FEP Solubility

Tutorial Created with Software Release: 2024-3
Topics: Free Energy Perturbation (FEP), Pharmaceutical Formulations
Methodology: Free Energy Perturbation (FEP)
Products Used: FEP+, MS Maestro

Tutorial files

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This tutorial is written for use with a 3-button mouse with a scroll wheel.
Words found in the Glossary of Terms are shown like this: Workspacethe 3D display area in the center of the main window, where molecular structures are displayed

 

Tip: You can hover over a glossary term to display its definition. You can click on an image to expand it in the page.
Abstract:

 

In this tutorial, we will learn to calculate the free energy of solubility.

 

Tutorial Content

  1. Introduction to FEP Solubility

  1. Creating Projects and Importing Structures

  1. Performing an FEP Solubility Simulation

  1. Analyzing an FEP Solubility Simulation

  1. Conclusion and References

  1. Glossary of Terms

1. Introduction to FEP Solubility

The free energy of solubility of a small molecule is determined by considering the transfer of a molecule from the surface of a solid in contact with the solvent into bulk solvent. Since free energy is a thermodynamic state function,  the exact mechanism of dissolution can be overlooked and we can instead focus on the energetic difference between the two end states. Quantification of this energetic difference is made amenable to simulation techniques by breaking it into two parts (or legs): (1) sublimation (ΔG(sublimation)), where a molecule (L) is removed from the solid (s) into the gas (g) phase, and (2) solvation (ΔG(solvation)), where the molecule is transferred from the gas phase to the solution (solv) phase—or, in the actual simulation, from the solution phase to the gas phase. The difference of the free energy for these two processes is the free energy of solubility (ΔG(solubility)).

ΔG(sublimation): Ln(s) → Ln-1(s) + L(g)

−ΔG(solvation): L(solv) → L(g)

ΔG(solubility) = ΔG(sublimation) + ΔG(solvation) : Ln(s) → Ln-1(s) + L(solv)

Two alchemical free energy perturbation (FEP) simulations are performed, both of which involve annihilation of a small molecule. In the first, a molecule on the surface of the solid phase that is in contact with the solvent is annihilated (sublimation). In the second, a molecule in pure solvent is annihilated (desolvation). For both simulations, existing solvent molecules fill the space that was occupied by the small molecule.

In this tutorial, we will calculate the solubility of ibuprofen using the FEP Solubility panel in Materials Science (MS) Maestro. Then we will analyze the results with the FEP+ panel.

The workflow is summarized in the following schematic:

2. Creating Projects and Importing Structures

At the start of the session, change the file path to your chosen Working Directorythe location where files are saved in MS Maestro to make file navigation easier. Each session in MS Maestro begins with a default Scratch Projecta temporary project in which work is not saved, closing a scratch project removes all current work and begins a new scratch project, which is not saved. A MS Maestro project stores all your data and has a .prj extension. A project may contain numerous entries corresponding to imported structures, as well as the output of modeling-related tasks. Once a project is saved, the project is automatically saved each time a change is made.

Structures can be built in MS Maestro or can be imported using File > Import Structures (or drag-and-dropped), and are added to the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data. The Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion is located to the left of the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed. The Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data can be accessed by Ctrl+T (Cmd+T) or Window > Project Table if you would like to see an expanded view of your project data.

OR

  1. Double click the Maestro or Materials Science icon to start Maestro or MS Maestro
    • (No icon? See Starting Maestro)
    • This tutorial uses MS Maestro, but this workflow can be performed in Maestro or MS Maestro. Use whichever interface you are comfortable with or typically use for your projects.

Figure 2-1. Change Working Directory option.

  1. Go to File > Change Working Directory
  2. Find your directory, and click Choose
  3. Pre-generated files are included for running jobs or examining output. Download the zip file here: schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/fep_solubility.zip
  4. After downloading the zip file, unzip the contents in your Working Directorythe location where files are saved for ease of access throughout the tutorial

Figure 2-2. Save Project panel.

  1. Go to File > Save Project As
  2. Change the File name to FEP_solubility_tutorial, click Save
    • The project is now named FEP_solubililty_tutorial.prj

Figure 2-3. The entry list after importing.

Let’s import an ibuprofen structure:

  1. Go to File > Import Structures
  2. Navigate to where the downloaded provided tutorial files are, choose ibuprofen.mae and click Open
    • A new entry is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

If you would prefer to practice preparing the component yourself, draw the molecule in the 2D Sketcher. For background on using this tool, see the Introduction to Materials Science Maestro tutorial.

