US20150265694A1 - Vaccines and methods for creating a vaccine for inducing immunity to all dengue virus serotypes - Google Patents

Vaccines and methods for creating a vaccine for inducing immunity to all dengue virus serotypes Download PDF

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US20150265694A1
US20150265694A1 US13/660,653 US201213660653A US2015265694A1 US 20150265694 A1 US20150265694 A1 US 20150265694A1 US 201213660653 A US201213660653 A US 201213660653A US 2015265694 A1 US2015265694 A1 US 2015265694A1
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amino acids
seq
envelope protein
protein
fever virus
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Sharon ISERN
Scott F. Michael
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Florida Gulf Coast University
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/12—Viral antigens
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A61P31/14—Antivirals for RNA viruses
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/005—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N7/00—Viruses; Bacteriophages; Compositions thereof; Preparation or purification thereof
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/70—Multivalent vaccine
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/40—Fusion polypeptide containing a tag for immunodetection, or an epitope for immunisation
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
    • C12N2770/00011—Details
    • C12N2770/24011—Flaviviridae
    • C12N2770/24111—Flavivirus, e.g. yellow fever virus, dengue, JEV
    • C12N2770/24122—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
    • C12N2770/00011—Details
    • C12N2770/24011—Flaviviridae
    • C12N2770/24111—Flavivirus, e.g. yellow fever virus, dengue, JEV
    • C12N2770/24134—Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
    • C12N2770/00011—Details
    • C12N2770/24011—Flaviviridae
    • C12N2770/24111—Flavivirus, e.g. yellow fever virus, dengue, JEV
    • C12N2770/24151—Methods of production or purification of viral material
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

  • Dengue viruses members of the genus Flavivirus
  • DF dengue fever
  • DHF dengue hemorrhagic fever
  • DSS dengue shock syndrome
  • a method of forming a chimeric protein comprising the steps of providing a yellow fever virus 17-D envelope protein having SEQ ID No. 1; providing a dengue fever virus envelope protein selected from the group consisting of SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, or SEQ ID No. 5; and substituting one or more of amino acids 1-11, 28-30, 32, 42, 44, 46, 70-81, 95-99, 110-115, 142-147, 149-157, 236-242, 304-324, 333, 335, 337, 350-352, 355, 356, 362-370, 377, 379, 386, 388-393 of SEQ ID No. 1 with the corresponding amino acid of the selected dengue fever virus envelope protein to create a chimeric envelope protein.
  • Also described here is a method of creating a treatment composition, comprising the steps of providing a portion of an envelope protein from a flavivirus; providing a dengue fever virus envelope protein selecting from the group consisting of SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, or SEQ ID No. 5; substituting a portion of the envelope protein amino acids of the flavivirus with a the corresponding envelope protein amino acids of the selected dengue fever virus to create a chimeric envelope protein; providing a pharmaceutically acceptable excipient; and mixing the chimeric envelope protein and the excipient.
  • a chimeric protein comprising: an envelope protein comprised of yellow fever virus 17-D envelope protein having SEQ ID No. 1, wherein selected amino acids of the yellow fever virus 17-D envelope protein are substituted with corresponding amino acids of dengue fever virus envelope protein selected from the group consisting of SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, or SEQ ID No. 5.
  • compositions for treatment of dengue fever virus comprising: a chimeric envelope protein comprised of a flavivirus envelope protein, wherein selected amino acids of the flavivirus envelope protein are substituted with corresponding amino acids of dengue fever virus envelope protein selected from the group consisting of SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, or SEQ ID No. 5; and a pharmaceutically acceptable excipient.
  • FIG. 1 shows the results of ELISA assays with immobilized virus envelope glycoproteins, patient sera, and monoclonal antibodies from DENV infected patients.
  • FIG. 2 shows the results of immunofluorescence assays with DENV-1 to 4 infected LLC-MK-2 cells exposed to monoclonal antibodies from DENV infected patients.
  • FIG. 3 shows the results of neutralization assays with DENV-1 to 4 infected LLC-MK-2 cells, patient sera, monoclonal antibodies from DENV infected patients.
  • FIG. 4 shows the viral uptake results from enhancement assays performed in the presence of monoclonal antibodies from DENV infected patients.
  • FIG. 5 shows the results from virus-cell binding inhibition assays performed in the presence of monoclonal antibodies from DENV infected patients.
