Chimeric proteins

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in text format and is hereby incorporated by reference in its entirety. Said text file, created on Mar. 17, 2020, is named 119691-10103 seq_listing.txt and is 1,111 kb in size.

FIELD

This invention relates to chimeric proteins and their production and uses.

BACKGROUND

A priority area in medicine, particularly cancer research, is the expansion of the ‘druggable’ proteome, which is currently limited to narrow classes of molecular targets. For example, protein-protein interactions (PPIs) are fundamental to all biological processes and represent a large proportion of potential drug targets, but they are not readily amenable to conventional small molecule inhibition. The architecture of tandem repeat proteins has tremendous scope for rational design (Kobe & Kajava 2000, Longo & Blaber, 2014, Rowling et al., 2015). The key features of tandem repeat proteins are relatively small size, modularity and extremely high stability (and therefore recombinant production) without the need of disulphide bonds. Individual consensus-designed repeats are self-compatible and can be put together in any order; function is therefore also modular, which means that multiple functions can be independently designed and incorporated in a combinatorial fashion within a single molecule (WO2017106728).

Novel repeat protein functions, e.g. DARPins (Tamaskovic et al., 2012), have been developed based on the natural type of PPI interface of these proteins i.e. spanning many repeat units to create an extended, high-affinity binding interface for the target. Mutations have been introduced into the surface residues in the tetratricopeptide (TPR) repeats of the cytosolic receptor peroxin 5 (Sampathkumar et al. (2008) J. Mol. Biol., 381, 867-880). Binding of peptide ligands to peroxin 5 is shown to be mediated by residues located in several different TPR repeats. The interactions of TPR containing protein kinesin-1 with different cargo proteins has also been reported (Zhu et al PLoS One 2012 7 3 e33943). The specificity and stability of ankyrin repeat proteins has been modified through the introduction of mutations into ankyrin repeat sequences (Li et al (2006) Biochemistry 45 15168-15178).

SUMMARY OF THE INVENTION

The present inventors have found that chimeric proteins which comprise peptidyl ligands, such as short linear motifs (SLiMs), on scaffolds. Such chimeric proteins (i.e., modular binding proteins), may be useful for example, as single- or multi-function protein therapeutics.

An aspect of the invention provides a chimeric protein comprising:

- a scaffold comprising a first end and a second end, and two or more repeat domains linked by inter-repeat loops between the ends; and
- one or more peptide ligands, wherein a single peptide ligand is located in the scaffold in (i), an inter-repeat loop, (ii) at the first end, or (iii) at the second end of the scaffold, thereby forming a chimeric protein (a grafted scaffold).

In a preferred embodiment, the scaffold is a continuous polypeptide strand such that the first end is the N terminus and the second end is the C terminus of the scaffold.

In some preferred embodiments, the chimeric protein may comprise a first peptide ligand that binds a first target molecule and a second peptide ligand that binds a second target molecule. One of the first or second target molecules may be an E3 ubiquitin ligase. Where a chimeric protein comprises two or more peptide ligands, the ligands are different ligands (bind to different targets) and are not located in the same loop or at the same end of a scaffold.

Another aspect of the invention provides a method of producing a chimeric protein comprising;

- inserting a first nucleic acid encoding a peptide ligand into a second nucleic acid encoding a scaffold comprising two or more repeat domains linked by inter-repeat loops, to produce a chimeric nucleic acid encoding a chimeric protein as described herein; and
- expressing the chimeric nucleic acid to produce the chimeric protein.

Another aspect of the invention provides a method of producing a chimeric protein that binds to a first target molecule and a second target molecule comprising;

- providing a nucleic acid encoding a scaffold comprising two or more repeat domains linked by inter-repeat loops, and
- incorporating into the nucleic acid a first nucleotide sequence encoding a first peptide ligand that binds to a first target molecule and a second nucleotide sequence encoding a second peptide ligand that binds to a second target molecule to generate a nucleic acid encoding a chimeric protein comprising the first and second peptide ligands, wherein the peptide ligands are independently located in an inter-repeat loop or at the N or C terminus of the chimeric protein; and
- expressing the nucleic acid to produce the protein.

In some preferred embodiments, one of the first or second target molecules is an E3 ubiquitin ligase.

In another aspect, the invention provides a chimeric protein, comprising

(i) a tetratricopeptide (TPR) scaffold comprising first and second α-helices linked by an inter-repeat loop, and,

(ii) a first heterologous peptide that binds to a target protein, and

(iii) a second heterologous peptide that binds to an E3 ubiquitin ligase, wherein the first and second heterologous peptides are, independently, located in an inter-repeat loop or at the N or at the C terminus of the chimeric protein.

In a preferred embodiment, each of the first and second α-helices comprises the amino acid sequence Y-X1X2X3X4; wherein Y is an amino acid sequence shown in Tables 4 to 6 and X1, X2, X3, X4 are independently any amino acid, and optionally wherein X1 is D and/or optionally wherein X2 is P.

In another preferred embodiment, the first and second α-helices each comprise the amino acid sequence:

(SEQ ID NO: 1)

AEAWYNLGNAYYKQGDYQKAIEYYQKALEL-X1X2X3X4;

or

(SEQ ID NO: 307)

AEALNNLGNVYREQGDYQKAIEYYQKALEL-X1X2X3X4;

or

(SEQ ID NO: 2)

AEAWYNLGNAYYRQGDYQRAIEYYQRALEL-X1X2X3X4;

or

(SEQ ID NO: 3)

AEALNNLGNVYREQGDYQRAIEYYQRALEL-X1X2X3X4;

or

(SEQ ID NO: 308)

AEALRNLGRVYRRQGRYQRAIEYYRRALEL-X1X2X3X4,

wherein X1, X2, X3, X4 are independently any amino acid, and optionally wherein X1 is D and/or optionally wherein X2 is P.

In another preferred embodiment, the chimeric protein comprising third, fourth and fifth TPR repeats.

The invention also provides a chimeric protein comprising

(i) a TPR scaffold comprising first and second α-helices linked by an inter-repeat loop, and,

(ii) a heterologous peptide ligand that binds an E3 ligase, wherein the heterologous peptide is located in an inter-repeat loop or at the N or at the C terminus of the chimeric protein.

The invention also provides a chimeric protein comprising

(i) a TPR scaffold comprising first and second α-helices linked by an inter-repeat loop, and,

(ii) a heterologous peptide ligand that binds a target protein,

- wherein the heterologous peptide ligand is located in an inter-repeat loop or at the N or at the C terminus of the chimeric protein.

Another aspect of the invention provides a library comprising chimeric proteins, each chimeric protein in the library comprising;

- (i) two or more repeat domains,
- (ii) inter-repeat loops linking the repeat domains; and
- (iii) one or more peptide ligands, each the peptide ligand being located in an inter-repeat loop or at the N or C terminus of the chimeric protein,
  - wherein at least one amino acid residue in the peptide ligands in the library is diverse.

Another aspect of the invention provides a library comprising a first and a second sub-library of chimeric proteins, each chimeric protein in the first and second sub-libraries comprising;

- (i) two or more repeat domains,
- (ii) inter-repeat loops linking the repeat domains; and
- (iii) a peptide ligand comprising at least one diverse amino acid residue, wherein the peptide ligand in the chimeric proteins in the first sub-library binds to a first target molecule and is located in one of (i) an inter-repeat loop; (ii) the N terminus or (iii) the C terminus of the chimeric protein, and
- the peptide ligand in the chimeric proteins in the second sub-library binds to a second target molecule and is located in another of (i) an inter-repeat loop; (ii) the N terminus or (iii) the C terminus of the chimeric protein.

Another aspect of the invention provides a method of producing a library of chimeric proteins comprising;

- (a) providing a population of nucleic acids encoding a diverse population of chimeric proteins comprising
  - (i) two or more repeat domains,
  - (ii) inter-repeat loops linking the repeat domains; and
  - (iii) one or more peptide ligands, each the peptide ligand being located in an inter-repeat loop or at the N or C terminus of the chimeric protein,
  - wherein the peptide ligands in the population are diverse, and
- (b) expressing the population of nucleic acids to produce the diverse population,
  - thereby producing a library of chimeric proteins.

Another aspect of the invention provides a method of screening a library comprising;

- (a) providing a library of chimeric proteins, each chimeric protein in the library comprising;
  - (i) two or more repeat domains,
  - (ii) inter-repeat loops linking the repeat domains; and
  - (iii) a peptide ligand located in the inter-repeat loop, at the N terminus or at the C terminus of the protein.
  - wherein at least one amino acid residue in the peptide ligands in the library is diverse,
- (b) screening the library for chimeric proteins which display a binding activity, and
- (c) identifying one or more chimeric proteins in the library which display the binding activity.

Other aspects and embodiments of the invention are described in more detail below.

Other Embodiments

From the foregoing description, it will be apparent that variations and modifications may be made to the invention described herein to adopt it to various usages and conditions. Such embodiments are also within the scope of the following claims.

The recitation of a listing of elements in any definition of a variable herein includes definitions of that variable as any single element or combination (or subcombination) of listed elements. The recitation of an embodiment herein includes that embodiment as any single embodiment or in combination with any other embodiments or portions thereof.

All publications and patent applications mentioned in the specification are indicative of the level of skill of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference

BRIEF DESCRIPTION OF FIGURES

FIG. 1 shows the thermostability of consensus-designed tetratricopeptide (CTPR) proteins containing loop- or helix-grafted binding motifs: Thermal denaturation, monitored by circular dichroism, of 2-repeat RTPR (a CTPR in which lysine residues have been replaced with arginine residues) proteins: RTPR2 (in diamonds), RTPR2 containing a loop binding-module (circles) and RTPR2 containing a helix binding-module (squares). All samples are at 20 μM in 10 mM sodium phosphate buffer pH 7.4, 150 mM NaCl.

FIG. 2 shows the thermostability of CTPR proteins of increasing length containing an increasing number of binding modules (alternating with blank modules): Thermal denaturation curves, monitored by circular dichroism, of TPR proteins containing 1, 2, 3 and 4 loops comprising a tankyrase-binding sequence: 1TBP-CTPR2, 2TBP-CTPR4, 3TBP-CTPR6, 4TBP-CTPR8. All samples are at 20 μM in 10 mM sodium phosphate buffer pH 7.4, 150 mM NaCl.

FIGS. 3A-3D show a examples of helix grafting. FIG. 3A shows the crystal structures of SOS1 (son-of-sevenless homologue 1) bound to KRAS (Kirsten rat sarcoma) (PDB 1NVU, Margarit et al. Cell (2003) 112(5):685-95), FIG. 3B shows the SOS1 helix grafted onto a helix at the N-terminus of a CTPR2 protein. The modelled structure of SOS-RTPR2 is shown, and the sequence of the helix is given with the key KRAS-binding residues in grey and the residues that form the interface with the CTPR helices in black. FIG. 3C shows the modelled structure of SOS-TPR2 in complex with KRAS. FIG. 3D shows binding of SOS-TPR2 to KRAS measured by competitive fluorescence polarization (FP). The complex between mant-GTP and KRAS was pre-formed, and 0.1-300 μM SOS-RTPR2 was then titrated in to the complex, displacing the mant-GTP from KRAS resulting in a decrease in FP. EC50 is 3 μM.

FIG. 4A-4B show another example of helix grafting. FIG. 4A shows the modelled structure of the Mdm2 (Mouse double minute 2 homolog) N-terminal domain in complex with the p53-TPR2 comprising the Mdm2-binding helix of p53 grafted onto a helix at the C-terminus of a CTPR2 protein. FIG. 4B shows an ITC analysis of the interaction between p53-TPR2 and Mdm2 N-terminal domain. The N-terminal domain of Mdm2 was titrated into the cell containing 10 μM p53-TPR2.

FIGS. 5A-5B show examples of single and multivalent loop-grafted CTPRs. FIG. 5A shows an ITC analysis of the interaction between a series of tankyrase-binding loop-grafted CTPR2 proteins (TBP-CTPR2) and the substrate-binding ARC4 (ankyrin-repeat cluster) domain of tankyrase. There is an enhancement of both binding affinity and dissociation constant with increasing number of binding modules. FIG. 5B shows native gel analysis (using a native gel in Tris-Glycine buffer pH 8.0, 40 μM protein concentration) of multivalent TBP-CTPR proteins expressed as fusion constructs with the foldon trimerisation domain (Boudko et al 2002; Meier et al. 2004). 1TBP-CTPR2, 2TBP-CTPR4 and 4TBP-CTPR8 (all lacking the foldon domain) were purified and run as monomeric controls. Constructs having the foldon domain run at much higher molecular weights than their monomeric counterparts.

FIGS. 6A-6B show examples of loop-grafted CTPRs comprising the 10-residue Skp2-binding sequence derived from p27 grafted into a loop of a CTPR protein (CTPR-p27). FIG. 6A shows that HA-CTPR2-p27 is able to co-IP FLAG-Skp2 from HEK293T cells. FIG. 6B shows E. coli-expressed and purified TPR5-p27 inhibits p27 ubiquitination in vitro.

FIGS. 7A-7B show another example of loop-grafted CTPRs. FIG. 7A shows (left) ITC analysis of the interaction between the Keap1 (Ketch-like ECH-associated protein 1) KELCH domain and a CTPR2 protein containing a loop-grafted Keap1-binding sequence derived from the protein Nrf2 (Nuclear factor (erythroid-derived 2)-like 2) (Nrf-CTPR2). No binding is observed for the blank CPTR2 protein (right). FIG. 7B shows that three variants of Nrf-CTPR2 (Nrf-CTPR2 (i), Nrf-CTPR2 (ii), Nrf-CTPR2 (iii) can co-IP Keap1 from HEK293T cells.

FIG. 8 shows live-cell imaging of intracellular delivery of an RTPR achieved by resurfacing (by introducing Arginine residues at surface sites). PC3 (left) and U2OS (right) cells incubated with 10 μM FITC-labelled resurfaced TBP-RTPR2 for 3 hours at 37° C., 5% CO2. Overlay of DIC (differential interference contrast) and confocal image. Intracellular fluorescence was also observed at lower concentrations of protein.

FIGS. 9A-9B show the induced degradation of the target protein beta-catenin by designed hetero-bifunctional RTPRs. FIG. 9A shows the beta-catenin levels in cells transfected with either HA-tagged beta-catenin plasmid alone or HA-tagged beta-catenin plasmid together with one of two different hetero-bifunctional RTPR plasmids (LRH1-TPR-p27 and axin-TPR-p27, designed to bind simultaneously to beta-catenin and to E3 ligase SCF^Skp2). FIG. 9B shows a quantitative analysis of the beta-catenin levels in the presence of different hetero-bifunctional RTPRs designed to bind simultaneously to beta-catenin and to either E3 ligase SCF^Skp2or E3 ligase Mdm2. The analysis was performed using densitometry of the bands detected by Western blots corresponding to HA-tagged beta-catenin normalised to actin bands using ImageJ. Negative controls used were single-function TPRs or blank (non-functional) TPRs.

FIGS. 10A-10E show examples of different chimeric protein formats. A chimeric protein may comprise: two repeat domains with a helical target-binding peptide ligand and a helical E3-binding peptide ligand at the N and C termini (FIG. 10A); three repeat domains with a helical E3-binding peptide ligand at the C terminus and a target-binding peptide ligand in the first inter-repeat loop from the N terminus (FIG. 10B); three repeat domains with a helical target-binding peptide ligand at the N terminus and an E3-binding peptide ligand in the second inter-repeat loop from the N terminus (FIG. 10C):, four repeat domains with a target-binding peptide ligand and an E3-binding peptide ligand in the first and third inter-repeat loop from the N terminus (FIG. 10D); and four repeat domains with an E3-binding peptide ligand and a target-binding peptide ligand in the first and third inter-repeat loop from the N terminus (FIG. 10E).

FIG. 11 shows a schematic of a chimeric protein with four peptide ligands located in alternate inter-repeat loops. The binding sites are arrayed at 90° to each other.

FIG. 12 shows a schematic of a chimeric protein engineered so that peptide ligands in alternate inter-repeat loops bind adjacent epitopes on the target.

FIG. 13 shows the modelled structure of a hetero-bifunctional chimeric protein comprising TPR repeat domains, an LRH1-derived peptide ligand designed to bind target beta-catenin, and a p53-derived N-terminal peptide ligand designed to bind to the E3 ubiquitin ligase mdm2.

FIG. 14 shows a schematic of the combinatorial assembly of a module comprising a repeat domain and a terminal helical peptide ligand and a module comprising repeat domains and an inter-repeat loop peptide ligand to generate a chimeric protein.

FIGS. 15A-15F show examples of different chimeric protein formats. 15A shows the blank proteins; 15B shows binding peptides inserted into one or more inter-repeat loops. 15C shows helical binding peptides at one or both of the termini; 15D is a combination of loop and helical binding peptides; 15E and 15F show examples of how multivalency can be achieved.

FIG. 16 shows a schematic of the assembly of a chimeric protein by the progressive screening of chimeric proteins comprising modules with a diverse peptide ligand in addition to modules already identified in previous rounds of screening.

FIG. 17 shows the effect of designed multi-valent tankyrase-binding TPR proteins on Wnt signalling. HEK293T cells were transfected with TPR-encoding plasmids using Lipofectamine2000. The TPR proteins contained 1-4 copies of a tankyrase-binding peptide (TBP) grafted onto the inter-repeat loop(s). For example, 2TBP-CTPR4 is a protein comprising 4 TPR modules with one TBP grafted onto the loop between the first and second TPR and one between the third and fourth TPR. ‘Foldon’ indicates a trimeric TPR-foldon fusion protein.

FIG. 18 shows characterisation of the size and charge of liposome-encapsulated TPR proteins.

FIG. 19 shows the delivery of TPR proteins into cells by liposome encapsulation. FITC dye-labelled liposomes stain the cell membrane upon membrane fusion (red panel), and RITC-labelled TPR protein cargo is then delivered into the cytoplasm. The green panel and red-green merge show that the proteins have entered the cells and are spread diffusely in the cytoplasm.

FIG. 20 shows that liposome-encapsulated TPR proteins are not toxic to HEK293T cells at the concentrations used.

FIG. 21 shows the effect of designed TPR proteins delivered by liposome encapsulation. The TPR proteins contained a tankyrase-binding peptide. Cells were treated with liposomes for 2 hr.

FIG. 22 shows the effect of designed TPR proteins delivered by liposome encapsulation. Cells were treated with liposomes encapsulating 32 μg protein for variable times (2-8 h) indicated in the figure.

FIG. 23 shows the effect of designed hetero-bifunctional TPR proteins on KRAS levels in HEK 293T cells. The TPR proteins contained a binding sequence for KRAS (a non-helical peptide sequence, referred to as KBL, grafted onto an inter-repeat loop of the RTPR) and a degron derived from p27 grafted onto another inter-repeat loop. Cells were transiently transfected with 50 ng or 500 ng of TPR encoding plasmids, as indicated, and with KRAS plasmid or empty vector as control. 24 hours post transfection the cells were lysed, and KRAS levels were evaluated by western blot. In dark grey are cells treated transfected with single-function TPR plasmid (containing degron only).

FIG. 24 shows the effect of hetero-bifunctional TPR proteins targeting endogenous KRAS to the CMA (chaperone-mediated autophagy) pathway. The TPR proteins contained a binding sequence for KRAS (either a grafted helix derived from son-of-sevenless-homolog 1 (SOS) or a non-helical peptide sequence (referred to as ‘KBL’) displayed in a loop of the RTPR) and targeted for degradation using two different chaperone-mediated autophagy peptides (referred to as ‘CMA_Q’ or ‘CMA_K’) at the N- or C-terminus of the construct. Constructs or empty vector (light grey) were transiently transfected into either HEK293T or DLD1 (colorectal cancer cell line). 24 hours post transfection the cells were lysed, and KRAS levels were evaluated by western blot. Those constructs that resulted in significant reduction in KRAS compared to the empty vector control are shown in white.

FIG. 25 shows examples of variations in the linker sequence connecting a peptide ligand to an inter-repeat loop in order to optimise the binding affinity for the target. The example shown is Nrf-TPR, a TPR protein designed to bind to Keap1 (see FIG. 7 of the original patent application). Glycine residues were introduced into the linker to provide flexibility and increased spatial sampling. The introduction of this more flexible linker sequence was found to increase the binding affinity of the Nrf-TPR protein (labelled ‘Flexible’) when compared with the consensus-like linker sequence. Altering the charge content of the linker sequence (‘labelled ‘Charged’) and altering the conformational properties (based on the predictions of the program CIDER (Holehouse et al. Biophys. J. 112, 16-21 (2017)) of the loop by changing the amino acid composition of the linker sequence (labelled ‘CIDER-optimised’) also affected the Keap1-binding affinity.

FIG. 26 shows the schematic representation of a matrix of degradation-inducing chimeric proteins. The matrix shown is for use in targeting β-catenin for degradation. These proteins comprise a scaffold (grey rectangles) onto which are grafted: (1) a target-binding peptide ligand and (2) a binding peptide for an E3 ubiquitin ligase or a component of another degradation pathway. Each of the target-binding peptides is derived from a different protein that interacts with β-catenin (see Table 2). Each of the degradation pathway-binding peptides (referred to as “degrons”) is derived from a substrate or binding partner of one of many different E3s or from a binding partner for one of a component of another cellular degradation pathway (including chaperone-mediated autophagy, selective autophagy and ESCRT (endosome-lysosome) pathways); ‘etc.’ denotes the fact that there are many such proteins that can be harnessed for degradation, as detailed further in Table 3 The schematic illustrates the combinatioral “plug-and-play” nature of these matrices, in terms of the ability to slot in any target-recruiting peptide and degradation-pathway-recruiting peptide. The other factor that can be varied in the matrix arises from the fact that the two peptides can also be grafted onto different positions in the scaffold so as to present the target in different configurations with respect to the E3 or other degradation machinery. Once the matrix is constructed, it can then be screened in cell-based assay in order to identify the best combination of two peptides and their positions within the scaffold that induces the greatest reduction in target protein levels. The same panel of diverse degradation pathway components can be used for screen for degradation of any target

DETAILED DESCRIPTION

This invention relates to the chimeric proteins that comprise multiple repeat domains. These repeat domains are linked to each other in the polypeptide chain by inter-repeat loops. One or more peptide ligands (i.e., peptidyl binding motifs or binding domains), are located in one or more of the inter-repeat loops and/or in N or C terminal helices of the chimeric protein. The peptide ligands may be to the same or different target molecules and the chimeric protein may be multi-functional and/or multi-valent. The geometrical display of the grafted binding sites may be precisely and predictably tuned by adjusting the positions of the binding sites and the number and shape of the repeat domains. Chimeric proteins as described herein may be useful in a range of therapeutic and diagnostic applications.

A “repeat domain” is a repetitive structural element of 30 to 100 amino acids that forms a defined secondary structure. Multiple (two or more) repeat domains stack sequentially in a modular fashion to form a stable protein, which may for example have a solenoid or toroid structure. Repeat domains may be synthetic or may be naturally-occurring repeats from tandem repeat proteins, or variants thereof.

Due to the identical form of their building blocks, solenoid domains can only assume a limited number of shapes. Two main topologies are possible: linear (or open, generally with some degree of helical curvature) and circular (or closed). Patthy, László (2007). Protein Evolution. Wiley-Blackwell. ISBN 978-1-4051-5166-5.

If the two terminal repeats in a solenoid do not physically interact, it leads to an open or linear structure. Members of this group are frequently rod- or crescent-shaped. The number of individual repeats can range from 2 to over 50. A clear advantage of this topology is that both the N- and C-terminal ends are free to add new repeats and folds, or even remove existing ones during evolution without any gross impact on the structural stability of the entire domain. Kinch L N, Grishin N V (June 2002). Curr. Opin. Struct. Biol. 12 (3): 400-8. doi:10.1016/s0959-440x(02)00338-x. PMID 12127461. This type of domain is extremely common among extracellular segments of receptors or cell adhesion molecules. A non-exhaustive list of examples include: EGF repeats, cadherin repeats, leucine-rich repeats, HEAT repeats, ankyrin repeats, armadillo repeats, tetratricopeptide repeats, etc. Whenever a linear solenoid domain structure participates in protein-protein interactions, frequently at least 3 or more repetitive subunits form the ligand-binding sites. Thus—while individual repeats might have a (limited) ability to fold on their own—they usually cannot perform the functions of the entire domain alone.

In the case when the N- and C-terminal repeats lie in close physical contact in a solenoid domain, the result is a topologically compact, closed structure. Such domains typically display a high rotational symmetry (unlike open solenoids that only have translational symmetries), and assume a wheel-like shape. Because of the limitations of this structure, the number of individual repeats is not arbitrary. In the case of WD40 repeats (perhaps the largest family of closed solenoids) the number of repeats can range from 4 to 10 (more usually between 5 and 7). (Vogel C, Berzuini C, Bashton M, Gough J, Teichmann S A (February 2004). J. Mol. Biol. 336 (3): 809-23). Kelch repeats, beta-barrels and beta-trefoil repeats are further examples for this architecture.

A repeat domain may have the structure of a solenoid repeat. The structures of solenoid repeats are well known in the art (see for example Kobe & Kajava Trends in Biochemical Sciences 2000; 25(10):509-15). For example, a repeat domain may have an α/α or α/3₁₀(helix-turn-helix or hth) structure, for example a tetratricopeptide repeat structure; α/α/α (helix-turn-helix-turn-helix or hthth) structure, for example an armadillo repeat structure; a β/β/α/α structure; a α/β or 3₁₀/β structure, for example a leucine rich repeat (LRR) structure; a β/β/β structure, for example, an IGF1RL, HPR or PelC repeat structure; or a β/β structure, for example a serralysin or EGF repeat structure.

A “scaffold” refers to two or more repeat domains, and a “grafted scaffold” refers to a continuous polypeptide comprising a scaffold and a heterologous binding site (e.g., a peptide ligand).

Ankyrin repeat, one of the most widely existing protein motifs in nature, consists of 30-34 amino acid residues and exclusively functions to mediate protein-protein interactions, some of which are directly involved in the development of human cancer and other diseases. Each ankyrin repeat exhibits a helix-turn-helix conformation, and strings of such tandem repeats are packed in a nearly linear array to form helix-turn-helix bundles with relatively flexible loops. The loops between adjacent Ankyrin repeats are semi-structured and therefore are quite rigid. The global structure of an ankyrin repeat protein is mainly stabilized by intra- and inter-repeat hydrophobic and hydrogen bonding interactions. The repetitive and elongated nature of ankyrin repeat proteins provides the molecular bases of the unique characteristics.

The armadillo (Arm) repeat is an approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila melanogaster segment polarity gene armadillo involved in signal transduction through wingless. Animal Arm-repeat proteins function in various processes, including intracellular signalling and cytoskeletal regulation, and include such proteins as beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumour suppressor protein, and the nuclear transport factor importin-alpha, amongst others [(PUBMED:9770300)].

Suitable repeat domains may include domains of the Ankyrin clan (Pfam: CL0465), such as ankyrin (PF00023), which may comprise a 30-34 amino-acid repeat composed of two beta strands and two alpha helices; domains of the leucine-rich repeat (LRR) clan (Pfam; CL0022), such as LRR1 (PF00560), which may comprise a 20-30 amino acid repeat composed of an α/β horseshoe fold; domains of the Pec Lyase-like (CL0268) clan, such as pec lyase C (PF00544), which may comprise a right handed beta helix; domains of the beta-Roll (CL0592) clan such as Haemolysin-type calcium-binding repeat (PF000353), which may comprise short repeat units (e.g. 9-mers) that form a beta-roll made up of a super-helix of beta-strand-turns of two short strands each, stabilised by Ca²⁺ ions; domains of the PSI clan (CL0630), such as trefoil (PF00088); and domains of the tetratricopeptide clan (CL0020), such as TPR-1 (PR00515), which may comprise a 24 to 30, or 24 to 40, or 24 to 90 amino acid repeat composed of a helix-turn-helix.

Consensus Sequences for ANK Repeats

SMART database, see Table 10) include the following:

O04242/1-30
NGHTALHIAASK------------------GDEQCVKLLLEHGA------DPNA

(SEQ ID NO: 722)

CONSENSUS/80%
.t.sslhhsh.t..................tp.phhphllp.t.......pht.

CONSENSUS/65%
pstosLphAstp..................sphphlphLlptss......shsh

CONSENSUS/50%
sGpTsLHhAsps..................sshcllchLlspus......slst

Consensus Sequence for ARM repeats (SMART database, see Table 11) include the following:

IMO2HUMANb
PND-KIQAVIDAG--VCRRLVELLM----------------------

HNDYKVVSPALRA (SEQ ID NO: 1158)

CONSENSUS/80%
pt...h..hhp.t.hl..lhphlt.........................p.pl.t.shhs

CONSENSUS/65%
ssp.ptphlhpts..slshLlpLLp......................pts.plhptsshs

CONSENSUS/50%
ssc..sppsllcsG..slstLlpLLs......................sscsclppsAstA

IMO2HUMANb
VGNIVT (SEQ ID NO: 3100)

CONSENSUS/80%
ltpls.

CONSENSUS/65%
LpNlst

CONSENSUS/50%
LsNlus

Suitable repeat domains may be identified using the PFAM database (see for example Finn et al Nucleic Acids Research (2016) Database Issue 44:D279-D285).

In some preferred embodiments, the repeat domain may have the structure of an α/α-solenoid repeat domain, such as a helix-turn-helix. A helix-turn-helix domain comprises two antiparallel α-helices of 12-45 amino acids.

Suitable helix-turn-helix domains include tetratricopeptide-like repeat domains. Tetratricopeptide-like repeats may include domains of the TPR clan (CL0020), for example and Arm domains (see for example Armadillo; PF00514; Huber et al Cell 1997; 90: 871-882), HEAT domains (Huntingtin, EF3, PP2A, TOR1; PF02985; see for example Groves et al. Cell. 96 (1): 99-110), PPR domains (pentatricopeptide repeat PF01535; see for example Small (2000) Trends Biochem. Sci. 25 (2): 46-7), TALE domains (TAL (transcription activator-like) effector; PF03377; see for example Zhang et al Nature Biotechnology. 29 (2): 149-53) and TPR1 domains (tetratricopeptide repeat-1; PF00515; see for example Blatch et al BioEssays. 21 (11): 932-9).

Other suitable helix-turn-helix domain may be synthetic, for example DHR1 to DHR83 as disclosed in Brunette et al., Nature 2015 528 580-584.

In some preferred embodiments, the helix-turn-helix scaffold may be a tetratricopeptide repeat domain (TPR) (D'Andrea & Regan, 2003) or a variant thereof. TPR repeat domains may include naturally occurring or synthetic TPR domains. Suitable TPR repeat domains are well known in the art (see for example Parmeggiani et al., J. Mol. Biol. 427 563-575) and may have the amino acid sequence:

(SEQ ID NO: 1)

AEAWYNLGNAYYKQGDYQKAIEYYQKALEL-X₁X₂X₃X₄,

- wherein X_1-4are independently any amino acid, preferably X₁and X₂being D and P respectively, or may be a variant of this sequence.

Additional TPR repeat consensus sequences (SMART database, see Table 9) include the following:

S75991
ALTLNNIGTI YYAREDYDQA LNYYEQALSL SRAV

(SEQ ID NO: 309)

CONSENSUS/80%
XXhhXthuXh hXXXtphppA htXhppsltht XpX

CONSENSUS/65%
spshhphGth hhphsphppA lphappAlpl pspX

CONSENSUS/50%
spsatslGps atptucaccA lcsap+ALcl sPss

Other TPR repeat domain sequences are shown in Tables 4-6 and 9 below.

The grouping of amino acids to classes and class abbreviation (the key) used within consensus sequences are shown below.

Class
Key
Residues

alcohol
o
S, T

aliphatic
l
I, L, V

any
.
A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T,

V, W, Y

aromatic
a
F, H, W, Y

charged
c
D, E, H, K, R

hydrophobic
h
A, C, F, G, H, I, K, L, M, R, T, V, W, Y

negative
−
D, E

polar
p
C, D, E, H, K, N, Q, R, S, T

positive
+
H, K, R

small
s
A, C, D, G, N, P, S, T, V

tiny
u
A, G, S

turnlike
t
A, C, D, E, G, H, K, N, Q, R, S, T

Preferred TPR domains may include CTPR, RTPRa, RTPRb and KTPRb domains, for example a domain having a sequence shown in Table 4 or Table 6 or a variant of a sequence shown in Table 4 or Table 6.

In some embodiments, a TPR repeat domain may be a human TPR repeat domain, preferably a TPR repeat domain from a human protein in blood. TPR repeat domains from human blood may have reduced immunogenicity in vivo. Suitable human blood TPR repeat domains may include repeat domains from IFIT1, IFIT2 or IFIT3. Other examples of human blood repeat domains identified in the plasma proteome database are shown in Table 5.

