Patent Grant
10294279
This application is a national phase entry under 35 U.S.C. § 371 of International Patent Application PCT/EP2014/062655, filed Jun. 17, 2014, designating the United States of America and published in English as International Patent Publication WO 2014/202570 A1 on Dec. 24, 2014, which claims the benefit under Article 8 of the Patent Cooperation Treaty to European Patent Application Serial No. 13172256.3, filed Jun. 17, 2013.
Pursuant to 37 C.F.R. § 1.821(c) or (e), a file containing a TXT version and a PDF version of the Sequence Listing has been submitted concomitant with this application, the contents of which are hereby incorporated by reference.
This disclosure relates to the field of medicine and biotechnology. The disclosure, in particular, relates to recombinant pre-fusion RSV F polypeptides and uses thereof, e.g., in immunogenic compositions.
Respiratory syncytial virus (RSV) is an enveloped non-segmented negative-strand RNA virus in the family Paramyxoviridae, genus Pneumovirus. Worldwide, it is estimated that 64 million RSV infections occur each year resulting in 160,000 deaths (WHO Acute Respiratory Infections Update September 2009). The most severe disease occurs particularly in premature infants, the elderly and immune-compromised individuals. In children younger than 2 years, RSV is the most common respiratory tract pathogen, accounting for approximately 50% of the hospitalizations due to respiratory infections, with a peak of hospitalization occurring at 2-4 months of age. It has been reported that almost all children have been infected by RSV by the age of two. Repeated infection during lifetime is attributed to ineffective natural immunity. The level of RSV disease burden, mortality and morbidity in the elderly are second only to those caused by non-pandemic influenza A infections.
To infect a host cell, RSV, like other enveloped viruses such as influenza virus and HIV, require fusion of the viral membrane with a host cell membrane. For RSV, the conserved fusion protein (RSV F protein) fuses the viral and host cell cellular membranes. In current models, based on paramyxovirus studies, the RSV F protein initially folds into a “pre-fusion” conformation. The metastable structure has recently been solved in complex with a stabilizing neutralizing antibody Fab fragment (McLellan et al., Science 340(6136):1113-7, 2013). During cell entry, the pre-fusion conformation undergoes refolding and conformational changes to its “post-fusion” conformation (McLellan, J. Vivol. 85(15):7788-96, 2010; Swanson, PNAS 108(23):9619-24, 2011). Thus, the RSV F protein is a metastable protein that drives membrane fusion by coupling irreversible protein refolding to membrane juxtaposition by initially folding into a metastable form (pre-fusion conformation) that subsequently undergoes discrete/stepwise conformational changes to a lower energy conformation (post-fusion conformation).
These observations suggest that pre-fusion and post-fusion RSV F protein are antigenically distinct (L. J. Calder et al., Virology 271:122-131 (2000)).
A vaccine against RSV infection is not currently available, but is desired. Vaccine candidates based on the RSV F protein have failed due to problems with, e.g., stability, purity, reproducibility, and potency. As indicated above, crystal structures have revealed a large conformational change between the pre-fusion and post-fusion states. The magnitude of the rearrangement suggested that only a portion of antibodies directed to the post-fusion conformation of RSV F will be able to cross react with the native conformation of the pre-fusion spike on the surface of the virus. Accordingly, efforts to produce a vaccine against RSV have focused on developing vaccines that contain pre-fusion forms of RSV F protein (see, e.g., WO 2010/149745, WO 2010/149743, WO 2009/079796, and WO 2012/158613). However, these efforts have not yet yielded stable pre-fusion RSV F polypeptides that could be used as candidates for testing in humans.
Provided are stable, recombinant, pre-fusion respiratory syncytial virus (RSV) fusion (F) polypeptides, i.e., recombinant RSV F polypeptides that are stabilized in the pre-fusion conformation. The RSV F polypeptides of the disclosure comprise at least one epitope that is specific to the pre-fusion conformation F protein. In certain embodiments, the pre-fusion RSV F polypeptides are soluble. The disclosure also provides nucleic acid molecules encoding the pre-fusion RSV F polypeptides according to the disclosure and vectors comprising such nucleic acid molecules.
The disclosure also relates to compositions, preferably immunogenic compositions, comprising a RSV F polypeptide, a nucleic acid molecule and/or a vector, and to the use thereof in inducing an immune response against RSV F protein, in particular, use thereof as a vaccine. The disclosure also relates to methods for inducing an anti-respiratory syncytial virus (RSV) immune response in a subject, comprising administering to the subject an effective amount of a pre-fusion RSV F polypeptide, a nucleic acid molecule encoding the RSV F polypeptide, and/or a vector comprising the nucleic acid molecule. Preferably, the induced immune response is characterized by neutralizing antibodies to RSV and/or protective immunity against RSV. In particular aspects, the disclosure relates to a method for inducing neutralizing anti-respiratory syncytial virus (RSV) F protein antibodies in a subject, comprising administering to the subject an effective amount of an immunogenic composition comprising a pre-fusion RSV F polypeptide, a nucleic acid molecule encoding the RSV F polypeptide, and/or a vector comprising the nucleic acid molecule.
The fusion protein (F) of the respiratory syncytial virus (RSV) is involved in fusion of the viral membrane with a host cell membrane, which is required for infection. The RSV F mRNA is translated into a 574-amino acid precursor protein designated F0, which contains a signal peptide sequence at the N-terminus (e.g., amino acid residues 1-26 of SEQ ID NO:1) that is removed by a signal peptidase in the endoplasmic reticulum. F0 is cleaved at two sites (between amino acid residues 109/110 and 136/137) by cellular proteases (in particular, furin, or furin-like)) removing a short glycosylated intervening sequence (also referred to as a p27 region, comprising the amino acid residues 110 to 136, and generating two domains or subunits designated F1 and F2. The F1 domain (amino acid residues 137-574) contains a hydrophobic fusion peptide at its N-terminus and the C-terminus contains the transmembrane (TM) (amino acid residues 530-550) and cytoplasmic region (amino acid residues 551-574). The F2 domain (amino acid residues 27-109) is covalently linked to F1 by two disulfide bridges. The F1-F2 heterodimers are assembled as homotrimers in the virion.
A vaccine against RSV infection is not currently available, but is desired. One potential approach to producing a vaccine is a subunit vaccine based on purified RSV F protein. However, for this approach, it is desirable that the purified RSV F protein is in a conformation that resembles the conformation of the pre-fusion state of RSV F protein, that is stable over time, and can be produced in sufficient quantities. In addition, for a subunit-based vaccine, the RSV F protein needs to be truncated by deletion of the transmembrane (TM) and the cytoplasmic region to create a soluble secreted F protein (sF). Because the TM region is responsible for membrane anchoring and trimerization, the anchorless soluble F protein is considerably more labile than the full-length protein and will readily refold into the post-fusion end-state. In order to obtain soluble F protein in the stable pre-fusion conformation that shows high expression levels and high stability, the pre-fusion conformation thus needs to be stabilized.
Stabilization of another paramyxovirus F protein in the pre-fusion conformation has been successfully accomplished for parainfluenza type 5 (PIV5). Yin et al. (Nature 439:38-44 (2006)) thus stabilized the pre-fusion structure of PIV-5 F protein by mutation of the furin cleavage site in F0, which blocked processing into F1 and F2. Furthermore, the transmembrane (TM) and cytoplasmic domain were replaced by a well-known helical trimerization domain: GCN4pII. This domain forms a trimeric helical coiled coil structure and is a modification of the natural dimeric helical coiled coil peptide GCN4 (O'Shea et al., Science 243:538-542 (1989)). The GCN4-pII peptide, in which the amino acid sequence of the GCN4 Leucine zipper was substituted with Isoleucine residues at every a and d position of the heptad, was shown to form a triple-stranded parallel alpha-helical coiled coil (Harbury et al., Science 262:1401-1407 (1993)).
For the stabilization of RSV F in the pre-fusion conformation, the same strategy has been tried, i.e., mutation of the furin cleavage site and fusion of the RSV F ectodomain to a GCN4pII trimerization domain (as disclosed in e.g., WO 2010/149743, WO 2010/149745, WO 2009/079796, and WO 2012/158613) or to the fibritin trimerization domain (McLellan et al., Nature Struct. Biol. 17:2-248-250 (2010); McLellan et al., Science 340(6136):1113-7 (2013)). This fibritin domain or “foldon” is derived from T4 fibritin and was described earlier as an artificial natural trimerization domain (Letarov et al., Biochemistry Moscow 64:817-823 (1993); S-Guthe et al., J. Mol. Biol. 337:905-915 (2004)). However, these efforts have not resulted in stable pre-fusion RSV F protein. Moreover, these efforts have not yet resulted in candidates suitable for testing in humans.
Now provided are recombinant stable pre-fusion RSV F polypeptides, i.e., RSV F polypeptides that are stabilized in the pre-fusion conformation. In the research that led to this disclosure, several modification steps were introduced and/or combined in order to obtain the stable soluble pre-fusion RSV F polypeptides. The stable pre-fusion RSV F polypeptides of the disclosure are in the pre-fusion conformation, i.e., they comprise (display) at least one epitope that is specific to the pre-fusion conformation F protein. An epitope that is specific to the pre-fusion conformation F protein is an epitope that is not presented in the post-fusion conformation. Without wishing to be bound by any particular theory, it is believed that the pre-fusion conformation of RSV F protein may contain epitopes that are the same as those on the RSV F protein expressed on natural RSV virions and, therefore, may provide advantages for eliciting protective neutralizing antibodies.
