Bookmark and Share
BioAssay: AID 680

Factor XIa Mixture HTS

Factor XI (FXI) circulates as a complex with high molecular weight kininogen (HK) in the plasma at a concentration of 5 ug/ml (equivalent to 31.3 nM, dimeric concentration) as a homodimeric glycosylated blood plasma zymogen of approximately 160 kDa, containing monomeric subunits of 80 kDa each (1). Thrombin (2, 3), factor XIa (FXIa) (3), and factor XIIa alpha (FXIIa) (4), all cleave an internal R369-I370 bond in each monomer of FXI, yielding the enzyme FXIa. ..more
 Tested Compounds
 Tested Compounds
 Tested Substances
 Tested Substances
 Related BioAssays
 Related BioAssays
AID: 680
BioAssay Type: Primary, Primary Screening, Single Concentration Activity Observed
Depositor Category: NIH Molecular Libraries Screening Center Network
BioAssay Version:
Deposit Date: 2007-04-19
Modify Date: 2008-10-07

Data Table ( Complete ):           Active    All
BioActive Compounds: 120
Depositor Specified Assays
679Factor XIa Dose Response ConfirmationconfirmatoryFactor XIa dose-response confirmation of hits from 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


Factor XI (FXI) circulates as a complex with high molecular weight kininogen (HK) in the plasma at a concentration of 5 ug/ml (equivalent to 31.3 nM, dimeric concentration) as a homodimeric glycosylated blood plasma zymogen of approximately 160 kDa, containing monomeric subunits of 80 kDa each (1). Thrombin (2, 3), factor XIa (FXIa) (3), and factor XIIa alpha (FXIIa) (4), all cleave an internal R369-I370 bond in each monomer of FXI, yielding the enzyme FXIa.

After activation from FXI to FXIa, FXIa possesses a heavy chain of 369 residues and a light chain of 238 residues. The heavy chain consists of four apple domains (A1-A4) and the light chain represents a trypsin-like serine protease domain with active site residues at H413, D464, and S557 (1, 5-7). FXIa catalyzes FIX to FIXa activation by cleaving two scissile bonds at R145 and R180 (8). The FIXa generated can catalyze FXa formation on the platelet surface with the active cofactor factor VIIIa (FVIIIa), with FVIIIa increasing the Vmax of FX activation by FIXa by 100,000 fold (9). After activation of sufficient levels of FXa by the consolidation pathway, FXa can go on to form a ternary complex with FVa and prothrombin on the platelet surface, to give sufficient levels of thrombin for activation of fibrinogen to fibrin. Formation of this ternary prothrombinase complex in the presence of phospholipids has been shown to increase the rate of prothrombin to thrombin activation by 300,000-fold more than with FXa and prothrombin alone (10).

Thrombin catalyzes activation of fibrinogen to fibrin, cleaving peptides 14-16 amino acids in length, called fibrinopeptides, from the A alpha and B beta subunits of fibrinogen (11, 12). The fibrin monomers produced by thrombin form a noncovalent meshwork with other fibrin molecules to produce a fibrin clot that stabilizes and retracts the initial platelet plug described above. This stable fibrin clot formation stabilizes the primary platelet plug, and reduces the volume of the plug in order to arrest blood loss.

The role of FXI in thrombosis was investigated using a mouse double knockout of FXI and protein C (PC). First, the single FXI knockout in the mouse did not cause a significant bleeding problem in mice, shown by comparable tail bleeding times between FXI knockout mice and wt mice, as opposed to the FIX knockout mouse which had a tail bleeding time increase of > 5.8-fold over wt mice (13). Additionally, using a FXI deficient mouse model, mice were partially protected from arterial occlusion in a FeCl3 model of thrombosis (13). Thus, by this model, controlling or limiting FXI activity can have a protective effect on hemostasis by preventing pathologic thrombus formation. Further studies of FXI under rapid arterial flow conditions simulating rapid thrombus growth with an anti-FXI antibody that reduced intraluminal thrombus growth did suggest that inhibiting FXI can have a mild, yet controlled antithrombotic effect that may be of significant use clinically (14). A recent report found that increased risk of cerebrovascular events is associated with elevated FXI activity and antigenic levels, implicating FXI as a risk factor in deep venous thrombosis (15). When double knockout mice lacking both FXI and activated protein C (aPC) were examined, the mice possessed greater control over thrombosis than the aPC knockouts, suggesting that FXI deficiency helped these mice to survive past the neonatal period. Thus, the absence of FXI prevented the occurrence of fatal disseminated intravascular coagulation (DIC) in this model (16).