Suitable human blood repeat domains may be identified from the plasma proteome database (Nanjappa et al Nucl Acids Res 2014 January; 42 (Database issue):D959-65) for example by searching for sequences with high sequence identity to the TPR repeat domain using standard sequence analysis tools (e.g. Altschul et al Nucleic Acids Res. 25:3389-34021; Altschul et al FEBS J. 272:5101-5109).

A variant of a reference repeat domain or binding site sequence set out herein may comprise an amino acid sequence having at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or at least 98% sequence identity to the reference sequence. Particular amino acid sequence variants may differ from a repeat domain shown above by insertion, addition, substitution or deletion of 1 amino acid, 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more than 10 amino acids. Preferred variants of a TPR repeat domain may comprise one or more conserved residues, for example, 1, 2, 3, 4, 5, 6 or more preferably all of Leu at position 7, Gly or Ala at position 8, Tyr at position 11, Ala at position 20, Ala at position 27, Leu or Ile at positions 28 and 30 and Pro at position 32.

Sequence similarity and identity are commonly defined with reference to the algorithm GAP (Wisconsin Package, Accelerys, San Diego USA). GAP uses the Needleman and Wunsch algorithm to align two complete sequences that maximizes the number of matches and minimizes the number of gaps. Generally, default parameters are used, with a gap creation penalty=12 and gap extension penalty=4. Use of GAP may be preferred but other algorithms may be used, e.g. BLAST (which uses the method of Altschul et al. (1990) J. Mol. Biol. 215: 405-410), FASTA (which uses the method of Pearson and Lipman (1988) PNAS USA 85: 2444-2448), or the Smith-Waterman algorithm (Smith and Waterman (1981) J. Mol Biol. 147: 195-197), or the TBLASTN program, of Altschul et al. (1990) supra, generally employing default parameters. In particular, the psi-Blast algorithm (Nucl. Acids Res. (1997) 25 3389-3402) may be used.

Sequence comparison may be made over the full-length of the relevant sequence described herein.

For example, a repeat domain may comprise one or more point mutations to facilitate grafting of hydrophobic peptide ligands. For example, aromatic residues in the repeat domain may be substituted for polar or charged residues. Suitable substitutions may be identified in a rational manner, for example using Hidden Markov plots of repeat domain sequences to identify non-aromatic residues that are found in nature in consensus aromatic positions. A suitable TPR repeat domain for grafting hydrophobic peptide ligands may have the amino acid sequence:

(SEQ ID NO: 2)

AEAWYNLGNAYYRQGDYQRAIEYYQRALEL-X₁X₂X₃X₄,

- wherein X_1-4are independently any amino acid, preferably X₁and X₂being D and P

In some embodiments, lysine residues in the repeat domain may be replaced by arginine residues to prevent ubiquitination and subsequent degradation. This may be particularly useful when the chimeric protein comprises an E3 ubiquitin ligase-peptide ligand, for example in a proteolysis targeting chimera (PROTAC). For example, a suitable TPR repeat domain may have the amino acid sequence:

(SEQ ID NO: 307)

AEALNNLGNVYREQGDYQRAIEYYQRALEL-X₁X₂X₃X₄,

- wherein X_1-4are independently any amino acid, preferably X₁and X₂being D and P respectively.

In preferred embodiments, the chimeric protein may comprise 2, 3, 4, 5, 6, 7, 8, 9, 10 or more than 10 repeat domains. Preferably, the chimeric protein comprises 2 to 5 repeat domains. Chimeric proteins with fewer repeat domains may display increased cell penetration. For example, a chimeric protein with 2-3 repeat domains may be useful in binding intracellular target molecule. Chimeric proteins with more repeat domains may display increased stability and functionality. For example, a chimeric protein with 4 or more repeat domains may be useful in binding extracellular target molecules. A chimeric protein with 6 or more repeat domains may be useful in producing long linear molecules for targeting or assembling extracellular complexes in bi- or multivalent formats.

In other embodiments, sufficient stability and functionality may be conferred by a single repeat domain with N and C terminal peptide ligands. For example, a chimeric protein may comprise:

- (i) a repeat domain, and
- (ii) peptide ligands at the N and C terminal of the repeat domain.

The repeat domains of a chimeric protein may lack binding activity i.e. the binding activity of the chimeric protein is mediated by the peptide ligands and not by residues within the repeat domains.

A “binding domain” (“peptide ligand”) is a contiguous amino acid sequence that specifically binds to a target molecule. Suitable peptide ligands that are capable of grafting onto a terminal helix or inter-repeat loop are well-known in the art and include peptide sequences selected from a library, antigen epitopes, natural protein-protein interactions (helical, extended or turn-like) and short linear motifs (SLiMs). Viral SLiMs (that hijack the host machinery) may be particularly useful because they may display high binding affinities (Davey et al (2011) Trends Biochem. Sci. 36, 159-169).

A suitable peptide ligand for a target molecule may be selected from a library, for example using phage or ribosome display, or identified or designed using rational approaches or computational design, for example using the crystal structure of a complex or an interaction. In some embodiments, peptide ligands may be identified in an amino acid sequence using standard sequence analysis tools (e.g. Davey et al Nucleic Acids Res. 2011 Jul. 1; 39 (Web Server issue): W56-W60).

Peptide ligands may be 5 to 25 amino acids in length, preferably 8 to 15 amino acids, although in some embodiments, longer peptide ligands may be employed.

Generally in chimeric proteins of the invention, the two or more peptide ligands are 40 angstroms apart from each other, they may be 35 angstroms, 30 angstroms, 25 angstroms, 20 angstroms, 15 angstroms but no less than 10 angstroms apart. A person of skill in art can use a 3D structural software such as Chimera or Pymol to determine the minimum distances between positions for ideal positioning in three dimensional orientation.

The peptide ligands and the repeat domains of the chimeric protein are heterologous i.e. the peptide ligand is not associated with the repeat domain in naturally occurring proteins and the binding and repeat domains are artificially associated in the chimeric protein by recombinant means.

A chimeric protein described herein may comprise 1 to n+1 peptide ligands, where n is the number of repeat domains in the chimeric protein. The number of peptide ligands is determined by the required functionality and valency of the chimeric protein. For example, one peptide ligand may be suitable for a mono-functional chimeric protein and two or more peptide ligands may be suitable for a bi-functional or multi-functional chimeric protein.

Chimeric proteins may be monovalent. A target molecule may be bound by a single peptide ligand in a monovalent chimeric protein. Chimeric proteins may be multivalent. A target molecule may be bound by two or more of the same or different peptide ligands in a multivalent chimeric protein.

Chimeric proteins may be monospecific. The peptide ligands in a monospecific chimeric protein may all bind to the same target molecule, more preferably the same site or epitope of the target molecule.

Chimeric proteins may be multi-specific. The peptide ligands in a multi-specific chimeric protein may bind to different target molecules. For example, a bi-specific chimeric protein may comprise one or more peptide ligands that bind to a first target molecule and one or more peptide ligands that bind to a second target molecule and a tri-specific chimeric protein may comprise one or more peptide ligands that bind to a first target molecule, one or more peptide ligands that bind to a second target molecule and one or more peptide ligands that bind to third target molecule.

A bi-specific chimeric protein may bind to the two different target molecules concurrently. This may be useful in bringing the first and second target molecules into close proximity.

When the target molecules are located on different cells, concurrent binding of the target molecules to the chimeric protein may bring the cells into close proximity, for example to promote or enhance the interaction of the cells. For example, a chimeric protein which binds to a tumour specific antigen and a T cell antigen, such as CD3, may be useful in bringing T cells into proximity to tumour cells. When the target molecules are from different biological pathways, this may be may be useful in achieving synergistic effects and also for minimising resistance.

A tri-specific chimeric protein may bind to three different target molecules concurrently. In some embodiments, one of the target molecules may be an E3 ubiquitin ligase. For example, tri-specific chimeric protein may binding to a first target molecule from a first biological pathway and a second target molecule from a second biological pathway as well as an E3 ubiquitin ligase. This may be useful in achieving synergistic effects and also for minimising resistance.

A peptide ligand may be located in an inter-repeat loop of the chimeric protein.

An “inter-repeat binding domain” or “inter-repeat peptide ligand” may comprise 5 to 25 amino acid residues, preferably 8 to 15 amino acids. However, since there is no intrinsic restriction on the size of the inter-loop peptide ligand, longer sequences of more than 25 amino acid residues may be used in some embodiments.

In some embodiments, an unstructured peptide ligand may be inserted into an inter-repeat loop.

One or more, two or more, three or more, four or more or five or more of the inter-repeat loops in the chimeric protein may comprise peptide ligands. The peptide ligands may be located on consecutive inter-repeat loops or may have a different distribution in the inter-repeat loops of the chimeric protein. For example, inter-repeat loops comprising a peptide ligand may be separated in the modular protein by one or more, two or more, three or more or four or more inter-repeat loops which lack a peptide ligand.

A peptide ligand may be connected to an inter-repeat loop directly or via one or more additional residues or linkers. Additional residues or linkers may be useful for example when a peptide ligand requires conformational flexibility in order to bind to a target molecule, or when the amino acid residues that are adjacent to the minimal peptide ligand favourably influence the micro-environment of the binding interface.

Additional residues or linkers may be positioned at the N terminus of the peptide ligand, the C terminus of the peptide ligand, or both. For example, the sequence of an inter-repeat loop containing a peptide ligand may be [X_1-i]-[X_1-n]-[X_1-z], where each residue denoted by X is independently any amino acid and may be the same amino acid or a different amino acid to any other residue that is also denoted by X, [X_1-n] is the peptide ligand, n is 1 to 100, [X_1-i] is a linker and i is independently any number between 1 to 10. In some embodiments, D may be preferred at the first position of the linker [X_1-i], P may be preferred at the second position of linker [X_1-i], D may be preferred at the last position of the linker [X_1-z] and/or P may be preferred at the penultimate position of linker [X_1-z]. Examples of preferred inter-repeat loop sequences may include DP-[X_1-n]-PX (SEQ ID NO:4); DPXX-[X_1-n]-XXPX (SEQ ID NO:5); DPXX-[X_1-n]-XPXX (SEQ ID NO:6); DPXX-[X_1-n]-PXXX (SEQ ID NO:7); PXX-[X_1-i]-[X_1-n]-[X_1-i]-XXPX (SEQ ID NO:8), DPXX-[X_1-i]-[X_1-n]-[X_1-n]-XPXX (SEQ ID NO:9), DPXX-[X_1-i]-[X_1-n]-[X_1-i]-PXXX (SEQ ID NO:10), DPXX-[X_1-i]-[X_1-n]-XPXX (SEQ ID NO:11), DPXX-[X_1-i]-[X_1-n]-XPXX (SEQ ID NO:12), DPXX-[X_1-i]-[X_1-n]-XPXX (SEQ ID NO:13), DPXX-[X_1-n]-[X_1-i]-XXPX (SEQ ID NO:14), DPXX-[X_1-n]-[X_1-i]-XPXX (SEQ ID NO:15) and DPXX-[X_1-n]-[X_1-i]-PXXX (SEQ ID NO:16).

The precise sequence of the residues or linkers used to connect a peptide ligand to an inter-repeat loop depends on the peptide ligand and may be readily determined for any peptide ligand of interest using standard techniques. For example, small, non-hydrophobic amino acids, such as glycine, may be used to provide flexibility and increased spatial sampling, for example when a peptide ligand needs to adopt a specific conformation, or proline residues may be used to increase rigidity, for example, when the peptide ligands are short.

In some preferred embodiments, an inter-repeat peptide ligand may be non-hydrophobic. For example, at least 40% of the amino acids in the peptide ligand may be charged (e.g. D, E, R or K) or polar (e.g. Q, N, H, T, Y, C or W). Alternatively, the repeat domains may be modified to accommodate a hydrophobic peptide ligand, for example by replacing aromatic residues with charged or polar residues.

A peptide ligand may be located at one or both termini of the chimeric protein.

A peptide ligand may be located in a helical region of the scaffold in the chimeric protein. A helical region or “helix” is a portion of a scaffold which assumes an α-helical structure.

The precise length of a helical peptide ligand is dependent on the length of the helical region of the scaffold. In general, the helical peptide ligand is no longer than the length of the helical region of the scaffold. However, if the helical region of the scaffold is located at one or other termini or is flanked by unstructured or loosely structured residues, then it may be possible to extend it to accommodate a longer helical peptide ligand.

A helical peptide ligand may comprise 3 to 25 amino acid residues, preferably 8 to 15 amino acids in length. In some embodiments, a helical peptide ligand may comprise 3-10 or 3-12 or 3-15 or 8-10 or 8-12 or 8-13 or 8-14 or 8-15 or 3-18 or 3-20 or 3-21 or 3-22 or 3-24 or 3- 25 amino acids. In some embodiments, a helical peptide ligand may comprise 3 or 4 or 5 or 6 or 7 or 8 or 9 or 10 or 11 or 12 or 13 or 14 or 15 or 16 or 17 or 18 or 19 or 20 or 21 or 22 or 23 or 24 or 25 amino acid residues.

In some embodiments, a peptide ligand located at the N or C terminus may comprise an α-helical structure and may comprise all or part of a half-repeat (i.e. all or part of a single α-helix) that stacks against an adjacent repeat domain. The α-helix of the terminal peptide ligand makes stabilising interactions with an adjacent repeat domain and is stable and folded. Only a few of the positions that structurally define an α-helix are required for the correct interfacial interaction with the adjacent repeat domain. The residues in some of these positions are defined (Tyr (i)-Ile (1+4)-Tyr (i+7)-Leu (1+11) for the N-terminal α-helix and Ala (i)-Leu (i+4)-Ala/Val (i+7) for the C-terminal helix), but the remaining positions of the α-helix may be modified to form a helical peptide ligand.

A helical peptide ligand may be located at the N terminus of the protein. The N terminal peptide ligand may be helical and may comprise all or part of the sequence X_n-(X)₁₅-X₁X₂XX (SEQ ID NO:17), preferably all or part of the sequence X_n-XYXXXIXXYXXXOCX-X₁X₂XX (SEQ ID NO:18), where each residue denoted by X is independently any amino acid and may be the same amino acid or a different amino acid to any other residue in the sequence that is also denoted by X, X₁is independently any amino acid, preferably D, and X₂is independently any amino acid, preferably P, and n is 0 or any number. In some embodiments, the Y, I, and/or L residues in the N terminal peptide ligand may be substituted for an amino acid residue with similar properties (i.e. a conservative substitution).

A helical peptide ligand may be located at the C terminus of the scaffold. The C terminal peptide ligand may be helical and may comprise all or part of the sequence X_n-(X)₁₅-X₁X₂XX, preferably all or part of the sequence X₁X₂XX-XXAXXXLXX[A or V]XXXXX-X_n, (SEQ ID NO:19) where X is independently any amino acid and may be the same amino acid or a different amino acid to any other residue in the sequence that is also denoted by X, X₁is independently any amino acid, preferably D, and X₂is independently any amino acid, preferably P, and n is 0 or any number. In some embodiments, the A, L and/or V residues in the C terminal peptide ligand may be substituted for an amino acid residue with similar properties (i.e. a conservative substitution).

The minimum length of the terminal peptide ligand is determined by the number of residues required to form a helix that binds to the target molecule. There is no intrinsic maximum length of the terminal peptide ligand and n may be any number.

It is within the skill in the art to graft selected residues of a peptide ligand into a helix portion of a scaffold containing a helix, and the invention contemplates this variation of grafting as an equivalent to grafting a peptide ligand itself. The residues of the peptide ligand that are in contact with the peptide ligand binding partner (the target protein) are those whose side chains are outward facing and are exposed to solvent. These residues are suitable for grafting to a helical portion of a scaffold. The residues of the scaffold helix whose side chains face inwards and pack against the rest of the scaffold should not be substituted, and this way their interactions with the rest of the scaffold are maintained. It is within the skill in the art to visualize the scaffold structure to identify which of the residues of the helix selected for grafting are facing outwards. PDB codes from any protein databank provide three dimensional co-ordinates that allow one of skill in the art to visualize the structure of the domain using programs such as PYMOL®, CHIMERA® and RASMOL®. At the same time, it is well within the skill in the art to identify residues of the helix peptide ligand that face outwards form noncovalent interactions (hydrogen bonds and/or Van der Waals and/or hydrophobic interactions) with its binding partner, using a program such as PYMOL®, CHIMERA® and RASMOL® to visualize a peptide ligand complexed with its binding partner. Helix grafting is performed by selectively replacing the outward-facing residues of the helix with corresponding outward-facing residues of the peptide ligand. The inward-facing residues of the helix are undisturbed, and hence the resultant grafted scaffold will have a grafted helix that comprises a mixture of outward facing residues derived from the helix peptide and the native inward facing residues of the helix that were undisturbed.

For instance, the following example shows a nine-residue helix peptide ligand (X1-X2-X3-X4-X5-X6-X7-X8-X9). A 3-dimensional view of the peptide ligand in complex with the target protein (using one of the above-noted programs) shows that residues X1, X2, X5, X8 and X9 (for example) of the peptide ligand interact with the target protein and thus are outward facing. Similarly, a helical portion of a given scaffold may be thirty amino acids in length (Y1-Y2-Y3- . . . -Y28-Y29-Y30). A 3-dimensional view of the scaffold shows the helical region and that residues Y3, Y4, Y6, Y7, and Y10 (for example) are inward facing and thus interact with the rest of the scaffold. One of skill in the art would recognize Y1, Y2, Y5, Y8 and Y9 as outward facing, thus identifying these residues as scaffold helical residues that may be replaced with peptide ligand outward facing residues. Therefore, peptide ligand residues X1, X2, X5, X8 and X9 are grafted to the scaffold replacing residues Y1, Y2, Y5, Y8 and Y9 with the corresponding outward facing residues peptide ligand residues X1, X2, X5, X8 and X9, thereby creating an isomorphic replacement. The resultant grafted scaffold will have a grafted helix whose sequence would include the following residues:

- X1 X2 Y3 Y4 X5 Y6 Y7 X8 X9 (Y10-30)
  
  The resulting grafted helix preserves the native hydrogen bonding within the scaffold and at the same time preserves the noncovalent interactions required for specific binding of the peptide ligand to its target protein.

The “peptide ligand” may also contain more than one consecutive set of outward facing residues to graft into the scaffold, in which case the grafted scaffold may contain invariant scaffold residues between the grafted peptide residues (e, g “X1 X2 Y3 Y4 X5 Y6 Y7 X8 X9”).

A helical peptide ligand may comprise all or part of the sequence C₁X₁X₂C₂X₃X₄C₃X₅X₆C₄, where X₁to X6 are independently any amino acid and, C₁, C₂, C₃and C₄are A, B, C and D, respectively.

In some embodiments, a helical peptide ligand may be non-hydrophobic. For example, at least 20% of the amino acids in the peptide ligand may be charged (e.g. D, E, R or K) or polar (e.g. Q, N, H, T, Y, C or W).

In other embodiments, a peptide ligand located at the N or C terminus may comprise a non-helical structure. For example, a peptide ligand that is an obligate N- or C-terminal domain (for example because the terminal amino or carboxylate group mediates the binding interaction) may be located at the beginning or end of the one or more repeat domains.

In some embodiments, one or more positions in a peptide ligand may be diverse or randomised. A chimeric protein comprising one or more diverse or randomised residues may form a library as described below.

In some embodiments, the N and C terminal peptide ligands may be non-hydrophobic. For example, at least 20% of the amino acids in the peptide ligand may be charged (e.g. D, E, R or K) or polar (e.g. Q, N, H, T, Y, C or W). Alternatively, the helix turn helix scaffold of the repeat domains may be modified, for example by replacing aromatic residues with charged or polar residues in order to accommodate a hydrophobic peptide ligand.

A chimeric protein as described herein may comprise peptide ligands in any arrangement or combination. For example, peptide ligands may be located at both the N and C terminus and optionally one or more inter-repeat loops of a chimeric protein; at the N terminus and optionally one or more loops of a chimeric protein; at the C terminus and optionally one or more loops of a chimeric protein; or in one or more inter-repeat loops of a chimeric protein.

The location of the peptide ligands within a chimeric protein may be determined by rational design, for example using modelling to identify the optimal arrangement for the presentation of two target molecules to each other (e.g. for substrate presentation to an E3 ubiquitin ligase); and/or by screening for example using populations of chimeric proteins with different arrangements of peptide ligands to identify the arrangement which confers the optimal interaction of target molecules.

Target Proteins and Targeting Peptide Ligands

Target proteins and peptide ligands that bind such proteins are described herein and are listed, without limitation, in the tables.

Suitable target molecules for chimeric proteins described herein include biological macromolecules, such as proteins. The target molecule may be a receptor, enzyme, antigen, oligosaccharide, oligonucleotide, integral membrane protein, transcription factor, transcriptional regulator, G protein coupled receptor (GPCR) or any other target of interest. Proteins that are difficult to target with small molecules, such as PPIs, proteins that accumulate in neurodegenerative diseases and proteins overexpressed in disease conditions, such as cancer, may be particularly suitable target molecules. Target molecules may include α-synuclein; β-amyloid; tau; superoxide dismutase; huntingtin; β-catenin; KRAS; components of superenhancers and other types of transcriptional regulators, such as N-Myc, C-Myc, Notch, aurora A, EWS-FLI1 (Ewing's sarcoma-friend leukemia integration 1), TEL-AML1, TAL1 (T-cell acute lymphocytic leukemia protein 1) and Sox2 ((sex determining region Y)-box 2); tankyrases; phosphatases such as PP2A; epigenetic writers, readers and erasers, such as histone deacetylases and histone methyltransferases; BRD4 and other bromodomain proteins; and kinases, such as PLK1 (polo-like kinase 1), c-ABL (Abelson murine leukemia viral oncogene homolog 1) and BCR (breakpoint cluster region)-ABL.

In some embodiments, a chimeric protein may neutralise a biological activity of the target molecule, for example by inhibiting or antagonising its activity or binding to another molecule or by tagging it for ubiquitination and proteasomal degradation or for degradation via autophagy. In other embodiments, a chimeric protein may activate a biological activity of the target molecule.

In some embodiments, the target molecule may be β-catenin. Suitable peptide ligands that specifically bind to 3-catenin are well-known in the art and include β-catenin-peptide ligands derived from axin (e.g. GAYPEYILDIHVYRVQLEL (SEQ ID NO:20) and variants thereof), Bcl-9 (e.g. SQEQLEHRYRSLITLYDIQLML (SEQ ID NO:21) and variants thereof), TCF7L2 (e.g. QELGDNDELMHFSYESTQD (SEQ ID NO:22) and variants thereof), ICAT (e.g. YAYQRAIVEYMLRLMS (SEQ ID NO:23) and variants thereof), LRH-1 (e.g. YEQAIAAYLDALMC (SEQ ID NO:24) and variants thereof) or APC (e.g. SCSEELEALEALELDE (SEQ ID NO:25) and variants thereof).

In some embodiments, the target molecule may be KRAS. Suitable peptide ligands that specifically bind to KRAS are well-known in the art and include a KRAS-peptide ligand from SOS-1 (e.g. FEGIALTNYLKALEG (SEQ ID NO:26) and variants thereof) and KRAS-peptide ligands identified by phage display (see for example Sakamoto et al. Biochem. Biophys. Res. Comm. (2017) 484 605-611).

In some embodiments, the target molecule may be tankyrase. Suitable peptide ligands that specifically bind to tankyrase are well-known in the art and include tankyrase peptide ligands from Axin (e.g. REAGDGEE (SEQ ID NO:27) and HLQREAGDGEEFRS (SEQ ID NO:28) or variants thereof).

In some embodiments, the target molecule may be EWS-FLI1. Suitable peptide ligands that specifically bind to EWS-FLI1 are well-known in the art and include the ESAP1 peptide TMRGKKKRTRAN (SEQ ID NO:29) and variants thereof. Other suitable sequences may be identified by phage display (see for example Erkizan et al. Cell Cycle (2011) 10, 3397-408).

In some embodiments, the target molecule may be Aurora-A. Suitable peptide ligands that specifically bind to Aurora-A are well-known in the art and include Aurora-A binding sequences from TPX2, such as SYSYDAPSDFINFSS (SEQ ID NO:30) (Bayliss et al. Mol. Cell (2003) 12, 851-62) and Aurora-A binding sequences from N-myc, such as N-myc residues 19-47 or 61-89 (see for example Richards et al. PNAS (2016) 113, 13726-31).

In some embodiments, the target molecule may be N-Myc or C-Myc. Suitable peptide ligands that specifically bind to N-myc or C-myc are well-known in the art and include helical binding sequences from Aurora-A (see for example Richards et al. PNAS (2016) 113, 13726-31).

In some embodiments, the target molecule may be WDR5 (WD repeat-containing protein 5). Suitable peptide ligands that specifically bind to WDR5 are well-known in the art and include the WDR5-interacting motif (WIN) of MLL1 (mixed lineage leukemia protein 1) (see for example Song & Kingston J. Biol. Chem. (2008) 283, 35258-64; Patel et al. J. Biol. Chem. (2008) 283, 32158-61), e.g. EPPLNPHGSARAEVHLRKS (SEQ ID NO:31) and variants thereof.

In some embodiments, the target molecule may be BRD4 or a Bromodomain protein. Suitable peptide ligands that specifically bind to BRD4 are well-known in the art and include sequences derived from histone protein ligands.

In some embodiments, the target molecule may be a HDAC (histone deacetylase). Suitable peptide ligands that specifically bind to HDAC are well-known in the art and include binding sequences derived from SMRT and other proteins that recruit HDACs to specific transcriptional regulatory complexes or binding sequences derived from histone proteins (see for example Watson et al. Nat. Comm. (2016) 7, 11262; Dowling et al. Biochem. (2008) 47, 13554-63).

In some embodiments, the target molecule may be Notch. Suitable peptide ligands that specifically bind to Notch are well-known in the art and include binding sequences from the N-terminus of MAML1 (mastermind like protein 1), e.g. SAVMERLRRRIELCRRHHST (SEQ ID NO:32) and variants thereof (see for example Moellering et al. Nature (2009) 462, 182-8).

In some embodiments, the target molecule may be a Cdk (cyclin-dependent kinase). Suitable peptide ligands that specifically bind to Cdks are well-known in the art and include substrate-based peptides, for example, Cdk2 sequences derived from cyclin A, such as TYTKKQVLRMEHLVLKVLTFDL (SEQ ID NO:33) and variants thereof (see for example Gondeau et al. J. Biol. Chem. (2005) 280, 13793-800; Mendoza et al. Cancer Res. (2003) 63, 1020-4).

In some embodiments, the target molecule may be PLK1 (polo-like kinase 1). Suitable peptide ligands that specifically bind to PLK1 are well-known in the art and include optimised substrate-derived sequences that bind to the substrate-binding PBD (polo-box domain), such as MAGPMQSEPLMGAKK (SEQ ID NO:34) and variants thereof.

In some embodiments, the target molecule may be Tau. Suitable peptide ligands that specifically bind to Tau are well-known in the art and include tau-binding sequences derived from alpha- and beta-tubulin, such as KDYEEVGVDSVE (SEQ ID NO:35) and YQQYQDATADEQG (SEQ ID NO:36) and variants thereof (see for example Maccioni et al. EMBO J. (1988) 7, 1957-63; Rivas et al. PNAS (1988) 85, 6092-6).

In some embodiments, the target molecule may be BCR-ABL. Suitable peptide ligands that specifically bind to BCR-ABL are well-known in the art and include optimized substrate-derived sequences, such as EAIYAAPFAKKK (SEQ ID NO:37) and variants thereof.

In some embodiments, the target molecule may be PP2A (protein phosphatase 2A). Suitable peptide ligands that specifically bind to PP2A are well-known in the art and include sequences that bind the B56 regulatory subunit, such as LQTIQEEE (SEQ ID NO:38) and variants thereof (see for example Hetz et al. Mol. Cell (2016), 63 686-95).

some embodiments, the target molecule may be EED (Embryonic ectoderm development). Suitable peptide ligands that specifically bind to EED are well-known in the art and include helical binding sequences from co-factor EZH2 (enhancer of zeste homolog 2), such as FSSNRQKILERTEILNQEWKQRRIQPV (SEQ ID NO:39) and variants thereof (see for example Kim et al. Nat. Chem. Biol. (2013) 9, 643-50.)

In some embodiments, the target molecule may be MCL-1 (induced myeloid leukemia cell differentiation protein). Suitable peptide ligands that specifically bind to MCL-1 are well-known in the art and include sequences from BCL2, e.g. KALETLRRVGDGVQRNHETAF (SEQ ID NO:40) and variants thereof (see for example Stewart et al. Nat. Chem. Biol. (2010) 6, 595-601).

In some embodiments, the target molecule may be RAS. Suitable RAS peptide ligands are well-known in the art and include RAS-binding peptides identified by phage display, such as RRRRCPLYISYDPVCRRRR (SEQ ID NO:41) and variants thereof (see for example Sakamoto et al. BBRC (2017) 484, 605-11).

In some embodiments, the target molecule may be GSK3 (glycogen synthase kinase 3). Suitable GSK3 peptide ligands are well-known in the art and include substrate-competitive binding sequences such as KEAPPAPPQDP (SEQ ID NO:42), LSRRPDYR (SEQ ID NO:1436), RREGGMSRPADVDG (SEQ ID NO:44), and YRRAAVPPSPSLSRHSSPSQDEDEEE (SEQ ID NO:45) and variants thereof (see for example Ilouz et al. J. Biol. Chem. 281 (2006), 30621-30630. Plotkin et al. J. Pharmacol. Exp. Ther. (2003) 305, 974-980).

In some embodiments, the target molecule may be CtBP (C-terminal binding protein). Suitable CtBP peptide ligands are well-known in the art and include sequences identified from a cyclic peptide library screen, such as SGWTVVRMY (SEQ ID NO:46) and variants thereof (see for example Birts et al. Chem. Sci. (2013) 4, 3046-57).

Examples of suitable peptide ligands for target molecules that may be used in a chimeric protein as described herein are shown in Tables 2 and 7.

E3 Ligase Peptide Ligands

In some preferred embodiments, a chimeric protein as described herein may comprise a peptide ligand for an E3 ubiquitin ligase. Examples of suitable E3 ubiquitin ligases include MDM2, SCF^Skp2, BTB-CUL3-RBX1, APC/C, SIAH, CHIP, Cul4-DDB1, SCF-family, β-TrCP, Fbw7 and Fbx4.

E3 Ligase Peptide Ligands

Suitable peptide ligands for E3 ubiquitin ligases (degrons) are well known in the art and may be 5 to 20 amino acids. For example, a suitable peptide ligand for MDM2 may include a peptide ligand from p53 (e.g. FAAYWNLLSAYG) (SEQ ID NO:47) and or a variant thereof. A suitable peptide ligand for SCF^Skp2may include a peptide ligand from p27 (e.g. AGSNEQEPKKRS) (SEQ ID NO:48) and variants thereof. A suitable peptide ligand for Keap1-Cul3 may include a peptide ligand from Nrf2 (e.g. DPETGEL) (SEQ ID NO:49) or a variant thereof. A suitable peptide ligand for SPOP-Cul3 may be include a peptide ligand from Puc (e.g. LACDEVTSTTSSSTA (SEQ ID NO:50) or a variant thereof. A suitable peptide ligand for APC/C may include the degrons termed ABBA (e.g. SLSSAFHVFEDGNKEN) (SEQ ID NO:51), KEN (e.g. SEDKENVPP) (SEQ ID NO:52), or DBOX (e.g. PRLPLGDVSNN) (SEQ ID NO:53) or a variant thereof. In some instances, a combination of these degrons for may be used (mimicking the bipartite or tripartite degrons found in some natural substrates). A suitable peptide ligand for SIAH may include a peptide ligand from PHYL (e.g. LRPVAMVRPTV) (SEQ ID NO:54) or a variant thereof. A suitable peptide ligand for CHIP (carboxyl terminus of Hsc70-interacting protein) may include peptide sequences such as ASRMEEVD (SEQ ID NO:55) (from Hsp90 C-terminus) and GPTIEEVD (SEQ ID NO:56) (from Hsp70 C-terminus) or a variant thereof. A suitable peptide ligand for beta-TrCP may include a degron sequence motif (including phosphomimetic amino acids), such as DDGYFD (SEQ ID NO:57) or a variant thereof. A suitable peptide ligand for Fbx4 may include sequences derived from TRF1, such as MPIFWKAHRMSKMGTG (SEQ ID NO:58) or a variant thereof (see for example Lee et al. Chembiochem (2013) 14, 445-451). A suitable peptide ligand for FBw7 may include degron sequence motifs (including phosphomimetic amino acids), such as LPSGLLEPPQD (SEQ ID NO:59). A suitable peptide ligand for DDB1-Cul4 may include sequences derived from HBx (hepatitis B virus X protein) and similar proteins from other viruses and from DCAFs (DDB1-CUL4-associated factors) including helical motifs such as ILPKVLHKRTLGL (SEQ ID NO:60), NFVSWHANRQLGM (SEQ ID NO:61), NTVEYFTSQQVTG (SEQ ID NO:62), and NITRDLIRRQIKE (SEQ ID NO:63) (see for example Li et al. Nat. Struct. Mol. Biol. (2010) 17, 105-111).

