Bump-‐and-‐hole and PROTACs Alessio Ciulli School of Life Sciences, University of Dundee ELRIG Drug Discovery 2016, Liverpool 14th October 2016 TargeBng Protein-‐Protein InteracBons (PPIs) with Chemical Probes Context and Vision Chemical probes to study biology and to aid therapeuBcs Drugs DNA CRISPR RNA RNAi Protein AnIbodies Chemical Probes Receptor ligands Enzyme inhibitors Nat. Rev. Drug Discov 2002, 1, 727 Drug Discov. Today 2005, 10, 1607 ! " protein-protein networks protein-protein complexes # challenging targets ~1,000 Å2 Transcription factors posttranslational Regulatory complexes modifications Multisubunit enzymes …. TargeBng Protein-‐Protein InteracBons (PPIs) with Chemical Probes Context and Vision Chemical probes to study biology and to aid therapeuBcs Drugs DNA RNA Protein CRISPR RNAi AnIbodies Chemical Probes commentary Nature America, Inc. All rights reserved. The promise and peril of chemical probes Cheryl H Arrowsmith1,2, James E Audia3, Christopher Austin4, Jonathan Baell5, Jonathan Bennett6, Julian Blagg7, Chas Bountra8, Paul E Brennan8,9, Peter J Brown1, Mark E Bunnage10, Carolyn Buser-Doepner11, Robert M Campbell12, Adrian J Carter13, Philip Cohen14, Robert A Copeland15, Ben Cravatt16, Jayme L Dahlin17, Dashyant Dhanak18, Aled M Edwards1*, Stephen V Frye19, Nathanael Gray20, Charles E Grimshaw21, David Hepworth10, Trevor Howe22, Kilian V M Huber23, Jian Jin24–26, Stefan Knapp8,9, Joanne D Kotz27, Ryan G Kruger28, Derek Lowe29, Mary M Mader12, Brian Marsden8, Anke Mueller-Fahrnow30, Susanne Müller8,9, Ronan C O’Hagan31, John P Overington32,33, Dafydd R Owen10, Saul H Rosenberg34, Brian Roth35, Ruth Ross36, Matthieu Schapira1,36, Stuart L Schreiber27, Brian Shoichet37, Michael Sundström38,39, Giulio Superti-Furga23,40, Jack Taunton41,42, Leticia Toledo-Sherman43, Chris Walpole44, Michael A Walters45, Timothy M Willson35,46, Paul Workman7, Robert N Young47 & William J Zuercher35,46 Chemical probes are powerful reagents with increasing impacts on biomedical research. However, probes of poor quality or that are used incorrectly generate misleading results. To help address these shortcomings, we will create a community-driven wiki resource to improve quality and convey current best practice. A bout a decade ago, academia substantially increased its efforts in chemical biology and drug discovery. These efforts arose in part because of the availability of large numbers of uncharacterized potential drug targets emerging from genome sequencing efforts, from the development and commoditization of new screening technologies and from the possibility of inventing new medicines. Some of these efforts, perhaps in appreciation of the complexity and as powerful research tools and as seeds to spur the development of new medicines (Table 1). Second, chemical reagents, akin to any other protein-targeted reagent, are only useful if they are potent, have known selectivity and have a proven mechanism of action. During the past decade, we have gained a greater appreciation that probes of this quality are difficult to produce and require substantial resources, commitment and skills. We learned that many of the occurring artifacts in chemical