3. Performing an FEP Solubility Simulation

In this section, we will perform an FEP solubility simulation on an ibuprofen molecule using the FEP Solubility panel.

Figure 3-1. Opening the FEP Solubility panel.

  1. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includethe entry is represented in the Workspace, the circle in the In column is blue the ibuprofen entry
  2. Go to Tasks > Browse All > Free Energy Perturbation > Solubility FEP
    • The FEP Solubility panel opens in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Let’s first learn a bit more about the FEP Solubility panel.

 

The solid phase can be represented by an amorphous cluster of 64 molecules or a crystal structure. The cluster is built from a single structure by arranging the molecules in a simulation box, minimizing the overall volume while avoiding steric clashes. MD relaxation simulations of this cluster of molecules is then performed, followed by a production equilibration MD simulation at 300 K in the NPT ensemble. The structure from the final frame of this simulation is then merged into a pre-equilibrated water box, removing water molecules that overlap with the ibuprofen molecules.

 

Alternatively, one can use a crystal structure that has at least eight copies of the small molecule. Like the amorphous cluster, the structure is merged into a pre-equilibrated water box, removing overlapping water molecules.

 

The system is immersed in the solvent on all sides, with a 10 Å buffer. The system is therefore simulating a very small particle that is dissolving in the solvent.

 

The sublimation simulations are repeated 5 times and the solvation simulations are run once for the molecules with the highest solvent exposure. The solubility free energy is taken as the median value from the results of these simulations.

Figure 3-2. Loading the ibuprofen structure.

  1. Ensure that Project Table (1 selected entry) is selected for Use compounds from
  2. Click Load
    • A check is run to ensure that the structure meets the MS Maestro criteria for a small molecule. Any structure that does not meet the criteria is not loaded, and a warning is issued indicating how many molecules were not loaded.
    • The molecules are added to the Project Table as locked entries.

This calculation will be performed with the default settings. To change the default settings, open the Advanced Options… dialog box. View the help documentation to learn more about the FEP Solubility - Advanced Options panel or for more information, see the FEP Solubility Best Practices documentation.

 

Figure 3-3. Running the FEP Solubility calculation.

  1. For Job name, enter fep_sol_ibuprofen
  2. Adjust the job settings () as needed
    • This job requires a CPU and GPU host. The job can be completed in about 2 days.
    • FEP calculations can use a large amount of memory. There is a script that you can use to estimate the memory required for an FEP job—see fep_memory_estimation.py Command Help for more information.
  3. If you would like to run the job, click Run. Otherwise, pre-generated results are provided to view the structure
  4. Close the FEP Solubility panel

4. Analyzing an FEP Solubility Simulation

In this section, we will analyze the FEP solubility simulation performed in Section 3 using the FEP+ panel.

Figure 4-1. Opening the FEP+ panel.

  1. Go to Tasks > Browse All > Free Energy Perturbation > FEP+
  2. Click Browse

Figure 4-2. Importing the output file.

  1. Navigate to where you downloaded the provided tutorial files, choose Section_04 > fep_sol_ibuprofen > fep_sol_ibuprofen_out.fmp and click Open
  2. Click Next

 

 

Figure 4-3. The FEP+ Overview tab.

The Overview tab contains a table with information for solubility FEP.

  1. Click the Analysis tab

 

 

Figure 4-4. The FEP+ Analysis tab.

The Analysis tab analyzes the results of FEP calculations for solubility. The analysis produces estimates of the solubility.

The solubility free energy ΔG(solubility) for ibuprofen was calculated to be 3.4 kcal/mol.

 

  1. Click View

Let’s learn more about the Analysis tab before viewing the results.

 

FEP - The solubility free energy ΔG(solubility) in kcal/mol of the small molecule.

 

Energy conv - Classification of energy convergence for the process as GOOD, FAIR, or BAD. This classifier tracks the rate at which both FEP legs (solvation and sublimation) converge, measured in the last nanosecond (ns) of the simulation. Two criteria are used: a global variation, which is the maximum change in ΔΔG or ΔG divided by the time span in which convergence is measured (the last ns, ideally), and a local variation, which is the maximum change in ΔΔG or ΔG for any time step in that time span divided by the time step. Both criteria yield a value in kcal/mol*ns. The energy convergence can be improved by expanding the simulation runtime.

 

REST Exch  - Classification of replica exchange density profiles as GOOD, FAIR, or BAD. A good profile is one in which all replicas are sampled adequately in all lambda windows. This classifier monitors the mixing of replicas throughout the FEP simulation and can be visualized through a PDF report of each edge. Replica mixing is assigned a score from 0 to 1, where one is perfect mixing while zero is no mixing.

