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Computer AidedDrug DesignDocking and other Virtual ScreeningMethods

Drug Design Lingo: Target: any macromolecule whose function can bemanipulated/altered to result in diseasetreatment! Ligand: compound (typically small molecule) thatmay bind to a target, with hopes of it serving as atreatment HTS: High Throughput Screening; experimentalmethod of assaying many (thousands) ofcompounds for activity Binding Mode: orientation of ligand in a bindingsite

Goals/objectives of CADD: Find/design ligands to bind/regulate targetmacromolecules

Goals/objectives of CADD: Find/design ligands to bind/regulate targetmacromolecules Virtual High Throughput Screening Thousands of ligands/1-2 targets Target Structure/Binding Site Prediction 1-2 targets Off-path Target Screening 10-20 ligands/10-20 targets Binding Mode Analysis/Prediction 10-20 ligands/1-2 targets

Goals/objectives of CADD: Find/design ligands to bind/regulate targetmacromolecules Virtual High Throughput Screening Thousands of ligands/1-2 targetsDocking,Pharmacophore Modeling Target Structure/Binding Site Prediction 1-2 targetsHomology Modeling, Binding Site Prediction Off-path Target ScreeningBinding Site Comparison, 10-20 ligands/10-20 targets Cross-Docking Binding Mode Analysis/Prediction 10-20 ligands/1-2 targetsFlexible Docking

An Example of CADD Success!Doman, T. N., et al. Molecular Docking and HighThroughput Screening for Novel Inhibitors of ProteinTyrosine Phosphatase-1B J. Med. Chem. 2002. 45,2213-2221

What functionalityare you lookingfor? What information do you have? What information do you want? Directory of Computer Aided DrugDesign Tools (very great link! cross referencesfunctionality by software!)c

What functionalityare you lookingfor? What information do you have? What information do you want? Directory of Computer Aided DrugDesign Tools (very great link! cross referencesfunctionality by software!)cYou know the structure of thetarget binding site!You know a ligandconfirmed to bind target!Saturday Morning!!

What functionalityare you lookingfor? What information do you have? What information do you want? Directory of Computer Aided DrugDesign Tools (very great link! cross referencesfunctionality by software!)cLet’s take 5 minutes, to all follow this link separately youmight find something that interests you!

Molecular Docking Simulations:Introduction and Tutorial

Docking What is it?

“In the field of molecular modeling, docking is a method which predicts the preferred orientation ofone molecule to a second when bound to each other to form a stable complex. Knowledge of thepreferred orientation in turn may be used to predict the strength of association or bindingaffinity between two molecules using, for example, scoring functions.” (from king (molecular)Lengauer T, Rarey M. Computational methods for biomolecular docking. 1996. 6(3), 402-406

“In the field of molecular modeling, docking is a method which predicts the preferred orientation ofone molecule to a second when bound to each other to form a stable complex. Knowledge of thepreferred orientation in turn may be used to predict the strength of association or bindingaffinity between two molecules using, for example, scoring functions.” (from Wikipedia)fun sunshineget into Docking (molecular)Lengauer T, Rarey M. Computational methods for biomolecular docking. 1996. 6(3), 402-406

Docking Goals:1. Identify false positives and falsenegatives before experimentalscreening (narrow compoundlibrary)2. Predict binding modes & relativebinding affinity3. Suggest possible successfulcompounds

Docking can predict binding modes as well as possible binders!Number ofCompoundLigand PubChem IDNumberDocking 09909190104361206398761 (Maxacalcitol)ChemSpider ID: 1466931135253652895489935197446912452895015288670 504-10.49947-10.07298-9.211291-8.99854-7.881713

There are many docking programs .1-Click DockingAADSADAMAutoDockAutoDock d ODOCKSOFTDockingSurflex-DockSwissDockVoteDockYUCCA

Why so many different docking programs? Protein, Ligands, etc. Ligand Whole molecule Fragment Based Protein Rigid DockingFlexible Receptor DockingSemi-flexible dockingFull Protein Flexible Docking Water / co-factors / metals Explicit Implicit Scoring Function EmpiricalForce FieldKnowledge BasedConsensus

The Specifics: What do we need to predict a binding mode?Ligand ofInterestConformationalSearch AlgorithmEnergetic ScoringFunctionPredictedBinding Mode

The Specifics: What do we need to predict a binding mode?may be a database ofligands .Ligand ofInterestConformationalSearch Algorithm Molecular DynamicsSimulations Genetic Algorithm Systematic Searching (i.e.,rotamer libraries and such)Energetic ScoringFunctionPredictedBinding Mode

AutoDock Vina: A Rigid, Grid-based Docking ProcedureVina represents shape and properties of the receptor as a gridof points, where each point in space is assigned a value in afield! (ligand flexible, protein rigid)(draw grid here on board)The non-bonded energetic terms of a docked ligand are then minimizedwithin this grid/field, rather minimized via explicit atom-atom calculations.

