Patent Grant
11725028
This application claims priority to EP 21151126.6, filed Jan. 12, 2021, the disclosure of which is incorporated herein by reference in its entirety.
This application contains a sequence listing, which is submitted electronically via EFS-Web as an ASCII formatted sequence listing with a file name “004852_12055_195US1_SeqList.txt” and a creation date of Jan. 11, 2022, and having a size of 16 kb. The sequence listing submitted via EFS-Web is part of the specification and is herein incorporated by reference in its entirety.
This invention relates to the fields of medical microbiology and vaccines. In particular, the invention relates to polypeptides comprising a FimH lectin domain comprising at least one amino acid mutation that causes the FimH lectin domain to be in a conformation with low affinity for mannose and inducing high levels of antibody-mediated inhibition of adhesion of E. coli to bladder epithelial cells upon administration to a subject. Furthermore, the invention relates to compositions which comprise such polypeptides and to methods of stimulating an immune response in a subject in need thereof by administration of the immunogenic polypeptide.
Strains of E. coli responsible for extra-intestinal infections have been termed extra-intestinal pathogenic E. coli (ExPEC). ExPEC are the most common enteric Gram-negative organisms to cause extra-intestinal infection in the ambulatory, long-term-care, and hospital settings. Typical extra-intestinal infections due to E. coli include urinary tract infection (UTI), bacteremia, and sepsis. E. coli is a leading cause of severe sepsis and it is responsible for high morbidity and mortality rates.
ExPEC, as other members of the Enterobacteriaceae family, produces type I fimbriae, which aid in the attachment to mucosal epithelial surfaces. These type I fimbriae are hair-like structures which emanate from the surface members of the Enterobacteriaceae family. The major component of Type I fimbriae is repeating subunits of FimA arranged in a right-handed helix to form a filament approximately 1 μm in length and 7 nm in diameter with a central axial hole. Along with FimA as the major subunit, the fimbrial filament also contains FimF, FimG and FimH as minor protein subunits. The minor protein subunit FimH is a mannan-binding adhesin that promotes adherence of Type I-fimbriated bacteria to mannose-containing glycoproteins on eukaryotic cell surfaces and represents a family of proteins which bind to various targets, including mannan and fibronectin. Immune electron microscopy studies have revealed that FimH is strategically placed at the distal tips of Type I fimbriae where it appears to be complexed with FimG, forming a flexible fibrillum structure, and is also placed longitudinally at various intervals along the filament.
The FimH adhesin protein has been shown to induce protection when used as vaccine in various pre-clinical models against UTI (Langermann S, et al., 1997, Science, 276: 607-611; Langermann S, et al., 2000, J Infect Dis, 181: 774-778; O'Brien VP et al., 2016, Nat Microbiol, 2:16196).
It has been shown that during E. coli infection, the lectin domain of the adhesin FimH, that binds to mannosylated receptors, can adopt two distinct conformations: low-affinity for mannose (tense) and high-affinity for mannose (elongated/relaxed) (Kalas et al, 2017, Sci Adv 10; 3(2)). The low affinity conformation promotes bacterial motility and colonization of new tissues. The high-affinity conformation ensures tight bacterial adhesion under the mechanical forces of urine excretion. Furthermore, antibodies against low-affinity variant were shown to block bacterial binding to uroepithelial cells and reduce CFU counts in the bladder (Tchesnokoca, 2011 Infect Immun. 79(10):3895-904; Kisiela, 2013 Proc Natl Acad Sci, 19; 110(47):19089-94).
WO02102974 describes a number of FimH mutants that all comprise an amino acid modification in the canyon region of the molecule. Specifically, WO02102974 describes variants wherein mannose interacting residues in the binding pocket are mutated. This location of the mutation is selected because it would keep the FimH mutant in a more open conformation and thereby expose epitopes that are poorly accessible in the wild-type protein. However, to date, to the best of our knowledge, none of these mutants have been further pursued as vaccine candidates. In clinical trials, only wild-type FimH has been used.
Thus, there remains a need in the art for vaccines that can induce highly inhibitory antibodies against bacterial infections caused by E. coli.
In a first aspect, the invention provides for a polypeptide comprising a FimH lectin domain comprising an amino acid other than phenylalanine (F) at the position corresponding to position 71 in the amino acid sequence of SEQ ID NO: 1.
In a second aspect, the invention provides for a polypeptide comprising a FimH lectin domain according to the first aspect wherein the polypeptide further comprises an amino acid other than phenylalanine (F) at the position corresponding to position 144 in the amino acid sequence of SEQ ID NO: 1.
In a third aspect, the invention provides a polynucleotide encoding a polypeptide according to the invention.
In a fourth aspect, the invention provides for a vector comprising the polynucleotide according to the invention.
In a fifth aspect, the invention provides for a host cell comprising a polynucleotide or a vector according to the invention.
In a sixth aspect, the invention provides for a pharmaceutical composition comprising a polypeptide, polynucleotide, or vector according to the invention.
In a seventh aspect, the invention provides for a polypeptide according to the invention, a polynucleotide according to the invention, a vector according to the invention, or a pharmaceutical composition according to the invention for use in inducing an immune response against a bacterium of the family of Enterobacteriaceae. The invention further relates to a method for treating or preventing an enterobacillus-related condition a subject in need thereof the method comprising administering an effective amount of a polypeptide according to the invention, a polynucleotide according to the invention, a vector according to the invention, or a pharmaceutical composition according to the invention.
In an eighth aspect the invention further provides for a method for producing a polypeptide comprising expressing the polypeptide from a recombinant cell containing the polynucleotide of the invention and/or the vector of the invention, optionally the method further comprises recovering the polypeptide which is optionally followed by formulation into a pharmaceutical composition of the polypeptide.
The invention provides for a novel polypeptide comprising a FimH lectin domain wherein the FimH lectin domain is “locked” in a conformation with low affinity for mannose, also referred to herein as the ‘low affinity conformation’. The present invention is based in part on the observation that FimH antigen in the low affinity for mannose conformation is capable of inducing antibodies that can inhibit mannoside-mediated adhesion. These antibodies are highly inhibitory and have an enhanced effect in preventing or treating bacterial infections. It was found herein that a FimH lectin domain with an F71Y mutation has a surprisingly good combination of desirable properties that for instance makes it very suitable for use in vaccines against UTI, e.g. to prevent or reduce recurrent UTI.
Accordingly, in a first aspect, the invention provides for a polypeptide, preferably an immunogenic polypeptide, comprising a FimH lectin domain, comprising an amino acid other than phenylalanine (F) at a position corresponding to position 71 in the reference amino acid sequence of SEQ ID NO: 1.
In a second aspect, the invention further provides for a polypeptide, preferably an immunogenic polypeptide, comprising a FimH lectin domain, comprising an amino acid other than phenylalanine (F) at both positions corresponding to positions 71 and 144, respectively, in the reference amino acid sequence of SEQ ID NO: 1. This “double-mutant” remains locked in the low affinity conformation and is thus equally capable of inducing antibodies that can inhibit mannoside-mediated adhesion. In addition to inducing these inhibitory antibodies, it was found herein that the F71Y and F144V double mutant of the FimH lectin domain is unable to switch back to the high affinity conformation which gives the double mutant a surprisingly high stability. This inability to switch back to the high affinity conformation is a very desirable property that makes the double-mutant very suitable for instance for use in vaccines against UTI, e.g. to prevent or reduce recurrent UTI, as it inter alia ensures that no additional quality or stability controls are needed to test whether the conformation is stable during storage or under other storage- or use conditions.
The amino acid positions 71 and 144 as used herein refer to positions 71 and 144, respectively, in the reference amino acid sequence of the FimH lectin domain of SEQ ID NO: 1. In amino acid sequences of the invention other than SEQ ID NO: 1, preferably, the amino acid positions 71 and 144 are present at a position in that other amino acid sequence that correspond to the positions 71 and 144, respectively, in SEQ ID NO: 1, in a sequence alignment, preferably in a ClustalW (1.83) sequence alignment using default settings. The skilled person will know how to identify corresponding amino acid positions in FimH lectin domain amino acid sequences other than SEQ ID NO: 1 using amino acid sequence alignment algorithms as defined hereinabove.
Throughout the application, a polypeptide of the invention comprising a FimH lectin domain that comprises an amino acid other than phenylalanine (F) at the position corresponding to position 71 in the amino acid sequence of SEQ ID NO:1 will be referred to herein as “FimH(F71mut)”. Likewise, a polypeptide of the invention comprising a FimH lectin domain that comprises an amino acid other than phenylalanine (F) at both the positions corresponding to positions 71 and 144, respectively, in the amino acid sequence of SEQ ID NO:1 will be referred to herein as “FimH(F71mut/F144mut)”.
In certain embodiments, FimH(F71mut) comprises an amino acid selected from the group of tyrosine (Y) and tryptophan (W) at the position that corresponds to position 71 in SEQ ID NO: 1.
