Patent Application
20210087238
The present disclosure generally is directed to cell penetrating peptides (CPPs) and related compositions and methods.
Peptides are attractive diagnostic and therapeutic agents due to their high potency and target specificity. In particular, peptides are very promising as inhibitors of intracellular protein-protein interactions (e.g., p53 interactions), which have typically been quite difficult to target using small molecule therapeutics. However, one of the challenges to more widespread adoption of peptides as therapeutics is the inability of most peptides to access intracellular targets, as the cell membrane generally acts as a barrier to intracellular entry of peptides. Further, existing cell penetrating peptides (CPPs) and any associated cargo typically become entrapped in the endosomal and lysosomal compartment. Thus, in order to fully exploit the advantages of peptide therapeutics there is an ongoing need to develop compositions and methods for intracellular/cytosolic delivery of peptides and associated payloads.
The present disclosure provides cell penetrating peptides (CPPs) and related compositions. Such compositions are particularly useful for enhancing cytosolic delivery of a linked cargo, e.g, a heterologous peptide, a heterologous, protein, or a small molecule therapeutic agent linked to a CPP. Such reagents and methods can provide for additional stability of a peptide.
Accordingly, the present disclosure provides a non-naturally occurring cell-penetrating peptide (CPP) comprising an amino acid sequence corresponding to the following structure:
X1-X2-X3-X4-X5 (Formula I), wherein:
X1 is an optional amino acid sequence selected from the group consisting of: QE; KTQE (SEQ ID NO:1); and RTQE (SEQ ID NO:2);
X2 is any combination of 3 to 8 lysine and/or arginine residues;
X3 is an amino acid sequence selected from the group consisting of: QPAKPRPKTQE (SEQ ID NO:3), QPPKPKKPKTQE (SEQ ID NO:4), QPPRPRRPRTQE (SEQ ID NO:5), QTTKTKKTKTQE (SEQ ID NO:6), QPAKKKPKTQE (SEQ ID NO:7), and QAPKQPPKPKKPKTQE (SEQ ID NO:8)
X4 is any combination of 3 to 8 arginine and/or lysine residues; and
X5 is an amino acid sequence selected from the group consisting of QPPKPKR (SEQ ID NO:9); QTTKTKR (SEQ ID NO:10); QPPKPK (SEQ ID NO:11); and QPPRPRR (SEQ ID NO:12), wherein the amino acid sequence of the non-naturally occurring CPP does not consist of the amino acid corresponding to:
The present disclosure also provides a non-naturally occurring cell-penetrating peptide (CPP) comprising an amino acid sequence corresponding to the following structure:
X1-X2-X3-X4-X5 (Formula II), wherein:
X1 is an optional amino acid sequence selected from the group consisting of: P; QE; KTQE (SEQ ID NO:1); RTQE (SEQ ID NO:2); QPPKPKR (SEQ ID NO:223); and RKPKPPQ (SEQ ID NO:224);
X2 is any combination of 3 to 8 lysine and/or arginine residues;
X3 is an amino acid sequence selected from the group consisting of SEQ ID NOs:3-8 and 225-248;
X4 is any combination of 3 to 8 arginine and/or lysine residues; and
X5 is an optional amino acid sequence selected from the group consisting of SEQ ID NOS:9-12, 249-260, and PKR, wherein the amino acid sequence of the non-naturally occurring CPP does not consist of the amino acid corresponding to:
In some examples X2 or X4 consists of only arginine residues. In some examples X2 consists of only arginine residues. In other examples X4 consists of only arginine residues. In some examples X2 and X4 consist of only arginine residues.
In some examples X2 or X4 consists of only lysine residues. In some embodiments X2 consists of only lysine residues. In some examples X2 consists of only arginine residues. In other examples X4 consists of only lysine residues. In some examples X2 and X4 consist of only lysine residues.
In some examples X2 or X4 consists of both arginine and lysine residues. In some examples X2 and X4 consist of both arginine and lysine residues.
In some examples the length of the amino acid sequence of the CPP consists of 25 to 100 residues. In other examples the length of the amino acid sequence of the CPP consists of 30 to 70 residues. In other examples the length of the amino acid sequence of the CPP consists of 40 to 60 residues. In other examples the length of the amino acid sequence of the CPP consists of 25 to 50 residues.
In some examples the amino acid sequence of the CPP consists of Formula I or Formula II.
In some examples the amino acid sequence of the CPP comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 39, 64, 67, 69, 73-81, and SEQ ID NOs:113-167. In some examples the amino acid sequence of the CPP comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 64, 74-81, and 113-167.
In some examples any of the above-mentioned CPPs comprises multiple copies of an amino acid sequence corresponding to Formula I or Formula II. In one example, the CPP comprising multiple copies of Formula I or Formula II, comprises at least two copies of the amino acid sequence corresponding to SEQ ID NO:88. In other examples the amino acid sequence of a CPP consists of Formula I or Formula II.
In some examples a CPP is a modified CPP comprising a moiety other than a canonical amino acid. In some examples, where the CPP is a modified CPP, the moiety is selected from the group consisting of a detectable label, a non-canonical amino acid, a reactive group, a fatty acid, cholesterol, a lipid, a bioactive carbohydrate, a nanoparticle, a small molecule drug, and a polynucleotide. In some examples the moiety in a modified CPP is a D-amino acid.
In some examples the moiety is a detectable label. In some examples the detectable label is selected from the group consisting of a fluorophore, a fluorogenic substrate, a luminogenic substrate, and a biotin.
In some examples, the detectable label is a fluorophore. In some examples the fluorophore is a pH-sensitive fluorescent probe. In some examples the pH-sensitive fluorescent probe is naphthofluorescein. In other examples the moiety is a fluorogenic substrate.
In some examples, where the CPP is a modified CPP, a moiety is non-covalently linked to the CPP. In other examples the moiety is covalently linked to the CPP. In some examples the moiety is covalently linked at the N-terminal of the CPP amino acid sequence. In other examples the moiety is covalently linked at the C-terminal of the CPP amino acid sequence. In other examples the moiety is covalently linked to a sidechain of the CPP amino acid sequence. In some examples, the amino acid sequence of a CPP is the retro-inverso sequence of the amino acid sequence of the amino acid sequence of any of the foregoing CPPs.
The present disclosure also provides a CPP fusion protein comprising the amino acid sequence of any of the CPPs disclosed herein and a heterologous amino acid sequence. In some examples the heterologous amino acid sequence in the CPP fusion protein comprises an amino acid sequence selected from the group consisting of a SpyTag peptide (SEQ ID NO:84), a Phylomer™ as defined herein, a reporter protein, a pro-apoptotic peptide, a targeting protein, a bioactive peptide, a dominant negative peptide, a cytotoxic protein, an enzyme, an antibody, and a SpyC peptide (SEQ ID NO:83). In some examples the heterologous amino acid sequence comprises the amino acid sequence of a dominant negative peptide. In some examples the dominant negative peptide comprises the amino acid sequence of Omomyc (SEQ ID NO:99). In some examples the heterologous amino acid sequence comprises the amino acid sequence of β-lactamase (SEQ ID NO:112). In some examples the heterologous amino acid sequence comprises the amino acid sequence of a dominant negative peptide. In some examples the dominant negative peptide peptide comprises the amino acid sequence of Omomyc (SEQ ID NO:99). In other examples the heterologous amino acid sequence comprises the amino acid sequence of a proapoptotic peptide. In some examples the amino acid sequence of the proapoptotic peptide comprises the amino acid sequence corresponding to SEQ ID NO:61 or SEQ ID NO:63. In other examples the heterologous amino acid sequence comprises the amino acid sequence of an enzyme. In some examples the enzyme is a therapeutic enzyme. In other examples the heterologous amino acid sequence comprises the amino acid sequence of a SpyTag peptide (SEQ ID NO:84).
In some examples a CPP fusion protein comprises a flexible linker linking the CPP and the heterologous amino acid sequence.
The present disclosure further provides a CPP conjugate comprising a CPP fusion protein covalently linked to a SpyCatcher fusion protein comprising the amino acid sequence of SEQ ID NO:83 and a heterologous amino acid sequence, wherein the SpyCatcher fusion protein is covalently linked to the CPP fusion protein by an isopeptide bond to the SpyTag peptide. In some examples the SpyCatcher fusion protein in the CPP conjugate comprises an amino acid sequence selected from the group consisting of a Phylomer™ as defined herein, a reporter protein, a pro-apoptotic peptide, a targeting protein, a cytotoxic protein, an enzyme, a dominant negative peptide, and an antibody. In some examples the heterologous amino acid sequence in the SpyCatcher fusion protein comprises the amino acid sequence of a pro-apoptotic peptide. In some example the amino acid sequence of the pro-apoptotic peptide comprises the amino acid sequence of any one of SEQ ID NOs:61 and 63.
In other examples the SpyCatcher fusion protein comprises the amino acid sequence of a reporter protein in the form of an enzyme. In some examples the reporter protein comprises the amino acid sequence of a β-lactamase.
The present disclosure also provides a modified cell comprising a CPP, a CPP fusion protein, or a CPP conjugate.
The present disclosure also provides any of the above-mentioned CPPs, CPP fusion proteins, CPP conjugates, and modified cells for use as a medicament or diagnostic agent.
Also provided by the present disclosure is a method for delivering a CPP, a CPP fusion protein, or a CPP conjugate to a cell by contacting the cell with any of the CPPs, CPP fusion proteins, or CPP conjugate provided herein. In some examples the contacting is performed ex vivo. In other examples the contacting is performed in vivo.
Throughout this specification, unless specifically stated otherwise or the context requires otherwise, reference to a single step, composition of matter, group of steps or group of compositions of matter shall be taken to encompass one and a plurality (i.e. one or more) of those steps, compositions of matter, groups of steps or groups of compositions of matter. Thus, as used herein, the singular forms “a”, “an” and “the” include plural aspects unless the context clearly dictates otherwise. For example, reference to “a” includes a single as well as two or more; reference to “an” includes a single as well as two or more; reference to “the” includes a single as well as two or more and so forth.
Each example of the present disclosure described herein is to be applied mutatis mutandis to each and every other example unless specifically stated otherwise.
