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WO 2017/070742 Al 4 May 2017 (04.05.2017) P O P C T

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WO 2017/070742 Al 4 May 2017 (04.05.2017) P O P C T (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2017/070742 Al 4 May 2017 (04.05.2017) P O P C T (51) International Patent Classification: Mark; c/- Phylogica Limited, 15 Lovegrove Close, Mount C07K 14/315 (2006.01) C12N 7/01 (2006.01) Claremont, Western Australia 6010 (AU). C07K 19/00 (2006.01) C12N 15/31 (2006.01) (74) Agent: FB RICE; Level 14, 90 Collins St, Melbourne, (21) International Application Number: Victoria 3000 (AU). PCT/AU2016/051017 (81) Designated States (unless otherwise indicated, for every (22) International Filing Date: kind of national protection available): AE, AG, AL, AM, 28 October 2016 (28.10.201 6) AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, (25) Filing Language: English DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (26) Publication Language: English HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, (30) Priority Data: MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, 2015904465 30 October 2015 (30. 10.2015) AU OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, (71) Applicant: PHYLOGICA LIMITED [AU/AU]; 15 Love- SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, grove Close, Mount Claremont, Western Australia 6010 TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, (AU). ZW. (72) Inventors: STONE, Shane Ramsay; c/- Phylogica Lim (84) Designated States (unless otherwise indicated, for every ited, 15 Lovegrove Close, Mount Claremont, Western Aus kind of regional protection available): ARIPO (BW, GH, tralia 6010 (AU). HEINRICH, Tatjana; c/- Phylogica GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, Limited, 15 Lovegrove Close, Mount Claremont, Western TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, Australia 6010 (AU). CUNNINGHAM, Paula; c/- Phylo TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, gica Limited, 15 Lovegrove Close, Mount Claremont, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, Western Australia 6010 (AU). BOGDAWA, Heique; c/- LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, Phylogica Limited, 15 Lovegrove Close, Mount Clar e mont, Western Australia 6010 (AU). HOFFMANN, Kat- GW, KM, ML, MR, NE, SN, TD, TG). rin; c/- Phylogica Limited, 15 Lovegrove Close, Mount Published: Claremont, Western Australia 6010 (AU). WATT, Paul; — with international search report (Art. 21(3)) c/- Phylogica Limited, 15 Lovegrove Close, Mount Clar e mont, Western Australia 6010 (AU). ANASTASAS, — with sequence listing part of description (Rule 5.2(a)) o o (54) Title: USE OF SPYCATCHER AS A PROTEIN SCAFFOLD FOR PEPTIDE DISPLAY; AND SPYCATCHER/SPYTAG o CYCLISED PEPTIDES DISPLAYED ON BACTERIOPHAGE (57) Abstract: Described herein is a modified SpyCatcher protein (comprising an amino acid sequence having at least 80% identity to SEQ ID NO: 1) wherein the modification comprises a peptide inserted into a region of the protein corresponding to amino acid residues 12- 22, 27-31, 38-43, 48-50 or 59-68 of SEQ ID NO: 1. Also described are bacteriophage particles displaying a chimeric protein comprising SpyCatcher, a peptide of interest, and SpyTag, where SpyCatcher and SpyTag are linked via an isopeptide bond. USE OF SPYCATCHER AS A PROTEIN SCAFFOLD FOR PEPTIDE DISPLAY; AND SPYCATCHER/SPYTAG CYCLISED PEPTIDES DISPLAYED ON BACTERIOPHAGE Technical Field The present disclosure generally relates to binding proteins and protein binding partners for display of peptides and various uses thereof. Background Peptides are attractive diagnostic and therapeutic targets due to their varied physiological roles and potentially high potency and target specificity. However, the identification and development of such peptides remains challenging. Peptides sometimes bind to their targets with modest affinity due to entropic thermodynamic reasons because the exhibit insufficient conformational constraint. While constraint may be conferred through cyclisation of the peptides, but this can involve complex chemistries which may not be feasible for the construction of large libraries. Many peptides when expressed in a host cell are susceptible to degradation by proteases and peptidases. This is normally because these peptides are unable to form stable tertiary structures. While one or more disulfide bonds may be added to increase the stability of certain peptides, disulfide bonds are susceptible to reduction in certain extracellular environments such as in blood and within cells. Moreover, a significant proportion of peptides that are stably expressed accumulate in insoluble aggregates. Peptides that are present in inclusion bodies may be misfolded, inactive and/or denatured. The process of obtaining bioactive