Small Molecule – Oligonucleotide Docking with Glide

Tutorial Created with Software Release: 2025-3
Topics: Hit Discovery, Small Molecule Drug Discovery, Virtual Screening
Products Used: Glide, Maestro

Tutorial files

8 MB
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:

 

This tutorial will guide you through essential steps to perform docking calculations for an RNA receptor. It covers how to generate a receptor, validate the docking protocol by docking the co-crystal ligand, dock a set of congeneric ligands into the receptor grid, and analyze the docking results.

 

Tutorial Content

  1. Introduction to Glide Docking to Nucleic Acid Targets

  1. Creating Projects and Importing Structures

  1. Running and Analyzing the Docking Job

  1. Conclusion and References

  1. Glossary of Terms

1. Introduction to Glide Docking to Nucleic Acid Targets

In virtual screening campaigns, the primary objective is to find novel small molecules that selectively interact with specific biological targets. Given a well-defined structure of a target, Glide is a powerful tool to identify compounds that are likely to bind, regardless of whether the target is a protein or an oligonucleotide. Glide examines the geometric and electrostatic complementarity between the small molecule and the oligonucleotide, generating plausible binding orientations (poses) and assigning a score to each, which quantifies how well the molecule fits in the binding pocket. It has an alternative scoring function that is tuned for RNA receptors, with reweighted coulomb, vdW, and internal energy terms.

In order to enable screening of thousands of compounds, Glide treats the receptor (oligonucleotide) as rigid, and the ligand as conformationally flexible to explore the optimal fit. Consequently, Glide scoring functions are primarily optimized for enriching true binders from a diverse set of compounds, rather than providing precise quantitative predictions of binding affinity.

This tutorial uses the prepared 6DN3 RNA structure, which is a flavin mononucleotide (FMN) riboswitch bound to a flavin analog ligand BRX1555. If you are following along with a different structure, please make sure that your structure is prepared as shown in the Preparing Nucleic Acid Structures tutorial.

Glide can be used both as a key part of a virtual screening funnel and a tool to obtain bound poses of ligands or ligand ideas to enable more in-depth methods like molecular dynamics or FEP+ simulations.

In this tutorial, you will set up a docking model and dock flavin analogs to the 6DN3 FMN riboswitch with the goal of determining ligand poses in the RNA binding pocket. These flavin analogs constitute a congeneric series of ligands, i.e. they have a common core scaffold (the isoalloxazine ring system) but possess different substituents at one or more positions. You will validate the docking model by re-docking the cognate ligand.

If you want to learn more about using Glide for performing structure-based virtual screening, see the corresponding tutorial.

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  Maestro to make file navigation easier. Each session in 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 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 Maestro or can be imported using File > Import Structures (or drag-and-dropped), and are added to the Entriesa 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 Entriesa 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.

  1. Double-click the Maestro icon.

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: https://www.schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/docking_nucleic_acid.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. Saving the project in the Save Project panel.

  1. Go to File > Save Project As.
  2. Change the File name to RNA_docking.
  3. Click Save.
    • The project is now named RNA_docking.prj.

Figure 2-3. Importing the prepared structure.

  1. Go to File > Import Structures.
  2. Navigate to and find RNAprep_6DN3-out.maegz.
  3. Click Open.
    • A new entry titled 6DN3 - prepared is added to the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and a banner appears confirming successful import of the structure.

Note: Imported structures in Maestro are includedthe entry is represented in the Workspace, the circle in the In column is blue in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed and 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 Entries (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries in the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion by default. Please refer to the Glossary of Terms for the difference between includedthe entry is represented in the Workspace, the circle in the In column is blue and 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 Entries (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries.

3. Running and Analyzing the Docking Job

In this section, you will dock flavin analogs to the 6DN3 FMN riboswitch. For performing docking calculations, you will first generate a receptor grid file and re-dock the cognate ligand (BRX1555) to validate the docking protocol. The validated protocol can then be used to dock other flavin analogs. To save time, the cognate ligand and the flavin analogs have been prepared using the LigPrep panel and are included in the zip archive. The ligands were prepared using the same global pH (7.4) as used for the RNA preparation. All the possible tautomers and ionization states at this pH were generated using Epik Classic. Additionally, the specified chiralities of the ligands were retained while varying other chiral centers for generating all the possible stereoisomers. If you are following along with a different set of compounds, make sure that you have prepared them using the LigPrep panel. For more information, please refer to the LigPrep panel documentation.

