Journal of Computer-Aided Molecular Design

, Volume 29, Issue 8, pp 707–712

Molecular dynamics to enhance structure-based virtual screening on cathepsin B

  • Mitja Ogrizek
  • Samo Turk
  • Samo Lešnik
  • Izidor Sosič
  • Milan Hodošček
  • Bojana Mirković
  • Janko Kos
  • Dušanka Janežič
  • Stanislav Gobec
  • Janez Konc
Article

DOI: 10.1007/s10822-015-9847-2

Cite this article as:
Ogrizek, M., Turk, S., Lešnik, S. et al. J Comput Aided Mol Des (2015) 29: 707. doi:10.1007/s10822-015-9847-2

Abstract

Molecular dynamics (MD) and molecular docking are commonly used to study molecular interactions in drug discovery. Most docking approaches consider proteins as rigid, which can decrease the accuracy of predicted docked poses. Therefore MD simulations can be used prior to docking to add flexibility to proteins. We evaluated the contribution of using MD together with docking in a docking study on human cathepsin B, a well-studied protein involved in numerous pathological processes. Using CHARMM biomolecular simulation program and AutoDock Vina molecular docking program, we found, that short MD simulations significantly improved molecular docking. Our results, expressed with the area under the receiver operating characteristic curves, show an increase in discriminatory power i.e. the ability to discriminate active from inactive compounds of molecular docking, when docking is performed to selected snapshots from MD simulations.

Keywords

Cathepsin B Molecular dynamics Molecular docking Protein flexibility 

Supplementary material

10822_2015_9847_MOESM1_ESM.doc (552 kb)
Supplementary material 1 (DOC 552 kb)

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Mitja Ogrizek
    • 1
  • Samo Turk
    • 2
    • 4
  • Samo Lešnik
    • 1
  • Izidor Sosič
    • 2
  • Milan Hodošček
    • 1
  • Bojana Mirković
    • 2
  • Janko Kos
    • 2
  • Dušanka Janežič
    • 3
  • Stanislav Gobec
    • 2
  • Janez Konc
    • 1
    • 3
  1. 1.National Institute of ChemistryLjubljanaSlovenia
  2. 2.Faculty of PharmacyUniversity of LjubljanaLjubljanaSlovenia
  3. 3.Faculty of Mathematics, Natural Sciences, and Information TechnologiesUniversity of PrimorskaKoperSlovenia
  4. 4.BioMed X GmbHHeidelbergGermany