Teaching with Schrödinger

Updated: 1-23-22

Structure-Based Virtual Screening
Created with: Release 2021-3
Prerequisites: working knowledge of Maestro
Files Supplied: SBVS_worksheet
Categories:
biochemistry, medicinal chemistry

About this Lesson
This lesson will focus on an important early stage of drug discovery in which protein
structures and molecular modeling are utilized to identify molecules that can be further
developed into drugs.
Using Maestro, students will learn how to perform a virtual screen for potential
inhibitors of FXa using the ligand docking application Glide. Students will learn how to
generate a protein receptor grid, dock a set of ligands into the receptor grid, andanalyze the docking results. Students can then sketch their own inhibitor designs andevaluate their value.

Learning Objectives
Learn the steps of a molecular docking workflow using Schrödinger’s Glide● Perform a structure-based virtual screen of a small set of ligands● Design your own inhibitor for FXa and determine its docking score●

1
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Standards●

ACS Guidelines○●

ETS Chemistry GRE○●

Biological macromolecules (Section 5.1)
Organic Chemistry – Amino acids, Peptides (3F)

AAMC MCAT○

Structure, function, and reactivity of biologically-relevant molecules (5D)

Assessments
The following types of formative assessments are embedded in this lesson:●●

Assessment of student understanding through discussion of warm-up questions andfilling in any knowledge gaps about structure-based virtual screen steps
Visual assessment of student-generated docking scores from their own set of ligands

Warm-Up Questions: To be done on their own or at the beginning of class
Read the article “Structure-Based Virtual Screening: From Classical to Artificial Intelligence”
and answer the following questions.
1) What is a typical drug development timeline from drug target identification to clinical
trials?

2) What are some advantages and disadvantages to performing structure-based virtual
screens?

Lesson Outline
1.
2.
3.
4.
5.
6.
7.

What you will need for this lesson - p. 3
Introduction to Structure-Based Virtual Screening - p. 5
Generating a Receptor Grid - p. 6
Docking the Cognate Ligand and Screening Compounds - p. 11
Analyzing Results and Binding-Site Characterization- p. 17
Individual Exercises - p. 23
Summary, Additional Resources, and References - p. 24

2
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

1. What you will need for this lesson
1. Go to the ‘Data’ folder and open yourClass Folder found on the virtual
cluster’s desktop.
2. Right-click on the folder called“Structure_Based_Virtual_Screen”
and copy folder to Desktop● Here, you will find the lesson
plan, worksheet, and any
additional resources
3. Open Maestro
a. See Starting Maestro if you
need help
Figure 1-1. Open Maestro.
4. Go to File > Change Working
Directory
5. Find your“Structure_Based_Virtual_Screen”
folder that you duplicated to yourDesktop, and click Choose

Figure 1-2. Change Working Directory option.

3
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

6. Next, go to File > Save Project As
7. Type “SBVS_tutorial” and click Savea. The project will be titled
SBVS_tutorial.prj

Figure 1-3. Save Project panel.

Figure 1-4. Choose the best mouse option foryour set up.

8. Finally, check your Mouse Actions
a. PC : Edit > Customize Mouse
Actionsb. Mac : Workspace >Customize Mouse Actions
9. Make sure you have the best option
chosen for your set up. This lesson
was written with a three-button mousewith a scroll wheel, meaning the scroll
wheel is a button as well as a wheel. If
you do not have a mouse, choose
Trackpad.

4
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

2. Introduction to Structure-Based Virtual
Screening
Molecular modeling encompasses a wide array of approaches that impact theearly stages of drug discovery: hit ID, hit-to-lead, and lead optimization. Generally, thesemolecular modeling approaches are broken down into two categories: ligand-based andstructure-based approaches. Ligand-based approaches use information from a hit orseries of hits to inform on next stages in drug discovery. This information includes
molecular fingerprints, shape, charge, and more. Structure-based approaches use
information not only from a ligand structure but also from a target structure. A target isanother term for a protein or other macromolecule that is being targeted by a drug. Bothof these approaches are often used synergistically in all stages of computer-aided drug
discovery and in combination with fragment-based approaches as well.
In this lesson, we will be performing a structure-based virtual screen of potential
FXa inhibitors. Structure-based approaches allow for the identification of key residues
around the ligand and water energetics in the binding site that could modify or enhance
the binding of one compound over another. A binding site is a pocket or surface of atarget protein where a compound or drug binds to elicit a downstream effect in adisease pathway.
Figure 1 below shows a schematic for the steps involved in a structure-based
virtual screen. Structure files obtained from the PDB, vendors, and other sources often
lack necessary information for performing modeling-related tasks. Typically, these files
are missing hydrogens, partial charges, side chains, and/or whole loop regions. In orderto make these structures suitable for modeling tasks, we use the Protein Preparation
Workflow to resolve issues. Similarly, ligand files can be sourced from numerous places,such as vendors or databases, often in the form of 1D or 2D structures withunstandardized chemistry. LigPrep can convert ligand files to 3D structures, with thechemistry properly standardized and extrapolated, ready for use in virtual screening.
In this lesson, the protein, cognate ligand, and virtual screening ligands havealready been prepared in order to save time. However, these preparation steps are anecessary part of a virtual screen and must be done before docking. Please see thelesson on Protein-Ligand Interactions for guidance on using the Protein Preparation
Workflow and LigPrep.

