Calcula&ng)mul&scale)rela&onships) …nkhuri/files/systems-pharmacology-lecture4-01262015.pdf ·...
Transcript of Calcula&ng)mul&scale)rela&onships) …nkhuri/files/systems-pharmacology-lecture4-01262015.pdf ·...
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Calcula&ng)mul&scale)rela&onships)among)drugs,)targets,)and)side)effects)
Michael(Keiser,(PhD(Assistant(Professor(of(Pharmaceu6cal(Chemistry(NS416A(Sandler(Neurosciences(Center,(Mission(Bay(Ins6tute(for(Neurodegenera6ve(Diseases(([email protected](
Pharmacogenomics(245B(26(Jan(2015(
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How(do(we(know(if(we’ve(found(all(of(a(drug’s(targets?(
nausea vomiting fatigue dizziness dry mouth headache itching muscle pains abdominal pain blurred vision constipation diarrhea loss of appetite memory loss failure to thrive palpitations problems with coordination ringing in the ears skin rashes or hives swelling of hands or feet heart attack syncope cafe-au-lait spots ecchymosis jaundice livedo reticularis necrolytic migratory erythema
heart attack
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This(is(the(sort(of(thing(we’d(like(to(avoid(
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$6(billion(in(claims$
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culprit:(5VHT2b(off6target(
1997( heart(valve(disorder(
already(cost(Wyeth(
$21$billion$by(2004$
But(which(sorts(of(toxicity(could(we(predict?(
OffVtarget( FenPhen(
1996(
Liver((metabolic)(
Rezulin((2000)(–(Parke(Davis(–(430+(pa6ents(suffered(liver(failures(
OnVtarget( Vioxx((2004)(–(Merck(–($6(billion(
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TODAY$1. known(pharmacology(2. rela6ng(targets(to(other(targets(3. predic6ng(drug(offVtargets(4. wholeVorganism(effects(
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Ligands(link(disparate(proteins(
An6folate(targets(lack(sequence(or(structural(similarity.((
✗$✗$
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Cysteine(proteases(
Metalloproteases(
Serine(proteases(
Aspartyl(proteases(
Kinases(
Nuclear(hormone(receptors(
Ion(Channels(
Phosphodiesterases(
Aminergic(GPCRs(
Pep6de(GPCRs(
GPCRs((others)(
Enzymes(((others)(
Miscellaneous((
Paolini, Nat. Biotech, 2006
Polypharmacology(recapitulates(biology(
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Aminergic(GPCRs((
Aspartyl(Proteases((
Cysteine(Proteases((
Enzymes((others)((
GPCRs(Class(AV(others((
GPCRs(Class(B((
GPCRs(Class(C((
Hydrolases((
Ion(ChannelsV(Ligand(Gated((
Ion(ChannelsV(others((
KinasesV(others((
Metalloproteases((
Nuclear(hormone(receptors((
Miscellaneous((
Oxidoreductases((
Phosphodiesterases((
Pep6de(GPCRs((
Protein(Kinases((
Serine(Proteases((
Transferases(
Aminergic(GP
CRs(
Aspartyl(Proteases(
Cysteine
(Proteases(
Enzymes((o
thers)(
GPCR
s(others(
GPCR
s(Class(B(
GPCR
s(Class(C(
Hydrolases(
Ion(Ch
anne
lsV(LG(
Ion(Ch
anne
lsV(
KinasesV(others(
Metalloproteases(
Nuclear(re
ceptors(
Misc
ellane
ous(
Oxido
redu
ctases(
Phosph
odiesterases(
Pep6
de(GPC
Rs(
Protein(Kinases(
Serin
e(Proteases(
Transferases(
Promiscuity((Gkl)(value(0((((((((((((((((((((((((((((60(
No(data(available(
Paolini,(Nat.(Biotech,(2006(
Promiscuity$in$&$across$gene$families$
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How(can(we(predict(drug(&(target(networks?(
• Hypothesis:(Proteins(can(be(interVrelated(through(their(ligands.(
– We(represent(proteins(solely(by(their(ligands.(
– This(works(for(protein(targets(that(are(unrelated(by(biological(criteria((sequence(&(structure).(
– We(can(predict(new(links(known(between(targets(and(known(drugs.(
