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Principal Investigator: Alexander Deiters
Organization: UNIVERSITY OF PITTSBURGH AT PITTSBURGH
Fiscal Year: 2024
Award: $356,542
Funding agency: National Institute of General Medical Sciences
PROJECT SUMMARY
The overall goal of this proposal is to develop a fundamentally new class of oligonucleotide agents – covalent
aptamers – that will have a major impact on nucleic acid-based reagents and therapeutics. Covalent aptamers
will be an enabling methodology behind new aptamer applications and will provide new solutions to persistent
limitations of this compound class. Aptamers are engineered oligonucleotides that bind protein targets and have
found applications in a multitude of areas, including therapeutics, diagnostics, drug delivery, and imaging. They
bind their targets with affinity and specificity that rivals those of antibodies, while displaying lower production
cost, higher production consistency, and the ability to easily introduce chemical modifications. Capitalizing on
the ability to amplify and sequence nucleic acids, aptamers are being generated through SELEX, a powerful in
vitro selection process. Our central hypothesis is that the formation of a covalent bond between an aptamer – or
a functional motif delivered by the aptamer – and its target protein will provide unprecedented residence time,
increase nuclease stability (or obviate the need for it), and facilitate aptamer selection. Furthermore, covalent
bond formation enables new applications based on the aptamer platform. The following aims will test this hy-
pothesis. Aim 1: The chemistry of covalent aptamers. To gain a comprehensive understanding of the design
principles behind covalent aptamers and to enable broad applicability, we will explore their chemistry based on
our promising preliminary results. We will explore applications in antibody drug conjugate assembly, as well as
catalytic covalent bond formation. Aim 2: Cell-based applications of covalent aptamers. We will develop several
applications that are enabled by covalent aptamers and that showcase their utility as chemical biology probes.
We are focusing on cell-surface proteins due to the rich collection of aptamers that have been reported. Aim 3:
Selection of covalent aptamers. For the de novo generation of covalent aptamers capable of selectively cross-
linking to any chosen protein target without prior sequence and/or structural information, we will develop a gen-
eralized in vitro selection process that adds distinct advantages to traditional SELEX.
Terms: <2019-nCoV S protein><2019-nCoV spike glycoprotein><2019-nCoV spike protein><Affinity><Amino Acids><Animal Model><Animal Models and Related Studies><Antibodies><Antibody-drug conjugates><Antisense Agent><Antisense Oligonucleotides><Area><Basal Transcription Factor><Basal transcription factor genes><Base Sequence><Binding><Binding Proteins><Biologic Models><Biological><Biological Models><Biology><Brachydanio rerio><COVID-19 S protein><COVID-19 spike><COVID-19 spike glycoprotein><COVID-19 spike protein><Cell Body><Cell Surface Proteins><Cell model><Cell surface><Cells><Cellular model><Chemicals><Chemistry><Collection><Danio rerio><Data><Detection><Development><Diagnostic><Disease><Disorder><Drug Delivery><Drug Delivery Systems><Embryo><Embryonic><Engineering><Evaluation><General Transcription Factor Gene><General Transcription Factors><Generations><Goals><Government><Image><Immobilization><Immune Targeting><Immune response><Immunological response><In Vitro><Investigators><Kinetics><Label><Libraries><Ligand Binding Protein><Ligand Binding Protein Gene><Ligands><Literature><Mediating><Metabolic Protein Degradation><Methodology><Mice><Mice Mammals><Model System><Modification><Molecular Interaction><Murine><Mus><Nucleic Acids><Nucleotide Sequence><Nucleotides><Oligo><Oligonucleotides><Persons><Position><Positioning Attribute><Post-Translational Modification Protein/Amino Acid Biochemistry><Post-Translational Modifications><Post-Translational Protein Modification><Post-Translational Protein Processing><Posttranslational Modifications><Posttranslational Protein Processing><Preparation><Process><Production><Protein Binding><Protein Modification><Protein Turnover><Proteins><RNA vaccine><RNA-based vaccine><Rationalization><Reaction><Reagent><Regulatory Protein Degradation><Reporting><Research><Research Personnel><Researchers><SARS-CoV-2 S><SARS-CoV-2 S protein><SARS-CoV-2 spike><SARS-CoV-2 spike glycoprotein><SARS-CoV-2 spike protein><Severe acute respiratory syndrome coronavirus 2 S protein><Severe acute respiratory syndrome coronavirus 2 spike glycoprotein><Severe acute respiratory syndrome coronavirus 2 spike protein><Site><Specificity><Structure-Activity Relationship><Testing><Therapeutic><Thrombase><Thrombin><Time><Transcription Factor Proto-Oncogene><Transcription factor genes><Virus><Zebra Danio><Zebra Fish><Zebrafish><aminoacid><antisense oligo><aptamer><biologic><bound protein><chemical structure function><circulating cancer cell><coronavirus disease 2019 S protein><coronavirus disease 2019 spike glycoprotein><coronavirus disease 2019 spike protein><cost><covalent bond><crosslink><design><designing><developmental><experience><fibrinogenase><host response><imaging><immune system response><immunoresponse><improved><in vivo><mRNA vaccine><mRNA-based vaccine><model of animal><novel><nuclease><nucleic acid chemical synthesis><nucleic acid sequence><nucleic acid therapy><nucleic acid-based therapeutics><oligos><orthopedic freezing><preparations><programs><protein degradation><protein purification><residence><residential building><residential site><small molecular inhibitor><small molecule inhibitor><spike proteins on SARS-CoV-2><structure function relationship><success><therapeutic nucleic acids><tool><transcription factor>