Small Molecules Rotamers: Generating and Testingrosettadesigngroup.com/workshops/RCW2008/...2008.pdf · Predicting Bioactive Conformations • Test set taken from PDBBind a collection
Post on 28-Jun-2020
2 Views
Preview:
Transcript
SmallMoleculesRotamers:GeneratingandTesting
KristianKaufmannVanderbiltUniversityRosettaCon2008July22nd‐25th2008
Unpublished and Confidential
GeneratingandUsingRotamersforSmallMolecules
• Rotamersconstructionstrategy• Predictionsofconformationsonasetof628smallmolecules
• ModificationstoRGHIJJKLMNKOPtoincorporatesmallmoleculerotamers
• EvaluationofDockingonasetof7proteinsincomplexwith10smallmolecules
Buildingmolecularmodelsfromfragmentsmoleculescapturedincrystalstructures
hasprovenfruitful
• Fragmentsfordenovoproteinmodelling
• Rotamersforproteinsidechainmodelling
• Corinagenerates3DstructuresfromstatisticsgarneredfromtheCambridgeStructuralDatabase(CSD)ofsmallmolecules.
• FleXXanincrementalconstructionalgorithmforsmallmoleculedockinganddesignalsomakesuseoftheCSDinitsmallmoleculeconstruction
Rohletal.MethodsEnzymol.2004383p.66‐93DunbrackandKarplusJMolBiol.1993230p.543‐74Gasteigeretal.TetrahedronComp.Method.1990,3,537‐547Rareyetal.JMolBiol.1996261470‐89
PowerfulEnergyfunctionscanbederivedfromcrystalstructures
• Hydrogenbondingfunctionderivedthroughanalysisofhighresolutionproteincrystalstructures.
• DunbrackrotamerenergyderivedfromtheprobabilityofobservingtherotamerinthePDB
• VanderWaalsforcesderivedfromatomicdistancesincrystalstructures
Simonsetal.Proteins.199934p.82‐95Kuhlmanetal.Science.2003302p.1364‐8
Pre‐computeinteractionsforrotamerlibraryoflikely
aminoacidsconformations
ProteinSmallMolecule
Pre‐computeinteractionsforsmallmoleculelibraryoflikelyconformations
Replacementofsidechainconformations
Replacementofsmallmoleculeconformations
1(Setup)
2(coarsediscreteoptimization)
ImplementingSmallMoleculeFlexibilityusingRotamerswhileRetainingRosetta’sFunctionality
SimultaneousoptimizationofProteinbindingsite
Selectrotamersfromsidechainconformationsseenin
thePDB
Constructrotamersfromtorsionprofilesseeninthe
CSD
GeneratingTorsionProfilefromtheCambridgeStructuralDatabase
X
XX
X
DefineAtomTypestocapturechemicalcharacteristicsofdihedralangles
SearchCambridgeStructuralDatabaseforallatompairsexcludingthoseinringsystemsandmeasuredihedral.Bineverytendegrees.
0
1000
2000
3000
4000
5000
‐180
‐160
‐140
‐120
‐100
‐80
‐60
‐40
‐20 0 20
40
60
80
100
120
140
160
180
Freq
uency
DihedralAngle
AromaticCarbonEtherOxygenBond
GeneratingEnergiesfromaTorsionProfile
• Energiescanbegeneratedbycomputingthenegativelogofthepropensityofastate
• Thepropensityistheprobabilitynormalizedbytherandomprobabilityofselectingastate.
• Anyanglewithaenergylessthanzerohasagreaterthanrandomprobability.
• Minimaintheenergyprofilecanthenbeusedinconstructingsmallmoleculeconformations
010002000300040005000
‐180 ‐120 ‐60 0 60 120 180
Freq
uency
AromaticCarbonEtherOxygenBond
‐2‐10123456
‐180 ‐120 ‐60 0 60 120 180
Dihed
ralEne
rgy
DihedralAngle
CSD
AMBER
GeneratingSmallMoleculeRotamers
Pickarandomsetofoptimaldihedralanglesforallrotatablebonds
Doesitclash?
Storeconformation.10000acceptedconformations?
Acceptconformationwithlowestenergy.Createlistofallconformationswithin2*numberof
rotatablebondsenergyunitsofthelowestenergyconformation.Acceptmaximalspanningensemble
ofconformations.
Yes
Yes
No
No
PredictingBioactiveConformations• Testsettakenfrom
PDBBindacollectionofcrystalstructuresforsmallmoleculesfromproteincomplexeswithknownbindingconstants
• PDBBindwasculledtocontainonlymoleculeswith≤6rotatablebonds
• Upto500rotamersweregeneratedforeachsmallmolecule
Wangetal.JMedChem.200548p.4111‐9.
