1 IntelliSyn

IntelliSyn RD

Fragment assisted drug discovery

Jeffrey AlbertJuly 22, 2014, Punta Cana

Fragment applications to:- PDE10 Inhibitors- CCR2 Antagonists

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Continuing to expand the scope of fragment applications

Fragment based drug discovery• Optimize weak affinity hits through knowledge-based

design• Crystallography• NMR

Fragment assisted drug discovery• Limited structural knowledge• Fragments serve as a bridge with various other

approaches• Mark Whittaker, Evotec; DDT, 2009, 13, 623

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Fragment assisted drug discovery (1)Lepre (Vertex); Exp. Opin. Drug Discov. 2007, 2, 1555

Fragments influence combinatorial libraries• Regulatory erythroid kinase (REDK) inhibitors• Lepre (Vertex); Exp. Opin. Drug Discov. 2007, 2, 1555

S

N NH2

O

S

N NH2O

Initial NMR screen (100 uM)

10% activity at 100 uM

Follow-up NMR screen

IC50 ~200 uM

OH

N

N NH

Directed combinatorial library

IC50 0.61 uM

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Fragment assisted drug discovery (2)

• Fragments influence combinatorial libraries• AstraZeneca; Curr. Topics Med. Chem., 2007, 7, 1600• Melanocortin 4 receptor antagonists (MCr4); Class A GPCR

ON

NH O

ON

N OSN

Cl

Biological HCS at 1 mM; 660 fragments

IC50 631 uM

Focused screen

IC50 4 uM

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Fragment screening across different targets

Target class Screen conc. (mM)

Screening method

Library size

X-ray avail.? Hit rate (%)

Protein-protein interact. 0.05 HCS 40000 N 0.2Aspartyl protease 1 1D NMR 2500 Y 1.2Metalloproteinase 1 HCS 600 N 1Serine Protease 1 2D NMR & HCS 150 N 6GPCR Class A 1 HCS 1000 N 15GPCR Class B 1 HCS 600 N 1.5Nuclear hormone recep. 0.3 1D NMR 500 Y 2ATPase 1 2D NMR 1000 Y 6.3Kinase 0.6 2D NMR 2500 Y 0.4Glycosyl hydrolase 0.1 HCS 2000 N 1.5Ion channel 0.3 1D NMR 500 N 0

Albert, JS; Blomberg, N; Breeze, AL; Brown, AJH; et al. An integrated approach to fragment-based lead generation: Philosophy, strategy and case studies from AstraZeneca's drug discovery programmes. Curr. Top. Med. Chem. 2007, 7, 1600.

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Integrated application of multiple methods

• Use all the knowledge available• Literature, target, in-house experience, fragments, HTS, others…

Integrated knowledge

Fragments HTS

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PDE10 as a key new target for schizophrenia

• Target rationale• PDE10 catabolizes cAMP and regulates striatal cAMP

(critical second messenger)• Alters signaling processes downstream of D2• Offers the potential to treat schizophrenia without the liabilities of all existing D2

antagonists

Papavarine Pfizer AZ Mölndal Pfizer

NO

O

O

O

NH

N

N

ON

N

N

NO

O

ON

N N

NH

OOH

NF

O

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Biacore-based screening assay

N

F

NHO

O

ONH

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Fragment screen

Fragment screen3k cmpds

Target based

Ligand based

Diversity based

368 hits

80 90 100 110

0

100

200

300

400

500

600

ΔPM

V (p

m)

Time (min)

Addition of protein

Addition of compounds

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LE

<0.25

>0.40

0.30-0.350.35-0.40

0.25-0.30

LE>0.40

0.30-0.350.35-0.40

0.25-0.30

LE>0.40

0.30-0.350.35-0.40

LE>0.400.35-0.30

LE>0.4

N

N

NN

N

N

NH2

N

NS

N

N

N

N

N

S

N

NNH

O

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Fragment assisted lead generation

Ligand efficiency

IC50

Fragment knowledge

HTS data mining, triage and validation

NNH

O S

NN

IC50 324 μMLE 0.40

IC50 851 μMLE 0.38

AA

AHet

Chemotype

IC50 3.8 μMLE 0.32

NNH

NH

O

NH

N

ON

HTS

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Fragment elaboration

20 compound

diversity setNN

H

NH

O

NH

N

ON

NNH

NH

O

NH

N

Cl

IC50 3.8 μMLE 0.32

cLogP 1.7

IC50 100 nMLE 0.38

cLogP 4.4

IC50 16 nMLE 0.41

cLogP 4.6

IC50 120 nMLE 0.36

cLogP 3.3

N

NH

S

O

N

N

CN

N

NH

S

O

N

N

Cl

~40 cmpds, 4 weeks

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NH

N

N

ON

N

NH

S

O

N

N

Cl

IC50 16 nM (model)

Pfizer (X-ray)

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CCR2

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Fragment screen: Strategy

Binding FLIPR

3000 fragments

Retest actives Retest actives

Conc. resp. Conc. resp.

