Search for Similar Binding Sites with SiteHopper

SiteHopper is a tool to superpose and compare protein binding sites. The input is a protein-ligand (or apo) complex where the binding site is converted to a searchable site called a patch. SiteHopper can efficiently compare this patch to other binding site patches, which are stored in a pre-generated database.

A search for similar binding sites can be useful for a number of different reasons, two of which are:

  • A similar binding site in a related or unrelated protein can indicate possible off-target risks. Finding and comparing these binding sites can be helpful for improving compound selectivity.

  • A ligand from a similar binding site can potentially be used as tool compound or as an early stage hit for a target. Especially interesting are results where the binding site similarity is high while the ligand similarity is low - think of this as scaffold hopping based on binding site similarity.

In this tutorial a dataset of binding site patches will be searched with a query structure from the HSP90 target using the SiteHopper Search Floe. The results will be visualized in both the analyze page and the 3D viewer. The patch database preparation should only be run once and is afterwards shareable with others.

This tutorial uses the following Floes

  • Make SiteHopper Patch Database from the OpenEye Biomodeler Floes package.

  • Classic Spruce - Prep from PDB Codes from the OpenEye Classic Floes package.

  • SiteHopper Search from the OpenEye Biomodeler Floes package.

Create a Tutorial Project

Note

If you have already created a Tutorial project you can re-use the existing one.

Log into Orion and click the home button at the top of the blue ribbon on the left of the Orion Interface. Then click on the ‘Create New Project’ button and in the pop up window enter Tutorial for the name of the project and click ‘Save’.

create_project_ui

Orion home page

Prepare Patch Dataset

Note

If you have already created a patch dataset you can re-use it

The steps from the video are detailed here below

OEDesignUnits must be converted to SiteHopper patches before they can be searched with the SiteHopper Search Floe. Openeye has pre-generated the Guide to Pharmacology prepared design unit collection for you, it contains prepared design units for ~21k PDB structures for targets in the Guide to Pharmacology database; with biological unit expansion and alternate conformation enumeration that turns into ~39k prepared design units.

Locate the Make SiteHopper Patch Database Floe as follows

  1. Click on the ‘Floes’ button in the left menu bar

  2. Click on the ‘Floes’ tab

  3. Set the ‘Browse Workfloes’ drop down menu to ‘Show all packages’

  4. Select ‘All’ under Browse Workfloes

  5. In the search bar enter Make SiteHopper Patch Database

The Make SiteHopper Patch Database floe will be visible to the right (see below)

find_sitehopper_floes

Click on the Make SiteHopper Patch Database Floe to bring up the Job Form and set the following parameters.

  1. Inputs -> Input Collection : GtoP DU Collection.

    To select this collection

    • Click the ‘Choose Input Button’

    • Click on ‘<Organization> Data’ under collections in the Select Input Collection modal. <Organization> is the name of your company/entity/organization. This name is set during Orion installation or configuration; however, an Organization admin can also change the name.

    • Select the Guide to Pharmacology Design Units Collection OEv1.0 collection.

    • Click ‘Use Collection as Input’

    select_gtop_du__collection
  2. Outputs

    • Type or enter GtoP Patch Dataset in the Output Dataset (Dataset Writer) input field:

    • Type or enter Failed GtoP Patch Dataset in the Output Dataset (Failed Dataset Writer) input field

    • Type or enter GtoP Patch Collection in the Collection Name input field

launch_filter_collection

Scroll down to the bottom of the Job Form and click click ‘Start Job’. The job will take about 10-15 min to run. Once the Floe has finished move on to the next step of the tutorial. Note that when finished the results will show a dataset with a single (1) record for the successes. This single record holds a link to a collection with >38,000 patches. The failed dataset will have 300-some failures.

Prepare Query Protein

The steps from the video are detailed here below

This tutorial will use the HSP90 crystal structure 1uyg from the protein data bank. To import this structure into Orion and prepare it for docking locate the Floe Classic Spruce - Prep from PDB Codes in the ‘Floes’ page as follows

  1. Click on the ‘Floes’ button in the left menu bar

  2. Click on the ‘Floes’ tab

  3. Set the ‘Browse Workfloes’ drop down menu to ‘Show all packages’

  4. Select ‘All’ under Browse Workfloes

  5. In the search bar enter Spruce

A list of three spruce Floes will now be visible to the right (see below)

find_spruce_floe

Click on the Classic Spruce - Prep from PDB Codes and a Job Form will pop up. Specify the following parameter settings in the Job Form.

  1. Enter or type hsp90_design_unit in the Outputs Dataset input field

  2. Enter or type 1uyg in the PDB Code(s) To Download input field

spruce_launch_ui

Click the ‘Start Job’ button to launch the Floe. Wait for the Floe status to be complete before moving on to the next step in the tutorial (without loop modeling this will take on the order of ~2-3 min, with loop modeling as used in this tutorial more like 10 min).

View Prepared Site

Once the Classic Spruce - Prep from PDB Codes job finishes make the resulting dataset active as follows:

  1. Go to the Project Data page by clicking on the blue ‘Data’ button on the left menu bar.

  2. Select ‘Project Data’ from the list of options to the left of the page

  3. Set the ‘Type’ drop down menu to Datasets if it is not already.

  4. Check to make sure you no datasets set as active by clicking on ‘Active Datasets’ in the top right of the window

  5. Locate the dataset named hsp90_design_unit and make it active by clicking on the circle with the plus symbol in the Active column next to the hsp90_design_unit.

make_spruce_du_active

Now you can see the query in the 3D viewer, clicking on the 3D button in the left menu bar.

Search Patch Dataset

The steps from the video are detailed here below, except for the more detailed data analysis.

Locate the SiteHopper Search Floe as follows

  1. Click on the ‘Floes’ button on the left menu bar

  2. Click on the ‘Floes’ tab

  3. Set the ‘Browse Workfloes’ drop down menu to ‘Show all packages’

  4. Select ‘All’ under Browse Workfloes

  5. In the search bar enter SiteHopper Search

The SiteHopper Search Floe will be visible to the right (see below)

find_search_docking_floe

Click on the SiteHopper Search Floe to bring up the Job Form and set the following parameters.

  1. Inputs -> Query Dataset : hsp90_design_unit

    This is the dataset with the protein we prepared

  2. Inputs -> SiteHoper DB Dataset: : GtoP Patch Dataset

    This is the dataset with all the patches we created at the beginning of this tutorial.

  3. Outputs -> Output Dataset: : HSP90 Similar Sites

Once the parameters are set scroll to the bottom of the page and click ‘Start Job’. The job will take 5-10 min depending on the query.

View Results

Once the search job has completed make the output datasets active as follows

  1. Press the ‘Project Data’ button in left menu bar

  2. Clear current active datasets by clicking on ‘Active Datasets’ and clicking ‘Clear All’ in the menu that pops up.

  3. Make the output datasets active by clicking on the + icon in the Actives column.

Once the datasets are active switch to the 3D viewer by clicking the 3D button in the menu bar. The 3D results will be overlaid to the input query. This is similar to how FastROCS results are shown for small molecules. Analysis of the scores and drilling down to interesting results can also be done in the Analyze page based on SiteHopper scores and sequence similarity scores.