SMART Drugs Engineering Nature’s Solution to the Undruggable Target Challenge

SMART Drugs:
Engineering Nature’s Solution to the
Undruggable Target Challenge

Warp Drive’s Mission
To build the premiere company advancing
transformative medicines that harness the
molecules and mechanisms of Nature
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The Problem of Intractable Targets
80-90% of human proteins cannot be targeted by established modali:es
Universe of
potential targets
Small Molecule-Assisted
Receptor TargeCng
(SMART)
Small
Molecules
Limited to targets with
hydrophobic pockets
(10%)
Biologics
Limited to targets
outside the cell
(10%)
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Nature’s Solution to Undruggable Targets
Rapamycin and FKBP cooperate to bind a flat, funcFonal surface of mTor
A
B
Rapamycin
C
Rap|FKBP
mTor
• Cell-penetrant small molecule, creates a
composite surface that binds a flat
undruggable target surface
• Follows rules of naturally occurring
protein-protein interactions
• Binding is cooperativeà high affinity and
selectivity
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How Does Nature Achieve the ‘Impossible’?
By Mimicking Typical Protein-Protein Interactions
hGH:hGHR 1
Common Characteristics of Many Protein-
Protein Interactions
• Flat protein-protein interface
• Large contact surface area 1,200-2,000 Å 2
• High surface complementarity
• Central hydrophobic residues provide most
of the binding energy (‘hydrophobic hotspot’)
• Non-hydrophobic residues around the
periphery contribute to selectivity
Hotspot residues
Non-hotspot residues
Hydrophobicity
1. Adapted from Clackson, T., …Wells, J., J Mol Biol 1998; Lo Conte, L., Chothia, C., Janin, J., J Mol Biol 1999
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Hydrophobicity
Rap|FK Binding Follows the Rules of
Natural Protein-Protein Interactions
Rapamycin provides the missing hydrophobic hotspot to FKBP12;
Enables engagement of mTor’s hotspot normally reserved for substrate binding
mTOR FRB Domain
Hydrophobic Hotspot
Rapamycin
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Cooperative Binding Mimics Natural Protein-
Protein Interactions
• Rapamycin, FKBP12 each contributes ~half of the contact surface area w/ mTor
• Total contact surface area (~1,550 Å 2 ) comparable to natural PPIs
mTor
mTor residues that interact
with FKBP12 (780 Å 2 )
mTor residues that
interact with Rap (790 Å 2 )
Note: FKBP12 not shown
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No Target is Too Flat
• WDB has discovered mulFple Rapamycin family members w/ novel target selecFvity
• Example: WDB-002 cooperates with FKBP12 to bind with sub-nanomolar affinity to a
coiled-coil (an archetypal ‘undruggable’ structural moFf)
FKBP12
Kd = 290 pM
CEP250 11.4
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Nature Can Reprogram Target Selectivity
FKBP = 758 Å 2
Rap = 790 Å 2
=
FKBP
Rapamycin
Tor
FKBP/Rapamycin/Tor
=
FKBP
FK506
Calcineurin
FKBP/FK506/Calcineurin
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How Nature Reprograms Target Selectivity
Variable Region: Target Binding
Constant Region: FKBP Binding
HO
Me
Me
OMe
O
O
H H
O
OH
N
Me
H
O O
HO
O
Me
Me
OMe
OMe
HO
Me
OMe
Me
MeO
Me
O
O
H H
O
N
O
Me
OH
Me
H
O O
HO
O
Me
Me
O
O
H
N
HO
H
O O
HO
FK506 (Calcineurin) Rapamycin (mTor) WDB002 (CEP250)
Me
OMe
O
Me
Me
Me
Variable Region
Constant Region
v Like Mabs, members of the Rapamycin/FK506 family of natural products have a
variable and a constant region
v The variable region confers target specificity; The constant region confers presentation
v Unlike Mabs, these drugs are orally bioavailable and can access intracellular targets
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Surface of FKBP12 Adapts Itself to Multiple Targets
FKBP12 Uses a Distinct Repertoire of Residues to Engage Each Target
