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BioAssay: AID 2195

QFRET-based biochemical high throughput dose response assay for inhibitors of the Plasmodium falciparum M18 Aspartyl Aminopeptidase (PFM18AAP).

Grant Proposal PI: John Dalton and Donald Gardiner, Queensland Institute of Medical Research, Australia ..more
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 Tested Compounds
 Tested Compounds
All(125)
 
 
Active(125)
 
 
 Tested Substances
 Tested Substances
All(125)
 
 
Active(125)
 
 
AID: 2195
Data Source: The Scripps Research Institute Molecular Screening Center (PFM18AAP_INH_QFRET_1536_3XIC50)
BioAssay Type: Confirmatory, Concentration-Response Relationship Observed
Depositor Category: NIH Molecular Libraries Probe Production Network
BioAssay Version:
Deposit Date: 2009-12-09
Hold-until Date: 2010-03-01
Modify Date: 2010-03-01

Data Table ( Complete ):           Active    All
Target
BioActive Compounds: 125
Depositor Specified Assays
AIDNameTypeComment
1855Summary of probe development efforts to identify inhibitors of the Plasmodium falciparum M18 Aspartyl Aminopeptidase (M18AAP)summarySummary AID.
2170QFRET-based biochemical high throughput confirmation assay for inhibitors of the Plasmodium falciparum M18 Aspartyl Aminopeptidase (PFM18AAP).screeningConfirmation screen (PFM18AAP inhibitors).
489011Late stage assay provider results from the probe development effort to identify inhibitors of the Plasmodium falciparum M18 Aspartyl Aminopeptidase (M18AAP): radiolabel-based cell-based dose response assay to identify compounds that inhibit P. falciparum growth in RBCsconfirmatory
720736Late stage assay provider results from the probe development effort to identify inhibitors of the Plasmodium falciparum M18 Aspartyl Aminopeptidase (M18AAP): radiolabel-based cell-based assay to identify compounds that inhibit P. falciparum growth in RBCs, Set2other
743024Late stage assay provider results from the probe development effort to identify inhibitors of the Plasmodium falciparum M18 Aspartyl Aminopeptidase (M18AAP): radiolabel-based cell-based dose response assay to identify compounds that inhibit P. falciparum growth in RBCs, Set 2.confirmatory
492975Late stage assay provider results from the probe development effort to identify inhibitors of the Plasmodium falciparum M18 Alanyl Aminopeptidase (PfM18AAP): fluorescence-based biochemical assay to identify inhibitors of malaria cell lysatescreening
492974Late stage assay provider results from the probe development effort to identify inhibitors of the Plasmodium falciparum M18 Alanyl Aminopeptidase (PfM18AAP): fluorescence-based biochemical assay to identify inhibitors of rPfM18AAPscreening
489015Late stage assay provider results from the probe development effort to identify inhibitors of the Plasmodium falciparum M18 Aspartyl Aminopeptidase (M18AAP): radiolabel-based cell-based assay to identify compounds that inhibit P. falciparum growth in RBCsother
Description:
Source (MLPCN Center Name): The Scripps Research Institute Molecular Screening Center
Affiliation: The Scripps Research Institute, TSRI
Assay Provider: John Dalton and Donald Gardiner, Queensland Institute of Medical Research, Australia
Network: Molecular Library Probe Production Centers Network (MLPCN)
Grant Proposal Number: 1 R03 MH084103-01
Grant Proposal PI: John Dalton and Donald Gardiner, Queensland Institute of Medical Research, Australia
External Assay ID: PFM18AAP_INH_QFRET_1536_3XIC50

Name: QFRET-based biochemical high throughput dose response assay for inhibitors of the Plasmodium falciparum M18 Aspartyl Aminopeptidase (PFM18AAP).

