Chemical Genetics
Chemical genetics is how small molecules regulate the function of a protein. Small molecules are molecules that weigh less than 1000 daltons. Most drugs are small molecules because of their ability to modify proteins which alters the proteins function. When a small molecule binds to a protein depending on where the molecule bound can change the function of the protein. Proteins have areas on them where inactivation can occur and other sites where activation can occur, this makes understanding small molecule interactions extremely important when researching a particular protein. Researchers that do this process often, must have a sort of "library" where they can keep a large amount of small molecules that can be used to interact with a multitude of proteins at a time. There are two types:
Diversity-oriented libraries- have small molecules that are structurally unrelated, this is typically used first in order to figure out what type of general molecule the protein interacts with
Target-Oriented libraries - have highly related small molecules that are structurally similar,but they also have slightly different side chains that are used to decipher what chemical group reacts the most with the protein
Diversity-oriented libraries- have small molecules that are structurally unrelated, this is typically used first in order to figure out what type of general molecule the protein interacts with
Target-Oriented libraries - have highly related small molecules that are structurally similar,but they also have slightly different side chains that are used to decipher what chemical group reacts the most with the protein
After you choose/make up your library you will then screen the small molecules to see how they bind to the targeted protein. We set this up using microarrays with labeled dyes to detect where we see binding from our small molecules to our targeted protein.
Below is a video that explains Microarrays however this looks at DNA instead of proteins but it is the same concept for the last step of chemical genetics with small molecules.
Small Molecules and DNA Polymerase Gamma
From the literature found at PubChem we notice that assays using kasanosins A and B to attempt to inhibit DNA polymerase gamma. They were unsuccessful in there assays to inhibit the DNA polymerase gamma but they were able to inhibit DNA polymerase lambda and beta. There were also assays that used 3,4-di-O-galloyl-5-O-digalloylquinic acid a type of tetragalloylquinic acid, because of its percieved ability to inhibit HIV reverse transcriptase by inhibiting the cells ability to replicate. However this was also unsuccessful in inhibiting DNA polymerase. Finally the last assay that had confirmed results of some kind was involving a pateamine A molecule that was also unsuccessful in inhibiting DNA polymerase gamma.
Analysis
Some of assays conducted didn't produce any results that show'd successful inhibition. The assays made sense to their chemical compounds and in some cases they were successful in inhibiting other DNA polymerases however they were unable to inhibit the DNA polymerase thats responsible for correct mitochondrial function. This could be due to the DNA polymerase being highly regulated and found in the mitochondria and not the nucleus as other DNA polymerases are located. The mitochondria may also be more difficult to manipulate with drugs which could be affecting these results and could make finding a good chemical molecule to react with our desired protein difficult. However one did successfully inhibit DNA polymerase gamma, the researchers used 3,4-dihydro-1H-[1]-benzothieno[2,3-c]pyran and 3,4-dihydro-1H-pyrano[3,4-b]benzofuran derivatives to look at non-nucleoside inhibitors of HCV NS5B RNA dependent RNA polymerase.
This molecule was successful in inhibiting DNA polymerase gamma with a concentrations of up to 50uM. What is interesting is that these molecules are known as RNA polymerase inhibitors not DNA polymerase inhibitors. In the future we could engineer molecules that contain the general structure pictured above and manipulate substituents like the Nitrogen and the Fluorine and see how the molecule reacts in those conditions in order to further study the protein.
References
- "Inhibition of Human DNA Polymerase Gamma at 100 UM." AID 385390. PubChem, n.d. Web. 26 Mar. 2015
- "Inhibitory Activity against Human Mitochondrial DNA Polymerase Gamma Upto 50 UM." AID 259170. PubChem, May 2010. Web. 26 Mar. 2015.
- "Bugs, Drugs and Chemical Genomics." Nature.comB. Nature Publishing Group, 15 Dec. 2011. Web. 1 Mar. 2015.