# Patent

## Title
Compositions and methods for diagnosing and/or treating influenza infection

## Abstract

The present invention provides HA polypeptides (e.g., H1 HA polypeptides) that bind to umbrella-topology glycans, and reagents and methods relating thereto. The present invention provides binding agents that bind to HA polypeptides (e.g., H1 HA polypeptides), and reagents and methods relating thereto. The present invention provides interfering agents that inhibit the binding of HA polypeptides (e.g., H1 HA polypeptides) to HA receptors, and reagents and methods relating thereto. The present invention provides compositions and methods for treating, preventing, and/or diagnosing influenza infection utilizing HA polypeptides, HA polypeptide binding agents, HA polypeptide interfering agents, and/or vaccine compositions comprising any of the foregoing.

## Background
RELATED APPLICATIONS
This application is related to and claims priority under 35 U.S.C. §119(e) to U.S. provisional patent application No. 61/222,889, filed Jul. 2, 2009 (“the '889 application”). The entire contents of the '889 application are incorporated herein by reference.
SEQUENCE LISTING
In accordance with 37 C.F.R. §1.52(e)(5), a Sequence Listing in the form of a text file (entitled “Sequence_Listing,” created on Oct. 20, 2010 and 205 kilobytes) is incorporated herein by reference in its entirety.


GOVERNMENT SUPPORT
This invention was made with United States government support awarded by the National Institute of General Medical Sciences of the National Institute of Health (contract numbers GM57073 and U54 GM62116). The United States Government has certain rights in the invention.


BACKGROUND OF THE INVENTION
On Jun. 11, 2009 the World Health Organization raised the global pandemic alert level to phase 6, the pandemic phase, in response to the emergence and global spread of a novel influenza A (H1N1) virus henceforth referred to as 2009 A/H1N1 virus containing a unique combination of genes of swine origin (Garten et al., “Antigenic and Genetic Characteristics of Swine-Origin 2009 A(H1N1) Influenza Viruses Circulating in Humans” Science, May 22, 2009, Science Express Online; incorporated herein by reference). The emergence of this new strain can be traced back to March-April 2009 when there were reports of increased numbers of patients with influenza-like illness and associated hospitalizations and deaths in several areas of Mexico. In the period Mar.-Jun. 19, 2009, there have been over 44,000 laboratory-confirmed human cases of influenza 2009 A/H1N1 infections reported in 85 countries on 6 continents.
Given the rapid outbreak of this virus, there have been uncertainties associated with its virulence, transmissibility and its origins. Recent studies using epidemiological models to interpret data on outbreaks of the 2009H1N1 virus have indicated that its transmissibility is on the lower end of what was estimated for the 1918H1N1 pandemic. In most of the cases of human infection with the 2009H1N1 viruses, the symptoms have been relatively mild, however, there have been over 150 deaths reported. Additionally, a substantial portion ( ̃40%) of infected individuals experience gastrointestinal distress and vomiting, a percentage that is higher than what is typically observed for seasonal flu.
SUMMARY OF THE INVENTION
The present invention provides compositions and methods for the treatment, prevention, and/or diagnosis of infection with an H1N1 influenza virus. In some embodiments, the invention provides compositions and methods for treatment, prevention, and/or diagnosis of infection with an H1N1 influenza virus that has acquired significant human infectivity.
Among other things, the present invention defines H1N1 HA variants with enhanced human binding and/or infectivity as compared with H1N1 influenza strains. Such variants may be utilized, among other things, as components of vaccines and/or therapeutics to treat, reduce, and/or prevent human infection by and H1N1 virus, and particularly by a variant with enhanced human binding and/or infectivity. Alternatively or additionally, such variants may be utilized as standards in systems for detecting occurrence of and/or infection with an H1N1 variant with enhanced human infectivity.
In some aspects, the present invention provides agents that bind specifically to an H1N1 HA polypeptide, for example for use in detecting H1N1 infection. In some embodiments, the present invention provides agents that bind specifically to an H1N1 variant with enhanced human binding and/or infectivity. In some embodiments, the present invention provides agents that discriminate between H1N1 variants with enhanced human infectivity and H1N1 variants without enhanced human infectivity.
In some aspects, the present invention provides agents that interfere (and/or compete) with binding interactions between an H1N1 HA polypeptide and one or more glycans, for example umbrella-topology glycans. In some embodiments, the present invention provides agents that interfere (and/or compete with) binding interactions between an H1N1 HA polypeptide and one or more α2-6 sialylated glycans. In some embodiments, the present invention provides agents that interfere (and/or compete) with binding interactions between an H1N1 HA polypeptide and one or more 6′SLN-LN glycans. In some embodiments, the H1N1 HA polypeptide whose binding interaction is interfered with is an H1N1 variant with enhanced human binding and/or infectivity.
As already noted, in some embodiments, the present invention provides systems for performing surveillance to detect presence of and/or infection with H1N1 influenza. In some embodiments, the present invention provides systems for performing surveillance to detect presence of and/or infection with an H1N1 influenza variant with enhanced human binding and/or infectivity.
In some embodiments, the present invention provides strategies for vaccinating and/or treating populations (e.g., human populations) against infection with H1N1 influenza strains. In some embodiments, the present invention provides strategies for vaccinating and/or treating populations (e.g., human populations) against infection with an H1N1 influenza variant with enhanced human binding and/or infectivity.
In some embodiments, the present invention provides strategies for stratifying patient populations, e.g., identifying subjects previously exposed to one or more viruses showing similarity with 2009 A/H1N1. In this manner, it is envisioned that patient populations can be identified that are at reduced or increased risk for contracting 2009 A/H1N1 virus and/or potentially have a delayed immune response due to the lack of previous humoral immunity to one or more viruses showing similarity to 2009 A/H1N1.



BRIEF DESCRIPTION OF THE DRAWING
FIGS. 1A-C. Alignment of exemplary sequences of wild type HAs. Sequences were obtained from the NCBI influenza virus sequence database (http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html). FIGS. 1A, 1B, and 1C represent the sequence alignment of the amino acid residues of the following wild type HAs: H1_Av (SEQ ID NO: 1). H1_Hu1 (SEQ ID NO: 2). H1_Hu2 (SEQ ID NO: 3). H2_Av (SEQ ID NO: 4). H2_Hu (SEQ ID NO: 5). H3_Av (SEQ ID NO: 6). H3 Hu1 (SEQ ID NO: 7). H3_Hu2 (SEQ ID NO: 8). H4_Av (SEQ ID NO: 9). H5_Av1 (SEQ ID NO: 10). H5_Av2 (SEQ ID NO: 11). H6_Av (SEQ ID NO: 12). H7_Av (SEQ ID NO: 13). H8_Av (SEQ ID NO: 14). H9_Av (SEQ ID NO: 15). H10_Av (SEQ ID NO: 16). H11_Av (SEQ ID NO: 17). H12_Av (SEQ ID NO: 18). H13_Av (SEQ ID NO: 19). H14_Av (SEQ ID NO: 20). H15_Av (SEQ ID NO: 21). H16_Av (SEQ ID NO: 22).
FIGS. 2A-B. Sequence alignment of HA glycan binding domains. FIGS. 2A and 2B represent the sequence alignment of the amino acid residues of HA glycan binding domains: ADA76, ASI30, APR34, ASC18, AT91, ANY18, ADU63, AAI68, AM99, ADS97, and Viet04. Residues at positions 98, 136, 153, 155, 183, and 194 are conserved amino acids involved in binding to sialic acid. Residues at positions 190 and 226 are particular amino acids involved in binding to Neu5Acα2-3/6Gal motifs. Residues at positions 186 and 228 are amino acids that influence positioning of Q226 (137, 138) and E190 (186, 228). Residues at positions 189, 193, 222, and 225 are amino acids involved in binding to other monosaccharides (or modifications) attached to Neu5Acα2-3/6Gal motif. The sequence for ASI30, APR34, ADU63, ADS97 and Viet04 were obtained from their respective crystal structures. The other sequences were obtained from SwissProt (http://us.expasy.org). Abbreviations: ADA76, A/duck/Alberta/35/76 (H1N1) (SEQ ID NO: 23); ASI30, A/Swine/Iowa/30 (H1N1) (SEQ ID NO: 24); APR34, A/Puerto Rico/8/34 (H1N1) (SEQ ID NO: 25); ASC18, A/South Carolina/1/18 (H1N1) (SEQ ID NO: 26); AT91, A/Texas/36/91 (H1N1) (SEQ ID NO: 27); ANY18, A/New York/1/18 (H1N1) (SEQ ID NO: 28); ADU63, A/Duck/Ukraine/1/63 (H3N8) (SEQ ID NO: 29); AAI68, A/Aichi/2/68 (H3N2) (SEQ ID NO: 30); AM99, A/Moscow/10/99 (H3N2) (SEQ ID NO: 31); ADS97, A/Duck/Singapore/3/97 (H5N3) (SEQ ID NO: 32); Viet04, A/Vietnam/1203/2004 (H5N1) (SEQ ID NO: 33).
FIGS. 3A-B. Sequence alignment illustrating conserved subsequences characteristic of H1 HAs. FIG. 3A presents the same alignment that was presented in FIG. 1A, except that FIG. 3A indicates the presence of an additional conserved subsequence. FIG. 3B presents the same alignment that was presented in FIG. 1C, except that FIG. 3B indicates the presence of an additional conserved subsequence.
FIGS. 4A-C. (A) Sequence alignment of 2009 A/H1N1 HA (CA—04—09) and its mutant forms (Mut—1) and (Mut—2) along with human adapted HAs (SC—1—18, Solls—3—06, Bris—50—07). Residues marked contribute directly or indirectly to α2-6 binding. Residues 186 (P), 189 (T), and 227 (A) for CA—04—09_Mut2 and 219 (K) for CA—04—09_Mut1 are residues that are altered in H1N1 variants with enhanced human binding and/or infectivity as compared with 2009 A/H1N1 HA (CA—04—09). CA—04—09 (SEQ ID NO: 34). CA—04—09_Mut1 (SEQ ID NO: 35). CA—04—09_Mut2 (SEQ ID NO: 36). SC—1—18 (SEQ ID NO: 37). SolIs—3—06 (SEQ ID NO: 38). Bris—59—07 (SEQ ID NO: 39). (B) Sequence alignment of influenza H1N1 HA from a 2009 seasonal strain (Aichi—9—09), 2007-2008 seasonal strain (Bris—59—07) and a “swine flu” strain (Cal—04—09). AAichi—9—09 (SEQ ID NO: 40)=A/Aichi/9/2009; ABris—59—07 (SEQ ID NO: 41)=A/Brisbane/59/2007; ACal—04—09 (SEQ ID NO: 42)=A/California/04/2009. Residues that are directly or indirectly involved in α2-6 binding are marked. (C) Sequence alignment of influenza H1N1 HA from 1918 pandemic (SC—1—18), 1930 swine isolate (SwIA—15—30) and a “swine flu” strain (Cal—04—09). SC—1—18 (SEQ ID NO: 43)=A/South Carolina/1/1918; SwIA—15—30 (SEQ ID NO: 44)=A/Swine/IA/15/1930; ACal—04—09 (SEQ ID NO: 45)=A/California/04/2009. Residues that are directly or indirectly involved in α2-6 binding are marked.
FIGS. 5A-C. Frameworks for understanding glycan receptor specificity. α2-3- and/or α2-6-linked glycans can adopt different topologies. According to the present invention, the ability of an HA polypeptide to bind to certain of these topologies confers upon it the ability to mediate infection of different hosts, for example, humans. As illustrated in Panel A of this figure, the present invention defines two particularly relevant topologies, a “cone” topology and an “umbrella” topology. The cone topology can be adopted by α2-3- and/or α2-6-linked glycans, and is typical of short oligosaccharides or branched oligosaccharides attached to a core (although this topology can be adopted by certain long oligosaccharides). The umbrella topology can only be adopted by α2-6-linked glycans (presumably due to the increased conformational plurality afforded by the extra C5-C6 bond that is present in the α2-6 linkage), and is predominantly adopted by long oligosaccharides or branched glycans with long oligosaccharide branches, particularly containing the motif Neu5Acα2-6Galβ1-3/4GlcNAc-. As described herein, ability of HA polypeptides to bind the umbrella glycan topology, confers binding to human receptors and/or ability to mediate infection of humans. Panel B of this Figure specifically shows the topology of α2-3 and α2-6 as governed by the glycosidic torsion angles of the trisaccharide motifs—Neu5Acα2-3Galβ1-3/4GlcNAc and Neu5Acα2-6Galβ1-4GlcNAc respectively. A parameter (θ)-angle between C2 atom of Neu5Ac and C1 atoms of the subsequent Gal and GlcNAc sugars in these trisaccharide motifs was defined to characterize the topology. Superimposition of the θ contour and the conformational maps of the α2-3 and α2-6 motifs shows that α2-3 motifs adopt 100% cone-like topology and α2-6 motifs sampled both cone-like and umbrella-like topologies (Panel C). In the cone-like topology sampled by α2-3 and α2-6, GlcNAc and subsequent sugars are positioned along a region spanning a cone. Interactions of HA with cone-like topology primarily involve contacts of amino acids at the numbered positions (based on H3 HA numbering) with Neu5Ac and Gal sugars. On the other hand, in umbrella-like topology, which is unique to α2-6, \ GlcNAc and subsequent sugars bend towards the HA binding site (as observed in HA-α2-6 co-crystal structures). Longer α2-6 oligosaccharides (e.g., at least a tetrasaccharide) would favor this conformation since it is stabilized by intra-sugar van der Waals contact between acetyl groups of GlcNAc and Neu5Ac. HA interactions with umbrella-like topology involve contacts of amino acids at the numbered positions (based on H3 HA numbering) with GlcNAc and subsequent sugars in addition to contacts with Neu5Ac and Gal sugars. Panel C of this Figure depicts conformational sampling of cone- and umbrella-like topology by α2-3 and α2-6. Sections (1)-(4) show the conformational (φ, ψ) maps of Neu5Acα2-3Gal, Neu5Acα2-6Gal, Galβ1-3GlcNAc, and Galβ1-4GlcNAc linkages, respectively. These maps obtained from GlycoMaps DB (http://www.glycosciences.de/modeling/glycomapsdb/) were generated using ab initio MD simulations using MM3 force field. Energy distribution is coded starting from dark shading (representing highest energy) to light shading representing lowest energy. Encircled regions 1-5 represent (φ,ψ), values observed for the α2-3 and α2-6 oligosaccharides in the HA-glycan co-crystal structures. The trans conformation (encircled region 1) of Neu5Acα2-3Gal predominates in HA binding pocket with the exception of the co-crystal structure of A/Aichi/2/68 H3N2 HA with α2-3 where this conformation is gauche (encircled region 2). On the other hand, the cis conformation of Neu5Acα2-6Gal (encircled region 3) predominates in HA binding pocket. The cone-like topology is sampled by encircled regions 1 and 2 and the umbrella-like topology is sampled by encircled region 3. Sections (5)-(6) show sampling of cone-like and umbrella-like topologies by α2-3 and α2-6 motifs, respectively. Regions marked in dark shading in the conformational maps were used as the outer boundaries to calculate the θ parameter (angle between C2 atom of Neu5Ac and C1 atoms of subsequent Gal and GlcNAc sugars) for a given set of (φ,ψ) values. Based on the energy cutoff, the value of θ>110° was used to characterize cone-like topology and θ<100° was used to characterize umbrella-like topology. Superimposition of the θ contour with the conformational energy map indicated that α2-3 motif adopts 100% cone-like topology since it was energetically unfavorable to adopt umbrella-like topology. On the other hand, the α2-6 motif sampled both the cone-like and umbrella-like topologies and this sampling was classified based on the ω angle (O—C6-C5-H5) of Neu5Acα2-6Gal linkage.
FIG. 6. Interactions of HA residues with cone vs. umbrella glycan topologies. Analysis of HA-glycan co-crystals reveals that the position of Neu5Ac relative to the HA binding site is almost invariant. Contacts with Neu5Ac involve highly conserved residues such as F98, S/T136, W153, H183 and L/I194. Contacts with other sugars involve different residues, depending on whether the sugar linkage is α2-3 or α2-6 and whether the glycan topology is cone or umbrella. For example, in the cone topology, the primary contacts are with Neu5Ac and with Gal sugars. E190 and Q226 play particularly important roles in this binding. This Figure also illustrates other positions (e.g., 137, 145, 186, 187, 193, 222) that can participate in binding to cone structures. In some cases, different residues can make different contacts with different glycan structures. The type of amino acid in these positions can influence ability of an HA polypeptide to bind to receptors with different modification and/or branching patterns in the glycan structures. In the umbrella topology, contacts are made with sugars beyond Neu5Ac and Gal. This Figure illustrates residues (e.g., 137, 145, 156, 159, 186, 187, 189, 190, 192, 193, 196, 222, 225, 226) that can participate in binding to umbrella structures. In some cases, different residues can make different contacts with different glycan structures. The type of amino acid in these positions can influence ability of an HA polypeptide to bind to receptors with different modification and/or branching patterns in the glycan structures. In some embodiments, a D residue at position 190 and/or a D residue at position 225 contribute(s) to binding to umbrella topologies.
FIG. 7. Exemplary cone topologies. This Figure illustrates certain exemplary (but not exhaustive) glycan structures that adopt cone topologies.
FIGS. 8A-B. Exemplary umbrella topologies. (A) Certain exemplary (but not exhaustive) N- and O-linked glycan structures that can adopt umbrella topologies. (B) Certain exemplary (but not exhaustive) O-linked glycan structures that can adopt umbrella topologies.
FIGS. 9A-B. Dose dependent direct receptor binding of CA/04 (A) and SC18 (B) HAs. A streptavidin plate array comprising of representative biotinylated α2-3 and α2-6 sialylated glycans (shown in legend) were used for the assay. LN corresponds to lactosamine (Galβ1-4GlcNAc) and 3′ SLN and 6′ SLN respectively correspond to Neu5Acα2-3 and Neu5Acα2-6 linked to LN. The assay was carried out as described previously (Srinivasan et al., Proc Natl Acad Sci USA 105:2800, 2008) for an entire range of HA concentration from 0.01-40 μg/ml by pre-complexing HA:primary antibody:secondary antibody in the ratio 4:2:1 to enhance the multivalent presentation of HA. The pattern of binding selectively to 6′ SLN-LN is similar for both the HAs. Note that no detectable binding signals are observed for CA/04 HA below 2 μg/ml concentrations whereas SC—18 HA shows substantial binding at these concentrations indicating a much higher binding affinity than CA/04 HA.
FIG. 10: Human lung tissue binding of CA/04 HA. Shown in the top is the binding of CA/04 HA at 20 μg/ml concentration to apical surface (white arrow) of human tracheal tissue sections. Note the binding of HA to the apical surface of tracheal tissue which is known to predominantly express α2-6 sialylated glycans. Shown in the bottom is the minimal binding of HA at 20 μg/ml concentration to the alveolar tissue section. The sialic acid specific binding of HA to the tracheal tissue section was confirmed by the minimal binding of HA to the tissue section pre-treated with 0.2 U of Sialidase A (recombinantly expressed in Arthrobacter ureafaciens). The binding of the recombinantly expressed HA to the human tissues was carried out as described previously (Chandrasekaran, et al., Nat Biotechnol 26:107, 2008; incorporated herein by reference) by precomplexing HA:primary antibody:secondary antibody in the ratio 4:2:1 to enhance multivalent presentation of HA.
FIG. 11. Glycan binding residues of H1N1 HAs. The residues are organized into network forming clusters. The sugar unit (numbered as shown in FIG. 12), which makes contact with the clusters, is shown in the last row. The unique amino acids in 2009 H1N1 HAs are “K”, shown in column 145. The key for the virus strains SolIS—3—06 (A/Solomon Islands/3/06); Bris—59—07 (A/Brisbane/59/07); NewCal—20—99 (A/New Caledonia/20/99); TX/15 (A/Texas/15/2009); MX/4482 (A/Mexico/4482/2009).
FIG. 12: Structural model of CA/04 HA bound to α2-6 oligosaccharide. The contacts of CA/04 HA with an α2-6 oligosaccharide (Neu5Acα2-6Galβ1-4GlcNAcβ1-3Galβ1-4Glc) were analyzed by constructing a structural model as described previously (Soundararajan, et al., Nat Biotechnol 27, 510, 2009; incorporated herein by reference). Shown in the figure is the cartoon representation of the glycan binding site of CA/04 HA where the side chains of the key amino acids are shown in stick representation. The α2-6 oligosaccharide is shown as a stick representation and labeled starting from non-reducing end Neu5Ac-1 to reducing end Glc-5. The potential destabilization of the interaction network due to the Ile219/Glu227 combination is highlighted in dotted circle.
FIGS. 13A-D: Fixing the mismatched interaction in RBS of CA04 HA. (A) Structural complex of RBS of CA04 HA with human receptor (mismatched Ile219-Glu227 contacts highlighted in circle). (B) RBS of CA04M1 complexed with human receptor where Lys219 makes ionic contacts with Glu227. (C) RBS of CA04M2 complexed with the human receptor. (D) RBS of SC—18 HA complexed with human receptor. The hydrophobic interactions between Ile219, Pro186, and Ala227 and interactions between Ser187, Thr189, and Asp190 in RBS of CA04M2 HA are similar to that between analogous residues in SC18 HA. The structural complexes are shown in stereo with RBS represented as a cartoon schematic with side chains of key amino acids. The substituted amino acids are shown. Stick representation of human receptor is shown with carbon atoms.
FIG. 14: Nomenclature of glycans used in the glycan array
FIGS. 15A-D: Glycan receptor-binding properties of CA04M1 and CA04M2 HAs. (A) Dose dependent direct glycan array binding of CA04M1. (B) Dose-dependent direct glycan array binding of CA04M2. (C) Binding curves of CA04, CA04M1, CA04M2 and SC18 HAs to 6′SLN-LN. The experimental data (disconnected markers indicated using “Data”) is shown along with the theoretical binding curve (line indicated using “Model”) generated as described in Example 4. The Kd′ of SC18 HA is around 6 pM (in the same range as that of CA04M2 HA) and hence is indicated using the same label. (D) Human tracheal tissue binding of CA04, CA04M1, and CA04M2 HA (staining of HA against propidium iodide). The apical surface of the tracheal tissue sections is indicated using a white arrow. The sialic acid specific binding of HA to the tracheal tissue sections was confirmed by loss of staining upon pre-treatment of the tissue sections with Sialidase A (from Arthrobacter ureafaciens) and enzyme that cleaves terminal sialic acid from both avian and human receptors.
FIG. 16: Dose-dependent direct glycan array binding of CA04 HA in comparison with the natural variants CA04M3 (Asp225Glu), CA04M4 (Asp225Asn) and CA04M5 (Asp225Gly) HAs. Also shown in the bottom panel are the binding curves of these HAs to the representative human receptor (6′SLN-LN) along with the binding strengths quantified using Kd'. Although CA04M3 and CA04M4 show same the human receptor binding specificity of CA04, the binding strength of CA04M4>CA04>>CA04M3 HA. CA04M5, on the other hand, shows dose-dependent binding to human receptors at dramatically lower signal values and to avian receptors as well. These observations suggest that length (as compared to polarity) of the side chain at position 225 might influence human-receptor binding.