• Lounkine(&(Keiser(et(al.(LargeVscale(predic6on(and(tes6ng(of(drug(ac6vity(on(sideVeffect(targets.(Nature.(2012.(
• Keiser(&(Setola(et(al.(Predic6ng(new(molecular(targets(for(known(drugs.(Nature.(2009.(• Keiser(et(al.(Rela6ng(protein(pharmacology(by(ligand(chemistry.(Nat)Biotech.(2007.(
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1. known(pharmacology(2. rela6ng(targets(to(other(targets(3. predic6ng(drug(offVtargets(4. wholeVorganism(effects(
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Core(idea:(Link(small(molecules(to(protein(targets(by(ligands,(not(by(sequence(or(structure(
• Many(drugs(&(ligands(simultaneously(act(through(dissimilar(proteins.(
• Methadone:(– μ(opioid(receptor((GPCR)(– NMDA(receptor((Ion(channel)(
• Ligands(are(a(func6onal(link(between(molecular(targets.(
G*protein$coupled$receptor$(GPCR)$
Ion$channel$
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Where(do(we(get(the(ligands?(
• From(compound(ac6vity(databases(
DHFR(
Database$ Ligands$ Targets$ Data$points$MDDR((2005)( 201,761( 631( 391,406(
WOMBAT((2008)( 254,679( 2,100( 760,605(ChEMBLV14VB((2013)( 241,749( 2,657$ 1,165,336(
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How(can(we(compare(two(proteins?(
Calculate(all(pairVwise(similari6es(among(ligands(across(the(sets(
?(DHFR( TS(
DHFR( TS(
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How(do(we(encode(a(molecule?(
Fingerprint$
Bond(paTern(1(
Bond(paTern(2(
…(
F$T$
.(
.(
.(
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How(similar(are(two(molecules?(
• Use(Tanimoto(coefficients(to(compare(their(fingerprints(
• TC ( (=(bC(((/ ((b1 (+(b2 (–(bC)(• 0.29( (=(2( (/ ((4( (+(5( (–(2)(
1
2
Comparative performance metrics: Chen et al. (2002) J Chem Inf Comput Sci. 42(6), 1407-14.
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How(can(we(compare(two(ligand(sets?(
TC(a1,b1)(=(0.91(TC(a1,b2)(=(0.34(TC(a2,b1)(=(0.28(
TC(a2,b2)(=(0.31(TC(a3,b1)(=(0.43(TC(a3,b2)(=(0.39(
TC(=(Tanimoto(coefficient,(using(ECFP4(fingerprints(
Sa( Sb(
Similarity(distribu6on(for(Sa(vs.(Sb(
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How(similar(are(ligands(across(targets?(
TS$
�Raw$Score�$
Similarity(to(Thymidylate(synthetase((TS)(ligands(
Num
ber(o
f(ligand(pairs(
Pairwise(ligand(similarity((%)(
Thrombin$
DHFR$
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What(similarity(is(significant?(
Product(of(ligand(set(sizes(
Random)raw)scores)
Raw)score)standard)dev)
Raw(sc
ore(means(
Raw(sc
ore(std(de
vs(
Extreme$Value$Distribu\on$(EVD)$
ZVscore(Freq
uency(
Probability(of(any(given(raw(score(happening(by(random(chance(alone:(
Product(of(ligand(set(sizes(
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But(wait;(how(should(we(choose(a(threshold?(
0.50(Tc(Threshold(chosen(by(fit(to(EVD(
0.48(Tc(Threshold(chosen(by(best(singleVmolecule(crossVfold(valida6on(performance((
Note:(Data(shown(uses(Daylight,(but(this(also(applies(to(ECFP4,(etc(
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Similarity(ensemble(approach((for(targets)(
A( A(
1(Choose(target( 2(Build(ligand(set(
4(Rank(by(significance(
ZVscore(
Freq
uency(
A(vs.(B(
A(vs.(C(
Sta6s6cal(model(
…$
B(
3(Compare(against(database(sets(
?(?(
C(
,$
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Similar(drug(targets(group(together(
?$Ligand(set(
Ligand(sets(
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Similarity(paTerns(among(ligand(sets(
Similar MDDR Activity Classes E-value
Dihydrofolate Reductase Inhibitor 1.8e-247
