Teaching with Schrödinger

Updated: 10-28-22

EnzymesCreated with:

Release 2022-2

Prerequisites:

working knowledge of Maestro

Files Supplied:

Enzymes_worksheet

Categories:

AP/college general biology, AP/college biochemistry

About this Lesson:
Enzymes are biological catalysts, and nearly all of them are proteins. Understanding
the structure and function of enzymes is crucial because they accelerate key metabolic
processes that are necessary to sustain life.
Using Maestro, students will learn how to use the protein preparation workflow andglide docking panels to prepare a quality enzyme structure, predict substrate binding
modes, as well as analyze enzyme-substrate interactions within the binding site.

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.

Learning Objectives:
Define a catalyst and explain how enzymes work, including inhibitory
mechanisms● Prepare and visualize the enzyme structure using the protein preparation panel● Assess enzymatic activity by simulating enzyme-substrate binding using Glide● Analyze enzyme-substrate interactions using the Ligand Interaction panel●Standards:●

NY State Core Curriculum:○●

Enzymes in the Human Body (Standard 4, Key Idea 3.4)

Connections to AP:○

Enzyme Structure and Catalysis (ENE 1 & 3)

● IB Diploma Programme:○ Enzymes (Core Topic 2.5)
● ACS Guidelines:○●

Biological Reactions - (Conceptual Topics)

AAMC MCAT:○

Biological and Biochemical Foundations of Living Systems (1A)

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 the structure and function of enzymes
Visual assessment of student-prepared enzyme structure, simulated substrate-active
site binding, and creation of 2D interaction diagrams

Warm-Up Questions: To be done on their own or at the beginning of class
Read the Khan Academy article on Enzymes and answer the following questions:
1)

What is a catalyst? How do they work?

2) Give an example of catalysis in your daily life. Identify the catalyst in your example.

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.

Lesson Outline:
1.
2.
3.
4.
5.
6.
7.
8.

1.

What you will need for this lesson - p. 3
What are enzymes? - p. 5
Enzyme structure - p. 6
Enzyme classification - p. 8
Simulating enzyme-substrate binding - p. 9
Individual Exercises - p. 27
Summary, Additional Resources, and References - p. 30
Glossary of Terms - p. 31

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“Enzymes” 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.

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.

4. Go to File > Change Working
Directory
5. Find your “Enzymes” folder that you
duplicated to your Desktop, and click
ChooseFigure 1-2. Change Working Directory option.

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

What are enzymes?

Enzymes are biological polymers that catalyze biochemical reactions in our
body. They are crucial players in the human body and are very important for cells to live
and function. For example, the food that you eat is broken down by different enzymes
known as digestive enzymes, such as amylases, proteases, and lipases. Most enzymes
also happen to be proteins and constitute a linear chain of amino acids. The sequenceof amino acids in an enzyme specifies its three-dimensional structure, which in turn
determines its catalytic activity.
Enzymes are catalysts, which means that they speed up the rate of reactions
without being consumed by it. The molecules that enzymes act upon are called
substrates and the part of the enzyme where the substrate binds is called the activesite. This is where all the catalytic activity takes place, and results in the formation ofdifferent molecules known as products as can be seen in Figure 2-1.

Figure 2-1. Basic stages of an enzymatic reaction

Although enzymes help catalyze important chemical reactions in livingorganisms, in order to function effectively, biological systems must also be able toregulate the activity of enzymes. This is where special agents called inhibitors comeinto play. Inhibitors are substrates that bind onto enzymes in order to block the5
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.

enzyme’s activity. There are many different types of inhibitors. Competitive inhibitors
are chemicals that typically resemble the substrate and can therefore directly bind to theactive site of the enzyme. Once bound, the competitive inhibitor prevents the substratefrom occupying the active site. Noncompetitive inhibitors, also known as allostericinhibitors, do not compete with the substrate for the active site. Rather, they bind to adifferent area on the enzyme known as the allosteric site. Both competitive andnon-competitive inhibitors can be reversible or irreversible. Finally, feedback
inhibitors are the end products of an enzymatic reaction. They inhibit the enzyme that
helped produce them by binding to the allosteric site. To visualize the mechanism ofinhibition, take a look at Figure 2-2 below.