DESCRIPTION OF HA SEQUENCE ELEMENTS
HA Sequence Element 1
HA Sequence Element 1 is a sequence element corresponding approximately to residues 97-185 (where residue positions are assigned using H3 HA as reference) of many HA proteins found in natural influenza isolates. This sequence element has the basic structure:

    
    
        C(Y/F) P X1 C X2 W X3 W X4H H P, wherein:
        X1 is approximately 30-45 amino acids long;
        X2 is approximately 5-20 amino acids long;
        X3 is approximately 25-30 amino acids long; and
        X4 is approximately 2 amino acids long.
    
    


In some embodiments, X1 is about 35-45, or about 35-43, or about 35, 36, 37, 38, 38, 40, 41, 42, or 43 amino acids long. In some embodiments, X2 is about 9-15, or about 9-14, or about 9, 10, 11, 12, 13, or 14 amino acids long. In some embodiments, X3 is about 26-28, or about 26, 27, or 28 amino acids long. In some embodiments, X4 has the sequence (G/A) (I/V). In some embodiments, X4 has the sequence GI; in some embodiments, X4 has the sequence GV; in some embodiments, X4 has the sequence AI; in some embodiments, X4 has the sequence AV. In some embodiments, HA Sequence Element 1 comprises a disulfide bond. In some embodiments, this disulfide bond bridges residues corresponding to positions 97 and 139 (based on the canonical H3 numbering system utilized herein).
In some embodiments, and particularly in H1 polypeptides, X1 is about 43 amino acids long, and/or X2 is about 13 amino acids long, and/or X3 is about 26 amino acids long. In some embodiments, and particularly in H1 polypeptides, HA Sequence Element 1 has the structure:

    
    
        C Y P X1A T (A/T) (A/S) C X2 W X3 W X4H H P, wherein:
        X1A is approximately 27-42, or approximately 32-42, or approximately 32-40, or approximately 26-41, or approximately 31-41, or approximately 31-39, or approximately 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 amino acids long, and X2-X4 are as above.
    
    


In some embodiments, and particularly in H1 polypeptides, HA Sequence Element 1 has the structure:

    
    
        C Y P X1A T (A/T) (A/S) C X2 W (I/L) (T/V) X3A W X4H H P, wherein:
        X1A is approximately 27-42, or approximately 32-42, or approximately 32-40, or approximately 32, 33, 34, 35, 36, 37, 38, 39, or 40 amino acids long,
        X3A is approximately 23-28, or approximately 24-26, or approximately 24, 25, or 26 amino acids long, and X2 and X4 are as above.
    
    


In some embodiments, and particularly in H1 polypeptides, HA Sequence Element 1 includes the sequence:









Q L S S I S S F E K,






typically within X1, (including within X1A) and especially beginning about residue 12 of X1 (as illustrated, for example, in FIGS. 1-3).

In some embodiments, and particularly in H3 polypeptides, X1 is about 39 amino acids long, and/or X2 is about 13 amino acids long, and/or X3 is about 26 amino acids long.
In some embodiments, and particularly in H3 polypeptides, HA Sequence Element 1 has the structure:

    
    
        C Y P X1A S(S/N) (A/S) C X2 W X3 W X4H H P, wherein:
        X1A is approximately 27-42, or approximately 32-42, or approximately 32-40, or approximately 23-38, or approximately 28-38, or approximately 28-36, or approximately 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 amino acids long, and X2-X4 are as above.
    
    


In some embodiments, and particularly in H3 polypeptides, HA Sequence Element 1 has the structure:

    
    
        C Y P X1A S(S/N) (A/S) C X2 W L (T/H) X3A W X4H H P, wherein:
        X1A is approximately 27-42, or approximately 32-42, or approximately 32-40, or approximately 32, 33, 34, 35, 36, 37, 38, 39, or 40 amino acids long,
        X3A is approximately 23-28, or approximately 24-26, or approximately 24, 25, or 26 amino acids long, and X2 and X4 are as above.
    
    


In some embodiments, and particularly in H3 polypeptides, HA Sequence Element 1 includes the sequence:









(L/I) (V/I) A S S G T L E F,






typically within X1 (including within X1A), and especially beginning about residue 12 of X1 (as illustrated, for example, in FIGS. 1 and 2).

In some embodiments, and particularly in H5 polypeptides, X1 is about 42 amino acids long, and/or X2 is about 13 amino acids long, and/or X3 is about 26 amino acids long.
In some embodiments, and particularly in H5 polypeptides, HA Sequence Element 1 has the structure:

    
    
        C Y P X1A S S AC X2 W X3 W X4H H P, wherein:
        X1A is approximately 27-42, or approximately 32-42, or approximately 32-40, or approximately 23-38, or approximately 28-38, or approximately 28-36, or approximately 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 amino acids long, and X2-X4 are as.
    
    


In some embodiments, and particularly in H5 polypeptides, HA Sequence Element 1 has the structure:

    
    
        C Y P X1A S S AC X2 W L I X3A W X4H H P, wherein:
        X1A is approximately 27-42, or approximately 32-42, or approximately 32-40, or approximately 32, 33, 34, 35, 36, 37, 38, 39, or 40 amino acids long, and
        X3A is approximately 23-28, or approximately 24-26, or approximately 24, 25, or 26 amino acids long, and X2 and X4 are as above.
    
    


In some embodiments, and particularly in H5 polypeptides, HA Sequence Element 1 is extended (i.e., at a position corresponding to residues 186-193) by the sequence:









N D A A E X X (K/R)






In some embodiments, and particularly in H5 polypeptides, HA Sequence Element 1 includes the sequence:









Y E E L K H L X S X X N H F E K,






typically within X1, and especially beginning about residue 6 of X1 (as illustrated, for example, in FIGS. 1 and 2).

HA Sequence Element 2
HA Sequence Element 2 is a sequence element corresponding approximately to residues 324-340 (again using a numbering system based on H3 HA) of many HA proteins found in natural influenza isolates. This sequence element has the basic structure:









G A I A G F I E






In some embodiments, HA Sequence Element 2 has the sequence:










PX1G A I A G F I E,






wherein:

    
    
        X1 is approximately 4-14 amino acids long, or about 8-12 amino acids long, or about 12, 11, 10, 9 or 8 amino acids long. In some embodiments, this sequence element provides the HA0 cleavage site, allowing production of HA1 and HA2.
    
    


In some embodiments, and particularly in H1 polypeptides, HA Sequence Element 2 has the structure:

    
    
        P S (I/V) Q S R X1A G A I A G F I E, wherein:
        X1A is approximately 3 amino acids long; in some embodiments, X1A is G (L/I) F.
    
    


In some embodiments, and particularly in H3 polypeptides, HA Sequence Element 2 has the structure:

    
    
        P X K X T R X1A G A I A G F I E, wherein:
        X1A is approximately 3 amino acids long; in some embodiments, X1A is G (L/I) F.
    
    


In some embodiments, and particularly in H5 polypeptides, HA Sequence Element 2 has the structure:

    
    
        P Q R X X X R X X R X1A G A I A G F I E, wherein:
        X1A is approximately 3 amino acids long; in some embodiments, X1A is G (L/I) F.
    