The polypeptides of the disclosure comprise at least one epitope that is recognized by a pre-fusion specific monoclonal antibody, comprising a heavy chain CDR1 region of SEQ ID NO:54, a heavy chain CDR2 region of SEQ ID NO:55, a heavy chain CDR3 region of SEQ ID NO:56 and a light chain CDR1 region of SEQ ID NO:62, a light chain CDR2 region of SEQ ID NO:63, and a light chain CDR3 region of SEQ ID NO:64 (hereafter referred to as “CR9501”) and/or a pre-fusion specific monoclonal antibody comprising a heavy chain CDR1 region of SEQ ID NO:58, a heavy chain CDR2 region of SEQ ID NO:59, a heavy chain CDR3 region of SEQ ID NO:60 and a light chain CDR1 region of SEQ ID NO:66, a light chain CDR2 region of SEQ ID NO:67, and a light chain CDR3 region of SEQ ID NO:68 (referred to as “CR9502”). CR9501 and CR9502 comprise the heavy and light chain variable regions and, thus, the binding specificities of the antibodies 58C5 and 30D8, respectively, which have previously been shown to bind specifically to RSV F protein in its pre-fusion conformation and not to the post-fusion conformation (see WO 2012/006596).
In certain embodiments, the recombinant pre-fusion RSV F polypeptides comprise at least one epitope that is recognized by at least one pre-fusion-specific monoclonal antibody as described above and are trimeric.
The stable pre-fusion RSV F polypeptides according to the disclosure comprise an F1 domain and an F2 domain, wherein the polypeptides comprise at least one mutation, as compared to wild-type F1 and F2 domains, selected from the group consisting of:
In certain embodiments, the stable pre-fusion RSV F polypeptides comprise an F1 domain and an F2 domain, wherein the polypeptides comprise at least one mutation selected from the group consisting of:
In certain embodiments, the pre-fusion RSV F polypeptides further comprise a mutation of the amino acid residue at position 67 and/or a mutation of the amino acid residue at position 215.
In certain embodiments, the stable pre-fusion RSV F polypeptides thus comprise an F1 domain and an F2 domain, wherein the polypeptides comprise a mutation of the amino acid residue at position 67 and/or a mutation of the amino acid residue at position 215, and at least one further mutation selected from the group consisting of:
In certain embodiments, the stable pre-fusion RSV F polypeptides comprise an F1 domain and an F2 domain, wherein the polypeptides comprise a mutation of the amino acid residue N or T at position 67 and/or a mutation of amino acid residue S at position 215, and wherein the polypeptides further comprise at least one further mutation selected from the group consisting of:
In certain embodiments, the stable pre-fusion RSV F polypeptides comprise a linking sequence comprising from 1 to 10 amino acids, linking the F1 domain and F2 domain.
In certain embodiments, the stable pre-fusion RSV F polypeptides according to the disclosure thus comprise an F1 domain and an F2 domain, and a linking sequence comprising from 1 to 10 amino acid residues, linking the F1 domain to the F2 domain, wherein the polypeptides comprise at least one mutation selected from the group consisting of:
In certain embodiments, the stable pre-fusion RSV F polypeptides further comprise a mutation of the amino acid residue N or T at position 67 and/or a mutation of amino acid residue S at position 215. In certain embodiments, the stable pre-fusion RSV F polypeptides further comprise a mutation of the amino acid residue N or T at position 67 (N/T67I) into I and/or a mutation of amino acid residue S at position 215 into P (S215P).
In certain embodiments, the stable pre-fusion RSV F polypeptides according to the disclosure comprise a truncated F1 domain.
In certain embodiments, the stable pre-fusion RSV F polypeptides according to the disclosure thus comprise a truncated F1 domain and an F2 domain and, optionally, a linking sequence comprising from 1 to 10 amino acid residues, linking the truncated F1 domain to the F2 domain, wherein the polypeptides comprise at least one further mutation selected from the group consisting of:
In certain embodiments, the polypeptides further comprise a mutation of the amino acid residue N or T at position 67 and/or a mutation of amino acid residue S at position 215. In certain embodiments, the stable pre-fusion RSV F polypeptides further comprise a mutation of the amino acid residue N or T at position 67 (N/T67I) into I and/or a mutation of amino acid residue S at position 215 into P (S215P).
According to the disclosure, the polypeptides of the disclosure thus comprise at least one stabilizing mutation in the F1 and/or F2 domain as compared to the RSV F1 and/or F2 domain in a wild-type RSV F protein. It is known that RSV exists as a single serotype having two antigenic subgroups: A and B. The amino acid sequences of the mature processed F proteins of the two groups are about 93% identical. As used throughout this disclosure, the amino acid positions are given in reference to the sequence of RSV F protein from the A2 strain (SEQ ID NO:1). As used in this disclosure, the wording “the amino acid at position “x” of the RSV F protein” thus means the amino acid corresponding to the amino acid at position “x” in the RSV F protein of the RSV A2 strain of SEQ ID NO:1. Note that, in the numbering system used throughout this disclosure, “1” refers to the N-terminal amino acid of an immature F0 protein (SEQ ID NO:1). When an RSV strain other than the A2 strain is used, the amino acid positions of the F protein are to be numbered with reference to the numbering of the F protein of the A2 strain of SEQ ID NO:1 by aligning the sequences of the other RSV strain with the F protein of SEQ ID NO:1 with the insertion of gaps as needed. Sequence alignments can be done using methods well known in the art, e.g., by CLUSTALW, Bioedit or CLC Workbench.
An amino acid according to the disclosure can be any of the twenty naturally occurring (or “standard”) amino acids or variants thereof, such as, e.g., D-amino acids (the D-enantiomers of amino acids with a chiral center), or any variants that are not naturally found in proteins, such as, e.g., norleucine. The standard amino acids can be divided into several groups based on their properties. Important factors are charge, hydrophilicity or hydrophobicity, size and functional groups. These properties are important for protein structure and protein-protein interactions. Some amino acids have special properties, such as cysteine, that can form covalent disulfide bonds (or disulfide bridges) to other cysteine residues, proline that induces turns of the polypeptide backbone, and glycine that is more flexible than other amino acids. Table 17 shows the abbreviations and properties of the standard amino acids.
It will be appreciated by a skilled person that the mutations can be made to the protein by routine molecular biology procedures. The mutations according to the disclosure preferably result in increased expression levels and/or increased stabilization of the pre-fusion RSV F polypeptides as compared to RSV F polypeptides that do not comprise these mutation(s).
In certain embodiments, the pre-fusion RSV F polypeptides are full length.
In certain embodiments, the pre-fusion RSV F polypeptides are soluble.
In certain embodiments, the pre-fusion RSV F polypeptides further comprise a heterologous trimerization domain linked to the truncated F1 domain. According to the disclosure, it was shown that by linking a heterologous trimerization domain to the C-terminal amino acid residue of a truncated F1 domain, optionally combined with a linking sequence linking the F1 and F2 domains and the stabilizing mutation(s), RSV F polypeptides are provided that show high expression and that bind to pre-fusion-specific antibodies, indicating that the polypeptides are in the pre-fusion conformation. In addition, the RSV F polypeptides are stabilized in the pre-fusion conformation, i.e., even after processing of the polypeptides, they still bind to the pre-fusion-specific antibodies CR9501 and/or CR9502, indicating that the pre-fusion-specific epitope is retained.
In further embodiments, the pre-fusion RSV F polypeptides comprise one or more further mutations (as compared to the wild-type RSV F protein), selected from the group consisting of:
In preferred embodiments, the one or more further mutations are selected from the group consisting of:
As described above, in certain embodiments, the pre-fusion RSV F polypeptides comprise a mutation of the amino acid residue D at position 486 into C (D486C) in combination with D489C or E487C. These double mutations to two extra cysteine residues result in an inter-subunit disulfide bridge between the F1 proteins to establish a covalent bond between the protomers and to stabilize the pre-fusion RSV F structure.
It is again noted that for the positions of the amino acid residues, reference is made to SEQ ID NO:1. A skilled person will be able to determine the corresponding amino acid residues in F proteins of other RSV strains.
In certain embodiments, the pre-fusion RSV F polypeptides comprise at least two mutations (as compared to a wild-type RSV F protein).
In certain embodiments, the polypeptides comprise at least three mutations.
In certain embodiments, the polypeptides comprise at least four, five or six mutations.
In certain embodiments, the heterologous trimerization domain comprises the amino acid sequence EKKIEAIEKKIEAIEKKIEA (SEQ ID NO:3). In certain other embodiments, the heterologous trimerization domain comprises the amino acid sequence GYIPEAPRDGQAYVRKDGEWVLLSTFL (SEQ ID NO:4).
As described above, in certain embodiments, the polypeptides of the disclosure comprise a truncated F1 domain. As used herein, a “truncated” F1 domain refers to an F1 domain that is not a full-length F1 domain, i.e., wherein either N-terminally or C-terminally, one or more amino acid residues have been deleted. According to the disclosure, at least the transmembrane domain and cytoplasmic tail have been deleted to permit expression as a soluble ectodomain.
