Compositions and methods for treating arenavirus infection
11191823 · 2021-12-07
Assignee
- Children's Medical Center Corporation (Boston, MA)
- Dana-Farber Cancer Institute, Inc. (Boston, MA, US)
Inventors
- Jonathan Abraham (Boston, MA, US)
- Stephen Harrison (Boston, MA, US)
- Kai Wucherpfennig (Boston, MA, US)
Cpc classification
C12N2760/10022
CHEMISTRY; METALLURGY
C12N2760/16134
CHEMISTRY; METALLURGY
C07K2317/33
CHEMISTRY; METALLURGY
G16B15/00
PHYSICS
C07K2317/76
CHEMISTRY; METALLURGY
G01N33/53
PHYSICS
C12N15/86
CHEMISTRY; METALLURGY
C12N2760/10043
CHEMISTRY; METALLURGY
C12N2760/10031
CHEMISTRY; METALLURGY
International classification
C12N15/86
CHEMISTRY; METALLURGY
A61K39/395
HUMAN NECESSITIES
G01N33/53
PHYSICS
Abstract
The invention generally provides compositions and methods of treating or preventing an arenavirus infection, using an agent that inhibits binding of an arenavirus glycoprotein 1 (GP1) polypeptide to transferrin receptor 1 (TfR1). The invention also provides methods of designing or identifying therapeutic agents that bind to or target a GP1 receptor-binding site (RBS) to inhibit arenavirus attachment to a cell, and therapeutic agents identified using the methods.
Claims
1. An isolated antibody or an antigen-binding fragment thereof that specifically binds to arenavirus glycoprotein 1 (GP1), wherein the antibody or the antigen binding fragment thereof comprises a heavy chain comprising three complementary determining region (CDR) sequences as follows: TABLE-US-00015 CDR H1 sequence (SEQ ID NO: 1) GFTFGTSI CDR H2 sequence (SEQ ID NO: 2) ISHDESRK CDR H3 sequence (SEQ ID NO: 3) AKDLSPPYSYAWDIFQYW and a light chain comprising three CDR sequences as follows: TABLE-US-00016 CDR L1 sequence (SEQ ID NO: 4) QSVLYSSRSDNKY CDR L2 sequence (SEQ ID NO: 36) WAS CDR L3 sequence (SEQ ID NO: 5) QQYYSSPPTF; or wherein the antibody or the antigen binding fragment thereof comprises a heavy chain comprising three CDR sequences as follows: TABLE-US-00017 CDR H1 sequence (SEQ ID NO: 6) GFTFSSA CDR H2 sequence (SEQ ID NO: 7) IWSDGSNE CDR H3 sequence (SEQ ID NO: 8) ATDKTYVSGYTSTWYYFNY and a light chain comprising three CDR sequences as follows: TABLE-US-00018 CDR L1 sequence (SEQ ID NO: 9) QSIDNW CDR L2 sequence (SEQ ID NO: 37) KAS; and CDR L3 sequence (SEQ ID NO: 10) QHRT.
2. The isolated antibody or antigen-binding fragment thereof of claim 1, wherein the antibody comprises the heavy chain sequence TABLE-US-00019 (SEQ ID NO: 11) QVQLVESGGGVVQPGRSLRLSCAASGFTFSSSAMHWVRQAPGKGLE WVAVIWSDGSNENYADSVKGRFTISRDNSKNTLYLQMSSLRAEDTAVYY CATDKTYVSGYTSTWYYFNYWGQGTLVTVS and the light chain sequence TABLE-US-00020 (SEQ ID NO: 12) DIQMTQSPSTLSASVGDRVTITCRASQSIDNWLAWYQQKPGKAPKLLIY TASRLESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQHRTFGQG TKVEIK or an antibody comprises the heavy chain sequence TABLE-US-00021 (SEQ ID NO: 13) QVQLVESGGGVVHPGRSLRLSCAASGFTFGTSIMHWVRQAPGKGM QWVAQISHDESRKFYSDSVKGRFTVSRDNSKNTLFLEMSSLRIEDTA VYYCAKDLSPPYSYAWDIFQYWGQGSLVTVS and the light chain sequence TABLE-US-00022 (SEQ ID NO: 14) DIVMTQSPESLAVSLGERATINCKSSQSVLYSSRSDNKDYLAWYQQK PGQSPKLLIYWASTRESGVPERFTGSGSGTDFTLSISSLQAEDVAVY YCQQYYSSPPTFGGGTKVELK.
3. The isolated antibody or antigen-binding fragment thereof of claim 1, that inhibits binding of GP1 and a transferrin receptor 1 (TfR1).
4. The isolated antibody or antigen-binding fragment thereof of claim 1, that binds a TfR1 receptor binding site of GP1.
5. The isolated antibody or antigen-binding fragment thereof of claim 1, wherein the TfR1 receptor binding site comprises amino acids 87-235 of JUNV GP1 as shown in
6. The isolated antibody or antigen-binding fragment thereof of claim 1, wherein the TfR1 receptor binding site comprises one or more of amino acids Serine 111, Aspartate 113, Isoleucine 115, and Lysine 216, amino acids 113-124 (JUNV GP1 loop 3), and amino acids 166-174 (JUNV GP1 loop 3) of JUNV GP1 as shown in
7. The isolated antibody or antigen-binding fragment thereof of claim 1, wherein the antibody or the antigen-binding fragment thereof binds to an arenavirus glycoprotein 1 (GP1) in a subject who is infected or at risk of infection with a New World arenavirus.
8. The isolated antibody or antigen-binding fragment thereof of claim 1, wherein the antibody or the antigen-binding fragment thereof binds to an arenavirus glycoprotein 1 (GP1) of a New World arenavirus selected from Junin (JUNV), Machupo (MACV), Guanarito (GTOV), Sabiá (SBAV), Chapare virus (CHPV), Tacaribe virus (TCRV), or White Water Arroyo virus (WWAV).
9. A method of inhibiting or preventing binding of a transferrin receptor 1 (TfR1) and an arenavirus glycoprotein 1 (GP1), the method comprising contacting a TfR1 with the isolated antibody or the antigen-binding fragment thereof of claim 1.
10. A method of treating or preventing a New World arenavirus infection, the method comprising administering to a subject in need thereof the isolated antibody or the antigen-binding fragment thereof of claim 1.
11. A kit comprising the antibody or antigen-binding fragment thereof of claim 1.
12. The method of claim 9, wherein the method is in vivo or in vitro.
13. The method of claim 9, wherein the antibody or the antigen-binding fragment thereof binds a TfR1 receptor binding site of GP1.
14. The method of claim 13, wherein the PRI receptor binding site comprises amino acids 87-235 of JUNV GP1 or corresponding amino acids of an arenavirus GP1.
15. The method of claim 13, wherein the TfR1 receptor binding site comprises one or more of amino acids Serine 111, Aspartate 113, Isoleucine 115, and Lysine 216, amino acids 113-124 (JUNV GP1 loop and amino acids 166-174 (JUNV GP1 loop 3) of JUNV GP1 or corresponding amino acids of an arenavirus GP1.
16. The method of claim 13, wherein the TfR1 receptor binding site interacts with Tyr211 of TfR1.
17. The method of claim 9, wherein the arenavirus GP1 is from a New World arenavirus selected from Junin (JUNV), Machupo (MACV), Guanarito (GTOV), Sabia (SBA Chapare virus (CHPV), Tacaribe virus (TCRV), or White Water Arroyo virus (WWAV).
18. The method of claim 10, wherein the subject has or is at risk of developing viral hemorrhagic fever.
19. The method of claim 10, wherein the isolated antibody or the antigen-binding fragment thereof has neutralizing activity against New World arenavirus in the subject.
Description
BRIEF DESCRIPTION OF THE DRAWINGS
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(11) The atomic coordinates of the protein structure of a CR1-10/JUNV/CR1-28 complex are deposited in the Protein Data Bank (PDB) under Accession No. PDB ID 5W1K. The atomic coordinates of the protein structure of a MACV/CR1-07 complex are deposited in the Protein Data Bank (PDB) under Accession No. PDB ID 5W1M. The PDB file for JUNV GP1 bound to GD01 is available at Protein Data Bank Accession No. PDB ID 5EN2. The PDB file for MACV bound to transferrin is available at Protein Data Bank Accession No. PDB ID 3KAS. The atomic coordinates of the protein structure of an unliganded Fab fragment of CR1-07 is deposited at Protein Database (PDB) ID 5W1G. The entire contents of the protein structural data and atomic coordinates of these deposits are incorporated herein.
