
As also shown in Table 1, SB-3CT and BB-94 are two in-
hibitors known for their inhibitory activity against MMPs.
In our assay, BB-94 and SB-3CT impaired MMP-9 FL
gelatinolytic activity in the nmol/L range, with BB-94 be-
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Vandooren J
et al
. Gelatinase test for structure-function analysis

ing the best inhibitor (Figure 4). EGCG impaired MMP-9
gelatinolytic activity in the μmol/L range.
Inuence of DMSO on the uorogenic gelatin assay:
Since most commercially available compound libraries are
dissolved in DMSO, we tested whether DMSO had an
influence on the assay. This was expected, since DMSO
disrupts the binding of MMP-9 to gelatin[13]. Figure 5A
shows the enzyme velocity as a function of DMSO con-
centration. With the used conditions, DMSO signicantly
inhibited the enzyme activity with an IC50 of 56 mmol/L
DMSO. Therefore, we tested different DMSO concen-
trations to define a low concentration at which the net
inhibitory effect could still be measured (Figure 5B). At a
concentration of 44 mmol/L DMSO (0.3% DMSO), the
interference was ± 42% of the signal and at 22 mmol/L
(0.15% DMSO), the DMSO interference was ± 24%.
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2000
1500
1000
500
0
Fluorescence
0.1 nmol/L MMP-9
2.5 μg/mL DQ™-gelatin
0 1 2 4
MMP-9 (nmol/L)
4000
3000
2000
1000
0
Fluorescence
2.5 μg/mL DQ™-gelatin
0.1 nmol/L MMP-9
0 10 20 30 40
DQ™-gelatin (μg/mL)
14
12
10
8
6
4
2
0
Signal/noise
40
20
10
5
2.5
1.25
0.625
0.3125
DQ™-gelatin (μg/mL)
0.000152
0.000457
0.001372
0.004115
0.037037
0.111111
0.333333
0.012346
1.000000
3.000000
MMP-9 (nmol/L)
A
CB
Figure 1 Optimization of enzyme and substrate concentrations. A: 3D surface representation of the signal uorescence divided by the noise uorescence (signal/
noise) as a function of the enzyme [matrix metalloproteinase (MMP)-9 FL] and substrate (DQ™-gelatin) concentration. Data were obtained after an incubation period
of 2 h. The red line represents the signal-to-noise ratio as a function of variable enzyme concentration and at a constant substrate concentration of 2.5 μg/mL. The
yellow line shows the signal-to-noise ratio at variable substrate concentrations and at a constant enzyme concentration of approximately 0.1 nmol/L. These enzyme
and substrate concentrations were chosen for further testing; B: The uorescence signal (light blue surface) and noise uorescence (dark blue surface) under different
enzyme concentrations and at a constant substrate concentration of 2.5 μg/mL is shown; C: The uorescence signal (light blue surface) and noise uorescence (dark
blue surface) under different substrate concentrations and at a constant concentration of 0.1 nmol/L MMP-9 FL is plotted.
6000
4000
2000
0
Fluorescence
Standard (12 h):
y = x48 200 ± 90.25
Standard (46 h):
y = x45 150 ± 108.7
0.00 0.02 0.04 0.06 0.08 0.10
DQ™-gelatin (μmol/L)
Figure 2 Standard curves of the correlations between uorescence and
product (DQ™-gelatin) concentration. The full line represents a linear regres-
sion of uorescence data obtained after 12 h incubation. The dashed line repre-
sents a linear regression of the uorescence data obtained after 46 h. The drop
in uorescence was signicant (P < 0.05). Data represent mean ± SE (n = 32).
Vandooren J
et al
. Gelatinase test for structure-function analysis

Therefore, in subsequent experiments the DMSO concen-
tration was always kept as low as possible. We recommend
keeping the DMSO concentration at 0.2% or lower, if
possible.
