Patent Grant
11459358
This application is a U.S. National Stage Application of International Patent Application No. PCT/EP2017/079349, filed Nov. 15, 2017, which claims the benefit of priority of European Patent Application No. 16199033.8, filed Nov. 16, 2016, the disclosure of each of which is incorporated by reference for all purposes herein in its entirety.
A Sequence Listing in Computer Readable Form (“CRF”), which is an ASCII text file of 206,884 bytes in size entitled 11808-409-999_Substitute_SEQ_LISTING.TXT, created on Jan. 17, 2020, is incorporated by reference herein in its entirety.
The present invention is in the field of targeting and provides substances that home to, bind to, and are taken up by various organs or tissues.
Most therapeutic compounds are delivered to the target organ or tissue through the circulation. However, in most cases the drug or other treatment will not only target the diseased organ or tissues, but will also be taken up by other organs and tissues in the body. This can result in undesirable side effects due to, for example, generalized toxic effects throughout the patient's body. Thus, it would be desirable to selectively target specific organs or tissues. In addition, linking a therapeutic compound to a targeting moiety can improve the uptake properties of the therapeutic compound into the targeted tissue or cells, resulting in a more effective substance. Similarly, linking a diagnostic compound to a targeting moiety can improve the uptake properties of the diagnostic compound into the targeted tissue or cells, resulting in a more effective substance. Therefore, linking to targeting moieties yields substances that are more effective and less toxic than the parental substances, see Curnis et al., 2000, Nature Biotechnol. 18, 1185-1190. This can be applied to a wide range of substances, such as peptides, proteins, cytostatic agents, antibiotic agents, antibodies, and antiviral agents.
In the case of muscle diseases such as Duchenne muscular dystrophy (DMD), Becker Muscular Dystrophy (BMD), myotonic dystrophy (DM) or spinal muscular atrophy (SMA), muscle-specific peptides can be conjugated to, or formulated with, for example, an antisense oligonucleotide (AON) besides other nucleic acid-based therapeutics such as single- or double stranded small interfering RNA (siRNA), synthetic mRNA, or short hairpin RNA (shRNA). Such oligonucleotides have high potency to be applied as new classes of medicines for treatment of specific diseases by modulating undesired gene expression. In the field of DMD therapy antisense-induced exon skipping is gaining attention as a promising tool for correction of the translational reading frame of the dystrophin transcript. The aim is to manipulate splicing in such a manner that the targeted exon will be skipped (through binding of the AONs to pre-mRNA) and a slightly shorter but in-frame transcript will be generated. This would allow correction of the translational reading frame, and induction of the synthesis of a Becker muscular dystrophy (BMD)-like dystrophin protein that may significantly alleviate progression of the disease.
During the last decade, this therapeutic approach has emerged as a promising therapy for DMD (van Ommen et al., 2008; Yokota et al., 2007; van Deutekom et al., 2007; Goemans et al., 2011; Voit et al., 2014; Cirak et al., 2011). AON-induced exon skipping provides a mutation-specific, and thus personalized therapeutic approach for DMD patients. As the majority of the mutations cluster around exons 45 to 55, the skipping of one specific exon may be therapeutic for many patients with different mutations. The skipping of exon 51 applies to the largest subset of patients (˜13%), including those with deletions of exons 45 to 50, 48 to 50, 50, or 52. The AONs applied are chemically modified to resist endonucleases, exonucleases, and RNaseH, and to promote RNA binding and duplex stability. Different AON chemistries are currently being explored for inducing corrective exon skipping for DMD, including 2′-O-methyl phosphorothioate RNA (2OMePS; Voit et al., 2014), phosphorodiamidate morpholino (PMO; Cirak et al., 2011), tricyclo DNA (tcDNA; Goyenvalle et al, 2015), and peptide nucleic acid (PNA; Gao et al., 2015). Although AONs are typically not well taken up by healthy muscle fibers, the dystrophin deficiency in DMD and the resulting pathology, characterized by activated satellite cells and damaged and thus more permeable fiber membranes, may actually facilitate a better uptake. Nevertheless, to improve the clinical applicability and therapeutic index of nucleic acid/oligonucleotide-based therapies, the field is challenged to develop oligonucleotides with improved delivery to, and uptake by, muscle tissue throughout the body.
An efficient therapy for muscle wasting diseases will require that essentially all of the skeletal muscles including those of arms and legs and the muscles involved in respiration as well as the cardiac muscle are targeted. None of the mechanisms investigated to date have the ability to specifically deliver (antisense) oligonucleotides, let alone entire genes, to essentially all muscle tissues/cells simultaneously over the entire body. Methods for the in vivo delivery of genes or other compounds into muscle that have been published so far include injection of naked DNA with for example electrotransfer, use of microbubbles (Lu et al. 2003, Gene Ther. 10, 396-405) and systemic delivery using poloxamer (a poly(oxy-ethylene)poly(oxypropylene)poly(oxy-ethylene) triblock copolymer). It was shown in mdx mice that systemic delivery of morpholino AONs with this poloxamer resulted in an increased dystrophin expression in several muscles (Alter et al., 2006, Nature Med. 12, 1-3). However, even after repeated administration, dystrophin expression was limited in diaphragm and heart muscle. Furthermore, in these mdx mice the AONs are taken up into the muscles at least in part because the muscle membranes are compromised. In other muscle diseases like SMA and DM, delivery of AONs is more complicated due to the fact that in this case the muscle fiber membranes are not similarly compromised.
Strategies for improving the delivery of AONs that are not muscle-specific are the use of nanoparticles, cell penetrating peptides (CPPs) conjugation or co-administration of additive compounds to enhance cellular uptake (Bassi et al., 2012; Betts et al., 2015; Ferlini et al., 2010; Hu et al., 2010; Kendall et al., 2012; Lehto et al., 2013; Moulton & Moulton, 2010; Mumcuoglu, Sardan, Tekinay, Guler, & Tekinay, 2015; Rimessi et al., 2009; Verhaart & Aartsma-Rus, 2012; Wang et al., 2013; Yin et al., 2011). Some of these methods, such as cationic CPPs, are unsuitable for conjugation to anionic AONs such as 2′-O-methyl phosphorothioate AONs (2OMePS) due to aggregation issues.
Ideally, whole-body muscle therapy would use systemic delivery (e.g. intravenously or subcutaneously) of a compound endowed with a cell specific targeting ability. Some substances have been described that have potential for muscle cell targeting. The first report is of a peptide sequence with enhanced in vivo skeletal and cardiac muscle binding that was identified by screening a random phage display library (Samoylova and Smith, 1999, Muscle Nerve 22, 460-466). However, it was not shown whether or not this linear peptide can be used for in vivo targeting of conjugated compounds to muscle cells. Also a number of linear 7-mer peptide sequences that were recovered from human skeletal muscle after in vivo screening of phage random peptide library have been described (Arap et al., 2002, Nature Medicine 8, 121-127). No information was given on binding to cardiac muscle cells. Also here it was not shown whether or not these peptides can be used for in vivo targeting of conjugated compounds to muscle cells. Another substance that has been described is an Fv part of a monoclonal antibody (mAb) that is selectively transported into skeletal muscle in vivo (Weisbart et al., 2003, Mol. Immunol. 39, 783-789). Single chain Fv fragments of the murine mAb were injected into the tail veins of mice and 4 hours later the fragments were found in 20% of skeletal muscle cells, primarily localized in the nucleus. It was shown that the mAb binds to the protein myosin IIb in lysates of skeletal muscle cells, but it did not bind any protein in lysates of heart muscle cells. Therefore, this antibody might be useful for targeting to skeletal muscles, but not to the heart muscle. Linear 7-mer peptides, identified through phage display experiments, were described to enhance tissue levels of the oligonucleotide they were attached to, albeit a modest increase (Jirka SMG et al. Nucl. Acid Ther. 2014, 24, 25).
Peptides that target muscle cells were reported in WO2009/008727. These peptides were identified using technology where a phage display library (Ph.D.-7™, New England Biolabs) expresses a few copies of a linear 7-mer peptide at the N-terminus of the PIII protein of the phage. This technique is known for identifying target-specific peptides (Smith, 1985) but this approach can be cumbersome and it is well known that many false positive peptides can be identified (Huang, Ru, Li, Lin, & Guo, 2010).
In the case of lysosomal storage disease a problem in the enzyme replacement therapy is poor in vivo uptake of the therapeutic recombinant enzyme into the muscle cells. For example in Pompe's disease (glycogen storage disease type II) the doses of recombinant human acid α-glucosidase (rhGAA) that were needed in clinical studies were very high, due to poor uptake of the rhGAA into the skeletal muscle (Winkel et al., 2004, Ann. Neurol. 55, 495-502).
In light of the above, it is very clear that further improvements in delivery systems are necessary to achieve specific uptake of agents such as AONs in vivo. There is an ongoing need for improved targeting moieties.
It is an object of the present invention to provide compounds, preferably peptides or peptidomimetics, that target an organ or tissue or cell type of interest, especially muscle cells including the heart. By coupling diagnostic moieties or biologically active moieties to such targeting compounds, said moieties are targeted to the specific organs or tissues or cells.
