USC NancyDeng MolecularDockingStudies

8/10/2019 USC NancyDeng MolecularDockingStudies

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Structure-based Drug Design:Structure-based Drug Design:Molecular Docking StudiesMolecular Docking Studies

Jinxia (Nancy) Deng, PhDJinxia (Nancy) Deng, PhDSept 25, 2007Sept 25, 2007


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OutlineOutline

Review of Structure Based DrugReview of Structure Based Drug

DesignDesign

Molecular dockingMolecular docking

Docking case studyDocking case study


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http://www-personal.engin.umich.edu/~wildd/mfg501/lecture.ppt

Identify disease

Isolate protein

involved in

disease (2-5 years)

Find a drug effective

against disease protein

(2-5 years)

Preclinical testing

(1-3 years)

Formulation

Human clinical trials

(2-10 years)

Scale-up

FDA approval

(2-3 years)

F i l e

I N D

F i l e

N D A

http://images.google.com/imgres?imgurl=www.elements.nb.ca/theme/health/patty/sick.jpg&imgrefurl=http://www.elements.nb.ca/theme/health/theme.htm&h=128&w=75&prev=/images%3Fq%3Dsick%2Bclipart%26svnum%3D10%26hl%3Den%26lr%3D%26ie%3DUTF-8%26safe%3Doff


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Database searchingDatabase searching

3D structure searching3D structure searching pharmacophore modelspharmacophore models exclusion zones to represent receptorexclusion zones to represent receptor

DockingDocking prediction of the structure and binding free energyprediction of the structure and binding free energy

of a ligand-receptor complex given only theof a ligand-receptor complex given only thestructures of the free ligand and receptorstructures of the free ligand and receptor

examine binding model of known ligands toexamine binding model of known ligands tosuggest modificationsuggest modification

screen databases of 3D structure to find novelscreen databases of 3D structure to find novelligandsligands


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It includesIt includes ligand-protein docking, one branch ofligand-protein docking, one branch of

rational drug design to predict whichrational drug design to predict which

molecules can displace others frommolecules can displace others fromthe surface of a protein, or changethe surface of a protein, or change

protein function.protein function.

Protein-protein interactionProtein-protein interaction

Protein – DNA interactionProtein – DNA interaction


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Ligand docking(lock & key model)


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Structure

determination

Design new

inhibitors

Targetstructure Small

molecule

database


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•Ligand-protein docking:

• Docking of a small molecule (the ligand) on

a large molecule (the protein, so called-receptor)

•Protein-protein docking:

• Usually the docking site is a more "planar" surface than inthe ligand-protein docking

•Protein-DNA simulation*

Nucleic Acids Research 2006, Vol34, No. 11 3317-3325


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Evaluating a structureEvaluating a structure

X-ray crystallographyX-ray crystallography Most commonMost common Must have better than 2.5Must have better than 2.5ÅÅ

resolutionresolution

NMRNMR May be possible to determineMay be possible to determine

dynamicsdynamics

Homology modelingHomology modeling When no experimental structureWhen no experimental structure

is availableis available Uses a known structure as aUses a known structure as a

template for the unknowntemplate for the unknown


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Growth of the PDBGrowth of the PDB

0

5000

10000

15000

20000

25000

30000

1977 1982 1987 1992 1997 2002

Year

N u m b e r o

f E n t r i e s

http://www.rcsb.org


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Identification of target siteIdentification of target site

Ideally a pocket or protuberance withIdeally a pocket or protuberance with Hydrogen bond donors and acceptorsHydrogen bond donors and acceptors

Hydrophobic characteristicsHydrophobic characteristics

Variety of sizes of molecular surfacesVariety of sizes of molecular surfaces Can be an active site, an assembly site,Can be an active site, an assembly site,

or a communication siteor a communication site

Co-crystallized protein-ligand complexesCo-crystallized protein-ligand complexescan be invaluable for determining targetcan be invaluable for determining target

sitessites


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Docking algorithmsDocking algorithms

Molecular flexibilityMolecular flexibility both ligand and protein rigidboth ligand and protein rigid flexible ligand and rigid proteinflexible ligand and rigid protein both ligand and protein flexibleboth ligand and protein flexible

search algorithmsearch algorithm use to explore optimal positions of the ligand withinuse to explore optimal positions of the ligand within

the active sitethe active site

scoring functionscoring function value should correspond to preferred binding modevalue should correspond to preferred binding mode

efficiency very important for database searchingefficiency very important for database searching


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TODAY’S FOCUSTODAY’S FOCUS

eHITSeHITS:: EElectroniclectronic HiHighgh

TThroughputhroughput SScreeningcreening

((SimBioSys Inc.)SimBioSys Inc.)

