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Definitions

• the present invention relates to a biosynthetic random coil polypeptide or a biosynthetic random coil polypeptide segment or a conjugate, said biosynthetic random coil polypeptide or a biosynthetic random coil polypeptide segment or a conjugate comprising an amino acid sequence consisting solely of proline and alanine amino acid residues, wherein said amino acid sequence consists of at least about 50 proline (Pro) and alanine (Ala) amino acid residues.
• Said at least about 50 proline (Pro) and alanine (Ala) amino acid residues may be (a) constituent(s) of a heterologous polypeptide or an heterologous polypeptide construct.
• biosynthetic random coil polypeptide or biosynthetic random coil polypeptide segment consists of at least about 50, of at least about 100, of at least about 150, of at least about 200, of at least about 250, of at least about 300, of at least about 350 or of at least about 400 proline (Pro) and alanine (Ala) amino acid residues.
• proline (Pro) and alanine (Ala) amino acid residues are preferably (a) a constituent of a heterologous polypeptide or a heterologous polypeptide construct or are preferably (b) a constituent of a conjugate, like a drug conjugate, like a conjugate with a food or cosmetic ingredient or additive, like a conjugate with a biologically active compound or like a conjugate with a spectroscopically active compound.
• heterologous proteins are provided herein whereby these proteins comprise at least two domains, wherein a first domain of said at least two domains comprises an amino acid sequence having and/or mediating an activity, like a biological activity, and a second domain of said at least two domains comprising the biosynthetic random coil proline/alanine polypeptide or proline/alanine polypeptide segment of the present invention.
• the present invention relates in particular to a drug conjugate comprising (i) a biosynthetic random coil polypeptide or polypeptide segment comprising an amino acid sequence consisting solely of proline and alanine amino acid residues, wherein said amino acid sequence consists of at least 50 proline (Pro) and alanine (Ala) amino acid residues, and (ii) a drug selected from the group consisting of (a) a biologically active protein or a polypeptide that comprises or that is an amino acid sequence that has or mediates a biological activity and (b) a small molecule drug.
• a further subject of the present invention is a drug conjugate comprising the biosynthetic random coil proline/alanine polypeptide or proline/alanine polypeptide segment as provided herein and, additionally, (a) pharmaceutically or medically useful molecule(s), like small molecules, peptides or biomacromolecules (such as proteins, nucleic acids, carbohydrates, lipid vesicles) and the like, linked and/or coupled to said biosynthetic random coil proline/alanine polypeptide or proline/alanine polypeptide segment.
• pharmaceutically or medically useful molecule(s) like small molecules, peptides or biomacromolecules (such as proteins, nucleic acids, carbohydrates, lipid vesicles) and the like, linked and/or coupled to said biosynthetic random coil proline/alanine polypeptide or proline/alanine polypeptide segment.
• nucleic acid molecules encoding the biosynthetic random coil polypeptide or polypeptide segment and/or the biologically active, heterologous proteins as well as vectors and cells comprising said nucleic acid molecules are disclosed.
• methods for the production of the herein described inventive biosynthetic random coil polypeptides or polypeptide segments and corresponding drug or food conjugates, i.e. conjugates comprising the herein defined biosynthetic random coil polypeptides or polypeptide segments and a food ingredient or a food additive are disclosed.
• compositions comprising the compounds of the invention (i.e.
• random coil polypeptides or random coil polypeptide segments comprising an amino acid sequence consisting solely of proline and alanine amino acid residues and nucleic acid molecules encoding the same) as well as specific uses of said random coil polypeptide or polypeptide segment, of the biologically active proteins comprising said random coil polype random coil polypeptides or random coil polypeptide segments prides or random coil polypeptide segments , the drug conjugates, the food conjugates or the nucleic acid molecules, vectors and cells of the invention.
• biosynthetic random coil polypeptides or polypeptide segments as well as of producing and/or obtaining the inventive biologically active, heterologous proteins, and/or polypeptide constructs or drug conjugates are provided.
• medical, pharmaceutical as well as diagnostic uses are provided herein for the biosynthetic random coil polypeptide or polypeptide segment comprising an amino acid sequence consisting solely of proline and alanine amino acid residues (or for molecules and conjugates comprising the same) as defined herein.
• Such a medical or pharmaceutical use can comprise the use of said biosynthetic random coil polypeptide or polypeptide segment as plasma expander and the like.
• the means and methods provided herein are not limited to pharmaceutical, medical and biological uses but can also be employed in other industrial areas, like in the paper industry, in oil recovery, etc.
• PEGylation technology has several drawbacks: clinical grade PEG derivatives are expensive and their covalent coupling to a recombinant protein requires additional downstream processing and purification steps, thus lowering yield and raising the costs. Furthermore, PEG is not biodegradable, which can cause side effects such as vacuolation of kidney epithelium upon continuous treatment; see, e.g., Gaberc-Porekar (2008) Curr Opin Drug Discov Devel 1 1 :242-50; Knop (2010) Angew Chem Int Ed Engl 49:6288-308 or Armstrong in: Veronese (Ed.), "PEGylated Protein Drugs: Basic Science and Clinical Applications”; Birkhauser Verlag, Basel 2009.
• Gelatin hydrolyzed and denatured animal collagen, contains long stretches of Gly-Xaa-Yaa repeats, wherein Xaa and Yaa mostly constitute proline and 4-hydroxyproline, respectively.
• Succinylation of gelatin primarily via the ⁇ -amino groups of naturally interspersed lysine side chains, increases the hydrophilicity of this biopolymer and lowers its isoelectric point (pi).
• the intramolecular electrostatic repulsion between the negatively charged carboxylate groups of the modified side chains supposedly spreads out the molecule into a more or less extended conformation.
• the resulting expanded volume makes succinylated gelatin a macromolecule for use as plasma expander in humans and is, inter alia, marketed as Volplex ® (Beacon Pharmaceuticals Ltd) or Gelofusine ® (B. Braun Melsungen AG). Furthermore, a half-life extending effect was achieved by genetic fusion of granulocyte-colon -stimulating factor (G-CSF) to an artificial gelatin-like polypeptide (Huang (2010) Eur J Pharm Biopharm 74:435-41).
