Patent Grant
9879249
The field of protein and small molecule therapeutics has advanced greatly, providing a number of clinically beneficial drugs and promising to provide more with the years to come. Protein therapeutics can provide several advantages in therapies, due to, for example, exquisite specificity, multiplicity of functions and relatively low off-target activity, resulting in fewer side effects. With the development of sophisticated screening methods, small molecule drugs have also advanced in specificity of action.
Often, though, such therapeutics can be further improved by providing for enhanced activity following administration. For example, it is often desirable to increase the serum half-life of the therapeutic (e.g., in order to reduce the overall dose and/or the number of administrations required over a dosage period). Alternatively or in addition, therapeutics could benefit from improving their bioavailability. For example, some drugs may benefit from improving solubility in the relevant physiological environment and/or to facilitation formulation (e.g., to increase shelf-life). Moreover, conjugation of a drug to a carrier protein can be difficult to control, resulting in a heterogeneous mixture of conjugates that differ in the number of drug molecules attached. This can make controlling the amount administered to a patient difficult.
There is a need for methods and compositions that provide drug conjugates.
The disclosure provides aldehyde-tagged protein carriers that can be covalently and site-specifically bound to drug to provide a drug-containing scaffold. The disclosure also provides methods of production of such drug-containing scaffolds and intermediates, as well as methods of use.
Accordingly, the present disclosure provides carrier protein-drug conjugates composed of a carrier protein and a covalently bound drug, wherein the carrier protein comprises a modified sulfatase motif of the formula:
X1(FGly′)X2Z2X3Z3
where FGly′ is of the formula:
wherein J1 is the covalently bound drug;
each L1 is a divalent moiety independently selected from alkylene, substituted alkylene, alkenylene, substituted alkenylene, alkynylene, alkynylene, arylene, substituted arylene, cycloalkylene, substituted cycloalkylene, heteroarylene, substituted heteroarylene, heterocyclene, substituted heterocyclene, acyl, amido, acyloxy, urethanylene, thioester, sulfonyl, sulfonamide, sulfonyl ester, —O—, —S—, —NH—, and substituted amine;
n is a number selected from zero to 40;
Z2 is a proline or alanine residue;
X1 is present or absent and, when present, is any amino acid, with the proviso that when the sulfatase motif is at an N-terminus of the polypeptide, X1 is present;
X2 and X3 are each independently any amino acid; and
Z3 is a basic amino acid, and
wherein the carrier protein presents the covalently bound drug on a solvent-accessible surface when in a folded state.
In some embodiments, the carrier protein-drug conjugate contains two or more modified sulfatase motifs, and can contain three or more modified sulfatase motifs.
In further embodiments the modified sulfatase motifs of the carrier protein-drug conjugate are positioned in the carrier protein-drug conjugate at at least one of an N-terminus of the carrier protein, a C-terminus of the carrier protein, and a solvent-accessible loop of the carrier protein.
The modified sulfatase motifs of the carrier protein-drug conjugate can be provided as a concatamer composed of modified sulfatase motifs separated by a flexible linker.
In one exemplar, the carrier protein of the carrier protein-drug conjugate is albumin. The covalently bound drug can be a peptide drug, such as glucagon-like peptide 1 (GLP-1) or a biologically active variant thereof, or calcitonin or a biologically active variant thereof. The covalently bound drug of the carrier protein-drug conjugate can be a small molecule drug (e.g., doxorubicin).
Exemplary carrier protein-drug conjugates include those where Z3 is arginine (R). In exemplary embodiments, X1, when present, X2, and X3 are each independently an aliphatic amino acid, a sulfur-containing amino acid, or a polar, uncharged amino acid. In specific examples, X1, when present, is L, M, V, S or T. In specific examples, X2 and X3 are each independently S, T, A, V, G, or C.
The disclosure also provides aldehyde-tagged carrier proteins having an amino acid sequence of:
X1Z1X2Z2X3Z3
where
Z1 is a cysteine, a serine, or a 2-formylglycine residue;
Z2 is a proline or alanine residue;
X1 is present or absent and, when present, is any amino acid, with the proviso that when the heterologous sulfatase motif is at an N-terminus of the aldehyde tagged polypeptide, X1 is present; and
X2 and X3 are each independently any amino acid; and
Z3 is a basic amino acid;
wherein the carrier protein presents the covalently bound drug on a solvent-accessible surface when in a folded state.
In some examples the aldehyde-tagged carrier protein contains two or more modified sulfatase motifs, and can contain three or more modified sulfatase motifs. In some examples, the modified sulfatase motifs are positioned in the aldehyde-tagged carrier protein at at least one of an N-terminus of the carrier protein, a C-terminus of the carrier protein, and a solvent-accessible loop of the carrier protein. In one example, the carrier protein is albumin
Exemplary aldehyde-tagged carrier proteins include those in which Z3 is arginine (R). Exemplary aldehyde-tagged carrier proteins include those in which X1, when present, X2, and X3 are each independently an aliphatic amino acid, a sulfur-containing amino acid, or a polar, uncharged amino acid. In specific examples of aldehyde-tagged carrier protein, X1, when present, is L, M, V, S or T. In specific examples of aldehyde-tagged carrier protein, X2 and X3 are each independently S, T, A, V, G, or C.
The disclosure also provides libraries of modified carrier proteins containing a population of aldehyde-tagged carrier proteins according to the present disclosure, or nucleic acid constructs encoding the aldehyde-tagged carrier proteins, where Z1 is a cysteine or serine residue, wherein the population comprises members having differently aldehyde-tagged carrier proteins. In some examples, the population of the library includes aldehyde-tagged carrier proteins having two or more aldehyde tags. In some examples, the wherein the population of the library includes aldehyde-tagged carrier proteins having at least one aldehyde tag at one or more of the N-terminus, the C-terminus, or an interior loop and the carrier protein. In some embodiments, the library is provided as a population of recombinant cells genetically modified to express the nucleic acid constructs.
The disclosure also provides methods of producing a carrier protein-drug conjugate by combining in a reaction mixture an aldehyde-tagged carrier protein having a 2-formyl-glycine residue (FGly′ at Z1) and a drug for conjugation to the carrier protein, wherein the drug has an aminooxy or hydrazide reactive group. The drug is provided in the reaction mixture in an amount sufficient to provide for a desired ratio of drug to carrier protein, said combining being under conditions suitable to promote reaction between an aldehyde of the carrier protein and reactive group of the drug to generate a carrier protein-drug conjugate. The carrier protein-drug conjugate is then isolated from the reaction mixture. In specific embodiments, the aldehyde-tagged carrier protein is folded prior to said combining.
The disclosure also provides formulations containing a carrier protein-drug conjugate of the present disclosure and a pharmaceutically acceptable excipient.
The disclosure also provides methods of treating a subject having or at risk of having condition amenable to treatment with glucagon-like peptide 1 (GLP-1) by administering to a subject in of treatment a carrier protein-drug conjugate of the present disclosure in which the covalently bound drug is glucagon-like peptide 1 (GLP-1) or a biologically active variant thereof, where administration is effective to treat the condition in the subject. The disclosure also provides methods of treating a subject having or at risk of having condition amenable to treatment with calcitonin by administering to a subject in of treatment a carrier protein-drug conjugate of the present disclosure in which the covalently bound drug is calcitonin or a biologically active variant thereof, where administration is effective to treat the condition in the subject.
The disclosure also provides recombinant nucleic acids having nucleic acid encoding an aldehyde-tagged carrier protein of the present disclosure in which Z1 is a cysteine residue or a serine residue.
Other features are provided below, and will be readily apparent to the ordinarily skilled artisan upon reading the present disclosure.
It is emphasized that, according to common practice, the various features of the drawings may not be to-scale. On the contrary, the dimensions of the various features are arbitrarily expanded or reduced for clarity. Included in the drawings are the following figures:
Before the present invention is described, it is to be understood that this invention is not limited to particular embodiments described, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only by the appended claims.
Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limits of that range is also specifically disclosed. Each smaller range between any stated value or intervening value in a stated range and any other stated or intervening value in that stated range is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included or excluded in the range, and each range where either, neither or both limits are included in the smaller ranges is also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the invention.
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, some potential and exemplary methods and materials are now described. All publications mentioned herein are incorporated herein by reference to disclose and describe the methods and/or materials in connection with which the publications are cited. It is understood that the present disclosure supersedes any disclosure of an incorporated publication to the extent there is a contradiction.
It must be noted that as used herein and in the appended claims, the singular forms “a”, “an”, and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “an aldehyde tag” includes a plurality of such tags and reference to “the polypeptide” includes reference to one or more polypeptides and equivalents thereof known to those skilled in the art, and so forth.
It is further noted that the claims may be drafted to exclude any element which may be optional. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as “solely”, “only” and the like in connection with the recitation of claim elements, or the use of a “negative” limitation.
It is appreciated that certain features of the invention, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the invention, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable sub-combination. All combinations of the embodiments pertaining to the invention are specifically embraced by the present invention and are disclosed herein just as if each and every combination was individually and explicitly disclosed, to the extent that such combinations embrace subject matter that are, for example, compounds that are stable compounds (i.e., compounds that can be made, isolated, characterized, and tested for biological activity). In addition, all sub-combinations of the various embodiments and elements thereof (e.g., elements of the chemical groups listed in the embodiments describing such variables) are also specifically embraced by the present invention and are disclosed herein just as if each and every such sub-combination was individually and explicitly disclosed herein.
The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention. Further, the dates of publication provided may be different from the actual publication dates which may need to be independently confirmed.
Definitions
The terms “polypeptide”, “peptide” and “protein” are used interchangeably herein to refer to a polymeric form of amino acids of any length. Unless specifically indicated otherwise, “polypeptide”, “peptide” and “protein” can include genetically coded and non-coded amino acids, chemically or biochemically modified or derivatized amino acids, and polypeptides having modified peptide backbones. The term includes fusion proteins, including, but not limited to, fusion proteins with a heterologous amino acid sequence, fusions with heterologous and homologous leader sequences, proteins which contain at least one N-terminal methionine residue (e.g., to facilitate production in a recombinant bacterial host cell); immunologically tagged proteins; and the like.
“Native amino acid sequence” or “parent amino acid sequence” are used interchangeably herein in the context of a carrier protein to refer to the amino acid sequence of the carrier protein prior to modification to include a heterologous aldehyde tag.
By “aldehyde tag” or “ald-tag” is meant an amino acid sequence that contains an amino acid sequence derived from a sulfatase motif which is capable of being converted, or which has been converted, by action of a formylglycine generating enzyme (FGE) to contain a 2-formylglycine residue (referred to herein as “FGly”). Although this is technically incorrect, the FGly residue generated by an FGE is often referred to in the literature as a “formylglycine”. Stated differently, the term “aldehyde tag” is used herein to refer to an amino acid sequence comprising an “unconverted” sulfatase motif (i.e., a sulfatase motif in which the cysteine or serine residues has not been converted to FGly by an FGE, but is capable of being converted) as well as to an amino acid sequence comprising a “converted” sulfatase motif (i.e., a sulfatase motif in which the cysteine or serine residues has been converted to FGly by action of an FGE).
By “conversion” as used in the context of action of a formylglycine generating enzyme (FGE) on a sulfatase motif refers to biochemical modification of a cysteine or serine residue in a sulfatase motif to a formylglycine (FGly) residue (e.g., Cys to FGly, or Ser to FGly).
“Modification” encompasses addition, removal, or alteration of a moiety. As used in the context of a polypeptide having a converted sulfatase motif, “modification” is meant to refer to chemical or biochemical modification of an FGly residue of an aldehyde tag of a polypeptide through reaction of the FGly aldehyde moiety with a reactive partner. As discussed above, the term “conversion” refers to a type of biochemical modification of an FGly residue of an aldehyde tag mediated by an FGE. An aldehyde tag that is modified by reaction of an FGly with a reactive partner as described herein is sometimes referred to as a “modified ald tag” or an aldehyde tag containing “FGly′”.
