Investigations of albumin-insulin detemir complexes using molecular dynamics simulations and free energy calculations

Line A. Ryberg*, Pernille Sønderby, Jens T. Bukrinski, Pernille Harris, Günther H. J. Peters

*Corresponding author for this work

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Abstract

Insulin detemir is a lipidated insulin analogue that obtains a half-life extension by oligomerization and reversible binding to human serum albumin. In the present study, the complex between a detemir hexamer and albumin is investigated by an integrative approach combining molecular dynamics (MD) simulations, molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculations and dynamic light scattering (DLS) experiments. Recent reported small angle X-ray scattering data could not unambiguously resolve the exact binding site of detemir on albumin. We therefore applied MD simulations to deduce the binding site and key protein-protein interactions. MD simulations were started from initial complex structures based on the SAXS models and free energies of binding were estimated from the simulations by using the MM-PBSA approach for the different binding positions. The results suggest that the overlapping FA3-FA4 binding site (named FA4) is the most favorable site with a calculated free energy of binding of -28±6 kcal/mol and a good fit to the reported SAXS data throughout the simulations. Multiple salt bridges, hydrogen bonds and favorable van der Waals interactions are observed in the binding interface that promote complexation. The binding to FA4 is further supported by DLS competition experiments with the prototypical FA4 ligand, ibuprofen, showing displacement of detemir by ibuprofen. This study provides information on albumin-detemir binding on a molecular level, which could be utilized in a rational design of future lipidated albumin-binding peptides.
Original languageEnglish
JournalMolecular Pharmaceutics
Volume17
Issue number1
Pages (from-to)132-144
ISSN1543-8384
DOIs
Publication statusPublished - 2020

Keywords

  • Human serum albumin
  • Insulin detemir
  • protein-protein complexes
  • Molecular dynamics simulation
  • Dynamic light scattering
  • Small-angle X-ray scattering
  • Free energy calculations

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