Cross check

Validated fragment hits

SPR

Test at 300 and 1000 uMBinding

Retest actives

Conc. resp.

Fragment-to-hit chemistry

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Fragment screen set design (3000 compounds)

cLogP mw

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CCR2 Fragment screen: Binding assay

~25 Initial hits

Prioritized hits withIC50 <100 uM or LE >0.4

Validated leads

67 initial actives

1350 fragments tested (1st set)

SP binding assay at 1000 uMCutoff: 80% displacement

Displacement cutoff at 1000 uM # Cmpds Hit rate

30% 266 20%50% 125 9%80% 67 5%

Dose/response in binding assay

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CCR2 Fragment screen: Flipr assay

2495 Fragments in at 1000 uM

2495 Fragments in at 1000 uM

528 in 7p CR 528 in 7p CR

256 actives

256 actives

Even low UV absorbance confounds the binding assay. Worse in the Fliprassay.

8%

64%

28%

5-100 uM

100-1000 uM

>1000 uM

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Integrated screening profile

• Chemokine receptors

Bin

ding

affi

nity

IC50

(μM

)

Function

Validatedfragment hits

Binding

Select best 3000 fragments

Biacore

Antagonist functional potency, IC50 (μM)

A

B

C

A. Potential orthosteric binders/antagonistsB. Potential allosteric antagonistsC. Potential orthsteric binders (SAMs?)

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Initial actives

ID

Binding IC50 (uM)

IT19232

Flipr IC50 (uM)

IT19233

LE Binding

LE FLIPR

MoA Cmpd

1 221 140 0.26 0.28 AZ10003110

2 301 467 0.3 0.28 AZ10080126

3 145 75 0.35 0.37 AZ10371873

4 297 213 0.37 0.38 AZ10168494

5 412 406 0.38 0.38 AZ10498119

6 102 709 0.49 0.39 AZ10350370

7 139 294 0.44 0.4 AZ10305347

8 204 130 0.39 0.41 AZ10373784

9 150 458 0.47 0.41 AZ10277394

10 7 618 0.78 0.48 NAM AZ10289990

11 18 11 0.5 0.52 AZ10028094

12 220 212 0.71 0.71 AZ10065909

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Surface Plasmon Resonance (SPR)

• Provides direct confirmation of target/ligand engagement• Extremely sensitive (can detect binding as weak as 1 mM affinity)

SPR sensor chip

Immobilize membrane bound CCR2

Ligand

Ligand

Detect ligand binding

SPR sensor chip SPR sensor chip

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IntelliSyn RDSpin-out from the legacy Montreal Pharma community

Major-pharma personnel and facilities• Capitalizing on major site closures by AstraZeneca, Merck,

Boehringer Ingelheim• 75% of staff have Ph.D. and 10+ years training inside major

pharma

Integrated capabilities• Synthesis• Med chem, comp chem• Biological screening• In vivo DMPK (on-site rodent vivarium)

Our core therapeutic areas• Oncology• CNS drugs

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Biology screening capabilities

Cellular functional screening recombinant and primary cells• Label free screening technology (EPIC)• Calcium imaging (Hammamatsu FDSS7000, FLIPR 384)

Biochemical assays• Intracellular signaling (cAMP, IP3, beta arrestin, ERK 1/2)

Radioligand binding• GTPγS binding (SPA and filtration)• Peptidic and small molecules binding assays

Electrophysiology• PatchXpress• Q-Patch

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Company highlights over our first 24 months

Client Type IntelliSyn delivers to client

1 Pharma • Route development and tech transfer for their most difficult syntheses

2 Biotech• Pharmacophore model → 2 clinical candidates in

18 months• Filed 2 patents for client

3 Biotech• Hit → in vivo active lead in 3 months. • Filed 1 patent for client• Enabled client to secure round-2 financing

4 Biotech• New target → Validated lead series• Filed 1 new patent• Facilitated new company spin-out

“IntelliSyn has the right expertise on epigenetic targets—specifically,BRD inhibitors—to develop it.” Mounia Azzi, Neomed; director of scientific affairs. SciBX April 2014

Grant 447277: 2013-2014: "Novel epigenetic anti-cancer drug candidates“

Grant 832369 2014-2015: “Hypoxia response modulators for cancer”

High impact for our clients• 4 Patent filings• 3/3 Successful milestone transitions• 2 Clinical candidates• 1 Project spun out to new investor group• 2 Grants awarded from government sponsorsEvery client has renewed their initial contracts