1 CrossMiner: Federated CSD and PDB 3D searching Version 1.0 – July 2016 CrossMiner ver. 1.2 Table of Contents CrossMiner Terminology .................................................................... 2 Introduction ....................................................................................... 2 Overview of CrossMiner ..................................................................... 3 Example 1: Searching with a Pharmacophore ..................................... 4 Example 2: Editing a Pharmacophore ................................................. 8 Example 3: Creating a Pharmacophore from a Reference Molecule & Scaffold Hopping ...............................................................................11 Exercise 4: Building your Own Feature Database ...............................13
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8. Foreaseofviewing,changethestyleintheupperlefttoCappedSticks.Take a few moments to explore how the returned result matches thepharmacophorequery.Inparticulartonote:
• Feature matching is based on size of sphere (and thus the tolerancelevel).Tinysphereswithtighttolerancewillresultinhitswithveryclose
areaforalignment.• Therearenoexplicithydrogens in theproteinsites –hydrogenbond
donors and acceptors are defined in this database based on featuredefinitions,whichcomefromexpertknowledgeaboutprotonationandtautomerstate.Thus,thereisnowaytodisplayhydrogens,astheyareinferred. See the referencepaper listed in the introduction formoreinformation.
Therearealotofresults,likelyduetothelargeradiusofthefeatures.Lowerthetoleranceofthefeaturestogetasmallerresultsetwithmoreprecisealignmentto the pharmacophore centres. To do this, you will need to edit thepharmacophore,whichcannotbedonewhenviewingresults.
9. Clickthestop buttontocleartheresultsandenableediting.10. EnsurethatPickingmodeissettoEditPharmacophore.11. In editing mode, you can double click on the radius sizes in the feature
Tanimoto value. If clustered, youwill see representativesof thosesimilargroups in the resultsviewer (and thus fewer hits thanactually returned).Unchecktheboxtoseeallhits,includingthosewhichareverysimilartoeachother.
The lowestRMSDresultshereare2XU1and2XU3–whichareunsurprisinglycathepsinLPDBentries.Ifyouexplorethetopresult(2XU1_001),you’llseethatthehitmatchesthepharmacophorealmostexactly.
Example2:EditingaPharmacophoreOneofthepowersofCrossMineristheabilitytomanuallyinteractwithandeditapharmacophoreatanytime(evenwhileasearchisrunning).Forthisexample,you will be editing the cathepsin L pharmacophore. For ease, start with thedefaultcathepsinLpharmacophore.Reloaditasperstep1inexample1.Ifthesearchstartsagain,justclickstop.1. Make sure you are in Edit Pharmacophore mode. Right click on the
hydrophobic feature to bring up the editingmenu. ClickMorph Into andwater.YouwillalsoneedtoclickAnyMolecule,asthewateristechnicallynotapartoftheproteinorsmallmolecule.
thelowRMSDresultsandvisualizeit.CrossMinerallowsyoutovisuallyinteractwiththepharmacophore.Youcaneditthefeaturesnumerically in thefeaturebrowser,andalsomanually inviewer.Whilethisisnotarigorousapproach,itishelpfulforexploringchemicalspace.
button.Thiswillchangetheradiusofthewatersphere.Thislargersphereallows formore flexibility inawaterplacementaround the ligand. If youhavetroublegettingthiswork,ensurethatInteractiveeditingmodebuttonis on (see step 7 below). Change the radius back to1.00 in the featurebrowser.
loadthemoleculeintotheviewer,withallfeaturesdefined.Thismeansthatprojection lines betweenbase and virtual features are shown, aswell ascentroidsandprojectedaromaticvirtualpoints.
pharmacophore.Ctrl+z(orEdit>>Undo)isveryhelpful.Itwillundothelastchangemadetothepharmacophore. However, the search will start over again, so form goodCrossMinerhabitsearly!
editingmodeon,dragthenewfluorineneartothereferencepoint.Whenthenewfluorinefeature is clearlyclosertothatreferencepointthananyotherreferencepoint,right-clickthefeature,andselectSnapToAtom.Thiswillalignthefeaturetothenearestatomicreferencepoint.
This new search probably won’t find any results. This step was just todemonstratehowtoaddandmanoeuvrenewfeatures.11. SaveyoureditedpharmacophorebyclickingFile>>SavePharmacophore.
12 This demonstrates how easy scaffold hopping could be carried out withCrossMiner.Asanotherexample,youwillexperimentwithscaffoldhoppingofPD180970,theco-crystallizedligandoftheABLkinasedomain.5. Load the file 2hzi_ligand.sdf as you did previously. Define the
pharmacophore as indicated. For the acceptor_projected, two points areindicated – ensure that bothprojected virtual points are set to features.Ensurethatthefeaturesareallsettointraconstraints,asabove.
Forthissearch,leaveboththeCSDandPDBdatabasesselected.You’llseethatthere is no shortage of great results from the CSD to match this query. Tryexperimentingwithnarrowingthisresultsetdown.Tryrestrictingsomeoftheradii,oraddinginanewfeaturethatyourchemistryexperiencesaysmightbeimportant.
planar_ring_projected
hydrophobicexit_vector
acceptor_projected(2)
13
Exercise4:BuildingyourOwnFeatureDatabaseForthisexerciseyouwillbebuildingyourownfeaturedatabasefromasetofligands. These ligands do not have pre-configured features, and will rely onCrossMinertodetectandaddthefeatures.1. SelectFeatureDatabase>>Create.Select‘Add’andnavigatetothetutorial
datafolderandloadfviia_ligands01.sdf.2. You will also need to load the feature definitions – this step allows for
flexibilityinhowfeaturesaredefined,ifyouwanttoaddcustomfeatures.Click on Add Substructures, and navigate to [CrossMinerInstallation]\feature_definitions.Selecteveryentrystartingwithfeatures_,usingtheshiftkey.ClickOK.
for a save location – indicate the tutorial data directory, and name itfviaa_ligands01.feat.Oncetheindexinghascompleted,clickOKtoclosetheCreateFeatureDatabasewindow.