peptide

Abstract

The present invention provides a non-toxic method for producing cyclic peptides in mammalian cells, the method comprising: (a) introducing a vector into a mammalian cell, the vector comprising a C-terminal intein domain, a polypeptide sequence to be cyclized, an N-terminal intein domain, and a degradation tag, the degradation tag being linked to at least one intein domain; and (b) expressing the construct to produce an intermediate comprising an active intein and a polypeptide sequence, the active intein being spliced ​​upon formation to cyclize the polypeptide, and the degradation tag degrading the active intein. The present invention also provides a cyclic peptide library produced according to this method, and the incorporation of the non-toxic cyclic peptide-producing construct of the above method into a genetic construct, vector, or mammalian cell.

Description

[Technical field]

[0001] The present invention relates to the non-toxic production of cyclic peptides by modifying the split intein cyclic ligation of peptides and proteins (SICLOPPS) methodology to increase efficiency in mammalian cells. [Background technology]

[0002] The use of cyclic peptides in the early stages of drug discovery is becoming increasingly prevalent in pharmaceutical research and development. These peptides, which vary in length from only two amino acids linked together to peptides containing hundreds of such residues, are particularly useful in identifying protein-protein interaction inhibitors and have further applications in serving as important starting points for the design of drug-like small molecules.

[0003] Peptides have special utility as ligands for otherwise "undruggable" targets. Such undruggable targets may be intracellular molecules, specific protein-protein interactions, and are generally unsuitable for small molecules and biologics. Further cyclization or ring closure of peptides extends the lifespan of such molecules in vivo and subsequently significantly improves their pharmacokinetics. Although the range of useful cyclic peptides found in nature is somewhat limited, the production of synthetic polypeptides in the laboratory itself paves the way for the possibility of discovering drug candidates.

[0004] As a result, the generation of large libraries of synthetic cyclic peptides has become a cornerstone of modern drug discovery with enormous economic and commercial implications. Such genetically encoded libraries allow high-throughput screening and rapid deconvolution of target protein-binding hits by sequencing the DNA or mRNA tags that may be attached to each peptide.

[0005] One increasingly used method for intracellular cyclic peptide library generation is termed split intein cyclic ligation of peptides and proteins (SICLOPPS). This easily accessible method can generate libraries of over 100 million members with great speed and simplicity, and its intracellular nature allows for integrated functional assays in vivo.

[0006] This approach utilizes intein splicing to cyclize each peptide of interest, or "extein." Inteins are unique autoprocessing protein domains that can undergo a self-excision event from a larger precursor polypeptide through the cleavage of two peptide bonds while ligating the N- and C-termini of adjacent extein sequences with new peptide bonds. "Split inteins" are more specifically those whose polypeptide sequence is derived from two genes, resulting in two separate N- and C-intein domains flanking the extein. After translation, the two domains non-covalently reassemble into a canonical active intein that carries out protein splicing.

[0007] The SICLOPPS construct encodes a C-terminal intein domain followed by an extein polypeptide sequence to be cyclized, and an N-terminal intein domain. Upon transcription and translation, the flanking regions assemble to give an active intein that, as a result of splicing, self-excises and cyclizes the remaining polypeptide sequence between the C-terminal and N-terminal intein domains. Peptides of various lengths and amino acid compositions can be incorporated into the SICLOPPS method, provided that the first amino acid of the target peptide is a nucleophilic cysteine, serine, or threonine.

[0008] This technique provides a simple method for generating cyclic peptide libraries that requires only SICLOPPS plasmids, degenerate oligonucleotides, and a few simple molecular biology steps. The degenerate oligonucleotides will be designed to determine the ring size of the cyclic peptide, the number of randomized amino acids, and any set amino acids to be incorporated. Each oligonucleotide containing a unique extein sequence of interest is incorporated into the SICLOPPS plasmid via PCR digestion and ligation techniques to create the library. The plasmid library can then be screened after transformation into cells, for example, with a phenotypic assay. The identity of the active cyclic peptides is revealed by isolating the SICLOPPS plasmid from cells exhibiting the desired phenotype, followed by DNA sequencing (Tavassoli 2017, Curr Opin Chem Biol 38:30-35).

[0009] The advent of SICLOPPS offered the advantage of interfacing cyclic peptide libraries with assays in a variety of organisms, including E. coli, yeast, and mammalian cells. Intracellular functional assays can be performed against a variety of targets, allowing the assessment of not only the affinity of each member of the library, but also its function against a given target. Because SICLOPPS libraries are DNA-encoded, there is a great deal of control over the composition of the library, and a variety of libraries can be easily created and screened against such targets. Examples of SICLOPPS library variations that are easy to implement include cyclic peptides of different ring sizes, libraries of different amino acid compositions, or the inclusion of a given amino acid or motif at a set position in all members of the library. This allows the user full control over the composition of the cyclic peptide library via the degenerate oligonucleotides that encode it.

[0010] SICLOPPS originally uses the DnaE split intein from Synechocystis sp. PCC6803. The Ssp intein has a relatively slow splicing rate and is quite sensitive to amino acid changes near the splice junctions, meaning that a significant portion of the cyclic peptide library may not actually be cyclic peptides, but rather exist as partially spliced ​​inteins. However, such limitations of the technique have been overcome by adapting the faster splicing and broader host range "Npu" intein engineered from Nostoc punctiforme.

[0011] Despite the clear advances from using alternative intein types, the use of inteins themselves still poses issues with regard to the low level of efficiency of the technique in cells. Townend and Tavassoli (2016) investigated the effects of SICLOPPS-generated cyclic peptide libraries on E. coli cell viability (Townend & Tavassoli 2016, ACS Chem Biol 11(6):1624-1630). The data show that, despite a fast rate of splicing and tolerance to variation in the extein sequence, approximately 42% of the Npu SICLOPPS library was found to be cytotoxic to the E. coli host, greatly reducing its usefulness. As the study utilized three different E. coli strains (DH5α, BW27786, and BL21), it was deemed unlikely that such observed effects were strain-specific. The assay was further performed with the less favorable Ssp intein, and results show that approximately 14% of the library members also affected host viability. Although some of the cyclic peptides encoded by the libraries are likely to be intrinsically toxic to E. coli, for example through interference with critical proteins or pathways, in our experiments both intein sets encoded the same library, so any higher levels of toxicity than observed with the Npu intein could only be attributable to the Npu intein itself.

[0012] In a 2016 study, scientists engineered an SsrA tag (AANDENYALAA, SEQ ID NO: 11) at the C-terminus of a protein of interest to target the spliced ​​intein for intracellular degradation (Townend & Tavassoli 2016, ACS Chem Biol 11(6):1624-1630). The addition of the SsrA sequence was shown to guide the tagged protein to the ClpXP machinery specific to E. coli for degradation, shortening the half-life of the tagged protein to approximately 5 minutes.

[0013] Although investigations are ongoing to reduce the cytotoxicity of the Npu SICLOPPS intein in E. coli, there are no such described alternative approaches applicable for use in mammalian cells, where cellular functions differ from prokaryotic cells. With an ever-increasing demand for functional assays of cyclic peptides in mammalian cells for drug discovery, modifications of SICLOPPS to improve efficiency will aid in elucidating compounds against mammalian-specific targets.

