Patent Application
20230381293
This disclosure relates to recombinant Norovirus Virus-Like Particles and their use.
Norovirus is a non-enveloped virus that belongs to the family Caliciviridae. It constitutes the major cause of epidemic gastroenteritis in close settings and since the introduction of rotavirus vaccines, Norovirus has become the leading cause of medically attended acute gastroenteritis in U.S. children, associated with nearly 1 million health care visits annually. A gastroenteritis episode due to Norovirus is incapacitating during the acute phase that usually lasts from 1 to 3 days and includes explosive vomiting, stomach cramps and diarrhea Immunocompetent patients usually recover completely from the illness, but the gastroenteritis may be severe in young children, the elderly and immunocompromised, increasing the risk for morbidity and mortality. It has been estimated that around 200,000 people die annually because of Norovirus gastroenteritis, mostly in developing countries. In immunocompromised patients, Norovirus is recognized as an important cause of chronic gastroenteritis, with long-term virus shedding and increased morbidity in this population. In immunocompetent patients the virus shedding after infection lasts for approximately days, while in immunocompromised patients virus shedding has been detected for up to 3 years. It has been proposed that long term virus shedding may contribute to the spread of the virus. Overall, the societal costs associated with Norovirus infection worldwide has been estimated to be upward of $60 billion.
The Norovirus genome is composed of a single-stranded positive-sense RNA molecule that contains three open reading frames. The genome is surrounded by a non-enveloped capsid composed of the major capsid protein, VP1, encoded by ORF2, and a minor structural protein, VP2, encoded by ORF3. Crystallographic cryoEM analyses have showed that the Norovirus capsid is formed by 180 molecules of VP1, organized into 90 dimers. Each VP1 monomer is divided into two domains designated shell (S) and protruding (P), linked by a flexible hinge. The P domain is further divided into P1 and P2 subdomains, with P2 as the outermost domain exposed on the surface.
Noroviruses are divided into six major genogroups designated Genogroup (G)I through GVI. GI and GII contain the majority of Norovirus strains associated with human disease. The Norovirus GI.1 was the first genotype described, and the GII.4 genotype has been associated with the majority of global outbreaks. Despite extensive effort, an approved vaccine for Norovirus infection remains elusive.
Disclosed herein are recombinant Norovirus VLPs formed from self-assembled recombinant Norovirus VP1 proteins comprising one or more amino acid substitutions that increase stability of the recombinant Norovirus VLP compared to Norovirus VLPs formed from unmodified recombinant Norovirus VP1 proteins.
In some embodiments, the recombinant Norovirus VLP comprises a multimer of a recombinant Norovirus GI VP1 protein comprising amino acid substitutions set forth as one or more of the following pairs of cysteine substitutions that form a non-natural interprotomer disulfide bond: N116C/G193C, A37C/A44C, Q62C/A140C, L144C/P221C, G131C/N172C, and N167C/L169C, and/or one or more of the following pairs of hydrophobic amino acid substitutions: Q141V/P221L and A37I/A44L substitutions, wherein the amino acid positions are according to the reference GI VP1 protein sequence set forth as SEQ ID NO: 1.
In some embodiments, the recombinant Norovirus VLP comprises a multimer of a recombinant Norovirus GII VP1 protein comprising amino acid substitutions set forth as one or more of the following pairs of cysteine substitutions that form a non-natural interprotomer disulfide bond: N112C/A116C, N189C/D194C, P60C/S134C, M140C/P217C, P129C/R223C, wherein the amino acid positions are according to the reference GII VP1 protein sequence set forth as SEQ ID NO: 51.
In some embodiments, the recombinant VP1 protein further comprises one or more additional amino acid substitutions or deletions, such as amino acid substitutions that increase thermostability of the recombinant Norovirus VLP.
Immunogenic compositions including the recombinant Norovirus VLP that are suitable for administration to a subject are provided, and may also be contained in a unit dosage form. The compositions can further include an adjuvant.
Methods of inducing an immune response in a subject are disclosed, as are methods of treating, inhibiting or preventing a Norovirus infection in a subject, by administering to the subject an effective amount of a disclosed recombinant Norovirus VLP. Additionally, methods of identifying an antibody that specifically binds to a solvent-accessible epitope on a Norovirus VLP, as well as methods for identifying a sample from a subject with a neutralizing antibody response to Norovirus, are provided.
The foregoing and other features and advantages of this disclosure will become more apparent from the following detailed description of several embodiments which proceeds with reference to the accompanying figures.
Fabs and intact VLPs decorated with a layer of 512 Fabs. (
The nucleic and amino acid sequences listed in the accompanying sequence listing are shown using standard letter abbreviations for nucleotide bases, and three letter code for amino acids, as defined in 37 C.F.R. 1.822. Only one strand of each nucleic acid sequence is shown, but the complementary strand is understood as included by any reference to the displayed strand. The Sequence Listing is submitted as an ASCII text file in the form of the file named “Sequence.txt” (˜260 kb), which was created on Oct. 9, 2021 which is incorporated by reference herein.
This disclosure provides recombinant Norovirus VLPs that include one or more amino acid substitutions that stabilize the VP1 assembly of the VLP and which are useful, for example, to elicit a neutralizing immune response to Norovirus in a subject.
Unless otherwise noted, technical terms are used according to conventional usage. Definitions of common terms in molecular biology may be found in Benjamin Lewin, Genes X, published by Jones & Bartlett Publishers, 2009; and Meyers et al. (eds.), The Encyclopedia of Cell Biology and Molecular Medicine, published by Wiley-VCH in 16 volumes, 2008; and other similar references.
As used herein, the singular forms “a,” “an,” and “the,” refer to both the singular as well as plural, unless the context clearly indicates otherwise. For example, the term “an antigen” includes single or plural antigens and can be considered equivalent to the phrase “at least one antigen.” As used herein, the term “comprises” means “includes.” It is further to be understood that any and all base sizes or amino acid sizes, and all molecular weight or molecular mass values, given for nucleic acids or polypeptides are approximate, and are provided for descriptive purposes, unless otherwise indicated. Although many methods and materials similar or equivalent to those described herein can be used, particular suitable methods and materials are described herein. In case of conflict, the present specification, including explanations of terms, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting. To facilitate review of the various embodiments, the following explanations of terms are provided:
About: Plus or minus 5% relative to a reference value. For example, about 100 refers to from 95 to 105.
Adjuvant: A vehicle used to enhance antigenicity. In some embodiments, an adjuvant can include a suspension of minerals (alum, aluminum hydroxide, or phosphate) on which antigen is adsorbed; or water-in-oil emulsion, for example, in which antigen solution is emulsified in mineral oil (Freund incomplete adjuvant), sometimes with the inclusion of killed mycobacteria (Freund's complete adjuvant) to further enhance antigenicity (inhibits degradation of antigen and/or causes influx of macrophages). In some embodiments, the adjuvant used in a disclosed immunogenic composition is a combination of lecithin and carbomer homopolymer (such as the ADJUPLEX™ adjuvant available from Advanced BioAdjuvants, LLC, see also Wegmann, Clin Vaccine Immunol, 22(9): 1004-1012, 2015). Additional adjuvants for use in the disclosed immunogenic compositions include the QS21 purified plant extract, Matrix M, AS01, MF59, and ALFQ adjuvants. Immunostimulatory oligonucleotides (such as those including a CpG motif) can also be used as adjuvants. Adjuvants include biological molecules (a “biological adjuvant”), such as costimulatory molecules. Exemplary adjuvants include IL-2, RANTES, GM-CSF, TNF-α, IFN-γ, G-CSF, LFA-3, CD72, B7-1, B7-2, OX-40L, 4-1BBL and toll-like receptor (TLR) agonists, such as TLR-9 agonists. Additional description of adjuvants can be found, for example, in Singh (ed.) Vaccine Adjuvants and Delivery Systems. Wiley-Interscience, 2007). Adjuvants can be used in combination with the disclosed immunogens.
Administration: The introduction of an agent, such as a disclosed immunogen, into a subject by a chosen route. Administration can be local or systemic. Exemplary routes of administration include, but are not limited to, oral, injection (such as subcutaneous, intramuscular, intradermal, intraperitoneal, and intravenous), sublingual, rectal, transdermal (for example, topical), intranasal, vaginal, and inhalation routes.
Amino Acid Substitution: The replacement of one amino acid in a polypeptide with a different amino acid.
Antibody: An immunoglobulin, antigen-binding fragment, or derivative thereof, that specifically binds and recognizes an analyte (antigen) such as a recombinant Norovirus VP1 protein or multimer of the antigen. The term “antibody” is used herein in the broadest sense and encompasses various antibody structures, including but not limited to monoclonal antibodies, polyclonal antibodies, multispecific antibodies (e.g., bispecific antibodies), and antibody fragments, so long as they exhibit the desired antigen-binding activity. Non-limiting examples of antibodies include, for example, intact immunoglobulins and variants and fragments thereof that retain binding affinity for the antigen. Examples of antibody fragments include but are not limited to Fv, Fab, Fab′, Fab′-SH, F(ab′)2; diabodies; linear antibodies; single-chain antibody molecules (e.g. scFv); and multispecific antibodies formed from antibody fragments. Antibody fragments include antigen binding fragments either produced by the modification of whole antibodies or those synthesized de novo using recombinant DNA methodologies (see, e.g., Kontermann and Dubel (Ed), Antibody Engineering, Vols. 1-2, 2nd Ed., Springer Press, 2010).
A “neutralizing” antibody reduces the infectious titer of an infectious agent by binding to a specific antigen on the infectious agent. In some examples the infectious agent is a virus, such as a Norovirus, for example a Genogroup I or Genogroup II Norovirus, such as a Norwalk virus or MD2004 virus. In some examples, an antibody that is specific for a Norovirus polypeptide neutralizes the infectious titer of the virus. In some examples, an antibody specific for Norovirus VP1 neutralizes the infectious titer of the virus. In vitro assays for neutralization are known in the art. Thus, in some non-limiting examples, an assay for neutralization activity is blocking the binding of Norovirus-like particles (VLPs) to HBGA synthetic carbohydrates, for example H1 or H3 type HBGA, in a dose dependent manner In other non-limiting examples an assay for neutralization activity is blocking the binding of Norovirus VLPs to pig gastric mucin or saliva, in a dose dependent manner.
Biological Sample: A sample obtained from a subject. Biological samples include all clinical samples useful for detection of disease or infection (for example, Norovirus infection) in subjects, including, but not limited to, cells, tissues, and bodily fluids, such as blood, derivatives and fractions of blood (such as serum), cerebrospinal fluid; as well as biopsied or surgically removed tissue, for example tissues that are unfixed, frozen, or fixed in formalin or paraffin. In a particular example, a biological sample is obtained from a subject having or suspected of having a Norovirus infection.
Carrier: An immunogenic molecule to which an antigen can be linked. When linked to a carrier, the antigen may become more immunogenic. Carriers are chosen to increase the immunogenicity of the antigen and/or to elicit antibodies against the carrier which are diagnostically, analytically, and/or therapeutically beneficial. Useful carriers include polymeric carriers, which can be natural (for example, proteins from bacteria or viruses), semi-synthetic or synthetic materials containing one or more functional groups to which a reactant moiety can be attached.
Conditions sufficient to form an immune complex: Conditions which allow an antibody or antigen binding fragment to bind to its cognate epitope to a detectably greater degree than, and/or to the substantial exclusion of, binding to substantially all other epitopes. Conditions sufficient to form an immune complex are dependent upon the format of the binding reaction and typically are those utilized in immunoassay protocols or those conditions encountered in vivo. See Greenfield (Ed.), Antibodies: A Laboratory Manual, 2nd ed. New York: Cold Spring Harbor Laboratory Press, 2014, for a description of immunoassay formats and conditions. The conditions employed in the methods are “physiological conditions” which include reference to conditions (e.g., temperature, osmolarity, pH) that are typical inside a living mammal or a mammalian cell. While it is recognized that some organs are subject to extreme conditions, the intra-organismal and intracellular environment normally lies around pH 7 (e.g., from pH 6.0 to pH 8.0, more typically pH 6.5 to 7.5), contains water as the predominant solvent, and exists at a temperature above 0° C. and below 50° C. Osmolarity is within the range that is supportive of cell viability and proliferation.
The formation of an immune complex can be detected, for example, through conventional methods such as immunohistochemistry (IHC), immunoprecipitation (IP), flow cytometry, immunofluorescence microscopy, ELISA, immunoblotting (for example, Western blot), magnetic resonance imaging (MRI), computed tomography (CT) scans, radiography, and affinity chromatography.
Conservative variants: “Conservative” amino acid substitutions are those substitutions that do not substantially affect or decrease a function of a protein, such as the ability of the protein to induce an immune response when administered to a subject. The term conservative variation also includes the use of a substituted amino acid in place of an unsubstituted parent amino acid. Furthermore, deletions or additions which alter, add or delete a single amino acid or a small percentage of amino acids (for instance less than 5%, in some embodiments less than 1%) in an encoded sequence are conservative variations where the alterations result in the substitution of an amino acid with a chemically similar amino acid.
The following six groups are examples of amino acids that are considered to be conservative substitutions for one another:
Non-conservative substitutions are those that reduce an activity or function of a recombinant VP1 protein as described herein, such as the ability to self-assemble into a VLP. For instance, if an amino acid residue is essential for a function of the protein, even an otherwise conservative substitution may disrupt that activity. Thus, a conservative substitution does not alter the basic function of a protein of interest.