Description:

Aminopeptidases (APs) are metalloproteases that cleave amino-terminal (N-terminal) amino acids during protein synthesis (1, 2) These enzymes are characterized in part by their post-translational removal of leucine, aspartate, proline, methionine, etc from proteins and peptides, in order that proteins are properly regulated, targeted for degradation, and trafficked within both animal and plant cells (3). As a result, these enzymes are involved in diverse processes, including meiosis (1), cellular senescence (1), blood pressure control (4, 5), angiogenesis (6), and inflammation (7). PFM18AAP is the sole aspartyl aminopeptidase (AAP) present in the genome of the malaria parasite Plasmodium falciparum (8). It exhibits exopeptidase activity exclusively against the N-terminal acidic amino acids glutamate and aspartate (9-11), is found in all intra-erythrocytic stages of the parasite (9), and functions to complete the hydrolysis of host hemoglobin into amino acids for use in de novo protein synthesis by the parasite (12, 13). Studies demonstrating that genetic knockdown of PFM18AAP results in a lethal parasite phenotype (9), and that inhibitors of methionine (14) and leucine (12, 15) aminopeptidases prevent malaria growth in culture and hemoglobin degradation, suggest that these enzymes are essential for parasite survival. As a result, the identification of selective inhibitors of PFM18AAP would elucidate this enzyme#s role in the P. falciparum lifecycle, and serve as potential therapeutic agents to control malaria infection.

References:

1. Walling, L.L., Recycling or regulation? The role of amino-terminal modifying enzymes. Curr Opin Plant Biol, 2006. 9(3): p. 227-33.
2. Meinnel, T., Serero, A., and Giglione, C., Impact of the N-terminal amino acid on targeted protein degradation. Biol Chem, 2006. 387(7): p. 839-51.
3. Jankiewicz, U. and Bielawski, W., The properties and functions of bacterial aminopeptidases. Acta Microbiol Pol, 2003. 52(3): p. 217-31.
4. Banegas, I., Prieto, I., Vives, F., Alba, F., de Gasparo, M., Segarra, A.B., Hermoso, F., Duran, R., and Ramirez, M., Brain aminopeptidases and hypertension. J Renin Angiotensin Aldosterone Syst, 2006. 7(3): p. 129-34.
5. Silveira, P.F., Gil, J., Casis, L., and Irazusta, J., Peptide metabolism and the control of body fluid homeostasis. Curr Med Chem Cardiovasc Hematol Agents, 2004. 2(3): p. 219-38.
6. Zhong, H. and Bowen, J.P., Antiangiogenesis drug design: multiple pathways targeting tumor vasculature. Curr Med Chem, 2006. 13(8): p. 849-62.
7. Proost, P., Struyf, S., and Van Damme, J., Natural post-translational modifications of chemokines. Biochem Soc Trans, 2006. 34(Pt 6): p. 997-1001.
8. Wilk, S., Wilk, E., and Magnusson, R.P., Purification, characterization, and cloning of a cytosolic aspartyl aminopeptidase. J Biol Chem, 1998. 273(26): p. 15961-70.
9. Teuscher, F., Lowther, J., Skinner-Adams, T.S., Spielmann, T., Dixon, M.W., Stack, C.M., Donnelly, S., Mucha, A., Kafarski, P., Vassiliou, S., Gardiner, D.L., Dalton, J.P., and Trenholme, K.R., The M18 aspartyl aminopeptidase of the human malaria parasite Plasmodium falciparum. J Biol Chem, 2007. 282(42): p. 30817-26.
10. Gyang, F.N., Poole, B., and Trager, W., Peptidases from Plasmodium falciparum cultured in vitro. Mol Biochem Parasitol, 1982. 5(4): p. 263-73.
11. Vander Jagt, D.L., Baack, B.R., and Hunsaker, L.A., Purification and characterization of an aminopeptidase from Plasmodium falciparum. Mol Biochem Parasitol, 1984. 10(1): p. 45-54.
12. Nankya-Kitaka, M.F., Curley, G.P., Gavigan, C.S., Bell, A., and Dalton, J.P., Plasmodium chabaudi chabaudi and P. falciparum: inhibition of aminopeptidase and parasite growth by bestatin and nitrobestatin. Parasitol Res, 1998. 84(6): p. 552-8.
13. Lauterbach, S.B. and Coetzer, T.L., The M18 aspartyl aminopeptidase of Plasmodium falciparum binds to human erythrocyte spectrin in vitro. Malar J, 2008. 7: p. 161.
14. Chen, X., Chong, C.R., Shi, L., Yoshimoto, T., Sullivan, D.J., Jr., and Liu, J.O., Inhibitors of Plasmodium falciparum methionine aminopeptidase 1b possess antimalarial activity. Proc Natl Acad Sci U S A, 2006. 103(39): p. 14548-53.
15. Stack, C.M., Lowther, J., Cunningham, E., Donnelly, S., Gardiner, D.L., Trenholme, K.R., Skinner-Adams, T.S., Teuscher, F., Grembecka, J., Mucha, A., Kafarski, P., Lua, L., Bell, A., and Dalton, J.P., Characterization of the Plasmodium falciparum M17 leucyl aminopeptidase. A protease involved in amino acid regulation with potential for antimalarial drug development. J Biol Chem, 2007. 282(3): p. 2069-80.