[0014] Thus, there is a need for a modified SICLOPPS approach to generate cyclic peptides in mammalian cells in a more efficient manner. Kinsella et al 2002 JBC 277:37512-37518 describe the production of cyclic peptide libraries with up to 160,000 members in mammalian cells using the Ssp SICLOPPS intein, but do not mention or investigate toxicity associated with the intein. Summary of the Invention

[0015] The toxicity of inteins in mammalian cells was not investigated by Kinsella et al. The inventors surprisingly found that mammalian cells are also susceptible to toxicity resulting from active inteins. Prior to this, the problem of intein-associated toxicity in mammalian cells had not been recognized. The inventors devised a degradation tag system that is suitable for use in mammalian cells, obviates intein-associated toxicity, and allows the split intein system to be widely used in mammalian cells for the production of cyclic peptides.

[0016] The present invention is based on the surprising discovery that it is possible to modify mammalian cell-based SICLOPPS methodology to include a degradation tag attached to the intein to minimize any resulting intein-induced cytotoxicity. Attaching a degradation tag to either the N- or C-terminal intein domain allows a standard active intein to be targeted for degradation via the mammalian cell degradation pathway following splicing and cyclization of the extein of interest. This approach thus prevents the formation of deleterious accumulations of cytotoxic inteins during cyclic peptide production in mammalian cells. Thus, such degradation-tagged inteins can be used in the modified SICLOPPS methodology to generate cyclic peptide libraries more efficiently in mammalian cells. Importantly, the intein can be spliced ​​before being degraded.

[0017] Thus, in a first aspect of the present invention, a method is provided for the non-toxic production of cyclic peptides in mammalian cells, the method comprising: a) introducing a vector into a mammalian cell, the vector comprising a C-terminal intein domain, a polypeptide sequence to be cyclized, an N-terminal intein domain, and a degradation tag, the degradation tag being bound to at least one of the intein domains; and b) expressing the construct to produce an intermediate comprising an active intein and the polypeptide sequence, the active intein, once formed, undergoes splicing to cyclize the polypeptide, and the degradation tag degrades the active intein.

[0018] The invention also provides a mammalian cell produced by the method of the first aspect of the invention. For example, the invention provides a cell expressing a cyclic peptide, wherein the mammalian cell is a) introducing into a mammalian cell a vector, the vector comprising a construct encoding the C-terminal and N-terminal intein domains of a split intein, a polypeptide sequence to be cyclized, and a degradation tag, the degradation tag being linked to at least one of the intein domains; b) expressing the construct to produce an intermediate comprising an active intein and a polypeptide sequence, whereby the active intein undergoes splicing, circularizing the polypeptide, and expressing a degradation tag that degrades the active intein.

[0019] The present invention also provides a library of mammalian cells produced according to the first aspect of the invention. That is, the library comprises a number of mammalian cells each containing a different nucleic acid encoding a different cyclic peptide, where the nucleic acid is a nucleic acid of the invention described herein. In some embodiments, the library of mammalian cells produced by the method according to the first aspect of the invention comprises at least 128,000 members at the cyclic peptide level, optionally at least 150,000 or at least 200,000 members at the cyclic peptide level, for example. As the skilled artisan will appreciate, it is possible to create libraries containing millions of different gene constructs, but if the protein or peptide that the gene encodes (in this case a cyclic peptide) is toxic to the cells, those cells will be lost, reducing the number of members in the library at the protein level. For example, a library of 2 million members is created at the gene level, but if the active intein is toxic, only 1 million members expressing, for example, a cyclic peptide will be obtained. Because the present invention addresses the toxicity associated with inteins, it is possible to generate much larger cyclic peptide libraries, or much larger libraries of mammalian cells generated according to the method of the first aspect of the invention.

[0020] In some embodiments, the library of mammalian cells generated by the method according to the first aspect of the invention comprises at least 128,000 members at the protein level, such as at least 130,000, 150,000, 200,000, 300,000, 400,000, 500,000, 600,000, 700,000, 800,000, 900,000, 1 million, 1.5 million, 2 million, 2.5 million, 3 million, 3.2 million, 3.5 million, or at least 4 million members.

[0021] By at the protein level we include the meaning at the level of expressed cyclized peptide.

[0022] As reported in the art, the use of split inteins to generate cyclic peptides in mammalian cells results in mammalian cells that contain an active intein that may be toxic, whereas the cells of the invention resulting from the use of a degradation tag are free of active inteins or substantially free of active inteins, e.g., free of or substantially free of toxic active inteins.

[0023] The invention also provides a cell lysate prepared from the mammalian cells of the invention.

[0024] In a second aspect of the invention there is provided a cyclic peptide library produced by a method according to the first aspect of the invention.

[0025] In a third aspect of the invention, there is provided a genetic construct comprising a polypeptide cassette encoding a C-terminal intein domain, a polypeptide sequence to be cyclized, an N-terminal intein domain, and a degradation tag suitable for use in a mammalian cell, where the degradation tag is attached to at least the intein domain and, upon expression, forms an active intein.

[0026] In a fourth aspect of the invention there is provided a vector comprising a genetic construct according to the third aspect of the invention.

[0027] In a fifth aspect of the present invention, there is provided a mammalian cell comprising a vector according to the fourth aspect of the present invention or a genetic construct according to the third aspect of the present invention. The present invention also provides a library of mammalian cells comprising a vector according to the fourth aspect of the present invention or a genetic construct according to the third aspect of the present invention. In some embodiments, the library of mammalian cells comprises at least 200,000 members, such as at least 300,000, 400,000, 500,000, 600,000, 700,000, 800,000, 900,000, 1 million, 1.5 million, 2 million, 2.5 million, 3 million, 3.2 million, 3.5 million, or at least 4 million members.

[0028] In a sixth aspect of the invention, there is provided a method of generating a cyclic library according to the method of the first aspect of the invention. [Brief description of the drawings]