Contacting: Placement in direct physical association; includes both in solid and liquid form, which can take place either in vivo or in vitro. Contacting includes contact between one molecule and another molecule, for example the amino acid on the surface of one polypeptide, such as an antigen, that contacts another polypeptide, such as an antibody. Contacting can also include contacting a cell for example by placing an antibody in direct physical association with a cell.
Control: A reference standard. In some embodiments, the control is a sample obtained from a healthy patient. In other embodiments, the control is a tissue sample obtained from a patient diagnosed with a Norovirus infection, such as a Norwalk virus infection that serves as a positive control. In still other embodiments, the control is a historical control or standard reference value or range of values (such as a previously tested control sample, such as a group of infected patients with known prognosis or outcome, or group of samples that represent baseline or normal values).
A difference between a test sample and a control can be an increase or conversely a decrease. The difference can be a qualitative difference or a quantitative difference, for example a statistically significant difference. In some examples, a difference is an increase or decrease, relative to a control, of at least about 5%, such as at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 100%, at least about 150%, at least about 200%, at least about 250%, at least about 300%, at least about 350%, at least about 400%, at least about 500%, or greater than 500%.
Detectable Marker: A detectable molecule (also known as a label) that is conjugated directly or indirectly to a second molecule, such as an antibody, to facilitate detection of the second molecule. For example, the detectable marker can be capable of detection by ELISA, spectrophotometry, flow cytometry, microscopy or diagnostic imaging techniques (such as CT scans, MRIs, ultrasound, fiberoptic examination, and laparoscopic examination). Specific, non-limiting examples of detectable markers include fluorophores, chemiluminescent agents, enzymatic linkages, radioactive isotopes and heavy metals or compounds (for example super paramagnetic iron oxide nanocrystals for detection by MRI). Methods for using detectable markers and guidance in the choice of detectable markers appropriate for various purposes are discussed for example in Green and Sambrook (Molecular Cloning: A Laboratory Manual, 4th ed., New York: Cold Spring Harbor Laboratory Press, 2012) and Ausubel et al. (Eds.) (Current Protocols in Molecular Biology, New York: John Wiley and Sons, including supplements, 2017).
Detecting: To identify the existence, presence, or fact of something.
Effective Amount: An amount of agent, such as a recombinant Norovirus VLP as described herein, that is sufficient to elicit a desired response, such as an immune response in a subject. It is understood that to obtain a protective immune response against Norovirus infection can require multiple administrations of a disclosed recombinant Norovirus VLP, and/or administration of a disclosed recombinant Norovirus VLP as the “prime” in a prime boost protocol wherein the boost immunogen can be different from the prime immunogen. Accordingly, an effective amount of a disclosed recombinant Norovirus VLP can be the amount of the recombinant Norovirus VLP sufficient to elicit a priming immune response in a subject that can be subsequently boosted with the same or a different immunogen to elicit a protective immune response.
In one example, a desired response is to inhibit or reduce or prevent Norovirus infection. The Norovirus infection does not need to be completely eliminated or reduced or prevented for the method to be effective. For example, administration of an effective amount of the immunogen can induce an immune response that decreases the Norovirus infection (for example, as measured by infection of cells, or by number or percentage of subjects infected by the Norovirus) by a desired amount, for example by at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or even at least 100% (elimination or prevention of detectable 2 Norovirus infection), as compared to a suitable control.
Epitope: An antigenic determinant These are particular chemical groups or peptide sequences on a molecule that are antigenic, such that they elicit a specific immune response, for example, an epitope is the region of an antigen to which B and/or T cells respond. An antibody can bind to a particular antigenic epitope, such as an epitope on a recombinant Norovirus VLP. Epitopes can be formed both from contiguous amino acids or noncontiguous amino acids juxtaposed by tertiary folding of a protein.
Expression: Transcription or translation of a nucleic acid sequence. For example, a gene is expressed when its DNA is transcribed into an RNA or RNA fragment, which in some examples is processed to become mRNA. A gene may also be expressed when its mRNA is translated into an amino acid sequence, such as a protein or a protein fragment. In a particular example, a heterologous gene is expressed when it is transcribed into an RNA. In another example, a heterologous gene is expressed when its RNA is translated into an amino acid sequence. The term “expression” is used herein to denote either transcription or translation. Regulation of expression can include controls on transcription, translation, RNA transport and processing, degradation of intermediary molecules such as mRNA, or through activation, inactivation, compartmentalization or degradation of specific protein molecules after they are produced.
Expression Control Sequences: Nucleic acid sequences that regulate the expression of a heterologous nucleic acid sequence to which it is operatively linked. Expression control sequences are operatively linked to a nucleic acid sequence when the expression control sequences control and regulate the transcription and, as appropriate, translation of the nucleic acid sequence. Thus expression control sequences can include appropriate promoters, enhancers, transcription terminators, a start codon (ATG) in front of a protein-encoding gene, splicing signal for introns, maintenance of the correct reading frame of that gene to permit proper translation of mRNA, and stop codons. The term “control sequences” is intended to include, at a minimum, components whose presence can influence expression, and can also include additional components whose presence is advantageous, for example, leader sequences and fusion partner sequences. Expression control sequences can include a promoter.
A promoter is a minimal sequence sufficient to direct transcription. Also included are those promoter elements which are sufficient to render promoter-dependent gene expression controllable for cell-type specific, tissue-specific, or inducible by external signals or agents; such elements may be located in the 5′ or 3′ regions of the gene. Both constitutive and inducible promoters are included (see for example, Bitter et al., Methods in Enzymology 153:516-544, 1987). For example, when cloning in bacterial systems, inducible promoters such as pL of bacteriophage lambda, plac, ptrp, ptac (ptrp-lac hybrid promoter) and the like may be used. In one embodiment, when cloning in mammalian cell systems, promoters derived from the genome of mammalian cells (such as metallothionein promoter) or from mammalian viruses (such as the retrovirus long terminal repeat; the adenovirus late promoter; the vaccinia virus 7.5K promoter) can be used. Promoters produced by recombinant DNA or synthetic techniques may also be used to provide for transcription of the nucleic acid sequences.
Expression Vector: A vector comprising a recombinant polynucleotide comprising expression control sequences operatively linked to a nucleotide sequence to be expressed. An expression vector comprises sufficient cis-acting elements for expression; other elements for expression can be supplied by the host cell or in an in vitro expression system. Expression vectors include all those known in the art, such as cosmids, plasmids (e.g., naked or contained in liposomes) and viruses (e.g., lentiviruses, retroviruses, adenoviruses, and adeno-associated viruses) that incorporate the recombinant polynucleotide.
Host Cells: Cells in which a vector can be propagated and its DNA expressed. The cell may be prokaryotic or eukaryotic. The term also includes any progeny of the subject host cell. It is understood that all progeny may not be identical to the parental cell since there may be mutations that occur during replication. However, such progeny is included when the term “host cell” is used.
Immune Complex: The binding of antibody or antigen binding fragment to a soluble antigen forms an immune complex. The formation of an immune complex can be detected through conventional methods, for instance immunohistochemistry, immunoprecipitation, flow cytometry, immunofluorescence microscopy, ELISA, immunoblotting (for example, Western blot), magnetic resonance imaging, CT scans, radiography, and affinity chromatography.
Immune response: A response of a cell of the immune system, such as a B cell, T cell, or monocyte, to a stimulus. In one embodiment, the response is specific for a particular antigen (an “antigen-specific response”). In one embodiment, an immune response is a T cell response, such as a CD4+ response or a CD8+ response. In another embodiment, the response is a B cell response, and results in the production of specific antibodies.
Immunogen: A compound, composition, or substance (for example, a recombinant Norovirus VLP) that can elicit an immune response in an animal, including compositions that are injected or absorbed into an animal. Administration of an immunogen to a subject can lead to protective immunity against a pathogen of interest.
Immunogenic Composition: A composition comprising a disclosed recombinant Norovirus VLP that induces a measurable CTL response, or induces a measurable B cell response (such as production of antibodies), against the genotype and strain of the Norovirus, when administered to a subject. For in vivo use, the immunogenic composition will typically include the recombinant Norovirus VLP in a pharmaceutically acceptable carrier and may also include other agents, such as an adjuvant.
Inhibiting or Treating a Disease: Inhibiting the full development of a disease or condition, for example, in a subject who is at risk for a disease such as a Norovirus infection. “Treatment” refers to a therapeutic intervention that ameliorates a sign or symptom of a disease or pathological condition after it has begun to develop. The term “ameliorating,” with reference to a disease or pathological condition, refers to any observable beneficial effect of the treatment. Inhibiting a disease can include preventing or reducing the risk of the disease, such as preventing or reducing the risk of viral infection. The beneficial effect can be evidenced, for example, by a delayed onset of clinical symptoms of the disease in a susceptible subject, a reduction in severity of some or all clinical symptoms of the disease, a slower progression of the disease, a reduction in the viral load, an improvement in the overall health or well-being of the subject, or by other parameters that are specific to the particular disease. A “prophylactic” treatment is a treatment administered to a subject who does not exhibit signs of a disease or exhibits only early signs for the purpose of decreasing the risk of developing pathology.
Isolated: An “isolated” biological component has been substantially separated or purified away from other biological components, such as other biological components in which the component naturally occurs, such as other chromosomal and extrachromosomal DNA, RNA, and proteins. Proteins, peptides, nucleic acids, and viruses that have been “isolated” include those purified by standard purification methods. Isolated does not require absolute purity, and can include protein, peptide, nucleic acid, or virus molecules that are at least 50% isolated, such as at least 75%, 80%, 90%, 95%, 98%, 99%, or even 99.9% isolated.
Native Protein, Sequence, or disulfide Bond: A polypeptide, sequence or disulfide bond that has not been modified, for example, by selective mutation. For example, selective mutation to focus the antigenicity of the antigen to a target epitope, or to introduce a disulfide bond into a protein that does not occur in the native protein. Native protein or native sequence are also referred to as wild-type protein or wild-type sequence. A non-native disulfide bond is a disulfide bond that is not present in a native protein, for example, a disulfide bond that forms in a protein due to introduction of one or more cysteine residues into the protein by genetic engineering.
Norovirus (NoV): A non-enveloped virus that belongs to the family Caliciviridae. It constitutes the major cause of epidemic gastroenteritis in close settings and since the introduction of rotavirus vaccines, has become the leading cause of medically attended acute gastroenteritis in U.S. children, associated with nearly 1 million health care visits annually. A gastroenteritis episode due to Norovirus is incapacitating during the acute phase that usually lasts from 1 to 3 days and includes explosive vomiting, stomach cramps and diarrhea Immunocompetent patients usually recover completely from the illness, but the gastroenteritis may be severe in young children, the elderly and immunocompromised, increasing the risk for morbidity and mortality. It has been estimated that around 200,000 people die annually because of Norovirus gastroenteritis, especially in developing countries. In immunocompromised patients, Norovirus is recognized as an important cause of chronic gastroenteritis, with long-term virus shedding and increased morbidity in this population. In immunocompetent patients the virus shedding after infection lasts for approximately days, while in immunocompromised patients virus shedding has been detected for up to 3 years. It has been proposed that long term virus shedding may contribute to the spread of the virus.
The Norovirus genome is composed of a single-stranded positive-sense RNA molecule that contains three open reading frames. The genome is surrounded by a non-enveloped capsid composed of the major capsid protein, VP1, encoded by ORF2, and a minor structural protein, VP2, encoded by ORF3. Crystallographic analysis showed that the Norovirus capsid is formed by 180 molecules of VP1, organized into 90 dimers. Each VP1 monomer is divided into two domains designated shell (S) and protruding (P), linked by a flexible hinge. The P domain is further divided into P1 and P2 subdomains, with P2 as the outermost domain exposed on the surface (Prasad et al., Science 286(5438): 287-90, 1999).
Noroviruses are divided into six major genogroups designated Genogroup (G)I through GVI. GI and GII contain the majority of Norovirus strains associated with human disease and are further divided into 9 and 21 genotypes, respectively (Kroneman et al., Arch Virol 158(10): 2059-68, 2013). The Norovirus GI.1 was the first genotype described, the GII.4 genotype has been associated with the majority of global outbreaks since the mid-1990s, when active surveillance with molecular diagnostic techniques was initiated.
Non-limiting examples of Noroviruses include Norwalk virus (GI.1, GenBank M87661, NP_056821.2), Jingzhou virus (GI.2, GenBank KF306212.1), Desert Shield virus (GI.3, GenBank AAA16285.1), Chiba virus (G1.4, GenBank BAB18267.1), Musgrove (GI.5, GenBank AJ277614.1), Hawaii virus (GII.1, GenBank AAB97768.2), Snow Mountain virus (GII.2, GenBank AAB16915.1), Mexico virus (GII.3, GenBank AAB06271.1), and Sydney virus (GII.4, GenBank AAZ31411.2). The nucleic acid and corresponding amino acid sequences of each are all incorporated by reference in their entirety.
Standard methods for detecting viral infection may be used to detect Norovirus infection in a subject, including but not limited to, assessment of patient symptoms and background and genetic tests such as reverse transcription-polymerase chain reaction (rRT-PCR). The test can be done on patient samples such as stool, vomit, or blood samples.