DETAILED DESCRIPTION OF THE INVENTION
(12) The invention provides compositions and methods for treating or preventing arenavirus infection, as well as methods for the discovery or identification of therapeutic agents useful for inhibiting arenavirus infection. As described herein, the structure of the JUNV surface glycoprotein receptor-binding subunit (GP1) bound to a neutralizing monoclonal antibody was determined. The antibody engages the GP1 site that binds transferrin receptor 1 (TfR1)—the host cell surface receptor for all New World hemorrhagic fever arenaviruses—and mimics an important receptor contact. The invention is based, at least in part, on the discovery that the GP1 receptor-binding site (RBS) with which the New World hemorrhagic fever arenaviruses engage their obligate cell surface receptor, TfR1, is readily accessible to neutralizing antibodies. Several enveloped RNA viruses cause human viral hemorrhagic fevers, but passive immunotherapy has been rigorously shown to be effective in humans only for the treatment of JUNV infection. Without being bound by theory, it is proposed that RBS accessibility explains the effectiveness of convalescent-phase plasma therapy against JUNV. It is proposed that this functionally conserved epitope is a potential target for therapeutics and vaccines to limit infection by all New World hemorrhagic fever arenaviruses and also antibodies with cross-neutralizing activity against various viruses within the group. Thus, deploying and adapting this approach has the potential to limit outbreaks of the New World mammarenaviruses which depend on TfR1 for cellular entry, including the related arenaviruses MACV, GTOV, CHAPV, and SBAV.
(13) Arenaviruses
(14) Arenaviruses are enveloped viruses that carry single-stranded, bi-segmented RNA genomes. They include viruses found in captive alethinophidian snakes (the reptarenaviruses) and viruses that circulate mostly in rodents (the mammarenaviruses) (Radoshitzky et al., 2015). The arenaviruses are divided into two groups—‘Old World’ and ‘New World’—based on their serology and geographic distribution. They cause acute human viral hemorrhagic fevers with high case fatality rates (Paessler and Walker, 2013). The pathogenic Old World arenaviruses include Lassa (LASV) and Lujo (LUJV) viruses (Briese et al., 2009; Charrel and de Lamballerie, 2003). The New World arenaviruses include Junin (JUNV), Machupo (MACV), Guanarito (GTOV), and Sabia (SBAV) viruses, which respectively cause Argentine (AHF), Bolivian, Venezuelan, and “Brazilian” hemorrhagic fever (Charrel and de Lamballerie, 2003; Oldstone, 2002; Salas et al., 1991). The most recently described member, Chapare virus (CHPV), was isolated from a small outbreak in Bolivia from 2003 to 2004 (Delgado et al., 2008). All cause severe human disease associated with hemorrhage and hemodynamic shock. Argentine hemorrhagic fever (AHF) is unique among viral hemorrhagic fevers because infusion of polyclonal neutralizing antibody-containing immune plasma derived from survivors (‘passive immunity’) is a well-established means of treating acute human infection (Maiztegui et al., 1979; Ruggiero et al., 1986). When provided within 8 days of illness, it decreases the case fatality rate from 15-30% to less than 1% (Maiztegui et al., 1979; Ruggiero et al., 1986). For it to be effective, the immune plasma has to be administered in defined doses of neutralizing activity (Enria et al., 1984). Without being bound by theory, this indicates that antibody-mediated virus neutralization is its main mode of action.
(15) Arenavirus Surface Envelope Glycoprotein (GPC)
(16) The arenavirus surface envelope glycoprotein (GPC) is the target of neutralizing antibodies. GPC comprises three non-covalently associated polypeptides; the stable signal peptide (SSP), GP1, and GP2 (Burri et al., 2012). GP1 binds cellular receptors, and GP2 contains a transmembrane segment and promotes fusion of the viral and host cell membranes. The ubiquitously expressed iron-uptake protein TfR1 is a cellular receptor for all New World hemorrhagic fever arenaviruses (Helguera et al., 2012; Radoshitzky et al., 2007). TfR1 orthologs from the natural hosts of all tested clade B New World arenaviruses are receptors for their corresponding virus, but only the New World arenaviruses that cause human disease bind human TfR1 (Choe et al., 2011).
(17) Previously the structure of a MACV GP1-TfR1 complex was determined (Abraham et al., 2010). MACV GP1 binds TfR1 through an extensive network of contacts with the lateral surface of the apical domain of TfR1. Sequence comparison for the five New World hemorrhagic fever arenavirus GP1s show these to be complementary to the same TfR1 surface. A pocket on GP1 that accepts a tyrosine on the βII-2 strand of the TfR1 apical domain (Tyr211.sub.TfR1) is a central feature of the GP1 receptor-binding site (RBS) (Abraham et al., 2010). This tyrosine is present on all the TfR1 orthologs that support entry of New World arenaviruses and is an important determinant of host specificity (Abraham et al., 2009; Radoshitzky et al., 2008).
(18) Arenavirus Neutralizing Antibodies
(19) GD01-AG02 (GD01) and QC03-BF11 (QC03) are antibodies that were generated in mice by immunization with inactivated JUNV (Sanchez et al., 1989). They belong to a small group of described monoclonal antibodies that neutralize JUNV, and they are active against infectious virus (Sanchez et al., 1989). However, their epitopes have not previously been characterized. As described herein, the X-ray crystal structure of JUNV GP1 complexed with the antigen-binding fragment (Fab) of GD01 was determined to understand how antibodies neutralize JUNV. The structure reveals that the antibody and receptor have similar modes of GP1 recognition and that the antibody's complementarity-determining region (CDR) H3 mimics the Tyr211.sub.TfR1 receptor contact. GD01 and QC03 compete for the same GP1 surface. Without being bound by theory, this indicates that both antibodies neutralize the virus by a similar mechanism. It is further shown that survivor immune plasma with neutralizing activity contains antibodies that target the Tyr211 TfR1 pocket and GP1 RBS. The GP1 RBS is thus an accessible target for therapeutics and vaccines to limit infection caused by this important group of emerging human pathogens.
(20) Therapeutic Methods
(21) The methods and compositions provided herein can be used to treat or prevent an arenavirus infection. The methods and compositions provided herein can generate or enhance an immune response in a subject against an arenavirus infection. In general, arenavirus GP1 polypeptides and/or antibodies specific to arenavirus GP1 polypeptides described herein can be administered therapeutically and/or prophylactically to simulate an immune response specific for arenavirus GP1 antigen. The methods include administering an immunologically effective amount of an immunogenic GP1 polypeptide provided herein, and/or an immunologically effective amount of an antibody provided herein (e.g., CR1-07, CR1-28) to an individual in a physiologically acceptable carrier. In certain embodiments, the serum or plasma of an arenavirus immune survivor is used to treat or prevent the infection of another or different species of arenavirus.
(22) The present invention provides methods of treating or preventing an arenavirus infection (e.g., a New World arenavirus infection), and/or disorders or symptoms thereof, which comprise administering a therapeutically effective amount of an anti-arenavirus GP1 agent as described herein (e.g., CR1-07, CR1-28, and/or a compound that specifically binds the TfR1 RBS of GP1), to a subject (e.g., a mammal such as a human). Thus, one embodiment is a method of treating a subject suffering from or susceptible to an arenavirus infection, disease or symptom thereof (e.g., viral hemorrhagic fever). The method includes the step of administering to the mammal a therapeutic amount of an anti-GP1 agent (e.g., anti-GP1 antibody) sufficient to treat the infection, disease or symptom thereof, under conditions such that the infection, disease or disorder is treated.