Figure 2-2. Competitive versus non-competitive inhibition

2.1 Enzyme structure
Enzymes are generally globular proteins that react in highly regio- andstereo-specific ways with dissolved solutes. The specificity of enzymatic activity is inturn determined by the enzyme’s amino acid sequence. While some amino acids do notplay a role in catalytic reactions, the amino acids that do get involved in chemical
catalysis are called catalytic residues. These residues have side chains that can belarge or small, hydrophilic or hydrophobic, and acidic or basic. It is these characteristics
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.

that determine the properties of an enzyme’s active site. The sequence of amino acids
found in the enzyme’s active site, along with their positions in 3D space, give the active
site a very specific shape and size that makes it suited to bind only to a particular
substrate. Enzyme active sites also typically create non-polar environments in whichbonds can be broken and formed more easily. Unless water participates in the actual
reaction, it is usually excluded from the active site. This hydrophobic effect, along withother noncovalent interactions like hydrogen bonds and van der Waals forces, helps thesubstrate bind to the active site, while simultaneously preventing any unwanted
reactions.
Active sites are much smaller than the actual size of an enzyme, and enzymes
are much larger than the substrate molecules they bind with. On the smaller end,
enzymes can range in size from 62 amino acid residues, such as in 4-oxalocrotonate
tautomerase (4-OT), and on the larger end, enzymes can also comprise of over 27,000
amino acid residues, like in the enzyme titin.

Figure 2-3. Zooming into the active site of enzyme 4-OT
Lukesch, M.S.; Pavkov-Keller, T.; Gruber, K.; Zangger, K. Substituting the catalytic proline of 4-oxalocrotonate
tautomerase with non-canonical analogues reveals a finely tuned catalytic system. Scientific Reports. 2019, 9 (1).
DOI:10.1038/s41598-019-39484-9

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.

Example #1. Name the catalytic residues visible in the active site of 4-OT. Which aminoacid residue in Figure 2-3 contributes to the hydrophobic effects of substrate-active site
binding? Hint: nonpolar residues are often hydrophobic.

3.

Enzyme classification

According to the International Union of Biochemistry and Molecular Biology(IUBMB), there are six major classes of enzymes. These classifications were formed
based on the type of reaction in which the enzymes are used to catalyze and aredetailed in Figure 3-1 below.

Figure 3-1. Major classifications of enzymes
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.

Example #2. Look up the role and function of the following enzymes and classify themaccording to the IUBMB nomenclature.
1) Pyruvate dehydrogenase

2) DNA ligase

3) Kinase4) Phosphoglucomutase

5) GTPase

4.

Simulating enzyme-substrate binding

In this activity, you will be analyzing the TBK1 (TANK-binding Kinase 1) enzyme boundto an inhibitor compound. TBK1 is an enzyme with kinase activity. Specifically, TBK1 is a
protein kinase that catalyzes the transfer of phosphate groups from high-energy,
phosphate-donating molecules to specific substrates.
Why are we examining TBK1? Well, TBK1 happens to play a critical role in inflammatory
signaling and is overexpressed and activated in bladder, lung, breast, and colon cancers. TBK1
is also thought to drive oncogenesis by phosphorylating and activating the AKT1 gene, whichfurther promotes cancer growth. TBK1 is thus a potentially interesting target in cancer therapy.

Computational Exercise: Enzyme-substrate binding in Maestro
This exercise involves five parts:
1) Import and prepare the TBK1-inhibitor complex in Maestro using protein
preparation workflow
2) Prepare the inhibitor compound using ligprep3) Generate a receptor grid to prepare for docking
4) Predict and analyze substrate binding poses using Glide Docking5) Visualize enzyme-substrate interactions after docking

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.

Part 1. Import and prepare TBK1-inhibitor
complex
When you import a protein directly from a
PDB file, it is not a prepared protein, rather it
is a protein in its raw state. This means thatthe structure might have missing hydrogens,partial charges, side chains or whole loop
regions. So, you cannot directly run
calculations on this structure, such as Glide
docking for instance. To resolve these issues,
we must first prepare the protein using theProtein Preparation Workflow.