Norovirus VP1 Protein: A capsid polypeptide that is encoded by open reading frame (ORF) 2 of the Norovirus genome. The VP1 proteins self-assemble under suitable conditions to form the Norovirus capsid. In the native virus, VP1 self assembles to form an icosahedral capsid with a T=3 symmetry, about 38 nm in diameter, and consisting of 180 VP1 proteins, organized into dimers. In the native virus, the capsid encapsulates the genomic RNA and VP2 proteins, and attaches virion to target cells by binding histo-blood group antigens present on gastroduodenal epithelial cells. Each VP1 monomer is divided into two domains designated shell (S) and protruding (P), linked by a flexible hinge. The P domain is further divided into P1 and P2 subdomains, with P2 as the outermost domain exposed on the surface (Prasad et al., Science 286(5438): 287-90, 1999).
An exemplary GI VP1 is provided in GenBank Accession No. M87661 (Norwalk virus), which is incorporated herein by reference and provided herein as SEQ ID NO: 1. The numbering used for the disclosed recombinant Norovirus GI VP1 proteins is relative to the Norovirus GI.1 VP1 protein sequence provided as SEQ ID NO: 1.
An exemplary GII VP1 is provided in GenBank Accession No. JX459908.1(GII.4 2012 Sydney strain), which is incorporated herein by reference and provided herein as SEQ ID NO: 29. The numbering used for the disclosed recombinant Norovirus GII VP1 proteins is relative to the Norovirus GII.4 VP1 protein sequence provided as SEQ ID NO: 29.
Norovirus Virus-Like Particle (VLP): A non-replicating genome-free viral shell formed from a self-assembly of Norovirus VP1 (capsid) proteins. The VP1 proteins in the VLP self assemble to form an icosahedral shaped structure including 180 VP1 proteins, organized into 90 dimers, and are about 38 nm in diameter. The icosahedral structure with T=3 symmetry, shows the characteristic 3-fold and 5-fold symmetry axes. The icosahedral asymmetric unit is made of three quasi-equivalent monomers termed A, B and C. (see
Nucleic Acid Molecule: A polymeric form of nucleotides, which may include both sense and anti-sense strands of RNA, cDNA, genomic DNA, and synthetic forms and mixed polymers of the above. A nucleotide refers to a ribonucleotide, deoxynucleotide or a modified form of either type of nucleotide. The term “nucleic acid molecule” as used herein is synonymous with “nucleic acid” and “polynucleotide.” A nucleic acid molecule is usually at least 10 bases in length, unless otherwise specified. The term includes single- and double-stranded forms of DNA. A polynucleotide may include either or both naturally occurring and modified nucleotides linked together by naturally occurring and/or non-naturally occurring nucleotide linkages. “cDNA” refers to a DNA that is complementary or identical to an mRNA, in either single stranded or double stranded form. “Encoding” refers to the inherent property of specific sequences of nucleotides in a polynucleotide, such as a gene, a cDNA, or an mRNA, to serve as templates for synthesis of other polymers and macromolecules in biological processes having either a defined sequence of nucleotides (i.e., rRNA, tRNA and mRNA) or a defined sequence of amino acids and the biological properties resulting therefrom.
Operably Linked: A first nucleic acid sequence is operably linked with a second nucleic acid sequence when the first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence. For instance, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. Generally, operably linked nucleic acid sequences are contiguous and, where necessary to join two protein-coding regions, in the same reading frame.
Pharmaceutically Acceptable Carriers: The pharmaceutically acceptable carriers of use are conventional. Remington's Pharmaceutical Sciences, by E. W. Martin, Mack Publishing Co., Easton, PA, 19th Edition, 1995, describes compositions and formulations suitable for pharmaceutical delivery of the disclosed immunogens.
In general, the nature of the carrier will depend on the particular mode of administration being employed. For instance, parenteral formulations usually comprise injectable fluids that include pharmaceutically and physiologically acceptable fluids such as water, physiological saline, balanced salt solutions, aqueous dextrose, glycerol or the like as a vehicle. For solid compositions (e.g., powder, pill, tablet, or capsule forms), conventional non-toxic solid carriers can include, for example, pharmaceutical grades of mannitol, lactose, starch, or magnesium stearate. In addition to biologically neutral carriers, pharmaceutical compositions (such as immunogenic compositions) to be administered can contain minor amounts of non-toxic auxiliary substances, such as wetting or emulsifying agents, preservatives, and pH buffering agents and the like, for example sodium acetate or sorbitan monolaurate. In particular embodiments, suitable for administration to a subject the carrier may be sterile, and/or suspended or otherwise contained in a unit dosage form containing one or more measured doses of the composition suitable to induce the desired immune response. It may also be accompanied by medications for its use for treatment purposes. The unit dosage form may be, for example, in a sealed vial that contains sterile contents or a syringe for injection into a subject, or lyophilized for subsequent solubilization and administration or in a solid or controlled release dosage.
Polypeptide: Any chain of amino acids, regardless of length or post-translational modification (e.g., glycosylation or phosphorylation). “Polypeptide” applies to amino acid polymers including naturally occurring amino acid polymers and non-naturally occurring amino acid polymer as well as in which one or more amino acid residue is a non-natural amino acid, for example, an artificial chemical mimetic of a corresponding naturally occurring amino acid. A “residue” refers to an amino acid or amino acid mimetic incorporated in a polypeptide by an amide bond or amide bond mimetic. A polypeptide has an amino terminal (N-terminal) end and a carboxy terminal (C-terminal) end. “Polypeptide” is used interchangeably with peptide or protein, and is used herein to refer to a polymer of amino acid residues.
Prime-Boost Vaccination: An immunotherapy including administration of a first immunogenic composition (the primary vaccine) followed by administration of a second immunogenic composition (the booster vaccine) to a subject to induce an immune response. The priming vaccine and/or the booster vaccine include a vector (such as a viral vector, RNA, or DNA vector) expressing the antigen to which the immune response is directed. The booster vaccine is administered to the subject after the priming vaccine; a suitable time interval between administration of the priming vaccine and the booster vaccine, and examples of such timeframes are disclosed herein. In some embodiments, the priming vaccine, the booster vaccine, or both primer vaccine and the booster vaccine additionally include an adjuvant. In one non-limiting example, the priming vaccine is a DNA-based vaccine (or other vaccine based on gene delivery), and the booster vaccine is a protein subunit or protein nanoparticle based vaccine.
Recombinant: A recombinant nucleic acid molecule is one that has a sequence that is not naturally occurring, for example, includes one or more nucleic acid substitutions, deletions or insertions, and/or has a sequence that is made by an artificial combination of two otherwise separated segments of sequence. This artificial combination can be accomplished by chemical synthesis or, more commonly, by the artificial manipulation of isolated segments of nucleic acids, for example, by genetic engineering techniques. A recombinant virus is one that includes a genome that includes a recombinant nucleic acid molecule. A recombinant protein is one that has a sequence that is not naturally occurring or has a sequence that is made by an artificial combination of two otherwise separated segments of sequence. In several embodiments, a recombinant protein is encoded by a heterologous (for example, recombinant) nucleic acid that has been introduced into a host cell, such as a bacterial or eukaryotic cell, or into the genome of a recombinant virus.
Sequence Identity: The similarity between amino acid sequences is expressed in terms of the similarity between the sequences, otherwise referred to as sequence identity. Sequence identity is frequently measured in terms of percentage identity; the higher the percentage, the more similar the two sequences are. Homologs, orthologs, or variants of a polypeptide will possess a relatively high degree of sequence identity when aligned using standard methods.
Methods of alignment of sequences for comparison are well known in the art. Various programs and alignment algorithms are described in: Smith & Waterman, Adv. Appl. Math. 2:482, 1981; Needleman & Wunsch, J. Mol. Biol. 48:443, 1970; Pearson & Lipman, Proc. Natl. Acad. Sci. USA 85:2444, 1988; Higgins & Sharp, Gene, 73:237-44, 1988; Higgins & Sharp, CABIOS 5:151-3, 1989; Corpet et al., Nuc. Acids Res. 16:10881-90, 1988; Huang et al. Computer Appls. in the Biosciences 8, 155-65, 1992; and Pearson et al., Meth. Mol. Bio. 24:307-31, 1994. Altschul et al., J. Mol. Biol. 215:403-10, 1990, presents a detailed consideration of sequence alignment methods and homology calculations.
Homologs and variants of a polypeptide (such as a Norovirus VP1 protein) are typically characterized by possession of at least about 75%, for example at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity counted over the full length alignment with the amino acid sequence of interest. Proteins with even greater similarity to the reference sequences will show increasing percentage identities when assessed by this method, such as at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity. When less than the entire sequence is being compared for sequence identity, homologs and variants will typically possess at least 80% sequence identity over short windows of 10-20 amino acids, and may possess sequence identities of at least 85% or at least 90% or 95% depending on their similarity to the reference sequence. Methods for determining sequence identity over such short windows are available at the NCBI website on the internet.
As used herein, reference to “at least 90% identity” or similar language refers to “at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or even 100% identity” to a specified reference sequence.
Subject: Living multi-cellular vertebrate organisms, a category that includes human and non-human mammals, such as non-human primates, pigs, camels, bats, sheep, cows, dogs, cats, rodents, and the like. In an example, a subject is a human. In a particular example, the subject is a human. In an additional example, a subject is selected that is in need of inhibiting a Norovirus infection. For example, the subject is either uninfected and at risk of the Norovirus infection or is infected and in need of treatment.
Vaccine: A pharmaceutical composition that induces a prophylactic or therapeutic immune response in a subject. In some cases, the immune response is a protective immune response. Typically, a vaccine induces an antigen-specific immune response to an antigen of a pathogen, for example a viral pathogen, or to a cellular constituent correlated with a pathological condition. A vaccine may include a polynucleotide (such as a nucleic acid encoding a disclosed antigen), a peptide or polypeptide (such as a disclosed Norovirus VP1 VLP), a virus, a cell or one or more cellular constituents. In a non-limiting example, a vaccine induces an immune response that reduces the severity of the symptoms associated with a Norovirus infection (such as a GI.1 or GII.4 Norovirus infection) and/or decreases the viral load compared to a control. In another non-limiting example, a vaccine induces an immune response that reduces and/or prevents a Norovirus infection (such as a GI.1 or GII.4 Norovirus infection) compared to a control.
Disclosed herein are embodiments of a recombinant Norovirus VLP comprising a multimer of a recombinant Norovirus VP1 proteins comprising one or more amino acid substitutions that stabilize the recombinant Norovirus VLP in its assembled form. The recombinant Norovirus VLPs provided herein elicit a superior immune response in an animal model compared to corresponding Norovirus VLPs that lack the stabilizing amino acid substitutions.
In some embodiments, the recombinant Norovirus VP1 VLP is composed of GI VP1 proteins as provided herein. Non-limiting examples of native Norovirus GI VP1 proteins that can be modified as described herein by incorporation of one or more amino acid substitutions that stabilize the recombinant Norovirus VLP in its assembled form include:
The amino acid numbering used herein for residues of the GI VP1 protein is with reference to the GI.1 VP1 sequence provided as SEQ ID NO: 1. With reference to the GI.1 VP1sequence provided as SEQ ID NO: 1, the shell (S) domain comprises residues 1-225, the Protruding domain (P) comprises residues 226-530) and is divided into sub-domains P1 (residues 226-278 (P1 subdomain 1) and 406-530 (P1 subdomain 2) and P2 (amino acids 279-405). The position numbering of the VP1 protein may vary between GI VP1 protein stains, but the sequences can be aligned to determine relevant structural domains and residues of interest.
In some embodiments, the recombinant Norovirus VP1 VLP composed of GI VP1 proteins comprises a self-assembly of 90 Norovirus VP1 dimers into an icosahedral shaped VLP. The diameter of the recombinant Norovirus VP1 VLP composed of GI VP1 proteins is from about 35 to about 45 nm in the T=3 symmetry, such as from about 38 to about 40 nm, for example, about 37 nm, about 38 nm, about 39 nm, or about 40 nm. Human Norovirus VLPs can also self-assemble in T=1 and T=4 configuration. T=1 VLPs contain 60 VP1 monomers and are about 23 nm in diameter, while T=4 VLPs have 240 VP1 monomers and are about 55 nm in diameter. In several embodiments, the recombinant Norovirus VP1 VLP composed of GI VP1 proteins does not comprise a VP2 protein and/or genetic material.
Modification of the GI VP1 proteins with the one or more amino acid substitutions as described herein increases the stability (such as maintaining the assembled icosahedral VLP structure) of the corresponding VLP in the assembled compared to VLPs formed from unmodified GI VP1 proteins. For example, recombinant VLPs formed from the recombinant GI VP1 proteins comprising the one or more amino acid substitutions as described herein have increased thermal stability (such as maintaining the assembled icosahedral VLP structure at increased temperature) compared to VLPs formed from unmodified GI VP1 proteins.
As described in the examples, VLPs formed from native Norovirus GI VP1 proteins are prone to disassembly and in the presence of certain antibodies, such as mAb1227, the disassembly may be accelerated. Accordingly, VLPs formed from the recombinant GI VP1 proteins as described herein have increased resistance to disassembly when incubated with mAb1227, for example at a 1:2 molar ratio (1 VP1: 2 Fab) for 1 hour at room temperature in phosphate buffered saline (PBS), compared to corresponding VLPs formed from native GI VP1 proteins.
In some embodiments, a recombinant Norovirus VLP comprising a multimer of a recombinant Norovirus GI VP1 proteins is provided. In some embodiments, the recombinant Norovirus GI VP1 proteins in the VLP comprise amino acid substitutions set forth as one or more of the following pairs of cysteine substitutions that form a non-natural interprotomer disulfide bond: N116C/G193C, A37C/A44C, Q62C/A140C, L144C/P221C, G131C/N172C, and N167C/L169C. Formation of the interprotomer disulfide bond stabilizes the VLP in its assembled form.