1 Glycinamide Ribonucleotide Formyltransferase Inhibitor 8.5e-157
2 Thymidylate Synthetase Inhibitor 1.7e-94
3 Folylpolyglutamate Synthetase Inhibitor 7.1e-88
4 Uridine Phosphorylase Inhibitor 4.3e+3
1$
2$
3$
4$
Ligand(sets(form(archipelagos.(((
Does(this(feature(lead(to(an(informa6ve(global(map?(
Query:$Dihydrofolate(Reductase(Inhibitor(
MDDR$MDL(Drug(Data(Report((100k(compounds(annotated(by(patent(literature)(
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Biological(clusters(emerge(from(chemistry(
Keiser(MJ,(et(al.(Rela6ng(protein(pharmacology(by(ligand(chemistry.(Nat)Biotech((2007).(
Node(A(set(of(ligands(that(represents(a(single(target((Edge(A(SEA(score(between(two(targets(
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Sequence(&(pharmacology(are(complementary(
Sequence$similarity:$Log((PSIVBLAST(EVvalues)(
Pharmacological$similarity:$Log((SEA(EVvalues)(
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1. known(pharmacology(2. rela6ng(targets(to(other(targets(3. predic6ng(drug(offVtargets(4. wholeVorganism(effects(
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• Although(drugs(are(intended(to(be(selec6ve,(at(least(some(bind(to(several(physiological(targets,(explaining(side(effects(and(efficacy.(
• But(how(common(is(this?(
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Known(network(pharmacology.(
(
Is(it(comprehensive?(
Drug((
Protein(target((
≤(1(uM(IC50(
Keiser(&(Setola,(et(al.(Nature,)2009(
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3(Rank(by(significance((SEA(EVvalue)(
ZVscore(
Freq
uency(
vs.(DHFR(
vs.(thrombin(
Sta6s6cal(model(
DHFR(
Similarity(Ensemble(Approach((SEA)(predicts(targets((2000(targets,(300,000+(ligands)(
1(For(a(small(molecule,(
Keiser(et(al.,(Nature)Biotech.(2007;(Keiser(&(Setola(et(al.,(Nature,(2009.(
DHFR(
2(Compare(it(against(each(target’s(ligands(
…$,$thrombin(
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First(tests:(Methadone(is(an(an6muscarinic(
Keiser(et(al,(Nat)Biotechnol,(2007(
$( Ac\vity( SEA$E*value(
1( An6muscarinic( 4.5(×(10V50(
2( Muscarinic(M3(Antagonist( 1.2(×(10V11(
3( Opioid(Agonist( 1.8(×(100(
4( NMDA(Receptor(Antagonist( 9.0(×(100(
%(of(kno
wn(ligand(bo
und(
Drug(concentra6on( Time((seconds)(
M3(ac6vity
((RFU
)(
Ac6vity(blocked(
((SEA(predic6ons(above(used(MDDR(v2005()(
Methadone(
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Drugs(aren’t(always(“magic(bullets”(
Revanil((lysuride)(An6parkinsonian(that(inhibits(D1/2,(and(prolac6n(secre6on.(
α2(Antagonist(SEA:(8.9x10V82(
0.055(nM(
Permax((pergolide)(An6parkinsonian(withdrawn(due(to(heart(valve(disease.(
5VHT1D(Antagonist(SEA:(8.7x10V29(
13.1(nM(
Zyvox((linezolid)(An6Vinfec6ve(that(inhibits(bacterial(protein(synthesis(by(binding(to(23S(rRNA.(Also(affects(blood(pressure.(
MAOVB(Inhibitor(SEA:(1.3x10V27(
17(uM(
…We(found(>40(more(manual(and(182(more(automa6callyVvalidated(predic6ons(with(SEA(EVvalues(<(10V10(
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…but(some(may(be(“magic(shotguns”(Dapsone(Old(use:((Leprosy((New(use:(Malaria(Why?(�CA(may(have(essen6al(roles(in(the(parasite(metabolism.(Thus,(the(aroma6c(sulfonamide(CA(inhibitors(may(have(poten6al(for(development(of(novel(an6malarial(drugs."(
Carbonic(anhydrase(
(
SEA:(2.9x10V12(
Miltefosine(Old(use:(Cancer(New(use:(Visceral(leishmania(Why?(�[analogues(of(sphingosine](have(been(assayed(in(vitro(against(Leishmania(spp.(and(Trypanosoma(cruzi.(Most(of(the(compounds(were(potent(parasi6cides..."(
SphingosineV1Vphosphate(
(
SEA:(1.9x10V6(
These(drugs(have(both(been(successfully(�repurposed�(
