Evolution of Cyclic Peptide Scaffolds to Target Nucleic Acids

G-quadruplex;Nucleic Acids;RNA;bTAR;bTat;cyclic peptide;phage display

Burns, Virginia Abigail ; Dr. Christian Melander, Committee Chair,Dr. Reza Ghiladi, Committee Member,Dr. John Cavanagh, Committee Member,Dr. Tatyana Smirnova, Committee Member,Burns, Virginia Abigail ; Dr. Christian Melander ; Committee Chair ; Dr. Reza Ghiladi ; Committee Member ; Dr. John Cavanagh ; Committee Member ; Dr. Tatyana Smirnova ; Committee Member

University:North Carolina State University

关键词: G-quadruplex;    Nucleic Acids;    RNA;    bTAR;    bTat;    cyclic peptide;    phage display;   

Others  :  https://repository.lib.ncsu.edu/bitstream/handle/1840.16/4174/etd.pdf?sequence=1&isAllowed=y

美国|英语

来源: null

【 摘 要 】

Given the great strides that have taken place over the past few decades in our understandingof nucleic acid’s role in cellular processes, it has become abundantly clear that DNA andRNA can provide a great tool and target for drug development. The human genome projecthas provided a major impetus in identifying human genes implicated in diseases and hasopened the door to new possibilities with DNA-based therapeutics. Further developments intranscriptomics and proteomics will provide an additional momentum for the advancement oftherapeutics by supplying novel targets for drug design, screening, and selection. As newdiscoveries are made and our knowledge of nucleic acid’s role in life processes is expanding,the area of chemistry focused on learning how to target and exploit these nucleic acids forcontrol of their relative processes is also expanding. New strategies to develop molecules thatcan both identify DNA or RNA targets and modulate their activity are of great interest tomedicinal chemistry. The goal of this research was to delineate an efficient approach totargeting nucleic acids that yields cell permeable, biologically stable molecules that can beexploited in vivo applications.Herein describes our approach which utilizes cyclic peptide phage display for the evolutionof novel cyclic peptide scaffolds that target a given oligonucleotide. Evolved scaffolds arethen tested in vitro as discrete entities to assess their binding capabilities. Given that thephage display scaffolds employ a disulfide linker for cyclization, alternative redox stablemacrocylic linkers were developed and synthesized. Second and third generation analogueswere subsequently assessed for the retention of the desired binding activity.The details of this pragmatic approach were developed using the bTAR RNA oligo as amodel system. Results indicated that not only could we evolve bTAR binders form a pool of1.2 billion possible scaffolds in a relatively short time, but that these scaffolds bound withaffinities in the low micromolar range when tested as discrete entities. We also successful indeveloping an alternative dicarbon macrocyclic linker to yield redox stable analogues.Subsequent testing of the analogue scaffolds indicated the retention of the desired bindingproperties.