Small-molecule inhibitors identify the RAD52-ssDNA interaction as critical for recovery from replication stress and for survival of BRCA2 deficient cells
- University of Iowa, United States
- Istituto Superiore di Sanita, Italy
- Carver College of Medicine, University of Iowa, United States
Figures
Figure 1
High throughput screening of the MicroSource SPECTRUM collection identifies 12 compounds that inhibit the RAD52-ssDNA interaction.
(a) Control lanes from a 384 well: 16 negative control wells contain stoichiometric RAD52- Cy3-dT30-Cy5 complexes (red filled circles), while 16 positive control wells contain a stoichiometric …
Figure 2 with 4 supplements
Biochemical characterization of ‘1’.
(a) Aromatic region of the 1D 1H NMR spectrum of compound ‘1’ alone (black) and the WaterLOGSY spectrum of 20 μM compound ‘1’ in the presence of 3.3 μM RAD52 (red). The nonexchangeable proton peaks …
Figure 2—figure supplement 1
Stoichiometric complexes of RAD52 with ssDNA, RPA-coated ssDNA and dsDNA yield characteristic FRET values.
(a) FRET measurements were performed by titrating RAD52 protein into a solution containing 1 nM Cy3-dT30-Cy5 ssDNA. The Cy3 fluorescence was excited directly and the emissions of Cy3 and Cy5 dyes …
Figure 2—figure supplement 2
RAD52 FRET based ssDNA annealing assay in the presence of small molecules.
(a) Schematic of the FRET based annealing reaction. In two half-reactions, stoichiometric amounts of RAD52 were incubated with Target28Cy3 and Probe28Cy5 oligonucleotides, respectively. Upon mixing …
Figure 2—figure supplement 3
None of the tested compounds affect the oligomeric state of RAD52 protein.
A possible effect of the identified compounds on the oligomeric state of RAD52 protein was probed in the dynamic light scattering experiments, which measured the average hydrodynamic radius of RAD52 …
Figure 2—figure supplement 4
Compounds ‘1’ and ‘6’ have no effect on the interaction between RAD52 and RPA proteins.
Ni-NTA Agarose (15 uL buffer equilibrated bead slurry) was incubated with 3 μM RAD52, 3 μM RPA in the presence or absence of 3 μM ‘1’ or ‘6’, in the binding buffer (30 mM Tris-Acetate pH7.5, 1 mM …
Figure 3
Biochemical characterization of ‘6’.
(a) Aromatic region of the 1D 1H NMR spectrum of compound ‘6’ alone (black) and the WaterLOGSY spectrum of 40 μM compound ‘6’ in the presence of 3.3 μM RAD52 (red). The nonexchangeable proton peaks …
Figure 4
Virtual screening places the RAD52 inhibitors within the ssDNA binding groove.
(a) Three individual monomers of the RAD52-NTD undecameric ring (PDB 1KNO) are colored yellow, green and blue respectively. ‘1’ and ‘6’ occupy similar sites at the interface of two subunits. Two …
Figure 5 with 1 supplement
Inhibiting the RAD52-ssDNA interaction interferes with RAD52/MUS81-mediated DSB formation essential for replication fork recovery in check point deficient cells.
(a) Representative images showing fields of cells from the comet assay for untreated, as well as from UCN01 (300 nM) and HU (2 mM) treated cells in the presence and absence of ‘1’, ‘6’, and siRAD52. …
Figure 5—figure supplement 1
Compound ‘1’ does not affect MUS81 activity.
(a) GM01604 wild-type fibroblasts were transfected with CTRL or MUS81 siRNA. Forty eight hours after transfection the fibroblasts were lysed and analysed by WB with the indicated antibodies. (b) …
Figure 6
Inhibition of ssDNA binding by RAD52 is sufficient to stimulate cell death in the absence of the MUS81 nuclease or BRCA2 tumor suppressor.