• G-CSF granulocyte-colon -stimulating factor
• GLK 1 16 amino acid gelatin-like protein
• G-CSF was fused at its N-terminus with 4 copies of this GLK sequence and secreted in Pichia pastoris.
• Pichia pastor is appeared as a favourable production organism for GLK fusion proteins; yet, if GLKs can also be produced in other organisms remains to be determined as it is known that recombinant gelatin fragments can be expressed with only low yield in E. coli, for example, as illustrated in 01 sen (2003), Adv Drug Deliv Rev 55: 1547-67.
• Elastin is a component of the extracellular matrix in many tissues. It is formed from the soluble precursor tropoelastin, which consists of a hydrophilic Lys/ Ala-rich domain and a hydrophobic, elastomeric domain with repetitive sequence. Enzymatic crosslinking of lysine side chains within the hydrophilic domain leads to insoluble elastin formation. Elastin-like polypeptides (ELPs) are artifically designed, repetitive amino acid sequences derived from the hydrophobic domain of tropoelastin.
• ELPs The most common repeat sequence motif of ELPs is V- P-G-X-G, wherein "X” can be any amino acid except Pro (MacEwan (2010) Biopolymers 94:60-77; Kim (2010) Adv Drug Deliv Rev 62: 1468-78).
• Suitable ELPs can be fused with therapeutic proteins and produced in E. coli. Consequently, the ability of ELPs to form gellike depots after injection can significantly prolong the in vivo half-life of an attached biologic, albeit by a mechanism different from the other unstructured polypeptides. Yet, ELP attachment can hamper the bioactivity of the fusion partner as demonstrated for the interleukin-1 receptor antagonist in an IL-1 -induced lymphocyte proliferation bioassay (Shamji (2007) Arthritis Rheum. 1 1 :3650- 3661). In addition, ELPs are subject to degradation by endogenous proteases such as collagenase. Also, aggregated proteins are generally more susceptible to immunogenicity.
• WO 2006/081249 describes a polypeptide sequence with about 2 to 500 repeat units of 3 to 6 amino acids, wherein G, N or Q represent the major constituents while minor constituents can be A, S, T, D or E.
• This amino acid composition allows integration of the glycosylation sequon Asn-Xaa-Ser/Thr (where Xaa is any amino acid except Pro) for N-linked glycosylation of the Asn side chain in eukaryotic expression systems.
• the increased macromolecular size of a resulting fusion protein, including posttranslational modification with bulky solvated carbohydrate structures, can extend the pharmacokinetics of the genetically conjugated protein.
• oligosaccharide attachments in general can both reduce susceptibility to proteolysis and increase the hydrodynamic volume (Sinclair (2005) J Pharm Sci 94: 1626-35).
• a disadvantage is the intrinsic molecular heterogeneity of the glycosylated biomacromolecule, which causes additional effort during biotechnological production and quality control.
• WO 2010/091122 and WO 2007/103515
• Schellenberger (2009) Nat Biotechnol 27: 1 186-90 disclose unstructured non-repetitive amino acid polymers encompassing and comprising the residues P, E, S, T, A and G.
• This set of amino acids which shows a composition not unlike the PSTAD repeat described further above, was systematically screened for sequences to yield a solvated polypeptide with large molecular size, suitable for biopharmaceutical development, by avoiding hydrophobic side chains - in particular F, I, L, M, V and W - that can give rise to aggregation and may cause an HLA/MHC-II mediated immune response. Also, potentially crosslinking Cys residues, the cationic amino acids K, R and H, which could interact with negatively charged cell membranes, and the amide side chains of N and Q, which are potentially prone to hydrolysis, were excluded (see Schellenberger (2009) loc. cit).
• the fusion proteins - typically carrying a cellulose binding domain, which was later cleaved off - were produced in a soluble state in the cytoplasm of E. coli and isolated.
• Investigation of of E-XTEN by circular dichroism (CD) spectroscopy revealed lack of secondary structure while during size exclusion chromatography (SEC) the fusion protein showed substantially less retention than expected for a 84 kDa protein, thus demonstrating an increased hydrodynamic volume (Schellenberg (2009) loc. cit.).
• the disordered structure of the PESTAG polypeptide and the associated increase in hydrodynamic radius may be favoured by the electrostatic repulsion between amino acids that carry a high net negative charge which are distributed across the XTEN sequence (see WO 2010/091 122).
• polyglycine is a linear unbranched polyamide that shows certain resemblance to the polyether PEG in so far as both are essentially one-dimensional macromolecules with many rotational degrees of freedom along the chain, which are made of repeated short hydrocarbon units that are regularly interrupted by hydrogen-bonding and highly solvated polar groups. Consequently, polyglycine should constitute the simplest genetically encodable PEG mimetic with prospects for extending the plasma half-life of therapeutic proteins.
• copolypeptides of proline and alanine are partially soluble in water, while other copolypeptides were completely insoluble. It is speculated in Izuka that proline/alanine copolypeptides may have a partial disordered conformation. Izuka emphasizes that chemically synthesized polypeptides with a random proline/alanine sequence occur predominantly in a collagen-like conformation, i.e. in a structured conformation.
• the invention relates to the provision and use of a biosynthetic random coil polypeptide or polypeptide segment comprising an amino acid sequence consisting of at least about 50, in particular of at least about 100, in particular of at least about 150, in particular of at least about 200, in particular of at least about 250, in particular of at least about 300, in particular of at least about 350, in particular of at least about 400 proline and alanine amino acid residues.
• the invention therefore relates to the provision of biosynthetic random coil polypeptides or polypeptide segments comprising an amino acid sequence of at least 50 amino acid residues, said amino acid sequence consisting solely of proline and alanine amino acid residues and comprising at least one proline and at least one alanine.
• the invention also provides for a drug conjugate comprising (i) a biosynthetic random coil polypeptide or polypeptide segment comprising an amino acid sequence consisting solely of proline and alanine amino acid residues, wherein said amino acid sequence consists of at least 50 proline (Pro) and alanine (Ala) amino acid residues, and (ii) a drug selected from the group consisting of (a) a biologically active protein or a polypeptide that comprises or that is an amino acid sequence that has or mediates a biological activity and (b) a small molecule drug.