Those skilled in the art will appreciate that the disclosure herein is susceptible to variations and modifications other than those specifically described. It is to be understood that the disclosure includes all such variations and modifications. The disclosure also includes all of the steps, features, compositions and compounds referred to or indicated in this specification, individually or collectively, and any and all combinations or any two or more of said steps or features.
The present disclosure is not to be limited in scope by the specific examples described herein, which are intended for the purpose of exemplification only. Functionally-equivalent products, compositions and methods are clearly within the scope of the disclosure, as described herein.
The present disclosure is performed without undue experimentation using, unless otherwise indicated, conventional techniques of molecular biology, microbiology, virology, recombinant DNA technology, peptide synthesis in solution, solid phase peptide synthesis, and immunology. Such techniques are described and explained throughout the literature in sources such as Perbal 1984, Sambrook et al., 2001, Brown (editor) 1991, Glover and Hames (editors) 1995 and 1996, Ausubel et al. including all updates until present, Coligan et al. (editors) (including all updates until present), Maniatis et al. 1982, Gait (editor) 1984, Hames and Higgins (editors) 1984, Freshney (editor) 1986.
The term “and/or”, e.g, “X and/or Y” shall be understood to mean either “X and Y” or “X or Y” and shall be taken to provide explicit support for both meanings or for either meaning.
The term “about”, unless stated to the contrary, refers to +/−20%, more preferably +/−10%, of the designated value. For the avoidance of doubt, the term “about” followed by a designated value is to be interpreted as also encompassing the exact designated value itself (for example, “about 10” also encompasses 10 exactly).
Throughout this specification the word “comprise”, or variations such as “comprises” or “comprising”, will be understood to imply the inclusion of a stated element, integer or step, or group of elements, integers or steps, but not the exclusion of any other element, integer or step, or group of elements, integers or steps.
The term antibody” as used herein includes polyclonal antibodies, monoclonal antibodies, bispecific antibodies, fusion diabodies, triabodies, heteroconjugate antibodies, and chimeric antibodies. Also contemplated are antibody fragments that retain at least substantial (about 10%) antigen binding relative to the corresponding full length antibody. Antibodies include modifications in a variety of forms including, for example, but not limited to, domain antibodies including either the VH or VL domain, a dimer of the heavy chain variable region (VHH, as described for a camelid), a dimer of the light chain variable region (VLL), Fv fragments containing only the light (VL) and heavy chain (VH) variable regions which may be joined directly or through a linker, or Fd fragments containing the heavy chain variable region and the CH1 domain.
A scFv consisting of the variable regions of the heavy and light chains linked together to form a single-chain antibody and oligomers of scFvs such as diabodies and triabodies are also encompassed by the term “antibody”. Also encompassed are fragments of antibodies such as Fab, (Fab′)2 and FabFc2 fragments which contain the variable regions and parts of the constant regions. Complementarity determining region (CDR)-grafted antibody fragments and oligomers of antibody fragments are also encompassed. The heavy and light chain components of an Fv may be derived from the same antibody or different antibodies thereby producing a chimeric Fv region. The antibody may be of animal (for example mouse, rabbit or rat) or human origin or may be chimeric or humanize.
The antibodies may be Fv regions comprising a variable light (VL) and a variable heavy (VH) chain in which the light and heavy chains may be joined directly or through a linker. As used herein a linker refers to a molecule that is covalently linked to the light and heavy chain and provides enough spacing and flexibility between the two chains such that they are able to achieve a conformation in which they are capable of specifically binding the epitope to which they are directed. Protein linkers are particularly preferred as they may be expressed as an intrinsic component of the Ig portion of the fusion polypeptide.
In some examples, an antibody is a recombinantly produced single chain scFv antibody, preferably a humanized scFv. Methods for generating antibody fusion proteins are known in the art as exemplified in, e.g., U.S. Pat. No. 8,142,781.
The term “canonical amino acid” refers to an amino acid encoded directly by the codons of the universal genetic code. The canonical amino acids are: Alanine, Arginine, Asparagine, Aspartic acid, Cysteine, Glutamic acid, Glutamine, Glycine, Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Proline, Serine, Threonine, Tryptophan, Tyrosine, and Valine.
The term “conjugate,” as used herein, refers to two or more peptides or proteins that are covalently linked by a means other than an amide bond between the C-terminus of one protein and the N-terminus of the other. Typically, the covalent bond is by means of an isopeptide bond formed between a sidechain carboxylic acid of one protein or peptide to be conjugated.
The term “endogenous” or “endogenously encoded” in reference to a nucleotide or amino acid sequence indicates that sequence in question is native to a virus, cell, or organism that has not been experimentally modified to encode or express the amino acid sequence in question.
A “heterologous amino acid sequence” refers to an amino acid sequence that does not naturally occur as a sequence that is contiguous with the amino acid sequence of a reference sequence. For example, green fluorescent protein is a heterologous amino acid sequence with respect to a cell penetrating peptide (CPP) derived from a Sindbis viral coat.
A “nanoparticle” refers to a microscopic particle with at least one dimension less than 100 nm. Examples of nanoparticles include, but are not limited to, derivatized gold nanoparticles, quantum dots, and polymeric nanoparticles.
The term “non-naturally occurring” in reference to a peptide will be understood to indicate that: (i) there is no endogenous gene or open reading frame that encodes an amino acid sequence consisting of the amino acid sequence of the peptide in question; and (ii) there is no endogenous protein fragment the amino acid sequence of which consists of the peptide in question. For example, a peptide consisting of the amino acid sequence of a fragment of an endogenously expressed protein is considered a non-naturally occurring peptide if the protein fragment itself is not naturally expressed or does not ordinarily occur as a byproduct of the endogenously expressed protein.
The term “Phylomer™” refers to a peptide of about 8 to about 180 amino acids encoded by nucleic acid fragments obtainable from genome(s) of a microorganisms and/or a eukaryotic species having a compact genome.
The term “peptide” is intended to include compounds composed of amino acid residues linked by amide bonds. A peptide may be natural or unnatural, ribosome encoded or synthetically derived. Typically, a peptide will consist of between 2 and 200 amino acids. For example, the peptide may have a length in the range of 10 to 20 amino acids or 10 to 30 amino acids or 10 to 40 amino acids or 10 to 50 amino acids or 10 to 60 amino acids or 10 to 70 amino acids or 10 to 80 amino acids or 10 to 90 amino acids or 10 to 100 amino acids, including any length within said range(s). The peptide may comprise or consist of fewer than about 150 amino acids or fewer than about 125 amino acids or fewer than about 100 amino acids or fewer than about 90 amino acids or fewer than about 80 amino acids or fewer than about 70 amino acids or fewer than about 60 amino acids or fewer than about 50 amino acids.
Peptides, as referred to herein, include “inverso” peptides in which all L-amino acids are substituted with the corresponding D-amino acids, “retro-inverso” peptides in which the sequence of amino acids is reversed and all L-amino acids are replaced with D-amino acids.
Peptides may comprise amino acids in both L- and/or D-form. For example, both L- and D-forms may be used for different amino acids within the same peptide sequence. In some examples the amino acids within the peptide sequence are in L-form, such as natural amino acids. In some examples the amino acids within the peptide sequence are a combination of L- and D-form.
Peptides may be encoded by nucleic acid fragments of genomic DNA or cDNA obtained from an evolutionary diverse range of organisms from Viruses, Bacteria, Archaea, and Eukarya. For example, nucleic acid fragments may be obtained from Aeropyrum pernix, Aquifex aeolicus, Archaeoglobus fulgidis, Bacillus subtilis, Bordetella pertussis, Borrelia burgdorferi, Chlamydia trachomatis, Escherichia coli, Haemophilus influenzae, Helicobacter pylori, Methanobacterium thermoautotrophicum, Methanocaldococcus jannaschii, Mycoplasma pneumoniae, Neisseria meningitidis, Pseudomonas aeruginosa, Pyrococcus horikoshii, Synechocystis PCC 6803, Thermoplasma volcanium and Thermotoga maritima. Alternatively, peptides may be synthesized using well known solid phase peptide synthesis techniques, and purification techniques.
Nucleic acid fragments may be generated using one or more of a variety of methods known to those skilled in the art. Suitable methods include, as well as those described in the examples below, for example, mechanical shearing (e.g by sonication or passing the nucleic acid through a fine gauge needle), digestion with a nuclease (e.g DNAse 1), partial or complete digestion with one or more restriction enzymes, preferably frequent cutting enzymes that recognize 4-base restriction enzyme sites and treating the DNA samples with radiation (e.g gamma radiation or ultra-violet radiation).
The term “protein” shall be taken to include a single polypeptide chain, i.e., a series of contiguous amino acids linked by peptide bonds or a series of polypeptide chains covalently or non-covalently linked to one another (i.e., a polypeptide complex). For example, the series of polypeptide chains can be covalently linked using a suitable chemical bond or a disulfide bond. Examples of non-covalent bonds include hydrogen bonds, ionic bonds, Van der Waals forces, and hydrophobic interactions.
Percentage amino acid sequence identity with respect to a given amino acid sequence is defined as the percentage of amino acid residues in a candidate sequence that are identical to the amino acid residues in the reference sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Amino acid sequence identity may be determined using the EMBOSS Pairwise Alignment Algorithms tool available from The European Bioinformatics Institute (EMBL-EBI), which is part of the European Molecular Biology Laboratory. This tool is accessible at the website located at www.ebi.ac.uk/Tools/emboss/align/. This tool utilizes the Needleman-Wunsch global alignment algorithm (Needleman and Wunsch, 1970). Default settings are utilized which include Gap Open: 10.0 and Gap Extend 0.5. The default matrix “Blosum62” is utilized for amino acid sequences and the default matrix.
The term “cell penetrating peptide” (CPP) refers to a peptide that is capable of crossing a cellular membrane. In one example, a CPP is capable of translocating across a mammalian cell membrane and entering into a cell. In another example, a CPP may direct a conjugate to a desired subcellular compartment. Thus, a CPP may direct or facilitate penetration of a molecule of interest across a phospholipid, mitochondrial, endosomal, lysosomal, vesicular, or nuclear membrane. CPPs that are able to “escape” the endosomal and lysosomal compartments for cytosolic delivery can be referred to as “FPPs” as described herein. A CPP may be translocated across the membrane with its amino acid sequence complete and intact, or alternatively partially degraded.