  • FIG. 6 shows the results from virus-liposome binding inhibition assays performed in the presence of monoclonal antibodies from DENV infected patients.
  • FIG. 7 shows the results from Western blot assays performed with purified DENV-2 and probed with monoclonal antibodies from DENV infected patients.
  • FIG. 8 shows the results from Western blot assays performed with soluble protein E and probed with monoclonal antibodies from DENV infected patients.
  • FIG. 9 shows the results from epitope mapping and gives the dissociation constants of monoclonal antibodies from DENV infected patients to soluble protein E.
  • FIG. 10 shows the results from binding competition ELISA assays with monoclonal antibodies from DENV infected patients and 4G2.
  • FIG. 11 shows the results from Western blot assays performed with DI/II and DIII and probed with monoclonal antibodies from DENV infected patients.
  • FIG. 12 shows the residues for monoclonal antibodies from DENV infected patients mapped to E protein crystal structure.
  • FIG. 13 shows an amino acid sequence alignment of DENV-1 to 4 and the yellow fever 17-D envelope protein.
  • FIG. 14 shows the protein crystal structure of the DENV envelope protein and demonstrates the location of the fusion loop (black) and 5 ⁇ (green) and 14 ⁇ (teal) surrounding amino acids.
  • DHF dengue hemorrhagic fever
  • DSS shock syndromes
  • Dengue virus is a mosquito-transmitted virus and is expanding in geographic range and also in disease severity. There are four distinct serotypes of dengue that cause similar disease symptoms, serotypes 1-4. Infection with a single serotype results in an immune response that is protective against that same serotype, but causes a cross-reactive antibody response against the other serotypes (and other flaviviruses as well). Epidemiological studies have shown that the presence of cross-reactive antibodies correlates with a more severe disease outcome during subsequent infections with a different serotype. The mechanism for this effect appears to be an antibody-dependent enhancement of infection of macrophage and macrophage like cells that express Fc receptors. These cells are normally not infected efficiently by dengue, but become highly infectable in the presence of dengue virus binding antibodies that then target the virus particles directly to the macrophages through the interaction of the antibody heavy chains and the cellular Fc receptors.
  • the invention relates to a chimeric protein and methods for producing a chimeric protein for immunizing an individual against dengue and dengue clinical outcomes, and for treating an individual susceptible to infection or infected with dengue virus.
  • the chimeric protein could be used to create a treatment composition for an infected individual, while in others the chimeric protein could be used to produce a live attenuated vaccine, or a subunit vaccine that is not replicative.
  • the chimeric protein is created by substituting a portion of yellow fever virus (YFV) envelope protein, Flavivirus yellow fever virus, with a portion of any of the strains of dengue virus (DENV) envelope protein, Flavivirus dengue virus.
  • the chimeric protein of the invention is created using YFV 17D strain envelope protein.
  • the example is limited to YFV envelope protein, in other embodiments it is envisioned the chimeric protein may be created using the envelope protein of any flavivirus, for example West Nile Virus, St. Louis encephalitis, Dengue Fever virus, Japanese encephalitis, and Kunjin virus, and substituting any of the four strains of DENV envelope protein.
  • YFV 17D strain envelope protein has the following sequence, identified as SEQ ID No. 1:
  • DENV strain 1 envelope protein has the following sequence, identified as SEQ ID No. 2:
  • DENV strain 2 envelope protein has the following sequence, identified as SEQ ID No. 3:
  • DENV strain 3 envelope protein has the following sequence, identified as SEQ ID No. 4:
  • DENV strain 4 envelope protein has the following sequence, identified as SEQ ID No. 5:
  • FIG. 13 shows an alignment of the YFV 17D strain envelope protein of and all four strains of DENV envelope protein.
  • a “corresponding amino acid” is defined as follows.
  • FIG. 13 may be used to calculate which amino acids of the DENV envelope protein corresponds to the amino acid of the YFV envelope protein.
  • FIG. 13 shows that the first amino acid of YFV envelope protein, alanine, corresponds to the first amino acid of all four strains of DENV envelope protein, methionine.