    


Definitions
Affinity: As is known in the art, “affinity” is a measure of the tightness with a particular ligand (e.g., an HA polypeptide) binds to its partner (e.g., and HA receptor). In some embodiments, affinity refers to strength of binding of one entity to another. Affinities can be measured in different ways.
Amino acid: As used herein, term “amino acid,” in its broadest sense, refers to any compound and/or substance that can be incorporated into a polypeptide chain. In some embodiments, an amino acid has the general structure H2N—C(H)(R)—COOH. In some embodiments, an amino acid is a naturally occurring amino acid. In some embodiments, an amino acid is a synthetic amino acid; in some embodiments, an amino acid is a D-amino acid; in some embodiments, an amino acid is an L-amino acid. “Standard amino acid” refers to any of the twenty standard L-amino acids commonly found in naturally occurring peptides. “Nonstandard amino acid” refers to any amino acid, other than the standard amino acids, regardless of whether it is prepared synthetically or obtained from a natural source. As used herein, “synthetic amino acid” encompasses chemically modified amino acids, including but not limited to salts, amino acid derivatives (such as amides), substitutions, and/or those modified through chemical reactions and/or biosynthetically. Amino acids, including carboxy- and/or amino-terminal amino acids in peptides, can be modified by methylation, amidation, acetylation, protecting groups, and/or substitution with other chemical groups that can change the peptide's circulating half-life without adversely affecting their activity. Amino acids may participate in a disulfide bond. Amino acids may comprise one or posttranslational modifications, such as association with one or more chemical entities (e.g., methyl groups, acetate groups, acetyl groups, phosphate groups, formyl moieties, isoprenoid groups, sulfate groups, polyethylene glycol moieties, lipid moieties, carbohydrate moieties, biotin moieties, etc.). The term “amino acid” is used interchangeably with “amino acid residue,” and may refer to a free amino acid and/or to an amino acid residue of a peptide. It will be apparent from the context in which the term is used whether it refers to a free amino acid or a residue of a peptide.
Animal: As used herein, the term “animal” refers to any member of the animal kingdom. In some embodiments, “animal” refers to humans, of either sex and at any stage of development. In some embodiments, “animal” refers to non-human animals, at any stage of development. In certain embodiments, the non-human animal is a mammal (e.g., a rodent, a mouse, a rat, a rabbit, a monkey, a dog, a cat, a sheep, cattle, a primate, and/or a pig). In some embodiments, animals include, but are not limited to, mammals, birds, reptiles, amphibians, fish, insects, and/or worms. In certain embodiments, the animal is susceptible to infection by influenza. In some embodiments, an animal may be a transgenic animal, genetically engineered animal, and/or a clone.
Approximately: As used herein, the term “approximately” or “about,” as applied to one or more values of interest, refers to a value that is similar to a stated reference value. In certain embodiments, the term “approximately” or “about” refers to a range of values that fall within 25%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, or less in either direction (greater than or less than) of the stated reference value unless otherwise stated or otherwise evident from the context (except where such number would exceed 100% of a possible value).
Binding: It will be understood that the term “binding”, as used herein, typically refers to a non-covalent association between or among agents. In many embodiments herein, binding is addressed with respect to particular glycans (e.g., umbrella topology glycans or cone topology glycans). It will be appreciated by those of ordinary skill in the art that such binding may be assessed in any of a variety of contexts. In some embodiments, binding is assessed with respect to free glycans. In some embodiments, binding is assessed with respect to glycans attached (e.g., covalently linked to) a carrier. In some such embodiments, the carrier is a polypeptide. In some embodiments, binding is assessed with respect to glycans attached to an HA receptor. In such embodiments, reference may be made to receptor binding or to glycan binding. In some embodiments, binding is specific in that a binding agent discriminates between its target binding partner and other potential binding partners in its environment.
Binding agent: In general, the term “binding agent” is used herein to refer to any entity that binds to an agent of interest. For example, an HA binding agent binds to one or more HA polypeptides (and/or to variants, fragments, and/or characteristic portions thereof), as described herein. Binding agents may be of any chemical type. In some embodiments, binding agents are polypeptides (including, e.g., antibodies or antibody fragments). In some embodiments, binding agents are small molecules. In some embodiments, binding agents are nucleic acids. In some embodiments, binding agents are aptamers. In some embodiments, binding agents are polymers; in some embodiments, binding agents are non-polymeric. In some embodiments, binding agents are carbohydrates. In some embodiments, binding agents are lectins. In some embodiments, H1 HA binding agents bind to H1 HA polypeptides. In some embodiments, binding agents bind to H1 HA polypeptide variants with enhanced human binding and/or infectivity. In some embodiments, a binding agent provided herein is an umbrella topology blocking agent. In some embodiments, a binding agent provided herein is an umbrella topology specific blocking agent.
Biologically active: As used herein, the phrase “biologically active” refers to a characteristic of any agent that has activity in a biological system, and particularly in an organism. For instance, an agent that, when administered to an organism, has a biological effect on that organism, is considered to be biologically active. In particular embodiments, where a protein or polypeptide is biologically active, a portion of that protein or polypeptide that shares at least one biological activity of the protein or polypeptide is typically referred to as a “biologically active” portion.
Characteristic portion: As used herein, the phrase a “characteristic portion” of a protein or polypeptide is one that contains a continuous stretch of amino acids, or a collection of continuous stretches of amino acids, that together are characteristic of a protein or polypeptide. Each such continuous stretch generally will contain at least two amino acids. Furthermore, those of ordinary skill in the art will appreciate that typically at least 5, 10, 15, 20 or more amino acids are required to be characteristic of a protein. In general, a characteristic portion is one that, in addition to the sequence identity specified above, shares at least one functional characteristic with the relevant intact protein.
Characteristic sequence: A “characteristic sequence” is a sequence that is found in all members of a family of polypeptides or nucleic acids, and therefore can be used by those of ordinary skill in the art to define members of the family.
Cone topology: The phrase “cone topology” is used herein to refer to a 3-dimensional arrangement adopted by certain glycans and in particular by glycans on HA receptors. As illustrated in FIGS. 5 and 7, cone topology can be adopted by α2-3 sialylated glycans or by α2-6 sialylated glycans, and is typical of short oligonucleotide chains, though some long oligonucleotides can also adopt this conformation. The cone topology is characterized by the glycosidic torsion angles of Neu5Acα2-3Gal linkage which samples three regions of minimum energy conformations given by φ (C1-C2-O—C3/C6) value of around −60, 60 or 180 and ψ (C2-O—C3/C6-H3/C5) samples −60 to 60. FIG. 7 presents certain representative (though not exhaustive) examples of glycans that adopt a cone topology.
Corresponding to: As used herein, the term “corresponding to” is often used to designate the position/identity of an amino acid residue in an HA polypeptide. Those of ordinary skill will appreciate that, for purposes of simplicity, a canonical numbering system (based on wild type H3 HA) is utilized herein (as illustrated, for example, in FIGS. 1-4), so that an amino acid “corresponding to” a residue at position 190, for example, need not actually be the 190th amino acid in a particular amino acid chain but rather corresponds to the residue found at 190 in wild type H3 HA; those of ordinary skill in the art readily appreciate how to identify corresponding amino acids.
Degree of separation removed: As used herein, amino acids that are a “degree of separation removed” are HA amino acids that have indirect effects on glycan binding. For example, one-degree-of-separation-removed amino acids may either: (1) interact with the direct-binding amino acids; and/or (2) otherwise affect the ability of direct-binding amino acids to interact with glycan that is associated with host cell HA receptors; such one-degree-of-separation-removed amino acids may or may not directly bind to glycan themselves. Two-degree-of-separation-removed amino acids either (1) interact with one-degree-of-separation-removed amino acids; and/or (2) otherwise affect the ability of the one-degree-of-separation-removed amino acids to interact with direct-binding amino acids, etc.
Direct-binding amino acids: As used herein, the phrase “direct-binding amino acids” refers to HA polypeptide amino acids which interact directly with one or more glycans that is associated with host cell HA receptors.
Engineered: The term “engineered”, as used herein, describes a polypeptide whose amino acid sequence has been selected by man. For example, an engineered HA polypeptide has an amino acid sequence that differs from the amino acid sequences of HA polypeptides found in natural influenza isolates. In some embodiments, an engineered HA polypeptide has an amino acid sequence that differs from the amino acid sequence of HA polypeptides included in the NCBI database.
Enhanced human binding and/or infectivity variant HA: As used herein, the phrase “enhanced human binding and/or infectivity variant HA” refers to a version of an HA polypeptide (e.g., of an H1 HA polypeptide) that binds to HA receptors found in human epithelial tissues, and particularly to human HA receptors having α2-6 sialylated glycans. In some embodiments, enhanced human binding and/or infectivity variant HAs bind to umbrella topology glycans. In some embodiments, enhanced human binding and/or infectivity variant HAs bind α2-6 sialylated glycans. In some embodiments, enhanced human binding and/or infectivity variant HAs bind long α2-6 sialylated glycans. In some embodiments, enhanced human binding and/or infectivity variant HAs bind 6′SLN-LN glycans. In some embodiments, “enhanced human binding” means that, for example, a variant HA polypeptide shows increased binding relative to that observed with its cognate wild type HA polypeptide (e.g., a control H1 HA polypeptide strain, such as those provided in Table 1). In some embodiments, “enhanced human binding” means that, for example, a variant HA polypeptide shows at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, at least 10-fold, at least 20-fold, at least 50-fold, at least 100-fold, at least 500-fold, or at least 1000-fold increased binding relative to that observed with its cognate wild type HA polypeptide (e.g., a control H1 HA polypeptide strain, such as those provided in Table 1). In some embodiments, “enhanced infectivity” means that, for example, influenza having a variant HA polypeptide shows increased infectivity of a subject relative to that observed with its cognate wild type HA polypeptide (e.g., a control H1 HA polypeptide strain, such as those provided in Table 1). In some embodiments, “enhanced infectivity” means that, for example, influenza having a variant HA polypeptide shows at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, at least 10-fold, at least 20-fold, at least 50-fold, at least 100-fold, at least 500-fold, or at least 1000-fold increased infectivity of a subject relative to that observed with its cognate wild type HA polypeptide (e.g., a control H1 HA polypeptide strain, such as those provided in Table 1). In some embodiments, “enhanced human binding” means that, relative to that observed with its cognate wild type HA polypeptide (e.g., a control H1 HA polypeptide strain, such as those provided in Table 1), a variant H1 HA polypeptide shows binding that is increased to substantially the same degree as H1 HA present in one or more of influenza strains A/South Carolina/1/1918, 2009 A/H1N1 (e.g., A/CA/4/2009), and A/Swine/Iowa/15/1930. In some embodiments, “enhanced infectivity” means that, relative to that observed with its cognate wild type HA polypeptide (e.g., a control H1 HA polypeptide strain, such as those provided in Table 1), influenza having a variant H1 HA polypeptide shows infectivity that is increased to substantially the same degree as H1 HA present in one or more of influenza strains A/South Carolina/1/1918, 2009 A/H1N1 (e.g., A/CA/4/2009), and A/Swine/Iowa/15/1930. In general, an enhanced human binding H1 HA polypeptide as described herein shows enhanced binding to umbrella-topology glycans (e.g., at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, at least 10-fold, at least 20-fold, at least 50-fold, at least 100-fold, at least 500-fold, or at least 1000-fold enhanced binding) and/or enhanced discrimination in binding to umbrella-topology glycans as compared with cone-topology glycans (e.g., at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, at least 10-fold, at least 20-fold, at least 50-fold, at least 100-fold, at least 500-fold, or at least 1000-fold enhanced binding) as compared with an H1 HA polypeptide found in 2009 A/H1N1 (see, e.g., Table 1). In some embodiments, an enhanced human binding H1 HA shows increased binding to α2-6 sialylated, e.g., long α-2-6 sialylated, e.g., 6′SLN-LN glycans, as compared with an H1 HA polypeptide found in 2009 A/H1N1 (see, e.g., Table 1). As will be appreciated by those of ordinary skill in the art, such enhanced binding and/or infectivity may be assessed using any of a variety of assays including, for example, those described herein.
H1 polypeptide: An “H1 polypeptide”, as that term is used herein, is an HA polypeptide whose amino acid sequence includes at least one sequence element that is characteristic of H1 and distinguishes H1 from other HA subtypes. Representative such sequence elements can be determined by alignments such as, for example, those illustrated in FIGS. 1-4 and include, for example, those described herein with regard to H1-specific embodiments of HA Sequence Elements.
H3 polypeptide: An “H3 polypeptide”, as that term is used herein, is an HA polypeptide whose amino acid sequence includes at least one sequence element that is characteristic of H3 and distinguishes H3 from other HA subtypes. Representative such sequence elements can be determined by alignments such as, for example, those illustrated in FIGS. 1 and 2 and include, for example, those described herein with regard to H3-specific embodiments of HA Sequence Elements.
H5 polypeptide: An “H5 polypeptide”, as that term is used herein, is an HA polypeptide whose amino acid sequence includes at least one sequence element that is characteristic of H5 and distinguishes H5 from other HA subtypes. Representative such sequence elements can be determined by alignments such as, for example, those illustrated in FIGS. 1 and 2 and include, for example, those described herein with regard to H5-specific embodiments of HA Sequence Elements.
Hemagglutinin (HA) polypeptide: As used herein, the term “hemagglutinin polypeptide” (or “HA polypeptide”) refers to a polypeptide whose amino acid sequence includes at least one characteristic sequence of HA. A wide variety of HA sequences from influenza isolates are known in the art; indeed, the National Center for Biotechnology Information (NCBI) maintains a database (www.ncbi.nlm.nih.gov/genomes/FLU/flu.html) that, as of the filing of the present application included 9796 HA sequences. Those of ordinary skill in the art, referring to this database, can readily identify sequences that are characteristic of HA polypeptides generally, and/or of particular HA polypeptides (e.g., H1, H2, H3, H4, H5, H6, H7, H8, H9, H10, H11, H12, H13, H14, H15, or H16 polypeptides); or of HAs that mediate infection of particular hosts, e.g., avian, camel, canine, cat, civet, environment, equine, human, leopard, mink, mouse, seal, stone martin, swine, tiger, whale, etc. For example, in some embodiments, an HA polypeptide includes one or more characteristic sequence elements found between about residues 97 and 185, 324 and 340, 96 and 100, and/or 130-230 of an HA protein found in a natural isolate of an influenza virus. In some embodiments, an HA polypeptide has an amino acid sequence comprising at least one of HA Sequence Elements 1 and 2, as defined herein. In some embodiments, an HA polypeptide has an amino acid sequence comprising HA Sequence Elements 1 and 2, in some embodiments separated from one another by about 100 to about 200, or by about 125 to about 175, or about 125 to about 160, or about 125 to about 150, or about 129 to about 139, or about 129, about 130, about 131, about 132, about 133, about 134, about 135, about 136, about 137, about 138, or about 139 amino acids. In some embodiments, an HA polypeptide has an amino acid sequence that includes residues at positions within the regions 96-100 and/or 130-230 that participate in glycan binding. For example, many HA polypeptides include one or more of the following residues: Tyr98, Ser/Thr136, Trp153, His183, and Leu/Ile194. In some embodiments, an HA polypeptide includes at least 2, at least 3, at least 4, or at least all 5 of these residues.
Identity: As used herein, the term “identity” refers to the overall relatedness between polymeric molecules, e.g., between nucleic acid molecules (e.g., DNA molecules and/or RNA molecules) and/or between polypeptide molecules. Calculation of the percent identity of two nucleic acid sequences, for example, can be performed by aligning the two sequences for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second nucleic acid sequences for optimal alignment and non-identical sequences can be disregarded for comparison purposes). In certain embodiments, the length of a sequence aligned for comparison purposes is at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or substantially 100% of the length of the reference sequence. The nucleotides at corresponding nucleotide positions are then compared. When a position in the first sequence is occupied by the same nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which needs to be introduced for optimal alignment of the two sequences. The comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm.
Interfering agent: As used herein, the term “interfering agent” refers to any entity that binds to a designated target (e.g., to a particular HA polypeptide and/or to particular glycans, such as umbrella-topology glycans) as described herein. Interfering agents may be of any chemical type. In some embodiments, interfering agents are polypeptides (including, e.g., antibodies or antibody fragments); in some such embodiments, interfering agents are HA polypeptides; in other embodiments, interfering agents are polypeptides whose amino acid sequence does not include an HA characteristic sequence (i.e., “non-HA polypeptides”). In some embodiments, interfering agents are small molecules. In some embodiments, interfering agents are nucleic acids. In some embodiments, interfering agents are aptamers. In some embodiments, interfering agents are polymers; in some embodiments, interfering agents are non-polymeric. In some embodiments, interfering agents are carbohydrates. In some embodiments, interfering agents are lectins. In some embodiments, interfering agents as described herein bind to one or more HA polypeptides. In some embodiments, interfering agents bind to H1 HA polypeptides. In some embodiments, interfering agents bind to H1 HA polypeptide variants having enhanced human binding and/or infectivity. In some embodiments, interfering agents as described herein bind to sialylated glycans having an umbrella-like topology. In certain embodiments, interfering agents bind to umbrella-topology glycans with high affinity and/or specificity. In some embodiments, interfering agents show a binding preference for umbrella-topology glycans as compared with cone-topology glycans. In some embodiments, interfering agents compete with hemagglutinin for binding to glycans on hemagglutinin receptors. In some embodiments, interfering agents compete with hemagglutinin for binding to umbrella-topology glycans. In some embodiments, an interfering agent provided herein is an umbrella topology blocking agent. In some embodiments, an interfering agent provided herein is an umbrella topology specific blocking agent. In some embodiments, interfering agents bind to umbrella topology glycan mimics.
Isolated: The term “isolated”, as used herein, refers to an agent or entity that has either (i) been separated from at least some of the components with which it was associated when initially produced (whether in nature or in an experimental setting); or (ii) produced by the hand of man. Isolated agents or entities may be separated from at least about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, or more of the other components with which they were initially associated. In some embodiments, isolated agents are more than 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% pure. In some embodiments, calculation of percent purity of isolated substances and/or entities does not include excipients (e.g., buffer, solvent, water, etc.)
Linkage Specific Blocking Agent (LSBA): As used herein, the term “linkage specific blocking agent” refers to an agent which binds to an HA receptor having an α2-6 sialylated glycan. In some embodiments, an LSBA selectively binds to an HA receptor having an α2-6 sialylated glycan with at least about 40, about 50, or about 75% of the affinity of that for an HA receptor having an α2-3 sialylated glycan. In some embodiments, an LSBA selectively binds to an HA receptor having an α2-6 sialylated glycan with at least about 2, about 4, about 5, or about 10 times greater affinity than that for an HA receptor having an α2-3 sialylated glycan. In some embodiments, an LSBA has an affinity for an α2-6 sialylated glycan that is at least 50, 100, 150, or 200% of its affinity for an α2-3 sialylated glycan. In some embodiments, an LSBA may compete with hemagglutinin for binding to an HA receptor. For example, an LSBA may selectively inhibit the binding of an influenza virus particle (e.g., human or avian influenza virus) to an HA receptor based on the linkage characteristics (e.g., α2-6 sialylated glycan or α2-3 sialylated glycan). In some embodiments, an LSBA is a polypeptide. In some such embodiments, an LSBA polypeptide has an amino acid sequence that is substantially identical or substantially homologous to that of a naturally-occurring polypeptide. In some embodiments, an LSBA polypeptide is an HA polypeptide. In some embodiments, an LSBA polypeptide is a naturally-occurring HA polypeptide, or a fragment thereof. In some embodiments, an LSBA polypeptide has an amino acid sequence that is not related to that of an HA polypeptide. In some embodiments, an LSBA polypeptide is an antibody or fragment thereof. In some embodiments, an LSBA polypeptide is a lectin (e.g., SNA-1). In some embodiments, an LSBA is not a polypeptide. In some embodiments, an LSBA is a small molecule. In some embodiments, an LSBA is a nucleic acid.
Long oligosaccharide: For purposes of the present disclosure, an oligosaccharide is typically considered to be “long” if it includes at least one linear chain that has at least four saccharide residues.
Non-natural amino acid: The phrase “non-natural amino acid” refers to an entity having the chemical structure of an amino acid (i.e.:




and therefore being capable of participating in at least two peptide bonds, but having an R group that differs from those found in nature. In some embodiments, non-natural amino acids may also have a second R group rather than a hydrogen, and/or may have one or more other substitutions on the amino or carboxylic acid moieties.

Polypeptide: A “polypeptide”, generally speaking, is a string of at least two amino acids attached to one another by a peptide bond. In some embodiments, a polypeptide may include at least 3-5 amino acids, each of which is attached to others by way of at least one peptide bond. Those of ordinary skill in the art will appreciate that polypeptides sometimes include “non-natural” amino acids or other entities that nonetheless are capable of integrating into a polypeptide chain, optionally.
Preferentially: As used herein, a first entity “preferentially” binds to second entity as compared to a reference entity if the first entity demonstrates enhanced binding to the second entity than the reference entity. In some embodiments, a first entity will bind to a second entity with a binding affinity that is about 1.5-fold, about 2-fold, about 3-fold, about 4-fold, about 5-fold, about 6-fold, about 7-fold, about 8-fold, about 9-fold, about 10-fold, about 20-fold, about 50-fold, about 100-fold, about 500-fold, or about 1000-fold that of the reference entity.
Pure: As used herein, an agent or entity is “pure” if it is substantially free of other components. For example, a preparation that contains more than about 90% of a particular agent or entity is typically considered to be a pure preparation. In some embodiments, an agent or entity is at least 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% pure.
Short oligosaccharide: For purposes of the present disclosure, an oligosaccharide is typically considered to be “short” if it has fewer than 4, or certainly fewer than 3, residues in any linear chain.
Specificity: As is known in the art, “specificity” is a measure of the ability of a particular ligand (e.g., an HA polypeptide) to distinguish its binding partner (e.g., a human HA receptor, and particularly a human upper respiratory tract HA receptor) from other potential binding partners (e.g., an avian HA receptor).
Substantial homology: The phrase “substantial homology” is used herein to refer to a comparison between amino acid or nucleic acid sequences. As will be appreciated by those of ordinary skill in the art, two sequences are generally considered to be “substantially homologous” if they contain homologous residues in corresponding positions. Homologous residues may be identical residues. Alternatively, homologous residues may be non-identical residues will appropriately similar structural and/or functional characteristics. For example, as is well known by those of ordinary skill in the art, certain amino acids are typically classified as “hydrophobic” or “hydrophilic” amino acids, and/or as having “polar” or “non-polar” side chains. Substitution of one amino acid for another of the same type may often be considered a “homologous” substitution. Typical amino acid categorizations are summarized below:

















Alanine
Ala
A
nonpolar
Neutral
1.8


Arginine
Arg
R
polar
Positive
−4.5


Asparagine
Asn
N
polar
Neutral
−3.5


Aspartic acid
Asp
D
polar
Negative
−3.5


Cysteine
Cys
C
nonpolar
Neutral
2.5


Glutamic acid
Glu
E
polar
Negative
−3.5


Glutamine
Gln
Q
polar
Neutral
−3.5


Glycine
Gly
G
nonpolar
Neutral
−0.4


Histidine
His
H
polar
Positive
−3.2


Isoleucine
Ile
I
nonpolar
Neutral
4.5


Leucine
Leu
L
nonpolar
Neutral
3.8


Lysine
Lys
K
polar
Positive
−3.9


Methionine
Met
M
nonpolar
Neutral
1.9


Phenylalanine
Phe
F
nonpolar
Neutral
2.8


Proline
Pro
P
nonpolar
Neutral
−1.6


Serine
Ser
S
polar
Neutral
−0.8


Threonine
Thr
T
polar
Neutral
−0.7


Tryptophan
Trp
W
nonpolar
Neutral
−0.9


Tyrosine
Tyr
Y
polar
Neutral
−1.3


Valine
Val
V
nonpolar
Neutral
4.2
























Ambiguous Amino Acids
3-Letter
1-Letter









Asparagine or aspartic acid
Asx
B



Glutamine or glutamic acid
Glx
Z



Leucine or Isoleucine
Xle
J



Unspecified or unknown amino acid
Xaa
X










As is well known in this art, amino acid or nucleic acid sequences may be compared using any of a variety of algorithms, including those available in commercial computer programs such as BLASTN for nucleotide sequences and BLASTP, gapped BLAST, and PSI-BLAST for amino acid sequences. Exemplary such programs are described in Altschul, et al., Basic local alignment search tool, J. Mol. Biol., 215(3): 403-410, 1990; Altschul, et al., Methods in Enzymology; Altschul, et al., “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,” Nucleic Acids Res. 25:3389-3402, 1997; Baxevanis, et al., Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Wiley, 1998; and Misener, et al., (eds.), Bioinformatics Methods and Protocols (Methods in Molecular Biology, Vol. 132), Humana Press, 1999; all of which are incorporated herein by reference. In addition to identifying homologous sequences, the programs mentioned above typically provide an indication of the degree of homology. In some embodiments, two sequences are considered to be substantially homologous if at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more of their corresponding residues are homologous over a relevant stretch of residues. In some embodiments, the relevant stretch is a complete sequence. In some embodiments, the relevant stretch is at least 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500 or more residues.

Substantial identity: The phrase “substantial identity” is used herein to refer to a comparison between amino acid or nucleic acid sequences. As will be appreciated by those of ordinary skill in the art, two sequences are generally considered to be “substantially identical” if they contain identical residues in corresponding positions. As is well known in this art, amino acid or nucleic acid sequences may be compared using any of a variety of algorithms, including those available in commercial computer programs such as BLASTN for nucleotide sequences and BLASTP, gapped BLAST, and PSI-BLAST for amino acid sequences. Exemplary such programs are described in Altschul, et al., Basic local alignment search tool, J. Mol. Biol., 215(3): 403-410, 1990; Altschul, et al., Methods in Enzymology; Altschul, et al., “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs”, Nucleic Acids Res. 25:3389-3402, 1997; Baxevanis, et al., Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Wiley, 1998; and Misener, et al., (eds.), Bioinformatics Methods and Protocols (Methods in Molecular Biology, Vol. 132), Humana Press, 1999; all of which are incorporated herein by reference. In addition to identifying identical sequences, the programs mentioned above typically provide an indication of the degree of identity. In some embodiments, two sequences are considered to be substantially identical if at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more of their corresponding residues are identical over a relevant stretch of residues. In some embodiments, the relevant stretch is a complete sequence. In some embodiments, the relevant stretch is at least 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500 or more residues.
Suffering from: An individual who is “suffering from” a disease, disorder, and/or condition (e.g., influenza infection) has been diagnosed with and/or displays one or more symptoms of a disease, disorder, and/or condition.
Susceptible to: An individual who is “susceptible to” a disease, disorder, and/or condition (e.g., influenza infection) has not been diagnosed with a disease, disorder, and/or condition. In some embodiments, an individual who is susceptible to a disease, disorder, and/or condition may exhibit symptoms of the disease, disorder, and/or condition. In some embodiments, an individual who is susceptible to a disease, disorder, and/or condition may not exhibit symptoms of the disease, disorder, and/or condition. In some embodiments, an individual who is susceptible to a disease, disorder, and/or condition will develop the disease, disorder, and/or condition. In some embodiments, an individual who is susceptible to a disease, disorder, and/or condition will not develop the disease, disorder, and/or condition.
Therapeutic agent: As used herein, the phrase “therapeutic agent” refers to any agent that, when administered to a subject, has a therapeutic effect and/or elicits a desired biological and/or pharmacological effect. In some embodiments, a therapeutic agent is any substance that can be used to alleviate, ameliorate, relieve, inhibit, prevent, delay onset of, reduce severity of and/or reduce incidence of one or more symptoms or features of influenza infection.
Therapeutically effective amount: As used herein, the term “therapeutically effective amount” means an amount of inventive composition that is sufficient, when administered to a subject suffering from or susceptible to a disease, disorder, and/or condition (e.g., influenza infection), to treat, diagnose, prevent, and/or delay the onset of the disease, disorder, and/or condition.
Treatment: As used herein, the term “treat,” “treatment,” or “treating” refers to any method used to partially or completely alleviate, ameliorate, relieve, inhibit, prevent, delay onset of, reduce severity of and/or reduce incidence of one or more symptoms or features of a disease, disorder, and/or condition (e.g., influenza infection). Treatment may be administered to a subject who does not exhibit signs of a disease, disorder, and/or condition. In some embodiments, treatment may be administered to a subject who exhibits only early signs of the disease, disorder, and/or condition for the purpose of decreasing the risk of developing pathology associated with the disease, disorder, and/or condition.
Umbrella topology: The phrase “umbrella topology” is used herein to refer to a 3-dimensional arrangement adopted by certain glycans and in particular by glycans bound to HA receptors. The present invention encompasses the recognition that binding to umbrella topology glycans is characteristic of HA proteins that mediate infection of human hosts. As illustrated in FIG. 5, the umbrella topology is typically adopted only by α2-6 sialylated glycans, and is typical of long (e.g., greater than tetrasaccharide) oligosaccharides. In some embodiments, umbrella-topology glycans are glycans exhibiting a three-dimensional structure substantially similar to the structure presented in FIG. 5A (right panel). In some embodiments, umbrella-topology glycans are glycans which contact HA polypeptides via the amino acid residues shown in FIG. 5B-2 (right panel) and FIG. 6 (right panel). In some embodiments, umbrella-topology glycans are glycans which are able to contact and/or specifically bind to the amino acid binding pocket shown in FIG. 5B-2 (right panel). In some embodiments, glycan structural topology is classified based on parameter θ defined as angle between C2 of Sia, C1 of Gal, and C1 of GlcNAc. Values of θ<100° represent cone-like topology adopted by α2-3 and short α2-6 glycans. Values of θ>110° represent umbrella-like topology, such as topology adopted by long α2-6 glycans (FIG. 6). An example of umbrella topology is given by φ angle of Neu5Acα2-6Gal linkage of around −60. FIG. 8 presents certain representative (though not exhaustive) examples of glycans that can adopt an umbrella topology. The long α2-6 motifs presented in FIG. 8 include Neu5Acα2-6 linked at the non-reducing end to a long chain (e.g., at least a trisaccharide) found as a part of biological N-linked glycans, O-linked glycans, and glycolipids. The boxed inset shows examples of the umbrella-topology long α2-6 glycan moieties that are found as a part of biological glycans that bind to high affinity with HA. In some embodiments, umbrella-topology glycans (e.g., at a site) comprise a greater proportion of long (e.g., multiple lactosamine units) α2-6 oligosaccharide branches than short α2-6 (e.g., single lactosamine) branches. In some embodiments, umbrella-topology glycans (e.g., at a site) comprise about 2-fold, about 3-fold, about 4-fold, about 5-fold, about 10-fold, about 20-fold, about 50-fold, or greater than about 50-fold more long α2-6 oligosaccharide branches than short α2-6 (e.g., single lactosamine) branches. In certain embodiments, the unique characteristic of HA interactions with umbrella-topology glycans and/or glycan decoys is the HA contact with a glycan comprising sialic acid (SA) and/or SA analogs at the non-reducing end. In some embodiments, chain length of the oligosaccharide is at least a trisaccharide (excluding the SA or SA analog). In some embodiments, a combination of the numbered residues shown in FIGS. 5A and 5B-2 (right-hand panels) is involved in contacts with umbrella-like topology. In certain embodiments, umbrella topology glycans are oligosaccharides of the following form:
Neu5Acα2-6Sug1-Sug2-Sug3
where:
(a) Neu5Ac α2-6 is typically (but not essentially) at the non-reducing end;
(b) Sug1:

    
    
        (i) is a hexose (frequently Gal or Glc) or hexosamine (GlcNAc or GalNAc) in α or β configuration (frequently β- for N- and O-linked extension and α- in the case of GalNAcα- that is O-linked to glycoprotein);
        (ii) no sugars other than Neu5Acα2-6 are attached to any of the non-reducing positions of Sug1 (except when Sug1 is GalNAcα- that is O-linked to the glycoprotein); and/or
        (iii) non-sugar moieties such as sulfate, phosphate, guanidium, amine, N-acetyl, etc. can be attached to non-reducing positions (typically 6 position) of Sug1 (e.g., to improve contacts with HA);
    
    


(c) Sug2 and/or Sug3 is/are:

    
    
        (i) hexose (frequently Gal or Glc) or hexosamine (GlcNAc or GalNAc) in α or β configuration (frequently β); and/or
        (ii) sugars (such as Fuc) or non-sugar moieties such as sulfate, phosphate, guanidium, amine, N-acetyl, etc. can be attached to non-reducing positions of Sug2, Sug3, and/or Sug4;
    
    


