Patent Application
20230233663
The content of the following submission on ASCII text file is incorporated herein by reference in its entirety: a computer readable form (CRF) of the Sequence Listing (file name: 165762000442SEQLIST.TXT, date recorded: Jun. 9, 2021, size: 186 KB).
The present disclosure relates in some aspects to immunogenic compositions including recombinant peptides and proteins comprising human immunodeficiency virus (HIV) 1 viral antigens and immunogens, e.g., gp120 protein peptides, for treating and/or preventing an HIV infection.
Human immunodeficiency viruses (HIV) include two species of lentivirus that infect humans, and over time can cause acquired immunodeficiency syndrome (AIDS). Immunization against HIV 1 is currently not available. Clinical trials have been unsuccessful in generating broadly neutralizing antibodies against all tiers of HIV. Improved strategies are needed.
In some embodiments, disclosed herein are recombinant subunit vaccines that comprise an ecto-domain (e.g., without transmembrane and cytoplasmic domains) of an HIV protein or its fragments, such as the HIV gp120 protein, which is fused in-frame to a C-propeptide of a collagen that is capable of forming disulfide bond-linked homo-trimer. The resulting recombinant subunit vaccines, such as an gp120-trimer, can be expressed and purified from transfected cells, and are expected to be in native-like conformation in trimeric form. This solves the problems of mis-folding of a viral antigen often encountered when it is expressed as a recombinant peptide or protein in soluble forms without the transmembrane and/or cytoplasmic domains. Such mis-folded viral antigens do not faithfully preserve the native viral antigen conformation, and often fail to evoke neutralizing antibodies.
In one aspect, provided herein is a protein comprising a plurality of recombinant polypeptides, each recombinant polypeptide comprising a HIV gp120 protein peptide or a fragment or epitope thereof linked to a C-terminal propeptide of collagen, wherein the C-terminal propeptides of the recombinant polypeptides form inter-polypeptide disulfide bonds.
In some of any embodiments, the HIV is an HIV-1, optionally a tier 1B, tier 1A, tier 2, or tier 3 virus. In some of any embodiments, the epitope is a linear epitope or a conformational epitope.
In some of any embodiments, the gp120 protein peptide comprises an outer domain subunit peptide, an inner domain subunit peptide, or any combination thereof, and wherein the protein comprises three recombinant polypeptides. In some of any embodiments, the gp120 protein comprises one, two, three, four, or five C regions, and one, two, three, four, or five variable regions, optionally separated by a bridging sheet. In some embodiments, the gp120 protein peptide comprises an outer subunit or an inner subunit the gp120 protein. In some of any embodiments, the gp120 protein peptide comprises an inner subunit and an outer subunit of the gp120 protein, optionally wherein the outer subunit and the inner subunit are linked by a disulfide bond or an artificially introduced linker. In some of any embodiments, the gp120 protein peptide does not comprise a transmembrane (TM) domain peptide and/or a cytoplasm (CP) domain peptide.
In some of any embodiments, the gp120 protein peptide comprises a protease cleavage site, wherein the protease is optionally furin, a transmembrane serine protease such as TMPRSS2, trypsin, factor Xa, thrombin, or cathepsin L. In some of any embodiments, the gp120 protein peptide does not comprise a protease cleavage site, wherein the protease is optionally furin, a transmembrane serine protease such as TMPRSS2, trypsin, factor Xa, thrombin, or cathepsin L.
In some of any embodiments, the gp120 protein peptide is soluble or does not directly bind to a lipid bilayer, e.g., a membrane or viral envelope. In some of any embodiments, the gp120 protein peptides are the same or different among the recombinant polypeptides of the protein. In some of any of the embodiments, the gp120 protein peptide is directly fused to the C-terminal propeptide, or is linked to the C-terminal propeptide via a linker, such as a linker comprising glycine-X-Y repeats, wherein X and Y and independently any amino acid and optionally proline or hydroxyproline.
In some of any embodiments, the provided protein is soluble. In some of any embodiments, the protein does not directly bind to a lipid bilayer, e.g., a membrane or viral envelope. In some of any embodiments, the protein is capable of binding to a cell surface attachment factor or receptor of a subject, optionally wherein the subject is a mammal such as a primate, e.g., human.
In some of any embodiments, the C-terminal propeptide is of human collagen. In some of any embodiments, the C-terminal propeptide comprises a C-terminal polypeptide of proα1(I), proα1(II), proα1(III), proα1(V), proα1(XI), proα2(I), proα2(V), proα2(XI), or proα3(XI), or a fragment thereof. In some of any embodiments, the C-terminal propeptides are the same or different among the recombinant polypeptides.
In some of any embodiments, the C-terminal propeptide comprises any one of SEQ ID NOs: 31-46 or an amino acid sequence at least 90% identical thereto capable of forming inter-polypeptide disulfide bonds and trimerizing the recombinant polypeptides.
In some of any embodiments, the gp120 protein peptide in each recombinant polypeptide is in a prefusion conformation or a postfusion conformation.
In some of any embodiments, the gp120 protein peptide in each recombinant polypeptide comprises any of SEQ ID NOs: 19-30 or an amino acid sequence at least 80% identical thereto.
In some of any embodiments, the recombinant polypeptide comprises any of SEQ ID NOS: 1-18 or an amino acid sequence at least 80% identical thereto.
Provided herein is an immunogen, such as an immunogen comprising any of the provided proteins. Also provided herein is a protein nanoparticle, such as a protein nanoparticle comprising any of the provided proteins directly or indirectly linked to a nanoparticle. Also provided here in a virus-like particle (VLP), such as a VLP comprising any of the provided proteins
Also provided herein is a nucleic acid, such as an isolated nucleic acid encoding one, two, three or more of the recombinant polypeptides of any of the provided proteins. In some embodiments, a polypeptide encoding the gp120 protein peptide is fused in-frame to a polypeptide encoding the C-terminal propeptide of collagen.
In some embodiments, the isolated nucleic acid is operably linked to a promoter. In some embodiments, the isolated nucleic acid is operably linked to a promoter. In some embodiments, the isolated nucleic acid is DNA molecule.
In some embodiments, the isolated nucleic acid is an RNA molecule. Optionally, an mRNA molecule such as a nucleoside-modified mRNA, a non-amplifying mRNA, a self-amplifying mRNA, or a trans-amplifying mRNA.
Provided herein is a vector, such as a vector comprising any of the provided nucleic acids. In some embodiments, the vector is a viral vector.
Also provided herein is a virus, a pseudovirus, or a cell comprising any of the vector provided herein. Optionally, wherein the virus or cell has a recombinant genome.
Provided herein is an immunogenic composition comprising any of the provided proteins, immunogens, protein nanoparticle, VLP, isolated nucleic acid, vector, virus, pseudovirus, or cell and a pharmaceutically acceptable carrier.
Provided herein is a vaccine comprising any of the provided immunogenic compositions. Optionally, in an adjuvant, wherein the vaccine is optionally a subunit vaccine. In some embodiments, the vaccine is a prophylactic and/or therapeutic vaccine.
Also provided herein is a method of producing a protein, said method comprising expressing any of the provided isolated nucleic acids or vectors in a host cell to produce any of the provided proteins; and purifying the protein. Provided herein are proteins produced by this method.
Provided herein is a method for generating an immune response to an gp120 protein peptide or fragment or epitope thereof of an HIV virus in a subject, the method comprising administering to the subject an effective amount of any of the provided protein, immunogen, protein nanoparticle, VLP, isolated nucleic acid, vector, virus, pseudovirus, cell, immunogenic composition, or vaccine to generate the immune response.
In some of any embodiments, the method is for treating or preventing infection with the HIV virus. In some embodiments, generating the immune response inhibits or reduces replication of HIV in the subject. In some embodiments, the immune response comprises a cell-mediated response and/or a humoral response, optionally comprising production of one or more neutralizing antibody, such as a polyclonal antibody or a monoclonal antibody. In some embodiments, the immune response is against the gp120 protein peptide or fragment or epitope thereof of HIV but not against the C-terminal propeptide.
In some of any embodiments, the administering does not lead to antibody dependent enhancement (ADE) in the subject due to prior exposure to one or more HIV virus. In some embodiments, the administering does not lead to antibody dependent enhancement (ADE) in the subject when subsequently exposed to one or more HIV virus.
In some of any embodiments, the method further comprises a priming step and/or a boosting step.
In some of any embodiments, the administering step is performed via topical, transdermal, subcutaneous, intradermal, oral, intranasal (e.g., intranasal spray), intratracheal, sublingual, buccal, rectal, vaginal, inhaled, intravenous (e.g., intravenous injection), intraarterial, intramuscular (e.g., intramuscular injection), intracardiac, intraosseous, intraperitoneal, transmucosal, intravitreal, subretinal, intraarticular, peri-articular, local, or epicutaneous administration. In some of any embodiments, the effective amount is administered in a single dose or a series of doses separated by one or more interval. In some of any embodiments, the effective amount is administered without an adjuvant. In some of any embodiments, the effective amount is administered with an adjuvant.
Provided herein is a method comprising administering to a subject an effective amount of any of the provided proteins to generate in the subject a neutralizing antibody or neutralizing antisera to the HIV virus. In some embodiments, the subject is a mammal. Optionally, a human or a non-human primate.
In some of any embodiments, the method further comprises isolating the neutralizing antibody or neutralizing antisera from the subject. In some of any embodiments, the method further comprises administering an effective amount of the isolated neutralizing antibody or neutralizing antisera to a human subject via passive immunization to prevent or treat an infection by the HIV virus. In some of any embodiments, the neutralizing antisera comprises polyclonal antibodies to the gp120 protein peptide or fragment or epitope thereof, optionally wherein the neutralizing antibody is free or substantially free of antibodies to the C-terminal propeptide of collagen. In some of any embodiments, the neutralizing antibody comprises a monoclonal antibody to the gp120 protein peptide or fragment or epitope thereof, optionally wherein the neutralizing antibody is free or substantially free of antibodies to the C-terminal propeptide of collagen.
In some of any embodiments, any of the provided proteins, immunogens, protein nanoparticles, VLPs, isolated nucleic acids, vectors, viruses, pseudoviruses, cells, immunogenic compositions, or vaccines, are for use in inducing an immune response to an HIV virus in a subject, and/or in treating or preventing an infection by the HIV virus.
Provided herein is the use of any of the provided protein, immunogen, protein nanoparticle, VLP, isolated nucleic acid, vector, virus, pseudovirus, cell, immunogenic composition, or vaccine for inducing an immune response to an HIV virus in a subject, and/or for treating or preventing an infection by the HIV virus.
Provided herein is the use of any of the provided protein, immunogen, protein nanoparticle, VLP, isolated nucleic acid, vector, virus, pseudovirus, cell, immunogenic composition, or vaccine for the manufacture of a medicament or a prophylactic for inducing an immune response to an HIV virus in a subject, and/or for treating or preventing an infection by the HIV virus.
Also provided herein is a method for analyzing a sample, the method comprising: contacting a sample with any of the provided proteins, and detecting a binding between the protein and an analyte capable of specific binding to the gp120 protein peptide or fragment or epitope thereof of the HIV virus.
In some of any embodiments, the analyte is an antibody, a receptor, or a cell recognizing the gp120 protein peptide or fragment or epitope thereof. In some of any embodiments, the binding indicates the presence of the analyte in the sample, and/or an infection by HIV in a subject from which the sample is derived.
Also provided herein is a kit, the kit comprising any of the provided proteins and a substrate, pad, or vial containing or immobilizing the protein, optionally wherein the kit is an ELISA or lateral flow assay kit.
The construct was stably transfected into the CHO-S dhfr−/− cell line and supernatants were first run over a 5 mL Blue-Sepharose affinity purification column. The trimeric fractions were isolated with purity of the isolated exemplary fusion protein comprising HIV gp120 shown in
Binding kinetics of the exemplary fusion protein comprising HIV gp120 were assessed against several broadly neutralizing antibodies (bNAbs) are depicted in
The exemplary fusion proteins were biotin labeled with 20 mM EZ-Link NHS-PEG4-biotin (ThermoFisher), then attached to the streptavidin (SA) sensors and loaded within the plate coating with 10 μg/mL biotin-gp120-Trimer for 300 s. Binding kinetics were additional measured at 30° C. by fortebio OCTET QKe Bio-layer interferometry (BLI) system (Pall Life Science Corp) and are shown in
The binding kinetics to bNAb, such as NIH45-46, PG9 and 447-52D, is depicted in
Immunization with exemplary HIV gp120 fusion protein was observed to induce HIV-1 neutralizing antibodies, including against Tier 1A and 1B (
In some embodiments, compositions and methods of use of recombinant soluble surface antigens from RNA viruses in covalently linked trimeric forms are disclosed. In some embodiments, the resulting fusion proteins are secreted as disulfide bond-linked homo-trimers, which are more stable in structure, while preserving the conformations of native-like trimeric viral antigens, thereby can be used as more effective vaccines against these dangerous pathogens.
In some embodiments, disclosed herein are methods for using viral antigen trimers as a vaccine or as part of a multivalent vaccine to prevent viral infections, without or with adjuvant, or with more than one adjuvant, optionally via either intra-muscular injections or intra-nasal administrations.
In some embodiments, disclosed herein are methods for using viral antigen trimers as an antigen for diagnosis of viral infections through detection of antibodies, e.g., IgM or IgG, that recognize the viral antigen, such as neutralizing antibodies.