By “genetically-encodable” as used in reference to an amino acid sequence of polypeptide, peptide or protein means that the amino acid sequence is composed of amino acid residues that are capable of production by transcription and translation of a nucleic acid encoding the amino acid sequence, where transcription and/or translation may occur in a cell or in a cell-free in vitro transcription/translation system.
The term “control sequences” refers to DNA sequences to facilitate expression of an operably linked coding sequence in a particular expression system, e.g. mammalian cell, bacterial cell, cell-free synthesis, etc. The control sequences that are suitable for prokaryote systems, for example, include a promoter, optionally an operator sequence, and a ribosome binding site. Eukaryotic cell systems may utilize promoters, polyadenylation signals, and enhancers.
A nucleic acid is “operably linked” when it is placed into a functional relationship with another nucleic acid sequence. For example, DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide; a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate the initiation of translation. Generally, “operably linked” means that the DNA sequences being linked are contiguous, and, in the case of a secretory leader, contiguous and in reading frame. Linking is accomplished by ligation or through amplification reactions. Synthetic oligonucleotide adaptors or linkers may be used for linking sequences in accordance with conventional practice.
The term “expression cassette” as used herein refers to a segment of nucleic acid, usually DNA, that can be inserted into a nucleic acid (e.g., by use of restriction sites compatible with ligation into a construct of interest or by homologous recombination into a construct of interest or into a host cell genome). In general, the nucleic acid segment comprises a polynucleotide that encodes a polypeptide of interest (e.g., an aldehyde tagged-carrier protein), and the cassette and restriction sites are designed to facilitate insertion of the cassette in the proper reading frame for transcription and translation. Expression cassettes can also comprise elements that facilitate expression of a polynucleotide encoding a polypeptide of interest in a host cell. These elements may include, but are not limited to: a promoter, a minimal promoter, an enhancer, a response element, a terminator sequence, a polyadenylation sequence, and the like.
As used herein the term “isolated” is meant to describe a compound of interest that is in an environment different from that in which the compound naturally occurs. “Isolated” is meant to include compounds that are within samples that are substantially enriched for the compound of interest and/or in which the compound of interest is partially or substantially purified.
As used herein, the term “substantially purified” refers to a compound that is removed from its natural environment and is at least 60% free, usually 75% free, and most usually 90% free from other components with which it is naturally associated.
The term “physiological conditions” is meant to encompass those conditions compatible with living cells, e.g., predominantly aqueous conditions of a temperature, pH, salinity, etc. that are compatible with living cells.
By “heterologous” is meant that a first entity and second entity are provided in an association that is not normally found in nature. For example, a protein containing a “heterologous” sulfatase motif or “heterologous” ald-tag is a protein that does not normally contain a sulfatase motif at that position within its amino acid sequence (e.g., proteins which have a single, native sulfatase motif can contain a second sulfatase motif that is “heterologous”; further proteins which contain a sulfatase motif can be modified so as to reposition the sulfatase motif, rendering the re-positioned sulfatase motif “heterologous” to the protein). In some embodiments, a heterologous sulfatase motif is present in a polypeptide which contains no native sulfatase motif.
By “reactive partner” is meant a molecule or molecular moiety that specifically reacts with another reactive partner to produce a reaction product. Exemplary reactive partners include an cysteine or serine of sulfatase motif and a formylglycine generating enzyme (FGE), which react to form a reaction product of a converted aldehyde tag containing a FGly in lieu of cysteine or serine in the motif. Other exemplary reactive partners include an aldehyde of a formylglycine (FGly) residue of a converted aldehyde tag and a reactive partner reagent comprising a moiety of interest, which react to form a reaction product of a modified aldehyde tagged polypeptide having the moiety of interest conjugated to the aldehyde tagged polypeptide at the FGly residue.
“N-terminus” refers to the terminal amino acid residue of a polypeptide having a free amine group, which amine group in non-N-terminus amino acid residues normally forms part of the covalent backbone of the polypeptide.
“C-terminus” refers to the terminal amino acid residue of a polypeptide having a free carboxyl group, which carboxyl group in non-C-terminus amino acid residues normally forms part of the covalent backbone of the polypeptide.
By “N-terminal” is meant the region of a polypeptide that is closer to the N-terminus than to the C-terminus.
By “C-terminal” is meant the region of a polypeptide that is closer to the C-terminus than to the N-terminus.
By “internal site” as used in referenced to a polypeptide or an amino acid sequence of a polypeptide means a region of the polypeptide that is not at the N-terminus or at the C-terminus, and includes both N-terminal and C-terminal regions of the polypeptide.
Introduction
The present disclosure provides aldehyde-tagged protein carriers that can be covalently and site-specifically bound to drug to provide a drug-containing scaffold, as well as methods of production of such drug-containing scaffolds and intermediates, as well as methods of use. Aldehyde-tagged carrier proteins may also be referred to herein as “ald-tagged carrier proteins”, “ald-tagged protein scaffolds” or “ald-tagged scaffolds”. Such Ald-tagged scaffolds can be site-specifically decorated with a covalently bound molecule of interest, such as a drug (e.g., a peptide, a small molecule drug, and the like). Such drug-scaffold conjugates can provide for enhanced serum half-life of the drug.
The compositions and methods of the present disclosure exploit a naturally-occurring, genetically-encodable sulfatase motif for use as a tag, referred to herein as an “aldehyde tag” or “ald tag”, to direct site-specific modification of the carrier protein. The sulfatase motif of the aldehyde tag, which is based on a motif found in active sites of sulfatases, contains a serine or cysteine residue that is capable of being converted (oxidized) to a 2-formylglycine (FGly) residue by action of a formylglycine generating enzyme (FGE) either in vivo (e.g., at the time of translation of an ald tag-containing protein in a cell) or in vitro (e.g., by contacting an ald tag-containing protein with an FGE in a cell-free system). The aldehyde moiety of the resulting FGly residue can be used as a “chemical handle” to facilitate site-specific chemical modification of the protein, and thus site-specific attachment of a drug of interest. For example, a peptide modified to contain an α-nucleophile-containing moiety (e.g., an aminooxy or hydrazide moiety) can be reacted with the FGly-containing carrier protein to yield a conjugate in which the carrier protein and peptide are linked by a hydrazone or oxime bond, respectively. The reactivity of the aldehyde thus allows for bioorthongonal and chemoselective modification of the carrier protein, and thus provides a site-specific means for chemical modification that in turn can be exploited to provide for site-specific attachment of a moiety of interest in the final conjugate.
For illustrative purposes, a schematic of production of an ald-tagged carrier protein is provided in
Exemplary methods and compositions for practice of the invention will now be described in more detail.
Aldehyde Tags
In general, an aldehyde tag (“ald tag”) can be based on any amino acid sequence derived from a sulfatase motif (also referred to as a “sulfatase domain”), which is capable of being converted by action of a formylglycine generating enzyme (FGE) to contain a formylglycine (FGly). Action of FGE is directed in a sequence-specific manner in that the FGE acts at a sulfatase motif, but this sulfatase motif can be positioned within any region of carrier protein. Thus, FGE-mediated conversion of a sulfatase motif is site-specific (i.e., in that FGE acts at the amino acid sequence of a sulfatase motif) but the ability of FGE to act upon the sulfatase motif is sequence context-independent (i.e., the ability of the FGE to convert a cysteine/serine of a sulfatase motif is independent of the sequence context in which the sulfatase motif is presented in the carrier protein).
Exemplary Aldehyde Tags
A minimal sulfatase motif of an aldehyde tag is usually about 5 or 6 amino acid residues in length, usually no more than 6 amino acid residues in length. In general, it is normally desirable to minimize the extent of modification of the native amino acid sequence of the carrier protein, so as to minimize the number of amino acid residues that are inserted, deleted, substituted (replaced), or added (e.g., to the N- or C-terminus). Minimizing the extent of amino acid sequence modification of the carrier protein is usually desirable so as to minimize the impact such modifications may have upon carrier protein structure and/or immunogenicity. Thus, aldehyde tags of particular interest include those that require modification (insertion, addition, deletion, substitution/replacement) of less than 16, 15, 14, 13, 12, 11, 10, 9, 8, or 7 amino acid residues of the amino acid sequence of the carrier protein (e.g., the carrier polypeptide).
It should be noted that while aldehyde tags of particular interest are those based on a minimal sulfatase motif, it will be readily appreciated that longer aldehyde tags are both contemplated and encompassed by the present disclosure and can find use in the compositions and methods of the invention. Aldehyde tags can thus comprise a minimal sulfatase motif of 5 or 6 residues, or can be longer and comprise a minimal sulfatase motif which can be flanked at the N- and/or C-terminal sides of the motif by additional amino acid residues. Aldehyde tags of, for example, 5 or 6 amino acid residues are contemplated, as well as longer amino acid sequences of more than 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more amino acid residues.
In general, sulfatase motifs useful in aldehyde tags as described herein are of the formula:
X1Z1X2Z2X3Z3 (I)
or, in an exemplary embodiment
X1Z1X2Z2X3R (Ia)
where
Z1 is cysteine or serine (which can also be represented by (C/S));
Z2 is either a proline or alanine residue (which can also be represented by (P/A));
Z3 is a basic amino acid, and may be arginine (R), lysine (K) or histidine (H), usually lysine), or an aliphatic amino acid (alanine (A), glycine (G), leucine (L), valine (V), isoleucine (I), or proline (P), usually A, G, L, V, or I (in Formula (Ia) Z3 is arginine (R));
X1 is present or absent and, when present, can be any amino acid, though usually an aliphatic amino acid, a sulfur-containing amino acid, or a polar, uncharged amino acid, (i.e., other than a aromatic amino acid or a charged amino acid), usually L, M, V, S or T, more usually L, M, S or V, with the proviso that when the sulfatase motif is at the N-terminus of the carrier protein, X1 is present; and
X2 and X3 independently can be any amino acid, though usually an aliphatic amino acid, a polar, uncharged amino acid, or a sulfur containing amino acid (i.e., other than a aromatic amino acid or a charged amino acid), usually S, T, A, V, G or C, more usually S, T, A, V or G.
It should be noted that, following action of an FGE on the sulfatase motif, Z1 is oxidized to generate a 2-formylglycine (FGly) residue. Furthermore, following both FGE-mediated conversion and reaction with a reactive partner of a drug of interest, FGly position at Z1 in the formula above is covalently bound to the drug (e.g., a peptide drug, etc). The reactive partner generally is an α-nucleophile, such as an aminooxy or hydrazide group, and provides for linkage of the carrier protein to the drug through an oxime or hydrazone linkage. Thus the carrier protein and drug are not linked through an amide bond, as may be found in other drug conjugates based on recombinant fusion protein technology.
Where the aldehyde tag is present at a location other than the N-terminus of the carrier protein, X1 of the formula above can be provided by an amino acid residue of the native amino acid sequence of the carrier protein. Therefore, in some embodiments, and when present at a location other than the N-terminus of a carrier protein, sulfatase motifs are of the formula:
(C/S)X1(P/A)X2Z3 (II)
or, in an exemplary embodiment
(C/S)X1(P/A)X2R (IIa)
where X1 and X2 independently can be any amino acid, though usually an aliphatic amino acid, a polar, uncharged amino acid, or a sulfur-containing amino acid (i.e., other than an aromatic amino acid or a charged amino acid), usually S, T, A, V, or C, more usually S, T, A, or V. Z3 in Formula II is defined as above.