(23) The present invention also provides methods of treating or preventing an arenavirus infection (e.g., a New World arenavirus infection), and/or disorders or symptoms thereof, which comprise administering a therapeutically effective amount of an immunogenic composition or vaccine as described herein (e.g., comprising a polypeptide comprising the TfR1 RBS of GP1), to a subject (e.g., a mammal such as a human). Thus, one embodiment is a method of preventing an arenavirus infection in a subject susceptible to an arenavirus infection, disease or symptom thereof (e.g., viral hemorrhagic fever). The method includes the step of administering to the mammal a prophylactic amount of an immunogenic GP1 polypeptide (e.g., comprising the TfR1 RBS of GP1) sufficient to prevent the infection, disease or symptom thereof, under conditions such that the infection, disease or disorder is prevent.
(24) Treatment will be suitably administered to subjects, particularly humans, suffering from, having, susceptible to, or at risk for an arenavirus infection, disease or symptom thereof. Determination of those subjects “at risk” can be made by any objective or subjective determination by a diagnostic test or opinion of a subject or health care provider (e.g., genetic test, enzyme or protein marker (such as levels of S100 ligands), family history, and the like). The methods herein also include administering to the subject (including a subject identified as in need of such treatment) an effective amount of an anti-arenavirus GP1 antibody, an immunogenic composition or vaccine as described herein. Identifying a subject in need of such treatment can be in the judgment of a subject or a health care professional and can be subjective (e.g. opinion) or objective (e.g. measurable by a test or diagnostic method).
(25) In some aspects, the invention features methods of treating or preventing an arenavirus arenavirus infection or arenavirus-associated disease or condition (e.g., hemorrhagic fever) in a subject, the methods comprising administering to the subject an effective amount of a composition comprising an anti-arenavirus agent (e.g., an anti-GP1 antibody or therapeutic vaccine as described herein). Optionally, an anti-arenavirus therapeutic of the invention (e.g., an anti-GP1 antibody or therapeutic vaccine as described herein) may be administered in combination with one or more of any other standard anti-arenavirus therapies (see e.g., Vela et al., 2012). For example, an anti-GP1 antibody or therapeutic vaccine as described herein may be administered in combination with other antibodies or antibody cocktails with antiviral activity (including e.g., immune plasma), in combination with a vaccine (including e.g., a therapeutic vaccine), or in combination with a drug with anti-arenavirus activity (Ribavirin). Methods for administering combination therapies (e.g., concurrently or otherwise) are known to the skilled artisan and are described for example in Remington's Pharmaceutical Sciences by E. W. Martin.
(26) Antibodies
(27) As reported herein, antibodies that specifically bind arenavirus GP1 are useful in therapeutic methods. For example, antibodies that inhibit or target the binding of transferrin receptor 1 (TfR1) to glycoprotein 1 (GP1), are particularly useful in the methods of the invention. In particular embodiments, the invention provides methods of using anti-GP1 antibodies for the treatment or prevention of arenavirus infection and/or hemorrhagic disease. Exemplary anti-GP1 antibodies include one or more of GD01, CR1-28, and CR1-07, and antibodies obtained or isolated from survivors of arenavirus infection (e.g., from blood, serum, or plasma).
(28) Methods of preparing antibodies are well known to those of ordinary skill in the science of immunology. As used herein, the term “antibody” means not only intact antibody molecules, but also fragments of antibody molecules that retain immunogen-binding ability. Such fragments are also well known in the art and are regularly employed both in vitro and in vivo. Accordingly, as used herein, the term “antibody” means not only intact immunoglobulin molecules but also the well-known active fragments F(ab′).sub.2, and Fab. F(ab′).sub.2, and Fab fragments that lack the Fc fragment of an intact antibody, clear more rapidly from the circulation, and may have less non-specific tissue binding than an intact antibody (Wahl et al., J. Nucl. Med. 24:316-325 (1983). The antibodies of the invention comprise whole native antibodies, bispecific antibodies; chimeric antibodies; Fab, Fab′, single chain V region fragments (scFv), fusion polypeptides, and unconventional antibodies.
(29) Unconventional antibodies include, but are not limited to, nanobodies, linear antibodies (Zapata et al., Protein Eng. 8(10): 1057-1062, 1995), single domain antibodies, single chain antibodies, and antibodies having multiple valencies (e.g., diabodies, tribodies, tetrabodies, and pentabodies). Nanobodies are the smallest fragments of naturally occurring heavy-chain antibodies that have evolved to be fully functional in the absence of a light chain. Nanobodies have the affinity and specificity of conventional antibodies although they are only half of the size of a single chain Fv fragment. The consequence of this unique structure, combined with their extreme stability and a high degree of homology with human antibody frameworks, is that nanobodies can bind therapeutic targets not accessible to conventional antibodies. Recombinant antibody fragments with multiple valencies provide high binding avidity and unique targeting specificity to cancer cells. These multimeric scFvs (e.g., diabodies, tetrabodies) offer an improvement over the parent antibody since small molecules of ˜60-100 kDa in size provide faster blood clearance and rapid tissue uptake. See Power et al., (Generation of recombinant multimeric antibody fragments for tumor diagnosis and therapy. Methods Mol Biol, 207, 335-50, 2003); and Wu et al. (Anti-carcinoembryonic antigen (CEA) diabody for rapid tumor targeting and imaging. Tumor Targeting, 4, 47-58, 1999).
(30) Various techniques for making and using unconventional antibodies have been described. Bispecific antibodies produced using leucine zippers are described by Kostelny et al. (J. Immunol. 148(5):1547-1553, 1992). Diabody technology is described by Hollinger et al. (Proc. Natl. Acad. Sci. USA 90:6444-6448, 1993). Another strategy for making bispecific antibody fragments by the use of single-chain Fv (sFv) diners is described by Gruber et al. (J. Immunol. 152:5368, 1994). Trispecific antibodies are described by Tutt et al. (J. Immunol. 147:60, 1991). Single chain Fv polypeptide antibodies include a covalently linked VH::VL heterodimer which can be expressed from a nucleic acid including V.sub.H- and V.sub.L-encoding sequences either joined directly or joined by a peptide-encoding linker as described by Huston, et al. (Proc. Nat. Acad. Sci. USA, 85:5879-5883, 1988). See, also, U.S. Pat. Nos. 5,091,513, 5,132,405 and 4,956,778; and U.S. Patent Publication Nos. 20050196754 and 20050196754.
(31) In various embodiments, an antibody that binds arenavirus GP1 is monoclonal. Alternatively, the anti-arenavirus GP1 antibody is a polyclonal antibody. In various embodiments, the antibody that binds arenavirus GP1 is obtained from the serum or plasma of an arenavirus immune survivor. The preparation and use of polyclonal antibodies are also known the skilled artisan. The invention also encompasses hybrid antibodies, in which one pair of heavy and light chains is obtained from a first antibody, while the other pair of heavy and light chains is obtained from a different second antibody. Such hybrids may also be formed using humanized heavy and light chains. Such antibodies are often referred to as “chimeric” antibodies.
(32) In general, intact antibodies are said to contain “Fc” and “Fab” regions. The Fc regions are involved in complement activation and are not involved in antigen binding. An antibody from which the Fc′ region has been enzymatically cleaved, or which has been produced without the Fc′ region, designated an “F(ab′)2” fragment, retains both of the antigen binding sites of the intact antibody. Similarly, an antibody from which the Fc region has been enzymatically cleaved, or which has been produced without the Fc region, designated an “Fab′” fragment, retains one of the antigen binding sites of the intact antibody. Fab fragments consist of a covalently bound antibody light chain and a portion of the antibody heavy chain, denoted “Fd.” The Fd fragments are the major determinants of antibody specificity (a single Fd fragment may be associated with up to ten different light chains without altering antibody specificity). Isolated Fd fragments retain the ability to specifically bind to immunogenic epitopes.
(33) Antibodies can be made by any of the methods known in the art utilizing soluble polypeptides, or immunogenic fragments thereof, as an immunogen. One method of obtaining antibodies is to immunize suitable host animals with an immunogen and to follow standard procedures for polyclonal or monoclonal antibody production. The immunogen will facilitate presentation of the immunogen on the cell surface. Immunization of a suitable host can be carried out in a number of ways. Nucleic acid sequences encoding human arenavirus GP1 or immunogenic fragments thereof, can be provided to the host in a delivery vehicle that is taken up by immune cells of the host. The cells will in turn express the human arenavirus GP1 thereby generating an immunogenic response in the host. Alternatively, nucleic acid sequences encoding human arenavirus GP1 or immunogenic fragments thereof can be expressed in cells in vitro, followed by isolation of the human arenavirus GP1 and administration of the arenavirus GP1 to a suitable host in which antibodies are raised.