5
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Figure 1. Workflow for a Structure-Based Virtual Screening

3.

Generating a Receptor Grid

Grid generation must be performed prior to running a virtual screen with Glide. The
shape and properties of the receptor are represented in a grid by fields that become
progressively more discriminating during the docking process. To add more information
to a receptor grid, different kinds of constraints can be applied during the grid
generation stage. For a comprehensive overview of constraint options, see the grid
generation videos on our website or the Glide User Manual (Help > Help > User
Manuals > Glide User Manual). In this tutorial, we will set a hydrogen bond constraint
in our receptor grid.

6
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

3.1

Identify the binding site

Figure 3-1. Receptor Grid Generation
option in Receptor-Based Virtual
Screening.

Figure 3-2. The Receptor tab of Receptor
Grid Generation.

1. Click the In circle next to
1fjs_prep_complex to include it in
the Workspace
2. Double-click Presets○ 1fjs_prep_complex isrendered using the Custom
Preset
3. Go to Tasks > Browse >Receptor-Based Virtual
Screening > Receptor Grid
Generation○ The Receptor Grid
Generation panel opens
4. Under Define Receptor, check theboxes for Pick to Identify theligand (Molecule) and Show
Markers○ A banner in the Workspace
will prompt you to click on
an atom in the ligand

7
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

5. Click on the ligand○ The ligand is now
highlighted with a purple
box around it○ The ligand will be excluded
from the grid generation
Note: The purple bounding box defines
the region that the docked molecule(s)can occupy to satisfy the initial stages of
docking

Figure 3-3. The ligand is defined to be
excluded from grid generation.

3.2

Define the bounding box dimensions
1. Click the Site tab
2. Select Centroid of Workspace
ligand (selected in the Receptortab)
3. Click Advanced Settings○ A green inner bounding box
appears

Figure 3-4. The Site tab of Receptor Grid
Generation.

Note: The green bounding box defines
the region in which the centroid of thedocked molecule(s) must occupy to pass
the initial stages docking

8
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

4. Adjust the settings for X, Y, and Z
sizes to 10, 8, and 6 Å ,respectively.
○ The shape of the green box
is changed
5. Click OK

Figure 3-5. Ligand diameter midpoint box
panel.

3.3

Set a hydrogen bonding constraint
1. Type L to zoom to the ligand
2. In the Structure Hierarchy, click
the magnifying glass
3. In the search field, type ASP 189
4. Select ASP 189

Figure 3-6. Search in the Structure
Hierarchy.

Note: Please see the Introduction to
Structure Preparation and Visualization
tutorial for instructions on how to add
residue labels and show H-bonds
5. Under Fit, click Fit view toselected atoms

Figure 3-7. Zoom to selected atoms.

9
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

6. In the Receptor Grid Generation
panel, click the Constraints tab
7. Click the H-bond/Metal (0) tab○ A banner appears
prompting selection of thereceptor atom to be theconstraint

Figure 3-8. The Constraints tab of
Receptor Grid Generation.
8. Click an oxygen atom of the ASP
189 sidechain○ Both oxygens arehighlighted○ An H-bond constraint isdefined in the Receptor
atoms table

Figure 3-9. Constraint defined on ASP
189.

10
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

9. Change Job name toglide-grid_1fjs
10. Click Run○ This job will take about aminute○ A folder named
glide-grid_1fjs is written to
your Working Directory

Figure 3-10. Run receptor grid generation
job.
Question #1:
Why is it necessary to generate a receptor grid? What would happen if you proceededwith docking a ligand without a receptor grid?

