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StructurebasedDrugDesign:

MolecularDockingStudies

Jinxia(Nancy)Deng,PhD
Sept25,2007

Outline

ReviewofStructureBasedDrug
Design

Moleculardocking

Dockingcasestudy

Drugdiscoveryprocess

Identifydisease

DA

Formulation

Humanclinicaltrials
(210years)

Fi
le
N

Preclinicaltesting
(13years)

Fil
eI
ND

Isolateprotein
involvedin
disease(25years)

Findadrugeffective
againstdiseaseprotein
(25years)
Scaleup

FDAapproval
(23years)
http://wwwpersonal.engin.umich.edu/~wildd/mfg501/lecture.ppt

Databasesearching

3Dstructuresearching

pharmacophoremodels
exclusionzonestorepresentreceptor

Docking

predictionofthestructureandbindingfreeenergy
ofaligandreceptorcomplexgivenonlythe
structuresofthefreeligandandreceptor
examinebindingmodelofknownligandsto
suggestmodification
screendatabasesof3Dstructuretofindnovel
ligands

Itincludes
ligandproteindocking,onebranchof
rationaldrugdesigntopredictwhich
moleculescandisplaceothersfrom
thesurfaceofaprotein,orchange
proteinfunction.
Proteinproteininteraction
ProteinDNAinteraction

Liganddocking
(lock&keymodel)

Target
structure

Small
molecule
database

Structure
determination

Designnew
inhibitors

Ligandproteindocking:
Dockingofasmallmolecule(theligand)on
alargemolecule(theprotein,socalledreceptor)

Proteinproteindocking:
Usuallythedockingsiteisamore"planar"surfacethanin
theligandproteindocking
B
ProteinDNAsimulation*

NucleicAcidsResearch2006,Vol
34,No.1133173325

Evaluatingastructure
Xraycrystallography

Mostcommon
Musthavebetterthan2.5
resolution

NMR

Maybepossibletodetermine
dynamics

Homologymodeling

Whennoexperimentalstructure
isavailable
Usesaknownstructureasa
templatefortheunknown

GrowthofthePDB
30000

NumberofEntries

25000
20000
15000
10000
5000
0

1977

1982

1987

1992
Year

http://www.rcsb.org

1997

2002

Identificationoftargetsite

Ideallyapocketorprotuberancewith

Hydrogenbonddonorsandacceptors
Hydrophobiccharacteristics
Varietyofsizesofmolecularsurfaces

Canbeanactivesite,anassemblysite,
oracommunicationsite
Cocrystallizedproteinligandcomplexes
canbeinvaluablefordeterminingtarget
sites

Dockingalgorithms

Molecularflexibility
bothligandandproteinrigid
flexibleligandandrigidprotein
bothligandandproteinflexible
searchalgorithm
usetoexploreoptimalpositionsoftheligandwithin
theactivesite
scoringfunction
valueshouldcorrespondtopreferredbindingmode
efficiencyveryimportantfordatabasesearching

TODAYSFOCUS
eHITS:ElectronicHigh

ThroughputScreening
(SimBioSysInc.)

GOLD:GeneticOptimization

forLigandDocking (CCDC)

eHITS:ElectronicHighThroughput
Screening(SimBioSysInc.)

Fast,felxibible
dockingofwholeand
partialstructuresto
targetreceptors

Designedforlibrary
screening

eHiTSSearch

Ligandisdividedinto

rigidfragmentsand
connectingflexiblechains

Allrigidfragmentsare
dockedindependently

Graphmatching

Flexiblechainfitting

Localenergyminimisation

eHiTSScoring

Empiricalbasedscoring

Manycomponents;Hydrogen
bonding,HydrophobicityElectrostatic
potential,VanderWaalscontact
energy,Metalioninteractions,etc.

Allparametersareconfigurable

Chemicalpropertiesmappedto
Connollysurface

Flagcompatibilitymatrixscorefor
receptorligandcontacts

Therearemanydockingprograms
eHITSisafullysystematicandexhaustive

dockingprogram

19.FragmentBasedeHiTS

Algorithm

Ligandsaredividedintorigid
fragmentsandflexibleconnecting
chains
RigidDock:Eachfragmentis
dockedINDEPENDENTLY
everywhereinthereceptor
PoseMatch:Afastgraph
matchingalgorithmfindsall
matchingsolutionstoreconstruct
theoriginalmolecule
LocalEnergyOptimization:
structureisoptimizedwithinthe
receptor
Ranking:structuresareranked
basedonscoringfunction

HN

H2

HN

H2

H2

HN

H2

NH

HN
O
O

H2

HN

N
N

H2

H2

HN

HN

H2

Reconnecte
dLigand
Pose:

O
N

HN
N

H2

20.DockingFragmentsRigiDock

Rigidfragmentdockingbasedon
Chemicalfeaturemappedpolyhedra
Polyhedronshrinkwrappedonto
molecularsurface(Connolly)
Chemicalfeatureflagsonvertices
Analoguecavityrepresentation
Rapidmappingofligandandcavity
polyhedra

21.FragmentBasedDocking

22.DockingFragment1

TheFragmentisdocked
everywhereinthereceptor
site,andclusteredtogive
asetnumberofposes
NOTE: In the illustrations shown, only 250 poses are displayed,
default parameters of eHiTS uses 640 for each fragment

23.DockingFragment2

24.DockingFragment3

25.DockingFragment4

26.Closebutdifferent

Fragment2:EtherOxygen

Fragment4:AlcoholOxygen

PolarCharacter

27.Posematching

Eachrigidfragmentisnowindividually
dockedtoseveralalternativesites
Taskistofindsetsofposessuchthat:

fragmentscanbelinkedbyflexiblechains

theydonotbumpintoeachother

Algorithm

Graphnodes:ligandfragmentposes

Graphedges:posepairsatdistance
compatiblewithchainlength

Cliquesencodedockingsolutions

Frag1

Frag2

Frag3

Frag4

TopRankedPose
RMSD:0.699
Score:8.507

29.SummaryofeHiTSFeatures
Fragmentbaseddockingengine
Speedupduetodatabasestorage
Statisticallyderivedempiricalscoring

function
Usertrainablescoringfunction(Family
based)
Automatichandlingofprotonationstate

DHFRCaseStudy

ExperimentObjectives

Showabilitytoreproducecrystal
structures

ShowthateHiTScanselectactiveligands
ofhumanDHFRfromadrugdatabase

IllustratetheeaseofuseofeHiTS
Nopdbpreparation,noligand
preparation
ShoweHiTScanbeusedinHTS

DihydrofolateReductase
(DHFR)

Playsanessentialroleinthe
buildingofDNA

jugglestwomoleculesin
thisreaction

Folate(purple)andNADPH
(green)

Thefirstenzymetargetedfor
cancerchemotherapy

Oct.2002PDBMoleculeoftheMonth:
http://www.rcsb.org/pdb/molecules/pdb34_3.html

DHFRBindingsite

Thedrugmethotrexateisdesignedto
mimicfolate,blockingtheenzyme'saction

Notetheinteractionbetweenfolateand
NADPH,thisisessentialfortheenzyme's
function

ActivesSelection

SearchedforDHFRcomplexesinthePDB

Obtained88complexes,allsources

Uponquickvisualinspection,eliminated17
complexes

Containednoligandinthebindingsite

Containedmultipleligandsinthebindingsite

Selected71DHFRcomplexesforstudy

Including19humancomplexes

19HumanDHFRcomplex
Com plex
1dhf
1dlr
1dls
1drf
1hfp
1hfq
1hfr
1km s
1km v
1m vs
1m vt
1ohj
1ohk
1pd8
1pd9
1s3 u
1s3 v
1s3 w
2dhf

Ligand
Form ula
# at om s
FOL 2(C19H17 N7 O6)
49
MXA C17 H19N5O2
43
MTX C20H22N8O5
55
FOL C19H17 N7 O6
49
MOT C20H22N6O6
54
MOT C20H22N6O6
54
MOT C20H22N6O6
54
LIH
C18H17 N7
42
LII
C18H19N5O2
44
DTM C18H22N6O3
49
DTM C18H22N6O3
49
COP C27 H27 N9O6
69
COP C27 H27 N9O6
69
CO4 C19H24N6O3
52
CO4 C19H24N6O3
52
TQD C19H3 9N5O3
66
TQD C19H3 9N5O3
66
TQT C17 H3 3 N5
55
DZF 2(C20H18N6O6)
50

CoF

Form ula

NDP C21H27 N7 O17 P3


NDP C21H27 N7 O17 P3
NAP
NAP
NAP
NDP
NDP

C21H28N7 O17 P3
C21H28N7 O17 P3
C21H28N7 O17 P3
C21H3 0N7 O17 P3
C21H3 0N7 O17 P3

NDP C21H3 0N7 O17 P3


NDP C21H3 0N7 O17 P3
NDP C21H3 0N7 O17 P3

NAP C21H28N7 O17 P3

Validation

EachDHFRligandwasremovedfromthe
proteinanddockedbackintoitsbindingsite

EHiTSwasallowedtodothissplitautomatically

Resultswerethenjudgedbyevaluatingthe
RMSDbetweenthecrystalstructurebinding
positionandthecomputeddockingpose

Standard(default)parametersforeHiTSwere
usedinalltheruns

ValidationAllSources
71PDBs

29Unique
Ligands

Topranked Closest
< 0.5
3.23%
17.74%
< 1.0
22.58%
51.61%
< 1.5
59.68%
69.35%
< 2.0
67.74%
85.48%
< 2.5
83.87%
91.94%
< 3.0
88.71%
91.94%
Av eRMSD
1.94
1.41