E3 Ligases and E3 Ligase Peptide Ligands

Examples of suitable peptide ligands for E3 ubiquitin ligases that may be used in a chimeric protein as described herein are shown in Table 3.

A chimeric protein comprising a peptide ligand for an E3 ubiquitin ligase may also comprise a peptide ligand for a target molecule. Without being bound to any one hypothesis, binding of the chimeric protein to both the target molecule and the E3 ubiquitin ligase may cause the target molecule to be ubiquitinated by the E3 ubiquitin ligase. Ubiquitinylated target molecules may then degraded by the proteasome. This allows the specific targeting of molecules for proteolysis by the chimeric protein. The ubiquitination and subsequent degradation of a target protein has been shown for hetero-bifunctional small molecules (PROTACs; proteolysis targeting chimeras) that bind the target protein and a ubiquitin ligase simultaneously (see for example Bondeson et al. Nat. Chem. Biol. 2015; Deshaies 2015; Lu et al. 2015).

In some embodiments, the chimeric protein may lack lysine residues, so that it avoids ubiquitination by the E3 ubiquitin ligase.

Examples of chimeric proteins that bind E3 ubiquitin ligase and a target molecule are shown in Tables 1 and 8.

A suitable chimeric protein may comprise an N terminal peptide ligand that binds a target protein, such as β catenin, and a C terminal peptide ligand that binds an E3 ubiquitin ligase. For example, the N terminal peptide ligand may be a β catenin-binding sequence derived from Bcl9 and the C terminal peptide ligand may be an Mdm2-binding sequence derived from p53. Alternatively, a chimeric protein may comprise a C terminal peptide ligand that binds a target protein, such as β catenin, and an N terminal peptide ligand that binds an E3 ubiquitin ligase (see FIG. 10A).

Another suitable chimeric protein may comprise three repeat domains, a peptide ligand located in an inter-repeat loop that binds a target protein, such as β catenin, and a C terminal peptide ligand that binds an E3 ubiquitin ligase. For example, the inter-repeat loop peptide ligand may be derived from the phosphorylated region of APC (adenomentous polyposis coli) and the C terminal peptide ligand may be an Mdm2-binding sequence derived from p53. Alternatively, the chimeric protein may comprise a peptide ligand located in an inter-repeat loop that binds an E3 ubiquitin ligase, and a C terminal peptide ligand that binds a target protein, such as β catenin (See FIG. 10B).

Another suitable chimeric protein may comprise three repeat domains, an N terminal peptide ligand that binds a target protein, such as β catenin, and a peptide ligand located in an inter-module loop that binds an E3 ubiquitin ligase. For example, the N terminal peptide ligand may be a β catenin-binding sequence derived from LRH1 (liver receptor homolog 1) and the inter-module loop peptide ligand may be a sequence derived from the Skp2-targeting region of p27. Alternatively, the chimeric protein may comprise an N terminal peptide ligand that binds an E3 ubiquitin ligase and a peptide ligand located in an inter-module loop that binds a target protein, such as β catenin (see FIG. 10C).

Another suitable chimeric protein may comprise four repeat domains, a first peptide ligand located in an inter-repeat loop that binds an E3 ubiquitin ligase and a second peptide ligand located in an inter-repeat loop that binds a target molecule. The first and second inter-repeat loops may be separate by an inter-repeat loop lacking a peptide ligand. For example, the first peptide ligand may be located in the first inter-repeat loop inter-repeat loop from the N terminus and the second peptide ligand may be located in the third inter-repeat loop from the N terminus or vice versa.

In some preferred embodiments, a chimeric protein as described herein may comprise an amino acid shown in Table 8 or a variant thereof.

In other preferred embodiments, a chimeric protein as described herein may comprise a peptide ligand that binds to a component of a target-selective autophagy pathway, such as chaperone-mediated autophagy (CMA). The chimeric protein and target molecules bound thereto are thus recognised by the autophagy pathway and the target molecules are subsequently degraded. Suitable components of the CMA pathway include heat shock cognate protein of 70 kDa (hsc70, HSPA8, Gene ID: 3312). Suitable peptide ligands are well known in the art (Dice J. F. (1990). Trends Biochem. Sci. 15, 305-309) and include Lys-Phe-Glu-Arg-Gln (KFERQ (SEQ ID NO:64)) and variants thereof, such as CMA_Q and CMA_K, as described herein. These domains have been demonstrated to be capable of targeting heterologous proteins to the autophagy pathway (Fan, X. et al; (2014) Nature Neuroscience 17, 471-480).

In addition to repeat domains and peptide ligands, a chimeric protein may further comprise one or more additional domains which confer additional functionality, such as targeting domains, intracellular transport domains, stabilising domains or oligomerisation domains. Additional domains may for example be located at the N or C terminus of the chimeric protein or in a loop between repeats.

A targeting domain may be useful in targeting the chimeric protein to a particular destination in vivo, such as a target tissue, cell, membrane or intracellular organelle. Suitable targeting domains include chimeric antigen receptors (CARs).

An intracellular transport domain may facilitate the passage of the chimeric protein through the cell membrane into cells, for example to bind intracellular target molecules. Suitable intracellular transfer domains are well known in the art (see for example Bechara et al FEBS Letters 587 1 (2013) 1693-1702) and include cell-penetrating peptides (CPPs), such as Antennapedia (43-58), Tat (48-60), Cadherin (615-632) and poly-Arg.

A stabilising domain may increase the half-life of the chimeric protein in vivo. Suitable stabilising domains are well known in the art and include Fc domains, serum albumin, unstructured peptides such as XTEN⁹⁸or PAS⁹⁹and polyethylene glycol (PEG).

An oligomerisation domain may facilitate the formation of multi-protein complexes, for example to increase avidity against multi-valent targets. Suitable oligomerisation domains include the ‘foldon’ domain, the natural trimerisation domain of T4 fibritin (Meier et al., J. Mol. Biol. (2004) 344(4):1051-69).

In addition to repeat domains, peptide ligands and optionally one or more additional domains, a chimeric protein may further comprise a cytotoxic or therapeutic agent and/or or detectable label.

Suitable cytotoxic agents include, for example, chemotherapeutic agents, such as methotrexate, auristatin adriamicin, doxorubicin, melphalan, mitomycin C, ozogamicin, chlorambucil, maytansine, emtansine, daunorubicin or other intercalating agents, enzymatically active toxins of bacterial, fungal, plant, or animal origin, such as diphtheria A chain, nonbinding active fragments of diphtheria toxin, exotoxin A chain, ricin A chain, abrin A chain, modeccin A chain, α-amanitin, alpha-sarcin, Aleurites fordii proteins, tubulysins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII, and PAP-S), Momordica charantia inhibitor, curcin, crotin, Sapaonaria officinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin, pyrrolobenzodiazepines, and the tricothecenes and fragments of any of these. Suitable cytotoxic agents may also include radioisotopes. A variety of radionuclides are available for the production of radioconjugated chimeric proteins including, but not limited to, ⁹⁰Y, ¹²⁵I, ¹³¹I, ¹²³I, ¹³¹In, ¹⁰⁵Rh, ¹⁵³Sm, ⁶⁷Cu, ⁶⁷Ga, ¹⁶⁶Ho, ¹⁷⁷Lu, ¹⁸⁶Re, ¹⁸⁸Re and ²¹²Bi. Conjugates of a chimeric protein and one or more small anti-cancer molecules, for example toxins, such as a calicheamicin, maytansinoids, a trichothene, and CC1065, and the derivatives of these toxins that have toxin activity, may also be used.

Suitable therapeutic agents may include cytokines (e.g. IL2, IL12 and TNF), chemokines, pro-coagulant factors (e.g. tissue factor), enzymes, liposomes, and immune response factors.

A detectable label may be any molecule that produces or can be induced to produce a signal, including but not limited to fluorescers, radiolabels, enzymes, chemiluminescers or photosensitizers. Thus, binding may be detected and/or measured by detecting fluorescence or luminescence, radioactivity, enzyme activity or light absorbance. Detectable labels may be attached to chimeric proteins using conventional chemistry known in the art.

There are numerous methods by which the label can produce a signal detectable by external means, for example, by visual examination, electromagnetic radiation, heat, and chemical reagents. The label can also be bound to another specific binding member that binds the chimeric protein, or to a support.

In some embodiments, a chimeric protein may be configured for display on a particle or molecular complex, such as a cell, ribosome or phage, for example for screening and selection. A suitable chimeric protein may further comprise a display moiety, such as phage coat protein, to facilitate display on a particle or molecular complex. The phage coat protein may be fused or covalently linked to the chimeric protein.

Providing a Chimeric Protein According to the Invention

Chimeric proteins as described herein may be produced by recombinant means. For example, a method of producing a chimeric protein as described herein may comprise expressing a nucleic acid encoding the chimeric protein. A nucleic acid may be expressed in a host cell and the expressed chimeric protein may then be isolated and/or purified from the cell culture.

In some embodiments, the recombinant method may comprise;

- inserting a first nucleic acid encoding a peptide ligand into a second nucleic acid encoding two or more repeat domains, e.g, a TPR repeat as described herein, e.g., CTPR or RTPR2, to produce a chimeric nucleic acid encoding a chimeric protein comprising a peptide ligand. The first nucleic acid may be inserted into an inter-repeat loop (for example, the RTPR2 scaffold contains a 20 amino acid loop and the first peptide ligand may be inserted anywhere between codons encoding two loop amino acids. Alternatively, the first nucleic acid may be inserted into the second nucleic acid at the codon encoding the N-terminus or the C-terminus of the scaffold such that the peptide is in-frame with the scaffold, thereby forming a chimeric nucleic acid encoding a chimeric protein (a grafted scaffold); and,
- expressing the chimeric nucleic acid to produce the chimeric protein.

Methods described herein may be useful in producing a chimeric protein that binds to a first target molecule and a second target molecule. For example, a method may comprise;

- providing a nucleic acid encoding two or more repeat domains linked by inter-repeat loops, each repeat domain; and
- incorporating into the nucleic acid a first nucleotide sequence encoding a first peptide ligand that binds to a first target molecule and a second nucleotide sequence encoding a second peptide ligand that binds to a second target molecule to generate a nucleic acid encoding a chimeric protein comprising the first and second peptide ligands, wherein the first nucleotide sequence encoding the first peptide ligand is located in an inter-repeat loop or at the N or C terminus of the grafted scaffold and the second nucleotide sequence encoding the second peptide ligand is located in a different inter-repeat loop than the first peptide ligand or is located at the N or C terminus wherein the first peptide ligand is not located; and
- expressing the nucleic acid to produce the chimeric protein.

One of the first and second target molecules may be an E3 ubiquitin ligase. For example, a method may comprise;

- providing a nucleic acid encoding two or more repeat domains linked by inter-repeat loops between the repeat domains; and
- incorporating into the nucleic acid a first nucleotide sequence encoding a first peptide ligand that binds to a target molecule and a second nucleotide sequence encoding a second peptide ligand that binds to an E3 ubiquitin ligase to generate a nucleic acid encoding a chimeric protein comprising the first and second peptide ligands, wherein the first and second peptide ligands are located (i) in different inter-repeat loops or (ii) the first ligand is located in an inter-repeat loop while the second peptide ligand is located at the N or C terminus of the scaffold, or (iii) the first and second peptide ligands are located at the N and C termini of the scaffold, respectively; and
- expressing the nucleic acid to produce the protein.

An isolated nucleic acid encoding a chimeric protein as described herein is provided as an aspect of the invention. The nucleic acid may be comprised within an expression vector. Suitable vectors can be chosen or constructed, containing appropriate regulatory sequences, including promoter sequences, terminator fragments, polyadenylation sequences, enhancer sequences, marker genes and other sequences as appropriate. Preferably, the vector contains appropriate regulatory sequences to drive the expression of the nucleic acid in a host cell.

Suitable regulatory sequences to drive the expression of heterologous nucleic acid coding sequences in expression systems are well-known in the art and include constitutive promoters, for example viral promoters such as CMV or SV40, and inducible promoters, such as Tet-on controlled promoters. A vector may also comprise sequences, such as origins of replication and selectable markers, which allow for its selection and replication and expression in bacterial hosts such as E. coli and/or in eukaryotic cells.

Many techniques and protocols that are suitable for the expression of recombinant chimeric proteins in cell culture and their subsequent isolation and purification are known in the art (see for example Protocols in Molecular Biology, Second Edition, Ausubel et al. eds. John Wiley & Sons, 1992; Recombinant Gene Expression Protocols Ed RS Tuan (March 1997) Humana Press Inc).

A host cell comprising a nucleic acid encoding a chimeric protein as described herein or vector containing such a nucleic acid is also provided as an aspect of the invention. Suitable host cells include bacteria, mammalian cells, plant cells, filamentous fungi, yeast and baculovirus systems and transgenic plants and animals. The expression of proteins in prokaryotic cells is well established in the art. A common bacterial host is E. coli. A chimeric protein may also be produced by expression in eukaryotic cells in culture. Mammalian cell lines available in the art for expression of a chimeric protein include Chinese hamster ovary (CHO) cells, HeLa cells, baby hamster kidney cells, NS0 mouse melanoma cells, YB2/0 rat myeloma cells, human embryonic kidney cells (e.g. HEK293 cells), human embryonic retina cells (e.g. PerC6 cells) and many others.

The following procedures and assays may be used according to the invention.

Preparation of Grafted Scaffold Protein

Large-Scale Protein Purification (His-Tagged) from E. coli

The pRSET B (His-tag) constructs are transformed into chemically competent E. coli C41 cells by heat shock and plated on LB-Amp plates. Colonies are grown in 2TY media containing ampicillin (50 micrograms/mL) at 37° C., 220 rpm until the optical density (O.D.) at 600 nm reached 0.6. Cultures are then induced with IPTG (0.5 mM) for 16-20 h at 20° C. or 4 h at 37° C. Cells are pelleted by centrifugation at 3000 g (4° C., 10 min) and resuspended in lysis buffer (10 mM sodium phosphate pH 7.4, 150 mM NaCl, 1 tablet of SIGMAFAST protease inhibitor cocktail (EDTA-free per 100 mL of solution), then lysed on a Emulsiflex C5 homogenizer at 15000 psi. Cell debris is pelleted by centrifugation at 15,000 g at 4° C. for 45 mM. Ni-NTA beads 50% bed volume (GE Healthcare) (5 mL) are washed once with phosphate buffer (10 mM sodium phosphate pH 7.4, 150 mM NaCl) before the supernatant of the cell lysate is bound to them for 1 hr at 4° C. in batch. The loaded beads are washed three times with phosphate buffer (40 mL) containing 30 mM of imidazole to prevent non-specific interaction of lysate proteins with the beads. Samples are eluted using phosphate buffer with 300 mM imidazole, and purified by size-exclusion chromatography using a HiLoad 16/60 SuperdexG75 column (GE Life-Science) pre-equilibrated in phosphate buffer (10 mM sodium phosphate, pH 7.4, 150 mM NaCl) and proteins separated in isocratic conditions. Purity is checked on NuPage protein gel (Invitrogen), and fractions found to be over 95% pure are pooled. Purified protein is flash-frozen and stored at −80° C. until further use. Concentrations are determined by measuring absorbance at 280 nm and using a calculated extinction coefficient from ExPASy ProtParam (Gasteiger et al. 2005) for each variant. Molecular weight and purity is confirmed using mass spectrometry (MALDI).

Large-Scale Protein Purification (Heat Treatment) from E. coli

Many of the chimeric proteins described herein are thermally very stable, with melting temperatures above 80° C. This means that the chimeric proteins could be separated from E. coli proteins by incubating the cell lysates at 65° C. for 20 mM. Very few of the E. coli proteins will remain folded at such temperatures, and therefore, they will unfold and aggregate. Aggregated proteins are removed by centrifugation, leaving 80-90% pure sample of the desired protein. Constructs that fold reversibly can be further purified by methods such as acetone or salt precipitation to remove DNA and other contaminants.

This approach allows the production of large amounts of functional proteins without expensive affinity purification methods such as antibodies or His tags and is potentially scalable to industrial production and bioreactors.

Small-Scale Purification of His-Tagged Proteins for Higher-Throughput Testing

Plasmids are transformed into E. coli C41 cells and plated overnight. 15 mls of 2TY medium (Roche) containing 50 micrograms/ml ampicillin is placed in each one f multiple 50 ml tubes. Several colonies are picked from the plates and resuspended in each 15 ml culture. For sufficient aeration it is important to only loosely tighten the lids of the 50 ml tubes. Cells are grown at 37° C. until OD600 of 0.6 and then induced with 0.5 mM IPTG overnight. Cells are pelleted at 3000 g (Eppendorf Centrifuge 5804) and then resuspended in 1 ml of BugBuster® cell lysis reagent. Alternatively, sonication in combination with lysozyme and DNAse I treatment is used. The lysate is spun at 12000 g for 1 minute to pellet any insoluble protein and cell debris.

The supernatant is added to 100 μl bed volume of pre-washed Ni-NTA agarose beads. The subsequent affinity purification is performed in batch, by washing the beads 4 times with 1 ml of buffer each time (alternatively, Qiagen Ni-NTA Spin Columns can be used). The first ish contained 10% BugBuster® solution and 30 mM imidazole in the chosen buffer. Here we used 50 mM sodium phosphate buffer pH 6.8, 150 mM NaCl. The three successive ishes had 30 mM of imidazole in the chosen buffer. Beads are washed thoroughly to remove the detergent present in the BugBuster® solution. Protein is eluted from the beads in a single step using 1 ml of chosen buffer containing 300 mM imidazole. The combination of Bugbuster® and imidazole and the repeat washes in small bead volumes yielded >95% pure protein. Imidazole is removed using a NAP-5 disposable gel-filtration column (GE Healthcare).

Measuring Binding of Grafted Scaffold Protein to Target Protein

Competition Fluorescence Polarisation (FP) Assay

To measure the binding of a grafted scaffold to a target protein, Competition FP can be performed using 384-well black opaque optiplate microplates and a CLARIOstar microplate reader. The grafted scaffold protein is titrated into a solution containing a mixture of FITC-labelled peptide ligand and target binding partner (target protein). The prepared plates are incubated for 30 minutes at room temperature before readings are taken. The grafted scaffold is then titrated into the preformed FITC-peptide-target protein complex. A decrease in polarisation with increasing concentrations of grafted scaffold indicates displacement of FITC-peptide upon binding of the grafted scaffold to its target.

Isothermal Titration calorimetry (ITC)

ITC can be performed using a VP-ITC instrument (Microcal). Grafted scaffolds are dialysed into 10 mM sodium phosphate buffer pH 7.4, 150 mM NaCl, 0.5 mM TCEP. Dialysed target protein (200 μM) is titrated into the sample cell containing the grafted scaffold at 20 μM. Injections of target protein into the cell are initiated with a 5 μL injection, followed by 29 injections of 10 μL. The reference power is set at 15 μCal/s with an initial delay of 1000 s and a stirring speed of 485 rpm. Data are fitted using the instrument software a one-site binding model.

Cell Culture and Cell Transfection

HEK293T cells are cultured in Dulbecco's Modified Eagle's Medium (Sigma Aldrich) supplemented with 10% fetal bovine serum and penicillin/streptomycin (LifeTech) at 37° C. with 5% CO₂air supply.

HEK293T are seeded in 6-well tissue culture plates (500,000 cells per well) and transfected the next day using the Lipofectamine2000 transfection reagent (Invitrogen) according to the manufacturer's protocol.

Western Blot Assay of Target-Protein Engagement and of Target-Protein Levels

Plasmid encoding the target protein (1 μg) alone and with plasmid encoding one of various target-specific grafted scaffolds (1 μg) is transfected in HEK293T cells in 6-well plates using Lipofectamine2000. After 48 hours of transfection, the cells are lysed in 200 μL of Laemmli buffer. After sample is boiled at 95° C. for 20 min proteins are resolved by SDS-PAGE and transferred to a PVDF membrane, and immunoblotting is performed using anti-HA (C29F4, Cell Signaling Technologies) and anti-actin (A2066, Sigma-Aldrich) antibodies. Changes in target protein levels upon co-transfection with bifunctional grafted scaffolds are evaluated by the densitometry of the bands corresponding to the target protein normalised to actin levels using ImageJ. Co-immunoprecipitation can also be used to show that the grafted scaffold binds to the target protein and/or to the desired component of the degradation machinery.

Liposomal Formulation and Cytotoxicity Assay

To make liposomal formulations of proteins (LFP), lipids (DOTAP (cationic): DOPE (neutral): DiR (aromatic)=1:1:0.1 w/w) are dissolved in chloroform, and solvent is evaporated under vacuum overnight. Resulting mixed lipid cake is hydrated with 10 mM HEPES pH 7.4, containing 27 μM protein, so that the total lipid concentration is 4 mg/ml. This mixture is vortexed for 2 minutes and then sonicated for 20 minutes at room temperature. Liposomes encapsulating proteins are stored at 4° C. until further use. To make empty liposomes (EL, empty liposomes without proteins), lipid cake is hydrated with 10 mM HEPES pH 7.4 without proteins.

An ATP assay is used to investigate whether there is any cytotoxicity associated with EL and LFP. In a typical procedure, 2×10⁵HEK 293T cells/well in 500 μL of Dulbecco's Modified Eagles Medium (DMEM) supplemented with 10% fetal bovine serum are grown for 24 hours in a 24-well cell culture plate. Cells are incubated with liposome (EL/LFP)-media (DMEM without FBS) mix, having different volumes (0-60 μL) of EL and LFP, for 15 minutes at 37° C. After washing twice with 1×PBS, 500 μL of CellTiter-Glo® Reagent (Promega) is added and luminescence is measured using a microplate reader as par the manufacture's protocol. Untreated cells are used as control. Data are obtained from triplicate samples, and the standard deviations are calculated from two independent experiments.

HiBit Split-Luciferase Assay

An alternative method for measuring target protein levels is the Nano-Glo® HiBiT Lytic Detection System from Promega Corporation. It is based on the split NanoLuc assay, which consists of a large N-terminal fragment (LgBiT) and a small C-terminal region (SmBiT). Five of the SmBiT amino acids have been replaced to produce the HiBiT (VSGWRLFKKIS) (SEQ ID NO: 3102) fragment, which has greater affinity for the LgBiT fragment and maintains NanoLuc luciferase activity. Either the HiBiT-tagged target DNA can be transient transfected or the endogenous target can be monitored by knock-in of the HiBiT tag sequence using CRISPR/Cas9 technology. Subsequent introduction of the complementary polypeptide, LgBiT, results in spontaneous and high affinity interaction between the HiBiT tag and LgBiT to reconstitute the luminescent NanoBit® enzyme. Detection of tagged protein levels is possible from live or lysed cells.

Protein is introduced into HEK293T cells by either DNA transient transfection or encapsulation within fusogenic liposomes. HEK293T cells are seeded into either 24-well or 96-well plates After 24 hours, DNA encoding the HiBiT-tagged target protein (20 ng for 96-well plate; 100 ng for 24-well plate) is transiently transfected into cells. Chimeric protein DNA (100 ng) is either transiently transfected into cells at the same time as HiBiT-target DNA transfection or encapsulated into liposomes and introduced 24 hours into the cells after transfection. Cells are treated with chimeric protein-containing liposomes for 15 minutes before 2 hours of incubation.

Nano-Glo® HiBiT Lytic Buffer (LgBiT protein (1:100), Nano-Glo® HiBiT Lytic Substrate (1:50) 1×PBS (1:1)) is added to the cells 24 hours after transient transfection or 2 hours after liposomal treatment. The plates are shaken on an orbital shaker (1,000 rpm, 10 min) to ensure homogenous cell lysis and equilibration of LgBiT and HiBiT in the cell lysate. The luminescence measurements are performed in white Nunclon™ Delta 96-well plates at 25° C. using a CLARIOstar plate reader using a 460-480 emission filter.

Determining Properties of a Grafted Scaffold

The biophysical properties of a grafted scaffold may be assessed as follows: The molar ellipticity at 222 nm (a measure of helical structure content) is monitored as a function of increasing temperature. A decrease in the molar ellipticity with increasing temperature indicates a loss of structure and the unfolding of the protein. This thermal unfolding experiment is used to determine the melting temperature of the scaffold and thereby to assess whether or not the grafting process has had a detrimental effect on the thermostability of the scaffold.

An alternative method to determine the thermodynamic stability of the proteins is to measure chemical-induced denaturation (either guanidine hydrochloride (GdnHCl) or urea) monitored by intrinsic protein fluorescence (tryptophan and tyrosine residues). Solutions are dispensed into Corning® 96-well, half-area, black polystyrene plates (CLS3993) with a Microlab ML510B dispenser (Hamilton) and measurements are carried out on a CLARIOstar Plate Reader (BMG Labtech). The buffer is added first into the wells, followed by 15 μl aliquots of protein stock. A stock solution of chemical denaturant (either 7 M GdnHCl or 9 M urea) is then dispensed into the wells to create a chemical-denaturant concentration gradient.

Preparation of a Helix-Grafted Scaffold that Binds to a Target Protein

First, the helix of a given protein that interacts with its target binding partner is mapped onto the heptad distribution, and the stapled side of the peptide is set so as to form the hydrophobic interface with the rest of the scaffold protein. The grafted scaffold may then be docked against the target protein using Haddock software (de Vries & Bonvin 2011; de Vries et al. 2010). Haddock is a data-driven docking algorithm that uses known information about the interaction for its calculations. The active (primary interaction residues) and the passive (5 Å proximity to active) residues are extracted and inputted into the calculations. Docking is not necessary to validate helical grafted scaffold, and inspection of the structure of the helix-target protein structure and of the scaffold structure may be sufficient: The geometry of alpha-helices permits selection of amino acid positions of the scaffold that accommodate outward facing target binding residues of the peptide ligand.

Preparation of a Grafted Scaffold with a Single Binding Function Grafted onto an Inter-Repeat Loop

First, a peptide ligand that binds to a given target protein is grafted onto the scaffold in a loop. Binding of the loop-grafted scaffold may be tested using ITC. ITC is particularly useful to assess these interactions, as it can measure the stoichiometry (n) of the interaction, and thus inform as to which loops (if there is more than one loop) are more or less accessible to the target protein, and can inform as to whether a multi-loop scaffold affords multivalency. An advantage of a multivalent grafted scaffold is that one may achieve an avidity effect. This is particularly useful where a target molecule has multiple domains that can be bound by a peptide ligand. Binding of a multivalent grafted scaffold to such a target protein would produce an increased binding affinity and a decreased off rate according to the number of repeats in the grafted scaffold, thus achieving an avidity effect.

Introducing Multivalency into a Single Binding Function Scaffold

The function of a multi-valent grafted scaffold containing variable numbers of the peptide ligand binding motif that binds to a given target protein can be tested using the same assays as for the mono-valent grafted scaffold. The results are used to assess whether increased potency can be achieved by increasing the valency.

Preparing a Loop-Grafted Scaffold Using a Peptide Ligand that Binds to an E3 Ubiquitin Ligase

A peptide ligand that is known to bind the substrate recognition subunit of an E3 ligase (see Table 3 for such peptides and ligases) is inserted into the scaffold loop. Immunoprecipitation is used to confirm binding of the grafted scaffold to the E3 ligase. ITC analysis is used to assess the affinity of the interaction.

Preparation of Hetero-Bifunctional Scaffolds that Direct Target Proteins for Ubiquitination and Subsequent Degradation

A bispecific grafted scaffold is constructed using a peptide ligand specific for a target protein (see Table 2) and a peptide ligand specific for an E3 ligase.

To test whether these bispecific grafted scaffolds are capable of directing the target protein for ubiquitination and degradation, a plasmid encoding the hetero-bifunctional scaffold is transfected into HEK293T cells using Lipofectamine2000 together with HA-tagged β-catenin plasmid (using cells transfected with HA-tagged β-catenin plasmid alone as a control). After 48 hours of transfection, the cells are lysed, the sample is boiled and proteins are resolved by SDS-PAGE and immunoblotting is performed using anti-HA and anti-actin antibodies. Changes in target protein levels are evaluated by the densitometry of the bands corresponding to HA-target protein normalised to actin levels. In this way, different combinations of target protein binding peptides and E3 ligase peptide ligands can be compared for their abilities to reduce the levels of target protein.

Delivering a Grafted Scaffold Protein into Cells

A grafted scaffold protein is encapsulated within fusogenic liposomes made from cationic, neutral, and aromatic lipids, and then delivered into cells. Empty liposomes and liposomes encapsulating grafted scaffolds have been determined to be non-toxic to cells.

Libraries

Chimeric proteins as described herein may be used to produce libraries. For example, where a given chimeric protein (grafted scaffold) is demonstrated to binds bispecifically to a target protein and to an E3 ligase may be further optimized by changing amino acid residues of the grafted scaffold and selecting for stronger or weaker binders.

Chimeric proteins which are demonstrated to bind may be further engineered to improve an activity or property or introduce a new activity or property, for example a binding property such as affinity and/or specificity, an in vivo property such as solubility, plasma stability, or cell penetration, or an activity such as increased neutralization of the target molecule and/or modulation of a specific activity of the target molecule or an analytical property. Chimeric proteins may also be engineered to improve stability, solubility or expression level.

Alternatively, a library may be used to screen in order to identify and isolate chimeric proteins with specific binding activity.

A library may comprise chimeric proteins, each chimeric protein in the library comprising:

- (i) two or more repeat domains,
- (ii) inter-repeat loops linking the repeat domains; and
- (iii) one or more peptide ligands, each the peptide ligand being located in an inter-repeat loop or at the N or C terminus of the chimeric protein,
- wherein at least one amino acid residue in the peptide ligands in the library is diverse.

The residues at one or more positions in the peptide ligand of the chimeric proteins in the library may be diverse or randomised i.e. the residue located at the one or more positions may be different in different molecules in a population.

For example, 1 to 12 positions within a helical peptide ligand at the N or C terminus of the chimeric proteins in the library may be diverse or randomised. In addition, the non-constrained sequence of the peptide ligand may contain additional diversity. Alternatively or additionally, 1 to n positions within an inter-repeat peptide ligand of the chimeric proteins in the library may be diverse or randomised, where n is the number of amino acids in the peptide ligand.

In some embodiments, peptide ligands may be screened individually and a chimeric protein progressively assembled from repeat domains comprising peptide ligands identified in different rounds of screening. For example, a library may comprise chimeric proteins, each chimeric protein in the library comprising:

- (i) two or more repeat domains,
- (ii) inter-repeat loops linking the repeat domains; and
- (iii) one or more constant peptide ligands having the same amino acid sequence in each chimeric protein in the library and one or more diverse peptide ligands, preferably one diverse peptide ligand, having a different amino acid sequence in each chimeric protein in the library,
- the peptide ligands being located in an inter-repeat loop or at the N or C terminus of the chimeric protein.

At least one amino acid residue in the diverse peptide ligands in the library may be diverse.

A library may be produced by a method comprising:

- (a) providing a population of nucleic acids encoding a diverse population of chimeric proteins comprising
  - (i) two or more repeat domains,
  - (ii) inter-repeat loops linking the two or more repeat domains; and
  - (iii) one or more peptide ligands, each the peptide ligand being located in an inter-repeat loop or at the N or C terminus of the chimeric protein,
  - wherein one or more residues of a peptide ligand in each chimeric protein is diverse in the library, and
- (b) expressing the population of nucleic acids to produce the diverse population, thereby producing a library of chimeric proteins.

The population of nucleic acids may be provided by a method comprising inserting a first population of nucleic acids encoding a diverse peptide ligand into a second population of nucleic acids encoding the two or more repeat domains linked by inter-repeat loops, optionally wherein the first and second nucleic acids are linked with a third population of nucleic acids encoding linkers of up to 10 amino acids.

The nucleic acids may be contained in vectors, for example expression vectors. Suitable vectors include phage-based or phagemid-based phage display vectors.

The nucleic acids may be recombinantly expressed in a cell or in solution using a cell-free in vitro translation system such as a ribosome, to generate the library. In some preferred embodiments, the library is expressed in a system in which the function of the chimeric protein enables isolation of its encoding nucleic acid. For example, the chimeric protein may be displayed on a particle or molecular complex to enable selection and/or screening. In some embodiments, the library of chimeric proteins may be displayed on beads, cell-free ribosomes, bacteriophage, prokaryotic cells or eukaryotic cells. Alternatively, the encoded chimeric protein may be presented within an emulsion where activity of the chimeric protein causes an identifiable change. Alternatively, the encoded chimeric protein may be expressed within or in proximity of a cell where activity of the chimeric protein causes a phenotypic change or changes in the expression of a reporter gene.