In some embodiments, disclosed herein are methods for using viral antigen trimers as an antigen to generate polyclonal or monoclonal antibodies which can be used for passive immunization, e.g., neutralizing mAb for preventing or treating an HIV infection.
In some embodiments, disclosed herein is a viral antigen trimer as a vaccine or as part of a multivalent vaccine, wherein the vaccine comprises a plurality of trimeric subunit vaccines comprising viral antigens of the same protein of a virus or comprising viral antigens of two or more different proteins of one or more viruses or one or more strains of the same virus.
In some embodiments, disclosed herein is a monovalent vaccine comprising a viral antigen trimer disclosed herein. In some embodiments, disclosed herein is a bi-valent vaccine comprising a viral antigen trimer disclosed herein. In some embodiments, disclosed herein is a tri-valent vaccine comprising a viral antigen trimer disclosed herein. In some embodiments, disclosed herein is a quadrivalent vaccine comprising a viral antigen trimer disclosed herein.
In some embodiments, disclosed herein is a monovalent vaccine comprising an envelope glycoprotein-trimer (e.g., gp160- or gp120- or gp41-Trimer) disclosed herein. In some embodiments, disclosed herein is a bi-valent vaccine comprising an envelope glycoprotein-trimer (e.g., gp160- or gp120- or gp41-Trimer) disclosed herein. In some embodiments, disclosed herein is a bi-valent vaccine comprising at least one envelope glycoprotein-trimer (e.g., gp160- or gp120- or gp41-Trimer) comprising a first envelope glycoprotein antigen and at least one envelope glycoprotein-trimer (e.g., gp160- or gp120- or gp41-Trimer) comprising a second envelope glycoprotein antigen. In some embodiments, the first and second envelope glycoprotein antigens are from the same envelope glycoprotein of one or more virus species or strains/subtypes, or from two or more different envelope glycoproteins of one or more virus species or one or more strains/subtypes of the same virus species. In some embodiments, disclosed herein is a tri-valent vaccine comprising an envelope glycoprotein-trimer (e.g., gp160- or gp120- or gp41-Trimer) disclosed herein. In some embodiments, disclosed herein is a tri-valent vaccine comprising at least one envelope glycoprotein-trimer (e.g., gp160- or gp120- or gp41-Trimer) comprising a first envelope glycoprotein antigen, at least one envelope glycoprotein-trimer (e.g., gp160- or gp120- or gp41-Trimer) comprising a second envelope glycoprotein antigen, and at least one envelope glycoprotein-trimer (e.g., gp160- or gp120- or gp41-Trimer) comprising a third envelope glycoprotein antigen. In some embodiments, the first, second and third envelope glycoprotein antigens are from the same envelope glycoprotein of one or more virus species or strains/subtypes, or from two, three, or more different envelope glycoproteins of one or more virus species or one or more strains/subtypes of the same virus species. In some embodiments, disclosed herein is a quadrivalent vaccine comprising an envelope glycoprotein-trimer (e.g., gp160- or gp120- or gp41-Trimer) disclosed herein. In some embodiments, disclosed herein is quadrivalent vaccine comprising at least one envelope glycoprotein-trimer (e.g., gp160- or gp120- or gp41-Trimer) comprising a first envelope glycoprotein antigen, at least one envelope glycoprotein-trimer (e.g., gp160- or gp120- or gp41-Trimer) comprising a second envelope glycoprotein antigen, at least one envelope glycoprotein-trimer (e.g., gp160- or gp120- or gp41-Trimer) comprising a third envelope glycoprotein antigen, and at least one envelope glycoprotein-trimer (e.g., gp160- or gp120- or gp41-Trimer) comprising a fourth envelope glycoprotein antigen. In some embodiments, the first, second, third, and fourth envelope glycoprotein antigens are from the same envelope glycoprotein of one or more virus species or strains/subtypes, or from two, three, four, or more different envelope glycoproteins of one or more virus species or one or more strains/subtypes of the same virus species. In some embodiments, disclosed herein is a vaccine comprising at least one gp120-Trimer from BG505, at least one gp120-Trimer from B41, and at least one gp120-Trimer from CH505.
Provided herein are immunogenic compositions, methods, and uses of recombinant polypeptides peptides and proteins comprising HIV viral antigens or immunogens for the treatment, e.g., prophylactic, therapeutic, of HIV infection. HIV includes two species of lentivirus that infect humans, and over time can cause acquired immunodeficiency syndrome (AIDS). AIDS is a condition in which progressive failure of the immune system allows life-threatening infections and cancers to thrive. In the absence of treatment, the average survival time after infection with HIV is estimated to be 9 to 11 years.
HIV infection can be sexually transmitted by contact with or transfer of blood, pre-ejaculate, semen, and vaginal fluids. HIV infection can also be transmitted non-sexually, for example from an infected mother to her infant during pregnancy, birth, and/or breast milk.
The primary immunologic abnormality resulting from infection by human immunodeficiency virus (HIV) is the progressive depletion and functional impairment of T lymphocytes expressing the CD4 cell surface glycoprotein. The loss of CD4 helper/inducer T cell function probably underlies the profound defects in cellular and humoral immunity leading to the opportunistic infections and malignancies characteristic of AIDS (Lane et al., Ann. Rev. Immunol., 3: 477, 1985). Studies of HIV-1 infection of fractionated CD4 and CD8 T-cells from normal donors and AIDS patients have revealed that depletion of CD4 T-cells results from the ability of HIV-1 to selectively infect, replicate in, and ultimately destroy this T lymphocyte subset (Klatzmann et al., Science, 225: 59, 1984). Since its discovery in the early 1980s, AIDS has become a pandemic and caused more than 25 million deaths. Approximately 35 million people are currently living with HIV/AIDS globally, urgently in need of effective, affordable, long-term treatment and management of the disease.
While HIV can infect a variety of cell types, CD4+ T cells and macrophages are the primary cellular targets in vivo. Entry into host cells is an essential step in HIV-1 life cycle that can be targeted by anti-HIV-1 drugs. HIV-1 entry is mediated by the viral spike (Env), which comprises three gp120 and three gp41 subunits (
The widespread use of highly active antiretroviral therapy (HAART) has dramatically improved the clinical course for many individuals infected with HIV (Berrey et al., J. Infect. Dis., 183, (10): 1466, 2001). However, toxicities associated with long term HAART have put a high priority on the design and development of less toxic therapies.
Prior unsuccessful HIV vaccine attempts include utilizing gp120 monomers, non-native gp140 proteins, gp120 core and outer domain (OD) proteins, epitope-specific scaffolds and epitope-based peptides (Sliepen 2016). One well-studied approach for making soluble trimers is BG505 SOSIP.664, which attempts to mimic the natural gp140-trimer conformation by introducing an intermolecular disulfide bond to strengthen the gp120-gp41ECTO interaction (Binley 2000, Binley 2002, Sanders 2002, Klasse 2013, Khayat 2013). BG505 SOSIP.664 adopts a stable trimer conformation based on electron microscopy (EM) (Sanders 2015), and it displays many known bNAb epitopes while binding to non-NAbs weakly (Sanders 2013). However, in rabbit immunization studies, BG505 SOSIP.664 only induced NAbs against autologous Tier-2 virus, while bNAbs against heterologous Tier-2 viruses were not observed (Sanders 2015).
Since the discovery of human immunodeficiency virus (HIV) as the cause for AIDS in 1983 (Gallo, 2003), the development of an effective vaccine has been an ongoing global health priority. A successful vaccine must be able to induce broadly neutralizing antibodies (bNAbs) conferring protective immunity against the vast genetic diversity of circulating HIV-1 isolates, especially neutralization resistant Tier-2 viruses (M. S. Seaman, 2010). Unfortunately, after decades of intensive efforts, a vaccine candidate capable of inducing bNAbs remains elusive, with success yet to be achieved even in animal models let alone humans.
The proteins and recombinant polypeptides comprising HIV viral antigens and immunogens provided herein are useful for effectively and safely treating (e.g., therapeutically, prophylactically) IRV infection. In some aspects, the provided methods allow for a subunit vaccine to be produced safely, with a simple and robust manufacturing process. In some aspects, the provided compositions and methods allow for the IRV viral antigens or immunogens to maintain their native conformation. This may be advantageous for eliciting an immune response to native antigenic sites, e.g., linear or conformational epitopes.
In some embodiments, the HIV viral antigen or immunogen is a gp120 protein peptide, or a fragment or epitope thereof. In some embodiments, the HIV viral antigen or immunogen, e.g., gp120 protein peptide, as described herein, is linked to a C-terminal propeptide of collagen to form the recombinant polypeptide, wherein the C-terminal propeptides of the recombinant polypeptides form inter-polypeptide disulfide bonds. In some embodiments, the C-terminal propeptides of the recombinant polypeptides form inter-polypeptide disulfide bonds resulting in multimerization, e.g., trimerization, of the recombinant polypeptides. In some aspects, multimerization, e.g., trimerization, allows for the gp120 protein peptide to acquire a native gp120 trimeric conformation, for example resembling the organization of the gp120 on the native viral surface. In some embodiments, the native confirmation elicits robust immune responses targeting protective conformational epitopes in the gp120.
In some embodiments, a protein as described herein contains a plurality of recombinant proteins described here. In some embodiments, the protein forms a macrostructure. In some embodiments, the proteins or recombinant polypeptides provided herein are comprised in nanoparticles or virus-like-particles (VLPs). Also provided are nucleic acids, e.g., isolated nucleic acids, encoding the recombinant polypeptides. In some embodiments, the nucleic acids encoding the recombinant polypeptides are contained in vectors, such as viral vectors or pseudovirus vectors. In some embodiments, the nucleic acids encoding the recombinant polypeptides or the vectors containing the nucleic acid vectors are comprised in cells. In some embodiments, cells containing the nucleic acids or vectors may be used to produce the recombinant polypeptides.
In some embodiments, the proteins, recombinant receptors, protein nanoparticles, VLPs, nucleic acids, vectors, viruses, pseudoviruses, or cells are or comprise an immunogenic composition. In some embodiments, the immunogenic composition contains a pharmaceutically acceptable carrier. In some embodiments, the immunogenic composition is used as a vaccine. In some embodiments, the vaccine contains or is administered in combination with one or more adjuvants.
Also provided herein are methods of producing proteins provided herein, methods of treating subjects with proteins and compositions provided herein, and kits.
All publications, including patent documents, scientific articles and databases, referred to in this application are incorporated by reference in their entirety for all purposes to the same extent as if each individual publication were individually incorporated by reference. If a definition set forth herein is contrary to or otherwise inconsistent with a definition set forth in the patents, applications, published applications and other publications that are herein incorporated by reference, the definition set forth herein prevails over the definition that is incorporated herein by reference.
The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described.
The proteins provided herein comprise HIV viral antigens and immunogens. The HIV viral antigens and immunogens contemplated herein are capable of promoting or stimulating a cell-mediated response and/or a humoral response. In some embodiments, the response, e.g., cell-mediated or humoral response, comprises the production of antibodies, e.g., neutralizing antibodies.
Genomic viral RNA must be packaged inside of viral particles so that the virus is transmitted. Some viral RNA capsids are enveloped, or enclosed by lipid membranes of the infected host cell and others have an outer shell of viral protein without a lipid bilayer. Viral proteins are generally classified as structural and non-structural proteins. In general, the non-structural proteins are involved in genomic replication, transcriptional regulation, and packaging. Structural proteins generally perform three major functions that include: (1) Genomic RNA binding (i.e., the nucleocapsid protein for HIV A virus), (2) Maintaining the relationship between packaged RNA and other proteins (i.e. matrix protein) and (3) Building the outermost external viral layer (i.e. surface proteins, such as gp120). Assembly into viral particles ensures the effective transmission of the viral RNA genome to another host within the same species or across species.
In some embodiments, the virus is a human immunodeficiency virus (HIV). In some embodiments, the HIV is HIV-1. HIV-1 isolates are often classified on the basis of neutralization ‘tier’ phenotype. Four tiers are defined in relationship with the at least three confirmations through which the trimeric HIV-1 envelope glycoprotein spike can spontaneously transition. Neutralization tier phenotypes correspond to the frequency by which the trimer exists in an open (tier 1A), closed (tiers 2 and 3), or intermediate (tier 1B) conformation. In some respects, an open confirmation exposes more internal epitopes. In some cases, the closed conformation is stabilized and can be bound by many broadly neutralizing antibodies.
Tier 1A is the most sensitive neutralization phenotype and represents a very minor fraction of circulating strains. Tier 1B is the next most sensitive and represents a larger but still relatively small fraction of circulating strains. Most circulating strains exhibit a moderately sensitive tier 2 phenotype that is considered the most important to target with vaccines; this phenotype comprises the majority of reference strains. Tier 3 is the least sensitive phenotype (Montefiori et al., Curr Opin HIV AIDS (13)2:128-136, 2018).
In some embodiments, the viral antigen or immunogen is an HIV gp120 protein peptide or a fragment or epitope thereof.
The envelope protein of HIV is initially synthesized as a longer precursor gp160 protein of 845-870 amino acids in size. Gp160 can form a homotrimer and undergoes glycosylation within the Golgi apparatus of an infected host cell. In vivo, gp160 is then cleaved by a cellular furin protease into gp120 and gp41. Gp41 contains a transmembrane domain and remains in a trimeric configuration. Gp120 contains most of the cell surface external domains of the envelope glycoprotein complex. Gp120 binds both to the cellular CD4 receptor and to the cellular chemokine receptors (such as CCR5), which facilitates viral entry into host cells. Gp41 and gp120 can interact via non-covalent bonding.