A CPP may direct a molecule of interest from outside a cell through the plasma membrane, and into the cytoplasm or a desired subcellular compartment. Alternatively, or in addition, a CPP may direct a molecule of interest across the blood-brain, trans-mucosal, hematoretinal, skin, gastrointestinal and/or pulmonary barriers.
Accordingly, a CPP may be linked to a molecule of interest. Such molecules include a further peptide or protein, an RNAi agent, a therapeutic agent, a toxin, or a detectable label. The linkage may be through a covalent bond or non-covalent interactions. For example, a CPP may be linked to a further peptide or protein via a “peptide linker”. Alternatively, a CPP may be linked to another moiety (including a peptide) by a non-peptide synthetic linker. The further peptide or protein may be designed to act upon a particular intracellular target or to direct its transport to particular subcellular compartment. In some examples, a “therapeutic agent” is a small molecule compound (generally less than about 900 daltons in size). In some examples a small molecule compound is a chemotherapeutic agent, a cytotoxic molecule, or a cytostatic molecule.
The capability to translocate across membranes of a CPP may be energy dependent or independent, and/or receptor dependent or independent. In some examples, the CPP is a peptide which is demonstrated to translocate across a plasma membrane as determined by the methods described herein. CPPs encompass: (i) peptides that become internalized by cells but subsequently entrapped within endosomes or lysosomes; and (ii) peptides that not only become internalized by cells, but also are able to escape endosomal and/or lysosomal compartments once internalized by cells. The latter are referred to as “functional penetrating peptides,” (FPPs) as described herein.
The term “functional penetrating peptide” (FPP) refers to a subset of CPPs that in addition being able to mediate intracellular delivery, is also able to escape from endosomal and/or lysosomal compartments for delivery into cytosol
The term “basic amino acid” relates to any amino acid, including natural and non-natural amino acids, that has an isoelectric point above 6.3, as measured according to Kice & Marvell “Modern Principles of organic Chemistry” (Macmillan, 1974) or Matthews and van Holde “Biochemistry” Cummings Publishing Company, 1996. Included within this definition are Arginine, Lysine, Homoarginine (Har), and Histidine as well as derivatives thereof. Suitable non-natural basic amino acids are described in U.S. Pat. No. 6,858,396.
Accordingly, in some examples provided herein is a non-naturally occurring cell-penetrating peptide (CPP) comprising an amino acid sequence corresponding to the following structure:
X4-X2-X3-X4-X5 (Formula I), wherein:
X1 is an optional amino acid sequence selected from the group consisting of: QE; KTQE (SEQ ID NO:1); and RTQE (SEQ ID NO:2);
X2 is any combination of 3 to 8 lysine and/or arginine residues;
X3 is an amino acid sequence selected from the group consisting of:
X4 is any combination of 3 to 8 arginine and/or lysine residues; and
X5 is an amino acid sequence selected from the group consisting of QPPKPKR (SEQ ID NO:9); QTTKTKR (SEQ ID NO:10); QPPKPK (SEQ ID NO:11); and QPPRPRR (SEQ ID NO:12), wherein the amino acid sequence of the non-naturally occurring CPP does not consist of the amino acid corresponding to:
Also provided herein is provides a non-naturally occurring cell-penetrating peptide (CPP) comprising an amino acid sequence corresponding to the following structure:
X1-X2-X3-X4-X5 (Formula II), wherein:
X1 is an optional amino acid sequence selected from the group consisting of: P; QE; KTQE (SEQ ID NO:1); RTQE (SEQ ID NO:2); QPPKPKR (SEQ ID NO:223); and RKPKPPQ (SEQ ID NO:224);
X2 is any combination of 3 to 8 lysine and/or arginine residues;
X3 is an amino acid sequence selected from the group consisting of SEQ ID NOs:3-8 and 225-248;
X4 is any combination of 3 to 8 arginine and/or lysine residues; and
X5 is an optional amino acid sequence selected from the group consisting of SEQ ID NOS:9-12, 249-260, and PKR, wherein the amino acid sequence of the non-naturally occurring CPP does not consist of the amino acid corresponding to:
In some examples, X2 or X4 consists of only arginine residues. In some examples, X2 and X4 consist of only arginine residues. In other examples, X2 or X4 consists of only lysine residues. In some examples, X2 and X4 consist of only arginine residues. In further examples, X2 or X4 consists of both arginine and lysine residues. In other examples, each of X2 and X4 consist of both arginine and lysine residues.
In some examples, a CPP will comprise between one and ten conservative amino acid substitutions relative to any sequence described herein, e.g, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 conservative amino acid substitutions.
A “conservative” amino acid substitution is one in which an amino acid residue is replaced with another amino acid residue having a side chain with similar physicochemical properties. Amino acid residues having side chains with similar physiochemical properties are known in the art, and include amino acids with basic side chains (e.g, lysine, arginine, histidine), acidic side chains (e.g, aspartic acid, glutamic acid), uncharged polar side chains (e.g, glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine, tryptophan), nonpolar side chains (e.g, alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine), beta-branched side 10 chains (e.g, threonine, valine, isoleucine) and aromatic side chains (e.g, tyrosine, phenylalanine, tryptophan, histidine). Conservative amino acid substitutions include those with amino acids, which have been substituted with non-naturally occurring amino acids and non-proteogenic amino acids, which are therefore not among the regular amino acids encoded by the genetic code. Examples of non-proteogenic amino acids include, but are not limited to, ornithine, citrulline (Cit), diaminobutyric acid (Dab), diaminopropionic acid (Dap), 2-Aminoisobutyric acid, α-Amino-n-butyric acid, Norvaline, Norleucine, Alloisoleucine, t-leucine, Ornithine, Allothreonine, β-Alanine, β-Amino-n-butyric acid, N-isopropyl glycine, Isoserine, and Sarcosine and pyroglutamic acid. Conservative amino acid substitutions further include D-amino acids. In some examples the amino acid sequence of a CPP is a retro-inverso amino acid sequence.
In some examples the amino acid sequence of any of the foregoing CPPs consists of 25 to 100 residues, e.g, 30, 35, 40, 45, 48, 50, 52, 60, 65, 70, 75, 80, 85, 90, 95, or another number of residues from 25 to 100. In other examples the amino acid sequence of any of the foregoing CPPs consists of 30 to 70 residues, e.g, 35, 40, 45, 48, 50, 52, 60, 65, or another number of residues from 30 to 70 residues. In other examples the amino acid sequence of any of the foregoing CPPs consists of 40 to 60 residues, e.g, 42, 43, 45, 48, 50, 52, 54, 57, 58, or another number of residues from 40 to 60 residues. In some examples, the amino acid sequence of any of the foregoing CPPs consists of 35 to 50 residues, e.g, 36, 38, 40, 42, 43, 45, 57, 58, or another number of residues from 35 to 50 residues. In yet other examples the amino acid sequence of any of the foregoing CPPs consists of 25 to 50 residues, e.g, 27, 28, 30, 32, 35, 37, 38, 40, 42, 46, 48, or another number of residues from 25 to 50.
In one example the amino acid sequence of the CPP consists of an amino acid sequence corresponding to Formula I. For the avoidance of doubt, it is to be understood that in such examples, while the amino acid sequence of the CPP consists of an amino acid sequence corresponding to Formula I, the CPP may, nevertheless, comprise chemical modifications that do not alter the amino acid sequence. Such modifications include, but are not limited to, non-peptide linkers, non-peptide therapeutic agents (e.g, a chemotherapeutic agent), and detectable labels. In such examples the CPP is generally referred to as a “modified CPP,” as described in further detail herein. In other examples the CPP consists of an amino acid sequence corresponding to Formula I.
In particular examples, the amino acid sequence of the CPP comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 39, 64, 67, 69, 73-81, and SEQ ID NOs:113-167. In other examples, the amino acid sequence of the CPP consists of an amino acid sequence selected from the group consisting of SEQ ID NOs: 64, 74-81, and 113-167.
In some examples any of the above-mentioned CPPs comprise multiple copies of an amino acid sequence corresponding to Formula I or Formula II, referred to herein as a multimeric CPP. In some examples, a multimeric CPP comprises between two and ten copies of an amino acid sequence corresponding to Formula I or Formula II, e.g, 2, 3, 4, 5, 6, 7, 8, 9, or 10 copies of an amino acid sequence corresponding to Formula I or Formula II. In some examples, the multimeric CPP corresponding comprises at least two amino acid sequences selected from the group consisting of 39, 64, 67, 69, 73-81, and 113-167. In one example, the CPP comprising multiple copies of Formula I or Formula II, comprises at least two copies of the amino acid sequence corresponding to SEQ ID NO:88.
In some examples a CPP is a modified CPP comprising a moiety other than a canonical amino acid. Such modified CPPs may confer additional functionalities to a CPP, such as facilitating detection of CPP entry, localisation within cells, enhanced cell entry, and/or reduced CPP degradation in vitro or in vivo. Suitable moieties for a modified CPP include, but are not limited to any moiety selected from the group consisting of: a detectable label, a non-canonical amino acid, a reactive group, a fatty acid, cholesterol, a bioactive carbohydrate, a lipid, a nanoparticle, a small molecule drug, and a polynucleotide. In some examples the moiety in a modified CPP is a D-amino acid. In some examples the moiety in a modified CPP is a detectable label.
The term “detectable label” refers to any type of molecule which can be detected by optical, fluorescent, isotopic imaging or by mass spectroscopic techniques, or by performing simple enzymatic assays. Any detectable label known in the art may be used. In some examples the detectable label is selected from among a fluorophore, a fluorogenic substrate, a luminogenic substrate, and a biotin.