Preferably, the nucleic acids are expressed in a prokaryotic cell, such as E coli. For example, the nucleic acids may be expressed in a prokaryotic cell to generate a library of recombine binding proteins that is displayed on the surface of bacteriophage. Suitable prokaryotic phage display systems are well known in the art, and are described for example in Kontermann, R & Dubel, S, Antibody Engineering, Springer-Verlag New York, LLC; 2001, ISBN: 3540413545, WO92/01047, U.S. Pat. Nos. 5,969,108, 5,565,332, 5,733,743, 5,858,657, 5,871,907, 5,872,215, 5,885,793, 5,962,255, 6,140,471, 6,172,197, 6,225,447, 6,291,650, 6,492,160 and 6,521,404. Phage display systems allow the production of large libraries, for example libraries with 10⁸or more, 10⁹or more, or 10¹⁰or more members.

In other embodiments, the cell may be a eukaryotic cell, such as a yeast, insect, plant or mammalian cell.

A diverse sequence as described herein is a sequence which varies between the members of a population i.e. the sequence is different in different members of the population. A diverse sequence may be random i.e. the identity of the amino acid or nucleotide at each position in the diverse sequence may be randomly selected from the complete set of naturally occurring amino acids or nucleotides or a sub-set thereof. Diversity may be introduced into the peptide ligand using approaches known to those skilled in the art, such as oligonucleotide-directed mutagenesis ²², Molecular Cloning: a Laboratory Manual: 3rd edition, Russell et al., 2001, Cold Spring Harbor Laboratory Press, and references therein).

Diverse sequences may be contiguous or may be distributed within the peptide ligand. Suitable methods for introducing diverse sequences into peptide ligand are well-described in the art and include oligonucleotide-directed mutagenesis (see Molecular Cloning: a Laboratory Manual: 3rd edition, Russell et al., 2001, Cold Spring Harbor Laboratory Press, and references therein). For example, diversification may be generated using oligonucleotide mixes created using partial or complete randomisation of nucleotides or created using codons mixtures, for example using trinucleotides. Alternatively, a population of diverse oligonucleotides may be synthesised using high throughput gene synthesis methods and combined to create a precisely defined and controlled population of peptide ligands. Alternatively, “doping” techniques in which the original nucleotide predominates with alternative nucleotide(s) present at lower frequency may be used.

Preferably, the library is a display library. The chimeric proteins in the library may be displayed on the surface of particles, or molecular complexes such as beads, for example, plastic or resin beads, ribosomes, cells or viruses, including replicable genetic packages, such as yeast, bacteria or bacteriophage (e.g. Fd, M13 or T7) particles, viruses, cells, including mammalian cells, or covalent, ribosomal or other in vitro display systems. Techniques for the production of display libraries, such as phage display libraries are well known in the art. Each particle or molecular complex may comprise nucleic acid that encodes the chimeric protein that is displayed by the particle.

In some preferred embodiments, the chimeric proteins in the library are displayed on the surface of a viral particle such as a bacteriophage. Each chimeric protein in the library may further comprise a phage coat protein to facilitate display. Each viral particle may comprise nucleic acid encoding the chimeric protein displayed on the particle. Suitable viral particles include bacteriophage, for example filamentous bacteriophage such as M13 and Fd.

Suitable methods for the generation and screening of phage display libraries are well known in the art. Phage display is described for example in WO92/01047 and U.S. Pat. Nos. 5,969,108, 5,565,332, 5,733,743, 5,858,657, 5,871,907, 5,872,215, 5,885,793, 5,962,255, 6,140,471, 6,172,197, 6,225,447, 6,291,650, 6,492,160 and 6,521,404.

Libraries as described herein may be screened for chimeric proteins which display binding activity, for example binding to a target molecule. Binding may be measured directly or may be measured indirectly through agonistic or antagonistic effects resulting from binding. A method of screening may comprise;

- (a) providing a library of chimeric proteins, each chimeric protein in the library comprising;
  - (i) two or more repeat domains,
  - (ii) inter-repeat loops linking the repeat domains; and
  - (iii) one or more peptide ligands, each the peptide ligand being located in an inter-repeat loop or at the N or C terminus of the chimeric protein,
  - wherein one or more residues of the one or more peptide ligands are diverse in the library,
- (b) screening the library for chimeric proteins which display a binding activity, and
- (c) identifying one or more chimeric proteins in the library which display the binding activity.

In some embodiments, the chimeric proteins in the library may comprise one peptide ligand with at least one diverse amino acid residue. Conveniently the chimeric proteins in the library comprise two repeat domains. The library may be screened for peptide ligands that bind to a target molecule. Peptide ligands identified in this fashion can be assembled in a modular fashion to generate a chimeric protein as described herein that is multi-specific.

For example, a first library may be screened for a first peptide ligand that binds to a first target molecule and a second library may be screened for a second peptide ligand that binds to a second target molecule. The first and second peptide ligands are in different locations in the chimeric protein i.e. they are not both N terminal peptide ligands, C terminal peptide ligands or inter-repeat peptide ligands. First and second peptide ligands that bind to the first and second target molecules, respectively, are identified from the first and second libraries. The identified first and second peptide ligands may then be incorporated into a chimeric protein that binds to the first and second target molecules.

A first library may comprise chimeric proteins in the library with a first diverse peptide ligand having at least one diverse amino acid residue. A first peptide ligand that binds to a target molecule may be identified from the first library. Chimeric proteins comprising the first peptide ligand may be used to generate a second library comprising a second diverse peptide ligand having at least one diverse amino acid residue. For example, the chimeric protein from the first library may be modified by addition of a second diverse peptide ligand at the N or C terminal or by the addition of additional repeat domains comprising the second diverse peptide ligand in an inter-repeat loop. A second peptide ligand that binds to the same or a different target molecule may be identified from the second library. Chimeric proteins comprising the first and second peptide ligands may be used to generate a third library comprising a third diverse peptide ligand having at least one diverse amino acid residue. For example, the chimeric protein from the second library may be modified by addition of a third diverse peptide ligand at the N or C terminal or by the addition of additional repeat domains comprising the third diverse peptide ligand in an inter-repeat loop. A third peptide ligand that binds to the same target molecule as the first and/or second peptide ligands or a different target molecule may be identified from the third library. In this way, a chimeric protein containing multiple peptide ligands may be sequentially assembled (see FIG. 16).

The use of separate libraries for each peptide ligand allows large numbers of different variants of each peptide ligand to be screened independently and then combined. For example, a phage library of 10⁸-10¹²first peptide ligand variants may be combined with a phage library of 10⁸-10¹²second peptide ligand variants and a phage library of 10⁸-10¹²third peptide ligand variants. In some embodiments, a phage library of 10⁸-10¹²N terminal peptide ligand variants may be combined with a phage library of 10⁸-10¹²C terminal peptide ligand variants to generate a chimeric protein with N and C terminal peptide ligands.

Screening a library for binding activity may comprise providing a target molecule and identifying or selecting members of the library that bind to the target, or expressing the library in a population of cells and identifying or selecting members of the library that elicit a cell phenotype. The one or more identified or selected chimeric proteins may be recovered and subjected to further selection and/or screening.

In other embodiments, the chimeric proteins in the library may comprise a first peptide ligand for a first target molecule, which has at least one diverse amino acid residue, and a second peptide ligand for a second target molecule, which has at least one diverse amino acid residue. The library may be screened for peptide ligands that bind to the first and second target molecules. For example, the library may be screened for chimeric proteins comprising a first peptide ligand that binds to a first target molecule and a second peptide ligand that binds to a second target molecule.

Screening a library for binding activity may comprise providing a target molecule and identifying or selecting members of the library that bind to the target, or expressing the library in a population of cells and identifying or selecting members of the library that elicit a cell phenotype. The one or more identified or selected chimeric protein may be recovered and subjected to further selection and/or screening.

Chimeric proteins as described herein may be used to produce libraries comprising different combinations of peptide ligands grafted into an scaffold. The combinations of ligands may comprise first peptide ligands that bind to a members of a protein degradation pathway, such as an E3 ubiquitin ligase, and second peptide ligands that bind to a target molecule. A library may be screened in order to identify and isolate chimeric proteins which display an activity selected from (i) binding to the member of a protein degradation pathway and the target molecule, (ii) causing degradation of the target molecule in a cell through the protein degradation pathway.

A library may comprise chimeric proteins, each chimeric protein in the library comprising:

(i) a scaffold;

(ii) a first peptide ligand for a member of a protein degradation pathway and

(iii) a second peptide ligand for a target molecule, the peptide ligands being located at and of the scaffold of the chimeric domain,

wherein different chimeric proteins in the library comprise different first peptide ligands for different members of the protein degradation pathway and different second peptide ligands for the target molecule, the chimeric proteins in the library comprising different combinations of the first and second peptide ligands.

Suitable chimeric proteins, target molecules and members of protein degradation pathways and examples of peptide ligands thereto are described elsewhere herein.

Preferably, the member of a protein degradation pathway is an E3 ubiquitin ligase. For example, each chimeric protein in a library of chimeric proteins may comprise:

(i) a scaffold;

(ii) a first peptide ligand for an E3 ubiquitin ligase and

(iii) a second peptide ligand for a target molecule, the peptide ligands being located at and of the scaffold of the chimeric domain,

Different chimeric proteins in the library may comprise a peptide ligand for a different E3 ubiquitin ligase. For example, the chimeric proteins in the library may comprise peptide ligands for a panel of E3 ubiquitin ligases, each chimeric protein in the library comprising a peptide ligand for one of the E3 ubiquitin ligases in the panel.

Numerous E3 ubiquitin ligases are known in the art. A suitable panel of E3 ubiquitin ligases may for example, comprise two, three, four, five or more of Mdm2, SCF(Skp2), Cul3-Keap1, Cul3-SPOP, APC/C, SIAH, SCF^Fbw7, SCF^Fbw8, Cul4-DDB1-Cdt2, DDB1-Cul4, DDB1-Cul5, SOCS box-Cul5-SPSB2, SOCS box-Cul5-SPSB4, CHIP, CRL4(COP1/DET), UBR5, CRL2(KLHDC2), GID4, TRIM21, Nedd4, Elongin C and β-TRP. Examples of peptide ligands for E3 ubiquitin ligases are shown in Table 3.

The target molecule may be a target molecule as described above, for example, β-catenin, KRAS, or myc. The chimeric proteins in the library may comprise different peptide ligands for the target molecule i.e. different chimeric proteins in the library may comprise different peptide ligands for the same target molecule. Each chimeric protein in the library may comprise a different peptide ligand for the target molecule. Examples of peptide ligands target molecules are shown in Table 3. For example, the target molecule may be β-cateran, KRAS, or myc and the chimeric proteins in the library may comprise different peptide ligands for β-catenin, KRAS, or myc, respectively. Examples of different peptide ligands for β-catenin, KRAS, and myc are shown in Table 3.

A method of screening a library of chimeric proteins may comprise;

(a) providing a library of chimeric proteins, each chimeric protein in the library comprising:

(i) a scaffold;

(ii) a first peptide ligand for a member of a protein degradation pathway and

(iii) a second peptide ligand for a target molecule, the peptide ligands being located at and of the scaffold of the chimeric domain,

wherein the chimeric proteins in the library comprise first peptide ligands for different members of a protein degradation pathway and different second peptide ligands for the target molecule, the chimeric proteins comprising different combinations of the first and second peptide ligands,

(b) screening the library for chimeric proteins which display an activity selected from (i) binding to the member of a protein degradation pathway and the target molecule and (ii) causing degradation of the target molecule in a cell through the protein degradation pathway,

(c) identifying one or more chimeric proteins in the library which display the activity.

In some embodiments, the member of a protein degradation pathway may be an E3 ubiquitin ligase. A method of screening a library of chimeric proteins may comprise;

(a) providing a library of chimeric proteins, each chimeric protein in the library comprising:

(i) a scaffold;

(ii) a first peptide ligand for an E3 ubiquitin ligase and

(iii) a second peptide ligand for a target molecule, the peptide ligands being located at and of the scaffold of the chimeric domain,

wherein the chimeric proteins in the library comprise first peptide ligands for different E3 ubiquitin ligases and different second peptide ligands for the target molecule, the chimeric proteins comprising different combinations of the first and second peptide ligands,

(b) screening the library for chimeric proteins which display an activity selected from (i) binding to an E3 ubiquitin ligase and the target molecule, (ii) causing ubiquitination of the target molecule by an E3 ubiquitin ligase in a cell and (iii) causing degradation of the target molecule in a cell,

(c) identifying one or more chimeric proteins in the library which display the activity.

A method may further comprise identifying one or more combinations of first and second peptide ligands in chimeric proteins in the library which display the activity.

Determination of Binding of a Chimeric Protein

Binding of a chimeric protein may be determined by any suitable technique, described below and in the examples herein.

Suitable methods for determining binding of a chimeric protein to a target molecule are well known in the art and include ELISA, bead-based binding assays (e.g. using streptavidin-coated beads in conjunction with biotinylated target molecules, surface plasmon resonance, flow cytometry, Western blotting, immunocytochemistry, immunoprecipitation, and affinity chromatography. Alternatively, biochemical or cell-based assays, such as fluorescence-based or luminescence-based reporter assays may be employed. For example, Isothermal Titration calorimetry, Cell transfection followed by assaying for expressed chimeric protein, Liposomal formulation and cytotoxicity assays, a dual-Luciferase Reporter Assay System such as TOPFLASH®, and a competition fluorescence polarisation (FP) assay to measure the binding of a chimeric protein to its targets.

In some embodiments, binding may be determined by detecting agonism or antagonism resulting from the binding of a chimeric protein to a target molecule, such as a ligand, receptor or enzyme.

Where a library is in use, the library may be contacted with the target molecule under binding conditions for a time period sufficient for the target molecule to interact with the library and form a binding reaction complex with a least one member thereof. Binding conditions are those conditions compatible with the known natural binding function of the target molecule. Those compatible conditions are buffer, pH and temperature conditions that maintain the biological activity of the target molecule, thereby maintaining the ability of the molecule to participate in its preselected binding interaction. Typically, those conditions include an aqueous, physiologic solution of pH and ionic strength normally associated with the target molecule of interest. The library may be contacted with the target molecule in the form of a heterogeneous or homogeneous admixture. Thus, the members of the library can be in the solid phase with the target molecule present in the liquid phase. Alternatively, the target molecule can be in the solid phase with the members of the library present in the liquid phase. Still further, both the library members and the target molecule can be in the liquid phase.

Multiple rounds of panning may be performed in order to identify chimeric proteins which display the binding activity. For example, a population of chimeric proteins enriched for the binding activity may be recovered or isolated from the library and subjected to one or more further rounds of screening for the binding activity to produce one or further enriched populations. Chimeric proteins which display binding activity may be identified from the one or more further enriched populations and recovered, isolated and/or further investigated.

In some embodiments, binding may be determined by detecting agonism or antagonism resulting from the binding of a chimeric protein to a target molecule, such as a ligand, receptor or enzyme. For example, the library may be screened by expressing the library in reporter cells and identifying one or more reporter cells with altered gene expression or phenotype. Suitable functional screening techniques for screening recombinant populations of chimeric proteins are well-known in the art.

Further rounds of screening may be employed to identify chimeric proteins which display the improved property or activity. For example, a population of chimeric proteins enriched for binding to the target molecule may be recovered or isolated from the library and subjected to one or more further rounds of screening for the improved or new property or activity to produce one or further enriched populations. Optionally, this may be repeated one or more times. Chimeric proteins which display the improved property or activity may be identified from the one or more further enriched populations and recovered, isolated and/or further investigated.

A chimeric protein as described herein may be encapsulated in a liposome, for example for delivery into a cell. Preferred liposomes include fusogenic liposomes. Suitable fusogenic liposomes may comprise a cationic lipid, such as 1, 2-dioleoyl-3-trimethylammoniumpropane (DOTAP), and a neutral lipid, such as dioleoylphosphatidylethanolamine (DOPE) for example in a 1:1 (w/w) ratio. Optionally, a liposome may further comprise an aromatic lipid, such as DiO (3, 3′-dioctadecyloxacarbocyanine perchlorate), DiR (1, 1′-dioctadecyl-3, 3, 3′, 3′-tetramethylindotricarbocyanine iodide), N-(4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-sindacene-3-propionyl)-1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine (triethylammonium salt) (BODIPY FL-DHPE), and 2-(4,4-difluoro-5-methyl-4-bora-3a,4a-diazas-indacene-3-dodecanoyl)-1-hexadecanoyl-sn-glycero-3-phosphocholine (BODIPY-C12HPC) for example in a 0.1:1:1 (w/w) ratio relative to the neutral and cationic lipid. Suitable techniques for the encapsulation of proteins in liposomes and their delivery into cells are established in the art (see for example, Kube et al Langmuir (2017) 33 1051-1059; Kolaginac et al (2018) Int. J. Mol. Sci. 19 346).

A method described herein may comprise admixing a chimeric protein or encoding nucleic acid as described herein with a solution of lipids, for example in an organic solvent, such as chloroform, and evaporating the solvent to produce liposomes encapsulating the chimeric protein. Liposome encapsulations comprising a chimeric protein as described herein are provided as an aspect of the invention.

A chimeric protein or encoding nucleic acid as described herein may be admixed with a pharmaceutically acceptable excipient. A pharmaceutical composition comprising a chimeric protein or nucleic acid as described herein and a pharmaceutically acceptable excipient is provided as an aspect of the invention.

The term “pharmaceutically acceptable” as used herein pertains to compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgement, suitable for use in contact with the tissues of a subject (e.g., human) without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio. Each carrier, excipient, etc. must also be “acceptable” in the sense of being compatible with the other ingredients of the formulation. Suitable carriers, excipients, etc. can be found in standard pharmaceutical texts, for example, Remington's Pharmaceutical Sciences, 18th edition, Mack Publishing Company, Easton, Pa., 1990.

Pharmaceutical Compositions and Formulations

The pharmaceutical composition may conveniently be presented in unit dosage form and may be prepared by any methods well-known in the art of pharmacy. Such methods include the step of bringing the chimeric protein into association with a carrier which may constitute one or more accessory ingredients. In general, pharmaceutical compositions are prepared by uniformly and intimately bringing into association the active compound with liquid carriers or finely divided solid carriers or both, and then if necessary shaping the product.

Pharmaceutical compositions may be in the form of liquids, solutions, suspensions, emulsions, elixirs, syrups, tablets, lozenges, granules, powders, capsules, cachets, pills, ampoules, suppositories, pessaries, ointments, gels, pastes, creams, sprays, mists, foams, lotions, oils, boluses, electuaries, or aerosols.

Dosage and Mode of Administration

A chimeric protein, encoding nucleic acid or pharmaceutical composition comprising the chimeric protein or encoding nucleic acid may be administered to a subject by any convenient route of administration, whether systemically/peripherally or at the site of desired action, including but not limited to, oral (e.g. by ingestion); topical (including e.g. transdermal, intranasal, ocular, buccal, and sublingual); pulmonary (e.g. by inhalation or insufflation therapy using, e.g. an aerosol, e.g. through mouth or nose); rectal; vaginal; parenteral, for example, by injection, including subcutaneous, intradermal, intramuscular, intravenous, intraarterial, intracardiac, intrathecal, intraspinal, intracapsular, subcapsular, intraorbital, intraperitoneal, intratracheal, subcuticular, intraarticular, subarachnoid, and intrasternal; by implant of a depot, for example, subcutaneously or intramuscularly.

Pharmaceutical compositions suitable for oral administration (e.g., by ingestion) may be presented as discrete units such as capsules, cachets or tablets, each containing a predetermined amount of the active compound; as a powder or granules; as a solution or suspension in an aqueous or non-aqueous liquid; or as an oil-in-water liquid emulsion or a water-in-oil liquid emulsion; as a bolus; as an electuary; or as a paste.

Pharmaceutical compositions suitable for parenteral administration (e.g. by injection, including cutaneous, subcutaneous, intramuscular, intravenous and intradermal), include aqueous and non-aqueous isotonic, pyrogen-free, sterile injection solutions which may contain anti-oxidants, buffers, preservatives, stabilisers, bacteriostats, and solutes which render the formulation isotonic with the blood of the intended recipient; and aqueous and non-aqueous sterile suspensions which may include suspending agents and thickening agents, and liposomes or other microparticulate systems which are designed to target the compound to cells, tissue or organs. Examples of suitable isotonic vehicles for use in such formulations include Sodium Chloride Injection, Ringer's Solution, or Lactated Ringer's Injection. Typically, the concentration of the active compound in the solution is from about 1 ng/ml to about 10 μg/ml, for example, from about 10 ng/ml to about 1 μg/ml. The formulations may be presented in unit-dose or multi-dose sealed containers, for example, ampoules and vials, and may be stored in a freeze-dried (lyophilised) condition requiring only the addition of the sterile liquid carrier, for example water for injections, immediately prior to use.

It will be appreciated that appropriate dosages of the chimeric protein, can vary from patient to patient. Determining the optimal dosage will generally involve the balancing of the level of diagnostic benefit against any risk or deleterious side effects of the administration. The selected dosage level will depend on a variety of factors including, but not limited to, the route of administration, the time of administration, the rate of excretion of the imaging agent, the amount of contrast required, other drugs, compounds, and/or materials used in combination, and the age, sex, weight, condition, general health, and prior medical history of the patient. The amount of imaging agent and route of administration will ultimately be at the discretion of the physician, although generally the dosage will be to achieve concentrations of the imaging agent at a site, such as a tumour, a tissue of interest or the whole body, which allow for imaging without causing substantial harmful or deleterious side-effects.

Administration in vivo can be effected in one dose, continuously or intermittently (e.g., in divided doses at appropriate intervals). Methods of determining the most effective means and dosage of administration are well known to those of skill in the art and will vary with the formulation used for therapy, the purpose of the therapy, the target cell being treated, and the subject being treated. Single or multiple administrations can be carried out with the dose level and pattern being selected by the physician.

Chimeric proteins described herein may be used in methods of diagnosis or treatment in human or animal subjects, e.g. human. Chimeric proteins for a target molecule may be used to treat disorders associated with the target molecule.

Other aspects and embodiments of the invention provide the aspects and embodiments described above with the term “comprising” replaced by the term “consisting of” and the aspects and embodiments described above with the term “comprising” replaced by the term “consisting essentially of”.

It is to be understood that the application discloses all combinations of any of the above aspects and embodiments described above with each other, unless the context demands otherwise. Similarly, the application discloses all combinations of the preferred and/or optional features either singly or together with any of the other aspects, unless the context demands otherwise.

Modifications of the above embodiments, further embodiments and modifications thereof will be apparent to the skilled person on reading this disclosure, and as such, these are within the scope of the present invention.

All documents and sequence database entries mentioned in this specification are incorporated herein by reference in their entirety for all purposes.

“and/or” where used herein is to be taken as specific disclosure of each of the two specified features or components with or without the other. For example “A and/or B” is to be taken as specific disclosure of each of (i) A, (ii) B and (iii) A and B, just as if each is set out individually herein.

Certain aspects and embodiments of the invention will now be illustrated by way of example and with reference to the figures described above.

Experiments

1. Methods

1.1 Large-Scale Protein Purification (His-Tagged) from E. coli

The pRSET B (His-tag) constructs were transformed into chemically competent E. coli C41 cells by heat shock and plated on LB-Amp plates. Colonies were grown in 2TY media containing ampicillin (50 micrograms/mL) at 37° C., 220 rpm until the optical density (O.D.) at 600 nm reached 0.6. Cultures were then induced with IPTG (0.5 mM) for 16-20 h at 20° C. or 4 h at 37° C. Cells were pelleted by centrifugation at 3000 g (4° C., 10 min) and resuspended in lysis buffer (10 mM sodium phosphate pH 7.4, 150 mM NaCl, 1 tablet of SIGMAFAST protease inhibitor cocktail (EDTA-free per 100 mL of solution), then lysed on a Emulsiflex C5 homogenizer at 15000 psi. Cell debris was pelleted by centrifugation at 15,000 g at 4° C. for 45 min. Ni-NTA beads 50% bed volume (GE Healthcare) (5 mL) were washed once with phosphate buffer (10 mM sodium phosphate pH 7.4, 150 mM NaCl) before the supernatant of the cell lysate was bound to them for 1 hr at 4° C. in batch. The loaded beads were washed three times with phosphate buffer (40 mL) containing 30 mM of imidazole to prevent non-specific interaction of lysate proteins with the beads. Samples were eluted using phosphate buffer with 300 mM imidazole, and purified by size-exclusion chromatography using a HiLoad 16/60 SuperdexG75 column (GE Life-Science) pre-equilibrated in phosphate buffer (10 mM sodium phosphate, pH 7.4, 150 mM NaCl) and proteins separated in isocratic conditions. Purity was checked on NuPage protein gel (Invitrogen), and fractions found to be over 95% pure were pooled. Purified protein was flash-frozen and stored at −80° C. until further use. Concentrations were determined by measuring absorbance at 280 nm and using a calculated extinction coefficient from ExPASy ProtParam (Gasteiger et al. 2005) for each variant. Molecular weight and purity was confirmed using mass spectrometry (MALDI.

1.2 Large-Scale Protein Purification (Heat Treatment) from E. coli

All chimeric proteins described herein are thermally very stable, with melting temperatures above 80° C. This means that the chimeric proteins could be separated from E. coli proteins by incubating the cell lysates at 65° C. for 20 min. Very few of the E. coli proteins survive such temperatures, and therefore, they will unfold and aggregate. Aggregated proteins were removed by centrifugation, leaving 80-90% pure sample of the desired protein. All our constructs folded reversibly, and therefore could be further purified by methods such as acetone or salt precipitation to remove DNA and other contaminants.

This approach allowed the production of large amounts of functional proteins without expensive affinity purification methods such as antibodies or His tags and is scalable to industrial production and bioreactors.

1.3 Small-Scale Purification of His-Tagged Proteins for Higher-Throughput Testing

Plasmids were transformed into E. coli C41 cells and plated overnight. 15 mls of 2TY medium (Roche) containing 50 micrograms/ml ampicillin was placed in multiple 50 ml tubes. Several colonies were picked and resuspended in each 15 ml culture. For sufficient aeration it is important to only loosely tighten the lids of the 50 ml tubes. Cells were grown at 37° C. until OD600 of 0.6 and then induced with 0.5 mM IPTG overnight. Cells were pelleted at 3000 g (Eppendorf Centrifuge 5804) and then resuspended in 1 ml of BugBuster® cell lysis reagent. Alternatively, sonication in combination with lysozyme and DNAse I treatment was used. The lysate was spun at 12000 g for 1 minute to pellet any insoluble protein and cell debris.

The supernatant was added to 100 μl bed volume of pre-washed Ni-NTA agarose beads. The subsequent affinity purification was performed in batch, by washing the beads 4 times with 1 ml of buffer each time (alternatively, Qiagen Ni-NTA Spin Columns can be used). The first wash contained 10% BugBuster® solution and 30 mM imidazole in the chosen buffer. Here we used 50 mM sodium phosphate buffer pH 6.8, 150 mM NaCl. The three successive washes had 30 mM of imidazole in the chosen buffer. Beads were washed thoroughly to remove the detergent present in the BugBuster® solution. Protein was eluted from the beads in a single step using 1 ml of chosen buffer containing 300 mM imidazole. The combination of Bugbuster® and imidazole and the repeat washes in small bead volumes yielded >95% pure protein. Imidazole was removed using a NAP-5 disposable gel-filtration column (GE Healthcare).

1.4 Competition Fluorescence Polarization (FP)

To assay the binding of the designed SOS-TPR protein to KRAS, Competition FP was performed using purified KRAS Q61H mutant and (2′-(or -3′)-O-(N-Methylanthraniloyl) Guanosine 5′-Triphosphate, a fluorescent version of GTP, also known as mant-GTP. SOS-TPR was titrated using a 2-fold serial dilution against a 1:1 complex of KRAS Q61H and mant-GTP (1 μM) in a black 96-well plate (CLS3993 SIGMA). Plates were prepared under reduced light conditions and incubated at room temperature. Readings were taken on the CLARIOstar microplate reader, using an excitation filter at 360 nm and emission filter at 440 nm.

1.5 Isothermal Titration Calorimetry (ITC)

ITC was performed at 25° C. using a VP-ITC (Microcal). 1TBP-CTPR2, 2TBP-CTPR4, 3TBP-CTPR6 and TNKS2 ARC4 were dialysed into 10 mM sodium phosphate buffer pH 7.4, 150 mM NaCl, 0.5 mM TCEP. Dialysed TNKS2 ARC4 (200 μM) was titrated into the sample cell containing 1TBP-CTPR2 at 20 μM. Similar experiments were performed for 2TBP-CTPR4 and 3TBP-CTPR6. Injections of TNKS2 ARC4 into the cell were initiated with a 5 μL injection, followed by 29 injections of 10 μL. The reference power was set at 15 μCal/s with an initial delay of 1000 s and a stirring speed of 485 rpm. Data were fitted using the instrument software a one-site binding model.

1.6 Cell Culture

HEK293T cells were cultured in Dulbecco's Modified Eagle's Medium (Sigma Aldrich) supplemented with 10% fetal bovine serum and penicillin/streptomycin (LifeTech) at 37° C. with 5% CO₂air supply.

1.7 Cell Transfection

HEK293T were seeded in 6-well tissue culture plates (500,000 cells per well) and transfected the next day using the Lipofectamine2000 transfection reagent (Invitrogen) according to the manufacturer's protocol.

1.8 β-Catenin Levels Western Blot Assay

HA-β-catenin (1 μg) alone and with various PROTACs (1 μg) was transfected in HEK293T cells in 6-well plates using Lipofectamine2000. After 48 hours of transfection, the cells were lysed in 200 μL of Laemmli buffer. After sample was boiled at 95° C. for 20 min proteins were resolved by SDS-PAGE and transferred to a PVDF membrane, and immunoblotting was performed using anti-HA (C29F4, Cell Signaling Technologies) and anti-actin (A2066, Sigma-Aldrich) antibodies. Changes in β-catenin levels were evaluated by the densitometry of the bands corresponding to HA-β-catenin normalised to actin levels using ImageJ.

1.9 Liposomal Formulation and Cytotoxicity Assay

To make liposomal formulations of proteins (LFP), lipids (DOTAP (cationic): DOPE (neutral): DiR (aromatic)=1:1:0.1 w/w) were dissolved in chloroform, and solvent was evaporated under vacuum overnight. Resulting mixed lipid cake was hydrated with 10 mM HEPES pH 7.4, containing 27 μM protein, so that the total lipid concentration is 4 mg/ml. This mixture was vortexed for 2 minutes and then sonicated for 20 minutes at room temperature. Liposomes encapsulating proteins were stored at 4° C. until further use. To make empty liposomes (EL, empty liposomes without proteins), lipid cake was hydrated with 10 mM HEPES pH 7.4 without proteins.

An ATP assay was used to investigate whether there is any cytotoxicity associated with EL and LFP. In a typical procedure, 2×10⁵HEK 293T cells/well in 500 μL of Dulbecco's Modified Eagles Medium (DMEM) supplemented with 10% fetal bovine serum were grown for 24 hours in a 24-well cell culture plate. Cells were incubated with liposome (EL/LFP)-media (DMEM without FBS) mix, having different volumes (0-60 μL) of EL and LFP, for 15 minutes at 37° C. After washing twice with 1×PBS, 500 μL of CellTiter-Glo® Reagent (Promega) was added and luminescence was measured using a microplate reader as par the manufacture's protocol. Untreated cells were used as control. Data were obtained from triplicate samples, and the standard deviations were calculated from two independent experiments.

1.10 TOPFLASH Assay

The Wnt pathway was activated by treating HEK293T cells with Wnt-conditioned media obtained from L-cells expressing Wnt3A for 8 days. To perform the assay, 10⁵HEK293T cells/well were seeded on a 24-well plate Nunclon Delta Surface plate (NUNC) and incubated overnight at 37° C., 5% CO2. The following day, cells were transfected with 100 ng of TOPflash TCF7L2-firefly luciferase plasmid, 10 ng of CMV-Renilla plasmid (as internal control) and 100 ng of the corresponding TPR construct. Plasmids were mixed with 0.5 μL of Lipofectamine 2000 transfection reagent according to the manufacturer's protocol (invitrogen). Transfected cells were allowed to recover for 8 h, then they were treated with Wnt-conditioned media (1:2 final concentration) for a further 16 h. The TOPflash assay was performed using the Dual-Luciferase Reporter Assay System (Promega) (Korinek et al., 1997 Science 275(5307):1784-7) following the manufacturer's instructions. The activities of firefly and Renilla luciferases were measured sequentially from a single sample, using the CLARIOstar plate reader. Relative luciferase values were obtained from triplicate samples dividing the firefly luminescence activity by the CMV-induced Renilla activity, and standard deviation was calculated.

