WO2023064909A1 - Agents anti-pathogènes bifonctionnels - Google Patents

Agents anti-pathogènes bifonctionnels Download PDF

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Publication number
WO2023064909A1
WO2023064909A1 PCT/US2022/078127 US2022078127W WO2023064909A1 WO 2023064909 A1 WO2023064909 A1 WO 2023064909A1 US 2022078127 W US2022078127 W US 2022078127W WO 2023064909 A1 WO2023064909 A1 WO 2023064909A1
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seq
composition
amino acid
acid sequence
single chain
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PCT/US2022/078127
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English (en)
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Neil Goldstein
Karla FRIETZE
Jeffrey Wolf
Matthew Seavey
John Prendergast
Kamala ANUMUKONDA
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Nighthawk Biosciences, Inc.
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Publication of WO2023064909A1 publication Critical patent/WO2023064909A1/fr

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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A61P37/04—Immunostimulants
    • 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
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/08—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses
    • C07K16/10—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses from RNA viruses
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/08—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses
    • C07K16/10—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses from RNA viruses
    • C07K16/1027—Paramyxoviridae, e.g. respiratory syncytial virus
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/12—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from bacteria
    • C07K16/1267—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from bacteria from Gram-positive bacteria
    • C07K16/1282—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from bacteria from Gram-positive bacteria from Clostridium (G)
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2896—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against molecules with a "CD"-designation, not provided for elsewhere
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
    • C07K2317/31—Immunoglobulins specific features characterized by aspects of specificity or valency multispecific
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
    • C07K2317/565—Complementarity determining region [CDR]
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/60—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments
    • C07K2317/62—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments comprising only variable region components
    • C07K2317/622—Single chain antibody (scFv)

Definitions

  • the disclosure is related to bifunctional molecules for clearing pathogens.
  • a C3b/immune complex can bind to cluster of differentiation 35 (CD35), expressed on the surface of erythrocytes via the C3b molecule attached to the immune complex. This allows the immune complex to be transited to the reticuloendothial system in the liver and spleen by the erythrocyte and eventual neutralization.
  • Certain RES cells, inclusive of Kupffer cells recognize the C3b/immune complex and sever the C3b receptor-RBC junction, freeing the erythrocyte and the C3b/immune complex. The C3b/immune complex is then engulfed and destroyed by the Kupffer cells.
  • the present disclosure relates to bispecific molecules, and uses thereof, which allow the formation of a synapse between a pathogen antigen or cell and a scavenger receptor on an immune cell to increase a subj ect’ s ability to clear pathogens and, in turn, prevent or treat infection.
  • composition comprising a bispecific molecule comprising (a) a first antigen recognition domain that binds to an antigenic pathogen molecule; (b) a second antigen recognition domain that binds to cluster of differentiation 35 (CD35); and a linker comprising a hinge-CH2-CH3 Fc domain displaced between (a) and (b).
  • a method of promoting antigen specific pathogen sequestration and/or destruction comprising administering an effective amount of the composition described herein or the pharmaceutical composition described herein to a subject in need thereof.
  • a method of promoting liver and/or spleen clearance of a pathogen comprising administering an effective amount of the composition described herein or the pharmaceutical composition described herein to a subject in need thereof, wherein the clearance is optionally mediated by a macrophage, optionally a Kupffer cell.
  • a monospecific molecule comprising an antigen recognition domain that binds to an antigenic pathogen molecule.
  • a method of treating or preventing Marburg virus disease comprising administering an effective amount of the composition described herein or the pharmaceutical composition described herein to a subject in need thereof.
  • a method of treating or preventing Ebola virus disease comprising administering an effective amount of the composition described herein or the pharmaceutical composition described herein to a subject in need thereof.
  • a method of treating or preventing a hemorrhagic fever comprising administering an effective amount of the composition described herein or the pharmaceutical composition described herein to a subject in need thereof.
  • a method of treating or preventing infection by MRSA comprising administering an effective amount of the composition described herein or the pharmaceutical composition described herein to a subject in need thereof.
  • a method of treating or preventing infection by NIP AH virus comprising administering an effective amount of the composition described herein or the pharmaceutical composition described herein to a subject in need thereof.
  • a method of treating or preventing infection by botulinum toxin comprising administering an effective amount of the composition described herein or the pharmaceutical composition described herein to a subject in need thereof.
  • a method of treating or preventing infection by anthrax toxin comprising administering an effective amount of the composition described herein or the pharmaceutical composition described herein to a subject in need thereof.
  • a method of reversing or mitigating adverse vaccination comprising administering an effective amount of the composition described herein or the pharmaceutical composition described herein to a subject in need thereof.
  • FIG. 1 shows a non-limiting schematic of embodiments of the disclosure (where “T-800” is one of the present compositions).
  • FIG. 2 shows proof of concept data for the configuration of an Fc linker between the first antigen recognition domain and second antigen recognition domain.
  • FIG. 3 shows a bar graph comparing the results of the Ebola Virus Like Particles (VLP) phagocytosis assay with Fc block in THP-1 cells.
  • VLP Ebola Virus Like Particles
  • FIG. 4 shows a bar graph comparing the results of Ebola VLP phagocytosis assay with Fc block in RAW cells
  • FIG. 5 shows a bar graph comparing the percentage of phagocytic cells after treatment with various CD35-ebola bispecific constructs.
  • FIG. 6 shows a bar graph comparing the results of the THP-1 macrophage dose response curve after treatment with Ebola 8 constructs.
  • composition comprising a bispecific molecule comprising (a) a first antigen recognition domain that binds to an antigenic pathogen molecule; (b) a second antigen recognition domain that binds to cluster of differentiation 35 (CD35); and a linker comprising a hinge-CH2-CH3 Fc domain displaced between (a) and (b).
  • the composition is suitable for creating a linkage between one or more antigenic pathogen molecule and CD35.
  • the composition is suitable for creating a linkage between one or more antigenic pathogen molecule and one or more a erythrocytes, macrophages, and/or B-cells.
  • the composition is suitable for creating a linkage between one or more pathogens and one or more a erythrocytes, macrophages, and/or B-cells.
  • the composition is suitable for promoting liver and/or spleen clearance of the pathogen associated therewith, optionally by engulfment by a macrophage, optionally a Kupffer cell.
  • the composition is suitable interacting with the erythrocyte, macrophage, and/or B-cell in non-deleterious manner.
  • compositions described herein create a temporary state of “instant immunity”.
  • the compositions described herein (and associated methods described herein) find use in pre-exposure prophylaxis, e.g. for neutralization and/or sequestration.
  • the compositions described herein (and associated methods described herein) find use in post-exposure intervention, e.g. for therapeutic clearance.
  • the compositions described herein (and associated methods described herein) find use in clearing pathogen antibodies, e.g. in autoimmunity or adverse vaccine responses.
  • the first antigen recognition domain binds and neutralizes the antigenic pathogen molecule or binds and does not neutralize the antigenic pathogen molecule.
  • the first antigen recognition domain and/or the second antigen recognition domain comprises an antibody, antibody derivative or format.
  • the first antigen recognition domain and/or the second antigen recognition domain is a single-chain antibody (scFv), a single-domain antibody, a microprotein, a DARPin; a Tetranectin; an Affibody; a Transbody; an Anticalin; an AdNectin; an Affilin; an Affimer, a Microbody; a recombinant heavy-chain-only antibody (VHH), a shark heavy-chain-only antibody (VNAR), a plastic antibody; a stradobody; a maxibody; an evibody; a probody, an immunobody, a triomab, a troybody; a pepbody; a vaccibody, a UniBody; a DuoBody, a Fv, a Fab, a Fab', a F(ab') 2 .
  • scFv single-chain antibody
  • a single-domain antibody a microprotein, a
  • the first antigen recognition domain and/or the second antigen recognition domain is a scFv.
  • the first antigen recognition domain and/or the second antigen recognition domain each independently comprise a single chain antibody, or fragment thereof, having a heavy chain variable domain.
  • the variable domain determines the specificity of the antibody.
  • each variable region comprises three hypervariable regions also known as complementarity determining regions (CDRs) flanked by four relatively conserved framework regions (FRs).
  • CDRs complementarity determining regions
  • FRs relatively conserved framework regions
  • the three CDRs referred to as CDR1, CDR2, and CDR3, contribute to the antibody binding specificity.
  • the variable region FW sequences are human.
  • the first antigen recognition domain and/or the second antigen recognition domain is or comprises a chimeric antibody.
  • the first antigen recognition domain and/or the second antigen recognition domain is or comprises a humanized antibody.
  • the antigenic pathogen molecule is any substance that is present in the circulation that is potentially injurious to or undesirable in the subj ect to be treated, including but is not limited to proteins, toxins, autoantibodies or autoantigens, or a molecule of any infectious agent or its products.
  • the antigenic pathogen molecule is any molecule containing an antigenic determinant (or otherwise capable of being bound by a recognition domain) that is or is part of a substance (e.g., a pathogen) that is the cause of a disease or disorder or any other undesirable condition
  • the antigenic pathogen molecule is a cell surface antigen of a pathogen, a toxin, and/or an antibody. In embodiments, the antigenic pathogen molecule is an antigen derived from a virus, bacterium, fungus, parasite, or protozoan.
  • the antigenic pathogen molecule is an antigen derived from a virus of the family Filoviridae.
  • the antigenic pathogen molecule is an antigen derived from Marburg virus.
  • the Marburg virus is an isolate or strain of Marburg Marburgvirus species, optionally selected from a Marburg Popp strain, Ratayczak strain, Ozolin strain, Musoke strain (MARV-Musoke), Angola strain (MARV-Angola), and Ravn strain.
  • the first antigen recognition domain binds an antigen derived from Marburg virus and optionally is or comprises a single chain antibody.
  • the Marburg recognition domain has a variable domain of three complementarity determining regions (CDRs).
  • the CDR1 of the Marburg recognition domain comprises an amino acid sequence of SEQ ID NO: 43, or a variant thereof having a substitution or deletion.
  • the CDR1 of the Marburg recognition domain comprises an amino acid sequence of SEQ ID NO: 43, or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • the CDR2 of the Marburg recognition domain comprises an amino acid sequence of SEQ ID NO: 44, or a variant thereof having a substitution or deletion.
