Tutorials

Classic Gameplan Tutorial

The Classic Gameplan Floe uses SZMAP to analyze ways to modify ligand chemistry based on water structure and energetics in the immediate environment of the ligand. By testing a limited number of coordinates based on the structure of the ligand and the binding site, the Floe quickly generates:

  • A description of how compatible the ligand is with the binding site.

  • A series of hypotheses for ligand variants, and stabilizing or destabilizing waters.

Floes used in the Tutorials

Prepare Protein and Bound Ligand from PDB Codes

To run the Spruce Prep from PDB Codes Floe, in the Floe tab on Orion 1) select “OpenEye Classic Floes” in the dropdown list, 2) type “PDB” in the search box, 3) click “Classic Spruce Prep from PDB Codes” to open the Job Form.

Run Spruce Floe

Run the Classic Spruce Prep from PDB Codes Floe

An extracellular signal-regulated kinase 1/2 inhibitor is used in the tutorials. The PDB code is 5K4J and it is straightforward to prepare the protein and bound ligand using the Classic Spruce - Prep from PDB Codes Floe.

Spruce Floe Parameters

Spruce Floe Parameters

The preparation steps of the Floe involves:

  1. Expansion of the asymmetric unit to the biological unit (if structure is from an X-ray crystallography experiment and it is necessary).

  2. Enumeration (default) or collapse of alternate locations.

  3. Building missing pieces e.g. partial sidechains, capping chain breaks, and modeling missing loops.

  4. Placement and optimization of hydrogen atoms including tautomer enumeration of ligands and cofactors, as well as evaluation of those tautomer states in the biomolecule structure.

The protein and ligand are also assigned partial charges (AmberFF99SB and Am1bcc respectively) by the Spruce Prep Floe and the output dataset Spruce_prep_dataset_5K4J is ready for the Gameplan Floe.

Run the Classic Gameplan Floe

To run the Classic Gameplan Floe, in the Floe tab on Orion 1) select “OpenEye Classic Floes” in the dropdown list, 2) type “Gameplan” in the search box, 3) click “Classic Gameplan” to open the Job Form.

Run Gameplan Floe

Run the Classic Gameplan Floe

There are two required inputs: protein and ligands. Click “Choose input…” and select Spruce_prep_dataset_5K4J as input for both the protein and ligands.

Select Gameplan Input

Select Inputs for the Classic Gameplan Floe

By default, the Classic Gameplan Floe hypotheses respect the hybridization of aromatic atoms in the input ligand. Specifying the switch “Sample Sp3 Hybridization” will permit the Floe to explore the effect of a change of hybridization of aromatic atoms. Note that only the local hybridization at the attachment site is altered, often leading to odd-looking geometry. But the point is to generate fresh ideas for how you might modify your ligand. To turn this option on, 1) turn “Show cube parameters” on, 2) select “Gameplan” Cube, 3) turn “Sample Sp3 Hybridization” on. And then click “Start Job” to run the Floe.

Turn Sample Sp3 Hybridizaiton On

Turn “Sample Sp3 Hybridization” On

Gameplan Results

Once the Classic Gameplan Floe job finishes, click the “Show in Project Data” in the job status page.

Open Project Data

Open Project Data

And then click “Add to active data” to add the Gameplan hypothesis dataset.

Add Data to Active

Add Gameplan Hypothesis to Active Data

Click the “3D Modeling” button. This will open the 3D Viewer pre-populated with the Gameplan hypothesis results.

Gameplan Results in 3D Modeling

Gameplan Results in 3D Modeling Page

Gameplan results are organized into three main sections (click “maximize” to show full list):

  • An analysis of how well the ligand compares to the solvent in the binding site with colored annotation around atoms that indicates the type of site (Figure Ligand Compared to apo Binding Site). The protein is also included here for context.

  • A series of hypotheses for substituents that could be added to the ligand. Each attachment is modeled using dummy atoms with annotation that indicates the type of site: polar, nonpolar and van der Waals (see Figures Hypothesis for a Polar Substituent and Hypothesis for a Nonpolar/VDW Substituent).

  • A (possibly empty) section showing stabilizing and destabilizing water sites (Figure Stabilizing Site and Figure Destablizing Site).

Full List of Gameplan Hypothesis

Full List of Gameplean Hypothesis

Click “restore” to show other tabs in the 3D Viewer Page and click the grey circle in the list to turn on/off a specific hypothesis in the 3D viewer.

Apo Site Image

Ligand Compared to apo Binding Site

Polar Image

Hypothesis for a Polar Substituent

Nonpolar Image

Hypothesis for a Nonpolar Substituent

Vdw Image

Hypothesis for a VDW Substituent

Stabilizing Image

Stabilizing Site

Destabilizing Image

Destabilizing Site

Annotations are:

  • Yellow sphere: polar site; the size of the sphere indicates the magnitude of the polar interaction.

  • Green sphere: van der Waals site; the size of the sphere indicates the magnitude of the VDW interaction.

  • Bluish Green sphere: non-polar site.

  • Purple top: mismatch site, where the ligand polarity does not match that of the solvent.

  • Small green and blue spheres: stabilizing and destabilizing points, respectively.

Click the Analyze button, energies of the Gameplan Hypotheses are shown in the spreadsheet.

Results in Analyze Image

Gameplan Results in Analyze Page

There are also 2D depiction of interactions. Click “Magnify” icon to show a large version of the depiction.

../../../../_images/apo_2d.png
../../../../_images/polar_2d.png

Suggested further experiments, you may want to modify your ligand to make it more compatible with the apo pocket solvent electrostatics, add a substituent based on the suggested hypotheses, displace a destabilizing water or carefully replace a stabilizing water, mimicking the interactions of the water.