As noted above, the sulfatase motif can contain additional residues at one or both of the N- and C-terminus of the sequence, e.g., such that the aldehyde tag includes both a sulfatase motif and an “auxiliary motif”. In one embodiment, the sulfatase motif includes an auxiliary motif at the C-terminus (i.e., following the arginine residue in the formula above) 1, 2, 3, 4, 5, 6, or all 7 of the contiguous residues of an amino acid sequence of AALLTGR (SEQ ID NO:46), SQLLTGR (SEQ ID NO:47), AAFMTGR (SEQ ID NO:48), AAFLTGR (SEQ ID NO:49), SAFLTGR (SEQ ID NO:50), ASILTGK (SEQ ID NO:51), VSFLTGR (SEQ ID NO:52), ASLLTGL (SEQ ID NO:53), ASILITG (SEQ ID NO:54), VSFLTGR (SEQ ID NO:55), SAIMTGR (SEQ ID NO:56), SAIVTGR (SEQ ID NO:57), TNLWRG (SEQ ID NO:58), TNLWRGQ (SEQ ID NO:59), TNLCAAS (SEQ ID NO:60), VSLWTGK (SEQ ID NO:61), SMLLTG (SEQ ID NO:62), SMLLTGN (SEQ ID NO:63), SMLLTGT (SEQ ID NO:64), ASFMAGQ (SEQ ID NO:65), or ASLLTGL (SEQ ID NO:66), (see, e.g., Dierks et al. (1999) EMBO J 18(8): 2084-2091), or of GSLFTGR (SEQ ID NO:67). Additional C-terminal amino acid residues are not required for FGE-mediated conversion of the sulfatase motif of the aldehyde tag, and thus are only optional and may be specifically excluded from the aldehyde tags described herein. In some embodiments the aldehyde tag does not contain an amino acid sequence CGPSR(M/A)S (SEQ ID NO:68) or CGPSR(M/A) (SEQ ID NO:69), which may be present as a native amino acid sequence in phosphonate monoester hydrolases.
The sulfatase motif of the aldehyde tag is generally selected so as to be capable of conversion by a selected FGE, e.g., an FGE present in a host cell in which the aldehyde tagged polypeptide is expressed or an FGE which is to be contacted with the aldehyde tagged polypeptide in a cell-free in vitro method.
Selection of aldehyde tags and an FGE that provide for suitable reactive partners to provide for generation of an FGly in the aldehyde tagged carrier protein can be readily accomplished in light of information available in the art. In general, sulfatase motifs susceptible to conversion by a eukaryotic FGE contain a cysteine and a proline (i.e., a cysteine and proline at Z1 and Z2, respectively, in Formula I above (e.g., X1CX2PX3R); CX1PX2R in Formula II above) and are modified by the “SUMF1-type” FGE (Cosma et al. Cell 2003, 113, (4), 445-56; Dierks et al. Cell 2003, 113, (4), 435-44). Sulfatase motifs susceptible to conversion by a prokaryotic FGE contain either a cysteine or a serine, and a proline in the sulfatase motif (i.e., a cysteine or serine at Z1, and a proline at Z2, respectively, in Formula I above (e.g., X1(C/S)X2PX3R); (C/S)X1PX2R in Formula II above) are modified either by the “SUMF1-type” FGE or the “AtsB-type” FGE, respectively (Szameit et al. J Biol Chem 1999, 274, (22), 15375-81). Other sulfatase motifs susceptible to conversion by a prokaryotic FGE contain either a cysteine or a serine, and either a proline or an alanine in the sulfatase motif (i.e., a cysteine or serine at Z1, and a proline or alanine at Z2, respectively, e.g, SX1AX2R; X1CX2PX3Z3; X1SX2PX2Z3; X1CX2AX3Z3; X1SX2AX3Z3; CX1PX2Z3; SX1PX2Z3; CX1AX2Z3; SX1AX2Z3 (in Formula I above); CX1PX2Z3 (in Formula II above); X1CX2PX3R; X1SX2PX2R; X1CX2AX3R; X1SX2AX3R (in Formula Ia above); CX1PX2R; SX1PX2R; CX1AX2R; SX1AX2R (in Formula IIa above), and are susceptible to modification by, for example, can be modified by an FGE of a Firmicutes (e.g., Clostridium perfringens) (see Berteau et al. J. Biol. Chem. 2006; 281:22464-22470).
Therefore, for example, where the FGE is a eukaryotic FGE (e.g., a mammalian FGE, including a human FGE), the sulfatase motif is usually of the formula:
X1CX2PX3Z3 (III)
or, in an exemplary embodiment
X1CX2PX3R (IIIa)
where
X1 may be present or absent and, when present, can be any amino acid, though usually an aliphatic amino acid, a sulfur-containing amino acid, or a polar, uncharged amino acid, (i.e., other than a aromatic amino acid or a charged amino acid), usually L, M, S or V, with the proviso that when the sulfatase motif is at the N-terminus of the carrier protein, X1 is present;
X2 and X3 independently can be any amino acid, though usually an aliphatic amino acid, a sulfur-containing amino acid, or a polar, uncharged amino acid, (i.e., other than a aromatic amino acid or a charged amino acid), usually S, T, A, V, G, or C, more usually S, T, A, V or G; and
Z3 is a basic amino acid (which may be other than arginine (R), and may be lysine (K) or histidine (H), usually lysine), or an aliphatic amino acid (alanine (A), glycine (G), leucine (L), valine (V), isoleucine (I), or proline (P), usually A, G, L, V, or I, where Z3 is arginine (R) in Formula IIIa.
Specific examples of sulfatase motifs include LCTPSR (SEQ ID NO:1), MCTPSR (SEQ ID NO:2), VCTPSR(SEQ ID NO:3), LCSPSR (SEQ ID NO:4), LCAPSR (SEQ ID NO:5) LCVPSR (SEQ ID NO:6), LCGPSR(SEQ ID NO:7), ICTPAR(SEQ ID NO:8), LCTPSK(SEQ ID NO:9), MCTPSK (SEQ ID NO:10), VCTPSK (SEQ ID NO:11), LCSPSK (SEQ ID NO:12), LCAPSK (SEQ ID NO:13), LCVPSK(SEQ ID NO:14), LCGPSK(SEQ ID NO:15), LCTPSA (SEQ ID NO:16), ICTPAA (SEQ ID NO:17), MCTPSA (SEQ ID NO:18), VCTPSA (SEQ ID NO:19), LCSPSA (SEQ ID NO:20), LCAPSA (SEQ ID NO:21), LCVPSA (SEQ ID NO:22), and LCGPSA (SEQ ID NO:23). Other specific sulfatase motifs are readily apparent from the disclosure provided herein.
As described in more detail below, a converted aldehyde tagged polypeptide is reacted with a reactive partner of a moiety of interest to provide for conjugation between the moiety of interest to the FGly residue of the converted aldehyde tagged polypeptide, and production of a modified polypeptide (e.g., a conjugate of the ald-tagged carrier protein and a peptide drug). Modified polypeptides having a modified aldehyde tag are generally described by comprising a modified sulfatase motif of the formula:
X1(FGly′)X2Z2X3Z3 (I′)
or, in an exemplary embodiment
X1(FGly′)X2Z2X3R (Ia′)
where
FGly′ is a formylglycine residue having a covalently attached moiety (e.g., a peptide drug);
Z2 is either a proline or alanine residue (which can also be represented by (P/A));
Z3 in Formula I′ is a basic amino acid, and may be arginine (R) (as in Formula Ia′), lysine (K) or histidine (H), usually lysine), or an aliphatic amino acid (alanine (A), glycine (G), leucine (L), valine (V), isoleucine (I), or proline (P), usually A, G, L, V, or I;
X1 may be present or absent and, when present, can be any amino acid, though usually an aliphatic amino acid, a sulfur-containing amino acid, or a polar, uncharged amino acid, (i.e., other than a aromatic amino acid or a charged amino acid), usually L, M, V, S or T, more usually L, M or V, with the proviso that when the sulfatase motif is at the N-terminus of the carrier protein, X1 is present; and
X2 and X3 independently can be any amino acid, though usually an aliphatic amino acid, a sulfur-containing amino acid, or a polar, uncharged amino acid, (i.e., other than a aromatic amino acid or a charged amino acid), usually S, T, A, V, G or C, more usually S, T, A, V or G.
Specific examples of converted sulfatase motifs include L(FGly)TPSR (SEQ ID NO:24), M(FGly)TPSR (SEQ ID NO:25), V(FGly)TPSR (SEQ ID NO:26), L(FGly)SPSR (SEQ ID NO:27), L(FGly)APSR (SEQ ID NO:28), L(FGly)VPSR (SEQ ID NO:29), L(FGly)GPSR (SEQ ID NO:30), I(FGly)TPAR (SEQ ID NO:31), L(FGly)TPSK (SEQ ID NO:32), M(FGly)TPSK (SEQ ID NO:33), V(FGly)TPSK (SEQ ID NO:34), L(FGly)SPSK (SEQ ID NO:35), L(FGly)APSK (SEQ ID NO:36), L(FGly)VPSK (SEQ ID NO:37), L(FGly)GPSK (SEQ ID NO:38), L(FGly)TPSA (SEQ ID NO:39), M(FGly)TPSA (SEQ ID NO:40), V(FGly)TPSA (SEQ ID NO:41), L(FGly)SPSA (SEQ ID NO:42), L(FGly)APSA (SEQ ID NO:43), L(FGly)VPSA (SEQ ID NO:44), and L(FGly)GPSA (SEQ ID NO:45). It will be appreciated that exemplary carrier proteins that are covalently bound to drug through reaction with the aldehyde of the FGly residue include those having the amino acid sequences described above, but the modified FGly (represented above by FGly′) in lieu of the unmodified FGly.
Carrier Proteins
In general a “carrier protein” is a protein that is biologically inert, is susceptible to modification by use of the ald tag technology as disclosed herein, and which can provide for solvent-accessible presentation of drug conjugated to the carrier protein through a modified ald-tag positioned in the carrier protein (e.g., through an oxime or hydrazone bond within the converted sulfatase motif of the ald tagged carrier protein) in a physiological environment. “Biologically inert” is meant to indicate the carrier protein exhibits clinically insignificant or no detectable biological activity when administered to the appropriate subject, particularly when administered to a human subject. Thus, carrier proteins are biologically inert in that they, for example, are of low immunogenicity, do not exhibit significant or detectable targeting properties (e.g., do not exhibit significant or detectable activity in binding to a specific receptor), and exhibit little or no detectable biological activity that may interfere with activity of a drug to be conjugated to the ald-tagged carrier protein. By “low immunogenicity” is meant that the carrier protein elicits little or no detectable immune response upon administration to a subject, especially a mammalian subject, more especially a human subject. Carrier proteins can be provided in monomeric or multimeric (e.g., dimeric) forms.
Carrier proteins having a three-dimensional structure when folded that provides for multiple different solvent-accessible sites that are amenable to ald-tag modification (and thus conjugation to a drug) are of particular interest. In general, carrier proteins of interest are those that are of a size and three-dimensional folded structure so as to provide for presentation of conjugated drug on solvent accessible surfaces in a manner that is sufficient spatially separated so as to provide for activity and bioavailability of the conjugated drug molecules are of particular interest. The carrier protein will be selected according to a variety of factors including, but not limited to, the drug to be conjugated to the carrier.
Accordingly, any of a wide variety of polypeptides can be suitable for use as ald-tagged carrier proteins for use in the drug-carrier proteins conjugates of the present disclosure. Such carrier proteins can include those having a naturally-occurring amino acid sequence, a native amino acid sequence having an N-terminal methionine, fragments of naturally-occurring polypeptides, and non-naturally occurring polypeptides and fragments thereof.
Exemplary carrier proteins include, but are not necessarily limited to, albumin and fragments thereof (e.g., human serum albumin, bovine serum albumin, and the like), transferrin and fragments thereof (e.g. human transferrin), and Fc fragments having reduced binding to a mammalian Fc receptor, particularly a human Fc receptor (e.g., a modified Fc fragment of an antibody (e.g., IgG), particularly a mammalian antibody, e.g., a human antibody). Exemplary modified Fc fragments having reduced Fc receptor binding are exemplified by the Fc fragments of Herceptin (trastuzumab) and Rituxan (Rituximab), which contain point mutations that provide for reduced Fc receptor binding (see, e.g., Clynes et al Nature Medicine 2000, 6, 443-446). Alternatively or in addition, the isotype of the Fc fragment can be selected according to a desired level of Fc receptor binding (e.g., use of an Fc fragment of an IgG4 isotype human heavy chain constant region rather than from IgG1 or IgG3. (see, e.g, Fridman FASEB J 1991 September; 5 (12): 2684-90) In general, carrier proteins can be at least about 4 kDa (e.g., about 50 amino acid residues in length), usually at least about 25 kDa, and can be larger in size (e.g., transferrin has a molecular weight of 90 kDa while Fc fragments can have molecular weights of 30 kDa to 50 kDa).