In additional embodiments, the recombinant Norovirus GI VP1 proteins in the VLP comprise amino acid substitutions set forth as one or more of the following pairs of hydrophobic amino acid substitutions: Q141V/P221L and A37I/A44L substitutions. The hydrophobic residues are proximate to one another between protomers of the assembled VLP, and form hydrophobic interactions that stabilize the VLP in its assembled form.
The recombinant Norovirus GI VP1 protein in the VLP can be selected from any GI VP1 protein, such as a GI.1, GI.2, GI.3, GI.4, GI.7, or GI.8 VP1 protein that comprises the one or more amino acid substitutions. In several embodiments, the recombinant Norovirus GI VP1 protein in the VLP is a GI.1 VP1 protein comprising the one or more amino acid substitutions.
In some embodiments, the recombinant Norovirus GI VP1 protein comprises one or more of the following pairs of cysteine substitutions that form a non-natural interprotomer disulfide bond: N116C/G193C, A37C/A44C, Q62C/A140C, L144C/P221C, G131C/N172C, and N167C/L169C, and an amino acid sequence at least 80% (such as at least 90%, at least 95%, or at least 99%) identical to any one of SEQ ID NOs: 1-6.
In some embodiments, the recombinant Norovirus GI VP1 protein comprises N116C/G193C substitutions that form a non-natural interprotomer disulfide bond, and an amino acid sequence at least 80% (such as at least 90%, at least 95%, or at least 99%) identical to any one of SEQ ID NOs: 1-6. In some embodiments, the recombinant Norovirus GI VP1 protein comprises N116C/G193C substitutions that form a non-natural interprotomer disulfide bond, and an amino acid sequence at least 80% (such as at least 90%, at least 95%, or at least 99%) identical to SEQ ID NO: 1. The non-natural interprotomer disulfide bond formed by the N116C/G193C substitutions is located at the interface between each A-A monomer pair around the 5-fold symmetry axes and between each B-C monomer pair around the 3-fold symmetry axes in the capsid.
In some embodiments, the recombinant Norovirus GI VP1 protein comprises A37C/A44C substitutions that form a non-natural interprotomer disulfide bond, and an amino acid sequence at least 80% (such as at least 90%, at least 95%, or at least 99%) identical to any one of SEQ ID NOs: 1-6. In some embodiments, the recombinant Norovirus GI VP1 protein comprises A37C/A44C substitutions that form a non-natural interprotomer disulfide bond, and an amino acid sequence at least 80% (such as at least 90%, at least 95%, or at least 99%) identical to SEQ ID NO: 1. The non-natural interprotomer disulfide bond formed by the A37C/A44C substitutions is located within the icosahedral asymmetric unit of the VLP and links monomers A-B, B-C, and C-A).
In some embodiments, the recombinant Norovirus GI VP1 protein comprises Q62C/A140C substitutions that form a non-natural interprotomer disulfide bond, and an amino acid sequence at least 80% (such as at least 90%, at least 95%, or at least 99%) identical to any one of SEQ ID NOs: 1-6. In some embodiments, the recombinant Norovirus GI VP1 protein comprises Q62C/A140C substitutions that form a non-natural interprotomer disulfide bond, and an amino acid sequence at least 80% (such as at least 90%, at least 95%, or at least 99%) identical to SEQ ID NO: 1. The non-natural interprotomer disulfide bond formed by the Q62C/A140C substitutions is located at the interface between each A-A monomer pair around the 5-fold symmetry axes and between each B-C monomer pair around the 3-fold symmetry axes in the capsid.
In some embodiments, the recombinant Norovirus GI VP1 protein comprises L144C/P221C substitutions that form a non-natural interprotomer disulfide bond, and an amino acid sequence at least 80% (such as at least 90%, at least 95%, or at least 99%) identical to any one of SEQ ID NOs: 1-6. In some embodiments, the recombinant Norovirus GI VP1 protein comprises L144C/P221C substitutions that form a non-natural interprotomer disulfide bond, and an amino acid sequence at least 80% (such as at least 90%, at least 95%, or at least 99%) identical to SEQ ID NO: 1. The non-natural interprotomer disulfide bond formed by the L144C/P221C substitutions is located at the interface between each A-A monomer pair around the 5-fold symmetry axes and between each B-C monomer pair around the 3-fold symmetry axes in the capsid.
In some embodiments, the recombinant Norovirus GI VP1 protein comprises G131C/N172C substitutions that form a non-natural interprotomer disulfide bond, and an amino acid sequence at least 80% (such as at least 90%, at least 95%, or at least 99%) identical to any one of SEQ ID NOs: 1-6. In some embodiments, the recombinant Norovirus GI VP1 protein comprises G131C/N172C substitutions that form a non-natural interprotomer disulfide bond, and an amino acid sequence at least 80% (such as at least 90%, at least 95%, or at least 99%) identical to SEQ ID NO: 1. The non-natural interprotomer disulfide bond formed by the G131C/N172C substitutions is located at the interface between each A-A monomer pair around the 5-fold symmetry axes and between each B-C monomer pair around the 3-fold symmetry axes in the capsid.
In some embodiments, the recombinant Norovirus GI VP1 protein comprises N167C/L169C substitutions that form a non-natural interprotomer disulfide bond, and an amino acid sequence at least 80% (such as at least 90%, at least 95%, or at least 99%) identical to any one of SEQ ID NOs: 1-6. In some embodiments, the recombinant Norovirus GI VP1 protein comprises N167C/L169C substitutions that form a non-natural interprotomer disulfide bond, and an amino acid sequence at least 80% (such as at least 90%, at least 95%, or at least 99%) identical to SEQ ID NO: 1. The non-natural interprotomer disulfide bond formed by the N167C/L169C substitutions is located at the interface between each A-A monomer pair around the 5-fold symmetry axes and between each B-C monomer pair around the 3-fold symmetry axes in the capsid.
In some embodiments, the recombinant Norovirus GI VP1 protein further comprises one or more additional amino acid substitutions that stabilize the assembly of the recombinant Norovirus GI VP1 proteins in the VLP.
Exemplary protein sequences of recombinant GI VP1 proteins containing the amino acid substitutions as described herein are provided below. Norovirus VLPs composed of these recombinant VP1 proteins have increased stability (such as increased thermal stability) compared to Norovirus VLPs composed of corresponding unmodified VP1 proteins
In some embodiments, the recombinant Norovirus VP1 VLP is composed of GII VP1 proteins as provided herein. Non-limiting examples of native Norovirus GII VP1 proteins that can be modified as described herein by incorporation of one or more amino acid substitutions that stabilize the recombinant Norovirus VLP in its assembled form include:
In some embodiments, the one or more amino acid substitutions that stabilize the recombinant Norovirus VLP in its assembled form are incorporated into a modified GII VP1 sequence that represents a consensus of the GII VP1 protein strains, such as the consensus GII.4 VP1 protein described in Para et al. (Vaccine, 2012; 30(24:3580-3586) and provided as: GII.4c VP1 sequence (GenBank Accession No. QEN95698.1) (SEQ ID NO: 51)
The amino acid numbering used herein for residues of the GII VP1 protein is with reference to the GII.4 VP1 sequence provided as SEQ ID NO: 29. With reference to the GII.4 VP1 sequence provided as SEQ ID NO: 29, the shell (S) domain comprises residues 1-221, the Protruding domain (P) comprises residues 222-540) and is divided into sub-domains P1 (residues 222-274 (P1 subdomain 1) and 406-540 (P1 subdomain 2) and P2 (residues 275-405). The position numbering of the VP1 protein may vary between GII VP1 protein stains, but the sequences can be aligned to determine relevant structural domains and residues of interest.
In some embodiments, the recombinant Norovirus VP1 VLP composed of GII VP1 proteins comprises a self-assembly of 90 Norovirus VP1 dimers into an icosahedral shaped VLP. The diameter of the recombinant Norovirus VP1 VLP composed of GII VP1 proteins is from about 35 to about 45 nm in the T=3 symmetry, such as from about 38 to about 40 nm, for example, about 37 nm, about 38 nm, about 39 nm, or about 40 nm. Human Norovirus VLPs can also self-assemble in T=1 and T=4 configuration. T=1 VLPs contain 60 VP1 monomers and are about 23 nm in diameter, while T=4 VLPs have 240 VP1 monomers and are about 55 nm in diameter. In several embodiments, the recombinant Norovirus VP1 VLP composed of GII VP1 proteins does not comprise a VP2 protein and/or genetic material.
Modification of the GII VP1 proteins with the one or more amino acid substitutions as described herein increases the stability (such as maintaining the assembled icosahedral VLP structure) of the corresponding VLP in the assembled compared to VLPs formed from unmodified GII VP1 proteins. For example, recombinant VLPs formed from the recombinant GII VP1 proteins comprising the one or more amino acid substitutions as described herein have increased thermal stability (such as maintaining the assembled icosahedral VLP structure at increased temperature) compared to VLPs formed from unmodified GII VP1 proteins.
As described in the examples, VLPs formed from native Norovirus I VP1 proteins are prone to disassembly in the presence of certain antibodies, such as mAb1227. Accordingly, VLPs formed from the recombinant GII VP1 proteins as described herein have increased resistance to disassembly when incubated with mAb1227, for example at 1:2 molar ratio (1 VP1: 2 Fab) for 1 hour at room temperature in PBS, compared to corresponding VLPs formed from native GII VP1 proteins.
In some embodiments, a recombinant Norovirus VLP comprising a multimer of a recombinant Norovirus GII VP1 proteins is provided. In some embodiments, the recombinant Norovirus GII VP1 proteins in the VLP comprise amino acid substitutions set forth as one or more of the following pairs of cysteine substitutions that form a non-natural interprotomer disulfide bond: N112C/A116C, N189C/D194C, S134C/P60C, M140C/P217C, and P129C/R223C. Formation of the interprotomer disulfide bond stabilizes the VLP in its assembled form.
The recombinant Norovirus GI VP1 protein in the VLP can be selected from any GI VP1 protein, such as a GII.1, GII.2, GII.3, GII.4, GII.4c, GII.5, GII.6, GII.7, GII.8, GII.9, GII.10, GII.11, GII.12, GII.13, GII.14, GII.15, GII.16, GII.17, GII.18, GII.19, GII.20, GII.21, GII.22, GII.23, GII.24, or GII.25 VP1 protein that comprises the one or more amino acid substitutions. In several embodiments, the recombinant Norovirus GII VP1 protein in the VLP is a GII.4c VP1 protein comprising the one or more amino acid substitutions.
In some embodiments, the recombinant Norovirus GII VP1 protein comprises one or more of the following pairs of cysteine substitutions that form a non-natural interprotomer disulfide bond: N112C/A116C, N189C/D194C, S134C/P60C, M140C/P217C, and P129C/R223C, and an amino acid sequence at least 80% (such as at least 90%, at least 95%, or at least 99%) identical to any one of SEQ ID NOs: 26-51.
In some embodiments, the recombinant Norovirus GII VP1 protein comprises N112C/A116C substitutions that form a non-natural interprotomer disulfide bond, and an amino acid sequence at least 80% (such as at least 90%, at least 95%, or at least 99%) identical to any one of SEQ ID NOs: 26-51. In some embodiments, the recombinant Norovirus GII VP1 protein comprises N112C/A116C substitutions that form a non-natural interprotomer disulfide bond, and an amino acid sequence at least 80% (such as at least 90%, at least 95%, or at least 99%) identical to SEQ ID NO: 51. The non-natural interprotomer disulfide bond formed by the N112C/A116C substitutions is located at the interface between each A-A monomer pair around the 5-fold symmetry axes and between each B-C monomer pair around the 3-fold symmetry axes in the capsid.
In some embodiments, the recombinant Norovirus GII VP1 protein comprises N189C/D194C substitutions that form a non-natural interprotomer disulfide bond, and an amino acid sequence at least 80% (such as at least 90%, at least 95%, or at least 99%) identical to any one of SEQ ID NOs: 26-51. In some embodiments, the recombinant Norovirus GII VP1 protein comprises N189C/D194C substitutions that form a non-natural interprotomer disulfide bond, and an amino acid sequence at least 80% (such as at least 90%, at least 95%, or at least 99%) identical to SEQ ID NO: 51. The non-natural interprotomer disulfide bond formed by the N189C/D194C substitutions located at the interface between each A-A monomer pair around the 5-fold symmetry axes and between each B-C monomer pair around the 3-fold symmetry axes in the capsid.
In some embodiments, the recombinant Norovirus GII VP1 protein comprises S134C/P60C substitutions that form a non-natural interprotomer disulfide bond, and an amino acid sequence at least 80% (such as at least 90%, at least 95%, or at least 99%) identical to any one of SEQ ID NOs: 26-51. In some embodiments, the recombinant Norovirus GII VP1 protein comprises S134C/P60C substitutions that form a non-natural interprotomer disulfide bond, and an amino acid sequence at least 80% (such as at least 90%, at least 95%, or at least 99%) identical to SEQ ID NO: 51. The non-natural interprotomer disulfide bond formed by the S134C/P60C substitutions is located at the interface between each A-A monomer pair around the 5-fold symmetry axes and between each B-C monomer pair around the 3-fold symmetry axes in the capsid.