screening and chemical biology3,7 and countless ‘case-by-case’ papers describing the serious deficiencies of specific chemical probes, nonselective and/or poorly characterized compounds continue to be widely used. Thus, the evidence suggests that the literature is an ineffective vehicle to provide guidance to the community about the quality of new chemical probes or to reduce the use of low-quality chemical probes. We argue that a complementary approach is Nat. Chem. Biol. 2015, 11, 536 O H N O N Adequate characterizaIon of chemical probes is paramount to aid reproducible results A major challenge lies in achieving target selecIvity and establishing on-‐target acIvity Challenges to Chemical GeneBcs for EpigeneBcs • Growing understanding of the links between epigeneIc effector proteins and disease 3. Probe selecBvity. Domains are clustered in large families with highly conserved binding sites 1. Complex phenotypic changes 2. Cell-‐type, cell-‐state dependent Runcie et al. Curr. Opin. Chem. Biol. 2016, 33, 186 Talk outline 1. Engineering selecBvity: Allele-‐specific inhibiBon 2. Added layer of selecBvity: From inhibitors to degraders PROTAC Ligand for E3 ligase VHL Science, 2014, 346, 638 J. Med. Chem., 2016, 59, 1492 linker BET Bromodomain Inhibitor proteasome ubiquitin VHL$ E3$ Brd4$ Brd4$ ACS Chem. Biol., 2015, 10, 1770 Talk outline 1. Engineering selecBvity: Allele-‐specific inhibiBon 2. Added layer of selecBvity: From inhibitors to degraders PROTAC Ligand for E3 ligase VHL Science, 2014, 346, 638 J. Med. Chem., 2016, 59, 1492 linker BET Bromodomain Inhibitor proteasome ubiquitin VHL$ E3$ Brd4$ Brd4$ ACS Chem. Biol., 2015, 10, 1770 BET bromodomain proteins and BET inhibitors Bromo and Extra-‐Terminal (BET) proteins BRD2 BRD3 BRD4 BRDT BD1 BD2 BD1 BD2 BD1 BD2 BD2 BD1 ET ET ET ET H4 pepIde Kac binding pocket BET bromodomain Structurally conserved ~ 110 aa in size BET bromodomain proteins and BET inhibitors Bromo and Extra-‐Terminal (BET) proteins BRD2 BRD3 BRD4 BRDT BD1 BD2 BD1 BD2 BD1 BD2 BD2 BD1 Target genes TF ET RNA Pol-II ET MYC BCL2 …. ET ET Mediator H4 pepIde BD1 PTef-β BD2 N ET C BRD4 Kac binding pocket BET bromodomain Structurally conserved ~ 110 aa in size BET transcripBonal co-‐regulators, involved in many biological processes and linked to diseases including: Trends Biochem Sci, 2015, 40, 468 Cancer Nat Rev. Cancer 2012, 12, 465 Rare translocaIons e.g. BRD3 or BRD4 with NUT in NMC Cancer Genet Cyto. 2010, 203, 16 Obesity Nat Rev. Cancer 2012, 12, 465 InflammaIon J. Immunol. 2013, 190, 3670 Viral processes Cell 2014, 117, 349 amongst many others… BET bromodomain proteins and BET inhibitors Bromo and Extra-‐Terminal (BET) proteins N N O N N BRD2 BRD3 BRD4 BRDT BD1 BD2 BD1 BD2 BD1 BD2 BD2 BD1 O N NH O N S ET N N O ET ET I-‐BET762 Cl ET JQ1 Cl Filippakopoulos et al., Nature 2010, 468, 1067-‐1073; Nicodeme et al., Nature 2010, 468, 1119-‐1123. H4 pepIde Pubmed%search%for%"JQ1"%or%"JQ81"%or%"I8BET"%or% "BRD4"%or%"BET%bromodomains"% 180 No. of Publications 160 140 120 100 80 60 40 20 15 14 13 16 20 20 20 20 11 12 20 10 09 08 07 06 20 20 20 20 20 20 04 05 20 20 03 0 20 Kac binding pocket Year%of%Publica.on% BET bromodomain Structurally conserved ~ 110 aa in size 10 BET inhibitors in 18 running trials (NMC, AML, ALL and other solid/hematological cancers) Nat Rev. Drug Discov. 