Fragment-based drug discovery to identify small molecule ......the RAS/MAPK pathway using fragment...
Transcript of Fragment-based drug discovery to identify small molecule ......the RAS/MAPK pathway using fragment...
Astex Pharmaceuticals
Fragment-based drug discovery to identify small molecule allosteric inhibitors of SHP2
AACR, April 2020
Christopher N. Johnson
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Disclosure
• The presenter and co-authors are employees of Astex Pharmaceuticals or Taiho Pharmaceutical Co. Ltd.
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Src Homology Phosphatase 2 (SHP2)
• Protein tyrosine phosphatase family member– Downstream of multiple RTKs– Regulator of RAS/MAPK signalling– Clinically validated pathway– Many opportunities in KRAS & RTK driven cancers for
SHP2 inhibitor as single agent or in combination– Astex has a fragment-derived ERK1/2 kinase inhibitor in
Phase 1
• Talk describes the SHP2 fragment screen and early hit-to-lead program
SHP2
RAF
MEK
ERK
p90RSKProliferation
Differentiation
Survivalnucleus
AKT
Growth factor signalling
RTK
PI3K
RASpY
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Why Use a Fragment-Based Approach?
• Proven approach: many fragment-derived compounds currently in clinical development, with three approved drugs
– Vemurafenib (BRAF-V600E), venetoclax (BCL-2), erdafitinib (FGFR)
• Astex has successfully targeted another node downstream of SHP2 in the RAS/MAPK pathway using fragment-based drug design: ERK1/2
Fragment IC50 76 μM Lead IC50 0.0030 μM
Heightman et al., J. Med. Chem. 2018, 61, 4978−4992
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Fragment-Based Drug Discovery at Astex - PyramidTM
INTEGRATED BIOPHYSICAL SCREENING
STRUCTURE-LED OPTIMIZATIONFRAGMENT SELECTION
Astex ProprietaryFragment Library
<HAC> 12 <MW> 176
Targeted & Virtual Screening Sets
NH
N
ONH2
Cl
NN
NN
N
N NH2ClN NH2
N
NNH2
ClOH
NH
NH
NH2
O
OCl
NN
NH
S
X-Ray
-0.5 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5
-6
-4
-2
0
-0.6
-0.5
-0.4
-0.3
-0.2
-0.1
0.0
0.10 20 40 60 80 100
Time (min)
µcal
/sec
Molar Ratio
kcal
/mol
e of
inje
ctan
t
305 310 315 320 325 330 335
1x105
2x105
3x105
4x105
5x105
Flu
orescence (a.u
.)
Temperature (K)
NMR
Tm
ITC
Astex PYRAMID™Screening
Fragment-to-Candidate Chemistry
AutoSolve
Jhoti, et al. Nature Reviews Drug Discovery, 12, 644 (2013)
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• Historically phosphatase enzymes were deemed undruggable– Targeting direct inhibition of catalytic site has proven very difficult– Opportunity to use fragment screening to identify allosteric sites
• Objective: to discover an allosteric inhibitor stabilizing the closed, catalytically-inactive, form of the protein
The Challenge for Drugging SHP2
C-SH2 N-SH2
PTPClosed, inactive conformation
Open, active conformationsubstrate
pY
N-SH2 C-SH2 PTPpY
PTP = protein tyrosine phosphatase (catalytic) domain
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SHP2 Fragment Screen
• No hits obtained for phosphatase-only construct
• Fragment screen was carried out on two constructs– Closed autoinhibited C-terminal truncated form having catalytic + both SH2 domains– Phosphatase domain only form– Screened using ligand-observed NMR and X-ray crystallography
N-SH2
Tunnel site
C-SH2
Phosphatase
• Multiple hits obtained for C-terminal truncated form
– >70 structurally validated hits bound in tunnel-like site
– Additional sites identified• Tunnel site does not exist for other
phosphatases: high selectivity potential
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SHP2 Fragment Hit to Early Lead Compound
• Example of a millimolar-affinity fragment hit binding to tunnel site
• Isothermal titration calorimetry (ITC) used to characterise affinity of weakly binding compounds
• Structure-guided growing of fragment hit into adjacent pockets gave an Early Lead with ~ 1000-fold increase in affinity
Apo Tunnel Site Fragment Early Lead
SHP2 ITC KD/µM 1000 1.1
Ligand Efficiency 0.34 0.39
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SHP2 Enzyme Inhibitory Activity Demonstrated
Phosphatase Activity
• Early Lead inhibits activity of C-terminal truncated construct expressing N-SH2, C-SH2 and catalytic domains
• No inhibition of phosphatase catalytic domain-only construct• Promising starting point for further optimization
0 1 2 30
50
100
Tunnel site SHP2 inhibitor
log10([AT36746] /µM)
%
Act
ivity
SHP2SHP2 phosphatase domain
log10([compound]/μM)
IC50 = 2.1 μM
N-SH2
Tunnel site
C-SH2
Phosphatase
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Summary and Current Project Status
• Novel allosteric SHP2 inhibitor series identified using fragment-based
drug discovery
• Lead series has subsequently been optimised to single-digit nanomolar-
affinity orally bioavailable preclinical candidate using structure-led design
– No inhibitory activity versus catalytic-domain-only construct
– No inhibition across a panel of 20 phosphatases, including closest relative SHP1
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Acknowledgements
Valerio BerdiniJuan CastroGianni ChessariThomas G. DaviesJames E. H. DayPhilip J. DaySatoshi FukayaChris HamlettKeisha HearnSteve HiscockRhian Holvey
Satoru ItoChristopher N. JohnsonYasuo KodamaKenichi MatsuoYoko NakatsuruNick PalmerAmanda PriceTadashi ShimamuraJeffrey D. St. DenisNicola G. WallisGlyn Williams
Affiliation: Astex Taiho