A fluorescent tag may be a fluorophore. For example, a fluorophore may be fluorescein isothiocyanate, fluorescein thiosemicarbazide, rhodamine, Texas Red, a CyDye such as Cy3, Cy5 and Cy5.5, a Alexa Fluor such as Alexa488, Alexa555, Alexa594 and Alexa647) or a near infrared fluorescent dye. A fluorophore may be a pH-sensitive fluorescent probe. For example, a pH-sensitive fluorescent probe may be naphthofluorescein, A fluorescent tag may be a fluorescent protein. For example, a fluorescent protein may be green fluorescent protein (GFP), enhanced green fluorescent protein (EGFP), AcGFP or TurboGFP, Emerald, Azami Green, ZsGreen, EBFP, Sapphire, T-Sapphire, ECFP, mCFP, Cerulean, CyPet, AmCyanl, Midori-Ishi Cyan, mTFPl (Teal), enhanced yellow fluorescent protein (EYFP), Topaz, Venus, mCitrine, YPet, PhiYFP, ZsYellow1, mBanana, Kusabira, ange, mOrange, dTomato, dTomato-Tandem, AsRed2, mRFP1, Jred, mCherry, HcRed1, mRaspberry, HcRed1, HcRed-Tandem, mPlum, AQ 143. A fluorescent tag may be a quantum dot. In some examples, where the detectable label is a fluorophore, the fluorophore is a pH-sensitive fluorescent probe. Suitable pH-sensitive fluorescent probes include, but are not limited to, naphthofluorescein, pHrodo™ Green (ThermoFisher), and pHrodo™ Red (ThermoFisher). Fluorescent tags may be detected using fluorescent microscopes such as epifluorescence or confocal microscopes, fluorescence scanners such as microarray readers, spectrofluorometers, microplate readers and/or flow cytometers.
In some examples the detectable label is a fluorogenic substrate. Suitable fluorogenic substrates include fluorogenic substrates of β-lactamase (e.g, CCF-2-AM, CCF4-AM, and any of those described in U.S. Pat. No. 7,427,680) and β-gal (e.g, HMRef-βGal described in Asanuma et al 2015, Nature Comm., 6:6463).
In some examples the detectable label is a luminogenic substrate. Suitable luminogenic substrates include, but are not limited to, D-Luciferin, L-Luciferin, Coelenterazine,
An epitope tag may be a poly-histidine tag such as a hexahistidine tag or a dodecahistidine, a FLAG tag, a Myc tag, a HA tag, a GST tag or a V5 tag. Epitope tags are routinely detected with commercially available antibodies. A person skilled in the art will be aware that an epitope tag may facilitate purification and/or detection. For example, a conjugate containing a hexahistidine tag may be purified using methods known in the art, such as, by contacting a sample comprising the protein with nickel-nitrilotriacetic acid (Ni-NTA) that specifically binds a hexahistidine tag immobilized on a solid or semi-solid support, washing the sample to remove unbound protein, and subsequently eluting the bound protein. Alternatively, or in addition a ligand or antibody that binds to an epitope tag may be used in an affinity purification method.
An isobaric tag may be a mass tag or an isobaric tag for relative absolute quantification (iTRAQ). A mass tag is a chemical label used for mass spectrometry based quantification of proteins and peptides. In such methods mass spectrometers recognise the mass difference between the labeled and unlabeled forms of a protein or peptide, and quantification is achieved by comparing their respective signal intensities as described, for example, in Bantscheff et al. 2007. Examples of mass tags include TMTzero, TMTduplex, TMTsixplex and TMT 10-plex. An isobaric tag for relative absolute quantification (iTRAQ) is a chemical tag used in quantitative proteomics by tandem mass spectrometry to determine the amount of proteins from different sources in a single experiment as described, for example, in Wiese et al. 2007.
In some examples the moiety is a non-canonical amino acid. Suitable non-canonical amino acids include, but are not limited to, ornithine, citrulline (Cit), diaminobutyric acid (Dab), diaminopropionic acid (Dap), 2-Aminoisobutyric acid α-Amino-n-butyric acid, Norvaline, Norleucine, Alloisoleucine, t-leucine, Ornithine, Allothreonine, β-Alanine, β-Amino-n-butyric acid, N-isopropyl glycine, Isoserine, and Sarcosine.
In other examples a moiety in a modified CPP is a reactive group. Suitable reactive groups include, but are not limited to, azide groups, amine-reactive groups, thiol-reactive groups, and carbonyl-reactive groups. In some examples the reactive groups are part of a chemical tag. Suitable chemical tags include, but are not limited to, a SNAP tag, a CLIP tag, a HaloTag or a TMP-tag. In one example, the chemical tag is a SNAP-tag or a CLIP-tag. SNAP and CLIP fusion proteins enable the specific, covalent attachment of virtually any molecule to a protein or peptide of interest as described, for example, in Correa 2015 (Methods Mol Biol, 1266:55-79). In another example, the chemical tag is a HaloTag. HaloTag involves a modular protein tagging system that allows different molecules to be covalently linked, either in solution, in living cells, or in chemically fixed cells. In another example, the chemical tag is a TMP-tag. TMP-tags are able to label intracellular, as opposed to cell-surface, proteins with high selectivity.
In some examples the moiety in a modified CPP is a fatty acid. Suitable fatty acids for modified peptides include, but are not limited to, palmitic acid, myristic acid, caprylic acid, lauric acid, n-octanoic acid, and n-decanoic acid.
In other examples the moiety in a modified CPP is cholesterol.
In some examples, where the moiety on a modified CPP is a polynucleotide, the polynucleotide is an RNAi, an antisense RNA, a single stranded DNA or RNA oligonucleotide, a double stranded DNA oligonucleotide, an mRNA, or a plasmid.
In some examples the moiety of a modified CPP is covalently linked to an amino acid in the CPP. In one example the covalently linked moiety is covalently linked to the N-terminal of the CPP amino acid sequence. In another example the covalently linked moiety is covalently linked to the C-terminal of the CPP amino acid sequence. In other examples, the covalently linked moiety is covalently linked through an amino acid residue side chain (e.g, at an internal lysine or cysteine residue). In some examples the moiety is non-covalently linked to the CPP, e.g, via non-covalent interactions between one or more charged amino acid residues in the CPP and one or more functional groups in the moiety that are of opposite charge to the one or more CPP amino acid residues.
In some examples the moiety in a modified CPP is a D-amino acid. In some examples, the amino acid sequence of a CPP is the retro-inverso sequence of the amino acid sequence of any of the foregoing CPPs.
Also described herein are CPP fusion proteins comprising the amino acid sequence of any CPP described herein, including a modified CPP and a heterologous amino acid sequence, Le, an amino acid sequence that is not naturally found as a sequence that is contiguous with the amino acid sequence of a CPP. In some examples, the heterologous amino acid sequence comprises the amino acid sequence of a protein selected from the group consisting of a SpyTag protein (SEQ ID NO:84), a Phylomer™ as defined herein, a reporter protein, a pro-apoptotic peptide, a targeting protein, a cytotoxic protein, a bioactive peptide, a dominant negative peptide, an enzyme, an antibody, and a SpyC peptide (SEQ ID NO:83). Examples of bioactive peptides include, but are not limited to, Glucagon (GCG), Glucose-dependent insulinotropic peptide (GIP, Cholecystokinin B (CCKB), Glucagon-like peptide 2 (GLP-2), as described in, e.g., Fosgerau et al (2015), Peptide therapeutics: current status and future directions, 20(1):122-128. Examples of suitable enzymes (e.g., therapeutic enzymes) include, but are not limited to, Acid Sphingomyelinase, Glucocerebrosidase, and I-L-Iduronidase.
In some examples the heterologous amino acid sequence in the CPP fusion protein is that of a SpyTag peptide (SEQ ID NO:84), which allows covalent isopeptide bond formation between the CPP fusion protein and a SpyCatcher protein as described in Zakeri et al 2012 (PNAS-USA, 109(12):E690-697). In other examples the CPP fusion protein comprises the amino acid sequence of a SpyTag peptide (SEQ ID NO:84), which is referred to herein as a CPP-SpyTag fusion protein.
In some examples a CPP-SpyTag fusion protein comprises the amino acid sequence of any one of SEQ ID NOs:42-60, 97, or 168-222.
In some examples the heterologous amino acid sequence comprises the amino acid sequence of a dominant negative peptide, e.g., the amino acid sequence of Omomyc (SEQ ID NO:99). In other examples the heterologous amino acid sequence comprises the amino acid sequence of a proapoptotic peptide. In some examples the amino acid sequence of the proapoptotic peptide comprises the amino acid sequence of SEQ ID NO:61 or SEQ ID NO:63. In other examples the heterologous amino acid sequence comprises the amino acid sequence of an enzyme. In some examples the enzyme is a therapeutic enzyme. In some examples the reporter protein comprises the amino acid sequence of β-lactamase (SEQ ID NO:112).
In some examples, the CPP fusion protein comprises a flexible linker linking the CPP and the heterologous amino acid sequence. Examples of flexible linkers include, but are not limited to, GGGGS (SEQ ID NO:262), GGGGSGGGGS (SEQ ID NO:263), GAS, GGG, GSG, GTG, and GGTAGSTGG (SEQ ID NO:264). Other examples of such flexible linkers are known in the art as described in, e.g., Chen et al (2013), Adv Drug Deliv Rev., 65(10):1357-1369.
Also described herein is a CPP conjugate comprising a CPP-SpyTag peptide fusion protein comprising the amino acid sequence of any Phylomer™-derived CPP disclosed herein and a SpyCatcher fusion protein comprising the amino acid sequence of SEQ ID NO:83 and a heterologous amino acid sequence, wherein the SpyCatcher fusion protein is covalently linked to the CPP fusion protein by an isopeptide bond to the SpyTag peptide. One of skill in the art will appreciate that such conjugates are readily generated by reacting a CPP fusion protein with a SpyCatcher fusion protein, whereby the SpyTag peptide and SpyCatcher peptide react with each other to form an amide bond as described in Zakeri, supra. Conveniently, such CPP conjugates allow the modular functionalization of a CPP with various peptides or proteins thereby avoiding the need to separate CPP fusion proteins with different functionalities (e.g, a CPP-β-lactamase fusion protein, a CPP-fluorescent protein fusion protein, etc.
In some examples the heterologous amino acid sequence in the above-mentioned CPP fusion proteins or conjugates is the amino acid sequence of a Phylomer™, a reporter protein, a pro-apoptotic peptide, an enzyme (e.g., Caspase-9), a targeting protein (e.g, a receptor affibody such as an EGFR affibody), a cytotoxic protein (e.g., Bouganin), a dominant-negative peptide (e.g, Omomyc, SEQ ID NO:99), an antibody, or a SpyC peptide (SEQ ID NO:83).
In some examples the heterologous amino acid sequence is the amino acid sequence of a Phylomer™.