4. Docking the Cognate Ligand and Screening
Compounds
The minimum requirements for running a Glide virtual screen are a grid file and a ligand
file. It is strongly recommended that the grid file be generated from a protein preparedusing the Protein Preparation Workflow and the ligand file be prepared using LigPrep.
Additionally, you can choose the scoring function, set ligand- and receptor-based
constraints, and define the output. Please see the Glide User Manual for more detail. In
this section, we will include the hydrogen bonding constraint that was created in theprevious step.
First, we will dock the cognate ligand, which is a helpful way to benchmark a virtual
screen of compounds with unknown binding activity against a target. The information
11
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

gained from this step can help with evaluating poses and beneficial interactions, which
is useful for hit finding. Second, we will dock the screening compounds from aprepared ligand file, 50ligs_epik.mae.gz. Both jobs will use the receptor grid file thatwas generated in the previous step.

4.1

Prepare the cognate ligand
1. Include 1fjs_prep_lig in theWorkspace
2. Go to Tasks > Browse > LigPrep○ The LigPrep panel opens

Figure 4-1. Include 1fjs_prep_lig.
3. For Use structures from, choose
Workspace (1 included entry)
4. Under Stereoisomers, selectDetermine chiralities from 3D
structure
5. Change Job name to ligprep_1fjs
6. Click Run○ A banner appears when thejob has been incorporated○ A new group is added to
the Entry List

Figure 4-2. The LigPrep panel.

12
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Question #2:
Preparing a ligand using LigPrep may produce multiple output structures for each input
structure by generating different protonation states, stereochemical outcomes,
tautomers, and ring conformations. Why is it important to prepare a ligand before
proceeding with docking?

4.2

Dock the cognate ligand
1. Go to Tasks > Browse >Receptor-Based Virtual
Screening > Ligand Docking○ The Ligand Docking panel
opens
2. Next to Receptor grid, click
Browse and choose
glide-grid_1fjs.zip

Figure 4-3. The Ligands tab of the Ligand
Docking panel.

3. In the Ligands tab, for Use ligands
from, choose Files
4. Next to File name, click Browse
and choose
ligprep_1FJS-out.maegz

13
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

5. Click the Constraints tab
6. Click on the Grid-based tab
7. Under Use, check the H-bondconstraint for ASP 189
8. Change Job name toglide_1FJS_cognate
9. Click Run○ This job takes about aminute○ A banner appears to showthat files have been
incorporated○ A new group is added to
the Entry List
Figure 4-4. The Constraints tab of the
Ligand Docking panel.

14
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Note: The 1fjs_prep_complex entry isfixed in the Workspace, the top
1fjs_prep_lig entry is included, and thePose Viewer panel appears
10. Include other ligand results○ H-bonds to ASP 189 areconserved
11. Double-click Presets
12. Double-click the In circle next to
1fjs_prep_complex○ The entry is no longer fixedin the Workspace

Figure 4-5. Binding pose of the top
docked cognate ligand (pink) comparedto the crystal structure (gray).

Note: Though only the top ranked result
is in strong agreement with the
crystallographic pose, all three results
accurately capture the pose of the ligand
in the binding site (with varying degrees
of success in capturing the solvent
exposed region)

Question #3:
What important protein-ligand interactions do you see when the cognate ligand isdocked? List specific residues and define specific interactions that may play animportant role in binding.

15
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

4.3

Dock the screening compounds
1. In the Entry List, select the group
50ligs_epik

Figure 4-6. Select 50ligs_epik in the Entry
List.
2. In the Ligand Docking panel, click
the Ligands tab
3. For Use ligands from, choose
Project Table (selected entries)

Figure 4-7. Use ligands from selected
entries.

Note: Keep glide-grid_1fjs.zip as
the receptor grid16
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

4. Click the Output tab
5. Check Write per-residue
interaction scores
6. Change Job name toglide_1FJS_screening
7. Click Run○ This job takes a few
minutes○ A banner appears to showthat files have been
incorporated○ A new group is added to
the Entry List

Figure 4-8. The Output tab of the Ligand
Docking panel.

5. Analyzing Results and Binding-Site
Characterization
Multiple Glide docking results can be viewed in the Entry List and be identified by the
job name. Docked results will show the receptor in the first row and the docked
ligand(s) in the subsequent row(s), where they are ordered by best to worst docking
score, or Glide Gscore if Epik state penalties were not applied in LigPrep. The Glide
Gscore is broken down by van der Waals electrostatic components and can be seen in
the Project Table, using the Property Tree. You can read more about how docking
scores/poses are generated here and here and what dependencies they have here and
here.

17
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

5.1

Visualize the results using Pose Viewer

Figure 5-1. Pose Viewer panel.