  • FIG. 13 may also be used to calculate that the 160 th amino acid of the YFV envelope protein, lysine, corresponds to the following amino acids of the four strains of DENV envelope protein:
  • a similar amino acid alignment may be created by practitioners in the art with other flavivirus envelope proteins, for example with West Nile Virus, St. Louis encephalitis, Dengue Fever virus, Japanese encephalitis, and Kunjin virus envelope proteins. These amino acid alignments could be used to determine which amino acid of the flavivirus envelope protein corresponded to any of the four strains of DENV envelope protein.
  • Any or all of amino acids 1-11, 28-30, 32, 42, 44, 46, 70-81, 95-99, 110-115, 142-147, 149-157, 236-242, 304-324, 333, 335, 337, 350-352, 355, 356, 362-370, 377, 379, 386, 388-393 of YFV envelope protein, SEQ ID No. 1, may be substituted with the corresponding amino acid of the desired strain of DENV envelope (E) protein to create the chimeric protein of the invention.
  • E DENV envelope
  • the substitution may be made according to methods known to practitioners in the art. For example, site directed mutagenesis of the envelope protein may be performed to create the chimeric protein.
  • this method makes use of a short mutant DNA primer that binds specifically to the region being changed, but contains one or a small number of specific base changes that will result in a coding change to substitute the new specifically desired amino acid.
  • the bacterial plasmid with the E gene is replicated using PCR amplification to generate new full-length mutant DNA strands. Then the original DNA strand is degraded, leaving only the remaining specifically mutated DNA strand.
  • the chimeric protein is created by substituting amino acids of YFV envelope protein proximal to the domain II fusion loop.
  • amino acids “proximal to” the domain II fusion loop are those amino acids which are near the domain II fusion loop of the YFV envelope protein, shown in FIG. 13 .
  • amino acids which are within 5 ⁇ of the fusion loop are proximal to the fusion loop.
  • those amino acids which are within 14 ⁇ of the fusion loop are proximal to the fusion loop are proximal to the fusion loop.
  • Amino acids within 5 ⁇ and 14 ⁇ of the fusion loop are also shown in FIG. 13 .
  • the fusion loop is a structural feature of flavivirus envelope proteins that is found on the tip of domain II and is responsible for direct interaction of the envelope (E) protein with the target cell lipid membrane.
  • E envelope
  • the fusion loop is projected outward by a structural rearrangement of the E protein, resulting in the fusion loop “harpooning” into the target cell membrane. This interaction is critical for the subsequent membrane fusion step, mediated by a further E protein movement that pulls the cell and virus membranes together.
  • the fusion loop is highly conserved in dengue and yellow fever viruses.
  • the cysteine (C) at position 105 in the fusion loop forms a disulfide bond with the conserved cysteine (C) at position 74. This disulfide is important for the correct folding of the fusion loop. Amino acids within 5 ⁇ and 14 ⁇ of the fusion loop are important in YFV and DENV infection as well.
  • the chimeric protein may be used as a treatment composition for DENV infected individuals. It is further envisioned the chimeric protein may be used to create a treatment composition for preventing infection, or a vaccine effective against one or all four strains of DENV.
  • the chimeric protein may use a small portion of the yellow fever virus (YFV) 17D vaccine strain envelope protein to be replaced by the corresponding portion from the dengue virus envelope protein.
  • the vaccine may use a replication competent YFV with the DENV/YFV hybrid E protein.
  • An attenuated vaccine is created by reducing the virulence of a pathogen like YFV, but still keeping it viable (or “live”). Attenuation takes an infectious agent and alters it so that it becomes harmless or less virulent. These vaccines contrast to those produced by “killing” the virus (inactivated vaccine).
  • the invention could be used to develop a subunit vaccine that is not replicative. Rather than introducing an inactivated or attenuated micro-organism to an immune system (which would constitute a “whole-agent” vaccine), a fragment of it can create an immune response, and relate to producing a subunit vaccine.
  • Flaviviridae contains at least 70 arthropod-transmitted viruses, many of which infect humans and other vertebrates.
  • Subgroups of the Flaviviridae family include West Nile, Japanese Encephalitis, tick borne encephalitis, etc.
  • the Japanese encephalitis serocomplex includes West Nile Virus, St. Louis encephalitis, Murray Valley encephalitis, kunjin and other viruses.
  • the invention may swap out the dengue neutralizing epitopes into any other related flavivirus.
  • flaviviruses including West Nile Virus, St Louis encephalitis, dengue, Japanese encephalitis, yellow fever and kunjin viruses share similar size, symmetry and appearance.