  • the CDR2 of the Marburg recognition domain comprises an amino acid sequence of SEQ ID NO: 44, or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • the CDR3 of the Marburg recognition domain comprises an amino acid sequence selected from CDR3 of marburgHlO (SEQ ID NO: 45), CDR3 of marburgClO (SEQ ID NO: 46), or CDR3 of marburgF7 (SEQ ID NO: 47), or a variant thereof having a substitution or deletion.
  • the CDR3 of the Marburg recognition domain comprises an amino acid sequence selected from CDR3 of marburgHlO (SEQ ID NO: 45), CDR3 of marburgClO (SEQ ID NO: 46), or CDR3 of marburgF7 (SEQ ID NO: 47), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • the first antigen recognition domain is a Marburg single chain antibody, comprising an amino acid sequence selected from marburgHlO (SEQ ID NO: 1), marburgClO (SEQ ID NO: 2), and marburgF7 (SEQ ID NO: 3), or an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% thereto.
  • marburgHlO SEQ ID NO: 1
  • marburgClO SEQ ID NO: 2
  • marburgF7 SEQ ID NO: 3
  • the antigenic pathogen molecule is an antigen derived from Marburg virus selected from Marburg virus glycoproteins (GPs) and nucleoproteins (NPs). In embodiments, the antigenic pathogen molecule is an antigen derived from Marburg virus selected from nucleoprotein (NP), polymerase cofactor (VP35), (VP40), GP, transcription activator (VP30), VP24, and RNA- dependent RNA polymerase (L). In embodiments, the antigenic pathogen molecule is Marburg GP1.
  • the antigenic pathogen molecule is an antigen derived from Ebola virus.
  • the first antigen recognition domain binds an antigen derived from Ebola virus and optionally is or comprises a single chain antibody.
  • the Ebola recognition domain has a variable domain of three complementarity determining regions (CDRs).
  • the CDR1 of the Ebola recognition domain comprises an amino acid sequence selected from CDR1 of ebolaGl l (SEQ ID NO: 63), CDR1 of ebolaG2&3 (SEQ ID NO: 63), CDR1 of ebolaMGl 1 (SEQ ID NO: 76), and CDR1 of ebolaMG2&3 (SEQ ID NO: 76), or a variant thereof having a substitution or deletion.
  • the CDR1 of the Ebola recognition domain comprises an amino acid sequence selected from CDR1 of ebolaGl l (SEQ ID NO: 63), CDR1 of ebolaG2&3 (SEQ ID NO: 63), CDR1 of ebolaMGl 1 (SEQ ID NO: 76), and CDR1 of ebolaMG2&3 (SEQ ID NO: 76), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • the CDR2 of the Ebola recognition domain comprises an amino acid sequence selected from CDR2 of ebolaGl l (SEQ ID NO: 63), CDR2 of ebolaG2&3 (SEQ ID NO: 63), CDR2 of ebolaMGl 1 (SEQ ID NO: 77), and CDR2 of ebolaMG2&3 (SEQ ID NO: 77), or a variant thereof having a substitution or deletion.
  • the CDR2 of the Ebola recognition domain comprises an amino acid sequence selected from CDR2 of ebolaGl l (SEQ ID NO: 63), CDR2 of ebolaG2&3 (SEQ ID NO: 63), CDR2 of ebolaMGl 1 (SEQ ID NO: 77), and CDR2 of ebolaMG2&3 (SEQ ID NO: 77), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • the CDR3 of the Ebola recognition domain comprises an amino acid sequence selected from CDR3 of ebolaGl l (SEQ ID NO: 64), CDR3 of ebolaG2&3 (SEQ ID NO: 65), CDR3 of ebolaMGl 1 (SEQ ID NO: 64), and CDR3 of ebolaMG2&3 (SEQ ID NO: 65), or a variant thereof having a substitution or deletion.
  • the CDR3 of the Ebola recognition domain comprises an amino acid sequence selected from CDR3 of ebolaGl l (SEQ ID NO: 64), CDR3 of ebolaG2&3 (SEQ ID NO: 65), CDR3 of ebolaMGl 1 (SEQ ID NO: 64), and CDR3 of ebolaMG2&3 (SEQ ID NO: 65), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • the first antigen recognition domain is a Ebola single chain antibody, comprising an amino acid sequence selected from ebolaGl 1 (SEQ ID NO: 61), ebolaG2&3 (SEQ ID NO: 62), ebolaMGl 1 (SEQ ID NO: 74), and ebolaMG2&3 (SEQ ID NO: 75), or an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% thereto.
  • the Ebola virus is selected from Zaire ebolavirus, Sudan ebolavirus, Reston ebolavirus, Tai Forest ebolavirus, and Bundibugyo ebolavirus.
  • the antigenic pathogen molecule is an antigen derived from Ebola virus selected from nucleoprotein (NP), polymerase cofactor (VP35), (VP40), GP, transcription activator (VP30), VP24, and RNA- dependent RNA polymerase (L).
  • the antigenic pathogen molecule is Ebola GP1, e.g. comprising an epitope within amino acid positions 389 to 493 thereof.
  • the antigenic pathogen molecule is an antigen derived from Staphylococcus aureus, optionally methicillin-resistant Staphylococcus aureus (MRSA).
  • MRSA methicillin-resistant Staphylococcus aureus
  • the antigenic pathogen molecule is an antigen derived from NIP AH virus.
  • the NIP AH virus is selected from NIP AH virus Malaysia strain (NiVM) and NIP AH virus Bangladesh strain (NiVn).
  • the first antigen recognition domain binds an antigen derived from NIP AH virus and optionally is or comprises a single chain antibody.
  • the NIP AH recognition domain has a variable domain of three complementarity determining regions (CDRs).
  • the CDR1 of the NIP AH recognition domain comprises an amino acid sequence of SEQ ID NO: 54, or a variant thereof having a substitution or deletion.
  • the CDR1 of the NIP AH recognition domain comprises an amino acid sequence of SEQ ID NO: 54, or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • the CDR2 of the NIP AH recognition domain comprises an amino acid sequence of SEQ ID NO: 55, or a variant thereof having a substitution or deletion.
  • the CDR2 of the NIP AH recognition domain comprises an amino acid sequence of SEQ ID NO: 55, or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • the CDR3 of the NIP AH recognition domain comprises an amino acid sequence of CDR3 of nipahEl (SEQ ID NO: 56), CDR3 of nipahE6 (SEQ ID NO: 57), CDR3 of nipahlO (SEQ ID NO: 58), or CDR3 of nipahG4R (SEQ ID NO: 59), or a variant thereof having a substitution or deletion.
  • the CDR3 of the NIP AH recognition domain comprises an amino acid sequence of CDR3 of nipahEl (SEQ ID NO: 56), CDR3 of nipahE6 (SEQ ID NO: 57), CDR3 of nipahlO (SEQ ID NO: 58), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • the first antigen recognition domain is a NIP AH single chain antibody, comprising an amino acid sequence selected from nipahEl (SEQ ID NO: 23), nipahE6 (SEQ ID NO: 24), nipahDIO (SEQ ID NO: 25) and nipahG4R (SEQ ID NO: 26), or an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% thereto.
  • the antigenic pathogen molecule is an antigen derived from Clostridium, optionally Clostridium botulinum. In embodiments, the antigenic pathogen molecule is an antigen derived from botulinum toxin.
  • the first antigen recognition domain binds an antigen derived from botulinum toxin and optionally is or comprises a single chain antibody.
  • the botulinum toxin recognition domain has a variable domain of three complementarity determining regions (CDRs).
  • the CDRs of the botulinum toxin recognition domain comprise amino acid sequences set forth in CDR1 of BoNT-993A (SEQ ID NO: 88), CDR2 of BoNT-993A (SEQ ID NO: 89), CDR3 of BoNT-993A (SEQ ID NO: 90), or a variant thereof having a substitution or deletion.
  • the CDRs of the botulinum toxin recognition domain comprise amino acid sequences set forth in CDR1 of BoNT-993A (SEQ ID NO: 88), CDR2 of BoNT-993A (SEQ ID NO: 89), CDR3 of BoNT-993A (SEQ ID NO: 90), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • the CDRs of the botulinum toxin recognition domain comprise amino acid sequences set forth in CDR1 of BoNT-990 (SEQ ID NO: 91), CDR2 of BoNT-990 (SEQ ID NO: 92), CDR3 of BoNT-990 (SEQ ID NO: 93), or a variant thereof having a substitution or deletion.
  • the CDRs of the botulinum toxin recognition domain comprise amino acid sequences set forth in CDR1 of BoNT-990 (SEQ ID NO: 91), CDR2 of BoNT-990 (SEQ ID NO: 92), CDR3 of BoNT-990 (SEQ ID NO: 93), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • the first antigen recognition domain is a botulinum toxin single chain antibody, comprising an amino acid sequence selected from BoNT-993A (SEQ ID NO: 86), and BoNT-990 (SEQ ID NO: 87), or an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% thereto.
  • the botulinum toxin is a serotype of Clostridium botulinum, optionally selected from serotypes A, B, E, F, or H.
  • the antigenic pathogen molecule is an antigen derived from Bacillus, optionally bacillus anthracis.
  • the antigenic pathogen molecule is an antigen derived from anthrax toxin.
  • the first antigen recognition domain binds an antigen derived from anthrax toxin and optionally is or comprises a single chain antibody.
  • the anthrax recognition domain has a variable domain of three complementarity determining regions (CDRs)
  • the anthrax recognition domain has a light chain variable domain of three complementarity determining regions (CDRs) and/or a heavy chain variable domain of three complementarity determining regions (CDRs).
  • CDRs complementarity determining regions
  • CDRs heavy chain variable domain of three complementarity determining regions
  • the light chain variable domain comprises CDR1, CDR2, and CDR3 sequences, wherein the CDR1 comprises RASQDIRNYLN (SEQ ID NO: 103), CDR2 comprises YTSRLLP (SEQ ID NO: 104), CDR3 comprises QQGNTLPWT (SEQ ID NO: 105), or a variant thereof having a substitution or deletion.
