Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation: application to the D3R Grand Challenge 2

Eko Aditya Rifai, Marc van Dijk, Nico P E Vermeulen, Daan P Geerke

Research output: Contribution to JournalArticleAcademicpeer-review

Abstract

Computational protein binding affinity prediction can play an important role in drug research but performing efficient and accurate binding free energy calculations is still challenging. In the context of phase 2 of the Drug Design Data Resource (D3R) Grand Challenge 2 we used our automated eTOX ALLIES approach to apply the (iterative) linear interaction energy (LIE) method and we evaluated its performance in predicting binding affinities for farnesoid X receptor (FXR) agonists. Efficiency was obtained by our pre-calibrated LIE models and molecular dynamics (MD) simulations at the nanosecond scale, while predictive accuracy was obtained for a small subset of compounds. Using our recently introduced reliability estimation metrics, we could classify predictions with higher confidence by featuring an applicability domain (AD) analysis in combination with protein-ligand interaction profiling. The outcomes of and agreement between our AD and interaction-profile analyses to distinguish and rationalize the performance of our predictions highlighted the relevance of sufficiently exploring protein-ligand interactions during training and it demonstrated the possibility to quantitatively and efficiently evaluate if this is achieved by using simulation data only.

Original languageEnglish
Pages (from-to)239-249
Number of pages11
JournalJournal of Computer-aided Molecular Design
Volume32
Issue number1
Early online date9 Sept 2017
DOIs
Publication statusPublished - 2017

Funding

EAR received financial support from Indonesia Endowment Fund for Education, Ministry of Finance, Republic of Indonesia (LPDP). We also gratefully acknowledge financial support by The Netherlands Organization for Scientific Research (NWO, VIDI Grant 723.012.105). Acknowledgements EAR received financial support from Indone-

FundersFunder number
LPDP
Ministry of Finance, Republic of Indonesia
Netherlands Organization for Scientific Research
Nederlandse Organisatie voor Wetenschappelijk Onderzoek723.012.105

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    • Human Health and Life Sciences
    • Science for Sustainability

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