Academic Commons

Theses Doctoral

Application and development of methods towards the target identification of biologically-active small molecules

SriRamaratnam, Rohitha

Small molecules have played an important role in defining the functions and identities of numerous proteins involved in fundamental biological processes as well as pathways involved in disease. Chemical genetics represents the formalization of this process into a defined field desiring to achieve the breadth and specificity of classical genetics. In order to gain full advantage of a small molecule's ability to perturb the cell for novel or desired phenotypes, a complete understanding of the molecule's mechanism of action must be achieved. Identification of the biological targets of a molecule represents the most direct approach to attaining this knowledge.
In our strategy to find novel mechanisms to target cancers with oncogenic RAS mutations, we have used small molecules to probe specific weaknesses of this cancerous network through synthetic lethal screening. One molecule identified in these screens, RSL3, attracted interest as a candidate for target identification studies because of its potent lethality and potentially unique mechanism of action. We used an affinity chromatography approach to directly isolate binding partners of RSL3 by modifying the molecules structure to incorporate various affinity tags. Through these experiments we ultimately identified a number of interesting candidate targets. Investigations validating these targets suggest that multi-targeted modulation of antioxidant and prostaglandin networks may be a mechanism for selectively killing cancers with oncogenic RAS.
The identification of biological targets of small molecules poses a difficult challenge to the field of forward chemical genetics. Thus, we attempted to optimize a unique method for target identification, the yeast three-hybrid system (Y3H), which detects small molecule-protein interactions through a transcriptional assay in vivo. We created a version of our Y3H system that incorporated a covalent anchor and compared it with the existing state-of-the-art, which uses a high affinity non-covalent anchor. Transcriptional assays indicated our new system was functional, but surprisingly could not improve upon the original Y3H system. These results highlight the complexities of manipulating ligand-receptor interactions in vivo.


  • thumnail for SriRamaratnam_columbia_0054D_10415.pdf SriRamaratnam_columbia_0054D_10415.pdf application/pdf 4.47 MB Download File

More About This Work

Academic Units
Thesis Advisors
Stockwell, Brent R.
Cornish, Virginia W.
Ph.D., Columbia University
Published Here
December 12, 2017