Happy to share that our recently published collaborative article on aptamer simulation has been selected for the front cover of 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.
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
