Molecular dynamics of transferrin receptor binder peptides: unlocking blood-brain barrier for enhanced CNS drug delivery

A cystine-dense peptide (CDP) named TfRB1 was identified for its ability to bind to the transferrin receptor (TfR). CDPs are stabilized by their disulfide bonds, and variants of TfRB1 - specifically TfRB1G1, TfRB1G2, and TfRB1G3 - are explored for their potential to transport molecules across the blood-brain barrier (BBB) into the central nervous system (CNS). This study employed molecular modeling and dynamics simulations to characterize the interactions between these TfRB1 variants and TfR. Binding free energy calculations showed a strong correlation with experimental binding affinities of -10.99 kcal/mol for TfRB1G2 and -13.18 kcal/mol for TfRB1G3, with a relative error of 1.98%. The key forces driving these interactions include electrostatic and van der Waals forces, with mutations in TfRB1G3 (T9M and A13D) enhancing its binding affinity through improved interactions with residues such as Arg633. The free energy landscape analysis revealed that TfRB1G3 maintains the N-terminal residues of TfR in an α-helical conformation, unlike TfRB1G2. Per-residue free energy decomposition identified key residues - Leu619, Arg629, Tyr643, and Phe650 - as crucial for TfR binding, underscoring their competitive nature with transferrin. Additionally, Glu612, which is favorable for binding in TfRB1G2, becomes unfavorable in TfRB1G3. Conversely, Arg633 shifts from unfavorable in TfRB1G2 to favorable in TfRB1G3, compensating for the loss of favorable interaction with Glu612. These findings provide valuable molecular insights into the TfRB1 peptides' potential as drug carriers, highlighting their capability to deliver molecules to the CNS and compete with transferrin for BBB transport.