TopRankedandClosestRMSD
Comparison
100.00%
90.00%

PercentofStructures

80.00%
70.00%
60.00%

Topranked
Closest

50.00%
40.00%
30.00%
20.00%
10.00%
0.00%
<0.5

<1.0

<1.5

<2.0

RMSD

<2.5

<3.0

ValidationHuman
19PDBs

12Unique
Ligands

Topranked Closest
< 0 .5
10 .53% 21.0 5%
< 1.0
21.0 5% 63.16%
< 1.5
68 .42% 73.68 %
< 2.0
73.68 % 8 4.21%
< 2.5
8 4.21% 94.74%
< 3.0
8 9.47% 94.74%
AveRMSD
1.98
1.18

TopRankedandClosestRMSD
ComparisonHumanDHFR
100.00%
90.00%

PercentofStructures

80.00%
70.00%
60.00%

Topranked
Closest

50.00%
40.00%
30.00%
20.00%
10.00%
0.00%
<0.5

<1.0

<1.5

<2.0

RMSD

<2.5

<3.0

ResultsTheGood
1dyiComplexxrayligandinwhite

Closest,105.77
0.76RMS

TopRank,139.6
0.85RMS

ResultsTheBad
1ly4Complexxrayligandinwhite
Closest,50.32
0.89RMS

TopRank,55.11
2.23RMS

ResultsTheUgly
1rc4Complexxrayligandinwhite
Closest,43.22
4.38RMS

TopRank,7.87
4.90RMS

ValidationSummary

EHiTSwasabletoreproduceaccurately
(RMS<2.0)thecrystalstructurepositionof
DHFRligands85%ofthetime

67%ofthetime,eHiTS'highestranking
(bestscoring)posehadaRMS<2.0

ThisnumberimprovesforHumanDHFR
ligands,74%

ThisshowsthateHiTSisabletopredict
dockingposesforDHFRligands

GOLD:GeneticOptimizationfor
LigandDocking( CCDC)

calculatingdockingmodesofsmall
moleculesintoproteinbindingsites
geneticalgorithmforproteinligand
docking
fullligandandpartialproteinflexibility
energyfunctionspartlybasedon
conformationalandnonbondedcontact
informationfromtheCSD
choiceofscoringfunctions:GoldScore,
ChemScoreandUserdefinedscore
virtuallibraryscreening

GOLDcontains:
Ascoringfunction:
GOLDFitness=Shbext+Svdwex+Shbint+Svdwint

Searchingmechanismtoexplorebinding
mode:Geneticalgorithm.

Dockingoftheligand
in1BL7,aMAP
kinaseP38complex.
TheGOLDdocked
solution(red)is
comparedwiththat
observedinthePDB
(colouredby
element).RMSD=
0.5Angstroms.

Dockingoftheligandin
1JAP,amatrix
metalloprotease
complex.TheGOLD
dockedsolution(red)is
comparedwiththat
observedinthePDB
(colouredbyelement)
RMSD=0.8Angstroms

GeneticAlgorithm:selection,crossover,andmutation
operatorstofindtheoptimalsolution

Solutionsareencodedasgenome,i.e.
chromsome
ChromosomeA:
101100101100101011100101
ChromosomeB:
111111100000110000011111

Reproduction:viacrossover,whichpicks
randomlyfromparentgenometoproduce
newgeneration.

Mutation:chromosomecanundergo
spontaneouschanges(withsmall
probability)toproducenewgenerationsto
samplingdifferentpartofthesolution
space.
Afitnessfunction(orobjectivefunction)is
usedtoevaluateeachsolution.

Dockingapplications

Bindingmodeprediction

Novelleaddesignoroptimization

Databasescreeningtoidentifyhits

Designnovelleadsfrom
fragment
Docking
fragment

target

Linkage

Perfectligand

Challenging:receptorflexibility

Ligandbindingtothereceptorinducesarangeof
conformationalchanges:

Twoproblems

Localrearrangementofsidechains
Hingemotionsofdomain
Predictingconformationalchange
samplingthepossiblechangedconformationduring
dockingbecausetoomanydegreeoffreedomavailableto
abindingsiteandnumberofbindingsiteconformations
growsexponentiallywiththem.

VirtualScreening/Docking
eHiTS
DOCK
FlexX
FlexE
SLIDE
Flo98
ADAM
Hammerhead

GLIDE

GRAMM

GOLD

PPD

HINT

BIGGER

LIGPLOT
SITUS

ZDOCK/
RDOCK

VEGA

RosettaDock

FRED

Affinity

FlexiDock

CombiBUILD

MCSAPCR
AUTODOCK
MCDOCK
ProDOCK
ICM
DockVision
3DDock
HEX

eHiTSDemo
(A)