 

Analysis - Click the View button to display an analysis for the complex defined in this row, in the Solubility FEP+ — Analysis Panel.

 

Hydration Trajectory     - This column displays the total simulation time for the solvation leg. The time is a link (in blue) which you can click to view the trajectory for the solvation leg in the Trajectory Player.

 

Sublimation Trajectory - This column displays the total simulation time for the sublimation leg. The time is a link (in blue) which you can click to view the trajectory for the sublimation leg in the Trajectory Player.

Figure 4-5.The analysis summary report.

 

The Summary tab shows all the Sublimation energies from the 5 different calculations and the overall median value.

 

  1. Click the Free Energy tab

 

Figure 4-6. The free energy results.

This tab displays information on free energy convergence. Free energy differences given in kcal/mol in solvent and complex legs are plotted as a function of time over the course of the simulation. Three plots for each leg show the accumulated data during different time window schemes: forward; reverse; and sliding window.

  1. Click the Exchange Densities tab

 

Figure 4-7. The exchange densities results.

The Exchange Densities tab displays charts showing the replicas and how they are exchanged between lambda windows. There are two subtabs, one for the complex leg and one for the solvent leg.

Each replica is color coded and the plot shows how the replicas occupy different lambda windows during the course of the simulation. The height of a color block for a given replica and lambda window represents the fraction of time the replica spent in the lambda window. Ideally, each replica will sample all lambda windows uniformly; however, non-uniform sampling is sufficient in most instances.

Note: In the Analysis tab, the user can increase the number of lambda windows to improve the exchange profiles.

 

  1. Click the Molecular Environment tab

 

Figure 4-8. The molecular environment results.

This plot shows the different interaction types in the system.

 

A PDF file that reports all of the information presented in the panel with plots and explanatory text can be generated or any images can be saved.

 

Figure 4-9. Output structure of ibuprofen in a box of water molecules.

  1. To view the system of 64 ibuprofen molecules, navigate to where you downloaded the provided tutorial files, choose Section_04 > fep_sol_ibuprofen > fep_sol_ibuprofen_5 > fep_sol_ibuprofen_ddc56a4_subilmation_0-out.mae.

 

This entry group contains 3 entries: the ibuprofen + water system, the 64 ibuprofen molecules, and the box of water molecules. The report lists which 5 ibuprofen molecules were used to determine the median sublimation value (#45, 7, 20, 57, and 42). Feel free to explore these molecules and view their interactions with other ibuprofen molecules or water molecules.

Shown below, molecule 45 is highlighted in red and the non-covalent bonds and pi interactions are shown by the dashed lines.

 

5. Conclusion and References

In this tutorial, we learned how to perform an FEP Solubility simulation of ibuprofen and analyze the results.

For further learning:

For introductory content, focused on navigating the Schrödinger Materials Science interface, an Introduction to Materials Science Maestro tutorial is available. Please visit the materials science training website for access to 70+ tutorials. For scientific inquiries or technical troubleshooting, submit a ticket to our Technical Support Scientists at help@schrodinger.com.

For self-paced, asynchronous, online courses in Materials Science modeling, including access to Schrödinger software, please visit the Schrödinger Online Learning portal on our website.

For some related practice, proceed to explore other relevant tutorials:

For further reading:
  • See the help documentation on the FEP Solubility and FEP+ panels
  • A Free Energy Perturbation Approach to Estimate the Intrinsic Solubilities of Drug-like Small Molecules. DOI: 10.26434/chemrxiv.10263077
  • Free Energy Perturbation Approach for Accurate Crystalline Aqueous Solubility Predictions. DOI: 10.1021/acs.jmedchem.3c01339
  • Novel Physics-Based Ensemble Modeling Approach That Utilizes 3D Molecular Conformation and Packing to Access Aqueous Thermodynamic Solubility: A Case Study of Orally Available Bromodomain and Extraterminal Domain Inhibitor Lead Optimization Series. DOI: /10.1021/acs.jcim.0c01410

6. Glossary of Terms

Entry List - a simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

Included - the entry is represented in the Workspace, the circle in the In column is blue

Project Table - displays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data

Recent actions - This is a list of your recent actions, which you can use to reopen a panel, displayed below the Browse row. (Right-click to delete.)

Scratch Project - a temporary project in which work is not saved, closing a scratch project removes all current work and begins a new scratch project

Selected - (1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries

Working Directory - the location where files are saved

Workspace - the 3D display area in the center of the main window, where molecular structures are displayed