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Principal Investigator: Pranam Chatterjee
Organization: DUKE UNIVERSITY
Fiscal Year: 2023
Award: $331,981
Funding agency: National Cancer Institute
Summary
Over 600 human proteins have been recently prioritized as key cancer targets, with nearly half being
considered ‘intractable’ by standard small-molecule inhibition approaches, due to target instability and active
site accessibility constraints. By redirecting the ubiquitin-proteasomal pathway (UPS) for targeted protein
degradation, the proteolysis-targeting chimera (PROTAC) technology provides a potential solution, enabling
rapid and continuous target consumption as well as the stronger pharmacological effects than small molecule
inhibition. Nonetheless, PROTACs suffer from similar developmental hurdles as small molecules and cannot be
easily designed for motif or post-translational modification-specific targeting. To address these hurdles,
research efforts have shifted toward gene therapy approaches by introducing the concept of protein-mediated
protein degradation. Here, E3 ubiquitin ligases are redirected by replacing their natural substrate binding
domains with “off-the-shelf” binding domains, including nanobodies, antibodies, and DARPins, to generate
target-specific ubiquibodies. To augment this platform, we recently exploited natural protein-protein interaction
information to develop algorithmic pipelines that prioritize target-selective peptides which can be fused to the
E3 ubiquitin ligase conjugation domains to induce target protein degradation. In this project, we will augment
our current methods to enable the development of these ubiquibodies (uAbs) for any protein, including those
deemed ‘intractable’ by small molecule-based means. To do this, we will automate a bipartite algorithmic
pipeline that leverages recent advancements in protein language modeling as well as existing co-complex
databases to design peptide binders to diverse protein targets, including those with solved co-crystals as well
as those with minimal structural information. Specifically, our pipeline will take user-specified target proteins as
inputs, and generate prioritized lists of candidate peptide binders as outputs, enabling subsequent generation
of uAbs for target degradation. Through library-on-library fluorescence-based assays in human cells and
subsequent encapsulation of uAb mRNA in lipid nanoparticles (LNPs), we will develop a scalable method to
test and translate our degraders for downstream in vivo validation. In total, this work will generate a robust
peptide design tool that will enhance targeted protein degradation efforts and lay the foundation for
programmable proteome editing.
Terms: <2019 novel corona virus><2019 novel coronavirus><2019-nCoV><Active Sites><Address><Algorithms><Amino Acid Sequence><Antibodies><Architecture><Assay><Base Sequence><Binding><Bioassay><Biologic Assays><Biological Assay><COVID-19 virus><COVID19 virus><CRISPR approach><CRISPR based approach><CRISPR method><CRISPR methodology><CRISPR technique><CRISPR technology><CRISPR tools><CRISPR-CAS-9><CRISPR-based method><CRISPR-based technique><CRISPR-based technology><CRISPR-based tool><CRISPR/CAS approach><CRISPR/Cas method><CRISPR/Cas technology><CRISPR/Cas9><CRISPR/Cas9 technology><Cancers><Cas nuclease technology><Cell Body><Cells><Chemistry><Chimera><Chimera Protein><Chimera organism><Chimeric Proteins><Clustered Regularly Interspaced Short Palindromic Repeats approach><Clustered Regularly Interspaced Short Palindromic Repeats method><Clustered Regularly Interspaced Short Palindromic Repeats methodology><Clustered Regularly Interspaced Short Palindromic Repeats technique><Clustered Regularly Interspaced Short Palindromic Repeats technology><CoV-2><CoV2><Code><Coding System><Cold-Insoluble Globulins><Complex><Consumption><DNA><DNA Therapy><Data Bases><Data Set><Databases><Deoxyribonucleic Acid><Development><Disease><Disorder><E3 Ligase><E3 Ubiquitin Ligase><Employment><Encapsulated><Engineering><Engineering / Architecture><FN1><Fibronectin 1><Fibronectins><Fluorescence><Formulation><Foundations><Fusion Protein><Gene Delivery><Gene Transfer Clinical><Generations><Genetic><Genetic Intervention><Genetics-Mutagenesis><Goals><Grips><Human><In Vitro><Isoforms><Kinases><LETS Proteins><Laboratories><Language><Large External Transformation-Sensitive Protein><Learning><Length><Libraries><Malignant Neoplasms><Malignant Tumor><Masks><Mediating><Messenger RNA><Metabolic Protein Degradation><Methodology><Methods><Modality><Modeling><Modern Man><Molecular Configuration><Molecular Conformation><Molecular Interaction><Molecular Stereochemistry><Mutagenesis><Mutagenesis Molecular Biology><Non-Polyadenylated RNA><Nucleotide Sequence><Opsonic Glycoprotein><Opsonic alpha(2)SB Glycoprotein><Output><Pathogenicity><Peptides><Phosphatases><Phosphohydrolases><Phosphomonoesterases><Phosphoric Monoester Hydrolases><Phosphotransferase Gene><Phosphotransferases><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><Primary Protein Structure><Protac><Protein Engineering><Protein Isoforms><Protein Modification><Protein Turnover><Proteins><Proteolysis targeting chimeric><Proteome><Protocol><Protocols documentation><RNA><RNA Gene Products><Rapid screening><Regulatory Protein Degradation><Research><Ribonucleic Acid><Role of Parkin in the Ubiquitin-Proteasomal Pathway><SARS corona virus 2><SARS-CO-V2><SARS-COVID-2><SARS-CoV-2><SARS-CoV2><SARS-associated corona virus 2><SARS-associated coronavirus 2><SARS-coronavirus-2><SARS-related corona virus 2><SARS-related coronavirus 2><SARSCoV2><Severe Acute Respiratory Coronavirus 2><Severe Acute Respiratory Distress Syndrome CoV 2><Severe Acute Respiratory Distress Syndrome Corona Virus 2><Severe Acute Respiratory Distress Syndrome Coronavirus 2><Severe Acute Respiratory Syndrome CoV 2><Severe Acute Respiratory Syndrome-associated coronavirus 2><Severe Acute Respiratory Syndrome-related coronavirus 2><Severe acute respiratory syndrome associated corona virus 2><Severe acute respiratory syndrome coronavirus 2><Severe acute respiratory syndrome related corona virus 2><Specific qualifier value><Specified><Structure><Techniques><Technology><Testing><Therapeutic><Training><Translating><Translations><Transphosphorylases><Ubiquitin Protein Ligase><Ubiquitin-Proteasomal Pathway><Ubiquitin-Protein Ligase Complexes><Ubiquitin-Protein Ligase E3><Validation><Variant><Variation><Work><Wuhan coronavirus><alpha 2-Surface Binding Glycoprotein><chimeras><conformation><conformational><conformational state><conformationally><conformations><coronavirus disease 2019 virus><coronavirus disease-19 virus><data base><design><designing><developmental><disease phenotype><experimental analysis><gene repair therapy><gene therapy><gene-based therapy><genetic protein engineering><genetic therapy><genomic therapy><grasp><hCoV19><in silico><in vivo><in vivo evaluation><in vivo testing><interest><iterative design><lipid based nanoparticle><lipid nanoparticle><mRNA><malignancy><mutant><nCoV2><nanobodies><nanobody><neoplasm/cancer><new drug treatments><new drugs><new pharmacological therapeutic><new therapeutic approach><new therapeutic intervention><new therapeutic strategies><new therapeutics><new therapy><new therapy approaches><new treatment approach><new treatment strategy><next generation therapeutics><novel drug treatments><novel drugs><novel pharmaco-therapeutic><novel pharmacological therapeutic><novel therapeutic approach><novel therapeutic intervention><novel therapeutic strategies><novel therapeutics><novel therapy><novel therapy approach><nucleic acid sequence><peptide aminoacid sequence><peptide sequence><pharmacologic><protein aminoacid sequence><protein complex><protein degradation><protein design><protein protein interaction><protein sequence><proteolysis targeting chimera><rapid testing><scaffold><scaffolding><screening><screenings><sdAb><single domain antibodies><small molecule><small molecule inhibitor><tool><translation><ubiquitin-protein ligase><validations>