2014, 13, 337 Nat. Biotechnol. 2016, 34, 361 LimitaIon of BET inhibitors: lack of intra-‐BET selecIvity Target genes Pan-BET inhibitors MYC BCL2 …. BD1 BD2 N ET C Pan-inhibition of Brd2, Brd3 and Brd4 BET proteins • BET proteins and domains have different physiological roles (Shi & Vakoc, Mol. Cell. 2014) • Genome occupancy paherns of BET proteins not idenIcal (Anders et al. Nat Biotech. 2014) • TradiIonal geneIc techniques have proven challenging • The pleotropic role of BET proteins have raised concerns about safety of BET inhibitors • Need for selecBve targeBng of individual BET bromodomains A GOAL: to engineer controlled selecIvity of BET bromodomain chemical probes Pan-selective probe inhibits multiple targets B Synthesis Bump Approach: Bump-‐and-‐Hole (Schreiber, Clackson, Shokat, Gray) Mutation Hole C Mutant-selective probe inhibits single target Runcie et al. Curr. Opin. Chem. Biol. 2016, 33, 186 A bump-and-hole approach to engineer controlled selectivity of BET bromodomain inhibitors Matthias Baud Enrique Lin-Shiao L/G, L/A L/I V/A ! W/F W/H I-BET762 bound to Brd4-BD1 Baud, Lin-Shiao et al. Science, 2014, 346, 638 Baud, Lin-Shiao et al. J. Med. Chem., 2016, 59, 1492 A bump-and-hole approach to engineer controlled selectivity of BET bromodomain inhibitors Matthias Baud Enrique Lin-Shiao L/A Baud, Lin-Shiao et al. Science, 2014, 346, 638 Baud, Lin-Shiao et al. J. Med. Chem., 2016, 59, 1492 Leu BD* Ala L/A mutant ! I-BET762 bound to Brd4-BD1 BD • • • stable retains histone binding and Kac selectivity pattern functionally silent NN N NOO NN N OO I KHMDS THF -78 °C 10-56% 19-56% NN (+-)-IBET O O Cl N O N O N O ET shows 40–540 fold (average 160) overall selecBvity for L/A vs WT across the enBre BET subfamily * L/A mutants Cl Wild-‐types Cl = 0" ΔTm"/"degrees"C" 5" 10" I-‐BET762 iBET% ME% BD1"L/A" ET% O BD1"WT" BD2"WT" N N O N N BD2"L/A" O ET Cl PR% cPR% Matt Baud, Enrique Lin-Shiao ET vs L/A Kd = 85 nM ET vs WT Kd = 20 µM O N N O N N Cl O ET X-‐ray crystal structures confirm “bump-‐and-‐hole” design raIonale Brd2(BD2) L383A mutant Co-‐crystallized with ET bound 1.7 Å res. Baud, et al. Science, 2014, 346, 638 Cynthia Tallant SelecIvity of ET is validated in vitro within tandem BET bromodomain constructs Teresa Cardote WT/WT + iBET WT/WT + ET LA/WT + ET WT/LA + ET LA/LA + ET Baud, et al. Science, 2014, 346, 638 n Kd (nM) 1.8 360 n.d. >10,000 1.0 150 1.0 140 1.9 24 Fluorescence Recovery Aser Photobleaching (FRAP) in U2OS cell nuclei EGFP-Brd4 10 µm bleach event WT/WT + DMSO! WT/WT + 1µM iBET! WT/WT + 1µM ET! LA/WT + 1µM ET! WT/LA + 1µM ET! LA/LA + 1µM ET! Annica Pschibul t = 1.5s t = 3.2s • TargeIng BD1 is sufficient to displace Brd4 from chromaIn 4! n.s. * *** *** 3! *** 2! t = 15.4s t1/2 (seconds)! pre-‐bleach 1! LA/WT WT/LA LA/LA WT/WT ET I-‐BET ET DMSO 1 µM 1 µM 1 µM BD1 0! N ET BD2 C A revised model Baud, et al. Science, 2014, 346, 638 Summary – Part 1 ‘Bumping’ selecIvity onto BET inhibitors • • • • Developed and opImized bump-‐and-‐hole vs a PPI target Developed new syntheIc routes to triazolo-‐BZP