In certain embodiments, FimH(F71mut) comprises Tyrosine (Y) at the position that corresponds to position 71 in SEQ ID NO: 1.
In certain embodiments, the FimH(F71mut/F144mut) comprises an amino acid selected from the group consisting of valine (V), isoleucine (I), leucine (L), glycine (G), methionine (M), and alanine (A) at the position that corresponds to position 144 in SEQ ID NO: 1.
In certain embodiments, the FimH(F71mut/F144mut) comprises Valine (V) at the position that corresponds to position 144 in SEQ ID NO: 1.
In certain embodiments, at least one of the FimH(F71mut) and the FimH(F71mut/F144mut) lectin domains have an amino acid sequence having at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity with SEQ ID NO: 1.
In one embodiment, the FimH(F71mut) or FimH(F71mut/F144mut) comprise at least one mutation that causes the FimH lectin domain to be in the low affinity for mannose conformation. In one embodiment, the FimH(F71mut) has been mutated at a position that corresponds to position 71 in SEQ ID NO: 1. In one embodiment, FimH(F71mut/F144mut) has been mutated at the positions that corresponds to positions 71 and 144 in SEQ ID NO: 1.
A FimH lectin domain with low affinity for mannose in this context is defined herein as a FimH lectin domain binding to a mannoside ligand with a dissociation constant (KD) of at least 1000 nM or higher, as measured using surface plasmon resonance, e.g. under the conditions specified in example 2. A FimH lectin domain with high affinity for mannose is defined herein as a FimH lectin domain binding to a mannoside ligand with a KD that is 100 nM or lower, under the same conditions; typically wild-type FimH falls in this category. FimH lectin domains with a KD between 100 nM and 1000 nM under these conditions is referred to herein as having intermediate affinity for mannose.
The terms ‘mutant’, ‘mutation’, ‘mutated’ or ‘substitution’, ‘substituted’ in this context mean that another amino acid is present on the indicated position than in the corresponding parent molecule, which here is a polypeptide comprising a FimH lectin domain with F at positions 71 and 144. Such parent molecule may exist physically as polypeptide or in the form of nucleic acid encoding such polypeptide, but may also merely exist in silico or on paper as amino acid sequence or a corresponding nucleic acid sequence encoding the amino acid sequence. A mutation or substitution in this context is therefore also considered present for instance if a protein is expressed from a nucleic acid that has been synthesized such that it encodes the mutation or substitution, even though the nucleic acid encoding the corresponding parent molecule was not initially actually prepared during the process, e.g. when the nucleic acid molecule has been prepared entirely by chemical synthesis.
Preferably, the mutation is a substitution of a single amino acid residue. The mutation is preferably a substitution of an amino acid residue that corresponds to at least one of the positions 71 and 144 in SEQ ID NO: 1, respectively. Preferably, the mutation is a substitution of a phenylalanine (F) by another amino acid at a position corresponding to position 71 in SEQ ID NO: 1. Preferably the polypeptide of the invention further comprises a substitution of a phenylalanine (F) by another amino acid at a position corresponding to position 144 in SEQ ID NO: 1. In FimH(F71mut), the position that corresponds to position 71 in SEQ ID NO: 1 is preferably substituted for an amino acid selected from the group consisting of tyrosine (Y) and tryptophan (W). In one preferred embodiment, FimH(F71mut) comprises the substitution of phenylalanine (F) to tyrosine (Y) at position 71. In certain embodiments, FimH(F71mut) is a non-naturally occurring polypeptide which comprises a tyrosine at position 71. In certain embodiments, FimH(F71mut) has a tyrosine at position 71 instead of the naturally occurring phenylalanine (referred to as “FimH(F71Y)”). In certain embodiments, FimH(F71mut) has a tyrosine at position 71 instead of a naturally occurring amino acid other than phenylalanine (‘FimH(x71Y)’, wherein x would be an amino acid other than phenylalanine or tyrosine in a parent molecule).
In one embodiment, FimH(F71mut/F144mut) comprises a mutation at the positions that corresponds to positions 71 and 144 in SEQ ID NO: 1. The mutation at position 71 is preferably a substitution as described herein. The mutation at position 144 is preferably a substitution of an amino acid residue that corresponds to position 144 in SEQ ID NO: 1. Preferably, the mutation is a substitution of a phenylalanine (F) amino acid residue at a position corresponding to position 144 in SEQ ID NO: 1. Preferably, the amino acid at position 144 is substituted by an amino acid selected from the group consisting of valine (V), isoleucine (I), leucine (L), glycine (G), methionine (M), and alanine (A). In one preferred embodiment, FimH(F71mut/F144mut) comprises the substitution of phenylalanine (F) to valine (V) at position 144.
In certain embodiments FimH(F71mut/F144mut) is a non-naturally occurring polypeptide which comprises a tyrosine at position 71 and a valine at position 144. In certain embodiments, FimH(F71mut/F144mut) has a tyrosine at position 71 instead of the naturally occurring phenyalanine and a valine at position 144 instead of the naturally occurring phenylalanine. In certain embodiments, FimH(F71mut/F144mut) has a tyrosine at position 71 instead of a naturally occurring amino acid other than phenylalanine as well as a valine at position 144 instead of the naturally occurring amino acid other than phenylalanine.
Full-length FimH (FimHFL) is composed of two domains: the N-terminal lectin domain (FimHLD) connected to the C-terminal pilin domain (FimHPD) by a short tetra-peptides loop linker. In certain embodiments of the invention, the polypeptide comprising the FimH lectin domain according to the invention does not comprise a FimH pilin domain. In another embodiment of the invention, the polypeptide comprising the FimH lectin domain according to the invention further comprises a FimH pilin domain. In one embodiment, FimH(F71mut) or FimH(F71mut/F144mut) is a full length FimH polypeptide wherein the FimH lectin domain comprises an amino acid sequence as herein defined above for FimH(F71mut) and FimH(F71mut/F144mut), respectively. In certain embodiments of the invention, the polypeptide comprising the FimH lectin domain according to the invention is a fusion polypeptide of the FimH lectin domain fused to another polypeptide, which other polypeptide may be any polypeptide of interest, and this needs neither to be related to FimH nor to be associated with FimH in nature. In certain embodiments, the polypeptide comprising the FimH lectin domain of the invention is a fusion polypeptide that further comprises a FimH pilin domain and in addition comprises another polypeptide, which other polypeptide may be any polypeptide of interest, and this needs neither to be related to FimH nor to be associated with FimH in nature. The fusion polypeptides of the invention can for instance also be used as immunogens for vaccination purposes.
In one embodiment, the FimHFL polypeptide comprises an amino acid sequence having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity with SEQ ID NO: 2, whereby, preferably the positions 71 or 71 and 144 comprise amino acid residues as herein defined above for FimH(F71mut) and FimH(F71mut/F144mut), respectively. In certain embodiments, the FimHFL polypeptide may comprise a sequence having SEQ ID NO: 2, with the exception of the F71Y and optionally the F144V substitution as described herein. In another embodiment, the polypeptide is a FimHFL having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity with SEQ ID NO: 4 or preferably at least with amino acids 22-300 thereof, whereby, the positions 71 or 71 and 144 comprise amino acid residues as herein defined above for FimH(F71mut) and FimH(F71mut/F144mut), respectively. In certain embodiments, the FimHFL polypeptide may comprise a sequence having SEQ ID NO: 4 or at least amino acids 22-300 thereof, with the exception of the F71Y and/or the F144V substitution as described herein.
In certain embodiments, the FimHFL polypeptide comprises an amino acid sequence having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity with SEQ ID NO: 23-45 and 55 as described in U.S. Pat. No. 6,737,063, which is incorporated herein in its entirety, whereby, the positions 71 or 71 and 144 comprise amino acid residues as herein defined above for FimH(F71mut) and FimH(F71mut/F144mut), respectively.
FimH polypeptides are highly conserved between various strains of E. coli, and they are also highly conserved among a wide range of gram-negative bacteria. Moreover, the amino acid changes that occur between strains generally occur at similar amino acid positions. As a result of the high conservation of FimH between E. coli strains, FimH polypeptides from one strain are capable of inducing antibody responses that inhibit or prevent other E. coli strains from binding to cells by a FimH lectin and/or provide protection and/or treatment against infection caused by other E. coli strains. Accordingly, in one embodiment the FimHFL polypeptide comprises an amino acid sequence that has at least about 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity with SEQ ID NO: 5, or preferably at least with amino acids 22-300 thereof, whereby, the positions 71 or 71 and 144 comprise amino acid residues as herein defined above for FimH(F71mut) and FimH(F71mut/F144mut), respectively. In certain embodiments, the FimHFL polypeptide may comprise a sequence having SEQ ID NO: 5 or at least amino acids 22-300 thereof, with the exception of the F71Y substitution and optionally the F144V substitution as described herein. In another embodiment, the FimHFL polypeptide comprises an amino acid sequence that has at least about 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity with SEQ ID NO: 6, whereby, the positions 71 or 71 and 144 comprise amino acid residues as herein defined above for FimH(F71mut) and FimH(F71mut/F144mut), respectively. In certain embodiments, the FimHFL polypeptide may comprise a sequence having SEQ ID NO: 6, with the exception of the F71Y substitution, and optionally the F144V substitution, as described herein.
