Spatial overlap of peptide hotspots and canonical drug pockets in a model enzyme. From molecular display peptides to small molecule inhibitors.

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1 partnerships in biologics discovery Spatial overlap of peptide hotspots and canonical drug pockets in a model enzyme Walraj S. Gosal June 205 From molecular display peptides to small molecule inhibitors. In collaboration with: With funding from:

2 Display technology is pivotal for biologics discovery Humira (monoclonal antibody) is the biggest selling drug worldwide ($3bn in sales). Primary seq. 00 amino acid protein = x0 30 sequences Humira FAB Approved: RA, UC, CD fold into precise 3D structures TNFα" chemical reactions of life through the precise arrangement & dynamics of atoms Computational approaches are showing evermore promise (e.g. Rosetta),2. Design Crystal structure Kuhlman,B. et al. Science (2003). 2 Fleishman,S.J. et al. Science (20). 2

3 Display technology is pivotal for the emergence of biologics Recent emergence of over a dozen scaffolds ranging in size (~ 20 to 70 amino acids),2. Humira FAB DARPin Approved: RA, UC, CD TNFα" Anticalin e.g. PRS-050 (Phase I: angiogenesis) e.g. Abicipar pegol (Phase III: macular degeneration) Adnectin / Centyrin e.g. Angiocept (phase II glioblastoma) Affibody e.g. SOBI002 (Phase I: inflammation) Knottin e.g. Ziconotide (Approved: pain relief) Lofblom,J. et al. Current Opinion in Biotechnology (20). 2 Gronwall, C. et al. Journal of Biotechnology (2009).

4 pept random library Display technology is pivotal for biologics discovery Basic idea is to enrich phenotypes in a library and be able to read genotypes. CIS Display2-4 First described by George Smith in 985 using bacterial filamentous phage (phage display). Incubation with PCR amplification of binders random library random library Smith,G.P. 4Patel,S. random library In vitro transcription & translation Science (985). 2Odegrip,R. et al. PNAS (2004).3Eldridge,B. et al. Protein Eng. Des. Eng. (2009). et al. Protein Eng. Des. Eng. (203). 4

5 CIS display & NGS random peptide library selection, amplifiction & NGS. CIS display & NGS Protein VLSEGEWQLVLHVWAKVEADV peptide site I 05 AQGAMNKALELFRKDIAAKYK site II peptide Residue hotspots & field calculation 3. Structure determination Computation (mutational analysis, Rosetta, & XED force field) (NMR or X-ray) VLSEGEWQLVLHVWAKVEADV 05 AQGAMNKALELFRKDIAAKYK site II h2 5. Virtual molecule (>07 small m -ve/hbd h3 Target-binding peptide candidates 2. Peptide hit validation (ELISA, truncation, binding, activity, epitope mapping) h & screening site I random peptide library Small&-binding peptides 4. selection, amplifiction NGS 2. Peptide hit validation (ELISA, truncation, binding, activity, epitope mapping). CIS display & NGS Target-binding peptide candidates rget X-ray / NMR Can molecular display be used to inform small molecule discovery? VdW surface h4 +ve/hba hydrophobic Small -binding peptides 3. Structure determination (NMR or X-ray) Peptide field map 6. Focused experimental screen O H N NH O H N OH O

6 Target of choice: thrombin - a serine protease 40 year race in the drug industry to replace anticoagulants - Warfarin (953) & Heparin (937),2. Large body of public information that covers all major discovery platforms (fragment screening, structurebased design & HTS). S S S S2 S4 S2 S4 S2 S4 Substrate: FPA Dabigatran Melagatran Unique structure based solutions from Nature 3. s-variegin 3 (32 aa) Tropical bont tick Anophelin 3 (3 aa) Mosquito Hirudin 3 (65aa) Medicinal leech Gustafsson,D. Nature Reviews Drug Discovery (2004). 2 Nar, H. Trends in Pharm. Sci (202). 3 Huntington, J. A. Thromb. Haemost., (204). 6

7 Summary & Acknowledgements. In a retrospective study, CIS display peptide hot-spots spatially overlap with known drug pockets in thrombin, although novel pockets are induced. 2. Peptides cover the chemical solution space for the primary S pocket. 3. Field patterns based on peptides can be used to find new inhibitors. Chris Ullman Neil Cooley Kevin Matthews Gabriela Ivanova Amanda Hallott Shabana Vohra Contact Walraj S. Gosal walraj.gosal@isogenica.com Steve Gardner Dirk Gewert Peter Campbell Robert Scoffin Andy Vinter Mark Mackey Gordon Woodrow Stephan Krapp Tom Blundell Jim Huntington Ty Adams With funding from: 7