High-throughput screening for MMP-9 inhibition with the
use of the uorogenic gelatin assay
Initial screening: The results of the initial screening are
shown in Table 3. Four hundred and fifty seven com-
pounds reduced the uorescence within a range of 1%-10%
compared to the control with an equivalent amount of
DMSO. We assumed that these small percentages were in
the error-range of the assay. One hundred and twenty six
compounds reduced the signal between 11%-20% and 37
compounds inhibited the uorescence signal by more than
20%. The increase in uorescence as a function of incuba-
tion time with and without an active compound is shown
in Figure 6. All assays were replicated three times and in-
hibitory compounds were defined on the basis of thrice
concordant results.
Further testing of active compounds: Out of the 37
MMP-9 inhibitors, 5 showed an IC50 value below 40 μmol/L.
The dose response graphs, IC50s and molecular structures
are shown in Figure 7. The two most active compounds
had an IC50 of 15 μmol/L and 19 μmol/L. One of these
compounds was compound 6994210 (ChemBridge) or
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Table 2 Michaelis-Menten parameters for different enzyme variants
MMP-9 FL MMP-9 ∆Hem MMP-9 ∆OGHem MMP-9 MMP-9 MutEC
Vmax (nmol/L per minute) 3.643 2.686 2.314 1.117 -
kcat/KM (nmol/L per minute) 0.097 0.086 0.088 0.058 -
Goodness of t (R2) 0.9977 0.9900 0.9861 0.9470 0.7096
Difference from MMP-9 FL - P = 0.0207 P = 0.0049 P = 0.0020 P = 0.0010
The corresponding Michaelis-Menten curves are shown in Figure 3. The P-values were calculated with a Wilcoxon signed rank test. The Vmax and KM
values could not be determined for the matrix metalloproteinase (MMP)-9 MutEC.
4
3
2
1
0
Enzyme velocity
(nmol/L product/min)
MMP-9 DOGHemb
MMP-9 DHema
MMP-9 FL
MMP-9 DOGb
MMP-9 MutECb
0 100 200 300 400
DQ™-gelatin (nmol/L)
Figure 3 Enzyme velocity as a function of the amount of substrate
(nmol/L DQ™-gelatin) (at a concentration of 1 nmol/L). Prism 5 (GraphPad
Software, Inc) was used to t the data with the corresponding Michaelis-Menten
curve and to calculate the Vmax and KM values (Table 2). By using a Wilcoxon
signed rank test we determined that all mutants had a significantly different
activity from that of matrix metalloproteinase (MMP)-9 FL (aP < 0.05, bP < 0.01).
The graphs are representative of three independent experiments.
2.0
1.5
1.0
0.5
0.0
Enzyme velocity (nmol/min)
0.0 0.5 1.0 1.5
Log (SB-3CT) (μmol/L)
SB-3CT
2.0
1.5
1.0
0.5
0.0
Enzyme velocity (nmol/min)
0.0 0.5 1.0 1.5
Log (BB-94) (μmol/L)
BB-94
Enzyme velocity (nmol/min)
0.0 0.5 1.0 1.5
Log (EGCG) (μmol/L)
EGCG
2.0
1.8
1.6
1.4
1.2
1.0
Figure 4 Dose-response curves of the inhibitory activities of SB-3CT,
BB-94 and EGCG. With GraphPad prism software, the IC50 of SB-3CT and
BB-94 was predicted to be in the nmol/L range and the IC50 of EGCG in the
μmol/L range. The data points correspond to inhibitor concentrations of: 1.25,
2.5, 5, 10 and 20 μmol/L, respectively. The horizontal line shows the enzyme
velocity in the absence of inhibitor.
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5-[(2-hydroxy-6-methyl-3-quinolinyl)methylene]-2,4,-
(1H,3H,5H)-pyrimidinetrione. Pyrimidine-triones have
already been described as metalloproteinase inhibitors.