Figure 4-1. Importing structure from PDB
database

1. Go to > File > Get PDB
2. For PDB IDs, type “6RST”
3. Click > Download○ 6RST is loaded into theWorkspace○ A banner appears
Note: Banners appear when files have been
imported, jobs incorporated into the Entry
List, or to prompt a common next step. Here,preparing the enzyme complex will becovered below.
4. In the Favorites toolbar, click Protein
Preparation○ The Protein Preparation
Workflow opens

Figure 4-2. Get PDB File panel

Note: You can also click Prepare in thebanner or find the Protein Preparation
Workflow in the Task Tool

Figure 4-2. The Protein Preparation Workflow
in the Favorites toolbar.

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.

Figure 4-3. The Protein Preparation Workflow
in Automatic mode.

5. In the Preparation Workflow tab,confirm the INTERACTIVE button isoff○ When on, the pane will readProtein Preparation Workflow(interactive)
Note: INTERACTIVE mode can be used for
exploring manual options, or to run a single
protein in a step-by-step manner. This tutorial
will be running an automatic protein
preparation.

Figure 4-4. Specify the protein from theWorkspace.

6. In the Specify Protein section, choose
use structures from: Workspace
7. Select Global Settings○ A dropdown opens showing
the simulation pH and the PDB
pH as well as small molecule
options○

The Non-water solvents option
is left unchecked. This saves
computational resources
because the glycerols in ourWorkspace will not be
preparedNote: The Specify Protein tool provides you
with the option to prepare a protein from theWorkspace, Project Table, File, or directlyfrom the PDB.
8. Select Review Structure○ The substructures tab opens
to show Ligands, Metals,
Other, Waters, and Chains
Note: our structure only contains one chain.
Figure 4-5. View protein issues in the
Diagnostics tab.

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.

9. Select the Diagnostics tab○ Valence errors were found, butthese bond order issues will be
resolved in the protein
preparation○ The Missing tab indicates one
missing side chain.
10. Select Reports to view other issues
with the protein that must resolved
prior to modeling

Figure 4-6. View missing side chain in the
Diagnostics tab.

Figure 4-7. Preprocess default settings.

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.

Figure 4-8. Optimize H-Bond Assignment
default settings.

Figure 4-9. Running the protein preparation
workflow.

11. Return to the Preparation Workflow
tab
12. Confirm Preprocess is toggled on○ Notice Fill in missing side
chains is checked by default.
Since these are missing in our
structure, they will become
populated during this step.
13. Under Preprocess, select More
Options○ Among the options provided,
notice that missing loops may
be filled in using Prime
14. Check the pH range for generating het
states with Epik
○ This should align with thephysiological or assay pH.
Note: Depending on your system andresearch question, you may want to keep
certain waters. See Protein Preparation
Workflow Panel Help for more details.
15. Confirm Optimize H-bondAssignment is toggled on
16. Click Settings○ Overlapping atoms caused by
the addition of hydrogens
during the Preprocess step will
be corrected, and side chains
may be flipped when this job isrun
17. Check the pH for Optimization○ This value should be captured
in the pH range chosen during
the Preprocess step
18. Change the job name to
6RST_Prepared
19. Click Run

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.

○This job will take a few
minutes as all toggled jobs are
running consecutively○ A new group will be added to
the Entry List
20. In the Entry List, click 6RST_
prepared

Figure 4-10. Select the protein preparation
outputNote: In Interactive mode, multiple entries will
be added to the Entry List as each individual
preparation task will be run as anindependent job

Figure 4-11. Load workspace entry in thesubstructures tab.

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.

Figure 4-12. Confirm issues have been
resolved during preparation.

21. Return to the Protein Preparation
tool
22. Click the Substructures tab
23. Choose Load Workspace Entry
24. In the Waters table, you can see that
all waters have been removed during
processing.
Note: Depending on your system andresearch question, you may want to keep
certain waters. See Protein Structure
Preparation using the Protein Preparation
Workflow or Protein Preparation Workflow
Panel Help for more details.
25. Click the Diagnostics tab to makesure there are no issues missed
during the preparation. You may needto click Check Workspace Entry
26. Exit the Protein Preparation Workflow
Note: If issues persist after preparation,
perform specific interactive protein
preparations on the modified protein withadjusted settings. The job type will depend on
which problems were found.