The mature gp120 polypeptide has about 500 amino acids in the primary sequence. Gp120 is a heavily N-glycosylated protein in vivo, giving rise to an molecular weight of 120 kD when visualized via western blot and it's name. The gp120 polypeptide is comprised of five conserved regions (C1-C5) and five regions of high variability (V1-V5). Exemplary sequences of wild type gp160 polypeptides are shown on GENBANK, for example accession numbers AAB05604 and AAD12142, as available on Sep. 6, 2007, which are incorporated herein by reference.
The gp120 core has a unique molecular structure, which comprises two domains: an “inner” domain (which faces gp41) and an “outer” domain (which is mostly exposed on the surface of the oligomeric envelope glycoprotein complex). The two gp120 domains are separated by a “bridging sheet” that is not part of either domain. The gp120 core comprises 25 beta strands, 5 a1pgp120 helices, and 10 defined loop segments.
Gp120 polypeptides also include “gp120-derived molecules” which encompasses analogs (non-protein organic molecules), derivatives (chemically functionalized protein molecules obtained starting with the disclosed protein sequences) or mimetics (three-dimensionally similar chemicals) of the native gp120 structure, as well as proteins sequence variants (such as mutants), genetic alleles, fusions proteins of gp120, or combinations thereof. In some embodiments, the gp120 is a peptide fragment, epitope, or a derivative thereof.
The third variable region referred to herein as the V3 loop is a loop of about 35 amino acids critical for the binding of the co-receptor and determination of which of the co-receptors will bind. In some embodiments, the V3 loop comprises residues 296-331.
Gp120 is the most common target for neutralizing antibodies against HIV-1 due to its exposed nature on the trimeric complex, while gp41 antigenic epitopes are typically unexposed, are located near the viral membrane, or are only transiently exposed during the fusion process of the HIV-1 virus and CD4+T lymphocyte membranes (Burton 2004). Interestingly, gp120 commonly elicits non-neutralizing antibodies during the course of natural infection. Such non-neutralizing antibodies may be directed against gp120 regions that are occluded on the assembled trimer but are subsequently exposed upon gp120 shedding from gp41 into soluble gp120 monomers (Moore 1996, Wyatt 1997). In contrast, neutralizing antibodies typically bind to the mature trimeric complex with higher affinity than to gp120 monomers, and such binding can be trimer-specific (Sattentau 1995, Burton 2004, de Taeye 2016).
The amino acids residues in gp120 can be numbered using the HXB2 numbering scheme as set forth in Numbering Positions in HIV Relative to HXB2CG Bette Korber et al., Human Retroviruses and AIDS 1998: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. Korber B, Kuiken C L, Foley B, Hahn B, McCutchan F, Mellors J W, and Sodroski J, Eds. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, N. Mex. which is incorporated by reference herein in its entirety.
In some embodiments, gp120 protein peptide comprises an outer domain subunit peptide, an inner domain subunit peptide, or any combination thereof. In some embodiments, the protein comprises three recombinant polypeptides. In some embodiments, the gp120 protein comprises one, two, three, four, or five C regions, and one, two, three, four, or five variable regions, optionally separated by a bridging sheet. In some embodiments, the gp120 protein peptide comprises an outer subunit or an inner subunit of the gp120 protein. In some embodiments, the gp120 protein peptide comprises an inner subunit and an outer subunit of the gp120 protein, optionally wherein the outer subunit and the inner subunit are linked by a disulfide bond or an artificially introduced linker. In some embodiments, the gp120 protein peptide does not comprise a transmembrane (TM) domain peptide and/or a cytoplasm (CP) domain peptide. In some embodiments, the gp120 protein peptide comprises a protease cleavage site, wherein the protease is optionally furin, a transmembrane serine protease such as TMPRSS2, trypsin, factor Xa, or cathepsin L. In some embodiments, the gp120 protein peptide does not comprise a protease cleavage site, wherein the protease is optionally furin, a transmembrane serine protease such as TMPRSS2, trypsin, factor Xa, or cathepsin L. In some embodiments, the gp120 protein peptide is soluble or does not directly bind to a lipid bilayer, e.g., a membrane or viral envelope. In some embodiments, the gp120 protein peptides are the same or different among the recombinant polypeptides of the protein.
In some embodiments, the gp120 protein peptide in each recombinant polypeptide is in a prefusion conformation or a postfusion conformation. In some embodiments, the gp120 protein peptide in each recombinant polypeptide is or includes the sequence set forth in any of SEQ ID NOs: 19-30. In some embodiments, the gp120 protein peptide in each recombinant polypeptide is or includes a sequence of amino acids that exhibits at least or about 85%, at least or about 90%, at least or about 92%, at least or about 95%, at least or about 97% sequence identity to the sequence set forth in any of SEQ ID NOs: 19-30.
In some embodiments, the viral antigen or immunogen comprises an amino acid sequence having at least or about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to any of SEQ ID NOs: 19-30, including a sequence comprising substitution, deletion, and/or insertion at one or more amino acid positions.
Provided herein are polynucleic acids encoding recombinant peptides, such as HIV gp120. In some embodiments, the polynucleic acid encodes one, two, three, or more of the recombinant peptides.
In some embodiments, the viral antigen or immunogen is produced from a nucleic acid sequence that has been codon optimized. In some embodiments, the viral antigen or immunogen is produced from a nucleic acid sequence that has not been codon optimized.
In some embodiments, compositions and methods of use of recombinant soluble surface antigens from RNA viruses in covalently linked trimeric forms are disclosed. In some embodiments, the resulting fusion proteins are secreted as disulfide bond-linked homo-trimers, which are more stable in structure, while preserving the conformations of native-like trimeric viral antigens, thereby can be used as more effective vaccines against these dangerous pathogens.
It is contemplated that the HIV viral antigens and immunogens provided herein, e.g., gp120 protein peptides (see, Section I-1), can be combined, e.g., linked, to other proteins or peptides to form recombinant polypeptides, including fusion peptides. In some embodiments, individual recombinant polypeptides (e.g., monomers) provided herein associate to form multimers, e.g., trimers, of recombinant polypeptides. In some embodiments, association of the individual recombinant polypeptide monomers occurs via covalent interactions. In some embodiments, association of the individual recombinant polypeptide monomers occurs via non-covalent interactions. In some embodiments, the interaction, e.g., covalent or non-covalent, is effected by the protein or peptide to which the HIV viral antigen or immunogen, e.g., gp120 protein peptide, is linked. In some embodiments, for example when the HIV viral antigen or immunogen is a gp120 protein peptide as described herein, the protein or peptide to which it will be linked can be selected such that the native homotrimeric structure of the glycoprotein is preserved. This can be advantageous for evoking a strong and effective immunogenic response to the gp120 protein peptide. For example, preservation and/or maintenance of the native conformation of the HIV viral antigens or immunogens (e.g., gp120 protein peptide) may improve or allow access to antigenic sites capable to generating an immune response. In some cases, the recombinant polypeptide comprising a gp120 protein peptide described herein, e.g., see Section I-1, is referred to herein alternatively as a recombinant HIV antigen, recombinant HIV immunogen, or a recombinant HIV protein. a recombinant HIV gp120 antigen.
It is further contemplated that in some cases, the recombinant polypeptides or multimerized recombinant polypeptides thereof aggregate or can be aggregated to form a protein comprising a plurality of HIV viral antigen and/or immunogen recombinant polypeptides. Formation of such proteins may be advantageous for generating a strong and effective immunogenic response to the HIV viral antigens and/or immunogens. For instance, formation of a protein comprising a plurality of recombinant polypeptides, and thus a plurality of HIV viral antigens, e.g., gp120 protein peptides, may preserve the tertiary and/or quaternary structures of the viral antigen, allowing an immune response to be mounted against the native structure. In some cases, the aggregation may confer structural stability of the HIV viral antigen or immunogen, which in turn can afford access to potentially antigenic sites capable of promoting an immune response.
In some embodiments, the HIV viral antigen or immunogen can be linked at their C-terminus (C-terminal linkage) to a trimerization domain to promote trimerization of the monomers. In some embodiments, the trimerization stabilizes the membrane proximal aspect of the HIV viral antigen or immunogen in a trimeric configuration.
Non-limiting examples of exogenous multimerization domains that promote stable trimers of soluble recombinant proteins include: the GCN4 leucine zipper (Harbury et al. 1993 Science 262:1401-1407), the trimerization motif from the lung surfactant protein (Hoppe et al. 1994 FEBS Lett 344:191-195), collagen (McAlinden et al. 2003 J Biol Chem 278:42200-42207), and the phage T4 fibritin Foldon (Miroshnikov et al. 1998 Protein Eng 11:329-414), any of which can be linked to a recombinant HIV viral antigen or immunogen described herein (e.g., by linkage to the C-terminus of a gp120 domain) to promote trimerization of the recombinant viral antigen or immunogen. See also U.S. Pat. Nos. 7,268,116, 7,666,837, 7,691,815, 10,618,949, 10,906,944, and 10,960,070, and US 2020/0009244, which are incorporated herein by reference in their entireties for all purposes.
In some embodiments, one or more peptide linkers (such as a gly-ser linker, for example, a 10 amino acid glycine-serine peptide linker can be used to link the recombinant viral antigen or immunogen to the transmembrane domain. The trimer can include any of the stabilizing mutations provided herein (or combinations thereof) as long as the recombinant viral antigen or immunogen trimer retains the desired properties (e.g., the prefusion conformation).
To be therapeutically feasible, a desired trimerizing protein moiety for biologic drug designs should satisfy the following criteria. Ideally it should be part of a naturally secreted protein, like immunoglobulin Fc, that is also abundant (non-toxic) in the circulation, human in origin (lack of immunogenicity), relatively stable (long half-life) and capable of efficient self-trimerization which is strengthened by inter-chain covalent disulfide bonds so the trimerized HIV viral antigens or immunogens are structurally stable.
Collagen is a family of fibrous proteins that are the major components of the extracellular matrix. It is the most abundant protein in mammals, constituting nearly 25% of the total protein in the body. Collagen plays a major structural role in the formation of bone, tendon, skin, cornea, cartilage, blood vessels, and teeth. The fibrillar types of collagen I, II, III, IV, V, and XI are all synthesized as larger trimeric precursors, called procollagens, in which the central uninterrupted triple-helical domain consisting of hundreds of “G-X-Y” repeats (or glycine repeats) is flanked by non-collagenous domains (NC), the N-propeptide and the C-propeptide. Both the C- and N-terminal extensions are processed proteolytically upon secretion of the procollagen, an event that triggers the assembly of the mature protein into collagen fibrils which forms an insoluble cell matrix. BMP-1 is a protease that recognizes a specific peptide sequence of procollagen near the junction between the glycine repeats and the C-prodomain of collagens and is responsible for the removal of the propeptide. The shed trimeric C-propeptide of type I collagen is found in human sera of normal adults at a concentration in the range of 50-300 ng/mL, with children having a much higher level which is indicative of active bone formation. In people with familial high serum concentration of C-propeptide of type I collagen, the level could reach as high as 1-6 μg/mL with no apparent abnormality, suggesting the C-propeptide is not toxic. Structural study of the trimeric C-propeptide of collagen suggested that it is a tri-lobed structure with all three subunits coming together in a junction region near their N-termini to connect to the rest of the procollagen molecule. Such geometry in projecting proteins to be fused in one direction is similar to that of Fc dimer.
Type I, IV, V and XI collagens are mainly assembled into heterotrimeric forms consisting of either two α-1 chains and one α-2 chain (for Type I, IV, V), or three different a chains (for Type XI), which are highly homologous in sequence. The type II and III collagens are both homotrimers of α-1 chain. For type I collagen, the most abundant form of collagen, stable α(I) homotrimer is also formed and is present at variable levels in different tissues. Most of these collagen C-propeptide chains can self-assemble into homotrimers, when over-expressed alone in a cell. Although the N-propeptide domains are synthesized first, molecular assembly into trimeric collagen begins with the in-register association of the C-propeptides. It is believed the C-propeptide complex is stabilized by the formation of interchain disulfide bonds, but the necessity of disulfide bond formation for proper chain registration is not clear. The triple helix of the glycine repeats and is then propagated from the associated C-termini to the N-termini in a zipper-like manner. This knowledge has led to the creation of non-natural types of collagen matrix by swapping the C-propeptides of different collagen chains using recombinant DNA technology. Non-collagenous proteins, such as cytokines and growth factors, also have been fused to the N-termini of either procollagens or mature collagens to allow new collagen matrix formation, which is intended to allow slow release of the noncollagenous proteins from the cell matrix. However, under both circumstances, the C-propeptides are required to be cleaved before recombinant collagen fibril assembly into an insoluble cell matrix.
Although other protein trimerization domains, such as those from GCN4 from yeast fibritin from bacteria phage T4 and aspartate transcarbamoylase of Escherichia coli, have been described previously to allow trimerization of heterologous proteins, none of these trimerizing proteins are human in nature, nor are they naturally secreted proteins. As such, any trimeric fusion proteins would have to be made intracellularly, which not only may fold incorrectly for naturally secreted proteins such as soluble receptors, but also make purification of such fusion proteins from thousands of other intracellular proteins difficult. Moreover, the fatal drawback of using such non-human protein trimerization domains (e.g. from yeast, bacteria phage and bacteria) for trimeric biologic drug design is their presumed immunogenicity in the human body, rendering such fusion proteins ineffective shortly after injecting them into the human body.
