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Discovery and Optimization of Ras Inhibitors Through Combinatorial and Medicinal Chemistry

Upadhyaya, Punit
http://rave.ohiolink.edu/etdc/view?acc_num=osu1405516420

Abstract Details

2014, Doctor of Philosophy, Ohio State University, Chemistry.
Ras is a small family of proteins that are ubiquitously expressed and play critical roles in cell proliferation, differentiation and survival. Mutations in the Ras gene are present in approximately 30 % of human cancers. These mutations result in the functional activation of Ras due to the impairment of GTP hydrolysis. Despite half a century of extensive research, no therapeutics has been very successful in clinical trials. Most of the efforts to discover inhibitors of Ras have focused on small molecules. However, this approach may not be successful, as Ras does not contain any deep binding pockets ideal for small molecule binding. The mutant K-Ras G12V is prevalent in major neoplasms that result in a high level of mortality. Unlike G12C and G12D mutants that contain a reactive moiety (thiol and carboxyl groups respectively) that can be specifically targeted with covalent inhibitors, K-Ras G12V presents a much more challenging target. Since inhibition of Ras function requires a molecule that can compete with large effector proteins for binding to Ras, we chose to screen monocyclic and bicyclic peptide libraries to obtain binders and inhibitors against K-Ras G12V. These macrocycles occupy a unique chemical space between small molecules and antibodies and currently underexplored as inhibitors of Protein Protein Interactions (PPI’s). The one bead two compound (OBTC) approach was used to design bicyclic and monocyclic libraries with the potential inhibitor displayed on the surface and the corresponding encoding tag for hit identification. We successfully incorporated unique features in the library such as the ability to selective cleave and screen cyclic peptides in solution. This feature enhances our screening procedure and reduces the time and expense associated with the screening process. The bicyclic library screening produced compounds that bound to K-Ras G12V with high affinity. Some of these inhibitors bound to the effector binding surface of Ras and inhibited their function. Other molecules bound to a different site on Ras and were unable to inhibit Ras-effector protein interaction. We were successful in finding molecules that bound specifically to activated GTP bound K-Ras G12V with 10-fold selectivity. Although the usefulness of these molecules is blunted by their lack of cellular activity, we are currently in the process of improving their properties such as cell permeability and binding affinities to address that issues. The monocyclic library produced compounds that in addition to inhibiting K-Ras in vitro, were able to inhibit growth of lung cancer cells. Despite a lack of structural information on the binding mode of these compounds with the protein, we were able to use SAR studies to obtain molecules with improved potency and cell permeability. The most potent compound, 9A5 bound to GTP-K-Ras with 6-fold selectivity. 9A5 also downregulated major signaling pathways of K-Ras and induced apoptosis in lung cancer cell lines. These compounds represent the most potent inhibitors of K-Ras (in addition to other Ras proteins) to date and may serve as lead compounds for further drug development.
Dehua Pei (Advisor)
Jon Parquette (Committee Member)
Mark Foster (Committee Member)
140 p.
Biochemistry; Chemistry
Combinatorial Chemistry, Cyclic Peptides, Bicyclic Peptides, Ras Inhibitors

Recommended Citations

Citations

  • Upadhyaya, P. (2014). Discovery and Optimization of Ras Inhibitors Through Combinatorial and Medicinal Chemistry [Doctoral dissertation, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu1405516420

    APA Style (7th edition)

  • Upadhyaya, Punit. Discovery and Optimization of Ras Inhibitors Through Combinatorial and Medicinal Chemistry. 2014. Ohio State University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=osu1405516420.

    MLA Style (8th edition)

  • Upadhyaya, Punit. "Discovery and Optimization of Ras Inhibitors Through Combinatorial and Medicinal Chemistry." Doctoral dissertation, Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1405516420

    Chicago Manual of Style (17th edition)

osu1405516420
44
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This open access ETD is published by The Ohio State University and OhioLINK.