Tosteson Medical Education Center (TMEC), Room 246
260 Longwood Ave, Boston, MA 02215
Self-Assembling Protein Nanoparticles for Cytosolic Delivery of Therapeutic Macromolecules
Nucleic acid- and protein-based drugs have transformative therapeutic potential across many diseases, through modulating intracellular targets, enabling cytosolic protein production, and editing the genome. Achieving safe, effective, and specific delivery of these drugs to extrahepatic target cell types in vivo remains a critical bottleneck preventing the full realization of this potential. Recombinant, non-viral protein nanoparticles hold great promise as macromolecular drug delivery vehicles given their biocompatibility, genetic control over material properties, and the ability to directly integrate functional protein domains in a modular fashion, but inefficient endosomal escape and poor particle stability have limited their use to date.
In this thesis, we develop recombinant elastin-like polypeptide (ELP) nanoparticles as a modular protein nanoparticle platform for therapeutic macromolecule delivery. Through an iterative design process, we first developed ELPs that self-assemble into pH-responsive micellar nanoparticles and incorporate cationic endosomal escape peptides (EEPs) to promote cytosolic delivery of diverse biomacromolecules, including antisense RNAs, mRNA, DNA, and gene editor proteins, to multiple cell lines and primary cell types. We show that ELP-EEPs enable effective in vivo delivery of a model recombinase through intranasal administration in reporter mice. To enhance potency, we next implement a directed evolution-inspired, machine learning-guided design approach to develop de novo EEPs using a hybrid fitness function combining model predicted activity and empirical physicochemical metrics. This approach yielded an 8-fold increase in average protein delivery efficiency over four generations, as well as a lead construct with double the mRNA delivery potency of a prior lead. EEP feature analysis highlights both known and novel physicochemical drivers of activity, and predictive model generalization into underrepresented feature spaces enabled the design of shorter, less cationic, and deimmunized peptides with retained activity. Finally, we adapt ELP nanoparticles for targeted delivery to hematopoietic stem and progenitor cells (HSPCs) through recombinant functionalization with stem cell factor (SCF) to promote CD117-mediated internalization. SCF-functionalized nanoparticles demonstrated improved functional delivery of a model recombinase to reporter mouse-derived CD117+ bone marrow cells and HSCs ex vivo and promoted increased binding of ELP nanoparticles to HSPCs in vivo. Altogether, this work demonstrates the promise of ELP nanoparticles as a modular platform for nonviral delivery of nucleic acid and protein therapeutics.
Thesis Supervisor:
Elliot Chaikof, MD, PhD.
Johnson and Johnson Professor of Surgery, Harvard Medical School
Thesis Committee Chair:
Sangeeta Bhatia, MD, PhD.
John J. and Dorothy Wilson Professor of Health Sciences and Technology and Professor of Electrical Engineering and Computer Science, MIT
Thesis Readers:
Daniel Bauer, MD, PhD.
Donald S. Fredrickson, MD Associate Professor of Pediatrics, Harvard Medical School
Rafael Gómez-Bombarelli, PhD.
Paul M. Cook Career Development Professor and Associate Professor of Materials Science and Engineering, MIT
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Feyisayo Eweje is inviting you to a scheduled Zoom meeting
Topic: Feyisayo Eweje MEMP PhD Thesis Defense
Time: Tuesday, April 29, 2025, 10:00 AM Eastern Time (US and Canada)
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