In some embodiments, the recombinant Norovirus GII VP1 protein comprises M140C/P217C substitutions that form a non-natural interprotomer disulfide bond, and an amino acid sequence at least 80% (such as at least 90%, at least 95%, or at least 99%) identical to any one of SEQ ID NOs: 26-51. In some embodiments, the recombinant Norovirus GII VP1 protein comprises M140C/P217C substitutions that form a non-natural interprotomer disulfide bond, and an amino acid sequence at least 80% (such as at least 90%, at least 95%, or at least 99%) identical to SEQ ID NO: 51. The non-natural interprotomer disulfide bond formed by the M140C/P217C substitutions is located within the icosahedral asymmetric unit of the VLP and links monomers A-B, B-C, and C-A).
In some embodiments, the recombinant Norovirus GII VP1 protein comprises P129C/R223C substitutions that form a non-natural interprotomer disulfide bond, and an amino acid sequence at least 80% (such as at least 90%, at least 95%, or at least 99%) identical to any one of SEQ ID NOs: 26-51. In some embodiments, the recombinant Norovirus GII VP1 protein comprises P129C/R223C substitutions that form a non-natural interprotomer disulfide bond, and an amino acid sequence at least 80% (such as at least 90%, at least 95%, or at least 99%) identical to SEQ ID NO: 51. The non-natural interprotomer disulfide bond formed by the P129C/R223C substitutions is located within the icosahedral asymmetric unit of the VLP and links monomers A-B, B-C, and C-A).
In some embodiments, the recombinant Norovirus GII VP1 protein further comprises one or more additional amino acid substitutions that stabilize the assembly of the recombinant Norovirus GII VP1 proteins in the VLP.
Exemplary protein sequences of recombinant GII VP1 proteins containing the amino acid substitutions as described herein are provided below. Norovirus VLPs composed of these recombinant VP1 proteins have increased stability (such as increased thermal stability) compared to Norovirus VLPs composed of corresponding unmodified VP1 proteins:
Analogs and variants of the recombinant Norovirus VP1 protein may be used in the methods and systems of the present disclosure. Through the use of recombinant DNA technology, variants of the recombinant Norovirus VP1 protein may be prepared by altering the underlying DNA. All such variations or alterations in the structure of the recombinant Norovirus VP1 protein resulting in variants are included within the scope of this disclosure. Such variants include insertions, substitutions, or deletions of one or more amino acid residues, glycosylation variants, unglycosylated recombinant Norovirus VP1 protein, organic and inorganic salts, covalently modified derivatives of the recombinant Norovirus VP1 protein, or a precursor thereof. Such variants may maintain one or more of the functional, biological activities of the recombinant Norovirus VP1 protein, such as binding to cell surface receptor. The recombinant Norovirus VP1 protein thereof can be modified, for example, by PEGylation, to increase the half-life of the protein in the recipient, to retard clearance from the pericardial space, and/or to make the protein more stable for delivery to a subject.
In some embodiments, a recombinant Norovirus VP1 protein useful within the disclosure is modified by replacement of one or more naturally occurring side chains of the 20 genetically encoded amino acids (or D-amino acids) with other side chains, for example with groups such as alkyl, lower alkyl, cyclic 4-, 5-, 6-, to 7-membered alkyl, amide, amide lower alkyl, amide di(lower alkyl), lower alkoxy, hydroxy, carboxy and the lower ester derivatives thereof, and with 4-, 5-, 6-, to 7-membered heterocyclics. For example, proline analogs can be made in which the ring size of the proline residue is changed from a 5-membered ring to a 4-, 6-, or 7-membered ring. Cyclic groups can be saturated or unsaturated, and if unsaturated, can be aromatic or non-aromatic. Heterocyclic groups can contain one or more nitrogen, oxygen, and/or sulphur heteroatoms. Examples of such groups include furazanyl, furyl, imidazolidinyl, imidazolyl, imidazolinyl, isothiazolyl, isoxazolyl, morpholinyl (e.g., morpholino), oxazolyl, piperazinyl (e.g., 1-piperazinyl), piperidyl (e.g., 1-piperidyl, piperidino), pyranyl, pyrazinyl, pyrazolidinyl, pyrazolinyl, pyrazolyl, pyridazinyl, pyridyl, pyrimidinyl, pyrrolidinyl (e.g., 1-pyrrolidinyl), pyrrolinyl, pyrrolyl, thiadiazolyl, thiazolyl, thienyl, thiomorpholinyl (e.g., thiomorpholino), and triazolyl groups. These heterocyclic groups can be substituted or unsubstituted. Where a group is substituted, the substituent can be alkyl, alkoxy, halogen, oxygen, or substituted or unsubstituted phenyl. Peptides, as well as peptide analogs and mimetics, can also be covalently bound to one or more of a variety of nonproteinaceous polymers, for example, polyethylene glycol, polypropylene glycol, or polyoxyalkenes, as described in U.S. Pat. Nos. 4,640,835; 4,496,668; 4,301,144; 4,668,417; 4,791,192; and 4,179,337.
Polynucleotides encoding a recombinant VP1 protein of any of the disclosed recombinant Norovirus VLPs are also provided. These polynucleotides include DNA, cDNA and RNA sequences which encode the recombinant VP1 protein, as well as vectors including the DNA, cDNA and RNA sequences. The genetic code to construct a variety of functionally equivalent nucleic acids, such as nucleic acids which differ in sequence but which encode the same protein sequence, or encode a conjugate or fusion protein including the nucleic acid sequence.
Exemplary nucleic acids can be prepared by cloning techniques. Examples of appropriate cloning and sequencing techniques, and instructions sufficient to direct persons of skill through many cloning exercises are known (see, e.g., Sambrook et al. (Molecular Cloning: A Laboratory Manual, 4th ed, Cold Spring Harbor, New York, 2012) and Ausubel et al. (In Current Protocols in Molecular Biology, John Wiley & Sons, New York, through supplement 104, 2013).
Nucleic acids can also be prepared by amplification methods Amplification methods include polymerase chain reaction (PCR), the ligase chain reaction (LCR), the transcription-based amplification system (TAS), the self-sustained sequence replication system (3SR). A wide variety of cloning methods, host cells, and in vitro amplification methodologies are well known to persons of skill.
The polynucleotides encoding a disclosed recombinant Norovirus VP1 protein can include a recombinant DNA which is incorporated into a vector (such as an expression vector) into an autonomously replicating plasmid or virus or into the genomic DNA of a prokaryote or eukaryote, or which exists as a separate molecule (such as a cDNA) independent of other sequences. The nucleotides can be ribonucleotides, deoxyribonucleotides, or modified forms of either nucleotide. The term includes single and double forms of DNA.
Polynucleotide sequences encoding a disclosed recombinant Norovirus VP1 protein can be operatively linked to expression control sequences. An expression control sequence operatively linked to a coding sequence is ligated such that expression of the coding sequence is achieved under conditions compatible with the expression control sequences. The expression control sequences include, but are not limited to, appropriate promoters, enhancers, transcription terminators, a start codon (i.e., ATG) in front of a protein-encoding gene, splicing signal for introns, maintenance of the correct reading frame of that gene to permit proper translation of mRNA, and stop codons.
DNA sequences encoding the disclosed recombinant VP1 protein can be expressed in vitro by DNA transfer into a suitable host cell. The cell may be prokaryotic or eukaryotic. The term also includes any progeny of the subject host cell. It is understood that all progeny may not be identical to the parental cell since there may be mutations that occur during replication. Methods of stable transfer, meaning that the foreign DNA is continuously maintained in the host, are known in the art.
Hosts can include microbial, yeast, insect and mammalian organisms. Methods of expressing DNA sequences having eukaryotic or viral sequences in prokaryotes are well known in the art. Non-limiting examples of suitable host cells include bacteria, archea, insect, fungi (for example, yeast), plant, and animal cells (for example, mammalian cells, such as human). Exemplary cells of use include Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Salmonella typhimurium, SF9 cells, C129 cells, 293 cells, Neurospora, and immortalized mammalian myeloid and lymphoid cell lines. Techniques for the propagation of mammalian cells in culture are well-known (see, e.g., Helgason and Miller (Eds.), 2012, Basic Cell Culture Protocols (Methods in Molecular Biology), 4th Ed., Humana Press). Examples of commonly used mammalian host cell lines are VERO and HeLa cells, CHO cells, and WI38, BHK, and COS cell lines, although cell lines may be used, such as cells designed to provide higher expression, desirable glycosylation patterns, or other features. In some embodiments, the host cells include HEK293 cells or derivatives thereof, such as GnTI−/31 cells (ATCC® No. CRL-3022), or HEK-293F cells.
Transformation of a host cell with recombinant DNA can be carried out by conventional techniques. Where the host is prokaryotic, such as, but not limited to, E. coli, competent cells which are capable of DNA uptake can be prepared from cells harvested after exponential growth phase and subsequently treated by the CaCl2 method using standard procedures. Alternatively, MgCl2 or RbCl can be used. Transformation can also be performed after forming a protoplast of the host cell if desired, or by electroporation.
When the host is a eukaryote, such methods of transfection of DNA as calcium phosphate coprecipitates, conventional mechanical procedures such as microinjection, electroporation, insertion of a plasmid encased in liposomes, or viral vectors can be used. Eukaryotic cells can also be co-transformed with polynucleotide sequences encoding a disclosed antigen, and a second foreign DNA molecule encoding a selectable phenotype, such as the herpes simplex thymidine kinase gene. Another method is to use a eukaryotic viral vector, such as simian virus 40 (SV40) or bovine papilloma virus, to transiently infect or transform eukaryotic cells and express the protein (see for example, Viral Expression Vectors, Springer press, Muzyczka ed., 2011). Appropriate expression systems such as plasmids and vectors of use in producing proteins in cells including higher eukaryotic cells such as the COS, CHO, HeLa and myeloma cell lines.
Modifications can be made to a nucleic acid encoding a disclosed recombinant Norovirus VP1 protein without diminishing its biological activity. Some modifications can be made to facilitate the cloning, expression, or incorporation of the targeting molecule into a fusion protein. Such modifications are well known to those of skill in the art and include, for example, termination codons, a methionine added at the amino terminus to provide an initiation, site, additional amino acids placed on either terminus to create conveniently located restriction sites, or additional amino acids (such as poly His) to aid in purification steps.
In some embodiments, the disclosed recombinant Norovirus VP1 protein can be expressed in cells under conditions where the recombinant Norovirus VP1 protein self-assembles into VLPs which are secreted from the cells into the cell media, such as described in the examples. The medium can be centrifuged and the recombinant Norovirus VLPs purified from the supernatant.
The presence of Norovirus VLPs following recombinant expression of viral proteins can be detected using any suitable techniques, such as by electron microscopy, biophysical characterization, dynamic light scattering (DLS), selective chromatographic separation (e.g., ion exchange, hydrophobic interaction, and/or size exclusion chromatographic separation of the VLPs) and density gradient centrifugation. Further, Norovirus VLPs can be isolated by any suitable technique, such as density gradient centrifugation and identified by characteristic density banding.
Immunogenic compositions comprising one or more of the disclosed recombinant Norovirus VLPs and a pharmaceutically acceptable carrier are also provided. Such pharmaceutical compositions can be administered to subjects by a variety of administration modes known to the person of ordinary skill in the art, for example, intramuscular, intradermal, subcutaneous, intravenous, intra-arterial, intra-articular, intraperitoneal, intranasal, sublingual, tonsillar, oropharyngeal, or other parenteral and mucosal routes. In several embodiments, pharmaceutical compositions including one or more of the disclosed immunogens are immunogenic compositions. Actual methods for preparing administrable compositions will be known or apparent to those skilled in the art and are described in more detail in such publications as Remingtons Pharmaceutical Sciences, 19th Ed., Mack Publishing Company, Easton, Pennsylvania, 1995.
Thus, an immunogen described herein can be formulated with pharmaceutically acceptable carriers to help retain biological activity while also promoting increased stability during storage within an acceptable temperature range. Potential carriers include, but are not limited to, physiologically balanced culture medium, phosphate buffer saline solution, water, emulsions (e.g., oil/water or water/oil emulsions), various types of wetting agents, cryoprotective additives or stabilizers such as proteins, peptides or hydrolysates (e.g., albumin, gelatin), sugars (e.g., sucrose, lactose, sorbitol), amino acids (e.g., sodium glutamate), or other protective agents. The resulting aqueous solutions may be packaged for use as is or lyophilized. Lyophilized preparations are combined with a sterile solution prior to administration for either single or multiple dosing.
Formulated compositions, especially liquid formulations, may contain a bacteriostat to prevent or minimize degradation during storage, including but not limited to effective concentrations (usually ≤1% w/v) of benzyl alcohol, phenol, m-cresol, chlorobutanol, methylparaben, and/or propylparaben. A bacteriostat may be contraindicated for some patients; therefore, a lyophilized formulation may be reconstituted in a solution either containing or not containing such a component.
The immunogenic compositions of the disclosure can contain as pharmaceutically acceptable vehicles substances as required to approximate physiological conditions, such as pH adjusting and buffering agents, tonicity adjusting agents, wetting agents and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, and triethanolamine oleate.
The immunogenic composition may optionally include an adjuvant to enhance an immune response of the host. Suitable adjuvants are, for example, toll-like receptor agonists, alum, AlPO4, alhydrogel, Lipid-A and derivatives or variants thereof, oil-emulsions, saponins, neutral liposomes, liposomes containing the vaccine and cytokines, non-ionic block copolymers, and chemokines. Non-ionic block polymers containing polyoxyethylene (POE) and polyxylpropylene (POP), such as POE-POP-POE block copolymers, MPL™ (3-O-deacylated monophosphoryl lipid A; Corixa, Hamilton, IN) and IL-12 (Genetics Institute, Cambridge, MA), among many other suitable adjuvants well known in the art, may be used as an adjuvant (Newman et al., 1998, Critical Reviews in Therapeutic Drug Carrier Systems 15:89-142). These adjuvants have the advantage in that they help to stimulate the immune system in a non-specific way, thus enhancing the immune response to a pharmaceutical product.