In other examples the heterologous amino sequence is a reporter protein. Suitable reporter proteins include a fluorescent protein as described herein, a β-lactamase as described in Qureshi (2007), Biotechniques, 42(1):91-95, a haloalkane dehalogenase, or a luciferase. In some examples the reporter protein comprises the amino acid sequence of a β-lactamase.
In some examples the heterologous amino acid sequence is the amino acid sequence of a pro-apoptotic peptide. In some examples the amino acid sequence of the pro-apoptotic peptide corresponds to SEQ ID NO:61 or SEQ ID NO:63. In some examples a SpyCatcher-pro-apoptotic peptide fusion protein in the CPP conjugate comprises the amino acid sequence of SEQ ID NO:62.
In some examples the heterologous amino acid sequence is a targeting moiety. A targeting moiety may provide increased specificity to CPP conjugates by binding to a specific cell surface antigen (e.g, a receptor), which is then internalized into endosomes. The CPPs disclosed herein can provide the added advantage relative to conventional CPPs of increased escape from endosomes and enhanced cytosolic delivery of conjugate “cargoes.” Examples of targeting proteins include, but are not limited to, Affibodies, scFvs, single chain antibodies, and other selective binding proteins using alternative scaffolds (e.g, peptide aptamers). In some examples the targeting moiety is an EGFR affibody. In other examples the heterologous amino acid sequence is a cytotoxic protein (e.g, Bouganin or diphtheria toxin) that induces rapid cell death upon internalization and escape from endosomes.
In some examples the heterologous amino acid sequence is a dominant negative peptide. Dominant negative peptides generally act to interfere with one or more functions of a protein from which they are derived and/or with that of an interacting partner of the full length protein. Typically, they act by interfering with the interaction of a protein and one or more of its binding partners. In some examples the dominant negative transcription factor peptide is an anti-cancer peptide. Suitable anti-cancer peptides include, but are not limited to, Omomyc (SEQ ID NO:99), an Activating Transcription Factor 5 (ATF5) dominant negative peptide d/n-ATF5-S1 (SEQ ID NO:85) described in Massler et al (2016), Clin Cancer Res, 22(18):4698-4711, anti-Ras-p21 dominant negative peptides such as ras-p21 96-110 (PNC-2) (SEQ ID NO:86) and ras-p21 35-47 (SEQ ID NO:87) as described in Adler et al (2008), Cancer Chemother Pharmacol, 62(3):491-498. In other examples, the heterologous amino acid sequence is an enzyme. In some examples the enzyme is a genomic targeting protein (e.g, a CRISPR-associated protein 9/Cas9 genomic targeting protein or a Cpf1 genomic targeting protein). In other examples the enzyme is a caspase (e.g., Caspase-9).
Any protein or peptide of the present disclosure may be synthesized using a chemical method known to the skilled artisan. For example, synthetic proteins and peptides are prepared using known techniques of solid phase, liquid phase, or peptide condensation, or any combination thereof, and can include natural and/or unnatural amino acids.
Any protein of the present disclosure may be expressed by recombinant means. For example, the nucleic acid encoding the CPP may be placed in operable connection with a promoter or other regulatory sequence capable of regulating expression in cellular system or organism.
Typical promoters suitable for expression in bacterial cells include, for example, the lacz promoter, the Ipp promoter, temperature-sensitive μL or λR promoters, T7 promoter, T3 promoter, SP6 promoter or semi-artificial promoters such as the IPTG-inducible tac promoter or lacUV5 promoter. A number of other gene construct systems for expressing the nucleic acid fragment of the invention in bacterial cells are well-known in the art and are described, for example, in Ausubel et al. (1988), and Sambrook et al. (2001).
Numerous expression vectors for expression of recombinant polypeptides in bacterial cells have been described, and include, for example, PKC3, pKK173-3, pET28, the pCR vector suite (Invitrogen), pGEM-T Easy vectors (Promega), the pL expression vector suite (Invitrogen) or pBAD/thio—TOPO series of vectors containing an arabinose-inducible promoter (Invitrogen), amongst others.
Typical promoters suitable for expression in yeast cells such as, for example, a yeast cell selected from the group comprising Pichia pastoris, S. cerevisiae and S. pombe, include, but are not limited to, the ADH1 promoter, the GAL1 promoter, the GAL4 promoter, the CUP1 promoter, the PHO5 promoter, the nmt promoter, the RPR1 promoter, or the TEF1 promoter.
Expression vectors for expression in yeast cells are preferred and include, for example, the pACT vector (Clontech), the pDBleu-X vector, the pPIC vector suite (Invitrogen), the pGAPZ vector suite (Invitrogen), the pHYB vector (Invitrogen), the pYD 1 vector (Invitrogen), and the pNMT 1, pNMT41, pNMT81 TOPO vectors (Invitrogen), the pPC86-Y vector (Invitrogen), the pRH series of vectors (Invitrogen), pYESTrp series of vectors (Invitrogen).
Preferred vectors for expression in mammalian cells include, for example, the pcDNA vector suite (Invitrogen), the pTARGET series of vectors (Promega), and the pSV vector suite (Promega).
Suitable methods for transforming and transfecting host cells can be found in Sambrook et al. 2001 and other laboratory textbooks. In one example, nucleic acid may be introduced into prokaryotic cells using for example, electroporation or calcium-chloride mediated transformation. In another example, nucleic acid may be introduced into mammalian cells using, for example, microinjection, calcium phosphate or calcium chloride co-precipitation, DEAE-dextran mediated transfection, transfection mediated by liposomes such as by using Lipofectamine (Invitrogen) and/or cellfectin (Invitrogen), PEG mediated DNA uptake, electroporation, transduction by Adenoviuses, Herpesviruses, Togaviruses or Retroviruses and microparticle bombardment such as by using DNA-coated tungsten or gold particles. Alternatively, nucleic acid may be introduced into yeast cells using conventional techniques such as, for example, electroporation, and PEG mediated transformation.
Following production/expression/synthesis, any protein or peptide of the present disclosure can be purified using a method known in the art such as HPLC See e.g, Scopes (In: Protein purification: principles and practice, Third Edition, Springer Verlag, 1994).
The present disclosure provides a method of identifying a peptide capable of translocating a membrane of a cell comprising:
A CPP may be modified to facilitate detection. For example, a CPP may be linked to a detectable label, such as naphthofluorescein (CAS No. 61419-02-1; λex=594 nm, λem=663 nm). Naphthofluorescein is a pH sensitive fluorophore that ranges from non-fluorescent at pH≤5.5 to maximal fluorescence at pH≥9.0, with 50% fluorescence intensity at pH≈7.5. Such pH sensitive fluorophores are advantageous because they are non-fluorescent in the acidic endosomal or lysosomal environment but become fluorescent when released into the neutral cytosol. Therefore, pH sensitive fluorophores may be conjugated to a CPP to measure its ability to escape the endosome. For convenience, CPPs that can not only enter cells, but can also escape endosomal or lysosomal compartment can be referred to as “functional penetrating peptides” (FPPs).
Alternatively, the ability of a peptide to not only translocate a membrane, but also to escape an endosomal compartment can be assessed using a phenotypic endpoint that discriminates selectively identifies CPPs that are localized in the cytoplasm (FPPs) and not entrapped in an endosomal compartment. For example, the ability of a test CPP-pro-apoptotic peptide conjugate to be delivered to target cells can be assessed by measuring cell death of the target cells following contact with the test CPP-pro-apoptotic peptide conjugate versus the level of cell death following contact with the unconjugated pro-apoptotic peptide or CPP peptide separately. Alternatively, a CPP conjugated to a pH-sensitive fluorescent probe (e.g., naphthofluorescein) can be used to discriminate between CPP localization to acidic endosomal/vesicular compartments versus the neutral cytoplasm.
Also described herein is a modified cell comprising any of the CPPs, CPP fusion proteins, or CPP conjugates described herein. In some examples a modified cell is a prokaryotic cell. In other examples the modified cell is a eukaryotic cell. Suitable eukaryotic cells include yeast cells, and mammalian cells including, but not limited to human cells. In some examples modified mammalian cells are from a cell line. Suitable cell lines include, but are not limited to, CHO-K1, HEK-293, COS7, HeLa, N2a, and NIH 3T3.
In some examples a modified cell expresses one or more genetically encoded CPPs or CPP fusion proteins. In other examples a modified cell is a primary mammalian cell.
In other examples a modified cell does not comprise exogenous nucleic acids encoding a CPP or CPP fusion protein, but is modified by protein transduction of a CPP or CPP fusion protein.
Preferably the modified cells are eukaryotic cells. More preferably the eukaryotic cells are mammalian cells. Most preferably the mammalian cells are human cells. In some examples the human cells are human stem cells. Such human stem cells include, but are not limited to, embryonic stem cells, induced pluripotent stem cells, and mesenchymal stem cells. In further examples human cells include, but are not limited to, cardiomyocytes, neurons, hepatocytes, and pancreatic islet cells. In other examples, the mammalian cells are cancer cells (e.g., human cancer cells).
The present disclosure also provides any one of the CPPs, CPP fusion proteins, CPP conjugates, or modified cells for use as a medicament or diagnostic agent. The present disclosure also provides any one of the CPPs, CPP fusion proteins, CPP conjugates, or modified cells for use in the manufacture of a medicament or diagnostic agent.
The present disclosure also provides a method for delivering any of the CPPs, CPP fusion proteins, or CPP conjugates disclosed herein to a cell by contacting the cell with any of these. In some examples the contacting is performed ex vivo, e.g., in cultured eukaryotic cells. In other examples the contacting is performed in vivo, e.g., in a human subject.
The invention will now be further described with reference to the following, non-limiting examples.