• biosynthetic random coil polypeptide or biosynthetic random coil polypeptide segment as described herein and to be used in drug or food conjugates as provided herein and comprising an amino acid sequence consisting of at least about 50, of at least about 100, of at least about 150, of at least about 200, of at least about 250, of at least about 300, of at least about 350, of at least about 400 proline (P) and alanine (A) amino acid residues is, inter alia, to be used in a heterologous context, i.e.
• biologically active in context of herein disclosed conjugates is not limited to pure biological molecules but also comprise medically active, therapeutically active, pharmacuticlly active molecules and the like. It is evident for the skilled artisan that the means and methods provided herein are not limited to pharmaceutical and medical uses, but can be employed in a wide variety of technologies, including, but not limited to cosmetic, food, beverage and nutrition technologies, oil industry, paper industry and the like.
• the produced polypeptides are essentially uniform and share the above characteristics (i.e. defined sequence, defined length and/or defined amino acid ratio).
• the random coil polypeptides consisting of at least about 50, in particular of at least about 100, in particular of at least about 150, in particular of at least about 200, in particular of at least about 250, in particular of at least about 300, in particular of at least about 350, in particular of at least about 400 proline and alanine amino acid residues are, in accordance with this invention for example comprised in biologically active, heterologous polypeptides/polypeptide constructs and/or in drug or food conjugates as well as in other conjugates useful in further industrial areas, like, but not limited to paper industry, oil industry and the like.
• buffers in particular in experimental settings (for example in the determination of protein structures, in particular in CD measurements and other methods that allow the person skilled in the art to determine the structural properties of a protein/amino acid stretch) or in buffers, solvents and/or excipients for pharmaceutical compositions, are considered to represent "physiological solutions" / "physiological conditions" in vitro.
• buffers are, e.g. phosphate-buffered saline (PBS: 1 15 mM NaCl, 4 mM H 2 P0 4 , 16 mM Na 2 HP0 4 pH 7.4), Tris buffers, acetate buffers, citrate buffers or similar buffers such as those used in the appended examples.
• the inventive biosynthetic amino acid sequence comprises about 200 to about 3000 proline and alanine residues, about 200 to about 2500 proline and alanine residues, about 200 to about 2000 proline and alanine residues, about 200 to about 1500 proline and alanine residues, about 200 to about 1000 proline and alanine residues, about 300 to about 3000 proline and alanine residues, about 300 to about 2500 proline and alanine residues, about 300 to about 2000 proline and alanine residues, about 300 to about 1500 proline and alanine residues, about 300 to about 1000 proline and alanine residues, about 400 to about 3000 proline and alanine residues, about 400 to about 2500 proline and alanine residues, about 400 to about 2000 proline and alanine residues, about 400 to about 1500 proline and alanine residues, about 400 to about 1000 proline and alanine residues, about 500 to about 3000 proline
• biosynthetic random coil polypeptides are characterised by a defined content or ratio of amino acid residues, in particular of the main constituents proline and alanine.
• the present invention relates to a biosynthetic random coil polypeptide or polypeptide segment comprising an amino acid sequence consisting solely of proline and alanine amino acid residues, wherein said amino acid sequence consists of at least about 50, of at least about 100, of at least about 150, of at least about 200 of at least about 250, of at least about 300, of at least about 350, of at least about 400 proline (Pro) and alanine (Ala) amino acid residues in particular when comprised in a heterologous biological active protein/protein construct/polypeptide or drug conjugate.
• the present invention relates in one embodiment to a biosynthetic random coil polypeptide (or segment thereof) whereby the amino acid sequence consists mainly of proline and alanine, and wherein the proline residues constitute more than about 10 % and less than 75 % of the amino acid sequence.
• the alanine residues comprise the remaining at least 25 % to 90 % of said amino acid sequence (or the random coil polypeptide or polypeptide segment if it consists of the amino acid sequence).
• the amino acid sequence comprises more than about 10 %, preferably more than about 12 %, even more preferably more than about 14 %, particularly preferably more than about 18 %, more particularly preferably more than about 20 %, even more particularly preferably more than about 22 %, 23 % or 24 % and most preferably more than about 25 % proline residues.
• the amino acid sequence preferably comprises less than about 75 %, more preferably less than 70 %, 65 %, 60 %, 55 % or 50 % proline residues, wherein the lower values are preferred. Even more preferably, the amino acid sequence comprises less than about 48 %, 46 %, 44 %, 42 % proline residues.
• the random coil polypeptide may comprise an amino acid sequence consisting of about 25 % proline residues, and about 75 % alanine residues.
• the random coil polypeptide (or segment thereof) may comprise an amino acid sequence consisting of about 35 % proline residues and about 65 % alanine residues.
• the term "about X %" as used herein above is not limited to the concise number of the percentage, but also comprises values of additional 10 % to 20 % or 10 % to 20 % less residues.
• 10 % may also relate to 1 1 % or 12 % and to 9 % and 8 %, respectively.
• amino acid sequence/polypeptide may also form random coil conformation when other residues than proline and alanine are comprised as a minor constituent in said amino acid sequence/ polypeptide (polypeptide segment).
• minor constituent means that maximally 5 % or maximally 10 % amino acid residues are different from proline or alanine in the inventive biosynthetic random coil polypepitdes/polymers of this invention.- This means that maximally 10 of 100 amino acids may be different from proline and alanine, preferably maximally 8 %, i.e. maximally 8 of 100 amino acids may be different from proline and alanine, more preferably maximally 6 %, i.e.
• maximally 6 of 100 amino acids may be different from proline and alanine, even more preferably maximally 5 %, i.e. maximally 5 of 100 amino acids may be different from proline and alanine, particularly preferably maximally 4 %, i.e. maximally 4 of 100 amino acids may be different from proline and alanine, more particularly preferably maximally 3 %, i.e. maximally 3 of 100 amino acids may be different from proline and alanine, even more particularly preferably maximally 2 %, i.e. maximally 2 of 100 amino acids may be different from proline and alanine and most preferably maximally 1 %, i.e.
• maximally 1 of 100 of the amino acids that are comprised in the random coil polypeptide (or segment thereof) may be different from proline and alanine.