  • the light chain variable domain comprises CDR1, CDR2, and CDR3 sequences, wherein the CDR1 comprises RASQDIRNYLN (SEQ ID NO: 103), CDR2 comprises YTSRLLP (SEQ ID NO: 104), CDR3 comprises QQGNTLPWT (SEQ ID NO: 105), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • the heavy chain variable domain comprises CDR1, CDR2, and CDR3 sequences, wherein the CDR1 comprises YAFSSSWMN (SEQ ID NO: 106), CDR2 comprises RIYPGDGDTNYNGKFQG (SEQ ID NO: 107), and CDR3 comprises SGLLRYAMDY (SEQ ID NO: 108), or a variant thereof having a substitution or deletion.
  • CDR1 comprises YAFSSSWMN (SEQ ID NO: 106)
  • CDR2 comprises RIYPGDGDTNYNGKFQG (SEQ ID NO: 107)
  • CDR3 comprises SGLLRYAMDY (SEQ ID NO: 108), or a variant thereof having a substitution or deletion.
  • the heavy chain variable domain comprises CDR1, CDR2, and CDR3 sequences, wherein the CDR1 comprises YAFSSSWMN (SEQ ID NO: 106), CDR2 comprises RIYPGDGDTNYNGKFQG (SEQ ID NO: 107), and CDR3 comprises SGLLRYAMDY (SEQ ID NO: 108), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • the light chain variable domain comprises CDR1, CDR2, and CDR3 sequences, wherein the CDR1 comprises RASQDIRNYLN (SEQ ID NO: 103), CDR2 comprises YTSRLLP (SEQ ID NO: 104), and CDR3 comprises QQGNTLPWT (SEQ ID NO: 105), and the heavy chain variable domain comprises CDR1, CDR2, and CDR3 sequences, wherein the CDR1 comprises YAFSSSWMN (SEQ ID NO: 106), CDR2 comprises RIYPGDGDTNYNGKFQG (SEQ ID NO: 107), CDR3 comprises SGLLRYAMDY (SEQ ID NO: 108), or a variant thereof having a substitution or deletion.
  • the CDR1 comprises RASQDIRNYLN (SEQ ID NO: 103)
  • CDR2 comprises YTSRLLP (SEQ ID NO: 104)
  • CDR3 comprises QQGNTLPWT (SEQ ID NO: 105)
  • the heavy chain variable domain comprises
  • the light chain variable domain comprises CDR1, CDR2, and CDR3 sequences, wherein the CDR1 comprises RASQDIRNYLN (SEQ ID NO: 103), CDR2 comprises YTSRLLP (SEQ ID NO: 104), and CDR3 comprises QQGNTLPWT (SEQ ID NO: 105), and the heavy chain variable domain comprises CDR1, CDR2, and CDR3 sequences, wherein the CDR1 comprises YAFSSSWMN (SEQ ID NO: 106), CDR2 comprises RIYPGDGDTNYNGKFQG (SEQ ID NO: 107), CDR3 comprises SGLLRYAMDY (SEQ ID NO: 108), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • the first antigen recognition domain is an anthrax single chain antibody, comprising an amino acid sequence selected from AnthimVl-VH (SEQ ID NO: 102), AnthimVh- VI (SEQ ID NO: 109), AnthimVl (SEQ ID NO: 110), and AnthimVh (SEQ ID NO: 111), or an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% thereto.
  • the antigenic pathogen molecule is expressed on the surface on a pathogen.
  • the antigenic pathogen molecule is another antibody, e.g. autoantibodies.
  • the present methods are useful in treating or preventing a disease characterized by autoantibodies, e.g. lupus.
  • the antigenic pathogen molecule is an antigen specific T-cell when used as an MHC tetramer, e.g. for use in treating or preventing multiple sclerosis.
  • the second antigen recognition domain binds a scavenger receptor. In embodiments, the second antigen recognition domain binds a scavenger receptor expressed on the surface of a cell, optionally a red blood cell, macrophage, and/or B-cell.
  • the second antigen recognition domain binds CD35.
  • the CD35 is human CD35.
  • the second antigen recognition domain binds the extracellular domain of CD35.
  • the second antigen recognition domain is a CD35/CR1 antibody, optionally a single chain antibody.
  • the CD35/CR1 antibody has a variable domain of three complementarity determining regions (CDRs).
  • the CDR1 of the CD35/CR1 antibody comprises an amino acid sequence set forth in SEQ ID NO: 48, or a variant thereof having a substitution or deletion.
  • the CDR1 of the CD35/CR1 antibody comprises an amino acid sequence set forth in SEQ ID NO: 48, or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • the CDR2 of the CD35/CR1 antibody comprises an amino acid sequence set forth in SEQ ID NO: 49, or a variant thereof having a substitution or deletion.
  • the CDR2 of the CD35/CR1 antibody comprises an amino acid sequence set forth in SEQ ID NO: 49, or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • the CDR3 of the CD35/CR1 antibody comprises an amino acid sequence of CDR3 of CD35/CR1-3512 (SEQ ID NO: 50), CDR3 of CD35/CR 1-3511 (SEQ ID NO: 51), CDR3 of CD35/CR1-358 (SEQ ID NO: 52), or CDR3 of CD35/CR1-353 (SEQ ID NO: 53), or a variant thereof having a substitution or deletion.
  • the CDR3 of the CD35/CR1 antibody comprises an amino acid sequence of CDR3 of CD35/CR1-3512 (SEQ ID NO: 50), CDR3 of CD35/CR 1-3511 (SEQ ID NO: 51), CDR3 of CD35/CR1-358 (SEQ ID NO: 52), or CDR3 of CD35/CR1-353 (SEQ ID NO: 53), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • the CD35/CR1 single chain antibody comprises an amino acid sequence selected from CD35/CR1-3512 (SEQ ID NO: 4), CD35/CR1-3511 (SEQ ID NO: 5), CD35/CR1-358 (SEQ ID NO: 6) or CD35/CR1-353 (SEQ ID NO: 7), or an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% thereto.
  • the second antigen recognition domain binds CD35 expressed on the surface of a cell, optionally a red blood cell, macrophage, and/or B-cell.
  • the first antigen recognition domain binds and neutralizes CD35 or binds and does not neutralize CD35.
  • the composition is suitable for contemporaneous binding of the antigenic pathogen molecule and CD35.
  • the bispecific molecule comprises the first antigen recognition domain which is a Marburg single chain antibody and the second antigen recognition domain which is a CD35/CR1 single chain antibody.
  • the Marburg single chain antibody comprises an amino acid sequence selected from marburgHlO (SEQ ID NO: 1), marburgClO (SEQ ID NO: 2), or marburgF7 (SEQ ID NO: 3) and the CD35/CR1 single chain antibody comprises an amino acid sequence selected from 3512 (SEQ ID NO: 4), 3511 (SEQ ID NO: 5), 358 (SEQ ID NO: 6) or 353 (SEQ ID NO: 7), or an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% thereto.
  • the Marburg-CD35/CR1 bispecific molecule comprises an amino acid sequence selected from marburgH10-3512 (SEQ ID NO: 11), marburgH10-3511 (SEQ ID NO: 12), marburgH10-358 (SEQ ID NO: 13), marburgH10-353 (SEQ ID NO: 14), marburgC10-3512 (SEQ ID NO: 15), marburgC10-3511 (SEQ ID NO: 16), marburgC10-358 (SEQ ID NO: 17), marburgC10-353 (SEQ ID NO: 18), marburgF7-3512 (SEQ ID NO: 19), marburgF7-3511 (SEQ ID NO: 20), marburgF7-358 (SEQ ID NO: 21), marburgF7-353 (SEQ ID NO: 22) constructs, or an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% thereto.
  • the bispecific molecule comprises the first antigen recognition domain which is an Ebola single chain antibody and the second antigen recognition domain which is a CD35/CR1 single chain antibody.
  • the Ebola single chain antibody comprises an amino acid sequence selected from ebolaGl 1 (SEQ ID NO: 61), ebolaG2&3 (SEQ ID NO: 62), ebolaMGl l (SEQ ID NO: 74), and ebolaMG2&3 (SEQ ID NO: 75) and the CD35/CR1 single chain antibody comprises an amino acid sequence selected from 3512 (SEQ ID NO: 4), 3511 (SEQ ID NO: 5), 358 (SEQ ID NO: 6) or 353 (SEQ ID NO: 7), or an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% thereto.
  • the Ebola-CD35/CR1 bispecific molecule comprises an amino acid sequence selected from ebolaGl 1-3512 (SEQ ID NO: 66), ebolaGl 1-3511 (SEQ ID NO: 67), ebolaGl 1-358 (SEQ ID NO: 68), ebolaGl 1-353 (SEQ ID NO: 69), ebolaG2&3-3512 (SEQ ID NO: 70), ebolaG2&3-3511 (SEQ ID NO: 71), ebolaG2&3-358 (SEQ ID NO: 72), ebolaG2&3-353 (SEQ ID NO: 73), ebolaMGl 1-3512 (SEQ ID NO: 78), ebolaMGl 1-3511 (SEQ ID NO: 79), ebolaMGl 1-358 (SEQ ID NO: 80), ebolaMGl 1-353 (SEQ ID NO: 81), ebolaMG2&3-3512 (SEQ ID NO
  • the bispecific molecule comprises the first antigen recognition domain which is a NIP AH single chain antibody and the second antigen recognition domain which is a CD35/CR1 single chain antibody.
  • the NIP AH single chain antibody comprises an amino acid sequence selected from nipahEl (SEQ ID NO: 23), nipahE6 (SEQ ID NO: 24), nipahDIO (SEQ ID NO: 25) or nipahG4R (SEQ ID NO: 26) and the CD35/CR1 single chain antibody comprises an amino acid sequence selected from CD35/CR1-3512 (SEQ ID NO: 4), CD35/CR1-3511 (SEQ ID NO: 5), CD35/CR1-358 (SEQ ID NO: 6) and CD35/CR1-353 (SEQ ID NO: 7), or an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% thereto.
