Late stage assay provider results from the probe development effort to identify inhibitors of PAFAH2: absorbance-based cell-based dose response assay to determine cytotoxicity of inhibitor compounds
Name: Late stage assay provider results from the probe development effort to identify inhibitors of PAFAH2: absorbance-based cell-based dose response assay to determine cytotoxicity of inhibitor compounds. ..more
Source (MLPCN Center Name): The Scripps Research Institute Molecular Screening Center (SRIMSC)
Center Affiliation: The Scripps Research Institute (TSRI)
Assay Provider: Benjamin Cravatt, TSRI
Network: Molecular Libraries Probe Production Centers Network (MLPCN)
Grant Proposal Number: 1R01HL084366
Grant Proposal PI: Brian Bahnson, Univ. of Delaware, Benjamin Cravatt, TSRI
External Assay ID: TCELLCYTOX_INH_ABSORB_4XCC50_PAFAH2
Name: Late stage assay provider results from the probe development effort to identify inhibitors of PAFAH2: absorbance-based cell-based dose response assay to determine cytotoxicity of inhibitor compounds.
Oxidative stress has been implicated as an underlying inflammatory factor in several disease pathologies, including cancer, atherosclerosis, aging, and various neurodegenerative disorders (1-5). Phospholipids in particular are susceptible to oxidative damage, and (per)oxidized phospholipids can have deleterious effects, including disruption of membrane bilayers and production of toxic byproducts (4, 6-8). One hypothesized pathway for removal of oxidatively damaged species involves hydrolysis by phospholipase A2-type enzymes. Candidate hydrolytic enzymes include the platelet-activating factor acetylhydrolases (PAFAHs) (4,9). The initial role assigned to the PAFAHs was the hydrolysis of platelet activating factor (PAF) (10,11), a potent pro-inflammatory phospholipid signaling molecule (12), which plays a role in myriad physiological processes including inflammation, anaphylaxis, fetal development, and reproduction (4,13). The PAFAHs are subdivided into three classes: plasma (p)PAFAH, and intracellular types 1 and 2. In terms of sequence homology, pPAFAH and PAFAH2 are close homologs and show little similarity to type 1 enzymes. This project aims to develop specific inhibitors for pPAFAH and three counterscreen enzymes: PAFAH2, PAFAH1b2, and PAFAH1b3.
pPAFAH is associated with inflammatory pathways involved in atherosclerosis, asthma, anaphylactic shock, and other allergic reactions (14,15). Numerous studies have also linked increases in pPAFAH concentration and/or activity to an increased risk of various cardiovascular diseases (16,17); however, the biological function of pPAFAH in the development of coronary heart diseases is controversial, with both anti- and proinflammatory roles attributed to it (18,19). Dr. Bahnson and colleagues recently reported the first high-resolution crystal structure of pPAFAH (20), and would like to expand their studies to co-crystallize pPAFAH with substrate-mimetic inhibitors to further define the active site and substrate specificity of pPAFAH. While one selective pPAFAH inhibitor has been reported (21), its properties are not suitable for the proposed studies.
PAFAH2 has also been shown to play a role in inflammatory processes via hydrolysis of oxidized phospholipids. Over-expression of PAFAH2 has been shown to reduce oxidative stress-induced cell death (22,23) and to mediate repair of oxidative-stress induced tissue injury (4). The enzyme also undergoes N-terminal myristoylation and subsequent translocation to the membrane under conditions of oxidative stress (22,23). This evidence suggests that PAFAH2 functions as an important, and perhaps primary, antioxidant enzyme in certain tissues (4); however, its substrate specificity and pathway involvement are far from being fully elucidated. Currently no suitable inhibitors exist for co-crystallization or biochemical studies of PAFAH2.
Given the complex biology of the PAFAH enzymes, chemical tools capable of interrogating enzyme architecture and providing precise temporal control over PAFAH activity are necessary for complete characterization of patho/physiological roles of the PAFAHs in phospholipid metabolism and inflammatory disease processes. Towards that goal, we developed a HTS assay for inhibitor discovery for four PAFAH enzymes: pPAFAH, PAFAH2, PAFAH1b2, and PAFAH1b3, based on their reactivity with the serine-hydrolase-specific fluorophosphonate (FP) (24) activity-based protein profiling (ABPP) probe. This reactivity can be exploited for inhibitor discovery using a competitive-ABPP platform, whereby small molecule enzyme inhibition is assessed by the ability to out-compete ABPP probe labeling (25). Competitive ABPP has also been configured to operate in a high-throughput manner via fluorescence polarization readout, FluoPol-ABPP (26). Following the HTS campaign, top inhibitors for each enzyme will be characterized and medchem optimized with the goal of delivering key reagents for elucidating the biology of the PAFAH enzymes.