Modification of Carrier Proteins to Contain an Aldehyde Tag
An aldehyde tag can be provided in a carrier protein by insertion (e.g., so as to provide a 5 or 6 amino acid residue insertion within the native amino acid sequence) and/or by addition (e.g., at an N- or C-terminus of the carrier protein). An aldehyde tag can also be provided by complete or partial substitution of native amino acid residues of the carrier protein with the contiguous amino acid sequence of an aldehyde tag. For example, a heterologous aldehyde tag of 5 (or 6) amino acid residues can be provided in a carrier protein by replacing 1, 2, 3, 4, or 5 (or 1, 2, 3, 4, 5, or 6) amino acid residues of the native amino acid sequence with the corresponding amino acid residues of the aldehyde tag.
Modification of a carrier protein to include one or more aldehyde tags can be accomplished using recombinant molecular genetic techniques, so as produce nucleic acid encoding the desired aldehyde tagged carrier protein. Such methods are well known in the art, and include cloning methods, site-specific mutation methods, and the like (see, e.g., Sambrook et al., In “Molecular Cloning: A Laboratory Manual” (Cold Spring Harbor Laboratory Press 1989); “Current Protocols in Molecular Biology” (eds., Ausubel et al.; Greene Publishing Associates, Inc., and John Wiley & Sons, Inc. 1990 and supplements). Alternatively, an aldehyde tag can be added using non-recombinant techniques, e.g., using native chemical ligation or pseudo-native chemical ligation, e.g., to add an aldehyde tag to a C-terminus of the carrier protein (see, e.g., U.S. Pat. Nos. 6,184,344; 6,307,018; 6,451,543; 6,570,040; US 2006/0173159; US 2006/0149039). See also Rush et al. (Jan. 5, 2006) Org Lett. 8(1):131-4.
Aldehyde tags can be positioned at any suitable location within a carrier protein, with the proviso that the site of the aldehyde tag is accessible for conversion by an FGE and subsequent modification at the FGly, or can be rendered accessible (e.g., by denaturing the protein). The carrier protein can include one or more aldehyde tags. The number of aldehyde tags that can be present in a carrier protein will vary with the carrier protein selected, and may include 1, 2, 3, 4, 5, or more aldehyde tags.
Carrier Proteins Containing Multiple Ald Tags
Multiple ald tags can be positioned in the ald-tagged carrier protein so as to distribute the tags over the surface of the folded carrier protein. Where the carrier protein is modified to contain multiple ald tags, the ald tags can be spaced apart in the carrier protein by amino acid residues native to the carrier protein. Alternatively or in addition, the carrier protein can include ald tags spaced apart by a linker, where the linker has an amino acid sequence heterologous to the carrier protein.
Alternatively or in addition, the ald tags can be provided in the ald-tagged carrier protein as a concatameric construct of 2, 3, 4 or more ald tags, where the expression construct thus encodes for 2, 3, 4 or more sulfatase motifs in a contiguous sequence of the modified carrier protein, wherein the sulfatase motifs are separated by a linker] The linkers of the concatemeric constructs may be designed so as to facilitate presentation of drug conjugated to the ald tag in the final carrier protein-drug conjugate. For example, the linker can be selected so as to provide flexibility between the ald tags, thus allowing for rotation of covalently-bound drug molecules so as to enhance presentation of biologically active drug on the carrier protein-drug conjugate surface. Such linkers can also be used in where the ald tags are not provided as a concatamer, e.g., where an ald tag is positioned at a C- or N-terminus of a carrier protein. Ald tags, including those provided as concatamers, can be positioned at or near the C-terminus of the carrier protein, at or near the N-terminus of the carrier protein, and/or in one or more solvent-accessible loops of the carrier protein.
Linkers will be selected according to a variety of factors (e.g., the ald tag used, the number of ald tags in the concatamer, the degree of flexibility desired), and will be variable length, such as from about 3 amino acids to about 25 amino acids, including about 4 amino acids to about 23 amino acids, about 5 amino acids to about 20 amino acids, about 6 amino acids to about 18 amino acids, about 7 amino acids to about 16 amino acids, about 8 amino acids to about 14 amino acids, and about 9 amino acids to about 12 amino acids. Exemplary flexible linkers include glycine polymers (G)n, glycine-serine polymers (including, for example, (GS)n, (GSGGS)n (SEQ ID NO:90) and (GGGS)n (SEQ ID NO:91), where n is an integer of at least one), glycine-alanine polymers, alanine-serine polymers, and other flexible linkers such as the tether for the shaker potassium channel, and a large variety of other flexible linkers, as will be appreciated by those in the art. Glycine and glycine-serine polymers are of interest since both of these amino acids are relatively unstructured, and therefore may be able to serve as a neutral tether between components. Glycine polymers are of particular interests glycine accesses significantly more phi-psi space than even alanine, and is much less restricted tan residues with longer side chains (see Scheraga, Rev. Computational Chem. 11173-142 (1992)). Exemplary flexible linkers include, but are not limited Gly-Gly-Ser-Gly-Gly (SEQ ID NO:92), Gly-Ser-Gly-Ser-Gly (SEQ ID NO:93), Gly-Ser-Gly-Gly-Gly (SEQ ID NO:94), Gly-Gly-Gly-Ser-Gly (SEQ ID NO:95), Gly-Ser-Ser-Ser-Gly (SEQ ID NO:96), and the like.
Concatameric ald tag constructs containing a linker can be described by the general formula:
T1-Ln-T2
where T1 and T2 are the same or different ald tags as described herein (see, e.g., formulae I, Ia, I′, Ia′, II, IIa, III, and IIIa), L is a linker peptide, and n is an integer of 1 or more, and may be 2, 3, 4, 5, 6, 7, 8 or more. An exemplary amino acid sequence of a concatameric ald tag containing a linker is LCTPSR GGGG LCTPSR (SEQ ID NO:97), where the cysteine (C) is modified to an FGly by action of an FGE, and can be reacted with a reactive partner-containing drug to provide for covalently bound drug as described herein.
The aldehyde tag(s) can be positioned in the carrier protein so as to take into account its structure when folded (e.g., in a cell-free environment, usually a cell-free physiological environment), e.g., so as to provide the aldehyde tag at a solvent accessible site in the folded carrier protein. The solvent accessible aldehyde tag can thus be accessed in the folded, unconverted ald-tagged carrier protein so as to be accessible to an FGE for conversion of the serine or cysteine to an FGly and/or to a reactive partner reagent for conjugation to a drug of interest. Where an aldehyde tag is positioned at a solvent accessible site, in vitro FGE-mediated conversion and modification with a moiety by reaction with a reactive partner can be performed without the need to denature the protein. Solvent accessible sites can also include carrier protein regions that are exposed at an extracellular or intracellular cell surface when expressed in a host cell.
Accordingly, or more aldehyde tags can be provided at sites independently selected from, for example, a solvent accessible N-terminus, a solvent accessible N-terminal region, a solvent accessible C-terminus, a solvent accessible C-terminal region, and/or a loop structure. In some embodiments, the aldehyde tag is positioned at a site other than the C-terminus of the polypeptide. In other embodiments, the polypeptide in which the aldehyde tag is positioned is a full-length polypeptide.
In other embodiments, an aldehyde tag site is positioned at a site which is post-translationally modified in the parent carrier protein (e.g., a naturally-occurring site). For example, an aldehyde tag can be introduced at a site of glycosylation (e.g., N-glycosylation, O-glycosylation), phosphorylation, sulftation, ubiquitination, acylation, methylation, prenylation, hydroxylation, carboxylation, and the like in the native carrier protein. In addition or alternatively the site of post-translational modification can be one that has been engineered (e.g., through recombinant techniques) and does not occur naturally in the carrier protein.
Nucleic and amino acid sequences of polypeptides suitable for use as ald-tagged carrier proteins as described herein are available in the art. For example,
Further exemplary ald-tagged carrier proteins include ald-tagged Fc fragment.
Ald-tagged Carrier Protein Libraries
As exemplified in the schematic of
Such libraries can serve as a “plug and play” system for reaction of the produced ald-tagged carrier proteins with a candidate drug having a reactive partner (e.g., an aminooxy or hydrazide moiety). The reaction productions of drug-carrier protein conjugates can then be screened for desired characteristics (e.g., biological activity of the drug, low immunogenicity of the conjugate, and the like).
Formylglycine Generating Enzymes (FGEs)
A formylglycine generating enzyme (FGE) is an enzyme that oxidizes cysteine or serine in a sulfatase motif to FGly. It should be noted that in general, the literature refers to FGly-generating enzymes that convert a cysteine (C to FGly in a sulfatase motif as FGEs, and refers to enzymes that convert serine (S) to FGly in a sulfatase motif as Ats-B-like. However, for purposes of the present disclosure “FGE” is used generically to refer to both types of FGly-generating enzymes, with the understanding that an appropriate FGE will be selected according to the sulfatase motif (i.e., C-containing or S-containing) present in the modified carrier protein.
In general, the FGE used to facilitate conversion of cysteine or serine to FGly in a sulfatase motif of an aldehyde tag of a carrier protein is selected according to the sulfatase motif present in the aldehyde tag. The FGE can be native to the host cell in which the aldehyde tagged carrier protein is expressed, or the host cell can be genetically modified to express an appropriate FGE. Eukaryotic sulfatases generally contain a cysteine in their sulfatase motif and are modified by the “SUMF1-type” FGE (Cosma et al. Cell 2003, 113, (4), 445-56; Dierks et al. Cell 2003, 113, (4), 435-44). Prokaryotic sulfatases generally contain either a cysteine or a serine in their sulfatase motif and are modified either by the “SUMF1-type” FGE or the “AtsB-type” FGE, respectively (Szameit et al. J Biol Chem 1999, 274, (22), 15375-81). An FGE has been described in Mycobacterium tuberculosis (see, e.e.g GenBank Acc. No. NP_215226 (gi:15607852) and WO 2008/036350). FGEs have also been described in deuterostomia, including vertebrates and echinodermata (see, e.g., Pepe et al. (2003) Cell 113, 445-456, Dierks et al. (2003) Cell 113, 435-444; Cosma et al. (2004) Hum. Mutat. 23, 576-581). In some embodiments it may be desired to use a sulfatase motif compatible with a human FGE (e.g., the SUMF1-type FGE, see, e.g., Cosma et al. Cell 113, 445-56 (2003); Dierks et al. Cell 113, 435-44 (2003)), and express the aldehyde tagged protein in a human cell that expresses the FGE or in a host cell, usually a mammalian cell, genetically modified to express a human FGE.
In general, an FGE for use in the methods disclosed herein can be obtained from naturally occurring sources or synthetically produced. For example, an appropriate FGE can be derived from biological sources which naturally produce an FGE or which are genetically modified to express a recombinant gene encoding an FGE. Nucleic acids encoding a number of FGEs are known in the art and readily available (see, e.g., Preusser et al. 2005 J. Biol. Chem. 280(15):14900-10 (Epub 2005 Jan. 18); Fang et al. 2004 J Biol Chem. 79(15):14570-8 (Epub 2004 Jan. 28); Landgrebe et al. Gene. 2003 Oct. 16; 316:47-56; Dierks et al. 1998 FEBS Lett. 423(1):61-5; Dierks et al. Cell. 2003 May 16; 113(4):435-44; Cosma et al. (2003 May 16) Cell 113(4):445-56; Baenziger (2003 May 16) Cell 113(4):421-2 (review); Dierks et al. Cell. 2005 May 20; 121(4):541-52; Roeser et al. (2006 Jan. 3)Proc Natl Acad Sci USA 103(1):81-6; Sardiello et al. (2005 Nov. 1) Hum Mol Genet. 14(21):3203-17; WO 2004/072275; GenBank Accession No. NM_182760; and WO 2008/036350). Accordingly, the disclosure here provides for recombinant host cells genetically modified to express an FGE that is compatible for use with an aldehyde tag of a tagged carrier protein.
