Computationally Guided Engineering of Short Peptides for Targeted RNA-Loaded pBAE Nanoparticles

Abstract Nanoparticles encapsulating therapeutic RNA have emerged as a transformative strategy in precision medicine, enabling a wide range of applications such as gene therapy for rare diseases, the silencing of toxic gene products, and the mobilization of the immune system to induce specific responses ranging from immune tolerance to fighting tumors. However, most current preclinical and clinical efforts rely on non-targeted delivery systems, limiting their safety, therapeutic efficacy, and selectivity. To enhance the therapeutic index of RNA-based therapeutic systems, we report on the design of a novel Clec9A-targeted polymeric nanoparticle aimed at exploring strategies to enhance delivery toward CLEC9A-expressing immune cells as a proof of concept in the field of mRNA vaccination. We began by evaluating in silico the binding potential of the previously reported 12-amino-acid WH peptide, known for its high affinity to mouse Clec9A, the human ortholog. Using computational tools, we designed and screened truncated variants of the peptide and identified promising candidates with retained, or even enhanced, binding capacity to human Clec9A. These optimized short peptides were synthesized and covalently conjugated to our proprietary poly(beta-amino ester) (pBAE) polymers. We evaluated the impact of the conjugation site on receptor targeting by comparing terminal versus lateral chain attachment. We show that peptide orientation significantly influences transfection efficiency in human THP-1 cells, used as a monocytic robust in vitro model. Additionally, we computationally generated and validated shorter mutant peptide variants with improved Clec9A affinity over the original sequences. Our findings demonstrate that rationally engineered short peptides improve transfection in a human monocytic cell model, which is consistent with the proposed Clec9A-targeting strategy suggested by computational modeling. This strategy lays the groundwork for the next generation of targeted RNA-based (immune)therapeutics, offering improved selectivity and consequent therapeutic potential.