Free energy perturbation calculations
SchrödingerRelease2016v2/Maestro10.6/Desmondv4.6/FEP+/ProteinPreparationWizard/Epikv3.6/Primev4.4/Impactv71014
OPLS3 force field
Windows per transformation: 12
Assumed pH 7.4
Typical simulation time per window: 5 ns
Water Model: SPC
Ensemble for production run: NPT
Free Energy Perturbation Protocol
The free energy calculations were repeated for this set of congeneric ligands, using as reference the native binding mode.
Crystal structure 1hqmf was prepared with Protein Preparation Wizard of Schrodinger.
The protein preparation took place using the following procedure from within the Protein Preparation Wizard, Schrödinger Release 2016-2, Maestro 10.6:
1) Crystal structure 1hqmf imported
2) Automatically added missing hydrogen atoms
3) Enumerate bond orders to HET groups
4) Removed or kept co-crystallized water molecules as described below (see following section)
5) Capped protein termini with ACE and NMA residues
6) Highlighted residues with missing atoms or multiple occupancies
7) Pre-processed structures for Prime, Schrödinger's program for protein structure prediction
8) Determined the most likely ligand protonation state as well as the energy penalties associated with alternate protonation states with Epik
9) Determined optimal protonation states for histidine residues
10) Corrected potentially transposed heavy atoms in arginine, glutamine, and histidine side chains
11) Optimize the protein's hydrogen bond network by means of a systematic, cluster-based approach, which greatly decreases preparation times
12) Perform a restrained minimization that allows hydrogen atoms to be freely minimized, while allowing for sufficient heavy-atom movement to relax strained bonds, angles, and clashes using Impact
Schrödinger Release 2016-3: Schrödinger Suite 2016-3 Protein Preparation Wizard; Epik, Schrödinger, LLC, New York, NY, 2016; Impact, Schrödinger, LLC, New York, NY, 2016; Prime, Schrödinger, LLC, New York, NY, 2016.
Initial poses of the ligands were calculated by alignment of their structures with the native ligand of crystal structure ID 1hqmf (FXR_17). For the alignment of the ligands we used the Flexible Ligand Alignment tool of Maestro, Schrodinger.
The above poses were constructed with the assumption that the binding mode of FXR_17 is conserved in all lignds. Because during Free Energy perturbation calculations the charge cannot change, the ligand FXR_101 was calculated in its protonated state.
Subsequently, the free energy calculations were conducted with the aid of FEP+ module of Schrodinger. The aligned ligands were imported to FEP Mapper module, and the FEP map was costructed according to LOMAP algorithm.
FEP+ gave us the final relative free energy differences ranking.
We submitted the final snapshot of the MD trajectory for each ligand. All water molecules were removed.
Contributors: Christina Athanasiou, Sofia Vasilakaki, Dimitris Ntellis, Zoe Cournia
Biomedical Research Foundation, Academy of Athens, Greece
Pose prediction for free energy perurbation calculations
Schrödinger Release 2016-2: /SchrödingerRelease2016v2/Maestro 10.6/ProteinPreparationWizard/Primev4.4/Impactv71014/Desmondv4.6/Phasev4.7/Epikv3.6
Using Schrödinger's Protein Preparation Wizard, we converted the raw PDB structure into an all-atom, fully prepared protein model.
The protein preparation took place using the following procedure from within the Protein Preparation Wizard, Schrödinger Release 2016-2, Maestro 10.6:
1) Imported 1hqmf crystal structure
2) Automatically added missing hydrogen atoms
3) Enumerate bond orders to HET groups
4) Removed or kept co-crystallized water molecules
5) Capped protein termini with ACE and NMA residues
6) Highlighted residues with missing atoms or multiple occupancies
7) Pre-processed structures for Prime, Schrödinger's program for protein structure prediction
8) Determined the most likely ligand protonation state as well as the energy penalties associated with alternate protonation states with Epik
9) Determined optimal protonation states for histidine residues
10) Corrected potentially transposed heavy atoms in arginine, glutamine, and histidine side chains
11) Optimize the protein's hydrogen bond network by means of a systematic, cluster-based approach, which greatly decreases preparation times
12) Perform a restrained minimization that allows hydrogen atoms to be freely minimized, while allowing for sufficient heavy-atom movement to relax strained bonds, angles, and clashes using Impact
Schrödinger Release 2016-3: Schrödinger Suite 2016-3 Protein Preparation Wizard; Epik, Schrödinger, LLC, New York, NY, 2016; Impact, Schrödinger, LLC, New York, NY, 2016; Prime, Schrödinger, LLC, New York, NY, 2016.
Sastry, G.M.; Adzhigirey, M.; Day, T.; Annabhimoju, R.; Sherman, W., "Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments," J. Comput. Aid. Mol. Des., 2013, 27(3), 221-234
Flexible ligand alignment: align maximum common substructure
The pose prediction methodology is described below.
1) Protein Preparation of 1hqmf crystal structure
The default parameters from Maestro Protein Preparation Module were used as described above.
2) Flexible ligand alignment
All compounds were aligned to the native ligand of 1hqmf crystal structure. We made the assumption that all ligands have the same binding mode.
Contributors: Christina Athanasiou, Sofia Vasilakaki, Dimitris Ntellis, Zoe Cournia
Biomedical Research Foundation, Academy of Athens, Greece