Keywords:

Aspartyl aminopeptidase, PFM18AAP, M18AAP, rPFAAP, malaria, parasite, plasmodium falciparum, exopeptidase, dose response, HTS, high throughput screen, 1536, inhibitor, inhibition, fluorescence, FLINT, peptide, cleavage, Scripps, Scripps Florida, The Scripps Research Institute Molecular Screening Center, SRIMSC, Molecular Libraries Probe Production Centers Network, MLPCN.
Protocol
Assay Overview:

The purpose of this assay is to determine dose response curves for compounds identified as active in a set of previous experiments entitled, #QFRET-based biochemical high throughput confirmation assay for inhibitors of the Plasmodium falciparum M18 Aspartyl Aminopeptidase (PFM18AAP) (AID 2170). In this biochemical assay, a commercially available fluorogenic peptide substrate (H-Glu-NHMec) is incubated with purified recombinant PFM18AAP enzyme (rPFM18AAP) in the presence of test compounds. Cleavage of the substrate by rPFM18AAP enzyme liberates the NHMec leaving group from the peptide, leading to increased well fluorescence. As designed, compounds that inhibit PFM18AAP will block rPFM18AAP-mediated cleavage of HGlu-NHMec and liberation of the NHMec leaving group from the substrate, resulting in decreased well fluorescence as measured at 340 nm excitation and 450 nm emission. Test compounds were assayed in triplicate in a 10-point 1:3 dilution series starting at a nominal test concentration of 73.5 micromolar.

Protocol Summary:

Prior to the start of the assay, 2.5 microliters of assay buffer (50mM Tris HCl pH7.5, 4mM CoCl2, 0.1% BSA) containing 5micrograms/mL rPFM18AAP were dispensed into a 1536 microtiter plate. Next, 37 nL of test compound in DMSO, ZnCl2 (2mM final concentration), or DMSO alone (0.74% final concentration) were added to the appropriate wells. The plates were then incubated for 30 minutes at 25 degrees Celsius.

The assay was started by dispensing 2.5 microliters of 100 micromolar H-Glu-NHMec substrate in buffer (50 mM Tris HCl, pH 8.8) into all wells. Well fluorescence was read immediately (T0) on the Viewlux (Perkin-Elmer) and again after 90 minutes (T90) of incubation at 25 degrees Celsius.

Prior to further calculations, T0 was subtracted from T90 for each individual well. The difference between RFU values read at T0 (RFU_T0) and T90 (RFU_T90), named delta RFU, was calculated as follows:

delta RFU = RFU_T90 - RFU_T0

The percent inhibition for each well was then calculated as follows:

Percent inhibition = (test_compound_delta RFU - negative_control_ delta RFU)/(positive_control_ delta RFU - negative_control_ delta RFU)*100

Where:

Test_Compound is defined as wells containing test compound.
Negative_Control is defined as the median of the wells containing rPFM18AAP.
Positive_Control is defined as the median of the wells containing ZnCl2.

For each test compound, percent inhibition was plotted against compound concentration. A four parameter equation describing a sigmoidal dose-response curve was then fitted with adjustable baseline using Assay Explorer software (Symyx Technologies Inc). The reported IC50 values were generated from fitted curves by solving for the X-intercept value at the 50% inhibition level of the Y-intercept value. In cases where the highest concentration tested (i.e. 73.5 micromolar) did not result in greater than 50% inhibition, the IC50 was determined manually as greater than 73.5 micromolar. Compounds with an IC50 greater than 10 micromolar were considered inactive. Compounds with an IC50 equal to or less than 10 micromolar were considered active.

Any compound with a percent activity value <50% at all test concentrations was assigned an activity score of zero. Any compound with a percent activity value >50% at any test concentration was assigned an activity score greater than zero. Activity score was then ranked by the potency, with the most potent compounds assigned the highest activity scores.

The activity score range for active compounds is 100-1. There are no inactive compounds.