In certain other embodiments, the F1 domain is truncated after amino acid residue 495 of the RSV F protein (referring to SEQ ID NO:1), i.e., the C-terminal part of the F1 domain starting from amino acid residue 496 (referring to SEQ ID NO:1) has been deleted. In certain other embodiments, the F1 domain is truncated after amino acid residue 513 of the RSV F protein. In certain embodiments, the F1 domain is truncated after amino acid residue 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 512, 513, 514, 515, 516, 517, 518, 519, 520, 521, 522, 523, 524 or 525.
In certain embodiments, the trimerization domain is linked to amino acid residue 495 of the RSV F1 domain. In certain embodiments, the trimerization domain comprises SEQ ID NO:4 and is linked to amino acid residue 495 of the RSV F1 domain.
In certain other embodiments, the trimerization domain is linked to amino acid residue 513 of the RSV F1 domain. In certain embodiments, the trimerization domain comprises SEQ ID NO:3 and is linked to amino acid residue 513 of the RSV F1 domain.
As described above, in certain embodiments, the F1 domain, which is optionally truncated, and the F2 domain are linked by a linking sequence, linking the C-terminal amino acid of the F2 domain to the N-terminal amino acid of the (optionally truncated) F2 domain. In certain embodiments, the linking sequence (or linker) comprises from 1-10 amino acid residues, preferably from 2-9 amino acid residues, preferably from 3-8 amino acid residues, preferably from 4-7 amino acid residues, and more preferably, the linker comprises 5 or 6 amino acid residues. Numerous conformationally neutral linkers are known in the art that can be used according to the disclosure without disrupting the conformation of the pre-fusion RSV F polypeptides. In preferred embodiments, the linker comprises the amino acid sequence GSGSG (SEQ ID NO:5).
In certain embodiments, the F1 domain and/or the F domain are from an RSV A strain. In certain embodiments, the F1 and/or F2 domain are from the RSV A2 strain of SEQ ID NO:1.
In certain embodiments, the F1 and/or F2 domain are from the RSV A2 strain of SEQ ID NO:69.
In certain embodiments, the F1 domain and/or the F domain are from an RSV B strain. In certain embodiments, the F1 and/or F2 domain are from the RSV B strain of SEQ ID NO:2.
In certain embodiments, the F1 and F2 domains are from the same RSV strain. In certain embodiments, the pre-fusion RSV F polypeptides are chimeric polypeptides, i.e., comprising F1 and F2 domains that are from different RSV strains.
In certain embodiments, the level of expression of the pre-fusion RSV F polypeptides of the disclosure is increased, as compared to a full-length wild-type RSV F polypeptide or a wild-type ectodomain (i.e., without the transmembrane and cytoplasmic region) without the mutation(s). In certain embodiments, the level of expression is increased at least five-fold, preferably up to ten-fold. In certain embodiments, the level of expression is increased more than ten-fold.
The pre-fusion RSV F polypeptides according to the disclosure are stable, i.e., do not readily change into the post-fusion conformation upon processing of the polypeptides, such as, e.g., purification, freeze-thaw cycles, and/or storage, etc.
In certain embodiments, the pre-fusion RSV F polypeptides according to the disclosure have an increased stability upon storage at 4° C. as compared to an RSV F polypeptide without the mutation(s). In certain embodiments, the polypeptides are stable upon storage at 4° C. for at least 30 days, preferably at least 60 days, preferably at least 6 months, even more preferably at least 1 year. With “stable upon storage,” it is meant that the polypeptides still display the at least one epitope specific for the pre-fusion-specific antibody (e.g., CR9501) upon storage of the polypeptide in solution (e.g., culture medium) at 4° C. for at least 30 days, e.g., as determined using a method as described in Example 8 or 10. In certain embodiments, the polypeptides display the at least one pre-fusion-specific epitope for at least 6 months, preferably for at least 1 year upon storage of the pre-fusion RSV F polypeptides at 4° C.
In certain embodiments, the pre-fusion RSV F polypeptides according to the disclosure have an increased stability when subjected to heat, as compared to RSV F polypeptides without the mutation(s). In certain embodiments, the pre-fusion RSV F polypeptides are heat stable for at least 30 minutes at a temperature of 55° C., preferably at 58° C., more preferably at 60° C. With “heat stable” it is meant that the polypeptides still display the at least one pre-fusion-specific epitope after having been subjected for at least 30 minutes to an increased temperature (i.e., a temperature of 55° C. or above), e.g., as determined using a method as described in Example 9.
In certain embodiments, the polypeptides display the at least one pre-fusion-specific epitope after being subjected to 1 to 6 freeze-thaw cycles in an appropriate formulation buffer.
In certain preferred embodiments, the pre-fusion RSV F polypeptide of the disclosure comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:90-94. In certain embodiments, the pre-fusion RSV F polypeptide of the disclosure consists of an amino acid sequence selected from the group consisting of SEQ ID NOS:90-94.
As used throughout this disclosure, nucleotide sequences are provided from 5′ to 3′ direction, and amino acid sequences from N-terminus to C-terminus, as customary in the art.
In certain embodiments, the encoded polypeptides according to the disclosure further comprise a leader sequence, also referred to as “signal sequence” or “signal peptide,” corresponding to amino acids 1-26 of SEQ ID NO:1, SEQ ID NO:2 or SEQ ID NO:69. This is a short (typically 5-30 amino acids long) peptide present at the N-terminus of the majority of newly synthesized proteins that are destined toward the secretory pathway. In certain embodiments, the polypeptides according to the disclosure do not comprise a leader sequence.
In certain embodiments, the polypeptides comprise a HIS-Tag. A His-Tag or polyhistidine-tag is an amino acid motif in proteins that consists of at least five histidine (H) residues, often at the N- or C-terminus of the protein, which is generally used for purification purposes.
In certain embodiments, the polypeptides do not comprise a HIS-Tag. According to the disclosure, it has surprisingly been shown that when the HIS-tag is deleted, the level of expression and the stability are increased as compared to polypeptides with a HIS-tag.
This disclosure further provides nucleic acid molecules encoding the RSV F polypeptides according to the disclosure.
In preferred embodiments, the nucleic acid molecules encoding the polypeptides according to the disclosure are codon-optimized for expression in mammalian cells, preferably human cells. Methods of codon-optimization are known and have been described previously (e.g., WO 96/09378). A sequence is considered codon-optimized if at least one non-preferred codon as compared to a wild-type sequence is replaced by a codon that is more preferred. Herein, a non-preferred codon is a codon that is used less frequently in an organism than another codon coding for the same amino acid, and a codon that is more preferred is a codon that is used more frequently in an organism than a non-preferred codon. The frequency of codon usage for a specific organism can be found in codon frequency tables, such as. Preferably, more than one non-preferred codon, preferably most or all non-preferred codons, are replaced by codons that are more preferred. Preferably, the most frequently used codons in an organism are used in a codon-optimized sequence. Replacement by preferred codons generally leads to higher expression.
It will be understood by a skilled person that numerous different polynucleotides and nucleic acid molecules can encode the same polypeptide as a result of the degeneracy of the genetic code. It is also understood that skilled persons may, using routine techniques, make nucleotide substitutions that do not affect the polypeptide sequence encoded by the nucleic acid molecules to reflect the codon usage of any particular host organism in which the polypeptides are to be expressed. Therefore, unless otherwise specified, a “nucleotide sequence encoding an amino acid sequence” includes all nucleotide sequences that are degenerate versions of each other and that encode the same amino acid sequence. Nucleotide sequences that encode proteins and RNA may or may not include introns.
Nucleic acid sequences can be cloned using routine molecular biology techniques, or generated de novo by DNA synthesis, which can be performed using routine procedures by service companies having business in the field of DNA synthesis and/or molecular cloning (e.g., GENEART®, G
The disclosure also provides vectors comprising a nucleic acid molecule as described above. In certain embodiments, a nucleic acid molecule according to the disclosure thus is part of a vector. Such vectors can easily be manipulated by methods well known to the person skilled in the art and can, for instance, be designed for being capable of replication in prokaryotic and/or eukaryotic cells. In addition, many vectors can be used for transformation of eukaryotic cells and will integrate in whole or in part into the genome of such cells, resulting in stable host cells comprising the desired nucleic acid in their genome. The vector used can be any vector that is suitable for cloning DNA and that can be used for transcription of a nucleic acid of interest. Suitable vectors according to the disclosure are, e.g., adenovectors, such as, e.g., Ad26 or Ad35, alphavirus, paramyxovirus, vaccinia virus, herpes virus, retroviral vectors, etc. The person skilled in the art is capable of choosing suitable expression vectors and inserting the nucleic acid sequences of the disclosure in a functional manner.