5.2

1. Step through the results using theright and left arrow keys
○ Ligand poses are displayedin the Workspace○ Residues are coloredaccording to theirinteraction energies, ranging
from green (favorable) to red(unfavorable)
2. Close the Pose Viewer panel

Analyze the results

Figure 5-2. Glide Primary properties
shown in the Project Table.

1. In the Project Table, click theProperty Tree icon
○ The Property Tree appearson the right of the ProjectTable
2. Click the All box twice○ All boxes are deselected
3. Click the Glide box
4. Click Primary○ Only the Glide Primary
properties are shown
Note: Please see Knowledge Base Article
1027 for more information on the
difference between docking score, Glide
gscore, and glide emodel score.

Question #4:
18
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

In the table below, select your top 5 ligands with the best docking scores. Rememberthat the lower the value, the better the docking score. For each ligand, i) write theligand name and take a screenshot of the pose, ii) list the docking score that can befound in the Project Table, and iii) identify at least 2 types of protein-ligand interactions
between that particular ligand and residues within the active site.
Ligand Name &a Screenshot of the Pose

Docking Score(found in Project Table)

Protein-Ligand
Interactions

19
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

5.3

Identify a binding site with SiteMap

We will analyze the binding site using SiteMap. SiteMap characterizes hydrophilic,hydrophobic, acceptor, and donor regions of a receptor. This is useful for learning more
about an active site, predicting a binding site in an apo structure, or identifying possible
allosteric sites. SiteMap ranks the potential binding sites with a druggability score,
which can be viewed in the Project Table. The output from a Glide virtual screen can beoverlaid with SiteMap information to examine how well the docked ligands explore thevarious regions in the binding cavity. Sites identified by SiteMap can also be used tocreate receptor grids for virtual screening experiments. This can be useful for exploringsites without a known active compound.
1. Right-click an empty area in theWorkspace choose Clear
Workspace

Figure 5-3. Clear Workspace.

Figure 5-4. Fix 1fjs_prep_complex in theWorkspace.

2. Double-click the In circle to fix
1fjs_prep_complex (in row 3) inthe Entry List
3. Go to Tasks > Browse >Structure Analysis > Binding Site
Detection○ The SiteMap panel opens

20
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

4. Under Task, select Evaluate aSingle binding site region
5. Click on the ligand in theWorkspace○ The ligand is highlighted○ SiteMap removes the ligandfrom the calculation
6. Change the Job name tositemap_1fjs
7. Click Run○ A banner appears when thejob has incorporated○ A new group is added to
the Entry List

Figure 5-5. SiteMap panel.

21
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

8. Include the sitemap_1fjs_site_1,
sitemap_1fjs_ligand, and
1fjs_protein
9. Type L○ Various surfaces are shown
representing different
regions of hydrophilic
property; hydrophobic(yellow), acceptor (red),
donor (blue)○ The white site-point
spheres each represent ~1
Å3

Figure 5-6. SiteMap results in theWorkspace.

10. In the Entry List, click the S next tositemap_1fjs_site1 to toggle thesurfaces associated with the
SiteMap
Note: To find all possible binding sites
using SiteMap, under Task select Identify
top-ranked potential receptor bindingsites. If you want to detect all pockets,
you will need to exclude the cognate
ligand from the Workspace.

Question #5:
SiteMap visualization uses a grid of points to identify potential hydrophobic andhydrophilic regions; the hydrophilic regions are further classified into hydrogen-bonddonor, hydrogen-bond acceptor, and metal-binding regions, and the surface of theprotein is contoured. Take a screenshot of your SiteMap results. Identify which regionsof your receptor are hydrophilic and hydrophobic.

22
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

6.

Individual Exercise

Using the information that you gained from docking the screening ligands, design a
new inhibitor that may have a better docking score. Perform LigPrep on your moleculeand use Glide to obtain its docking score. Take a screenshot of its pose and paste it
below. Then list its docking score. Provide analysis as to why you chose to design thisparticular inhibitor.

23
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

7.

Summary, Additional Resources, and References

In this lesson, we completed a workflow for virtual screening using Glide. We generated
a receptor grid with a hydrogen bond constraint, which was used in cognate ligand
docking as a positive control to set up a virtual screen of test ligands. Then, a series ofscreening compounds were docked and the results were viewed using Pose Viewer,with known actives being found as the top hits. SiteMap was used to explore thebinding site.
For further information, please see:
Maestro 11 Training Portal
Introduction to Structure Preparation and Visualization
Glide User Manual
Glossary of Terms
cognate ligand - a ligand that is bound to its protein target
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
incorporated - once a job is finished, output files from the working directory are added
to the project and shown in the Entry List and Project Table
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
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 theselected 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 that files are saved

24
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

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

25
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.