(a) The WB shows the analysis of RNAi. (b) Evaluation of cell death after replication stress. Forty eight hours after transfection with the BRCA2 or MUS81 siRNAs, alone or in combination, the …
Figure 7
Inhibition of ssDNA binding to RAD52 is sufficient to stimulate cell death in the absence of the BRCA2 tumor suppressor.
(a) Western blot analysis of BRCA2, RAD52, and GAPDH (loading control) protein levels in GM01604 cells treated with Ctrl, BRCA2, and RAD52 siRNAs. (b) Evaluation of cell death after replication …
Figure 8
In silico screening campaign identifies novel small molecule that inhibits the RAD52-ssDNA interaction.
(a) Docking workflow involved RAD52-NTD undecameric ring (PDB 1KNO) pre-processing, AnalytiCon Discovery MEGx Natural Products Screening Library pre-processing, and classical docking using the Dock …
Figure 9
Biochemical characterization of NP-004255.
(a) Aromatic region of the 1D 1H NMR spectrum of compound NP-004255 alone (black) and the WaterLOGSY spectrum of 40 μM compound NP-004255 in the presence of 3.3 μM RAD52 (red). The nonexchangeable …
Author response image 1
The RAD52 inhibitor interferes with the ability of RAD52 to localize in nuclear foci after DSBs.
https://doi.org/10.7554/eLife.14740.018Tables
Table 1
The twelve hits from the FRET-based HTS assay aimed at finding inhibitors of the RAD52-ssDNA interaction.
| # | Small molecule name; CAS # | Small molecule structure | IC50 (DNA binding); FRET value at saturation | IC50 (Annealing extent) | SAEM ΔG (kcal/mol) |
|---|---|---|---|---|---|
| ‘1’ | (−)−Epigallocatechin; 970-74-1 |  | ssDNA: 1.8 ± 0.1 µM; 0.45 ± 0.004 ssDNA-RPA: 1.6 ± 0.1 µM; | ssDNA: 4.9 ± 0.4 µM ssDNA-RPA 4.8 ± 1.8 µM; | −8.60 |
| ‘3’ | Methacycline Hydrochloride; 3963-95-9 |  | 2.0 ± 0.17 µM; 0.47 ± 0.01 | 3.8 ± 0.2 µM | −4.61 |
| ‘4’ | Rolitetracycline; 751-97-3 |  | 29 ± 8.2 µM; 0.56 ± 0.04 | NI | −10.5 |
| ‘5’ | (−)−Epicatechin gallate; 1257-08-5 |  | 255 ± 16 nM; 0.41 ± 0.004 | 20 ± 0.7 µM | −9.87 |
| ‘6’ | Epigallocatechin-3-monogallate; 989-51-5 |  | ssDNA: 277 ± 22 nM; 0.46 ± 0.01 ssDNA-RPA: 1.6 ± 0.5 µM; | ssDNA: 6.7 ± 2.1 µM ssDNA-RPA: 3.7 ± 0.5 µM; | −10.69 |
| ‘7’ | (−)−Epicatechin; 490-46-0 |  | 1.45 ± 0.11 µM; 0.51 ± 0.01 | NI | −9.03 |
| ‘14’ | Oxidopamine; 28094-15-7 1199-18-4 |  | 779 ± 51 nM; 0.50 ± 0.01 | NI | −5.71 |
| ‘15’ | Quinalizarin; 81-61-8 |  | 563 ± 40 nM; 0.51 ± 0.01 | 5.6 ± 0.6 µM | −9.17 |
| ‘16’ | Cisapride Monohydrate; 260779-88-2 81098-60-4 |  | 1.06 ± 0.05 µM; 0.50 ± 0.01 | NI | −8.39 |
| ‘17’ | Cedrelone; 1254-85-9 |  | >300 µM | NI | −10.0 |
| ‘18’ | Asiatic Acid; 464-92-6 18449-41-7 |  | >800 µM | >100 µM | −11.33 |
| ‘19’ | Gossypetin; 489-35-0 |  | 913 ± 58 nM; 0.49 ± 0.01 | 6.0 ± 2.3 µM | −9.30 |