We previously identified a series of Phylomer™ sequences in a genetic screen designed to enrich for peptides not only able to penetrate eukaryotic cells, but also able to escape the endosomal and lysosomal compartments following uptake into cells. Such peptides are referred to here as “functional penetrating peptides” (FPPs) to distinguish them from CPPs that only penetrate the cell membrane but become entrapped in the endosomal or lysosomal compartments. This screen resulted in the identification of various Phylomer™ sequences, including a series of Sindbis capsid-derived peptides (corresponding to SEQ ID Nos:13-41 shown in
CPP sequences, (derived from parental sequences corresponding to SEQ ID NOs:13-41, and encompassing N-terminal truncations, C-terminal truncations, truncations, deletions, point and contiguous sequence mutations and all variations thereof), were synthesized by Pepscan (Netherlands) and Mimotopes (Australia) as fusion proteins N-terminal to the SpyTag sequence (SEQ ID NOs:42-60). The CPP sequences used in the fusion proteins are shown in
pET28a+ SpyCatcher-PAP (SpyC-PAP; SEQ ID NO:62) was codon optimized for E. coli expression and synthesized (DNA 2.0, Menlo Park, Calif., USA). The synthesised cassette is cloned into the NcoI/XhoI of the pET28a+ expression vector (Novagen). The cassette includes a hexahistidine tag and prescission protease cleavage site to aid purification. This cassette comprises the SpyCatcher sequence (SEQ ID NO:83) and the 14 amino acid PAP sequence (SEQ ID NO:61).
DNA sequences were synthesized and cloned (ATUM) into NcoI and XhoI sites of pET28a+ vector (Merck Millipore). Recombinant proteins were expressed as His6-N-terminally tagged fusion proteins in E. coli strain BL21 (DE3) Gold (Agilent Technologies). Proteins were purified using IMAC as previously described (Milech et al 2015, Sci Rep 5, 18329) with an additional purification step performed for some proteins after IMAC using Ion Exchange Chromatography (IEX). Proteins with an isoelectric point (pI) ranging from 8 to 10 were desalted into binding buffer containing 20 mM Sodium Phosphate, pH 6.8. Samples were loaded on a HiTrap SP HP 5 mL column (GE Healthcare), and eluted with a 0-1M. NaCl gradient. All the other proteins were desalted into 20 mM Tris, pH 8.0 binding buffer and purified through a HiTrap Q HP 5 mL column (GE Healthcare). Proteins were eluted using a 0-1M NaCl gradient. Final proteins were desalted into PBS pH 7.4, and purity was confirmed by analysis on 4-16% SDS-PAGE stained with Gel Code Blue Reagent. Recombinant Omomyc proteins were expressed and purified similarly by the UQ Protein Expression Facility (University of Queensland, Australia).
Recombinant His_SpyC_BLA (SEQ ID NO:90) and His_SpyC_BLA_FPP1.1 (SEQ ID NO:91) proteins were made as previously described (Milech, supra) with the following modifications: Pellets from 100 ml cultures grown at 28° C. for 18 h were purified by the IMAC gravity flow protocol with 1 ml of Ni Sepharose High Performance slurry. To avoid precipitation due to the high protein yield, the eluted proteins were diluted 1:4 in a buffer containing 20 mM phosphate, 500 mM NaCl and 20 mM imidazole, pH 8.0 and dialysed slowly (SnakeSkin Pleated Dialysis Tubing, 7,000 MWCO; Thermo Scientific) against 50 mM Tris pH 7.5, 200 mM NaCl buffer overnight at 4° C. The protein solutions were sterile-filtered (0.22 μm) and concentrated (Amicon Ultra-15, MWCO 10K; Merck Millipore).
SpyC-free Omomyc recombinant proteins were expressed with an N-terminal Thioredoxin (Trx) solubility tag, containing an His6_HRV3C (Human Rhinovirus 3C protease) cleavage sequence positioned at the C-terminus of Trx. After IMAC purification, proteins were desalted into IEX buffer, followed by tag removal using HRV3C enzymatic digestion overnight at 4° C. with agitation. Digested samples were further purified using IEXC, desalted into PBS pH 7.4, and analyzed as described above. SpyC_PAS protein, where SpyC is expressed as a recombinant fusion protein with PAS (PAS sequence described in Schlapsky et al. 2013, Protein Engineering, Design & Selection, 26(8):489-501) was provided by Professor Arne Skerra, Technical University of Munich, Munich, Germany.
With the exception of SpyC PAS proteins, conjugations were set up at a SpyCatcher:SpyTag ratio of 1:1.25, with a 40 μM final concentration for the SpyCatcher moiety. SpyC proteins and SpyTag peptides were incubated for 2 h at 22° C. with gentle mixing, and then left at 4° C. overnight. Conjugation efficiencies were analyzed on 4-16% SDS-PAGE gels stained with Gel Code Blue Reagent (Thermo Fisher Scientific). SpyC_PAS proteins were conjugated with SpyTag peptides at ratio 1:1.1, mixed and incubated at room temperature for 30 mins before being stored overnight at 4° C.
All cell lines were maintained in a humidified incubator at 37° C. with 5% CO2. HEK-293 and A431 cells were cultured in DMEM supplemented with 10% FCS, 2 mM L-glutamine, 100 U/ml penicillin, and 100 μg/ml streptomycin. CHO-K1, T47D and AMO-1 cells were cultured in RPMI 1640 supplemented with 10% FCS (heat-inactivated), 2 mM L-glutamine or 2 mM Glutamax (LifeTech), 100 U/ml penicillin, and 100 μg/ml streptomycin. HL-60 cells were cultured in RPMI 1640 supplemented with 20% FCS (heat-inactivated), 100 U/ml penicillin, 100 μg/ml streptomycin, 2 mM L-glutamine. Stable cell lines HEK-293 EGFR and HEK-293_BirA were cultured in HEK-293 complete medium additionally supplemented with 300 μg/ml and 500 μg/ml Geneticin, respectively. CHO-K1 EGFR stable cell line was made using FlpIn™ technology (ThermoFisher Scientific) and cultured in F-12K medium supplemented with 10% FCS (heat-inactivated), 100 U/ml penicillin, 100 μg/ml streptomycin, 2 mM L-glutamine and 800 μg/ml Hygromycin B. Stable cell line A431_BirA (made by lentiviral infection, Genscript) was cultured in A431 complete medium additionally supplemented with 1 μg/ml Puromycin.
HEK-293_BirA cells were electro-transfected with plasmid DNA (pcDNA4/TO_β-actin, pcDNA4/TO_β-actin_AviTag) using the Neon transfection system (LifeTech). Briefly 3×105 cells/100 μL were prepared according to manufacturer's instructions (Neon, LifeTech) and transfected with 0.5 μg DNA with the following pulse conditions: 1100 V, 20 ms, 2 pulses. Following transfection cells were transferred to 8 well glass chamber slides (Nalgene Nunc International) pre-coated with gelatin and were maintained in media+/−5 μM biotin for 18 h. Media was changed to biotin-free media for 2 h prior to processing to reduce non-specific background. At 20 h post transfection cells were fixed (4% formaldehyde/PBS) and permeabilized (0.4% Saponin/PBS) for 1 h at 4° C. Successful biotinylation of the AviTag was detected by incubation with Streptavidin-FITC (1:100 in the permabilization buffer) for 60 min. For wells that were counterstained a second incubation with β-actin red (LifeTech) was performed following manufacturer's instructions. Wells were then washed and mounted with Vectashield antifade mounting media with DAPI (Vector Laboratories, USA). Cell images were captured at 100× magnification using an Olympus BX53 with DP72 camera. Image overlays were compiled using the ImageJ software.
Peptide/protein conjugates were prepared in parallel, with SpyC moieties at 40 μM concentration and the SpyT peptides at 50 μM concentration. Conjugations were incubated at room temperature for 1 h and then buffers and BirA ligase (2.9 ng/μl final concentration) were spiked into one tube for in vitro biotinylation. All conjugations were then incubated overnight at 4° C. in the cold room with gentle rotation.
HEK-293_BirA cells were seeded in 6-well plates (8×105 cells/well) and incubated overnight. The following day, cells were treated with either FPP1.1_Avi_SpyT (SEQ ID NO:111)/SpyC_Omomyc (SEQ ID NO:110) conjugate or in vitro biotinylated conjugate for 30 mins or 60 mins. Treated samples were then lysed with M-PER mammalian protein extraction reagent (Thermo Fisher Scientific), supplemented with 1× cOmplete protease inhibitors cocktail (Sigma) and 1 mM sodium pyrophosphate (BirA inhibitor, Sigma). Supernatants were clarified by centrifugation (10,000 rpm, 20 s). Clarified lysates (˜800 μl each sample) were then incubated with 40 μl of 1:1 slurry of washed Dynabeads™ M-280 streptavidin magnetic beads (Thermo Fisher Scientific) in PBS overnight with gentle rotation at 4° C. according to manufacturer's instructions, to bind any biotinylated proteins in the samples. The following day, bead samples were washed and proteins denatured in Laemmli buffer according to manufacturer's instructions.
Proteins were separated on Bis-Tris gels (Thermo Fisher Scientific) by SDS-PAGE and transferred to PVDF membranes by iBLOT (Thermo Fisher Scientific). Immunoblots were processed as previously described, (Milech, supra) using primary and secondary antibodies according to manufacturer's instructions.
For detection of V5-tagged protein conjugates and peptides, immunoblots were probed with anti-V5 primary antibody (Thermo Fisher Scientific, clone E10) and secondary anti-Mouse-HRP antibody (Amersham) before visualizing using Clarity ECL reagent (BioRad) and imaged on a ChemiDoc Gel Imaging System (BioRad).
Cells in were seeded at 2000-6000 cells/well, depending on cell line, in 96-well plates (PAP assays: CHO-K1, 3000 cells/well; peptide cytotoxicity assays: CHO-K1, 5000 cells/well; Bouganin assay: CHO-K1 and CHO-K1 EGFR, 2500 cells/well; DPMIα assays: T47D, 5000 cells/well; Omomyc assays: all cell lines, 5000 cells/well). In brief, adherent cells were allowed to attach for 24 h prior to addition of treatments whereas suspension cell lines were treated immediately following seeding. Following 2-48 h incubations with treatments, cell viability was measure by a variety of methods. Membrane integrity was assessed by the release of LDH into the media via the CytoTox-ONE reagent (Promega). Metabolic activity was measured either by resazurin reduction potential using PrestoBlue (LifeTech) or ATP activity using CellTitre-Glo (Promega). All assays followed manufacturer's instructions. IC50 values were calculated using Prism (version 7.0a, GraphPad).
SpyC-PAP/CPP-SpyT complex IC50s were ranked according to potency to determine impact of changes to primary CPP sequence. Sequence variations positively impacting on potency are retained for further optimization, whereas sequence variations deleterious to potency are excluded, thus establishing sequence activity relationships for the CPP peptide. SpyC_BLA/CPP-SpyT complex median cell fluorescence at 4 μM concentration was ranked according to intensity to determine impact of changes to primary CPP sequence. Sequence variations positively impacting on intensity were retained for further optimization, whereas sequence variations deleterious to intensity were excluded, thus establishing sequence activity relationships for the CPP peptide.