analogues Applied the approach to dissect the role of individual PPIs Extension to other bromodomains / epigeneIc reader families warranted • New tool for enhanced validaIon of BET proteins as targets N N N O S N O A single Target is inhibited Cl Selective Target inhibition Talk outline 1. Engineering selecBvity: Allele-‐specific inhibiBon 2. Added layer of selecBvity: From inhibitors to degraders PROTAC Ligand for E3 ligase VHL Science, 2014, 346, 638 J. Med. Chem., 2016, 59, 1492 linker BET Bromodomain Inhibitor proteasome ubiquitin VHL$ E3$ Brd4$ Brd4$ ACS Chem. Biol., 2015, 10, 1770 Natural pathway S Ub Ub Ub proteasome E2 SRS r to Adap RING Cullin S = Substrate SRS = Substrate RecogniIon Subunit = Post-‐translaIonal modificaIon Cullin RING E3 ligases (>200 in humans; up to 20% of proteasome-‐dependent degradaIon can be CRL-‐dependent) (Deshaies, PavleIch, Zheng, Schulman, Peters, Bullock et al.) Natural pathway S Ub Ub Ub Ub proteasome E2 SRS tor Adap RING Cullin S = Substrate SRS = Substrate RecogniIon Subunit = Post-‐translaIonal modificaIon Cullin RING E3 ligases (>200 in humans; up to 20% of proteasome-‐dependent degradaIon can be CRL-‐dependent) (Deshaies, PavleIch, Zheng, Schulman, Peters, Bullock et al.) Natural pathway proteasome E2 SRS tor Adap RING Cullin Proteolysis TargeIng Chimeras (PROTACs) (Crews, Deshaies, Sakamoto) Ligand for E3 Ligand for Target Linker Target Ub Ub Ub E2 RING SRS r to Adap Cullin Natural pathway proteasome E2 SRS RING Cullin tor Adap Proteolysis TargeIng Chimeras (PROTACs) 2nd generation PROTAC.2 b) Ligand for E3 Ligand for Target Linker AR ligand Target Ub Ub Ub H poly-Arg tag HN H ALA(Hyp)YIP-(D-Arg)8 O E2 RING SRS r O H Ub NH O to Adap (Crews, Deshaies, Sakamoto) O H Cullin heptapeptide HIF-1α motif O (2001-‐2005) Design and optimization of VHL ligands (2010-2014) Dennis Buckley (Yale) J. Am. Chem. Soc. 2012 134, 4465 Chem. Biol. 2012 19, 1300 Angew. Chem. Int. Ed. 2012 51, 11463 Inge David van Molle Dias (Cambridge) ACS Med. Chem. Lett. 2014, 5, 23 J. Med. Chem. 2014, 57, 8657 unpublished Kd (µM) LE 5.0 0.24 1.0 0.26 0.18 0.04 0.28 0.28 Hif-1α peptide bound to VHL ! capped-Hyp Structure-based design >60 ligand-bound structures OH S OH O N Group Efficiency N H N O O N H O O NH LHS Hyp RHS1 RHS2 • Initiated collaboratively with the Crews Lab (2010-12) • Led to founding of GSK DPU and Arvinas (2013) N O VH032 N 1" 0" N O Kd = 180 nM NHA = 33; MW = 472 Da LogD7.4 = 0.62; cLogP = 1.7 Morgan Carles Gadd Galdeano (Dundee) Galdeano et al. J. Med. Chem, 2014, 57, 8657 (top most read arBcle in J. Med. Chem. for 2015) VHL Cul2 E3 ubiquitin ligase and hypoxic signalling OH PHD inhibitors IOX-2, FG-4592 S N O N H O NH O VHL inhibitors HRE EPO N VHL Cul2 E3 ubiquitin ligase and hypoxic signalling OH PHD inhibitors IOX-2, FG-4592 S N O N H O NH O VHL inhibitors HRE EPO N Discovery of VH298, a potent and selecIve VHL inhibitor as chemical probe of the hypoxic signalling pathway OH Time (min) S N O NC NH O 0 NH N 10 20 30 40 0.00 O Carles Galdeano CollaboraIon with Sonia Rocha, Doreen Cantrell, Kevin Read (SLS Dundee) and Paola Grandi (Cellzome-‐GSK) Frost et al., Nature Comm. In Press ITC -0.50 0.0 kcal mol of