1.11 TOPFLASH Assay Using Liposome Encapsulation to Deliver Designed TPR Proteins into the Cell

10⁵HEK 293T cells in 500 μL of Dulbecco's Modified Eagles Medium (DMEM) supplemented with 10% fetal bovine serum were grown overnight in each well of a 24-well cell culture plate. For TOPFLASH reporter assays, 100 ng/well of TOPFLASH plasmid and 10 ng/well of CMV-Renilla plasmid (as internal control) were used to transfect cells in 24-well plates. Cells were transfected with the Lipofectamine 2000 transfection reagent according to the manufacturer's protocol (Invitrogen). Transfected cells were allowed to recover for 8 hours, and Wnt signalling was activated by addition of Wnt3A-conditioned media obtained from L-cells. 16 hours post Wnt pathway activation, proteins were delivered into the cells by liposomal treatment. Cells were incubated with liposome (LFP)-media (DMEM without FBS) mix for 15 minutes at 37° C. followed by one PBS wash. Wnt3A conditioned media was replaced and cells were incubated for variable time durations (2-8 hours). Following incubation, TOPFLASH assays were performed using the Dual-Luciferase Reporter Assay System (Promega) (Korinek et al., 1997) following the manufacturer's instructions. Relative luciferase values were obtained from triplicate samples (from two independent experiments) by dividing the firefly luciferase values (from TOPFLASH) by the Renilla luciferase values (from CMV Renilla), and standard deviations were calculated.

1.12. Competition Fluorescence Polarisation (FP) Assay to Measure the Binding of Designed Nrf-TPR Proteins to Keap1

To measure the binding of the designed Nrf-TPR proteins to Keap1, Competition FP was performed using 384-well black opaque optiplate microplates and a CLARIOstar microplate reader. Nrf-TPR proteins were titrated into a solution containing a mixture of FITC-labelled Nrf2 peptide and Keap1 protein. The prepared plates were incubated for 30 minutes at room temperature before readings were taken.

2. Results

Tetratricopeptide repeat (TPR) is a 34-residue motif that can be repeated in tandem to generate modular proteins. TPRs are used here as an example of helix-turn-helix tandem-repeats arrays, but any tandem repeat array may be used.

RTPR proteins comprising TPRs were derived from the consensus TPR sequence (CTPR). Two repeats were found to be sufficient to generate a highly stable mini-protein of 68 amino acids (RTPR2). The biophysical properties of two types of engineering strategy; loop insertions and terminal helix grafting, were assessed. The molar ellipticity at 222 nm (a measure of helical secondary structure content) of three different RTPR modules was monitored as a function of increasing temperature. A decrease in the absolute molar ellipticity with increasing temperature indicates a loss of structure and the unfolding of the protein. Even at the highest temperature recorded (85° C.), the RTPR2 protein without insertion was not fully denatured (FIG. 1). RTPR2 with a 20-residue unstructured loop between the two repeats showed a small shift to a lower melting temperature (FIG. 1), but the protein remains fully folded up to 55° C. This is well above physiologically relevant temperatures. RTPR2 with an additional N-terminal helix showed an increase in absolute molar ellipticity, indicating that the additional helical domain is folded. Moreover, unlike the loop insertion, the helix domain was capable of stabilising the RTPR2 module, shifting the transition midpoint to above 90° C. (FIG. 1). These results showed that the two engineering strategies generated folded and stable modular mini-proteins capable of withstanding high temperatures.

A key feature of the TPR scaffold was its modular nature. This modularity allowed display any number of binding modules in tandem to obtain bi- and multi-valent and multi-functional molecules against one, two or more targets. The stability of these proteins was shown to be modular. The stabilities of proteins comprising TBP-CTPR2 (a two-repeat CTPR with a loop insertion that binds to the protein tankyrase (Guettler et al. 2011)) repeated in tandem were measured. The TBP-CTPR2-containing proteins had two, four, six, and eight repeats, and they displayed one, two, three and four binding loops, respectively. The helical content of the proteins, monitored by molar ellipticity at 222 nm, was found to increase in proportion to the number of repeats, as did the stability, indicating that they were behaving like classic helical repeat proteins (FIG. 2). These results demonstrate that bi- or multi-functional chimeric proteins have a high thermostability.

2.1. Demonstration of Proteins with a Single Binding Function Grafted onto an Alpha-Helix

2.1.1 SOS1-TPR, a Helix-Grafted Binding Module Designed to Bind to Oncoprotein KRAS

First, we mapped the helix of SOS1 that interacts with KRAS (Margarit et al. 2003 Cell 112 5 685-695) onto the heptad distribution. We matched the heptad positions with the stapled SOS1 helical peptide produced by Leshchiner et al. (PNAS 2015 112 (6) 1761-1766) and set the stapled side of the peptide to form the hydrophobic interface with the rest of the TPR protein (FIG. 3A). The length of the helix is important. An N-terminal solvating CTPR helix ends in the sequence DPNN, which forms a short loop that leads into the next repeat. CTPR-mediated “stapling” (constraining) of binding helices therefore occurred through residues Tyr (i)-Ile (i+4)-Tyr (i+7)-Leu (i+11), fully stapling a 15-residue helix.

We created a hydrophobic interface between the grafted helix and the adjacent repeat and allowed the formation of the DPNN loop at the C-terminal end of the grafted helix. We then grafted the final sequence onto the crystal structure of a CTPR B helix for further validation of the interaction. Our designed KRAS-binding protein, SOS1-TPR, was docked against KRAS using the Haddock software (de Vries & Bonvin 2011; de Vries et al. 2010). Haddock is a data-driven docking algorithm that uses known information about the interaction for its calculations. The crystal structure of SOS1-KRAS (PDB: 1NVU) (Margarit et al. 2003) was originally used to design the stapled peptide. The active (primary interaction residues) and the passive (5 Å proximity to active) residues were extracted and inputted into the calculations.

Docking is not necessary to validate helical grafted scaffold. The geometry of α-helices permits selection of amino acid positions of the scaffold that accommodate outward facing target binding residues of the peptide ligand. TPR repeat scaffolds are exceptional for display of binding helices, as they grow linearly in the opposite direction of the helix, thereby avoiding steric clashes with the target protein.

KRAS binding of the grafted scaffold can be assessed using the change in fluorescence polarisation of mant-GTP (2′-/3′-O—(N′-Methylanthraniloyl) guanosine-5′-O-triphosphate), a fluorescent analog of GTP (FIG. 3B). The fluorescence of mant-GTP is dependent on the hydrophobicity of its environment (excitation at 360 nm, emission at 440 nm). An increase in fluorescence intensity and fluorescence polarization was observed previously upon binding to KRAS (Leshchiner et al. 2015). SOS-TPR2 was then titrated into the preformed mant-GTP-KRAS complex. There was a clear decrease in polarisation with increasing concentrations of SOS-TPR2, indicating displacement of mant-GTP upon binding of SOS-TRP2 to KRAS (FIG. 3B). Fitting the data gave an EC50 of 3.4 μM. In contrast, a blank protein, CTPR3, had no effect on the fluorescence polarisation.

2.1.2 p53-TPR, a Helix-Grafted Binding Module Designed to Bind to Mdm2

Many degrons (region within the substrate that is recognized by the E3 ubiquitin ligase) are unstructured. However, p53 binds to the Mdm2 E3 through an alpha helix (FIG. 4A). Stapled versions of the p53 helix, as well as circular peptides and grafted coiled coils, have been developed by many groups, and the sequences have been optimised to give nanomolar affinities in some cases (see for example, Ji et al. 2013; Lee et al. 2014; Kritzer et al. 2006). The p53 helix has a favourable geometry to be grafted onto the C-terminal solvating helix of the CTPR scaffold, and moreover the two helices have 30% sequence identity.

Proof of binding of p53-CTPR2 to Mdm2 (N-terminal domain) was obtained using isothermal titration calorimetry (ITC). Mdm2 was titrated into a solution containing 10 μM of p53-TPR2. ITC measures the heat released upon binding. A high-affinity interaction was observed with a dissociation constant of approximately 50 nM (FIG. 4B).

2.2. Demonstration of Proteins with a Single Binding Function Grafted onto an Inter-Repeat Loop

2.2.1 TPB2-TPR, a Loop Module Designed to Bind to Oncoprotein Tankyrase

First, we introduced the SLiM “3BP2”, a sequence that binds to the substrate-binding ankyrin-repeat clusters (ARC) of the protein tankyrase, a multi-domain poly ADP-ribose polymerase that is upregulated in many cancers (Guettler et al. 2011) onto the CTPR scaffold. Grafting SLiMs in folded domains led to an increase of proteolysis resistance; showing the potential to expand the interaction surface through further rational engineering, in silico methods and/or directed evolution; controlled geometric arrangement; and bi- or multivalency of interactions.

We tested the binding of 1TBP-CTPR2, 2TBP-CTPR4 and 3TBP-CTPR6 to the ARC4 domain of tankyrase using ITC (FIG. 5A). This technique is particularly useful for these interactions, as it can measure the stoichiometry (n) of the interaction. We showed that n increased with the number of binding loops, meaning that there were as many tankyrase molecules bound to one TBP-CTPR as loops in the protein. Thus, all loops are accessible to the binding partner. Moreover, the binding affinity increases and the off rate decreases with the number of repeats indicative of an avidity effect. This type of multivalent molecule would be particularly useful for full-length tankyrase, as it has four ARC domains capable of binding the 3BP2 peptide.

Multivalency in this system was increased further via oligomerisation of the binding modules by fusing them to the foldon domain of T4 fibritin (FIG. 5B). This trimerisation domain comprises of a C-terminal helix, such as that of p53-CTPR, ending with the foldon domain, a short β-sheet peptide capable of homo-trimerising. The foldon domain has been shown to be highly stable and independently folded (Boudko et al 2002; Meier et al. 2004). In this way, multiple binding modules can be arranged with specified geometries to inhibit complex multivalent molecules that cannot be targeted with monovalent interactions due to their natural tendency to interact with other multivalent networks with high avidity.

2.2.2 Effect of Introducing Multivalency into a Single Binding Function TPR

We tested the function of multi-valent CTPR proteins containing variable numbers of the “3BP2” motif that binds to the protein tankyrase. (1TBP-CTPR2, 2TBP-CTPR4 and 3TBP-CTPR6 etc.). Multi-valency was increased further via oligomerisation of the TPRs by fusing them to the foldon domain of T4 fibritin (1TBP-CTPR2-Foldon, 2TBP-CTPR4-Foldon etc.). The inhibitory effect of the TBP-grafted TPRs was assayed using a beta-catenin reporter gene assay (TOPFLASH assay). Increasing the number of functional units increased the inhibitory effect of the proteins, as mentioned using a Wnt signalling assay (FIG. 17).

2.2.3 Skp2-RTPR, a Loop Module Designed to Bind to E3 Ubiquitin Ligase SCF^Skp2

Skp2 is the substrate recognition subunit of the SCF^Skp2ubiquitin ligase. The Skp2-binding sequence that we inserted into the RTPR loop was based on the previously published degron peptide sequence derived from the substrate p27 that binds to Skp2 in complex with Cks1 (an accessory protein) (Hao et al. 2005). We used only 10 residues of this peptide. Although ideally the Skp2-binding sequence would include a phospho-threonine (as this residues makes some key contacts with Skp2 and Cks1), we instead explored whether we could replace the phospho-threonine with a phosphomimetic (glutamate) without affecting binding affinity. We found using co-immunoprecipitation that the resulting p27-TPR protein was able to bind to Skp2 (FIG. 6A) and that it was able to inhibit the ubiquitination of p27 in vitro with a high efficiency indicating a dissociation constant of the order of 30 nM (FIG. 6B). As the peptide adopts a turn-like conformation in its Skp2/Cks1-bound state, constraining it within the RTPR scaffold leads to a large enhancement in binding affinity that outweighs any loss in affinity arising from replacing the phosphothreonine with a phosphomimetic.

2.2.4 Nrf-TPR, a Loop Module Designed to Bind to E3 Ubiquitin Ligase Keap1-Cul3

Keap1 is the substrate recognition subunit of the Keap1-Cul3 ubiquitin ligase. A Keap1-binding sequence that we inserted into the CTPR loop was based on the previously published degron peptide sequence derived from the Keap1 substrate Nrf2. We found using co-immunoprecipitation that the resulting Nrf-TPR protein was able to bind to Keap1 (FIG. 7A) and that the interaction had a high affinity in the low nanomolar range as measured by ITC analysis (FIG. 7B).

2.3. Engineering the RTPR Scaffold for Delivery into the Cell

Combining our RTPR sequences with an alternative consensus TPR sequence (Parmeggiani et al. 2015) we included additional solvent-exposed Arginine residues, as such ‘resurfacing’ or ‘supercharging’ has been shown previously to facilitate the entry of proteins into cells (Chapman & McNaughton 2016; Thompson et al. 2012). FIG. 8 shows that this approach was successful in delivering a fluorescent-labelled resurfaced TBP-RTPR2 protein into two different cell lines.

2.4. Design of Hetero-Bifunctional TPRs to Direct Proteins for Ubiquitination and Subsequent Degradation

The Wnt/β-catenin signalling pathway is deregulated in many cancers and in neurodegenerative diseases, and therefore β-catenin is an important drug target. There are a large number of known binding sequences (both helical and non-helical) for 3-catenin that appear suitable for grafting onto the TPR scaffold, and therefore we chose it as the first target for our design of hetero-bifunctional TPRs to induce protein degradation. We selected Mdm2 and SCF^Skp2to test as E3 ubiquitin ligases, as we had successfully generated single-function TPRs to bind to them (FIGS. 4 and 6). We generated structural models of some of the hetero-bifunctional molecules and used these as a crude assessment of whether the resulting presentation of β-catenin to the E3 looked appropriate. We then generated a small library of plasmids encoding proteins comprising three or four TPRs functionalized with different combinations of the β-catenin-binding module and the two E3 ligase-binding modules.

We transfected HA-tagged β-catenin plasmid alone or HA-tagged β-catenin plasmid together with one of the various hetero-bifunctional TPR plasmids in HEK293T cells using Lipofectamine2000. After 48 hours of transfection, the cells were lysed, the sample was boiled and proteins were resolved by SDS-PAGE and immunoblotting was performed using anti-HA and anti-actin antibodies. Changes in β-catenin levels were evaluated by the densitometry of the bands corresponding to HA-β-catenin normalised to actin levels (FIG. 9). The results show that a number of the hetero-bifunctional molecules are capable of reducing β-catenin levels by up to 70%. In contrast, neither a blank TPR nor single-function TPRs have any effect on β-catenin levels.

A range of different factors contribute to efficient ubiquitination and target degradation by these hetero-bifunctional molecules, hence the power of screening different combinations of single-function modules and potentially also different lengths of intervening blank modules.

2.5 Using a Delivery Vehicle to Introduce the Modular TPR Proteins into Cells

We encapsulated the designed TPR proteins within fusogenic liposomes made from cationic, neutral, and aromatic lipids, and we showed that they were thereby delivered into cells (FIGS. 18 and 19). Empty liposomes and liposomes encapsulating TPR proteins are not toxic to the cell (FIG. 20).

2.6 Further Examples of TPRs to Direct Proteins for Ubiquitination and Subsequent Degradation

TPR proteins were designed to target either tankyrase (FIG. 21, FIG. 22) or KRAS (FIG. 23). TPR proteins targeting tankyrase or were delivered into cells using liposome encapsulation, and the effect on Wnt signalling was assayed using a TOPFLASH assay. The results show that the TPR proteins are able to inhibit Wnt signalling. For KRAS, we transfected KRAS plasmid alone or KRAS plasmid together with one of the TPR plasmids in HEK293T cells using Lipofectamine2000. 24 hours post transfection the cells were lysed, and KRAS levels were evaluated by western blot. The results show that the designed hetero-bifunctional TPR is capable of reducing KRAS levels.

2.7 Hetero-Bifunctional TPRs to Direct KRAS for Degradation Via Chaperone-Mediated Autophagy (CMA)

Hetero-bifunctional TPR proteins were designed to target endogenous KRAS for degradation via CMA (FIG. 24). TPR constructs or empty vector (light grey) were transiently transfected into either HEK293T or DLD1 (colorectal cancer cell line) using Lipofectamine2000. 24 hours post transfection the cells were lysed, and KRAS levels were evaluated by western blot. The designed hetero-bifunctional TPRs that resulted in reduction of KRAS levels compared to the empty vector control are shown in white.

2.8 Variations in the Linker Sequence Connecting a Peptide Ligand to an Inter-Repeat Loop

The linker sequence connecting a peptide ligand to an inter-repeat loop was varied in order to optimise the binding affinity for the target for Nrf-TPR, a TPR protein designed to bind to the protein Keap1 (see FIG. 7). Glycine residues were introduced into the linker to provide flexibility and increased spatial sampling. The introduction of this more flexible linker sequence was found to increase the binding affinity of the Nrf-TPR protein (labelled ‘Flexible’) when compared with the consensus-like linker sequence altering the charge content of the linker sequence (‘labelled ‘Charged’) and altering the conformational properties (based on the predictions of the program CIDER (Holehouse et al. Biophys. J. 112, 16-21 (2017)) of the loop by changing the amino acid composition of the linker sequence (labelled ‘CIDER-optimised’) also affected the Keap1-binding affinity (FIG. 25).

TABLE 1

Degron

β-catenin-

sequence
Targeted
binding

Targeted
derived
protein for
sequence

Ubiquitin Ligase
from
Degradation
derived from:
Scaffold

Mdm2
p53
β-catenin
axin
RTPR

Mdm2
p53
β-catenin
Bcl-9
RTPR

Mdm2
p53
β-catenin
TCF-4
RTPR

Mdm2
p53
β-catenin
ICAT
RTPR

Mdm2
p53
β-catenin
LRH-1
RTPR

Mdm2
p53
β-catenin
APC
RTPR

SCF^skp2
p27
β-catenin
axin
RTPR

SCF^skp2
p27
β-catenin
Bcl-9
RTPR

SCF^skp2
p27
β-catenin
TCF-4
RTPR

SCF^skp2
p27
β-catenin
ICAT
RTPR

SCF^skp2
p27
β-catenin
LRH-1
RTPR

SCF^skp2
p27
β-catenin
APC
RTPR

BTB-CUL3-RBX1
Nrf2
β-catenin
Bcl-9
RTPR

BTB-CUL3-RBX1
SPOP
β-catenin
Bcl-9
RTPR

APC/C
ABBA
β-catenin
Bcl-9
RTPR

APC/C
KEN
β-catenin
Bcl-9
RTPR

APC/C
DBOX
β-catenin
Bcl-9
RTPR

SIAH
PHYL
β-catenin
Bcl-9
RTPR

BTB-CUL3-RBX1
Nrf2
β-catenin
axin
RTPR

BTB-CUL3-RBX1
SPOP
β-catenin
axin
RTPR

APC/C
ABBA
β-catenin
axin
RTPR

APC/C
KEN
β-catenin
axin
RTPR

APC/C
DBOX
β-catenin
axin
RTPR

SIAH
PHYL
β-catenin
axin
RTPR

BTB-CUL3-RBX1
Nrf2
β-catenin
TCF-4
RTPR

BTB-CUL3-RBX1
Nrf2
β-catenin
APC
RTPR

TABLE 2

Target protein
Grafting

and binding
site in

DNA sequence optimised

partner
scaffold
Amino acid sequence
for E. coli expression

β-catenin

axin
helix
GAYPEYILDIHVYRVQL
GGTGCATATCCGGAATACATC

EL (SEQ ID NO: 20)
CTGGATATTCATGTTTATCGTG

TTCAGCTGGAACTG (SEQ ID

NO: 65)

Bcl-9
helix
SQEQLEHRYRSLITLYD
AGCCAAGAACAGCTGGAACAT

IQLML (SEQ ID NO: 21)
CGTTATCGTAGCCTGATTACCC

TGTATGATATTCAGCTGATGCT

G (SEQ ID NO: 67)

TCF-4
loop
QELGDNDELMHFSYES
CAAGAACTGGGCGATAATGAT

TQD (SEQ ID NO: 22)
GAACTGATGCACTTTAGCTAT

GAAAGCACCCAGGAT (SEQ ID

NO: 69)

ICAT
helix
YAYQRAIVEYMLRLMS
TATGCATATCAGCGTGCCATC

(SEQ ID NO: 23)
GTTGAATATATGCTGCGTCTG

ATGAGC (SEQ ID NO: 71)

LRH-1
helix
YEQAIAAYLDALMC
TATGAACAGGCAATTGCAGCA

(SEQ ID NO: 24)
TATCTGGATGCACTGATGTGT

(SEQ ID NO: 73)

APC
loop
SCSEELEALEALELDE
AGCTGTAGCGAAGAACTGGAA

(SEQ ID NO: 25)
GCCCTGGAAGCATTAGAACTG

GATGAA (SEQ ID NO: 75)

α-catenin
helix
RSKKAHVLAASVEQAT
CGCAGCAAAAAAGCGCATGTG

QNFLEKGEQIAKESQ
CTGGCGGCGAGCGTGGAACAG

(SEQ ID NO: 1327)
GCGACCCAGAACTTTCTGGAA

AAAGGCGAACAGATTGCGAA

AGAAAGCCAG (SEQ ID NO:

2136)

α-catenin
helix
RTLTVERLLEPLVTQVT
CGCACCCTGACCGTGGAACGC

TLV (SEQ ID NO: 1328)
CTGCTGGAACCGCTGGTGACC

CAGGTGACCACCCTGGTG

(SEQ ID NO: 2137)

APC Membrance
loop
RREQLEAQEARAREAH
CGCCGCGAACAGCTGGAAGCG

recruitment

AREAHAREAYTREAYG
CAGGAAGCGCGCGCGCGCGA

protein

REAYAREAHTWEAHG
AGCGCATGCGCGCGAAGCGCA

REARTREAQA (SEQ ID
TGCGCGCGAAGCGTATACCCG

NO: 1329)
CGAAGCGTATGGCCGCGAAGC

GTATGCGCGCGAAGCGCATAC

CTGGGAAGCGCATGGCCGCGA

AGCGCGCACCCGCGAAGCGCA

GGCG (SEQ ID NO: 2138)

SOX
loop
D..EFDQYL (SEQ ID NO:
GATNNNNNGAATTTGATCAG

1330)
TATCTG (SEQ ID NO: 2139)

kindlin 2
loop
QALLDKAKINQ
CAGGCGCTGCTGGATAAAGCG

GWLDSSRSLMEQDKEN
AAAATTAACCAGGGCTGGCTG

EALLRF (SEQ ID NO:
GATAGCAGCCGCAGCCTGATG

1331)
GAACAGGATAAAGAAAACGA

AGCGCTGCTGCGCTTT (SEQ ID

NO: 2140)

KRAS

SOS1
helix
FEGIALTNYLKALEG
TTTGAAGGTATTGCACTGACC

(SEQ ID NO: 1332)
AATTATCTGAAAGCACTGGAA

GGT (SEQ ID NO: 2141)

phage-display
loop
PLYISY (SEQ ID NO:
CCCCTGTACATCAGCTAC (SEQ

library peptide

1333)
ID NO: 2142)

KR-pep1

Synthetic peptide
helix
SIEDLHEYWARLWNYL
AGCATTGAAGATCTGCATGAA

225-1

YVA (SEQ ID NO: 1334)
TATTGGGCGCGCCTGTGGAAC

TATCTGTATGTGGCG (SEQ ID

NO: 2143)

Synthetic peptide
helix
QASLEELHEYWARLW
CAGGCGAGCCTGGAAGAACTG

225-15a

NYRVA (SEQ ID NO:
CATGAATATTGGGCGCGCCTG

1335)
TGGAACTATCGCGTGGCG

(SEQ ID NO: 2144)

Synthetic peptide
helix
NASIKQLHAYWQRLYA
AACGCGAGCATTAAACAGCTG

225-15b

YLAAVA (SEQ ID NO:
CATGCGTATTGGCAGCGCCTG

1336)
TATGCGTATCTGGCGGCGGTG

GCG (SEQ ID NO: 2145)

phage-display
loop
CMWWREICPVWW
TGCATGTGGTGGCGCGAAATT

library peptide

(SEQ ID NO: 1337)
TGCCCGGTGTGGTGG (SEQ ID

KR-pep3

NO: 2146)

Raf-S
loop
FARKTFLKLAF (SEQ ID
TTTGCGCGCAAAACCTTTCTG

NO: 1338)
AAACTGGCGTTT (SEQ ID NO:

2147)

NF1
loop
ARRFFLDIAD (SEQ ID
GCGCGCCGCTTCTTTCTGGATA

NO: 1339)
TTGCGGAT (SEQ ID NO: 2148)

RasIn peptide 2
loop
FRWP..RL.. (SEQ ID NO:
TTTCGCTGGCCGNNNNNNCGC

1340)
CTGNNNNNN (SEQ ID NO: 2149)

RasIn peptide 1
loop
t.VFXh.p (SEQ ID NO:
AGCATTGTGTTTGGCGCGCAT

1341)
GAT (SEQ ID NO: 2150)

NF1 monobody
loop
YGHGQVYYY (SEQ ID
TATGGCCATGGCCAGGTGTAT

peptide (74-84)

NO: 1342)
TATTAT (SEQ ID NO: 2151)

farnesyl
loop
ENPKQN (SEQ ID NO:
GAAAACCCGAAACAGAAC

transferase 1

1343)
(SEQ ID NO: 2152)

farnesyl
loop
DAYECLDASRPW (SEQ
GATGCGTATGAATGCCTGGAT

transferase 2

ID NO: 1344)
GCGAGCCGCCCGTGG (SEQ ID

NO: 2153)

farnesyl
loop
KSRDFYH (SEQ ID NO:
AAATCCCGCGATTTCTATCAT

transferase 3

1345)
(SEQ ID NO: 2154)

c-Myc

Aurora A
helix
AGVEHQLRREVEIQSH
GCGGGCGTGGAACATCAGCTG

(SEQ ID NO: 1346)
CGCCGCGAAGTGGAAATTCAG

AGCCAT (SEQ ID NO: 2155)

Aurora A
loop
WSVHAPSSRRTTpLAGT
TGGAGCGTGCATGCGCCGAGC

LDYLPPEMI (SEQ ID
AGCCGCCGCACCGAACTGGCG

NO: 1347)
GGCACCCTGGATTATCTGCCG

CCGGAAATGATT (SEQ ID NO:

2156)

Aurora A
helix
TYQETY (SEQ ID NO:
ACCTATCAGGAAACCTAT

1348)
(SEQ ID NO: 2157)

Omomyc
helix
QAEEQKLSEEDLLR
CAGGCGGAAGAACAGAAACT

KRREQLKHKLEQLRNS
GAGCGAAGAAGATCTGCTGCG

CA (SEQ ID NO: 1349)
CAAACGCCGCGAACAGCTGAA

ACATAAACTGGAACAGCTGCG

CAACAGCTGCGCG (SEQ ID

NO: 2158)

Myc H1 F8A

NELKRSFAALRDQI
AACGAACTGAAACGCAGCTTT

(SEQ ID NO: 1350)
GCGGCGCTGCGCGATCAGATT

(SEQ ID NO: 2159)

Myc H1 F8A

NELKRAFAALRDQI
AACGAACTGAAACGCGCGTTT

S6A

(SEQ ID NO: 1351)
GCGGCGCTGCGCGATCAGATT

(SEQ ID NO: 2160)

MIP
helix
IREKNHYHRQEVDDLR
ATTCGCGAAAAAAACCATTAT

RQNALLEQQVRAL
CATCGCCAGGAAGTGGATGAT

(SEQ ID NO: 1352)
CTGCGCCGCCAGAACGCGCTG

CTGGAACAGCAGGTGCGCGCG

CTG (SEQ ID NO: 2161)

PIN1
loop
FNHITNASQWE (SEQ ID
TTTAACCATATTACCAACGCG

NO: 1353)
AGCCAGTGGGAA (SEQ ID NO:

2162)

PIN2
loop
GDLGAFSRGQM (SEQ
GGCGATCTGGGCGCGTTTAGC

ID NO: 1354)
CGCGGCCAGATG (SEQ ID NO:

2163)

9E10 paratrope
loop
RSEFYYYGNTYYYSAM
CGCAGCGAATTTTATTATTATG

D (SEQ ID NO: 1355)
GCAACACCTATTATTATAGCG

CGATGGAT (SEQ ID NO: 2164)

BIN1
loop
QHDYTATDE (SEQ ID
CAGCATGATTATACCGCGACC

NO: 1356)
GATGAA (SEQ ID NO: 2165)

BIN1
loop
QNPEEQDEGW (SEQ ID
CAGAACCCGGAAGAACAGGA

NO: 1357)
TGAAGGCTGG (SEQ ID NO:

2166)

BIN1
loop
EKCRGVFPENF (SEQ ID
GAAAAGTGCCGCGGCGTGTTT

NO: 1358)
CCGGAAAACTTT (SEQ ID NO:

2167)

BRD4

JMJD6
loop
KWTLERLKRKYRN
AAATGGACCCTGGAACGTCTG

(SEQ ID NO: 1522)
AAACGTAAATACCGTAAC

(SEQ ID NO: 2303)

murine leukemia
loop
TWRVQRSQNPLKIRLT
ACCTGGCGTGTTCAGCGTTCTC

virus integrase

R (SEQ ID NO: 1523)
AGAACCCGCTGAAAATCCGTC

TGACCCGT (SEQ ID NO: 2304)

EWS-FLI1

ESAP1
loop
TMRGKKKRTRAN (SEQ
ACCATGCGCGGCAAAAAAAA

ID NO: 1524)
ACGCACCCGCGCGAAC (SEQ

ID NO: 2305)

Aurora A

TPX2
loop
SYSYDAPSDFINFSS
AGCTATAGCTATGATGCGCCG

(SEQ ID NO: 1525)
AGCGATTTTATTAACTTTAGCA

GC (SEQ ID NO: 2306)

TPX2
loop
SYSYDAPSDFINFSSLD
AGCTATAGCTATGATGCGCCG

DEGDTQNIDSWFEEKA
AGCGATTTTATTAACTTTAGCA

NLEN (SEQ ID NO: 1526)
GCCTGGATGATGAAGGCGATA

CCCAGAACATTGATAGCTGGT

TTGAAGAAAAAGCGAACCTGG

AAAAC (SEQ ID NO: 2307)

TPX3
loop
MSQVKSSYSYDAPSDFI
ATGAGCCAGGTGAAGTCATCT

NFSSLDD (SEQ ID NO:
TATTCCTATGATGCCCCCAGC

1527)
GATTTCATCAATTTTTCATCCT

TGGATGATGAA (SEQ ID NO:

2308)

N-myc
helix
MALSPSRGFAEHSSEPP
ATGGCGCTGAGCCCGAGCCGC

SWVTIMLYENELWI
GGCTTTGCGGAACATAGCAGC

(SEQ ID NO: 1528)
GAACCGCCGAGCTGGGTGACC

ATTATGCTGTATGAAAACGAA

CTGTGGATT (SEQ ID NO: 2309)

N-myc
loop
LEFDSLQPCFYPDEDDF
CTGGAATTTGATAGCCTGCAG

YFGGPDSTPPGE (SEQ
CCGTGCTTTTATCCGGATGAA

ID NO: 1529)
GATGATTTTTATTTTGGCGGCC

CGGATAGCACCCCGCCGGGCG

AA (SEQ ID NO: 2310)

CK2alpha

CK2beta
loop
RLYGFKIHPMAYQLQ
CGCCTGTATGGCTTTAAAATTC

(SEQ ID NO: 1530)
ATCCGATGGCGTATCAGCTGC

AG (SEQ ID NO: 2311)

WDR5

MLL1
loop
EPPLNPHGSARAEVHLR
GAACCGCCGCTGAACCCGCAT

KS (SEQ ID NO: 1531)
GGCAGCGCGCGCGCGGAAGTG

CATCTGCGCAAAAGC (SEQ ID

NO: 2312)

Notch

MAML1
helix
SAVMERLRRRIELCRRH
AGCGCGGTGATGGAACGCCTG

HST (SEQ ID NO: 1532)
CGCCGCCGCATTGAACTGTGC

CGCCGCCATCATAGCACC

(SEQ ID NO: 2313)