CHO-K1 cells (seeded at 1×105 cells/well in 24-well plates) were incubated with purified SpyC_BLA (SEQ ID NO:90) and SpyC_BLA_FPP1.1 (SEQ ID NO:91) proteins at 3° C./5% CO2 for 2 hours. Cells were washed, detached by 5 mins incubation with trypsin, washed, loaded with the β-lactamase substrate CCF2-AM and analysed by Flow Cytometry; intracellular β-lactamase activity caused an emission shift from 510 nm to 450 nm. The percentages of β-lactamase positive cells for each sample were graphed against the concentration of protein added to the cells.
Exon skipping assays and RT-PCR detection were performed according to published protocols (Morgan et al 1994, Developmental Biology, 162, 486-498) treating murine H-2Kb-tsA58 myoblast cells with 25 nM-1 μM of FPP1.1_M23D(+7-18) PMO or M23D(+7-18) PMO (Mann et al 2002, Gene Med, 4, 644-654) alone.
Animal experiments and the detection of dystrophin expression by immunofluorescence microscopy were carried out according to published protocols (Fletcher et al 2007, Mol. Ther., 15, 1587-1592). Mice were treated with five intra-peritoneal injections, at 4 nmoles per dose, over two weeks of FPP1.1_M23D(+7-18) PMO or M23D(+7-18) PMO alone. Each treatment group consisted of two animals. Two weeks after cessation of treatment, tissue samples were taken for detection of dystrophin by immunofluorescence.
C57BL/10ScSnArcmdx mice carry a nonsense mutation in exon 23 of the dystrophin gene. Control wild type mice are C57BL10/ScSnArc. All mice were supplied by the Animal Resources Centre (Murdoch, Western Australia) and housed according to National Health and Medical Research Council (Australia) guidelines. All animal work was approved and carried out under Murdoch University Animal ethics permit number R2625/13.
Flow cytometry and analysis of carboxynaphthofluoroscein (NF)-labeled peptides was performed according to published protocols (Qian et al 2015, Chem. Commun. (Camb), 51, 2162-2165; and Qian et al 2016, Biochemistry, 55, 2601-2612). Seeding density for the HEK-293_BirA cells was 3.6×105 cells/well in 12-well plates. Peptides and cells were incubated in treatment media (phenol-red free high glucose DMEM, 1% FCS, 10 mM HEPES and 2 mM L-glutamine) unless otherwise specified.
For endocytotic inhibitor assays, HEK-293_BirA cells were pre-treated with endocytotic inhibitors (100 μM dimethylamiloride (DMA, Abcam) or 20 μM Dyngo4a (Abcam) or vehicle control (1% DMSO in treatment media) for 30 min at 37° C. The washed cells were treated with 5 μM recombinant FPP1.1_SpyC protein conjugated to NF-LL1-SpyT (SEQ ID NO:94). For heparinase experiments, HEK-293_BirA cells were pre-incubated with 3 milli-Inhibitory Units (mIU) of heparinase III (Sigma) in DMEM containing 1% FCS for 1 h at 37° C. Then washed cells were treated with 5 μM FPP1.1_SpyC (SEQ ID NO:100) or SpyC (non-CPP control; SEQ ID NO:83) conjugated to NF-LL1-SpyT in serum-free media and incubated for 30 minutes at 37° C. For HSPG experiments, 5 μM FPP1.1_SpyC or SpyC were conjugated to NF-LL1-SpyT, then pre-incubated with 0, 5 or 10 μg/ml HSPG (Sigma) in serum free medium for 25 mins at 37° C. Then peptide-HSPG mixtures were added to HEK-293_BirA cells and further incubated for 30 minutes at 37° C. In all assays, peptide/protein conjugate uptake was measured by flow cytometry to detect the NF fluorescence signal.
For the first readout of functional activity we chose the proapoptotic peptide PAP (SEQ ID NO:61; Ellerby et al 1999, Nat Med, 5, 1032-1038) as a functional cargo and expressed it recombinantly, fused to SpyCatcher (SEQ ID NO:83) (abbreviated as “SpyC_PAP” or “SpyC-PAP”; SEQ ID NO:62) to enable subsequent conjugation with synthetic CPP-SpyTag fusion proteins. Mammalian cells were incubated with SpyC_PAP-CPP protein conjugates, which induce apoptosis if successfully delivered into cells. SpyC-PAP conjugated with FPP1 (SEQ ID NO:39) caused significant cell death compared to TAT (SEQ ID NO:93) or Penetratin (SEQ ID NO:92)-delivered SpyC_PAP, with the SpyC only control showing no effect (
We designed a range of amino acid substitution variants and N- and C-terminal truncations to reduce the size and charge of the peptide, as well as sequence extensions based on larger members of the identified Sindbis Phylomer™ family and assessed the potency of these variants and the effect of the different truncations and sequence modifications. Overall, N-terminal truncations of parental FPP1 by up to 11 amino acids marginally improved potency, whereas an N-terminal reduction of 13 amino acids (FPP1-SAR5) resulted in a 3-fold loss of activity. In contrast, potency was unaffected for the N-terminal 7 amino acid truncated variant (FPP1-P_T). C-terminal truncations of FPP1 were deleterious to CPP potency, with even a single amino acid truncation (FPP1-SAR12) resulting in approximately 2.2-fold reduction. Mutation of Proline to Threonine (P to T) for full length FPP1 improved activity by 1.7-fold (FPP1-SAR16), whereas activity was unaffected for the N-terminal 7 amino acid truncated variant (FPP1-P_T). Mutation of Lysine to Arginine (K to R, FPP1-SAR17) resulted in a 1.5-fold reduction in potency. Taken altogether, these data suggest that the C-terminal arginine residue is critical for full activity, C-terminal truncation is deleterious, and that Proline is not essential for full potency but multiple Lysine residues are. The data also highlights that the C-terminal 27 residues (FPP1.1; SEQ ID NO:81) comprised the minimum domain sufficient for potent activity (
When delivering therapeutics into a cell, it is critical that the delivery molecule itself is not cytotoxic. To assess innate cytotoxicity we tested the effects of FPPs alone on cell viability at 24 h (
The method described here outlines the measurement of peptide cell-penetrating and endosomal escape ability by coupling it to an enzyme and measuring cytoplasmic enzyme activity, where increased enzyme activity is indicative of increased cell penetration and delivery of enzyme.
β-Lactamase is a bacterial enzyme that catalyses the opening of β-lactam rings. It does not occur naturally in eukaryotic cells. β-Lactamase is also not intrinsically cell-penetrating and requires the addition of a cell-internalising agent to access the eukaryotic cytoplasm. To address this need, β-Lactamase was expressed as C-terminal SpyC fusion, making SpyC-BLA (SEQ ID NO:90). Cell-penetrating peptides were then added by conjugating to various synthetic CPP-SpyT fusion peptides (SEQ ID NOs:42-60 and 102), and the SpyC-BLA was independently reacted with each CPP-SpyT peptide to be tested to form a CPP conjugate as schematically illustrated in
CCF2-AM (Thermofisher Scientific, Australia) is a Fluorescence Resonance Energy Transfer (FRET) substrate that is enzymatically cleaved by β-Lactamase. CCF2-AM is an esterified form of 7-hydroxycoumarin linked to fluorescein by a cephalosporin core. Esterification facilitates cell entry of the molecule. Once inside, the molecule is transformed into its anionic form by endogenous cytoplasmic esterases which trap the molecule inside the cell. When excited at 409 nm, uncleaved CCF2-AM emits a FRET signal at 520 nm (green). In the presence of β-Lactamase, the fluorescein moiety of CCF2 is enzymatically cleaved, resulting in the emission wavelength shifting to 447 nm (blue). β-Lactamase activity is quantified by measuring the ratio of blue fluorescence to green fluorescence.
The cell-penetrating and endosomal escape ability of FPP1.1 (SEQ ID NO:39) and sequence variant SpyC-BLA/CCP-SpyT conjugates was assessed by flow cytometry to determine cytosolic CCF2-AM cleavage by internalized β-Lactamase. The ratio of blue to green fluorescence was assessed to determine the cell-penetrating and endosomal escape ability of the various CPP sequences.
Various SpyC-BLA-FPP variant conjugates including CPPs corresponding to the parental sequence “FPP1” (SEQ ID NO:39), a derivative “FPP1.1” (SEQ ID NO:81), and other variants (SEQ ID NOs:64-80, and 82) all shown in
We evaluated the versatility of several of the identified Phylomer™-based FPPs in a variety of cell types using bioassays where readout is dependent on delivery of a cargo into the cytoplasm. In the previous experiment, we demonstrated that the FPPs could deliver a functional protein cargo (i.e., active β-lactamase). Thus, we strategically chose a range of additional cargo types from biologic or therapeutically-relevant categories such as small peptides (DPMIα, Liu et al 2010, Proc. Natl. Acad. Sci. USA, 107, 14321-14326) and oligonucleotides (M23D(+7-18), a phosphorodiamidate morpholino oligomer (PMO), Mann et al 2002, Gene Med, 4, 644-654). Overall, Phylomer™ FPPs were successful in delivering all three cargo types into cells at lower doses than conventional CPPs.