(34) Alternatively, antibodies against arenavirus GP1 may, if desired, be derived from an antibody phage display library. A bacteriophage is capable of infecting and reproducing within bacteria, which can be engineered, when combined with human antibody genes, to display human antibody proteins. Phage display is the process by which the phage is made to ‘display’ the human antibody proteins on its surface. Genes from the human antibody gene libraries are inserted into a population of phage. Each phage carries the genes for a different antibody and thus displays a different antibody on its surface.
(35) Antibodies made by any method known in the art can then be purified from the host. Antibody purification methods may include salt precipitation (for example, with ammonium sulfate), ion exchange chromatography (for example, on a cationic or anionic exchange column preferably run at neutral pH and eluted with step gradients of increasing ionic strength), gel filtration chromatography (including gel filtration HPLC), and chromatography on affinity resins such as protein A, protein G, hydroxyapatite, and anti-immunoglobulin.
(36) Antibodies can be conveniently produced from hybridoma cells engineered to express the antibody. Methods of making hybridomas are well known in the art. The hybridoma cells can be cultured in a suitable medium, and spent medium can be used as an antibody source. Polynucleotides encoding the antibody of interest can in turn be obtained from the hybridoma that produces the antibody, and then the antibody may be produced synthetically or recombinantly from these DNA sequences. For the production of large amounts of antibody, it is generally more convenient to obtain an ascites fluid. The method of raising ascites generally comprises injecting hybridoma cells into an immunologically naive histocompatible or immunotolerant mammal, especially a mouse. The mammal may be primed for ascites production by prior administration of a suitable composition (e.g., Pristane).
(37) Monoclonal antibodies (Mabs) produced by methods of the invention can be “humanized” by methods known in the art. “Humanized” antibodies are antibodies in which at least part of the sequence has been altered from its initial form to render it more like human immunoglobulins. Techniques to humanize antibodies are particularly useful when non-human animal (e.g., murine) antibodies are generated. Examples of methods for humanizing a murine antibody are provided in U.S. Pat. Nos. 4,816,567, 5,530,101, 5,225,539, 5,585,089, 5,693,762 and 5,859,205.
(38) Pharmaceutical Compositions
(39) The present invention features compositions useful for treating or preventing arenavirus infection in a subject. The methods include administering an immunologically effective amount of a polypeptide provided herein, and/or an immunologically effective amount of an antibody provided herein to an individual in a physiologically acceptable carrier. In some embodiments, the composition comprises an anti-GP1 agent, such as an anti-GP1 antibody, or fragment thereof, as described herein. In other embodiments, the composition comprises an immunogenic GP1 polypeptide, such as a polypeptide comprising the TfR1 RBS of GP1, or fragment thereof, as described herein.
(40) Typically, the carrier or excipient for the immunogenic composition or vaccine provided herein is a pharmaceutically acceptable carrier or excipient, such as sterile water, aqueous saline solution, aqueous buffered saline solutions, aqueous dextrose solutions, aqueous glycerol solutions, ethanol, or combinations thereof. The preparation of such solutions ensuring sterility, pH, isotonicity, and stability is effected according to protocols established in the art. Generally, a carrier or excipient is selected to minimize allergic and other undesirable effects, and to suit the particular route of administration, e.g., subcutaneous, intramuscular, intranasal, and the like. Such methods also include administering an adjuvant, such as an oil-in-water emulsion, a saponin, a cholesterol, a phospholipid, a CpG, a polysaccharide, variants thereof, and a combination thereof, with the composition of the invention. Optionally, a formulation for prophylactic administration also contains one or more adjuvants for enhancing the immune response to the GP1 polypeptide antigens. Suitable adjuvants include: complete Freund's adjuvant, incomplete Freund's adjuvant, saponin, mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil or hydrocarbon emulsions, bacille Calmette-Guerin (BCG), Corynebacterium parvum, and the synthetic adjuvants QS-21 and MF59.
(41) The administration of a composition comprising an anti-arenavirus agent herein (e.g., anti-GP1) for the treatment or prevention of an arenavirus infection or arenavirus-associated disease or condition (e.g., hemorrhagic fever) may be by any suitable means that results in a concentration of the therapeutic that, combined with other components, is effective in ameliorating, reducing, or stabilizing the disease symptoms in a subject. The composition may be administered systemically, for example, formulated in a pharmaceutically-acceptable buffer such as physiological saline. Preferable routes of administration include, for example, subcutaneous, intravenous, intraperitoneally, intramuscular, intrathecal, or intradermal injections that provide continuous, sustained levels of the agent in the patient. The amount of the therapeutic agent to be administered varies depending upon the manner of administration, the age and body weight of the patient, and with the clinical symptoms of the arenavirus infection or disease. Generally, amounts will be in the range of those used for other agents used in the treatment of cardiac dysfunction, although in certain instances lower amounts will be needed because of the increased specificity of the agent. A composition is administered at a dosage that ameliorates or decreases effects of the arenavirus infection or disease (e.g., hemorrhagic fever and symptoms thereof) as determined by a method known to one skilled in the art.
(42) The therapeutic or prophylactic composition may be contained in any appropriate amount in any suitable carrier substance, and is generally present in an amount of 1-95% by weight of the total weight of the composition. The composition may be provided in a dosage form that is suitable for parenteral (e.g., subcutaneously, intravenously, intramuscularly, intrathecally, or intraperitoneally) administration route. The pharmaceutical compositions may be formulated according to conventional pharmaceutical practice (see, e.g., Remington: The Science and Practice of Pharmacy (20th ed.), ed. A. R. Gennaro, Lippincott Williams & Wilkins, 2000 and Encyclopedia of Pharmaceutical Technology, eds. J. Swarbrick and J. C. Boylan, 1988-1999, Marcel Dekker, New York).
(43) Pharmaceutical compositions according to the invention may be formulated to release the active agent substantially immediately upon administration or at any predetermined time or time period after administration. The latter types of compositions are generally known as controlled release formulations, which include (i) formulations that create a substantially constant concentration of the drug within the body over an extended period of time; (ii) formulations that after a predetermined lag time create a substantially constant concentration of the drug within the body over an extended period of time; (iii) formulations that sustain action during a predetermined time period by maintaining a relatively, constant, effective level in the body with concomitant minimization of undesirable side effects associated with fluctuations in the plasma level of the active substance (sawtooth kinetic pattern); (iv) formulations that localize action by, e.g., spatial placement of a controlled release composition adjacent to or in contact with an organ, such as the heart; (v) formulations that allow for convenient dosing, such that doses are administered, for example, once every one or two weeks; and (vi) formulations that target a disease using carriers or chemical derivatives to deliver the therapeutic agent to a particular cell type. For some applications, controlled release formulations obviate the need for frequent dosing during the day to sustain the plasma level at a therapeutic level.
(44) Any of a number of strategies can be pursued in order to obtain controlled release in which the rate of release outweighs the rate of metabolism of the agent in question. In one example, controlled release is obtained by appropriate selection of various formulation parameters and ingredients, including, e.g., various types of controlled release compositions and coatings. Thus, the therapeutic is formulated with appropriate excipients into a pharmaceutical composition that, upon administration, releases the therapeutic in a controlled manner. Examples include single or multiple unit tablet or capsule compositions, oil solutions, suspensions, emulsions, microcapsules, microspheres, molecular complexes, nanoparticles, patches, and liposomes.
(45) The pharmaceutical composition may be administered parenterally by injection, infusion or implantation (subcutaneous, intravenous, intramuscular, intraperitoneal, intrathecal, or the like) in dosage forms, formulations, or via suitable delivery devices or implants containing conventional, non-toxic pharmaceutically acceptable carriers and adjuvants. The formulation and preparation of such compositions are well known to those skilled in the art of pharmaceutical formulation. Formulations can be found in Remington: The Science and Practice of Pharmacy, supra.