In certain embodiments, FimH preferably is E. coli FimH.
As used herein, the term “periplasmic chaperone” is defined as a protein localized in the periplasm of bacteria that is capable of forming complexes with a variety of chaperone-binding proteins via recognition of a common binding epitope (or epitopes). Chaperones serve as templates upon which proteins exported from the bacterial cell into the periplasm fold into their native conformations. Association of the chaperone-binding protein with the chaperone also serves to protect the binding proteins from degradation by proteases localized within the periplasm, increases their solubility in aqueous solution, and leads to their sequentially correct incorporation into an assembling pilus. Chaperone proteins are a class of proteins in gram-negative bacteria that are involved in the assembly of pili by mediating such assembly, but are not incorporated into the structure. FimC is the periplasmic chaperone protein of FimH. A FimC polypeptide for use in the instant invention has an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or about 100% sequence identity with SEQ ID NO: 3. In certain embodiments, the FimC polypeptide has an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or about 100% sequence identity with SEQ ID NO: 29 as described in U.S. Pat. No. 6,737,063, which is incorporated herein in its entirety. The non-covalent complex of FimC and FimH is named FimCH.
Accordingly, in a further aspect, the invention provides for a complex comprising a polypeptide comprising a FimH(F71mut) or FimH(F71mut/F144mut) as defined herein and further comprising a FimH pilin domain or a full length FimH as defined herein, and a FimC polypeptide as defined herein.
In one embodiment of the invention, the FimH(F71mut) or FimH(F71mut/F144mut) lectin domains are part of a polypeptide further comprising a FimH pilin domain, which polypeptide is complexed with FimC to form a FimCH complex.
The inventors of the present application have created several FimH lectin domain variants with different amino acid changes and tested them for efficiency in various assays (see the examples).
The herein described FimH(F71mut) and FimH(F71mut/F144mut) were both capable of forming FimCH complex.
In one embodiment, the FimH(F71mut) or FimH(F71mut/F144mut) lectin domains are part of a FimHFL polypeptide having at least about 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity with SEQ ID NO: 2, which optionally is complexed with a FimC polypeptide to form a FimCH complex. A FimHFL polypeptide in its final form, i.e. a mature FimHFL polypeptide does typically not include the signal peptide, which is for instance shown as amino acids 1-21 of SEQ ID NOs: 4 and 5, i.e. a mature FimHFL polypeptide of SEQ ID NO: 4 or SEQ ID NO: 5 is understood to include amino acids 22-300 of these sequences while typically lacking amino acids 1-21 thereof. For recombinant production of a FimHFL polypeptide it is useful to encode a mature FimHFL polypeptide that includes the signal peptide in the recombinant host cell, to get transport across the inner (cytoplasmic) membrane via the general secretory pathway leading to periplasmic location of the polypeptide (sometimes referred to as ‘periplasmic expression’), but in the final mature FimHFL polypeptide as isolated and for instance used in pharmaceutical compositions, the signal peptide typically is no longer present as a result of processing by the recombinant cell that is expressing the polypeptide.
In one embodiment, the FimCH complex comprises or consists of a FimC protein having at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or at least about 99%, or 100% sequence identity with SEQ ID NO: 3 and a FimH protein comprising a FimH(F71mut) or FimH(F71mut/F144mut) lectin domain as herein defined above. In certain embodiments, the FimCH complex comprises or consists of a FimC protein having at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or at least about 99%, or 100% sequence identity with SEQ ID NO: 3 and a FimH protein or a FimHFL protein that comprises FimH(F71mut) or FimH(F71mut/F144mut) lectin domain as herein defined above, whereby the FimHFL, protein preferably comprises a F92 substitution (e.g. in SEQ ID NOs: 4 or 5 that still include the signal peptide). Optionally, the FimCH complex comprises or consists of a FimC protein having at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or at least about 99%, or 100% sequence identity with SEQ ID NO: 3 and a FimH protein that comprises a F71(Y) and a F144(V) substitution in the lectin domain or a full-length FimH protein that comprises a F92(Y) and a F165(V) substitution (e.g. in SEQ ID NOs: 4 or 5 that still include the signal peptide)
In a full length FimH that would still include the signal peptide amino acid position 92 corresponds to amino acid position 71 and position 165 corresponds to amino acid position 144 in the FimH lectin domain. The skilled person will know how to identify corresponding amino acid positions in full length FimH amino acid sequences and in FimH lectin domain amino acid sequences using amino acid sequence alignment algorithms as defined hereinabove.
In one embodiment, complexes comprising the E. coli chaperone FimC and polypeptides comprising FimH(F71mut) or FimH(F71mut/F144mut) may be formed by co-expressing the FimH(F71mut)- or FimH(F71mut/F144mut)-comprising polypeptides along with FimC, from a recombinant cell.
In one embodiment, the FimCH complex comprises a FimC originating from one bacterial strain while FimH originates from a different bacterial strain. In another embodiment, the FimCH complex comprises a FimC and a FimH both originating from the same bacterial strain. In certain embodiments, FimH or FimC or both FimH and FimC may be artificial sequences not from actual bacterial isolates that exist in nature, e.g. they can also be based upon consensus sequences or combinations of natural isolates.
In one embodiment, the FimCH complex comprises at least one polypeptide that comprises a His-tag. In one embodiment, the full-length FimH as described herein comprises a His-tag or the FimC as described herein comprises a His-tag. Preferably, in the FimCH complex, the FimC comprises the His-tag. A His-tag as used herein is a stretch of histidine (His) residues, e.g. six His residues, which may be added internally or preferably at the N- or C-terminus of a protein. Such a tag has well-known use for ease of purification.
In a further aspect, the invention pertains to a polynucleotide encoding a polypeptide comprising a FimH(F71mut) or FimH(F71mut/F144mut) lectin domain as defined herein above. The polynucleotide may be preceded by a promoter operably linked thereto. In certain embodiments, the promoter is endogenous to the FimH coding sequence. In certain embodiments, the promotor is an endogenous promoter driving the expression of FimH in a bacterium of the Enterobacteriaceae family. In other embodiments, the promoter is heterologous to the FimH coding sequence, e.g. a strong promoter known to the skilled person for use in recombinant expression systems is used. For example, a pET-DUET vector comprising an inducible Lac promoter can be used for expression of a FimH(F71mut) or FimH(F71mut/F144mut) polypeptide of the invention and/or for expression of a FimC polypeptide. In case of an inducible promotor such as a Lac promoter or Tac promoter, IPTG can be used to induce expression. Preferably, the polynucleotide is isolated from its natural environment. In certain embodiments, the invention provides an isolated polynucleotide according to the invention. The polypeptide can be a recombinant, synthetic or artificial polynucleotide. The polynucleotide may be in any form of nucleic acid, e.g. DNA or RNA, preferably DNA. The polynucleotide may comprise one or more nucleotides that are not present in a naturally occurring FimH encoding polynucleotide. Preferably, the polynucleotide has one or more nucleotides that are not present in a naturally occurring FimH-encoding polynucleotide at its 5′-end and/or 3′-end. The sequences of the encoded mature FimC and/or FimH may preferably be preceded by a signal peptide in the polypeptides as encoded by the respective polynucleotides, and the signal peptides may be endogenous signal peptides to the FimC and/or FimH polypeptides (i.e. signal peptides as occurring in nature for these proteins) respectively, or they may be heterologous signal peptides, i.e. signal peptides from other proteins or synthetic signal peptides. The signal peptides are useful for periplasmic expression, but are typically cleaved off and not present in the finally produced and purified FimC and/or FimH, respectively.
In a further aspect, the invention relates to vector comprising a polynucleotide encoding a FimH(F71mut) or FimH(F71mut/F144mut) polypeptide of the invention. In certain embodiments, the vector is a plasmid or a viral vector, preferably a plasmid. The vector is preferably in the form of DNA, e.g. a DNA plasmid. In certain embodiments, the vector comprises the polynucleotide of the invention operably linked to a promoter, meaning that the polynucleotide is under control of a promoter. The promoter may be located upstream of the polynucleotide that encodes the polypeptide of the invention, e.g. in an expression cassette in a plasmid.