3.1 Identify the binding site

Setup of a Glide docking model consists of two steps. Initially, a reduced representation of the receptor-induced environment of the binding pocket – called receptor grid – must be generated. This transformation drastically speeds up the second docking step by allowing ligand-receptor interactions to be efficiently calculated and infeasible ligands discarded early in the process.

Figure 3-1. Applying Default Custom Preset to the structure.

Feel free to adjust the visualization to your preference.

 

  1. Go to Presets and choose Apply Default Custom Preset.
    • The structure is rendered in the default custom preset.

Figure 3-2. The Receptor Grid Generation in Tasks.

  1. Go to Tasks > Browse > Receptor-Based Virtual Screening > Receptor Grid Generation.
    • The Receptor Grid Generation panel opens in the Receptor tab.

Figure 3-3. Receptor Grid Generation default settings.

  1. Under Define receptor, make sure that the boxes for Pick to Identify the ligand (Molecule) and Show Markers are checked.
    • A banner in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed prompts you to click on an atom in the ligand.  

Note: If you don’t know where the binding site of your target is, you can use SiteMap to identify putative binding sites as described in the Analyzing Binding Sites of Nucleic Acids with SiteMap tutorial. If you do know where the binding site is, but don’t have a ligand in the structure you are using, you can specify the binding site in the “Site” tab of the receptor grid Generation panel by selecting residues or spatial coordinates as described here.

Figure 3-4. Defining the binding pocket and excluding the ligand from grid generation.

  1. Click on an atom in the ligand.
    • A purple box appears around the ligand with all the atoms highlighted. This box defines the region that the docked molecule(s) can occupy.
    • The ligand will be excluded from the grid generation.
  2. Click the Fit-all button to see the entire structure with the purple box around the ligand.

 

 

Figure 3-5. Generating the receptor grid.

  1. Change the Job name to glide-grid_6DN3.
  2. Click Run.
    • This job takes ~1 minute.
    • A folder named glide-grid_6DN3 is written to your Working Directorythe location where files are saved which contains the receptor grid.
  3. Close the Receptor Grid Generation panel.


Note: Glide supports various receptor-based constraints, which can be used to bias the model to preserve certain interactions or atom positions. For more details, see the panel documentation.

3.2 Dock the co-crystal/cognate ligand

Docking the cognate ligand (if available) is an essential part of validating a docking model. The ligand should be prepared in the same manner as the screening library or ligand series.

Figure 3-6. The Ligand Docking in Tasks.

To set up the docking job, you must first specify the receptor grid to be used.

 

  1. Go to Tasks > Browse > Receptor-Based Virtual Screening > Ligand Docking.

Figure 3-7. Selecting the generated receptor grid.

  1. For Receptor grid, choose From file.
  2. Next to File name, click Browse.
  3. Navigate to and find glide-grid_6DN3.zip in your Working Directorythe location where files are saved.

Figure 3-8. Loading the prepared cognate ligand for docking.

You can find the results of running LigPrep for the cognate ligand in the tutorial zip archive. For this ligand, there is only one state that is predicted to be accessible at pH 7.4.

 

  1. In the Ligands tab, for Use ligands from, choose Files.
  2. Next to File name, click Browse.
  3. Navigate to the ligprep-6DN3_cognate_ligand folder in the tutorial files and select ligprep-6DN3_cognate_ligand-out.maegz.
  4. Click Open.

Figure 3-9. Enabling the RNA receptor scoring function and running the docking job.

Glide’s default scoring function is parametrized for protein receptors, so you have to explicitly enable the scoring function for RNA. For the details of RNA specific parametrization of the scoring function, see this publication.

 

  1. Go to the Settings tab.
  2. Enable Use RNA receptor scoring (beta).
  3. Change the Job name to glide-dock_6DN3_cognate.
  4. Click Run.
    • This job takes ~1 minute.
    • A banner appears and a new group glide-dock_6DN3_cognate_pv is added to the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.

Figure 3-10. Setting up the Workspace for viewing the docked pose.

Now, you can compare the Glide pose to the crystallographic pose.

 

  1. Click the Workflow icon next to the glide-dock_6DN3_cognate_pv group and select View Poses.
    • The 6DN3 - prepared entry is fixed in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
    • The Pose Viewer panel opens.