Cdk2

cyclin A
helix
TYTKKQVLRMEHLVLK
ACCTATACCAAAAAACAGGTG

VLTFDL (SEQ ID NO:
CTGCGCATGGAACATCTGGTG

1533)
CTGAAAGTGCTGACCTTT (SEQ

ID NO: 2314)

aptmer library

LVCKSYRLDWEAGALF
CTGGTGTGCAAAAGCTATCGC

RSLF (SEQ ID NO: 1534)
CTGGATTGGGAAGCGGGCGCG

CTGTTTCGCAGCCTGTTT (SEQ

ID NO: 2315)

aptmer library

YSFVHHGFFNFRVSWR
TATAGCTTTGTGCATCATGGCT

EMLA (SEQ ID NO:
TTTTTAACTTTCGCGTGAGCTG

1535)
GCGCGAAATGCTGGCG (SEQ

ID NO: 2316)

peptide
loop
TAALS (SEQ ID NO:
ACCGCGGCGCTGAGC (SEQ ID

1536)
NO: 2317)

peptide
loop
TALLS (SEQ ID NO:
ACCGCGCTGCTGAGC (SEQ ID

1537)
NO: 2318)

peptide
loop
LAALS (SEQ ID NO:
CTGGCGGCGCTGAGC (SEQ ID

1538)
NO: 2319)

peptide
loop
DAALT (SEQ ID NO:
GATGCGGCGCTGACC (SEQ ID

1539)
NO: 2320)

peptide
loop
YAALQ (SEQ ID NO:
TATGCGGCGCTGCAG (SEQ ID

1540)
NO: 2321)

peptide
loop
SKL.RFTGCSC (SEQ ID
AGCAAACTGNNNCGCTTTACC

NO: 1541)
GGCTGCAGCTGC (SEQ ID NO:

2322)

RXL peptide
loop
PVKRRLFL (SEQ ID NO:
CCGGTGAAACGCCGCCTGTTT

1542)
CTG (SEQ ID NO: 2323)

p21
loop
GRKRRQTSMTDFYHSK
GGCCGCAAACGCCGCCAGACC

RRLIFSKRKP (SEQ ID
AGCATGACCGATTTTTATCAT

NO: 1543)
AGCAAACGCCGCCTGATTTTT

AGCAAACGCAAACCG (SEQ ID

NO: 2324)

PLK1

peptide
loop
MAGPMQTSpTPKNAGK
ATGGCGGGCCCGATGCAGACC

K (SEQ ID NO: 1544)
AGCACCCCGAAAAACGCGGGC

AAAAAA (SEQ ID NO: 2325)

PBIP1
loop
FDPPLHSpTA (SEQ ID
TTTGATCCGCCGCTGCATAGC

NO: 1545)
ACCGCG (SEQ ID NO: 2326)

designed peptide
loop
PLHSpTAI (SEQ ID NO:
CCGCTGCATAGCACCGCGATT

1546)
(SEQ ID NO: 2327)

designed peptide
loop
MDSpTPL (SEQ ID NO:
ATGGATAGCACCCCGCTG

1547)
(SEQ ID NO: 2328)

Emi2
loop
FSQHKpTI (SEQ ID NO:
TTTAGCCAGCATAAAACCAGC

1548)
ATT (SEQ ID NO: 2329)

HEF1
loop
LHYPSpTTALQE (SEQ
CTGCATTATCCGAGCACCACC

ID NO: 1549)
GCGCTGCAGGAA (SEQ ID NO:

2330)

cdc-25
loop
LLCSpTPNGL (SEQ ID
CTGCTGTGCAGCACCCCGAAC

NO: 1550)
GGCCTG (SEQ ID NO: 2331)

BCR-ABL

optimised
loop
EAIYAAPFAKKK (SEQ
GAAGCGATTTATGCGGCGCCG

substrate peptide

ID NO: 1551)
TTTGCGAAAAAAAAA (SEQ ID

NO: 2332)

proline-rich
helix
APSYPPPPP (SEQ ID NO:
GCGCCGAGCTATCCGCCGCCG

peptide

1552)
CCGCCG (SEQ ID NO: 2333)

PP2A

optimised
loop
LQTIQEEE (SEQ ID NO:
CTGCAGACCATTCAGGAAGAA

substate peptide

1553)
GAA (SEQ ID NO: 2334)

PP1c

consensus
loop
RV.F
CGCGTGNNNTTT (SEQ ID NO:

sequence

2335)

consensus
loop
SILK (SEQ ID NO: 1554)
AGCATTCTGAAA (SEQ ID NO:

sequence

2336)

KNL1
loop
SRRVSFADTIKVFQT
AGCCGCCGCGTGAGCTTTGCG

(SEQ ID NO: 1555)
GATACCATTAAAGTGTTTCAG

ACC (SEQ ID NO: 2337)

EED

(Embryonic

ectoderm

development)

EZH2
helix
FSSNRQKILERTEILNQE
TTTAGCAGCAACCGCCAGAAA

WKQRRIQPV (SEQ ID
ATTCTGGAACGCACCGAAATT

NO: 1556)
CTGAACCAGGAATGGAAACAG

CGCCGCATTCAGCCGGTG

(SEQ ID NO: 2338)

MCL-1

EZH2
helix
KALETLRRVGDGVQRN
AAAGCGCTGGAAACCCTGCGC

HETAF (SEQ ID NO:
CGCGTGGGCGATGGCGTGCAG

1557)
CGCAACCATGAAACCGCGTTT

(SEQ ID NO: 2339)

NOXA BH3
helix
AELEVESATQLRRFGD
GCGGAACTGGAAGTGGAAAG

KLNFRQKLL (SEQ ID
CGCGACCCAGCTGCGCCGCTT

NO: 1558)
TGGCGATAAACTGAACTTTCG

CCAGAAACTGCTG (SEQ ID NO:

2340)

MCL-1 BH3
helix
KALETLR.VGD.VQRNH
AAAGCGCTGGAAACCCTGCGC

ETAF (SEQ ID NO: 1559)
NNNGTGGGCGATNNNGTGCAG

CGCAACCATGAAACCGCGTTT

(SEQ ID NO: 2341)

GSK3

Substrate-
loop
KEAPPAPPQDP (SEQ ID
AAAGAAGCGCCGCCGGCGCCG

competitive

NO: 1723)
CCGCAGGATCCG (SEQ ID NO:

binding peptide

2477)

Substrate-
loop
LSRRPDYR (SEQ ID NO:
CTGAGCCGCCGCCCGGATTAT

competitive

1724)
CGC (SEQ ID NO: 2478)

binding peptide

Substrate-
loop
RREGGMSRPADVDG
CGCCGCGAAGGCGGCATGAGC

competitive

(SEQ ID NO: 1725)
CGCCCGGCGGATGTGGATGGC

binding peptide

(SEQ ID NO: 2479)

Substrate-
loop
YRRAAVPPSPSLSRHSS
TATCGCCGCGCGGCGGTGCCG

competitive

PSQDEDEEE (SEQ ID
CCGAGCCCGAGCCTGAGCCGC

binding peptide

NO: 1726)
CATAGCAGCCCGAGCCAGGAT

GAAGATGAAGAAGAA (SEQ ID

NO: 2480)

CtBP

From cyclic
loop
SGWTVVRMY (SEQ ID
AGCGGCTGGACCGTGGTGCGC

peptide library

NO: 1890)
ATGTAT (SEQ ID NO: 2616)

tankyrase

consensus
loop
REAGDGEE (SEQ ID
CGTGAAGCCGGTGATGGTGAA

substrate peptide

NO: 1891)
GAA (SEQ ID NO: 2617)

consensus
loop
HLQREAGDGEEFRS
CATCTGCAGCGTGAAGCCGGT

substrate peptide

(SEQ ID NO: 1892)
GATGGTGAAGAATTTCGTAGC

(SEQ ID NO: 2618)

Bcl-2 and BCL-

XL

Bim BH3
helix
IWIAQELRRIGDEFNAY
ATTTGGATTGCGCAGGAACTG

YARR (SEQ ID NO:
CGCCGCATTGGCGATGAATTT

2056)
AACGCGTATTATGCGCGCCGC

(SEQ ID NO: 2754)

Bak BH3
helix
GQVGRQLAIIGDDINR
GGCCAGGTGGGCCGCCAGCTG

(SEQ ID NO: 2057)
GCGATTATTGGCGATGATATT

AACCGC (SEQ ID NO: 2755)

Bad BH3
helix
NLWAAQRYGRELRRM
AACCTGTGGGCGGCGCAGCGC

SDEFVDSFKK (SEQ ID
TATGGCCGCGAACTGCGCCGC

NO: 2058)
ATGAGCGATGAATTTGTGGAT

AGCTTTAAAAAA (SEQ ID NO:

2756)

Jun

library-selected
helix
SIAATLEKEEANLEKM
AGCATCGCCGCCACCCTGGAG

peptide

NKKLAAEIESLLKEKDK
AAGGAGGAGGCCAACCTGGA

LESVLNYHE (SEQ ID
GAAGATGAACAAGAAGCTGG

NO: 2059)
CCGCCGAGATCGAGAGCCTGC

TGAAGGAGAAGGACAAGCTG

GAGAGCGTGCTGAACTACCAC

GAG (SEQ ID NO: 2757)

library-selected
helix
VQEIEQEIQELEKRIKQI
GTTCAGGAAATCGAACAGGAA

peptide

QQEFQEIEQQIALL (SEQ
ATCCAGGAACTGGAAAAACGT

ID NO: 2060)
ATCAAACAGATCCAGCAGGAA

TTCCAGGAAATCGAACAGCAG

ATCGCGCTGCTG (SEQ ID NO:

2758)

BFL1

NOXA BH3
helix
ATQLRRFGDKLNFRQ
GCGACCCAGCTGCGCCGCTTT

(SEQ ID NO: 2061)
GGCGATAAACTGAACTTTCGC

CAG (SEQ ID NO: 2759)

BAX

Bcl-2 BH3
helix and
EIVAKYIHYKLSQRGYE
GAAATTGTGGCGAAATATATT

loop
WDA (SEQ ID NO: 2062)
CATTATAAACTGAGCCAGCGC

GGCTATGAATGGGATGCG

(SEQ ID NO: 2760)

eIF4E

eIF4G
helix
KKRYDREFLLGFQF
AAAAAACGCTATGATCGCGAA

(SEQ ID NO: 2063)
TTTCTGCTGGGCTTTCAGTTT

(SEQ ID NO: 2761)

eIF4G
helix and
GKKRYDREFLLGFQFIF
GGCAAAAAACGCTATGATCGC

loop
ASMQKPEGLPHISDVVL
GAATTTCTGCTGGGCTTTCAGT

(SEQ ID NO: 2064)
TTATTTTTGCGAGCATGCAGA

AACCGGAAGGCCTGCCGCATA

TTAGCGATGTGGTGCTG (SEQ

ID NO: 2762)

optimised
helix and
TKLIYERAFMKNLRGSP
ACCAAACTGATTTATGAACGC

peptide
loop
LSQTPPSNVPSCLLRGT
GCGTTTATGAAAAACCTGCGC

(SEQ ID NO: 2065)
GGCAGCCCGCTGAGCCAGACC

CCGCCGAGCAACGTGCCGAGC

TGCCTGCTGCGCGGCACC (SEQ

ID NO: 2763)

Fos

library-selected
helix

AIARLEERVKTLKAEIY
GCGATTGCGCGCCTGGAAGAA

peptide

ELRSKANMLREQIAQL
CGCGTGAAAACCCTGAAAGCG

GAP (SEQ ID NO: 2066)
GAAATTTATGAACTGCGCAGC

AAAGCGAACATGCTGCGCGAA

CAGATTGCGCAGCTGGGCGCG

CCG (SEQ ID NO: 2764)

library-selected
helix

AIARLEERVKTLKAEIY
GCGATTGCGCGCCTGGAAGAA

peptide

ELQSEANMLREQIAQL
CGCGTGAAAACCCTGAAAGCG

GAP (SEQ ID NO: 2067)
GAAATTTATGAACTGCGCAGC

AAAGCGAACATGCTGCGCGAA

CAGATTGCGCAGCTGGGCGCG

CCG (SEQ ID NO: 2765)

HDAC4

SMRT
loop
HIRGSITQGIPRSYV
CACATCCGTGGTTCTATCACCC

corepressor

(SEQ ID NO: 2068)
AGGGTATCCCGCGTTCTTACG

TT (SEQ ID NO: 2766)

BCL6

SMRT and N-
loop
GRSIHEIPR (SEQ ID NO:
GGCCGCAGCATTCATGAAATT

CoR

2069)
CCGCGC (SEQ ID NO: 2767)

corepressors

SMRT and N-
loop
GLVATVKEAGRSIHEIP
GGCCTGGTGGCGACCGTGAAA

CoR

REEL (SEQ ID NO: 2070)
GAAGCGGGCCGCAGCATTCAT

corepressors

GAAATTCCGCGCGAAGAACTG

(SEQ ID NO: 2768)

Tau

alpha-tubulin
loop
KDYEEVGVDSVE (SEQ
AAAGATTATGAAGAAGTGGGC

ID NO: 2071)
GTGGATAGCGTGGAA (SEQ ID

NO: 2769)

beta-tubulin
loop
YQQYQDATADEQG
TATCAGCAGTATCAGGATGCG

(SEQ ID NO: 2072)
ACCGCGGATGAACAGGGC

(SEQ ID NO: 2770)

PD-L1

HIP1R
loop
DAVRRIEDMMNQARH
GATGCGGTGCGCCGCATTGAA

ASSGV (SEQ ID NO:
GATATGATGAACCAGGCGCGC

2073)
CATGCGAGCAGCGGCGTG

(SEQ ID NO: 2771)

KDM4A

library-selected
loop
YVYNTRSGWRWYT
TACGTTTACAACACCCGTTCTG

peptide

(SEQ ID NO: 2074)
GTTGGCGTTGGTACACC (SEQ

ID NO: 2772)

EGFR

EGFR
helix
VRKRTLRRLLQERELV
GTGCGCAAACGCACCCTGCGC

(juxtamembrane

E (SEQ ID NO: 2075)
CGCCTGCTGCAGGAACGCGAA

coiled-coil

CTGGTGGAA (SEQ ID NO: 2773)

domain)

RAB25

RFIP1
helix
RQVRELENYIDRLVRV
CGCCAGGTGCGCGAACTGGAA

MEETPNILRIPR (SEQ ID
AACTATATTGATCGCCTGGTG

NO: 2076)
CGCGTGATGGAAGAAACCCCG

AACATTCTGCGCATTCCGCGC

(SEQ ID NO: 2774)

GPCRs and

other

transmembrane

proteins

PAR1 pepducin
N-term
pal-KKSRALF-NH2 (pal- =
synthetic peptide

palmitoyl; —NH2 = amino

group) (SEQ ID NO: 2077)

PAR1 pepducin
N-term
pal-RCLSSSAVANRS-
synthetic peptide

NH2 (SEQ ID NO: 2078)

PAR1 pepducin
N-term
pal-RSLSSSAVANRS-
synthetic peptide

NH2 (SEQ ID NO: 2079)

PAR1 pepducin
N-term
pal-AVANRSKKSRALF-
synthetic peptide

NH2 (SEQ ID NO: 2080)

PAR1 pepducin
N-term
pal-
synthetic peptide

RCESSSAEANRSKKERE

LF-NH2 (SEQ ID NO:

2081)

PAR1 pepducin
N-term
pal-ASSESQRYVYSIL-
synthetic peptide

NH2 (SEQ ID NO: 2082)

PAR1 pepducin
N-term
pal-ASSASQEYVYSIL-
synthetic peptide

NH2 (SEQ ID NO: 2083)

PAR2 pepducin
N-term
pal-
synthetic peptide

RSSAMDENSEKKRKSAI

K-NH2 (SEQ ID NO:

2084)

PAR2 pepducin
N-term
pal-
synthetic peptide

GDENSEKKRKQAIK-

NH2 (SEQ ID NO: 2085)

PAR4 pepducin
N-term
pal-SGRRYGHALR-NH2
synthetic peptide

(SEQ ID NO: 2086)

PAR4 pepducin
N-term
pal-ATGAPRLPST-NH2
synthetic peptide

(SEQ ID NO: 2087)

PAR4 pepducin
N-term
pal-RLAHGYRRGS-NH2
synthetic peptide

(SEQ ID NO: 2088)

CXCR1/2
N-term
pal-RTLFKAHMGQKHR-
synthetic peptide

pepducin

NH2 (SEQ ID NO: 2089)

CXCR1/2
N-term
pal-LCA-YSRVGRSVTD-
synthetic peptide

pepducin

NH2 (LCA- = lithocholic

acid) (SEQ ID NO: 2090)

CXCR4
N-term
pal-HSKGHQKRKALK-
synthetic peptide

pepducin

NH2 (SEQ ID NO: 2091)

CXCR4
N-term
pal-MGYQKKLRSMTD-
synthetic peptide

pepducin

NH2 (SEQ ID NO: 2092)

CXCR4
N-term
pal-
synthetic peptide

pepducin

MGYQKKLRSMTDKYR

L-NH2 (SEQ ID NO:

2093)

S1P3 pepducin
N-term
myristoyl-
synthetic peptide

GMRPYDANKR-NH2

(SEQ ID NO: 2094)

S1P3 pepducin
N-term
myristoyl-GRPYDAN-
synthetic peptide

NH2 (SEQ ID NO: 2095)

FRP2 pepducin
N-term
pal-
synthetic peptide

KIHKKGMIKSSRPLRV-

NH2 (SEQ ID NO: 2096)

FRP2 pepducin
N-term
pal-KIHKKGMIKS-NH2
synthetic peptide

(SEQ ID NO: 2097)

FRP2 pepducin
N-term
pal-KIHKKGMIKSSR-
synthetic peptide

NH2 (SEQ ID NO: 2098)

LGR7 pepducin
N-term
pal-
synthetic peptide

KRKALKALILNEKKVQ-

H (—H = hydrogen) (SEQ

ID NO: 2099)

SMO pepducin
N-term
pal-TFVADWRNSNRY-H
synthetic peptide

(SEQ ID NO: 2100)

SMO pepducin
N-term
pal-
synthetic peptide

TWAWHTSFKALGTTY

QPLSGKTS-H (SEQ ID

NO: 2101)

SMO pepducin
N-term
pal-
synthetic peptide

RGVMTLFSIKSNHPGLL

SEKAASKINETMLR-H

(SEQ ID NO: 2102)

IGF1R pepducin
N-term
pal-RNNSRLGNGVLY-
synthetic peptide

NH2 (SEQ ID NO: 2103)

CD226 pepducin
N-term
pal-RRERRDLFTE-NH2
synthetic peptide

(SEQ ID NO: 2104)

TRPV1
N-term
pal-MGETVNKIAQES-
synthetic peptide

TRPducin

NH2 (SEQ ID NO: 2105)

Nrp1/2

paratrope
loop
RASQYFSSYLA (SEQ ID
CGCGCGAGCCAGTATTTTAGC

NO: 2106)
AGCTATCTGGCG (SEQ ID NO:

2775)

paratrope
helix
AREDFRNRRLWYVMD
GCGCGCGAAGATTTTCGCAAC

Y (SEQ ID NO: 2107)
CGCCGCCTGTGGTATGTGATG

GATTAT (SEQ ID NO: 2776)

IL18

paratrope
helix
KASGYSFTDYFIY (SEQ
AAAGCGAGCGGCTATAGCTTT

ID NO: 2108)
ACCGATTATTTTATTTAT (SEQ

ID NO: 2777)

IL15

paratrope
loop
YRDRRRPS (SEQ ID NO:
TATCGCGATCGCCGCCGCCCG

2109)
AGC (SEQ ID NO: 2778)

Thyroid

stimulating

hormone

receptor

paratrope
loop
SGSSSDIGSNYVS (SEQ
AGCGGCAGCAGCAGCGATATT

ID NO: 2110)
GGCAGCAACTATGTGAGC

(SEQ ID NO: 2779)

EGF receptor

paratrope
loop
QQWSSHIFT (SEQ ID
CAGCAGTGGAGCAGCCATATT

NO: 2111)
TTTACC (SEQ ID NO: 2780)

paratrope
helix
ASRDYDYAGRYFDY
GCGAGCCGCGATTATGATTAT

(SEQ ID NO: 2112)
GCGGGCCGCTATTTTGATTAT

(SEQ ID NO: 2781)

IL23

paratrope
loop
QNGHSFPFT (SEQ ID
CAGAACGGCCATAGCTTTCCG

NO: 2113)
TTTACC (SEQ ID NO: 2782)

paratrope
helix
YINPYNDGTK (SEQ ID
TATATTAACCCGTATAACGAT

NO: 2114)
GGCACCAAA (SEQ ID NO: 2783)

paratrope
helix
ARNWDVAY (SEQ ID
GCGCGCAACTGGGATGTGGCG

NO: 2115)
TAT (SEQ ID NO: 2784)

Lymphocyte

function-

associated

antigen 1 (LFA-

1)

paratrope
helix
SGYSFTGHWMN (SEQ
AGCGGCTATAGCTTTACCGGC

ID NO: 2116)
CATTGGATGAAC (SEQ ID NO:

2785)

paratrope
helix
MIHPSDSETR (SEQ ID
ATGATTCATCCGAGCGATAGC

NO: 2117)
GAAACCCGC (SEQ ID NO: 2786)

paratrope
helix
ARGIYFYGTTYFDY
GCGCGCGGCATTTATTTTTATG

(SEQ ID NO: 2118)
GCACCACCTATTTTGATTAT

(SEQ ID NO: 2787)

C3b

paratrope
helix
SGFSFTSSVS (SEQ ID
AGCGGCTTTAGCTTTACCAGC

NO: 2119)
AGCGTGAGC (SEQ ID NO: 2788)

paratrope
helix
LIYPYNGFN (SEQ ID
CTGATTTATCCGTATAACGGCT

NO: 2120)
TTAAC (SEQ ID NO: 2789)

FGF receptor 3

paratrope
helix
AASGFTFTSTGIS (SEQ
GCGGCGAGCGGCTTTACCTTT

ID NO: 2121)
ACCAGCACCGGCATTAGC

(SEQ ID NO: 2790)

paratrope
helix
ARTYGIYDLYVDYTE
GCGCGCACCTATGGCATTTAT

(SEQ ID NO: 2122)
GATCTGTATGTGGATTATACC

GAA (SEQ ID NO: 2791)

IL2

paratrope
helix
SRDYGYYFD (SEQ ID
AGCCGCGATTATGGCTATTAT

NO: 2123)
TTTGAT (SEQ ID NO: 2792)

paratrope
helix
GYSFTRYWMH (SEQ ID
GGCTATAGCTTTACCCGCTATT

NO: 2124)
GGATGCAT (SEQ ID NO: 2793)

HER2

paratrope
loop
QWWWWPST (SEQ ID
CAGTGGTGGTGGTGGCCGAGC

NO: 2125)
ACC (SEQ ID NO: 2794)

paratrope
helix
ASGFSIWWSWIH (SEQ
GCGAGCGGCTTTAGCATTTGG

ID NO: 2126)
TGGAGCTGGATTCAT (SEQ ID

NO: 2795)

membrane-type

serine protease

1

paratrope
loop
YDNNQRPS (SEQ ID
TATGATAACAACCAGCGCCCG

NO: 2127)
AGC (SEQ ID NO: 2796)

paratrope
helix
TFHIRRYRSGYYDKMD
ACCTTTCATATTCGCCGCTATC

H (SEQ ID NO: 2128)
GCAGCGGCTATTATGATAAAA

TGGATCAT (SEQ ID NO: 2797)

beta-secretase

paratrope
helix
ARGPFSPWVMDY (SEQ
GCGCGCGGCCCGTTTAGCCCG

ID NO: 2129)
TGGGTGATGGATTAT (SEQ ID

NO: 2798)

VEGF-R

paratrope
helix
TRHDGTNFD (SEQ ID
ACCCGCCATGATGGCACCAAC

NO: 2130)
TTTGAT (SEQ ID NO: 2799)

paratrope
helix
QQAKAFPPT (SEQ ID
CAGCAGGCGAAAGCGTTTCCG

NO: 2131)
CCGACC (SEQ ID NO: 2800)

lrp5/6 receptor

paratrope
helix
SGHVNAVKNYGY (SEQ
AGCGGCCATGTGAACGCGGTG

ID NO: 2132)
AAAAACTATGGCTAT (SEQ ID

NO: 2801)

hepsin protease

paratrope
helix
WINTETGS (SEQ ID NO:
TGGATTAACACCGAAACCGGC

2133)
AGC (SEQ ID NO: 2802)

Factor D

paratrope
helix
WINTYTGE (SEQ ID NO:
TGGATTAACACCTATACCGGC

2134)
GAA (SEQ ID NO: 2803)

paratrope
helix
GYTFTNYGMN (SEQ ID
GGCTATACCTTTACCAACTAT

NO: 2135)
GGCATGAAC (SEQ ID NO: 2804)

TABLE 3

Degron
Grafting

Ubiquitin
sequence
site in

DNA sequence E. Coli codon optimised

Ligase
derived from
scaffold
Amino acid sequence
5′ to 3′

Mdm2
Consensus
helix
F[∨P]{3}W[∨P]{2,3}[VIL]
TTT[NNNNNNNN(EXCEPT CCN)]TGG[NNN{2,3}

(∨CCN)][GTG/ATT/CTG]

(SEQ ID NO: 2945)

Mdm2
p53
helix
FAAYWNLLSAYG
TTTGCAGCCTATTGGAATCTGCTGAGCGCATATGGT

(SEQ ID NO: 2805)
(SEQ ID NO: 2946)

Mdm2
p53
helix
RFMDYWEGL
CGCTTCATGGATTATTGGGAAGGTCTG

(SEQ ID NO: 2806)
(SEQ ID NO: 2947)

Mdm2
p53
helix
TSFAEYWALLAENL
ACCAGCTTTGCCGAGTATTGGGCCCTGCTGGCCGAG

(SEQ ID NO: 2807)
AATCTG

(SEQ ID NO: 2948)

Mdm2
p53
helix
EAQWAAL
GAAGCGCAGTGGGCGGCGCTG

(SEQ ID NO: 2808)
(SEQ ID NO: 2949)

Mdm2
p53
helix
FEAQWAAL
TTTGAAGCGCAGTGGGCGGCGCTG

(SEQ ID NO: 2809)
(SEQ ID NO: 2950)

Mdm2
p63
helix
FQHIWDFL
TTTCAGCATATTTGGGATTTTCTG

(SEQ ID NO: 2810)
(SEQ ID NO: 2951)

Mdm2
p73
helix
FEHLWSSL
TTTGAACATCTGTGGAGCAGCCTG

(SEQ ID NO: 2811)
(SEQ ID NO: 2952)

SCF(Skp2)
Consensus
loop
.[DE].pTP.K
NNN[GAT/GAA]NNNACCCCGNNNAAA

(SEQ ID NO: 2953)

SCF(Skp2)
p27
loop
AGSNEQEPKKRS
GCAGGTAGCAATGAACAAGAACCGAAAAAACGTAGT

(SEQ ID NO: 2812)
(SEQ ID NO: 2954)

Cul3-Keap1
Consensus
loop
[DNS].[DES][TNS] GE
[GAC/AAC/AGC]NNN[GAC/GAA/AGC][ACC/

AAC/AGC]GGCGAA

(SEQ ID NO: 2955)

Cul3-Keap1
Nrf2
loop
DPETGEL
GATCCGGAAACCGGTGAACTG

(SEQ ID NO: 2813)
(SEQ ID NO: 2956)

Cul3-Keap1
Sequestosome-1
loop
DPSTGEL
GATCCGAGCACCGGCGAACTG

(SEQ ID NO: 2814)
(SEQ ID NO: 2957)

Cul3-Keap1
IKKB
loop
NQETGE
AACCAGGAAACCGGCGAA

(SEQ ID NO: 2815)
(SEQ ID NO: 2958)

Cul3-KEAP1
APC membrane
loop
SPETGE
AGCCCGGAAACCGGCGAA

recruitment

(SEQ ID NO: 2816)
(SEQ ID NO: 2959)

protein 1

Cul3-KEAP1
Prothymosin
loop
NEENGE
AACGAAGAAAACGGCGAA

alpha

(SEQ ID NO: 2817)
(SEQ ID NO: 2960)

Cul3-KEAP1
Nucleosome-
oop
DPENGE
GATCCGGAAAACGGCGAA

remodeling

(SEQ ID NO: 2818)
(SEQ ID NO: 2961)

factor

subunit

BPTF

Cul3-KEAP1
Serine/
loop
NVESGE
AACGTGGAAAGCGGCGAA

threonine-

(SEQ ID NO: 2819)
(SEQ ID NO: 2962)

protein

phosphatase

PGAM5,

mitochondrial

Cul3-KEAP1
Nuclear
loop
DEETGE
GATGAAGAAACCGGCGAA

factor

(SEQ ID NO: 2820)
(SEQ ID NO: 2963)

erythroid 2-

related

factor 2

Cul3-KEAP1
Partner and
loop
DEETGE
GATGAAGAAACCGGCGAA

localizer of

(SEQ ID NO: 2821)
(SEQ ID NO: 2964)

BRAC2

Cul3-KEAP1_2
Consensus
loop
QD.DLGV
CAGGATNNNGATCTGGGTGTG

(SEQ ID NO: 2822)
(SEQ ID NO: 2965)

Cul3-SPOP
Consensus
loop
[AVP].[ST][ST][ST]
[GCG/GTG/CCG]NNN[AGC/ACC][AGC/ACC]

[AGC/ACC]

Cul3-SPOP
Map kinase
loop
ELDSPSSTSSSS
GAACTGGATAGCCCGAGCAGCACCAGCAGCAGCAGC

phosphatase

(SEQ ID NO: 2823)
(SEQ ID NO: 2966)

Cul3-SPOP
SBC
loop
LACDEVTSTTSSSTA
CTGGCATGTGATGAAGTTACCAGCACCACCAGTAGC

(SEQ ID NO: 2824)
AGCACCGCA

(SEQ ID NO: 2967)

Cul3-SPOP
Androgen
loop
ASSTT
GCGAGCAGCACCACC

receptor

(SEQ ID NO: 2825)
(SEQ ID NO: 2968)

Cul3-SPOP
Map kinase
loop
DEVTSTTSSST
GATGAAGTGACCAGCACCACCAGCAGCAGCACC

phosphatase

(SEQ ID NO: 2826)
(SEQ ID NO: 2969)

Cul3-KELCH
Consensus
loop
E.EE.E[AV]DQH
GAANNNGAAGAANNNGAA[GCG/GTG]GATAACCAT

(SEQ ID NO: 2827)
(SEQ ID NO: 2970)

Cul3-KELCH
Serine/
helix/loop
EPEEPEADQH
GAACCGGAAGAACCGGAAGCGGATCAGCAT

threonine-

(SEQ ID NO: 2828)
(SEQ ID NO: 2971)

protein

kinase WNK1

Cul3-KELCH
Serine/
helix/loop
ECEETEVDQH
GAATGCGAAGAAACCGAAGTGGATCAGCAT

threonine-

(SEQ ID NO: 2829)
(SEQ ID NO: 2972)

protein

kinase WNK3

Cul3-KELCH
Serine/
helix/loop
EPEEPEADQH
GAACCGGAAGAACCGGAAGCGGATCAGCAT

threonine-

(SEQ ID NO: 2830)
(SEQ ID NO: 2973)

protein

kinase WNK4

Cul3-KELCH
Nuclear
helix/loop
ILWRQDIDLGV
ATTCTGTGGCGCCAGGATATTGATCTGGGCGTG

factor

(SEQ ID NO: 2831)
(SEQ ID NO: 2974)

erythroid

2-related

factor 2

KELCH
Consensus
loop
[AP]P[MV][IM]V
[GCG/CCG]CCG[ATG/GTG][ATT/ATG]GTG

actinfilin

(SEQ ID NO: 3099)

APC/C
ABBA
loop
[FIVL].[ILMVP][FHY].
[TTT/ATT/GTG/CTG]NNN[ATT/CTG/ATG/

[DE].{O,3}{DEST}
GTG/CCG][TTT/CAT/TAT][NNN{0,3}]

[GAT/GAA/AGC/ACC]

APC/C
ABBA
loop
SLSSAFHVFEDGNKEN
AGCCTGAGCAGCGCGTTTCATGTGTTTGAAGATGGC

(SEQ ID NO: 2832)
AACAAAGAAAAC

(SEQ ID NO: 2975)

APC/C
Cyclin-A2:
loop
FTIHVD
TTTACCATTCATGTGGAT

ABBA

(SEQ ID NO: 2833)
(SEQ ID NO: 2976)

APC/C
ABOX
loop
QRVL
CAGCGTGTTCTG

(SEQ ID NO: 2977)

APC/C
Consensus
loop
.KEN.
NNNAAAGAAAACNNN

(SEQ ID NO: 2834)
(SEQ ID NO: 2978)

APC/C
KEN
loop
SEDKENVPP
AGCGAGGATAAAGAAAATGTTCCGCCT

(SEQ ID NO: 2835)
(SEQ ID NO: 2979)

APC/C
DBOX consensus
loop
.R..L..[LIVM].
NNNCGTNNNNNNCTGNNNNNN[CTG/ATT/GTG/

ATG]NNN

(SEQ ID NO: 2980)

APC/C
Shugoshin 1:
loop
RLSLSPKKN
CGCCTGAGCCTGAGCCCGAAAAAAAAC

DBOX

(SEQ ID NO: 2836)
(SEQ ID NO: 2981)