• Said amino acids different from proline and alanine may be selected from the group consisting of Arg, Asn, Asp, Cys, Gin, Glu, Gly, His, lie, Leu, Lys, Met, Phe, Thr, Trp, Tyr, and Val, including posttranslationally modified amino acids or non-natural amino acids (see, e.g., Budisa (2004) Angew Chem Int Ed Engl 43:6426-6463 or Young (2010) J Biol Chem 285:11039-1 1044).
• the "minor constituent" i.e.
• an amino acid other than proline and alanine) of the biosynthetic random coil polypeptide/construct/polymer comprises as "other amino acid'V'different amino acid" (a) Ser(s), said Ser amino acid/Ser amino acids constitute preferably less than 50 %, more preferably less than 40 %, less than 30 %, less than 20 % or less than 10 % of these (minor) amino acid residues.
• the biosynthetic random coil polypeptide/construct/polymer as described herein or the random coil polypeptide part of a (e.g.) fusion protein as described herein does not comprise (a) serine residue(s).
• biosynthetic random coil polypeptide/construct/polymer as described herein or the random coil polypeptide part of a (e.g.) fusion protein.
• a biosynthetic random coil polypeptide (or segment thereof)/the amino acid sequence may, in particular, consist exclusively of proline and alanine amino acid residues (i.e. no other amino acid residues are present in the random coil polypeptide or in the amino acid sequence).
• An illustrative "building block” is, e.g. "AP” and this has also been provided in the appended illustrative examples as functional biosynthetic random coil domain of the present invention.
• This illustrative example is the sequence "P1A1" as also provided in form of APAPAPAPAPAPAPAP (SEQ ID NO: 51). i.e. a "poly PA” "amino acid repeat'V'amino acid cassette'V'cassette repeat".
• the amino acid sequence/polypeptide comprising the above defined “amino acid repeats'V'amino acid cassettes'V'cassette repeats" and the like comprises no more than 5 identical consecutive amino acid residues.
• Other alternative embodiments are provided herein below in context of exemplified, individual building blocks.
• such a termed “repeat” may comprise even more than 50 amino acid residues, for example in cases wherein said inventive biosynthetic random coil polypeptide/polymer comprises more than about, e.g., 100 amino acids, more than about 150 amino acids, more than about 200 amino acids, etc. Accordingly, the maximal amount of amino acid residues comprised in such a "repeat” is conditioned by the over-all length of the biosynthetic polypeptide (or segment thereofj/polymer as provided herein.
• the present invention provides for (a) biologically active, heterologous protein(s) or (a) protein construct(s) that is/are particularly useful in a pharmaceutical, medical and/or medicinal setting.
• biologically active, heterologous proteins/protein constructs comprise as at least one domain of said at least two domains the random coil polypeptide or polypeptide segment comprising an amino acid sequence consisting solely of proline and alanine residues, wherein said amino acid sequence consist of about 50, of about 100, of about 150, of about 200, of about 250, of about 300, of about 350, of about 400 to about 3000 proline (Pro) and alanine (Ala) residues.
• biosynthetic random coil polypeptide/polypeptide segment consisting solely of proline and alanine amino acid residues as provided herein and as employed in the biologically active, heterologous proteins/protein constructs of this invention are preferably not further (chemically) modified, for example they are preferably neither glycosylated nor hydroxylated.
• such a homologous hypothetical protein as deduced from a naturally occurring nucleic acid molecule or open reading frame, comprising a high proline and alanine content above average is not part of this invention.
• the invention is based on the fact that a rather large random coil polypeptide or polypeptide segment that does not occur in nature in an isolated manner and that comprises an amino acid sequence consisting solely of proline and alanine residues, wherein said amino acid sequence consist of about 50, of about 100, of about 150, of about 200, of about 250, of about 300, of about 350, of about 400 to about 3000 proline (Pro) and alanine (Ala) residues is provided that is particularly useful in medical/pharmaceutical context.
• isolated biosynthetic random coil polypeptides or polypeptide segments that do not occur in nature in an isolated manner are also comprised in the herein disclosed (a) biologically active, heterologous protein(s) or (a) protein construct(s) that is/arc particularly useful in a pharmaceutical, medical and/or medicinal setting.
• random coil polypeptide (or segment thereof)/amino acid sequence consists preferably of at least about 50, of at least about 100, of at least about 150, of at least about 200, of at least about 250, of at least about 300, of at least about 350, of at least about 400 amino acid residues and up to about 3000 amino acid residues.
• the polypeptides/amino acid sequences comprising the above concatemers or having the above formula (I) should preferably have the overall length and/or proline/alanine content as defined and explained herein above, i.e.
• the random coil polypeptide ((a) polypeptide segment(s) thereof)/amino acid sequence may comprise the amino acid stretch AAPAAPAPAAPAAPAPAAPA (SEQ ID NO: 1), AAPAAPAPAAPAAPAPAAPA (SEQ ID NO: 1 ); AAPAAAPAPAAPAAPAPAAP (SEQ ID NO: 2); AAAPAAAPAAAPAAAPAAAP (SEQ ID NO: 3); AAPAAPAAPAAPAAPAAPAAPAAP (SEQ ID NO: 4);
• the biosynthetic random coil polypeptides (or polypeptide segment)/polymers as provided herein are characterized by a relatively large hydrodynamic volume.
• This hydrodynamic volume also called apparent size, can easily be determined by analytical gel filtration (also known as size exclusion chromatography, SEC).
• the random coil polypeptide (or segment thereof) has an apparent size of at least 10 kDa, preferably of at least 25 kDa, more preferably of at least 50 kDa, even more preferably of at least 100 kDa, particularly preferably of at least 200 kDa and most preferably of at least 400 kDa.
• glycosylation analogs of biologically active proteins in which new N-linked glycosylation consensus sequences are introduced has been proposed to prolong plasma half- life; see WO 02/02597; Perlman (2003) J Clin Endocrinol Metab 88:2327-2335; or Elliott (2003) Nat Biotechnol 21 :414-420).
• the described glycoengineered proteins displayed an altered in vivo activity, which indicates that the new carbohydrate side chains influence the biological activity of the engineered protein.