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23+(novel((
offVtargets,(from(14(drugs(
…of$20$assays,$15$at$<$1$uM$5$at$<$100$nM$( )
Keiser,(et(al.(Nature)2009(
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New(offVtargets(cross(tradi6onal(boundaries(
Rescriptor((HIVV1(NNRTI)(
Vadilex((NMDA)(
ROV25V6981((NMDA)(
Xenazine((VMAT2)(
Enzyme$
GPCR$
Ion$channel$
Transporter$α2$
H4$μ$opioid$
SERT$D4$
NET$κ$opioid$
E:(2.4x10V7(
E:(10V30(
E:(10V13V10V5(
Keiser(&(Setola,(et(al.(Nature,)2009(
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Sequence(similarity(may(disagree(with(pharmacology(
ATempt(to(recapitulate(SEA(offVtargets(by(seq.(similarity(to(drug’s(known(targets(
Average(PSIVBLAST(rank:(43$
(of(244)(
(of(23)(
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Case(study:(“Off”Vtargets(can(be(potent(
Keiser(&(Setola,(et(al.(Nature,)2009(
SEA(EVvalue:(2.8×10V27(
But(it(has(an$18$nM$Ki(for(D4R(
Baratol((an(an6hypertensive):(
(
200*600$nM$Ki$(
for(α1$
adrenergic((receptors.(
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Target$$ SEA$E*value$$
1$ 5VHT1B(( 3.1(×(10V21(
2$ 5VHT2A( 1.2(×(10V13(
3$ 5VHT5A( 1.1(×(10V7(
4$ 5VHT7( 5.0(×(10V6(
Keiser(&(Setola,(et(al.(Nature,)2009(
Case(study:(Mode(of(ac6on(for(a(hallucinogen(
DMT$(dimethyltryptamine)(
What(is(the(target(behind(DMT’s(hallucinatory(effects?(
(A(2009(paper(implicated(the(σ1(receptor((14,750(nM(Kd)(
DMT:(129(nM(
Ergotamine((Ki(=(3.5(nM)((
DMT$
5*HT1B$receptor$
%([3H]5VCT
(binding(
log([drug](
DMT:(206(nM(%([3H]LSD(bind
ing(
log([drug](
Chlorpromazine((Ki(=(42(nM)((
DMT$
5*HT7A$receptor$
DMT:(127(nM(
%([3H]LSD(bind
ing(
Chlorpromazine((Ki(=(2.4(nM)((
DMT$
5*HT2A$receptor$
log([drug](
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DMT(no(longer(hallucinogenic(in(5VHT2A(KO(mice(
5VHT2A(may(be(primary(target(of(DMT�s(hallucinogenic(effects.(
Keiser(&(Setola,(et(al.(Nature)2009(
With(Bryan(Roth((UNC(PDSP)(
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Case(study:(OffVtarget(to(side(effect(
Target$ SEA$E*value$
1$ Adrenergic((β)(blocker( 3.9(×(10V15(
2$ 5(HT1A(Antagonist( 2.0(×(10V9(
3$ Acetylcholinesterase(Inhibitor(( 1.1(×(10+1(
Keiser,(et(al.(Nature,)2009;(Thomas,(et(al.(Psychopharmacol)Bulle&n,(2010.(
SSRI(discon6nua6on(syndrome(for(pa6ents(with(ADRB1(muta6on((SNP)(
Fluoxe6ne(binds(β1((4(uM)((
Paroxe6ne(binds(β1((10(uM)(%([1
25I]P
indo
lol(bou
nd(
Log([drug](
β1(receptor(
Alprenolol(Ki(=(2.0(nM((
Fluoxe\ne$Ki(=(4,385(nM(
Fluoxe6ne((Prozac)(( ((Using(MDDR(v2005()(
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$Binding$assays$
Test(predic6ons(
We(sought(to(predict(ADRs(on(a(broad(scale(
$SEA$
predic\ons$
650(drugs(vs.)70(targets(
Liability(targets(
explaining(ADRS(
Target(consistent(with(ADR?(
$ADR$
databases$
115$new$links(found(
Lounkine(&(Keiser(et(al.,(Nature,(2012.(
ADR:(Adverse(drug(reac6on(
With(Laszlo(Urban((Novar6s)(
No)human)interven&on)
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CTX(inhibits(platelet(aggrega6on(in(human(blood.(
In(silico,(in(vitro,(ex(vivo:(From(structure(to(ADR(
Chlorotrianisene((CTX)(is(a(synthe6c(
estrogen(causing(stomach(pain$
COXV1: (130(nM((Estrogen(receptor: (1,000(nM(
Lounkine(&(Keiser(et(al.,(Nature,(2012.(
v.s.(Indomethacin((230(nM(COXV1)(
?(
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26%(of(new(targets(cross(family(boundaries(
Confirmed, 1%
0%(
5%(
10%(
15%(
20%(
25%(
30%(
Frac
tion
of n
ovel
off-
targ
ets
-log10 (BLAST E-value)
Sequence similarity of new target to closest known
HRH2(–(SCN10A(Not)related)
NR3C1(–(PGR(
CHRM1(–(HRH1(Dis&nct)subclass)
