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BioAssay: AID 1215

Thrombin 1536 HTS Dose Response Confirmation

Prothrombin, a 72 kDa blood zymogen (plasma concentration = 2 uM, (1)) is converted to thrombin by factor Xa (FXa) in the prothrombinase complex on platelets by cleavage of R271 and R320. Thrombin then further processes itself by cleavage at R155 and R284 in order to remove prothrombin fragment 1 and fragment 2, which contain the kringle 1 and 2 domains, leaving fully active alpha-thrombin (2). more ..
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AID: 1215
Data Source: PCMD (Thrombin_1536_DR)
BioAssay Type: Confirmatory, Concentration-Response Relationship Observed
Depositor Category: NIH Molecular Libraries Screening Center Network
BioAssay Version:
Deposit Date: 2008-03-07
Modify Date: 2008-11-04

Data Table ( Complete ):           View Active Data    View All Data
BioActive Compounds: 223
Related Experiments
1046Thrombin 1536 HTSScreeningdepositor-specified cross reference: Thrombin 1536 HTS; hits were confirmed in this assay
Molecular Library Screening Center Network (MLSCN)
Penn Center for Molecular Discovery (PCMD)
Assay Provider: Scott L. Diamond, University of Pennsylvania
MLSCN Grant: X01-MH076406-01


Prothrombin, a 72 kDa blood zymogen (plasma concentration = 2 uM, (1)) is converted to thrombin by factor Xa (FXa) in the prothrombinase complex on platelets by cleavage of R271 and R320. Thrombin then further processes itself by cleavage at R155 and R284 in order to remove prothrombin fragment 1 and fragment 2, which contain the kringle 1 and 2 domains, leaving fully active alpha-thrombin (2). alpha-thrombin goes to activate other coagulation factors that are involved in its own production, including the cofactors factor V and factor VIII, as well as activating platelets through the protease activated receptor-1 (PAR-1) (3).

With respect to formation of the secondary blood clot, alpha-thrombin catalyzes activation of fibrinogen to fibrin, cleaving peptides 14-16 amino acids in length, called fibrinopeptides, from the Aalpha and Bbeta subunits of fibrinogen (4). Fibrinogen (plasma concentration = 10.6 uM (5)) is a dimeric protein consisting of three pairs of disulfide-bonded polypeptide chains, referred to as Aalpha, Bbeta, and gamma, which form a complex with a total MW of approximately 340 kDa (6).

Specifically, the sites uncovered by the release of the fibrinopeptides, which are located in central regions of their respective chains, allow for noncovalent multimer formation of fibrin polymers by interactions with complementary central and outer regions of other fibrin monomers, forming an extensive fibrin meshwork. In this way alpha-thrombin produces a fibrin clot that is stabilized by the crosslinking activity of FXIIIa, which is also activated by alpha-thrombin from its inactive zymogen, factor XIII (7). The fibrin monomers produced by alpha-thrombin form a noncovalent meshwork with other fibrin molecules to produce a fibrin clot that stabilizes the primary platelet plug already in place at the site of injury, and reduces the volume of the plug in order to arrest blood loss (8).

HTS was performed using 217,350 compounds of the MLSCN library individually plated into 10ul 1536 compound plates at a concentration of 2.5 mM each, which were diluted 500-fold into 5 ul 1536 well assay plates (final concentration 5 uM each compound). This assay was performed as a counterscreen to compare with a separate HTS campaign to isolate inhibitors of the strong protein-protein interactions among fibrin monomers responsible for fibrin gel formation. Since any inhibitors of the proteolytic activity of alpha-thrombin would inhibit an assay to detect fibrin formation, this counterscreen will identify direct alpha-thrombin inhibitors. The assay used to test for percent inhibition was a fluorescence assay utilizing hydrolysis of Boc-Val-Pro-Arg-AMC, as first described by Morita, et al. (9).

1. F. C. McDuffie et al., Thromb Res 16, 759 (1979).
2. T. Morita, C. M. Jackson, J Biol Chem 261, 4015 (Mar 25, 1986).
3. E. Di Cera, Q. D. Dang, Y. M. Ayala, Cell Mol Life Sci 53, 701 (Sep, 1997).
4. K. Bailey, F. R. Bettelheim, L. Lorand, W. R. Middlebrook, Nature 167, 233 (Feb 10, 1951).
5. Y. Takeda, J Clin Invest 45, 103 (Jan, 1966).
6. H. A. Scheraga, Biophys Chem 112, 117 (Dec 20, 2004).
7. J. E. Folk, S. I. Chung, Adv Enzymol Relat Areas Mol Biol 38, 109 (1973).
8. L. L. Shen, J. Hermans, J. McDonagh, R. P. McDonagh, M. Carr, Thromb Res 6, 255 (Mar, 1975).
9. T. Morita, H. Kato, S. Iwanaga, K. Takada, T. Kimura, J Biochem 82, 1495 (Nov, 1977).

