jeffrey albert | fbdd 2014 | fragment assisted drug discovery
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1 IntelliSyn
IntelliSyn RD
Fragment assisted drug discovery
Jeffrey AlbertJuly 22, 2014, Punta Cana
Fragment applications to:- PDE10 Inhibitors- CCR2 Antagonists
2 IntelliSyn
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
3 IntelliSyn
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
4 IntelliSyn
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
5 IntelliSyn
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
7 IntelliSyn
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
12 IntelliSyn
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
18 IntelliSyn
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
19 IntelliSyn
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
22 IntelliSyn
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
24 IntelliSyn
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
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