In yet a further aspect, the invention relates to a host cell comprising a polynucleotide encoding a FimH(F71mut) or FimH(F71mut/F144mut) polypeptide of the invention or a vector as described herein. The polynucleotide encoding the FimH(F71mut) or FimH(F71mut/F144mut) polypeptide of the invention can be introduced to the cell by common molecular biology methods. Such nucleic acid may be extrachromosomal, e.g. on a plasmid or other vector, or it may be integrated into the genome of the host cell. Preferably the nucleic acid encoding a protein is operably coupled to a sequence driving expression of the nucleic acid in the host cell, such as a promoter. The promoter may be a constitutive promoter, or it may be a promoter of which the activity can be regulated, e.g. repressed or induced upon certain conditions, e.g. temperature changes or presence of certain chemicals or proteins in the cell, all of which are as such well known in the art.
The host cell may be an isolated cell. The host cell may be cultured in a culture medium, e.g. in a culture vessel such as a bioreactor. The cell may be any microbial, prokaryotic or eukaryotic cell, which is suitable for expression of the polynucleotide encoding the FimH(F71mut) or FimH(F71mut/F144mut) polypeptide of the invention. Preferably, the host cell is bacterial host cell. Preferably the bacterial host cell is a gram-negative bacterial cell. Preferably the host cell is selected from E. coli and Klebsiella. Preferably, the host cell is E. coli.
If required and/or if desired, a FimH(F71mut) or FimH(F71mut/F144mut) polypeptide of the invention or the polynucleotide encoding a FimH(F71mut) or FimH(F71mut/F144mut) polypeptide of the invention can be incorporated into a pharmaceutically active mixture by adding a pharmaceutically acceptable carrier.
Accordingly, in a further aspect, the invention also provides for a composition, preferably a pharmaceutical composition comprising a FimH(F71mut) or FimH(F71mut/F144mut) polypeptide of the invention or a polynucleotide encoding a FimH(F71mut) or FimH(F71mut/F144mut) polypeptide of the invention.
The (pharmaceutical) compositions of the invention may comprise any pharmaceutically acceptable excipient including a carrier, filler, preservative, solubilizer and/or diluent. Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid carriers, particularly for injectable solutions. Suitable excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like. Examples of suitable pharmaceutical carriers are known and for instance described in textbooks and manuals.
In certain embodiments, the compositions of the invention additionally comprise one or more buffers, e.g., Tris-buffered saline, phosphate buffer, HEPES, or sucrose phosphate glutamate buffer.
In certain embodiments, the compositions of the invention additionally comprise one or more salts, e.g., Tris-hydrochloride, sodium chloride, calcium chloride, potassium chloride, sodium phosphate, monosodium glutamate, and aluminum salts (e.g., aluminum hydroxide, aluminum phosphate, potassium aluminum sulfate, or a mixture of such aluminum salts).
The compositions of the invention can be used for eliciting an immune response in a host to whom the composition is administered, i.e., are immunogenic. Thus, the compositions of the invention can be used as vaccines against an infection caused by a bacterium of the family of Enterobacteriaceae, preferably against an infection caused by Klebsiella or E. coli, more preferably E. coli and can thus may optionally comprise any additional components suitable for use in a vaccine. For example, an additional optional component of a vaccine composition is an adjuvant as described herein.
In certain embodiments, the compositions of the invention additionally comprise a preservative, such as phenol, benzethonium chloride, 2-phenoxyethanol, or thimerosal. In a specific embodiment, the (pharmaceutical) compositions of the invention comprise 0.001% to 0.01% preservative. In other embodiments, the (pharmaceutical) compositions of the invention do not comprise a preservative.
In certain embodiments, the compositions of the invention are formulated to be suitable for the intended route of administration to a subject. For example, the compositions of the invention can be formulated to be suitable for subcutaneous, parenteral, oral, intradermal, transdermal, colorectal, intraperitoneal, intravaginal, or rectal administration. In a specific embodiment, the pharmaceutical composition can be formulated for intravenous, oral, buccal, intraperitoneal, intranasal, intratracheal, subcutaneous, intramuscular, topical, intradermal, transdermal or pulmonary administration, preferably intramuscular administration.
The compositions of the invention can be included in a container, pack, or dispenser together with instructions for administration.
In certain embodiments, the compositions of the invention can be stored before use, e.g., the compositions can be stored frozen (e.g., at about −20° C. or at about −70° C.); stored in refrigerated conditions (e.g., at about 2-8° C., e.g. about 4° C.); or stored at room temperature.
In an embodiment, the pharmaceutical composition of the invention herein further comprises an adjuvant. As used herein, the term “adjuvant” refers to a compound that when administered in conjunction with or as part of a composition of the invention augments, enhances and/or boosts the immune response to FimH, but when the adjuvant compound is administered alone does not generate an immune response to the conjugate and/or FimH. Adjuvants can enhance an immune response by several mechanisms including, e.g., lymphocyte recruitment, stimulation of B and/or T cells, and stimulation of antigen presenting cells.
In certain embodiments, the pharmaceutical compositions of the invention comprise, or are administered in combination with, an adjuvant. The adjuvant for administration in combination with a composition of the invention can be administered before, concomitantly with, or after administration of the immunogenic compositions. In certain embodiments, FimH(F71mut) or FimH(F71mut/F144mut) and the adjuvant are administered in the form of a single composition.
In other embodiments, the pharmaceutical compositions of the invention do not comprise, and are not administered in combination with, an adjuvant.
Specific examples of adjuvants include, but are not limited to, aluminum salts (alum) (such as aluminum hydroxide, aluminum phosphate, aluminum sulfate, and aluminum oxide, including nanoparticles comprising alum or nanoalum formulations), calcium phosphate (e.g. Masson J D et al, 2017, Expert Rev Vaccines 16: 289-299), monophosphoryl lipid A (MPL) or 3-de-O-acylated monophosphoryl lipid A (3D-MPL) (see e.g., United Kingdom Patent GB2220211, EP0971739, EP1194166, U.S. Pat. No. 6,491,919), AS01, AS02, AS03 and AS04 (all GlaxoSmithKline; see e.g. EP1126876, U.S. Pat. No. 7,357,936 for AS04, EP0671948, EP0761231, U.S. Pat. No. 5,750,110 for AS02), imidazopyridine compounds (see WO2007/109812), imidazoquinoxaline compounds (see WO2007/109813), delta-inulin (e.g. Petrovsky N and PD Cooper, 2015, Vaccine 33: 5920-5926), STING-activating synthetic cyclic-di-nucleotides (e.g. US20150056224), combinations of lecithin and carbomer homopolymers (e.g. U.S. Pat. No. 6,676,958), and saponins, such as QUIL-A and QS21 (see e.g. Zhu D and W Tuo, 2016, Nat Prod Chem Res 3: e113 (doi:10.4172/2329-6836.1000e113), optionally in combination with QS7 (see Kensil et al., in Vaccine Design: The Subunit and Adjuvant Approach (eds. Powell & Newman, Plenum Press, N Y, 1995); U.S. Pat. No. 5,057,540). In some embodiments, the adjuvant is Freund's adjuvant (complete or incomplete). In certain embodiments, the adjuvant comprises QUIL-A, such as for instance commercially obtainable from Brenntag (now Croda) or Invivogen. QUIL-A contains the water-extractable fraction of saponins from the Quillaja saponaria Molina tree. These saponins belong to the group of triterpenoid saponins, that have a common triterpenoid backbone structure. Saponins are known to induce a strong adjuvant response to T-dependent as well as T-independent antigens, as well as strong cytotoxic CD8+ lymphocyte responses and potentiating the response to mucosal antigens. They can also be combined with cholesterol and phospholipids, to form immunostimulatory complexes (ISCOMs), wherein QUIL-A adjuvant can activate both antibody-mediated and cell-mediated immune responses to a broad range of antigens from different origins. In certain embodiments, the adjuvant is AS01, preferably AS01B. S01 is an Adjuvant System containing MPL (3-O-desacyl-4′-monophosphoryl lipid A), QS21 (Quillaja saponaria Molina, fraction 21) and liposomes. In certain embodiments, the AS01 is commercially available (GSK) or can be made as described in WO 96/33739, incorporated herein by reference. Certain adjuvants comprise emulsions, which are mixtures of two immiscible fluids, e.g. oil and water, one of which is suspended as small drops inside the other, and are stabilized by surface-active agents. Oil-in-water emulsions have water forming the continuous phase, surrounding small droplets of oil, while water-in-oil emulsions have oil forming the continuous phase. Certain emulsions comprise squalene (a metabolizable oil). Certain adjuvants comprise block copolymers, which are copolymers formed when two monomers cluster together and form blocks of repeating units. An example of a water in oil emulsion comprising a block copolymer, squalene and a microparticulate stabilizer is TiterMax®, which can be commercially obtained from Sigma-Aldrich. Optionally emulsions can be combined with or comprise further immunostimulating components, such as a TLR4 agonist. Certain adjuvants are oil in water emulsions (such as squalene or peanut oil) also used in MF59 (see e.g. EP0399843, U.S. Pat. Nos. 6,299,884, 6,451,325) and AS03, optionally in combination with immune stimulants, such as monophosphoryl lipid A and/or QS21 such as in AS02 (see Stoute et al., 1997, N. Engl. J. Med. 336, 86-91). Further examples of adjuvants are liposomes containing immune stimulants such as MPL and QS21 such as in AS01E and AS01B (e.g. US 2011/0206758). Other examples of adjuvants are CpG, and imidazoquinolines (such as imiquimod and R848). See, e.g., Reed G, et al., 2013, Nature Med, 19: 1597-1608.