  • the NIPAH-CD35/CR1 bispecific molecule comprises an amino acid sequence selected from nipahEl-3512 (SEQ ID NO: 27), nipahEl-3511 (SEQ ID NO: 28), nipahEl-358 (SEQ ID NO: 29), nipahEl-353 (SEQ ID NO: 30), nipahE6-3512 (SEQ ID NO: 31), nipahE6- 3511 (SEQ ID NO: 32), nipahE6-358 (SEQ ID NO: 33), nipahE6-353 (SEQ ID NO: 34), nipahD10-3512 (SEQ ID NO: 35), nipahD10-3511 (SEQ ID NO: 36), nipahD10-358 (SEQ ID NO: 37), nipahD10-353 (SEQ ID NO: 38), nipahG4R -3512 (SEQ ID NO:
  • the bispecific molecule comprises the first antigen recognition domain which is a botulinum toxin single chain antibody and the second antigen recognition domain which is a CD35/CR1 single chain antibody.
  • the botulinum toxin single chain antibody comprises an amino acid sequence selected from BoNT-993A (SEQ ID NO: 86) or BoNT-990 (SEQ ID NO: 87) and the CD35/CR1 single chain antibody comprises an amino acid sequence selected from CD35/CR1-3512 (SEQ ID NO: 4), CD35/CR1-3511 (SEQ ID NO: 5), CD35/CR1-358 (SEQ ID NO: 6) and CD35/CR1-353 (SEQ ID NO: 7), or an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% thereto.
  • the botulinum toxin-CD35/CRl bispecific molecule comprises an amino acid sequence selected from BoNT-993A-3512 (SEQ ID NO: 94), BoNT-993A -3511 (SEQ ID NO: 95), BoNT-993A-358 (SEQ ID NO: 96), BoNT-993A-353 (SEQ ID NO: 97), BoNT-990-3512 (SEQ ID NO: 98), BoNT-990-3511 (SEQ ID NO: 99), BoNT-990-358 (SEQ ID NO: 100), and BoNT-990-353 (SEQ ID NO: 101) constructs, or an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% thereto.
  • the bispecific molecule comprises the first antigen domain which is an anthrax single chain antibody and the second antigen recognition domain which is a CD35/CR1 single chain antibody.
  • the anthrax single chain antibody comprises an amino acid sequence selected from AnthimVl-Vh (SEQ ID NO: 102), AnthimVH-Vl (SEQ ID NO: 109), AnthimVl (SEQ ID NO: 110), and AnthimVh (SEQ ID NO: 111)
  • the CD35/CR1 single chain antibody comprises an amino acid sequence selected from CD35/CR1-3512 (SEQ ID NO: 4), CD35/CR1-3511 (SEQ ID NO: 5), CD35/CR1-358 (SEQ ID NO: 6), and CD35/CR1-353 (SEQ ID NO: 7), or an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% thereto.
  • the anthrax-CD35/CRl bispecific molecule comprises an amino acid sequence selected from AnthimVl-Vh -3512 (SEQ ID NO: 112), AnthimVl-Vh -3511 (SEQ ID NO: 113), AnthimVl-Vh -358 (SEQ ID NO: 114), AnthimVl-Vh -353 (SEQ ID NO: 115), AnthimVH-Vl - 3512 (SEQ ID NO: 116), AnthimVH-Vl -3511 (SEQ ID NO: 117), AnthimVH-Vl -358 (SEQ ID NO: 118), AnthimVH-Vl -353 (SEQ ID NO: 119), AnthimVl -3512 (SEQ ID NO: 120), AnthimVl -3511 (SEQ ID NO: 121), AnthimVl -358 (SEQ ID NO: 122), AnthimVl -353 (SEQ ID NO: 123), AnthimVh -3512 (SEQ ID NO: 11
  • compositions have optional tags (e.g., FLAG tags, His6 tags, and the like).
  • tags e.g., FLAG tags, His6 tags, and the like.
  • any of the amino acid sequences have a polyhistidine tag and/or any residues C- terminal thereto removed or omitted.
  • the composition is a Marburg single chain antibody or antigen binding fragment thereof, wherein the Marburg single chain antibody has a variable domain of three complementarity determining regions (CDRs); wherein the CDR1 sequence comprises an amino acid sequence set forth in SEQ ID NO: 43, the CDR2 sequence comprises an amino acid sequence set forth in SEQ ID NO: 44; and the CDR3 sequence comprises an amino acid sequence selected from marburgHlO (SEQ ID NO: 45), marburgClO (SEQ ID NO: 46), or marburgF7 (SEQ ID NO: 47), or a variant thereof having a substitution or deletion.
  • CDRs complementarity determining regions
  • the composition is a Marburg single chain antibody or antigen binding fragment thereof, wherein the Marburg single chain antibody has a variable domain of three complementarity determining regions (CDRs); wherein the CDR1 sequence comprises an amino acid sequence set forth in SEQ ID NO: 43, the CDR2 sequence comprises an amino acid sequence set forth in (SEQ ID NO: 44); and the CDR3 sequence comprises an amino acid sequence selected from marburg H10 (SEQ ID NO: 45), marburgClO (SEQ ID NO: 46), or marburgF7 (SEQ ID NO: 47), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • CDRs complementarity determining regions
  • the composition is a Marburg single chain antibody, comprising an amino acid sequence selected from marburgHlO (SEQ ID NO: 1), marburgClO (SEQ ID NO: 2), and marburgF7 (SEQ ID NO: 3), or an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% thereto.
  • marburgHlO SEQ ID NO: 1
  • marburgClO SEQ ID NO: 2
  • marburgF7 SEQ ID NO: 3
  • the composition is a Ebola single chain antibody or antigen binding fragment thereof, wherein the Ebola single chain antibody has a variable domain of three complementarity determining regions (CDRs); wherein the CDR1 sequence comprises an amino acid sequence set forth in SEQ ID NO: 63, the CDR2 sequence comprises an amino acid sequence set forth in SEQ ID NO: 63; and the CDR3 sequence comprises an amino acid sequence selected from ebolaGl l (SEQ ID NO: 64), or ebolaG2&3 (SEQ ID NO: 65), or a variant thereof having a substitution or deletion.
  • CDRs complementarity determining regions
  • the composition is a Ebola single chain antibody or antigen binding fragment thereof, wherein the Ebola single chain antibody has a variable domain of three complementarity determining regions (CDRs); wherein the CDR1 sequence comprises an amino acid sequence set forth in SEQ ID NO: 63, the CDR2 sequence comprises an amino acid sequence set forth in SEQ ID NO: 63; and the CDR3 sequence comprises an amino acid sequence selected from ebolaGl l (SEQ ID NO: 64), or ebolaG2&3 (SEQ ID NO: 65), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • CDRs complementarity determining regions
  • the composition is a Ebola single chain antibody or antigen binding fragment thereof, wherein the Ebola single chain antibody has a variable domain of three complementarity determining regions (CDRs); wherein the CDR1 sequence comprises an amino acid sequence set forth in SEQ ID NO: 76, the CDR2 sequence comprises an amino acid sequence set forth in SEQ ID NO: 77; and the CDR3 sequence comprises an amino acid sequence selected from ebolaMGl 1 (SEQ ID NO: 74), or ebolaMG2&3 (SEQ ID NO: 75), or a variant thereof having a substitution or deletion.
  • CDRs complementarity determining regions
  • the composition is a Ebola single chain antibody or antigen binding fragment thereof, wherein the Ebola single chain antibody has a variable domain of three complementarity determining regions (CDRs); wherein the CDR1 sequence comprises an amino acid sequence set forth in SEQ ID NO: 76, the CDR2 sequence comprises an amino acid sequence set forth in SEQ ID NO: 77; and the CDR3 sequence comprises an amino acid sequence selected from ebolaMGl 1 (SEQ ID NO: 64), or ebolaMG2&3 (SEQ ID NO: 65), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • CDRs complementarity determining regions
  • the composition is a Ebola single chain antibody, comprising an amino acid sequence selected from ebolaGl 1 (SEQ ID NO: 61), or ebolaG2&3 (SEQ ID NO: 62), or an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% thereto.
  • the composition is a Ebola single chain antibody, comprising an amino acid sequence selected from ebolaMGl 1 (SEQ ID NO: 74), or ebolaMG2&3 (SEQ ID NO: 75), or an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% thereto.
  • the composition is a NIP AH single chain antibody or antigen binding fragment thereof, wherein the NIP AH single chain antibody has a variable domain of three complementarity determining regions (CDRs), wherein the CDR1 sequence comprises an amino acid sequence set forth in SEQ ID NO: 54, the CDR2 sequence comprises an amino acid sequence set forth in SEQ ID NO: 55; and the CDR3 sequence comprises an amino acid sequence selected from nipahEl (SEQ ID NO: 56), nipahE6 (SEQ ID NO: 57), nipahDIO (SEQ ID NO: 58), or nipahG4R (SEQ ID NO: 59), or a variant thereof having a substitution or deletion.
  • CDRs complementarity determining regions
  • the composition is a NIP AH single chain antibody or antigen binding fragment thereof, wherein the NIP AH single chain antibody has a variable domain of three complementarity determining regions (CDRs), wherein the CDR1 sequence comprises an amino acid sequence set forth in SEQ ID NO: 54, the CDR2 sequence comprises an amino acid sequence set forth in SEQ ID NO: 55; and the CDR3 sequence comprises an amino acid sequence selected from nipahEl (SEQ ID NO: 56), nipahE6 (SEQ ID NO: 57), nipahDIO (SEQ ID NO: 58), or nipahG4R (SEQ ID NO: 59), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • CDRs complementarity determining regions
  • the composition is a NIP AH single chain antibody, comprising an amino acid sequence selected from nipahEl (SEQ ID NO: 23), nipahE6 (SEQ ID NO: 24), nipahDIO (SEQ ID NO: 25) and nipahG4R (SEQ ID NO: 26), or an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% thereto.
  • the composition is a botulinum toxin single chain antibody or antigen binding fragment thereof, wherein the botulinum toxin single chain antibody has a variable domain of three complementarity determining regions (CDRs), wherein the CDR1 sequence comprises an amino acid sequence set forth in SEQ ID NO: 88, the CDR2 sequence comprises an amino acid sequence set forth in SEQ ID NO: 89; and the CDR3 comprises an amino acid sequence set forth in SEQ ID NO: 90, or a variant thereof having a substitution or deletion.
