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In this study, we enhanced the data analysis capabilities of the DARTS experiment by monitoring the changes in protein stability and estimating the affinity of protein-ligand interactions. The interactions can be plotted into two curves: a proteolytic curve and a dose-dependence curve. We have used mTOR-rapamycin interaction as an exemplary case.
Drug Affinity Responsive Target Stability (DARTS) is a robust method for detection of novel small molecule protein targets. It can be used to verify known small molecule-protein interactions and to find potential protein targets for natural products. Compared with other methods, DARTS uses native, unmodified, small molecules and is simple and easy to operate. In this study, we further enhanced the data analysis capabilities of the DARTS experiment by monitoring the changes in protein stability and estimating the affinity of protein-ligand interactions. The protein-ligand interactions can be plotted into two curves: a proteolytic curve and a dose-dependence curve. We have used the mTOR-rapamycin interaction as an exemplary case for establishment of our protocol. From the proteolytic curve we saw that the proteolysis of mTOR by pronase was inhibited by the presence of rapamycin. The dose-dependency curve allowed us to estimate the binding affinity of rapamycin and mTOR. This method is likely to be a powerful and simple method for accurately identifying novel target proteins and for the optimization of drug target engagement.
Identifying small molecule target proteins is essential to the mechanistic understanding and development of potential therapeutic drugs1,2,3. Affinity chromatography, as a classical method for identifying the target proteins of small molecules, has yielded good results4,5. However, this method has limitations, in that chemical modification of small molecules often results in reduced or altered binding specificity or affinity. To overcome these limitations, several new strategies have recently been developed and applied to identify the small molecule targets without chemical modification of the small molecules. These direct methods for target identification of label-free small molecules include drug affinity responsive target stability (DARTS)6, stability of proteins from rates of oxidation (SPROX)7, cellular thermal shift assay (CETSA)8,9, and thermal proteome profiling (TPP)10. These methods are highly advantageous because they use natural, unmodified small molecules and rely only on direct binding interactions to find target proteins11.
Among these new methods, DARTS is a comparatively simple methodology that can easily be adopted by most labs12,13. DARTS depends on the concept that ligand-bound proteins demonstrate modified susceptibility to enzymatic degradation relative to unbound proteins. The new target protein can be detected by examination of the altered band in SDS-PAGE gel through liquid chromatography-mass spectrometry (LC-MS/MS). This approach has been successfully implemented for identification of previously unknown targets of natural products and drugs14,15,16,17,18,19. It is also powerful as a means to screen or validate binding of compounds to a specific protein20,21. In this study, we present an improvement to the experiment by monitoring the changes in protein stability with small molecules and identifying protein-ligand binding affinities. We use mTOR- rapamycin interaction as an example to demonstrate our approach.
1. Collect and lyse cells
2. Incubate protein lysates with the small molecule
3. Perform proteolysis
NOTE: For proteolysis, steps are carried out at room temperature unless otherwise noted
4. Quantification and analysis
The flow chart of the experiment is outlined in Figure 1. The result of Coomassie blue staining is shown in Figure 2. Incubation with the small molecule confers protection against proteolysis. Three bands that appear to be protected by incubation with rapamycin over vehicle control are found. The expected results from proteolytic curve experiment are shown in Figure 3. As a proof-of-principle, we examined the well-studied protein mT...
DARTS allows for identification of small molecule targets by exploiting the protective effect of protein binding against degradation. DARTS does not require any chemical modification or immobilization of the small molecule26. This allows small molecules to be used to determine their direct binding protein targets. Standard assessment criteria for the classical DARTS method include gel staining, mass spectrometry and western blotting12,13. ...
The authors have nothing to disclose.
This work was supported partly by NIH research grants R01NS103931, R01AR062207, R01AR061484, and a DOD research grant W81XWH-16-1-0482.
Name | Company | Catalog Number | Comments |
100X Protease inhibitor cocktail | Sigma-Aldrich | P8340 | Dilute to 20X with ultrapure water |
293T cell line | ATCC | CRL-3216 | DMEM medium with 10% FBS |
Acetic acid | Sigma-Aldrich | A6283 | |
BCA Protein Assay Kit | Thermo Fisher | 23225 | |
Calcium chloride | Sigma-Aldrich | C1016 | |
Cell scraper | Thermo Fisher | 179693 | |
Coomassie Brilliant Blue R-250 Staining Solution | Bio-Rad | 1610436 | |
Dimethyl sulfoxide(DMSO) | Sigma-Aldrich | D2650 | |
GraphPad Prism | GraphPad Software | Version 6.0 | statistical analysis and drawing software |
Hydrochloric acid | Sigma-Aldrich | H1758 | |
ImageJ | National Institutes of Health | Version 1.52 | image processing and analysis software |
M-PER Cell Lysis Reagent | Thermo Fisher | 78501 | |
Phosphate-buffered saline (PBS) | Corning | R21-040-CV | |
Pronase | Roche | PRON-RO | 10 mg/ml |
Sodium chloride | Sigma-Aldrich | S7653 | |
Sodium fluoride | Sigma-Aldrich | S7920 | |
Sodium orthovanadate | Sigma-Aldrich | 450243 | |
Sodium pyrophosphate | Sigma-Aldrich | 221368 | |
Trizma base | Sigma-Aldrich | T1503 | adjust to pH 8.0 |
β-glycerophosphate | Sigma-Aldrich | G9422 |
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