In certain embodiments, the adjuvant comprises saponins, preferably the water-extractable fraction of saponins obtained from Quillaja saponaria. In certain embodiments, the adjuvant comprises QS-21.
In certain embodiments, the adjuvant contains a toll-like receptor 4 (TLR4) agonist. TLR4 agonists are well known in the art, see e.g. Ireton G C and S G Reed, 2013, Expert Rev Vaccines 12: 793-807. In certain embodiments, the adjuvant is a TLR4 agonist comprising lipid A, or an analog or derivative thereof.
The adjuvant, for example including a TLR4 agonist, may be formulated in various ways, e.g. in emulsions such as water-in-oil (w/o) emulsions or oil-in-water (o/w) emulsions (examples are MF59, AS03), stable (nano-)emulsions (SE), lipid suspensions, liposomes, (polymeric) nanoparticles, virosomes, alum adsorbed, aqueous formulations (AF), and the like, representing various delivery systems for immunomodulatory molecules in the adjuvant and/or for the immunogens (see e.g. Reed et al, 2013, supra; Alving C R et al, 2012, Curr Opin Immunol 24: 310-315).
The immunostimulatory TLR4 agonist may optionally be combined with other immunomodulatory components, such as saponins (e.g. QUIL-A, QS7, QS21, Matrix M, Iscoms, Iscomatrix, etc), aluminum salts, activators for other TLRs (e.g. imidazoquinolines, flagellin, CpG, dsRNA analogs, etc.), and the like (see e.g. Reed et al, 2013, supra).
As used herein, the term “lipid A” refers to the hydrophobic lipid moiety of an LPS molecule that comprises glucosamine and is linked to keto-deoxyoctulosonate in the inner core of the LPS molecule through a ketosidic bond, which anchors the LPS molecule in the outer leaflet of the outer membrane of Gram-negative bacteria. For an overview of the synthesis of LPS and lipid A structures, see, e.g., Raetz, 1993, J. Bacteriology 175:5745-5753, Raetz C R and C Whitfield, 2002, Annu Rev Biochem 71: 635-700; U.S. Pat. Nos. 5,593,969 and 5,191,072. Lipid A, as used herein includes naturally occurring lipid A, mixtures, analogs, derivatives and precursors thereof. The term includes monosaccharides, e.g., the precursor of lipid A referred to as lipid X; disaccharide lipid A; hepta-acyl lipid A; hexa-acyl lipid A; penta-acyl lipid A; tetra-acyl lipid A, e.g., tetra-acyl precursor of lipid A, referred to as lipid IVA; dephosphorylated lipid A; monophosphoryl lipid A; diphosphoryl lipid A, such as lipid A from Escherichia coli and Rhodobacter sphaeroides. Several immune activating lipid A structures contain 6 acyl chains. Four primary acyl chains attached directly to the glucosamine sugars are 3-hydroxy acyl chains usually between 10 and 16 carbons in length. Two additional acyl chains are often attached to the 3-hydroxy groups of the primary acyl chains. E. coli lipid A, as an example, typically has four C14 3-hydroxy acyl chains attached to the sugars and one C12 and one C14 attached to the 3-hydroxy groups of the primary acyl chains at the 2′ and 3′ position, respectively.
As used herein, the term “lipid A analog or derivative” refers to a molecule that resembles the structure and immunological activity of lipid A, but that does not necessarily naturally occur in nature. Lipid A analogs or derivatives may be modified to e.g. be shortened or condensed, and/or to have their glucosamine residues substituted with another amine sugar residue, e.g. galactosamine residues, to contain a 2-deoxy-2-aminogluconate in place of the glucosamine-1-phosphate at the reducing end, to bear a galacturonic acid moiety instead of a phosphate at position 4′. Lipid A analogs or derivatives may be prepared from lipid A isolated from a bacterium, e.g., by chemical derivation, or chemically synthesized, e.g. by first determining the structure of the preferred lipid A and synthesizing analogs or derivatives thereof. Lipid A analogs or derivatives are also useful as TLR4 agonist adjuvants (see, e.g. Gregg K A et al, 2017, MBio 8, eDD492-17, doi: 10.1128/mBio.00492-17). For example, a lipid A analog or derivative can be obtained by deacylation of a wild-type lipid A molecule, e.g., by alkali treatment. Lipid A analogs or derivatives can for instance be prepared from lipid A isolated from bacteria. Such molecules could also be chemically synthesized. Another example of lipid A analogs or derivatives are lipid A molecules isolated from bacterial cells harboring mutations in, or deletions or insertions of enzymes involved in lipid A biosynthesis and/or lipid A modification. MPL and 3D-MPL are lipid A analogs or derivatives that have been modified to attenuate lipid A toxicity. Lipid A, MPL and 3D-MPL have a sugar backbone onto which long fatty acid chains are attached, wherein the backbone contains two 6-carbon sugars in glycosidic linkage, and a phosphoryl moiety at the 4 position. Typically, five to eight long chain fatty acids (usually 12-14 carbon atoms) are attached to the sugar backbone. Due to derivation of natural sources, MPL or 3D-MPL may be present as a composite or mixture of a number of fatty acid substitution patterns, e.g. hepta-acyl, hexa-acyl, penta-acyl, etc., with varying fatty acid lengths. This is also true for some of the other lipid A analogs or derivatives described herein, however synthetic lipid A variants may also be defined and homogeneous. MPL and its manufacture are for instance described in U.S. Pat. No. 4,436,727. 3D-MPL is for instance described in U.S. Pat. No. 4,912,094B1, and differs from MPL by selective removal of the 3-hydroxymyristic acyl residue that is ester linked to the reducing-end glucosamine at position 3 (compare for instance the structure of MPL in column 1 vs 3D-MPL in column 6 of U.S. Pat. No. 4,912,094B1). In the art often 3D-MPL is used, while sometimes referred to as MPL (e.g. the first structure in Table 1 of Ireton G C and S G Reed, 2013, supra, refers to this structure as MPL®, but actually depicts the structure of 3D-MPL). Examples of lipid A (analogs, derivatives) according to the invention include MPL, 3D-MPL, RC529 (e.g. EP1385541), PET-lipid A, GLA (glycopyranosyl lipid adjuvant, a synthetic disaccharide glycolipid; e.g. US20100310602, U.S. Pat. No. 8,722,064), SLA (e.g. Carter D et al, 2016, Clin Transl Immunology 5: e108 (doi: 10.1038/cti.2016.63)), PHAD (phosphorylated hexaacyl disaccharide; the structure of which is the same as that of GLA), 3D-PHAD, 3D-(6-acyl)-PHAD (3D(6A)-PHAD) (PHAD, 3D-PHAD, and 3D(6A)PHAD are synthetic lipid A variants, see e.g. avantilipids.com/divisions/adjuvants, which also provide structures of these molecules), E6020 (CAS Number 287180-63-6), 0N04007, OM-174, and the like. For exemplary chemical structures of 3D-MPL, RC529, PET-lipid A, GLA/PHAD, E6020, 0N04007, and OM-174, see e.g. Table 1 in Ireton G C and S G Reed, 2013, supra. For a structure of SLA, see e.g.
Exemplary adjuvants comprising a lipid A analog or derivative include GLA-LSQ (synthetic MPL [GLA], QS21, lipids formulated as liposomes), SLA-LSQ (synthetic MPL [SLA], QS21, lipids, formulated as liposomes), GLA-SE (synthetic MPL [GLA], squalene oil/water emulsion), SLA-SE (synthetic MPL [SLA], squalene oil/water emulsion), SLA-Nanoalum (synthetic MPL [SLA], aluminum salt), GLA-Nanoalum (synthetic MPL [GLA], aluminum salt), SLA-AF (synthetic MPL [SLA], aqueous suspension), GLA-AF (synthetic MPL [GLA], aqueous suspension), SLA-alum (synthetic MPL [SLA], aluminum salt), GLA-alum (synthetic MPL [GLA], aluminum salt), and several of the GSK ASxx series of adjuvants, including AS01 (MPL, QS21, liposomes), AS02 (MPL, QS21, oil/water emulsion), AS25 (MPL, oil/water emulsion), AS04 (MPL, aluminum salt), and AS15 (MPL, QS21, CpG, liposomes). See, e.g., WO 2013/119856, WO 2006/116423, U.S. Pat. Nos. 4,987,237, 4,436,727, 4,877,611, 4,866,034, 4,912,094, 4,987,237, U.S. Pat. Nos. 5,191,072, 5,593,969, 6,759,241, 9,017,698, 9,149,521, 9,149,522, 9,415,097, 9,415,101, 9,504,743, Reed G, et al., 2013, supra, Johnson et al., 1999, J Med Chem, 42:4640-4649, and Ulrich and Myers, 1995, Vaccine Design: The Subunit and Adjuvant Approach; Powell and Newman, Eds.; Plenum: New York, 495-524.