[0029] The invention is illustrated with reference to the following drawings. [Figure 1] We demonstrate the initiation of the SICLOPPS mechanism, in which N- and C-terminal intein domains flanking the extein peptide sequence of interest non-covalently bind to form a canonical active intein (adapted from Townend & Tavassoli 2016, ACS Chem Biol 11(6):1624-1630). [Diagram 2] The mechanism of SICLOPPS following formation of an active intein is shown. In a three-step process involving a thioester and a lariat intermediate, the active intein splices and cyclizes the target peptide extein. [Diagram 3] We show how a cyclic peptide library can be generated from a SICLOPPS plasmid library. A plasmid containing an appropriate origin of replication, a selectable marker and promoter, and the SICLOPPS construct of interest is transfected into mammalian cells. Following transcription and translation, the expressed intein, in this case the DnaE intein, cyclizes each peptide of interest to generate an intracellular library of such molecules. [Figure 4] SICLOPPS constructs of eGFP / YFP peptides engineered with a degradation tag attached to the N intein. The attached degradation tag is the oxygen-dependent degradation (ODD) domain of the hypoxia-inducible factor-1 alpha (HIF-1α) subunit. Further additions to the construct include an affinity tag, a fluorescent tag of mCherry, and a FLAG tag for antibody recognition. [Diagram 5]Shown are fluorescence microscopy images of SICLOPPS plasmids according to Figure 4 transfected into HeLa cells, which were then placed in the presence of oxygen with and without 100 μM deferoxamine (DFX) treatment. The intein should only degrade in the presence of oxygen and in the absence of DFX. The results show that the intein associated with mCherry fluorescence was degraded in normoxia compared to the DFX experiment, which showed mCherry fluorescence. The extein marked with GFP remained present under both conditions. [Figure 6] Shown is a fluorescent microscopy image of the SICLOPPS plasmid according to FIG. 4, further containing P564G in the degradation tag, transfected into HeLa cells, which were then placed in the presence of oxygen with and without 100 μM deferoxamine (DFX) treatment. In this mutant construct, the intein should never be degraded regardless of the conditions, as observed in the results. [Figure 7] Western blot analysis of wild-type (WT) and P564G mutant SICLOPPS plasmids transfected into HeLa cells and incubated under normoxic, hypoxic, or DFX-treated conditions shows no intein degradation in the wild-type plasmid, whereas normoxic conditions resulted in intein degradation. [Figure 8] Figure 1 shows cell counts over 48 hours for HeLa cells transfected with the above WT and P564G mutant SICLOPPS plasmids under normoxia or hypoxia. The trend indicates that under hypoxia, a decrease in cell number due to cytotoxicity occurs for both WT and P564G SICLOPPS plasmids over time without intein degradation. However, under normal conditions, cell number of WT transfected cells with intein degradation is maintained over time, compared to cells containing the proline mutant intein, whose numbers decrease due to cytotoxicity. [Figure 9]Trex293 cells transfected with a plasmid encoding GFP-Npu-ODDD-mCherry are shown, spliced ​​(WT) or non-spliced ​​(C1A). Gates represent Q1: mCherry+GFP-, Q2: mCherry+GFP+, Q3: mCherry-GFP+, Q4: mCherry-GFP-. A) GFP-WT without DFX. Q1: 2.53%, Q2: 47.5%, Q3: 32.1%, Q4: 17.8%. B) GFP-WT with DFX. Q1: 3.24%, Q2: 69.3%, Q3: 10.8%, Q4: 16.6%. C) GFP-C1A without DFX. Q1: 40.4%, Q2: 37.5%, Q3: 0.65%, Q4: 21.4%. D) GFP-C1A with DFX. Q1: 25.0%, Q2: 54.3%, Q3: 0.18%, Q4: 20.5%. E) Overlay of mCherry+ cells from A (dark grey; -DFX) and B (light grey; +DFX). Addition of DFX prevents degradation of mCherry (i.e., the intein). mCherry values ​​- median A: 265 units, B: 618 units. [Figure 10] Trex293 cells integrating a plasmid encoding GFP-Npu-ODDD-mCherry splicing (WT). Gates represent Q1: mCherry+GFP-, Q2: mCherry+GFP+, Q3: mCherry-GFP+, and Q4: mCherry-GFP-. A) GFP-WT without DFX. Q1: 0.035%, Q2: 0.84%, Q3: 67.4%, and Q4: 31.7%. B) GFP-WT with DFX. Q1: 0.17%, Q2: 35.1%, Q3: 29.4%, and Q4: 35.4%. [Figure 11] Cells without DFX (-dfx) and with DFX (+dfx) were assessed for viability after 24 hours of culture. Values ​​are in triplicate (+ / -SD). Viability was normalized to their -dfx control for each cell line. [Figure 12] 1 is a plasmid map of GFP-Npu-mCherry-ODDD used in Examples 5 and 6.

[0030] Description of sequence listing SEQ ID NO:1 is the amino acid sequence of the C-terminal intein domain of the Ssp DnaE split intein isolated from Synechocytis sp. strain PCC6803.

[0031] SEQ ID NO:2 is the amino acid sequence of the corresponding N-terminal intein domain of the Ssp DnaE split intein isolated from Synechocytis sp. strain PCC6803.

[0032] SEQ ID NO:3 is the amino acid sequence of the C-terminal intein domain of the Npu DnaE split intein isolated from Nostoc sp. strain PCC73102.

[0033] SEQ ID NO:4 is the amino acid sequence of the corresponding N-terminal intein domain of the Npu DnaE split intein isolated from Nostoc sp. strain PCC73102.

[0034] SEQ ID NO:5 is the amino acid sequence of the C-terminal intein domain of an artificial Cfa DnaE split intein engineered to enhance stability and activity.

[0035] SEQ ID NO:6 is the amino acid sequence of the corresponding N-terminal intein domain of an artificial Cfa DnaE split intein engineered to enhance stability and activity.

[0036] SEQ ID NO:7 is the amino acid sequence of the C-terminal intein domain of the "ultrafast" gp41-1DnaE split intein, which has been engineered to have extremely fast splicing activity.

[0037] SEQ ID NO:8 is the amino acid sequence of the corresponding N-terminal intein domain of the "ultrafast" gp41-1DnaE split intein, which has been engineered to have extremely fast splicing activity.

[0038] SEQ ID NO:9 is the amino acid sequence of a Homo sapiens hypoxia inducible factor-1 alpha (HIF-1α) subunit containing an oxygen-dependent degradation (ODD) domain, which can be used as a degradation tag.

[0039] SEQ ID NO:10 is the amino acid sequence of the oxygen-dependent degradation (ODD) domain of the Homo sapiens hypoxia-inducible factor-1 alpha (HIF-1α) subunit, which can be used as a degradation tag. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0040] The present invention is premised on the surprising discovery that the addition of a degradation tag to a SICLOPPS-based methodology allows for the generation of cyclic peptides in mammalian cells without generating an accumulation of cytotoxic intein by-products, such that cyclic peptides can be produced in mammalian cells without the reduced efficiency levels typically associated with such methods.

[0041] The term "cyclic peptide" as used herein refers to a polypeptide or protein that is "cyclized" in which its constituent atoms form a ring. For example, a linear peptide is cyclized when its free amino (N) terminus is covalently linked to its free carboxy (C) terminus, i.e., in a head-to-tail fashion, such that no free C-terminus or N-terminus remains in the peptide. As referred to herein, the terms "peptide" and "polypeptide" can be used interchangeably.

[0042] The present invention provides a method for producing cyclic peptides in mammalian cells by SICLOPPS methodology modified to incorporate the use of degradative tags.

[0043] The term "mammalian cells" refers to eukaryotic cells that have a structurally defined intracellular organization, in contrast to bacteria and archaea. Mammalian cells are often used in cell culture, an example being the use of Chinese Hamster Ovary (CHO) cells, the most common mammalian cell line used for the mass production of therapeutic proteins (Wurm 2004, Nat Biotech 22(11):1393-1398).

[0044] SICLOPPS or "split intein cyclic ligation of peptides and proteins" utilizes intein splicing to generate cyclic peptides.