Host cells comprising the nucleic acid molecules encoding the pre-fusion RSV F polypeptides also form part of the disclosure. The pre-fusion RSV F polypeptides may be produced through recombinant DNA technology involving expression of the molecules in host cells, e.g., Chinese hamster ovary (CHO) cells, tumor cell lines, BHK cells, human cell lines such as HEK293 cells, PER.C6® cells, or yeast, fungi, insect cells, and the like, or transgenic animals or plants. In certain embodiments, the cells are from a multicellular organism. In certain embodiments, they are of vertebrate or invertebrate origin. In certain embodiments, the cells are mammalian cells. In certain embodiments, the cells are human cells. In general, the production of recombinant proteins, such as the pre-fusion RSV F polypeptides of the disclosure, in a host cell comprises the introduction of a heterologous nucleic acid molecule encoding the polypeptide in expressible format into the host cell, culturing the cells under conditions conducive to expression of the nucleic acid molecule and allowing expression of the polypeptide in the cell. The nucleic acid molecule encoding a protein in expressible format may be in the form of an expression cassette, and usually requires sequences capable of bringing about expression of the nucleic acid, such as enhancer(s), promoter, polyadenylation signal, and the like. The person skilled in the art is aware that various promoters can be used to obtain expression of a gene in host cells. Promoters can be constitutive or regulated, and can be obtained from various sources, including viruses, prokaryotic, or eukaryotic sources, or artificially designed.
Cell culture media are available from various vendors, and a suitable medium can be routinely chosen for a host cell to express the protein of interest, here, the pre-fusion RSV F polypeptides. The suitable medium may or may not contain serum.
A “heterologous nucleic acid molecule” (also referred to herein as “transgene”) is a nucleic acid molecule that is not naturally present in the host cell. It is introduced into, for instance, a vector by standard molecular biology techniques. A transgene is generally operably linked to expression control sequences. This can, for instance, be done by placing the nucleic acid encoding the transgene(s) under the control of a promoter. Further regulatory sequences may be added. Many promoters can be used for expression of a transgene(s), and are known to the skilled person, e.g., these may comprise viral, mammalian, synthetic promoters, and the like. A non-limiting example of a suitable promoter for obtaining expression in eukaryotic cells is a CMV-promoter (U.S. Pat. No. 5,385,839), e.g., the CMV immediate early promoter, for instance, comprising nt. −735 to +95 from the CMV immediate early gene enhancer/promoter. A polyadenylation signal, for example, the bovine growth hormone polyA signal (U.S. Pat. No. 5,122,458), may be present behind the transgene(s). Alternatively, several widely used expression vectors are available in the art and from commercial sources, e.g., the pcDNA and pEF vector series of Invitrogen, pMSCV and pTK-Hyg from BD Sciences, pCMV-Script from Stratagene, etc., which can be used to recombinantly express the protein of interest, or to obtain suitable promoters and/or transcription terminator sequences, polyA sequences, and the like.
The cell culture can be any type of cell culture, including adherent cell culture, e.g., cells attached to the surface of a culture vessel or to microcarriers, as well as suspension culture. Most large-scale suspension cultures are operated as batch or fed-batch processes because they are the most straightforward to operate and scale up. Nowadays, continuous processes based on perfusion principles are becoming more common and are also suitable. Suitable culture media are also well known to the skilled person and can generally be obtained from commercial sources in large quantities, or custom-made according to standard protocols. Culturing can be done, for instance, in dishes, roller bottles or in bioreactors, using batch, fed-batch, continuous systems, and the like. Suitable conditions for culturing cells are known (see, e.g., Tissue Culture, Academic Press, Kruse and Paterson, editors (1973), and R. I. Freshney, Culture of animal cells: A manual of basic technique, fourth edition (Wiley-Liss Inc., 2000, ISBN 0-471-34889-9)).
Further provided are compositions comprising a pre-fusion RSV F polypeptide and/or a nucleic acid molecule, and/or a vector, as described above. Thus provided are compositions comprising a pre-fusion RSV F polypeptide that displays an epitope that is present in a pre-fusion conformation of the RSV F protein but is absent in the post-fusion conformation. Also provided are compositions comprising a nucleic acid molecule and/or a vector, encoding such pre-fusion RSV F polypeptide. Further provided are immunogenic compositions comprising a pre-fusion RSV F polypeptide, and/or a nucleic acid molecule, and/or a vector, as described above. The disclosure also provides the use of a stabilized pre-fusion RSV F polypeptide, a nucleic acid molecule, and/or a vector, according to the disclosure, for inducing an immune response against RSV F protein in a subject. Further provided are methods for inducing an immune response against RSV F protein in a subject, comprising administering to the subject a pre-fusion RSV F polypeptide, and/or a nucleic acid molecule, and/or a vector, according to the disclosure. Also provided are pre-fusion RSV F polypeptides, nucleic acid molecules, and/or vectors, according to the disclosure, for use in inducing an immune response against RSV F protein in a subject. Further provided is the use of the pre-fusion RSV F polypeptides, and/or nucleic acid molecules, and/or vectors according to the disclosure for the manufacture of a medicament for use in inducing an immune response against RSV F protein in a subject.
The pre-fusion RSV F polypeptides, nucleic acid molecules, or vectors of the disclosure may be used for prevention (prophylaxis) and/or treatment of RSV infections. In certain embodiments, the prevention and/or treatment may be targeted at patient groups that are susceptible to RSV infection. Such patient groups include, but are not limited to, e.g., the elderly (e.g., >50 years old, >60 years old, and preferably >65 years old), the young (e.g., <5 years old, <1 year old), hospitalized patients and patients who have been treated with an antiviral compound but have shown an inadequate antiviral response.
The pre-fusion RSV F polypeptides, nucleic acid molecules and/or vectors according to the disclosure may be used, e.g., in stand-alone treatment and/or prophylaxis of a disease or condition caused by RSV, or in combination with other prophylactic and/or therapeutic treatments, such as (existing or future) vaccines, antiviral agents and/or monoclonal antibodies.
The disclosure further provides methods for preventing and/or treating RSV infection in a subject utilizing the pre-fusion RSV F polypeptides, nucleic acid molecules and/or vectors according to the disclosure. In a specific embodiment, a method for preventing and/or treating RSV infection in a subject comprises administering to a subject in need thereof an effective amount of a pre-fusion RSV F polypeptide, nucleic acid molecule and/or a vector, as described above. A therapeutically effective amount refers to an amount of a polypeptide, nucleic acid molecule or vector that is effective for preventing, ameliorating and/or treating a disease or condition resulting from infection by RSV. Prevention encompasses inhibiting or reducing the spread of RSV or inhibiting or reducing the onset, development or progression of one or more of the symptoms associated with infection by RSV. “Amelioration” as used in herein may refer to the reduction of visible or perceptible disease symptoms, viremia, or any other measurable manifestation of RSV infection.
For administering to subjects, such as humans, the disclosure may employ pharmaceutical compositions comprising a pre-fusion RSV F polypeptide, a nucleic acid molecule and/or a vector as described herein, and a pharmaceutically acceptable carrier or excipient. In the present context, the term “pharmaceutically acceptable” means that the carrier or excipient, at the dosages and concentrations employed, will not cause any unwanted or harmful effects in the subjects to which they are administered. Such pharmaceutically acceptable carriers and excipients are well known in the art (see Remington's Pharmaceutical Sciences, 18th edition, A. R. Gennaro, Ed., Mack Publishing Company [1990]; Pharmaceutical Formulation Development of Peptides and Proteins, S. Frokjaer and L. Hovgaard, Eds., Taylor & Francis [2000]; and Handbook of Pharmaceutical Excipients, 3rd edition, A. Kibbe, Ed., Pharmaceutical Press [2000]). The RSV F polypeptides or nucleic acid molecules are preferably formulated and administered as a sterile solution, although it may also be possible to utilize lyophilized preparations. Sterile solutions are prepared by sterile filtration or by other methods known per se in the art. The solutions are then lyophilized or filled into pharmaceutical dosage containers. The pH of the solution generally is in the range of pH 3.0 to 9.5, e.g., pH 5.0 to 7.5. The RSV F polypeptides typically are in a solution having a suitable pharmaceutically acceptable buffer, and the composition may also contain a salt. Optionally, stabilizing agent may be present, such as albumin. In certain embodiments, detergent is added. In certain embodiments, the RSV F polypeptides may be formulated into an injectable preparation.
In certain embodiments, a composition according to the disclosure further comprises one or more adjuvants. Adjuvants are known in the art to further increase the immune response to an applied antigenic determinant. The terms “adjuvant” and “immune stimulant” are used interchangeably herein, and are defined as one or more substances that cause stimulation of the immune system. In this context, an adjuvant is used to enhance an immune response to the RSV F polypeptides of the disclosure. Examples of suitable adjuvants include aluminium salts such as aluminium hydroxide and/or aluminium phosphate; oil-emulsion compositions (or oil-in-water compositions), including squalene-water emulsions, such as MF59 (see, e.g., WO 90/14837); saponin formulations, such as, for example, QS21 and Immunostimulating Complexes (ISCOMS) (see, e.g., U.S. Pat. No. 5,057,540; WO 90/03184, WO 96/11711, WO 2004/004762, WO 2005/002620); bacterial or microbial derivatives, examples of which are monophosphoryl lipid A (MPL), 3-O-deacylated MPL (3dMPL), CpG-motif containing oligonucleotides, ADP-ribosylating bacterial toxins or mutants thereof, such as E. coli heat labile enterotoxin LT, cholera toxin CT, and the like; eukaryotic proteins (e.g., antibodies or fragments thereof (e.g., directed against the antigen itself or CD1a, CD3, CD7, CD80) and ligands to receptors (e.g., CD40L, GMCSF, GCSF, etc., which stimulate immune response upon interaction with recipient cells. In certain embodiments, the compositions of the disclosure comprise aluminium as an adjuvant, e.g., in the form of aluminium hydroxide, aluminium phosphate, aluminium potassium phosphate, or combinations thereof, in concentrations of 0.05 to 5 mg, e.g., from 0.075 to 1.0 mg, of aluminium content per dose.