Non-glycolipid molecules may also be used as TLR4 agonist adjuvants, e.g. synthetic molecules such as Neoseptin-3 or natural molecules such as LeIF, see e.g. Reed S G et al, 2016, supra.
In another aspect the invention relates to a FimH(F71mut) or FimH(F71mut/F144mut) polypeptide of the invention, a polynucleotide encoding a FimH(F71mut) or FimH(F71mut/F144mut) polypeptide of the invention or a pharmaceutical composition of the invention for use as a medicament.
In a further aspect the invention relates to the use of a FimH(F71mut) or FimH(F71mut/F144mut) polypeptide of the invention, a polynucleotide encoding a FimH(F71mut) or FimH(F71mut/F144mut) polypeptide of the invention or a pharmaceutical composition described herein as a medicament for inducing an immune response against a gram negative bacterium of the family of Enterobacteriaceae.
As used herein the terms “immunogen” or “immunogenic” or “antigen” are used interchangeably to describe a molecule capable of inducing an immunological response against itself on administration to a recipient, either alone, in conjunction with an adjuvant, or presented on a display vehicle.
As used herein, an “immunological response” or “immune response” to an antigen or composition refers to the development in a subject of a humoral and/or a cellular immune response to the antigen or an antigen present in the composition.
In a further aspect, the invention relates a FimH(F71mut) or FimH(F71mut/F144mut) polypeptide of the invention, a polynucleotide encoding a FimH(F71mut) or FimH(F71mut/F144mut) polypeptide of the invention or a pharmaceutical composition described herein for use in inducing an immune response against a bacterial infection caused a gram negative bacterium of the family Enterobacteriaceae. In certain embodiments the bacterial infection is caused by Klebsiella spp., or E. coli. In a preferred embodiment, the bacterial infection is caused by E. coli. Thus in one embodiment, the invention relates to the use of a FimH(F71mut) or FimH(F71mut/F144mut) polypeptide of the invention a FimH(F71mut) or FimH(F71mut/F144mut) polypeptide of the invention or a pharmaceutical composition described herein as a medicament for inducing an immune response against E. coli or Klebsiella, preferably E. coli.
In preferred embodiments, the bacterial infection, caused by a gram-negative bacterium of the family Enterobacteriaceae is an infection by E. coli, e.g. by ExPEC, for instance the infection can be a urinary tract infection (UTI). In one embodiment, the invention relates to the polypeptide comprising a FimH lectin domain as described herein, a polynucleotide as described or a pharmaceutical composition described herein for use in treating, preventing, or suppressing symptoms and/or sequelae associated with a UTI in a subject. In certain embodiments, said UTI is a rUTI. E. coli is one of the main causative agents of UTIs and rUTIs which are an important health care problem in young females and older adults. Thus, in preferred embodiments, the bacterial infection is a UTI or rUTI caused by E. coli.
In one embodiment, the invention relates to a method of treating, preventing, or suppressing symptoms and/or sequelae associated with an enterobacillus-related condition a subject in need thereof. The method comprises administering to the subject an effective amount of a FimH(F71mut) or FimH(F71mut/F144mut) polypeptide of the invention, a polynucleotide encoding a FimH(F71mut) or FimH(F71mut/F144mut) polypeptide of the invention or a pharmaceutical composition described herein. Preferably, the administration induces an immune response that is effective in treating or preventing an enterobacillus-related condition. Preferably, the enterobacillus-related condition is a urogenital tract infection, more particularly a UTI or rUTI.
The invention also relates to use of a FimH(F71mut) or FimH(F71mut/F144mut) polypeptide of the invention, a polynucleotide encoding a FimH(F71mut) or FimH(F71mut/F144mut) polypeptide of the invention or a pharmaceutical composition described herein for the manufacture of a medicament for treating, preventing, or suppressing a bacterial infection caused a gram negative bacterium of the family Enterobacteriaceae, preferably a bacterial infection caused by E. coli. More preferably, the bacterial infection is a UTI or recurrent UTI (rUTI) caused by E. coli.
The invention further relates to a method for the production of a polypeptide of the invention, the method comprising culturing a recombinant cell containing the polynucleotide encoding a FimH(F71mut) or FimH(F71mut/F144mut) polypeptide of the invention and/or the vector as described herein, wherein the culturing takes place under conditions conducive to the production of the polypeptide.
In certain embodiments, the method further comprises recovering the polypeptide, which is optionally followed by formulation into a pharmaceutical composition.
Preferably an E. coli cell, for example an E. coli BL21 derivative, cell is used in the method for producing a FimH(F71mut) or FimH(F71mut/F144mut) polypeptide of the invention.
The recovery of the polypeptide preferably includes a purification and/or isolation step which can be performed using conventional protein purification methods well known in the art. Such methods may for example include ammonium sulfate or ethanol precipitation, acid extraction, anion and/or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography, and/or lectin chromatography.
Typical examples for such purification and/or isolation may utilize an antibody to the protein or to a His tag or cleavable leader or tail that is expressing as part of the protein structure. In certain embodiments, the polypeptide described herein have a His-tag included and are purified by methods such as IMAC affinity purification. In certain embodiments, the polypeptides described herein do not comprise a His-tag, in such cases purification can be performed by chromatography, for example ion exchange chromatography (IEX), hydrophobic interaction chromatography (HIC) and/or size exclusion chromatography.
Definitions
Various publications, articles and patents are cited or described in the background and throughout the specification; each of these references is herein incorporated by reference in its entirety. Discussion of documents, acts, materials, devices, articles or the like which has been included in the present specification is for the purpose of providing context for the invention. Such discussion is not an admission that any or all of these matters form part of the prior art with respect to any inventions disclosed or claimed.
Unless defined otherwise, all technical and scientific terms used herein have the same meaning commonly understood to one of ordinary skill in the art to which this invention pertains. Otherwise, certain terms cited herein have the meanings as set in the specification. All patents, published patent applications and publications cited herein are incorporated by reference as if set forth fully herein. It must be noted that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural reference unless the context clearly dictates otherwise.
Throughout this description and the claims which follow, unless the context requires otherwise, the word “comprise”, and variations such as “comprises” and “comprising”, will be understood to imply the inclusion of a stated integer or step or group of integers or steps but not the exclusion of any other integer or step or group of integer or step. When used herein the term “comprising” can be substituted with the term “containing” or “including” or sometimes when used herein with the term “having”.
When used herein “consisting of” excludes any element, step, or ingredient not specified in the claim element. When used herein, “consisting essentially of” does not exclude materials or steps that do not materially affect the basic and novel characteristics of the claim. Any of the aforementioned terms of “comprising”, “containing”, “including”, and “having”, whenever used herein in the context of an aspect or embodiment of the invention can be replaced with the term “consisting of” or “consisting essentially of” to vary scopes of the disclosure.
As used herein, the conjunctive term “and/or” between multiple recited elements is understood as encompassing both individual and combined options. For instance, where two elements are conjoined by “and/or”, a first option refers to the applicability of the first element without the second. A second option refers to the applicability of the second element without the first. A third option refers to the applicability of the first and second elements together. Any one of these options is understood to fall within the meaning, and therefore satisfy the requirement of the term “and/or” as used herein. Concurrent applicability of more than one of the options is also understood to fall within the meaning, and therefore satisfy the requirement of the term “and/or.”
As used herein, the term “pharmaceutically acceptable carrier” refers to a non-toxic material that does not interfere with the effectiveness of a composition according to the invention or the biological activity of a composition according to the invention. A “pharmaceutically acceptable carrier” can include any excipient, diluent, filler, salt, buffer, stabilizer, solubilizer, oil, lipid, lipid containing vesicle, microsphere, liposomal encapsulation, or other material well known in the art for use in pharmaceutical formulations. It will be understood that the characteristics of the pharmaceutically acceptable carrier will depend on the route of administration for a particular application. According to particular embodiments, in view of the present disclosure, any pharmaceutically acceptable carrier suitable for use in a vaccine can be used in the invention. Suitable excipients include but are not limited to sterile water, saline, dextrose, glycerol, ethanol, or the like and combinations thereof, as well as stabilizers, e.g. Human Serum Albumin (HSA) or other suitable proteins and reducing sugars.