Analyzing the outcome of phage display experiments with next generation sequencing (NGS) can improve the chance of success ('t Hoen et al., 2012). NGS allows use of just a single screening round, preventing parasitic peptide sequences to dominate the outcome and making identification of parasitic peptide sequences easier and more reliable.
A cyclic 7-mer peptide library, Ph.D.-C7C™, is available (New England Biolabs). This C7C-peptide library shares it features with the linear library (Ph.D.-7™) but expresses peptides that are cyclized by the formation of disulfide bridges between the two cysteine amino acids, which are positioned at each end of the random 7-mer peptide. This imposes conformational restriction by cyclization on the displayed peptides.
After extensive research, the present inventors have identified a number of amino acid sequences that selectively bind to and are taken up by muscle cells, including the heart. This invention thus fulfills the need of improving the in vivo uptake of for example therapeutic recombinant enzyme or (antisense) oligonucleotides, by conjugating or otherwise linking of such enzymes or oligonucleotides to muscle-specific peptides. The conjugates are advantageously useful in anti-sense therapy methods for treatment of myopathies, gene therapy of diseases where muscles potentially serve as reservoirs of protein production and delivery of a wide variety of diagnostics or drugs to heart and muscle cells.
Thus the present invention relates to a peptide or a peptidomimetic comprising or consisting of a targeting sequence selected form the group consisting of SEQ ID NO: 1-63, preferably SEQ ID NO:24 or 25.SEQ ID NO: 1-63 are shown in table 1. Preferably, the peptide is cyclic.
Also the present invention concerns conjugates of one or more peptides according to the invention, wherein said peptide according to the invention is linked to at least one moiety selected from a biologically active moiety and a diagnostic moiety.
A conjugate as described above for use as a medicament is an aspect of this invention.
A molecule comprising a peptide according to the invention and a linker moiety, which is not a peptide, for linking the peptide according to the invention to a biologically active moiety or a diagnostic moiety, is a further aspect of this invention.
The present invention provides peptides or peptidomimetics for targeting diagnostic moieties or biologically active moieties to an organ or tissue or cell type of interest, especially muscle cells including the heart.
A peptide in the context of this invention comprises at least 7 amino acids. The peptide can be fully constructed of naturally occurring L-amino acids, or can contain one or more modifications to backbone and/or side chain(s). These modifications can be introduced by incorporation of amino acid mimetics that show similarity to the natural amino acid. The group of peptides described above comprising one or more mimetics of amino acids is referred to as peptidomimetics. In the context of this invention, mimetics of amino acids include, but are not limited to, β2- and β3-amino acids, β2,2-β2,3, and β3,3-disubstituted amino acids, α,α-disubstituted amino acids, statine derivatives of amino acids, D-amino acids, α-hydroxyacids, α-aminonitriles, N-alkylamino acids and the like. In addition, the C-terminus of the peptide might be carboxylic acid or carboxamide, or other resulting from incorporation of one of the above mentioned amino acid mimetics. Furthermore, the peptides described above may contain one or more replacements of native peptide bonds with groups including, but not limited to, sulfonamide, retroamide, aminooxy-containing bond, ester, alkylketone, α,α-difluoroketone, α-fluoroketone, peptoid bond (N-alkylated glycyl amide bond). Furthermore, the peptides mentioned above may contain substitutions in the amino acid side chain (referring to the side chain of the corresponding natural amino acid), for instance 4-fluorophenylalanine, 4-hydroxylysine, 3-aminoproline, 2-nitrotyrosine, N-alkylhistidine or β-branched amino acids or β-branched amino acid mimetics with chirality at the β-side chain carbon atom opposed to the natural chirality (e.g. allo-threonine, allo-isoleucine and derivatives). In one other embodiment, the above mentioned group of peptides may contain close natural or non-natural structural analogues of amino acid or amino acids mimetics, for instance ornithine instead of lysine, homophenylalanine or phenylglycine instead of phenylalanine, β-alanine instead of glycine, pyroglutamic acid instead of glutamic acid, norleucine instead of leucine or the sulfur-oxidized versions of methionine and/or cysteine.
Preferred peptides comprise or consist of a sequence selected from the group consisting of SEQ ID NO: 1-63 (i.e. SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63). More preferred peptides comprise or consist of SEQ ID NO:24 or 25. The group may therefore also be defined as: preferred peptides comprise or consist of a sequence selected from the group consisting of SEQ ID NO: 24, 25, 1-23, 26-63. The linear and cyclic forms of the peptides mentioned above are covered by this patent, as well as their retro, inverso and/or retroinverso analogues. Preferred peptides according to the invention are cyclic. To those skilled in the art many more close variations may be known, but the fact that these are not mentioned here does not limit the scope of the present invention. In one embodiment, a peptide or peptidomimetic according to the present invention is at most 30 amino acids in length, or at least 25 amino acids or 20 amino acids or 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8 or 7 amino acids in length.
Preferred cyclic peptides are cyclic peptides where a sequence consisting or comprising of a sequence selected from the group consisting of SEQ ID NO: 1-63 is flanked by amino acid residues, or other moieties, that are able to form a bond to yield a cyclic structure. More preferred cyclic peptides are cyclic peptides where a sequence comprising or consisting of SEQ ID NO:24 or 25 is flanked by amino acid residues, or other moieties, that are able to form a bond to yield a cyclic structure. Peptides or peptidomimetics such as described above are referred to herein as peptides according to the invention, or as cyclic peptides according to the invention when only cyclic peptides or cyclic peptidomimetics are intended, or as linear peptides according to the invention when only linear peptides or linear peptidomimetics are intended. When not further specified, peptides according to the invention encompass both cyclic and linear peptides or peptidomimetics.
Sequences represented by SEQ ID NO: 1-63 are herein referred to as targeting sequences. More preferred sequences are represented by SEQ ID NO: 24 or 25. A targeting sequence is a sequence of a peptide or of a peptidomimetic that binds to muscle cells or to muscle tissue, or that increases uptake in muscle cells or in muscle tissue. Preferred assays for determining whether a sequence is a targeting sequence are provided in the examples. For example, increased uptake can be determined by fluorescence microscopy when a targeting sequence is linked to a fluorescent label.
Herein, the use of the term peptide should be so construed that next to otherwise featureless peptides where each residue is a naturally occurring proteinogenic amino acid linked to its neighbor through a backbone amide bond, also peptides comprising non-natural amino acids, peptidomimetics, unconventional linkages, and many common variations are encompassed. This includes peptides comprising alkylated bonds, inverted bonds, or other types of bonds, such as esters, triazoles, carbamates, ureas, thioureas, imides, imines, halogenated bonds, alpha-halogenated bonds, ketones, or peptides comprising beta-amino acids, other extended amino acids, or peptoids where side chains of residues are attached to the backbone amide bonds instead of to the corresponding alpha carbon atoms, or bonds that involve side chains instead of backbone functional groups. Peptides can comprise amino acids of any chirality, such as L-amino acids or D-amino acids, or mixtures thereof. Accordingly, the term ‘amino acid’ as used in this invention should be interpreted as any moiety that can constitute a residue in a peptide as defined above. Most often, an amino acid is a molecular acid, preferably featuring a carboxylic acid, said amino acid featuring an amine at the alpha-carbon next to the carboxylic acid. However, the amine can also be more distant from the carboxylic acid. The most common naturally occurring proteinogenic amino acids and their three-letter abbreviations and one-letter codes are the following: alanine (Ala, A); arginine (Arg, R), asparagine (Asn, N); aspartic acid (Asp, D); cysteine (Cys, C); glutamic acid (Glu, E); glutamine (Gln, Q); glycine (Gly, G); histidine (His, H); isoleucine (Ile, I); leucine (Leu, L); lysine (Lys, K); methionine (Met, M); phenylalanine (Phe, F); proline (Pro, P); serine (Ser, S); threonine (Thr, T); tyrosine (Tyr, Y); tryptophan (Trp, W); valine (Val, V). In the context of this invention, naturally occurring amino acids are also called natural amino acids. Natural amino acids are often proteinogenic, which means that they are used by organisms in the biosynthesis of proteins. In some cases, natural amino acids can also be non-proteinogenic. Natural amino acids are those amino acids that can be found in nature, without further limiting their role or function. As known to a person skilled in the art, amino acids are often characterized by the nature of their side chains. Amino acids that are considered to be basic amino acids are lysine, arginine, and histidine. Amino acids that are considered to be acidic amino acids are aspartic acid and glutamic acid. Amino acids that are considered to be polar uncharged amino acids are serine, threonine, cysteine, tyrosine, asparagine, and glutamine. Amino acids that are considered to be hydrophobic amino acids are alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, proline, and tryptophan. Proline is considered to be a conformationally restrained amino acid. Glycine is achiral yet can be part of both D-peptides and L-peptides. Within the embodiments of this invention, peptides can be comprised in larger peptides, or in larger substances. Peptides are understood to possibly comprise capping groups such as terminal amides, acetamides, methyl esters, other terminating esters, or other terminal moieties that are known to a person skilled in the art. Peptides are further understood to possibly feature protecting groups such as acetyl, t-butyl carbamate, 9-fluorenylmethyl carbamate, benzyl carbamate, benzyl ester, t-butyl ester, methyl ester, or other protecting groups known in the art.