APC/C
Shugoshin 1:
loop
RSSLKKHCN
CGCAGCAGCCTGAAAAAACATTGCAAC

DBOX

(SEQ ID NO: 2837)
(SEQ ID NO: 2982)

APC/C
Shugoshin 1:
loop
HLSLKDITN
CATCTGAGCCTGAAAGATATTACCAAC

DBOX

(SEQ ID NO: 2838)
(SEQ ID NO: 2983)

APC/C
Bcl-2-like
loop
RSPLFIF
CGCAGCCCGCTGTTTATTTTT

protein 11:

(SEQ ID NO: 2839)
(SEQ ID NO: 2984)

DBOX

APC/C
Bcl-2-like
loop
RSSLLSR
CGCAGCAGCCTGCTGAGCCGC

protein 11:

(SEQ ID NO: 2840)
(SEQ ID NO: 2985)

DBOX

APC/C
Securin:
loop
RKALGTV
CGCAAAGCGCTGGGCACCGTG

DBOX

(SEQ ID NO: 2841)
(SEQ ID NO: 2986)

APC/C
Securin-2:
loop
RKALGTV
CGCAAAGCGCTGGGCACCGTG

DBOX

(SEQ ID NO: 2842)
(SEQ ID NO: 2987)

APC/C
Ski-like
loop
RLCLPQV
CGCCTGTGCCTGCCGCAGGTG

protein: DBOX

(SEQ ID NO: 2843)
(SEQ ID NO: 2988)

APC/C
Aurora kinase
loop
RLPLAQV
CGCCTGCCGCTGGCGCAGGTG

B: DBOX

(SEQ ID NO: 2844)
(SEQ ID NO: 2989)

APC/C
Serine/
loop
NRKPLTVLN
AACAGGAAGCCCCTGACCGTGCTGAAC

threonine-

(SEQ ID NO: 2845)
(SEQ ID NO: 2990)

protein

kinase

PLK1: DBOX

APC/C
Cyclin-A2:
loop
RAALAVL
CGCGCGGCGCTGGCGGTGCTG

DBOX

(SEQ ID NO: 2846)
(SEQ ID NO: 2991)

APC/C
G2/mitotic-
loop
PRTALGDIG
CCGCGCACCGCGCTGGGCGATATTGGC

specific

(SEQ ID NO: 2847)
(SEQ ID NO: 2992)

cyclin-B1:

DBOX

APC/C
G2/mitotic-
loop
RSAFEDLTN
CGCAGCGCGTTTGAAGATCTGACCAAC

specific

(SEQ ID NO: 2848)
(SEQ ID NO: 2993)

cyclin-B3:

DBOX

APC/C
S-phase
loop
HRKHLQEIP
CATCGCAAACATCTGCAGGAAATTCCG

kinase-

(SEQ ID NO: 2849)
(SEQ ID NO: 2994)

associated

protein 2:

DBOX

APC/C
Nuclear
loop
RSGLQLS
CGCAGCGGCCTGCAGCTGAGC

autoantigen

(SEQ ID NO: 2850)
(SEQ ID NO: 2995)

Sp-100:

DBOX

APC/C
Nucleolar and
loop
RRGLILA
CGCCGCGGCCTGATTCTGGCG

spindle-

(SEQ ID NO: 2851)
(SEQ ID NO: 2996)

associated

protien 1:

DBOX

APC/C
BRCA1-A
loop
RHCLPTL
CGCCATTGCCTGCCGACCCTG

complex

(SEQ ID NO: 2852)
(SEQ ID NO: 2997)

subunit

RAP80:

DBOX

APC/C
BARD1: DBOX
loop
RNLLHDN
CGCAACCTGCTGCATGATAAC

(SEQ ID NO: 2853)
(SEQ ID NO: 2998)

APC/C
BARD1: DBOX
loop
RAALDRL
CGCGCGGCGCTGGATCGCCTG

(SEQ ID NO: 2854)
(SEQ ID NO: 2999)

APC/C
E3 ubiquitin
loop
RKKL
CGCAAAAAACTG

ligase RNF157:

(SEQ ID NO: 2855)
(SEQ ID NO: 3000)

DBOX

APC/C
E3 ubiquitin
loop
RRRL
CGCCGCCGCCTG

ligase RNF157:

(SEQ ID NO: 2856)
(SEQ ID NO: 3001)

DBOX

APC/C
Nuclear-
loop
RARLCSS
CGCGCGCGCCTGTGCAGCAGC

interacting

(SEQ ID NO: 2857)
(SEQ ID NO: 3002)

partner of

ALK: DBOX

APC/C
Nuclear-
loop
RLPLVPE
CGCCTGCCGCTGGTGCCGGAA

interacting

(SEQ ID NO: 2858)
(SEQ ID NO: 3003)

partner of

ALK: DBOX

APC/C
Tribbles
loop
RKKLVLE
CGCAAAAAACTGGTGCTGGAA

homolog 3:

(SEQ ID NO: 2859)
(SEQ ID NO: 3004)

DBOX

APC/C
Anillin: DBOX
loop
RENLQRK
CGCGAAAACCTGCAGCGCAAA

(SEQ ID NO: 2860)
(SEQ ID NO: 3005)

APC/C
Anillin: DBOX
loop
RQPLSEA
CGCCAGCCGCTGAGCGAAGCG

(SEQ ID NO: 2861)
(SEQ ID NO: 3006)

APC/C
Ninein-like
loop
RTQLETK
CGCACCCAGCTGGAAACCAAA

(SEQ ID NO: 2862)
(SEQ ID NO: 3007)

protein: DBOX

APC/C
Dual
loop
RNSLRQT
CGCAACAGCCTGCGCCAGACC

specificity

(SEQ ID NO: 2863)
(SEQ ID NO: 3008)

protein

kinase TTK:

DBOX

APC/C
Inactive serine/
loop
RYGLHPD
CGCTATGGCCTGCATCCGGAT

threonine-

(SEQ ID NO: 2864)
(SEQ ID NO: 3009)

protein kinase

TEX14: DBOX

APC/C
DBOX
loop
PRLPLGDVSNN
CCGCGTCTGCCGCTGGGTGATGTTAGCAATAAT

(SEQ ID NO: 2865)
(SEQ ID NO: 3010)

APC/C
Bub1b
loop
AKENE
GCGAAAGAAAACGAA

(SEQ ID NO: 2866)
(SEQ ID NO: 3011)

APC/C
Bub1b
loop
SKENV
AGCAAAGAAAACGTG

(SEQ ID NO: 2867)
(SEQ ID NO: 3012)

APC/C TPR1
Consensus
loop
.[ILM]R$
NNN[ATT/CTG/ATG]CTG

SCF^Fbw7_1
Consensus
loop
[LIVMP].{0,2}pTP..
[CTG/ATT/GTT/ATG/CCG][NNN{0,2}]ACCCC

[pSpT]
GNNNNNN[AGC/ACC]

(SEQ ID NO: 3013)

SCF^Fbw7_1
Neurogenic
loop
PFLpTPpSPE
CCGTTTCTGACCCCGAGCCCGGAA

locus notch

(SEQ ID NO: 2868)
(SEQ ID NO: 3014)

homolog

protein 1

SCF^Fbw7_1
Uracil-DNA
loop
PGpTPPSpS
CCGGGCACCCCGCCGAGCAGC

glycosylase

(SEQ ID NO: 2869)
(SEQ ID NO: 3015)

SCF^Fbw7_1
G1/S-specific
loop
LLpTPPQpS
CTGCTGACCCCGCCGCAGAGC

cyclin-E1

(SEQ ID NO: 2870)
(SEQ ID NO: 3016)

SCF^Fbw7_2
Consensus
loop
[LIVMP].{0,2}pTP..E
[CTG/ATT/GTT/ATG/CCG][NNN{0,2}]ACCCC

GNNNNNNGAA

(SEQ ID NO: 3017)

SCF^Fbw7_2
Neurogenic
loop
PFLpTPSPE
CCGTTTCTGACCCCGAGCCCGGAA

locus notch

(SEQ ID NO: 2871)
(SEQ ID NO: 3018)

homolog

protein 1

SCF^Fbw7
G1/S-specific
loop
SLIPpTPDK
AGCCTGATTCCGACCCCGGATAAA

cyclin-E1

(SEQ ID NO: 2872)
(SEQ ID NO: 3019)

SCF^Fbw7
cyclin-D3
loop
PEQTSEPTDVAI
CCGGAACAGACCAGCGAACCGACCGATGTTGCAATT

(SEQ ID NO: 2873)
(SEQ ID NO: 3020)

SCF^Fbw7
Sterol
loop
SDSEPD
AGCGATAGCGAACCGGAT

regulatory

(SEQ ID NO: 2874)
(SEQ ID NO: 3021)

element-

binding

protein 1

SCF^Fbw7
SV40
loop
TPxxE
ACCCCGNNNNNNGAA

(SEQ ID NO: 3022)

SCF^Fbw7
cyclin E1
loop
SLIPEPDR
AGCCTGATTCCGGAACCGGATCGT

(SEQ ID NO: 2875)
(SEQ ID NO: 3023)

SCF^Fbw7
Nuclear factor
loop
pSGVETpSF
AGCGGCGTGGAAACCAGCTTT

NF-kappa-B

(SEQ ID NO: 2876)
(SEQ ID NO: 3024)

p105 subunit

SCF^Fbw7
E3 Ubiquitin
loop
LKLKKSL
CTGAAACTGAAAAAAAGCCTG

ligase RNF157

(SEQ ID NO: 2877)
(SEQ ID NO: 3025)

SCF^Fbw7
NF-kappa-B
loop
pSGLDpS
AGCGGCCTGGATAGC

inhibitor

(SEQ ID NO: 2878)
(SEQ ID NO: 3026)

alpha

SCF^Fbw7
NF-kappa-B
loop
DpSGIEpS
GATAGCGGCATTGAAAGC

inhibitor

(SEQ ID NO: 2879)
(SEQ ID NO: 3027)

epsilon

SCF^Fbw7
Programmed
loop
pSSRDSGRGDS
AGCAGCCGCGATAGCGGCCGCGGCGATAGC

cell death

(SEQ ID NO: 2880)
(SEQ ID NO: 3028)

protein 4

SCF^Fbw7
NF-kappa-B
loop
DpSGLGpS
GATAGCGGCCTGGGCAGC

inhibitor

(SEQ ID NO: 2881)
(SEQ ID NO: 3029)

beta

SCF^Fbw8
myc
loop
EPPLEP
GAACCGCCTCTGGAACCG

(SEQ ID NO: 2882)
(SEQ ID NO: 3030)

SCF_TIR1
Consensus
loop
.[VLIA][VLI]GWPP
NNN[GTG/CTG/ATT/GCG][GTG/CTG/ATT]GGT

[VLI]...R.
TATCCGCCG[GTG/CTG/ATT] NNNNNNCGTNNN

(SEQ ID NO: 2883)
(SEQ ID NO: 3031)

Cul4-DDB1-
Consensus
loop
[NQ]{0,1}..[ILMV]
[AAC/CAG{0,1}]NNNNNN[ATT/CTG/ATG/

Cdt2_1

[ST][DEN][FY][FY].
GTG][AGC/ACC][GAC/GAA/AAC][TTT/TAT]

{2,3}[KR]{2,3}[{circumflex over ( )}DE]
[TTT/TAT][NNN{0,3}][AAA/CGT{2,3}]

[NNN (∨GAA/GAT)]

Cul4-DDB1-
Consensus
loop
[NQ]{0,1}..[ILMV]T
[AAC/CAG{0,1}]NNNNNN[ATT/CTG/ATG/GTG]

Cdt2_2

[DEN][HMFY][FMY].
[ACC][GAC/GAA/AAC][CAT/ATG/TTT/TAT]

{2,3}[KR]{2,3}[{circumflex over ( )}DE]
[TTT/TAT/ATG][NNN{2,3}][AAA/CGT{2,3}]

[NNN (∨GAA/GAT)]

Cul4-DDB1-
PIP
loop
QRRMTDFYARRR
CAGCGTCGTATGACCGATTTTTATGCACGTCGTCGT

Cdt2

(SEQ ID NO: 2884)
(SEQ ID NO: 3032)

DDB1-CUL4
paramoxyvirus
helix
TVAYFTLQQVYG
ACCGTTGCATATTTTACCCTGCAGCAGGTTTATGGT

SV5-V protein

(SEQ ID NO: 2885)
(SEQ ID NO: 3033)

DDB1-CUL4
Hepatitis B
helix
ILPAVLHLRTVYG
ATTCTGCCTGCAGTTCTGCATCTGCGTACCGTTTAT

virus X protein

(SEQ ID NO: 2886)
GGT

(SEQ ID NO: 3034)

DDB1-CUL4
Woodchuck
helix
NFVAWHALRQVYG
AATTTTGTTGCATGGCATGCACTGCGTCAGGTTTAT

Hepatitis

(SEQ ID NO: 2887)
GGT

virus X

(SEQ ID NO: 3035)

protein

DDB1-CUL5
DCAF9
helix
NITADLILRQVYG
AACATTACCGCAGATCTGATTCTGCGTCAGGTTTAT

(SEQ ID NO: 2888)
GGT

(SEQ ID NO: 3036)

Unknown
Bonger
loop
RRRG
CGTCGTCGTGGT

(SEQ ID NO: 2889)
(SEQ ID NO: 3037)

SOCS box-
iNOS
loop
DINN
GACATCAACAAC

Cul5-SPSB2

(SEQ ID NO: 2890)
(SEQ ID NO: 3038)

SCF_TRCP1_1
Consensus
loop
DpSG.{2,3}[pSpt]
GATAGCGGC[NNN{2,3}][AGC/ACC]

(SEQ ID NO: 3039)

SCF_TRCP1_1
SETBP1
loop
DSGIGT
GATAGCGGCATTGGCACC

(SEQ ID NO: 2891)
(SEQ ID NO: 3040)

β-TRCP
β-catenin
loop
DEGNYE
GATGAAGGCAACTATGAA

(SEQ ID NO: 2892)
(SEQ ID NO: 3041)

β-TRCP
Vpu
loop
DSGxxS
GATAGCGGCNNNNNNAGC

(SEQ ID NO: 2893)
(SEQ ID NO: 3042)

β-TRCP
RE1-silencing
loop
SEGSDDSGL
AGCGAAGGCAGCGATGATAGCGGCCTG

transcription

(SEQ ID NO: 2894)
(SEQ ID NO: 3043)

factor

β-TRCP
Prolactin
loop
TDSGRGS
ACCGATAGCGGCCGCGGCAGC

receptor

(SEQ ID NO: 2895)
(SEQ ID NO: 3044)

β-TRCP
Protein aurora
loop
DSGYNT
GATAGCGGCTATAACACC

borealis

(SEQ ID NO: 2896)
(SEQ ID NO: 3045)

β-TRCP
Vaccinia virus
loop
YSGNLEpS
TATAGCGGCAACCTGGAAAGC

(SEQ ID NO: 2897)
(SEQ ID NO: 3046)

SCF^Fbw2
G1/S-specific
loop
pSQTSTPTDVTAIHL
AGCCAGACCAGCACCCCGACCGATGTGACCGCGATT

cyclin-D3

(SEQ ID NO: 2898)
CATCTG

(SEQ ID NO: 3047)

SCF^Fbw3
G1/S-specific
loop
PTDVTAI
CCGACCGATGTGACCGCGATT

cyclin-D3

(SEQ ID NO: 2899)
(SEQ ID NO: 3048)

SCF^Fbw4
cyclin D1
loop
EEEVSLASEPTDVRD
GAAGAAGAAGTTAGCCTGGCAAGCGAACCGACCGAT

(SEQ ID NO: 2900)
GTTCGTGAT

(SEQ ID NO: 3049)

OPDH VHL 1
consensus
loop
[IL]ApT.{6,8}[FLIVM].
[ATT/CTG]GCGACC[NNN{6,8}][TTT/CTG/

[FLIVM]
ATT/GTG/ATG]NNN[TTT/CTG/ATT/GTG/ATG]

(SEQ ID NO: 3050)

SCF coil
consensus
loop
[RK][RK].SL.F[FLM].
[CGT/AAA][CGT/AAA]NNNAGCCTGNNNTTT

[RK]R[HRK].
[TTT/CTA/ATG]NNN[CGT/AAA]CGT[CGT/

(SEQ ID NO: 2901)
AAA/CAT]NNN[CGT/AAA]

(SEQ ID NO: 3051)

CHIP
Hsp90
loop or
ASRMEEVD
GCAAGCCGTATGGAAGAAGTTGAT

C-
(SEQ ID NO: 2902)
(SEQ ID NO: 3052)

terminus

CHIP
Hsp70
loop or
GPTIEEVD
GGTCCGACCATTGAAGAAGTTGAT

C-
(SEQ ID NO: 2903)
(SEQ ID NO: 3053)

terminus

SOCS box-
VASA
loop
DINNNNNIVEDVERKREFYI
GACATCAACAACAACAACAACATCGTTGAAGACGTT

Cul5-SPSB4

(SEQ ID NO: 2904)
GAACGTAAACGTGAATTCTACATC

(SEQ ID NO: 3054)

UBR5
PAM2
loop
SKLSVNAPEFYPSG
TCTAAACTGTCTGTTAACGCGCCGGAATTCTACCCG

(SEQ ID NO: 2905)
TCTGGT

(SEQ ID NO: 3055)

CRL2(KLHDC2)
Usp1
C-
IGLLGG
ATCGGTCTGCTGGGTGGT

terminu
(SEQ ID NO: 2906)
(SEQ ID NO: 3056)

CID4
Pro/N-degron
N-
PGLW
CCGGGTCTGTGG

terminu
(SEQ ID NO: 2907)
(SEQ ID NO: 3057)

TRIM21
Fc fragment
loop
WxW
TGGNNNTGG

TRIM21
Fc fragment
loop
HNH
CATAACCAT

Nedd4
PPxY motif
loop
TAPPPAYATLG
ACCGCGCCGCCGCCGGCGTATGCGACCCTGGGC

(SEQ ID NO: 2908)
(SEQ ID NO: 3058)

Elongin C
Vif
loop
SLxxxLxxxI
AGCCTGNNNNNNNNNCTGNNNNNNNNNATT

(SEQ ID NO: 2909)
(SEQ ID NO: 3059)

Unknown
ID2
loop
SRTPLTTLN
AGCCGCACCCCGCTGACCACCCTGAAC

(SEQ ID NO: 2910)
(SEQ ID NO: 3060)

Unknown
ZAP70
loop
DGYTPEP
GATGGCTATACCCCGGAACCG

(SEQ ID NO: 2911)
(SEQ ID NO: 3061)

Unknown
SH3R1
loop
RPTAAVTPI
CGCCCGACCGCGGCGGTGACCCCGATT

(SEQ ID NO: 2912)
(SEQ ID NO: 3062)

Unknown
ETV1
loop
DEQFVPD
GATGAACAGTTTGTGCCGGAT

(SEQ ID NO: 2913)
(SEQ ID NO: 3063)

Unknown
EPAS1
loop
LAPYIPMDGEDFQL
CTGGCGCCGTATATTCCGATGGATGGCGAAGATTTT

(SEQ ID NO: 2914)
CAGCTG

(SEQ ID NO: 3064)

Unknown
hantavirus
loop
YVGLVWGVLLTTELIVWAASA
TATGTGGGCCTGGTGTGGGGCGTGCTGCTGACCACC

(SEQ ID NO: 2915)
GAACTGATTGTGTGGGCGGCGAGCGCG

(SEQ ID NO: 3065)

CRL4_CDT2_1
SETD8
loop
PKTPPSSCDSTN
CCGAAAACCCCGCCGAGCAGCTGCGATAGCACCAAC

(SEQ ID NO: 2916)
(SEQ ID NO: 3066)

CBL (PTK)
Consensus
loop
[DN].pY[ST].P
[GAT/AAC]NNNTAT[AGC/ACC]NNNCCG

(SEQ ID NO: 3067)

CBL (met)
Consensus
loop
DpYR
GATTATCGT

CBL
SH2B adapter
loop
RAIDNQYTPL
CGCGCGATTGATAACCAGTATACCCCGCTG

protein 3

(SEQ ID NO: 2917)
(SEQ ID NO: 3068)

CBL
Protein sprouty
loop
IRGSNEYTEGPS
ATTCGCGGCAGCAACGAATATACCGAAGGCCCGAGC

homolog 1

(SEQ ID NO: 2918)
(SEQ ID NO: 3069)

CBL
Protein sprouty
loop
IRNTNEYTEGPT
ATTCGCAACACCAACGAATATACCGAAGGCCCGACC

homolog 2

(SEQ ID NO: 2919)
(SEQ ID NO: 3070)

CBL
Protein sprouty
loop
HVENDYIDNPS
CATGTGGAAAACGATTATATTGATAACCCGAGC

homolog 4

(SEQ ID NO: 2920)
(SEQ ID NO: 3071)

CBL
Tyrosine-protein
loop
SFNPYEPELA
AGCTTTAACCCGTATGAACCGGAACTGGCG

kinase SYK

(SEQ ID NO: 2921)
(SEQ ID NO: 3072)

CBL
Tyrosine-protein
loop
TLNSDGpYTPEPA
ACCCTGAACAGCGATGGCTATACCCCGGAACCGGCG

kinase ZAP-70

(SEQ ID NO: 2922)
(SEQ ID NO: 3073)

CBL
Plexin-A3
loop
IPFLDYRTYAV
ATTCCGTTTCTGGATTATCGCACCTATGCGGTG

(SEQ ID NO: 2923)
(SEQ ID NO: 3074)

CBL
Plexin-A1
loop
IPFLDYRTYAM
ATTCCGTTTCTGGATTATCGCACCTATGCGATG

(SEQ ID NO: 2924)
(SEQ ID NO: 3075)

CBL
Platelet-
loop
SIFDNLYTTLSD
AGCATTTTTAACAGCCTGTATACCACCCTGAGCGAT

derived

(SEQ ID NO: 2925)
(SEQ ID NO: 3076)

growth factor

receptor alpha

CBL
Platelet-
loop
SIFNSLYTTLSD
AGCATTTTTAACAGCCTGTATACCACCCTGAGCGAT

derived

(SEQ ID NO: 2926)
(SEQ ID NO: 3077)

growth factor

receptor beta

CBL
Tumor necrosis
loop
KGDGGLYSSLPP
AAAGGCGATGGCGGCCTGTATAGCAGCCTGCCGCCG

factor receptor

(SEQ ID NO: 2927)
(SEQ ID NO: 3078)

superfamily

member 16

CRL4(COP1/
Trib1
loop
SDQIVPEY
TCTGACCAGATCGTTCCGGAATAC

DET)

(SEQ ID NO: 2928)
(SEQ ID NO: 3079)

SH3RF1
E3 Ubiquitin-
loop
RPTAAVTPI
CGCCCGACCGCGGCGGTGACCCCGATT

protein ligase

(SEQ ID NO: 2929)
(SEQ ID NO: 3080)

SH3RF1

COP-1
Consensus
loop
[D,E][D,E].{2,3}
[GAA/GAC][GAA/GACHNNNNNN/NNNNNNNNN]

VP[DE]
GTGCCG[GAA/GAC]

(SEQ ID NO: 3081)

COP-1
Tribbles
loop
SDQIVPEY
AGCGATCAGATTGTGCCGGAATAT

homolog 1

(SEQ ID NO: 2930)
(SEQ ID NO: 3082)

SIAH
Consensus
loop
.P.A.V.P[{circumflex over ( )}P]
NNNCCGNNNGCGNNNGTGNNNCCG[NNN EXCEPT

(SEQ ID NO: 2931)
CCN]

(SEQ ID NO: 3083)

SIAH
AF4/FMR2
loop (beta
KPTAYVRPM
AAACCGACCGCGTATGTGCGCCCGATG

family memeber
sttrand)
(SEQ ID NO: 2932)
(SEQ ID NO: 3084)

4

SIAH
calcyclin-
loop
KPAAVVAPI
AAACCGGCGGCGGTGGTGGCGCCGATT

binding

(SEQ ID NO: 2933)
(SEQ ID NO: 3085)

protein

SIAH
POU domain
loop
APTAVVLPH
GCGCCGACCGCGGTGGTGCTGCCGCAT

class 2-

(SEQ ID NO: 2934)
(SEQ ID NO: 3086)

associating

factor 1

SIAH
Retrotransposon-
loop
PPRALVLPH
CCGCCGCGCGCGCTGGTGCTGCCGCAT

derived

(SEQ ID NO: 2935)
(SEQ ID NO: 3087)

protein

PEG10

ERAD-C
CL1
amphipathic
ACKNWFSSLSHFVIHL
GCGTGCAAAAACTGGTTTAGCAGCCTGAGCCATTTT

helix
(SEQ ID NO: 2936)
GTGATTCATCTG

extension

(SEQ ID NO: 3088)

Nend_Nbox 2
N-terminal

^ΛM{0,1}[FLYIW][∨P]
[ATG{0,1}][TTT/CTG/TAT/TGG/ATT]

extension

[NNN∨CCG]

Nend_UBRbox 1
N-terminal

^ΛM{0,1}[RK][∨P]
[ATG{0,1}][AAA/CGT][NNN∨CCG]

extension

Nend_UBRbox 2
N-terminal

^ΛM{0,1}[ED]
[ATG{0,1}][GAT/GAA]

extension

Nend_UBRbox 3
N-terminal

^ΛM{0,1}[NQ]
[ATG{0,1}][CAG/AAC]

extension

Nend_UBRbox 4
N-terminal

^ΛM{0,1}[C]
[ATG{0,1}][TGC]

extension

Other

degradation

pathways:

pathway;

protein to
Degron
Intro-

which the
sequence
duction

degron
derived
to

DNA sequence E. Coli codon

binds
from
scaffold
Amino acid sequence
optimised 5′ to 3′

ESRCT; ALIX
Consensus,
loop
LYPxxxL,
GAACTGTACCCGCTGACCTCTCTGCGTTCT

e.g. HIV

(SEQ ID NO: 2937)
(SEQ ID NO: 3089)

Gag

e.g. ELYPLTSLRS

(SEQ ID NO: 2937)

ESCRT; AP-1
Nef
loop
ExxxLL
GAANNNNNNNNNCTGCTG

(SEQ ID NO: 3090)

ESCRT; AP-2
Env
loop
YxxL
TATNNNNNNCTG

(SEQ ID NO: 3091)

ESCRT; AP
viral
loop
SREKPYKEVTEDLLHLNSLF
AGCCGCGAAAAACCGTATAAAGAAGTGACCGAAGAT

adaptor

(SEQ ID NO: 2939)
CTGCTGCATCTGAACAGCCTGTTT

(SEQ ID NO: 3092)

ESCRT; AP
viral
loop
AAGAYDPARKLLEQYAKK
GCGGCGGGCGCGTATGATCCGGCGCGCAAACTGCTG

adaptor

(SEQ ID NO: 2940)
GAACAGTATGCGAAAAAA

(SEQ ID NO: 3093)

CMA
Consensus
loop
KFERQ
AAATTTGAACGCCAG

(SEQ ID NO: 2941)
(SEQ ID NO: 3094)

CMA
Consensus
loop
QRFFE
CAGCGCTTTTTTGAA

(SEQ ID NO: 2942)
(SEQ ID NO: 3095)

Autophagy;
Consensus
loop
[W/F/Y]xx[L/I/V]
(TGG/TTC/TAT)NNNNNN(CTG/ATC/GTG)

LC3/Atg8
LIR (LC3-

family
interacting)/

AIM (Atg8

family-

interacting)

motif

Autophagy;
CCPG1
loop
TASDDSDIVTLEPPK
ACCGCGTCTGACGACTCTGACATCGTTACCCTGGAA

FIP200

(SEQ ID NO: 2943)
CCGCCGAAA

(SEQ ID NO: 3096)

Autophagy;
DVL
loop
EVRDRMWLKITI
GAAGTTCGTGACCGTATGTGGCTGAAAATCACCATC

LC3

(SEQ ID NO: 2944)
(SEQ ID NO: 3097)

KEY

.
any amino acid

[X]
allowed amino acid at the

position

p
phosphorylated amino acid

$
C-terminal of chain

^ΛX
N-terminal of chain

X{x,y}
where x & y are the

minimum, maximum of X

aminoacids at the position

[∨X]
the position

NNN
any condon

[NNN/NNN/NNN]
on of these condons at the

position

[∨NNN]
any condon except this

[NNN{x,y}]
condon, where x & y are the

maximun & minimum of

condons

TABLE 4

Multiple Alignment of DNA sequences of all CTPR and RTPR used in hetero-

bifunctional CTPRs and RTPRs

CLUSTAL multiple sequence alignment by MUSCLE (3.8)

RTPRc
GCAGAAGCACTGCGTAATCTGGGTCGTGTTTATCGTCGTCAGGGTCGTTATCAGCGTGCA

RTPRa-ii-H
GCCGAAGCTTGGTATAATCTGGGGAATGCCTATTACAGACAGGGGGATTATCAGCGCGCC

RTPRa-i-E
GCAGAAGCATGGTATAATCTGGGTAATGCATATTATCGCCAGGGTGATTATCAGCGTGCC

RTPRa-iii-E
GCAGAAGCATGGTATAATCTGGGCAATGCATATTATCGTCAGGGTGATTATCAGCGTGCC

CTPRa-E
GCAGAAGCATGGTATAATCTGGGTAATGCATATTACAAACAGGGCGATTATCAGAAAGCC

CTPRb-E
GCAGAAGCACTGAATAATCTGGGTAATGTTTATCGTGAACAGGGCGATTATCAGAAAGCC

RTPRb-E
GCAGAAGCACTGAATAATCTGGGTAATGTTTATCGTGAACAGGGCGATTATCAGCGTGCC

RTPRa-ii-E
GCCGAGGCCTGGTATAACCTTGGCAACGCCTATTATCGTCAAGGCGACTACCAGAGAGCA

RTPRc-H
GCCGAGGCTCTGAGAAATCTGGGCAGAGTGTACAGACGGCAGGGCAGATACCAGCGGGCC

CTPRb-H
GCCGAGGCTCTGAACAACCTGGGCAACGTGTACAGAGAGCAGGGCGACTACCAGAAGGCC

RTPRb-H
GCCGAGGCTCTGAACAACCTGGGCAACGTGTACAGAGAGCAGGGCGACTACCAGCGGGCC

RTPRa-iv-E
GCCGAGGCCTGGTACAACCTGGGTAACGCCTATTATCGCCAAGGCGACTACCAGCGTGCA

CTPRa-H
GCCGAGGCCTGGTACAATCTGGGCAACGCCTACTACAAGCAGGGCGACTACCAGAAGGCC

RTPRa-i-H
GCCGAGGCCTGGTACAACCTGGGCAACGCCTACTACCGGCAGGGCGACTACCAGCGGGCC

** ** ** * ** ** ** * ** ** ** ** *** **

RTPRc
ATTGAATATTATCGTCGCGCACTGGAATTAGATCCGNNNNNN (SEQ ID NO: 148)

RTPRa-ii-H
ATTGAATATTATCAGCGGGCTCTGGAACTGGATCCTNNNNNN (SEQ ID NO: 149)

RTPRa-i-E
ATTGAATATTATCAACGTGCACTGGAACTGGACCCGNNNNNN (SEQ ID NO: 150)

RTPRa-iii-E
ATCGAATATTATCAACGTGCACTGGAACTGGACCCGNNNNNN (SEQ ID NO: 151)

CTPRa-E
ATCGAGTATTATCAAAAAGCACTGGAACTGGACCCGNNNNNN (SEQ ID NO: 152)

CTPRb-E
ATCGAATATTATCAAAAAGCGCTGGAACTGGACCCGNNNNNN (SEQ ID NO: 153)

RTPRb-E
ATTGAATATTATCAACGTGCGCTGGAATTAGATCCGNNNNNN (SEQ ID NO: 154)

RTPRa-ii-E
ATCGAATATTACCAGCGTGCGTTAGAATTAGATCCGNNNNNN (SEQ ID NO: 155)

RTPRc-H
ATCGAGTATTACCGCAGAGCCCTGGAACTGGACCCCNNNNNN (SEQ ID NO: 156)

CTPRb-H
ATCGAGTATTATCAGAAGGCCCTGGAACTGGACCCCNNNNNN (SEQ ID NO: 157)

RTPRb-H
ATCGAGTATTATCAGAGAGCCCTGGAACTGGACCCCNNNNNN (SEQ ID NO: 158)

RTPRa-iv-E
ATTGAGTACTACCAACGTGCCCTGGAACTGGACCCTNNNNNN (SEQ ID NO: 159)

CTPRa-H
ATCGAGTATTATCAGAAGGCCCTGGAACTGGACCCCNNNNNN (SEQ ID NO: 160)

RTPRa-i-H
ATCGAGTACTACCAGAGAGCCCTGGAACTGGACCCTNNNNNN (SEQ ID NO: 161)