  • CDRs complementarity determining regions
  • the composition is a botulinum toxin single chain antibody or antigen binding fragment thereof, wherein the botulinum toxin single chain antibody has a variable domain of three complementarity determining regions (CDRs), wherein the CDR1 sequence comprises an amino acid sequence set forth in SEQ ID NO: 88, the CDR2 sequence comprises an amino acid sequence set forth in SEQ ID NO: 89; and the CDR3 comprises an amino acid sequence set forth in SEQ ID NO: 90, or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • CDRs complementarity determining regions
  • the composition is a botulinum toxin single chain antibody or antigen binding fragment thereof, wherein the botulinum toxin single chain antibody has a variable domain of three complementarity determining regions (CDRs), wherein the CDR1 sequence comprises an amino acid sequence set forth in SEQ ID NO: 91, the CDR2 sequence comprises an amino acid sequence set forth in SEQ ID NO: 92; and the CDR3 comprises an amino acid sequence set forth in SEQ ID NO: 93, or a variant thereof having a substitution or deletion.
  • CDRs complementarity determining regions
  • the composition is a botulinum toxin single chain antibody or antigen binding fragment thereof, wherein the botulinum toxin single chain antibody has a variable domain of three complementarity determining regions (CDRs), wherein the CDR1 sequence comprises an amino acid sequence set forth in SEQ ID NO: 91, the CDR2 sequence comprises an amino acid sequence set forth in SEQ ID NO: 92; and the CDR3 comprises an amino acid sequence set forth in SEQ ID NO: 93, or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • CDRs complementarity determining regions
  • the composition is a botulinum toxin single chain antibody, comprising an amino acid sequence selected from BoNT-993A (SEQ ID NO: 86) and BoNT-990 (SEQ ID NO: 87), or an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% thereto.
  • the composition is an anthrax single chain antibody or antigen binding fragment thereof, wherein the anthrax single chain antibody comprises a light chain variable domain of three complementarity determining regions (CDRs) and/or a heavy chain variable domain of three complementarity determining regions (CDRs).
  • CDRs complementarity determining regions
  • CDRs heavy chain variable domain of three complementarity determining regions
  • the composition is an anthrax single chain antibody or antigen binding fragment thereof, wherein the anthrax single chain antibody has a light chain variable domain of three complementarity determining regions (CDRs), wherein the CDR1 sequence comprises an amino acid sequence set forth in SEQ ID NO: 103, the CDR2 sequence comprises an amino acid sequence set forth in SEQ ID NO: 104; and the CDR3 comprises an amino acid sequence set forth in SEQ ID NO: 105, or a variant thereof having a substitution or deletion.
  • CDRs complementarity determining regions
  • the composition is an anthrax single chain antibody or antigen binding fragment thereof, wherein the anthrax single chain antibody has a light chain variable domain of three complementarity determining regions (CDRs), wherein the CDR1 sequence comprises an amino acid sequence set forth in SEQ ID NO: 103, the CDR2 sequence comprises an amino acid sequence set forth in SEQ ID NO: 104; and the CDR3 comprises an amino acid sequence set forth in SEQ ID NO: 105, or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • CDRs complementarity determining regions
  • the composition is an anthrax single chain antibody or antigen binding fragment thereof, wherein the anthrax single chain antibody has a heavy chain variable domain of three complementarity determining regions (CDRs), wherein the CDR1 sequence comprises an amino acid sequence set forth in SEQ ID NO: 106, the CDR2 sequence comprises an amino acid sequence set forth in SEQ ID NO: 107; and the CDR3 comprises an amino acid sequence set forth in SEQ ID NO: 108, or a variant thereof having a substitution or deletion.
  • CDRs complementarity determining regions
  • the composition is an anthrax single chain antibody or antigen binding fragment thereof, wherein the anthrax single chain antibody has a heavy chain variable domain of three complementarity determining regions (CDRs), wherein the CDR1 sequence comprises an amino acid sequence set forth in SEQ ID NO: 106, the CDR2 sequence comprises an amino acid sequence set forth in SEQ ID NO: 107; and the CDR3 comprises an amino acid sequence set forth in SEQ ID NO: 108, or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • CDRs complementarity determining regions
  • the composition is an anthrax single chain antibody or antigen binding fragment thereof, wherein the anthrax single chain antibody has a light chain variable domain of three complementarity determining regions (CDRs) and a heavy chain variable domain of three complementarity determining regions (CDRs), wherein the light chain variable domain comprises CDR1, CDR2, and CDR3 sequences, wherein the CDR1 comprises RASQDIRNYLN (SEQ ID NO: 103), CDR2 comprises YTSRLLP (SEQ ID NO: 104), and CDR3 comprises QQGNTLPWT (SEQ ID NO: 105), and the heavy chain variable domain comprises CDR1, CDR2, and CDR3 sequences, wherein the CDR1 comprises YAFSSSWMN (SEQ ID NO: 106), CDR2 comprises RIYPGDGDTNYNGKFQG (SEQ ID NO: 107), CDR3 comprises SGLLRYAMDY (SEQ ID NO: 108), or a variant thereof having a substitution or deletion.
  • CDRs C
  • the composition is an anthrax single chain antibody or antigen binding fragment thereof, wherein the anthrax single chain antibody has a light chain variable domain of three complementarity determining regions (CDRs) and a heavy chain variable domain of three complementarity determining regions (CDRs), wherein the light chain variable domain comprises CDR1, CDR2, and CDR3 sequences, wherein the CDR1 comprises RASQDIRNYLN (SEQ ID NO: 103), CDR2 comprises YTSRLLP (SEQ ID NO: 104), and CDR3 comprises QQGNTLPWT (SEQ ID NO: 105), and the heavy chain variable domain comprises CDR1, CDR2, and CDR3 sequences, wherein the CDR1 comprises YAFSSSWMN (SEQ ID NO: 106), CDR2 comprises RIYPGDGDTNYNGKFQG (SEQ ID NO: 107), CDR3 comprises SGLLRYAMDY (SEQ ID NO: 108), or a variant thereof, wherein the variant comprises about 1, or about
  • the composition is an anthrax single chain antibody, comprising an amino acid sequence selected from AnthimVl-Vh (SEQ ID NO: 102), AnthimVl-Vh (SEQ ID NO: 109), AnthimVl (SEQ ID NO: 110), and AnthimVh (SEQ ID NO: 111), or an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% thereto.
  • the composition is a CD35/CR1 single chain antibody or antigen binding fragment thereof, wherein the CD35/CR1 single chain antibody has a variable domain of three complementarity determining regions (CDRs), wherein the CDR1 sequence comprises an amino acid sequence set forth in SEQ ID NO: 48, the CDR2 sequence comprises an amino acid sequence set forth in SEQ ID NO: 49; and the CDR3 sequence comprises an amino acid sequence selected from CD35/CR1-3512 (SEQ ID NO: 50), CD35/CR1-3511 (SEQ ID NO: 51), CD35/CR1-358 (SEQ ID NO: 52), or CD35/CR1-353 (SEQ ID NO: 53), or a variant thereof having a substitution or deletion.
  • CDRs complementarity determining regions
  • the composition is a CD35/CR1 single chain antibody or antigen binding fragment thereof, wherein the CD35/CR1 single chain antibody has a variable domain of three complementarity determining regions (CDRs), wherein the CDR1 sequence comprises an amino acid sequence set forth in SEQ ID NO: 48, the CDR2 sequence comprises an amino acid sequence set forth in SEQ ID NO: 49; and the CDR3 sequence comprises an amino acid sequence selected from CD35/CR1-3512 (SEQ ID NO: 50), CD35/CR1-3511 (SEQ ID NO: 51), CD35/CR1-358 (SEQ ID NO: 52), or CD35/CR1-353 (SEQ ID NO: 53), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • CDRs complementarity determining regions
  • the composition is a CD35/CR1 single chain antibody, comprising an amino acid sequence selected from CD35/CR1-3512 (SEQ ID NO: 4), CD35/CR1-3511 (SEQ ID NO: 5), CD35/CR1-358 (SEQ ID NO: 6) or CD35/CR1-353 (SEQ ID NO: 7), or an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% thereto.
  • the compositions have optional tags (e.g., FLAG tags, His6 tags, and the like) or these tags are removed from any of the sequences provided herein.
  • any of the amino acid sequences have a polyhistidine tag and/or any residues C- terminal thereto removed or omitted.
  • the composition is a nucleic acid encoding a Marburg single chain antibody or antigen binding fragment thereof.
  • the composition is a nucleic acid encoding a Ebola single chain antibody or antigen binding fragment thereof.
  • the composition is a nucleic acid encoding a NIP AH single chain antibody or antigen binding fragment thereof.
  • the composition is a nucleic acid encoding a botulinum toxin single chain antibody or antigen binding fragment thereof.
  • the composition is a nucleic acid encoding an anthrax single chain antibody or antigen binding fragment thereof.
  • the composition is a nucleic acid encoding a CD35/CR1 single chain antibody or antigen binding fragment thereof.
  • the hinge-CH2-CH3 Fc domain is from or is derived from IgG, IgA, IgD, or IgE.
  • the hinge-CH2-CH3 Fc domain is from or is derived from human IgG, IgA, IgD, or IgE.
  • the hinge-CH2-CH3 Fc domain is from or is derived from IgGl, IgG2, IgG3, IgG4, IgAl, or IgA2.
  • the hinge-CH2-CH3 Fc domain is from or is derived from human IgGl, IgG2, IgG3, IgG4, IgAl, or IgA2.
  • the hinge-CH2-CH3 Fc domain is from or is derived from IgG4.
  • the hinge-CH2-CH3 Fc domain is from or is derived from human IgG4.
  • the linker comprises an amino acid sequence of GPGGPEPKSSDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDP EVI ⁇ FNWYVDGVEVHNAI ⁇ TI ⁇ PREEQYNSTYRVVSVLTVLHQDWLNGI ⁇ EYI ⁇ CI ⁇ VSNI ⁇ A LPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPE NNYKTTPPVLD SDGSFFLYSKLTVDKSRWQQGNVF SC S VMHEALHNHYTQKSLSLSPG K (SEQ ID NO: 8), or an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% thereto.