(d) Linkage between any two sugars in the oligosaccharide apart from Neu5Acα2-6 linkage can be 1-2, 1-3, 1-4, and/or 1-6 (typically 1-3 or 1-4); and/or
(e) Structure where Neu5Acα2-6 is linked GalNAcα that is O-linked to the glycoprotein and additional sugars are linked to the non-reducing end of GalNAcα for example

    
    
        (i) Neu5Acα2-6(Neu5Acα2-3Galβ1-3)GalNAcα-
        (ii) Neu5Acα2-6(Galβ1-3)GalNAcα-
    
    


Umbrella topology blocking agent (UTBA): As used herein, the term “umbrella topology blocking agent” refers to an agent which binds to an HA receptor having an umbrella topology glycan. In some embodiments, a UTBA binds to an HA receptor having an umbrella topology glycan found in human upper airways. A UBTA can bind to either an umbrella topology glycan and/or to a cone topology glycan. In some embodiments, a UTBA selectively binds to an umbrella topology glycan with 50, 100, 150, or 200% of its affinity for a cone topology glycan. In some embodiments a UTBA selectively binds to an umbrella topology glycan with 50-150% of its affinity for a cone topology glycan. In some embodiments, a UTBA binds to an umbrella topology glycan with about the same affinity as for a cone topology glycan. For example, in some embodiments, a UTBA binds an umbrella topology glycan (e.g., 6′SLN-LN) with about 50-200%, 50-150%, or about the same affinity to which it binds a cone topology glycan (e.g., 3′SLN-LN). In some embodiments, a UTBA selectively inhibits the binding of an influenza virus particle (e.g., a human or avian influenza virus) to the HA receptor based on the glycan topology of the receptor (e.g., umbrella or cone). In some embodiments, a UTBA is a polypeptide. In some such embodiments, a UTBA polypeptide has an amino acid sequence that is substantially identical or substantially homologous to that of a naturally-occurring polypeptide. In some embodiments, a UTBA polypeptide is an HA polypeptide. In some embodiments, a UTBA polypeptide is a naturally-occurring HA polypeptide, or a fragment thereof. In some embodiments, a UTBA polypeptide has an amino acid sequence that is not related to that of an HA polypeptide. In some embodiments, a UTBA polypeptide is an antibody or fragment thereof. In some embodiments, a UTBA polypeptide is a lectin (e.g., SNA-1). In some embodiments, a UTBA is not a polypeptide. In some embodiments, a UTBA is a small molecule. In some embodiments, a UTBA is a nucleic acid.
Umbrella topology glycan mimic: An “umbrella topology glycan mimic” is an agent, other than an umbrella topology glycan, that binds to binding agents as described herein. In some embodiments, umbrella topology glycan mimics are agents that bind to HA polypeptides. In some such embodiments, umbrella topology glycan mimics are agents that interact with HA polypeptide residues selected from the group consisting of residues 136, 137, 145, 153, 155, 156, 159, 186, 187, 189, 190, 192, 193, 194, 196, 222, 225, 226, 228 and combinations thereof. In some such embodiments, umbrella topology glycan mimics are agents that interact with HA polypeptide residues selected from the group consisting of residues. In some such embodiments, umbrella topology glycan mimics are agents that interact with HA polypeptide residues selected from the group consisting of residues 156, 159, 189, 192, 193, 196, and combinations thereof. In some such embodiments, umbrella topology glycan mimics are agents that interact with HA polypeptide residues selected from the group consisting of residues 186, 187, 189, 190, and combinations thereof. In some such embodiments, umbrella topology glycan mimics are agents that interact with HA polypeptide residues selected from the group consisting of residues 137, 145, 190, 226, 228, and combinations thereof. In some such embodiments, umbrella topology glycan mimics are agents that interact with HA polypeptide residues selected from the group consisting of residues 190, 222, 225, 226, and combinations thereof. In some such embodiments, umbrella topology glycan mimics are agents that interact with HA polypeptide residues selected from the group consisting of residues 136, 153, 155, 194, and combinations thereof. In some such embodiments, umbrella topology glycan mimics are agents that interact with HA polypeptide residues selected from the group consisting of residues 190 and 226. In some such embodiments, umbrella topology glycan mimics are agents that interact with HA polypeptide residues selected from the group consisting of residues 222, 225, and 226. In some such embodiments, umbrella topology glycan mimics are agents that interact with HA polypeptide residues selected from the group consisting of residues 190, 192, 193, and 225. In some such embodiments, umbrella topology glycan mimics are agents that interact with HA polypeptide residues selected from the group consisting of residues 186, 193, and 222. Note that amino acid positions stated above are based on H3 HA numbering. In certain embodiments, an HA topology glycan mimic is an agent that competes with umbrella topology glycans for interaction with an HA polypeptide.
Umbrella topology specific blocking agent (UTSBA): As used herein, the term “umbrella topology specific blocking agent” refers to an agent which binds to an HA receptor having an umbrella topology glycan found in human upper airways. A UTSBA selectively binds an umbrella topology glycan HA. For example, a UTSBA binds an umbrella topology glycan (e.g., 6′SLN-LN) with about at least 2, 4, 5, or 10 times greater affinity than it binds to a cone topology glycan (e.g., 3′SLN-LN). Typically, the affinity of a UTSBA for an umbrella topology glycan is greater than 1 nM. Typically the affinity of a UTSBA for a cone topology glycan is less is at least within 2 to 3 orders of magnitude of the binding affinity of umbrella topology glycans to human adapted HAs such as SC18, Mos99, Tx91, etc., and α2-6 binding plant lectins such as SNA-I. The binding affinity of UTSBA as measured by the dose-dependent direct binding assay would typically be at least 1 nM. Typically the affinity of a UTSBA for a cone topology glycan is at most 1 to 3 orders of magnitude less than the binding affinity of cone topology glycans to avian HAs such as Viet0405, Av18, etc. In some embodiments, a UTSBA selectively inhibits binding of an influenza virus particle (e.g., a human or avian influenza virus) to the HA receptor (e.g., an H1, H2 or H3 or a human-adapted H5, H7 or H9) based on glycan topology (e.g., umbrella or cone). In some embodiments, a UTSBA is a polypeptide. In some such embodiments, a UTSBA polypeptide has an amino acid sequence that is that is substantially identical or substantially homologous to that of a naturally-occurring polypeptide. In some embodiments, a UTSBA polypeptide is an HA polypeptide. In some embodiments, a UTSBA polypeptide is a naturally-occurring HA polypeptide, or a fragment thereof. In some embodiments, a UTSBA polypeptide has an amino acid sequence that is not related to that of an HA polypeptide. In some embodiments, a UTSBA polypeptide is an antibody or fragment thereof. In some embodiments, a UTSBA polypeptide is a lectin (e.g., SNA-1). In some embodiments, a UTSBA is not a polypeptide. In some embodiments, a UTSBA is a small molecule. In some embodiments, a UTSBA is a nucleic acid.
Vaccination: As used herein, the term “vaccination” refers to the administration of a composition intended to generate an immune response, for example to a disease-causing agent. For the purposes of the present invention, vaccination can be administered before, during, and/or after exposure to a disease-causing agent, and in certain embodiments, before, during, and/or shortly after exposure to the agent. In some embodiments, vaccination includes multiple administrations, appropriately spaced in time, of a vaccinating composition.
Variant: As used herein, the term “variant” is a relative term that describes the relationship between a particular polypeptide (e.g., HA polypeptide) of interest and a “parent” polypeptide to which its sequence is being compared. A polypeptide of interest is considered to be a “variant” of a parent polypeptide if the polypeptide of interest has an amino acid sequence that is identical to that of the parent but for a small number of sequence alterations at particular positions. Typically, fewer than 20%, 15%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2% of the residues in the variant are substituted as compared with the parent. In some embodiments, a variant has 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 substituted residue as compared with a parent. Often, a variant has a very small number (e.g., fewer than 5, 4, 3, 2, or 1) number of substituted functional residues (i.e., residues that participate in a particular biological activity). Furthermore, a variant typically has not more than 5, 4, 3, 2, or 1 additions or deletions, and often has no additions or deletions, as compared with the parent. Moreover, any additions or deletions are typically fewer than about 25, 20, 19, 18, 17, 16, 15, 14, 13, 10, 9, 8, 7, 6, and commonly are fewer than about 5, 4, 3, or 2 residues. In some embodiments, the parent polypeptide is one found in nature. For example, a parent HA polypeptide may be one found in a natural (e.g., wild type) isolate of an influenza virus (e.g., a wild type HA). In some embodiments, an H1 HA parent polypeptide may correspond to the H1 polypeptide characteristic of any of the influenza strains presented in Table 1. In some embodiments, a variant H1 HA polypeptide has at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 50, 100, or more than 100 substitutions, deletions, and/or additions relative to one or more of the H1 polypeptides characteristic of any of the influenza strains presented in Table 1.
Vector: As used herein, “vector” refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. In some embodiment, vectors are capable of extra-chromosomal replication and/or expression of nucleic acids to which they are linked in a host cell such as a eukaryotic or prokaryotic cell. Vectors capable of directing the expression of operatively linked genes are referred to herein as “expression vectors.”
Wild type: As is understood in the art, the phrase “wild type” generally refers to a normal form of a protein or nucleic acid, as is found in nature. For example, wild type HA polypeptides are found in natural isolates of influenza virus. A variety of different wild type HA sequences can be found in the NCBI influenza virus sequence database, http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html.
Detailed Description of Certain Particular Embodiments of the Invention
Among other things, the present invention defines H1N1 HA variants with enhanced human binding and/or infectivity as compared with an H1 polypeptide found in H1N1 influenza strains (see, e.g., Table 1). Such variants may be utilized, among other things, as components of vaccines and/or therapeutics to treat, reduce, and/or prevent human infection by and H1N1 virus, and particularly by a variant with enhanced human binding and/or infectivity. Alternatively or additionally, such variants may be utilized as standards in systems for detecting occurrence of and/or infection with an H1N1 variant with enhanced human infectivity.
In some aspects, the present invention provides agents that bind specifically to an H1N1 HA polypeptides, for example for use in detecting H1N1 infection. In some embodiments, the present invention provides agents that bind specifically to an H1N1 variant with enhanced human infectivity. In some embodiments, the present invention provides agents that discriminate between H1N1 variants with enhanced human infectivity and H1N1 variants without enhanced human infectivity.
In some aspects, the present invention provides agents that interfere (and/or compete) with binding interactions between an H1N1 HA polypeptide and one or more glycans, for example umbrella-topology glycans. In some embodiments, the present invention provides agents that interfere (and/or compete with) binding interactions between an H1N1 HA polypeptide and one or more α2-6 sialylated glycans. In some embodiments, the present invention provides agents that interfere (and/or compete) with binding interactions between an H1N1 HA polypeptide and one or more 6′SLN-LN glycans. In some embodiments, the H1N1 HA polypeptide whose binding interaction is interfered with is an H1N1 variant with enhanced human infectivity.
Hemagglutinin (HA)
Influenza viruses are RNA viruses which are characterized by a lipid membrane envelope containing two glycoproteins, hemagglutinin (HA) and neuraminidase (NA), embedded in the membrane of the virus particular. There are 16 known HA subtypes and 9 NA subtypes, and different influenza strains are named based on the number of the strain's HA and NA subtypes. Based on comparisons of amino acid sequence identity and of crystal structures, the HA subtypes have been divided into two main groups and four smaller clades. The different HA subtypes do not necessarily share strong amino acid sequence identity, but the overall 3D structures of the different HA subtypes are similar to one another, with several subtle differences that can be used for classification purposes. For example, the particular orientation of the membrane-distal subdomains in relation to a central α-helix is one structural characteristic commonly used to determine HA subtype (Russell et al., Virology, 325:287, 2004).
HA exists in the membrane as a homotrimer of one of 16 subtypes, termed H1-H16. Only three of these subtypes (H1, H2, and H3) have thus far become adapted for human infection. One reported characteristic of HAs that have adapted to infect humans (e.g., of HAs from the pandemic H1N1 (1918) and H3N2 (1967-68) influenza subtypes) is their ability to preferentially bind to α2-6 sialylated glycans in comparison with their avian progenitors that preferentially bind to α2-3 sialylated glycans (Skehel & Wiley, Annu Rev Biochem, 69:531, 2000; Rogers, & Paulson, Virology, 127:361, 1983; Rogers et al., Nature, 304:76, 1983; Sauter et al., Biochemistry, 31:9609, 1992; Connor et al., Virology, 205:17, 1994; Tumpey et al., Science, 310:77, 2005; all of which are incorporated herein by reference). The present inventors, however, have discovered that ability to infect human hosts correlates less with binding to glycans of a particular linkage, and more with binding to glycans of a particular topology (see, e.g., US patent application publications 2009/0269342, 2010/0004195, and 2010/0125043, all of which are incorporated herein by reference). Thus, the present inventors have demonstrated that HAs that mediate infection of humans bind to umbrella topology glycans, often showing preference for umbrella topology glycans over cone topology glycans (even though cone-topology glycans may be or comprise α2-6 sialylated glycans).
Several crystal structures of HAs from H1 (human and swine), H3 (avian) and H5 (avian) subtypes bound to sialylated oligosaccharides (of both α2-3 and α2-6 linkages) are available and provide molecular insights into the specific amino acids that are involved in distinct interactions of the HAs with these glycans (Eisen et al., Virology, 232:19, 1997; Ha et al., Proc Natl Acad Sci USA, 98:11181, 2001; Ha et al., Virology, 309:209, 2003; Gamblin et al., Science, 303:1838, 2004; Stevens et al., Science, 303:1866, 2004; Russell et al., Glycoconj J 23:85, 2006; Stevens et al., Science, 312:404, 2006; all of which are incorporated herein by reference).
For example, the crystal structures of H5 (A/duck/Singapore/3/97) alone or bound to an α2-3 or an α2-6 sialylated oligosaccharide identifies certain amino acids that interact directly with bound glycans, and also amino acids that are one or more degree of separation removed (Stevens et al., Proc Natl Acad Sci USA 98:11181, 2001; incorporated herein by reference). In some cases, conformation of these residues is different in bound versus unbound states. For instance, Glu190, Lys193 and Gln226 all participate in direct-binding interactions and have different conformations in the bound versus the unbound state. The conformation of Asn186, which is proximal to Glu190, is also significantly different in the bound versus the unbound state.
HA Polypeptides
The present invention provides HA polypeptides. As used herein, the term “HA polypeptides” is understood to encompass fragments of HA polypeptides, portions (e.g., characteristic portions) of HA polypeptides, and/or variants of HA polypeptides. HA polypeptide fragments, portions of HA polypeptides, and variant HA polypeptides are described in further detail below, in the subsections below entitled “Portions and/or Fragments of HA Polypeptides” and “Variant HA Polypeptides.”
The present invention particularly provides HA H1 polypeptides. As used herein, the term “H1 polypeptides” is understood to encompass fragments of H1 polypeptides, portions (e.g., characteristic portions) of H1 polypeptides, and/or polypeptides that are H1 variants. H1 polypeptide fragments, portions of H1 polypeptides, and H1 variant polypeptides are described in further detail below, in the subsections below entitled “Portions and/or Fragments of HA Polypeptides” and “Variant HA Polypeptides.”
In some embodiments, HA polypeptides are isolated HA polypeptides with designated binding characteristics with respect to umbrella topology glycans. In some embodiments, HA polypeptides are engineered HA polypeptides with designated binding characteristics with respect to umbrella topology glycans.
In some embodiments, provided HA polypeptides with designated binding characteristics are H1 polypeptides. In some embodiments, provided HA polypeptides are H1 HA variant polypeptides that show enhanced human binding and/or infectivity as compared with a reference H1 HA polypeptide. In some embodiments, such H1 HA variant polypeptides are engineered. In some embodiments, such H1 HA variant polypeptides are isolated from influenza strains found in the environment. Exemplary H1 HA variant polypeptides with enhanced human binding and/or infectivity include, but are not limited to, H1 HA polypeptides (e.g., fragments thereof and/or characteristic portions thereof) present in influenza strains A/South Carolina/1/1918, 2009 A/H1N1 (e.g., A/CA/4/2009), A/Swine/Iowa/15/1930. In some embodiments, H1 HA variant polypeptides with enhanced human binding and/or infectivity, such as H1 HA polypeptides present in influenza strains A/South Carolina/1/1918, 2009 A/H1N1 (e.g., A/CA/4/2009), and A/Swine/Iowa/15/1930 are engineered to exhibit even more enhanced human binding and/or infectivity. In some embodiments, H1 HA polypeptides with enhanced human binding and/or infectivity specifically exclude H1 polypeptides found in influenza strains A/South Carolina/1/1918, 2009 A/H1N1 (e.g., A/CA/4/2009), A/Swine/Iowa/15/1930.
In some embodiments, reference H1 HA polypeptides include the HA protein from one or more of the strains presented in Table 1. In some embodiments, reference H1 HA polypeptides include any H1 HA found in a 2009 A/H1N1 “swine flu” isolate listed in one or both of the GISAID Influenza portal database (http://platform.gisaid.org/dante-cms/live/struktur.jdante?aid=1131) and/or the NCBI Flu database (http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html).