GOLDGOLD:: GGeneticenetic OOptimizationptimizationforfor LLigandigand DDocking (ocking (CCDC CCDC ))

http://www.ccdc.cam.ac.uk/prods/gold/index.htmlhttp://www.ccdc.cam.ac.uk/prods/gold/index.htmlhttp://www.ccdc.cam.ac.uk/prods/gold/index.html


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eHITS: Electronic High ThroughputeHITS: Electronic High Throughput

ScreeningScreening (SimBioSys Inc.)(SimBioSys Inc.)

Fast, felxibibleFast, felxibible

docking of whole anddocking of whole andpartial structures topartial structures totarget receptorstarget receptors

Designed for libraryDesigned for libraryscreeningscreening


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eHiTS - SearcheHiTS - Search

❑ Ligand is divided intoLigand is divided into❑ rigid fragments andrigid fragments and

❑ connecting flexible chainsconnecting flexible chains

❑ All rigid fragments areAll rigid fragments are

docked independentlydocked independently

❑ Graph matchingGraph matching

❑ Flexible chain fittingFlexible chain fitting

❑ Local energy minimisationLocal energy minimisation


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There are many docking programsThere are many docking programs eHITS is a fully systematic and exhaustiveeHITS is a fully systematic and exhaustive

docking programdocking program

19 F B d HiTSF t B d HiTS


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1919.. Fragment Based eHiTSFragment Based eHiTS

AlgorithmAlgorithm

Ligands are divided into rigidLigands are divided into rigidfragments and flexible connectingfragments and flexible connectingchainschains

Rigid Dock: Each fragment isRigid Dock: Each fragment isdocked INDEPENDENTLYdocked INDEPENDENTLY

everywhere in the receptoreverywhere in the receptor Pose Match: A fast graphPose Match: A fast graph

matching algorithm finds allmatching algorithm finds allmatching solutions to reconstructmatching solutions to reconstruct

the original moleculethe original molecule Local Energy Optimization:Local Energy Optimization:

structure is optimized within thestructure is optimized within thereceptorreceptor

Ranking: structures are rankedRanking: structures are rankedbased on scoring functionbased on scoring function

N

O

N

O

N

O

N

O

HN

N

N

OH2

HN

N

HN

NHN

N

HN

N

HN

N

NH

N

HN

N

H2H

2

H2

H2

H2

H2

H2

Reconnected LigandPose:

HN

N

N

O

H2


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2020.. Docking Fragments - RigiDockDocking Fragments - RigiDock

Rigid fragment docking based onRigid fragment docking based onChemical feature mapped polyhedraChemical feature mapped polyhedra

Polyhedron shrink-wrapped ontoPolyhedron shrink-wrapped onto

molecular surface (Connolly)molecular surface (Connolly)

Chemical feature flags on verticesChemical feature flags on vertices

Analogue cavity representationAnalogue cavity representation

Rapid mapping of ligand and cavityRapid mapping of ligand and cavity

polyhedrapolyhedra


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2121.. Fragment Based DockingFragment Based Docking


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2222.. Docking Fragment 1Docking Fragment 1

The Fragment is docked

everywhere in the receptorsite, and clustered to givea set number of poses

NOTE: In the illustrations shown, only 250 poses are displayed,default parameters of eHiTS uses 60 for ea!h fra"ment


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2626.. Close but differentClose but different

Polar CharacterFragment 4: Alcohol Oxygen

Fragment 2: Ether Oxygen


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F 1 F 2 F 3 F 4


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Top Ranked PoseRMSD: 0.699

Score: -8.507

Frag 1 Frag 2 Frag 3 Frag 4


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2929.. Summary of eHiTS FeaturesSummary of eHiTS Features

Fragment based docking engineFragment based docking engine

Speed-up due to database storageSpeed-up due to database storage

Statistically derived empirical scoringStatistically derived empirical scoringfunctionfunction

User-trainable scoring function (FamilyUser-trainable scoring function (Family

based)based) Automatic handling of protonation stateAutomatic handling of protonation state


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DHFR Case StudyDHFR Case Study


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Experiment ObjectivesExperiment Objectives

❑ Show ability to reproduce crystalShow ability to reproduce crystal

structuresstructures

❑ Show that eHiTS can select active ligandsShow that eHiTS can select active ligandsof human DHFR from a drug databaseof human DHFR from a drug database