The use of collagen in a recombinant polypeptide as described herein thus has many advantages, including: (1) collagen is the most abundant protein secreted in the body of a mammal, constituting nearly 25% of the total proteins in the body; (2) the major forms of collagen naturally occur as trimeric helixes, with their globular C-propeptides being responsible for the initiating of trimerization; (3) the trimeric C-propeptide of collagen proteolytically released from the mature collagen is found naturally at sub microgram/mL level in the blood of mammals and is not known to be toxic to the body; (4) the linear triple helical region of collagen can be included as a linker with predicted 2.9 Å spacing per residue, or excluded as part of the fusion protein so the distance between a protein to be trimerized and the C-propeptide of collagen can be precisely adjusted to achieve an optimal biological activity; (5) the recognition site of BMP1 which cleaves the C-propeptide off the pro-collagen can be mutated or deleted to prevent the disruption of a trimeric fusion protein; (6) the C-propeptide domain self-trimerizes via disulfide bonds and it provides a universal affinity tag, which can be used for purification of any secreted fusion proteins created. In some embodiments, the C-propeptide of collagen to which the HIV viral antigen and immunogen, e.g., gp120 protein peptide, enables the recombinant production of soluble, covalently-linked homotrimeric fusion proteins.
In some embodiments, the HIV viral antigen or immunogen is linked to a C-terminal propeptide of collagen to form a recombinant polypeptide. In some embodiments, the C-terminal propeptides of the recombinant polypeptides form inter-polypeptide disulfide bonds. In some embodiments, the recombinant proteins form trimers. In some embodiments, the HIV viral antigen or immunogen is a gp120 protein peptide as described in Section I-1.
In some embodiments, the C-terminal propeptide is of human collagen. In some embodiments, the C-terminal propeptide comprises a C-terminal polypeptide of proα1(1), proα1(II), proα1(III), proα1(V), proα1(XI), proα2(I), proα2(V), proα2(XI), or proα3(XI), or a fragment thereof. In some embodiments, the C-terminal propeptide is or comprises a C-terminal polypeptide of proα1(I).
In some embodiments, the C-terminal propeptide is or comprises the amino acid sequence set forth by any of SEQ ID NOs: 31-46. In some embodiments, the C-terminal propeptide is an amino acid sequence having at least or about 85%, 90%, 92%, 95%, or 97% sequence identity to sequence of any of SEQ ID NOs: 31-46.
In some embodiments, the C-terminal propeptide is or comprises the amino acid sequence of a collagen trimerization domain (e.g., C-propeptide of human α1(I) collagen) with an aspartic acid (D) to asparagine (N) substitution in the BMP-1 site, for instance where RAD is mutated to RAN. In some embodiments, the C-terminal propeptide is or comprises the amino acid sequence of a collagen trimerization domain (e.g., C-propeptide of human α1(I) collagen) with an alanine (A) to asparagine (N) substitution in the BMP-1 site, for instance where RAD is mutated to RND. In some embodiments, the C-terminal propeptide herein may comprise a mutated BMP-1 site, e.g., RSAN instead of DDAN. In some embodiments, the C-terminal propeptide herein may comprise a BMP-1 site, e.g., a sequence comprising the RAD (e.g., RADDAN) sequence instead of RAN (e.g., RANDAN) or RND (e.g., RNDDAN) may be used in a fusion polypeptide disclosed herein.
In some embodiments, the C-terminal propeptide can comprise a sequence comprising glycine-X-Y repeats linked to the N-terminus of any of SEQ ID NOs: 31-46, wherein X and Y are independently any amino acid, or an amino acid sequence at least 85%, 90%, 92%, 95%, or 97% identical thereto capable of forming inter-polypeptide disulfide bonds and trimerizing the recombinant polypeptides. In some embodiments, X and Y are independently proline or hydroxyproline.
In some cases where a gp120 peptide protein (e.g., HIV viral antigen or immunogen, e.g., see, Section I-1) is linked to the C-terminal propeptide to form the recombinant polypeptide, the recombinant polypeptides form a trimer resulting in a homotrimer of gp120 protein peptides. In some embodiments, the gp120 protein peptides of the trimerized recombinant polypeptides are in a prefusion conformation. In some embodiments, the gp120 protein peptides of the trimerized recombinant polypeptides are in a postfusion conformation. In some embodiments, the confirmation state allows for access to different antigenic sites on the gp120 protein peptides. In some embodiments, the antigenic sites are epitopes, such as linear epitopes or conformational epitopes. An advantage of having a trimerized recombinant polypeptides as described is that an immune response can be mounted against a variety of potential and diverse antigenic sites.
In some embodiments, trimerized recombinant polypeptides include individual recombinant polypeptides comprising the same viral antigen or immunogen. In some embodiments, trimerized recombinant polypeptides include individual recombinant polypeptides each comprising a different viral antigen or immunogen from the other recombinant polypeptides. In some embodiments, trimerized recombinant polypeptides include individual recombinant polypeptides wherein one of the individual recombinant polypeptides comprises a viral antigen or immunogen different from the other recombinant polypeptides. In some embodiments, trimerized recombinant polypeptides include individual recombinant polypeptides wherein two of the individual recombinant polypeptides comprise the same viral antigen or immunogen, and the viral antigen or immunogen is different from the viral antigen or immunogen comprised in the remaining recombinant polypeptide.
In some embodiments, the recombinant polypeptide comprises any HIV viral antigen or immunogen described in Section I-1. In some embodiments, the recombinant polypeptide comprises any HIV viral antigen or immunogen described in Section I-1 linked, as described herein, to the C-terminal propeptide of collagen as described herein.
In some embodiments, the recombinant polypeptide is or comprises the amino acid sequence set forth by any of SEQ ID NOs: 1-18. In some embodiments, the recombinant polypeptide is an amino acid sequence having at least or about 80%, 85%, 9/o, 92%, 95%, or 97% sequence identity to sequence of any of SEQ ID NOs: 1-18.
As indicated above, in some embodiments, the recombinant polypeptides provided herein associate not only to form trimers, but can also aggregate or be aggregated to generate proteins comprising a plurality of recombinant polypeptides. In some embodiments, the proteins formed have macrostructures. In some cases, the macrostructure may confer structural stability of the HIV viral antigen or immunogen recombinant polypeptides, which in turn can afford access to potentially antigenic sites capable of promoting an immune response.
In some embodiments, the proteins described herein comprising a plurality of recombinant polypeptides are an immunogen. In some embodiments, the proteins described herein comprising a plurality of recombinant polypeptides are comprised in a nanoparticle. For example, in some embodiments, the proteins are linked directly to a nanoparticle, e.g., protein nanoparticle. In some embodiments, the proteins are linked indirectly to a nanoparticle. In some embodiments, the proteins described herein comprising a plurality of recombinant polypeptides are comprised in virus-like particle (VLP).
Also provided are polynucleotides (nucleic acid molecules) encoding the HIV antigens or immunogens and recombinant polypeptides provided herein, and vectors for genetically engineering cells to express such HIV antigens or immunogens and recombinant polypeptides.
In some embodiments, provided are polynucleotides that encode recombinant polypeptides provided herein. In some aspects, the polynucleotide contains a single nucleic acid sequence, such as a nucleic acid sequence encoding a recombinant polypeptide. In other instances, the polynucleotide contains a first nucleic acid sequence encoding a recombinant polypeptide a particular HIV viral antigen or immunogen and a second nucleic acid sequence encoding a recombinant polypeptide comprising a different HIV viral antigen or immunogen.
In some embodiments, the polynucleotide encoding the recombinant polypeptide contains at least one promoter that is operatively linked to control expression of the recombinant polypeptide. In some embodiments, the polynucleotide contains two, three, or more promoters operatively linked to control expression of the recombinant polypeptide.
In some embodiments, for example when the polynucleotide contains two or more nucleic acid coding sequences, such as a sequences encoding recombinant polypeptides comprising different HIV viral antigens or immunogens, at least one promoter is operatively linked to control expression of the two or more nucleic acid sequences. In some embodiments, the polynucleotide contains two, three, or more promoters operatively linked to control expression of the recombinant polypeptides.
In some embodiments, expression of the recombinant polypeptide(s) is inducible or conditional. Thus, in some aspects, the polynucleotide encoding the recombinant polypeptide(s) contains a conditional promoter, enhancer, or transactivator. In some such aspects, the conditional promoter, enhancer, or transactivator is an inducible promoter, enhancer, or transactivator or a repressible promoter, enhancer, or transactivator. For example, in some embodiments, an inducible or conditional promoter can be used to restrict expression of the recombinant polypeptides to a specific microenvironment. In some embodiments, expression driven by the inducible or conditional promoter is regulated by exposure to an exogenous agent, such as heat, radiation, or drug.
In cases where the polynucleotide contains more than one nucleic acid sequence encoding a recombinant polypeptide, the polynucleotide may further include a nucleic acid sequence encoding a peptide between the one or more nucleic acid sequences. In some cases, the nucleic acid positioned between the nucleic acid sequences encodes a peptide that separates the translation products of the nucleic acid sequences during or after translation. In some embodiments, the peptide contains an internal ribosome entry site (IRES), a self-cleaving peptide, or a peptide that causes ribosome skipping, such as a T2A peptide.
In some embodiments, the polynucleotide encoding the recombinant polypeptide(s) is introduced into a composition containing cultured cells (e.g., host cells), such as by retroviral transduction, transfection, or transformation. In some embodiments, this can allow for expression (e.g., production) of the recombinant polypeptides. In some embodiments, the expressed recombinant polypeptides are purified.
In some embodiments, the polynucleotide (nucleic acid molecule) provided herein encodes an HIV viral antigen or immunogen as described herein. In some embodiments, the polynucleotide (nucleic acid molecule) provided herein encodes a recombinant polypeptide comprising HIV viral antigen or immunogen, e.g., HIV gp120 protein peptide, as described herein.
Also provided are vectors or constructs containing nucleic acid molecules as described herein. In some embodiments, the vectors or constructs contain one or more promoters operatively linked to the nucleic acid molecule encoding the recombinant polypeptide to drive expression thereof. In some embodiments, the promoter is operatively linked to one or more than one nucleic acid molecule, e.g., nucleic acid molecule encoding recombinant polypeptides containing different HIV viral antigens or immunogens.
In some embodiments, the vector is a viral vector. In some embodiments the viral vector is a retroviral vector. In some embodiments, the retroviral vector is a lentiviral vector. In some embodiments, the retroviral vector is a gammaretroviral vector.
In some embodiments, the vector or construct includes a single promoter that drives the expression of one or more nucleic acid molecules of the polynucleotide. In some embodiments, such promoters can be multicistronic (bicistronic or tricistronic, see e.g., U.S. Pat. No. 6,060,273). For example, in some embodiments, transcription units can be engineered as a bicistronic unit containing an IRES (internal ribosome entry site), which allows coexpression of gene products (e.g., encoding different recombinant polypeptides) by a message from a single promoter. In some embodiments, the vectors provided herein are bicistronic, allowing the vector to contain and express two nucleic acid sequences. In some embodiments, the vectors provided herein are tricistronic, allowing the vector to contain and express three nucleic acid sequences.
In some embodiments, a single promoter directs expression of an RNA that contains, in a single open reading frame (ORF), two or three genes (e.g. encoding the chimeric signaling receptor and encoding a recombinant receptor) separated from one another by sequences encoding a self-cleavage peptide (e.g., 2A sequences) or a protease recognition site (e.g., furin). The ORF thus encodes a single polypeptide, which, either during (in the case of 2A) or after translation, is processed into the individual proteins. In some cases, the peptide, such as T2A, can cause the ribosome to skip (ribosome skipping) synthesis of a peptide bond at the C-terminus of a 2A element, leading to separation between the end of the 2A sequence and the next peptide downstream (see, for example, de Felipe. Genetic Vaccines and Ther. 2:13 (2004) and deFelipe et al. Traffic 5:616-626 (2004)). Many 2A elements are known in the art. Examples of 2A sequences that can be used in the methods and nucleic acids disclosed herein include, without limitation, 2A sequences from the foot-and-mouth disease virus (F2A), equine rhinitis A virus (E2A), Thosea asigna virus (T2A), and porcine teschovirus-1 (P2A) as described in U.S. Patent Publication No. 20070116690.
In some embodiments, the vector is comprised in a virus. In some embodiments, the virus is a pseudovirus. In some embodiments, the virus is a viral-like particle. In some embodiments, the vector is comprised in a cell. In some embodiments, the virus or cell in which the vector is comprised contains a recombinant genome.
In some embodiments, provided herein is an immunogenic composition comprising a trimer of a recombinant polypeptide comprising a sequence selected from the group consisting of SEQ ID NOs: 1-18 or a fragment, variant, or mutant thereof, or a combination of any two or more of the trimers. In some embodiments, a unit dose of the immunogenic composition may comprise from about 10 μg to about 100 μg of the HIV antigen, preferably from about 25 μg to about 75 μg of the HIV antigen, preferably from about 40 μg to about 60 μg of the HIV antigen, or about 50 μg of the HIV antigen. In some embodiments, the dose contains 3 μg of the HIV antigen. In other embodiments, the dose contains 9 μg of the HIV antigen. In further embodiments, the dose contains 30 μg of the HIV antigen.