In a first aspect, the invention provides a conjugate of (i) a peptide or peptidomimetic comprising or consisting of a targeting sequence selected from the group consisting of SEQ ID NO: 1-63, wherein the peptide or peptidomimetic is linked to (ii) a moiety selected from a biologically active moiety and a diagnostic moiety. Such a conjugate is referred to herein as a conjugate according to the invention. Preferred targeting sequences comprise or consist of SEQ ID NO: 24 or 25. The conjugate according to the invention links a peptide according to the invention to a biologically active moiety or to a diagnostic moiety.
As known to a skilled person, a conjugate comprises at least a first characteristic part that is linked to at least a distinct second characteristic part. Non-limiting examples are a peptide as a first part linked to an oligonucleotide as a second part, a peptide as a first part linked to a distinct second peptide as a second part, an organic small molecule as a first part linked to a protein as a second part, et cetera. In the context of a conjugate according to the invention, a peptide or a peptidomimetic is linked to a further moiety selected from a biologically active moiety and a diagnostic moiety. It is not necessary that the biologically active or diagnostic moiety is covalently linked to the peptide or petidomimetic of the invention. It may also be linked via electrostatic interactions. A link can be a direct link such as a covalent bond between the peptide according to the invention and the biologically active moiety or the diagnostic moiety. Alternately, a linker moiety can be used. Linker moieties are known in the art. As defined herein, and as known to the person skilled in the art, Ahx represents 6-aminohexanoic acid, which is also known as aminocaproic acid, which in turn is abbreviated as Acp. Ahx is considered to be a linker moiety that links two further moieties together. In addition to Ahx, other linker moieties can be used instead of individual amino acid residues, such as, but not limited to, beta-alanine (also known as beta-aminopropionic acid, bAla), 4-Aminobutyric acid (also known as piperidinic acid, 4Abu), 3-aminoisobutyric acid (bAib), or other linker moieties known in the art. These linker moieties can be comprised in peptides according to the invention, or can be comprised in conjugates according to the invention, or can be comprised in molecules according to the invention.
In one embodiment the present invention also relates to a molecule comprising a peptide or peptidomimetic according to the invention and a linker moiety, which is not a peptide, for linking the molecule to a biologically active moiety or a diagnostic moiety. Thus, the invention also provides a molecule comprising:
Such a molecule is referred to herein as a molecule according to the invention.
The linker moiety for example may be a (poly)cationic group that complexes with a biologically active poly- or oligonucleotide. Such a (poly)cationic group may be a spermine or polyethyleneimine, polyethylene glycol, poly-L-lysine and derivatives and likes. A link that is to be effected by a linker moiety can be a covalent bond, a supramolecular bond, or any other bond that strongly associated the components of the conjugate with one another. Non-limiting examples of links are coiled coils such as leucine zippers, and host-guest interactions such as those involving biotin.
To prepare the conjugates according to the invention, coupling of the biologically active moiety or diagnostic moiety to the peptides or peptidomimetics according to the invention can occur via known methods to couple compounds to amino acids or peptides. A common method is to link a moiety to a free amino group or free hydroxyl group or free carboxylic acid group or free thiol group in a peptide or peptidomimetic. Common conjugation methods include thiol/maleimide coupling, amide or ester bond formation, or heterogeneous disulfide formation. The skilled person is well aware of standard chemistry that can be used to bring about the required coupling. The biologically active moiety or diagnostic moiety may be coupled directly to a peptide or peptidomimetic or may be coupled via a spacer or linker moiety. Examples of suitable linkers are those that result from the use of SMCC (which is succinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate) or of BMPS (which is (N-β-maleimidopropyloxy)succinimide ester).
As mentioned in one embodiment the peptide or peptidomimetic according to the present invention is linked to a biologically active moiety. For example the peptide or peptidomimetic can be linked to a biologically active or therapeutic peptide and in one embodiment can even be part of the peptide or peptidomimetic basic structure. For example the amino- or carboxy-terminus of a therapeutic peptide can be extended with a sequence comprising or consisting of the peptides described above. It is to be understood that such a peptide extended with a peptide or peptidomimetic according to the invention is encompassed by a conjugate according to the present invention. The preparation of such peptides can be achieved via standard amino acid or peptide coupling procedures.
In one embodiment the invention provides a conjugate according to the invention wherein the biologically active moiety is a protein or polypeptide and wherein the peptide or peptidomimetic is comprised in the protein or polypeptide backbone. Said conjugate is preferably prepared by recombinant expression of the peptide or peptidomimetic together with the biologically active protein. Preferably a DNA construct is prepared such that the peptide or peptidomimetic according to the invention is expressed at a terminus of the biologically active peptide, preferably at the C-terminus of the biologically active peptide. Such preparation of DNA constructs by recombinant DNA methodology and expression in a suitable host is common practice to the skilled person. Thus in one embodiment the present conjugate is a fusion protein of a peptide according to the present invention, e.g. a peptide of SEQ ID NO: 1-63 (preferably SEQ ID NO: 24 or 25) with a therapeutically active protein, e.g. antibody, or a diagnostic (e.g. fluorescent) protein or both, optionally also comprising a NLS. Such a fusion protein can be prepared by expression of the appropriate DNA construct.
In preferred embodiments, the conjugate according to the invention comprises a biologically active moiety. A biologically active moiety is a compound exerting (directly or indirectly) a biological function, preferably a therapeutic function, hence is preferably a therapeutically active compound. A therapeutically active compound can be any compound known in the art and preferably is a compound that has a therapeutic effect by modulating an intercellular process. A therapeutically active compound that has a (direct) modulating effect or (direct) biological function can be for instance any protein, enzyme inhibitor, oligonucleotide, siRNA, gene, natural compound, drug or pharmaceutical. Any biologically active compound or therapeutically active compound can be used as long as it can be linked to or can be made suitable to be linked to at least one peptide or peptidomimetic according to the present invention. The biologically active compound or therapeutically active compound so becomes the moiety in the compound according to the present invention. The skilled person will be able to identify suitable biologically active or therapeutically active compounds. A biologically active moiety can be a small organic molecule, a peptide, a depsipeptide, an acyldepsipeptide, an antibiotic, an antimicrobiotic, a polypeptide, a protein, a protein fragment, a nucleic acid, a nucleic acid analogue, or parts thereof, a chemotherapeutic, a decoy molecule, or any other entity or combination thereof. A nucleic acid can be selected from the group comprising DNA molecules, RNA molecules, PNA molecules, oligonucleotides, synthetic mRNAs, ss (single stranded) or ds (double stranded) siRNA molecules, miRNAs, gapmers, antisense molecules, ribozymes, aptamers, and spiegelmers. A biologically active moiety can be a drug, which is understood to be any entity that can assert a therapeutic effect, which can also be for vaccination.
In one embodiment the biologically active compound or therapeutically active compound is a compound comprising or consisting of nucleic acids or analogues thereof. Such compounds can be considered to exert (indirectly) a biological function, preferably a therapeutic function, by modulating the genetic machinery within a cell, in particular on the level of production of proteins. The nucleic acid may be a DNA, RNA or analogue thereof, such as compounds comprising analogue monomers such as 2′-F, 2′-O-alkyl or 2′-O-alkenyl (allyl) or 2′-O-alkynyl nucleotides, e.g. 2′-O-methyl-, specifically 2′-O-methyl phosphorothioate (2OMePS; Voit et al., 2014), phosphorodiamidate morpholino (PMO; Cirak et al., 2011), tricyclo DNA (tcDNA; Goyenvalle et al, 2015), peptide nucleic acid (PNA; Gao et al., 2015), 2′-O-methoxyethyl-(MOE) and 2′-O-allyl-nucleotides, bridged/bicyclic nucleic acids (BNAs, including for example LNA, alpha-L-LNA, 2′-aminoLNA, 2′-N-substituted-2′-aminoLNA, CBBN, ENA, CRN, cEt, BNANC[N-Me], tcDNA, and derivatives thereof), peptide nucleic acids (PNAs including derivatives as described in e.g. WO2009/113828 CTI Bio or WO2015/172889, WO2013/0131019 Ugichem), ethylene bridged nucleic acids (ENAs), phosphorothioate modified nucleotides, e.g. 2′-O-methoxyethyl phosphorothioate RNA nucleotides or 2′-O-methyl phosphorothioate RNA nucleotides, or chirally defined phosphorothioate nucleotides (such as those provided by WaVe Lifesciences, or Ontorii or Chiralgen), morpholino based nucleotides (for example PMO, PMO+, PMO-X such as those provided by Sarepta Therapeutics or AVI Biopharma or Shire or Nippon Shinyaku) and combinations thereof etc. The nucleic acid may be a gene, a polynucleotide or oligonucleotide, single or double stranded small interfering RNA, miRNA, or mRNA and the like.
