Systematic design of DMBT1-derived peptides correlating physicochemical properties and sequence motifs with siRNA delivery and efficacy in cancer therapy.

Abstract

Background: Molecules driving the cancer process are frequently difficult to target with traditional small-molecule drugs. Small interfering RNAs (siRNAs) offer high specificity, but their clinical translation is hindered by inefficient delivery and rapid degradation. We previously identified DMBT1-derived cell-penetrating peptides (CPPs) that encapsulate siRNA and improve serum stability in vitro.

Methods: We designed 37 DMBT1-derived peptides using a rational, high-throughput pipeline to enhance siRNA encapsulation, stability, and delivery. Binding, uptake, and silencing were assessed in A375 and MCF7 cells. Regression and motif discovery analyses were applied to link peptide physicochemical features with encapsulation efficiency, serum stability, and gene silencing.

Findings: Twenty-seven peptides showed improved siRNA binding and 20 achieved robust uptake in serum. We identified a conserved motif, SWGRVRVLRGDKW, enriched in complexes achieving >75% knockdown, associated with efficient cytosolic release. HE25 emerged as the lead peptide, delivering BRAF^V600E-siRNA and significantly reducing A375 proliferation in vitro. In female NOG CIEA mice xenografts, HE25 suppressed tumour growth, while repeated intravenous dosing in BALB/c mice confirmed biosafety.

Interpretation: Targeted optimisation combined with motif-based design establishes a framework for developing next-generation CPPs. The identification of a conserved motif driving efficient delivery highlights new opportunities for advancing siRNA therapeutics in cancer and beyond.

Funding: This work was supported by Novo Nordisk Foundation, Villum Foundation, Lundbeck Foundation, A.P. Møller Foundation, Dagmar Marshalls Foundation, Neye Foundation, Fabrikant Einar Willumsens Mindelegat, and Direktør Michael Hermann Nielsens Mindelegat.