  • the human IgG Fc comprises one or mutations to reduce or eliminate the effector function of the Fc domains.
  • the mutations are L234A and L235A (LALA) substitutions in human IgGl.
  • the human IgG Fc comprises one or mutations to stabilize a hinge region in the Fc domain.
  • the mutation is S228P.
  • the linker is flanked with one or more flexible linkers comprising one or more glycine and serine residues.
  • the linker is or comprises (GGS)n, wherein n is 1, or 2, or 3, or 4, or 5.
  • the linker is GGSGGSGGSG (SEQ ID NO: 9), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • the linker is GGGGSK (SEQ ID NO: 10), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.
  • the linker is flanked with one or more flexible linkers
  • a variant as used herein has or comprises about 1, or about 2, or about 3, or about 4, or about 5, or about 6, or about 7, or about 8, or about 9, or about 10 mutations.
  • the mutations are selected from substitutions or deletions.
  • a variant as used herein has at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98% identity to a sequence described herein.
  • disclosed herein are one or more (e.g. about 1, or about 2, or about 3, or about 4, or about 5, or about 6, or about 7, or about 8, or at least about 9, or about 10, or about 15, or about 20, or about 30) substitutions to a sequence described herein or a sequence with at least about 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 99.5, 99.8, 99.9% identity to a sequence described herein (or about 70%, or about 75%, or about 80%, or about 85%, or about 90, or about 95%, or about 9
  • one or more amino acids of a sequence described herein is substituted with a naturally occurring amino acid, such as a hydrophilic amino acid (e.g. a polar and positively charged hydrophilic amino acid, such as arginine I or lysine (K); a polar and neutral of charge hydrophilic amino acid, such as asparagine (N), glutamine (Q), serine (S), threonine (T), proline (P), and cysteine I, a polar and negatively charged hydrophilic amino acid, such as aspartate (D) or glutamate I, or an aromatic, polar and positively charged hydrophilic amino acid, such as histidine (H)) or a hydrophobic amino acid (e.g.
  • a hydrophilic amino acid e.g. a polar and positively charged hydrophilic amino acid, such as arginine I or lysine (K); a polar and neutral of charge hydrophilic amino acid, such as asparagine (N), glutamine (Q), serine (
  • a hydrophobic, aliphatic amino acid such as glycine (G), alanine (A), leucine (L), isoleucine (I), methionine (M), or valine (V)
  • a hydrophobic, aromatic amino acid such as phenylalanine (F), tryptophan (W), or tyrosine (Y) or a non-classical amino acid (e.g. selenocysteine, pyrrolysine, N-formylmethionine P-alanine, GABA and 6-Aminolevulinic acid.
  • 4-Aminobenzoic acid PABA
  • D-isomers of the common amino acids 2,4-diaminobutyric acid, a-amino isobutyric acid, 4-aminobutyric acid, Abu, 2-amino butyric acid, y-Abu, s-Ahx, 6-amino hexanoic acid, Aib, 2-amino isobutyric acid, 3-amino propionic acid, ornithine, norleucine, norvaline, hydroxyproline, sarcosme, citrulline, homocitrulline, cysteic acid, t-butylglycine, t-butylalanine, phenylglycine, cyclohexylalanine, P- alanine, fluoro-amino acids, designer amino acids such as P methyl amino acids, C a -methyl amino acids, N a -methyl amino acids, and amino acid analogs in general).
  • PABA 4-A
  • the amino acid mutations are amino acid substitutions, and may include conservative and/or non-conservative substitutions. “Conservative substitutions” may be made, for instance, on the basis of similarity in polarity, charge, size, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the amino acid residues involved.
  • the 20 naturally occurring amino acids can be grouped into the following six standard amino acid groups: (1) hydrophobic: Met, Ala, Vai, Leu, He; (2) neutral hydrophilic: Cys, Ser, Thr; Asn, Gin; (3) acidic: Asp, Glu; (4) basic: His, Lys, Arg; (5) residues that influence chain orientation: Gly, Pro; and (6) aromatic: Trp, Tyr, Phe.
  • “conservative substitutions” are exchanges of an amino acid by another amino acid listed within the same group of the six standard amino acid groups shown above. For example, the exchange of Asp by Glu retains one negative charge in the so modified polypeptide.
  • glycine and proline may be substituted for one another based on their ability to disrupt a-helices.
  • “non-conservative substitutions” are exchanges of an amino acid by another amino acid listed in a different group of the six standard amino acid groups (1) to (6) shown above.
  • compositions comprising a polynucleotide comprising a nucleic acid sequence encoding any one of the compositions described herein.
  • the polynucleotide is RNA or DNA.
  • the RNA is a messenger RNA (mRNA) or a modified mRNA.
  • composition comprising a vector composition comprising any one of the polynucleotides described herein.
  • compositions comprising a host cell comprising the polynucleotide described herein or the vector described herein.
  • Cells may be cultured in vitro or genetically engineered, for example.
  • Host cells can be obtained from normal or affected subjects, including healthy humans, private laboratory deposits, public culture collections such as the American Type Culture Collection, or from commercial suppliers.
  • compositions comprising the composition described herein, and a pharmaceutically acceptable excipient or carrier.
  • compositions that comprise compositions as described herein, in combination with a pharmaceutically acceptable carrier.
  • a “pharmaceutically acceptable carrier” (also referred to as an “excipient” or a “carrier”) is a pharmaceutically acceptable solvent, suspending agent, stabilizing agent, or any other pharmacologically inert vehicle for delivering one or more therapeutic compounds to a subject (e.g., a mammal, such as a human, non-human primate, dog, cat, sheep, pig, horse, cow, mouse, rat, or rabbit), which is nontoxic to the cell or subject being exposed thereto at the dosages and concentrations employed.
  • Pharmaceutically acceptable carriers can be liquid or solid, and can be selected with the planned manner of administration in mind so as to provide for the desired bulk, consistency, and other pertinent transport and chemical properties, when combined with one or more of therapeutic compounds and any other components of a given pharmaceutical composition.
  • Typical pharmaceutically acceptable carriers that do not deleteriously react with amino acids include, by way of example and not limitation: water, saline solution, binding agents (e.g., polyvinylpyrrolidone or hydroxypropyl methylcellulose), fillers (e.g., lactose and other sugars, gelatin, or calcium sulfate), lubricants (e.g., starch, polyethylene glycol, or sodium acetate), disintegrates (e.g., starch or sodium starch glycolate), and wetting agents (e.g., sodium lauryl sulfate).
  • binding agents e.g., polyvinylpyrrolidone or hydroxypropyl methylcellulose
  • fillers e.g., lacto
  • Pharmaceutically acceptable carriers also include aqueous pH buffered solutions or liposomes (small vesicles composed of various types of lipids, phospholipids and/or surfactants which are useful for delivery of a drug to a mammal).
  • Further examples of pharmaceutically acceptable carriers include buffers such as phosphate, citrate, and other organic acids, antioxidants such as ascorbic acid, low molecular weight (less than about 10 residues) polypeptides, proteins such as serum albumin, gelatin, or immunoglobulins, hydrophilic polymers such as polyvinylpyrrolidone, amino acids such as glycine, glutamine, asparagine, arginine or lysine, monosaccharides, disaccharides, and other carbohydrates including glucose, mannose or dextrins, chelating agents such as EDTA, sugar alcohols such as mannitol or sorbitol, salt-forming counterions such as sodium, and/or nonionic surfactants such as TWEENTM,
  • compositions can be formulated by mixing one or more active agents with one or more physiologically acceptable carriers, diluents, and/or adjuvants, and optionally other agents that are usually incorporated into formulations to provide improved transfer, delivery, tolerance, and the like.
  • a pharmaceutical composition can be formulated, e.g., in lyophilized formulations, aqueous solutions, dispersions, or solid preparations, such as tablets, dragees or capsules.
  • a multitude of appropriate formulations can be found in the formulary known to all pharmaceutical chemists: Remington’s Pharmaceutical Sciences (18 th ed, Mack Publishing Company, Easton, PA (1990)), particularly Chapter 87 by Block, Lawrence, therein.
  • formulations include, for example, powders, pastes, ointments, jellies, waxes, oils, lipids, lipid (cationic or anionic) containing vesicles (such as LIPOFECTINTM), DNA conjugates, anhydrous absorption pastes, oil- in-water and water-in-oil emulsions, emulsions carbowax (polyethylene glycols of various molecular weights), semi-solid gels, and semi-solid mixtures containing carbowax. Any of the foregoing mixtures may be appropriate in treatments and therapies as described herein, provided that the active agent in the formulation is not inactivated by the formulation and the formulation is physiologically compatible and tolerable with the route of administration.
  • compositions include, without limitation, solutions, emulsions, aqueous suspensions, and liposome-containing formulations. These compositions can be generated from a variety of components that include, for example, preformed liquids, self-emulsifying solids and self-emulsifying semisolids.
  • Emulsions are often biphasic systems comprising of two immiscible liquid phases intimately mixed and dispersed with each other; in general, emulsions are either of the water-in-oil (w/o) or oil-in-water (o/w) variety.
  • Emulsion formulations have been widely used for oral delivery of therapeutics due to their ease of formulation and efficacy of solubilization, absorption, and bioavailability.
  • compositions and formulations can contain sterile aqueous solutions, which also can contain buffers, diluents and other suitable additives (e.g., penetration enhancers, carrier compounds and other pharmaceutically acceptable carriers). Compositions additionally can contain other adjunct components conventionally found in pharmaceutical compositions. Thus, the compositions also can include compatible, pharmaceutically active materials such as, for example, antipruritics, astringents, local anesthetics or anti-inflammatory agents, or additional materials useful in physically formulating various dosage forms of the compositions provided herein, such as dyes, flavoring agents, preservatives, antioxidants, opacifiers, thickening agents and stabilizers.
  • suitable additives e.g., penetration enhancers, carrier compounds and other pharmaceutically acceptable carriers.
  • Compositions additionally can contain other adjunct components conventionally found in pharmaceutical compositions.