TABLE 1







Sequences of Exemplary H1 HA Polypeptides found in 2009 A/H1N1








Strain
H1 HA Sequence












A/California/04/2009
MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLEKNVT




VTHSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPEC



ESLSTASSWSYIVETPSSDNGTCYPGDFIDYEELREQLSSVSSF



ERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVK



KGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNA



DTYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPG



DKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQ



TPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNIPSIQ



SRGLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADL



KSTQNAIDEITNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLN



KKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKV



RSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYS



EEAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISF



WMCSNGSLQCRICI (SEQ ID NO: 46)


 


A/Texas/15/09
MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLEKNVT



VTHSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPEC



ESLSTASSWSYIVETSSSDNGTCYPGDFIDYEELREQLSSMSSF



ERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVK



KGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNA



DAYVFVGSSRYSKKLKPEIAIRPKVRDQEGRMNYYWTLVEPG



DKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQ



TPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNVPSIQ



SRGLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADL



KSTQNAIDEITNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLN



KKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKV



RSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYS



EEAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISF



WMCSNGSLQCRICI (SEQ ID NO: 47)


 


A/Mexico/4482/09
MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLEKNVT



VTHSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPEC



ESLSTASSWSYIVETSSSDNGTCYPGDFIDYEELREQLSSVSSF



ERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVK



KGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNA



DAYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPG



DKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQ



TPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNVPSIQ



SRGLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADL



KSTQNAIDEITNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLN



KKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKV



RSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYS



EEAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISF



WMCSNGSLQCRICI (SEQ ID NO: 48)









Sequences of H1 HA polypeptides found in influenza strains A/South Carolina/1/1918 and A/Swine/Iowa/15/1930 are found in Table 2.








TABLE 2







Sequences of Exemplary H1 HA Polypeptides from



Pandemic H1 Influenza Strains








Strain
H1 HA Sequence












A/South
MEARLLVLLCAFAATNADTICIGYHANNSTDTVDTVLEKNVT



Carolina/1/1918
VTHSVNLLEDSHNGKLCKLKGIAPLQLGKCNIAGWLLGNPEC



DLLLTASSWSYIVETSNSENGTCYPGDFIDYEELREQLSSVSSF



EKFEIFPKTSSWPNHETTKGVTAACSYAGASSFYRNLLWLTK



KGSSYPKLSKSYVNNKGKEVLVLWGVHHPPTGTDQQSLYQN



ADAYVSVGSSKYNRRFTPEIAARPKVRDQAGRMNYYWTLLE



PGDTITFEATGNLIAPWYAFALNRGSGSGIITSDAPVHDCNTK



CQTPHGAINSSLPFQNIHPVTIGECPKYVRSTKLRMATGLRNIP



SIQSRGLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAA



DQKSTQNAIDGITNKVNSVIEKMNTQFTAVGKEFNNLERRIEN



LNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVRNLYE



KVKSQLKNNAKEIGNGCFEFYHKCDDACMESVRNGTYDYPK



YSEESKLNREEIDGVKLESMGVYQILAIYSTVASSLVLLVSLG



AISFWMCSNGSLQCRICI (SEQ ID NO: 49)


 


A/Swine/IA/15/1930
MKAILLVLLCAFAATNADTLCIGYHANNSTDTVDTVLEKNVT



VTHSVNLLEDSHNGKLCRLGGIAPLQLGKCNIAGXXLGNPEC



DLLLTVSSWSYIVETSNSDNGTCYPGDFIDYEELREQLSSVSSF



EKFEIFPKTSSWPNHETTRGVTAACPYAGASSFYRNLLWLVK



KENSYPKLSKSYVNNKGKEVLVLWGVHHPPTSTDQQSLYQN



ADAYVSVGSSKYDRRFTPEIAARPKVRGQAGRMNYYWTLLE



PGDTITFEATGNLVAPRYAFALNRGSESGIITSDAPVHDCDTK



CQTPHGAINSSLPFQNIHPVTIGECPKYVKSTKLRMVTGLRNIP



SIQSRGLFGAIAGFIEGGWTGLIDGWYGYHHQNGQGSGYAAD



QKSTQNAIDGITNKVNSVIEKMNTQFTVVGKEFNNLERRIKNL



NKKVDDGFLDVWTYNAEMLVLLENERTLDFHDSNVKNLYE



KARSQLRNNAKEIGNGCFEFYHKCDDACMESVRNGTYDYPK



YSEESKLNREEIDGVKLESMMVYQILAIYSTVASSLVLLVSLG



AISFWMCSNGSLQCRICI (SEQ ID NO: 50)









