User:Mary Mendoza/Notebook/CHEM572 Exp. Biological Chemistry II/2013/01/30

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(Molecular Fingerprinting and Docking of Compounds to the ADA active site)
Current revision (17:11, 8 May 2013) (view source)
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==Molecular Fingerprinting of Compounds to the ADA active site==
 
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A. Opening Maestro
 
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* From the assigned computer, a new terminal was created from either of the following steps:
 
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1. Finder > Services > New terminal at folder
 
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-or-
 
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2. press the provided shortcut key F5
 
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* Then enter $maestro to open the suite.
 
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* 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.
 
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* 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.
 
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* The next step is to put the molecule under energy minimization to find a stable energetically conformation.
 
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B. Energy Minimization
 
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* To initiate energy minimization, go to the Applications option > Impact > Minimization.
 
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* Minimization analyzes the molecule using Classical Physics.
 
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* A dialog box appears with the force field set on OPLS 2005.
 
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* 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.
 
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* 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.
 
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* After all the parameters were set for minimization, the host zorro was chosen and the minimization was started.
 
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* Double-click the finished minimization on the monitor jobs (from applications option), then label the partial charges of the molecule.
 
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* Save the project entry.
 
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C. Calculation of Fingerprint
 
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* Opened Canvas from the Finder by typing $Canvas
 
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* Created a new project and named it as Aspirin_fingerprint.
 
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* Imported the energy minimized aspirin saved earlier from maestro.
 
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* Under applications option, click binary fingerprints > molprint2D
 
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* Click on the imported molecule and incorporate.
 
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* Export the molecule by saving it with an extension of .fp
 
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* A dialog box will appear, choose remove all properties and click ok.
 
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* Close the project.
 
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D. Screen Fingerprint
 
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* After closing the previous aspirin project, open the zinc database.
 
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* Imported the aspirin.fp molecule and allow duplicate mappings.
 
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* Go to the Applications > similar/distance screen > select aspirin.
 
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** Tanimoto similarity
 
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* Selected the fingerprint column and choose the fingerprint (aspirin)
 
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* Screened the molecules and then incorporate ~ 15,001
 
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* Clicked the fingerprint screen column and sort in descending order to show molecules closest to aspirin.
 
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* On the panel, select rows 1-15,001
 
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* Saved the selection by exporting the project as aspirin_15001.mae along with its properties and click OK.
 
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* Closed Canvas
 
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E. Docking Preparation
 
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[[Image:Prepwizard2.png|thumb|right|Protein Preparation Wizard_Import and Process Tab]]
 
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* Opened the protein databank (PDB) website, www.rcsb.org, and acquired two ADA Bovine structures. The two following structures were chosen by desirable resolutions:
 
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**1KRM (resolution 2.5 angstroms)
 
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**2Z7G (resolution 2.52 angstroms)
 
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* The pdb.txt of these structures were downloaded.
 
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* On Maestro, opened the aspirin.prj and imported the downloaded structures of ADA.
 
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* The structures of ADA were protonated according to the pH of 7.4. This was executed from:
 
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** Workflows > Protein preparation Wizard
 
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** On the Import and Process Tab, add H<sup>+</sup> (see image on the right side of the protein preparation wizard dialog box)
 
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** Uncheck the delete waters on the dialog box and click preprocess.
 
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** Moving to the Refine Tab, changed the default pH of 7.0 to 7.4 as shown below.
 
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** Then click Optimize
 
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[[Image:Refine75.png|center]]
 
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F. Superimposition of Proteins
 
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* After Optimization, navigated through Tools > Protein Structure Alignment
 
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** All > align
 
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** From the Undisplay icon, remove waters for both structures
 
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* Added ribbons for all residues to view the entire structure
 
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* Upon scanning the structure, subtracted all portions leaving only the ligand on display at 5 Angstroms.
 
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* Compared both structures by superimposing them.
 
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* Verified structure 1KRM has a better resolution and removed 2Z7G from the project table.
 
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* Showed ribbons for 1KRM and colored element entry carbons
 
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G. Docking
 
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* Duplicated the 1KRM H-minimized and deleted water molecules by manually clicking on each.
 
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* Changed ribbon color by residue position
 
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* Made a grid of the docking region by:
 
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** Application > Glide > Receptor Grid Generation
 
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** Select the ligand
 
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** Click site tab > center on ligand > change dock ligands to 15 Angstroms
 
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** Click Start
 
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* Changed the grid name and specified the host: zorro; click OK
 
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* Seeing the docking is done from the Monitor Jobs window:
 
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** Applications > Glide > Ligand Docking
 
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** Browse for the .zip grid previously created
 
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** Verify host: zorro and click start
 
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* Imported the glide.pv file
 
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* Excluded the protein structure leaving only the ligand
 
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* Superimposed the raw, crystallized PDB ADA ligand structure with the docked ligand
 
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* Imported flavonoids to compare with the docked ligand by superimposition
 
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* Database screening was initiated by going to Applications > Glide > Ligand Docking
 
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* Selected the entry with 15,000 compounds from the .pv file
 
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* Selected zorro host and clicked start
 
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