They are known for their zinc-chelating activity and
substituents have already been optimized to comparable
inhibitory efciency as batimastat (IC50 = 10 nmol/L for
MMP-2 and IC50 of 12 nmol/L for MMP-9) and specic-
ity for MMP-2 and MMP-9[18]. Therefore, the activity of
compound 6994210 may be caused by its zinc-binding
pyrimidine-trione group. Tochowicz et al[22] described
the interaction of compound RO-206-0222 (a barbitu-
ric acid inhibitor) with the MMP-9 catalytic site (of an
inactive E402Q mutant). This compound is a barbituric
acid derivative with two substituents: a phenoxyphenyl
and a pyrimidine-piperazine and gives a tight binding
in the active site of this MMP-9. The barbiturate ring
chelates the catalytic zinc and orients both substituents
into their respective subsites[22]. Intriguingly, compound
0204-5272 (ChemDiv) or N-[4-(6-methyl-1,3-benzothia-
zol-2-yl)phenyl]tetrahydrothiophene-2-carboxamide did
not show any similarity with existing inhibitors.
Compound 5805026 (ChemBridge) or N-(4-ethoxy-
8-methyl-2-quinazolinyl)guanidine was the third most active
compound (IC50 = 25 μmol/L). Compound STOCK1S-
82005 (InterBioScreen) displayed an IC50 of 27 μmol/L
100
80
60
40
20
0
% Activity
22 mmol/L
44 mmol/L
88 mmol/L
IC50 = 56 mmol/L
-2 -1 0 1
Log nal (DMSO) (mol/L)
Fluorescence
44 mmol/L DMSO
0 100 200 300
t
/min
1200
1000
800
600
400
200
0
Fluorescence
22 mmol/L DMSO
0 100 200 300
t
/min
1200
1000
800
600
400
200
0
Fluorescence
88 mmol/L DMSO
0 100 200 300
t
/min
1200
1000
800
600
400
200
0
DC
BA
Figure 5 The inuence of DMSO on the conversion of DQ™-gelatin into uorogenic gelatin by matrix metalloproteinase-9. A: By using a non-linear t, an
IC50 of 56 mmol/L DMSO (R2 = 0.9867) (horizontal dotted line) was determined. The vertical striped lines represent the concentrations used in panels B, C and D; B:
Inuences of 88 mmol/L (0.6% DMSO), 44 mmol/L (0.3% DMSO) and 22 mmol/L DMSO (0.15% DMSO) on the uorescence changes at different time points. The
solid lines show the uorescence evolutions measured in the absence of DMSO, the striped lines show the uorescence measured in the presence of DMSO at the
indicated concentrations. The vertical dotted lines represent uorescence data measured after 2 h.
Table 3 Results of the initial screening of 1612 compounds
Fluorescence decrease
1%-10% 11%-20% > 20%
ChemDiv (555 compounds) 217 57 4
(Max = 33%)
InterBioScreen (360 compounds) 106 19 18
(Max = 100%)
ChemBridge (697 compounds) 134 50 15
(Max = 100%)
800
600
400
200
0
Fluorescence
20 40 60 80 100 120
t
/min
59% decrease
Figure 6 Typical increase in uorescence (per time unit) between the posi-
tive control catalysis and in the presence of an active compound (Chem-
Bridge, 6994210). The percentage inhibition was measured after 2 h.
