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Title page for ETD etd-03252015-043915

Type of Document Dissertation
Author Sun, Qi
URN etd-03252015-043915
Title Discovery of K-Ras inhibitors for the treatment of cancer
Degree PhD
Department Biochemistry
Advisory Committee
Advisor Name Title
Stephen Fesik Committee Chair
Charles Sanders Committee Member
Lawrence Marnett Committee Member
Robert Coffey Committee Member
Walter Chazin Committee Member
  • Cancer
  • K-Ras
  • Fragment-based drug discovery
  • Structural-based drug design
Date of Defense 2015-01-15
Availability unrestricted
Ras is a small GTPase that functions as a molecular switch, cycling between inactive (GDP-bound) and active (GTP-bound) states. Mutations in Ras fix the protein in the active state and endow tumor cells with the ability to proliferate, evade apoptosis and metastasis. Indeed, aberrant K-Ras signaling plays a role in 30% of all human cancers, with the highest incidence of activating mutations found in pancreatic (70-90%), colon (30-50%), and lung (20-30%) carcinomas. Thus, Ras inhibition represents an attractive therapeutic strategy for many cancers. However, Ras activation and signaling is accomplished primarily through protein-protein interactions. Such protein interfaces typically lack well-defined binding pockets and have been difficult to target with small molecules.

My goal during my graduate studies was to discover potent Ras inhibitors using state-of-the-art methodologies such as fragment-based methods and structure-based design. To achieve this goal, I started by screening a fragment library of 11,000 compounds using NMR in which molecules were identified that bind to K-Ras. Based on the crystal structures of protein-ligand complexes, these compounds were found to bind to a hydrophobic pocket that is absent in ligand-free K-Ras. Using structure-based design, we synthesized analogs of the fragment hits with improved binding affinity as well as functional activity in a SOS-catalyzed nucleotide exchange assay. To further optimize the inhibitors, a second-site screen was conducted using a cysteine tethering strategy to block the first pocket. Using this approach, fragments that bind in a distinct pocket were identified. In addition, small molecules were also found that bind to the Ras/SOS complex and inhibit Ras signaling downstream, which can be used as an alternative approach to target K-Ras. This work provides an important starting point and a template for the rational design of more potent chemical probes for elucidating new insights into Ras signaling and for discovering Ras inhibitors for the treatment of Ras-driven cancers.

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