In vivo findings in rodent models of coagulation in addition to clinical data from patients at risk for pathologic cerebrovascular events have given rise to the recognition of FXI as a fine modulator and focal point in blood coagulation whose inhibition does not cause a severe bleeding diathesis, and suggest that drug design using the tools of high throughput chemical inhibitor screening may give rise to novel anticoagulant therapies (17).

HTS was performed using 62,107 compounds of the MLSCN library combined as mixtures of 10 orthogonally pooled compounds totaling 2.5 mM, which were diluted 50-fold into 10 ul 384 well assay plates (final concentration 5 uM each compound). The assay used to test for percent inhibition was a fluorescence assay utilizing hydrolysis of Boc-Glu-Ala-Arg-AMC, as first described by Kawabata et al. (18).

1. K. Fujikawa, D. W. Chung, L. E. Hendrickson, E. W. Davie, Biochemistry 25, 2417 (1986).
2. D. Gailani, G. J. Broze, Jr., Science 253, 909 (Aug 23, 1991).
3. K. Naito, K. Fujikawa, Journal of Biological Chemistry 266, 7353 (1991).
4. B. N. Bouma, J. H. Griffin, Journal of Biological Chemistry 252, 6432 (1977).
5. T. Koide, M. A. Hermodson, E. W. Davie, Nature 266, 729 (Apr 21, 1977).
6. F. van der Graaf, J. S. Greengard, B. N. Bouma, D. M. Kerbiriou, J. H. Griffin, Journal of Biological Chemistry 258, 9669 (1983).
7. B. A. McMullen, K. Fujikawa, E. W. Davie, Biochemistry 30, 2056 (Feb 26, 1991).
8. K. Fujikawa, M. E. Legaz, H. Kato, E. W. Davie, Biochemistry 13, 4508 (1974).
9. G. van Dieijen, G. Tans, J. Rosing, H. C. Hemker, J Biol Chem 256, 3433 (Apr 10, 1981).
10. J. P. Miletich, C. M. Jackson, P. W. Majerus, Journal of Biological Chemistry 253, 6908 (1978).
11. K. Bailey, F. R. Bettelheim, L. Lorand, W. R. Middlebrook, Nature 167, 233 (Feb 10, 1951).
12. B. Blomback, M. Blomback, Ann N Y Acad Sci 202, 77 (Dec 8, 1972).
13. X. Wang et al., J Thromb Haemost 3, 695 (Apr, 2005).
14. A. Gruber, S. R. Hanson, Blood 102, 953 (Aug 1, 2003).
15. D. T. Yang, Flanders, M.M., Rodgers, G.M., Blood 106, 2626 (November 16, 2005, 2005).
16. J. C. Chan et al., American Journal of Pathology 158, 469 (Feb, 2001).
17. A. Gruber, S. R. Hanson, Curr Pharm Des 9, 2367 (2003).
18. S. Kawabata et al., European Journal of Biochemistry 172, 17 (Feb 15, 1988).
Compound pooling

200 plates containing 64,000 compounds from the MLSCN library were arranged in two 10 x 10 grids of 100 plates each. Sets of ten plates were pooled as follows to give 20 mixture plates per 100 single compound plates:

Plate 1_2_3_4_5_6_7_8_9_10 pooled to mixture plate 1-10
Plate 11_12_13_14_15_16_17_18_19_20 pooled to mixture plate 11-20
Plate 21_22_23_24_25_26_27_28_29_30 pooled to mixture plate 21-30
Plate 31_32_33_34_35_36_37_38_39_40 pooled to mixture plate 31-40
Plate 41_42_43_44_45_46_47_48_49_50 pooled to mixture plate 41-50
Plate 51_52_53_54_55_56_57_58_59_60 pooled to mixture plate 51-60
Plate 61_62_63_64_65_66_67_68_69_70 pooled to mixture plate 61-70
Plate 71_72_73_74_75_76_77_78_79_80 pooled to mixture plate 71-80
Plate 81_82_83_84_85_86_87_88_89_90 pooled to mixture plate 81-90
Plate 91_92_93_94_95_96_97_98_99_100 pooled to mixture plate 91-100

Plates were also pooled 'vertically':

Plates 1, 11, 21, 31, 41, 51, 61, 71, 81, 91 pooled to mixture plate 1-91
Plates 2, 12, 22, 32, 42, 52, 62, 72, 82, 92 pooled to mixture plate 2-92
And so on until mixture plate 10-100.

For example, the single compound in well A3 in Plate 1 is mixed with 9 compounds in well A3 in mixture plate 1-10, and also with 9 different compounds in well A3 in mixture plate 1-91.