injectant -1 50 -8 Morgan Gadd -0.30 -0.40 0 Pedro Soares -0.20 Kd = 80 nM 100 % D is p la c e m e n t Julianty Frost FP µcal/sec -0.10 VH298 -7 -6 -5 -2.0 -4.0 AcIve trans InacIve cis -6.0 -4 0.0 lo g [ V H L in h ib it o r s ] 0.5 1.0 Molar Ratio SPR X-ray koff = 0.065 s-1 VH298 1.5 2.0 Discovery of VH298, a potent and selecIve VHL inhibitor as chemical probe of the hypoxic signalling pathway proteasome inhibitor HeLa 2 hr VH298 (µM) PHD inhibitors (100 µM) 250 148 HIF-1α (low) 98 250 148 HIF-1α (high) 98 250 148 98 50 Frost et al., Nature Comm. In Press HIF-1α-OH β-actin Discovery of VH298, a potent and selecIve VHL inhibitor as chemical probe of the hypoxic signalling pathway HIF-target genes CTLs – GLUT1 VH032 VH298 cis-‐VH032 cis-‐VH298 RelaBve EPO mRNA levels in RCC4 cells RelaBve mRNA levels 5 RCC4 – EPO producBon 4.5 4 3.5 3 2.5 2 1.5 1 0 50 100 150 200 ConcentraBon (µM) Frost et al., Nature Comm. In Press 250 3.50 DMSO VH298 * 3.00 2.50 2.00 1.50 1.00 0.50 0.00 HA HA-‐VHL Discovery of VH298, a potent and selecIve VHL inhibitor as chemical probe of the hypoxic signalling pathway HIF-target proteins HFF 24 hr; 100 µM 148 HIF-1α 98 148 HIF-2α 98 64 64 CA9 GLUT1 50 50 Frost et al., Nature Comm. In Press β-actin Discovery of MZ1, a selective Brd4 degrader Michael Zengerle Kwok-Ho Chan JQ1 MZ1 PROTAC Ligand for E3 ligase VHL linker BET Bromodomain Inhibitor proteasome ubiquitin VHL$ E3$ Brd4$ Brd4$ Zengerle et al, ACS Chem Biol, 2015, 10, 1770 VHL ligand Discovery of MZ1, a selective Brd4 degrader Michael Zengerle MZ1 MZ1 retained binding affinities of JQ1 and VH032 for BET-brd and VHL, respectively EGFP-Brd4 MZ1 Brd4 Kwok-Ho Chan Brd3 Brd2 EGFP-Brd4 β-Actin siRNA (48h) Compound (1 µM, 24h) mock Brd2 Brd3 cisMZ1 Brd4 cisMZ1 vehicle MZ1 JQ1 vehicle U2OS, 4h treatment Zengerle et al, ACS Chem Biol, 2015, 10, 1770 Discovery of MZ1, a selective Brd4 degrader DMSO MZ1 (24 hr) 10 µM 100 nM MZ1 BRD4 Brd4 BRD3 Brd3 BRD2 Brd2 β-‐AcIn β-Actin 0 4 8 12 16 24 36 (h) MZ1 preferenIally degrades Brd4 over Brd2 and Brd3 • MZ1 affects fewer genes compared to JQ1 in cancer cells, consistent with selective Brd4 knockdown Zengerle et al, ACS Chem Biol, 2015, 10, 1770 MZ1 treatment (1 µM) wash Brd4 long Brd4 short Brd3 Brd2 β-Actin 0 4 8 12 24 36 48 (h) Protein level recovered only 20 h aser compound wash: requires re-‐synthesis Zengerle et al, ACS Chem Biol, 2015, 10, 1770 OH N N O H N N S N O N O O N H O O N H O N S JQ1 VHL-binding moiety MZ1 Cl Zengerle et al. ACS Chem. Biol. 2015 H N HN N N O N O O O N NH O S JQ1 O N O dBET1 Winter, Buckley et al. Science 2015 Cl CRBN-binding moieties O O O O HN NH N N O N O N O N NH O S O ARV-825 Lu et al. Chem. Biol. 2015 Cl JQ1 OH O S O NH S O N O N O 4 N N H O O N H N S VHL-binding moiety PROTAC_RIPK2 Bondeson et al. Nat. Chem. Biol. 2015 OH N N O H N N S N O N O O N H O O N H O N S JQ1 VHL-binding moiety MZ1 Cl Zengerle et al. ACS Chem. Biol. 2015 H N HN N N O N O O O N NH O S JQ1 O N O dBET1 Winter, Buckley et al. Science 2015 Cl CRBN-binding moieties O O O O HN NH N N O N N O N NH O S “... the sky is the limit for PROTACs” Nat Chem Biol. 2015 Aug 18; 11:634-‐5 O O ARV-825 Lu et al. Chem. Biol. 2015 Cl JQ1 OH O