In some instances it may be desirable to combine a disclosed immunogen with other pharmaceutical products (e.g., vaccines) which induce protective responses to other agents. For example, a composition including a recombinant Norovirus VLP as described herein can be administered simultaneously (typically separately) or sequentially with other vaccines recommended by the Advisory Committee on Immunization Practices (ACIP; cdc.gov/vaccines/acip/index.html) for the targeted age group (e.g., infants from approximately one to six months of age), such as an influenza vaccine or a varicella zoster vaccine. As such, a disclosed immunogen including a recombinant Norovirus VLP as described herein may be administered simultaneously or sequentially with vaccines against, for example, hepatitis B (HepB), diphtheria, tetanus and pertussis (DTaP), pneumococcal bacteria (PCV), Haemophilus influenzae type b (Hib), polio, influenza and rotavirus.
In some embodiments, the composition can be provided as a sterile composition. The pharmaceutical composition typically contains an effective amount of a disclosed immunogen and can be prepared by conventional techniques. Typically, the amount of immunogen in each dose of the immunogenic composition is selected as an amount which induces an immune response without significant, adverse side effects. In some embodiments, the composition can be provided in unit dosage form for use to induce an immune response in a subject. A unit dosage form contains a suitable single preselected dosage for administration to a subject, or suitable marked or measured multiples of two or more preselected unit dosages, and/or a metering mechanism for administering the unit dose or multiples thereof. In other embodiments, the composition further includes an adjuvant.
The disclosed recombinant Norovirus VLPs can be administered to a subject to induce an immune response to the VP1 protein of the recombinant Norovirus VLP in the subject. In a particular example, the subject is a human The immune response can be a protective immune response, for example a response that inhibits subsequent infection with Norovirus. Elicitation of the immune response can also be used to treat or inhibit Norovirus infection and illnesses associated with the Norovirus infection.
A subject can be selected for treatment that has or is at risk for developing Norovirus infection, for example because of exposure or the possibility of exposure to the Norovirus. Following administration of a disclosed immunogen, the subject can be monitored for infection or symptoms associated with Norovirus infection.
Typical subjects intended for treatment with the therapeutics and methods of the present disclosure include humans, as well as non-human primates and other animals. To identify subjects for prophylaxis or treatment according to the methods of the disclosure, accepted screening methods are employed to determine risk factors associated with a targeted or suspected disease or condition, or to determine the status of an existing disease or condition in a subject. These screening methods include, for example, conventional work-ups to determine environmental, familial, occupational, and other such risk factors that may be associated with the targeted or suspected disease or condition, as well as diagnostic methods, such as various ELISA and other immunoassay methods to detect and/or characterize Norovirus infection. These and other routine methods allow the clinician to select patients in need of therapy using the methods and pharmaceutical compositions of the disclosure. In accordance with these methods and principles, a composition can be administered according to the teachings herein, or other conventional methods, as an independent prophylaxis or treatment program, or as a follow-up, adjunct or coordinate treatment regimen to other treatments.
The administration of a disclosed immunogen can be for prophylactic or therapeutic purpose. When provided prophylactically, the immunogen is provided in advance of any symptom, for example, in advance of infection. The prophylactic administration of the immunogen serves to prevent or ameliorate any subsequent infection. When provided therapeutically, the immunogen is provided at or after the onset of a symptom of infection, for example, after development of a symptom of Norovirus infection or after diagnosis with the Norovirus infection. The immunogen can thus be provided prior to the anticipated exposure to the Norovirus so as to attenuate the anticipated severity, duration or extent of an infection and/or associated disease symptoms, after exposure or suspected exposure to the Norovirus, or after the actual initiation of an infection.
The immunogens described herein, and immunogenic compositions thereof, are provided to a subject in an amount effective to induce or enhance an immune response against the recombinant VP1 protein in the Norovirus VLP in the subject, preferably a human. The actual dosage of disclosed immunogen will vary according to factors such as the disease indication and particular status of the subject (for example, the subject's age, size, fitness, extent of symptoms, susceptibility factors, and the like), time and route of administration, other drugs or treatments being administered concurrently, as well as the specific pharmacology of the composition for eliciting the desired activity or biological response in the subject. Dosage regimens can be adjusted to provide an optimum prophylactic or therapeutic response.
An immunogenic composition including one or more of the disclosed immunogens can be used in coordinate (or prime-boost) vaccination protocols or combinatorial formulations. In certain embodiments, novel combinatorial immunogenic compositions and coordinate immunization protocols employ separate immunogens or formulations, each directed toward eliciting an anti-viral immune response, such as an immune response to Norovirus VP1 protein. Separate immunogenic compositions that elicit the anti-viral immune response can be combined in a polyvalent immunogenic composition administered to a subject in a single immunization step, or they can be administered separately (in monovalent immunogenic compositions) in a coordinate (or prime-boost) immunization protocol.
There can be several boosts, and each boost can be a different disclosed immunogen. In some examples that the boost may be the same immunogen as another boost, or the prime. The prime and boost can be administered as a single dose or multiple doses, for example two doses, three doses, four doses, five doses, six doses or more can be administered to a subject over days, weeks or months. Multiple boosts can also be given, such one to five (e.g., 1, 2, 3, 4 or 5 boosts), or more. Different dosages can be used in a series of sequential immunizations. For example a relatively large dose in a primary immunization and then a boost with relatively smaller doses.
In some embodiments, the boost can be administered about two, about three to eight, or about four, weeks following the prime, or about several months after the prime. In some embodiments, the boost can be administered about 5, about 6, about 7, about 8, about 10, about 12, about 18, about 24, months after the prime, or more or less time after the prime. Periodic additional boosts can also be used at appropriate time points to enhance the subject's “immune memory.” The adequacy of the vaccination parameters chosen, e.g., formulation, dose, regimen and the like, can be determined by taking aliquots of serum from the subject and assaying antibody titers during the course of the immunization program. In addition, the clinical condition of the subject can be monitored for the desired effect, e.g., prevention of infection or improvement in disease state (e.g., reduction in viral load). If such monitoring indicates that vaccination is sub-optimal, the subject can be boosted with an additional dose of immunogenic composition, and the vaccination parameters can be modified in a fashion expected to potentiate the immune response.
In some embodiments, the prime-boost method can include DNA-primer and protein-boost vaccination protocol to a subject. The method can include two or more administrations of the nucleic acid molecule or the protein.
For protein therapeutics, typically, each human dose will comprise 1-1000 μg of protein, such as from about 1 μg to about 100 μg, for example, from about 1 μg to about 50 μg, such as about 1 μg, about 2 μg, about 5 μg, about 10 μg, about 15 μg, about 20 μg, about 25 μg, about 30 μg, about 40 μg, or about 50 μg.
In some embodiments, the recombinant Norovirus VLP is administered at a dose of 100 □g. In some embodiments, the does includes 100 □g of a first recombinant Norovirus VLP formed from GI.1 VP1 Proteins and 100 □g of a second recombinant Norovirus VLP formed from GII.4 VP1 proteins.
The amount utilized in an immunogenic composition is selected based on the subject population (e.g., infant or elderly). An optimal amount for a particular composition can be ascertained by standard studies involving observation of antibody titers and other responses in subjects. It is understood that a therapeutically effective amount of a disclosed immunogen, such as a disclosed recombinant Norovirus VLP, can include an amount that is ineffective at eliciting an immune response by administration of a single dose, but that is effective upon administration of multiple dosages, for example in a prime-boost administration protocol.
Upon administration of an immunogenic composition comprising a disclosed recombinant Norovirus VLP of this disclosure, the immune system of the subject typically responds to the immunogenic composition by producing antibodies specific for the recombinant Norovirus VLP included in the composition. Such a response signifies that an immunologically effective dose was delivered to the subject.
In some embodiments, the antibody response of a subject will be determined in the context of evaluating effective dosages/immunization protocols. In most instances it will be sufficient to assess the antibody titer in serum or plasma obtained from the subject. Decisions as to whether to administer booster inoculations and/or to change the amount of the therapeutic agent administered to the individual can be at least partially based on the antibody titer level. The antibody titer level can be based on, for example, an immunobinding assay which measures the concentration of antibodies in the serum which bind to an antigen including, for example, the recombinant Norovirus VLP included in the immunogenic composition.
Norovirus infection does not need to be completely eliminated or reduced or prevented for the methods to be effective. For example, elicitation of an immune response to the recombinant Norovirus VLP can reduce or inhibit Norovirus infection by a desired amount, for example, by at least 10%, at least 20%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or even at least 100% (elimination or prevention of detectable infected cells), as compared to Norovirus infection in the absence of the immunogen. In additional examples, Norovirus replication can be reduced or inhibited by the disclosed methods. Norovirus replication does not need to be completely eliminated for the method to be effective. For example, the immune response elicited using one or more of the disclosed immunogens can reduce Norovirus replication by a desired amount, for example, by at least 10%, at least 20%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or even at least 100% (elimination or prevention of detectable Norovirus replication, as compared to Norovirus replication in the absence of the immune response.
In some embodiments, the disclosed immunogen is administered to the subject simultaneously with the administration of the adjuvant. In other embodiments, the disclosed immunogen is administered to the subject after the administration of the adjuvant and within a sufficient amount of time to induce the immune response.
In some embodiments, administration of a therapeutically effective amount of one or more of the disclosed immunogens to a subject induces a neutralizing immune response in the subject. To assess neutralization activity, following immunization of a subject, serum can be collected from the subject at appropriate time points, frozen, and stored for neutralization testing. Methods to assay for neutralization activity include, but are not limited to, plaque reduction neutralization (PRNT) assays, microneutralization assays, flow cytometry based assays, single-cycle infection assays.
Methods are also provided for the detection of the presence of an antibody that specifically binds to a solvent-accessible epitope on a Norovirus VLP. In one example, the presence of an antibody that specifically binds to a solvent-accessible epitope on a stabilized Norovirus VLP as provided herein is detected in a biological sample from a subject and can be used to identify a subject with a neutralizing antibody response to Norovirus. The sample can be any sample, including, but not limited to, tissue from biopsies, autopsies, and pathology specimens. Biological samples also include sections of tissues, for example, frozen sections taken for histological purposes. Biological samples further include body fluids, such as blood, serum, plasma, sputum, spinal fluid or urine. The method of detection can include contacting a sample with a stabilized Norovirus VLP as described herein, or conjugate thereof under conditions sufficient to form an immune complex, and detecting the immune complex (e.g., by detecting a detectable marker conjugated to a secondary antibody that binds to antibodies in the biological sample).
In one embodiment, a method for identifying an antibody that specifically binds to a solvent-accessible epitope on a Norovirus VLP is provided. A stabilized Norovirus VLP as provided herein contacted with a test antibody under conditions sufficient to form an immune complex. Detecting the presence of the immune complex identifies that the test antibody specifically binds to a solvent-accessible epitope on the Norovirus VLP. Contacting the test antibody with the stabilized norovirus VLP, and detecting the presence of the immune complex, can be accomplished using any suitable means. In some embodiments, the stabilized Norovirus VLP is fixed to a solid support and contacted with the test antibody (the primary antibody). The primary antibody is unlabeled and a secondary antibody or other molecule that can bind the primary antibody is utilized for detection. The secondary antibody is chosen that is able to specifically bind the specific species and class of the primary antibody. For example, if the first antibody is a human IgG, then the secondary antibody may be an anti-human-IgG. Other molecules that can bind to antibodies include, without limitation, Protein A and Protein G, both of which are available commercially. Suitable labels for the antibody, antigen binding fragment or secondary antibody are known and described above, and include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, magnetic agents and radioactive materials.
In another embodiment, identifying a sample from a subject with a neutralizing antibody response to Norovirus is provided (for example, to confirm that the subject produced a neutralizing antibody response following vaccination). A stabilized Norovirus VLP as provided herein contacted with a biological sample comprising antibodies from a test subject under conditions sufficient to form an immune complex. Detecting the presence of the immune complex identifies the sample as from a subject with a neutralizing antibody response to Norovirus. Contacting the biological sample with the stabilized norovirus VLP, and detecting the presence of the immune complex, can be accomplished using any suitable means. In some embodiments, the stabilized Norovirus VLP is fixed to a solid support and contacted with the biological sample contacting antibodies (the primary antibodies). The primary antibodies are unlabeled and can be detected as noted above.
The following examples are provided to illustrate particular features of certain embodiments, but the scope of the claims should not be limited to those features exemplified.
This example shows that norovirus GI.1 VLPs are unstable and contain a substantial fraction of dissociated VLP components. Broadly reactive, non-neutralizing antibodies isolated from vaccinated donors bound to the dissociated particles, but not the intact VLPs. Engineering inter-protomer disulfide bonds within the shell domain prevented disassembly of the VLPs while preserving antibody accessibility to neutralizing epitopes. Mice immunized with stabilized GI.1 VLPs without adjuvant developed faster blockade antibody titers compared to wild-type GI.1 VLPs. Additionally, immunization with stabilized particles focused immune responses toward surface exposed epitopes and away from occluded epitopes. Thus, the recombinant Norovirus VLPs elicit a superior immune response in an animal model compared to VLPs formed from unmodified VP1 proteins.