Immunogenic compositions comprising a disclosed immunogen (e.g., a disclosed recombinant HIV gp120 trimer or nucleic acid molecule encoding a protomer of disclosed recombinant HIV gp120 trimer) and a pharmaceutically acceptable carrier are also provided. In some embodiments, the immunogenic composition comprises trimerized recombinant polypeptides provided herein, and optionally a pharmaceutically acceptable carrier. In some embodiments, the immunogenic composition comprises a protein comprising a plurality of trimerized recombinant polypeptides provided herein, and optionally a pharmaceutically acceptable carrier. In some embodiments, the immunogenic composition a protein nanoparticle provided herein, and optionally a pharmaceutically acceptable carrier. In some embodiments, the immunogenic composition comprises a VLP as provided herein, and optionally a pharmaceutically acceptable carrier. In some embodiments, the immunogenic composition comprises an isolated nucleic acid provided herein, and optionally a pharmaceutically acceptable carrier. In some embodiments, the immunogenic composition comprises a vector as provided herein, and optionally a pharmaceutically acceptable carrier. In some embodiments, the immunogenic composition comprises a virus as provided herein, and optionally a pharmaceutically acceptable carrier. In some embodiments, the immunogenic composition comprises a pseudovirus provided herein, and optionally a pharmaceutically acceptable carrier. In some embodiments, the immunogenic composition comprises a cell as provided herein, and optionally a pharmaceutically acceptable carrier. In some embodiments, the immunogenic composition, such as described herein, is a vaccine. In some embodiments, the vaccine is a prophylactic vaccine. In some embodiments, the vaccine is a therapeutic vaccine. In some embodiments, the vaccine is a prophylactic vaccine and a therapeutic vaccine. 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, Pa., 1995.
Thus, an immunogen, e.g., recombinant HIV gp120 antigen, e.g., trimer, protein 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 polyoxypropylene (POP), such as POE-POP-POE block copolymers, MPL™ (3-O-deacylated monophosphoryl lipid A; Corixa, Hamilton, Ind.) and IL-12 (Genetics Institute, Cambridge, Mass.), 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 embodiments, the immunogenic compositions of the disclosure may include or be administered with more than one adjuvant. In some embodiments, the immunogenic compositions of the disclosure may include or be administered with two adjuvants. In some embodiments, the immunogenic compositions of the disclosure may include or be administered with a plurality of adjuvants. For example, in some cases, a vaccine, e.g., comprising an immunogenic composition provided herein, may include or be administered in combination with a plurality of adjuvants.
For vaccine compositions, examples of suitable adjuvants include, e.g., aluminum hydroxide, lecithin, Freund's adjuvant, MPL™ and IL-12 In some embodiments, the vaccine compositions or nanoparticle immunogens disclosed herein (e.g., HIV vaccine composition) can be formulated as a controlled-release or time-release formulation. This can be achieved in a composition that contains a slow release polymer or via a microencapsulated delivery system or bioadhesive gel. The various pharmaceutical compositions can be prepared in accordance with standard procedures well known in the art.
In some embodiments, the immunogenic compositions of the disclosure can contain an adjuvant formulation comprising a metabolizable oil (e.g., squalene) and alpha tocopherol in the form of an oil-in-water emulsion, and polyoxyethylene sorbitan monooleate (Tween-80). In some embodiments, the adjuvant formulation can comprise from about 2% to about 10% squalene, from about 2 to about 10% alpha tocopherol (e.g., D-alpha-tocopherol) and from about 0.3 to about 3% polyoxyethylene sorbitan monooleate. In some embodiments, the adjuvant formulation can comprise about 5% squalene, about 5% tocopherol, and about 0.4% polyoxyethylene sorbitan monooleate. In some embodiments, the immunogenic compositions of the disclosure can contain 3 de-O-acylated monophosphoryl lipid A (3D-MPL), and an adjuvant in the form of an oil in water emulsion, which adjuvant contains a metabolizable oil, alpha tocopherol, and polyoxyethylene sorbitan monoleate. In some embodiments, the immunogenic compositions of the disclosure can contain QS21 (extract of Quillaja saponaria Molina: fraction 21), 3D-MPL and an oil in water emulsion wherein the oil in water emulsion comprises a metabolizable oil, alpha tocopherol and polyoxyethylene sorbitan monooleate. In some embodiments, the immunogenic compositions of the disclosure can contain QS21, 3D-MPL and an oil in water emulsion wherein the oil in water emulsion has the following composition: a metabolisible oil, such as squalene, alpha tocopherol and Tween-80. In some embodiments, the immunogenic compositions of the disclosure can contain an adjuvant in the form of a liposome composition.
In some embodiments, the immunogenic compositions of the disclosure can contain an adjuvant formulation comprising a metabolizable oil (e.g., squalene), polyoxyethylene sorbitan monooleate (Tween-80), and Span 85. In some embodiments, the adjuvant formulation can comprise about 5% (w/v) squalene, about 0.5% (w/v) polyoxyethylene sorbitan monooleate, and about 0.5% (w/v) Span 85.
In some embodiments, the immunogenic compositions of the disclosure can contain an adjuvant formulation comprising Quillaja saponins, cholesterol, and phosphorlipid, e.g., in the form of a nanoparticle composition. In some embodiments, the immunogenic compositions of the disclosure can contain a mixture of separately purified fractions of Quillaja saponaria Molina where are subsequently formulated with cholesterol and phospholipid.
In some embodiments, the immunogenic compositions of the disclosure can contain an adjuvant selected from the group consisting of MF59™, Matrix-A™, Matrix-C™, Matrix-M™, AS01, AS02, AS03, and AS04.
In some embodiments, the immunogenic compositions of the disclosure can contain a toll-like receptor 9 (TLR9) agonist, wherein the TLR9 agonist is an oligonucleotide of from 8 to 35 nucleotides in length comprising an unmethylated cytidine-phospho-guanosine (also referred to as CpG or cytosine-phosphate-guanosine) motif, and the HIV antigen (e.g., gp120 proteins) and the oligonucleotide are present in the immunogenic composition in amounts effective to stimulate an immune response against the HIV antigen in a mammalian subject, such as a human subject in need thereof. TLR9 (CD289) recognizes unmethylated cytidine-phospho-guanosine (CpG) motifs found in microbial DNA, which can be mimicked using synthetic CpG-containing oligodeoxynucleotides (CpG-ODNs). CpG-ODNs are known to enhance antibody production and to stimulate T helper 1 (Th1) cell responses (Coffman et al., Immunity, 33:492-503, 2010). Optimal oligonucleotide TLR9 agonists often contain a palindromic sequence following the general formula of: 5′-purine-purine-CG-pyrimidine-pyrimidine-3′, or 5′-purine-purine-CG-pyrimidine-pyrimidine-CG-3′. U.S. Pat. No. 6,589,940, which is incorporated herein by reference in its entirety. In some embodiments, the CpG oligonucleotide is linear. In other embodiments, the CpG oligonucleotide is circular or includes hairpin loop(s). The CpG oligonucleotide may be single stranded or double stranded. In some embodiments, the CpG oligonucleotide may contain modifications. Modifications include but are not limited to, modifications of the 3′OH or 5′OH group, modifications of the nucleotide base, modifications of the sugar component, and modifications of the phosphate group. Modified bases may be included in the palindromic sequence of the CpG oligonucleotide as long as the modified base(s) maintains the same specificity for its natural complement through Watson-Crick base pairing (e.g., the palindromic portion is still self-complementary). In some embodiments, the CpG oligonucleotide comprises a non-canonical base. In some embodiments, the CpG oligonucleotide comprises a modified nucleoside. In some embodiments, the modified nucleoside is selected from the group consisting of 2′-deoxy-7-deazaguanosine, 2′-deoxy-6-thioguanosine, arabinoguanosine, 2′-deoxy-2′substituted-arabinoguanosine, and 2′-O-substituted-arabinoguanosine. The CpG oligonucleotide may contain a modification of the phosphate group. For example, in addition to phosphodiester linkages, phosphate modifications include, but are not limited to, methyl phosphonate, phosphorothioate, phosphoramidate (bridging or non-bridging), phosphotriester and phosphorodithioate and may be used in any combination. Other non-phosphate linkages may also be used. In some embodiments, the oligonucleotides comprise only phosphorothioate backbones. In some embodiments, the oligonucleotides comprise only phosphodiester backbones. In some embodiments, the oligonucleotide comprises a combination of phosphate linkages in the phosphate backbone such as a combination of phosphodiester and phosphorothioate linkages. Oligonucleotides with phosphorothioate backbones can be more immunogenic than those with phosphodiester backbones and appear to be more resistant to degradation after injection into the host (Braun et al., J Immunol, 141:2084-2089, 1988; and Latimer et al., Mol Immunol, 32:1057-1064, 1995). The CpG oligonucleotides of the present disclosure include at least one, two or three internucleotide phosphorothioate ester linkages. In some embodiments, when a plurality of CpG oligonucleotide molecules are present in a pharmaceutical composition comprising at least one excipient, both stereoisomers of the phosphorothioate ester linkage are present in the plurality of CpG oligonucleotide molecules. In some embodiments, all of the internucleotide linkages of the CpG oligonucleotide are phosphorothioate linkages, or said another way, the CpG oligonucleotide has a phosphorothioate backbone.
Any suitable CpG oligodeoxynucleotides (ODNs) or combinations thereof can be used as adjuvants in the present disclosure. For instance, K-type ODNs (also referred to as B type) encode multiple CpG motifs on a phosphorothioate backbone. K-type ODNs may be based on the following sequence TCCATGGACGTTCCTGAGCGTT. The use of phosphorothioate nucleotides enhances resistance to nuclease digestion when compared with native phosphodiester nucleotides, resulting in a substantially longer in vivo half life. K-type ODNs trigger pDCs to differentiate and produce TNF-α, and B cells to proliferate and secrete IgM. D-type ODNs (also referred to as A type) are constructed of a mixed phosphodiester/phosphorothioate backbone, contain a single CpG motif flanked by palindromic sequences and have poly G tails at the 3′ and 5′ ends (a structural motif that facilitates the formation of concatamers). D-type ODNs may be based on the following sequence GGTGCATCGATGCAGGGGGG. D-type ODNs trigger pDCs to mature and secrete IFN-α, but have no effect on B cells. C-type ODNs resemble K-type in being composed entirely of phosphorothioate nucleotides, but resemble D-type in containing palindromic CpG motifs. C-type ODNs may be based on the following sequence TCGTCGTTCGAACGACGTTGAT. This class of ODNs stimulate B cells to secrete IL-6 and pDCs to produce IFN-α. P-type ODNs contain two palindromic sequences, enabling them to form higher ordered structures. P-type ODNs may be based on the following sequence TCGTCGACGATCGGCGCGCGCCG. P-type ODNs activate B cells and pDCs, and induce substantially greater IFN-α production when compared with C-type ODNs. In this paragraph, bold letters in ODN sequences indicate self-complementary palindromes and CpG motifs are underlined.
Exemplary CpG ODNs, e.g., CpG 7909 (5′-TCGTCGTTTTGTCGTTTTGTCGTT-3′) and CpG 1018 (5′-TGACTGTGAACGTTCGAGATGA-3′), are known and disclosed in U.S. Pat. Nos. 7,255,868, 7,491,706, 7,479,285, 7,745,598, 7,785,610, 8,003,115, 8,133,874, 8,114,418, 8,222,398, 8,333,980, 8,597,665, 8,669,237, 9,028,845, and 10,052,378; application publication US 2020/0002704; and Bode et al., “CpG DNA as a vaccine adjuvant”, Expert Rev Vaccines (2011), 10(4): 499-511, all of which are incorporated herein by reference in their entireties for all purposes.
One or more adjuvants may be used in combination and may include, but are not limited to, alum (aluminum salts), oil-in-water emulsions, water-in-oil emulsions, liposomes, and microparticles, such as poly(lactide-co-glycolide) microparticles (Shah et al., Methods Mol Biol, 1494:1-14, 2017). In some embodiments, the immunogenic compositions further comprises an aluminum salt adjuvant to which the HIV antigen is adsorbed. In some embodiments, the aluminum salt adjuvant comprises one or more of the group consisting of amorphous aluminum hydroxyphosphate sulfate, aluminum hydroxide, aluminum phosphate, and potassium aluminum sulfate. In some embodiments, the aluminum salt adjuvant comprises one or both of aluminum hydroxide and aluminum phosphate. In some embodiments, the aluminum salt adjuvant comprises aluminum hydroxide. In some embodiments, a unit dose of the immunogenic composition comprises from about 0.25 to about 0.50 mg Al3+, or about 0.35 mg Al3+. In some embodiments, the immunogenic composition further comprises an additional adjuvant. Other suitable adjuvants include, but are not limited to, squalene-in-water emulsion (e.g., MF59 or AS03), TLR3 agonists (e.g., poly-IC or poly-ICLC), TLR4 agonists (e.g., bacterial lipopolysaccharide derivatives such monophosphoryl lipid A (MPL), and/or a saponin such as Quil A or QS-21, as in AS01 or AS02), a TLR5 agonist (bacterial flagellin), and TLR7, TLR8 and/or TLR9 agonists (imidazoquinoline derivatives such as imiquimod, and resiquimod) (Coffman et al., Immunity, 33:492-503, 2010). In some embodiments, the additional adjuvant comprises MPL and alum (e.g., AS04). For veterinary use and for production of antibodies in non-human animals, mitogenic components of Freund's adjuvant (both complete and incomplete) can be used.