The pre-fusion RSV F polypeptides may also be administered in combination with or conjugated to nanoparticles, such as, e.g., polymers, liposomes, virosomes, and virus-like particles. The pre-fusion F polypeptides may be combined with, encapsidated in or conjugated to the nanoparticles with or without adjuvant. Encapsulation within liposomes is described, e.g., in U.S. Pat. No. 4,235,877. Conjugation to macromolecules is disclosed, for example, in U.S. Pat. No. 4,372,945 or U.S. Pat. No. 4,474,757.
In other embodiments, the compositions do not comprise adjuvants.
In certain embodiments, the disclosure provides methods for making a vaccine against respiratory syncytial virus (RSV) comprising providing a composition according to the disclosure and formulating it into a pharmaceutically acceptable composition. The term “vaccine” refers to an agent or composition containing an active component effective to induce a certain degree of immunity in a subject against a certain pathogen or disease, which will result in at least a decrease (up to complete absence) of the severity, duration or other manifestation of symptoms associated with infection by the pathogen or the disease. In this disclosure, the vaccine comprises an effective amount of a pre-fusion RSV F polypeptide and/or a nucleic acid molecule encoding a pre-fusion RSV F polypeptide, and/or a vector comprising the nucleic acid molecule, which results in an immune response against the F protein of RSV. This provides a method of preventing serious lower respiratory tract disease leading to hospitalization and the decrease in frequency of complications such as pneumonia and bronchiolitis due to RSV infection and replication in a subject. The term “vaccine” according to the disclosure implies that it is a pharmaceutical composition, and thus typically includes a pharmaceutically acceptable diluent, carrier or excipient. It may or may not comprise further active ingredients. In certain embodiments, it may be a combination vaccine that further comprises other components that induce an immune response, e.g., against other proteins of RSV and/or against other infectious agents. The administration of further active components may, for instance, be done by separate administration or by administering combination products of the vaccines of the disclosure and the further active components.
Compositions may be administered to a subject, e.g., a human subject. The total dose of the RSV F polypeptides in a composition for a single administration can, for instance, be about 0.01 μg to about 10 mg, e.g., 1 μg to 1 mg, e.g., 10 μg to 100 μg. Determining the recommended dose will be carried out by experimentation and is routine for those skilled in the art.
Administration of the compositions according to the disclosure can be performed using standard routes of administration. Non-limiting embodiments include parenteral administration, such as intradermal, intramuscular, subcutaneous, transcutaneous, or mucosal administration, e.g., intranasal, oral, and the like. In one embodiment, a composition is administered by intramuscular injection. The skilled person knows the various possibilities to administer a composition, e.g., a vaccine, in order to induce an immune response to the antigen(s) in the vaccine.
A “subject” as used herein preferably is a mammal, for instance, a rodent, e.g., a mouse, a cotton rat, or a non-human primate, or a human. Preferably, the subject is a human subject.
The polypeptides, nucleic acid molecules, vectors, and/or compositions may also be administered, either as prime, or as boost, in a homologous or heterologous prime-boost regimen. If a boosting vaccination is performed, typically, such a boosting vaccination will be administered to the same subject at a time between one week and one year, preferably between two weeks and four months, after administering the composition to the subject for the first time (which is, in such cases, referred to as “priming vaccination”). In certain embodiments, the administration comprises a prime and at least one booster administration.
In addition, the polypeptides of the disclosure may be used as a diagnostic tool, for example, to test the immune status of an individual by establishing whether there are antibodies in the serum of such individual capable of binding to the polypeptide of the disclosure. The disclosure thus also relates to an in vitro diagnostic method for detecting the presence of an RSV infection in a patient, the method comprising the steps of: a) contacting a biological sample obtained from the patient with a polypeptide according to the disclosure; and b) detecting the presence of antibody-polypeptide complexes.
The disclosure further provides a method for stabilizing the pre-fusion conformation of an RSV F polypeptide comprising introducing one or more mutations in an RSV F1 domain, as compared to the wild-type RSV F1 domain, wherein the one or more mutations are selected from the group consisting of:
In certain embodiments, the mutation in the HRA region is at position 161.
In certain embodiments, the mutation in the HRA region is at position 173.
In certain embodiments, the mutation in the HRA region is at position 182.
In certain embodiments, the introduction of two cysteine residues is at position 486 and 489.
In certain embodiments, the introduction of two cysteine residues is at position 486 and 487.
Stabilized pre-fusion RSV F polypeptides obtainable and/or obtained by such method also form part of the disclosure, as well as uses thereof as described above.
The disclosure is further explained in the following examples. The examples do not limit the disclosure in any way. They merely serve to clarify the disclosure.
In the patent application PCT/EP2014/058353 (now published as WO 2014/174018), stabilized variants of soluble pre-fusion F protein (sF) were designed by stabilizing the two main regions that initiate refolding. The first strategy was to arrest the fusion peptide in its position and prevent it from getting released from the head region by fixing and joining the F1-F2 domains by a short loop. Release of the fusion peptide can be prevented by re-establishing a covalent connection of the N-terminus of F1 to C-terminus of F2. As shown in this example, several different linkers have been tried. The insertion of a 5-amino acid loop between F1 and F2, in particular, comprising the amino acid sequence GSGSG (SEQ ID NO:5), was most successful.
The other unstable region is the second heptad repeat (HRB) region that forms the trimeric helical stem region in pre-fusion F protein. Deletion of the transmembrane domain (TM) in the soluble F protein further destabilizes this region, which was compensated by the addition of different heterologous trimerization domains. The fully processed mature RSV-F ectodomain was fused C-terminally to different trimerization domains and at different positions (i.e., the F1 domain was truncated at different amino acid residues).
Several constructs were made based on either RSV A2 or B1 strains. Different trimerization domains were linked to the RSV F1 domain, which was truncated at different positions. Trimerization domains that were tested included the Fibritin motif (comprising the amino acid sequence GYIPEAPRDGQAYVRKDGEWVLLSTFL (SEQ ID NO:4)), and the “Fibritin long” motif, a longer, N-terminal extended Fibritin domain that includes its natural helical regions (comprising the amino acid sequence SSLQGDVQALQEAGYIPEAPRDGQAYVRKDGEWVLLSTFL (SEQ ID NO:6)), that were added to the RSV F1 domain in frame (in register) with the presumed heptad repeat of the HRB region.
Further constructs that were made comprised heptad ideal helical trimeric coiled coils, or Isoleucine Zipper domains (IZ) (Suzuki et al., Protein Engineering 11:1051-1055 (1998)), comprising the amino acid sequence IEAIEKK (SEQ ID NO:7). According to the disclosure, different IZ domains were used, referred to as Isoleucine Zipper (L), comprising the amino acid sequence (I)EKKIEAIEKKIEAIEKKIEAIEAIEKKIEA (SEQ ID NO:8) and Isoleucine Zipper (S), comprising the amino acid sequence EKKIEAIEKKIEAIEKKIEA (SEQ ID NO:3).
These IZ domains are comparable in structure to GCN4; however, the IZ domains are not natural sequences but designed to be optimal trimerization domains and, therefore, more stable.
Further constructs were made with other known trimerization domains:
The following constructs were made:
All constructs comprised a HIS-tag.
The constructs were tested for expression levels, storage stability and antibody binding with the antibody CR9501. The amino acid sequences of the heavy and light chain variable regions, and of the heavy and light chain CDRs of this antibody are given below. CR9501 comprises the binding regions of the antibodies referred to as 58C5 in WO 2012/006596.
The constructs were synthesized and codon-optimized at GENEART® (Life Technologies, Carlsbad, Calif.). The constructs were cloned into pCDNA2004 or generated by standard methods widely known within the field involving site-directed mutagenesis and PCR and sequenced. The expression platform used was the 293Freestyle cells (Life Technologies). The cells were transiently transfected using 293Fectin (Life Technologies) according to the manufacturer's instructions and cultured for 5 days at 37° C. and 10% CO2. The culture supernatant was harvested and spun for 5 minutes at 300 g to remove cells and cellular debris. The spun supernatant was subsequently sterile filtered using a 0.22 μm vacuum filter and stored at 4° C. until use.
Supernatants from day 5 were evaluated for F protein expression by Western blot using the monoclonal antibody CR9503, which comprises the heavy and light chain variable regions of the RSV F antibody Motavizumab (referred to as CR9503). The approximate expression levels of the pre-fusion RSV F protein constructs were assessed using CR9503, an anti-human IR-dye-conjugated secondary antibody (Li-Cor, Lincoln, Nebr.) or an HRP-conjugated mouse anti-human IgG (Jackson ImmunoResearch, West Grove, Pa.). The protein quantities were then estimated using a dilution series of purified RSV standard protein, either by eye or using the Odyssey CLx infrared imaging system. To evaluate construct stability and to identify positive or negative stabilizing effects of introduced trimerization motifs, the constructs capable of binding CR9501 were treated at a range of temperatures from 45° C. to 65° C. for 30 minutes to test the stability of the CR9501 epitope. This procedure is described in detail in Example 9. The results are summarized in Table 1.