[0045] As used herein, the term "intein" refers to a naturally occurring or artificially constructed polypeptide sequence embedded within a precursor protein that can catalyze a splicing reaction during post-translational processing of the protein. An intein can excise itself from a precursor protein and join the remaining portion by a peptide bond in a process called "splicing". A "split intein" is an intein that has two or more separate components that are not fused to each other, encoded by two separate genes. In some cases, the split intein components will be flanked by polypeptide sequences therein that are referred to as "exteins". When flanked by exteins, the split intein components are referred to as N-terminal and C-terminal intein domains, with respect to the N- and C-termini of the extein.

[0046] In some embodiments of all of the aspects of the invention, the intein is an intein that is toxic to mammalian cells, including in the sense that the intein adversely affects the growth rate of mammalian cells or induces apoptosis or necrosis.

[0047] The mammalian cell may be any mammalian cell in which it is desired to express a cyclic peptide.

[0048] Currently, over 350 inteins are recognized, each of which may differ in the rate at which it catalyzes the splicing reaction. The nomenclature of an intein is based on the scientific name of the organism in which it is found. For example, the Ssp intein was first isolated from Synechocytis spp., while the faster splicing Npu intein was first isolated from Nostoc punctiforme. A database containing a list of some of the known inteins can be found at http: / / www.biocenter.helsinki.fi / bi / iwai / InBase / tools.neb.com / inbase / list.html.

[0049] The intein used in the present invention may be any intein that splices faster than its degradation time with an attached degradation tag. A person skilled in the art can select an appropriate intein for use with a corresponding degradation tag.

[0050] In one embodiment, the intein may be a Cfa intein. In a preferred embodiment, the intein may be a split Cfa intein comprising the amino acid sequences of SEQ ID NO:5 and SEQ ID NO:6 for the C-terminal and N-terminal intein domains, respectively.

[0051] In another preferred embodiment, the intein may be an Spp intein. In a further preferred embodiment, the intein may be a split Spp intein comprising the amino acid sequences of SEQ ID NO: 1 and SEQ ID NO: 2 for the C-terminal and N-terminal intein domains, respectively.

[0052] In another preferred embodiment, the intein may be a gp41-1 intein. In a further preferred embodiment, the intein may be a split gp41-1 intein comprising the amino acid sequences of SEQ ID NO: 7 and SEQ ID NO: 8 for the C-terminal and N-terminal intein domains, respectively.

[0053] In yet another preferred embodiment, the intein may be an Npu intein. In a most preferred embodiment, the intein may be a split Npu intein comprising the amino acid sequences of SEQ ID NO: 3 and SEQ ID NO: 4 for the C-terminal and N-terminal intein domains, respectively.

[0054] The process of SICLOPPS is known in the art, as referenced by Tavassoli 2017, Curr Opin Chem Biol 38:30-35. The SICLOPPS method utilizes a construct that includes a C-terminal intein domain followed by an extein polypeptide sequence to be circularized, and an N-terminal intein domain. The construct is arranged such that following translation of the mRNA sequence, the N- and C-terminal intein domains adjacent to the intervening extein non-covalently associate to form a functional active intein (Figure 1) that subsequently catalyzes a splicing reaction that produces a circular polypeptide.

[0055] As shown in Figure 2, the folded SICLOPPS construct, or "fusion protein," with its active standard intein will catalyze an N to S acyl shift at the N-terminal intein domain and extein junction to generate a thioester intermediate. The thioester intermediate will undergo transesterification with a side chain nucleophile at the opposite C-terminal intein domain and extein junction to form a lariat intermediate. Finally, cyclization of the asparagine side chain followed by an X to N acyl shift liberates the cyclic peptide from the intein (Scott et al., 1999, PNAS 96(24):13638-13643). Thus, such a method generates a cyclic peptide and a by-product that contains the now unwanted intein polypeptide.

[0056] Thus, in some embodiments of the invention, there is a modified SICLOPPS method that uses a polypeptide construct that includes an Npu split intein, which may include the following sequence: HHHHHHMIKIATRKYLGKQNVYDIGVERYHNFALKNGFIASN (SEQ ID NO:12; where "~" represents an additional X).

[0057] where X~~~~~ are the exteins and cyclic peptides to be generated, X being C, S, or T, and "~" indicating an amino acid in the cyclic peptide sequence. For splicing to function, it is necessary that the first position may be occupied by an invariant cysteine, serine, or threonine residue. It will be clear to one skilled in the art that any sequence may be inserted after "X" in the above sequence. This sequence may be one amino acid or more in length.

[0058] In preferred embodiments, the sequence may be 3 or more amino acids in length. In most preferred embodiments, the sequence may be at least 6 amino acids in length.

[0059] The above sequence includes the following components: 1. HHHHHH (SEQ ID NO: 13) An optional hexahistidine (6xHis) tag to aid in purification, or any other such affinity tag, may be included in the construct. Thus, in one embodiment, the underlying SICLOPPS construct will further comprise an affinity tag. In a preferred embodiment, the construct will comprise a 6xHis tag. In yet another preferred embodiment, the construct will comprise a 2xStrep tag. 2. MIKIATRKYLGKQNVYDIGVERYHNFALKNGFIASN (SEQ ID NO: 14) Contains the C-terminal intein domain. 3. X~~~~~ The polypeptide comprises an extein sequence that is to be cyclized. 4. CLSYDTEILTVEYGILPIGKIVEKRIECTVYSVDNNGNIYTQPVAQWHDRGEQEV FEYCLEDGCLIRATKDHKFMTVDGQMMPIDEIFERELDLMRVDNLPN (SEQ ID NO: 15) Contains the N-terminal intein domain.

[0060] In some embodiments, the SICLOPPS construct may be further modified to include a tag for antibody recognition. In a preferred embodiment, the tag for antibody recognition may be a FLAG tag.

[0061] The present invention provides a modified SICLOPPS method in which a SICLOPPS construct, as exemplified above, is modified by the addition of a degradation tag suitable for use in mammalian cells linked to either the N- or C-terminal intein domain.

[0062] The term "degradation tag" is intended to encompass peptide sequences that mark proteins for degradation by the cell's degradative machinery. In mammalian cells, the primary pathway for selective protein degradation is the ubiquitin-proteasome pathway. Ubiquitin-dependent protein degradation has a natural role in many biological processes, including signal transduction, cell cycle progression, and transcriptional regulation (Groulx & Lee 2002, Mol Cell Biol 22(15):5319-5336). Ubiquitin is a small regulatory protein that can be added to substrate proteins in a process called ubiquitination. Ubiquitin conjugation is an ATP-dependent process that involves three enzymes: E1 and E2 proteins prepare ubiquitin for conjugation, and E3 ubiquitin ligase recognizes specific protein substrates and catalyzes the transfer-activated ubiquitin molecule. Once a protein is tagged with a single ubiquitin molecule, other E3 ubiquitin ligases are signaled to attach additional ubiquitin molecules, resulting in polyubiquitin chains bound to substrate proteins.

[0063] Proteins tagged for ubiquitination are then targeted to the cellular proteasome complex where the ubiquitin chains are recognized by the proteasome and the bound protein is degraded into peptides 7-8 amino acids long. Thus, degradation tags can function by engaging the tagged protein with E3 ubiquitin ligases, resulting in the addition of polyubiquitin chains and subsequent degradation by the proteasome.

