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 2

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 Biologics Limited to targets outside the cell (10%) Limited to targets with hydrophobic pockets (10%) 3

Nature s Solution to Undruggable Targets Rapamycin and FKBP cooperate to bind a flat, funcfonal surface of mtor A B Rapamycin C Rap FKBP 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 mtor 4

How Does Nature Achieve the Impossible? By Mimicking Typical Protein-Protein Interactions hgh:hghr1 Common Characteristics of Many ProteinProtein Interactions Hotspot residues Non-hotspot residues Flat protein-protein interface Non-hydrophobic residues around the periphery contribute to selectivity Large contact surface area 1,200-2,000 Å2 High surface complementarity Central hydrophobic residues provide most of the binding energy ( hydrophobic hotspot ) Hydrophobicity 1. Adapted from Clackson, T., Wells, J., J Mol Biol 1998; Lo Conte, L., Chothia, C., Janin, J., J Mol Biol 1999 5

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 mtr FRB Domain Hydrophobic Hotspot Rapamycin Hydrophobicity 6

Cooperative Binding Mimics Natural ProteinProtein Interactions Rapamycin, FKBP12 each contributes ~half of the contact surface area w/ mtor Total contact surface area (~1,550 Å2) comparable to natural PPIs mtor mtor residues that interact with FKBP12 (780 Å2) mtor residues that interact with Rap (790 Å2) Note: FKBP12 not shown 7

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 CEP25011.4 8

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 9

How Nature Reprograms Target Selectivity Variable Region: Target Binding Constant Region: FKBP Binding H H H H N H H H H H N H H H H N H H H FK506 (Calcineurin) Rapamycin (mtor) WDB002 (CEP250) 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 10

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 Calcineurin T28 D33 K35 K36 F37 S39 R41 D42 N44 P46 Q54 FKBP12 (unbound) 7 Calcineurin 5 G20 T22 F49 K53 M50 CEP250 mtr P89 G90 I91 R43 K45 K48 H88 3 T86 Y83 G87 mtr CEP250 11

FKBP is Adaptable: Even Shared Residues Play Different Roles R43 H88 CEP250 t CEP250 Val K48 Ser Gln mtr mtr K45 Phe Tyr R43 Asp Arg Calcineurin Asn Lys Leu Gln H88 I91 G90 P89 Calcineurin Pro Tyr 12

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 13

Cyclophilins: A Parallel Universe CYPA/Cyclosporine/Calcineurin CYPA interface Cyclosporine interface 14

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 15

Small Molecule Assisted Receptor Targeting SMART Drugs: Engineering a New Modality 16

Two Presenters, Two Paths for SMART Drugs FKBP12 FK Cy Cyclophilin A 17

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 18

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 19

Mid-Scale Library Approaches (10^5) Cyclophillin Presented Library N N N H H H N N H 50,000 CsA-alogs synthesized to date N N H Boc FKBP Presented Library Cyclosporine Constant Region 1) 2) 3) 4) pool at stage of resins HTS H Bn N Ac Rapamycin Constant Region PepFde synthesis 20

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 21

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 22

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 23

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 24

Synthetic Crystallography: Concept Target 25

Synthetic Crystallography: Workflow S S N + H S / S S / Presenter Presenter + Ligand Target + Cys SyntheCc Complex Structure-Based Drug Design Crystal Structure w/o Linker CrystallizaCon Screening 26

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 27

Extensive Contact Surface Area Mimics Natural PPI, Drives Structure-Based Design Buried Surface Area (BSA) created by ternary complex formacon BSA (Å2) 3,500 Ligand Proteins 3,000 2,500 ~1,400 Å2 2,000 1,500 1,000 500 0 Cn mtr CEP250 G12C KRas FKBP12 Ligand 28

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 Å2 RalGDS BSA = 1,201 Å2 PI3K BSA = 1,305 Å2 29

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) 30

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 ther examples in early stages: PTP1b, Mcl1, beta-catenin Warp Drive is building pipeline of SMART Drugs -- independently and with partners 31