Calculate protein-ligand binding affinities with the extended linear interaction energy method: application on the Cathepsin S set in the D3R Grand Challenge 3

Journal of Computer-aided Molecular Design
Xibing HeJunmei Wang

Abstract

We participated in the Cathepsin S (CatS) sub-challenge of the Drug Design Data Resource (D3R) Grand Challenge 3 (GC3) in 2017 to blindly predict the binding poses of 24 CatS-bound ligands, the binding affinity ranking of 136 ligands, and the binding free energies of a subset of 33 ligands in Stage 1A and Stage 2. Our submitted predictions ranked relatively well compared to the submissions from other participants. Here we present our methodologies used in the challenge. For the binding pose prediction, we employed the Glide module in the Schrodinger Suite 2017 and AutoDock Vina. For the binding affinity/free energy prediction, we carried out molecular dynamics simulations of the complexes in explicit water solvent with counter ions, and then estimated the binding free energies with our newly developed model of extended linear interaction energy (ELIE), which is inspired by two other popular end-point approaches: the linear interaction energy (LIE) method, and the molecular mechanics with Poisson-Boltzmann surface area solvation method (MM/PBSA). Our studies suggest that ELIE is a good trade-off between efficiency and accuracy, and it is appropriate for filling the gap between the high-throughput docking and scoring methods and ...Continue Reading

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Citations

Dec 1, 2019·Journal of Computer-aided Molecular Design·Maria KadukovaSergei Grudinin
Sep 24, 2020·The Journal of Chemical Physics·Xibing HeJunmei Wang
Jan 25, 2020·Journal of Computer-aided Molecular Design·Conor D ParksMichael K Gilson
Aug 29, 2019·Journal of Chemical Information and Modeling·Eko Aditya RifaiDaan P Geerke
Nov 21, 2020·Journal of Chemical Information and Modeling·Dongxiao HaoJunmei Wang
Jun 3, 2020·The Journal of Physical Chemistry. B·Kiet HoMai Suan Li
Aug 31, 2021·Frontiers in Molecular Biosciences·Edward KingRay Luo

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