Figure 3-11. Comparing the docked pose with the crystallographic pose.

  1. Ctrl+Click (Cmd+Click) to includethe entry is represented in the Workspace, the circle in the In column is blue 6DN3 - prepared crystal structure in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
  2. Go to Presets and choose Binding Mode Comparison.
  3. Compare the docked pose with the co-crystal ligand pose.
  4. Clear the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
  5. Close the Pose Viewer panel.

The obtained ligand pose overlaps excellently with the co-crystal ligand pose. Our docking protocol is now validated for further use with other flavin analogs.

 

If you are working with a larger dataset, in particular in a virtual screening context, we recommend validating the docking model with a set of known actives and decoys, and evaluating whether the docking correctly recovers the binding poses of the actives. Additionally, you can also calculate enrichment which measures how well the active compounds are recovered and ranked compared to the inactive decoys.

3.3 Dock the flavin analogs

Figure 3-12. Loading the prepared flavin analogs for docking.

After having established that the cognate ligand docks sufficiently well, you will now dock other flavin analogs to the RNA receptor with the same receptor grid to predict their poses.

 

  1. In the Ligand Docking panel, next to File name, click Browse.
  2. Navigate to and select ligprep_flavin-analogs-out.maegz.
  3. Click Open.

Figure 3-13. Running the docking job.

  1. Make sure Use RNA receptor scoring (beta) option in the Settings tab is enabled.
  2. Change the Job name to glide-dock_flavin_analogs.
  3. Click Run.
    • This Job takes ~3 minutes.
    • A banner appears and a new group glide-dock_flavin_analogs_pv is added to the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.
  4. Close the Ligand Docking panel.

3.4 Analyze the results of the docking calculations

Figure 3-14. Setting up the Workspace for stepping through the poses.

The Pose Viewer is a helpful tool for looking at docking outputs. You can open it from the Tasks or the workflow action menu associated with the Entry group.

 

  1. Click the Workflow icon next to the glide-dock_flavin_analogs_pv group and select View Poses.
    • The 6DN3 - prepared entry is fixed in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed and the top docked pose is includedthe entry is represented in the Workspace, the circle in the In column is blue.

Figure 3-15. Applying the Binding Mode Comparison Preset.

You can unify the visualization for all ligands to make comparisons easier. Feel free to adjust this to your preference.

 

  1. Shift+Click to includethe entry is represented in the Workspace, the circle in the In column is blue all the docked flavin analogs.
  2. Click Continue if you see a warning about including many entries at the same time.
  3. Go to Presets and choose Binding Mode Comparison.

 

Figure 3-16. Visualizing the poses.

Visualizing the interactions can give you more insights into the complementarity between each ligand and the receptor.

 

  1. Includethe entry is represented in the Workspace, the circle in the In column is blue the top docked pose.
  2. Turn on the Interactions Toggle in the bottom right.
  3. Use the right and left arrow keys to visualize the poses one at a time.

 

Note: For comparing the ligand poses, it can be helpful to adjust the Auto-fit settings to your preference – if Auto-fit and Ligand are toggled on, the view will zoom to fit each ligand as you switch to its Entry. Turning auto-fit off will keep the view constant as you step through the poses.

All the flavin analogs successfully docked to the 6DN3 FMN riboswitch. If you are running a virtual screen with diverse ligands rather than generating bound poses for a congeneric series, check the Structure-Based Virtual Screening Using Glide tutorial for instructions on how to access and use the docking score. While docking provides valuable insights into potential binding poses and qualitative assessments of interactions, it is important to note that docking scores do not correlate with any binding affinity measurements, and are not suited for rank-ordering analogs or congeneric compounds. To rank-order the congeneric ligands, you can perform Free Energy Perturbation (FEP) calculations using FEP+, a physics-based free energy perturbation technology for computationally predicting receptor-ligand binding affinities.

4. Conclusion and References

In this tutorial, you learned how to perform docking calculations for an RNA receptor using Glide. You generated a receptor grid, docked the cognate ligand to validate the docking protocol, docked a series of compounds and analyzed the results using the Pose Viewer panel.

You can now for example use the insights into the receptor structure and ligand interactions for optimizing the ligand further using the Ligand Designer and predict binding affinities with the FEP+. See the further learning section below or the Oligonucleotide Modeling learning path for additional resources.

For further reading:

5. Glossary of Terms

Entries - 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 Entries (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