In-silico study of the interactions between acylated glucagon like-peptide-1 analogues and the native receptor

Abstract

We have performed a series of multiple molecular dynamics (MD) simulations of glucagon-like peptide-1 (GLP-1) and acylated GLP-1 analogues in complex with the endogenous receptor (GLP-1R) to obtain a molecular understanding of how fatty acid (FA) chain structure, acylation position on the peptide, and presence of a linker affect the binding. MD simulations were analysed to extract heatmaps of receptor–peptide interaction patterns and to determine the free energy of binding using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) approach. The extracted free energies from MM-PBSA calculations are in qualitative agreement with experimentally determined potencies. Furthermore, the interaction patterns seen in the receptor–GLP-1 complex simulations resemble previously reported binding interactions validating the simulations. Analysing the receptor–GLP-1 analogue complex simulations, we found that the major differences between the systems stem from FA interactions and positioning of acylation in the peptide. Hydrophobic interactions between the FA chain and a hydrophobic patch on the extracellular domain contribute significantly to the binding affinity. Acylation on Lys26 resulted in noticeably more interactions between the FA chain and the extracellular domain hydrophobic patch than found for acylation on Lys34 and Lys38, respectively. The presence of a charged linker between the peptide and FA chain can potentially stabilise the complex by forming hydrogen bonds to arginine residues in the linker region between the extracellular domain and the transmembrane domain. A molecular understanding of the fatty acid structure and its effect on binding provides important insights into designing acylated agonists for GLP-1R.

Communicated by Ramaswamy H. Sarma

Keywords:

• Acylated peptides
• binding free energy
• configurational entropy
• MM-PBSA
• molecular dynamics simulations
• peptide-receptor interactions

Acknowledgements

All simulations were performed at the DTU Chemistry GPU cluster.

Disclosure statement

No potential conflict of interest was reported by the authors.

Funding

TMF acknowledges financial support via an Academic Excellence Scholarship from the Department of Chemistry, Technical University at Denmark. SKK received a Ph.D. scholarship funded through the Technical University at Denmark Alliance program.