A Comparative Linear Interaction Energy and MM/PBSA Study on SIRT1-Ligand Binding Free Energy Calculation.

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ID: 22924
2019
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Abstract
Binding free energy (Δ) computation can play an important role in prioritizing compounds to be evaluated experimentally on their affinity for target proteins, yet fast and accurate Δ calculation remains an elusive task. In this study, we compare the performance of two popular end--point methods, i.e., linear interaction energy (LIE) and molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA), with respect to their ability to correlate calculated binding affinities of 27 thieno[3,2-d]pyrimidine-6-carboxamide-derived sirtuin 1 (SIRT1) inhibitors with experimental data. Compared with the standard single-trajectory setup of MM/PBSA, our study elucidates that LIE allows to obtain direct ('absolute') values for SIRT1 binding free energies with lower compute requirements, while the accuracy in calculating relative values for Δ is comparable (Pearson's r = 0.72 and 0.64 for LIE and MM/PBSA, respectively). We also investigate the potential of combining multiple docking poses in iterative LIE models and find that Boltzmann-like weighting of outcomes of simulations starting from different poses can retrieve appropriate binding orientations. In addition, we find that in this particular case study, the LIE and MM/PBSA models can be optimized by neglecting the contributions from electrostatic and polar interactions to the Δ calculations.
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rifai2019ajournal Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Rifai, Eko Aditya;van Dijk, Marc;Vermeulen, Nico P E;Yanuar, Arry;Geerke, Daan P;
Journal Journal of chemical information and modeling
Year 2019
DOI
10.1021/acs.jcim.9b00609
URL
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