(46) Compositions for parenteral use may be provided in unit dosage forms (e.g., in single-dose ampoules), or in vials containing several doses and in which a suitable preservative may be added (see below). The composition may be in the form of a solution, a suspension, an emulsion, an infusion device, or a delivery device for implantation, or it may be presented as a dry powder to be reconstituted with water or another suitable vehicle before use. Apart from the active agent that reduces or ameliorates a cardiac dysfunction or disease, the composition may include suitable parenterally acceptable carriers and/or excipients. The active therapeutic agent(s) (e.g., an anti-GP1 agent described herein) may be incorporated into microspheres, microcapsules, nanoparticles, liposomes, or the like for controlled release. Furthermore, the composition may include suspending, solubilizing, stabilizing, pH-adjusting agents, tonicity adjusting agents, and/or dispersing, agents.
(47) In some embodiments, the composition comprising the active therapeutic (i.e., an anti-GP1 antibody herein) is formulated for intravenous delivery. As indicated above, the pharmaceutical compositions according to the invention may be in the form suitable for sterile injection. To prepare such a composition, the suitable therapeutic(s) are dissolved or suspended in a parenterally acceptable liquid vehicle. Among acceptable vehicles and solvents that may be employed are water, water adjusted to a suitable pH by addition of an appropriate amount of hydrochloric acid, sodium hydroxide or a suitable buffer, 1,3-butanediol, Ringer's solution, and isotonic sodium chloride solution and dextrose solution. The aqueous formulation may also contain one or more preservatives (e.g., methyl, ethyl or n-propyl p-hydroxybenzoate). In cases where one of the agents is only sparingly or slightly soluble in water, a dissolution enhancing or solubilizing agent can be added, or the solvent may include 10-60% w/w of propylene glycol or the like.
(48) Methods of Identifying Agents that Inhibit Arenavirus GP1 Binding to Transferrin Receptor
(49) In Silico Drug Design
(50) The present invention permits the use of virtual design techniques (i.e., computer modeling or “in silico”) to design, select, and synthesize compounds capable of specifically binding arenavirus GP1, in particular, GP1-mediated cell attachment. In turn, these compounds may be effective in the treatment of an arenavirus infection or arenavirus-associated disease, such as hemorrhagic fever.
(51) In addition to the more traditional sources of test compounds, computer modeling and searching technologies permit the rational selection of test compounds by utilizing structural information from the ligand binding sites and functional antibody binding sites (e.g., binding sites of arenavirus-inhibitory antibodies) on proteins of the present invention (e.g., arenavirus GP1). Such rational selection of compounds may decrease the number of compounds that may need to be screened to identify a therapeutic candidate compound. In various embodiments, the functional antibody binding site of GP1 is a TfR1 binding site. In some embodiments, the functional site on arenavirus GP1 comprises any one or more of amino acid residues 87-235 (JUNV numbering) of arenavirus GP1 or a corresponding region of an arenavirus GP1 (see, e.g.,
(52) Knowledge of the protein sequences of the present invention may allow for generation of models of their binding sites that may be used to screen for potential agent(s) that bind to the binding sites. This process may be accomplished with the skills known in the art. One approach involves generating a sequence alignment of the protein sequence to a template (derived from the crystal structures or NMR-based model of a similar protein(s)), conversion of the amino acid structures and refining the model by molecular mechanics and visual examination. If a strong sequence alignment may not be obtained, then a model may also be generated by building models of the hydrophobic helices. Mutational data that point towards contact residues may also be used to position the helices relative to each other so that these contacts are achieved. During this process, docking of the known ligands into the binding site cavity within the helices may also be used to help position the helices by developing interactions that may stabilize the binding of the ligand. The model may be completed by refinement using molecular mechanics and loop building using standard homology modeling techniques. General information regarding modeling may be found in Schoneberg, T. et. al., Molecular and Cellular Endocrinology, 151:181-193 (1999), Flower, D., Biochim Biophys Acta, 1422, 207-234 (1999), and Sexton, P. M., Curr. Opin. Drug Discovery and Development, 2, 440-448 (1999).
(53) Once the model is completed, it may be used in conjunction with one of several computer programs to narrow the number of compounds to be screened, e.g., the DOCK program (UCSF Molecular Design Institute, San Francisco, Calif. 94143) or FLEXX (Tripos Inc., MO). One may also screen databases of commercial and/or proprietary compounds for steric fit and rough electrostatic complementarity to the binding site. In one embodiment, the docking program is ZDOCK (Pierce et al., Bioinformatics. 2014 Jun. 15; 30(12):1771-3). In another embodiment, the docking program is AutoDock Vina (Trott et al., Journal of Computational Chemistry 31 (2010) 455-461).
(54) In Silico Screening of Compounds
(55) In one aspect, the invention provides means to carry out virtual screening of compounds using the disclosed atomic coordinates or coordinates derived therefrom. The atomic coordinates of the three-dimensional structure elucidated by the invention are input into a computer so that images of the structure and various parameters are shown on the display. The resultant data are input into a virtual compound library. Since a virtual compound library is contained in a virtual screening software, the above-described data may be input into such a software. Compounds may be searched for, using a three-dimensional structure database of virtual or non-virtual compounds, such as MDDR (Prous Science, Spain).
(56) The potential interactions of a compound may be analyzed prior to its actual synthesis and testing by the use of computer modeling techniques. If the theoretical structure of the given compound suggests insufficient interactions with arenavirus GP1, synthesis and testing of the compound may be obviated. However, if computer modeling indicates sufficient interactions, the molecule may then be synthesized and tested for its ability to regulate arenavirus GP1, using various methods described herein and/or that are known to a person skilled in the art.
(57) Compounds may be computationally evaluated and designed by means of a series of steps in which chemical entities or fragments are screened and selected for their ability to bind with individual binding sites or combinations thereof (e.g., P0, P+1, P−1) or other areas of arenavirus GP1.
(58) One skilled in the art may use any of several methods to screen chemical entities or fragments for their ability to bind to arenavirus GP1 and more particularly with the specific binding sites or functional sites described herein (e.g., Protein Data Bank Accession No. PDB ID 5EN2, 3KAS, or those deposited under Protein Data Bank Accession No. PDB ID 5W1K and Protein Data Bank Accession No. PDB ID 5W1M. Sequences of arenavirus GP1, may also be threaded onto the protein backbone of an arenavirus GP1 crystal structure, with side chain positions optimized using methods known in the art. The resulting structural models may then be used to discover chemical entities or fragments that regulate arenavirus GP1 via in silico docking. The process may begin by visual inspection of, for example, the functional site on the computer screen based on the arenavirus GP1 coordinates presented in Protein Data Bank PDB ID 5EN2, 3KAS, or those deposited under Protein Data Bank Accession No. PDB ID 5W1K and Protein Data Bank Accession No. PDB ID 5W1M. Selected fragments or chemical entities may then be positioned in a variety of orientations, or docked, within a binding site of arenavirus GP1. Docking may be accomplished using software such as QUANTA™, SYBYL™ followed by energy minimization and molecular dynamics with molecular mechanics forcefields softwares, such as CHARMM™ and AIVIBER™.
(59) Specialized computer programs may also assist in the process of selecting fragments or chemical entities. These include, but are not limited to, GRID™ (Goodford, P. J., J. Med. Chem., 28, 849-857 (1985)); MCSS™ (Miranker, A. and M. Karplus, “Proteins: Structure, Function and Genetics, 11, 29-34 (1991)); (3) AUTODOCK™ (Goodsell, D. S. and A. J. Olsen, Proteins: Structure, Function, and Genetics, 8, 195-202 (1990; DOCK™ (Kuntz, I. D. et al., J. Mol. Biol., 161, pp. 269-288 (1982)); GLIDE™ (Schrodinger Inc.); FLEXX™ (Tripos Inc); (7) GOLD™ (Jones et al., J. Mol. Biol., 245, 43-53, 1995).