1 Expression level determined by Western Blot as described in Example 1.
As can be seen in Table 1, the only constructs that were expressed were the Fibritin variant (F18) and F23. Although F18 was trimeric and showed expression, it was unstable upon storage at 4° C. In contrast, F23 was stable at 4° C., binds to the pre-fusion-specific antibodies, but appeared to be monomeric. Therefore, both variants F18 and F23 were used to optimize for both stability and trimerization.
Next, several constructs were made in which the fusion peptide at the N-terminus of F1 was fixed by fusion to the C-terminus of the F2 domain. All constructs comprised a His-tag. Several constructs were made including constructs in which both furin cleavage sites were mutated, resulting in a soluble F protein that still contained the p27 peptide (i.e., F12, F15.1, and F17). In other constructs, the 27-residue region (P27 loop) that is cleaved from the precursor F0 was replaced by an alternative closed loop, either by replacing the region of RSV-F by the “homologous” region of PIV-5 F, the pre-fusion F protein that had been produced and crystallized successfully (F25), or by replacing the region by a minimal (GS)n loop that would bridge the termini of F2 and F1 (F24), or by replacing the region by the central conserved region of RSV-G (F26). Homology modeling of RSV-F based on PIV-5 and in silico measurements resulted in the choice of a minimal loop of five amino acid residues between residues 108 and 136. As a linker, Gly (G) and Ser (S) residues were chosen, which are flexible and polar and have a high chance to be accommodated (F24). Additionally, F137 was mutated to S because the local modifications caused by the loop could displace the hydrophobic F and cause instabilities. This is shown below. In addition, the R106 is mutated to Q and 27 residues (109-135) are replaced by GSGSG (SEQ ID NO:5).
As shown in Table 2, all variants showed very low or no expression except for the variant with the short GSGSG (SEQ ID NO:5) loop (F24), which showed a much higher expression (44 μg/ml) compared to wild-type RSV F construct, i.e., a similar construct, without the linker (F11). F24, which was trimeric, however, was unstable upon storage like all the other variants with a C-terminal Fibritin trimerization motif. All variants contained a HIS-tag.
Next, the most favorable modifications were combined to find the optimal pre-fusion F polypeptides. Combinations were made of variants with the GSGSG (SEQ ID NO:5) loop, C-terminal truncation of F1, and the addition of either fibritin (SEQ ID NO:4) or the Isoleucine Zipper (S) motif (SEQ ID NO:3) (see Table 3).
Addition of the GSGSG (SEQ ID NO:5) loop always increased the expression of functional constructs as well as the heat stability of the protein. Combination of the GSGSG (SEQ ID NO:5) loop with the truncated F and isoleucine zipper (S) motif (F43, F47) showed good expression, heat stability and good stability upon storage at 4° C. However, these variants were still monomeric. The isoleucine zipper (S) trimerization motif showed higher expression with an F variant that was C-terminally truncated F at position 495 (compare F43 with F56 and F23 with F46). In contrast, for variants with the Fibritin trimerization domain, a truncation at position 513 showed high expression compared to truncation at position 495, which showed no expression (compare F24 with F44).
Because the HIS-tag could interfere with the native folding of the trimers, variants were made without the HIS-tag for the Fibritin and the isoleucine zipper (S) variant (Table 4).
Strikingly, deletion of the HIS-tag increased expression in F47. Moreover, for F47, it increased the trimeric content slightly and, for F24, it only increased the expression level moderately.
Next, several alternative trimerization domains and truncations were tested in combination with the GSGSG (SEQ ID NO:5) loop stabilized F variant (F47) (see Table 5). All variants have a GSGSG (SEQ ID NO:5) loop and contain a HIS-tag.
Only the Matrillin 1 domain (S. A. Dames et al., Nat. Struc. Biol. 5(8), 1998) that contains both the N-terminal zipper domain and the C-terminal part with the cysteine residues that can potentially form inter-trimeric disulfide bridges was found to enable higher expression levels than F47 (Table 5, Matrillin long). Moreover, the variant with the Matrillin long trimerization motif shows trimeric F proteins. However, the product did not bind to the pre-fusion-specific Mab CR9501 and also showed hexameric species, which makes the Matrillin 1 trimerization domain not suitable for production of trimeric native F protein. None of the Matrillin-based or the GCN4II-based zipper motifs showed increased expression or stability relative to F47 (Table 5, Matrillin short, GCN4II optimized). Again, truncation at 495 results in higher expression levels. Addition of a GCN4 motif, which contained an optimized trigger sequence, showed no expression.
GCN4II is a trimerization domain that is used successfully for stabilizing the pre-fusion trimer of parainfluenza type 5 (Yin et al., Nature 439:38-44, 2006) and has also been tried by others to stabilize RSV pre-fusion F (as disclosed in, e.g., WO 2010/149743, WO 2010/149745, WO 2009/079796, and WO 2010/158613). The GCN4II trimerization domain was evaluated and compared with the constructs that contain the Isoleucine Zipper (S) domain (SEQ ID NO:3) or the Fibritin (SEQ ID NO:4) domain (results shown in Table 6). These variants were also compared with anther modifications, i.e., a short linker based on a single Lysine and the L512K mutation. All variants contained a HIS-tag.
The short linkage between F1 and F2 appears to be comparable to the GSGSG loop (SEQ ID NO:5). Addition of the GCN4II motif does not result in any F protein expression in any of the tested constructs (i.e., the RSV A2 F sequence described in WO 2010/149743 or WO 2010/149745, the RSV A2 F sequence used according to the disclosure, nor the RSV B1 F sequence).
It was shown that the introduction of these two types of modifications, i.e., introduction of a linking sequence and the heterologous trimerization domain, was not enough to enable the expression of stable trimeric pre-fusion F protein. Apart from the two main regions of instability that were stabilized, i.e., the HRB and the fusion peptide, as described above, other regions in the pre-fusion F protein also contribute and/or accommodate the dramatic refolding to post-fusion F, and more positions in the sequence can be optimized to stop the pre-fusion F protein from refolding. Therefore, different amino acid residues in the HRA and HRB domains and in all domains that contact these regions in pre-fusion F were mutated to increase the pre-fusion structure stability, as described in the following Examples.
Because the trimeric content (for construct F47) and storage stability (for construct F24) was not optimal, further variants were made that contained point mutations to increase expression levels, stability and native trimeric structure. The results are shown in Tables 7 and 8.
Nomenclature of mutations based on wt sequence (SEQ ID NO:1).
All constructs are variants of F47-: type A2, Isoleucine Zipper (S) motif (SEQ ID NO:3), GSGSG (SEQ ID NO:5) linker; termination point 495, no HIS-tag (SEQ ID NO:16). As shown in Table 7, many mutations increased the expression of F47-, but only the variant F47_S46G also showed a higher level of trimers besides the high expression.
Table 8 shows the results of the expression and stability of F24 variants. All variants were of RSV type A2, with fibritin motif, GSGSG (SEQ ID NO:5) linker; termination point 513, no HIS-tag.
Many mutations increased the expression of A2_F24-. For most mutations there was an apparent correlation between improved expression in F47- background (Table 7) and A2_F24- background (Table 8). N67I had more positive impact on F expression in A2_F24- background. The most significant increase in expression was obtained with the single point mutations: S46G, S215P, N67I, K80E, E92D, D486N, G184N, V185N, E487N, N175P, K209Q, E487I, E487Q, K77E, K201Q, N426S and K465Q. In the initial screening using the endpoint stability assay (Example 8), the variants with the highest expression showed the best stability upon storage as well (E92D, K465Q, K465E, N426S, S46G, S215P and N67I). To evaluate if these mutations indeed were stabilizing the pre-fusion conformation, culture supernatants were diluted to 5 and 10 μg/ml based on quantitative Western results and these were stored up to 33 days at 4° C. As single point mutants, only N67I and S215P were completely stable over time (see Example 10).
Subsequently, several mutations that showed high expression and good stability of the pre-fusion conformation were combined to evaluate whether the stabilizations were additive or had a possible synergistic effect (Table 9).
Storage stability refers to the association phase analysis illustrated in Example 10.
Expression level was determined as described in Example 1.
All variants are variants of F24-: type A2, fibritin motif, GSGSG (SEQ ID NO:5) linker; termination point 513, binding to all Mabs, no HIS-tag (SEQ ID NO:19).
When the previously identified point mutations were combined, very interesting synergistic effects could be observed especially in terms of expression levels with the combinations involving N67I as the most potent. All produced double mutants where either N67I and S215P was included were stable after more than 30 days storage at 4° C. (Example 10). Strikingly, the mutation N67I was found to have the strongest effect on expression levels of pre-fusion F when included in the double mutants. Next, combinations with the S215P mutations resulted in a reasonable expression. Combination of N67I with S215P was selected since it led to a very high expression level, and because both point mutations were stable upon storage. Additionally, it was observed that both N67I and S215P had the ability to stabilize some of the mutants that as single mutations were unstable indicating that the region where these two mutations are found is central for the conformation changes the protein undergoes during the transition to the post-fusion conformation.
It thus has been shown that at least some mutations resulted in increased expression levels and increased stabilization of the pre-fusion RSV protein. It is expected that these phenomena are linked. The mutations described in this Example all resulted in increased production of pre-fusion F polypeptides. Only a selection of these polypeptides remained stable upon long storage (see Example 10). The stability assay that was used is based on the loss of the pre-fusion-specific CR9501 epitope in the top of the pre-fusion F protein in a binding assay and it may not be sensitive enough to measure all contributions to stability of the whole protein. The mutation for which only increased expression is observed are therefore (very likely stabilizing) potential mutations that can be combined with other stabilizing mutations to obtain a pre-fusion F construct with high stability and high expression levels.