Question #1: List one error that you identified to be a problem prior to running the Protein
Preparation Workflow. Was it resolved after getting prepared?

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.

Part 2. Prepare inhibitor compound

Figure 4-13. Rename prepared enzyme to
6RST_prepared_dry

1. In the Entry List, double click 6RST_
prepared in the 6RST_prepared-out1group and rename the entry to
6RST_prepared_dry
2. Right-click on 6RST_prepared _dry
3. Choose Split > Into Ligands, Water,
Other○ Two new entries appear in the
Entry List
4. Include 6RST_prepared_dry_ligand○ Only the ligand is displayed in
the Workspace
5. Go to Tasks > Browse > LigPrep○ The LigPrep panel opens

Figure 4-14. Right-click to split an entry into
different components.

Figure 4-15. Include 6rst_prepared complex
into workspace

Figure 4-16. LigPrep application in the Task
toolbar.

16
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. For Use structures from, choose
Workspace (1 included entry)
7. Under Stereoisomers, choose
Determine chiralities from 3D
structure
8. Change Job name to ligprep_6rst
9. Click Run○ A banner appears when thejob has been incorporated○ A new group is added to the
Entry List
○ The number of ligands in thisgroup is shown in parentheses
Note: The Tile functionality is very useful forseeing the slight variations in chemistry forthe generated structures. The Tile View canbe turned on by clicking thein theWorkspace Configuration Toolbar in thebottom right corner and then clicking the Tile
button.

➕

Figure 4-17. The LigPrep panel.

10. Type Ctrl+T (Cmd+T) to open the
Project Table
11. Click Tree to open the Property Tree
○ Different calculated properties
can be toggled on and off○ Click the arrow next to eachapplication to view more
properties
Figure 4-18. The Project Table with theProperty Tree open.

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.

Question #2. What amino acid residues do you notice in the binding site of TBK1 and whatclassification of amino acid does it fall under (i.e. (1) non-polar and neutral, (2) polar andneutral, (3) acidic and polar, or (4) basic and polar)? List them and take a screenshot of thebinding site and paste it below.

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.

Figure 4-20. Double click presets.

Figure 4-21. Receptor Grid Generation option
in Receptor-Based Virtual Screening.

Figure 4-22. The Receptor tab of Receptor
Grid Generation.

Part 3. Receptor grid generation
Grid generation must be performed prior to
docking with Glide. The receptor grid
generation panel is used to specify a receptor
structure. The shape and properties of a
receptor structure are represented in a gridby fields that become progressively more
discriminating during the docking process.
These grid files represent the active site of
the receptor for Glide docking. A receptor gridalso ensures that any substrate you plan todock will stay within the shape and characterof the enzyme’s active site.
1. Click the In circle next to
6RST_prepared_dry to include it in
the Workspace
2. Double-click Presets○ 6RST_prepared_dry 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 the ligand(Molecule) and Show Markers○ A banner in the Workspace willprompt you to click on an atomin the ligand
Note: The purple bounding box defines theregion that the docked molecule(s) can
occupy to satisfy the initial stages of docking

Figure 4-23. The ligand is defined to be
excluded from grid generation.

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. Click the Site tab
6. Select Centroid of Workspace
ligand (selected in the Receptortab)
7. Click Advanced Settings○ A green inner bounding box
appears in the workspace

Figure 4-24. The Site tab of Receptor Grid
Generation.

Figure 4-25. Ligand diameter midpoint box
panel.

Note: The green bounding box defines theregion in which the centroid of the docked
molecule(s) must occupy to pass the initialstages docking
8. Leave the settings for X, Y, and Z
sizes to the default settings 10, 10,
and 10 Å, respectively.
9. Click OK
10. Change Job name to glide-grid_6rst
11. Click Run○ This job will take about aminute○ A folder named glide-grid_6rst
is written to your Working
Directory

Figure 4-26. Run receptor grid generation job.

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.

Part 4a. Docking inhibitor into active site
for Target Validation

Figure 4-27. The Ligands tab of the Ligand
Docking panel.