(60) Once suitable chemical entities or fragments have been selected, they may be assembled in silico or synthesized into a single compound. Chemical syntheses may be carried out by methods known in the art. In silico assembly may proceed by visual inspection of the relationship of the fragments to each other on the three-dimensional image displayed on a computer screen in relation to the structure coordinates of arenavirus GP1. This may be followed by manual model building using softwares such as QUANTA™ or SYBYL™.
(61) Useful programs for connecting the individual chemical entities or fragments include the following: CAVEAT™ (Bartlett, P. A. et al, Royal Chem. Soc., 78, 182-196 (1989)); 3D Database systems such as MACCS-3D™ (MDL Information Systems, San Leandro, Calif.); and HOOK™ (Molecular Simulations, Burlington, Mass.). In addition to building a compound in a step-wise fashion as described above, compounds may be designed as a whole or “de novo” using an empty active site or optionally including some portion(s) of a known compound. Such methods include, but are not limited to, LUDI™ (Bohm, H.-J., J. Com R. Aid. Molec. Design, 6, pp. 61-78 (1992)); LEGEND™ (Nishibata, Y. and A. Itai, Tetrahedron, 47, p. 8985 (1991)), and LEAPFROG™ (Tripos Inc., St. Louis, Mo.).
(62) Once a compound has been designed or selected, the molecular interactions or affinity with which that compound may bind arenavirus GP1 may be tested and optimized by computational evaluation. For example, a compound may demonstrate a relatively small difference in energy between its bound and unbound states (i.e., a small deformation energy of binding). A compound may interact with arenavirus GP1 in more than one conformation that is similar in overall binding energy. In those cases, the deformation energy of binding is taken to be the difference between the energy of the unbound compound and the average energy of the conformations observed.
(63) A compound that is designed or selected may be further computationally optimized so that in its bound state it may lack repulsive electrostatic interactions. Such interactions include repulsive charge-charge, dipole-dipole, and charge-dipole interactions. The sum of all electrostatic interactions between the compound and arenavirus GP1, may make a neutral or favorable contribution to the enthalpy of binding. Software programs to evaluate compound deformation energy and electrostatic interaction include, e.g., Gaussian 92™ (M. J. Frisch, Gaussian, Inc., Pittsburgh, Pa.); AIVIBER™ (P. A. Kollman, University of California at San Francisco, Calif.); QUANTA/CHARMM™ (Molecular Simulations, Inc., Burlington, Mass.); and Insight II/Discover™ (Biosysm Technologies Inc., San Diego, Calif.).
(64) Once a compound has been optimally selected or designed, substitutions may be made in some of its atoms or side groups in order to improve or modify its binding properties. Initial substitutions may be conservative, i.e., the replacement group will have approximately the same size, shape, hydrophobicity and charge as the original group. Such substituted compounds may then be analyzed for efficiency of fit to arenavirus GP1 by software programs similar to those described.
(65) Crystallographic Evaluation of Chemical Entities for Binding to Arenavirus GP1
(66) The invention allows one skilled in the art to study the binding of compounds to arenavirus GP1 by exposing either individual compounds or mixtures of compounds (such as may be obtained from combinatorial libraries) into arenavirus GP1 crystals or, alternatively, by co-crystallization of the compounds of interest with arenavirus GP1, using methods known in the art, or those described in the Examples herein. Acquisition and analysis of X-ray diffraction data from these crystals may then be performed using standard methods. If a compound binds to arenavirus GP1 then positive difference electron density will be observed in the Fourier maps calculated using the X-ray diffraction intensities and phases obtained from the arenavirus GP1 model presented herein. Models of the chemical entities may then be built into the electron density using standard methods, and the resulting structures may be refined against the X-ray diffraction data, providing experimental data describing the interaction of the compounds of interest. Those skilled in the art may use these models to design compounds based either on purely structural data; or on combination of structural data, biological/chemical activity based structure-activity relationship, and in silico drug design.
(67) The compounds that are thus designed or selected may further be tested in an in vitro, in vivo, or ex vivo assays to determine if they bind or neutralize arenavirus GP1. Such assays are known to one skilled in the art, including functional assays such as ELISA, gel filtration, immunoprecipitation, plasmon resonance, and the like.
(68) Kits
(69) The invention provides kits for the treatment or prevention of an arenavirus infection. In some embodiments, the kit includes a therapeutic or prophylactic composition containing an effective amount of an anti-GP1 agent (e.g., an anti-GP1 antibody) in unit dosage form. In other embodiments, the kit includes a therapeutic or prophylactic composition containing an effective amount of an immunogenic agent (e.g., a GP1 polypeptide) in unit dosage form. In some embodiments, the kit comprises a device (e.g., nebulizer, metered-dose inhaler) for dispersal of the composition or a sterile container which contains a pharmaceutical composition; such containers can be boxes, ampoules, bottles, vials, tubes, bags, pouches, blister-packs, or other suitable container forms known in the art. Such containers can be made of plastic, glass, laminated paper, metal foil, or other materials suitable for holding medicaments.
(70) If desired a pharmaceutical composition of the invention is provided together with instructions for administering the pharmaceutical composition to a subject having or at risk of contracting or developing an arenavirus infection. The instructions will generally include information about the use of the composition for the treatment or prevention of an arenavirus infection. In other embodiments, the instructions include at least one of the following: description of the therapeutic/prophylactic agent; dosage schedule and administration for treatment or prevention of arenavirus infection or symptoms thereof; precautions; warnings; indications; counter-indications; overdosage information; adverse reactions; animal pharmacology; clinical studies; and/or references. The instructions may be printed directly on the container (when present), or as a label applied to the container, or as a separate sheet, pamphlet, card, or folder supplied in or with the container.
(71) The practice of the present invention employs, unless otherwise indicated, conventional techniques of molecular biology (including recombinant techniques), microbiology, cell biology, biochemistry and immunology, which are well within the purview of the skilled artisan. Such techniques are explained fully in the literature, such as, “Molecular Cloning: A Laboratory Manual”, second edition (Sambrook, 1989); “Oligonucleotide Synthesis” (Gait, 1984); “Animal Cell Culture” (Freshney, 1987); “Methods in Enzymology” “Handbook of Experimental Immunology” (Weir, 1996); “Gene Transfer Vectors for Mammalian Cells” (Miller and Calos, 1987); “Current Protocols in Molecular Biology” (Ausubel, 1987); “PCR: The Polymerase Chain Reaction”, (Mullis, 1994); “Current Protocols in Immunology” (Coligan, 1991). These techniques are applicable to the production of the polynucleotides and polypeptides of the invention, and, as such, may be considered in making and practicing the invention. Particularly useful techniques for particular embodiments will be discussed in the sections that follow.
(72) The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the assay, screening, and therapeutic methods of the invention, and are not intended to limit the scope of what the inventors regard as their invention.
Example 1. The Structure of the Complex of JUNV
(73) GP1 with GD01 was Determined.
(74) Because GP1 is expected to be the most membrane distal subunit of GP on the virion surface, GD01 and QC03 Fabs were tested for JUNV GP1-reactivity. QC03 and GD01 both bound JUNV GP1 with high affinity as measured by surface plasmon resonance (1.5 nM and 12.5 nM, respectively;
(75) TABLE-US-00013 TABLE 1 Binding rate constants of surface plasmon resonance analysis (FIG. 7). k.sub.a k.sub.d K.sub.D Analyte Ligand (1/Ms) (1/s) (M) GD01 Fab JUNV GP1 2.08E5 2.61E−3 1.25E−8 QC03 Fab JUNV GP1 1.49E5 2.25E−4 1.51E−9
The structure of a GP1-neutralizing antibody complex was determined. A complex of JUNV GP1 with the GD01 Fab crystallized in space group P212121. Molecular replacement with MACV GP1 (Abraham et al., 2010) and an unrelated Fab (Aoki et al., 2009) as search models was used and the structure was refined with data extending to 1.8 Å (
(76) TABLE-US-00014 TABLE 2 Data collection and refinement statistics (molecular replacement) (FIG. 1). JUNV GP1:GD01 Data collection P2.sub.12.sub.12.sub.1 Cell dimensions a, b, c (Å) 52.1, 74.8, 177.6 Resolution (Å) 68.93 − 1.82 (1.92 − 1.82)* R.sub.merge 0.226 (1.418) Mean //σ/ 6.7 (1.5) Completeness (%) 99.9 (99.9) Redundancy 5.9 (5.7) Refinement Resolution (Å) 68.93 − 1.82 No. reflections 63032 R.sub.work/R.sub.free 0.181/0.224 (0.239/0.274) No. atoms 5473 Protein 4462 Ligand/ion 125 Water 886 B-factors Protein 21 Ligand/ion 59 Water 38 R.m.s. deviations Bond lengths (Å) 0.010 Bond angles (°) 1.06 One crystal was used to collect the dataset. *Values in parentheses are for the highest-resolution shell.