[0064] In one embodiment of the present invention, a modified SICLOPPS method is provided that uses constructs as described above, which may include a degradation tag attached to either the N- or C-terminal intein domain.

[0065] In a preferred embodiment, the attached degradation tag is capable of effecting degradation, at least in part, by ubiquitination.

[0066] In another preferred embodiment, the attached degradation tag may be a hypoxia inducible factor-1 alpha (HIF-1α) subunit. In a further preferred embodiment, the attached degradation tag may comprise an oxygen-dependent degradation domain of HIF-1α that engages with a ubiquitin ligase complex. In a most preferred embodiment, the attached degradation tag may comprise an amino acid sequence according to SEQ ID NO: 10.

[0067] In yet another embodiment, the attached degradation tag may be a tag or a proteolytic targeting chimera that engages an E3 ubiquitin ligase for protein degradation.

[0068] Hypoxia-inducible factor (HIF) is a heterodimeric transcription factor that contains the constitutively expressed HIF-1β subunit and the HIF-1α subunit, which is regulated by oxygen. HIF-1α contains an oxygen-dependent degradation (ODD) domain that contains the critical proline residue P564, which is hydroxylated under normoxia to target the HIF-1α subunit for proteasomal degradation by engaging with the ubiquitin ligase complex. The ubiquitin ligase complex contains the Hippel-Lindau tumor suppressor protein (VHL), which is involved in the recognition of the hydroxylated P564 residue of the ODD domain of HIF-1α.

[0069] Therefore, the addition of a sequence containing P564 from the ODD domain of HIF-1α as a degradation tag to the SICLOPPS construct polypeptide induces the degradation of the bound protein.In the present invention, upon expression of the SICLOPPS construct, the active intein binds to the ODD domain polypeptide containing P564 from either its N-terminal or C-terminal domain, following its self-excision and splicing and cyclization of the target extein.The hydroxylated P564 residue is recognized by VHL from the ubiquitin ligase complex, and is ubiquitinated and degraded by the proteasome together with the bound cytotoxic active intein.

[0070] Thus, in some embodiments, the above polypeptide constructs for use in the modified SICLOPPS methodology may further comprise amino acids 548-603 of the full length ODD domain of HIF-1α, including the key P564 for hydroxylation, linked to an N-terminal intein domain, consisting of the following sequence: HHHHHHMIKIATRKYLGKQNVYDIGVERYHNFALKNGFIASN X~~~~~CLSYDTEILTVEYGILPIGKIVEKRIECTVYSVDNNGNIYTQPVAQWHDR GEQEVFEYCLEDGCLIRATKDHKFMTVDGQMMPIDEIFERELDLMRVDNLPNNPFSTQDTDLDLEMLAPYIPMDDDFQLRSFDQLSPLESSSAS PESASPQSTVTVFQ (SEQ ID NO: 16) Where: NPFSTQDTDLDLEMLAPYIPMDDDFQLRSFDQLSPLESSSASPESASPQSTVTVFQ (SEQ ID NO: 17)

[0071] It contains amino acids 548 to 603 of the full-length ODD domain of HIF-1α.

[0072] Protein degradation targeting chimeras (PROTACs) function similarly as degradation tags. PROTACs are small molecules that contain two covalently linked protein-binding domains. One domain can engage an E3 ubiquitin ligase, while the other binds to a target protein for degradation. Thus, by incorporating a PROTAC as either an N- or C-terminal degradation tag, upon expression of the SICLOPPS construct, an E3 ubiquitin ligase is recruited to the excised active intein, resulting in its ubiquitination and proteasomal degradation.

[0073] Cleavage of the active intein is envisioned to allow production of cyclic peptides in mammalian cells without increased cytotoxicity, as has been shown to be associated with active inteins.

[0074] The term "cytotoxicity" as used herein refers to the toxic nature of a compound to cells, which may cause such cells to undergo necrosis, a condition in which cells die rapidly due to cell lysis from loss of membrane integrity, or apoptosis, a condition in which cells undergo programmed cell death. Cytotoxic effects may, for example, affect the level of efficiency in utilizing mammalian cells to produce cyclic peptides, as will be appreciated by those skilled in the art.

[0075] Degradation tags can induce degradation of the proteins or polypeptides to which they are attached, whether the attachment is direct or through a linker. Such linkers or spacers are short amino acid sequences that vary between 2 and 31 amino acids and are implemented to separate multiple domains of a single protein.

[0076] In one embodiment of the present invention, a modified SICLOPPS method is provided using a construct as described above, in which a degradation tag is attached to either the N- or C-terminal intein domain either through a direct linkage or via a linker. In a preferred embodiment, the degradation tag is attached via a direct linkage.

[0077] It is envisaged that a compatible degradation tag for the type of intein used will be incorporated into the SICLOPPS construct. It will be clear to the skilled artisan that an active intein will require splicing before it can be degraded by the included degradation tag, i.e. the degradation tag will need to induce degradation more slowly than the intein splice.

[0078] For the purpose of experimental visualization, it is common practice in the art to optionally include a fluorescent tag in the construct that codes for peptide.It is assumed that such a fluorescent tag can be bound to the degradation tag in the SICLOPPS construct, so that the resulting degradation of any expressed tagged protein can be visualized using fluorescence microscopy or other such techniques known in the art.There are a wide variety of fluorescent tags or fluorophores suitable for use in microscopy.A comprehensive list of fluorophores is available at https: / / www.biosyn.com.

[0079] In some embodiments of the present invention, the modified SICLOPPS method is provided by using the above-mentioned construct with the addition of any fluorescent tag.In another embodiment, the fluorescent tag is bound to the degradation tag incorporated in the SICLOPPS construct.In a preferred embodiment, the fluorescent tag is the DsRed fluorophore.

[0080] The method contemplates introducing the modified SICLOPPS construct into a mammalian cell within any suitable expression vector capable of promoting expression of the polynucleotide.

[0081] As used herein, the phrase "expression vector" refers to a vehicle that facilitates the transcription and / or translation of a nucleic acid molecule in a suitable in vitro or in vivo system. An expression vector is "inducible" if the addition of an exogenous material to a host system containing the expression vector causes the expression vector to be expressed, e.g., a nucleic acid molecule within the vector is transcribed into mRNA.

[0082] Such suitable vectors include plasmids (Figure 4), bacteriophage, and viral vectors. Many of these are known in the art, and many are commercially available or available from the scientific community. Those skilled in the art can select a suitable vector for use in a particular application based on the type of system selected, e.g., mammalian cells, and the expression conditions selected.

[0083] The expression vector used in this method may contain a stretch of nucleotides that encodes the target polypeptide construct and a stretch of nucleotides that functions as a regulatory domain that regulates or controls the expression of the nucleotide sequence in the vector. For example, the regulatory domain may be a promoter or an enhancer.