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_6rst.zip
3. In the Ligands tab, for Use ligands
from, choose Files
4. Next to File name, click Browse andchoose ligprep_6RST-out.maegz
5. Change Job name toglide-dock_6RST
6. Click Run○ This job takes about a minute○ A banner appears to show thatfiles have been incorporated

Figure 4-27. Run glide docking job.

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.

Note: The top 6rst_prep_lig entry is included,
and the Pose Viewer panel appears
7. A new group is added to the Entry List
8. Include other ligand results
9. Double-click Presets

Figure 4-28. Binding pose of the top docked
cognate ligand (pink) compared to the crystal
structure (gray).

Note: Though only the top ranked result is instrong agreement with the crystallographic
pose, all five results accurately capture thepose of the inhibitor compound in the bindingsite (with varying degrees of success in
capturing the solvent exposed region)

Learn more: 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 theProperty Tree. You can read more about how docking scores/poses are generated here andhere and what dependencies they have here and here.

Figure 4-29. Pose Viewer panel.

Part 4b. Analyzing binding poses
1. Open the Pose Viewer panel by
searching in the Tasks bar
2. Step through the results using theright and left arrow keys
○ Ligand poses are displayed in
the Workspace○ Residues are coloredaccording to their interactionenergies, ranging from green(favorable) to red(unfavorable)
3. Close the Pose Viewer panel

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.

Figure 4-30. Glide Primary properties shownin the Project Table.

4. Type Ctrl+T (Cmd+T) to open the
Project Table
5. In the Project Table, click the Property
Tree icon○ The Property Tree appears on
the right of the Project Table
6. Click the All box twice○ All boxes are deselected
7. Click the Glide box
8. Click Primary deselect Secondary○ 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, andglide emodel score.
Part 5a. Visualizing enzyme-substrateinteractions in Maestro

Figure 4-31. Include 6RST_prepared complex In this section, we will be analyzing 2Dinteractions between the inhibitor compoundand top performing ligand into workspaceand enzyme, and also visualizing the surfaceof the binding pocket and saving an image ofthe complex.

Figure 4-32. Ligand Interaction Diagram in
the Favorites toolbar.

1. Include only the 6RST_ prepared_dry
complex and the top performing ligand
in the workspace and exclude theother ligand results
2. In the Favorites toolbar, click Ligand
Interaction
a. The 2D Workspace - Ligand
Interaction Diagram opens

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.

3. Click on the clog and select > LID
Legend
4. Save an image of the 2D interaction
diagram by taking a screenshot
Note: The residue icon point indicates the
direction of the sidechain

Figure 4-33. Toggle on LID Legend.

Figure 4-34. The Ligand Interaction Diagramwith Sync with 3D turned on and LID legend
open.
Question #3. What important enzyme-substrate interactions do you see when the inhibitor
compound is docked? Take a screenshot of the Ligand Interaction Diagram and paste it
below. List specific residues that play an important role in the binding site.

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.

Part 5b. Generating a surface for thebinding pocket

Figure 4-37. More options in Quick Select.

1. Under the Quick Select panel in the
top-left corner of the Maestro
interface, click … and choose
Binding Sites
2. Click Style and choose Surface○ A solid gray surface is applied○ An S is next to the title in the
Entry List, click to see surface
options
Note: Click Surface (Binding Site) in theFavorites toolbar to perform the same task
3. Click on > Workspace > Surface >Manage Surfaces in the toolbar
4. Click on > Display Options

Figure 4-38. Opening the Manage Surfaces
panel.

Figure 4-39. Opening Display Options.

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.

5. Keep Style > as Solid
6. Change the Color Scheme >Electrostatic potential
7. Change the Min and Max values to-0.1 and 0.1, respectively
8. Click OK○ The intensity of the surface
colors is increased

Figure 4-40. Surface Display Options panel.
Question #4. Take a screenshot of the binding pocket with the surface view toggled on andpaste it below. What do you notice about the area surrounding the docked ligand/inhibitor?

26
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.