  • the compositions also can include compatible, pharmaceutically active materials such as, for example, antipruritics, astringents, local anesthetics or anti-inflammatory agents,
  • compositions can be mixed with auxiliary agents, e.g., lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, colorings, flavorings, and aromatic substances.
  • auxiliary agents e.g., lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, colorings, flavorings, and aromatic substances.
  • auxiliary agents e.g., lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, colorings, flavorings, and aromatic substances.
  • a composition containing a composition as provided herein can be in the form of a solution or powder with or without a diluent to make an injectable suspension.
  • the composition may contain additional ingredients including, without limitation, pharmaceutically acceptable vehicles, such as saline, water, lactic acid, mannitol, or combinations thereof, for example. Any appropriate method can be used to administer a composition as described herein to a mammal. Administration can be, for example, parenteral (e.g., by subcutaneous, intrathecal, intraventricular, intramuscular, or intraperitoneal injection, or by intravenous drip).
  • Administration can be rapid (e.g., by injection) or can occur over a period of time (e.g., by slow infusion or administration of slow release formulations).
  • administration can be topical (e.g., transdermal, sublingual, ophthalmic, or intranasal), pulmonary (e.g., by inhalation or insufflation of powders or aerosols), or oral.
  • a method of promoting antigen specific pathogen sequestration and/or destruction comprising administering an effective amount of the composition described herein or the pharmaceutical composition described herein to a subject in need thereof.
  • the composition contemporaneously binds to a pathogen cell and a erythrocyte, macrophage, and/or B-cell.
  • the composition homes to the liver and/or spleen for clearance, optionally by engulfment by a macrophage, optionally a Kupffer cell.
  • the erythrocyte, macrophage, and/or B-cell is unharmed.
  • a method of promoting liver and/or spleen clearance of a pathogen comprising administering an effective amount of the composition described herein or the pharmaceutical composition described herein to a subject in need thereof, wherein the clearance is optionally mediated by a macrophage, optionally a Kupffer cell.
  • the composition contemporaneously binds to a pathogen cell and a erythrocyte, macrophage, and/or B-cell.
  • the composition homes to the liver and/or spleen for clearance, optionally by engulfment by a macrophage, optionally a Kupffer cell.
  • the erythrocyte, macrophage, and/or B-cell is unharmed.
  • a method of treating or preventing Marburg virus disease comprising administering an effective amount of the composition described herein or the pharmaceutical composition described herein to a subject in need thereof.
  • a method of treating or preventing Ebola virus disease comprising administering an effective amount of the composition described herein or the pharmaceutical composition described herein to a subject in need thereof.
  • a method of treating or preventing Nipah virus disease comprising administering an effective amount of the composition described herein or the pharmaceutical composition described herein to a subject in need thereof.
  • a method of treating or preventing a hemorrhagic fever comprising administering an effective amount of the composition described herein or the pharmaceutical composition described herein to a subject in need thereof.
  • a method of treating or preventing infection by MRSA comprising administering an effective amount of the composition described herein or the pharmaceutical composition described herein to a subject in need thereof.
  • a method of treating or preventing botulism comprising administering an effective amount of the composition described herein or the pharmaceutical composition described herein to a subject in need thereof.
  • a method of treating or preventing anthrax comprising administering an effective amount of the composition described herein or the pharmaceutical composition described herein to a subject in need thereof.
  • a method of reversing or mitigating adverse vaccination comprising administering an effective amount of the composition described herein or the pharmaceutical composition described herein to a subject in need thereof.
  • a method of treating or preventing an autoimmune disease or disorder comprising administering an effective amount of the composition described herein or the pharmaceutical composition described herein to a subject in need thereof.
  • the autoimmune disease or disorder is selected from graft versus host disease, transplantation rejection (e.g., prevention of allograft rejection), multiple sclerosis, diabetes mellitus, lupus, celiac disease, Crohn’s disease, ulcerative colitis, Guillain-Barre syndrome, scleroderma, Goodpasture’s syndrome, Wegener’s granulomatosis, autoimmune epilepsy, Rasmussen’s encephalitis, Primary biliary sclerosis, Sclerosing cholangitis, Autoimmune hepatitis, Addison’s disease, Hashimoto’s thyroiditis, Fibromyalgia, Meniere’s syndrome; pernicious anemia, rheumatoid arthritis, systemic lupus erythematosus, dermatomyositis, Sjogren’s syndrome, lupus erythematosus, multiple sclerosis, myasthenia gravis, Reiter
  • any of the methods disclosed herein provide for clinically meaningful clearance of pathogen in about 2 hours.
  • the method provides for clinically meaningful clearance of pathogen with about 0.5 hour to about 2 hours, or about 1 hour to about 2 hours, or about 1.5 hour to about 2 hours, or about 0.5 hour to about 1.5 hours, or about 0.5 hour to about 1 hours.
  • clinically meaningful clearance of pathogen means clearance to a level at which disease symptoms are not detectable.
  • clinically meaningful clearance of pathogen means clearance to less than about 50,000 pathogens per milliliter of blood, or less than about 30,000 pathogens per milliliter of blood, or less than about 10,000 pathogens per milliliter of blood, or less than about 5,000 pathogens per milliliter of blood, or less than about 1,000 pathogens per milliliter of blood, or less than about 100 pathogens per milliliter of blood.
  • the present methods may further comprise administration of one or more other addition agents to increase or aid the treatment or prevention.
  • the addition agent is an antibiotic or antiviral agent.
  • the additional agent is one or more of atoltivimab, maftivimab, odesivimab, and ansuvimab-zykl.
  • the additional agent is a live-attenuated recombinant vesicular stomatitis virus (rVSV) vaccine vector, e.g.
  • rVSV-ZEBOV live-attenuated recombinant vesicular stomatitis virus
  • GP MBGV glycoprotein
  • the additional agent is an inhibitor of factor Vlla/tissue factor.
  • the additional agent is one or more of clindamycin, tetracyclines, and trimethoprim-sulfamethoxazole (TMP-SMX). Kits
  • kits containing the present compositions, or the compositions and one or more other addition agents that are synergistic in neutralization of a pathogen or antigenic pathogen molecule, in one or more containers.
  • Kits containing the pharmaceutical compositions of the invention are also provided in embodiments.
  • the word “include,” and its variants, is intended to be non-limiting, such that recitation of items in a list is not to the exclusion of other like items that may also be useful in the materials, compositions, devices, and methods of this technology.
  • the terms “can” and “may” and their variants are intended to be non-limiting, such that recitation that an embodiment can or may comprise certain elements or features does not exclude other embodiments of the present technology that do not contain those elements or features.
  • FIG. 2 shows proof of concept data for the configuration of an Fc linker between the first antigen recognition domain and second antigen recognition domain.
  • DR3 agonist antibodies as surrogate first antigen recognition domain and second antigen recognition domain
  • two configurations were constructed and tested: (1) Fc between first antigen recognition domain and second antigen recognition domain. (“2e-Fc-3D”) and (2) Fc after first antigen recognition domain and second antigen recognition domain. (“2E-3D-Fc”). Both have biological activity (FIG. 2).
  • scFV constructs specific for CD35 are constructed. Further, scFV constructs specific for one or more antigens of Ebola virus, or one or more antigens of Marburg virus, or one or more antigens of Nipah Virus, or one or more antigens of MRS A are generated. These scFv are fused via an Fc domain disposed between them to create the composition of FIG. 1 and as described herein.
  • CD35/CR1 single chain antibodies 3512 SEQ ID NO: 4
  • 3511 SEQ ID NO: 5
  • 358 SEQ ID NO: 6
  • 353 SEQ ID NO: 7
  • the CDR1 (SEQ ID NO: 48) and CDR2 (SEQ ID NO: 49) of the CD35/CR1 single chain antibodies were kept constant for all of the Marburg Virus- CD35 bispecific molecules.
  • the CDR3 of CD35/CR1 single chain antibodies 3512, 3511, 358 and 353 were modified (SEQ ID NO: 50-53).
  • marburgH10-3512 (SEQ ID NO: 11), marburgH10-3511 (SEQ ID NO: 12), marburgH10-358 (SEQ ID NO: 13), marburgH10-353 (SEQ ID NO: 14), marburgC10-3512 (SEQ ID NO: 15), marburgC10-3511 (SEQ ID NO: 16), marburgC10-358 (SEQ ID NO: 17), marburgC10-353 (SEQ ID NO: 18), marburgF7-3512 (SEQ ID NO: 19), marburgF7-3511 (SEQ ID NO: 20), marburgF7-358 (SEQ ID NO: 21), marburgF7-353 (SEQ ID NO: 22).
  • NIP AH virus-CD35 bispecific molecules Constructs were built for the NIP AH Virus-CD35 bispecific molecules.
  • the order of the construct is NIP AH virus single chain antibody — linker — human Fc (IgGl) — linker — CD35/CR1 single chain antibody — poly his tag.
  • the vector used is pcDNA3.1.
  • NIP AH virus single chain antibodies nipahEl (SEQ ID NO: 23), nipahE6 (SEQ ID NO: 24), nipahDIO (SEQ ID NO: 25) and nipahG4R (SEQ ID NO: 26).
  • the CDR1 (SEQ ID NO: 54) and CDR2 (SEQ ID NO: 55) of the NIP AH single chain antibodies were kept constant for all of the NIP AH Virus-CD35 bispecific molecules.
  • the CDR3 of NIP AH virus single chain antibodies, nipahEl, nipahE6, nipahDIO and nipahG4R were modified (SEQ ID NO: 56-59).
  • CD35/CR1 single chain antibodies 3512 (SEQ ID NO: 4), 3511 (SEQ ID NO: 5), 358 (SEQ ID NO: 6), and 353 (SEQ ID NO: 7).
  • the CDR1 (SEQ ID NO: 48) and CDR2 (SEQ ID NO: 49) of the CD35/CR1 single chain antibodies were kept constant for all of the NIP AH Virus-CD35 bispecific molecules.
  • the CDR3 of CD35/CR1 single chain antibodies 3512, 3511, 358 and 353 were modified (SEQ ID NO: 50-53).