Where a cell-free method is used to convert a sulfatase motif-containing carrier protein, an isolated FGE can be used. Any convenient protein purification procedures may be used to isolate an FGE, see, e.g., Guide to Protein Purification, (Deuthser ed.) (Academic Press, 1990). For example, a lysate may prepared from a cell the produces a desired FGE, and purified using HPLC, exclusion chromatography, gel electrophoresis, affinity chromatography, and the like.
Expression Vectors and Host Cells for Production of Aldehyde Tagged-Carrier Polypeptides
The present disclosure provides nucleic acid encoding ald-tagged carrier polypeptides, as well as constructs and host cells containing nucleic acid. Such nucleic acids comprise a sequence of DNA having an open reading frame that encodes an aldehyde tagged carrier protein and, in most embodiments, is capable, under appropriate conditions, of being expressed. “Nucleic acid” encompasses DNA, cDNA, mRNA, and vectors comprising such nucleic acids.
Nucleic acids contemplated herein can be provided as part of a vector (also referred to as a construct), a wide variety of which are known in the art and need not be elaborated upon herein. Exemplary vectors include, but are not limited to, plasmids; cosmids; viral vectors (e.g., retroviral vectors); non-viral vectors; artificial chromosomes (YAC's, BAC's, etc.); mini-chromosomes; and the like. The choice of vector will depend upon a variety of factors such as the type of cell in which propagation is desired and the purpose of propagation.
Vectors can provide for extrachromosomal maintenance in a host cell or can provide for integration into the host cell genome. Vectors are amply described in numerous publications well known to those in the art, including, e.g., Short Protocols in Molecular Biology, (1999) F. Ausubel, et al., eds., Wiley & Sons. Vectors may provide for expression of the nucleic acids encoding a polypeptide of interest (e.g., an aldehyde tagged polypeptide, an FGE, etc.), may provide for propagating the subject nucleic acids, or both.
Exemplary vectors that may be used include but are not limited to those derived from recombinant bacteriophage DNA, plasmid DNA or cosmid DNA. For example, plasmid vectors such as pBR322, pUC 19/18, pUC 118, 119 and the M13 mp series of vectors may be used. Bacteriophage vectors may include λgt10, λgt11, λgt18-23, λZAP/R and the EMBL series of bacteriophage vectors. Cosmid vectors that may be utilized include, but are not limited to, pJB8, pCV 103, pCV 107, pCV 108, pTM, pMCS, pNNL, pHSG274, COS202, COS203, pWE15, pWE16 and the charomid 9 series of vectors. Alternatively, recombinant virus vectors may be engineered, including but not limited to those derived from viruses such as herpes virus, retroviruses, vaccinia virus, poxviruses, adenoviruses, adeno-associated viruses or bovine papilloma virus.
For expression of a polypeptide of interest, an expression cassette may be employed. Thus, the present invention provides a recombinant expression vector comprising a subject nucleic acid. The expression vector provides a transcriptional and translational regulatory sequence, and may provide for inducible or constitutive expression, where the coding region is operably linked under the transcriptional control of the transcriptional initiation region, and a transcriptional and translational termination region. These control regions may be native to the gene encoding the polypeptide (e.g., the carrier protein or the FGE), or may be derived from exogenous sources. In general, the transcriptional and translational regulatory sequences may include, but are not limited to, promoter sequences, ribosomal binding sites, transcriptional start and stop sequences, translational start and stop sequences, and enhancer or activator sequences. In addition to constitutive and inducible promoters, strong promoters (e.g., T7, CMV, and the like) find use in the constructs described herein, particularly where high expression levels are desired in an in vivo (cell-based) or in an in vitro expression system. Further exemplary promoters include mouse mammary tumor virus (MMTV) promoters, Rous sarcoma virus (RSV) promoters, adenovirus promoters, the promoter from the immediate early gene of human CMV (Boshart et al., Cell 41:521-530, 1985), and the promoter from the long terminal repeat (LTR) of RSV (Gorman et al., Proc. Natl. Acad. Sci. USA 79:6777-6781, 1982). The promoter can also be provided by, for example, a 5′UTR of a retrovirus.
Expression vectors generally have convenient restriction sites located near the promoter sequence to provide for the insertion of nucleic acid sequences encoding proteins of interest. A selectable marker operative in the expression host may be present to facilitate selection of cells containing the vector. In addition, the expression construct may include additional elements. For example, the expression vector may have one or two replication systems, thus allowing it to be maintained in organisms, for example in mammalian or insect cells for expression and in a prokaryotic host for cloning and amplification. In addition the expression construct may contain a selectable marker gene to allow the selection of transformed host cells. Selection genes are well known in the art and will vary with the host cell used.
Expression constructs encoding aldehyde tagged carrier proteins can also be generated using amplification methods (e.g., polymerase chain reaction (PCR)), where at least one amplification primer (i.e., at least one of a forward or reverse primer) includes a nucleic acid sequence encoding an aldehyde tag. For example, an amplification primer having an aldehyde tag-encoding sequence is designed to provide for amplification of a nucleic acid encoding a carrier protein of interest. The extension product that results from polymerase-mediated synthesis from the aldehyde tag-containing forward primer produces a nucleic acid amplification product encoding a fusion protein composed of an aldehyde tagged-carrier protein. The amplification product is then inserted into an expression construct of choice to provide an aldehyde tagged polypeptide expression construct.
Host Cells
Any of a number of suitable host cells can be used in the production of an aldehyde tagged carrier protein. The host cell used for production of an aldehyde tagged-carrier protein can optionally provide for FGE-mediated conversion, so that the polypeptide produced contains an FGly-containing aldehyde tag following expression and post-translational modification by FGE. Alternatively the host cell can provide for production of an unconverted aldehyde tagged carrier protein (e.g., due to lack of expression of an FGE that facilitates conversion of the aldehyde tag).
In general, the polypeptides described herein may be expressed in prokaryotes or eukaryotes in accordance with conventional ways, depending upon the purpose for expression. Thus, the present invention further provides a host cell, e.g., a genetically modified host cell that comprises a nucleic acid encoding an aldehyde tagged polypeptide. The host cell can further optionally comprise a recombinant FGE, which may be endogenous or heterologous to the host cell.
Host cells for production (including large scale production) of an unconverted or (where the host cell expresses a suitable FGE) converted aldehyde tagged carrier protein, or for production of an FGE (e.g., for use in a cell-free method) can be selected from any of a variety of available host cells. Exemplary host cells include those of a prokaryotic or eukaryotic unicellular organism, such as bacteria (e.g., Escherichia coli strains, Bacillus spp. (e.g., B. subtilis), and the like) yeast or fungi (e.g., S. cerevisiae, Pichia spp., and the like), and other such host cells can be used. Exemplary host cells originally derived from a higher organism such as insects, vertebrates, particularly mammals, (e.g. CHO, HEK, and the like), may be used as the expression host cells.
Specific expression systems of interest include bacterial, yeast, insect cell and mammalian cell derived expression systems. Representative systems from each of these categories are provided below.
The product can be recovered by any appropriate means known in the art. Further, any convenient protein purification procedures may be employed, where suitable protein purification methodologies are described in Guide to Protein Purification, (Deuthser ed.) (Academic Press, 1990). For example, a lysate may prepared from a cell comprising the expression vector expressing the ald-tagged carrier protein, and purified using HPLC, exclusion chromatography, gel electrophoresis, affinity chromatography, and the like.
Methods for Conversion and Modification of an Aldehyde Tag
Conversion of an aldehyde tag present in an aldehyde tagged carrier protein can be accomplished by cell-based (in vivo) or cell-free methods (in vitro). Similarly, modification of a converted aldehyde tag of an aldehyde tagged polypeptide can be accomplished by cell-based (in vivo) or cell-free methods (in vitro). These are described in more detail below.
“In Vivo” Host Cells Conversion and Modification
Conversion of an aldehyde tag of an aldehyde tagged polypeptide can be accomplished by expression of the aldehyde tagged polypeptide in a cell that contains a suitable FGE. In this embodiment, conversion of the cysteine or serine of the aldehyde tag is occurs during or following translation in the host cell. The FGE of the host cell can be endogenous to the host cell, or the host cell can be recombinant for a suitable FGE that is heterologous to the host cell. FGE expression can be provided by an expression system endogenous to the FGE gene (e.g., expression is provided by a promoter and other control elements present in the native FGE gene of the host cell), or can be provided by from a recombinant expression system in which the FGE coding sequence is operably linked to a heterologous promoter to provide for constitutive or inducible expression.
Conditions suitable for use to accomplish conjugation of a reactive partner moiety to an aldehyde tagged polypeptide are similar to those described in Mahal et al. (1997 May 16) Science 276(5315):1125-8.
“In Vitro” (Cell-Free) Conversion and Modification
In vitro (cell-free) conversion of an aldehyde tag of an aldehyde tagged carrier protein can be accomplished by contacting an aldehyde tagged polypeptide with an FGE under conditions suitable for conversion of a cysteine or serine of a sulfatase motif of the aldehyde tag to a FGly. For example, nucleic acid encoding an aldehyde tagged polypeptide can be expressed in an in vitro transcription/translation system in the presence of a suitable FGE to provide for production of converted aldehyde tagged polypeptides.
Alternatively, isolated, unconverted aldehyde tagged carrier protein can be isolated following recombinant production in a host cell lacking a suitable FGE or by synthetic production. The isolated aldehyde tagged carrier protein is then contacted with a suitable FGE under conditions to provide for aldehyde tag conversion. The aldehyde tagged carrier protein can be unfolded by methods known in the art (e.g., using heat, adjustment of pH, chaotropic agents, (e.g., urea, and the like), organic solvents (e.g., hydrocarbons: octane, benzene, chloroform), etc.) and the denatured protein contacted with a suitable FGE. The ald-tagged carrier protein can then be refolded under suitable conditions.
With respect to modification of converted aldehyde tagged, modification is normally carried out in vitro. Converted aldehyde tagged carrier protein is isolated from a production source (e.g., recombinant host cell production, synthetic production), and contacted with a reactive partner-containing drug under conditions suitable to provide for conjugation of a moiety of the reactive partner to the FGly of the aldehyde tag.
Drugs for Conjugation to Ald-Tagged Carrier Proteins
Any of a number of drugs are suitable for use, or can be modified to be rendered suitable for use, as a reactive partner to conjugate to an ald tagged-carrier protein. Exemplary drugs include small molecule drugs and peptide drugs.
“Small molecule drug” as used herein refers to compound, usually an organic compound, which exhibits a pharmaceutical activity of interest and which is generally of a molecular weight of no greater than about 800 Da, and usually no greater than 2000 Da, but can encompass molecules of up to 5 kDa and can be as large as about 10 kDa. A small inorganic molecule refers to a molecule containing no carbon atoms, while a small organic molecules refers to a compound containing at least one carbon atom.
“Peptide drug” as used herein refers to amino-acid containing polymeric compounds, and is meant to encompass naturally-occurring and non-naturally-occurring peptides, oligopeptides, cyclic peptides, polypeptides, and proteins, as well as peptide mimetics. The peptide drugs may be obtained by chemical synthesis or be produced from a genetically encoded source (e.g., recombinant source). Peptide drugs can range in molecular weight, and can be from 200 Da to 10 kDa or greater in molecular weight.
Glucagon-like peptide 1 (GLP-1), calcitonin, and biologically active fragments and variants thereof are exemplary peptide drugs. By “variant” is meant a polypeptide that has an amino acid sequence that is not found in nature, and includes polypeptides having one or more amino acid substitutions, insertions and/or deletions relative to a naturally-occurring parent polypeptide. “Variant” polypeptides thus encompass a polypeptide having an N- or C-terminal truncation relative to a parent polypeptide. A “fragment” of a polypeptide is one that shares an amino acid sequence of a naturally-occurring polypeptide, but that is truncated at the N-terminus, C-terminus or both relative to a naturally-occurring parent polypeptide.