#of Rotatable Bonds
#of Molecule
Average RMSD of closest conformation
Average RMSD of furthest conformation
1 92 0.14±0.16 1.12±0.47 2 118 0.33±0.26 1.74±0.69 3 118 0.41±0.22 2.13±0.62 4 135 0.47±0.21 2.45±0.69 5 97 0.61±0.30 2.83±0.81 6 118 0.79±0.32 3.07±0.87
Overall Total 628 0.46±0.31 2.23±0.94
AtomicRMSDtocrystallizedconformation
DockingwithSmallMoleculeRotamersinRosetta
Proteincrystalstructureandlowenergysmallmoleculeconformation
Generateensembleofsmallmoleculeconformations
Translatesmallmoleculetorandompointinbindingsite
Pickrandomconformationtranslaterandomlyinside1Aboxrotaterandomlyaddconformation
tolist
X<1000
Selectfirst100nonclashingsmall
conformationsorbestseen
X++
yes
no
Performrotameroptimizationwithproteinsidechainandsmallmoleculerotamers
Performminimizationofproteinsidechainchianglesandrigidbodydegreesof
freedom
Outputstructure
FororiginalprotocolseeMeilerandBakerProteins.200665p.538‐48.
DockingBenchmarks
• 15crystalstructureswithsmallmolecules– 7proteins,10ligands
• 10selfdockingexamples– Verifiesprotocolsabilityto
sampleandidentifynativestate.
• 11crossdockingexamples– Testssensitivitytochanges
inbackboneaswouldbeexpectedfromahomologymodel.
DockingBenchmark
!15
!10
!5
0
0 2 4 6 8 10 12 14 16 18 20
Res
idue
Ene
rgy
RMSD in Å
modelsnative
2PRGdockingto1FM9ligand binding domain of the human peroxisome proliferator activated receptor γ
!15
!10
!5
0
0 2 4 6 8 10 12 14 16 18 20
Res
idue
Ene
rgy
RMSD in Å
modelsnative
1P8Ddockingto1P8DOxysterolsreceptorliverXreceptorβ.
DockingBenchmark
!15
!10
!5
0
0 2 4 6 8 10 12 14 16 18 20
Res
idue
Ene
rgy
RMSD in Å
modelsnative
2PRGdockingto1FM9ligand binding domain of the human peroxisome proliferator activated receptor γ
!15
!10
!5
0
0 2 4 6 8 10 12 14 16 18 20
Res
idue
Ene
rgy
RMSD in Å
modelsnative
1P8Ddockingto1P8DOxysterolsreceptorliverXreceptorβ.
PerformanceinaDockingBenchmark
In9outof10casesselfdockingwassuccessfulwhenlookingatthetop1%byenergy
Ligand Protein rank RMSD 1aq1 1aq1 1 0.56 1dm2 1dm2 1 0.31 1dbj 1dbj 1 1.36 2dbl 2dbl 1 1.45 1p8d 1p8d 1 1.63 4tim 4tim 1 1.87 6tim 6tim 1 1.77 2ctc 2ctc 3 0.82 1pph 1pph 6 1.49 2prg 2prg 639 1.94
SelfDockingResults
In8of11casescrossdockingsuccessfulwhenlookingatthetop1%byenergy
CrossDockingResultsLigand Protein rank RMSD 1dm2 1aq1 1 0.56 1dbj 2dbl 1 1.80 1pph 1ppc 2 1.96 4tim 6tim 2 1.90 2ctc 7cpa 3 0.95 6tim 4tim 5 1.77 1p8d 1pqc 10 1.28 2prg 1fm9 16 2.02 1p8d 1pq6 181 1.62 2dbl 1dbj 468 3.49 1aq1 1dm2 4296 1.87
ConclusionsandFutureDirections
• SmallmoleculerotamerspresentaviablemethodofrepresentingsmallmoleculeflexibilityinRosetta
• 90%ofofselfdockingcasesidentifiednative‐likestructureinthetop1%byenergy.
• 72%ofcrossdockingcasesidentifiedanative‐likestructureinthetop1%byenergy
• Optimizationofthescoringfunctionfordiscriminationofnativelikemodelsshouldyieldimprovedresults
• Meldingsmallmoleculerotamerapproachwithincrementalconstructionapproachisunderwayforapplicationtolargersmallmolecules.
Acknowledgements
• JensMeiler• RalfMueller
• KristinGlab• DARPAandNIHMolecularBiophysicsTrainingGrant
top related