In some embodiments, the immunogenic compositions comprise pharmaceutically acceptable excipients including for instance, solvents, bulking agents, buffering agents, tonicity adjusting agents, and preservatives (Pramanick et al., Pharma Times, 45:65-77, 2013). In some embodiments the immunogenic compositions may comprise an excipient that functions as one or more of a solvent, a bulking agent, a buffering agent, and a tonicity adjusting agent (e.g., sodium chloride in saline may serve as both an aqueous vehicle and a tonicity adjusting agent).
In some embodiments, the immunogenic compositions comprise an aqueous vehicle as a solvent. Suitable vehicles include for instance sterile water, saline solution, phosphate buffered saline, and Ringer's solution. In some embodiments, the composition is isotonic.
The immunogenic compositions may comprise a buffering agent. Buffering agents control pH to inhibit degradation of the active agent during processing, storage and optionally reconstitution. Suitable buffers include for instance salts comprising acetate, citrate, phosphate or sulfate. Other suitable buffers include for instance amino acids such as arginine, glycine, histidine, and lysine. The buffering agent may further comprise hydrochloric acid or sodium hydroxide. In some embodiments, the buffering agent maintains the pH of the composition within a range of 6 to 9. In some embodiments, the pH is greater than (lower limit) 6, 7 or 8. In some embodiments, the pH is less than (upper limit) 9, 8, or 7. That is, the pH is in the range of from about 6 to 9 in which the lower limit is less than the upper limit.
The immunogenic compositions may comprise a tonicity adjusting agent. Suitable tonicity adjusting agents include for instance dextrose, glycerol, sodium chloride, glycerin and mannitol.
The immunogenic compositions may comprise a bulking agent. Bulking agents are particularly useful when the pharmaceutical composition is to be lyophilized before administration. In some embodiments, the bulking agent is a protectant that aids in the stabilization and prevention of degradation of the active agents during freeze or spray drying and/or during storage. Suitable bulking agents are sugars (mono-, di- and polysaccharides) such as sucrose, lactose, trehalose, mannitol, sorbital, glucose and raffinose.
The immunogenic compositions may comprise a preservative. Suitable preservatives include for instance antioxidants and antimicrobial agents. However, in preferred embodiments, the immunogenic composition is prepared under sterile conditions and is in a single use container, and thus does not necessitate inclusion of a preservative.
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 paramyxovirus as described herein can be 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 HIV vaccine or a varicella zoster vaccine. As such, a disclosed immunogen including a recombinant HIV gp120 trimer 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 HIVe type b (Hib), polio, HIV and rotavirus.
Multivalent or combination vaccines provide protection against multiple pathogens. In some aspects, multivalent vaccines can protect against multiple strains of the same pathogen. In some aspects, multivalent vaccines protect against multiple pathogens, such as the combination vaccine Tdap, which protects against strains of tentus, pertussis, and diphtheria. Multivalent vaccines are highly desirable to minimize the number of immunizations required to confer protection against multiple pathogens or pathogenic strains, to reduce administration costs, and to increase coverage rates. This can be particularly useful, for example, when vaccinating babies or children.
In some embodiments, the vaccine, e.g., comprising an immunogenic composition described herein, is a multivalent vaccine. In some embodiments, the antigenic material for incorporation into the multivalent vaccine compositions of the invention is derived from HIV strains, or a combination thereof. Antigens for incorporation into the multivalent vaccine compositions of the invention may be derived from one strain of HIV or multiple strains, for example, between two and five strains, in order to provide a broader spectrum of protection. In one embodiment, antigens for incorporation into the multivalent vaccine compositions of the invention are derived from multiple strains of HIV. Other useful antigens include live, attenuated and inactivated viruses such as inactivated polio virus (Jiang et al., J. Biol. Stand., (1986) 14:103-9), attenuated strains of Hepatitis A virus (Bradley et al., J. Med. Virol., (1984) 14:373-86), attenuated measles virus (James et al., N. Engl. J. Med., (1995) 332:1262-6), and epitopes of pertussis virus (for example, ACEL-IMUNErM acellular DTP, Wyeth-Lederle Vaccines and Pediatrics).
In some aspects, a universal vaccine is a vaccine which protects against multiple strains of the same virus, such as multiple strains of HIV. Development of an effective universal HIV vaccine would reduce cost and labor with vaccine formulations and allow for more robust pandemic preparedness.
In some aspects, a universal vaccine is one comprised of multiple epitopes derived from distinct viral strains. In some aspects, a universal vaccine is comprised of a single epitope that is conserved across distinct viral strains. For example, a universal vaccine can be based on the relatively conserved domain(s) of an HIV surface protein, such as a conserved region of the gp120 protein.
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.
In some embodiments, disclosed herein are methods for using viral antigen trimers as a vaccine or as part of a multivalent vaccine to prevent viral infections, without or with adjuvant, or with more than one adjuvant, optionally via either intra-muscular injections or intra-nasal administrations.
In some embodiments, disclosed herein are methods for using viral antigen trimers as a vaccine or as part of a multivalent vaccine to prevent infections, without or with adjuvant, or with more than one adjuvant, optionally via either intra-muscular injections or intra-nasal administrations.
In some embodiments, disclosed herein are methods for using viral antigen trimers as an antigen for diagnosis of viral infections through detection of antibodies, e.g., IgM or IgG, that recognize the viral antigen, such as neutralizing antibodies.
In some embodiments, disclosed herein are methods for using viral antigen trimers as an antigen to generate polyclonal or monoclonal antibodies which can be used for passive immunization, e.g., neutralizing mAb for treating an HIV infection.
In some embodiments, disclosed herein is a viral antigen trimer as a vaccine or as part of a multivalent vaccine, wherein the vaccine comprises a plurality of trimeric subunit vaccines comprising viral antigens of the same protein of a virus or comprising viral antigens of two or more different proteins of one or more viruses or one or more strains of the same virus.
The disclosed immunogens (e.g., recombinant HIV gp120 trimer, a nucleic acid molecule (such as an RNA molecule) or vector encoding a protomer of a disclosed recombinant HIV gp120 trimer, or a protein nanoparticle or virus like particle comprising a disclosed recombinant HIV gp120 trimer) can be administered to a subject to induce an immune response to the corresponding HIV gp120 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 the corresponding HIV gp120. Elicitation of the immune response can also be used to treat or inhibit infection and illnesses associated with the corresponding HIV gp120.
A subject can be selected for treatment that has, or is at risk for developing infection with the HIV corresponding to the gp120 protein in the immunogen, for example because of exposure or the possibility of exposure to HIV. Following administration of a disclosed immunogen, the subject can be monitored for infection or symptoms associated with HIV, or both.
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 HIV 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 disclosed therapeutic agents are provided in advance of any symptom, for example, in advance of infection. The prophylactic administration of the disclosed therapeutic agents serves to prevent or ameliorate any subsequent infection. When provided therapeutically, the disclosed therapeutic agents are provided at or after the onset of a symptom of disease or infection, for example, after development of a symptom of infection with the HIV corresponding to the gp120 protein in the immunogen, or after diagnosis with the HIV infection. The therapeutic agents can thus be provided prior to the anticipated exposure to the HIV 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 virus, 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 HIV virus gp120 protein in the immunogen 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 HIV gp120 proteins. 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.
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 HIV gp120 trimer, viral vector, or nucleic acid molecule in a immunogenic composition, 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 a disclosed immunogen of this disclosure, the immune system of the subject typically responds to the immunogenic composition by producing antibodies specific for the HIV gp120 trimer included in the immunogen. 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 HIV gp120 trimer included in the immunogen.
HIV 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 HIV with one or more of the disclosed immunogens can reduce or inhibit infection with the HIV 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 infection with HIV in the absence of the immunogen. In additional examples, HIV replication can be reduced or inhibited by the disclosed methods. HIV 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 replication of the corresponding HIV 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 replication of HIV), as compared to replication of HIV 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.
One approach to administration of nucleic acids is direct immunization with plasmid DNA, such as with a mammalian expression plasmid. Immunization by nucleic acid constructs is well known in the art and taught, for example, in U.S. Pat. No. 5,643,578 (which describes methods of immunizing vertebrates by introducing DNA encoding a desired antigen to elicit a cell-mediated or a humoral response), and U.S. Pat. Nos. 5,593,972 and 5,817,637 (which describe operably linking a nucleic acid sequence encoding an antigen to regulatory sequences enabling expression). U.S. Pat. No. 5,880,103 describes several methods of delivery of nucleic acids encoding immunogenic peptides or other antigens to an organism. The methods include liposomal delivery of the nucleic acids (or of the synthetic peptides themselves), and immune-stimulating constructs, or ISCOMS™, negatively charged cage-like structures of 30-40 nm in size formed spontaneously on mixing cholesterol and Quil A™ (saponin). Protective immunity has been generated in a variety of experimental models of infection, including toxoplasmosis and Epstein-Barr virus-induced tumors, using ISCOMS™ as the delivery vehicle for antigens (Mowat and Donachie, Immunol. Today 12:383, 1991). Doses of antigen as low as 1 μg encapsulated in ISCOMS™ have been found to produce Class I mediated CTL responses (Takahashi et al., Nature 344:873, 1990).
In some embodiments, a plasmid DNA vaccine is used to express a disclosed immunogen in a subject. For example, a nucleic acid molecule encoding a disclosed immunogen can be administered to a subject to induce an immune response to the HIV gp120 protein included in the immunogen. In some embodiments, the nucleic acid molecule can be included on a plasmid vector for DNA immunization, such as the pVRC8400 vector (described in Barouch et al., J. Virol, 79, 8828-8834, 2005, which is incorporated by reference herein).
In another approach to using nucleic acids for immunization, a disclosed recombinant HIV gp120 or recombinant HIV gp120 trimer can be expressed by attenuated viral hosts or vectors or bacterial vectors. In another embodiments, a viral-vector based immunization protocol can be used to deliver a nucleic acid encoding a disclosed recombinant HIV gp120 or HIV gp120 trimer directly into cells. A number of viral based systems for gene transfer purposes have been described, such as retroviral and adenoviral systems. Recombinant vaccinia virus, adeno-associated virus (AAV), herpes virus, retrovirus, cytogmeglo virus or other viral vectors can be used to express the peptide or protein, thereby eliciting a CTL response. For example, vaccinia vectors and methods useful in immunization protocols are described in U.S. Pat. No. 4,722,848. BCG (Bacillus Calmette Guerin) provides another vector for expression of the peptides (see Stover, Nature 351:456-460, 1991).
In one embodiment, a nucleic acid encoding a disclosed recombinant HIV gp120 or HIV gp120 trimer is introduced directly into cells. For example, the nucleic acid can be loaded onto gold microspheres by standard methods and introduced into the skin by a device such as Bio-Rad's HELIOS™ Gene Gun. The nucleic acids can be “naked,” consisting of plasmids under control of a strong promoter. Typically, the DNA is injected into muscle, although it can also be injected directly into other sites. Dosages for injection are usually around 0.5 μg/kg to about 50 mg/kg, and typically are about 0.005 mg/kg to about 5 mg/kg (see, e.g., U.S. Pat. No. 5,589,466).
For example, the nucleic acid can be loaded onto gold microspheres by standard methods and introduced into the skin by a device such as Bio-Rad's HELIOS™ Gene Gun. The nucleic acids can be “naked,” consisting of plasmids under control of a strong promoter. Typically, the DNA is injected into muscle, although it can also be injected directly into other sites. Dosages for injection are usually around 0.5 μg/kg to about 50 mg/kg, and typically are about 0.005 mg/kg to about 5 mg/kg (see, e.g., U.S. Pat. No. 5,589,466).
In another embodiment, an mRNA-based immunization protocol can be used to deliver a nucleic acid encoding a disclosed recombinant HIV gp120 or HIV gp120 trimer directly into cells. In some embodiments, nucleic acid-based vaccines based on mRNA may provide a potent alternative to the previously mentioned approaches. mRNA vaccines preclude safety concerns about DNA integration into the host genome and can be directly translated in the host cell cytoplasm. Moreover, the simple cell-free, in vitro synthesis of RNA avoids the manufacturing complications associated with viral vectors. Two exemplary forms of RNA-based vaccination that can be used to deliver a nucleic acid encoding a disclosed recombinant HIV gp120 or HIV gp120 trimer include conventional non-amplifying mRNA immunization. Such methods have been used with viruses like HIV and are familiar to those of skill in the art (see, e.g., Petsch et al., “Protective efficacy of in vitro synthesized, specific mRNA vaccines against HIV virus infection,” Nature biotechnology, 30(12):1210-6, 2012) and self-amplifying mRNA immunization (see, e.g., Geall et al., “Nonviral delivery of self-amplifying RNA vaccines,” PNAS, 109(36): 14604-14609, 2012; Magini et al., “Self-Amplifying mRNA Vaccines Expressing Multiple Conserved Influenza Antigens Confer Protection against Homologous and Heterosubtypic Viral Challenge,” PLoS One, 11(8):e0161193, 2016; and Brito et al., “Self-amplifying mRNA vaccines,” Adv Genet., 89:179-233, 2015). In some embodiments, the isolated nucleic acid an RNA molecule. In some embodiments, the nucleic acid is an mRNA molecule, such as a nucleoside-modified mRNA, a non-amplifying mRNA, a self-amplifying mRNA, or a trans-amplifying mRNA.