The concentration of each mixture was 2.5 mM in DMSO (250 uM per compound). Pintool transfer into the HTS assay gave a final mixture concentration of 50 uM in 2% DMSO (5 uM per compound).


Human plasma factor XIa was purchased from Enzyme Research Laboratories (Cat # HFXIa 1111a). Substrate Boc-Glu-Ala-Arg-AMC was from Bachem (Cat #I-1575.0050). Assay buffer consisted of 50 mM Tris, pH 7.4, 150 mM sodium chloride, 0.02% Tween 20. Low-volume 384-well black plates were from Corning (Item #3676).


Factor XIa (0.23 ug/mL) was incubated with Boc-Glu-Ala-Arg-AMC substrate (15 uM) in 10 uL of assay buffer (see above) for 2 hr at room temperature. HTS was performed using 50 uM compound mixture (5 uM each of 10 compounds).

HTS protocol

1.Fill low-volume plate with 4 uL water using Multidrop-micro
2.Add 5 uL assay buffer to columns 1 and 23 using Multidrop-384
3.Add 200 nL of compound mixture (2.5 mM in DMSO) using Evolution pintool
4.Add 1 uL of Boc-Glu-Ala-Arg-AMC substrate (150 uM in 5x assay buffer) using Multidrop-micro
5.Add 5 uL enzyme (0.46 ug/mL in assay buffer) using Multidrop-384
6.Incubate for 2 hr at room temperature
7.Read fluorescence (excitation 355, emission 460) on Envision reader

Data analysis

Data were analyzed in IDBS ActivityBase. Each HTS plate contained compound mixtures (50 uM in 2% DMSO) in columns 3-22, controls (enzyme, no compound mixture) in columns 2 and 24, and blanks (no enzyme) in columns 1 and 23. HTS percent inhibition was calculated for each compound mixture 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:

% Inhibition = 100*(1-((signal-blank mean)/(control mean-blank mean)))

Assignment of percent inhibition to individual compounds---Mixture percent inhibition data were retrieved in IDBS SARgen, together with the 10 compounds contained in each mixture. The data were rearranged in Excel using VLookup functions such that each row contained a single compound and the two percent inhibition values corresponding to the location of the compound in the mixture plates.
Activity scoring

Activity scoring is complicated by the fact that the two percent inhibition values associated with each compound in fact represent two different mixtures of 10 compounds. Thus simple averaging of the two values is not meaningful. Instead each compound was assigned a percent inhibition score based on the lower of the two percent inhibition values. This system appropriately scores hits showing activity in both mixtures, but avoids assignment of an erroneously high score to inactives that shared one location with an active compound.

The activity score reported here is based on percent inhibition observed in the primary HTS (see above):

Percent inhibition scores were calculated from the lower of the two percent inhibition values associated with each compound as follows:

(1) For percent inhibition between 0 and 100, score = percent inhibition
(2) For negative percent inhibition, score = 0


This assay was submitted to the PCMD by Scott Diamond, assay development and HTS were conducted by Paul Riley, and data were submitted by Andrew Napper and Paul Riley, all of the University of Pennsylvania.
Result Definitions
Show more
OutcomeThe BioAssay activity outcomeOutcome
ScoreThe BioAssay activity ranking scoreInteger
1Percent inhibition in mixture #1 (5μM**)Float%
2Percent inhibition in mixture #2 (5μM**)Float%
3Percent inhibition #1 signal (FU)Float
4Percent inhibition #1 control mean (FU)Float
5Percent inhibition #1 control standard deviation (FU)Float
6Percent inhibition #1 number of control wellsInteger
7Percent inhibition #1 control percent CVFloat%
8Percent inhibition #1 blank mean (FU)Float
9Percent inhibition #1 blank standard deviation (FU)Float
10Percent inhibition #1 number of blank wellsInteger
11Percent inhibition #1 blank percent CVFloat%
12Percent inhibition #1 signal-to-background ratioFloat
13Percent inhibition #1 plate Z-factorFloat
14Percent inhibition #2 signal (FU)Float
15Percent inhibition #2 control mean (FU)Float
16Percent inhibition #2 control standard deviation (FU)Float
17Percent inhibition #2 number of control wellsInteger
18Percent inhibition #2 control percent CVFloat%
19Percent inhibition #2 blank mean (FU)Float
20Percent inhibition #2 blank standard deviation (FU)Float
21Percent inhibition #2 number of blank wellsInteger
22Percent inhibition #2 blank percent CVFloat%
23Percent inhibition #2 signal-to-background ratioFloat
24Percent inhibition #2 plate Z-factorFloat

** Test Concentration.

Data Table (Concise)