Accordingly, in preferred embodiments of the first aspect, the invention provides a conjugate according to the invention, wherein the biologically active moiety is selected from the group consisting of DNA, RNA, and analogues thereof, such as compounds comprising 2′-O-alkyl, in particular 2′-O-methoxyethyl- and 2′-O-methyl, bridged/bicyclic nucleic acid nucleotides (LNA, ENA, cEt, CBBN, CRN, alpha-L-LNA, cMOE, 2′-amino-LNA, 2′-(acylamino)LNA, 2′-thio-LNA, BNANC[N-Me], BNANC[NH]), tricyclo-DNA (tcDNA), peptide nucleic acid (PNA, PPNA), phosphorothioate modified nucleotides, chirally defined phosphorothioate modified nucleotides, phosphoryl guanidine modified oligonucleotides (PGOs), morpholino based nucleotides (PMO, PMO+, PMO-X, PPMO) and combinations thereof. In highly preferred embodiments, this DNA or RNA or analogue thereof such as described above is an antisense oligonucleotide (AON). Preferred AONs comprise one or more of the following:
The following is a non-exhaustive overview of literature references for DNA or RNA analogues that can be used as described above: cEt (2′-O,4′-C constrained ethyl) LNA (doi: 10.1021/ja710342q), cMOE (2′-O,4′-C constrained methoxyethyl) LNA (Seth et al., J. Org. Chem. 2010, 75, 1569-1581), 2′,4′-BNANC(N—H), 2′,4′-BNANC(N-Me), ethylene-bridged nucleic acid (ENA) (doi: 10.1093/nass/1.1.241), 2′-C-bridged bicyclic nucleotide (CBBN, as in e.g. WO 2014/145356 (MiRagen Therapeutics)), heterocyclic-bridged LNA (as in e.g. WO 2014/126229 (Mitsuoka Y et al.)), amido-bridged LNA (as in e.g. Yamamoto et al. Org. Biomol. Chem. 2015, 13, 3757), urea-bridged LNA (as in e.g. Nishida et al. Chem. Commun. 2010, 46, 5283), sulfonamide-bridged LNA (as in e.g. WO 2014/112463 (Obika S et al.)), bicyclic carbocyclic nucleosides (as in e.g. WO 2015/142910 (Ions Pharmaceuticals)), TriNA (Hanessian et al., J. Org. Chem., 2013, 78 (18), pp 9064-9075), α-L-TriNA, bicyclo DNA (bcDNA) (Bolli et al., Chem Biol. 1996 March; 3(3):197-206), F-bcDNA (DOI: 10.1021/jo402690j), tricyclo DNA (tcDNA) (Murray et al., Nucl. Acids Res., 2012, Vol. 40, No. 13 6135-6143), F-tcDNA (doi: 10.1021/acs.joc.5b00184), an oxetane nucleotide monomer (Nucleic Acids Res. 2004, 32, 5791-5799). For those not mentioned above, reference is made to WO 2011/097641 (ISIS/Ionis Pharmaceuticals) and WO2016/017422 (Osaka University), which are incorporated in their entirety by reference.
Preferred AONs that can be used as biologically active moiety are those wherein said AON induces pre-mRNA splicing modulation, preferably said pre-mRNA splicing modulation alters production or composition of protein, which preferably comprises exon skipping or exon inclusion, wherein said pre-mRNA splicing modulation most preferably comprises exon skipping. This pre-mRNA splicing modulation is preferably therapeutic.
The objective of pre-mRNA splicing modulation can be to alter production of a protein, most often the protein the RNA codes for. This production can be altered through increase or decrease of the level of said production. This production can also be altered through alteration of the composition of the protein that is actually produced, for example when pre-mRNA splicing modulation results in inclusion or exclusion of one or more exons, and in a protein that has a different amino acid sequence. Preferably, such a protein with a different amino acid sequence has more functionality, or has a better functionality, or has at least one altered property, as compared to the protein that is produced as a result of the disease or condition.
In the case of DMD, pre-mRNA splicing modulation can be applied to skip one or more specific exons in the dystrophin pre-mRNA in order to restore the open reading frame of the transcript and to induce the expression of a shorter but (more) functional dystrophin protein, with the ultimate goal to be able to interfere with the course of the disease. Similar strategies allow interference with the course of BMD. In the case of SMA, pre-mRNA splicing modulation can be applied to enhance inclusion of exon 7 in the SMN2 gene and to increase levels of the survival of motor neuron protein, which decreases loss of motor neurons in the spinal cord and subsequent atrophy of voluntary muscles. As such, in a preferred embodiment said oligonucleotide effects pre-mRNA splicing modulation, wherein said modulation alters production of protein that is related to a disease or a condition, preferably wherein said disease or condition is Duchenne Muscular Dystrophy (DMD), Becker Muscular Dystrophy (BMD), or Spinal Muscular Atrophy (SMA).
Other preferred AONs that can be used as biologically active moiety are those wherein said AON is effective for treating a human cis-element repeat instability associated genetic disorder. This also encompasses slowing the rate of decline of a subject suffering from such a disorder. A human cis-element repeat instability associated genetic disorder as identified herein is preferably a neuromuscular disorder. Therapeutic RNA modulation for repeat disorders involves an oligonucleotide which binds (or is able to bind), targets, hybridizes to (or is able to hybridize to) and/or is reverse complementary to a specific sequence of a transcript of a gene which is known to be associated with or involved in a human cis-element repeat instability associated genetic neuromuscular disorder. Examples include Huntington's disease (HD), several types of spinocerebellar ataxia (SCA), Friedreich's ataxia (FA), Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal dementia (FTD). A subset of neuropathies is caused by a cis-element repeat instability. For instance, HD is caused by a triplet (CAG)n repeat expansion in exon 1 of the HTT gene.
In preferred embodiments, a biologically active moiety is an AON, more preferably an AON for treating a human cis-element repeat instability associated genetic disorder or for inducing pre-mRNA splicing modulation, most preferably for inducing pre-mRNA splicing modulation. Suitable AONs are described in WO2013112053. Preferred AONs in this context comprise or consist of a sequence represented by any one of SEQ ID NOs: 84-330. Preferred AONs in this context comprise no more than 50 nucleotides or analogues thereof. Such AONs can optionally comprise 1, 2, 3, 4, or 5 additional nucleotides or analogues thereof that are not represented by any one of SEQ ID NOs: 84-330; preferably, such additional nucleotides or analogues thereof are comprised at the 5′ and/or the 3′ terminus of the sequence represented by any one of SEQ ID NOs: 84-330. More preferred oligonucleotides comprise a 2′-O-methyl phosphorothioate RNA monomer or consist of 2′-O-methyl phosphorothioate RNA and more preferably comprise a 5-methylpyrimidine (i.e. a 5-methylcytosine, and/or a 5-methyluracil) and/or a 2,6-diaminopurine base and are represented by a nucleotide or a base sequence comprising or consisting of any one of SEQ ID NOs: 84-330 or by a nucleotide or a base sequence comprising or consisting of a fragment of SEQ ID NO: 84-330. In this context, “a 5-methylpyrimidine” means at least one 5-methylpyrimidine. Accordingly “at least one 5-methylpyrimindine” means at least one 5-methylcytosine and/or at least one 5-methyluracile. In this context, a fragment of a SEQ ID NO refers to a sequence having a length of 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, or 33 nucleotides, and having 100% sequence identity with said SEQ ID NO over the length of the fragment. The invention also provides a conjugate according to the invention wherein the biologically active moiety is an AON comprising or consisting of a sequence represented by any one of SEQ ID NOs: 84-330 and comprising one or more of the following:
The invention provides a conjugate according to the invention wherein the biologically active moiety is an AON comprising or consisting of a sequence represented by any one of SEQ ID NOs: 84-330. In preferred embodiments the invention provides a conjugate according to the invention wherein the biologically active moiety is an AON comprising or consisting of a sequence represented by any one of SEQ ID NOs: 84-330 and comprising at least one analogue monomer.
In more preferred embodiments, the invention provides a conjugate according to the invention wherein the biologically active moiety is an AON comprising or consisting of a sequence represented by any one of SEQ ID NOs: 84-330 and comprising at least one analogue monomer selected from the group consisting of a 5-methyl pyrimidine monomer, a 2′-O-methyl phosphorothioate monomer, a BNA monomer, a PMO monomer, and a PNA monomer.
In a further more preferred embodiment, the invention provides a conjugate according to the invention wherein the biologically active moiety is an AON comprising or consisting of a sequence represented by any one of SEQ ID NOs: 84-330 and comprising only 2′-O-methyl phosphorothioate monomers.
In further more preferred embodiments, the invention provides a conjugate according to the invention wherein the biologically active moiety is an AON comprising or consisting of a sequence represented by any one of SEQ ID NOs: 84-330 and comprising at least one 5-methyl pyrimidine monomer.