• the additional carbohydrate side chains are likely to increase the antigenicity of the resulting biological active molecules, which raises substantial safety concerns.
• proteins comprising a herein defined, additional "second domain” adopting a random coil conformation in aqueous solution or under physiological conditions (for example polymers consisting of about 200 or about 400 or about 600 amino acid residues and comprising PA#1/SEQ ID NO. 1, PA#2/SEQ ID NO. 2, PA#3/SEQ ID NO. 3, PA#4/SEQ ID NO. 4, PA#5/SEQ ID NO. 5, PA#6/SEQ ID NO. 6 and/or P1A1/SEQ ID NO. 51 as "building blocks”) have an advantageous serum stability or plasma half-life, even in vivo, (in particular if intravenously administered) as compared to a control lacking said random coil conformation.
• polymers consisting of about 200 or about 400 or about 600 amino acid residues and comprising PA#1/SEQ ID NO. 1, PA#2/SEQ ID NO. 2, PA#3/SEQ ID NO. 3, PA#4/SEQ ID NO. 4, PA#5/SEQ ID NO. 5, PA#6/SEQ ID NO. 6 and/or P
• WO 2008/155134 (as discussed herein above) it has been shown that biologically active proteins which comprise a domain with an amino acid sequence adopting a random coil conformation have an increased in vivo and/or in vitro stability.
• the random coil domains disclosed in WO 2008/155134 consist, in particular, of proline, alanine, and serine (PAS) residues. The presence of these three residues is described in this prior art document as an essential requirement for the formation of a stable and soluble random coil in aqueous solution.
• domain relates to any region/part of an amino acid sequence that is capable of autonomously adopting a specific structure and/or function.
• a domain may represent a functional domain or a structural domain.
• the proteins of the present invention comprise at least one domain/part having and/or mediating biological activity and at least one domain/part forming random coil conformation.
• the proteins of the invention also may consist of more than two domains and may comprise e.g. an additional linker or spacer structure between the herein defined two domains/parts or another domain/part like, e.g.
• a protease sensitive cleavage site an affinity tag such as the His 6 -tag or the Strep-tag, a signal peptide, retention peptide, a targeting peptide like a membrane translocation peptide or additional effector domains like antibody fragments for tumour targeting associated with an anti-tumour toxin or an enzyme for prodrug-activation etc.
• exemplary biologically active proteins of interest include, but are not limited to, granulocyte colony stimulating factor, human growth hormone, alpha-interferon, beta- interferon, gamma -interferon, lambda-interferone, tumor necrosis factor, erythropoietin, coagulation factors such as coagulation factor VIII, coagulation factor Vila, coagulation factor IX, gpl20/gpl60, soluble tumor necrosis factor I and II receptor, thrombolytics such as reteplase, peptides with metabolic effects such as GLP-1 or exendin-4, immunosuppressive/immunoregulatory proteins like interleukin-1 receptor antagonists or anakinra, interleukin-2 and neutrophil gelatinase-associated lipocalin or other natural or engineered lipocalins or those proteins or
• hematide leptin, interleukin-20, interleukin-22 receptor subunit alpha (IL-22ra), interleukin-22, hyaluronidase, fibroblast growth factor 18, fibroblast growth factor 21 , glucagon-like peptide 1, osteoprotegerin, IL-18 binding protein, growth hormone releasing factor, soluble TACI receptor, thrombospondin- l .
• soluble VEGF receptor Flt-1 cx- galactosidase A, myostatin antagonist, gastric inhibitory polypeptide, alpha- 1 antitrypsin, IL- 4 mutein, and the like.
• the random coil polypeptide (or polypeptide segment) does not necessarily carry Pro or Ala residues at its amino or carboxyl terminus.
• the biologically active protein in accordance with the present invention may represent a protein conjugate wherein a protein of interest or a polypeptide/polypeptide stretch/peptide/amino acid sequence having and/or mediating biological activity is conjugated via a non-peptide bond to an amino acid sequence which forms/adopts random coil conformation, in particular, the random coil polypeptide (or polypeptide segment) as provided herein and consisting solely of proline and alanine residues.
• the present invention is not limited to "biologically or therapeutically active proteins" linked to the herein disclosed biosynthetic random coil polypeptide or polypeptide segment comprising an amino acid sequence consisting solely of proline and alanine amino acid residues, wherein said amino acid sequence consists of at least 50 proline (Pro) and alanine (Ala) amino acid residues.
• other proteins or molecules of interest as relevant for other industries, like food or beverage industry, cosmetic industry and the like, may be manufactured by the means and methods provided herein.
• amino acid sequence having and/or mediating said biological activity is located at the carboxy (C-) terminus and said "second domain” (i.e. the domain that comprises the herein provided random coil polypeptide (or segment thereof)) is located at the amino (N-) terminus of the biologically active protein.
• the domain order may, accordingly, be (from N-terminus to C-terminus): first domain (amino acid sequence having and/or mediating a biological activity) - second domain (random coil polypeptide (or segment thereof)).
• the domain order may be (from N-terminus to C-terminus): second domain (random coil polypeptide (or segment thereof)) - first domain (amino acid sequence having and/or mediating a biological activity).
• first domain amino acid sequence having and/or mediating a specific biological activity
• second domain random coil polypeptide (or segment thereof)
• first domain amino acid sequence having and/or mediating a specific biological activity
• second domain random coil polypeptide (or segment thereof)
• second domain random coil polypeptide (or segment thereof)
• domain orders in particular in cases where more than two "first domains” or “more than two “second domains” are comprised in the biologically active protein
• said domain(s) comprising an amino acid sequence having and/or mediating the said biological activity may also be a biologically active fragment of a given protein with a desired biological function.
• the herein defined "second domain” preferably comprising the herein provided random coil polypeptide (or segment thereof)
• the biologically active proteins of the invention which are modified to comprise a random coil polypeptide surprisingly exhibit an increased in vivo and/or in vitro stability when compared to unmodified biologically active proteins that lack said random coil domain.
• in vivo stability relates to the capacity of a specific substance that is administered to the living body to remain biologically available and biologically active. In vivo, a substance may be removed and/or inactivated due to excretion, kidney filtration, liver uptake, aggregation, degradation and/or other metabolic processes.