Next, it was verified whether the N67I-S215P double mutation, like the single mutations, was able to stabilize point mutations that as single mutants were deemed unstable based on the criteria used. Extra mutations were selected based on the favorable expression levels and stability according to Table 8. Triple mutant RSV-F variants were constructed and tested for expression levels and stability (Table 10).
Again, an additive effect on the expression levels was observed. As expected, D479N and E487R triple mutants express at somewhat lower levels because the single mutants were also among the lowest of the selected mutations (Table 8). Because of the stabilizing effect of the N67I+S215P mutation, additional mutations that are unstable as single mutants resulted in stable pre-fusion F variants when they were added to the A2_F24 N67I+S215P background. Some very illustrative examples are the triple mutants with the additional V185N, G184N or E487N, which showed high expression but low stability as single mutants (Table 8) but showed even higher expression and were highly stable when added to the A2_F24 N67I+S215P background.
Stabilizing Mutations Also Stabilize RSV-F Protein from Other Strains and Also in Processed F Variant.
Several mutations that showed high expression and good stability of the pre-fusion conformation were applied to RSV F proteins of other strains and were applied to a RSV A2 F variant without furin cleavage site mutations (F18: SEQ ID NO:71) to evaluate whether the modifications are a universal solution to stabilize RSV pre-fusion F (Table 11).
When the previously identified point mutations were introduced in A2_F18 (SEQ ID NO:71), the stability and expression levels were very similar compared with the single chain F24 (SEQ ID NO:21) variant that contained a short loop between F1 and F2. Again, synergism was observed showing higher expression and stability when mutations were added to variants that contained the N67I or the double mutation N67I, S215P. The double-point mutation N67I, S215P did not only stabilize the pre-fusion F of the A2 strain but also pre-fusion of B1 and CL57-v224 strain (Table 11).
Stabilizing Mutations Also Stabilize Full-Length RSV-F Protein.
Several mutations that showed high expression and good stability of the pre-fusion conformation in the soluble version of RSV-F corresponding to the ectodomain, were applied to the full-length RSV-F protein. The mutations were introduced in full-length RSV-F with or without furin cleavage site mutations. No trimerization domain was fused to these variants (Table 12).
The previously identified stabilizing point mutations were also stabilizing in the full-length F protein. The increase in expression level was less pronounced but showed the same trend. This may be caused by the different background the mutations were introduced in but may also be caused by the different quantification method (FACS versus Western blot) and a biological maximum of expression due to recycling of surface proteins. Introduction of the linking sequence (or short loop) increased expression and stability and the point mutations did so too. The point mutations were not or barely synergistic with the short loop (similar as to what was found for the soluble protein (Tables 9-11).
Because the point mutation at position 67 had such a positive effect on expression level and stability, all amino acid substitutions were tested for this position to study whether the most optimal were chosen or whether these positions can be improved (Table 13).
As shown in Table 13, primarily hydrophobic residues and particularly Ile, Leu and Met at position 67 were able to increase expression and stability. Ile is the residue that increased expression and stability most. Residues Glu and Gln, the smallest residue Gly and the positively charged residues Arg and Lys had the most destabilizing effect at position 67 on the pre-fusion conformation.
In the research that led to this disclosure, further stabilized variants of soluble pre-fusion F protein (sF) were designed by stabilizing the two main regions that initiate refolding. The first strategy was to prevent the refolding of the HRA region into a coiled coil. The second strategy was to construct disulfide bridges N-terminal to HRB to prevent the relocation of the HRB to form the six-helix bundle by docking onto the HRA coiled coil.
The constructs were tested for expression levels, storage stability and antibody binding with the antibody CR9501. The amino acid sequences of the heavy and light chain variable regions, and of the heavy and light chain CDRs of this antibody are given below. CR9501 comprises the binding regions of the antibodies referred to as 58C5 in WO 2012/006596. The constructs were synthesized and codon-optimized by GENEART® (Life Technologies, Carlsbad, Calif.). The constructs were cloned into pCDNA2004 or generated by standard methods widely known within the field involving site-directed mutagenesis and PCR and sequenced. The expression platform used was the 293Freestyle cells (Life Technologies). The cells were transiently transfected using 293Fectin (Life Technologies) according to the manufacturer's instructions and cultured for 5 days at 37° C. and 10% CO2. The culture supernatant was harvested and spun for 5 minutes at 300 g to remove cells and cellular debris. The spun supernatant was subsequently sterile filtered using a 0.22 μm vacuum filter and stored at 4° C. until use.
Supernatants from day 5 were evaluated for F protein expression by Western blot using the monoclonal antibody CR9503, which comprises the heavy and light chain variable regions of the RSV F antibody Motavizumab (referred to as CR9503). The approximate expression levels of the pre-fusion RSV F protein constructs were assessed using CR9503, an anti-human IR-dye-conjugated secondary antibody (Li-Cor, Lincoln, Nebr.) or an HRP-conjugated mouse anti-human IgG (Jackson ImmunoResearch, West Grove, Pa.). The protein quantities were then estimated using a dilution series of purified RSV standard protein, either by eye or using the Odyssey CLx infrared imaging system. To evaluate construct stability and to identify positive or negative stabilizing effects of introduced trimerization motifs, the constructs were tested for binding to pre-fusion-specific antibodies after 5, 14 or 30 days of storage at 4° C. This procedure is described in detail in Example 10.
Next, the most favorable modifications were combined to find the optimal pre-fusion F polypeptides. Combinations were made of variants with the GSGSG (SEQ ID NO:5) loop, C-terminal truncation of F1, and the addition of fibritin (SEQ ID NO:4). Variants were made that contained point mutations to increase expression levels, stability and native trimeric structure. All variants were of RSV type A2, with fibritin motif, GSGSG (SEQ ID NO:5) linker; termination point 513, no HIS-tag.
According to the disclosure, the amino acid mutations that stabilize the pre-fusion conformation of the RSV F protein can be grouped into different categories that stabilize the conformation in different manners.
Amino Acid Residues 161, 173, 174, 182 and 214
In order to refold from the pre-fusion to the post-fusion conformation, the region between residues 160 and 215 has to transform from an assembly of helices, loops and strands to a long continuous helix. This region demonstrates the most dramatic structural transition. Part of this region actually has the highest alpha-helix prediction. The actual helical structures in the pre-fusion crystal structure are shown below in gray highlights. This whole region is transformed into one large helix when it refolds to the post-fusion conformation. In the bottom sequence, the residues are highlighted in gray with the highest helix prediction based on Agadir (http://agadir.crg.es/). It is clear from this comparison that the C-terminal part that is maintained in a beta-hairpin, a connecting loop and a helix in the pre-fusion conformation (residues 187-202) has a high tendency to form an alpha-helix.
Underlined residues have bad angles according to Ramachandran-plot.
The sequence of residues 150-212 of RSV-F is shown above. On the second line, the secondary structures of the top line are indicated by h (for helix) and s (for strands) based on the crystal structure. Helices are highlighted with gray shading. The bottom line is the same sequence in which the helices are shaded gray, based on the helix propensity of the sequence.
The regions that need optimization are the loop regions in between the secondary structural elements (helices and strands) in the labile HRA of pre-fusion RSV-F. One of the positions in HRA that needs optimization in order to stabilize the pre-fusion conformation of RSV-F is position 161 in the turn between helices α2 (residues 148-157) and α3 (residues 163-172). There are several reasons why optimization of this position could increase the stability of this region:
In this example, residue Glu161 was replaced by Pro to reduce the negative repulsion and stabilize the turn and prevent it from refolding, or residue Glu161 was replaced by Gln to reduce the negative charge repulsion, or residue Glu161 was replaced by Gly because it allows a broader range of dihydral angles.
For the region of α2-turn-α3 (residues 153-168), the Brookhaven database was searched for a structurally homologous helix-turn-helix from a stable protein that does not refold in order to find a residue that could replace the unfavorable Glu161. A high structural homology was discovered with a turn in a helix-turn-helix of several proteins that all had a Proline at the homologous 161 position (PDB codes 2hgs, 3kal, 2o2z, 2zk3, and 2zqp). According to the alignment shown below, the substitution of Glu161 by Pro is a good structural solution to stabilize this turn and prevent it from refolding.
In certain embodiments, residue Ser173 was replaced by Pro to stabilize the turn and prevent it from refolding. In certain embodiments, residue Thr174 was replaced by Pro to stabilize the turn and prevent it from refolding.
The Ramachandran plot shows that the amino acid residue 182 in the turn between β3 and β4 also has bad/unfavorable dihydral angles. Optimization of this position could increase the stability of the turn and stabilize the β-hairpin.
For the region of β3-turn-β4 (residues 177-189), the Brookhaven database was searched for a structurally homologous β-hairpin from a stable protein that does not refold in order to find a residue that could replace the unfavorable Ser182. A high structural homology was discovered with a turn in a β-hairpin of a putative electron transfer protein that had a Proline at the homologous 182 position (PDB code 3me8). According to the alignment shown below, the substitution of Ser182 by Pro is a good structural solution to stabilize this turn and prevent it from refolding.