GLP-1 is one of several naturally occurring incretin compounds that possess biologic activity when released from the gut during digestion. GLP-1 naturally works on several deficient organs to lower blood sugar levels. It is able to significantly delay the progression of Type 2 diabetes, and is useful in treatment of hyperglycemis. Currently, GLP-1 is less useful as a drug because it is broken down within minutes by the enzyme DPP-4, which is present throughout the human body. Coupling of GLP1 to an ald-tagged carrier protein can provide for increased serum half-lifeGLP-1 and biologically active fragments and variants thereof represent an exemplary peptide drug of interest for conjugation to a ald-tagged carrier protein of the present disclosure. Exemplary fragments and variants of GLP-1 include, but are not necessarily limited to, those described in Green et al. 2007 Best Pract Res Clin Endocrinol Metab 21:497-516; Brubaker et al. 2007 Trends Endocrinol Metab 18:240-245; Boyle et al. 2007 J Am Osteopath Assoc 107(Suppl):S10-S16; and Drucker et al. 2006 The incretin system: glucagon-like peptide-1 receptor agonists and dipeptidyl peptidase-4 inhibitors in type 2 diabetes. Lancet 368:1696-1705 32. Exemplary biologically active GLP-1 variants include those having, for example, an amino acid substitution at amino acid residues His(7), Ala(8), or Glu(9) of the native GLP-1 amino acid sequence. Specific examples include (D-His7)GLP-1, (D-Ala8)GLP-1, (Gly8)GLP-1, (Ser8)GLP-1, (Aha8)GLP-1, (Thr8)GLP-1, (Aib8)GLP-1, (Abu8)GLP-1, (Va18)GLP-1, (Asp9)GLP-1, (Ala9)GLP-1, (Pro9)GLP-1, (Phe9)GLP-1, and (Lys9)GLP-1. Specific exemplary biologically active GLP-1 variants are known as Exenatide, LY548806, CJC-1131, and Lirglutide.
Calcitonin and biologically active variants thereof represent an exemplary peptide drug of interest for conjugation to an ald-tagged carrier protein of the present disclosure. Calcitonin is a 32 amino-acid linear polypeptide hormone that is produced in humans primarily by the parafollicular (also known as C-cells) of the thyroid. Calcitonin has short absorption and elimination half-lives of 10-15 minutes and 50-80 minutes, respectively and can be used therapeutically for the treatment of hypercalcaemia or osteoporosis. Conjugation of calcintonin to an ald-tagged carrier protein as disclosed herein can provide for enhanced serum half-life, and thus provide for a therapeutic that can be administered much less frequently then the peptide alone. Exemplary biologically active calcitonin variants include, but are not necessarily limited to, those described in Fowler et al. Proc Natl Acad Sci USA. 2005 Jul. 19; 102(29):10105-10.
The biological activity of drug conjugated to an ald-tagged carrier protein as disclosed herein can be assayed according to methods known in the art. Such conjugated drugs that retain at least one desired pharmacologic activity of the corresponding parent compound are of interest.
Methods for Modification of Drugs to Contain Reactive Partner for Reaction with 2-formylglycine
Peptide drugs to be conjugated to an ald-tagged carrier protein are modified to incorporate a reactive partner for reaction with an aldehyde of the FGly residue of the ald-tagged carrier protein. Since the methods of ald-tagged polypeptide modification are compatible with conventional chemical processes, any of a wide variety of commercially available reagents can be used to accomplish conjugation. For example, aminooxy, hydrazide, hydrazine, or thiosemicarbazide derivatives of a number of moieties of interest are suitable reactive partners, and are readily available or can be generated using standard chemical methods.
Where the drug is a peptide drug, the reactive moiety (e.g., aminooxy or hydrazide can be positioned at an N-terminal region, the N-terminus, a C-terminal region, the C-terminus, or at a position internal to the peptide.
Deprotection to expose the amino-oxy functionality is performed on the peptide comprising an N-protecting group. Deprotection of the N-oxysuccinimide group, for example, occurs according to standard deprotection conditions for a cyclic amide group. Deprotecting conditions can be found in Greene and Wuts, Protective Groups in Organic Chemistry, 3rd Ed., 1999, John Wiley & Sons, NY and Harrison et al. Certain deprotection conditions include a hydrazine reagent, amino reagent, or sodium borohydride. In
The ordinarily skilled artisan will appreciate that factors such as pH and steric hindrance (i.e., the accessibility of the aldehyde tag to reaction with a reactive partner of interest) are of importance, Modifying reaction conditions to provide for optimal conjugation conditions is well within the skill of the ordinary artisan, and is routine in the art. In general, it is normally desirable to conduction conjugation reactions at a pH below 7, with a pH of about 5.5, about 6, about 6.5, usually about 5.5 being optimal. Where conjugation is conducted with an aldehyde tagged polypeptide present in or on a living cell, the conditions are selected so as to be physiologically compatible. For example, the pH can be dropped temporarily for a time sufficient to allow for the reaction to occur but within a period tolerated by the cell having an aldehyde tag (e.g., from about 30 min to 1 hour). Physiological conditions for conducting modification of aldehyde tagged polypeptides on a cell surface can be similar to those used in a ketone-azide reaction in modification of cells bearing cell-surface azides (see, e.g., U.S. Pat. No. 6,570,040).
Small molecule compounds containing, or modified to contain, an α-nucleophilic group that serves as a reactive partner with an aldehyde of an FGly of an ald tag are also contemplated for use as drugs in the carrier protein-drug conjugates of the present disclosure. General methods are known in the art for chemical synthetic schemes and conditions useful for synthesizing a compound of interest (see, e.g., Smith and March, March's Advanced Organic Chemistry: Reactions, Mechanisms, and Structure, Fifth Edition, Wiley-Interscience, 2001; or Vogel, A Textbook of Practical Organic Chemistry, Including Qualitative Organic Analysis, Fourth Edition, New York: Longman, 1978).
Thus small molecules having an aminooxy or hydrazone group for reaction with an aldehyde of an FGly of an ald-tagged carrier protein group are available or can be readily synthesized. An aminooxy or hydrazone group can be installed onto a small molecule using standard synthetic chemistry techniques.
Peptide Drug—Carrier Protein Conjugates
The conjugates of the present disclosure are site-specifically decorated with covalently bound drug. The site-specificity of reaction of a reactive partner-containing drug with an aldehyde tag of the carrier protein allows for production of carrier proteins having multiple sites for chemical conjugation, thus providing a scaffold for production of carrier protein-drug conjugates have a desired drug payload per protein ratio. Moreover, the relative position of the ald tags in the ald-tagged carrier protein can be designed so as to provide for a desired presentation of covalently bound drug molecules on the surface of the final carrier protein-drug conjugate, thus allowing for control of spatial orientation of the displayed drug payload.
Further, the site-specific nature of chemical modification of ald tags to attach drug to the carrier protein can be exploited to provide for a composition composed of a substantially homogenous population carrier protein-drug conjugates. Such carrier protein-drug conjugates can provide for control of the stoichiometry of drug delivery.
Carrier protein-drug conjugates of the present disclosure are composed of a carrier protein and one or more covalently bound drug molecules, where the carrier protein comprises a modified sulfatase motif of the formula:
X1(FGly′)X2Z2X3Z3
where FGly′ is of the formula:
wherein J1 is the covalently bound drug;
each L1 is a divalent moiety independently selected from alkylene, substituted alkylene, alkenylene, substituted alkenylene, alkynylene, alkynylene, arylene, substituted arylene, cycloalkylene, substituted cycloalkylene, heteroarylene, substituted heteroarylene, heterocyclene, substituted heterocyclene, acyl, amido, acyloxy, urethanylene, thioester, sulfonyl, sulfonamide, sulfonyl ester, —O—, —S—, —NH—, and substituted amine;
n is a number selected from zero to 40;
Z2 is a proline or alanine residue;
X1 is present or absent and, when present, is any amino acid, with the proviso that when the sulfatase motif is at an N-terminus of the polypeptide, X1 is present;
X2 and X3 are each independently any amino acid; and
Z3 is a basic amino acid, and
wherein the carrier protein presents the covalently bound drug on a solvent-accessible surface when in a folded state. The X1, X2, Z2, X3, and Z3 can be further defined as discussed above.
As noted above, the ald-tagged carrier protein can be designed so as to provide for multiple sites for chemical conjugation, thus providing a scaffold for production of carrier protein-drug conjugates have a desired drug payload per protein ratio. The carrier protein-drug conjugates contemplated by the present disclosure generally include at least 2 modified sulfatase motifs having covalently bound drug molecules, and usually include 3 or more modified sulfatase motifs having covalently bound drug molecules. The carrier protein-drug conjugates of the present disclosure can provide for a 4 or more, 5 or more, or 6 or more covalently bound drug molecules in the carrier protein-drug conjugate. Carrier protein-drug conjugates of the present disclosure thus include those having a drug payload to protein carrier ratio of at least 2:1, at least 3:1, at least 4:1, at least 5:1 and, depending upon, for example, the size of the drug molecule relative to the size of the carrier protein and/or the available sites for insertion of an ald tag on the solvent-accessible surface area of the folded carrier protein.
As noted above, the relative position of the ald tags in the ald-tagged carrier protein can be designed so as to provide for a desired presentation of covalently bound drug molecules on the surface of the final carrier protein-drug conjugate. This feature allows for control of spatial orientation of the displayed drug payload on the surface of the final carrier protein-drug conjugate. Carrier protein-drug conjugates containing multiple ald tags, which may include concatameric ald tags separated by flexible linkers as described herein, can provide for greater drug payload:carrier protein ratios and enhanced presentation of drug to a physiological environment in which the carrier protein-drug conjugate is present. As such, the carrier protein-drug conjugates can be described as a modified carrier protein “decorated” with drug covalently bound to the carrier protein through an oxime or hydrazone linkage to the peptide backbone of the carrier protein.
For example, the ald tags of the carrier protein-drug conjugate can be positioned in the carrier protein-drug conjugate at at least one of an N-terminus of the carrier protein, a C-terminus of the carrier protein, and a solvent-accessible loop of the carrier protein. The ald tags can optionally be provided in connection with a linker, e.g., a flexible linker, as described above. The multiple ald tags can be localized to a particular region(s) of the carrier protein (e.g., provided in one or more of a solvent-accessible loop, N-terminal region (including N-terminus), C-terminal region (including C-terminus)), or can be distributed over the solvent-accessible surface area of the folded modified carrier protein.
In general, it may be desirable to space the ald tags of the ald-tagged carrier protein so that the final carrier protein-drug conjugate has covalently bound drug spaced apart at a distance sufficient to avoid interaction between the covalently bound drug molecules, e.g., so that drug molecules do not contact one another or otherwise interfere with their respective biological activities. The spatial orientation and positioning within the carrier protein will vary according to a variety of factors including the relative sizes of the drug to be conjugated and the carrier protein.
As noted above, the site-specific nature of chemical modification of ald tags to attach drug to the carrier protein can be exploited to provide for a composition composed of a substantially homogenous population carrier protein-drug conjugates. Such carrier protein-drug conjugates can provide for control of the stoichiometry of drug delivery. Such homogenous populations of carrier protein-drug conjugates include those in which at least 60%, at least 70%, at least 80% at least 90% or more of the carrier protein-drug conjugates of the population have the same drug payload to carrier protein ratio.
Methods of Making Carrier Protein-drug Conjugates
Methods of conjugation of an FGly-containing ald-tagged carrier protein with a reactive-partner containing-drug to provide a carrier protein-drug conjugate having a desired drug payload:carrier protein ratio are contemplated by the present disclosure. In general, such methods involve combining an FGly-containing, ald-tagged carrier protein with a reactive partner-containing drug (e.g., an aminooxy- or hydrazide-containing drug) in a reaction mixture under conditions suitable to promote reaction between the aldehyde(s) for the FGly(s) of the ald-tagged carrier protein with the reactive partner of the drug molecule(s), thereby producing a reaction product of a carrier protein-drug conjugate having drug covalently bound to the peptide backbone of the carrier protein through an oxime bond, hydrazide bond, or other aldehyde specific chemistries such as reductive aminations, or Wittig reactions.