[0084] In some embodiments, the expression vectors used in the method are generated with restriction sites both between and within the nucleic acid sequences encoding the split intein moieties to allow for cloning of a wide variety of circularization targets or splicing intermediates. In some embodiments, the expression vectors of the present invention can be inducible expression vectors, such as arabinose-inducible vectors. Such expression vectors can be generated using standard molecular biology techniques known to those skilled in the art. Plasmids can be transfected into mammalian cells for transient expression through several techniques well-practiced in the art, such as chemical-based or electroporation-based transfection.

[0085] It is envisaged that the expression vectors used within the present invention will contain an origin of replication (ORI) suitable for use in mammalian cells. Since there are no "natural" mammalian ORIs, viral-based ORIs are often used for expression vectors targeted to mammalian cells, such as the viral Epstein-Barr virus (EBC) or SV40 ORIs.

[0086] Thus, in one embodiment, a modified SICLOPPS method is provided that utilizes a plasmid containing a modified SICLOPPS construct as outlined above, suitable for expression in mammalian cells. In a preferred embodiment, the plasmid contains an SV40 origin of replication suitable for expression in mammalian cells.

[0087] In a second aspect, the present invention provides a cyclic peptide library produced by the modified SICLOPPS method according to the first aspect of the invention.

[0088] The term "cyclic peptide library" refers to a plurality of compartmentalized cyclic peptides, often containing over 100 million peptide members.

[0089] Each member of the library can be expressed in a mammalian cell from its own plasmid, as described in the first aspect of the invention. It is envisioned that the library will contain a number of randomized cyclic peptides from each expressed plasmid, generated such that the polypeptide or extein of interest is randomized. Randomized polypeptides are essentially degenerate oligonucleotides, where "degenerate" refers to the sequence containing a certain number of possible nucleotide bases. The resulting library will theoretically contain a large number of possible cyclic peptide structures that can then be used for pharmaceutical assays and other research purposes. The generation of cyclic peptide libraries in cells allows functional assays to be performed against a variety of targets.

[0090] SICLOPPS-based libraries, as outlined above, are DNA-encoded, allowing for a great deal of control over the composition of the library, and various libraries can be easily generated and screened against a given target (Figure 3). Such variations of SICLOPPS libraries that are easy to implement include cyclic peptides of different ring sizes, libraries of different amino acid compositions using limited codon sets, or the inclusion of a given amino acid or motif at a set position in all members of the library. This allows users of SICLOPPS full control over the composition of the cyclic peptide library via the degenerate oligonucleotides that encode it.

[0091] The length of the randomized polynucleotide inserted into the vector will depend on various factors that can be determined by one of skill in the art. The main consideration is the size of the final polypeptide to be expressed and the subsequent ring size of the cyclic peptide. In a preferred embodiment, the polypeptide is 6 amino acids long. Thus, a suitable randomized polynucleotide is 18 nucleic acids long. For cyclic peptide formation, one must consider whether the length of the polypeptide is sufficient to allow the cyclization reaction to proceed, i.e., whether the length allows the formation of a closed peptide cycle. In some embodiments, the peptide is cyclized by a linker of any length. Thus, a cyclic polypeptide may be achieved by encoding only two amino acids, in which case the randomized polynucleotide will be at least 6 nucleic acids long. Another consideration is the maximum insert size allowed by the vector and the corresponding replication system. In some embodiments, the randomized sequence may be longer, for example, at least 9, 30, 60, 90, 180, 300, 600, 900, 1,800, 3,000, or more nucleic acids long. In a preferred embodiment, the randomized nucleotide sequence is 6, 9, 12, 15, 18, 21, 24, 27, or 30 nucleotides long. The randomized sequence is intended to code for a polypeptide, but its length need not necessarily be a multiple of three. For example, it may be 7, 8, 10, 11, 13, 14, 16, 17, 19, 20, 22, 23, 25, 26, 28, or 29 nucleotides long. The randomized polynucleotide sequence may also be referred to herein as a variable sequence. In an embodiment, one or more positions of the "random" or "variable" sequence may actually be fixed. For example, in such a SICLOPPS method, a first position may be occupied by an invariant cysteine, serine, or threonine residue, followed by a variable or random amino acid sequence as described in the first aspect of the invention.

[0092] In a third aspect of the invention, there is provided a genetic construct comprising a polypeptide cassette encoding a C-terminal intein domain, a polypeptide sequence to be cyclized, an N-terminal intein domain, and a degradation tag suitable for use in a mammalian cell, where the degradation tag is attached to at least the intein domain and, upon expression, forms an active intein.

[0093] In some embodiments the genetic construct may further comprise any of the modifications or specifications according to the first aspect of the invention.

[0094] In a fourth aspect of the invention there is provided a vector comprising a genetic construct according to the third aspect of the invention.

[0095] In a fifth aspect of the invention there is provided a mammalian cell comprising a vector according to the fourth aspect of the invention.

[0096] In a sixth aspect of the invention, there is provided a method of generating a cyclic library according to the method of the first aspect of the invention.

[0097] In order that the invention may be more clearly understood, embodiments thereof will now be described, by way of example, with reference to the accompanying drawings, in which:

[0098] Example 1 SICLOPPS constructs were designed by adding a degradation domain to the N-terminal intein domain to deplete the spliced ​​intein product to prevent toxicity in mammalian cells. A Cfa intein containing an ERD to GEP mutation at residues 122-124 to increase amino acid tolerance at the +2 residue was used for rapid splicing and broad host range. Constructs were designed with the following sequences: C-terminal intein domain (+N-terminal 6xHis tag): MGHHHHHHGSGVKIISRKSLGTQNVYDIGVGEPHNFLLKNGLVASN (SEQ ID NO: 18) N-terminal intein domain: CLSYDTEILTVEYGFLPIGKIVEERIECTVYTVDKNGFVYTQPIAQWHNRGEQEV FEYCLEDGSIIRATKDHKFMTTDGQMLPIDEIFERGLDLKQVDGLP (SEQ ID NO: 19) In this example, eGFP was utilized in the extein (+N-terminal 2x Strep tag). To improve efficiency, wild-type Cfa splice junctions (CFN and AEY) were incorporated: Sequence List 1

[0099] JPEG0007665628000001.jpg49170.

[0100] The oxygen-dependent degradation (ODD) domain from HIF-1α, including the key residue P564 for hydroxylation, was engineered into the intein domain from the C-terminus to the N-terminus: Sequence Table 2

[0101] JPEG0007665628000002.jpg17170.

[0102] The fluorescent protein mCherry was further fused C-terminally to the ODD domain, followed by a FLAG tag for antibody recognition: JPEG0007665628000003.jpg40170.

[0103] Two versions of the eGFP extein plasmid (Figure 4) were generated. 1. Wild type or WT- splice and degrade. 2. Mutation of proline 564 in the P564G-ODD domain prevents degradation.

[0104] Example 2 The two plasmids from Example 1 were independently transfected into HeLa cells, which were then placed in the presence of oxygen with and without 100 μM DFX treatment to prevent intein degradation. In the wild-type plasmid, due to the inhibition of HIF prolyl hydroxylase domain (PHD), the intein should only degrade in the presence of oxygen and be stabilized in the absence of oxygen or in the presence of DFX. In contrast, in the P564G mutant, the intein should never be degraded, whether in the presence of oxygen or with DFX treatment. Proline is mutated to glycine, which prevents proline from being hydroxylated by PHD and subsequent protein degradation.