Positive control catalysis
Active compound
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Compound 0204-5272 (Chemdiv)
2.0
1.5
1.0
0.5
0.0
Velocity (nmol/min)
Compound 0204-5272 (Chemdiv)
IC50 = 14.73 μmol/L
-1.0 -0.5 0.0 0.5 1.0 1.5 2.0
Log (0204-5272)
Autouorescence
S
N
S
NH
O
H3C
2.0
1.5
1.0
0.5
0.0
8
6
4
2
0
D Fluorescence/min
Compound 6994210 (ChemBridge)
-1.0 -0.5 0.0 0.5 1.0 1.5 2.0
Log (6994210)
Velocity (nmol/min)
Compound 6994210 (ChemBridge)
IC50 = 18.55 μmol/L
-1.0 -0.5 0.0 0.5 1.0 1.5 2.0
Log (6994210)
NHHN
O
O
O
NOH
H3C
2.0
1.5
1.0
0.5
0.0
Velocity (nmol/min)
Compound 5805026 (ChemBridge)
IC50 = 24.83 μmol/L
-1.0 -0.5 0.0 0.5 1.0 1.5 2.0
Log (5805026)
Autouorescence
Compound 5805026 (ChemBridge)
CH3
CH3
O
N
N
NH
NH
NH2
8
6
4
2
0
D Fluorescence/min
Compound STOCK1S-82005 (InterBioScreen)
-1.0 -0.5 0.0 0.5 1.0 1.5 2.0
Log (STOCK1S-82005)
2.0
1.5
1.0
0.5
0.0
Velocity (nmol/min)
Compound STOCK1S-82005 (InterBioScreen)
IC50 = 27.48 μmol/L
-1.0 -0.5 0.0 0.5 1.0 1.5 2.0
Log (STOCK1S-82005)
O
CH3
N
N
N
N
H
F
2.0
1.5
1.0
0.5
0.0
Velocity (nmol/min)
Compound C920-1611 (ChemDiv)
IC50 = 29.99 μmol/L
-1.0 -0.5 0.0 0.5 1.0 1.5 2.0
Log (C920-1611)
Compound C920-1611 (ChemDiv)
Autouorescence
NH
CH3
O
N
N
S
Cl
Figure 7 Dose-response graph, IC50 and molecular structure of the 5 most active compounds (IC50 < 40 μmol/L) on conversion of DQ™-gelatin and a uo-
rescent peptide by matrix metalloproteinase-9. The results obtained with the DQ™-gelatin assay (including the IC50s) are shown in the left column. The chemical
structures are shown in the central column. Data with the uorescent peptide are shown in the right column.
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and com pound C920-1611 (Chem Div) or N -(2, 4 -
dimethylphenyl)-2-[(2-methyl-1,3-benzothiazol-6-yl)sulfo-
nylamino] acetamide had an IC50 of ± 30 μmol/L. For
these compounds, no structural similarity could be found
with existing MMP small-molecule inhibitors.
Inhibitor testing with the use of a small FP substrate:
As a comparison, we used a different assay with a FP
substrate to test the inhibitory potential of our 5 newly
discovered inhibitors. However, 3 of the 5 compounds
(compound 0204-5272, compound 5805026 and com-
pound C920-1611) were autofluorescent at the wave-
lengths required for this substrate (Figure 7 right column).
In addition, no inhibition was detected for the other two
compounds, illustrating the power of our new assay.
DISCUSSION
The DQ™-gelatin substrate was originally introduced for
the fluorometric determination of gelatinolytic activity
of cancer cells in vitro[23] but was, until now, mainly used
for the in situ demonstration of gelatinolytic activity[15,24,25].
Here, we show that the DQ™-gelatin assay is a useful tool
in many ways for the biochemical study of gelatinolysis
of puried proteases e.g. MMP-9. With low amounts of
substrate (2.5 μg/mL) and enzyme (0.1 nmol/L), MMP-9
activity was determined accurately. For comparison, with
the fluorogenic peptide {DNP-Pro-Cha-Gly-Cys(Me)-
His-Ala-Lys(N-Me-Abz)-NH2, the optimal substrate and
enzyme concentrations were 10 μg/mL and 1 nmol/L,
respectively. Although {DNP-Pro-Cha-Gly-Cys(Me)-His-
Ala-Lys(N-Me-Abz)-NH2 was originally described as a
good peptide for high-throughput screening efforts and
has compatible emission and excitation spectra with most
uorescent plate readers[21], the uorescent signal is not as
sensitive and stable as with the DQ™-gelatin substrate.