Lounkine(&(Keiser(et(al.,(Nature,(2012.(
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Physical(proper6es(only(loosely(predict(drug(promiscuity(
V4( 0(
Probucol(
Ibandronate(
Chlorhexidine(
Fluspirilene(
Zafirlukast(
Tegaserod(
Lounkine(&(Keiser(et(al.,(Nature,(2012.(
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1. known(pharmacology(2. rela6ng(targets(to(other(targets(3. predic6ng(drug(offVtargets(4. wholeVorganism(effects(
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Drugs(act(via(‘mul6scale(mechanisms’(
Zhao(&(Iyengar.(Annu.(Rev.(Pharmacol.(Toxicol.(2012.(
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channels((myocyte)(intermed.(+(target(intermediates(((drug(targets(drugs(
How(can(we(make(
this(simpler?(
Zhao(&(Iyengar.(Annu.(Rev.(Pharmacol.(Toxicol.(2012.(
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3(Test in vitro and genetically
ZVscore(
Freq
uency(
vs.(DHFR(
vs.(thrombin(
Sta6s6cal(model(
DHFR(
Predic6ng(phenotypic(mechanism(of(ac6on(with(SEA)
1(For each active molecule
DHFR(
2(Compare to ligands of 2500 targets
…$,$thrombin(
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Mul6Vphenotype(screen((3,200(cpds):(Some(compounds(affect(feeding(in(C.)elegans((measured(by(pharyngeal(pumping(rate).(
Kaveh’s(screen:(Can(we(find(mechanisms(systema6cally(
Food(source(
Posterior(pharynx(
Lemieux(et(al,(PLoS(Biology,(2013)
AR(8.6(nM( FltV3(
169(nM(
NK1(1.9(uM(
OTR(1.8(uM(
mGluR8(9.8(uM(
Using(SEA,(hits(were(antagonists(at(human(targets:(
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We(mapped(human(targets(back(to(C.)elegans)
V10(
V5(
0(
5(
10(
Interac6on:(• Addi6ve(• Epista6c(• Antagonis6c(
Change(in(fe
eding(rate(
Oxytocin(receptor((
(OTR)(antagonists(
Control((4.6(nM)(
From(screen:(F15((1.8(uM)(
Gene6c(condi6ons((gene(inac6va6ons)(
Lemieux(et(al,(PLoS(Biology,(2013)
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We(mapped(human(targets(back(to(C.)elegans)
V10(
V5(
0(
5(
10(
Interac6on:(• Addi6ve(• Epista6c(• Antagonis6c(
Change(in(fe
eding(rate(
Oxytocin(receptor((
(OTR)(antagonists(
Phenocopy$(4.6(nM)(
From(screen:(F15((1.8(uM)(
Gene6c(condi6ons((gene(inac6va6ons)(
gnrr*1$$
(3x10V30(by(BLAST(to(human(OTR)((
Lemieux(et(al,(PLoS(Biology,(2013)
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We(mapped(human(targets(back(to(C.)elegans)
V10(
V5(
0(
5(
10(
Gene6c(condi6ons(
Change(in(fe
eding(rate(
Chemical(condi6ons(Interac6on:(• Addi6ve(• Epista6c(• Antagonis6c(
Let’s(switch(a(topVdown(view(
Lemieux(et(al,(PLoS(Biology,(2013)
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mglV2(
verV3(
gnrrV1(
verV2(
tkrV1((RNAi)(
gnrrV3(
This(yielded(four(targets(newly(regula6ng(appe6te(
Interac6on:(• Addi6ve(• NonVaddi6ve(• Antagonis6c(
Gene6c(perturba6ons(
Chemical(perturba6ons(
3(
1(
2(
4(
mGluR8( FltV3( OTR( NK1/3( Human)(chemical))mglV2( verV3( gnrrV1( tkrV1( C.)elegans)(gene&c))
Lemieux,(Keiser,(et(al.(PLoS(Biol,(2013.) [c](=(posi6ve(control(compound(
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Winter(notes(on(summer(impressions(
• 1(People(usually(choose(targets(by(dint(of(domain(exper6se.(– If(we(didn’t,(would(we(just(get(‘useless�(offVtargets?(Or(learn(something(new?(
• 2(We(can(usually(cross(organisms.(– Zebrafish(<V>(human(– Worm(<V>(human(
• 3(One(phenotype(≠(one(target.(– How(many(of(these(are(stackable?(– What(happens(“offVdiagonal”?(
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Most(offVtargets(are(s6ll(unexplored(
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You(can(try(SEA(yourself(
hTp://sea.bkslab.org(