[0105] HeLa cells were imaged using a Zeiss fluorescence microscope to determine whether the extein (GFP) and intein (mCherry tagged) were present depending on the condition.

[0106] As shown in Figure 5, we found that the WT intein associated with mCherry fluorescence was degraded in normoxia compared to the DFX experiment, which showed mCherry fluorescence. The P564G mutant (Figure 6) showed both GFP and mCherry fluorescence in normoxia and DFX, indicating that no intein degradation occurred.

[0107] Example 3 The wild-type and P564G plasmids from Examples 1 and 2 were transfected into HeLa cells, which were then incubated for 24 hours under normoxic, hypoxic, or DFX-treated conditions. The cells were then lysed using RIPA buffer and a scraper. Total protein lysates were analyzed by Western blot, the results of which are shown in FIG. 7. Strep tag was used to capture GFP, and FLAG tag was used for mCherry. Anti-FLAG and anti-Strep tag antibodies were recognized using secondary antibodies conjugated to Alexa488 and Alexa568, respectively.

[0108] In the case of the wild type plasmid, more mCherry was displayed in hypoxic and DFX conditions, and no degradation of the intein was observed. Overall, the results show that under all conditions there was more GFP (associated with the extein) in the WT than in the P564G mutant. Actin, used as a control, was overall comparable between wells.

[0109] Example 4 Cell counts were performed from trypsinized cells independently transfected with the two plasmids from the previous example where HeLa cells were grown under normoxic and hypoxic conditions. Trypsinized cells were resuspended in complete medium. The cell suspension was then analyzed using a MOXI cell counter to count live and dead cells. Time points were obtained in triplicate or duplicate at 0, 6, 12, 24, 36, and 48 hours.

[0110] This trend indicates the maintenance of viable cell numbers in wild-type transfected cells compared to the decrease in viable cell numbers in P564G under normoxia, as shown in Figure 8. Cells incubated under hypoxic conditions can show a decrease in cell numbers from 48 hours, i.e., toxicity, for both plasmids, where no degradation of the intein has occurred.

[0111] Example 5 Transient transfection of spliced ​​(WT) and non-spliced ​​(C1A) GFP-Npu-mCherry-ODDD constructs into Trex cells Steps: 1.2×10 6 Trex293 cells were seeded in 6 cm dishes. The next day, cells were transfected with 1ug of plasmid and one well was left untransfected to serve as a negative control for setting the fluorescent gates. The next day, medium was changed and 1ug / mL doxycycline was added to each dish, and DFX was added to the dish of treated cells to a final concentration of 100mM. The next day, cells were analyzed by FACS.

[0112] Results: We investigated whether the intein fused to mCherry and an oxygen-dependent degradation domain (ODDD) was degraded in the presence of oxygen and whether adding DFX could prevent this oxygen-dependent degradation. Cells were analyzed by FACS and the GFP spliced ​​version (panel A of Figure 9) showed cells in the Q3 population (GFP+mCherry-), indicating that the GFP extein was spliced ​​out and that only the intein was degraded. Upon addition of DFX (panel B of Figure 9), much fewer cells were observed in Q3 and more in Q2 (GFP+mCherry+), indicating reduced degradation of the intein. This was confirmed in Figure 9 (panels C and D) for the non-spliced ​​variant. An overlay of the mCherry+ cells in panels A and B (presented in panel E of Figure 9) confirmed that the intensity of mCherry fluorescence was higher in the presence of DFX, suggesting less degradation of the intein via the ODDD pathway.

[0113] Example 6 Stable integration of GFP-Npu-mCherry-ODDD construct splicing (WT) into Trex cells Procedure: Trex293 cells stably integrated with GFP-WT-Npu-mCherry-ODDD were seeded in 6-well plates. Then, cells were treated with doxycycline to induce the expression of the intein. One condition was treated with DFX (100 mM) and the other condition was left untreated. The next day, cells were analyzed by FACS.

[0114] Results: We investigated whether the intein fused to mCherry and an oxygen-dependent degradation domain (ODDD) was degraded in the presence of oxygen, and whether adding DFX could prevent this oxygen-dependent degradation. Cells were analyzed by FACS, and in the absence of DFX (Figure 10, panel A), few cells were observed in Q1 and Q2 (mCherry+GFP- and mCherry+GFP+, respectively), with the majority of cells observed in Q3 (mCherry-GFP+; 67.4%). This indicates that splicing has occurred, separating GFP and mCherry, and that the mCherry-ODDD tagged intein is degraded in the presence of oxygen, leaving the spliced ​​GFP intact. Upon addition of DFX (Figure 10, panel B), more cells were found in Q2 (35.1%), suggesting that more mCherry is present as the intein degradation is reduced.

[0115] Example 7 Viability assay of Trex293 cells integrated with constructs encoding spliced ​​(WT) and non-spliced ​​(C1A) CFA intein-peptide extein-ODDD-mCherry Procedure: Trex cells integrated with CFA intein-peptide extein-ODDD-mCherry (spliced ​​and non-spliced) were seeded at a density of 1000 cells per well in 96-well plates. The next day, the medium was changed and replaced with fresh medium containing doxycycline (1 mg / mL) with or without DFX (final concentration 100 mM). The next day, cell viability was measured using the Cell Titer Glo Assay. [Table 1]

[0116] Results: This viability assay confirms that treatment with dfx, which has been shown to reduce intein degradation, significantly reduces cell viability (Figure 11). This suggests that the presence of the intein in the cells has a detrimental effect on cell viability. The -dfx control results in intein degradation and a subsequent increase in viability. The C1A non-spliced ​​control confirms that this is not a result of extein toxicity, as no spliced ​​extein is present.