In further more preferred embodiments, the invention provides a conjugate according to the invention wherein the biologically active moiety is an AON comprising or consisting of a sequence represented by any one of SEQ ID NOs: 84-330 and comprising at least one 5-methyl pyrimidine monomer and at least one 2′-O-methyl phosphorothioate monomer.
In further more preferred embodiments, the invention provides a conjugate according to the invention wherein the biologically active moiety is an AON comprising or consisting of a sequence represented by any one of SEQ ID NOs: 84-330 and comprising at least one 5-methyl pyrimidine monomer, at least one 2′-O-methyl phosphorothioate monomer, and at least one BNA monomer.
In further more preferred embodiments, the invention provides a conjugate according to the invention wherein the biologically active moiety is an AON comprising or consisting of a sequence represented by any one of SEQ ID NOs: 84-330 and comprising or consisting of PMO monomers.
In further more preferred embodiments, the invention provides a conjugate according to the invention wherein the biologically active moiety is an AON comprising or consisting of a sequence represented by any one of SEQ ID NOs: 84-330 and comprising or consisting of PNA monomers.
In preferred embodiments, the conjugate according to the invention comprises a diagnostic moiety. A diagnostic moiety is understood to be any moiety that facilitates detection using a method for detection, whereby such a diagnostic moiety is a fluorophore such as fluorescein, a chromophore, a radioactive tracer, a specific isotope, a diagnostic marker, or a hapten, wherein the hapten is preferably biotin. In a preferred embodiment, the diagnostic moiety renders the conjugate radioactively labeled, preferably by having incorporated a radioactively labeled amino acid, whereby more preferably the radioactively labeled amino acid is a tritium-labelled amino acid. The diagnostic moiety may be for in vivo, ex vivo, or in vitro diagnostic purposes. Commonly used imaging labels, radio labels or fluorescent labels such as FAM, FITC, VIC, Cy3, Cy5, Cy5.5 and the like, or green fluorescent protein (GFP) or other diagnostic proteins, possibly via recombinant expression may be used as diagnostic moieties. In preferred embodiments, the diagnostic moiety is not a phage or a part of a phage, more preferably it is not a phage.
In a preferred embodiment, this aspect provides a conjugate according to the invention, which is a fusion protein of a peptide according to claim 1 and the biologically active moiety or the diagnostic moiety, wherein the biologically active moiety is a therapeutically active protein and/or the diagnostic moiety is a diagnostic protein.
In a preferred embodiment this aspect provides a conjugate according to the invention, which further comprises a nuclear localisation signal and/or a cell penetrating peptide. In more preferred embodiments, the conjugate according to the invention further comprises a nuclear localisation signal. In other more preferred embodiments, the conjugate according to the invention further comprises a cell penetrating peptide. A cell-penetrating peptide is a peptide that can be used to promote entry into a cell of the compound itself, or of further compounds, or of conjugated or linked compounds. Skilled persons will be able to identify suitable cell-penetrating peptides.
In one embodiment the peptide or peptidomimetic according to the present invention is combined with a nuclear localization signal (NLS). In one embodiment a conjugate according to the present invention is combined with a NLS. In the context of the present invention the NLS functions to direct the present conjugates, e.g. the biologically active moiety or a diagnostic moiety, into a cell nucleus, presumably via its recognition by cytosolic nuclear transport receptors. The NLS may be part of the peptide or peptidomimetic according to the present invention, e.g. the amino- or carboxy-terminus of a NLS can be extended with a sequence comprising or consisting of the peptides described above. Also a NLS may be coupled at a different position than that of the peptide or peptidomimetic according to the present invention to a biologically active moiety or a diagnostic moiety. NLS sequences are known in the art. Typically a NLS signal consists of or comprises (a few) short sequences of positively charged lysines and/or arginines, for example a NLS consist of or comprises (K)KKR(K) (SEQ ID NO: 331), (K)KRS(K) (SEQ ID NO: 332), (K)(S)RK(R)(K) (SEQ ID NO: 333). Known NLSs are PKKKRKV (SEQ ID NO: 81), GKKRSKV (SEQ ID NO: 82), KSRKRKL (SEQ ID NO: 83). In one embodiment the peptide or peptidomimetic according to the invention is combined with a NLS selected from the group consisting of SEQ ID NO: 69-83.
In one embodiment the conjugates according to the invention can also be used as a tool for non-viral gene delivery or non-viral gene therapy. As a conjugate, the peptides or peptidomimetics according to the invention can target gene constructs to cells, in particular muscle cells. In one embodiment the gene construct allows for the production of an enzyme in an enzyme replacement therapy or the gene construct allows for the production of a therapeutical protein such as for example Factor VIII, Factor IX, Factor VII, bilirubin UDP glucuronosyltransferase, all lysosomal storage disorder proteins such as alpha-glucosidase or in particular Aldurazyme®, Cerezyme®, Fabrazyme® or Myozyme®.
One embodiment of the invention is the targeting of a virus or viral particle to cells. In a conjugate according to the invention the virus or viral particle is the biologically active moiety. In one embodiment the peptide or peptidomimetic according to the invention is linked to the viral biologically active moiety by including the DNA/RNA sequence of the peptide or peptidomimetic in the genome of a virus such that the peptide or peptidomimetic is expressed at the outer surface of the virus or viral particle. The recombinant methodology to bring such expression about is well known to the skilled person. The peptide or peptidomimetic thus targets the virus or viral particle to specific cells/tissue. This is of particular interest for targeted vaccination, gene therapy, gene replacement or viral exon skipping constructs (AAV vectors expressing antisense sequences fused to either U1 or U7 small nuclear RNA; Denti et al., 2006, Hum. Gene Ther. 17, 565-574).
A preferred peptide according to the invention is a cyclic peptide. As such, a preferred embodiment provides a conjugate according to the invention, wherein the peptide or peptidomimetic is cyclic. A cyclic peptide is a peptide that comprises a cycle formed by the peptide's backbone atoms. Such a cycle can be macrocycle, which is a cycle comprised of twelve or more atoms. The cycle is preferably closed by a bond, referred to herein as a closing bond. Preferred closing bonds are covalent bonds. A cyclic peptide may be more stable than a linear peptide. Compared to a linear peptide, a cyclic peptide often has fewer rotamers
The closing bond is formed between two moieties that are herein referred to as the flanking moieties. A cyclic peptide according to the invention comprises an even number of flanking moieties, because flanking moieties pair up in sets to form the closing bond. When reference is made to flanking moieties, context will make clear whether reference is made to a matching set of two flanking moieties, or to individual flanking moieties that are not necessarily part of a set. Within a set of flanking moieties, individual flanking moieties can comprise or consist of amino acid residues or of other moieties. Preferably, flanking moieties individually comprise or consist of amino acid residues. More preferably, flanking moieties individually comprise of one amino acid residue. As non-limiting examples this can be a natural amino acid such as cysteine, a derivatized amino acid such as a lysine that was modified at its ε-amine, or a non-natural amino acid such as allylglycine.
The closing bond connects two flanking moieties that flank the targeting sequence (SEQ ID NO: 1-63, preferably SEQ ID NO: 24 or 25). As such, the invention provides a conjugate according to the invention, wherein the peptide or the peptidomimetic comprises flanking moieties, wherein said flanking moieties comprise or consist of amino acid residues or other moieties that flank the targeting sequence, wherein said flanking moieties form a bond with each other. Preferably, this bond is a covalent bond. More preferably, the invention provides a conjugate according to the invention, wherein the cyclic peptide or the cyclic peptidomimetic comprises flanking moieties, wherein said flanking moieties comprise or consist of amino acid residues or other moieties that flank the targeting sequence, wherein said flanking moieties form a bond with each other. Preferably, this bond is a covalent bond.
The position of these flanking moieties with respect to the targeting sequence may vary and may be, in both cases independently, next to a terminus or not; for example, the targeting sequence may be flanked by two Cys residues that enable disulfide bridge formation; the position of such Cys residues may be directly next to the targeting sequence (generating for example Cys-Aa1-Aa2-Aa3-Aa4-Aa5-Aa6-Aa7-Cys with AaX referring to amino acid number X; AaX numbers 1 through 7 constitute the targeting sequence), or at other locations in the peptide (as in for example Cys-Ra0-Aa1-Aa2-Aa3-Aa4-Aa5-Aa6-Aa7-Ra8-Ra9-Ra10-Ra11-Cys with RaX meaning random amino acid number X; AaX numbers 1 through 7 constitute the targeting sequence, RaX are amino acid residues that function as a linker moiety between the targeting sequence and the flanking moieties). Other amino acid residues or chemical moieties may substitute the two Cys residues in the examples above.
Also encompassed by the invention are peptides as described above comprising other moieties that can form the closing bond. Examples of such moieties are a thiol and a maleimide, an acid and an amine, a thiol and an α-haloacetyl moiety, and moieties that can engage in bioorthogonal reactions such as an azide and an alkyne, an azide and a strained alkyne, an alkyne and a tetrazine, an alkyne and a nitrone, a tetrazine and a norbornene or other strained double or triple bond, and other so-called ‘click’ reactions known to a skilled person. Such moieties can be introduced through use of a non-natural amino acid carrying the moiety, or through conjugation of such a moiety to the side chain of a natural amino acid.