Human alpha-thrombin was purchased from Haematologic Technologies Inc. (Cat no. HCT-0020). Substrate Boc-Val-Pro-Arg-AMC was from Bachem (Cat no. I-1120.0050). Assay buffer consisted of 50 mM Tris, pH 7.5, 150mM NaCl, 0.05% Tween 20. 1536-well black plates were from Corning (Item no. 3728).


alpha-thrombin (5.5 ng/mL) was incubated with Boc-Val-Pro-Arg-AMC substrate (15 uM) in 5 uL of assay buffer (see above) for 30 min at room temperature. Hits from 1536 HTS were confirmed on single compounds by IC50 determination as described below.

IC50 protocol

1.Serial dilute single compounds at 50x concentration in DMSO (16 two-fold dilutions from 2.5 mM to 75 nM)
2.Fill low-volume plate with 4 uL water using Multidrop-micro
3.Add 5 uL assay buffer to columns 1 and 23 using Multidrop-384
4.Add 200 nL of compound (in DMSO from step 1) using 2 transfers of 100 nL with the Evolution 1536 pintool (washed with isopropanol after each transfer)
5.Add 1 uL of Boc-Val-Pro-Arg-AMC substrate (150 uM in 5x assay buffer) using Multidrop-micro
6.Add 5 uL enzyme (11 ng/mL in assay buffer) using Multidrop-384
7.Incubate for 2 hr at room temperature
8.Read fluorescence (excitation 355, emission 460) on Envision reader

Data analysis

IC50 plates contained compounds in columns 3-22, controls (enzyme, no compound) in columns 2 and 24, and blanks (no enzyme) in columns 1 and 23. Each column 3-22 contained 16 two-fold dilutions of a single compound, ranging in concentration from 50 uM to 1.5 nM. Percent activity was calculated for each dilution of each compound from the signal in fluorescence units (FU) and the mean of the plate controls and the mean of the plate blanks using the following equation:

% Activity = 100*((signal-blank mean)/(control mean-blank mean))

Dose response curves of percent activity were fit using XLfit equation 205 (four parameter logistic fit with maximum percent activity and minimum percent activity fixed at 100 and 0, respectively).
Activity scoring

The activity score reported here is based on follow-up IC50 testing on compounds that showed >40% inhibition in the primary HTS:

IC50 scores were calculated as follows:

(1) Score = 5.75 x (pIC50-3), where pIC50 = -log(10) of IC50 in mol/L
(2) For IC50 >50 uM, score was calculated from percent activity at maximum concentration tested in assay (50 uM):
Score = [5.75 x (0-3)] + [(100-percent activity at max concentration)/1.75]

Activity Outcome

Compounds that gave percent inhibition >40 in the primary HTS were judged to be hits and these compounds were selected for follow-up IC50 testing. IC50 values were determined as described in protocol above. The percent activity at the maximum concentration is reported and can be used to estimate the potency of compounds for which the IC50 values were >50 uM.

Activity outcome is reported as follows:

(1) IC50 <50 uM in all three IC50 determinations = active
(2) IC50 >50 uM, percent inhibition 30-50% at 50 uM = inconclusive
(3) IC50 >50 uM, percent inhibition <30% at 50 uM = inactive


This assay was submitted to the PCMD by Scott Diamond, assay development and HTS were conducted by Paul Riley and Abhishek Pratarphekar, and data were submitted by Andrew Napper and Paul Riley, all of the University of Pennsylvania.
Categorized Comment - additional comments and annotations
From ChEMBL:
Assay Type: Functional
Result Definitions
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OutcomeThe BioAssay activity outcomeOutcome
ScoreThe BioAssay activity ranking scoreInteger
1Number of IC50 determinationsInteger
4IC50 Hill slopeFloat
5IC50 R-squaredFloat
6IC50 min concentrationFloatμM
7IC50 percent activity at min concentrationFloat%
8IC50 max concentrationFloatμM
9IC50 percent activity at max concentrationFloat%
10IC50 signal at 0.00152 microM (0.00152μM**)Float
11IC50 signal at 0.00305 microM (0.00305μM**)Float
12IC50 signal at 0.00610 microM (0.0061μM**)Float
13IC50 signal at 0.01221 microM (0.01221μM**)Float
14IC50 signal at 0.02441 microM (0.02441μM**)Float
15IC50 signal at 0.04883 microM (0.04883μM**)Float
16IC50 signal at 0.09766 microM (0.09766μM**)Float
17IC50 signal at 0.19531 microM (0.19531μM**)Float
18IC50 signal at 0.39063 microM (0.39063μM**)Float
19IC50 signal at 0.78125 microM (0.78125μM**)Float
20IC50 signal at 1.5625 microM (1.5625μM**)Float
21IC50 signal at 3.125 microM (3.125μM**)Float
22IC50 signal at 6.25 microM (6.25μM**)Float
23IC50 signal at 12.5 microM (12.5μM**)Float
24IC50 signal at 25 microM (25μM**)Float
25IC50 signal at 50 microM (50μM**)Float
26IC50 control meanFloat
27IC50 control standard deviationFloat
28IC50 number of control wellsInteger
29IC50 control percent CVFloat%
30IC50 blank meanFloat
31IC50 blank standard deviationFloat
32IC50 number of blank wellsInteger
33IC50 blank percent CVFloat%
34IC50 signal-background ratioFloat
35IC50 plate Z-factorFloat

* Activity Concentration. ** Test Concentration.

Data Table (Concise)
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