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

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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.

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Acknowledgments

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

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Authors and Affiliations

  1. Center for Integrated Protein Science at the Department for Biosciences, Technische Universität München, Emil-Erlenmeyer-Forum 8, 85354, Freising, Germany

    Ilke Ugur, Maja Schroft, Antoine Marion, Manuel Glaser & Iris Antes

  2. Department of Chemistry, Middle East Technical University, 06800, Ankara, Turkey

    Ilke Ugur & Antoine Marion

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  1. Ilke Ugur
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  2. Maja Schroft
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  3. Antoine Marion
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  4. Manuel Glaser
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  5. Iris Antes
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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.

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Correspondence to Iris Antes.

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Ugur, I., Schroft, M., Marion, A. et al. Predicting the bioactive conformations of macrocycles: a molecular dynamics-based docking procedure with DynaDock. J Mol Model 25, 197 (2019). https://doi.org/10.1007/s00894-019-4077-5

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