In some embodiments, a nucleic acid encoding a disclosed recombinant HIV gp120 or HIV gp120 trimer is introduced directly into cells. For example, the nucleic acid or protein can be comprised within a virus-like particle (VLP). Virus-like particles (VLPs) are multiprotein structures that mimic the organization and structure of standard natural viruses, but lack the viral genome.
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 are known to the person of ordinary skill in the art and are further described herein, and include, but are not limited to, plaque reduction neutralization (PRNT) assays, microneutralization assays, flow cytometry based assays, single-cycle infection assays.
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 are known to the person of ordinary skill in the art and are further described herein, and include, but are not limited to, plaque reduction neutralization (PRNT) assays, microneutralization assays, flow cytometry based assays, single-cycle infection assays. In some embodiments, the serum neutralization activity can be assayed using a panel of HIV pseudoviruses.
In some embodiments, a neutralizing immune response induced by the disclosed immunogens herein generates a neutralizing antibody against an RNA virus such as HIV. In some embodiments, the neutralizing antibody herein binds to a cellular receptor of an RNA virus such as HIV or component thereof. In some embodiments, the viral receptor is retrovirus receptor or coreceptor, preferably an HIV-1 or HIV-2 receptor or coreceptor. In some embodiments, the neutralizing antibody herein modulates, decreases, antagonizes, mitigates, blocks, inhibits, abrogates and/or interferes with at least one RNA virus such as HIV activity or binding, or with an RNA virus receptor such as HIV receptor activity or binding, in vitro, in situ and/or in vivo, such as HIV release, HIV receptor signaling, membrane HIV cleavage, HIV activity, HIV production and/or synthesis. In some embodiments, the disclosed immunogens herein induce neutralizing antibodies against an RNA virus such as HIV that modulate, decrease, antagonize, mitigate, block, inhibit, abrogate and/or interfere with HIV virus binding to a receptor or coreceptor, such as CD4 and a co-receptor (e.g., CCR5 or CXCR4).
Also provided are articles of manufacture or kits containing the provided recombinant polypeptide, proteins, and immunogenic compositions provided herein. The articles of manufacture may include a container and a label or package insert on or associated with the container. Suitable containers include, for example, bottles, vials, syringes, test tubes, IV solution bags, etc. The containers may be formed from a variety of materials such as glass or plastic. In some embodiments, the container has a sterile access port. Exemplary containers include an intravenous solution bags, vials, including those with stoppers pierceable by a needle for injection. The article of manufacture or kit may further include a package insert indicating that the compositions can be used to treat a particular condition such as a condition described herein (e.g., HIV infection). Alternatively, or additionally, the article of manufacture or kit may further include another or the same container comprising a pharmaceutically-acceptable buffer. It may further include other materials such as other buffers, diluents, filters, needles, and/or syringes.
The label or package insert may indicate that the composition is used for treating an HIV infection in an individual. The label or a package insert, which is on or associated with the container, may indicate directions for reconstitution and/or use of the formulation. The label or package insert may further indicate that the formulation is useful or intended for subcutaneous, intravenous, or other modes of administration for treating or preventing an HIV infection in an individual.
The container in some embodiments holds a composition which is by itself or combined with another composition effective for treating, preventing and/or diagnosing the condition. The article of manufacture or kit may include (a) a first container with a composition contained therein (i.e., first medicament), wherein the composition includes the immunogenic composition or protein or recombinant polypeptide thereof: and (b) a second container with a composition contained therein (i.e., second medicament), wherein the composition includes a further agent, such as an adjuvant or otherwise therapeutic agent, and which article or kit further comprises instructions on the label or package insert for treating the subject with the second medicament, in an effective amount.
Unless defined otherwise, all terms of art, notations and other technical and scientific terms or terminology used herein are intended to have the same meaning as is commonly understood by one of ordinary skill in the art to which the claimed subject matter pertains. In some cases, terms with commonly understood meanings are defined herein for clarity and/or for ready reference, and the inclusion of such definitions herein should not necessarily be construed to represent a substantial difference over what is generally understood in the art.
The terms “polypeptide” and “protein” are used interchangeably to refer to a polymer of amino acid residues, and are not limited to a minimum length. Polypeptides, including the provided receptors and other polypeptides, e.g., linkers or peptides, may include amino acid residues including natural and/or non-natural amino acid residues. The terms also include post-expression modifications of the polypeptide, for example, glycosylation, sialylation, acetylation, and phosphorylation. In some aspects, the polypeptides may contain modifications with respect to a native or natural sequence, as long as the protein maintains the desired activity. These modifications may be deliberate, as through site-directed mutagenesis, or may be accidental, such as through mutations of hosts which produce the proteins or errors due to PCR amplification.
As used herein, a “subject” is a mammal, such as a human or other animal, and typically is human. In some embodiments, the subject, e.g., patient, to whom the agent or agents, cells, cell populations, or compositions are administered, is a mammal, typically a primate, such as a human. In some embodiments, the primate is a monkey or an ape. The subject can be male or female and can be any suitable age, including infant, juvenile, adolescent, adult, and geriatric subjects. In some embodiments, the subject is a non-primate mammal, such as a rodent.
As used herein, “treatment” (and grammatical variations thereof such as “treat” or “treating”) refers to complete or partial amelioration or reduction of a disease or condition or disorder, or a symptom, adverse effect or outcome, or phenotype associated therewith. Desirable effects of treatment include, but are not limited to, preventing occurrence or recurrence of disease, alleviation of symptoms, diminishment of any direct or indirect pathological consequences of the disease, preventing metastasis, decreasing the rate of disease progression, amelioration or palliation of the disease state, and remission or improved prognosis. The terms do not imply complete curing of a disease or complete elimination of any symptom or effect(s) on all symptoms or outcomes.
As used herein, “delaying development of a disease” means to defer, hinder, slow, retard, stabilize, suppress and/or postpone development of the disease (such as cancer). This delay can be of varying lengths of time, depending on the history of the disease and/or individual being treated. In some embodiments, sufficient or significant delay can, in effect, encompass prevention, in that the individual does not develop the disease. For example, a late stage cancer, such as development of metastasis, may be delayed.
“Preventing,” as used herein, includes providing prophylaxis with respect to the occurrence or recurrence of a disease in a subject that may be predisposed to the disease but has not yet been diagnosed with the disease. In some embodiments, the provided cells and compositions are used to delay development of a disease or to slow the progression of a disease.
As used herein, to “suppress” a function or activity is to reduce the function or activity when compared to otherwise same conditions except for a condition or parameter of interest, or alternatively, as compared to another condition. For example, cells that suppress tumor growth reduce the rate of growth of the tumor compared to the rate of growth of the tumor in the absence of the cells.
An “effective amount” of an agent, e.g., a pharmaceutical formulation, cells, or composition, in the context of administration, refers to an amount effective, at dosages/amounts and for periods of time necessary, to achieve a desired result, such as a therapeutic or prophylactic result.
A “therapeutically effective amount” of an agent, e.g., a pharmaceutical formulation or cells, refers to an amount effective, at dosages and for periods of time necessary, to achieve a desired therapeutic result, such as for treatment of a disease, condition, or disorder, and/or pharmacokinetic or pharmacodynamic effect of the treatment. The therapeutically effective amount may vary according to factors such as the disease state, age, sex, and weight of the subject, and the populations of cells administered. In some embodiments, the provided methods involve administering the cells and/or compositions at effective amounts, e.g., therapeutically effective amounts.
A “prophylactically effective amount” refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired prophylactic result. Typically but not necessarily, since a prophylactic dose is used in subjects prior to or at an earlier stage of disease, the prophylactically effective amount will be less than the therapeutically effective amount. In the context of lower tumor burden, the prophylactically effective amount in some aspects will be higher than the therapeutically effective amount.
The term “about” as used herein refers to the usual error range for the respective value readily known to the skilled person in this technical field. Reference to “about” a value or parameter herein includes (and describes) embodiments that are directed to that value or parameter per se.
As used herein, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise. For example, “a” or “an” means “at least one” or “one or more.”
Throughout this disclosure, various aspects of the claimed subject matter are presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the claimed subject matter. Accordingly, the description of a range should be considered to have specifically disclosed all the possible sub-ranges as well as individual numerical values within that range. For example, where a range of values is provided, it is understood that each intervening value, between the upper and lower limit of that range and any other stated or intervening value in that stated range is encompassed within the claimed subject matter. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges, and are also encompassed within the claimed subject matter, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the claimed subject matter. This applies regardless of the breadth of the range.
As used herein, a composition refers to any mixture of two or more products, substances, or compounds, including cells. It may be a solution, a suspension, liquid, powder, a paste, aqueous, non-aqueous or any combination thereof.
The term “vector,” as used herein, refers to a nucleic acid molecule capable of propagating another nucleic acid to which it is linked. The term includes the vector as a self-replicating nucleic acid structure as well as the vector incorporated into the genome of a host cell into which it has been introduced. Certain vectors are capable of directing the expression of nucleic acids to which they are operatively linked. Such vectors are referred to herein as “expression vectors.”
“Polyvalency” and “multivalency” are used interchangeably herein and refer to a feature of a nucleic acid or protein composition, e.g., protein or fragment thereof, that encodes or comprises a plurality of different proteins. Each nucleic acid, e.g., plasmid, encodes either a different HIV envelope glycoprotein (Env gp) or Env gp in the form of defective HIV viral particles, or an HIV envelope glycoprotein from different clades, or a combination of these possibilities, allowing for flexibility of this polyvalent nucleic acid, e.g., DNA plasmid, vaccine. As used herein, “envelope glycoproteins” (Env gps) refer not only to isolated Env gps, but also to Env gps in the form of defective viral particles. “3-valent” refers to a composition of three distinct antigens (e.g., an env gene of a clade A isolate, and env gene of a clade β isolate, and an env gene of a clade C isolate). Likewise, “4-valent” and “8-valent” refer to compositions with 4 and 8 unique antigens, respectively.
1. A protein comprising a plurality of recombinant polypeptides, each recombinant polypeptide comprising a human immunodeficiency virus gp120 protein peptide or a fragment or epitope thereof linked to a C-terminal propeptide of collagen, wherein the C-terminal propeptides of the recombinant polypeptides form inter-polypeptide disulfide bonds.
2. The protein of embodiment 1, wherein the HIV is an HIV-1, optionally a tier 1B, tier 1A, tier 2, or tier 3 virus.
3. The protein of embodiment 1 or 2, wherein the epitope is a linear epitope or a conformational epitope.
4. The protein of any of embodiments 1-3, wherein the gp120 protein peptide comprises an outer domain subunit peptide, an inner domain subunit peptide, or any combination thereof, and wherein the protein comprises three recombinant polypeptides.
5. The protein of any of embodiments 1-4, wherein the gp120 protein peptide comprises one, two, three, four, or five C regions, and one, two, three, four, or five variable regions, optionally separated by a bridging sheet.
6. The protein of any of embodiments 1-5, wherein the gp120 protein peptide comprises an outer subunit or an inner subunit of the gp120 protein.
7. The protein of any of embodiments 1-6, wherein the gp120 protein peptide comprises an inner subunit and an outer subunit of the gp120 protein, optionally wherein the outer subunit and the inner subunit are linked by a disulfide bond or an artificially introduced linker.
8. The protein of any of embodiments 1-7, wherein the gp120 protein peptide does not comprise a transmembrane (TM) domain peptide and/or a cytoplasm (CP) domain peptide.
9. The protein of any of embodiments 1-8, wherein the gp120 protein peptide comprises a protease cleavage site, wherein the protease is optionally furin, a transmembrane serine protease such as TMPRSS2, trypsin, factor Xa, or cathepsin L.
10. The protein of any of embodiments 1-8, wherein the gp120 protein peptide does not comprise a protease cleavage site, wherein the protease is optionally furin, a transmembrane serine protease such as TMPRSS2, trypsin, factor Xa, or cathepsin L.
11. The protein of any of embodiments 1-10, wherein the gp120 protein peptide is soluble or does not directly bind to a lipid bilayer, e.g., a membrane or viral envelope.
12. The protein of any of embodiments 1-11, wherein the gp120 protein peptides are the same or different among the recombinant polypeptides of the protein.
13. The protein of any of embodiments 1-12, wherein the gp120 protein peptide is directly fused to the C-terminal propeptide, or is linked to the C-terminal propeptide via a linker, such as a linker comprising glycine-X-Y repeats, wherein X and Y and independently any amino acid and optionally proline or hydroxyproline.
14. The protein of any of embodiments 1-13, which is soluble.
15. The protein of any of embodiments 1-14, wherein the protein does not directly bind to a lipid bilayer, e.g., a membrane or viral envelope.
16. The protein of any of embodiments 1-15, wherein the protein is capable of binding to a cell surface attachment factor or receptor of a subject, optionally wherein the subject is a mammal such as a primate, e.g., human.
17. The protein of any of embodiments 1-16, wherein the C-terminal propeptide is of human collagen.
18. The protein of any of embodiments 1-17, wherein the C-terminal propeptide comprises a C-terminal polypeptide of proα1(I), proα1(II), proα1(III), proα1(V), proα1(XI), proα2(I), proα2(V), proα2(XI), or proα3(XI), or a fragment thereof.
19. The protein of any of embodiments 1-18, wherein the C-terminal propeptides are the same or different among the recombinant polypeptides.
20. The protein of any of embodiments 1-19, wherein the C-terminal propeptide comprises any of SEQ ID NOs: 31-46 or an amino acid sequence at least 90% identical thereto capable of forming inter-polypeptide disulfide bonds and trimerizing the recombinant polypeptides.