  • nipahEl-3512 (SEQ ID NO: 27), nipahEl-3511 (SEQ ID NO: 28), nipahEl-358 (SEQ ID NO: 29), nipahEl-353 (SEQ ID NO: 30), nipahE6-3512 (SEQ ID NO: 31), nipahE6-3511 (SEQ ID NO: 32), nipahE6-358 (SEQ ID NO: 33), nipahE6-353 (SEQ ID NO: 34), nipahD10-3512 (SEQ ID NO: 35), nipahD10-3511 (SEQ ID NO: 36), nipahD10-358 (SEQ ID NO: 37), nipahD10-353 (SEQ ID NO: 38), nipahG4R-3512 (SEQ ID NO: 39), nipahG4R -3511 (SEQ ID NO:
  • Ebola virus single chain antibody linker — human Fc (IgGl) — linker — CD35/CR1 single chain antibody — poly his tag.
  • the vector used is pcDNA3.1.
  • Ebola virus single chain antibodies ebolaGl 1 (SEQ ID NO: 61 ), ebolaG2&3 (SEQ ID NO: 62), ebolaMGl 1 (SEQ ID NO: 74), ebolaMG2&3 (SEQ ID NO: 75).
  • the CDR1 (SEQ ID NO: 63) and CDR2 (SEQ ID NO: 63) of the ebolaGl 1 and ebolaG2&3 single chain antibodies were kept constant for the ebolaGl 1 and ebolaG2&3 bispecific molecules.
  • the CDR3 of ebolaGl 1 (SEQ ID NO: 64) and CDR3 of ebolaG2&3 (SEQ ID NO: 65) were modified.
  • the CDR1 (SEQ ID NO: 76) and CDR2 (SEQ ID NO: 77) of the ebolaMGl 1 and ebolaMG2&3 single chain antibodies were kept constant for the ebolaMGl 1 and ebolaMG2&3 bispecific molecules.
  • the CDR3 of ebolaMGl 1 (SEQ ID NO: 64) and CDR3 of ebolaMG2&3 (SEQ ID NO: 65) were modified.
  • CD35/CR1 single chain antibodies 3512 (SEQ ID NO: 4), 3511 (SEQ ID NO: 5), 358 (SEQ ID NO: 6), and 353 (SEQ ID NO: 7).
  • the CDR1 (SEQ ID NO: 48) and CDR2 (SEQ ID NO: 49) of the CD35/CR1 single chain antibodies were kept constant for all of the Ebola Virus- CD35 bispecific molecules.
  • the CDR3 of CD35/CR1 single chain antibodies 3512, 3511, 358 and 353 were modified (SEQ ID NO: 50-53).
  • ebolaGl 1-3512 (SEQ ID NO: 66), ebolaGl 1-3511 (SEQ ID NO: 67), ebolaGl 1-358 (SEQ ID NO: 68), ebolaGl 1-353 (SEQ ID NO: 69), ebolaG2&3-3512 (SEQ ID NO: 70), ebolaG2&3-3511 (SEQ ID NO: 71), ebolaG2&3-358 (SEQ ID NO: 72), ebolaG2&3-353 (SEQ ID NO: 73), ebolaMGl 1-3512 (SEQ ID NO: 78), ebolaMGl 1-3511 (SEQ ID NO: 79), ebolaMGl 1-358 (SEQ ID NO: 80), ebolaMGl 1-353 (SEQ ID NO: 81), ebolaMG2&3-3512 (SEQ ID NO: 82), ebolaMG2&3-
  • Botulinum Toxin-CD35 bispecific molecules were built for the Botulinum Toxin-CD35 bispecific molecules.
  • the order of the construct is botulinum toxin single chain antibody — linker — human Fc (IgGl) — linker — CD35/CR1 single chain antibody — poly his tag.
  • the vector used is pcDNA3.1.
  • BoNT-993A SEQ ID NO: 86
  • BoNT-990 SEQ ID NO: 87
  • the BoNT-993A single chain antibody has a variable domain of three CDRs, wherein CDR1 comprises an amino acid sequence set forth in SEQ ID NO: 88, CDR2 comprises an amino acid sequence set forth in SEQ ID NO: 89, CDR3 comprises an amino acid sequence set forth in SEQ ID NO: 90.
  • the BoNT-990 single chain antibody has a variable domain of three CDRs, wherein CDR1 comprises an amino acid sequence set forth in SEQ ID NO: 91, CDR2 comprises an amino acid sequence set forth in SEQ ID NO: 92, CDR3 comprises an amino acid sequence set forth in SEQ ID NO: 93.
  • CD35/CR1 single chain antibodies 3512 (SEQ ID NO: 4), 3511 (SEQ ID NO: 5), 358 (SEQ ID NO: 6), and 353 (SEQ ID NO: 7).
  • the CDR1 (SEQ ID NO: 48) and CDR2 (SEQ ID NO: 49) of the CD35/CR1 single chain antibodies were kept constant for all of the BoNT-CD35 bispecific molecules.
  • the CDR3 of CD35/CR1 single chain antibodies 3512, 3511, 358 and 353 were modified (SEQ ID NO: 50-53).
  • BoNT-993 A-3512 (SEQ ID NO: 94), BoNT-993 A -3511 (SEQ ID NO: 95), BoNT-993 A-358 (SEQ ID NO: 96), BoNT-993 A-353 (SEQ ID NO: 97), BoNT-990- 3512 (SEQ ID NO: 98), BoNT-990-3511 (SEQ ID NO: 99), BoNT-990-358 (SEQ ID NO: 100), BoNT-990-353 (SEQ ID NO: 101).
  • the AnthimVl single chain antibody has a variable domain of three CDRs, wherein CDR1 comprises an amino acid sequence set forth in SEQ ID NO: 103, CDR2 comprises an amino acid sequence set forth in SEQ ID NO: 104, and CDR3 comprises an amino acid sequence set forth in SEQ ID NO: 105.
  • the AnthimVh single chain antibody has a variable domain of three CDRs, wherein CDR1 comprises an amino acid sequence set forth in SEQ ID NO: 106, CDR2 comprises an amino acid sequence set forth in SEQ ID NO: 107, and CDR3 comprises an amino acid sequence set forth in SEQ ID NO: 108.
  • the AnthimVl-Vh single chain antibody has light chain variable domain comprises CDR1, CDR2, and CDR3 sequences, wherein the CDR1 comprises RASQDIRNYLN (SEQ ID NO: 103), CDR2 comprises YTSRLLP (SEQ ID NO: 104), and CDR3 comprises QQGNTLPWT (SEQ ID NO: 105), and the heavy chain variable domain comprises CDR1, CDR2, and CDR3 sequences, wherein the CDR1 comprises YAFSSSWMN (SEQ ID NO: 106), CDR2 comprises RIYPGDGDTNYNGKFQG (SEQ ID NO: 107), CDR3 comprises SGLLRYAMDY (SEQ ID NO: 108).
  • the AnthimVh-Vl single chain antibody has heavy chain variable domain comprises CDR1, CDR2, and CDR3 sequences, wherein the CDR1 comprises YAFSSSWMN (SEQ ID NO: 106), CDR2 comprises RIYPGDGDTNYNGKFQG (SEQ ID NO: 107), CDR3 comprises SGLLRYAMDY (SEQ ID NO: 108), and light chain variable domain comprises CDR1, CDR2, and CDR3 sequences, wherein the CDR1 comprises RASQDIRNYLN (SEQ ID NO: 103), CDR2 comprises YTSRLLP (SEQ ID NO: 104), and CDR3 comprises QQGNTLPWT (SEQ ID NO: 105).
  • the CDR1 comprises YAFSSSWMN (SEQ ID NO: 106)
  • CDR2 comprises RIYPGDGDTNYNGKFQG (SEQ ID NO: 107)
  • CDR3 comprises SGLLRYAMDY (SEQ ID NO: 108)
  • light chain variable domain
  • CD35/CR1 single chain antibodies 3512 (SEQ ID NO: 4), 3511 (SEQ ID NO: 5), 358 (SEQ ID NO: 6), and 353 (SEQ ID NO: 7).
  • the CDR1 (SEQ ID NO: 48) and CDR2 (SEQ ID NO: 49) of the CD35/CR1 single chain antibodies were kept constant for all of the anthrax- CD35 bispecific molecules.
  • the CDR3 of CD35/CR1 single chain antibodies 3512, 3511, 358 and 353 were modified (SEQ ID NO: 50-53).
  • AnthimVl-Vh -3512 (SEQ ID NO: 112), AnthimVl-Vh -3511 (SEQ ID NO: 113), AnthimVl-Vh -358 (SEQ ID NO: 114), AnthimVl-Vh -353 (SEQ ID NO: 115), AnthimVH-Vl -3512 (SEQ ID NO: 116), AnthimVH-Vl -3511 (SEQ ID NO: 117),
  • AnthimVH-Vl -358 (SEQ ID NO: 118), AnthimVH-Vl -353 (SEQ ID NO: 119), AnthimVl -3512 (SEQ ID NO: 120), AnthimVl -3511 (SEQ ID NO: 121), AnthimVl -358 (SEQ ID NO: 122), AnthimVl -353 (SEQ ID NO: 123), AnthimVh -3512 (SEQ ID NO: 124), AnthimVh -3511 (SEQ ID NO: 125), AnthimVh -358 (SEQ ID NO: 126), and AnthimVh -353 (SEQ ID NO: 127).
  • VLPs Virus Like Particles
  • Ebola glycoprotein were labeled using Cellbrite Membrane Stain.
  • CD35-ebola bispecific constructs were mixed with human (ThP-1 cells) or mouse (RAW) macrophages and fluorescence determined visually and by flow cytometry. The Fc receptors on the macrophages were blocked with antibody to eliminate non-specific uptake.
  • THP-1 cells expressing CD35 were identified by flow cytometry. Various CD35-ebola bispecific constructs were mixed with THP-1 cells. Results showed there was a quantitative/significant uptake of the labeled VLPs by Ebola 4, Ebola 7, and Ebola 8 constructs (FIG. 3).

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Abstract

La divulgation concerne des molécules à base d'anticorps bispécifiques pour, entre autres<i />, une clairance d'agents pathogènes.
PCT/US2022/078127 2021-10-14 2022-10-14 Agents anti-pathogènes bifonctionnels WO2023064909A1 (fr)

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