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

  • Ilke Ugur
  • Maja Schroft
  • Antoine Marion
  • Manuel Glaser
  • Iris AntesEmail author
Original Paper

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 (750 ns) simulations performed at moderately high temperature (370 K). 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 Å. 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.

Keywords

Macrocyclic compounds Protein–ligand docking Drug design Conformational sampling Molecular dynamics DynaDock 

Notes

Acknowledgments

Financial support from Deutsche Forschungsgemeinschaft (SFB 1035/A10 and CIPSM) is gratefully acknowledged.

Author contributions

I.U. and M.S. performed the computational studies. A.M. provided guidelines and established parameters of the macrocyles. M.G. gave advice regarding the DynaDock and MMGBSA calculations. I.A. and I.U. designed and supervised the study. All the authors contributed to the writing of the manuscript.

Supplementary material

894_2019_4077_MOESM1_ESM.pdf (3.8 mb)
ESM 1 (PDF 3840 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Center for Integrated Protein Science at the Department for BiosciencesTechnische Universität MünchenFreisingGermany
  2. 2.Department of ChemistryMiddle East Technical UniversityAnkaraTurkey

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