peptides from inclusion bodies requires extensive processing comprising isolation, solubilization, refolding and purification. Peptides can sometimes be used as receptor binding domains (RBD) for targeting specific cell types and/or concentrating drugs to diseased tissues such as tumours. However, such peptide-derived RBDs are often unstable and can be challenging to conjugate to their payloads. In the in vivo diagnostics and drug conjugate fields, there exists a desirability to combine a protein based functionality (such as receptor targeting, or an effect on a biological target) with a synthetic peptide component which can be used as a 'handle' to attach a moiety such as an imaging probe or a small molecule toxin molecule, respectively. Accordingly, there remains an unmet need for a system for displaying a wide range of constrained peptides and methods for screening constrained peptide libraries useful in biological and therapeutic applications. Summary The present disclosure provides reagents and methods for displaying peptides, e.g., in a constrained form. Such reagents and methods can provide for additional stability of a peptide. The reagents and methods of the disclosure additionally permit modular production of proteins and complexes displaying a plurality of peptides. For example, a protein or complex of the disclosure may display a peptide capable of inhibiting an intracellular protein interaction and a cell penetrating peptide to allow for intracellular delivery. Similarly, a protein or complex of the disclosure may display a therapeutic agent or peptide and a peptide that is a receptor binding domain to allow for cell targeting and concentration on a disease tissue or cell of interest. Likewise a protein or complex of the disclosure could be used for diagnostic or theranostic purposes. The present disclosure also provides reagents and methods to facilitate screening for peptides having various biological activities. The present disclosure provides a complex comprising: a) a binding protein comprising an amino acid sequence having at least 80% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO: 1; b) a peptide; and c) a protein binding partner; wherein the binding protein is linked to the protein binding partner via a covalent isopeptide bond, the binding protein is linked a first terminus of the peptide and the peptide tag is linked to a second terminus of the peptide. In one example, the complex comprises: a) a binding protein comprising an amino acid sequence having at least 80% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO: 1; b) a peptide; and c) a protein binding partner; wherein the binding protein is linked to the protein binding partner via a covalent isopeptide bond, the binding protein is linked the N' terminus of the peptide and the peptide tag is linked to the C terminus of the peptide. In another example, the complex comprises: a) a binding protein comprising an amino acid sequence having at least 80% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO: 1; b) a peptide; and c) a protein binding partner; wherein the binding protein is linked to the protein binding partner via a covalent isopeptide bond, the binding protein is linked the C terminus of the peptide and the peptide tag is linked to the N' terminus of the peptide. In one example, the binding protein disclosed herein comprises an amino acid sequence having at least 95% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO: 1. For example, the binding protein disclosed herein comprises the amino acid sequence set forth in SEQ ID NO: 2. For example, the binding protein disclosed herein comprises the amino acid sequence set forth in SEQ ID NO: 3. For example, the binding protein disclosed herein comprises the amino acid sequence set forth in SEQ ID NO: 4. For example, the binding protein disclosed herein comprises the amino acid sequence set forth in SEQ ID NO: 5. For example, the binding protein disclosed herein comprises the amino acid sequence set forth in SEQ ID NO: 6. For example , the binding protein disclosed herein comprises the amino acid sequence set forth in SEQ ID NO: 7. For example, the binding protein disclosed herein comprises the amino acid sequence set forth in SEQ ID NO: 8. For example, the binding protein disclosed herein comprises the amino acid sequence set forth in SEQ ID NO: 9. For example, the binding protein disclosed herein comprises the amino acid sequence set forth in SEQ ID NO: 10. For example, the binding protein disclosed herein comprises the amino acid sequence set forth in SEQ ID NO: 11. For example, the binding protein disclosed herein comprises the amino acid sequence set forth in SEQ ID NO: 12. For example, the binding protein disclosed herein comprises the amino acid sequence set forth in SEQ ID NO: 13.
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