30+ available residues on FKBP12, each with mulFple rotamer states,
enable very high combinatorial diversity for target recogniFon
FKBP contact residues
11
T28
D33 K35 K36 F37
S39 R41 D42 N44
P46 Q54
Calcineurin
FKBP12
(unbound)
Calcineurin
5
G20 T22
F49 K53
M50
7
P89 G90
I91 R43 K45
K48 H88
3
Y83
T86
G87
CEP250
mTOR
mTOR
CEP250
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FKBP is Adaptable:
Even Shared Residues Play Different Roles
R43
Met
CEP250
H88
Val
CEP250
Gln
K48
Ser
mTOR
K45
Phe
mTOR
Leu
Tyr
Asp
Gln
Calcineurin
Asn
Lys
R43
H88
I91
G90
P89
Tyr
Arg
Calcineurin
Pro
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Prolyl Isomerases (e.g., FKBP12) Are
Ideally Suited to Generalize the Modality
Abundant: Favorable stoichiometry vs. most targets of interest
Ubiquitous: Present in most/all tissue types
Safe: Minimal effect of inhibiting native function
Adaptable: Capable of engaging diverse protein surfaces
Selective: Capable of engaging protein surfaces selectively
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Cyclophilins: A Parallel Universe
CYPA/Cyclosporine/Calcineurin
CYPA interface
Cyclosporine interface
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Key Characteristics of SMART:
“Nature’s Modality”
• Combines advantages of small molecules (cell penetrant) and protein
therapeutics (able to engage flat surfaces) to bind ‘undruggable’ targets
• The modality is clinically validated: Three approved drugs exploit the binding
modality (Rapamycin, FK506, Cyclosporine)
• Follows rules of naturally occurring protein-protein interactions
o binding to functional hydrophobic hotspots
o cooperative binding mode, achieving high affinity and selectivity
• Exploits inherent adaptability of presenter protein binding surface
• Target selectivity of the modality is reprogrammable by modifying the variable
region of the small molecule
Warp Drive is Engineering this Modality to
Develop SMART Drugs with these Attributes
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Small Molecule Assisted Receptor Targeting
SMART Drugs:
Engineering a New Modality
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Two Presenters, Two Paths for SMART Drugs
FKBP12
FK
Cy
Cyclophilin A
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Two-Pronged Proprietary Discovery Platform
Screening Large Diverse SMART Libraries
SMART Structure-Based Design
Large-scale library of compounds (10 6 ) all capable
of high affinity binding with FKBP but with highly
diversified variable regions
FKBP
HT screening of library
for Target binding
Variable Region
…
Millions of
compounds
Target
FKBP
Target
Target
1. SyntheFc Crystallography
to solve Presenter-Target
Interface
2. Structure-Based Drug
Design to build Ligand-
Target interface
Novel hits and binding ligands to enable
hit-to-lead medicinal chemistry
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Two-Pronged Proprietary Discovery Platform
Screening Large Diverse SMART Libraries
SMART Structure-Based Design
Large-scale library of compounds (10 6 ) all capable
of high affinity binding with FKBP but with highly
diversified variable regions
FKBP
HT screening of library
for Target binding
Variable Region
…
Millions of
compounds
Target
FKBP
Target
Target
1. SyntheFc Crystallography
to solve Presenter-Target
Interface
2. Structure-Based Drug
Design to build Ligand-
Target interface
Novel hits and binding ligands to enable
hit-to-lead medicinal chemistry
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Mid-Scale Library Approaches (10^5)
Cyclophillin Presented Library
Me
Me
N
Me
Me O
N
N
O Me
OH
H H
N
O
O
N
Me
O
OH
50,000 CsA-alogs synthesized to date
O
Me
N
O
Me
N
H
Boc
FKBP Presented Library
Cyclosporine
Constant Region
1)
2)
3)
4)
pool at stage of resins
HTS
O
HO
Me
OBn
N
O
O
O
OMe
OAc
Rapamycin
Constant Region
PepFde
synthesis