[0117] Sequences used throughout this specification and which form part of the description: SEQ ID NO:1 (amino acid sequence of Ssp DnaE C-terminal intein domain) MVKVIGRRSLGVQRIFDIGLPQDHNFLLANGAIAANC SEQ ID NO: 2 (amino acid sequence of the Ssp DnaE N-terminal intein domain) AEYCLSFGTEILTVEYGPLPIGKIVSEEINCSVYSVDPEGRVYTQAIAQWHDRGE QEVLEYELEDGSVIRATSDHRFLTTDYQLLAIEEIFARQLDLLTLENIKQTEEALD NHRLPFPLLDAGTIK SEQ ID NO:3 (amino acid sequence of Npu DnaE C-terminal intein domain) MIKIATRKYLGKQNVYDIGVERDHNFALKNGFIASN SEQ ID NO: 4 (amino acid sequence of Npu DnaE N-terminal intein domain) CLSYETEILTVEYGLLPIGKIVEKRIECTVYSVDNNGNIYTQPVAQWHDRGEQEV FEYCLEDGSLIRATKDHKFMTVDGQMLPIDEIFERELDLMRVDNLPN SEQ ID NO: 5 (amino acid sequence of Cfa DnaE C-terminal intein domain) VKIISRKSLGTQNVYDIGVEKDHNFLLKNGLVASN SEQ ID NO:6 (amino acid sequence of Cfa DnaE N-terminal intein domain) CLSYDTEILTVEYGFLPIGKIVEERIECTVYTVDKNGFVYTQPIAQWHNRGEQEV FEYCLEDGSIRATKDHKFMTTDGQMLPIDEIFERGLDLKQVDGLP SEQ ID NO: 7 (amino acid sequence of gp41-1 C-terminal intein domain) MMLKKILKIEELDERELIDIEVSGNHLFYANDILTHNS SEQ ID NO:8 (amino acid sequence of gp41-1 N-terminal intein domain) CLDLKTQVQTPQGMKEISNIQVGDLVLSNTGYNEVLNVFPKSKKKSYKITLEDG KEIICSEEHLFPTQTGEMNISGGLKEGMCLYVKE SEQ ID NO:9 (Amino acid sequence of Homo sapiens hypoxia inducible factor-1 alpha [HIF-1α] subunit) MEGAGGANDKKKISSERRKEKSRDAARSRRSKESEVFYELAHQLPLPHNVSS HLDKASVMRLTISYLRVRKLLDAGDLDIEDDMKAQMNCFYLKALDGFVMVLTDD GDMIYISDNVNKYMGLTQFELTGHSVFDFTHPCDHEEMREMLTHRNGLVKKGK EQNTQRSFFLRMKCTLTSRGRTMNIKSATWKVLHCTGHIHVYDTNSNQPQCG YKKPPMTCLVLICEPIPHPSNIEIPLDSKTFLSRHSLDMKFSYCDERITELMGYEP EELLGRSIYEYYHALDSDHLTKTHHDMFTKGQVTTGQYRMLAKRGGYVWVET QATVIYNTKNSQPQCIVCVNYVVSGIIQHDLIFSLQQTECVLKPVESSDMKMTQL FTKVESEDTSSLFDKLKKEPDALTLLAPAAGDTIISLDFGSNDTETDDQQLEEVP LYNDVMLPSPNEKLQNINLAMSPLPTAETPKPLRSSADPALNQEVALKLEPNPE SLELSFTMPQIQDQTPSPSDGSTRQSSPEPNSPSEYCFYVDSDMVNEFKLELV EKLFAEDTEAKNPFSTQDTDLDLEMLAPYIPMDDDFQLRSFDQLSPLESSASP ESASPQSTVTVFQQTQIQEPTANATTTTATTDELKTVTKDRMEDIKILIASPSPTH IHKETTSATSSPYRDTQSRTASPNRAGKGVIEQTEKSHPRSPNVLSVALSQRTT VPEEELNPKILALQNAQRKRKMEHDGSLFQAVGIGTLLQQPDDHAATTSLSWK RVKGCKSSEQNGMEQKTIILIPSDLACRLLGQSMDESGLPQLTSYDCEVNAPIQ GSRNLLQGEELLRALDQVN SEQ ID NO:10 (Amino acid sequence of the oxygen-dependent degradation (ODD) domain of the Homo sapiens hypoxia-inducible factor-1 alpha [HIF-1α] subunit) NPFSTQDTDLDLEMLAPYIPMDDDFQLRSFDQLSPLESSSASPESASPQSTVT VFQ

Claims

1. 1. A method for the non-toxic production of cyclic peptides in mammalian cells comprising: a) introducing into said mammalian cell a vector, said vector comprising a construct encoding the C-terminal and N-terminal intein domains of a split intein, a polypeptide sequence to be cyclized, and a degradation tag, said degradation tag being linked to at least one intein domain; b) expressing the construct to produce an intermediate comprising an active intein and the polypeptide sequence, whereby the active intein undergoes splicing, circularizing the polypeptide, and the degradation tag is a peptide sequence that binds to the active intein for degradation, optionally by the ubiquitin-proteasome pathway.

2. A mammalian cell expressing a cyclic peptide, said mammalian cell comprising: a) introducing into said mammalian cell a vector, said vector comprising a construct encoding the C-terminal and N-terminal intein domains of a split intein, a polypeptide sequence to be cyclized, and a degradation tag, said degradation tag being linked to at least one intein domain; and b) expressing the construct to produce an intermediate comprising an active intein and the polypeptide sequence, whereby the active intein undergoes splicing, circularizing the polypeptide, and the degradation tag is a peptide sequence that attaches to the active intein for degradation, optionally by the ubiquitin-proteasome pathway.

3. 3. A library of mammalian cells comprising the mammalian cells of claim 2, wherein each mammalian cell comprises a different nucleic acid encoding a different cyclic peptide.

4. 1. A genetic construct comprising a polynucleotide cassette encoding the C-terminal and N-terminal intein domains of a split intein, a polypeptide sequence to be cyclized, and a degradation tag suitable for use in a mammalian cell, said degradation tag being linked to at least one intein domain, said degradation tag being a peptide sequence that binds to said active intein for degradation, optionally by the ubiquitin-proteasome pathway.

5. The genetic construct of claim 4 , wherein the active intein splices before being degraded by the degradation tag.

6. 6. The genetic construct of claim 4 or 5, wherein the degradation tag effects degradation at least in part by ubiquitination.

7. The genetic construct of any one of claims 4 to 6, wherein the degradation tag is a hypoxia inducible factor-1 alpha (HIF-1α) subunit or a protein degradation targeting chimera (PROTAC).

8. The genetic construct of any one of claims 4 to 7, wherein the degradation tag is the oxygen-dependent degradation (ODD) domain of the hypoxia-inducible factor-1 alpha (HIF-1α) subunit, including the key residue P564.

9. The gene construct according to claim 8, wherein the ODD domain of HIF-1α comprises a sequence length spanning amino acids 548 to 603.

10. The genetic construct of any one of claims 4 to 6, wherein the degradation tag is a protein degradation targeting chimera (PROTAC) small molecule capable of engaging an E3 ubiquitin ligase.

11. The genetic construct of any one of claims 4 to 10, wherein the active intein is a Cfa, Npu, Ssp, or gp41-1 intein.

12. The genetic construct according to any one of claims 4 to 10, wherein the active intein is an Npu intein.

13. The genetic construct according to any one of claims 4 to 12, wherein the link between the degradation tag and the intein is a direct link.

14. The genetic construct according to any one of claims 4 to 13, wherein the genetic construct further encodes at least one affinity tag.

15. 15. The genetic construct of claim 14, wherein the at least one encoded affinity tag is a FLAG tag for antibody recognition.

16. The genetic construct according to any one of claims 4 to 15, wherein said genetic construct further encodes a fluorescent tag, said tag being preferably DsRed.

17. A vector comprising a gene construct described in any one of claims 4 to 16.

18. A mammalian cell comprising a gene construct described in any one of claims 4 to 16 and / or a vector described in claim 17.

19. A library of mammalian cells comprising the mammalian cell of claim 18.

20. A method for non-toxic production of a cyclic peptide in a mammalian cell as described in claim 1, wherein the vector is a vector described in claim 17.

21. 21. A method for generating a cyclic peptide library using the method of claim 1 or 20.

22. 21. The method of claim 1 or 20, wherein the intein is toxic to mammalian cells.

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