1. Ames, B.N., Dietary carcinogens and anticarcinogens. Oxygen radicals and degenerative diseases. Science, 1983. 221(4617): p. 1256-64.
2. Halliwell, B. and J.M. Gutteridge, Role of free radicals and catalytic metal ions in human disease: an overview. Methods Enzymol., 1990. 186: p. 1-85.
3. Harman, D., The aging process. Proc. Natl. Acad. Sci. U. S. A., 1981. 78(11): p. 7124-8.
4. Kono, N., et al., Protection against oxidative stress-induced hepatic injury by intracellular type II platelet-activating factor acetylhydrolase by metabolism of oxidized phospholipids in vivo. J. Biol. Chem., 2008. 283(3): p. 1628-36.
5. Southorn, P.A. and G. Powis, Free radicals in medicine. II. Involvement in human disease. Mayo. Clin. Proc., 1988. 63(4): p. 390-408.
6. Kinnunen, P.K., On the principles of functional ordering in biological membranes. Chem. Phys. Lipids, 1991. 57(2-3): p. 375-99.
7. Uchida, K., 4-Hydroxy-2-nonenal: a product and mediator of oxidative stress. Prog. Lipid Res., 2003. 42(4): p. 318-43.
8. Fruhwirth, G.O., A. Loidl, and A. Hermetter, Oxidized phospholipids: from molecular properties to disease. Biochim. Et Biophys. Acta, 2007. 1772(7): p. 718-36.
9. Nigam, S. and T. Schewe, Phospholipase A(2)s and lipid peroxidation. Biochim. Et Biophys. Acta, 2000. 1488(1-2): p. 167-81.
10. Blank, M.L., et al., A specific acetylhydrolase for 1-alkyl-2-acetyl-sn-glycero-3-phosphocholine (a hypotensive and platelet-activating lipid). J. Biol. Chem., 1981. 256(1): p. 175-8.
11. Farr, R.S., et al., Preliminary studies of an acid-labile factor (ALF) in human sera that inactivates platelet-activating factor (PAF). Clin. Immunol. Immunopathol., 1980. 15(3): p. 318-330.
12. Zimmerman, G.A., et al., The platelet-activating factor signaling system and its regulators in syndromes of inflammation and thrombosis. Crit. Care Med., 2002. 30(5 Suppl): p. S294-301.
13. Prescott, S.M., et al., Platelet-activating factor and related lipid mediators. Annu. Rev. Biochem., 2000. 69: p. 419-45.
14. Karasawa, K., et al., Plasma platelet activating factor-acetylhydrolase (PAF-AH). Prog. Lipid Res., 2003. 42(2): p. 93-114.
15. Leitinger, N., Oxidized phospholipids as triggers of inflammation in atherosclerosis. Mol. Nutr. Food Res., 2005. 49(11): p. 1063-71.
16. Anderson, J.L., Lipoprotein-associated phospholipase A2: an independent predictor of coronary artery disease events in primary and secondary prevention. Am. J. Cardiol., 2008. 101(12A): p. 23F-33F.
17. Sudhir, K., Clinical review: Lipoprotein-associated phospholipase A2, a novel inflammatory biomarker and independent risk predictor for cardiovascular disease. J. Clin. Endocrinol. Metab., 2005. 90(5): p. 3100-5.
18. Wilensky, R.L. and C.H. Macphee, Lipoprotein-associated phospholipase A(2) and atherosclerosis. Curr. Opin. Lipidol., 2009. 20(5): p. 415-20.
19. Karabina, S.A. and E. Ninio, Plasma PAF-acetylhydrolase: an unfulfilled promise? Biochim. Et Biophys. Acta, 2006. 1761(11): p. 1351-8.
20. Samanta, U. and B.J. Bahnson, Crystal structure of human plasma platelet-activating factor acetylhydrolase: structural implication to lipoprotein binding and catalysis. J. Biol. Chem., 2008. 283(46): p. 31617-24.