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Primary Screening Assay: TR-FRET
Excita-on
Eu-α-His
(donor)
SA-APC
(acceptor)
TR-FRET
665 nm
Emission
615 nm
His-KRAS
BioCn-CypA
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Confirmed Screening Hits Against KRAS
Ternary Complex FormaFon
(Presenter|Ligand|KRAS)
Average: 91.2%
Hits = above 129.7% (3σ)
EC-50 ~ 1.2 uM
% ternary background
Pool
• ~50k CsA-alog compounds
screened to date
• Confirmed hit rate for singleton ~
0.06%
• Confirmed Hits Identified:
o
o
o
o
Presenter-dependent and targetspecific
binding
EC-50s ≤ 10 uM
Cell penetrant with in cellulo
presenter protein engagement
Further Hit validation in progress
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Large-Scale Library Approach (10^6)
Ligand Assisted Ternary-complex Identification Screen (LATIS)
Target Protein
CYPA
LATIS
CsA-log sub-library
pool (1,300 cmpds)
Size Exclusion
Chromatography
Screen in pools
Isolate Ternary Complex Area
& Analyze by LC-MS/MS for
CsA-log ID
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Two-Pronged Proprietary Discovery Platform
Screening Large Diverse SMART Libraries
SMART Structure-Based Design
Large-scale library of compounds (10 6 ) all capable
of high affinity binding with FKBP but with highly
diversified variable regions
FKBP
HT screening of library
for Target binding
Variable Region
…
Millions of
compounds
Target
FKBP
Target
Target
1. SyntheFc Crystallography
to solve Presenter-Target
Interface
2. Structure-Based Drug
Design to build Ligand-
Target interface
Novel hits and binding ligands to enable
hit-to-lead medicinal chemistry
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Synthetic Crystallography: Concept
Target
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Synthetic Crystallography: Workflow
O
H
N
S
S
N
+
O
H
N
H S
S
N
/
S
S
/
Presenter
Presenter + Ligand
Target + Cys
SyntheCc Complex
Structure-Based Drug Design
Crystal Structure w/o Linker
CrystallizaCon Screening
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Solving the Structure of KRAS-FKBP Ternary
Complex to Enable SMART
WDB is analyzing x-ray structure of FKBP12-bound, GTP-KRAS to drive
medicinal chemistry
FKBP12
FKBP12
K-Ras
K-Ras
ResoluFon: 1.4 Å
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Extensive Contact Surface Area Mimics Natural
PPI, Drives Structure-Based Design
Buried Surface Area (BSA) created
by ternary complex formaCon
BSA (Å 2 )
3,500
3,000
Ligand
Proteins
2,500
2,000
~1,400 Å 2
1,500
1,000
500
0
Cn mTOR CEP250 G12C
KRas
FKBP12
Ligand
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FKBP Competes for RAS Effector Binding Site
FKBP12 binds to the effector surface of KRAS, blocking access to
mulFple effectors
FKBP12
KRAS
B-Raf
BSA = 1,053 Å 2
RalGDS
BSA = 1,201 Å 2
PI3K
BSA = 1,305 Å 2
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Target Classes Accessible To SMART TM : Examples
• GTPases (e.g., RAS)
• Transcription factors (e.g., MYC)
• Phosphatases (e.g., PTP1b)
• Intracellular domains of cell-surface receptors (e.g., TNFR, IL-17R)
• Nuclear receptors (e.g., androgen receptor)
• Intracellular signaling PPIs (e.g., SHP2)
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Summary
• Nature has evolved a general mechanism to inhibit flat protein surfaces
o Pharmaceutically validated
o Exogenous small molecule mobilizes a flexible intracellular surface
o Follows rules of natural protein-protein interactions
• Warp Drive has developed a proprietary platform to deploy this natural
mechanism to develop SMART Drugs against challenging targets
o Proof of platform principle with KRAS (multiple surfaces)
o Other examples in early stages: PTP1b, Mcl1, beta-catenin
• Warp Drive is building pipeline of SMART Drugs -- independently and
with partners
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