Biopolym. Cell. 2026; 42(Special Issue):10.
Nucleic acid–based therapeutics and delivery technologies
Interaction of the IFN–IFNAR1 complex with ribonucleotides and D-mannitol: prospects for the development of next-generation interferon-based therapeutics
1Nikolaiev R. O., 1Tkachuk Z. Yu.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03143

Abstract

Aim. To elucidate the molecular mechanisms underlying the interaction of the IFN α-2b–IFNAR1 complex with ribonucleotides and D-mannitol to inform the development of next-generation interferon-based drugs. Methods. Fluorescence quenching experiments were performed using a Jasco FP-8200 spectrofluorimeter. Binding affinities (Kd) were calculated using the Stern–Volmer, Scatchard, Klotz, and Hill models. Molecular docking was performed with AutoDock Vina using AlphaFold-derived structures. Results. Free ribonucleotides (AMP, UMP and total oligoribonucleotide mix (ORNs)) showed the highest affinity for the heterodimeric IFN–IFNAR1 complex, with dissociation constants in the submicromolar range (Kd 0.14-0.56 µM). The highest affinity was observed for AMP in the complex with D-mannitol (Kd = 0.14 µM according to the Hill model). Converting ribonucleotides from the free acid to the disodium form led to a significant (3–10-fold) decrease in affinity. D-mannitol exhibited a clear, selective positive effect: it significantly enhanced the binding of AMP, UMP and ORNs, reducing Kd to up to 30% of the initial value, and this effect was most pronounced in the functional heterodimeric IFN–IFNAR1 complex. For isolated proteins (IFN α-2b and IFNAR1), the modulatory effect of mannitol was much weaker. Molecular docking confirmed the experimental data and revealed that GMP+D-mannitol forms the most stable complex with the IFN–IFNAR1 heterodimer (ΔG dock = –9.4 kcal/mol). Analysis of intermolecular contacts revealed an extensive network of hydrogen bonds and the participation of D-mannitol as a “bridging� modulator that stabilises the conformation of the binding site. We found significant differences in the GMP+D-mannitol binding profiles between individual proteins and their complex, indicating allosteric effects in the formation of a functional receptor heterodimer. Conclusions. The data demonstrate that free ribonucleotides and their D-mannitol complexes can serve as effective low-molecular-weight modulators of the interferon system. These findings provide a foundation for the development of next-generation interferon therapeutics with improved stability, enhanced receptor affinity, and potentially superior therapeutic efficacy. Grants. IMBG Simons Foundation Grant for Ukrainian institutions № SFI-PD-Ukraine-00017453.
Keywords: interferon α-2b, IFNAR1, ribonucleotides, D-mannitol, allosteric modulation, fluorescence spectroscopy, molecular docking, next-generation therapeutics