Thus, such cyclization can take many forms, all of which are known to those skilled in the art. Non-limiting examples are cyclization through disulfide, ester, ether, carbamate, alkylamine, amide, thioacyl, thioester, sulfone, sulfoxide, sulfonamide, thioether (e.g. thiol-maleimide coupling, CLIPS Technology from PepScan, The Netherlands), triazole (e.g. azide-alkynyl coupling), alkenyl (e.g. ring closing metathesis).
Preferred flanking moieties are amino acid residues that can form the closing bond via their side chains. In preferred embodiments the invention provides the conjugate according to the invention, wherein the flanking moieties form a disulfide bridge, preferably wherein the flanking moieties comprise or consist of cysteine residues.
In the context of the invention, when two moieties flank a sequence that is comprised in a peptide, the two flanking moieties constitute two residues in said peptide, and one of those two residues is comprised in that same peptide directly before or otherwise before the first residue of said sequence, or in other words N-terminal with regard to said sequence, and the other of those two residues is comprised in that same peptide directly after or otherwise after the last residue of said sequence, or in other words C-terminal with regard to said sequence. Preferably, the flanking moieties are separated from said sequence by no more than fifteen residues, or by no more than 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, or 0 residues. This can mean that the flanking moieties are adjacent to said sequence, or in other words that one of the two flanking moieties is directly before the first residue of the sequence, and the other of the two flanking moieties is directly after the last residue of the sequence. More preferably, the flanking moieties are separated from said sequence by no more than 4, 3, 2, 1, or 0 residues. Most preferably, the flanking moieties are adjacent to said sequence, which means that they are separated from said sequence by 0 residues. In this context, when residues are separated by a linker moiety such as 6-aminohexanoic acid (Ahx), such linker moieties can themselves be construed as residues.
Accordingly, in preferred peptides of the invention, the flanking moieties are separated from said sequence selected from the group consisting of SEQ ID NO: 1-63 (preferably SEQ ID NO: 24 or 25) by no more than 4, 3, 2, 1, or 0 residues, preferably the flanking moieties are adjacent to said sequence. Therefore the invention provides a conjugate according to the invention, wherein the flanking moieties are separated from the targeting sequence by 4, 3, 2, 1, or 0 residues, preferably wherein the flanking moieties are adjacent to the targeting sequence.
Preferably, within peptides according to the invention, the closing bond is a disulfide bridge. Within peptides according to the invention, the flanking moieties are preferably amino acid residues, more preferably cysteine or homocysteine residues, most preferably cysteine residues.
In preferred embodiments of aspects of this invention is provided a conjugate according to the invention, or a conjugate for use according to the invention, or the molecule according to the invention, wherein the targeting sequence is selected from the group consisting of SEQ ID NO: 1-25, preferably from the group consisting of SEQ ID NO: 14-25, more preferably from the group consisting of SEQ ID NO: 24-25.
Accordingly, in preferred embodiments is provided the peptide or peptidomimetic according to the invention wherein the targeting sequence is selected from the group consisting of
Preferably, the targeting sequence is selected from the group consisting of
More preferably, the targeting sequence is selected from the group consisting of
In most preferred embodiments of the aspects is provided a conjugate of (i) a peptide or peptidomimetic comprising or consisting of a targeting sequence which is LNSLFGS (SEQ ID NO: 339), wherein the peptide or peptidomimetic is linked to (ii) a moiety selected from a biologically active moiety and a diagnostic moiety. Preferably, said peptide is cyclic and the flanking moieties are cysteine residues that are directly adjacent to the targeting sequence LNSLFGS (SEQ ID NO: 339), and that form a disulfide bridge.
In other most preferred embodiments of the aspects is provided a conjugate of (i) a peptide or peptidomimetic comprising or consisting of a targeting sequence which is QLFPLFR (SEQ ID NO: 25), wherein the peptide or peptidomimetic is linked to (ii) a moiety selected from a biologically active moiety and a diagnostic moiety. Preferably, said peptide is cyclic and the flanking moieties are cysteine residues that are directly adjacent to the targeting sequence QLFPLFR (SEQ ID NO: 25), and that form a disulfide bridge.
Use
The present invention provides peptides or peptidomimetics for targeting biologically active moieties such as oligonucleotides, genes, proteins, pharmaceuticals and the like to various organs or tissues, especially muscle cells and the heart. Thus the invention also concerns the use of a peptide according to the invention or of a conjugate according to the invention as a medicament, preferably for targeting a biological active moiety or a diagnostic moiety to a muscle cell. Accordingly, in a second aspect the invention provides a peptide according to the invention, for use as a medicament. As such, the invention provides a peptide or peptidomimetic comprising or consisting of a targeting sequence selected from the group consisting of SEQ ID NO: 1-63 (preferably SEQ ID NO: 24 or 25) for use as a medicament. Preferably, such a peptide according to the invention is comprised in a conjugate according to the invention. Accordingly, in a second aspect the invention provides a conjugate according to the invention, for use as a medicament. These peptides for use are herein referred to as peptides for use according to the invention. These conjugates for use are herein referred to as conjugates for use according to the invention. In a preferred embodiment of this aspect the invention provides a peptide for use according to the invention, for targeting a biological active moiety or a diagnostic moiety to a muscle cell. In a preferred embodiment of this aspect the invention provides a conjugate for use according to the invention, for targeting the biological active moiety or the diagnostic moiety to a muscle cell.
In preferred embodiments, conjugates for use according to the invention or peptides for use according to the invention are administered systemically (e.g. intravenously, subcutaneously) or intramuscularly.
In one embodiment the medicament is for the treatment of a muscle-cell associated disorder including cardiac disorders. Accordingly, in preferred embodiments this aspect provides a conjugate for use according to the invention, wherein the medicament is for the treatment of a muscle-cell associated disorder, including cardiac disorders. In further preferred embodiments this aspect provides a peptide for use according to the invention, wherein the medicament is for the treatment of a muscle-cell associated disorder including cardiac disorders. Muscle-cell associated disorders include myopathies, muscular dystrophies and muscle wasting diseases. Accordingly, in preferred embodiments this aspect provides a conjugate for use according to the invention, wherein the medicament is for the treatment of a myopathy, muscular dystrophy, or muscle wasting disease. In further preferred embodiments this aspect provides a peptide for use according to the invention, wherein the medicament is for the treatment of a myopathy, muscular dystrophy, or muscle wasting disease. In one embodiment the medicament is for the treatment of disorders associated with myostatin. Myostatin has also been associated with autoimmune disease, metabolic disorders, obesity, and diabetes mellitus type II. Thus in one embodiment the medicament is for the treatment of autoimmune disease, metabolic disorders, obesity, and/or diabetes mellitus type II. Accordingly, in preferred embodiments this aspect provides a conjugate for use according to the invention, wherein the medicament is for the treatment of autoimmune disease, metabolic disorders, obesity, or diabetes mellitus type II. In further preferred embodiments this aspect provides a peptide for use according to the invention, wherein the medicament is for the treatment of autoimmune disease, metabolic disorders, obesity, or diabetes mellitus type II. In another embodiment the medicament is for the treatment of a muscle-cell associated disorder including cardiac disorders selected from the group consisting of Duchenne muscular dystrophy, Becker's muscular dystrophy, Emery-Dreifuss muscular dystrophy, Limb-girdle muscular dystrophy, Facioscapulohumeral muscular dystrophy, myotonic dystrophy type 1, myotonic dystrophy type 2, Oculopharyngeal muscular dystrophy Congenital muscular dystrophy, Distal muscular dystrophy, Amyotrophic lateral sclerosis, Infantile spinal muscular atrophy, (Juvenile-, Intermediate- and Adult-) spinal muscular atrophy, Spinal bulbar muscular atrophy, Dermatomyositis, Polymyositis, Inclusion body myositis, Myasthenia gravis, Lambert-Eaton myasthenic syndrome, Emery-Dreyfuss muscular dystrophy, Congenital myasthenic syndrome, Hyperthyroid myopathy, Hypothyroid myopathy, Charcot-Marie-Tooth disease, Friedreich's ataxia, Dejerine-Sottas disease, Myotonia congenita (both Thomsen's and Becker's Disease), Paramyotonia congenita, Central core disease, Nemaline myopathy, Myotubular myopathy (Centronuclear myopathy), Periodic paralysis (both Hypokalemic and Hyperkalemic), Mitochondrial myopathy and muscle diseases due to deficiencies in carnitine and the following enzymes Phosphorylase, Acid Maltase (Pompe's disease), Phosphofructokinase, Debrancher enzyme (also known as Amylo-1,6-glucosidase); a glycogen storage disease also known as Forbes disease, Carnitine palmityl transferase, Phosphoglycerate kinase, Phosphoglycerate mutase, Lactate dehydrogenase and Myoadenylate deaminase.