After production of the ald-tagged carrier protein, it is isolated using any of a variety of techniques available in the art (e.g., chromatography, e.g., HPLC, FPLC, immunoaffinity purification, and the like). In some embodiments, the carrier protein of the carrier protein-drug conjugate contains an immunotag (e.g., His tag, FLAG tag), usually positioned at an N- or C-terminus to facilitate isolation and purification prior to conjugation with drug. The FGly-containing ald-tagged carrier protein for use in a conjugation reaction with drug can be provided in denatured form or can be folder prior to combining in the reaction mixture. Usually, the FGly-containing ald-tagged carrier protein is provided in folded form in the conjugation reaction mixture. Where obtained from cells expressing the ald-tagged carrier protein and a compatible FGE, the FGly-containing ald-tagged carrier protein can be isolated in folded form from cells or, where secreted, from culture supernatant. Where needed, methods for folding of proteins are available in the art, and can be readily applied to the methods here.
In general, the ald-tagged carrier protein having FGly residues is isolated, and usually is purified. The carrier protein-drug conjugate is combined in a reaction mixture in buffered solution with a reactive partner-containing drug. The buffered solution can be at a physiological or near physiological pH, e.g., a pH of about 5 to 7, usually a pH of about 6.5. The reactive partner-containing drug is provided in the reaction mixture in excess to the aldehyde moieties of the FGly-containing ald-tagged carrier protein, usually at least 2 fold, 3 fold, 4 fold, 5 fold or more excess, in order drive the reaction to completion. After addition of reactive partner-containing drug to the reaction mixture, the mixture is stirred under suitable conditions of time and temperature (e.g., at room temperature for about 2 h). The resulting carrier protein-drug conjugate is isolated from the reaction mixture and can be further purified using standard techniques (e.g., chromatography, e.g., HPLC, FPLC).
Assessment of Carrier Protein-drug Conjugate Activity
Following isolation of a carrier protein-drug conjugate from a reaction mixture, the carrier protein-drug conjugate can be screened for activity in one or more assays. Such assays can be for one or more biological activities of the drug conjugated to the carrier protein-drug conjugate and/or for one or more characteristics of the carrier protein-drug conjugate (e.g., immunogenicity).
Methods for assessing immunogenicity are available in the art and can be adapted for use in assessing carrier protein-drug conjugates of the present disclosure. For example, the carrier protein-drug conjugate can be administered to a non-human animal (e.g., an animal that can serve as a model for a human immune response), and the immune response to the carrier protein-drug conjugate assessed. Carrier protein-drug conjugates can be assessed for their activity in eliciting a humoral and/or cellular immune response in a non-human animal. Of particular interest is the production of anti-carrier protein-drug conjugate antibodies by the immunized host. Methods for assessing antibody production in a host are well known in the art.
Methods for assessing activity of the drug conjugated to the carrier protein-drug conjugate are selected according to the drug bound to the carrier protein-drug conjugate and are available in the art. Such assays can be in vitro cell-free assays, in vitro cell-based assays, or in vivo assays (e.g., in an animal model). Usually the assay is a cell-based in vitro functional assay or an in vivo assay using a non-human animal model (e.g, an animal model of human disease).
For example, activity of a carrier protein-GLP-1 conjugate of the present disclosure can be assayed in a cellular receptor activity assay, as exemplified in the Example below. Activity of a carrier protein-calicitonin conjugate of the present disclosure can be assayed in a bone cell culture system to assess bone resorption of calcium.
Formulations
The carrier protein-drug conjugates of the present disclosure can be formulated in a variety of different ways. In general, the carrier protein-drug conjugate is formulated in a manner compatible with the drug conjugated to the carrier protein-drug conjugate, the condition to be treated, and the route of administration to be used.
The carrier protein-drug conjugate can be provided in any suitable form, e.g., in the form of a pharmaceutically acceptable salt, and can be formulated for any suitable route of administration, e.g., oral, topical or parenteral administration. Where the carrier protein-drug conjugate is provided as a liquid injectable (such as in those embodiments where they are administered intravenously or directly into a tissue), the carrier protein-drug conjugate can be provided as a ready-to-use dosage form, or as a reconstitutable storage-stable powder or liquid composed of pharmaceutically acceptable carriers and excipients.
Methods for formulating carrier protein-drug conjugates can be adapted from those available in the art. For example, carrier protein-drug conjugates can be provided in a pharmaceutical composition comprising an effective amount of a carrier protein-drug conjugate and a pharmaceutically acceptable carrier (e.g., saline). The pharmaceutical composition may optionally include other additives (e.g., buffers, stabilizers, preservatives, and the like). Of particular interest are formulations that are suitable for administration to a mammal, particularly those that are suitable for administration to a human.
Methods of Treatment
The carrier protein-drug conjugates of the present disclosure find use in treatment of a condition or disease in a subject that is amenable to treatment by administration of the parent drug (i.e., the drug prior to conjugation to the carrier protein. By “treatment” is meant that at least an amelioration of the symptoms associated with the condition afflicting the host is achieved, where amelioration is used in a broad sense to refer to at least a reduction in the magnitude of a parameter, e.g. symptom, associated with the condition being treated. As such, treatment also includes situations where the pathological condition, or at least symptoms associated therewith, are completely inhibited, e.g., prevented from happening, or stopped, e.g. terminated, such that the host no longer suffers from the condition, or at least the symptoms that characterize the condition. Thus treatment includes: (i) prevention, that is, reducing the risk of development of clinical symptoms, including causing the clinical symptoms not to develop, e.g., preventing disease progression to a harmful state; (ii) inhibition, that is, arresting the development or further development of clinical symptoms, e.g., mitigating or completely inhibiting an active disease; and/or (iii) relief, that is, causing the regression of clinical symptoms.
The subject to be treated can be one that is in need of therapy, where the host to be treated is one amenable to treatment using the parent drug. Accordingly, a variety of subjects may be amenable to treatment using the carrier protein-drug conjugates disclosed herein. Generally such subjects are “mammals”, with humans being of particular interest. Other subjects can include domestic pets (e.g., dogs and cats), livestock (e.g., cows, pigs, goats, horses, and the like), rodents (e.g., mice, guinea pigs, and rats, e.g., as in animal models of disease), as well as other primates (e.g., chimpanzees, and monkeys.
The amount of carrier protein-drug conjugate administered can be initially determined based on guidance of a dose and/or dosage regimen of the parent drug. In general, the carrier protein-drug conjugates can provide for enhanced blood serum half-life of the bound drug, thus providing for at least one of reduced dose or reduced administrations in a dosage regimen. Thus the carrier protein-drug conjugates can provide for reduced dose and/or reduced administration in a dosage regimen relative to the parent drug prior to conjugated in a carrier protein-drug conjugate of the present disclosure.
Furthermore, as noted above, because the carrier protein-drug conjugates can provide for controlled stoichiometry of drug delivery, dosages of carrier protein-drug conjugates can be calculated based on the number of drug molecules provided on a per carrier protein-drug conjugate basis.
Accordingly, the carrier protein-drug conjugates of the present disclosure where in the drug is GLP-1, or a biologically active variant thereof, can be used in treatment of conditions amenable to therapy by administration of GLP-1. Such conditions include Type II diabetes and hyperglycemia. Such methods involve administration of an effective amount of a carrier protein-GLP-1 conjugate (or a carrier protein-drug conjugate having a covalently bound variant of GLP-1) to a subject in need to treatment (e.g., a subject having or at risk of Type II diabetes and/or hyperglycemia, wherein administration of the carrier protein-drug conjugate is effect to treat the condition.
Where the drug of the carrier protein-drug conjugates of the present disclosure is Calcitonin, or a biologically active variant thereof, can be used in treatment of conditions amenable to therapy by administration of Calcitonin Such conditions include osteoporosis and hypercalcaemia. Such methods involve administration of an effective amount of a carrier protein-Calcitonin conjugate (or a carrier protein-drug conjugate having a covalently bound variant of Calcitonin) to a subject in need to treatment (e.g., a subject having or at risk of osteoporosis or hypercalcaemia, wherein administration of the carrier protein-drug conjugate is effect to treat the condition.
Kits and Systems
Kits and systems are provided to facilitate and, where desired, standardize the compositions of the invention and the uses thereof. Kits contemplated herein can include one or more of a construct encoding an aldehyde tagged carrier protein (and may encompass a library composed of constructs encoding a population of differently ald-tagged carrier proteins) for expression in a host cell; a host cell that produces an FGE compatible with an aldehyde tag of the kit, where the FGE may be endogenous, recombinant, or heterologous; a host cell genetically modified to express an aldehyde tagged carrier protein (and may encompass a library composed of recombinant host cells containing constructs encoding a population of differently ald-tagged carrier proteins), which host cell can further express an endogenous, recombinant, or heterologous FGE compatible for conversion of the aldehyde tag of the tagged polypeptide; reagents to provide for production of a reactive partner-containing drug; and reagents to promote a reaction between an ald-tagged carrier protein and a reactive partner-containing drug.
In addition, the kit can contain instructions for using the components of the kit, particularly the compositions of the invention that are contained in the kit.
The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the present invention, and are not intended to limit the scope of what the inventors regard as their invention nor are they intended to represent that the experiments below are all or the only experiments performed. Efforts have been made to ensure accuracy with respect to numbers used (e.g. amounts, temperature, etc.) but some experimental errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, molecular weight is weight average molecular weight, temperature is in degrees Centigrade, and pressure is at or near atmospheric.
The ald-tag technology is used to provide for high-efficiency modification of secreted carrier proteins in mammalian cell culture system. An FGE and sulfatase motifs are used to install aldehyde tags in a recombinant human serum albumin (rHSA) in a yeast expression system, e.g., Saccharomyces cerevisiae. The FGly-containing ald tag will be exploited to conjugate drugs (e.g., small molecule drugs) to the HSA carrier protein. HSA is trafficked through the secretory pathway, similar to native sulfatases and the previously studied secreted Fc proteins, and are therefore will be readily be recognized as substrates by ER-resident FGE when expressed in mammalian cells. When expressed in yeast, the recombinant HSA containing the aldehyde tag motif is purified and reacted with purified recombinant FGE to convert the cysteine to formylglycine ex vivo, the addition of purified FGE to a purified recombinant protein to give the enzymatic transformation. The converted aldehyde tagged HSA were chemically modified with small molecules to afford a final conjugated protein construct.
C-terminal Modified HSA as a Model Protein
The vector construction utilized the native (human) HSA leader sequence. Modifications to the sequence were made after initial cloning of HSA into a plasmid. A strong promoter was used (for example, Galactose inducible GAL or constitutively-active GPD promoter with -LEU2. For example, the vector p425-GAL1 or the vector p425GalL have a galactose-inducible strong promoter in place with a MCS that can receive the HSA sequence.
Yeast cell lines containing the HSA-Ald6 tag construct were generated using standard molecular biology techniques. After establishing and confirming transformed colonies by PCR, the expression of the Ald6 tagged-HSA was induced and production assayed by immunoblotting. In order to probe directly the aldehyde-modified protein, rHSA was reacted with aminooxy-FLAG peptide and analyzed by Western blot with an anti-FLAG antibody as well as an anti-HSA antibody. The percent conversion of Cys to FGly was quantified by isolation of the protein followed by tryptic digestion and mass spectrometry analysis.
Carrier proteins conjugated with multiple peptide drugs or small molecules can greatly enhance the efficacy of the biotherapeutic of interest. Thus multiple aldehyde tags will be installed into a single HSA carrier protein. An HSA carrier protein having Ald6 tags (LCTPSR, (SEQ ID NO:1)) placed in different locations along the peptide backbone of the carrier protein will be generated.