List of Reagents:

rPFM18AAP enzyme (supplied by Assay Provider)
H-Glu-NHMec substrate (Bachem, part I-1180)
1536-well plates (Greiner, part 789176)
Tris (Amresco, part 0497)
CoCl2 6H20 (Univar, part D3247)
ZnCl2 (Sigma, part 208086)
BSA (Calbiochem, part 126609)
Comment
Due to the increasing size of the MLPCN compound library, this assay may have been run as two or more separate campaigns, each campaign testing a unique set of compounds. In this case the results of each separate campaign were assigned #Active/Inactive# status based upon that campaign#s specific compound activity cutoff value. All data reported were normalized on a per-plate basis. In this assay, ZnCl2 had an IC50 of approximately 1.06 micromolar. Possible artifacts of this assay can include, but are not limited to: dust or lint located in or on wells of the microtiter plate, compounds that modulate well fluorescence. All test compound concentrations reported above and below are nominal; the specific test concentration(s) for a particular compound may vary based upon the actual sample provided by the MLSMR. The MLSMR was not able to provide all compounds selected for testing in this AID.
Result Definitions
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TIDNameDescriptionHistogramTypeUnit
OutcomeThe BioAssay activity outcomeOutcome
ScoreThe BioAssay activity ranking scoreInteger
1QualifierActivity Qualifier identifies if the resultant data IC50 came from a fitted curve or was determined manually to be less than or greater than its listed IC50 concentration.String
2IC50*The concentration at which 50 percent of the activity in the inhibitor assay is observed; (IC50) shown in micromolar.FloatμM
3LogIC50Log10 of the qualified IC50 (IC50) from the inhibitor assay in M concentration.Float
4Hill SlopeThe variable HillSlope describes the steepness of the curve. This variable is called the Hill slope, the slope factor, or the Hill coefficient. If it is positive, the curve increases as X increases. If it is negative, the curve decreases as X increases. A standard sigmoid dose-response curve (previous equation) has a Hill Slope of 1.0. When HillSlope is less than 1.0, the curve is more shallow. When HillSlope is greater than 1.0, the curve is steeper. The Hill slope has no units.Float
5Hill S0Y-min of the curve.Float
6Hill SinfY-max of the curve.Float
7Hill dSThe range of Y.Float
8Chi SquareA measure for the 'goodness' of a fit. The chi-square test (Snedecor and Cochran, 1989) is used to test if a sample of data came from a population with a specific distribution.Float
9RsquareThis statistic measures how successful the fit explains the variation of the data; R-square is the square of the correlation between the response values and the predicted response values.Float
10Number of DataPointsOverall number of data points of normalized percent inhibition that was used for calculations (includes all concentration points); in some cases a data point can be excluded as outlier.Integer
11Inhibition at 3.7 nM (0.0037μM**)Value of %inhibition at 3.7 nanomolar inhibitor concentration; average of triplicate measurement.Float%
12Inhibition at 11.2 nM (0.0112μM**)Value of %inhibition at 11.2 nanomolar inhibitor concentration; average of triplicate measurement.Float%
13Inhibition at 33.6 nM (0.0336μM**)Value of %inhibition at 33.6 nanomolar inhibitor concentration; average of triplicate measurement.Float%
14Inhibition at 100.8 nM (0.1008μM**)Value of %inhibition at 100.8 nanomolar inhibitor concentration; average of triplicate measurement.Float%
15Inhibition at 302.3 nM (0.3023μM**)Value of %inhibition at 302.3 nanomolar inhibitor concentration; average of triplicate measurement.Float%
16Inhibition at 906.9 nM (0.9069μM**)Value of %inhibition at 906.9 nanomolar inhibitor concentration; average of triplicate measurement.Float%
17Inhibition at 2.7 uM (2.7μM**)Value of %inhibition at 2.7 micromolar inhibitor concentration; average of triplicate measurement.Float%
18Inhibition at 8.2 uM (8.2μM**)Value of %inhibition at 8.2 micromolar inhibitor concentration; average of triplicate measurement.Float%
19Inhibition at 24.5 uM (24.5μM**)Value of %inhibition at 24.5 micromolar inhibitor concentration; average of triplicate measurement.Float%
20Inhibition at 73.5 uM (73.5μM**)Value of %inhibition at 73.5 micromolar inhibitor concentration; average of triplicate measurement.Float%

* Activity Concentration. ** Test Concentration.
Additional Information
Grant Number: 1 R03 MH084103-01

Data Table (Concise)
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