(77) The interface of JUNV GP1 with GD01 includes contacts from heavy-chain CDRs 1, 2 and 3 and light-chain CDRs 1 and 3, with the bulk of the interactions focusing on GP1 loops 3 and 7 (
Example 2. Neutralizing Anti-GP1 Antibody and TfR1 Receptor have a Shared Mode of GP1 Recognition
(78) JUNV GP1 is very similar to MACV GP1 (rmsd of 1.35 Å for Ca positions for residues 87-219 and 223-227), as expected from their sequences (48% identical for GP1 residues 87-235). However, there is a substantial difference in loop 10, in which MACV GP1 has a disulfide-linked insert with respect to JUNV (
(79) When viewed from the perspective of GP1, the lateral surface of the TfR1 apical domain presents two parallel ridges—one formed by the edge of the αII-2 helix and the βII-6-βII-7a loop, and the other by the βII-2 strand (
Example 3. GD01 Tyr98 (Kabat) Fits into the Position Occupied in the GP1 Receptor-Glycoprotein Complex by TfR1 Tyr211
(80) Close examination of the antibody-GP1 interface reveals that GD01 Tyr98 (Kabat numbering scheme) in CDR H3 fits precisely into the position occupied in the receptor-glycoprotein complex by Tyr211.sub.TfR1, even though most of the other specific interactions are different in character (
(81) A modified JUNV GP1 (designated JUNV GP1.sub.mut) was generated, in which the GP1 pocket that accepts Tyr211.sub.TfR1 was occluded by substituting residues that line it with bulkier ones (S111W, I115Y, and V117Y;
Example 4. AHF Survivor Plasma Contained RBS-Directed Antibodies
(82) Because survivor plasma transfusion is a very effective treatment for AHF (Enria et al., 1984; Maiztegui et al., 1979), it was determined whether immune plasma samples used for passive immunity contained RBS-directed antibodies. Nine survivor plasma samples (AHF1 through 9) were obtained with neutralizing antibody titers ranging from 1:10,240 to 1:40, and a survivor plasma sample with no neutralizing activity at the time of collection (AHF10) was also obtained (
(83) Single B-cell sorting was used to identify JUNV GP1-reactive antibodies from the blood of a recipient of the live attenuated vaccine Candid #1 (the individual is referred to as Candid #1 Recipient 1, or CR1) (
(84) Structures of GP1 complexes were determined for binding of the antibodies CR1-07, CR1-10, and CR1-28 isolated from single B-cell sorting to JUNV and MACV. The structure of MACV GP1 bound to TfR1 receptor (PDB 3KAS; see
(85) To determine if the Tyr211.sub.TfR1 pocket is a target for antibodies in human immune plasma, survivor IgG was tested for binding to JUNV GP1 and GP1.sub.mut. IgG purified from the plasma of AHF1 through AHF9 IgG bound JUNV GP1.sub.mut more weakly than they bound WT GP1 (
(86) Although the Tyr211.sub.TfR1 pocket is a central feature of the GP1 RBS, it is only a small part of the predicted TfR1 footprint (
(87) The lack of complete competition of GD01 with survivor IgGs in the ELISA shown in
(88) Receptor mimicry is a recurring phenomenon in antibody neutralization of enveloped RNA viruses. Receptor-mimicking antibodies neutralize influenza viruses (Schmidt et al., 2015; Xu et al., 2013) and HIV-1 (Scheid et al., 2011; Zhou et al., 2010). The results here reinforce the concept that host receptor mimicry is a general mode of antibody neutralization for diverse families of viruses.
(89) GD01 does not neutralize the other New World hemorrhagic fever arenaviruses (
(90) Because GD01 and TfR1 recognize GP1 similarly, the structure could serve as a template for in vitro or in silico design of antibodies that more faithfully mimic the receptor and neutralize some or all of the other viruses in this group. For example, the relatively prominent CDR H3 (17 residues) of GD01 projects substantially farther from the contact surface with GP1 than does the βII-2 strand of TfR1, and residues at its tip would collide with the MACV GP1-specific loop 10 insert (
(91) A less accessible RBS might explain why treatment with convalescent phase survivor plasma may be less effective against other viral hemorrhagic fevers. In the GP of the filoviruses Ebola virus (EBOV) and Sudan virus, for example, the GP1 RBS is hidden beneath a heavily glycosylated mucin-like domain that contains both O-linked and N-linked carbohydrates and becomes exposed only after this domain has been cleaved by cathepsin in acidified endosomes (Chandran et al., 2005; Lee et al., 2008). Neutralizing antibodies that target other sites, such as the GP1-GP2 interface (which lies near the viral membrane), appear to have a larger role in limiting these infections (Dias et al., 2011; Murin et al., 2014). The GP1 RBS for another filovirus that causes human hemorrhagic fevers, Marburg virus (MARV), is more exposed, and antibodies binding this site may be more important in controlling infection by this virus (Flyak et al., 2015). A MARV neutralizing antibody that probably mimics a viral glycoprotein-receptor contact has been described (Flyak et al., 2015; Hashiguchi et al., 2015).
(92) Like filoviruses, arenaviruses that are endemic to South America all lack adequate and rapidly scalable treatment options. Antibodies like GD01, CR1-28, and CR1-07 could eventually replace immune plasma in the treatment of AHF and perhaps of other New World hemorrhagic fevers. The findings described herein further indicate that a recombinant GP1 subunit-based immunization strategy, which focuses the immune response on the RBS by hiding other sites, has the potential to effectively protect against infection caused by these lethal agents.
(93) The results described herein were obtained using the following materials and methods.
(94) Cells and Plasmids
(95) HEK293T (human embryonic kidney cells, ATCC CRL-1268) were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% (v/v) fetal bovine serum (FBS). GnTI.sup.−/− 293S cells were maintained in serum free medium (FreeStyle™ 293 Expression Medium, Life Technologies). GP-expressor plasmids for JUNV, MACV, GTOV, SABV, CHAPV, TCRV, and LASV, and an expressor plasmid for vesicular stomatitis virus (VSIV) G, have been previously described (Abraham et al., 2009; Radoshitzky et al., 2007) (Helguera et al., 2012). LUJV GP (GenBank: NC_023776.1) was synthesized as a codon-optimized gene for mammalian expression, and subcloned into the pCAGGS vector. Hybridomas producing monoclonal antibodies GD01 and QC03 (clones GD01-AG02 and QC03-BF11, respectively) (Sanchez et al., 1989) were obtained from the NIAID Biodefense and Emerging Infections (BEI) repository. These cells in Hybridoma-SFM expression medium (Life Technologies). The pHLSec vector (Aricescu et al., 2006) was used to express secreted glycoproteins.
(96) Pseudotype Transduction
(97) Pseudotypes were packaged in 293T cells by transfecting plasmids encoding murine leukemia virus gag/pol, the arenaviral GP, and the pQCXIX transduction vector (BD Biosciences) expressing eGFP in a 1:1:1 ratio, as previously described (Radoshitzky et al., 2007). Virus-containing culture supernatant was harvested 24 hr and 48 hr later. Supernatants were filtered through a 0.45 μm membrane, and pseudotypes were stored at −80° C. until later use. For antibody neutralization experiments, pseudotypes were pre-incubated with polyclonal IgG or monoclonal antibodies for 30 min at 37° C. The pseudotypes and antibody mixture were then added to cells, and the media changed with 10% (v/v) FBS-supplemented DMEM 3 hr post transduction. Entry levels were measured by flow cytometry 48 hr post transduction.
