High Throughput Screening for Small Molecule Interactions with Nucleic Acid Binding Proteins

Nucleic acid binding proteins are critical nodes in almost all cell signaling networks. Cell network architecture depends on highly regulated nucleic acid binding to determine cell identity, developmental trajectory, environmental response, and homeostasis. These proteins govern all aspects of cancer, from oncogenesis to metastasis, as well as treatment resistance and tumor recurrence. Our ability to manipulate these entities in cells, and therefore our ability to understand their function precisely or to intervene in pathological processes, is extremely limited without genetic manipulation. To address this challenge, small molecule binding screens were implemented against transcription factor and RNA-binding protein targets. The MYC oncoprotein was successfully inhibited by an indirect strategy through stabilization of its obligate interacting partner MAX in an inactive form. A small molecule that binds to MAX shifts the equilibrium of the MYC/MAX system to favor transcriptionally repressive MAX homodimers, effectively reducing MYC transcriptional activity. Assays against the MYC target LIN28B were developed for further indirect inhibition of MYC; however, an unexpected biological interaction with cellular reporters prevents further biological characterization. Instead, biophysical secondary assays were implemented and expanded to include a panel of RNA-Binding Proteins implicated in cancer and neurodegeneration. Validation of assay positives demonstrates not only several starting points for chemical probe development, but also the fundamental chemical tractability of protein domains involved in RNA binding. Together, this work generates new chemical matter for inhibiting previously intractable targets and identifies a strategy for systematic discovery of inhibitors for protein-RNA interfaces.

Name thesis:degree_name

Doctoral

Department dc:contributor.department

Massachusetts Institute of Technology. Department of Biological Engineering

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2022

Author dc:creator

• Wilson, Robert M.

Advisor dc:contributor.advisor

• Koehler, Angela N.

Statement dc:rights

• In Copyright - Educational Use Permitted
• Copyright MIT

Licence dc:rights.uri

• http://rightsstatements.org/page/InC-EDU/1.0/

Handle dc:identifier.uri

https://hdl.handle.net/1721.1/147898

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/147898