S O NH S O N O N O 4 N N H O O N H N S VHL-binding moiety PROTAC_RIPK2 Bondeson et al. Nat. Chem. Biol. 2015 OH N N O H N N S N O N O O N H O O N H O N S JQ1 VHL-binding moiety MZ1 Cl Zengerle et al. ACS Chem. Biol. 2015 H N HN N N O N O O O N NH O S JQ1 O N O dBET1 Winter, Buckley et al. Science 2015 Cl CRBN-binding moieties O Press Release O O O HN NH N N O N N NH O Press Release th EMBARGOED: 14 July 2016, 10am (BST) Boehringer Ingelheim and University of Dundee collaborate to develop new class of medicines Collaboration aims to develop PROteolysis TArgeting Chimeric molecules (PROTACs) – a new therapeutic modality that is able to degrade proteins playing a central role in disease processes PROTACs and their new mechanism of action are expected to open new horizons for drug development allowing new drug targets to be accessible Research bears potential to develop innovative new treatment options for patients with high medical need Ellesfield Avenue Bracknell, Berkshire United Kingdom RG12 8YS Phone: +44 (0)1344 741155 Email: [email protected] ISDN: +44 (0)1344 311104 O ARV-825 Lu et al. Chem. Biol. 2015 Cl JQ1 OH O Contact: Boehringer Ingelheim Limited Communications O N S For UKttrade medical “... he s&ky is tmedia he lonly imit for PROTACs” Nat Chem Biol. 2015 Aug 18; 11:634-‐5 O S O NH S O N O N O 4 N N H O O N H N S VHL-binding moiety PROTAC_RIPK2 Bondeson et al. Nat. Chem. Biol. 2015 Outlook 1) inhibitor: N N O N S N O Several Targets are inhibited JQ1 Pan-inhibition Cl N 2) Bump and hole: N N O S N O A single Target is inhibited ET Cl Ad hoc selective inhibition 3) PROTAC: OH N O N H N N S N O O O O N N H O O S N H N MZ1 Cl A single Target is depleted Selective Target degradation Summary – Part 2 Turning inhibitors into selecIve degraders • ConjugaIng JQ1 to a VHL ligands yields PROTACs that induce preferenIal degradaIon of Brd4 leaving Brd2 and Brd3 untouched • MZ1 shows improvements over BET inhibitors as chemical probe and therapeuIc lead • Provides proof-‐of-‐concept for turning non-‐selecIve ligands into more selecIve degraders • Opportunity to validate the therapeuIc potenIal of degrading proteins using small molecules PROTAC A single Target is depleted Selective Target degradation Ciulli Laboratory Current members Anastasia Amato Alessio Bortoluzzi Elvira Bruno Teresa Cardote Guilherme Castro Kwok-‐Ho Chan Morgan Gadd Scoh Hughes Julianty Julianty Xavier Lucas Chiara Maniaci Ester Morreale Andrew Runcie Pedro Soares Andrea Testa Wei-‐Wei-‐Kung Funding Collaborators SGC Oxford: Stefan Knapp and colleagues at SGC Oxford Yale University: Craig Crews, Dennis Buckley and colleagues at Yale Cellzome: Paola Grandi, Marcus Batscheff and colleagues at Cellzome Dundee SLS: Dario Alessi, Doreen Cantrell, Axel Knebel, Kevin Read, Sonia Rocha, Helen Walden, DDU and colleagues Former members Ma}a Cocco Michael Zengerle Carles Galdeano Mahhias Baud Enrique Lian-‐Shiao Cynthia Tallant Annica Pschibul Jordi Rosello Lars van Beurden Inge Van Molle David Dias Emil Bulatov Fleur Ferguson Terence Kwan Charlohe Sutherell Mahhew Smith Sarah Hewih Lois Overvoorde Jemima Thomas Kyle Smith Ernie So
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