Also encompassed by the present invention is DNA consisting of or comprising a sequence encoding a peptide according to the present invention and the complementary DNA sequence thereof and the RNA transcript of a DNA sequence consisting of or comprising a sequence encoding a peptide according to the present invention and the complementary RNA sequence thereof.
The present invention also relates to pharmaceutical compositions comprising a conjugate according to the invention and a pharmaceutically acceptable carrier. Such compositions can be for use as a medicament as defined earlier herein.
In this application, ‘substances’ should be interpreted as pure molecules, complexes of multiple different molecules, oligomers, polymers, polypeptides, proteins, particles, or fragments thereof.
The term “adjacent” as used herein implies that no other matter is in between the adjacent matter. For example, adjacent residues in a peptide are directly next to one another. As a non-limiting example: when an amino acid residue is said to be adjacent to a particular sequence of amino acids, the residue is contiguous with said sequence and directly linked to it.
Conjugates according to the invention, peptides according to the invention, and molecules according to the invention can have simple variations in their molecular structure. Possible substituents are described here:
Unsubstituted alkyl groups have the general formula CnH2n+1 and may be linear or branched. Unsubstituted alkyl groups may also contain a cyclic moiety, and thus have the concomitant general formula CnH2n−1. Optionally, the alkyl groups are substituted by one or more substituents further specified in this document. Examples of alkyl groups include methyl, ethyl, propyl, 2-propyl, t-butyl, 1-hexyl, 1-dodecyl, etc.
Next to alkyl groups, possible substituents are halogens, amino groups, oxo and silyl groups, wherein the silyl groups can be represented by the formula (R2)3Si—, wherein R2 is independently selected from the group consisting of C1-C12 alkyl groups, C2-C12 alkenyl groups, C2-C12 alkynyl groups, C3-C12 cycloalkyl groups, C1-C12 alkoxy groups, C2-C12 alkenyloxy groups, C2-C12 alkynyloxy groups and C3-C12 cycloalkyloxy groups, wherein the alkyl groups, alkenyl groups, alkynyl groups, cycloalkyl groups, alkoxy groups, alkenyloxy groups, alkynyloxy groups and cycloalkyloxy groups are optionally substituted, the alkyl groups, the alkoxy groups, the cycloalkyl groups and the cycloalkoxy groups being optionally interrupted by one of more hetero-atoms selected from the group consisting of O, N and S.
When a structural formula or chemical name is understood by the skilled person to have chiral centers, yet no chirality is indicated, for each chiral center individual reference is made to all three of either the racemic mixture, the pure R enantiomer, and the pure S enantiomer.
Whenever a parameter of a substance is discussed in the context of this invention, it is assumed that unless otherwise specified, the parameter is determined, measured, or manifested under physiological conditions. Physiological conditions are known to a person skilled in the art, and comprise aqueous solvent systems, atmospheric pressure, pH-values between 6 and 8, a temperature ranging from room temperature to about 37° C. (from about 20° C. to about 40° C.), and a suitable concentration of buffer salts or other components. It is understood that charge is often associated with equilibrium. A moiety that is said to carry or bear a charge is a moiety that will be found in a state where it bears or carries such a charge more often than that it does not bear or carry such a charge. As such, an atom that is indicated in this disclosure to be charged could be non-charged under specific conditions, and a neutral moiety could be charged under specific conditions, as is understood by a person skilled in the art.
In the context of this invention, a decrease or increase of a parameter to be assessed means a change of at least 5% of the value corresponding to that parameter. More preferably, a decrease or increase of the value means a change of at least 10%, even more preferably at least 20%, at least 30%, at least 40%, at least 50%, at least 70%, at least 90%, or 100%. In this latter case, it can be the case that there is no longer a detectable value associated with the parameter.
The use of a substance as a medicament as described in this document can also be interpreted as the use of said substance in the manufacture of a medicament. Similarly, whenever a substance is used for treatment or as a medicament, it can also be used for the manufacture of a medicament for treatment. Substances for treatment are suitable for methods of treatment. Such a method can comprise administration of a substance to a subject, preferably such a method comprises administration of an effective amount of a substance to a subject in need thereof. A subject can be human or non-human, a preferred subject is a mammal. Within the description, different aspects of the invention are defined in more detail in the form of several embodiments. Each embodiment so defined may be combined with any other embodiment or embodiments unless clearly indicated to the contrary. In particular, any feature indicated as being preferred or advantageous may be combined with any other feature or features indicated as being preferred or advantageous.
In this document and in its claims, the verb “to comprise” and its conjugations are used in the non-limiting sense to mean that items following the word are included, but items not specifically mentioned are not excluded. In addition the verb “to consist” may be replaced by “to consist essentially of” meaning that a product or a combination or a composition as defined herein may comprise additional component(s) than the ones specifically identified; said additional component(s) not altering the unique characteristic of the invention. In addition, reference to an element by the indefinite article “a” or “an” does not exclude the possibility that more than one of the element is present, unless the context clearly requires that there be one and only one of the elements. The indefinite article “a” or “an” thus usually means “at least one”. Unless otherwise defined, all terms used in disclosing the invention, including technical and scientific terms, have the meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. By means of further guidance, term definitions are included to better appreciate the teaching of the present invention. The word “about” or “approximately” when used in association with a numerical value (e.g. about 10) preferably means that the value may be the given value (of 10) more or less 0.1% of the value.
All patent and literature references cited in the present specification are hereby incorporated by reference in their entirety. The following examples are offered for illustrative purposes only, and are not intended to limit the scope of the present invention in any way.
General Cell Cultures
All cells were cultured in an incubator at 37° C. and 5% CO2. Human control myoblasts (7304-1 cells (Zhu et al., 2007)), used for phage display biopanning) were grown in NutMix F-10 (Ham's) medium supplemented with GlutaMax-I, 20% fetal bovine serum (FBS) and 1% penicillin/streptomycin (P/S) (all from Gibco-BRL, the Netherlands) in flasks coated with purified bovine dermal collagen (collagen) for cell culture (Nutacon B.V. the Netherlands). Cells were plated on collagen coated petri-dishes and grown to 90% confluence before switching to differentiation medium (Dulbecco's medium (without phenol red) with 2% FBS, 1% P/S, 2% glutamax and 1% glucose (all from Gibco-BRL, the Netherlands)). Cells were allowed to differentiate for 7-14d.
Human control myoblasts (Km155.c25 cells, (Zhu et al., 2007)) were grown in skeletal muscle cell growth medium (Promocell, C-23160) supplemented with an extra 15% FBS (from, Gibco, the Netherlands) and 50 μg/ml gentamicin (PAA Laboratories) in uncoated flasks until 70-80% confluence was reached. Cells were plated in a 6 wells plate with 0.5% gelatin coated glass slides (Sigma Aldrich, the Netherlands), at a density of 1×105 cells per well, 48 hours prior to differentiation. Reaching 90% confluence, medium was switched to differentiation medium (Dulbecco's medium (without phenol red) with 2% FBS, 50 μg/ml gentamicin, 2% glutamax and 1% glucose (all from Gibco-BRL, the Netherlands)). Cells were allowed to differentiate for 3-5d.
Immortalized human cardiomyocytes (applied biological materials, Canada) were grown in Prigrow I medium supplemented with 10% FBS and 1% P/S in collagen coated flasks. Cells were plated in collagen coated glass slides in 6 wells plates and grown until confluence prior to experiments.
A schematic overview of the phage display selection experiments and candidate peptide identification (
In Vitro Biopanning
In vitro biopanning was performed as previously described by 't Hoen et al. ('t Hoen et al., 2012). Differentiated human control myoblasts cells were washed 3 times with phosphate buffered saline (PBS) and incubated with DMEM supplemented with 0.1% bovine serum albumin (BSA) for one hour at 37° C., 5% CO2. Cells were washed with PBS and incubated with 2×1011 phages from the Ph.D.-C7C™ Phage Display Peptide Library kit (New England Biolabs (NEB), Beverly, Md.) in 3 ml DMEM medium for 1 hour at 37° C., while shaking at 70 rounds per minute. After incubation, the cells were gently washed 6 times by incubating with 5 ml of ice cold DMEM containing 0.1% BSA, for 5 minutes. Subsequently, the cells were incubated for 10 minutes on ice with 3 ml of 0.1M HCl (pH 2.2) to elute cell-surface bound phages, which was neutralized by addition of 0.6 ml 0.5M Tris. To recover the cell-associated phages, cells were lysed for 1 hour on ice in 3 ml of 30 mM Tris.HCl, 1 mM EDTA, pH 8. Phages from each fraction were titrated and amplified according to the manufacturer's instruction (NEB).
In Vivo Biopanning
In total 3 mdx mice were injected intravenously (IV) with 2×10″ phages either from the first round in vitro cell-surface bound phages, in vitro cell-associated phages (i.e. second selection round in vivo) or the naïve Ph.D.-C7C™ library (i.e. first in vivo selection round). Phages were circulated for one hour after which mice were perfused. Left and right quadriceps muscles, heart and liver were isolated from mice injected with phages from the in vitro selection. Gastrocnemius and quadriceps muscles, heart, liver and kidney were isolated from the mouse injected with the naïve library. Tissues were homogenized in TBS buffer using the MagNalyzer according manufacturer's instruction (Roche Diagnostics). Phages were titrated and amplified according to manufacturer's instruction (NEB) (from here on referred to as enriched phage library).