As used herein, the term “effective amount” refers to an amount of an active ingredient or component that elicits the desired biological or medicinal response in a subject. An effective amount can be determined empirically and in a routine manner, in relation to the stated purpose. For example, in vitro assays can optionally be employed to help identify optimal dosage ranges.
As used herein, “subject” or “patient” means any animal, preferably a mammal, most preferably a human, who will be or has been vaccinated by a method or composition according to an embodiment of the invention. The term “mammal” as used herein, encompasses any mammal. Examples of mammals include, but are not limited to, cows, horses, sheep, pigs, cats, dogs, mice, rats, rabbits, guinea pigs, monkeys, humans, etc., most preferably a human. In certain embodiments, a subject is a human adult. As used herein, the term “human adult” refers to a human that is 18 years or older. In certain embodiments, a subject is less than 18 years old, e.g. 0-18 years old, e.g. 9-18 years old, or 12-18 years old. In certain embodiments, a subject is a human subject of about 18 to about 50 years. In certain embodiments, a subject is a human of about 50 to about 100 years, e.g. 50-85 years, 60-80 years, 50 years or older, 55 years or older, 60 years or older, 65 years or older, 70 years or older, 75 years or older, 80 years or older, 85 years or older. In some embodiments hereof the subject is not older than 85 years, not older than 80 years, not older than 75 years. In certain embodiments, a human subject is a male. In certain embodiments, a human subject is a female.
As used herein, a “UTI” means an infection of the kidney, bladder, ureter, or urethra. Symptoms of UTI may include one or more of burning feeling when urinating, frequent or intense urge to urinate, incomplete bladder emptying, urine having abnormal look and/or smell, elevated white blood cells in urine, feeling tired or shaky, feeling disoriented, fever or chills, malaise, pain or pressure in back, lower abdomen, pelvis or bladder. However, in some patients symptoms may be absent or non-specific. Sequelae of UTI may include systemic complications such as invasive disease and sepsis. In certain embodiments, a UTI is clinically and/or microbiologically documented, e.g. confirmed with bacterial culture of urine and/or with molecular or other methods. In certain embodiments, the subject is a human subject that previously has had or currently is having a UTI. In certain embodiments, the subject has had a UTI within the last two years, the last year, or the last 6 months. In certain embodiments, the subject has had or currently has a recurrent UTI (rUTI). A “rUTI” as used herein means at least two infections in six months or at least three UTIs in one year. In certain embodiments, a subject to whom the FimH(F71mut) or FimH(F71mut/F144mut), the FimCH complex of the invention, a fusion polypeptide of the invention, or a composition of the invention is administered, has suffered at least two UTIs within the last two years, within the last year, or within the last six months. In certain embodiments, the subject has suffered from complicated UTI. A ‘complicated UTI’ as used herein means a UTI associated with a condition, such as structural or functional abnormalities of the genitourinary tract or the presence of an underlying disease. In certain embodiments, a UTI leads to elevated numbers of white blood cells in urine or other urine abnormalities. In certain embodiments, a subject with UTI has a number of bacteria in urine, i.e. the urine is not sterile, e.g. a bacterial cell count of at least about 10 cells/mL, at least about 100 cells/mL, at least about 103 cells/mL, e.g. at least about 104 cells/mL, e.g. at least about 105 cells/mL.
As used herein, an “immunological response” or “immune response” to an antigen or composition refers to the development in a subject of a humoral and/or a cellular immune response to the antigen or an antigen present in the composition.
Unless otherwise indicated, the term “at least” preceding a series of elements is to be understood to refer to every element in the series.
The word “about” or “approximately” when used in association with a numerical value (e.g. about 10) preferably means that the value may be the given value (of 10) more or less 10%, preferably more or less 5% of the value.
The terms “homology”, “sequence identity” and the like are used interchangeably herein. Sequence identity is herein defined as a relationship between two or more amino acid (polypeptide or protein) sequences or two or more nucleic acid (polynucleotide) sequences, as determined by comparing the sequences. In the art, “identity” also means the degree of sequence relatedness between amino acid or nucleic acid sequences, as the case may be, as determined by the match between strings of such sequences. “Similarity” between two amino acid sequences is determined by comparing the amino acid sequence and its conserved amino acid substitutes of one polypeptide to the sequence of a second polypeptide. “Identity” and “similarity” can be readily calculated by known methods.
“Sequence identity” and “sequence similarity” can be determined by alignment of two peptide or two nucleotide sequences using global or local alignment algorithms, depending on the length of the two sequences. Sequences of similar lengths are preferably aligned using a global alignment algorithm (e.g. Needleman Wunsch) which aligns the sequences optimally over the entire length, while sequences of substantially different lengths are preferably aligned using a local alignment algorithm (e.g. Smith Waterman). Sequences may then be referred to as “substantially identical” or “essentially similar” when they (when optimally aligned by for example the programs GAP or BESTFIT using default parameters) share at least a certain minimal percentage of sequence identity (as defined below). GAP uses the Needleman and Wunsch global alignment algorithm to align two sequences over their entire length (full length), maximizing the number of matches and minimizing the number of gaps. A global alignment is suitably used to determine sequence identity when the two sequences have similar lengths. Generally, the GAP default parameters are used, with a gap creation penalty=50 (nucleotides)/8 (proteins) and gap extension penalty=3 (nucleotides)/2 (proteins). For nucleotides the default scoring matrix used is nwsgapdna and for proteins the default scoring matrix is Blosum62 (Henikoff & Henikoff, 1992, PNAS 89, 915-919). Sequence alignments and scores for percentage sequence identity may be determined using computer programs, such as the GCG Wisconsin Package, Version 10.3, available from Accelrys Inc., 9685 Scranton Road, San Diego, Calif. 92121-3752 USA, or using open source software, such as the program “needle” (using the global Needleman Wunsch algorithm) or “water” (using the local Smith Waterman algorithm) in EmbossWIN version 2.10.0, using the same parameters as for GAP above, or using the default settings (both for ‘needle’ and for ‘water’ and both for protein and for DNA alignments, the default Gap opening penalty is 10.0 and the default gap extension penalty is 0.5; default scoring matrices are Blosum62 for proteins and DNAFull for DNA). When sequences have a substantially different overall lengths, local alignments, such as those using the Smith Waterman algorithm, are preferred.
Alternatively, percentage similarity or identity may be determined by searching against public databases, using algorithms such as FASTA, BLAST, etc. Thus, the nucleic acid and protein sequences of the present invention can further be used as a “query sequence” to perform a search against public databases to, for example, identify other family members or related sequences. Such searches can be performed using the BLASTn and BLASTx programs (version 2.0) of Altschul, et al. (1990) J. Mol. Biol. 215:403-10. BLAST nucleotide searches can be performed with the NBLAST program, score=100, wordlength=12 to obtain nucleotide sequences homologous to nucleic acid molecules of the invention. BLAST protein searches can be performed with the BLASTx program, score=50, wordlength=3 to obtain amino acid sequences homologous to protein molecules of the invention. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul et al., (1997) Nucleic Acids Res. 25(17): 3389-3402. When utilizing BLAST and Gapped BLAST programs, the default parameters of the respective programs (e.g., BLASTx and BLASTn) can be used. See the homepage of the National Center for Biotechnology Information at hypertext transfer protocol://www.ncbi.nlm.nih.gov/.
Other examples of sequences for FimH polypeptides are described in U.S. Pat. No. 6,737,063, for example any one of SEQ ID NO: 23-45 or 55 therein, and these are all incorporated by reference herein.
The following examples of the invention are to further illustrate the nature of the invention. It should be understood that the following examples do not limit the invention and that the scope of the invention is to be determined by the appended claims.
To understand the impact of FimH conformational changes in the vaccine efficacy, several variants of FimH that contain different mutations that could potentially lock the protein in the low affinity status were designed, aiming to identify improved FimH variants that induce functional antibodies capable of reducing bacterial adhesion and colonization of the bladder. To optimize the chances of finding a suitable FimH lectin domain variant, variants with a different predicted mode of action were selected. The previously described mutants FimH_Q133K and FimH_R60P as well as a wild-type (WT) FimH were taken along as controls.
It has been shown that antibodies generated against FimH in the low affinity conformation are capable of blocking the bacterial cell and reducing colony formation in the bladder. Therefore as a first step, we evaluated the functionality of antibodies induced by the different variants of FimH locked in the low affinity conformation by using an adhesion inhibition assay (AIA).
Materials and Methods
FimH Design and Expression
FimC and FimH were expressed in a pET-DUET or pET-22b vector using heterologous signal sequences for expression in the periplasm and a C-terminal His-tag on FimC for affinity purification using immobilized metal affinity chromatography (IMAC). Expression was induced using IPTG and protein was extracted and purified using IMAC purification (Talon).