Noroviruses are single-stranded RNA viruses that cause pandemic outbreaks of acute gastroenteritis1. They are the major viral agents of food-borne diseases worldwide and they are responsible for more than 200,000 deaths per year (mostly among infants and elderly in developing countries)2. Due to high infectivity, noroviruses are also a significant threat to transplant patients and immunocompromised individuals3,4. Although discovered over 50 years ago, no vaccine nor drugs (antibodies or small molecules) are currently licensed to prevent or treat norovirus infections5.
In the absence of a widely available tissue-culture system that can sustain replication of human noroviruses, virus-like particles have been used as a surrogate to study the structural features of the capsid and as immunogens to elicit protective humoral responses6-8. Recently, VLPs have emerged as valuable immunogens for the elicitation of durable protective serological memory9,10. The most advanced norovirus vaccine candidate to date is a bivalent formulation comprising a mixture of GI.1 and GII.4 VLPs, administered intramuscularly11-13. Results from phase IIb clinical trials have revealed that the vaccine is highly immunogenic and can elicit high titers of blockade antibodies11,14. However, the vaccine is less than 50% protective against GI.1 challenge and, at least for GII.4, serum blockade titers wane rapidly following immunization15,16. In a recent study, ten antibodies were isolated from three donors after immunization with the bivalent vaccine17. The antibodies could be classified into two broad classes: 1) cross-reactive (capable of binding VLPs from genogroups I and II), but non-neutralizing and 2) genotype-specific (only targeting GII.4 variants) and neutralizing. Structural analysis of the antibody Fab fragments in complex with the P domain of GII.4 (2002 Farmington Hills strain) revealed cross GI-GII reactive antibodies to target a site on the P domain that would be completely buried in the context of the intact viral particle17. Similar antibodies (herein referred to as occluded-site antibodies) have been previously observed after immunization with norovirus VLPs in mice18-20. Two questions arise: how can such antibodies be elicited, and can vaccine performance be improved by preventing their elicitation? To shed light on these issues, we investigated the interaction between GI.1 norovirus VLPs and one antibody belonging to each class. First, we observed that GI.1 VLP preparations contained dissociated VP1 components even after extensive purification, with a substantial amount of VP1 dimers. The cross-reactive, but non-neutralizing, antibody A1227 bound strongly to VP1 dimers, but not to the intact particles, while the GI.1 specific and blockade antibody 512 could bind to VP1 dimers as well as to intact particles. Structure-based design of interprotomer disulfide bonds resulted in GI.1 VLPs that did not dissociate and did not bind occluded-site antibodies. Crucially, stabilization did not compromise accessibility to known neutralizing epitopes. Finally, immunization with stabilized VLPs elicited blockade titers more rapidly and appeared to focus the immune responses toward accessible (and potentially neutralizing) epitopes. Together, the data suggest interprotomer disulfide stabilization as an avenue to improve VLP-based norovirus vaccines.
GI.1 norovirus VLP preparations contain VP1 dimers and other oligomers that expose occluded-site epitopes. Serological analysis of antibody repertoires from humans vaccinated with a cocktail of GI.1 and GII.4 norovirus VLPs has identified broadly reactive, but non-neutralizing antibodies17. Binding data showed that one antibody belonging to this class (A1227) could bind to several VLPs from genogroup I and II, but no neutralization was observed against infectious GII.4 noroviruses in an organoid system17. The crystal structure of the A1227 Fab fragment bound to the GII.4 P domain revealed that the epitope for this antibody would be inaccessible when mapped on the surface of an intact GI.1 norovirus VLP (the only high-resolution structure of a human norovirus VLP available at the time)17. To determine how A1227 could interact with norovirus VLPs, we expressed the VP1 protein from GI.1 Norwalk strain (herein referred to as GI.1 WT) in insect cells and purified the self-assembled particles using a combination of gradient ultra-centrifugation and size-exclusion chromatography (
Next, we incubated A1227 Fab fragment with purified GI.1 WT VLPs. Surprisingly, after adding A1227 Fab (at a molar ratio of 1:2-VP1:Fab), we only observed complexes containing one VP1 dimer and two Fabs (
To rule out the possibility that VLP heterogeneity was due to artifacts from grid preparation for NS-EM, we used analytical size exclusion chromatography to assess particle dissociation and interaction with antibodies. In the absence of antibody A1227, GI.1 VLPs eluted in two main peaks (
In summary, expression of norovirus GI.1 VP1 protein in insect cells led to the production of intact VLPs as well a small population of dissociated particle components (primarily VP1 dimers). Cross-reactive, but non-neutralizing antibody A1227 bound only the dissociated VP1 dimers, while GI.1-specific and blockade antibody 512 bound to intact particles as well as to VP1 dimers.
Structure-Based Design of disulfide Bonds between VP1 Monomers Leads to Stabilized Particles. Disassembly of multivalent antigen particles can decrease immunogenicity 22 and expose epitopes that would otherwise be inaccessible on the surface of an intact particle. Due to their highly conserved nature, antibodies directed toward these occluded epitopes would tend to dominate the immune response. In the T=3 icosahedral particle arrangement, Norovirus capsids are made of 180 identical copies of the VP1 protein. The icosahedral asymmetric unit contains three quasi-equivalent VP1 monomers (designated A, B, and C)23. Each monomer associates with another monomer to form P domain dimers (in either A-B or C-C configuration). To prevent disassembly of VLP and exposure of occluded non-neutralizing epitopes, we engineered interprotomer disulfides in the shell domain of GI.1 VLPs. Because of the symmetry of the norovirus VLPs, a cysteine pair introduced near the 5-fold symmetry axes would yield disulfides between every A-A monomer pairs. The same cysteine pair at the 3-fold symmetry axes would yield disulfide bonds between every B-C monomer pair. (
To verify the formation of the disulfides, we determined the structure of the GI.1 DS1 VLP at 3.9 Å resolution using single-particle cryo-electron microscopy (
Introduction of second disulfide within the icosahedral asymmetric unit leads to further structural stabilization of the VLP (
Stabilized GI.1 VLPs do not Expose Occluded Epitopes but Retain Antigenicity of Blockade Epitopes. Stabilization of the VLPs should prevent the binding of occluded-site antibodies while maintaining accessibility of blockade epitopes. First, NS-EM analysis of GI.1 DS1 revealed very homogenous VLPs with undetectable amounts of dissociated particles (
To verify that the stabilization of the GI.1 VLPs did not compromise the blockade activity of GI.1 specific antibodies, we performed blockade and binding assays using pig gastric mucin (PGM)15 (
Stabilized VLPs Elicit Blockade Antibodies Faster than Wild Type and Focus Immune Responses toward Blockade Epitopes. Current clinical trials using norovirus VLPs have proven partially successful. The bivalent GI.1/GII4 VLP vaccine, currently in phase IIb clinical trials, is highly immunogenic; however blockade titers wane very quickly and, for some individuals, boosting fails to increase blockade responses15. We reasoned that lack of particle stability could promote exposure of immunodominant epitopes (mostly located at the base of the P domain and within the shell region). The resulting antibodies (targeting these occluded sites) would appear cross-reactive but would fail to neutralize the virus. Using stabilized particles would allow greater availability of intact particles to B cells in vivo for elicitation of higher blockade titers. In addition, since the stabilized particles would not present occluded site epitopes, they could help focus the immune response toward accessible (and potentially neutralizing) epitopes.
Accordingly, we immunized mice with GI.1 WT and GI.1 DS1 VLPs. Each group was tested with and without adjuvant (alum). The first boost was administered three weeks after the prime, followed by a second and third boost at week 6 and 9, respectively. Blood draws were performed at weeks 3, 5, 8 and 11 and final bleed was performed at week 22 (
Stabilized GI.1 VLPs should elicit higher titers of blockade antibodies (relative to GI.1—reactive antibody titers) compared to GI.1 WT. Indeed, immunization with stabilized particles led to a two-fold increase of blockade antibodies relative to total binding responses in the absence of alum (
Taken together, these data show that preventing norovirus particles from dissociating can lead to antibody responses that are more focused toward blockade epitopes; further, the stabilized VLPs showed faster development of blockade titers, compared to wild type VLPs.
In this study, we found that purification of GI.1 wild-type VLPs consistently resulted in a mixture of intact particles and partially dissociated VLP components. Even after extensive purification with size exclusion chromatography, it was still possible to detect disassembled particle components. Negative staining EM analysis of these smaller components revealed that the primary species were VP1 dimers. Interestingly, the cross-reactive but non-neutralizing antibody A1227 (Fab fragment) bound exclusively to VP1 dimers, while no Fab could be detected on the surface of intact particles. Conversely, the blocking antibody 512 could be found in complex with both intact particles and VP1 dimers. This suggests a potential route for the elicitation of cross-reactive but non-neutralizing antibodies, previously isolated from humans and mice immunized with norovirus VLPs17-19. When animals are immunized with VLPs, the partially dissociated particles expose highly conserved sites (mostly located at the base of the P domain and the shell domain) leading to the elicitation of antibodies capable of binding dissociated particles from several genogroups. It has been shown that cross-reactive but non-neutralizing antibodies are also elicited in people infected with GI.1 viruses, indicating that even infectious noroviruses could present occluded epitopes27. It is currently unclear if noroviruses can naturally present occluded sites as results of assembly defects or metastability of the capsid. It has been suggested that the flexibility of the P domain could allow some of these occluded epitopes to be (at least transiently) exposed28,29. On the other hand, to date, there are no EM studies showing direct evidence of VLPs bound to occluded-site antibodies. In our experiments, we could not detect any A1227 Fab bound to intact particles by NS-EM. However, we cannot exclude that binding of A1227 Fab at very low occupancy (few Fabs per VLP) could happen due to the transient exposure of occluded epitopes. The resolution of negatively stained samples is not sufficient to detect few Fabs that bind at the base of the P domain. Although infectious norovirus particles appear to be in a T=3 icosahedral configuration30, there is evidence that heterologous expression of VP1 proteins can lead to the assembly of T=1, T=3, and T=4 icosahedral VLPs24,30.
In addition to preventing disassembly, stabilization of VLPs also impacted immunogenicity. In particular, stabilized VLPs elicited a more focused immune response toward accessible epitopes and the development of blockade titers was much faster than immunization with wild type particles. Interestingly, the presence of adjuvant drastically improved the immunogenicity of wild type particles. We speculate that adsorption of VLPs on adjuvant could exert a stabilizing effect, thereby alleviating their propensity to dissociate. Furthermore, the particle stabilization can be used to improve immunogenicity of other human norovirus genogroups and genotypes, such as the medically important GII.4 or emerging strains such as GII.2 and GII.6. Finally, the ability of stabilized norovirus VLPs to discriminate between antibodies binding to irrelevant epitopes and surface-exposed epitopes can be exploited in antibody isolation campaigns to search for broadly neutralizing antibodies.
The gene for GI.1 VP1 protein (accession number: Q83884, identical VP1 sequence to GenBank Accession No. M87661) was synthesized, cloned in a pFastBacl vector and codon optimized for insect cell expression (GenScript). Mutation were performed by GeneImmune using the original pFastBac vector. All plasmids were sequenced before use. Generation of recombinant bacmid DNA was done using the Bac-to-Bac Baculovirus Expression System according to manufacturer instructions (Invitrogen).
Sf9 cells were maintained in ESF921 medium (Expression systems) and transfected with recombinant bacmid DNA using a mixture of 1 μg of DNA and 8 μL of Cellfectin II (Invitrogen) in a final volume of 100 μL. After incubation for 1 hour at room temperature, 800 μL of transfection reagent (Expression system) was added. Transfection was carried out in 6-well plates containing a total of 0.9×10{circumflex over ( )}6 cells per well by dropwise addition of transfection mixture. After incubation for 4 hours at 27° C., the medium was removed and 3 mL of ESF931 medium was added. Cells were incubated at 27° C. for 6 days. Cell culture medium containing recombinant baculovirus (P1 generation) was collected from each well and filter sterilized through 0.2 μm filters. High titer baculovirus was obtained by infecting 50 mL Sf9 cells at a density of 1×10{circumflex over ( )}6 cell/mL with 0.5 mL of P1 virus and incubating for 6 days (27° C., 140 rpm). Medium containing baculovirus (P2 generation) was subsequently clarified by centrifugation (4000 x g, 45 mM, 4° C.) and filter sterilized through 0.2 um filters and kept at 4° C. protected from light until needed. To test expression of VP1 proteins, 50 mL of Sf9 at 3×10{circumflex over ( )}6 cells/mL were infected with 5 mL of P2 virus and incubated for 4 days (27° C., 140 rpm) before clarification of medium. Expression levels were assessed by SDS-PAGE of samples from clarified medium.
