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Molecular Fingerprinting and Docking of Compounds to the ADA active site
A. Opening Maestro
From the assigned computer, a new terminal was created from either of the following steps:
1. Finder > Services > New terminal at folder
-or-
2. press the provided shortcut key F5
Then enter $maestro to open the suite.
Draw the molecule on the workspace area. Modifications can be made through the Edit panel > build > fragments > atom properties. Sponge the drawn molecule for clarity.
To save the molecule, create this entry on the project table -or- from the workspace option > project entry > name and create the project and then save.
The next step is to put the molecule under energy minimization to find a stable energetically conformation.
B. Energy Minimization
To initiate energy minimization, go to the Applications option > Impact > Minimization.
Minimization analyzes the molecule using Classical Physics.
A dialog box appears with the force field set on OPLS 2005.
Then click the Minimization tab. On the maximum cycles, this was changed to 10,000. The other standard parameters such as gradient criterion (0.01) and energy change criterion (1e-07) were kept. The pH was changed to the desired pH level of 7.4.
Knowing there are amino acids present, by changing the pH of the parameters, the structure must also be converted to its alkoxide form at pH 7.4. As a result, through atom types O3 was changed to OM.
After all the parameters were set for minimization, the host zorro was chosen and the minimization was started.
Double-click the finished minimization on the monitor jobs (from applications option), then label the partial charges of the molecule.
Save the project entry.
C. Calculation of Fingerprint
Opened Canvas from the Finder by typing $Canvas
Created a new project and named it as Aspirin_fingerprint.
Imported the energy minimized aspirin saved earlier from maestro.
Under applications option, click binary fingerprints > molprint2D
Click on the imported molecule and incorporate.
Export the molecule by saving it with an extension of .fp
A dialog box will appear, choose remove all properties and click ok.
Close the project.
D. Screen Fingerprint
After closing the previous aspirin project, open the zinc database.
Imported the aspirin.fp molecule and allow duplicate mappings.
Go to the Applications > similar/distance screen > select aspirin.
Tanimoto similarity
Selected the fingerprint column and choose the fingerprint (aspirin)
Screened the molecules and then incorporate ~ 15,001
Clicked the fingerprint screen column and sort in descending order to show molecules closest to aspirin.
On the panel, select rows 1-15,001
Saved the selection by exporting the project as aspirin_15001.mae along with its properties and click OK.
Closed Canvas
E. Docking Preparation
Protein Preparation Wizard_Import and Process Tab
Opened the protein databank (PDB) website, www.rcsb.org, and acquired two ADA Bovine structures. The two following structures were chosen by desirable resolutions:
1KRM (resolution 2.5 angstroms)
2Z7G (resolution 2.52 angstroms)
The pdb.txt of these structures were downloaded.
On Maestro, opened the aspirin.prj and imported the downloaded structures of ADA.
The structures of ADA were protonated according to the pH of 7.4. This was executed from:
Workflows > Protein preparation Wizard
On the Import and Process Tab, add H+ (see image on the right side of the protein preparation wizard dialog box)
Uncheck the delete waters on the dialog box and click preprocess.
Moving to the Refine Tab, changed the default pH of 7.0 to 7.4 as shown below.
Then click Optimize
F. Superimposition of Proteins
After Optimization, navigated through Tools > Protein Structure Alignment
All > align
From the Undisplay icon, remove waters for both structures
Added ribbons for all residues to view the entire structure
Upon scanning the structure, subtracted all portions leaving only the ligand on display at 5 Angstroms.
Compared both structures by superimposing them.
Verified structure 1KRM has a better resolution and removed 2Z7G from the project table.
Showed ribbons for 1KRM and colored element entry carbons
G. Docking
Duplicated the 1KRM H-minimized and deleted water molecules by manually clicking on each.
Changed ribbon color by residue position
Made a grid of the docking region by:
Application > Glide > Receptor Grid Generation
Select the ligand
Click site tab > center on ligand > change dock ligands to 15 Angstroms
Click Start
Changed the grid name and specified the host: zorro; click OK
Project name