• the present Figures and experimental information in the corresponding figure legends provide for illustrative examples, wherein the herein disclosed drug conjugates comprise (i) a biosynthetic random coil polypeptide or polypeptide segment comprising an amino acid sequence consisting solely of proline and alanine amino acid residues, wherein said amino acid sequence consists of at least 50 proline (Pro) and alanine (Ala) amino acid residues, and (ii) a small molecule, which is, as illustration, selected from digoxigenin and fluorescein. It is of note that these are not only academic examples.
• the N-terminal amino group can be chemically coupled with a wide variety of functional groups such as aldehydes and ketones (to form Schiff bases, which may be reduced to amines using sodium borohydride or sodium cyanoborohydride, for example) or to activated carbonic acid derivatives (anhydrides, chlorides, esters and the like, to form amides) or to other reactive chemicals such as isocyanates, isothiocyanates, sulfonly chlorides etc.
• functional groups such as aldehydes and ketones (to form Schiff bases, which may be reduced to amines using sodium borohydride or sodium cyanoborohydride, for example) or to activated carbonic acid derivatives (anhydrides, chlorides, esters and the like, to form amides) or to other reactive chemicals such as isocyanates, isothiocyanates, sulfonly chlorides etc.
• the present invention also relates to a nucleic acid molecule encoding the random coil polypeptide or polypeptide segment as comprised in the conjugates provided herein, like a drug conjugate as defined herein, or a nucleic acid molecule encoding a protein conjugate that comprises a biologically active protein as defined above and that comprises, additionally, a biosynthetic random coil polypeptide or polypeptide segment comprising an amino acid sequence consisting solely of proline and alanine amino acid residues, wherein said amino acid sequence consists of at least 50 proline (Pro) and alanine (Ala) amino acid residues.
• nucleic acid molecule as provided herein above said nucleic acid molecule parts/segments (ii) and (iii) are interchanged in their position on said nucleic acid molecule encoding for a conjugate, like a drug conjugate or a food conjugate.
• a nucleic acid molecule would comprise the following order of parts/segments:
• nucleic acid sequence that represents or is a translational stop codon.
• the nucleic acid molecules as provided herein above may also, optionally, comprise, between parts/segments (i) and (ii) and/or between parts/segments (ii) and (iii), a protease and/or a chemical cleavage site and/or a recognition site.
• chemical cleavage sites are well known in the art, and comprise for example specific, individual amino acid sequences (see, e.g. Lottspeich and Engels (Hrsg.) (2006) Bioanalytik. 2. Auflage. Spektrum Akademischer Verlag, Elsevier, Miinchen, Germany).
• nucleic acid molecule encoding the biosynthetic random coil polypeptide or polypeptide segment comprising an amino acid sequence consisting solely of proline and alanine amino acid residues of the present invention is useful in methods as also provided herein below and as illustrated in the appended examples and figures.
• Such an expressed random coil polypeptide or random coil polypeptide segment can be isolated form, e.g. host cells expressing such a random coil polypeptide or random coil polypeptide segment.
• host cells may be transfected cells, for example with an vector as provided herein. Therefore, it is envisaged to transfect cells with the nucleic acid molecule or vectors as described herein.
• the vectors containing the nucleic acid molecules of the invention can be transfected into the host cell by well known methods, which vary depending on the type of cell. Accordingly, the invention further relates to a cell comprising said nucleic acid molecule or said vector. Such methods, for example, include the techniques described in Sambrook (1989), loc. cit. and Ausubel (1989), loc. cit. Accordingly, calcium chloride transfection or electroporation is commonly utilized for prokaryotic cells, whereas calcium phosphate treatment or electroporation may be used for other cellular hosts (Sambrook (1989), loc. cit.). As a further alternative, the nucleic acid molecules and vectors of the invention can be reconstituted into liposomes for delivery to target cells.
• the random coil polypeptide (or segment thereof) per se of the present invention does, preferably not comprises any chemically reactive group, except for, possibly, one N-terminal primary (or, in the case of proline, secondary) amino group and one carboxylate group at the C-terminus of the polymer.
• the biosynthetic random coil polypeptide/polymer as provided herein may comprise a chemically reactive group, for example when said random coil polypeptide/polymer is part of a "fusion protein'V'fusion construct".
• said biosynthetic random coil polypeptide or polypeptide segment comprising an amino acid sequence consisting solely of proline and alanine amino acid residues may be chemically linked or coupled to a molecule of interest, as also shown in the appended examples.
• the molecule of interest may be enzymatically conjugated e.g. via transglutaminase (Besheer (2009) J Pharm Sci. 98:4420-8) or other enzymes (Subul (2009) Org. Biomol. Chem. 7:3361-3371) to the said biosynthetic random coil polypeptide or polypeptide segment comprising an amino acid sequence consisting of proline and alanine amino acid residues.
• the invention further relates to the use of the biologically active protein, the random coil polypeptide (or segment thereof) or the conjugates, like the drug conjugates of the invention, the nucleic acid molecule of the invention, the vector of the invention or the (host) cell of the invention for the preparation of a medicament, wherein said biologically active protein or drug (or any other small molecule or protein of interest) has an increased in vivo and/or in vitro stability as compared to a control molecule that does not comprise or that is not linked to a biosynthetic random coil polypeptide or polypeptide segment comprising an amino acid sequence consisting solely of proline and alanine amino acid residues, wherein said amino acid sequence consists of at least 50 proline (Pro) and alanine (Ala) amino acid residues.
• the present invention also relates to the use of the nucleic acid molecules, vectors as well as transfected cells as provided herein and comprising the nucleic acid molecules or vectors of the present invention in medical approaches, like, e.g. cell based gene therapy approaches or nucleic acid based gene therapy approaches.
• the present invention also provides for uses of the biosynthetic random coil polypeptide as provided herein in such industrial areas.
• the kit of the present invention may be advantageously used, inter alia, for carrying out the method of the invention and could be employed in a variety of applications referred herein, e.g., as diagnostic kits, as research tools or as medical tools. Additionally, the kit of the invention may contain means for detection suitable for scientific, medical and/or diagnostic purposes.