Large scale preparation of VLPs were carried out in 200 mL of SF9 cells at 3×106 cells/mL by addition of baculovirus at MOI of 1:5 (Sf9:PFU) for 4 days at 27° C. Clarified supernatant were prepared as described above. VLPs were concentrated by centrifugation (54,000 xg for 2 hours at 4° C.) on a cushion of 3 mL of 60% iodixanol (Optiprep). Most of the content of the tube was removed by pipetting, leaving the bottom 3 mL, the concentrated protein layer and additional 3 mL above the layer. The final concentration of the iodixanol in the sample being 30%. The mixture was transferred to 5.5 mL Quick-Seal® Ultra-Clear tubes (Beckmann) and centrifugation at 300,000 xg for 8 hours at 4° C. in a NVT100 rotor. The clearly visible VLP layer was collected by side-puncture and injected onto a 16/60 Sephacryl S-500 gel filtration column equilibrated with PBS. The VLP peak eluted at about 74 mL and fractions were pooled, concentrated to about 1 mg/mL in Amicon Ultra Filters (MWCO 30 kDa), and stored at 4° C. until needed. In the case of stabilized mutants, the pooled VLP peak was incubated with a final concentration of 20 mM diamide for one hour at room temperature and subsequently dialyzed overnight against PBS or re-injected onto Sephacryl S-500 columns to remove free diamide. Confirmation of disulfide formation was assessed by SDS-PAGE, with samples run in reducing and non-reducing conditions.
Antibodies and Fab fragments were produced as previously described7. Briefly, heavy and light chain plasmids (IgG format) containing secretion signals were co-transfected in Expi293F cells (ThermoFisher) using Turbo293 transfection reagent (Speed Biosystem). Cells were incubated for one day at 37° C., followed by 4 days at 37° C. All subsequent steps were performed at 4° C. Supernatant was collected by centrifugation and loaded onto Protein A resin (GE MabSelect) pre-equilibrated with PBS. Bound antibodies were washed with 50 ml of PBS and eluted dropwise in 1 mL fractions with Pierce IgG Elution buffer (Pierce). Elution was neutralized with 1M Tris-Cl, pH 8.0 (final concentration 0.1M). Fractions with highest A280 absorption were pooled and dialyzed overnight against PBS. Dialyzed protein concentrated to ˜10 mg/mL, filter sterilized and kept at 4° C. until needed. For the production of Fab fragment, the purified antibodies were incubated with HRV-3C protease (Millipore-Sigma) overnight at 4° C. Cleavage reaction was loaded onto Protein A resin and flow through was collected. Fabs were purified by size exclusion chromatography on a Superdex 200 16/60 column in PBS. Fractions corresponding to Fab were pooled, concentrated to ˜5 mg/mL, filter sterilized and kept at 4° C. until needed.
VLP samples were diluted to approximately 0.1 mg/ml with 10 mM HEPES, pH 7.0, 150 mM NaCl. Higher dilutions, in the range of 0.01-0.05 mg/ml, were used when dissociated VLP fragments or Fab fragments were present. Material was adsorbed to a glow-discharged carbon-coated copper grid, washed with the same buffer, and negatively stained with 0.75% uranyl formate. Datasets were collected at magnifications of 50,000 and 100,000 (pixel size: 0.44 and 0.22 nm, respectively) using SerialEM35 on an FEI Tecnai T20 electron microscope equipped with a 2 k x 2k Eagle CCD camera and operated at 200 kV, as well as at a magnification of 57,000 (pixel size: 0.25 nm) using EPU on a ThermoFisher Talos F200C electron microscope equipped with a ThermoFisher Ceta CCD camera and operated at 200 kV. Particles were picked automatically using in-house developed automatic software (unpublished) or using e2boxer from the EMAN2 software package36, followed by manual correction. Reference-free 2D classifications and 3D reconstructions were performed using Relion37.
Norovirus VLPs (200 μg) were incubated with either 512 Fab or A1227 Fab to a final molar ratio of 1:2 (VP1:Fab) on ice for 1 hour. Mixture was subsequently injected onto a Supredex 200 Increase 10/300 GL connected to an Äkta Pure system (GE Healthcare) equilibrated in PBS. Fractions (0.5 mL each) were collected and 20 μL from each fraction was mixed with 20 μL of 2X sample buffer (with and without reduction agent). Fifteen microliters of each fraction was loaded onto a NuPAGE™ 4 to 12%, Bis-Tris gel, which were subsequently stained with Coomassie. Each gel was derived from the same experiment and was processed in parallel. Integration of peaks from chromatograms was performed with the Evaluation option in the Unicorn 7.3 software.
VLP samples were prepared by diluting stock solutions (at 2 mg/mL) in PBS to a final concentration of 300 μg/mL. Four hundred microliter of diluted VLPs were loaded on a 96 well plate next to PBS only samples and heat capacities were measured using a high-precision differential scanning VP-DSC microcalorimeter (GE Healthcare/MicroCal). The scan rate was set at 1° C. per minute from 18° C. to 110° C.
Binding experiments by ITC were performed at 25° C. using a VP-ITC microcalorimeter from MicroCal-Malvern Instruments (Northampton, MA, USA). GI.1 VLP and the 512 and 1227 antibody fragments were prepared and dialyzed against PBS, pH 7.4. In each titration, the solution containing the antibody fragment was added stepwise in 10 μL aliquots to the stirred calorimetric cell (v ˜1.4 mL) containing GI.1 DS1 VLP at 12-17 nM. The concentration of Fab in the syringe was 16-27 μM. All reagents were thoroughly degassed prior to the experiments. The results are expressed per mole of Fab fragment and the stoichiometry, N, denotes the number of binding sites per mole of VLP. The heat evolved upon each injection was obtained from the integral of the calorimetric signal and the heat associated with binding was obtained after subtraction of the heat of dilution. The enthalpy change, ΔH, the association constant, Ka (the dissociation constant, Kd=1/Ka) and the stoichiometry, N, were obtained by nonlinear regression of the data to a single-site binding model using Origin with a fitting function made inhouse. Gibbs energy, ΔG, was calculated from the binding affinity using ΔG=−RT ln Ka, (R=1.987 cal/(K×mol)) and T is the absolute temperature in kelvin). The entropy contribution to Gibbs energy, −TΔS, was calculated from the relation ΔG=ΔH−TΔS.
GI.1 DS1 was deposited on a C-flat grid 1.2/1.3 (protochip.com) with 2.3 □1 of volume at 1 mg/ml concentration. The grid was vitrified with an FEI Vitrobot Mark IV with a wait time of 30 seconds, blot time of 3 seconds and a blot force of 1. Data collection was performed on a Titan Krios microscope using Leginon software38. The camera was a Gatan K2 Summit direct detection device. High magnification exposures were collected in movie mode for a 10 s with the total dose of 70.48 e-/Å2 fractionated over 50 raw frames. Images were initially processed using Appion39,41; frames were aligned using MotionCor241. CTFFind442,43 was used to calculate the CTF and DoG Picker39,40 was used for initial particle picking. RELION37 was then used for particle extraction and the particle stack was imported to cryoSPARC. CryoSPARC 2.1244 was used for 2D classifications, ab initio 3D reconstruction in C1, and the volume was subjected to homogeneous refinement using I1 symmetry.
UCSF Chimera45 was used to fit the asymmetric unit of human norovirus GI.1 Norwalk VLP (PDB 6OUT) into cryo-EM density and determine symmetry operators. Residues corresponding to the P domain were excluded from the model because the resolution in this region was insufficient for model building, leaving residues 51-222 of chains A-C. The model was subjected to alternating rounds of real space refinement in Phenix46 and manual building in Coot47.
Several loops located around the 3-fold symmetry axis were deleted because of weak density in this region. The FSC curve between the map and the model was calculated using phenix.mtriage. Model validation was performed with MolProbity48 and EMRinger49. Figures were generated in UCSF Chimera and PyMOL (www.pymol.org).
EIA and blockade assays were done as previously reported17. For VLP capture assays, plates were coated with PGM as for blockade assays, followed by addition of 0.25 μg/ml VLP for 1 hour at 37° C. and bound mAb detected as for EIA.
The competition between mouse polyclonal serum and human monoclonal antibodies for binding to immobilized VLPs (0.25 μg/ml) was measured by EIA as described previously50. Briefly, mouse s era were added to VLP-coated plates at different dilutions. After 1 h, human mAb were added at a concentration required to achieve 50% maximal binding [EC50] at room 37C for 1 h. The plates were then washed with phosphate-buffered saline (PBS)-0.05% Tween 20, and bound human mAb was detected using anti-human-IgG HRP (GE Healthcare). The concentration of sera that blocked binding of 50% of the mab was determined as described above for blockade of binding assays.
Mouse studies were executed in accordance with the recommendations for the care and use of animals by the Office of Laboratory Animal Welfare (OLAW) at NIH. The Institutional Animal Care and Use Committee (IACUC) at UNC-CH approved the animal studies performed here (protocol, IACUC 17-059). Six-week-old Balb/c mice (Jackson Labs) were immunized intramuscularly with 2 μg of VLP plus either PBS or 50 μg alhydrogel (Invivogen). Identical booster vaccinations were performed at week 3, 6, 9 with bleeds at week 3, 5, 8 and 11. Mice were euthanized with isoflurane at week 22, for terminal bleed. Each VLP group contained 8 mice, while 6 mice were used in PBS control groups.
Statistical analyses were performed using two-tailed Mann-Whitney tests with GraphPad Prism 8.0 software (La Jolla, CA). Differences were considered statistically significant at P<0.05.
A fortéBio Octet Red384 instrument was used to measure binding of sera from immunized mice after capture of VP1 dimer with 512 or A1227 IgG. All assays were performed at 1,000 rpm agitation. Assays were performed at 30° C. in tilted black 384-well plates (Geiger Bio-One) with final volumes of 50 μl/well. Anti Human-Fc sensor tips were used to capture either 512 or A1228 IgG. Biosensor tips were equilibrated for 30 minutes in PBS before each experiment. Capture levels were between 1.2 and 1.3 nm, and variability for each tip did not exceed 0.1 nm. Biosensor tips were then equilibrated for 300 s in PBS before a second association step (600 s) with VP1 dimers at 30 ug/mL. Biosensor tips were then equilibrated for 300 s in PBS prior to measuring association to serum samples from final bleed (300 s). All sera were diluted 50-fold in PBS. Initial slopes were determined by linear regression of the signal in first 30 seconds of association.
Stabilized Virus-Like Particles Formed from Recombinant GII.4 VP1 Proteins
Norovirus GII VLPs are metastable and can be disrupted by interaction with specific antibodies. Norovirus GII VLPs produced in insect cells using the baculovirus system have been 20 used extensively as immunogens in both mice and humans.
Using negative staining electron microscopy, the presence of distorted VLPs as well as VLP components were observed (
Further and surprisingly, adding A1227-Fab to GII.4.1997 VLPs lead to rapid (<60 min) 25 and complete disassembly of the VLP (
In contrast, A1227 has no inhibitory effect towards GII.4 viruses, as assessed by an enteroid culture system (Lindesmith et al., Immunity 50(6): 1530-1541, 2019). Therefore, it appears that A1227 (and other occluded site antibodies) bind partially disassembled VLPs, but do not interact with intact viruses.
Stabilization of GII VLPs
To prevent particle disassembly, intermolecular disulfide bonds and hydrophobic substitutions were designed within the shell domain of GII.4. The template GII.4 sequence used was the following:
Amino acid substitutions were introduced into the template sequence as follows:
GII.4 VP1 proteins with the sequences of variants 1-35 were expressed in insect cells as described in Example 1 for the GI VLPs. Supernatants from the insect cells were incubated with diamide (to establish an oxidizing environment) and subsequently separated by SDS-PAGE under reducing or non-reducing conditions. VLPs in which each protomer was covalently linked to the neighboring protomer by disulfide links, did not dissociate in the presence of SDS and thus failed to enter the separating gel due to the large size of the particle (˜10 MDa), remaining at the top of the well. In the presence of DTT, the disulfides were reduced, and the particle could be dissociated by SDS, resulting in a single band corresponding to the VP1 monomer. Three constructs showed significant stabilization after oxidation in diamide, variants 6, 7, and 20 (
This example describes use of the stabilized Norovirus VLPs described herein to detect and isolate antibodies that specifically bind to solvent-exposed epitopes on the surface of the VLPs.
The GI.1 DS1 VLPs (SEQ ID NO: 7) were fixed to detection plate surface in three difference ways (
Also, using Streptavidin coated plates makes the difference much larger than coating the VLP directly to the plate. This may be due to deformation of the particle when interacting with the plastic. Capturing of VLPs using the receptor (HBGA) is also not ideal because at higher concentration, the 512 antibody competes with the receptor and the particles detaches from the plate.
To further illustrate the effectiveness of the stabilized Norovirus VLP as diagnostic tools for identification of a subject that has produced a neutralizing antibody response to Norovirus VLP, assessment of total IgG, IgA and IgM antibody titers using stabilized GI.1 VLPs as probe was performed on samples from human patients before and after oral GI.1 Norovirus challenge. Serum from 15 different patients was collected before (day 1) and on day 28 following oral GI.1 Norovirus challenge. IgG, IgA and IgM antibody titers were determined against GI.1 DS1 VLP linked to plates using biotin/streptavidin as described above. As shown in
Accordingly, detection and/or isolation of antibodies that bind to solvent-exposed epitopes on the surface of the stabilized VLPS described herein can be used to identify a subject that elicits a neutralizing antibody response following Norovirus infection and/or receipt of a Norovirus vaccine, as also as tools to isolate neutralizing/blockade antibodies from immunized or naturally infected subjects.
It will be apparent that the precise details of the methods or compositions described may be varied or modified without departing from the spirit of the described embodiments. We claim all such modifications and variations that fall within the scope and spirit of the claims below.
This application claims priority to U.S. Provisional Application No. 63/091,824, filed on Oct. 1, 2020, which is incorporated herein by reference.
This invention was made with government support under Grant Nos. AI109761 and AI148260 awarded by the National Institutes of Health. The government has certain rights in the invention.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2021/055018 | 10/14/2021 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 63091824 | Oct 2020 | US |