Cysteine Bridge Formation in the Bottom of the Head Region Between Residues 486, 487, and 489
The negatively charged amino acid residues 486, 487 and 489 are part of a switch mechanism that controls the transition between the pre-fusion and post-fusion RSV-F structure. Mutation of Glu487 to Gln will impair this switch and stabilize contact between the protomers in the trimer. These same residue positions can also be used to engineer disulfide bridges between the protomers. Mutations of two residues by cysteines as described above will reduce the negative charge repulsion and allow disulfide bridges that will further stabilize the pre-fusion trimer.
Variants were made that contained point mutations that stabilize the turns between the secondary structural elements in the HRA region of RSV-F pre-fusion protein to increase stability and expression levels of the pre-fusion conformation. The results are shown in Table 14.
Of the single point mutations, substitution of positions 173, 182 and especially 161 to Proline resulted in higher expression levels and stability. Removing the charge of residue 161 did stabilize the proteins but did not increase expression levels. The same point mutations had a similar effect in a stabilized pre-fusion F sequence that contained the additional stabilizing N67I and S215P mutation. Mutation of residues 182, 173 and especially 161 to Proline showed the highest increase in stability and expression levels.
The E161P mutations that showed high expression and good stability of the pre-fusion conformation was also applied to soluble RSV A2 F ectodomain variants without furin cleavage site mutations (F18: SEQ ID NO:71) to evaluate whether the modifications are a universal solution to stabilize RSV pre-fusion F (Table 15).
The E161P mutation also showed a high increase in expression levels in the processed RSV-F protein. When combined with stabilizing point mutations at, e.g., positions 67, 215 and 487, the E161P mutation resulted in pre-fusion F variants with high expression levels and high stability.
Cysteine Bridge Formation in the Bottom of the Head Region Between Residues 486, 487, and 489
The negatively charged amino acid residues 486, 487 and 489 are part of a switch mechanism that controls the transition between the pre-fusion and post-fusion RSV-F structure. Mutation of Glu487 to Gln will impair this switch and stabilize contact between the protomers in the trimer (previous patent P00). These same residue positions can also be used to engineer disulfide bridges between the protomers. Mutations of two residues to cysteines of which one is a negatively charged residue 486, 486 or 489, will reduce the negative charge repulsion and allow disulfide bridges that will further stabilize the pre-fusion trimer. Several of such variants were tested for expression level and stability of the pre-fusion conformation (Table 16).
In the metastable F24 background (SEQ ID NO:19), only a disulfide bridge between residues 486 and 487 resulted in a pre-fusion protein with reasonable expression and stability. Because inter-protomeric disulfides need a correct alignment of opposing side chains, the disulfide connectivity may be more successful in a more stable F protein compared to the metastable F24 variant. Therefore, several of the disulfides were also engineered in the F24 variant that contained the two stabilizing mutations N67I and S215P. Indeed, in the stabilized background, the proteins with engineered disulfides expressed to much higher levels. Again, the variant with the cysteine mutations at positions 486 and 487 expressed to the highest level and expression level was 14 times higher compared with the unstabilized variant without the N67I and S215P mutation. Stability of the protein in the supernatant was reasonable and still contained 79% pre-fusion conformation. Higher stability may be reached when the protein is purified. Stability may not have reached 100% because not 100% of the cysteines were connected inter-protomeric as shown in Examples 4 and 5.
Culture supernatants were run reduced on 4-12% (w/v) Bis-Tris NuPAGE gels (Life Technology) and blotted using the IBLOT® technology (Life Technology). The blots were probed with CR9503 (sequences given below in Table 18) and developed with either a conjugated mouse anti-human IgG (Jackson ImmunoResearch, West Grove, Pa.) or an IRDye800CW-conjugated affinity-purified anti-human IgG (rabbit) (Rockland Immunochemicals, Gilbertsville, Pa.). In
For initial determination of the multimeric state of the pre-fusion F polypeptides according to the disclosure, culture supernatants from transiently transfected cells were analyzed in a NativePAGE Bis-Tris gel system (Life Technologies). Subsequently, the gels were blotted using the IBLOT® technology according to the manufacturer's instructions (Life Technologies). An RSV F protein-specific antibody CR9503 (sequences given below in Table 18) was used as primary probe for the detection of pre-fusion RSV F protein and followed by an HRP-conjugated mouse anti-human IgG (Jackson ImmunoResearch, West Grove, Pa.) or an IRDye800CW-conjugated affinity-purified anti-human IgG (rabbit) (Rockland Immunochemicals, Gilbertsville, Pa.). The blots were developed with either standard film (KODAK®) or using the Odyssey CLx infrared imaging system.
Expression plasmids encoding the recombinant pre-fusion RSV F protein were generated by standard methods widely known within the art, involving site-directed mutagenesis and PCR. The expression platform used was the 293Freestyle cells (Life Technologies, Renfreshire, UK). The cells were transiently transfected using 293Fectin (Life Technologies) according to the manufacturer's instructions and cultured in a shaking incubator for 5 days at 37° C. and 10% CO2. The culture supernatant was harvested and spun for 5 minutes at 300 g to remove cells and cellular debris. The spun supernatant was subsequently sterile filtered using a 0.22 μm vacuum filter and stored at 4° C. until use.
The recombinant polypeptides were purified by a two-step purification protocol applying a cat-ion exchange column for the initial purification and subsequently a SUPERDEX® 200 column for the polishing step to remove residual contaminants. For the initial ion-exchange step, the culture supernatant was diluted with 2 volumes of 50 mM NaOAc pH 5.0 and passed over a 5 ml HiTrap Capto S column at 5 ml per minute. Subsequently, the column was washed with 10 column volumes (CV) of 20 mM NaOAc, 50 mM NaCl, 0.01% (v/v) TWEEN® 20, pH 5 and eluted 2 CV of 20 mM NaOAc, I M NaCl, 0.01% (v/v) TWEEN® 20, pH 5. The eluate was concentrated using a spin concentrator and the protein was further purified using a SUPERDEX® 200 column using 40 mM Tris, 500 mM NaCl, 0.01% (v/v) TWEEN® 20, pH 7.4 as running buffer. In
The verification of the pre-fusion conformation of the expressed polypeptides according to the disclosure was done using the octet technology using the pre-fusion-specific antibodies CR9501 or CR9502, or the non-conformation-specific antibody CR9503, which comprises the heavy and light chain variable regions of the commercially available antibody Motavizumab. The antibodies were biotinylated by standard protocols and immobilized on streptavidin biosensors (F
The stabilizing potential of introduced features into the RSV F polypeptides was estimated by heat stress. For that purpose, culture supernatant from transiently transfected cells or purified protein was heated using a range of temperatures. The samples were subsequently cooled on ice to prevent further heat-induced conformational changes and probed using the CR9501 antibody on the octet technology platform as described in Example 11. The responses obtained at the end of the association phase at the different temperatures were plotted as a function of the temperature and fitted by non-linear regression using the Prism software. This resulted in an estimation of the temperature where the antibody binding level is 50% of the maximum and this value could be used to compare different constructs in terms of pre-fusion heat stability.
To assess the stability of various point mutations, the octet binding assay was developed by using association phase analysis. The CR9501 antibody or CR9502 antibody was used as probes for the pre-fusion conformation of the RSV-F protein. To reduce potential concentration bias of the endpoint assay, the data points were used from the entire association phase of the experiment. The data were compensated for the amount of bound antibody on the chip. The measurements were done at days 1, 5 and 33, and the shapes of the curves from the three days were compared. If identical curves were obtained, the construct was deemed stable and, if not, unstable.
To measure concentration of the pre-fusion RSV F protein in cell culture supernatants, quantitative Octet-based method was used. The CR9501 and CR9503 antibodies were biotinylated by standard protocols and immobilized on Streptavidin biosensors (F
To evaluate the immunogenicity of a stabilized pre-fusion RSV F (A2F24, N67I, S215P) (SEQ ID NO:21), mice were immunized according to Table 19 with 0.5 or 5 μg in a prime—boost regimen at week 0 and week 4. As shown in
Next, cotton rats were immunized with two different doses of RSV-F in either the post-fusion or the pre-fusion conformation (Table 20). Animals were immunized i.m. at week 0 and week 4.
Five days after challenge, the lung and nose viral load was measured (see
As shown, the pre-fusion F polypeptides according to the disclosure are able to induce a strong protective immune response that reduced viral load in the lung and even in the nose.
The amino acid sequence of several of the pre-fusion RSV F constructs is given below. It is noted that the amino acid numbering in the different constructs described herein is based on the wild-type sequence (SEQ ID NO:1), which means that all amino acids from position 1 to and including position 108 of the pre-fusion constructs correspond to the amino acid positions 1-108 of the wild-type sequence, whereas the numbering of the amino acids from position 138 to the end is shifted 22 amino acids, i.e., L138 in the wild-type sequence (SEQ ID NO:1) corresponds to L116 in all the pre-fusion constructs. This is due to the fact that a deletion has been made in the pre-fusion constructs, i.e., in the insertion of the GSGSG (SEQ ID NO:5) linker, the actual numbering in F1 is not the same between constructs. Thus, the numbering used with respect to the specific mutations according to the disclosure, e.g., S215P, refers to the position of the amino acid in the wild-type sequence.
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| 20160176932 A1 | Jun 2016 | US |