❑ Illustrate the ease of use of eHiTSIllustrate the ease of use of eHiTS

❑ No pdb preparation, no ligandNo pdb preparation, no ligand

preparationpreparation

❑

Show eHiTS can be used in HTSShow eHiTS can be used in HTS


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Dihydrofolate ReductaseDihydrofolate Reductase

(DHFR)(DHFR)❑ Plays an essential role in thePlays an essential role in the

building of DNAbuilding of DNA

❑

““ juggles” two molecules in juggles” two molecules inthis reactionthis reaction

❑ Folate (purple) and NADPHFolate (purple) and NADPH

(green)(green)❑ The first enzyme targeted forThe first enzyme targeted for

cancer chemotherapycancer chemotherapy Oct. 2002 PDB Molecule of the Month:http://www.rcsb.org/pdb/molecules/pdb34_3.html


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DHFR – Binding siteDHFR – Binding site

❑ The drug methotrexate is designed toThe drug methotrexate is designed to

mimic folate, blocking the enzyme's actionmimic folate, blocking the enzyme's action

❑

Note the interaction between folate andNote the interaction between folate andNADPH, this is essential for the enzyme'sNADPH, this is essential for the enzyme's

functionfunction


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““Actives” SelectionActives” Selection❑

Searched for DHFR complexes in the PDBSearched for DHFR complexes in the PDB❑ Obtained 88 complexes, all sourcesObtained 88 complexes, all sources

❑ Upon quick visual inspection, eliminated 17Upon quick visual inspection, eliminated 17

complexescomplexes❑ Contained no ligand in the binding siteContained no ligand in the binding site

❑ Contained multiple ligands in the binding siteContained multiple ligands in the binding site

❑ Selected 71 DHFR complexes for studySelected 71 DHFR complexes for study

❑ Including 19 human complexesIncluding 19 human complexes


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19 Human DHFR complex19 Human DHFR complex

Com plex Ligand Form ula # at om s CoF Form ula 1dhf FOL 2(C19 H17 N7 O6 --) 49

1dlr MXA C17 H19 N5 O2 43 NDP C21 H27 N7 O17 P 1dls MTX C20 H22 N8 O5 55 NDP C21 H27 N7 O17 P

1drf FOL C19 H17 N7 O6 -- 49 1hfp MOT C20 H22 N6 O6 54 NAP C21 H28 N7 O17 P

1hfq MOT C20 H22 N6 O6 54 NAP C21 H28 N7 O17 P 1hfr MOT C20 H22 N6 O6 54 NAP C21 H28 N7 O17 P 1km s LIH C18 H17 N7 42 NDP C21 H30 N7 O17 P 1km v LII C18 H19 N5 O2 44 NDP C21 H30 N7 O17 P

1m vs DTM C18 H22 N6 O3 49 1m vt DTM C18 H22 N6 O3 49

1ohj COP C27 H27 N9 O6 69 NDP C21 H30 N7 O17 P 1ohk COP C27 H27 N9 O6 69 NDP C21 H30 N7 O17 P 1pd8 CO4 C19 H24 N6 O3 52 NDP C21 H30 N7 O17 P

1pd9 CO4 C19 H24 N6 O3 52 1s3u TQD C19 H39 N5 O3 66 1s3v TQD C19 H39 N5 O3 66

1s3w TQT C17 H33 N5 55 NAP C21 H28 N7 O17 P 2dhf DZF 2(C20 H18 N6 O6 --) 50


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ValidationValidation

❑ Each DHFR ligand was removed from theEach DHFR ligand was removed from the

protein and docked back into its binding siteprotein and docked back into its binding site

❑ EHiTS was allowed to do this split automaticallyEHiTS was allowed to do this split automatically

❑ Results were then judged by evaluating theResults were then judged by evaluating the

RMSD between the crystal structure bindingRMSD between the crystal structure binding

position and the computed docking poseposition and the computed docking pose

❑ Standard (default) parameters for eHiTS wereStandard (default) parameters for eHiTS were

used in all the runsused in all the runs


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Validation – All SourcesValidation – All Sources

Top-ranked 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%Ave RMSD 1.94 1.41


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Validation - HumanValidation - Human


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Results – The GoodResults – The Good

1dyi Complex – x-ray ligand in white

Top-Rank, -139.60.85 RMS

Closest, -105.770.76 RMS


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Results – The BadResults – The Bad

1ly4 Complex – x-ray ligand in white


Closest, -50.320.89 RMS


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Results – The UglyResults – The Ugly


Closest, 43.224.38 RMS

1rc4 Complex – x-ray ligand in white


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Validation - SummaryValidation - Summary

❑ EHiTS was able to reproduce accuratelyEHiTS was able to reproduce accurately

(RMS < 2.0) the crystal structure position of(RMS < 2.0) the crystal structure position of