** ** ** ** * ** * *** * ** ** ******

TABLE 5

089
AEAYSNLGNVYKERGQLQEAIEHYRHALRL
118
NP_858058.1 (SEQ ID NO:162)

191
AVAWSNLGCVFNAQGEIWLAIHHFEKAVTL
220
(SEQ ID NO: 163)

327
ADSLNNLANIKREQGNIEEAVRLYRKALEV
356
(SEQ ID NO: 164)

264
NLACVYYEQGLIDLAIDTYRRAIEL
288
(SEQ ID NO: 165)

079
AEAYSNLGNVYKERGQLQEAIEHYRHALRL
108
NP_858059.1 (SEQ ID NO: 166)

181
AVAWSNLGCVFNAQGEIWLAIHHFEKAVTL
210
(SEQ ID NO: 167)

317
ADSLNNLANIKREQGNIEEAVRLYRKALEV
346
(SEQ ID NO: 168)

254
NLACVYYEQGLIDLAIDTYRRAIEL
278
(SEQ ID NO: 169)

079
AEAYSNLGNVYKERGQLQEAIEHYRHALRL
108
NP_003596.2 (SEQ ID NO: 170)

812
ESFYNLGRGLHQLGLIHLAIHYYQKALEL
840
NP_036218.1 (SEQ ID NO: 171)

637
AWYGLGMIYYKQEKFSLAEMHFQKALDI
664
NP_001247.2 (SEQ ID NO: 172)

568
EAWCAAGNCFSLQREHDIAIKFFQRAIQV
596
(SEQ ID NO: 173)

275
AQSCYSLGNTYTLLQDYEKAIDYHLKHLAI
304
(SEQ ID NO: 174)

058
YSQLGNAYFYLHDYAKALEYHHHDLTL
084
(SEQ ID NO: 175)

315
GRACWSLGNAYTALGNHDQAMHFAEKHLEI
344
(SEQ ID NO: 176)

247
NMGNIYLKQRNYSKAIKFYRMALD
270
NP_783195.2 (SEQ ID NO: 177)

495
ALTNKGNTVFANGDYEKAAEFYKEAL
520
(SEQ ID NO: 178)

238
NMGNIYLKQRNYSKAIKFYRMALD
261
NP_006522.2 (SEQ ID NO: 179)

486
ALTNKGNTVFANGDYEKAAEFYKEAL
511
(SEQ ID NO: 180)

715
AQAWMNMGGIQHIKGKYVSARAYYERALQL
744
NP_787057.2 (SEQ ID NO: 181)

575
AEILSPLGALYYNTGRYEEALQIYQEAAAL
604
(SEQ ID NO: 182)

114
AQAAKNKGNKYFKAGKYEQAIQCYTEAISL
143
NP_055635.3 (SEQ ID NO: 183)

610
YNLGKLYHEQGHYEEALSVYKEAIQ
634
NP_689801.1 (SEQ ID NO: 184)

586
AQAWMNMGGIQHIKGKYVSARAYYERALQL
615
NP_114126.2 (SEQ ID NO: 185)

446
AEILSPLGALYYNTGRYEEALQIYQEA
472
(SEQ ID NO: 186)

018
AETFKEQGNAYYAKKDYNEAYNYYTKAIDM
47
NP_003306.1 (SEQ ID NO: 187)

300
AKAYARIGNSYFKEEKYKDAIHFYNKSL
327
NP_006810.1 (SEQ ID NO: 188)

231
LGNDAYKKKDFDTALKHYDKAKEL
254
(SEQ ID NO: 189)

365
NKGNECFQKGDYPQAMKHYTEAI
387
(SEQ ID NO: 190)

028
AETFKEQGNAYYAKKDYNEAYNYYTKAIDM
057
AAH11837.2 (SEQ ID NO: 191)

228
AYSNLGNAHVFLGRFDVAAEYYKKTLQL
255
NP_056412.2 (SEQ ID NO: 192)

266
AQACYSLGNTYTLLQDYERAAEYHLRHL
293
(SEQ ID NO: 193)

28
AEELKTQANDYFKAKDYENAIKFYSQAIEL
57
NP_006238.1 (SEQ ID NO: 194)

318
DAYKSLGQAYRELGNFEAATESFQKALLL
346
NP_078801.2 (SEQ ID NO: 195)

1262
ETLKNLAVLSYEGGDFEKAAELYKRAMEI
1290
NP_694972.3 (SEQ ID NO: 196)

140
GNKYFKQGKYDEAIDCYTKGMD
161
NP_078880.1 (SEQ ID NO: 197)

289
GNGFFKEGKYERAIECYTRGI
309
(SEQ ID NO: 198)

600
CWESLGEAYLSRGGYTTALKSFTKASEL
627
NP_055454.1 (SEQ ID NO: 199)

172
KATYRAGIAFYHLGDYARALRYLQEA
197
NP_689692.2 (SEQ ID NO: 200)

174
LGKIHLLEGDLDKAIEVYKKAVE
196
NP_149017.2 (SEQ ID NO: 201)

158
LGDLFSKAGDFPRAAEAYQKQLRF
181
NP_038460.3 (SEQ ID NO: 202)

384
AYFNAGNIYFHHRQFSQASDYFSKALKF
411
NP_001007796.1 (SEQ ID NO: 203)

104
EAWNQLGEVYWKKGDVAAAHTCFSGAL
130
NP_612385.1 (SEQ ID NO: 204)

814
EAWQGLGEVLQAQGQNEAAVDCFLTALEL
842
NP_065191.2 (SEQ ID NO: 205)

446
AKLWNNVGHALENEKNFERALKYFLQA
472
NP_861448.1 (SEQ ID NO: 206)

597
ADLWYNLAIVHIELKEPNEALKNFNRALEL
626
(SEQ ID NO: 207)

251
YRRKGDLDKAIELFQRVLE
269
NP_001540.2 (SEQ ID NO: 208)

251
YRRKGDLDKAIELFQRVLE
269
NP_001026853.1 (SEQ ID NO: 209)

079
AKTYKDEGNDYFKEKDYKKAVISYTEGL
106
NP_004614.2 (SEQ ID NO: 210)

501
AKVHYNIGKNLADKGNQTAAIRYYREAVRL
530
NP_116202.2 (SEQ ID NO: 211)

482
AKVHYNIGKNLADKGNQTAAIRYYREAVRL
511
NP_001073137.1 (SEQ ID NO: 212)

200
GNELVKKGNHKKAIEKYSESL
220
NP_006800.2 (SEQ ID NO: 213)

123
GNEQFKKGDYIEAESSYSRALEM
145
NP_003305.1 (SEQ ID NO: 214)

438
ESLSLLGFVYKLEGNMNEALEYYERALRL
466
NP_001001887.1 (SEQ ID NO: 215)

438
ESLSLLGFVYKLEGNMNEALEYYERALRL
466
NP_001539.3 (SEQ ID NO: 216)

375
AKTKNNLASAYLKQNKYQQAEELYKEIL
402
NP_803136.2 (SEQ ID NO: 217)

564
WFSLGCAYLALEDYQGSAKAFQRCVTL
590
NP_060205.3 (SEQ ID NO: 218)

306
AESCYQLARSFHVQEDYDQAFQYYYQATQF
335
NP_055448.1 (SEQ ID NO: 219)

TABLE 6

CTPRa E. coli expression codon optimised

GCAGAAGCATGGTATAATCTGGGTAATGCATATTACAAACAGGGCGATTA

TCAGAAAGCCATCGAGTATTATCAAAAAGCACTGGAACTGGACCCGNNNN

NNAEAWYNLGNAYYKQGDYQKAIEYYQKALELDPXX

(SEQ ID NO: 220)

CTPRa H. Sapiens expression codon optimised

GCCGAGGCCTGGTACAATCTGGGCAACGCCTACTACAAGCAGGGCGACTA

CCAGAAGGCCATCGAGTATTATCAGAAGGCCCTGGAACTGGACCCCNNNN

NNAEAWYNLGNAYYKQGDYQKAIEYYQKALELDPXX

(SEQ ID NO: 220)

RTPRa-i H. sapiens expression codon optimised

GCCGAGGCCTGGTACAACCTGGGCAACGCCTACTACCGGCAGGGCGACTA

CCAGCGGGCCATCGAGTACTACCAGAGAGCCCTGGAACTGGACCCTNNNN

NNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPXX

(SEQ ID NO: 221)

RTPRa-ii H. sapiens expression codon optimised

GCCGAAGCTTGGTATAATCTGGGGAATGCCTATTACAGACAGGGGGATTA

TCAGCGCGCCATTGAATATTATCAGCGGGCTCTGGAACTGGATCCTNNNN

NNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPXX

(SEQ ID NO: 221)

RTPRa-i E. coli expression codon optimised

GCAGAAGCATGGTATAATCTGGGTAATGCATATTATCGCCAGGGTGATTA

TCAGCGTGCCATTGAATATTATCAACGTGCACTGGAACTGGACCCGNNNN

NNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPXX

(SEQ ID NO: 221)

RTPRa-ii E. coli expression codon optimised

GCCGAGGCCTGGTATAACCTTGGCAACGCCTATTATCGTCAAGGCGACTA

CCAGAGAGCAATCGAATATTACCAGCGTGCGTTAGAATTAGATCCGNNNN

NNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPXX

(SEQ ID NO: 221)

RTPRa-iii E. coli expression codon optimised

GCAGAAGCATGGTATAATCTGGGCAATGCATATTATCGTCAGGGTGATTA

TCAGCGTGCCATCGAATATTATCAACGTGCACTGGAACTGGACCCGNNNN

NNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPXX

(SEQ ID NO: 221)

RTPRa-iv E. coli expression codon optimised

GCCGAGGCCTGGTACAACCTGGGTAACGCCTATTATCGCCAAGGCGACTA

CCAGCGTGCAATTGAGTACTACCAACGTGCCCTGGAACTGGACCCTNNNN

NNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPXX

(SEQ ID NO: 221)

CTPRb E. coli expression codon optimised

GCAGAAGCACTGAATAATCTGGGTAATGTTTATCGTGAACAGGGCGATTA

TCAGAAAGCCATCGAATATTATCAAAAAGCGCTGGAACTGGACCCGNNNN

NNAEALNNLGNVYREQGDYQKAIEYYQKALEL-DPXX

(SEQ ID NO: 222)

CTPRb H. sapiens expression codon optimised

GCCGAGGCTCTGAACAACCTGGGCAACGTGTACAGAGAGCAGGGCGACTA

CCAGAAGGCCATCGAGTATTATCAGAAGGCCCTGGAACTGGACCCCNNNN

NNAEALNNLGNVYREQGDYQKAIEYYQKALEL-DPXX

(SEQ ID NO: 222)

RTPRb E. coli expression codon optimised

GCAGAAGCACTGAATAATCTGGGTAATGTTTATCGTGAACAGGGCGATTA

TCAGCGTGCCATTGAATATTATCAACGTGCGCTGGAATTAGATCCGNNNN

NNAEALNNLGNVYREQGDYQRAIEYYQRALEL-DPXX

(SEQ ID NO: 223)

RTPRb H. sapiens expression codon optimised

GCCGAGGCTCTGAACAACCTGGGCAACGTGTACAGAGAGCAGGGCGACTA

CCAGCGGGCCATCGAGTATTATCAGAGAGCCCTGGAACTGGACCCCNNNN

NNAEALNNLGNVYREQGDYQRAIEYYQRALELDPXX

(SEQ ID NO: 223)

RTPRc E. Coli expression codon optimised

GCAGAAGCACTGCGTAATCTGGGTCGTGTTTATCGTCGTCAGGGTCGTTA

TCAGCGTGCAATTGAATATTATCGTCGCGCACTGGAATTAGATCCGNNNN

NNAEALRNLGRVYRRQGRYQRAIEYYRRALELDPXX

(SEQ ID NO: 225)

RTPRc H. Sapiens expression codon optimised

GCCGAGGCTCTGAGAAATCTGGGCAGAGTGTACAGACGGCAGGGCAGATA

CCAGCGGGCCATCGAGTATTACCGCAGAGCCCTGGAACTGGACCCCNNNN

NNAEALRNLGRVYRRQGRYQRAIEYYRRALELDPXX

(SEQ ID NO: 225)

TABLE 7

Protein Target
Paratope
struct
RSCB no
therapeutic area

Nrp1/2
RASQYFSSYLA
loop
2qqn
anti-angiogenic

(SEQ ID NO: 226)

Nrp1/2
AREDFRNRRLWYVMDY
helix
2qql
anti-angiogenic

(SEQ ID NO: 227)

IL18
KASGYSFTDYFIY
helix
2yxt
anti-inflammatory

(SEQ ID NO: 228)

IL15
YRDRRRPS
loop
2xqb
anti-inflammatory

(SEQ ID NO: 229)

Thyroid stimulating hormone
SGSSSDIGSNYVS
loop
2xwt

receptor
(SEQ ID NO: 230)

EGF receptor
QQWSSHIFT
loop
3C09
cancer

(SEQ ID NO: 231)

EGF receptor
ASRDYDYAGRYFDY
helix
3C09
cancer

(SEQ ID NO: 232)

IL23
QNGHSFPFT
loop
3d85
anti-inflammatory

(SEQ ID NO: 233)

IL23
YINPYNDGTK
helix
3d85
anti-inflammatory

(SEQ ID NO: 234)

IL23
ARNWDVAY
helix
3d85
anti-inflammatory

(SEQ ID NO: 235)

Lymphocyte function-associated
SGYSFTGHWMN
helix
3eoa
auto-immune

antigen 1 (LFA-1)
(SEQ ID NO: 236)

Lymphocyte function-associated
MIHPSDSETR
helix
3eoa
auto-immune

antigen 1 (LFA-1)
(SEQ ID NO: 237)

Lymphocyte function-associated
ARGIYFYGTTYFDY
helix
3eoa
auto-immune

antigen 1 (LFA-1)
(SEQ ID NO: 238)

C3b
SGFSFTSSVS
helix
3g6j
anti-inflammatory

(SEQ ID NO: 239)

C3b
LIYPYNGFN
helix
3g6j
anti-inflammatory

(SEQ ID NO: 240)

FGF receptor 3
AASGFTFTSTGIS
helix
3grw
multiple myeloma

(SEQ ID NO: 241)

FGF receptor 3
ARTYGIYDLYVDYTE
helix
3grw
multiple myeloma

(SEQ ID NO: 242)

IL2
SRDYGYYFD
helix
3iu3
anti-inflammatory

(SEQ ID NO: 243)

IL2
GYSFTRYWMH
helix
3iu3
anti-inflammatory

(SEQ ID NO: 244)

HER2
QWWWWPST
loop
3n85
breast cancer

(SEQ ID NO: 245)

HER2
ASGFSIWWSWIH
helix
3n85
breast cancer

(SEQ ID NO: 246)

membrane-type serine protease 1
YDNNQRPS
loop
3nps
metastasis of

(SEQ ID NO: 247)

carcinomas

membrane-type serine protease 1
TFHIRRYRSGYYDKMDH
helix
3nps
metastasis of

(SEQ ID NO: 248)

carcinomas

beta-secretase
ARGPFSPWVMDY
helix
3r1g
Alzheimer's disease

(SEQ ID NO: 249)

VEGF-R
TRHDGTNFD
helix
3s35
anti-angiogenic

(SEQ ID NO: 250)

VEGF-R
QQAKAFPPT
loop
3s37
anti-angiogenic

(SEQ ID NO: 251)

Irp5/6 receptor
SGHVNAVKNYGY
helix
3sob
bone-loss

(SEQ ID NO: 252)

hepsin protease
WINTETGS
Helix
3t2n
prostrate cancer

(SEQ ID NO: 253)

Factor D
WINMGE
helix
4d9r
anti-inflammatory

(SEQ ID NO: 254)

Factor D
GYTFTNYGMN
helix
4d9r
anti-inflammatory

(SEQ ID NO: 255)

TABLE 8

1. Axin-RTPR-ABBA

MGSGAYPEYILDIHVYRVQLELDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAEAWYNLGNAYYRQG

DYQRAIEYYQRALELDPGGSLSSAFHVFEDGNKENGGPNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNN

(SEQ ID NO: 256)

2. Axin-RTPR-DBOX

MGSGAYPEYILDIHVYRVQLELDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAEAWYNLGNAYYRQG

DYQRAIEYYQRALELDPGGPRLPLGDVSNNGGPNAEAWYNLGNAYYRQGDYQRAIEyyQRALELDPNN

(SEQ ID NO: 257)

3. Axin-RTPR-KEN

MGSGAYPEYILDIHVYRVQLELDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAEAWYNLGNAyyRQG

DYQRAIEYYQRALELDPGGPRLPLGDVSNNGGPNAEAWYNLGNAyyRQGDYQRAIEYYQRALELDPNN

(SEQ ID NO: 258)

4. Axin-RTPR-Nrf2

MGSGAYPEYILDIHVYRVQLELDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAEAWYNLGNAYYRQG

DYQRAIEYYQRALELDPGGPRLPLGDVSNNGGPNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNN

(SEQ ID NO: 259)

5. Axin-RTPR-SIAH

MGSGAYPEYILDIHVYRVQLELDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAEAWYNLGNAYYRQG

DYQRAIEYYQRALELDPGGLRPVAMVRPTVGGPNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNN

(SEQ ID NO: 260)

6. Axin-RTPR-SPOP

MGSGAYPEYILDIHVYRVQLELDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPGGLACDEVTSTTSSSTA

GGPNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNN

(SEQ ID NO: 261)

7. Axin-RTPR-p27

MGSGAYPEYILDIHVYRVQLELDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAEAWYNLGNAYYRQG

DYQRAIEYYQRALELDPNNAGSNEQEPKKRSPDAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNN

(SEQ ID NO: 262)

8. Axin-RTPR-p53

MGSGAYPEYILDIHVYRVQLELDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAEAWYNLGNAYYRQG

DYQRAIEYYQRALELDPNNFAAYWNLLSAYG

(SEQ ID NO: 263)

10. Bcl9-RTPR-ABBA

MGSSQEQLEHRYRSLITLYDIQLMLDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAEAWYNLGNAYY

RQGDYQRAIEYYQRALELDPGGDPETGELGGPNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNN

(SEQ ID NO: 264)

11. Bcl9-RTPR-DBOX-v1

MGSSQEQLEHRYRSLITLYDIQLMLDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAEAWYNLGNAYY

RQGDYQRAIEYYQRALELDPGGPRLPLGDVSNNGGPNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNN

(SEQ ID NO: 265)

12. Bcl9-RTPR-DBOX-v2

MGSSQEQLEHRYRSLITLYDIQLMLDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPGGPRLPLGDVSNNG

GPNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNN

(SEQ ID NO: 266)

13. Bcl9-RTPR-KEN

MGSGAYPEYILDIHVYRVQLELDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAEAWYNLGNAYYRQG

DYQRAIEYYQRALELDPGGSLSSAFHVFEDGNKENGGPNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNN

(SEQ ID NO: 267)

14. Bcl9-RTPR-Nrf2

MGSSQEQLEHRYRSLITLYDIQLMLDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAEAWYNLGNAYY

RQGDYQRAIEYYQRALELDPGGDPETGELGGPNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNN

(SEQ ID NO: 268)

15. Bcl9-RTPR-p27

MGSSQEQLEHRYRSLITLYDIQLMLDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAEAWYNLGNAYY

RQGDYQRAIEYYQRALELDPNNAGSNEQEPKKRSPDAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNN

(SEQ ID NO: 269)

16. Bcl9-RTPR-p53

MGSSQEQLEHRYRSLITLYDIQLMLDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAEAWYNLGNAYY

RQGDYQRAIEYYQRALELDPNNFAAYWNLLSAYG

(SEQ ID NO: 270)

17. Bcl9-RTPR-SIAH

MGSSQEQLEHRYRSLITLYDIQLMLDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAEAWYNLGNAYY

RQGDYQRAIEYYQRALELDPGGLRPVAMVRPTVGGPNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNN

(SEQ ID NO: 271)

18. Bcl9-RTPR-SPOP

MGSSQEQLEHRYRSLITLYDIQLMLDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPGGLACDEVISTISS

STAGGPNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNN (SEQ ID NO: 272)

19. TCF7L2-RTPR-Nrf2

MGSAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPGGQELGDNDELMHFSYESTQDGGPNAEAWYNLGNAYYRQG

DYQRAIEYYQRALELDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPGGDPETGELGGPNAEAWYNLGNAY

YRQGDYQRAIEYYQRALELDPNN (SEQ ID NO: 273)

20. TCF7L2-RTPR-p27

MGSAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPGGQELGDNDELMHFSYESTQDGGPNAEAWYNLGNAYYRQG

DYQRAIEYYQRALELDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAGSNEQEPKKRSPDAEAWYNLG

NAYYRQGDYQRAIEYYQRALELDPNN (SEQ ID NO: 274)

21. p27-RTPR-TCF7L2

MRGSHHHHHHGLVPRGSAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAGSNEQEPKKRSPDAEAWYNLGNA

YYRQGDYQRAIEYYQRALELDPRSAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPGGQELGDNDELMHFSYEST

QDGGPNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPRS (SEQ ID NO: 275)

22. TCF7L2-RTPR-p53

MGSAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPGGQELGDNDELMHFSYESTQDGGPNAEAWYNLGNAYYRQG

DYQRAIEYYQRALELDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNFAAYWNLLSAYG

(SEQ ID NO: 276)

23. ICAT-RTPR-p27

MGSYAYQRAIVEYMLRLMSDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAEAWYNLGNAYYRQGDYQ

RAIEYYQRALELDPNNAGSNEQEPKKRSPDAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNN

(SEQ ID NO: 277)

24. ICAT-RTPR-p53

MGSYAYQRAIVEYMLRLMSDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAEAWYNLGNAYYRQGDYQ

RAIEYYQRALELDPNNFAAYWNLLSAYG (SEQ ID NO: 278)

25. LRH1-RTPR-ABBA

MGSYEQAIAAYLDALMCDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAEAWYNLGNAYYRQGDYQRA

IEYYQRALELDPGGSEDKENVPPGGPNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNN

(SEQ ID NO: 279)

26. LRH1-RTPR-DBOX

MGSYEQAIAAYLDALMCDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAEAWYNLGNAYYRQGDYQRA

IEYYQRALELDPGGPRLPLGDVSNNGGPNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNN

(SEQ ID NO: 280)

27. LRH1-RTPR-KEN

MGSYEQAIAAYLDALMCDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAEAWYNLGNAYYRQGDYQRA

IEYYQRALELDPGGSEDKENVPPGGPNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNN

(SEQ ID NO: 281)

28. LRH1-RTPR-Nrf2

MGSYEQAIAAYLDALMCDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAEAWYNLGNAYYRQGDYQRA

IEYYQRALELDPGGDPETGELGGPNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNN

(SEQ ID NO: 282)

29. LRH1-RTPR-p27

MGSYEQAIAAYLDALMCDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAEAWYNLGNAYYRQGDYQRA

IEYYQRALELDPNNAGSNEQEPKKRSPDAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNN

(SEQ ID NO: 283)

30. LRH1-RTPR-p53

MGSYEQAIAAYLDALMCDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAEAWYNLGNAYYRQGDYQRA

IEYYQRALELDPNNFAAYWNLLSAYG (SEQ ID NO: 284)

31. LRH1-RTPR-SIAH

MGSYEQAIAAYLDALMCDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAEAWYNLGNAYYRQGDYQRA

IEYYQRALELDPGGLRPVAMVRPTVGGPNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNN

(SEQ ID NO: 285)

32. LRH1-RTPR-SPOP

MGSYEQAIAAYLDALMCDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAEAWYNLGNAYYRQGDYQRA

IEYYQRALELDPGGLACDEVTSTTSSSTAGGPNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNN

(SEQ ID NO: 286)

33. APC-RTPR-Nrf2

MGSAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPGGSCSEELEALEALELDEGGPNAEAWYNLGNAYYRQGDYQ

RAIEYYQRALELDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPGGDPETGELGGPNAEAWYNLGNAYYRQ

GDYQRAIEYYQRALELDPNN (SEQ ID NO: 287)

34. APC-RTPR-p27

MGSAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPGGSCSEELEALEALELDEGGPNAEAWYNLGNAYYRQGDYQ

RAIEYYQRALELDPNN (SEQ ID NO: 288)

35. p27-RTPR-APC

MRGSHHHHHHGLVPRGSAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAGSNEQEPKKRSPDAEAWYNLGNA

YYRQGDYQRAIEYYQRALELDPRSAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPGGSCSEELEALEALELDEG

GPNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPRS (SEQ ID NO: 289)

36. APC-RTPR-p53

MGSAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPGGQELGDNDELMHFSYESTQDGGPNAEAWYNLGNAYYRQG

DYQRAIEYYQRALELDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNFAAYWNLLSAYG

(SEQ ID NO: 290)

37. 1TBP-CTPR2

MGSAEAWYNLGNAYYKQGDYQKAIEYYQKALELDPNNREAGDGEEDPRSAEAWYNLGNAYYKQGDYQKAIEYYQK

ALELDPRS (SEQ ID NO: 291)

38. 2TBP-CTPR4

MGSAEAWYNLGNAYYKQGDYQKAIEYYQKALELDPNNREAGDGEEDPRSAEAWYNLGNAYYKQGDYQKAIEYYQK

ALELDPRSAEAWYNLGNAYYKQGDYQKAIEYYQKALELDPNNREAGDGEEDPRSAEAWYNLGNAYYKQGDYQKAI

EYYQKALELDPRS (SEQ ID NO: 292)

39. 3TBP-CTPR6

MGSAEAWYNLGNAYYKQGDYQKAIEYYQKALELDPNNREAGDGEEDPRSAEAWYNLGNAYYKQGDYQKAIEYYQK

ALELDPRSAEAWYNLGNAYYKQGDYQKAIEYYQKALELDPNNREAGDGEEDPRSAEAWYNLGNAYYKQGDYQKAI

EYYQKALELDPRSAEAWYNLGNAYYKQGDYQKAIEYYQKALELDPNNREAGDGEEDPRSAEAWYNLGNAYYKQGD

YQKAIEYYQKALELDPRS (SEQ ID NO: 293)

40. 4TBP-CTPR8

MGSAEAWYNLGNAYYKQGDYQKAIEYYQKALELDPNNREAGDGEEDPRSAEAWYNLGNAYYKQGDYQKAIEYYQK

ALELDPRSAEAWYNLGNAYYKQGDYQKAIEYYQKALELDPNNREAGDGEEDPRSAEAWYNLGNAYYKQGDYQKAI

EYYQKALELDPRSAEAWYNLGNAYYKQGDYQKAIEYYQKALELDPNNREAGDGEEDPRSAEAWYNLGNAYYKQGD

YQKAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYQKAIEYYQKALELDPNNREAGDGEEDPRSAEAWYNLGNAY

YKQGDYQKAIEYYQKALELDPRS (SEQ ID NO: 294)

41. 1TBP-CTPR2-Foldon (Foldon sequence in bold)

MGSAEAWYNLGNAYYKQGDYQKAIEYYQKALELDPNNREAGDGEEDPRSAEAWYNLGNAYYKQGDYQKAIEYYQK

ALELDPRSAKASLNLANADIKTIQEAGYIPEAPRDGQAYVRKDGEWVLLSTFLRS (SEQ ID NO: 295)

42. 2TBP-CTPR4-Foldon (Foldon sequence in bold)

MGSAEAWYNLGNAYYKQGDYQKAIEYYQKALELDPNNREAGDGEEDPRSAEAWYNLGNAYYKQGDYQKAIEYYQK

ALELDPRSAEAWYNLGNAYYKQGDYQKAIEYYQKALELDPNNREAGDGEEDPRSAEAWYNLGNAYYKQGDYQKAI

EYYQKALELDPRSAKASLNLANADIKTIQEAGYIPEAPRDGQAYVRKDGEWVLLSTFLRS

(SEQ ID NO: 296)

43. 3TBP-CTPR6-Foldon (Foldon sequence in bold)

MGSAEAWYNLGNAYYKQGDYQKAIEYYQKALELDPNNREAGDGEEDPRSAEAWYNLGNAYYKQGDYQKAIEYYQK

ALELDPRSAEAWYNLGNAYYKQGDYQKAIEYYQKALELDPNNREAGDGEEDPRSAEAWYNLGNAYYKQGDYQKAI

EYYQKALELDPRSAEAWYNLGNAYYKQGDYQKAIEYYQKALELDPNNREAGDGEEDPRSAEAWYNLGNAYYKQGD

YQKAIEYYQKALELDPRSAKASLNLANADIKTIQEAGYIPEAPRDGQAYVRKDGEWVLLSTFLRS

(SEQ ID NO: 297)

44. 4TBP-CTPR8-Foldon (Foldon sequence in bold)

MGSAEAWYNLGNAYYKQGDYQKAIEYYQKALELDPNNREAGDGEEDPRSAEAWYNLGNAYYKQGDYQKAIEYYQK

ALELDPRSAEAWYNLGNAYYKQGDYQKAIEYYQKALELDPNNREAGDGEEDPRSAEAWYNLGNAYYKQGDYQKAI

EYYQKALELDPRSAEAWYNLGNAYYKQGDYQKAIEYYQKALELDPNNREAGDGEEDPRSAEAWYNLGNAYYKQGD

YQKAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYQKAIEYYQKALELDPNNREAGDGEEDPRSAEAWYNLGNAY

YKQGDYQKAIEYYQKALELDPRSAKASLNLANADIKTIQEAGYIPEAPRDGQAYVRKDGEWVLLSTFLRS

(SEQ ID NO: 298)

45. KBL-RTPR-CMA_Q

MGSIPNPLLGLDGSAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNPLYISYDPAEAWYNLGNAYYRQGDYQR

AIEYYQRALELDPRSAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNQRFFE (SEQ ID NO: 299)

46. CMA_Q-KBL-RTPR

MGSQRFFEGSAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNPLYISYDPAEAWYNLGNAYYRQGDYQRAIEY

YQRALELDPRSAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNN (SEQ ID NO: 300)

47. CMA_K-KBL-RTPR

MGSKFERQGSAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNPLYISYDPAEAWYNLGNAYYRQGDYQRAIEY

YQRALELDPRSAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNN (SEQ ID NO: 301)

48. SOS-RTPR-CMA_K

MGSFEGIALTNYLKALEGDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAEAWYNLGNAYYRQGDYQR

AIEYYQRALELDPRSKFERQ (SEQ ID NO: 302)

49. SOS-RTPR-CMA_Q

MGSFEGIALTNYLKALEGDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPRSIPNPLLGLDKFERQ

(SEQ ID NO: 303)

50. SOS-RTPR-p27

MGSFEGIALTNYLKALEGDPNNAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAEAWYNLGNAYYRQGDYQR

AIEYYQRALELDPRSAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAGSNEQEPKKRSPDAEAWYNLGNAYY

RQGDYQRAIEYYQRALELDPRS (SEQ ID NO: 304)

51. KBL-RTPR-p27

MGSAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNPLYISYDPAEAWYNLGNAYYRQGDYQRAIEYYQRALEL

DPRSAEAWYNLGNAYYRQGDYQRAIEYYQRALELDPNNAGSNEQEPKKRSAEAWYNLGNAYYRQGDYQRAIEYYQ

RALELDPNN (SEQ ID NO: 305)

TABLE 9-11

Abbreviations

Group name
Amino acids
Displayed as

Default
X
.

Single
X

custom character

Alanine
A
A

Cysteine
C
C

Aspartic Acid
D
D

Glutamic Acid
E
E

Phenylalanine
F
F

Glycine
G
G

Histidine
H
H

Isoleucine
I
I

Lysine
K
K

Leucine
L
L

Methionine
M
M

Asparagine
N
N

Proline
P
P

Glutamine
Q
Q

Arginine
R
R

Serine
S
S

Threonine
T
T

Valine
V
V

Tryptophan
W
W

Tyrosine
Y
Y

Negative
D, E
−

Ser/Thr
S, T
*

Aliphatic
I, L, V
l

Positive
H, K, R
+

Tiny
A, G, S
t

Aromatic
F, H, W, Y

a

Charged
D, E, H, K, R
c

Small
A, C, D, G, N, P, S, T, V
s

Polar
C, D, E, H, K, N, Q, R, S, T
p

Big
E, F, H, I, K, L, M, Q, R, W, Y

B

Hydrophobic
A, C, F, G, H, I, L, M, T, V, W, Y

h

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Number	Date	Country	Kind
1713316	Aug 2017	GB	national
1714038	Sep 2017	GB	national

Number	Date	Country
2009100990	Aug 2009	WO
2010060748	Jun 2010	WO
2019034332	Feb 2019	WO

	Number	Date	Country
Parent	16282155	Feb 2019	US
Child	16428451		US

	Number	Date	Country
Parent	PCT/EP2018/068580	Jul 2018	US
Child	16282155		US

Chimeric proteins

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