Date of Award
1-2023
Degree Type
Thesis
Degree Name
Master of Science (MS)
Department
Chemistry
First Advisor
Benjamin J. Alper, Ph.D.
Abstract
The CISH gene product (protein) SH2 domain binds to PLC Gamma l and inhibits the normal function of the T-cell signaling pathway and immune response. This is a pressing concern in tumorous blood cancers as the body's immune system cannot fight against a growing cancer. Dr. Steven Ansell from The Mayo Clinic hypothesized that there must be a way to create a molecule that will bind more readily to the CISH SH2 domain, mitigating the inhibitory impact of CISH on T-cell .
Homology modeling and computational peptide design were used to investigate the Ansell hypothesis. Fir t, homology models of the SH2 domain of CISH were generated using YASARA modeling software. Second, CISH SH2 homology models were tructurally aligned with the experimentally determined PLC gamma SH2/pTyr peptide complex u ing multiple algorithms (Mustang, MMLigner, Smith & Waterman, and Needleman & Wunsch). Third, the resulting CISH SH2/pTyr peptide complex models were evaluated for structural quality, resulting in the best homology model (2cish_smith) being selected as the structure used in the novel peptide inhibitor design. Fourth, the CISH SH2/pTyr peptide complex was visually assessed to identify protein-facing peptide side chains as potential sites for amino acid substitutions to enhance binding affinity; in this first design round, the pTyr peptide position was ignored. Fifth, the three identified peptide positions were mutated to all 20 common amino acids, resulting in 60 peptides. Sixth, the mutated peptides were scored for binding affinity using three computational approaches. Finally, the affinity core and mutant peptides were analyzed, and the most promising ones were selected for possible experimental testing. The plan is for Dr. Ansell and his team at the Mayo Clinic will obtain and test the proposed peptides in biochemical assays to determine their experimental activities and determine if the proposed peptides successfully inhibit the CISH protein from binding to PLC Gamma 1 and reactivate normal T- cell signaling pathway function.
Recommended Citation
Paquette, Evelyn, "Using Homology Modeling And Computational Protein-Peptide Design To Identify Potential Inhibitors Of Cish Binding To PLC-Gamma 1 In The T-Cell activation Pathway Of Blood Cancers" (2023). Chemistry Master’s Theses. 61.
https://digitalcommons.sacredheart.edu/chem_thes/61
Comments
Master's thesis submitted to the Faculty of the Department of Chemistry at Sacred Heart University in partial fulfillment of the requirements for the degree of Master of Science.