• the manufacture of the kits preferably follows standard procedures which are known to the person skilled in the art. The invention is further illustrated by the following, non-limiting Figures and Examples.
• the plasmid backbone outside the expression cassette flanked by the Xbal and Hindlll restriction sites is identical with that of the generic cloning and expression vector pASK75 (Skerra (1994) loc. cit). Singular restriction sites are indicated.
• the recombinant proteins were produced in E. coli KS272 (Strauch (1988) Proc. Natl. Acad. Sci. USA 85: 1576-80) via periplasmic secretion and purified by means of the His 6 -tag (Fab) or the Strep-tag II (IFNa2b) using immobilized metal or streptavidin affinity chromatography, respectively.
• Fab His 6 -tag
• IFNa2b Strep-tag II
• the structural gene for biologically active protein His6-PA#l(200)-hGH (comprising the bacterial OmpA signal peptide, the His6-tag, the PA#1 polymer/polypeptide segment with 200 residues, and human GH) is under transcriptional control of the tetracycline promoter/operator (tet p/o ) and ends with the lipoprotein terminator (ti pp ).
• the plasmid backbone outside the expression cassette flanked by the Xbal and HindlU restriction sites is identical with that of the generic cloning and expression vector pASK75 (Skerra (1994) loc. cit). Singular restriction sites are indicated.
• the structural gene comprising the human growth hormone signal peptide (Sp), the His 6 -tag, the PA#1 polymer/polypeptide sequence with 200 residues (PA# 1(200)), the human growth hormone (hGH), and containing the bovine growth hormone polyadenylation signal (bGH pA), is under transcriptional control of the cytomegalus virus promoter (CMV P ).
• CMV P cytomegalus virus promoter
• the two proteins appear as single bands indicated by arrows, with apparent molecular sizes of ca. 23 kDa (His6-hGH) and ca. 90 kDa (His6-PA#1- hGH). There is also a weak band around 60 kDa arising from serum proteins in the culture medium. Whereas the His6-tagged hGH appears at the calculated mass of 23.5 kDa, the apparent molecular size of His6-PA#l-hGH is significantly larger than its calculated mass of 39.5 kDa. This effect is due to the hydrophilic random coil nature of the Pro-Ala polymer.
• Figure 7 Theoretical prediction of secondary structure for the PA#1 Pro/Ala polypeptide/polymer sequence.
• the recombinant proteins were produced in E. coli KS272 via periplasmic secretion and purified by means of the His 6 -tag using immobilized metal affinity chromatography.
• the purified proteins were analyzed by 12 % SDS-PAGE.
• the gel shows 2 ⁇ g protein samples each of Fab-P1A1(200) and Fab-P1A3(200) as well as, for comparison, of the unfused Fab fragment (cf. Figure 3A). Samples on the left were reduced with 2- mercaptoethanol whereas analogous samples on the right were left unreduced. Sizes of protein markers - applied under reducing conditions - are indicated on the left margin.
• Example 2 Construction of pFab-PA#l(200) as expression vector for a Fab-PA#1 fusion protein.
• plasmid was prepared and the presence of the correct insert was confirmed by restriction analysis.
• the resulting plasmid was designated pPA#l(200)-IFNa2b (SEQ ID NO: 37) (Fig. 2F).
• Example 5 Bacterial production and purification of fusion proteins between IFNa2b and a genetically encoded PA#1 polymer/polypeptide.
• Periplasmic extraction in the presence of 500 mM sucrose, 1 mM EDTA, 100 mM Tris/HCl pH 8.0 containing 50 ⁇ ig/ml lysozyme was performed as described elsewhere (Breustedt (2005) loc. cit.) and followed by purification via the Strep-tag II using streptavidin affinity chromatography (Schmidt (2007) Nat. Protoc. 2: 1528-1535) in the presence of 150 mM NaCl, 1 mM EDTA, 100 mM Tris/HCl, pH 8.0.
• the fusion protein with the 200 residue PA#1 polymer/polypeptide exhibited a significantly larger size than corresponding globular proteins with the same molecular weight (Fig. 4D).
• the apparent size increase for PA#l(200)-IFNa2b was 10.2-fold compared with the unfused IFNa2b protein whereas the true mass was only larger by 1.8-fold.
• This observation clearly indicates a much increased hydrodynamic volume conferred to the biologically active interferon by the Pro/- Ala polymer/polypeptide according to this invention.
• Example 8 Detection of random coil conformation for the biosynthetic PA#1 polymer fused to a Fab fragment via circular dichroism spectroscopy.
• the vector pASK75-His6-PA#l(200)-hGH (SEQ ID NO: 46), a derivative of pASK75 (Skerra (1994) loc. cit), allowing prokaryotic production of the hGH PA#1 fusion protein, was cut with Nhel and HmdIII. This fragment was purified via agarose gel electrophoresis and ligated with the correspondingly cut vector pCHO (SEQ ID NO: 50). After transformation of E. coli XLl-Blue (Bullock (1987) loc. cit.), plasmid was prepared and the correct insertion of the fragment was verified via restriction analysis.
• the membrane was incubated with 10 ml of a 1 : 1000 dilution of anti human growth hormone antibody abl956 conjugated with horse radish peroxidase (Abeam, Cambridge, UK). After incubation for 1 h and washing the membrane twice for 5 min with 20 ml PBST and twice for 5 min with PBS, the chromogenic reaction was performed in the presence of 15 ml of SIGMAFASTTM 3,3-diaminobenzidine solution (Sigma-Aldrich Chemie, Kunststoff, Germany). The reaction was stopped by washing with water and air-drying of the membrane. The blot revealed signals for both recombinant protein samples (Fig. 6E), thus proving secretory production of the hGH fusion protein with the PA#1 polypeptide in CHO cells.
• Example 15 Measurement of binding affinity of human growth hormone and its PA#1 polymer fusions towards the extracellular domain of human growth hormone receptor using surface plasmon resonance.
• the wells of a 96 well microtiter plate were coated overnight at 4 °C with 50 ⁇ of a 10 ⁇ g/ml solution of recombinant Her2/ErbB2 ectodomain antigen in 50 mM NaHC0 3 pH 9.6. Then, the wells were blocked with 200 ⁇ of 3 % (w/v) BSA in PBS for 1 h and washed three times with PBS/T (PBS containing 0.1 % (v/v) Tween 20).