DPMIα is a small peptide (SEQ ID NO:105), which when conjugated to cationic CPPs can internalize into cells, bind to MDM2 (acting as a dominant negative peptide) and lift p53 suppression causing indiscriminate cytotoxicity (Liu, supra). FPP_DPMIα fusions were toxic to T47D cells, indicating they had been successfully delivered into the cell (
In another delivery assay a modified CPP was generated by linking FPP1.1 (SEQ ID NO:81) to a phosphorodiamidate-morpholino oligomer M23D(+7-18), which targets exon 23 of the Dystrophin gene that is mutated in in certain cases of Duchenne muscular dystrophy (DMD). Intracellular delivery of M23D(+7-18) induces exon skipping to produce a shorter, yet functional dystrophin protein. FPP1.1 successfully delivered M23D(+7-18) into murine H-2Kb-tsA58 myoblasts in vitro, with exon skipping detectable at the RNA level when cells were treated with as little as 50 nM of FPP1.1_M23D(+7-18) cargo (
In vivo delivery was assessed by treating C57BL/10ScSnmdx mice with five intra-peritoneal injections over two weeks at 4 nmoles per dose, of either FPP1.1_M23D(+7-18) or M23D(+7-18) oligonucleotide alone. Two weeks after end of treatment, tissue cryosections from mice treated with FPP1.1_M23D(+7-18) showed an increase in dystrophin expression and improved muscle architecture in the diaphragm compared to untreated and M23D(+7-18) only-treated mice. Moderate improvement was also seen in the tibialis anterior (
The potent cargo activities in diverse cell lines suggest that intracellular delivery by FPP1.1 is not cell-specific. To demonstrate the compatibility of a Phylomer™ FPP with cell targeting approaches, we generated a fusion protein (SEQ ID NO:109) linking AffibodyEGFR-1907, a well-characterized targeting domain (Friedman et al 2008, J Mol Biol, 376, 1388-1402) that binds hEGFR, a potent cytotoxic enzyme Bouganin (Hartog et al 2002, Eur J Biochem, 269, 1772-1779; Bolognesi et al 2000, Br J Haematol, 110, 351-361) and assessed its delivery, when conjugated with Phylomer™ FPPs in matched CHO-K1 cell lines (±hEGFR receptor). Importantly, the Phylomer™ FPP-delivered toxin was highly potent only in hEGFR-positive cells, showing that it retained Affibody-conferred cell-specificity (
We also performed preliminary assessment on the versatility of our FPPs in the context of drug development by assessing the effect of a standard half-life extension on the potency of a Phylomer™ FPP_Cargo. We expressed SpyC as a recombinant fusion with PAS protein, a large hydrophobic protein often used for half-life extension of biologics (Schlapschy et al 2013, Protein Eng Des Sel, 26, 489-501). PAS_SpyC was conjugated to SpyTag-containing FPP1.1 PAP fusion peptide (SEQ ID NO:97) using three proteolytically cleavable linker variants and then applied to T47D cells. The cleavable linker motifs used were Cathepsin B FKFL cleavage motif (BF) (Chu et al 2012 J. Contr. Rel., 157:445-454), Cathepsin B Valine-Citrulline cleavage motif (Ba) (Liang et al 2012, J. Contr. Rel., 160:618-629) and Furin RKKR cleavage motif (Fur) (Thomas 2002, Nat. Rev. Mol. Cell Biol. 3:753-766). While there was some decrease in potency from the addition of the large PAS molecule, FPP-dependent PAP-induced cytotoxicity was still detected for all PAS conjugates (
To assess potential mechanism and kinetics of uptake and endosomal release, we labelled FPP1.1 (SEQ ID NO:81) with the pH-sensitive fluorescent probe carboxynaphthofluorescein (NF), (Qian, supra) which is non-fluorescent at low pH values observed in the endosomes (pH<6).
Endosomal release and uptake occurred rapidly and could reliably be detected as early as 10 mins post addition of FPP1.1 modified by linkage to NF (NF-FPP1.1), with fluorescence levels plateauing at around 60 mins (
Finally, we assessed the ability of FPP1.1 to deliver a therapeutically-relevant cargo that directly acts on an intracellular target deemed to be “undruggable” by traditional biologic-therapeutics approaches. MYC is a prototypic example of an “undruggable target” whose deregulation is a hallmark of cancer due to its role as a master regulator of stem cell state, embryogenesis, tissue homeostasis, and aging. We used Omomyc (Soucek et al 1998, Oncogene, 17, 2463-2472; Soucek et al 2002, Cancer Res, 62, 3507-3510) a small structured dominant negative protein with known activity against cMYC, as our therapeutic cargo and recombinantly-expressed it as a direct fusion with FPP1.1.
We first validated intracellular delivery of recombinant SpyC_Omomyc protein (SEQ ID NO:110) conjugated to an FPP1.1_Avitag_SpyTag fusion peptide (SEQ ID NO:111) in HEK-293_BirA, biotin ligase-expressing cells (
When Myc-dependent blood cancer cell lines, AMO-1 and HL-60, and the breast cancer cell line, T47D, were treated with recombinant FPP1_Omomyc, we observed a dose-dependent decrease in cell viability (
In the above examples, we have demonstrated, identified and validated several Phylomer™-based CPPs as bona fide FPPs. FPP1 and several variants (e.g, FPP1.1) showed greater delivery activity than conventional CPPs, particularly at lower concentrations where uptake is less likely to be related to the phenomenon of non-specific flooding entry into cells (Verdurmen et al 2010, J of Controlled Release, 147, 171-179) When evaluating CPPs as therapeutic delivery agents the sequence needs to be versatile enough to accommodate various typical maturation modifications that may be required. Using clustering analysis of FPP1 to guide basic affinity maturation, we engineered peptide FPP1.1, which retains the strong potency of the parental sequence yet is amenable to synthesis. FPP1.1 is also potent as a dimer and as a retro-inverso sequence, a strategy often used to render peptides less susceptible to proteolytic cleavage (Fischer et al 2003, Curr Protein Pept. Sci., 4, 339-356). Finally, FPP1.1 was compatible with basic half-life extension and targeting technologies often employed to overcome the lack of specificity and quick clearance typically seen with traditional CPPs (Sarko et al 2010, Mol. Pharmaceutics, 7, 2224-2231) showing EGFR-dependent specificity when combined with a targeting Affibody and retaining a degree of potency after PASylation. Initial kinetics assessment of FPP1.1 established that uptake is rapid, is energy dependent and sensitive to inhibitors of endocytosis. This suggests that uptake occurs through clathrin-mediated endocytosis and is enhanced by heparin sulfate binding, consistent with its viral origin (Bomsel et al 2003, Nat Rev Mol Cell Biol, 4, 57-68) These mechanisms have been reported to function in a “piggyback” manner (Jones et al 2012, Journal of controlled release: official journal of the Controlled Release Society, 161, 582-591; Qian et al 2014, Biochemistry 53, 4034-4046) where the peptide is potentially internalized while bound to HSPG, facilitating endocytosis.
Here we deliberately chose a cargo-focused approach to validate our Phylomer FPPs and showed successful delivery of multiple larger and biologically relevant cargoes, evidence of which is rare in the CPP field (reviewed in Kauffman et al 2015, Trends Biochem Sci 40, 749-764). We recently reported a functional cytoplasmic delivery assay which showed striking differences between the potency of ten well-characterized canonical CPP (Milech, supra). Only TAT, R9 and Penetratin successfully delivered the protein cargo into the cytoplasm of cells. Of these, TAT-mediated delivery was the most successful at concentrations lower than 10 μM. In contrast, FPP1 retains strong potency and shows great versatility in delivering a variety of biological cargoes at concentrations down to single-digit micromolar to sub-micromolar-concentrations. This is highly desirable in the therapeutic context, as it avoids the need for dosing at high concentrations, which can induce translocation, toxicity, membrane disruption and increase the costs of manufacturing. As proof-of-concept for therapeutic application, we used a Phylomer™ FPP to deliver Omomyc, a well characterized protein inhibitor of cMYC with poor cellular penetration. Omomyc alone showed poor potency, causing only a slight reduction in cell viability at doses above 10 μM in one cell line. In sharp contrast, FPP1.1_Omomyc showed IC50s in the low single digit micromolar range (1.3-1.9 μM).
To our knowledge, these potencies are unprecedented for direct targeting of cMYC with a small molecule or protein-based biological therapy, and hence demonstrates the potential utility of Phylomer FPP-mediated delivery of a biologic therapeutic. We also have shown potent delivery of recombinant β-lactamase, detectable at sub-micromolar concentrations, as well as delivery of recombinant PAP and DPMIα peptide with greater potency compared to the conventional CPPs assessed alongside. Finally, when mice were treated with FPP-delivered morpholino oligos we observed a partial reversion of cell phenotype to normal morphology, providing strong evidence for the power of Phylomer FPPs to deliver high-potency therapeutics, including polynucleotides, in vivo.
In summary, we have identified a subset of Phylomer™-based CPPs that show functional cell penetration, endosomal escape and cytoplasmic uptake, which we refer to as “FPPs.” We have demonstrated that these FPPs are potent, versatile, and compatible with engineering solutions to further improve endosomal escape (Shin et al 2017, Nat Commun, 8, 15090. In addition, these FPPs are amenable to synthesis, and recombinant production where the FPP sequence encodes only naturally occurring (canonical) amino acids and thus compatible with cost-efficient scaled manufacturing. Further, these FPPs are generally not cytotoxic and importantly, are able to deliver into cells a wide range of biologic cargoes ranging from large proteins to small peptides and oligonucleotides, both in vitro and in vivo. We propose that the innate delivery efficiency of Phylomer™ FPPs addresses a key challenge for intracellular-targeted biologics by enabling more biologic drug payload to reach diverse disease targets within the cell.
X
1-X2-X3-X4-X5 (Formula I), wherein:
X
1 is an optional amino acid sequence selected from the group consisting of:
X
2 is any combination of 3 to 8 lysine and/or arginine residues;
X
3 is an amino acid sequence selected from the group consisting of:
X
4 is any combination of 3 to 8 arginine and/or lysine residues; and
X
5 is an amino acid sequence selected from the group consisting of QPPKPKR
It will be appreciated by persons skilled in the art that numerous variations and/or modifications may be made to the above-described examples, without departing from the broad general scope of the present disclosure. The present examples are, therefore, to be considered in all respects as illustrative and not restrictive.
The present application claims priority from AU 2017902976 filed 28 Jul. 2017, the entire contents of which are incorporated herein by reference.
All references cited herein, including patents, patent applications, papers, text books, and the like, and the references cited therein, to the extent that they are not already, are hereby incorporated herein by reference in their entirety.
Any discussion of documents, acts, materials, devices, articles or the like which has been included in the present specification is solely for the purpose of providing a context for the present invention. It is not to be taken as an admission that any or all of these matters form part of the prior art base or were common general knowledge in the field relevant to the present invention as it existed before the priority date of each claim of this application.
| Number | Date | Country | Kind |
|---|---|---|---|
| 2017902976 | Jul 2017 | AU | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/AU2018/050781 | 7/27/2018 | WO | 00 |