21. The protein of any of embodiments 1-20, wherein the C-terminal propeptide comprises SEQ ID NO: 31 or an amino acid sequence at least 90% identical thereto capable of forming inter-polypeptide disulfide bonds and trimerizing the recombinant polypeptides.
22. The protein of any of embodiments 1-20, wherein the C-terminal propeptide comprises SEQ ID NO: 32 or an amino acid sequence at least 9/o identical thereto capable of forming inter-polypeptide disulfide bonds and trimerizing the recombinant polypeptides.
23. The protein of any of embodiments 1-20, wherein the C-terminal propeptide comprises SEQ ID NO: 33 or an amino acid sequence at least 90% identical thereto capable of forming inter-polypeptide disulfide bonds and trimerizing the recombinant polypeptides.
24. The protein of any of embodiments 1-20, wherein the C-terminal propeptide comprises SEQ ID NO:34 or an amino acid sequence at least 90% identical thereto capable of forming inter-polypeptide disulfide bonds and trimerizing the recombinant polypeptides.
25. The protein of any of embodiments 1-20, wherein the C-terminal propeptide comprises SEQ ID NO: 35 or an amino acid sequence at least 90% identical thereto capable of forming inter-polypeptide disulfide bonds and trimerizing the recombinant polypeptides.
26. The protein of any of embodiments 1-20, wherein the C-terminal propeptide comprises SEQ ID NO: 36 or an amino acid sequence at least 90% identical thereto capable of forming inter-polypeptide disulfide bonds and trimerizing the recombinant polypeptides.
27. The protein of any of embodiments 1-20, wherein the C-terminal propeptide comprises SEQ ID NO: 37 or an amino acid sequence at least 90% identical thereto capable of forming inter-polypeptide disulfide bonds and trimerizing the recombinant polypeptides.
28. The protein of any of embodiments 1-20, wherein the C-terminal propeptide comprises SEQ ID NO: 38 or an amino acid sequence at least 90% identical thereto capable of forming inter-polypeptide disulfide bonds and trimerizing the recombinant polypeptides.
29. The protein of any of embodiments 1-20, wherein the C-terminal propeptide comprises SEQ ID NO: 39 or an amino acid sequence at least 90% identical thereto capable of forming inter-polypeptide disulfide bonds and trimerizing the recombinant polypeptides.
30. The protein of any of embodiments 1-29, wherein the C-terminal propeptide comprises a sequence comprising glycine-X-Y repeats linked to the N-terminus of any of SEQ ID NOs: 31-46, wherein X and Y and independently any amino acid and optionally proline or hydroxyproline, or an amino acid sequence at least 90% identical thereto capable of forming inter-polypeptide disulfide bonds and trimerizing the recombinant polypeptides.
31. The protein of any of embodiments 1-30, wherein the gp120 protein peptide in each recombinant polypeptide is in a prefusion conformation or a postfusion conformation.
32. The protein of any of embodiments 1-31, wherein the gp120 protein peptide in each recombinant polypeptide comprises SEQ ID NO: 19-30 or an amino acid sequence at least 80% identical thereto.
33. The protein of any of embodiments 1-32, wherein the recombinant polypeptide comprises SEQ ID NO: 1-18 or an amino acid sequence at least 80% identical thereto.
34. An immunogen comprising the protein of any of embodiments 1-33.
35. A protein nanoparticle comprising the protein of any of embodiments 1-33 directly or indirectly linked to a nanoparticle.
36. A virus-like particle (VLP) comprising the protein of any of embodiments 1-33.
37. An isolated nucleic acid encoding one, two, three or more of the recombinant polypeptides of the protein of any of embodiments 1-33.
38. The isolated nucleic acid of embodiment 37, wherein a polypeptide encoding the gp120 protein peptide is fused in-frame to a polypeptide encoding the C-terminal propeptide of collagen.
39. The isolated nucleic acid of embodiment 37 or 38, which is operably linked to a promoter.
40. The isolated nucleic acid of any of embodiments 37-39, which is a DNA molecule.
41. The isolated nucleic acid of any of embodiments 37-39, which is an RNA molecule, optionally an mRNA molecule such as a nucleoside-modified mRNA, a non-amplifying mRNA, a self-amplifying mRNA, or a trans-amplifying mRNA.
42. A vector comprising the isolated nucleic acid of any of embodiments 37-41.
43. The vector of embodiment 42, which is a viral vector.
44. A virus, a pseudovirus, or a cell comprising the vector of embodiment 42 or 43, optionally wherein the virus or cell has a recombinant genome.
45. An immunogenic composition comprising the protein, immunogen, protein nanoparticle, VLP, isolated nucleic acid, vector, virus, pseudovirus, or cell of any one of embodiments 1-44, and a pharmaceutically acceptable carrier.
46. A vaccine comprising the immunogenic composition of embodiment 45 and optionally an adjuvant, wherein the vaccine is optionally a subunit vaccine, and/or optionally wherein the vaccines is a prophylactic and/or therapeutic vaccine.
47. The vaccine of embodiment 46, wherein the vaccine comprises a plurality of different adjuvants.
48. A method of producing a protein, comprising: expressing the isolated nucleic acid or vector of any one of embodiments 37-43 in a host cell to produce the protein of any of embodiments 1-33; and purifying the protein.
49. The protein produced by the method of embodiment 48.
50. A method for generating an immune response to an gp120 protein peptide or fragment or epitope thereof of HIV in a subject, comprising administering to the subject an effective amount of the protein, immunogen, protein nanoparticle, VLP, isolated nucleic acid, vector, virus, pseudovirus, cell, immunogenic composition, or vaccine of any one of embodiments 1-47 and 49 to generate the immune response.
51. The method of embodiment 50, for treating or preventing infection with HIV.
52. The method of embodiment 50 or 51, wherein generating the immune response inhibits or reduces replication of HIV in the subject.
53. The method of any of embodiments 50-52, wherein the immune response comprises a cell-mediated response and/or a humoral response, optionally comprising production of one or more neutralizing antibody, such as a polyclonal antibody or a monoclonal antibody.
54. The method of any of embodiments 50-53, wherein the immune response is against the gp120 protein peptide or fragment or epitope thereof of HIV but not against the C-terminal propeptide.
55. The method of any of embodiments 50-54, wherein the administering does not lead to antibody dependent enhancement (ADE) in the subject due to prior exposure to one or more HIV viruses.
56. The method of any of embodiments 50-55, wherein the administering does not lead to antibody dependent enhancement (ADE) in the subject when subsequently exposed to one or more HIV viruses.
57. The method of any of embodiments 50-56, further comprising a priming step and/or a boosting step.
58. The method of any of embodiments 50-57, wherein the administering step is performed via topical, transdermal, subcutaneous, intradermal, oral, intranasal (e.g., intranasal spray), intratracheal, sublingual, buccal, rectal, vaginal, inhaled, intravenous (e.g., intravenous injection), intraarterial, intramuscular (e.g., intramuscular injection), intracardiac, intraosseous, intraperitoneal, transmucosal, intravitreal, subretinal, intraarticular, peri-articular, local, or epicutaneous administration.
59. The method of any of embodiments 50-58, wherein the effective amount is administered in a single dose or a series of doses separated by one or more interval.
60. The method of any of embodiments 50-59, wherein the effective amount is administered without an adjuvant.
61. The method of any of embodiments 50-59, wherein the effective amount is administered with an adjuvant.
62. A method comprising administering to a subject an effective amount of the protein of any one of embodiments 1-33 to generate in the subject a neutralizing antibody or neutralizing antisera to HIV.
63. The method of embodiment 62, wherein the subject is a mammal, optionally a human or a non-human primate.
64. The method of embodiment 62 or 63, further comprising isolating the neutralizing antibody or neutralizing antisera from the subject.
65. The method of embodiment 64, further comprising administering an effective amount of the isolated neutralizing antibody or neutralizing antisera to a human subject via passive immunization to prevent or treat an infection by HIV.
66. The method of any of embodiments 62-65, wherein the neutralizing antisera comprises polyclonal antibodies to the gp120 protein peptide or fragment or epitope thereof, optionally wherein the neutralizing antibody is free or substantially free of antibodies to the C-terminal propeptide of collagen.
67. The method of any of embodiments 62-65, wherein the neutralizing antibody comprises a monoclonal antibody to the gp120 protein peptide or fragment or epitope thereof, optionally wherein the neutralizing antibody is free or substantially free of antibodies to the C-terminal propeptide of collagen.
68. The protein, immunogen, protein nanoparticle, VLP, isolated nucleic acid, vector, virus, pseudovirus, cell, immunogenic composition, or vaccine of any one of embodiments 1-47 and 49, for use in inducing an immune response to HIV in a subject, and/or in treating or preventing an infection by HIV.
69. Use of the protein, immunogen, protein nanoparticle, VLP, isolated nucleic acid, vector, virus, pseudovirus, cell, immunogenic composition, or vaccine of any one of embodiments 1-47 and 49, for inducing an immune response to HIV in a subject, and/or for treating or preventing an infection by HIV.
70. Use of the protein, immunogen, protein nanoparticle, VLP, isolated nucleic acid, vector, virus, pseudovirus, cell, immunogenic composition, or vaccine of any one of embodiments 1-47 and 49, for the manufacture of a medicament or a prophylactic for inducing an immune response to an HIV in a subject, and/or for treating or preventing an infection by HIV.
71. A method for analyzing a sample, comprising: contacting a sample with the protein of any of embodiments 1-33, and detecting a binding between the protein and an analyte capable of specific binding to the gp120 protein peptide or fragment or epitope thereof of HIV.
72. The method of embodiment 71, wherein the analyte is an antibody, a receptor, or a cell recognizing the gp120 protein peptide or fragment or epitope thereof.
73. The method of embodiment 71 or 72, wherein the binding indicates the presence of the analyte in the sample, and/or an infection by HIV in a subject from which the sample is derived.
74. A kit comprising the protein of any of embodiments 1-33 and a substrate, pad, or vial containing or immobilizing the protein, optionally wherein the kit is an ELISA or lateral flow assay kit.
The following examples are included for illustrative purposes only and are not intended to limit the scope of the invention.
An exemplary gp120 fusion protein was generated, characterized in vitro and evaluated for in vivo efficacy. This exemplary gp120 fusion protein was observed to be highly native-like based on negative-stain electron microscopy. The exemplary gp120 fusion protein was observed to bind CD4 and various broadly neutralizing antibodies (bNAbs) with high affinity and tight binding kinetics. It was also demonstrated the exemplary gp120 fusion protein was able to induce bNAbs against a diverse panel of Tier-2 viruses in a rabbit immunization study.
85US_Ba-L gp120 env gene was synthesized after optimization for Chinese hamster ovary (CHO) expression by Genscript (Nanjing), using gp120 NCBI accession DQ318210.1. The gene fragment encoding the gp120 glycoprotein was cloned into the pTrimer-tag vector through HindIII and BglII sites as shown in
The construct was stably transfected into the CHO-S dhfr−/− cell line using 1 μg gp120-Trimer plasmid by FuGENE6. After clone selection, the high-expression clone was used to produce the exemplary fusion protein comprising HIV gp120 in Serum Free Medium (SFM). The supernatants in the bioreactor were harvested after 9 days by centrifugation at 4000 g for 20 min at 4° C. Cell debris were removed by 0.2 μm filter before purification. Supernatants were first run over a 5 mL Blue-Sepharose affinity purification column. The eluate was concentrated with 50 mL ultra-filters and immediately buffer exchanged into PBS, further purified by SEC using superdex 200 and elute with PBS, pH 7.4. The flow rate was maintained above at 5 mL/min. The trimeric fractions were isolated, concentrated and stored at −80° C. The protein concentrations were detected using BCA assay (ThermoFisher). Purity of the isolated exemplary fusion protein comprising HIV gp120 is shown in
Exemplary fusion protein alone and in complex with B12 or CD4 were analyzed by negative-stain electron microcopy as shown in
The binding kinetics of the exemplary fusion protein comprising HIV gp120 were assessed against several broadly neutralizing antibodies (bNAbs) is shown in
Binding kinetics were additional measured at 30° C. by fortebio OCTET QKe Bio-layer interferometry (BLI) system (Pall Life Science Corp), as shown in
Female New Zealand White rabbits were immunized intramuscularly with either 50 μg of exemplary fusion protein (n=2) or 50 μg of exemplary fusion protein plus alum adjuvant (n=2) on Days 0, 21, 42 and 140. As shown in
Immunization with exemplary HIV gp120 fusion protein was observed to induce HIV-1 neutralizing antibodies, including against Tier 1A and 1B (
The present invention is not intended to be limited in scope to the particular disclosed embodiments, which are provided, for example, to illustrate various aspects of the invention. Various modifications to the compositions and methods described will become apparent from the description and teachings herein. Such variations may be practiced without departing from the true scope and spirit of the disclosure and are intended to fall within the scope of the present disclosure.
| Number | Date | Country | Kind |
|---|---|---|---|
| PCT/CN2020/095335 | Jun 2020 | WO | international |
| PCT/CN2021/087054 | Apr 2021 | WO | international |
This application claims priority to and the benefit of International Patent Application Nos. PCT/CN2020/095335, filed Jun. 10, 2020, and PCT/CN2021/087054, filed Apr. 13, 2021, the disclosures of which applications are incorporated herein by reference in their entireties for all purposes.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/CN2021/099292 | 6/10/2021 | WO |