• the plasma samples were applied in dilution series in PBS/T containing 0.5 % (v/v) mouse plasma from an untreated animal and incubated for 1 h. The wells were then washed three times with PBS/T and incubated for 1 h with 50 ⁇ of a 1 : 1000 diluted solution of an anti-human CK antibody alkaline phosphatase conjugate in PBS/T. After washing twice with PBS/T and twice with PBS the chromogenic reaction was started by adding 50 ⁇ of 0.5 ⁇ g/ml p-nitrophenyl phosphate in 100 mM Tris/HCl pH 8.8, 100 mM NaCl.
• the fusion proteins with the 200 residue PlAl or P1A3 polymers/polypeptides exhibited significantly larger sizes than the corresponding unfused Fab fragment.
• the apparent size increase for Fab-P1A1(200) and Fab-P1A3(200) was 5.8-fold and 5.2-fold, respectively, compared with the Fab fragment (cf. Fig. 4B) whereas the true mass was only larger by 1.4-fold and 1.3-fold. This observation clearly indicates a much increased hydrodynamic volume conferred to the biologically active Fab fragment by the biosynthetic P1A1 and PI A3 polypeptide segments according to this invention.
• the 5 '-primer introduced an Ndel restriction site, containing a Met start codon (ATG) and an additional Lys codon, as well as the His6-tag encoding sequence while the 3 '-primer introduced a HmdIII and Sapl restriction site into the PGR product.
• the resulting DNA fragment was digested with Ndel and HmdIII and ligated with a correspondingly digested derivative of the plasmid pSAl (Schmidt (1994) J. Chromatogr. 676: 337-345), wherein the Sapl restriction site had been eliminated by silent mutation.
• the PA# 1 (200) polypeptide (calculated mass: 16.1 kDa) was initially produced as fusion protein with the small ubiquitin-like modifier (SUMO) protein (calculated mass: 12.2 kDa) in the cytoplasm of E. coli BLR(DE3) (NEB, Ipswich, MA, USA) harboring the expression plasmid pSUMO-PA# 1(200) (described in Example 21) together with the plasmid pLysE (Studier (1991) J. Mol. Biol. 219: 37-44), which suppresses the the T7 promoter.
• SUMO small ubiquitin-like modifier
• Bacterial production was performed at 30 °C in shake flask cultures with 2 L LB medium containing 2.5 g/L D-glucose, 0.5 g/L L-proline, 100 mg/1 ampicillin, and 30 mg/1 chloramphenicol. Recombinant gene expression was induced by addition of isopropyl- ⁇ - ⁇ - thiogalactopyranoside (IPTG) to a final concentration of 0.5 mM. Bacteria were harvested 3 h after induction, resuspended in 100 mM NaCl, 40 mM Na-phosphate pH 7.5 and lysed using a French pressure cell (Thermo Scientific, Waltham, MA, USA). After centrifugation (15 min, 15000 g) of the lysate no inclusion bodies were observed.
• IPTG isopropyl- ⁇ - ⁇ - thiogalactopyranoside
• biosynthetic PA# 1(200) polypeptide/polymer (SEQ ID NO: 61) prepared in this manner comprises altogether 201 amino acid residues, which arise from the encoded combined gene product of 10 ligated double-stranded oligodeoxynucleotide building blocks, each encoding 20 amino acid residues, as shown in Figure 1, and an additional Ala residue encoded by the triplet DNA overhang of the downstream Sapl restriction site that was used for cloning.
• Example 22 Preparation and characterization of small molecule/drug conjugates with PA# 1 (200).
• globular proteins for size calibration of the chromatography column ( Figure 13 L), 250 ⁇ of an appropriate mixture of the following globular proteins (Sigma-Aldrich) were applied in PBS at concentrations between 0.2 and 0.5 mg/ml: aprotinin, 6.5 kDa; cytochrome c, 12.4 kDa; carbonic anhydrase, 29.0 kDa; bovine serum albumin, 66.3 kDa; alcohol dehydrogenase, 150 kDa; ⁇ -amylase, 200 kDa; apo-fcrritin. 440 kDa.
• the present invention relates to and refers to the following exemplified sequences, whereby the appended sequence listing is presented as part of the description and is, accordingly a part of this specification.
• SEQ ID NO: 3 shows the amino acid sequence of PA#3.
• SEQ ID NO: 6 shows the amino acid sequence of PA#6.
• SEQ ID NO: 9 shows an amino acid sequence of a circular permutated version of SEQ ID NO: 1.
• SEQ ID NO: 10 shows an amino acid sequence of a circular permutated version of SEQ ID NO: 1.
• SEQ ID NO: 17 shows a nucleic acid sequence of the upper/coding strand oligodeoxynucleotide used for the generation of building block PA#1.
• SEQ ID NO: 21 shows an amino acid sequence of the C-terminus of the light chain of the Fab fragment as encoded on pASK88-Fab-2xSapI.
• SEQ ID NO: 29 shows the nucleic acid sequence (upper/coding strand) encoding the amino acid sequence of the N-terminus of INFa2b and Strep-tag II (only the last two amino acids).
• SEQ ID NO: 32 shows the nucleic acid sequence of pASK-IFNa2b.
• SEQ ID NO: 34 shows a nucleic acid sequence stretch (lower/non-coding strand) of the C- terminus of Strep-tag II and the N-terminus of IFNa2b after insertion of one PA#1 polymer sequence cassette.
• SEQ ID NO: 37 shows the nucleic acid sequence of pPA#l(200)-IFNa2b.
• SEQ ID NO: 53 shows the nucleic acid sequence of lower/non-coding strand oligodesoxynucleotide used for the generation of the building block for PI Al .
• SEQ ID NO: 58 shows the nucleic acid sequence of pFab-Pl Al(200).
• SEQ ID NO: 61 shows the PA# 1(200) polypeptide/polymer used for the preparation of drug conjugates (made by ligation of 10 20mer encoding gene cassettes, including one additional C-terminal Ala residue resulting from the downstream ligation site.

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