Individual Exercises

Part A: Enzymes at play in COVID-19
Now that you know what enzymes are, how they work, and how they interact with
substrates and inhibitors, it is time to apply our understanding of enzymes to areal-world problem, COVID-19.
SARS-CoV-2 is the virus behind the worldwide outbreak of COVID-19 disease. To
understand how SARS-CoV-2 works, as well as how other viruses work, we must firstzoom into the spike proteins (or S proteins) that cover the surface of SARS-CoV-2.
First, a large number of glycosylated S proteins on the surface of SARS-CoV-2 bind tothe host cell receptor angiotensin-converting enzyme 2 (ACE2), which helps mediateviral cell entry. When the S protein binds to the receptor, TM protease serine 2(TMPRSS2), a type 2 TM serine protease located on the host cell membrane, promotes
entry of the virus into the cell by activating the S protein. Once the virus enters the cell,
the viral RNA is released, and replication and translation take place (See our DNA &RNA lesson to learn more!).
Spike proteins thus play a critical role when it comes to eliciting an immune response,
particularly in the COVID-19 disease.
1) Based on the description of SARS-CoV-2 above, identify the enzymes involved in
the COVID-19 disease.

2) According to IUBMB nomenclature, what classification group(s) do the enzymes
from Question (1) fall under?

27
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) Who/What does “host cell” refer to?

4) Based on what you have learned in this lesson so far, list one possible
mechanism by which we can stop the activation of S proteins to prevent virus
entry.

Part B: Visualizing interactions in a SARS-CoV-2 enzyme-inhibitor complex

1. Go to > File > Import Structures
2. Select the file called“proteinprep_7MEQ-out.maegz”
Learn More: The raw 7MEQ protein
structure contains many valence issues
and a missing side loop which havealready been resolved for you using
PRIME. If you'd like to learn more aboutrefining loops, check out our docs on
PRIME.

Figure 5-4. Importing prepared 7MEQ
structure from working directory28
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. Click > Open
○ 7MEQ-prepared is loaded
into the workspace○ A banner appears

Figure 5-5. Import Structures panel

Figure 5-6. Double click presets.

Figure 5-7. Zooming into the ligand

Note: Banners appear when files havebeen imported, jobs incorporated into the
Entry List, or to prompt a common next
step.
Learn More: 7MEQ is a crystal structureof the enzyme TMPRSS2 in complex with
Nafamostat. Nafamostat is a serine
protease inhibitor that is underinvestigation as a potential COVID-19
therapeutic drug.
4. Double click on Presets
5. Zoom into the inhibitor compound(the ligand) in the workspace○ Play around with your scroll
wheel and look closely atthe binding site in theworkspace○ How many interactions canyou see in the binding site?

29
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 #1: Paste a screenshot of the binding pocket of TMPRSS2 below. Whatinteractions do you see in the binding site of TMPRSS2? Hint: use the Ligand
Interaction panel to more closely visualize the 2D interactions.

7.

Summary, Additional Resources, and References

In this lesson, students learned how to use the Protein Preparation Workflow and Glide
Docking panels to import and prepare an enzyme complex, dock an inhibitor compound,analyze enzyme-substrate interactions, as well as calculate binding stability after
residue mutations. Using Maestro, students were able to interact with the
enzyme-inhibitor complex by using the graphical user interface to zoom in/out, compare
various binding poses, and save images of the binding site.
For further learning:
●

●
●
●
●
●

Enzymes
Properties of SARS-CoV-2 spike protein
Webinar - Using Schrödinger tools to optimize enzyme design
Introduction to Computational Chemistry, 3rd Edition
Essentials of Computational Chemistry: Theories and Models, 2nd Edition
Molecular Modelling: Principles and Applications, 2nd Edition
30

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.

See the Protein Preparation Workflow help documentation● See the ligprep help documentation● See the Residue Scanning help documentation●

8.

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 apanel, 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 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
Workspace - the 3D display area in the center of the main window, where molecular
structures are displayed
Enzyme - a biological polymer that catalyzes biochemical reactions
Catalyst - a substance that increases the rate of a chemical reaction without itself
undergoing any permanent chemical change
Substrate - the molecules that enzymes act upon
Inhibitor - substrates that bind onto enzymes in order to block the enzyme’s activity
Catalytic residues - the amino acid residues in the enzyme's binding site that play arole in chemical catalysis
31
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.