In addition, the DQ™-gelatin substrate is a ‘natural’
MMP-9 substrate compared to short peptides. MMP-9
cooperatively binds gelatin with its fibronectin domain
and catalytic site, thereby orienting the substrate into the
catalytic site. The fibronectin domain is, therefore, also
essential for the gelatinolytic activity[26]. With the use of
gelatin as a natural substrate, the possibility exists of nd-
ing inhibitors targeting the fibronectin-like domain and
exclusively impairing gelatinolytic activity, without having
major implications on other MMP-9 proteolytic events.
Previous clinical trials with MMPIs have been somewhat
disappointing. One often invoked reason is the lack of
specicity, since most existing MMPIs target the catalytic
site, which is shown to be highly conserved and, there-
fore, similar amongst MMPs. Presently, attention is more
focused on distal surface residues and accessory domains
(called “MMP allosteric sites” or “exosites”) which may
allocate single or sets of MMPs and would, therefore, be
good targets for specic MMP inhibition[16]. Some efforts
in this direction have been made. Inhibitory peptides of
the MMP-2 collagen binding domain (CBD) have been
identified by Xu et al[27]. These peptides were also active
against MMP-9.
The possibility exists that the described inhibitory
effect of DMSO is related to the fibronectin domain
exosite. Indeed, recombinant MMP-2 CBD binds to gela-
tin and this complex dissociates in the presence of 2%
DMSO[28]. Furthermore, 2% DMSO, which corresponds
to 280 mmol/L, signicantly reduced the gelatinolytic ac-
tivity of MMP-2[29]. Our ndings suggest that 2% DMSO
has an even higher inhibitory effect (> 80% decreased
activity) on MMP-9. This difference may be due to the
known fact that MMP-9/gelatin binding (through the -
bronectin domain) is dependent on cooperativity between
the fibronectin type
Ⅰ and type Ⅱ modules, whereas
MMP-2 can bind gelatin without the need of cooperativ-
ity[28]. Also, in accordance with these ndings for MMP-2,
DMSO had no inuence on MMP-9 processing of a small
peptide substrate, suggesting that the CBD is not required
for positioning such short peptide substrates relative to
the active site[29].
A method for high throughput screening of potentially
selective MMP-13 (collagenase) exosite inhibitors was de-
veloped by Lauer-Fields et al[30]. They used a triple-helical
FRET substrate and found 34 active compounds includ-
ing two pyrimidine-trione derivatives and new compounds
which did not target the MMP-13 catalytic site. With the
DQ™-gelatin assay we tested 1612 small-molecule com-
pounds for their potential inhibition of MMP-9 FL gelati-
nolytic activity. We identied ve compounds with an IC50
below 30 μmol/L. One of these compounds (6994210)
was a pyrimidinetrione derivative. Barbiturates have previ-
ously been identied as Zn2+-binders[6]. We did not trace
the other small-molecules in the existing literature, mak-
ing these compounds additional candidates for further
development towards MMPIs. The finding of an exist-
ing MMP-9 zinc binder by using the DQ™-gelatin assay
endorses the suitability of this assay for high-throughput
drug screening. In line with this, we were able to perfectly
distinguish the three known MMP-9 inhibitors (SB-3CT,
BB-94 and EGCG) out of a set of 11 other protease
inhibitors with specificities for various (other) protease
classes.