Three different Ald6 tag sequences were appended to the recombinant HSA carrier protein. These constructs, containing Ald6 sequences, are shown in
A panel of ald-tagged rHSA carrier proteins was generated, with differently ald-tagged rHSA carrier proteins having aldehydes placed strategically throughout the scaffold. The panel thus serves as a library of differently ald-tagged rHSAs, where the members of the library differ in the number and/or position of ald tags in the scaffold. For example, as exemplified in
Short serum half-life has been a challenge in the development peptide therapeutics. Peptides are typically cleared from the bloodstream within minutes to hours after administration, and thus may not be sufficiently exposed in the target tissue for a desired clinical effect. Aldehyde tagged carrier proteins, such as ald tagged HSA can be used as a carrier protein to increase the serum half-life of the peptides.
Two carrier protein-drug conjugates are generated—one a conjugate with Calcitonin and one a conjugate with GLP-1. As mentioned previously, by coupling the peptides to the HSA carrier protein the absorption and elimination half-lives will be increased.
The peptides were synthesized via standard Fmoc-based solid phase peptide synthesis protocols. The final residue added at the N terminus was (t-Boc-aminooxy)acetic acid followed by cleavage under standard conditions. Deprotection to expose the amino-oxy functionality is followed by HPLC purification. Purified ald-tagged HSA is added to a buffered solution of peptide that has been functionalized with an N-terminus amino-oxy functionality. Upon coupling to the ald-tagged HSA, the final protein-peptide complex is purified using FPLC.
The HSA-GLP-1 conjugate is assayed for activity as compared to native GLP-1. GLP-1, released from intestinal L-cells, is known for its potent stimulation of insulin biosynthesis and release from pancreatic β-cells. For the identification of GLP-1 receptor agonist, a cellular receptor activation assay based on the formation of cAMP occurring due to receptor activation is used. Receptor activation studies are performed by incubating RINm5F cells, a rat insulinoma cell line, with or without the test peptides or the HSA-peptide conjugates at increasing concentrations. Activation of the GLP-1 receptor is measured by quantification of the intracellular cAMP after cell lysis. EC50 values (concentration of test compound leading to a half maximal stimulation of camp production) are calculated from the resulting dose response curves.
The HSA-Calcitonin conjugate is assayed for osteoclast activity as compared to native Calcitonin. The BD BioCoat Osteologic Bone Cell Culture System is used to assess the effect of treatment with the HSA-peptide conjugate and the native Calcitonin peptide on bone resorption of calcium. The BD BioCoat Osteologic Bone Cell Culture System involves sub-micron synthetic calcium phosphate thin films coated onto various culture vessels. This system has been used as an alternative method for compound screening for direct assessment of osteoclast and osteoblast activity in vitro. The thin film design permits easy and reliable quantification of results.
The following describes production of an exemplary ald-tagged HSA.
A. Primer Design:
A nucleic acid encoding the wildtype HSA was inserted into a vector which can be exploited for as a template for subcloning. Using a vector with the appropriate internal restriction sites the first PCR product was:
After insertion of this sequence in a vector, variants were made using longer primers such as:
The following primers were used for PCR cDNA amplification.
The double underline represents the native sequence, with the single underline the newly introduced restriction sites for further cloning.
A 1830 bp fragment was isolated after gel purification. This was followed by digestion with XmaI and XhoI, and the DNA fragment inserted in the expression vector. The open reading frame for HSA in the expression vector was as follows.
HSA-Encoding Nucleic Acid Sequence:
Amino Acid Sequence of Encoded HSA
The HSA native leader sequence (single and double underlined residues) is removed in 2-step process (in humans) before secretion of mature protein:
B. Construction of C-terminal Modified HSA
Using the plasmid with native HSA as a PCR template a new 3′ HSA PCR primer with additional restriction sites for appending C-terminal tags onto recombinant HSA was designed as follows:
ACTTG-3′
Double underline: native C-terminus of HSA sequence.
Single underline adjacent double underline: HinDIII site
Bold residues=Stop codon
Single underline 3′ of stop codon: SalI site
Single underline 5′ of stop codon: XhoI site
The SalI and HindIII were provided in the primer as these are not in the plasmid constructs. Used in conjunction with the same Forward primer used for original HSA amplification from cDNA, an 1863 residue PCR product was obtained as follows (with the predicted amino sequence following):
NPG
MKWVTFI SLLFLFSSAY S
RGVFRR
DAH KSEVAHRFKD LGEENFKALV LIAFAQYLQQ
The product was digested with XmaI and XhoI and inserted into the expression vector, then digested with HinDIII and SalI (sequentially) for insertion of a synthetic piece of double-stranded DNA with complementary sticky ends. The sequence of the synthetic DNA encoding the HSA having an ald tag LCTPSR (SEQ ID NO:1) at the C terminus is provided below (with the predicted amino sequence following):
The plasmid encoding recombinant HSA was further modified to include the FGE motif at the C-terminus. Primers, designed for the insertion of FGE motif and thrombin-cleavable affinity tag at C-terminus, were ligated into the vector using standard molecular biology techniques. The insert design was as follows:
PstI site allows for detection of insert via diagnostic digestion instead of sequencing each miniprep. LVPRGS is a thrombin cleavage site. The ORF translates to:
LV PRGSLQHHHH HHVD
The construct was expressed in S. cerevisae and purified using affinity column purification (
C. Construction of N-terminal Modified HSA
Generating the N-terminal aldehyde tagged HSA was accomplished by inserting an in-frame synthetic gene where the N-terminus of mature HSA was modified with the aldehyde tag. The synthetic gene was cloned into a yeast expression vector using standard molecular biology techniques. The designed sequence is as follows. Bold/underline=restriction site arrays
The expected ORF product was
The construct was expressed in S. cerevisae and purified using affinity column purification. The modified protein was reacted with purified FGE to convert the cysteine to formylglycine. The recombinant HSA was reacted with a fluorophore containing a hydrazide and the conversion and conjugation was quantified by measuring the resulting fluorescence of the modified protein.
D. Construction of Internal Modified HSA
Generating the internal aldehyde tagged HSA was accomplished by inserting an in-frame synthetic gene where key restriction sites are placed where mature HSA is to be modified with the aldehyde tag. The synthetic gene was cloned into a yeast expression vector using standard molecular biology techniques. The designed sequence was as follows:
The expected ORF was:
6×His-HSA synthetic gene was ligated into pCR blunt II-TOPO vector, followed by digestion of pRW33 with EcoRI and BamHI to cut out 6×His-HSA, which was purified and then ligated into pcDNA3.1 using the EcoRI and BamHI sites. The resulting vector was Digested with XhoI/SpeI and the annealed primers:
were ligated in generating the aldehyde tag. The designed sequence was as follows:
The expected ORF product was:
6×His-LCTPSR-HSA (HHHHHHLCTPSR (SEQ ID NO:127)) was expressed and purified from CHO cells. 6×His-LCTPSR-HSA (SEQ ID NO:127) was transfected in pcDNA3.1 into CHO cells in Opti-MEM serum-free medium using Lipofectin transfection reagent in a 10 cm dish. After 3 h at 37° C., the Opti-MEM medium was removed and added 10 mL of HAM'S F12 serum-free medium. After 3 days at 37° , the media was collected and added 10 mL Binding Buffer (20 mM Na2PO4, 500 mM NaCl, 20 mM Imidazole, pH 7.5) and 200 μl of Ni-NTA resin. After incubating with rotation for 1 h at 4° C., the mixture was applied to a column. The resin was washed with 5 mL Binding Buffer and then eluted with 5×500 μl Elution Buffer (20 mM Na2PO4, 500 mM NaCl, 500 mM Imidazole, pH 7.5). The samples were run on 10% Tric-HCl gels and either stained with Coomassie or transferred to nitrocellulose for immunoblotting with an anti-His antibody to verify the presence of protein.
E. Construction HSA Modified with Two Aldehyde Tags, Internally Modified and C-terminally Modified HSA
The vectors containing recombinant HSA was digested with XmaI/SacII and the annealed primers 5′-CCGGACTTTGTACCCCTAGCAGGGGGC-3′ (SEQ ID NO:123) and 5′-CCCCTGCTAGGGGTACAAAGT-3′ (SEQ ID NO:124) were ligated in resulting in the insertion of the aldehyde tag. The designed sequence was as follows:
The expected ORF product was:
Purified HSA modified with aldehyde tags was added to a buffered solution of peptide that has been functionalized with an N-terminus amino-oxy functionality. The conjugation reaction is carried out in a buffered solution at a pH of 6.0 with 100 mM aniline added. A three-fold excess of aminooxy peptide to aldehyde was added to the reaction mixture to drive the reaction to completion. After addition of peptide to a solution of the ald-tagged HSA, the mixture was stirred at room temp for 2 h, dialyzed and the protein-peptide conjugate purified using FPLC.
6×His-LCTPSR-HSA (SEQ ID NO:127) was transformed into the Pichia strain GS115using pRW39 (6×His-LCTPSR-HSA (SEQ ID NO:127) in pPIC3.5K). pRW39 was linearized with BglII. 20 μg of DNA in 10 μL water was added to 80 μL of freshly competent GS115 cells and electroporated in a 2 mm cuvette (2000V). 1 mL of ice cold 1M sorbitol was added immediately after electroporation. The cells were plated on regeneration dextrose Bacto agar plates (lacking histidine to select for HIS+transformants) and incubated 30° C. for 3 days. Colonies were isolated and tested for resistance to G418 to select for those colonies containing multiple copies of aldehyde-tagged-HSA integrated into the Pichia genome.
Colonies were grown 10 mL of buffered buffered glycerol-complex medium overnight at 30° C. Cultures were centrifuged the cells were resuspended in buffered methanol-complex medium to induce expression of 6×His-LCTPSR-HSA (SEO ID NO:127), integrated into the Pichia genome under the control of a methanol-inducible promoter. The cells were grown for 6 days at 30° C. Methanol was added to each culture every 24 h to 0.5%. After 6 days, cells were cleared from the media by centrifugation and 10 uL of the media was run on an SDS-PAGE gel, and the gel was stained with Coomassie Blue. As a negative control, the original untransformed GS115 strain was also grown and taken through the same procedure. As a positive control for methanol induction and secretion of a protein into the media, a GS115 strain containing wild-type HSA integrated into the Pichia genome under control of the methanol-inducible promoter was also grown. The colonies expressed aldehyde-tagged-HSA and secreted it into the media (see
24 μg of a DNA construct containing aldehyde-tagged-HSA in pcDNA3.1 (pRW38) was transfected into CHO-K1 cells in Opti-MEM serum-free medium using Lipofectin transfection reagent in a 10 cm dish. After 5 h at 37° C., the Opti-MEM was removed and Ex-Cell 325 protein-free medium (+1% FBS+L-glut+Pen/Strep) was added. After 72 h at 37°, the media was collected and cleared of debris. 10 mL Binding Buffer (20 mM Na2PO4, 500 mM NaCl, 20 mM Imidazole, pH 7.5) and 200 μl of Ni-NTA resin was added. After incubating with rotation for 1 h at 4° C., the mixture was added to a column and the flow-through fraction was collected. The resin was washed with 4 mL Binding Buffer and then eluted 5 times with 500 μL Elution Buffer (20 mM Na2PO4, 500 mM NaCl, 500 mM Imidazole, pH 7.5). 10 μL of the media was run on an SDS-PAGE gel, and the gel was stained with Coomassie Blue (
This application is a continuation of U.S. application Ser. No. 12/706,679 filed Feb. 16, 2010, now U.S. Pat. No. 9,238,878, which claims priority benefit of U.S. provisional application Ser. No. 61/153,162, filed Feb. 17, 2009, which applications are incorporated herein by reference in their entirety.
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| 20160160206 A1 | Jun 2016 | US |
| Number | Date | Country | |
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| 61153162 | Feb 2009 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 12706679 | Feb 2010 | US |
| Child | 14959360 | US |