  • flaviviruses may use different process to enter a host cell, such as endocytotis (described for West Nile Virus and Kunjin Virus) and direct fusion of the cell (described for dengue and Encephalitis Virus)
  • entry of all flaviviruses into the host-cell involves an interaction between the virus and a receptor of the cell.
  • the invention contemplates use of dengue neutralizing epitopes into any other related flavivirus.
  • the invention creates a vaccine that will induce broadly protective antibodies against dengue virus and reduce the induction of non-neutralizing antibodies that will cause enhancement.
  • the invention relates to a vaccine and methods of producing a vaccine using information from defining the regions of the E protein that are responsible for inducing a neutralizing antibody response to dengue.
  • Neutralizing antibodies can produce the infection enhancing effect, but they only do so at sub-neutralizing concentrations, while non-neutralizing antibodies produce enhancement at all concentrations.
  • the invention recognizes that if the human antibody response could be shifted away from a non-neutralizing response and towards a neutralizing response, this could considerably reduce the risk of post-vaccination disease enhancement.
  • the invention provides a vaccine that substantially reduces the risk of inducing an enhancing antibody response.
  • a vaccine formulation could accomplish this by only including the dengue E protein epitopes that induce a neutralizing response, and not including the epitopes that produce a non-neutralizing response.
  • the invention describes a common class of human, broadly neutralizing monoclonal antibodies and identifies their binding epitope, allowing the design a vaccine formulation.
  • the invention has confirmed the envelope portion from dengue virus that will be replaced in the yellow fever vaccine strain, and contemplates using common techniques to allow the resulting chimeric viruses to grow well enough to provide a suitable vaccine response.
  • the broadly neutralizing monoclonal antibodies were determined from each of three dengue patients infected in Jamaica, Singapore, and Sri Lanka, at time points two weeks, two months, and two years post infection. These antibodies (4.8A, D11Ck1, and 1.6D) show neutralization activity against all four serotypes of dengue and recognize a common epitope consisting of the E protein fusion loop and nearby regions. They target this region because they interfere with the binding of a previously characterized mouse monoclonal antibody that is known to target the fusion loop (4G2) and they interfere with each other's binding.
  • FIG. 1 establishes DENV specificity and broad reactivity of patient sera.
  • FIG. 2 establishes specificity for DENV antigens in the context of a cell.
  • FIG. 3 establishes neutralization activity of patient sera and of monoclonal antibodies from DENV infected patients.
  • FIG. 4 establishes that enhancing concentrations correlate with binding affinity to DENY-1 to 4, and also shows neutralization.
  • FIG. 5 rules out binding inhibition as mechanism.
  • FIG. 6 establishes mechanism as fusion inhibition for monoclonal antibody D11Ck1.
  • FIG. 7 shows that the monoclonal antibodies from DENV infected patients bind to protein consistent with size of E and the epitope is conformationally sensitive.
  • FIG. 8 confirms that the monoclonal antibodies from DENV infected patients bind to E, specifically to the ectodomain.
  • FIG. 9 determines how tightly the monoclonal antibodies from DENV infected patients bind to E protein.
  • FIG. 10 establishes that monoclonal antibodies from DENV infected patients compete for same domain as 4G2, a known fusion loop binder.
  • FIG. 11 establishes that monoclonal antibodies from DENV infected patients bind to DI/II consistent with fusion inhibition and competition assays.
  • FIG. 12 confirms monoclonal antibody 4.8 A epitope as fusion loop and/or vicinity.
  • FIG. 13 highlights the amino acids in yellow fever virus 17-D envelope protein which may be substituted with the DENV-1 to 4 envelope amino acids to create a chimeric E protein. It highlights the desirable amino acid substitution locations, as well as proposed amino acid substitutions.
  • FIG. 14 shows the protein crystal structure of the DENV envelope protein and demonstrates the location of the fusion loop at 10 and 5 ⁇ at 12 and 14 ⁇ at 14 surrounding amino acids.
  • the invention includes a vaccine for immunizing an individual against dengue hemorrhagic fever and/or dengue shock syndrome.
  • the vaccine includes one or more peptides of the type described, in a pharmaceutically acceptable adjuvant.
  • the invention provides a dengue vaccine and methods using a small portion of the yellow fever virus 17D vaccine strain envelope protein (or other related faviviruses) to be replaced by the corresponding portion from the dengue virus envelope protein.

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