Is “rigid” the best model forreceptor/ligand interaction?

Is “rigid” the best model forreceptor/ligand interaction?

Results: “Canonical” Cross Docking Test Set

“Lock and key” implies some element of rigidity“Hand and glove” model implies receptor and ligand are both flexibleThus we need:

“Lock and key” implies some element of rigidity“Hand and glove” model implies receptor and ligand are both flexibleThus we need:

“Lock and key” implies some element of rigidity“Hand and glove” model implies receptor and ligand are both flexibleThus we need:Flexible ligand/flexible receptor docking!

Induced Fit Docking (IFD) in Schrödinger:Initial ligand docking with Glide SP (using reducedvdW radii, can mutate large side-chains to alanine)Prime (protein structure prediction tool) used foreach initial pose to predict multiple receptorconformationsGlide XP “redocking” into different receptorconformersGlideScore calculated and complexes ranked, XPdescriptors written

CHARMM-based Flexible Receptor DockingO’Boyle, N. M.; Vandermeersch, T.; FlProtein 2acr contrast 900dpi.pngynn, C. J.; Maguire, A. R.;Hutchison, G. J. Cheminf., 2011, 3, 8-15.Lee M. S.: Feig, M.; Salsbury, Jr. F. R.; and Brooks III. C. L. J. Comp. Chem., 2003, 24, 1348-1356.Suárez, M, P. T.; and Alfonso J. Syst. Synth. Biol., 2008, 2.3, 105-113.Wu, X., Brooks, B.R. J. Chem. Phys., 2011, 135, 204101.

CHARMM-based Flexible Receptor Docking

So is rigid docking useless? NO! Use it to identify falsepositives and false negativesbefore further screening! rigid docking is computationallyinexpensive narrow the library before usingexpensive tools Use flexible docking to predictbinding modes and affinities

Tutorial:Docking with AutoDock VinaAutoDock Vina Publication

1. Navigate to the PDBwebsite(http://www.rcsb.org/pdb)and search for the PDB structureId 1MVC)2. Click “Download Files PDBFormat”, this will downloadthe 1MVC structure (a humanRxR) with bound BMS649agonist.

This is PyRx, a GUI for AutoDock Vina!The Navigator Panel is where you canload and organize molecules for jobs.The View Panel is where you can viewmolecules, documents, plots andcharts! You can also make plots,documents and charts. The Controlssection has a Vina wizard, an AutoDockWizard, a Babel wizard, and a pythonshell, as well as an error log.1.From the top toolbar in PyRx, clickthe “Load Molecule” icon.

This is PyRx, a GUI for AutoDock Vina!The Navigator Panel is where you canload and organize molecules for jobs.The View Panel is where you can viewmolecules, documents, plots andcharts! You can also make plots,documents and charts. The Controlssection has a Vina wizard, an AutoDockWizard, a Babel wizard, and a pythonshell, as well as an error log.1.From the top toolbar in PyRx, clickthe “Load Molecule” icon.2.A ‘Finder’ window (or windowsequivalent) will open. Navigate tothe downloads folder, select“1mvc.pdb” to open.

This is PyRx, a GUI for AutoDock Vina!The Navigator Panel is where you canload and organize molecules for jobs.The View Panel is where you can viewmolecules, documents, plots andcharts! You can also make plots,documents and charts. The Controlssection has a Vina wizard, an AutoDockWizard, a Babel wizard, and a pythonshell, as well as an error log.1.From the top toolbar in PyRx, clickthe “Load Molecule” icon.2.A ‘Finder’ window (or windowsequivalent) will open. Navigate tothe downloads folder, select“1mvc.pdb” to open.3.The macromolecule is now loadedin the 3D Scene!

Now we need to modify the 1mvc.pdbfile so that we can have themacromolecule (1mvc) and the ligand(bms649) in separate pdb files.1.In the “View” Panel, select the“Documents” Tab.