Immunization
Wistar rats received 4 intramuscular (i.m.) immunizations at days 0, 7, 10 and 18 with the different FimH variants (60 μg each variant/dose) combined with a non-Freund adjuvant (Speedy rat 28-Day model, Eurogentec). Functionality of serum antibodies was investigated at day 0 (pre-immunization) and day 28 (post-immunization) by Adhesion Inhibition Assay (AIA) as described below.
Adhesion Inhibition Assay (AIA)
Bacteria (E. coli strain J96) were labeled with a fluorescein isothiocyanate (FITC). Labeled bacteria were incubated with bladder urothelial cells (5637 cell line) for 1 h at 37° C. The % of adherent bacteria was measured by flow cytometry. For evaluation of serum inhibition, bacteria were previously incubated with serum samples for 30 minutes at 37° C. and then mixed with 5637 cells.
ELISA
96-well plates were coated overnight with 1 ug/mL of FimH. After washing, coated wells were incubated with blocking buffer [phosphate-buffered saline (PBS)+2% bovine serum albumin (BSA)] for 1 hour at room temperature. After washing with PBS+0.05% TWEEN 20, serum was added to the plates that were then incubated for 1 hour at room temperature. After washing, goat anti-rat antibody conjugated to horseradish peroxidase diluted in PBS with 2% BSA was added to each well for 1 hour at room temperature. After a final washing, the reaction was developed with tetramethylbenzidine substrate. The reaction was stopped with 1M phosphoric acid, and absorbance is measured at 450 nm.
Results
Serum antibody inhibitory titers were calculated as half maximal inhibitory concentration (IC50) based on a 4-parameter logistic (4PL) regression model. In addition, levels of serum antibodies induced by different FimH variants (total IgG) were evaluated by ELISA. IC50 titers, defined as half maximal effective concentration, were calculated based on duplicate 6-step titration curves that were analyzed with a 4PL nonlinear regression model.
In a preliminary experiment, several different FimH variants were tested for their ability to induce inhibitory antibodies. As can be seen in
The FimH(F71Y) and FimH(F144V) variants appear to be locked in the low affinity conformation by different mechanisms that induce a conformational change of the binding pocket. The substitution in the FimH(F71Y) variant prevents the residue to fold into a hydrophobic pocket (relaxed state) making the tense state more favorable whereas in the FimH(F144V) variant, the substitution is situated relatively close to the mannose binding pocket which stabilizes the low affinity conformation. Since the conformational change to the low affinity states is brought about by these two distinct mechanisms, we hypothesized that a lectin domain comprising both the F71Y and the F144V substitution could be even more stably locked in the low affinity conformation which would provide an extra advantage to a FimH variant of that kind. To test this hypothesis, we created a FimH double mutant which comprises both the F71Y and the F144V substitution it its lectin domain (FimH(F71Y/F144V)). As can be seen in
Based on these results, FimH(F71Y) and FimH(F71Y/F144V) were selected as the lead candidates. Their characteristics were further analyzed as described below.
SPR
To gain a detailed insight into the binding affinity and kinetics of the interaction of FimH lectin domain variants with the n-Heptyl-α-D-mannopyranoside ligand, surface plasmon resonance (SPR) measurements were performed. In brief, the FimH variants were titrated into the Mannoside ligand 5 surface (Rabbani S et al, J Biol. Chem., 2018, 293(5):1835-1849) with the top concentrations of either 3 or 10 μM in HBS-N (0.01 M HEPES, pH 7.4, 0.15 M NaCl, 3 mM EDTA, 0.05% surfactant P20). The proteins were injected from 0.12 to 10 μM or 0.036 to 3.0 μM using a single cycle kinetics injection.
Results
Previously described mutants FimH_Q133K and FimH_R60P have a mutation in the mannose interacting residues in the binding pocket. These mutations are predicted to directly influence the binding interaction with mannose. These mutants were taken as positive controls. The double mutant R60P_Q133K was taken along to check for potentially enhanced effects. Additionally, wild-type (WT) FimH lectin domain was taken along as a negative control.
The variants affinity for binding to mannose was assessed using SPR. The results are presented in table 2. As expected, the lectin domain variants having mutations in the mannoside binding pocket of FimH (Q133K and R60P_Q133K) did not bind to mannoside at all. The R60P mutant showed low affinity for mannoside, as expected.
Despite being capable of inducing high levels inhibitory antibodies, the variant comprising the F71Y substitution still showed some affinity for mannoside, indicating that this mutation did not completely abolish binding to mannoside. In the FimH lectin domain variants comprising the F144V substitution the binding to mannoside was completely abolished (as previously disclosed for the single F144V mutant in EP patent application number 20152217, filed in the name of Janssen Pharmaceuticals, Inc on 16 Jan. 2020, incorporated by reference herein). In the mutant comprising both F71Y and F144V binding to mannoside was also completely abolished.
Mutations in the lectin domain of FimH may cause the loss of epitopes that are crucial in eliciting a strong and functional immune response such as the epitopes that are present in the binding pocket of FimH. To ensure that the integrity of the binding pocket was not compromised by the mutations described herein, the binding of monoclonal antibodies (mAb) mAb475 and mAb926 to the mutant FimH lectin domains was assessed. mAb475 and mAb926, recognize overlapping but distinct epitopes on the FimH lectin domain within the mannose-binding pocket of the FimH (Kisiela et al. 2013 & 2015).
Results
Mutated FimH lectin domains have been previously described in WO02102974. WO02102974 describes an extensive list of possible mutations of mostly unspecified mutations (65 possible mutation sites are suggested in the lectin domain of FimH which is approximately 159 amino acids long). However, WO02102974 indicates that the FimH lectin domains having an amino acid substitution at position 54, 133 or 135 are the most promising candidates, FimH_Q133K is explicitly mentioned as a highly preferred option. It was therefore quite surprising that FimH-23-10_Q133K was not recognized by the functional mAb475, indicating integrity issues of the binding pocket (Table 3). In contrast, both FimH(F71Y) and FimH(F144V) were recognized by both mAb475 and mAb926 indicating that the binding pocket remained completely intact (Table 3). Also the FimH(F71Y/F144V) double mutant was still recognized by both antibodies, indicating that the binding pocket also remained intact in this double mutant (Table 3).
1H 15N heteronuclear single quantum coherence nuclear magnetic resonance (HSQC NMR) spectra of uniformly 15N-labeled FimHLD variants, produced as described in the method section with the addition of 15N to the growth media, were measured in the absence and presence of the n-Heptyl-α-D-mannopyranoside ligand to assess structural differences on a residue-based level. Protein was concentrated to 150 μM and measured in 20 mM phosphate buffer, pH 7.4, with 7%-10% D2O. The n-Heptyl-α-D-mannopyranoside ligand was dissolved in D2O and added stepwise to the protein up to a 10-fold molar excess. The spectra of each sample were compared to the publically available reference spectra (Rabbani S et al, J Biol. Chem., 2018, 293(5):1835-1849).
Results
FimH variants FimH(F71Y), FimH(F144V) and FimH(F71Y/F144V) were analyzed for their ability to remain in the low affinity confirmation in the presence of the mannoside ligand. In the absence of ligand, all three variants are in a low affinity confirmation when comparing chemical shifts of residues known to be indicative of the high affinity state (Rabbani S et al, J Biol. Chem., 2018, 293(5):1835-1849). In contrast, the FimHLD 23-10 wild type is locked in the high affinity conformation in absence of the mannoside ligand. However in the presence of ligand, FimH(F71Y) and FimH(F144V) switch back to the high affinity confirmation, while FimH (F71Y/F144V) stays in the low affinity confirmation, e.g. no chemical shift is observed after addition of ligand to the FimH(F71Y/F144V) (
Apart from two unknown residues that differ from the K12 wild-type, the FimHLD 23-10 wild type is considered to be already in the high affinity (H) conformation without ligand. The single mutant variants F71Y and F144V are in the low affinity (L) conformation without ligand but switch to H conformation in the presence of ligand, while the double mutant variant F71Y/F144V remained in the L conformation even in the presence of ligand. This inability to switch back to the high affinity conformation makes the FimH(F71Y/F144V) especially attractive for use in pharmaceutical compositions of vaccines, as it for instance ensures that no additional quality or stability controls are needed to test whether the conformation is stable during storage or under other storage conditions. Additionally, the inability to switch back into the high affinity conformation allows the use of the FimH(F71Y/F144V) as a research tool to study the mechanism of action or to gain conformational knowledge and it allows the FimH(F71Y/F144V) to be used to generate specific antibodies with useful research, diagnostic and possibly pharmaceutical applications.
Thus, in conclusion, of all of the FimH variants tested, FimH(F71Y), FimH(F144V), and FimH(F71Y/F144V) are capable of inducing the highest levels of functional inhibitory antibodies while keeping the binding pocket of FimH intact. FimH(F71Y/F144V) has the additional advantages of completely abolishing the binding to mannoside and of remaining locked in the low affinity conformation even in the presence of the ligand.
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