Small molecules
Organism phenotypes
RNAi
Small molecules
PubChem
Entering BRCA1 in the PubChem BioAssay search engine returned 7 screens. 5 of these screens, however, were protein-binding assays for small molecules that interact with the BRCA1-associated protein 1, not the BRCA1 protein itself. The two screens that found compounds that interact with BRCA1 were done by the same lab group using two different fluorophores (red and green). More specifically, this group was looking for drugs that inhibited the interaction between BRCT domain of BRCA1 with pBACH1 helicase, and thus preventing DNA repair. [1,2,3]
Red fluorophore screen
The screen done using a red fluorophore in the protein-binding screen resulted in 20 compounds with positive results. Figure 1 below shows a cluster diagram that rates the similarity in structure between the compounds isolated. The scores determined for each compound through analysis is shown at the right. Table 1 shows the structures of the compounds that resulted in scores over 80. The potency is also listed in this table, interestingly enough with the highest potency in the higher scoring higher (score is not based on the potency of the compound, but the effectiveness of the compound to bind).
Figure 1. Compound clustering tree for red fluorophore results. For interactive features, click on figure to link out to original website.
Table 1. Compound structures and scores for red fluorophore results. For interactive features, click on table to link out to original website.
Green fluorophore screen
The screen done using a green fluorophore in the protein-binding screen resulted in 34 compounds with positive results. Figure 2 below shows a cluster diagram that rates the similarity in structure between the compounds isolated. The scores determined for each compound through analysis is shown at the right. Table 2 shows the structures of the compounds that resulted in scores over 80. The potency is also listed in this table, again with the highest potency in the higher scoring higher.
Figure 2. Compound clustering tree for green fluorophore results. For interactive features, click on figure to link out to original website. Please refer to the key in Figure 1 above.
Table 2. Compound structures and scores for green fluorophore results. For interactive features, click on table to link out to original website.
Analysis
Between the two fluorophore assays used, a couple of the compounds found were common to both tests. For example, compound 2 in Table 1 is the same as compound 1 in Table 2. Interestingly, the potency of the same chemical was different between the two experiments, which may indicate interference of the fluorophore with the compound or protein or simply reflects error in the experiment. Regardless, the fact that some of the same compounds were detected in both experiments to bind BRCA1 further validates their data.
It is also interesting to note that the structure similarity does not indicate whether or not the compound will bind to BRCA1 similarly. This can be seen by examining the compound scores in Figures 1 and 2, which cluster the compounds based on structural similarity. This indicates that compounds diverse in their chemical structure may nevertheless be similar in biological function.
I would also like to point out that searching for compounds to be used for drug therapy for BRCA1 is futile. Most mutations in BRCA1 individuals are severe truncations in the protein, affecting its localization to the nucleus as well as abolishing function in DNA damage sensing pathways. Its role as a tumor suppressor would indicate that therapeutic drugs would need to reactivate function of the protein, which is nearly impossible if most of the protein is missing. Therefore, I can only see two purposes for screening these chemicals. First, they could be used in the laboratory as a way to knock-down BRCA1 function other than by mutating the gene, and thus allowing for temporal control. Second, knowing which compounds inhibit BRCA1 could lead to avoidance of these chemicals to prevent breast cancer if these are common compounds.
ChemBank and DrugBank were also searched for chemicals associated with BRCA1, but no results were returned.
[1] Inglese, J., Auld, D.S., Jadhav, A., Johnson, R.L., Simeonov, A., Yasgar, A., Zheng, W., and Austin, C.P. (2006).
Quantitative high-throughput screening: a titration-based approach that efficiently identifies biological
activities in large chemical libraries. Proc Natl Acad Sci 103(31):11473-11478.
doi:10.1073/pnas.0604348103.
[2] Lokesh, G.L., Muralidhara, B.K., Negi, S.S., and Natarajan, A. (2007). Thermodynamics of phosphopeptide
tethering to BRCT: the structural minima for inhibitor design. J Am Chem Soc 129(35):10658-10659.
doi:10.1021/ja0739178.
[3] Lokesh, G.L., Rachamallu, A., Kumar, G.D., and Natarajan, A. (2006). High-throughput fluorescence
polarization assay to identify small molecule inhibitors of BRCT domains of breast cancer gene 1. Anal
Biochem 352(1):135-141. doi:10.1016/j.ab.2006.01.025.
Site created by Jessica D. Kueck
Genetics 677 Assignment, Spring 2009
University of Wisconsin-Madison
