| Autor: |
Horton JT; School of Natural and Environmental Sciences, Newcastle University, Newcastle upon TyneNE1 7RU, United Kingdom., Boothroyd S; Boothroyd Scientific Consulting Ltd., 71-75 Shelton Street, LondonWC2H 9JQ, Greater London, United Kingdom., Wagner J; The Open Force Field Initiative, Open Molecular Software Foundation, Davis, California95616, United States., Mitchell JA; The Open Force Field Initiative, Open Molecular Software Foundation, Davis, California95616, United States., Gokey T; Department of Chemistry, University of California, Irvine, California92697, United States., Dotson DL; The Open Force Field Initiative, Open Molecular Software Foundation, Davis, California95616, United States., Behara PK; Department of Pharmaceutical Sciences, University of California, Irvine, California92697, United States., Ramaswamy VK; Cresset, New Cambridge House, Bassingbourn Road, LitlingtonSG8 0SS, Cambridgeshire, United Kingdom., Mackey M; Cresset, New Cambridge House, Bassingbourn Road, LitlingtonSG8 0SS, Cambridgeshire, United Kingdom., Chodera JD; Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York10065, United States., Anwar J; Department of Chemistry, Lancaster University, LancasterLA1 4YW, United Kingdom., Mobley DL; Department of Chemistry, University of California, Irvine, California92697, United States.; Department of Pharmaceutical Sciences, University of California, Irvine, California92697, United States., Cole DJ; School of Natural and Environmental Sciences, Newcastle University, Newcastle upon TyneNE1 7RU, United Kingdom. |
| Abstrakt: |
The development of accurate transferable force fields is key to realizing the full potential of atomistic modeling in the study of biological processes such as protein-ligand binding for drug discovery. State-of-the-art transferable force fields, such as those produced by the Open Force Field Initiative, use modern software engineering and automation techniques to yield accuracy improvements. However, force field torsion parameters, which must account for many stereoelectronic and steric effects, are considered to be less transferable than other force field parameters and are therefore often targets for bespoke parametrization. Here, we present the Open Force Field QCSubmit and BespokeFit software packages that, when combined, facilitate the fitting of torsion parameters to quantum mechanical reference data at scale. We demonstrate the use of QCSubmit for simplifying the process of creating and archiving large numbers of quantum chemical calculations, by generating a dataset of 671 torsion scans for druglike fragments. We use BespokeFit to derive individual torsion parameters for each of these molecules, thereby reducing the root-mean-square error in the potential energy surface from 1.1 kcal/mol, using the original transferable force field, to 0.4 kcal/mol using the bespoke version. Furthermore, we employ the bespoke force fields to compute the relative binding free energies of a congeneric series of inhibitors of the TYK2 protein, and demonstrate further improvements in accuracy, compared to the base force field (MUE reduced from 0.56 0.39 0.77 to 0.42 0.28 0.59 kcal/mol and R 2 correlation improved from 0.72 0.35 0.87 to 0.93 0.84 0.97 ). |
