Extracting ligands from receptors by reversed targeted molecular dynamics
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Short targeted MD trajectories are used to expel ligands from binding sites. The expulsion is governed by a linear increase of the target RMSD value, growing from zero to an arbitrary chosen final RMSD that forces the ligand to a selected distance outside of the receptor. The RMSD lag (i.e., the difference between the imposed and the actual RMSD) can be used to follow barriers encountered by the ligand during its way out of the receptor. The force constant used for the targeted MD can transform the RMSD lag into a strain energy. Integration of the (time-dependent) strain energy over time yields a value with the dimensions of “action” (i.e, energy multiplied by time) and can serve as a measure for the overall effort required to extract the ligand from its binding site. Possibilities to compare (numerically and graphically) the randomly detected exit pathways are discussed. As an example, the method is tested on the exit of bisphenol A from the human estrogen-related receptor \(\gamma\) and of GW0072 from the peroxysome proliferator activated receptor.
KeywordsReversed targeted MD Nuclear receptors Ligand exit pathways
The author thanks Anna Vulpetti and Rainer Wilcken for useful suggestions and for successfully testing the simulation protocols described here on various projects, and Richard Lewis for support and constructive comments.
- 17.Case DA, Babin V, Berryman JT, Betz RM, Cai Q, Cerutti DS, Cheatham TE III, Darden TA, Duke RE, Gohlke H, Goetz AW, Gusarov S, Homeyer N, Janowski P, Kaus J, Kolossváry I, Kovalenko A, Lee TS, LeGrand S, Luchko T, Luo R, Madej B, Merz KM, Paesani F, Roe DR, Roitberg A, Sagui C, Salomon-Ferrer R, Seabra G, Simmerling CL, Smith W, Swails J, Walker RC, Wang J, Wolf RM, Wu X, Kollman P (2014) Amber 14. University of California, San FranciscoGoogle Scholar
- 25.Schrödinger LLC (2012) The PyMOL Molecular Graphics System, Version 184.108.40.206. Schrödinger, LLCGoogle Scholar
- 26.Chovancova E, Pavelka A, Benes P, Strnad O, Brezovsky J, Kozlikova B, Gora A, Sustr V, Klvana M, Medek P, Biermannova L, Sochor J, Damborský J (2012) PLoS Comput Biol 8(10):1Google Scholar