Besides the above-mentioned application, the DQ™-
gelatin substrate was also useful in fundamental studies
of MMP-9 action. We tested different MMP-9 mutants
(MMP-9 ∆Hem, MMP-9 ∆OG, MMP-9 ∆OGHem and
MMP-9 MutEC) in the DQ™-gelatin assay. The fact that
the MMP-9 ∆OG mutant form was ± 40% less efficient
than the MMP-9 FL or the MMP-9 ∆OGHem form, sug-
gests an important role for the OG-domain in MMP-9 ge-
latinolytic activity. This has been suggested by Rosenblum
et al[31] on the basis of structural data. With the use of
single-molecule imaging statistical analysis and small-
angle X-ray scattering (SAXS), it was shown that MMP-9
FL is much more flexible than MMP-9 ∆OG. The OG
domain thus lends the MMP-9 molecule flexibility, sup-
porting multiple enzyme conformations[31]. With the use
of atomic force microscopy, it was recently shown that
MMP-9 FL can adopt an extended and a contracted con-
formation, addressed by the OG domain. Upon binding
of collagen, MMP-9 changes from the extended into the
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contracted form, thereby using the flexibility of the en-
zyme O-glycosylated domain to nd an appropriate bind-
ing site[32]. Removal of this exible linker may thus result
in a rigid structure which has fewer degrees of freedom
for interaction with the gelatin substrate. Removal of the
OG domain, also results in direct contact between the
catalytic and hemopexin domains. Our data on in vitro
gelatinolysis demonstrate functionally the importance of
the O-glycosylated domain in comparison with the hemo-
pexin domain, and further underline the possibilities of
the development of allosteric inhibitors.
We conclude that the DQ™-gelatin assay is useful in
high-throughput drug screening and exosite studies of
MMPs. The assay is easily applicable in multi-well plates
and the substrate is compatible with emission and excita-
tion spectra on most uorescent plate readers. In addition,
less autofluorescence of the compounds is measured at
these wavelengths. Because of the high resolution of the
assay, only small amounts of enzyme and substrate are
necessary, which implies low costs. Besides the technologi-
cal advancements, this study provides further insights into
the MMP inhibitory role of DMSO mediated through the
fibronectin domain and functionally defines the O-gly-
cosylated domain as a crucial entity for gelatin substrate
catalysis.
COMMENTS
Background
Matrix metalloproteinases (MMPs) are a family of Zn2+-dependent multidomain
enzymes, involved in pathological processes such as acute and chronic inam-
mation (e.g. rheumatoid arthritis and multiple sclerosis), cancer cell invasion
and metastasis, periodontal diseases, liver and lung diseases. Historically, the
MMPs were classified into gelatinases, collagenases, stromelysins, metallo-
elastases, matrilysins and membrane type MMPs (MT-MMPs), partially based
on substrate conversion. Gelatinase A/MMP-2 and Gelatinase B/MMP-9 repre-
sent the gelatinases, having gelatins as natural substrates.
Research frontiers
Several MMP inhibitors (MMPIs) have been developed over the past 20 years.
However, most clinical trials with MMPIs had poor outcomes and severe side-
effects were observed. Many reasons have been postulated for these results,
but one major problem was low selectivity of the used MMPIs. In order to
increase selectivity, inhibitors that target the distal surfaces of MMPs in addi-
tion to the highly conserved catalytic site, may be more promising. New high-
throughput screening assays which enable the identication of exosite inhibitors
are therefore needed. Instead of commonly used small peptide substrates,
we used high molecular weight gelatin in an attempt to mimic macromolecular
interactions in order to probe exosite interactions.
Innovations and breakthroughs
The present study validates Dye-quenched (DQ)™-gelatin, a uorogenic gelatin
substrate, for high-throughput drug screening of MMPIs. The presented assay
is easy, low cost and has a high resolution. In addition, this assay enables the
identication of exosite inhibitors for gelatinases, since DQ™-gelatin mimics the
natural substrate. Our study also stresses the crucial role of the O-glycosylated
domain in gelatin catalysis and provides further insights into how DMSO inhibits
MMP-9 through the bronectin domain.
Applications
The gelatin degradation assay is useful in fundamental studies of gelatinase ac-
tion and is applicable for high-throughput drug screening of MMPIs. It also has
potential for the identication of exosite inhibitors.
Peer review
The experiments have been carefully performed and the manuscript is clearly
written. A few issue need to be addressed before the paper should be pub-
lished.
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S- Editor Cheng JX L- Editor Webster JR E- Editor Zheng XM
Vandooren J
et al
. Gelatinase test for structure-function analysis