21. Blackie, J.A., et al., The identification of clinical candidate SB-480848: a potent inhibitor of lipoprotein-associated phospholipase A2. Bioorg. Med. Chem. Lett., 2003. 13(6): p. 1067-70.
22. Matsuzawa, A., et al., Protection against oxidative stress-induced cell death by intracellular platelet-activating factor-acetylhydrolase II. J. Biol. Chem., 1997. 272(51): p. 32315-20.
23. Marques, M., et al., Identification of platelet-activating factor acetylhydrolase II in human skin. J. Invest. Dermatol., 2002. 119(4): p. 913-9.
24. Jessani, N., et al., Enzyme activity profiles of the secreted and membrane proteome that depict cancer cell invasiveness. Proc. Natl. Acad. Sci. U. S. A., 2002. 99(16): p. 10335-40.
25. Leung, D., et al., Discovering potent and selective reversible inhibitors of enzymes in complex proteomes. Nat. Biotechnol., 2003. 21(6): p. 687-91.
26. Bachovchin, D.A., et al., Identification of selective inhibitors of uncharacterized enzymes by high-throughput screening with fluorescent activity-based probes. Nat. Biotechnol., 2009. 27(4): p. 387-94.
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The purpose of this assay is to determine cytotoxicity of inhibitor compounds belonging to the urea triazole scaffold. In this assay, BW5147-derived murine T-cells in either serum-free media (Assay 1) or media containing FCS (Assay 2) are incubated with test compounds, followed by determination of cell viability. The assay utilizes the WST-1 substrate which is converted into colorimetric formazan dye by the metabolic activity of viable cells. The amount of formed formazan directly correlates to the number of metabolically active cells in the culture. As designed, compounds that reduce cell viability will result in decreased absorbance of the dye. Compounds were tested in quadruplicate in a 7-point 1:5 dilution series starting at a nominal test concentration of 50 uM.
This assay was started by dispensing BW5147-derived murine T cells in RPMI media (100 uL, 10E4 cells/well) into a 96-well plate. Both serum-free media (Assay 1) and media supplemented with fetal calf serum (FCS) (Assay 2) were tested. Compound (5 uL of 0-1000 uM in media containing 5% DMSO) was added to each well, giving final compound concentrations of 0-50 uM. Cells were incubated for 48 hours at 37 degrees Celsius in a humidified incubator and cell viability was determined by the WST-1 assay (Roche) according to manufacturer instructions.
The % cell viability for each well was then calculated as follows:
%_Cell_Viability = ( ABS_Test_Compound - MedianABS_Low_Control ) / ( MedianABS_High_Control - MedianABS_Low_Control ) * 100
Test_Compound is defined as wells containing cells in the presence of test compound.
High_Control is defined as wells containing cells treated with media only (no compound).
Low_Control is defined as wells containing no cells (media only).
For each test compound, percent cell viability was plotted against the log of the compound concentration. The CC50 is reported as ">X uM" (where X = the highest concentration tested for which >50% cell survival was observed).
PubChem Activity Outcome and Score:
The following applies to each panel in this assay:
Compounds with a CC50 value of less than 5 uM were considered active (cytotoxic). Compounds with a CC50 value greater than or equal to 5 uM were considered inactive (non-cytotoxic).
Any compound with a percent cell viability value < 50% at all test concentrations was assigned an activity score of zero. Any compound with a percent cell viability value >= 50% at any test concentration was assigned an activity score greater than zero.
Activity score was then ranked by the potency of the compounds with fitted curves, with the most potent compounds assigned the highest activity scores.
Assay 1 Score: The PubChem Activity Score range for inactive compounds is 100-1. There are no active compounds.
Assay 2 Score: The PubChem Activity Score range for inactive compounds is 0-0. There are no active compounds.
Overall Outcome and Score:
The overall outcome was active if the compound was active in at least one panel, inactive otherwise.
The overall score is 0 if the compound was inactive, otherwise the score is taken as the fraction of panels where the compound is active, multiplied by 100.
The PubChem Activity Score range for inactive compounds is 0-0. There are no active compounds.
List of Reagents:
BW5147-derived murine T-cells (provided by Assay Provider)
RPMI Media (CellGro 10-040-CV)
FCS (Omega Scientific, FB-01)
WST-1 reagent (Roche)
96-well plates (Corning)
Categorized Comment - additional comments and annotations
* Activity Concentration. ** Test Concentration. § Panel component ID.