Now we need to modify the 1mvc.pdbfile so that we can have themacromolecule (1mvc) and the ligand(bms649) in separate pdb files.1.In the “View” Panel, select the“Documents” Tab.2.Click the “Open” icon (a Folder),again a “Finder” window will open,select “1mvc.pdb”.

Now we need to modify the 1mvc.pdbfile so that we can have themacromolecule (1mvc) and the ligand(bms649) in separate pdb files.1.In the “View” Panel, select the“Documents” Tab.2.Click the “Open” icon (a Folder),again a “Finder” window will open,select “1mvc.pdb”.3.This is what it should look likeafter opening the 1mvc.pdf file indocuments!

Now we need to modify the 1mvc.pdbfile so that we can have themacromolecule (1mvc) and the ligand(bms649) in separate pdb files.1.In the “View” Panel, select the“Documents” Tab.2.Click the “Open” icon (a Folder),again a “Finder” window will open,select “1mvc.pdb”.3.This is what it should look likeafter opening the 1mvc.pdf file indocuments!4.Scroll to nearly the bottom of1mvc.pdb, looking for lines thatstart with the word “HETATM”The lines of interest are:HETATM 1773 O1 BM6 A HETATM 1800 C24 BM6 A Ctrl C (copy) these lines of thepdb file!

Modifying 1mvc.pdb (cont.)5. Make a new document, this will bethe BMS649 ligand file, by clicking the“New” Icon (looks like a piece ofpaper).

Modifying 1mvc.pdb (cont.)5. Make a new document, this will bethe BMS649 ligand file, by clicking the“New” Icon (looks like a piece ofpaper).6. Paste the copied BM6 lines into thisnew untitled document.

Modifying 1mvc.pdb (cont.)5. Make a new document, this will bethe BMS649 ligand file, by clicking the“New” Icon (looks like a piece ofpaper).6. Paste the copied BM6 lines into thisnew untitled document.7. Click the yellow floppy disk icon tosave the new document.

Modifying 1mvc.pdb (cont.)5. Make a new document, this will bethe BMS649 ligand file, by clicking the“New” Icon (looks like a piece ofpaper).6. Paste the copied BM6 lines into thisnew untitled document.7. Click the yellow floppy disk icon tosave the new document.8. Save this new document as‘bms649.pdb’.

Modifying 1mvc.pdb (cont.)5. Make a new document, this will bethe BMS649 ligand file, by clicking the“New” Icon (looks like a piece ofpaper).6. Paste the copied BM6 lines into thisnew untitled document.7. Click the yellow floppy disk icon tosave the new document.8. Save this new document as‘bms649.pdb’.9. Return to the ‘1mvc.pdb’ file, findthe BM6 lines again, and delete them,we are making a macromolecular filewithout the ligand in it.

Modifying 1mvc.pdb (cont.)5. Make a new document, this will bethe BMS649 ligand file, by clicking the“New” Icon (looks like a piece ofpaper).6. Paste the copied BM6 lines into thisnew untitled document.7. Click the yellow floppy disk icon tosave the new document.8. Save this new document as‘bms649.pdb’.9. Return to the ‘1mvc.pdb’ file, findthe BM6 lines again, and delete them,we are making a macromolecular filewithout the ligand in it.10. Click “Save As” (blue floppy-disk)icon, and while saving, rename the fileto “1mvc-mod.pdb” just to distinguishit from the original file downloadedfrom the PDB

Modifying 1mvc.pdb (cont. 2)11. Now, we need to remove theoriginal 1mvc.pdb from the NavigationPane, so that we can instead includethe separate macromolecule and ligandfiles.

Modifying 1mvc.pdb (cont. 2)11. Now, we need to remove theoriginal 1mvc.pdb from the NavigationPane, so that we can instead includethe separate macromolecule and ligandfiles.12. With a newly cleared NavigationPane, load 1mvc-mod.pdb andbms649.pdb into PyRx (as done in steps1-2). You can see, ligands (as well assome elements of the macromolecularstructure) will be represented in “balland-stick:, while the protein isrepresented in “lines”. If you toggledbetween structures in the NavigationPane (by checking and uncheckingboxes) you can verify that the ligandand protein are in fact in separate files.

Modifying 1mvc.pdb (cont. 2)11. Now, we need to remove theoriginal 1mvc.pdb from the NavigationPane, so that we can instead includethe separate macromolecule and ligandfiles.12. With a newly cleared NavigationPane, load 1mvc-mod.pdb an