Excited to share our very study on in silico understanding of aptamer binding published in Biophysical Chemistry (IF 3.3). This study resulted from a collaboration with Daniel Vasconcelos (Imperial College, MedinUP, Apterna) and Nagid Habib (Imperial College, Apterna). In this study, we report an in silico protocol to study the molecular basis of recognition of a validated RNA aptamer with affinity to the human Transferrin Receptor-1. We combined molecular dynamics simulations, protein-RNA docking and free energy calculations, to characterize TfRapt-human TfR1 interaction. We examined the impact of hTfR1 recognition by the TfRapt, when conjugated to a short dsRNA with potential therapeutic use. The results provide design clues for other hTfR1 aptamers, by mapping the interactions of specific bases and amino acids, considering the spacer and dsRNA.
This computational approach can be expanded to other aptamers and to the conjugation of other therapeutically relevant oligonucleotides.
In silico analysis of aptamer-RNA conjugate interactions with human transferrin receptor
Daniel Vasconcelos, André Pina, Nagy Habib, Sérgio F. Sousa
Biophysical Chemistry (2024) | DOI: 10.1016/j.bpc.2024.107308
Abstract:
The human transmembrane protein Transferrin Receptor-1 is regarded as a promising target for the systemic delivery of therapeutic agents, particularly of nucleic acid therapeutics, such as short double stranded RNAs. This ubiquitous receptor is involved in cellular iron uptake, keeping intracellular homeostasis. It is overexpressed in multiple cancer cell types and is internalized via clathrin-mediated endocytosis. In previous studies, a human transferrin receptor-1 RNA aptamer, identified as TR14 ST1–3, was shown to be capable of effectively internalizing into cells in culture and to deliver small, double stranded RNAs in vitro and in vivo, via systemic administration.
To understand, at the molecular level, the aptamer binding to the receptor and the impact of conjugation with the therapeutic RNA, a multi-level in silico protocol was employed, including protein-aptamer docking, molecular dynamics simulations and free energy calculations. The competition for the binding pocket, between the aptamer and the natural ligand human Transferrin, was also evaluated.
The results show that the aptamer binds to the same region as Transferrin, with residues from the helical domain showing a critical role. Moreover, the conjugation to the therapeutic RNA, was shown not to affect aptamer binding. Overall, this study provides an atomic-level understanding of aptamer association to human Transferrin Receptor-1 and of its conjugation with a short model-therapeutic RNA, providing also important clues for futures studies aiming to deliver other oligonucleotide-based therapeutics via Transferrin Receptor.