DNA Isolation and Next Generation Sequencing
Total phage DNA was isolated from all enriched phage libraries, from the naïve unselected library and the naïve library after a single round of bacterial amplification. From each enriched phage library, 2×1011 phage particles were added to 500 μl LB growth media in a 1.5 ml tube. The phages were precipitated with 200 μl PEG 8000/NaCl for 3-4 h at room temperature. Phages were pelleted and DNA was isolated according to the manufacturer's instruction. The final pellet (phage DNA) was dissolved in milliQ water and DNA concentration determined by Nanodrop (Thermo scientific). Phage DNA was amplified by PCR using the following primers (* is a phosphorothioate bond):
XXX XXX XXX ATG GGA TTT TGC TAA ACA
The PCR primers used to amplify the phage DNA contain a subsequence that recognized the sequence flanking the 27 nucleotides long unknown insert sequence (including the two cysteines), the adapters necessary for binding to the Illumina flow cell and a unique barcode (underlined) for every enriched phage library. The PCR protocol applied was the following: 1 ng of phage DNA was incubated with 2.625 U high fidelity Taq polymerase (Roche Diagnostics, The Netherlands), 20 μM of primers in 1× high fidelity PCR buffer containing 15 mM MgCl2, and amplified for 20 cycles, each consisting of an incubation for 30 s at 94° C., 30 s at 67° C. and 30 s at 72° C. The PCR was stopped in exponential phase to mitigate PCR-induced sequence biases. The final PCR product was purified with the Qiaquick PCR purification kit (Qiagen, Valencia, Calif.). Concentrations as well as the correct length of the PCR products were established with an Agilent 2100 Bioanalyzer DNA 1000 assay. All PCR products from the enriched phage libraries were combined in a single lane. Phage fraction from the naïve unselected library (with and without amplification) were combined together in another lane of the Illumina flow cell. Both pools were subjected to solid phase amplification in the cluster station following manufacturer's specification (Illumina, San Diego, Calif.). Up to 50 cycles of single end sequencing were performed using a custom sequencing primer that started exactly at the first position of the unknown insert sequence
Sequencing was performed with the Illumina HiSeq 2000 with a v3 flow cell and reagents (Illumina, San Diego, Calif.).
Next Generation Sequencing Analyses
The Illumina CASAVA 1.8.2 software was used to extract fastq files from Illumina BCL files and to split the data based on the individual sample barcodes. For further analyses, sequences were filtered out if they did not fulfill the following criteria: sequences should start with GCT TGT followed by (NNK)7 and end with TGC GGT GGA GGT, with N being any nucleotide and K being G or T (SEQ ID NO: 344). Subsequently, sequences were translated to amino acid sequences with a custom perl script using conventional amino acid codon tables. When the stop codon TAG was encountered this was changed to a CAG codon (amino acid glutamine) according to manufacturer's instruction (NEB). An overview of the coverage is shown in table 2 and
Fluorescently labeled peptides were labeled using fluorescein isothiocyanate (FITC) and were obtained from Pepscan (Lelystad, the Netherlands). The FITC-label was attached to an Ahx (6-aminohexanoic acid) spacer which was added to the N-terminal end of the peptide, the C-terminal part was amidated and peptides were made circular by disulfide cyclization. Peptides according to the invention had cysteine flanking moieties wherein the flanking moieties were directly adjacent to the targeting sequences SEQ ID NOs: 14-25.
Human control myotubes and primary human cardiomyocytes were washed 2 times with PBS and incubated with 2.25 μM of FITC-labeled peptides in serum free media for 3 h at 37° C. and 5% CO2. Cells were washed 3 times with PBS and fixed with cold methanol (−20° C.) for 5 min (human control myotubes) or 10 min (human cardiomyocytes). Subsequently the glass slides were shortly air dried, and embedded on microscope slides with Vectashield hard set with 4′,6-diamidino-2-phenylindole (DAPI) mounting media (Vector laboratories). After drying 30 min, slides were analyzed with fluorescence microscopy (Leica DM5500 B) using a CCD camera (Leica DFC 360 FX). Representative pictures are shown. Brightest fluorescence in the cells is seen for peptides comprising SEQ ID NO: 24 and SEQ ID NO: 25 (
FITC-labeled peptides comprising SEQ ID NO:24 or SEQ ID NO: 25 were incubated at a dose of 2.25 μM, slides were imbedded in mounting media containing DAPI and analyzed with Leica microscopy using a CCD camera (Leica DFC 360 FX); Human control myotubes for 1 or 3 h (
The linear versions of the peptides comprising SEQ ID NO: 24 or SEQ ID NO: 25, in which the Cys residues were replaced with Ala residues, were labelled as described above and incubated with human control myotubes for 3 h (
5′-carboxylate linker phosphoramidite was purchased from Link Technologies (Bellshill, UK). All solvents and reagents were obtained from Sigma Aldrich (Zwijndrecht, The Netherlands) or Acros (Geel, Belgium) and used as received unless indicated otherwise. Observed molecular weights were corrected for reference standard values. Cyclic peptides were synthesized by PepScan (Lelystad, The Netherlands) or Bachem (Bubendorf, Switzerland) and contained an amidate C-terminus and addition of an Ahx (6-aminohexanoic acid) residue at the N-terminus.
AON Synthesis
2′-O-methyl phosphorothioate AONs modified with a 5′-carboxylate linker were prepared through standard phosphoramidite chemistry protocols, using a Clt-protected amidite for the last coupling (15 eq, 20 min modified coupling conditions) and final removal of the Clt group. Cleavage/deprotection (0.1M NaOH in MeOH/H2O 4/1 (v/v), 18 h, 55° C.), addition of NaCl and desalting by FPLC, and lyophilization yielded the desired AON.
Peptide-AON Conjugate Synthesis
Typical small scale procedure: the 5′-carboxylate modified AON h45 (with sequence 5′-UGCCGCUGCCCAAUGGGAUCCUG-3′, SEQ ID NO: 67, 1 μmol) for human exon 45 skip, was added to a solution of O-(6-chlorobenzotriazol-1-yl)-N,N,N′,N′-tetramethyluronium hexafluorophosphate (HCTU) (2.3 eq) and 1-hydroxybenzotriazole (HOBt)(2 eq) in DMSO (0.4 mL) to preactivate by shaking for 3 min at room temperature (RT). Cyclic peptide according to the invention with cysteine residues as flanking moieties directly adjacent to the targeting sequence (2 μmol and 2.3 eq N,N-diisopropylethylamine (DiPEA) in 0.1 mL N,N-dimethylformamide (DMF)) was added and the reaction mixture was shaken for 1 h at RT. Reverse phase (RP)-HPLC purification was followed by addition of a small excess of NaCl, desalted by FPLC and conjugates were evaporated to dryness 3 times from MilliQ, yielding the conjugate of the cyclic peptide comprising SEQ ID NO:25 with h45 (referred to as ID25-h45; yield 0.3 μmol (31%), MW (ESI) calc. 9211.9, found 9211.5). The two conjugates that were evaluated in vivo were obtained through similar procedure in larger scale from 6 separate pooled syntheses, using the AON m23 (with sequence 5′-GGCCAAACCUCGGCUUACCU-3′, SEQ ID NO: 68) for mouse exon 23 skip: ID24-m23 (yield 38 μmol (37%), MW (ESI) calc. 8005.8, found 8006.5) and ID25-m23 (yield 38 μmol (36%), MW (ESI) calc. 8189.1, found 8188.7).
The ID25-h45 conjugate was evaluated for activity to determine if the conjugation of a cyclic peptide has any influence on the exon skipping ability of the AON and was incubated with human control myotubes (at 2 μM) without any transfection reagent for 96 h (
4 wk-old mdx mice (n=4-5 per group) were administrated, 4× per week 50 mg/kg of m23 subcutaneously, a molar equivalent of ID24-m23, ID25-m23, or saline, for 8 wk. One week after the last injection tissues of interest were isolated. RNA was isolated and exon skipping levels evaluated by single RT-PCR (
For both peptide-m23 conjugates, tissue levels were improved. The levels of (CK) creatine kinase, a marker for muscle damage, were found decreased in both peptide-AON groups versus NT mdx mice (
Additionally, 1 wk after the last injection, blood was taken and evaluated for several safety markers (
| Number | Date | Country | Kind |
|---|---|---|---|
| 16199033 | Nov 2016 | EP | regional |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2017/079349 | 11/15/2017 | WO |
| Publishing Document | Publishing Date | Country | Kind |
|---|---|---|---|
| WO2018/091544 | 5/24/2018 | WO | A |
| Number | Name | Date | Kind |
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| 7504490 | Weinstock et al. | Mar 2009 | B1 |
| 20040123343 | La Rosa et al. | Jun 2004 | A1 |
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