DHFR ligands 85% of the timeDHFR ligands 85% of the time

❑ 67% of the time, eHiTS' highest ranking67% of the time, eHiTS' highest ranking

(best scoring) pose had a RMS < 2.0(best scoring) pose had a RMS < 2.0

❑

This number improves for Human DHFRThis number improves for Human DHFRligands, 74%ligands, 74%

❑ This shows that eHiTS is able to predictThis shows that eHiTS is able to predict

docking poses for DHFR ligandsdocking poses for DHFR ligands

GOLDGOLD:: GGeneticenetic OOptimization forptimization for



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calculating docking modes of smallcalculating docking modes of small

molecules into protein binding sitesmolecules into protein binding sites genetic algorithm for protein-ligandgenetic algorithm for protein-ligand

dockingdocking

full ligand and partial protein flexibilityfull ligand and partial protein flexibility energy functions partly based onenergy functions partly based onconformational and non-bonded contactconformational and non-bonded contactinformation from the CSDinformation from the CSD

choice of scoring functions: GoldScore,choice of scoring functions: GoldScore,ChemScore and User defined scoreChemScore and User defined score virtual library screeningvirtual library screening

GOLDGOLD:: GGeneticenetic OOptimization forptimization for

LLigandigand DDocking(ocking( CCDC CCDC ))

GOLD t iGOLD t i



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GOLD contains:GOLD contains:

A scoring function:A scoring function: GOLD Fitness =SGOLD Fitness =Shb-ext +hb-ext +SSvdw-exvdw-ex+S+Shb-inthb-int+S+Svdw-intvdw-int

Searching mechanism to explore bindingSearching mechanism to explore binding

mode: Genetic algorithm.mode: Genetic algorithm.

Docking of the ligandin 1BL7, a MAPkinase P38 complex.The GOLD dockedsolution (red) iscompared with thatobserved in the PDB(coloured by

element). RMSD =0.5 Angstroms.

Docking of the ligand in1JAP, a matrixmetalloproteasecomplex. The GOLDdocked solution (red) iscompared with thatobserved in the PDB(coloured by element)RMSD = 0.8 Angstroms

Genetic Algorithm: selection crossover and mutation


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Genetic Algorithm: selection , crossover , and mutationoperators to find the optimal solution

Solutions are encoded as genome, i.e.Solutions are encoded as genome, i.e.chromsomechromsome Chromosome A:Chromosome A:

101100101100101011100101101100101100101011100101 Chromosome B:Chromosome B:

111111100000110000011111111111100000110000011111


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Reproduction: via crossover, which picksReproduction: via crossover, which picks

randomly from parent genome to producerandomly from parent genome to producenew generation.new generation.


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Mutation: chromosome can undergoMutation: chromosome can undergo

spontaneous changes (with smallspontaneous changes (with smallprobability) to produce new generations toprobability) to produce new generations to

sampling different part of the solutionsampling different part of the solution

space.space.

AA fitness function fitness function (or(or objective function objective function ) is) is

used to evaluate each solution.used to evaluate each solution.


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Docking applicationsDocking applications

Binding mode predictionBinding mode prediction

Novel lead design or optimizationNovel lead design or optimization

Database screening to identify hitsDatabase screening to identify hits

Design novel leads from


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Design novel leads fromfragment

target

Docking

fragment

LinkagePerfect ligand


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Challenging: receptor flexibilityChallenging: receptor flexibility

Ligand binding to the receptor induces a range ofLigand binding to the receptor induces a range of

conformational changes:conformational changes: Local rearrangement of side-chainsLocal rearrangement of side-chains

Hinge motions of domainHinge motions of domain Two problemsTwo problems

Predicting conformational changePredicting conformational change

sampling the possible changed conformation duringsampling the possible changed conformation during

docking because too many degree of freedom available todocking because too many degree of freedom available toa binding site and number of binding site conformationsa binding site and number of binding site conformations

grows exponentially with them.grows exponentially with them.


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Virtual Screening / DockingVirtual Screening / Docking

eHiTSDOCK

FlexX

FlexE

SLIDE

Flo98

ADAM

Hammerhead

MCSA-PCRAUTODOCK

MCDOCK

ProDOCK

ICM

DockVision

3D-Dock

HEX

GRAMM

PPD

BIGGER

ZDOCK/RDOCK

RosettaDock

Affinity

CombiBUILD

GLIDE

GOLD

HINT

LIGPLOT

SITUS

VEGA

FRED

FlexiDock


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(A)

eHiTS Demo


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