Predicting the bioactive conformations of macrocycles: a molecular dynamics-based docking procedure with DynaDock

Ugur I., Schroft M., Marion A., Glaser M., Antes I.

JOURNAL OF MOLECULAR MODELING, vol.25, no.7, 2019 (SCI-Expanded) identifier identifier identifier

  • Publication Type: Article / Article
  • Volume: 25 Issue: 7
  • Publication Date: 2019
  • Doi Number: 10.1007/s00894-019-4077-5
  • Journal Name: JOURNAL OF MOLECULAR MODELING
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus
  • Keywords: Macrocyclic compounds, Protein-ligand docking, Drug design, Conformational sampling, Molecular dynamics, DynaDock, CYCLIC-PEPTIDES, DRUG DISCOVERY, AMINO-ACID, AMBER, SIMULATIONS, INHIBITORS, PROTEINS, ACCURACY, CHARGES, BINDING
  • Middle East Technical University Affiliated: Yes

Abstract

Macrocyclic compounds are of growing interest as a new class of therapeutics, especially as inhibitors binding to protein-protein interfaces. As molecular modeling is a well-established complimentary tool in modern drug design, the number of attempts to develop reliable docking strategies and algorithms to accurately predict the binding mode of macrocycles is rising continuously. Standard molecular docking approaches need to be adapted to this application, as a comprehensive yet efficient sampling of all ring conformations of the macrocycle is necessary. To overcome this issue, we designed a molecular dynamics-based docking protocol for macrocycles, in which the challenging sampling step is addressed by conventional molecular dynamics (750ns) simulations performed at moderately high temperature (370K). Consecutive flexible docking with the DynaDock approach based on multiple, pre-sampled ring conformations yields highly accurate poses with ligand RMSD values lower than 1.8 angstrom. We further investigated the value of molecular dynamics-based complex stability estimations for pose selection and discuss its applicability in combination with standard binding free energy estimations for assessing the quality of poses in future blind docking studies.