(98) Protein Expression and Purification
(99) To generate biotinylated proteins, JUNV GP1 (residues 87-235), MACV GP1 (residues 87-250), and LUJV GP1 (residues 59-217), were each subcloned along with an N-terminal His6-tag (SEQ ID NO: 26), followed by a Tobacco Etch Virus (TEV) protease site, a BirA ligase site (amino acids: GLNDIFEAQKIEWHE (SEQ ID NO: 27)), and a seven residue linker (amino acid sequence: GTGSGTG (SEQ ID NO: 28)), into the pHLSEC expression vector (Aricescu et al., 2006). JUNV GP1.sub.mut, which encodes JUNV GP1 residues 87-235 and contains the S111W, I115Y and V117Y mutations was generated by site directed mutagenesis. Proteins were produced by transfection using linear polyethylenimine in HEK293T cells grown in suspension, and the proteins purified using nickel affinity chromatography. The His6-tag (SEQ ID NO: 26) was removed with TEV protease and reverse nickel-affinity purification, and then site specific biotinylation was performed with BirA ligase followed by size-exclusion chromatography on a Superdex 200 column (GE Healthcare Sciences) to remove free biotin. For crystallography, JUNV GP1 (residues 87-235) was subcloned with the addition of N-terminal His6-Tag (SEQ ID NO: 26), a TEV protease site, and a short linker (amino acids: SGSG (SEQ ID NO: 29)), into the pHLSEC vector. The protein was produced in GnTI.sup.−/− 293S cells grown in suspension and purified by nickel affinity chromatography, and the tag was removed with TEV digestion, reverse nickel-affinity purification, and size exclusion on a Superdex 200 column. GD01 and QC03 Fabs were produced using a Pierce™ Fab Preparation Kit (Thermo scientific) from Protein G Ultralink® Resin (Thermo scientific) following the manufacturer's protocol.
(100) Surface Plasmon Resonance Binding Assays
(101) Binding experiments were performed in duplicate with a Biacore 3000 (GE Health Care Sciences), using streptavidin coated sensor chips, and biotinylated JUNV GP1. Approximately 600-800 response units of biotinylated JUNV GP1 were captured onto the chips to avoid rebinding events. Experiments were carried out in HBS-EP (10 mM HEPES pH 7.5, 150 mM NaCl, 3 mM EDTA, and 0.005% P-20). GD01, QC03, CR1-07, CR1-10, and CR1-28 Fabs were passed over the surface at various concentrations, and GP1-Fab interactions were analyzed using multi-cycle kinetic analysis with 2 min association and 5 min dissociation phases with a flow rate of 50 μL/min. Between each cycle, the surface was regenerated with two 5 μl injections of 35 mM NaOH, 1.3 M NaCl at 100 μL/min, and 2 minute stabilization after regeneration. For analysis, injections over blank surfaces were subtracted from the data, and the data was fit using a 1:1 Langmuir binding model in the BiaEvaluation software (GE Health Care Sciences).
(102) Data Collection and Structure Determination
(103) The JUNV GP1-GD01 Fab complex crystallized in the P212121 space group. X-ray diffraction data were collected at wavelength of 0.9789 and temperature of 100° K at NE-CAT beam line ID-24C at the Advanced Photon Source (Argonne National Laboratory). Data were processed using MOSFLM (Leslie and Powell, 2007), and the structure of the complex was determined by molecular replacement with PHASER (McCoy et al., 2007) with MACV GP1 (PBD ID: 3KAS) (Abraham et al., 2010) and the 4F8 Fab (PDB ID: 3FMG) (Aoki et al., 2009) as search models. Electron density was observed for residues 87-227 for JUNV GP1, residues 1 to 213 with the exception of residues 128-132 in the GD01 HC, and residues 1 to 212 in the GD01 LC. We could form a ternary complex of JUNV GP1 bound to the Fabs of CR1-28 and CR1-10. This complex yielded crystals in space group P1211 that diffracted to 3.99 Å. We determined its structure using molecular replacement, and identified four copies of the complex in the asymmetric unit (ASU). We obtained crystals of a complex of a MACV GP1-CR1-07 in space group P42212 that diffracted to 3.9 Å. Initial molecular replacement searches with MACV GP1 (PDB 3KAS). We determined the structure of the unliganded CR1-07 Fab, and used these coordinates along with MACV GP1 as search models to solve the structure of the complex. The model includes 4 copies of the complex per ASU.
(104) Sequence for the GD01 Fab was obtained using a previously described protocol for antibody gene recovery from the parent hybridoma (Fields et al., 2013), and performed iterative model building with COOT (Emsley et al., 2010) and refinement with PHENIX (Adams et al., 2010), yielding a final R.sub.work of 18.1% and R.sub.free of 22.4% (Table S2), with Ramachandran favored: 97.7% and Ramachandran outliers: 0.18%. The JUNV GP1 CR1-28/CR1-10 structure has R.sub.work 22.4% and R.sub.free of 28.1%, and the MACV GP1 CR1-07 structure has R.sub.work of 26.3% and R.sub.free of 27.8%. Figures were made with the PyMol Molecular Graphics System, Schrödinger, LLC.
(105) Human Immunoglobulin Purification
(106) Five (5) de-identified plasma samples from Argentine hemorrhagic fever survivors were obtained from the immune plasma bank at the Instituto Nacional de Enfermedades Virales Humanas (INEVH), based in Pergamino, Argentina, where these samples are routinely stored. Provision of the previously collected survivor plasma samples was approved by the INEVH Ethics Committee, and the Harvard University Faculty of Medicine Committee on Human Studies (identified as not involving human subjects under 45CFR46.102(f)). An additional 5 plasma survivor samples were obtained through INEVH under a Boston Children's Hospital Institutional Review Board and INEVH Ethics Committee approved protocol (IRB: IRB-P00007578) after informed consent was obtained from all subjects. Neutralizing antibody titers from the donors at the time of plasma collection had previously been determined by the fixed-virus/variable serum technique, with Vero cell monolayers infected with the XJC13 attenuated strain of JUNV virus, and defined as a plaque neutralization reduction of 80% (PRNT.sub.80). Because the heparin that is contained in the plasma samples could interfere with the interpretation of the results of the pseudotype assay, IgG from these samples were purified using Protein G Ultralink® Resin (Thermo scientific), according to manufacturer's instructions.
(107) ELISA Experiments
(108) Streptavidin-coated ELISA plates (Thermo scientific) were used. Wells were coated with biotinylated antigens at concentration of 0.2 μg/ml in PBS containing 2% bovine serum albumin. For ELISA-based competition assays, GD01 or 17b IgG were added at increasing concentrations during a pre-incubation step of 30 minutes, then the AHF survivor IgG was added at fixed concentrations (to obtain a baseline signal of 1.5-2 OD 450 nm). Bound antibody was detected with horse-radish peroxidase (HRP)-coupled anti-human antibody.
(109) Single B Cell Sorting
(110) Written informed consent was obtained from a healthy participant previously immunized with Candid #1 more than 2 years prior to study enrollment. This study was approved by the Boston Children's Hospital Institutional Review Board (IRB). Antigen-tetramers were prepared, and peripheral blood mononuclear cells were stained and washed as previously described (Franz et al., 2011), with the exception that phycoerythrein (PE)-labeled JUNV GP1 (Sort 1) and PE-labeled JUNV GP1 and PerCP-labeled JUNV GP1.sub.mut (Sort 2) were used for tetramer preparation and cell staining. The mRNA pre-amplification, RT-PCR, and nested PCR steps were carried out as previously described (Franz et al., 2011), with the exception that oligo-dT primers were used in the RT-PCR step.
OTHER EMBODIMENTS
(111) From the foregoing description, it will be apparent that variations and modifications may be made to the invention described herein to adopt it to various usages and conditions. Such embodiments are also within the scope of the following claims.
(112) The recitation of a listing of elements in any definition of a variable herein includes definitions of that variable as any single element or combination (or subcombination) of listed elements. The recitation of an embodiment herein includes that embodiment as any single embodiment or in combination with any other embodiments or portions thereof.
(113) All patents and publications mentioned in this specification are herein incorporated by reference to the same extent as if each independent patent and publication was specifically and individually indicated to be incorporated by reference.
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