In some embodiments, HA polypeptides (e.g., H1 polypeptides) are useful for developing and/or preparing influenza vaccines. In some embodiments, HA polypeptides (e.g., H1 polypeptides) are useful for developing and/or preparing influenza therapeutics. In some embodiments, HA polypeptides (e.g., H1 polypeptides) are useful for developing and/or preparing reagents useful for diagnosing influenza and/or determining whether a patient has been infected with an H1 HA influenza virus. In some embodiments, HA polypeptides (e.g., H1 polypeptides) are useful for surveillance of the emergence of a potential pandemic H1 HA influenza virus. Therapeutic, prophylactic, and diagnostic methods are described in further detail in the sections entitled “Detection of H1-Containing Influenzas” and “Treatment.”
Variant HA Polypeptides
In certain embodiments, a provided HA polypeptide (e.g., H1 polypeptide) is a variant of a parent HA polypeptide in that its amino acid sequence is identical to that of the parent HA but for a small number of particular sequence alterations. In some embodiments, the parent HA is an HA polypeptide found in a natural isolate of an influenza virus (e.g., a wild type HA polypeptide). In some embodiments, the parent HA is one of the HAs set forth in Table 1. Any of the portions and/or fragments described herein can be fragments and/or characteristic portions of HA polypeptides, as described in the section below entitled “Portions and/or Fragments of HA Polypeptides.”
In some embodiments, HA polypeptide variants have different glycan binding characteristics than their corresponding parent HA polypeptides. In some embodiments, HA variant polypeptides have greater affinity and/or specificity for umbrella glycans (e.g., as compared with for cone glycans) than do their cognate parent HA polypeptides. In certain embodiments, such HA polypeptide variants are engineered variants.
In some embodiments, HA variant polypeptides have a 2-fold, 3-fold, 4-fold, 5-fold, 10-fold, 15-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity and/or specificity for umbrella glycans (e.g., as compared with for cone glycans) than do their cognate parent HA polypeptides. In some embodiments, influenza virus expressing HA variant polypeptides has a 2-fold, 3-fold, 4-fold, 5-fold, 10-fold, 15-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold enhanced human infectivity than does an influenza virus expressing their cognate parent HA polypeptides.
In some embodiments, HA polypeptide variants with altered glycan binding characteristics have sequence alternations in residues within or affecting the glycan binding site. In some embodiments, such substitutions are of amino acids that interact directly with bound glycan; in other embodiments, such substitutions are of amino acids that are one degree of separation removed from those that interact with bound glycan, in that the one degree of separation removed-amino acids either (1) interact with the direct-binding amino acids; (2) otherwise affect the ability of the direct-binding amino acids to interact with glycan, but do not interact directly with glycan themselves; or (3) otherwise affect the ability of the direct-binding amino acids to interact with glycan, and also interact directly with glycan themselves. HA polypeptide variants contain substitutions of one or more direct-binding amino acids, one or more first degree of separation-amino acids, one or more second degree of separation-amino acids, or any combination of these. In some embodiments, HA polypeptide variants may contain substitutions of one or more amino acids with even higher degrees of separation.
In some embodiments, HA polypeptide variants with altered glycan binding characteristics have sequence alterations in residues that make contact with sugars beyond Neu5Ac and Gal (see, for example, FIG. 6).
In some embodiments, HA polypeptide variants have at least one amino acid substitution, as compared with a wild type parent HA. In certain embodiments, HA polypeptide variants have 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more than 20 amino acid substitutions as compared with a cognate wild type parent HA. In some embodiments, HA polypeptide variants have one or more amino acid substitutions separated by at least 1, at least 2, at least 3, at least 4, at least 5, at least 10, at least 20, at least 50, at least 100, at least 200, at least 300, at least 400, or at least 500 wild type amino acid residues. In some embodiments, about 70%, about 80%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99%, about 100% of such amino acid substitutions are located within the glycan binding site. In some embodiments, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% of such amino acid substitutions are located within the glycan binding site.
In some embodiments, HA polypeptide variants have at least one amino acid addition and/or deletion, as compared with a wild type parent HA. In some embodiments, HA polypeptide variants have 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more than 20 additions and/or deletions of residues. In some embodiments, HA polypeptide variants have one or more additions and/or deletions of residues separated by at least 1, at least 2, at least 3, at least 4, at least 5, at least 10, at least 20, at least 50, at least 100, at least 200, at least 300, at least 400, or at least 500 wild type amino acid residues. In some embodiments, about 70%, about 80%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99%, about 100% of such amino acid additions and/or deletions are located within the glycan binding site. In some embodiments, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% of such amino acid additions and/or deletions are located within the glycan binding site.
In some embodiments, HA polypeptide variants are about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to a cognate wild type parent HA.
In some embodiments, HA polypeptide variants are about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to a contiguous stretch of about 10, about 20, about 30, about 40, about 50, about 100, about 150, about 200, about 250, about 300, about 350, about 400, about 450, about 500, or about 550 amino acids of a cognate wild type parent HA.
In some embodiments, HA polypeptide variants have sequence substitutions, additions, and/or deletions at positions corresponding to one or more of residues 98, 136, 137, 138, 145, 153, 155, 156, 159, 183, 186, 187, 189, 190, 192, 193, 194, 195, 196, 215, 219, 222, 225, 226, 227, and 228. In some embodiments, HA polypeptide variants have sequence substitutions, additions, and/or deletions at positions corresponding to one or more of residues 156, 159, 189, 192, 193, and 196; and/or at positions corresponding to one or more of residues 186, 187, 189, and 190; and/or at positions corresponding to one or more of residues 190, 222, 225, and 226; and/or at positions corresponding to one or more of residues 137, 145, 190, 226 and 228. In some embodiments, HA polypeptide variants have sequence substitutions, additions, and/or deletions at positions corresponding to one or more of residues 190, 225, 226, and 228. In some embodiments, HA polypeptide variants, particularly H1 polypeptide variants, have sequence substitutions, additions, and/or deletions corresponding to one or more of residues 145, 186, 189, 219, and/or 227.
In some embodiments, HA polypeptide variants, and particularly H1 polypeptide variants, have one or more amino acid substitutions, additions, and/or deletions relative to a wild type parent HA at residues selected from amino acids located in the region of the polypeptide that directly binds to the glycan, including but not limited to residues 136, 145 (e.g., Lys145), 153, 155, 156, 183, 186, 189, 190, 192, 193, 194, 196, 215, 222, 225, 226 and/or 227. In some embodiments, an HA polypeptide variant, and particularly an H1 polypeptide variant, has one or more amino acid substitutions, additions, and/or deletions relative to a wild type parent HA at residues selected from amino acids located adjacent to the region of the polypeptide that directly binds the glycan, including but not limited to residues Ala/Thr137, Ala/Ser138, Pro/Ser186, Ser/Thr/Asn187, Ala/Thr189, Ile/Lys219, Glu/Ala227, and/or Lys222. In some embodiments, amino acids located adjacent to the region of the polypeptide that directly binds the glycan influence the ability of amino acids located in the region of the polypeptide that directly binds the glycan to mediate an interaction between the HA polypeptide and the receptor. To give but a few examples, in some embodiments, Ala/Thr137 and/or Ala/Ser138 influence Thr/Ser136 and/or Gln226; Pro/Ser186, Ser/Thr/Asn187, and/or Ala/Thr189 influence Asp190; Ile/Lys219 and/or Glu/Ala227 influence Pro/Ser186; Glu227 influences Lys222; and/or Lys222 influences Asp225.
In certain embodiments, an HA polypeptide variant, and particularly an H1 polypeptide variant has one or more amino acid substitutions, additions, and/or deletions relative to a wild type parent HA at residues selected from amino acids that are one degree of separation removed from those that interact with bound glycan, in that the one degree of separation removed-amino acids either (1) interact with the direct-binding amino acids; (2) otherwise affect the ability of the direct-binding amino acids to interact with glycan, but do not interact directly with glycan themselves; or (3) otherwise affect the ability of the direct-binding amino acids to interact with glycan, and also interact directly with glycan themselves, including but not limited to residues Ala/Thr137, Ala/Ser138, Pro/Ser186, Ser/Thr/Asn187, Ala/Thr189, Ile/Lys219, Glu/Ala227, and/or Lys222.
In certain embodiments, an HA polypeptide variant, and particularly an H1 polypeptide variant, has an amino acid substitution, addition, and/or deletion relative to a wild type parent HA at residue 145. In certain embodiments, an HA polypeptide variant, and particularly an H1 polypeptide variant, has an amino acid substitution, addition, and/or deletion relative to a wild type parent HA at residue 186. In certain embodiments, an HA polypeptide variant, and particularly an H1 polypeptide variant, has an amino acid substitution, addition, and/or deletion relative to a wild type parent HA at residue 189. In certain embodiments, an HA polypeptide variant, and particularly an H1 polypeptide variant, has an amino acid substitution, addition, and/or deletion relative to a wild type parent HA at residue 219. In certain embodiments, an HA polypeptide variant, and particularly an H1 polypeptide variant, has an amino acid substitution, addition, and/or deletion relative to a wild type parent HA at residue 227.
In some embodiments, an HA polypeptide variant, and particularly an H1 polypeptide variant, has one or more amino acid substitutions, additions, and/or deletions relative to a wild type parent HA at residues selected from 145, 186, 189, 219, and 227. In some embodiments, an HA polypeptide variant, and particularly an H1 polypeptide variant, has one or more amino acid substitutions, additions, and/or deletions relative to a wild type parent HA at residues 186, 189, and 227. In some embodiments, an HA polypeptide variant, and particularly an H1 polypeptide variant, has one or more amino acid substitutions, additions, and/or deletions relative to a wild type parent HA at residues 186, 189, 225, and 227. In some embodiments, an HA polypeptide variant, and particularly an H1 polypeptide variant, has one or more amino acid substitutions, additions, and/or deletions relative to a wild type parent HA at residues 219 and 225.
In some embodiments, an HA polypeptide variant, and particularly an H1 variant has one or more of the following amino acid substitutions: Lys145Ser, Lys145Asn, Ile219Lys, Ser 186Pro, Ala189Thr, Gly227Ala. In some embodiments, an HA polypeptide variant, and particularly an H1 variant has one or more of the following amino acid substitutions: Lys145Ser, Lys145Asn, Ile219Lys, Ser 186Pro, Ala189Thr, Asp225Glu, Asp225Asn, or Asp225Gly, and/or Gly227Ala. In some embodiments, an HA polypeptide variant has at least one addition and/or deletion at one or more of amino acid positions 145, 186, 189, 219, and/or 227. In some embodiments, an HA polypeptide variant has at least one addition and/or deletion at one or more of amino acid positions 145, 186, 189, 219, 225, and/or 227. In some embodiments, an HA polypeptide variant has at least one addition and/or deletion at one or more of amino acid positions 137, 156, 186, 187, 189, 190, 193, 225, 226, 227, and/or 228.
In some embodiments, an HA polypeptide variant, and particularly an H1 variant has one or more of the following sets of amino acid substitutions:
Ile219Lys
Ser186Pro, Ala189Thr, Glu227Ala
Ser186Pro, Ala189Thr
Ser186Pro, Glu227Ala
Ala189Thr, Glu227Ala
Ile219Lys, Ser186Pro, Ala189Thr, Glu227Ala
Ile219Lys, Ser186Pro, Ala189Thr
Ile219Lys, Ser186Pro
Ile219Lys, Ser186Pro, Glu227Ala
Ile219Lys, Glu227Ala
Ile219Lys, Ala189Thr, Glu227Ala
Ile219Lys, Glu227Ala
Lys145Ser or Lys145Asn
Lys145Ser or Lys145Asn, Ser186Pro, Ala189Thr, Glu227Ala
Lys145Ser or Lys145Asn, Ile219Lys
Asp225Asn, Ile219Lys
Asp225Asn, Ser186Pro, Ala189Thr, Glu227Ala
Asp225Gly, Ile219Lys
Asp225Gly, Ser186Pro, Ala189Thr, Glu227Ala
Asp225Glu, Ile219Lys
Asp225Glu, Ser186Pro, Ala189Thr, Glu227Ala
In some such embodiments, an HA polypeptide has at least one further substitution as compared with a wild type HA, such that affinity and/or specificity of the variant for umbrella glycans is increased. In other words, an HA polypeptide may comprise one or more of any of the sets of amino acid substitutions listed in this paragraph and one or more additional amino acid substitutions. To give but a few specific examples, an HA polypeptide may comprise one or more of any of the sets of amino acid substitutions listed in this paragraph and one or more additional amino acid substitutions, e.g., at positions 98, 136, 137, 138, 145, 153, 155, 156, 159, 183, 186, 187, 189, 190, 192, 193, 194, 195, 196, 215, 219, 222, 225, 226, 227, and 228, and/or combinations thereof.
In some embodiments, an HA polypeptide has at least one addition at and/or deletion of any of the amino acid positions and/or sets of amino acid positions described in this section.
In some embodiments, HA polypeptides (including HA polypeptide variants) have sequences that include S145, N145, L219, P186, T189, and/or A227. In some embodiments, HA polypeptides (including HA polypeptide variants) have sequences that include D190, D225, L226, and/or S228. In some embodiments, HA polypeptides have sequences that include D190 and D225; in some embodiments, HA polypeptides have sequences that include L226 and S228.
In some embodiments, HA polypeptide variants have an open binding site as compared with a parent HA, and particularly with a parent wild type HAs.
Portions and/or Fragments of HA Polypeptides
The present invention provides characteristic portions of HA polypeptides and nucleic acids that encode them. In general, a characteristic portion is one that contains a continuous stretch of amino acids, or a collection of continuous stretches of amino acids, that together are characteristic of the HA polypeptide. Each such continuous stretch generally will contain at least two amino acids. Furthermore, those of ordinary skill in the art will appreciate that typically at least 5, 10, 15, 20 or more amino acids are required to be characteristic of a H5 HA polypeptide. In general, a characteristic portion is one that, in addition to the sequence identity specified above, shares at least one functional characteristic with the relevant intact HA polypeptide. In some embodiments, characteristic portions of HA polypeptides share glycan binding characteristics with the relevant full-length HA polypeptides.
Any of the portions and/or fragments described herein can be variant HA polypeptide portions and/or fragments, as described in the section above entitled “Variant HA Polypeptides.”
In some embodiments, an HA polypeptide fragment and/or characteristic portion of an HA polypeptide corresponds to a contiguous stretch of about 10, about 20, about 30, about 40, about 50, about 100, about 150, about 200, about 250, about 300, about 350, about 400, about 450, about 500, or about 550 amino acids of a cognate wild type parent HA. In some embodiments, such a contiguous stretch is present within the context of non-HA polypeptide sequence at the 5′ end, at the 3′ end, or at both the 5′ and 3′ ends of the contiguous stretch. In some embodiments, the non-HA polypeptide sequence is about 1 amino acid, about 2 amino acids, about 3 amino acids, about 4 amino acids, about 5 amino acids, about 6 amino acids, about 7 amino acids, about 8 amino acids, about 9 amino acids, about 10 amino acids, about 15 amino acids, about 20 amino acids, about 25 amino acids, about 50 amino acids, about 75 amino acids, about 100 amino acids, about 250 amino acids, about 500 amino acids, about 750 amino acids, about 1000 amino acids, about 2000 amino acids, about 3000 amino acids, about 4000 amino acids, about 5000 amino acids, about 6000 amino acids, about 7000 amino acids, about 8000 amino acids, about 9000 amino acids, about 10,000 amino acids, or more than about 10,000 amino acids in length.
In some embodiments, two or more HA polypeptides, fragments thereof, and/or characteristic portions thereof (e.g., each of which corresponds to a contiguous stretch of about 10, about 20, about 30, about 40, about 50, about 100, about 150, about 200, about 250, about 300, about 350, about 400, about 450, about 500, or about 550 amino acids of a cognate wild type parent HA) are fused together in tandem. In some embodiments, tandem HA polypeptides comprise 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50, 100, or more than 100 HA polypeptides, fragments thereof, and/or characteristic portions thereof. In some embodiments, each HA polypeptide, fragment thereof, and/or characteristic portion thereof in such a tandem fusion is separated from each other fragment and/or portion by a non-HA polypeptide linker.
Non-HA Polypeptides
In some embodiments, the present invention provides polypeptides whose amino acid sequence does not include a characteristic HA sequence. Such polypeptides are referred to herein as “non-HA polypeptides.” In some embodiments, a non-HA polypeptide has an amino acid sequence selected in advance (e.g., via rational design, including for example, introduction of strategic amino acid alterations [additions, deletions, and/or substitutions] as compared with a reference sequence). In some embodiments, a non-HA polypeptide has an amino acid sequence that is determined stochastically and, for example, identified on the basis of the desirable binding characteristics defined herein. Non-HA polypeptides may be binding agents, interfering agents, etc., as described herein.
Production of Polypeptides
Polypeptides (e.g., HA polypeptides and/or non-HA polypeptides), variants thereof, fragments thereof, and/or characteristic portions thereof (and/or nucleic acids encoding any of these) may be produced by any available means.
Polypeptides (including variants, fragments, and/or characteristic portions thereof) may be produced, for example, by utilizing a host cell system engineered to express a polypeptide-encoding nucleic acid.
Any system can be used to produce polypeptides (including variants, fragments, and/or characteristic portions), such as egg, baculovirus, plant, yeast, Madin-Darby Canine Kidney cells (MDCK), or Vero (African green monkey kidney) cells. Alternatively or additionally, polypeptides (including variants, fragments, and/or characteristic portions thereof) can be expressed in cells using recombinant techniques, such as through the use of an expression vector (Sambrook et al., Molecular Cloning: A Laboratory Manual, CSHL Press, 1989; incorporated herein by reference).
Alternatively or additionally, polypeptides (including variants, fragments, and/or characteristic portions thereof) can be produced by synthetic means.
Alternatively or additionally, polypeptides (including variants, fragments, and/or characteristic portions thereof), and particularly HA polypeptides, may be produced in the context of intact virus, whether otherwise wild type, attenuated, killed, etc. Polypeptides (including variants, fragments, and/or characteristic portions thereof) may be produced in the context of virus like particles.
In some embodiments, HA polypeptides (including variants, fragments, and/or characteristic portions thereof) can be isolated and/or purified from influenza virus. For example, virus may be grown in eggs, such as embryonated hen eggs, in which case the harvested material is typically allantoic fluid. Alternatively or additionally, influenza virus may be derived from any method using tissue culture to grow the virus. Suitable cell substrates for growing the virus include, for example, dog kidney cells such as MDCK or cells from a clone of MDCK, MDCK-like cells, monkey kidney cells such as AGMK cells including Vero cells, cultured epithelial cells as continuous cell lines, 293T cells, BK-21 cells, CV-1 cells, or any other mammalian cell type suitable for the production of influenza virus for vaccine purposes, readily available from commercial sources (e.g., ATCC, Rockville, Md.). Suitable cell substrates also include human cells such as MRC-5 cells. Suitable cell substrates are not limited to cell lines; for example primary cells such as chicken embryo fibroblasts are also included.
It will be appreciated by those of ordinary skill in the art that polypeptides (including variants, fragments, and/or characteristic portions thereof) may be generated, identified, isolated, and/or produced by culturing cells or organisms that produce the polypeptide (whether alone or as part of a complex, including as part of a virus particle or virus) under conditions that allow ready screening and/or selection of polypeptides capable of binding to umbrella-topology glycans. To give but one example, in some embodiments, it may be useful to produce and/or study a collection of polypeptides (e.g., HA variant polypeptides) under conditions that reveal and/or favor those variants that bind to umbrella topology glycans (e.g., with particular specificity and/or affinity). In some embodiments, such a collection of polypeptides (e.g., HA variant polypeptides) results from evolution in nature. In some embodiments, such a collection of polypeptides (e.g., HA variant polypeptides) results from engineering. In some embodiments, such a collection of polypeptides (e.g., HA variant polypeptides) results from a combination of engineering and natural evolution.
Nucleic Acids
In certain embodiments, the present invention provides nucleic acids which encode an HA polypeptide (including a variant, fragment, and/or characteristic portion thereof). In other embodiments, the invention provides nucleic acids which are complementary to nucleic acids which encode an HA polypeptide (including a variant, fragment, and/or characteristic portion thereof).
In other embodiments, the invention provides nucleic acid molecules which hybridize to nucleic acids encoding an HA polypeptide (including a variant, fragment, and/or characteristic portion thereof). Such nucleic acids can be used, for example, as primers or as probes. To give but a few examples, such nucleic acids can be used as primers in polymerase chain reaction (PCR), as probes for hybridization (including in situ hybridization), and/or as primers for reverse transcription-PCR (RT-PCR).
In certain embodiments, nucleic acids can be DNA or RNA, and can be single stranded or double-stranded. In some embodiments, nucleic acids may include one or more non-natural nucleotides; in other embodiments, nucleic acids include only natural nucleotides.
HA Polypeptide Binding Agents
The invention provides HA polypeptide binding agents. In some embodiments, binding agents are entities that bind to one or more HA polypeptides (including variants, fragments, and/or characteristic portions thereof), as described herein. HA polypeptide binding agents may be of any chemical type. In some embodiments, binding agents are polypeptides (including, e.g., antibodies or antibody fragments). In some embodiments, such binding agents are small molecules. In some embodiments, such binding agents are nucleic acids. In some embodiments, such binding agents are aptamers. In some embodiments, binding agents are polymers; in some embodiments, HA polypeptide binding agents are non-polymeric. In some embodiments, binding agents are carbohydrates. In some embodiments, HA polypeptide binding agents are lectins.
In some embodiments, binding agents bind to H1 HA polypeptides (including variants, fragments, and/or characteristic portions thereof). In some embodiments, binding agents bind to H1 HA polypeptide variants (e.g., fragments and/or characteristic portions thereof) having enhanced human binding and/or infectivity. In some embodiments, an HA polypeptide binding agent binds to an H1 HA polypeptide variant with a greater affinity than it binds to a cognate parent H1 HA polypeptide. In some embodiments, an HA polypeptide binding agent binds to an H1 HA polypeptide enhanced human binding variant with a 2-fold, 3-fold, 4-fold, 5-fold, 10-fold, 15-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than it binds to a cognate parent H1 HA polypeptide. In some embodiments, an HA polypeptide binding agent binds to an influenza virus expressing an H1 HA polypeptide enhanced human binding variant with a 2-fold, 3-fold, 4-fold, 5-fold, 10-fold, 15-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than it binds to an influenza virus expressing its cognate parent HA polypeptide.
In some embodiments, HA polypeptide binding agents are entities that mimic the structure and/or three-dimensional characteristics of umbrella-topology glycans. In some embodiments, such binding agents are or comprise umbrella-topology glycans. In some embodiments, such binding agents are entities that more closely resemble umbrella-topology glycans than they resemble cone-topology glycans.
In some embodiments, when a binding agent binds to an HA polypeptide (and/or to variants, fragments, and/or characteristic portions thereof), the HA polypeptide is blocked from binding to HA receptors. Thus, in some embodiments, an HA polypeptide binding agent may also function as an “interfering agent,” as described in the section below entitled “HA Polypeptide Interfering Agents.”
In some embodiments, an HA polypeptide binding agent preferentially binds to a particular HA polypeptide (e.g., variants, fragments, and/or characteristic portions thereof). For example, in some embodiments, a binding agent preferentially binds to H1 HA polypeptides as compared with non-H1 HA polypeptides. In some embodiments, a binding agent binds to an H1 HA polypeptide with a 2-fold, 3-fold, 4-fold, 5-fold, 10-fold, 15-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than it binds to a non-H1 HA polypeptide. In some embodiments, a binding agent binds to an H1 HA polypeptide having one or more of the following mutations: Lys145Ser, Lys145Asn, Ile219Lys, Ser186Pro, Ala189Thr, and/or Glu227Ala with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than it binds to an H1 HA polypeptide not having one or more of those mutations. In some embodiments, a binding agent binds to an H1 HA polypeptide having a Ile219Lys mutation with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than it binds to an H1 HA polypeptide not having that mutation. In some embodiments, a binding agent binds to an H1 HA polypeptide having Ser186Pro, Ala189Thr, and Glu227Ala mutations with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than it binds to an H1 HA polypeptide not having those mutations. In some embodiments, a binding agent binds to an H1 HA polypeptide having Lys145Ser or Lys145Asn mutations with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than it binds to an H1 HA polypeptide not having those mutations. In some embodiments, a binding agent binds to an H1 HA polypeptide having Lys145Ser/Lys145Asn, Ser186Pro, Ala189Thr, and Glu227Ala mutations with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than it binds to an H1 HA polypeptide not having those mutations. In some embodiments, a binding agent binds to an H1 HA polypeptide having Lys145Ser/Lys145Asn and Ile219Lys mutations with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than it binds to an H1 HA polypeptide not having those mutations.
In some embodiments, a binding agent binds to an influenza virus expressing an H1 HA polypeptide with a 2-fold, 3-fold, 4-fold, 5-fold, 10-fold, 15-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than it binds to an influenza virus expressing a non-H1 HA polypeptide. In some embodiments, a binding agent binds to influenza virus expressing an H1 HA polypeptide having one or more of the following mutations: Ile219Lys, Ser186Pro, Ala189Thr, and/or Glu227Ala with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than it binds to influenza virus expressing an H1 HA polypeptide not having one or more of those mutations. In some embodiments, a binding agent binds to influenza virus expressing an H1 HA polypeptide having a Ile219Lys mutation with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than it binds to influenza virus expressing an H1 HA polypeptide not having that mutation. In some embodiments, a binding agent binds to influenza virus expressing an H1 HA polypeptide having Ser186Pro, Ala189Thr, and Glu227Ala mutations with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than it binds to influenza virus expressing an H1 HA polypeptide not having those mutations. In some embodiments, a binding agent binds to influenza virus expressing an H1 HA polypeptide having Lys145Ser or Lys145Asn mutations with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than it binds to influenza virus expressing an H1 HA polypeptide not having those mutations. In some embodiments, a binding agent binds to influenza virus expressing an H1 HA polypeptide having Lys145Ser/Lys145Asn, Ser186Pro, Ala189Thr, and Glu227Ala mutations with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than it binds to influenza virus expressing an H1 HA polypeptide not having those mutations. In some embodiments, a binding agent binds to influenza virus expressing an H1 HA polypeptide having Lys145Ser/Lys145Asn and Ile219Lys mutations with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than it binds to influenza virus expressing an H1 HA polypeptide not having those mutations.
In some embodiments, when administered to a subject, binding agents bind to at least about 10%, about 15%, about 20%, about 25%, about 30% about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or more of the HA polypeptides present with the subject (e.g., present within a subject's blood, mucosal tissues, etc.).
In certain embodiments, binding affinity of binding agents to HA polypeptides is assessed over a range of concentrations. Such a strategy provides significantly more information, particularly in multivalent binding assays, than do single-concentration analyses. In some embodiments, for example, binding affinities of binding agents are assessed over concentrations ranging over at least 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, or more than 10-fold.
In some embodiments, binding agents that preferentially bind to H1 HA polypeptides (e.g., variants, fragments, and/or characteristic portions thereof) are useful for various diagnostic and/or surveillance methods, including but not limited to those described in the section below called “Detection of H1-Containing Influenzas”
HA Polypeptide Interfering Agents
The present invention provides interfering agents. In some embodiments, interfering agents are entities that bind to designated targets (e.g., to a particular HA polypeptide and/or to particular glycans, such as umbrella-topology glycans) as described herein. Interfering agents may be of any chemical type. In some embodiments, interfering agents are polypeptides (including, e.g., antibodies or antibody fragments); in some such embodiments, interfering agents are HA polypeptides; in other embodiments, interfering agents are polypeptides whose amino acid sequence does not include an HA characteristic sequence (i.e., “non-HA polypeptides”). In some embodiments, interfering agents are small molecules. In some embodiments, interfering agents are nucleic acids. In some embodiments, interfering agents are aptamers. In some embodiments, interfering agents are polymers; in some embodiments, interfering agents are non-polymeric. In some embodiments, interfering agents are carbohydrates. In some embodiments, interfering agents are lectins.
In some embodiments, interfering agents as described herein bind to one or more HA polypeptides (and/or to variants, fragments, and/or characteristic portions thereof). In some embodiments, interfering agents bind to H1 HA polypeptides. In some embodiments, interfering agents bind to H1 HA polypeptide variants having enhanced human binding and/or infectivity.
In some embodiments, interfering agents compete with umbrella-topology glycans (e.g., on HA receptors) for binding to HA polypeptides (e.g., H1 HA polypeptides), including variants, fragments, and/or characteristic portions thereof). In some embodiments, interfering agents bind to HA polypeptides with a greater affinity than umbrella topology glycans bind to HA polypeptides. In some embodiments, interfering agents bind to HA polypeptides with a 2-fold, 3-fold, 4-fold, 5-fold, 10-fold, 15-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than umbrella topology glycans bind to HA polypeptides.
In some embodiments, interfering agents as described herein bind to sialylated glycans having an umbrella-like topology (e.g., on HA receptors). In certain embodiments, interfering agents bind to umbrella-topology glycans with high affinity and/or specificity. In some embodiments, interfering agents show a binding preference for umbrella-topology glycans as compared with cone-topology glycans. In some embodiments, interfering agents compete with HA for binding to glycans on HA receptors. In some embodiments, interfering agents compete with HA for binding to umbrella-topology glycans. In some embodiments, an interfering agent provided herein is an umbrella topology blocking agent. In some embodiments, an interfering agent provided herein is an umbrella topology specific blocking agent. In some embodiments, interfering agents bind to umbrella topology glycan mimics.
In some embodiments, interfering agents compete with HA polypeptides (and/or to variants, fragments, and/or characteristic portions thereof) for binding to umbrella topology glycans (e.g., on HA receptors). In some embodiments, interfering agents bind to umbrella topology glycans with a greater affinity than HA polypeptides bind to umbrella topology glycans. In some embodiments, interfering agents bind to umbrella topology glycans with a 2-fold, 3-fold, 4-fold, 5-fold, 10-fold, 15-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than HA polypeptides bind to umbrella topology glycans.
In certain embodiments, binding affinity of interfering agents is assessed over a range of concentrations. Such a strategy provides significantly more information, particularly in multivalent binding assays, than do single-concentration analyses. In some embodiments, for example, binding affinities of interfering agents are assessed over concentrations ranging over at least 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, or more than 10-fold.
In some embodiments, binding of an interfering agent to a target interferes with the ability of an HA polypeptide to bind to an HA receptor. In some embodiments, binding of an interfering agent to a target results in about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, about 95%, about 98%, about 99%, or about 100% reduction in binding of an HA polypeptide to bind to an HA receptor. In some embodiments, interfering agents are useful for treatment and/or prevention of influenza infection, for example, because they block the ability of an HA polypeptide to bind to an HA receptor.
Some particular types of interfering agents are discussed in more detail below.
Interfering Agents that Bind to Glycans
In some embodiments, interfering agents (e.g., HA polypeptides, LSBAs, UTBAs, UTSBAs, etc.) bind to umbrella glycans (and/or to umbrella topology glycan mimics), such as those present on HA receptors. In certain embodiments, interfering agents bind to umbrella topology glycans (and/or to umbrella topology glycan mimics) with high affinity. In some embodiments, interfering agents bind to umbrella topology glycans with greater affinity than they bind to cone topology glycans. In certain embodiments, interfering agents bind to a plurality of different umbrella topology glycans, often with high affinity and/or specificity.
In some embodiments, interfering agents bind to umbrella topology glycans (e.g., long α2-6 sialylated glycans such as, for example, Neu5Acα2-6Galβ1-4GlcNAcβ1-3Galβ1-4GlcNAc-) with high affinity. For example, in some embodiments, interfering agents bind to umbrella topology glycans with an affinity comparable to that observed for a wild type HA that mediates infection of a humans (e.g., H1N1 HA or H3N2 HA). In some embodiments, interfering agents bind to umbrella topology glycans with an affinity that is at least 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% of that observed under comparable conditions for a wild type HA that mediates infection of humans. In some embodiments, interfering agents bind to umbrella glycans with an affinity that is greater than that observed under comparable conditions for a wild type HA that mediates infection of humans. In some embodiments, exemplary interfering agents include LSBAs, UTBAs, and/or UTSBAs.
In certain embodiments, interfering agents show high affinity if they show a saturating signal in a multivalent glycan array binding assay such as those described herein. In some embodiments, interfering agents show high affinity if they show a signal above about 400000 or more (e.g., above about 500000, 600000, 700000, 800000, etc.) in such studies. In some embodiments, interfering agents as described herein show saturating binding to umbrella glycans over a concentration range of at least 2 fold, 3 fold, 4 fold, 5 fold or more, and in some embodiments over a concentration range as large as 10 fold or more.
Furthermore, in some embodiments, interfering agents bind to umbrella topology glycans (and/or to umbrella topology glycan mimics) more strongly than they bind to cone topology glycans. In some embodiments, interfering agents bind to umbrella topology glycans with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than they bind to cone topology glycans.
In some embodiments, interfering agents bind to α2-6 sialylated glycans; in some embodiments, interfering agents bind preferentially to α2-6 sialylated glycans. In certain embodiments, interfering agents bind to a plurality of different α2-6 sialylated glycans. In some embodiments, interfering agents are not able to bind to α2-3 sialylated glycans, and in other embodiments interfering agents are able to bind to α2-3 sialylated glycans.
In some embodiments, interfering agents bind to receptors found on human upper respiratory epithelial cells. In certain embodiments, interfering agents bind to HA receptors in the bronchus and/or trachea. In some embodiments, interfering agents are not able to bind receptors in the deep lung, and in other embodiments, interfering agents are able to bind receptors in the deep lung.
In some embodiments, interfering agents bind to at least about 10%, about 15%, about 20%, about 25%, about 30% about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or more of the glycans found on HA receptors in human upper respiratory tract tissues (e.g., epithelial cells).
In some embodiments, interfering agents bind to one or more of the glycans illustrated in FIG. 8. In some embodiments, interfering agents bind to multiple glycans illustrated in FIG. 8. In some embodiments, interfering agents bind with high affinity and/or specificity to glycans illustrated in FIG. 8. In some embodiments, interfering agents bind to glycans illustrated in FIG. 8 preferentially as compared with their binding to glycans illustrated in FIG. 7. In some embodiments, interfering agents bind to an oligosaccharide of the following form:
Neu5Acα2-6Sug1-Sug2-Sug3
where:

    1. Neu5Ac α2-6 is always or almost always at the non-reducing end;
    2. Sug1:
    
        a. is a hexose (frequently Gal or Glc) or hexosamine (GlcNAc or GalNAc) in α or β configuration (frequently β- for N- and O-linked extension and α- in the case of GalNAcα- that is O-linked to glycoprotein);
        b. no sugars other than Neu5Acα2-6 should be attached to any of the non-reducing positions of Sug1 (except when Sug1 is GalNAcα- that is O-linked to the glycoprotein); and/or
        c. non-sugar moieties such as sulfate, phosphate, guanidium, amine, N-acetyl, etc. can be attached to non-reducing positions (typically 6 position) of Sug1 to improve contacts with HA;
    
    
    3. Sug2 and/or Sug3:
    
        a. hexose (frequently Gal or Glc) or hexosamine (GlcNAc or GalNAc) in α or β configuration (frequently β); and/or
        b. sugars (such as Fuc) or non-sugar moieties such as sulfate, phosphate, guanidium, amine, N-acetyl, etc. can be attached to non-reducing positions of Sug2, Sug3, and/or Sug4;
    
    
    4. Linkage between any two sugars in the oligosaccharide apart from Neu5Acα2-6 linkage can be 1-2, 1-3, 1-4, and/or 1-6 (typically 1-3 or 1-4); and/or
    5. Structure where Neu5Acα2-6 is linked GalNAcα that is O-linked to the glycoprotein and additional sugars are linked to the non-reducing end of GalNAcα for example
    
        i. Neu5Acα2-6(Neu5Acα2-3Galβ1-3)GalNAcα-
        ii. Neu5Acα2-6(Galβ1-3)GalNAcα-
    
    


The present invention provides interfering agents with designated binding specificity, and also provides interfering agents with designated binding characteristics with respect to umbrella glycans.
HA Receptors
In some embodiments, interfering agents are entities that are or comprise HA receptors (e.g., fragments and/or characteristic portions thereof). HA interacts with cell surfaces by binding to a glycoprotein receptor. Binding of HA (e.g., H1 HA polypeptides and/or variants, fragments, and/or characteristic portions thereof) to HA receptors is predominantly mediated by N-linked glycans on the HA receptors. Specifically, HA on the surface of flu virus particles recognizes sialylated glycans that are associated with HA receptors on the surface of the cellular host. After recognition and binding, the host cell engulfs the viral cell and the virus is able to replicate and produce many more virus particles to be distributed to neighboring cells. Some crystal structures of exemplary HA-glycan interactions have been identified and are presented in Table 3:







TABLE 3







Crystal Structures of HA-Glycan Complexes









Abbreviation (PDB ID)
Virus Strain
Glycan (with assigned coordinates)





ASI30_H1_23 (1RV0)
A/Swine/Iowa/30 (H1N1)
Neu5Ac


ASI30_H1_26 (1RVT)
A/Swine/Iowa/30 (H1N1)
Neu5Acα6Galβ4GlcNAcβ3Galβ4Glc


APR34_H1_23 (1RVX)
A/Puerto Rico/8/34 (H1N1)
Neu5Acα3Galβ4GlcNAc


APR34_H1_26 (1RVZ)
A/Puerto Rico/8/34 (H1N1)
Neu5Acα6Galβ4GlcNAc


ADU63_H3_23 (1MQM)
A/Duck/Ukraine/1/63 (H3N8)
Neu5Acα3Gal


ADU63_H3_26 (1MQN)
A/Duck/Ukraine/1/63 (H3N8)
Neu5Acα6Gal


AAI68_H3_23 (1HGG)
A/Aichi/2/68 (H3N2)
Neu5Acα3Galβ4Glc


ADS97_H5_23 (1JSN)
A/Duck/Singapore/3/97 (H5N3)
Neu5Acα3Galβ3GlcNAc


ADS97_H5_26(1JSO)
A/Duck/Singapore/3/97 (H5N3)
Neu5Ac


Viet04_H5 (2FK0)
A/Vietnam/1203/2004 (H5N1)





HA - α2-6 sialylated glycan complexes were generated by superimposition of the CA trace of the HA1 subunit of ADU63_H3 and ADS97_H5 and Viet04_H5 on ASI30_H1_26 and APR34_H1_26 (H1). Although the structural complexes of the human A/Aichi/2/68 (H3N2) with α2-6 sialylated glycans are published (Eisen et al., 1997, Virology, 232: 19), their coordinates were not available in the Protein Data Bank. The SARF2 (http://123d.ncifcrf.gov/sarf2.html) program was used to obtain the structural alignment of the different HA1 subunits for superimposition.






HA receptors are modified by either α2-3 or α2-6 sialylated glycans near the receptor's HA-binding site, and the type of linkage of the receptor-bound glycan can affect the conformation of the receptor's HA-binding site, thus affecting the receptor's specificity for different HAs.
For example, the glycan binding pocket of avian HA is narrow. According to the present invention, this pocket binds to the trans conformation of α2-3 sialylated glycans, and/or to cone-topology glycans, whether α2-3 or α2-6 linked.
HA receptors in avian tissues, and also in human deep lung and gastrointestinal (GI) tract tissues are characterized by α2-3 sialylated glycan linkages, and furthermore (according to the present invention), are characterized by glycans, including α2-3 sialylated and/or α2-6 sialylated glycans, which predominantly adopt cone topologies. HA receptors having such cone-topology glycans may be referred to herein as CTHArs.
By contrast, human HA receptors in the bronchus and trachea of the upper respiratory tract are modified by α2-6 sialylated glycans. Unlike the α2-3 motif, the α2-6 motif has an additional degree of conformational freedom due to the C6-C5 bond (Russell et al., Glycoconj J 23:85, 2006; incorporated herein by reference). HAs that bind to such α2-6 sialylated glycans have a more open binding pocket to accommodate the diversity of structures arising from this conformational freedom. Moreover, according to the present invention, HAs may need to bind to glycans (e.g., α2-6 sialylated glycans) in an umbrella topology, and particularly may need to bind to such umbrella topology glycans with strong affinity and/or specificity, in order to effectively mediate infection of human upper respiratory tract tissues. HA receptors having umbrella-topology glycans may be referred to herein as UTHArs.
As a result of these spatially restricted glycosylation profiles, humans are not usually infected by viruses containing many wild type swine HAs (e.g., swine H1). Specifically, because the portions of the human respiratory tract that are most likely to encounter virus (i.e., the trachea and bronchi) lack receptors with cone glycans (e.g., α2-3 sialylated glycans, and/or short glycans) and wild type swine HAs typically bind primarily or exclusively to receptors associated with cone glycans (e.g., α2-3 sialylated glycans, and/or short glycans), humans rarely become infected with swine viruses. Only when in sufficiently close contact with virus that it can access the deep lung and/or gastrointestinal tract receptors having umbrella glycans (e.g., long α2-6 sialylated glycans) do humans become infected.
Lectins
In some embodiments, binding agents provided in accordance with the present invention are lectins. Lectins are sugar-binding proteins which may bind to a soluble carbohydrate or to a carbohydrate moiety which is a part of a glycoconjugate (e.g., a glycopeptide or glycolipid). Lectins typically agglutinate certain animal cells and/or precipitate glycoconjugates by recognizing a particular sugar moiety. For example, SNA-1 is a lectin that has a high affinity for α2-6 sialic acids. As yet another example, polyporus squamosus lectins (PSL1a and PSL1b) have high affinity for binding sialylated glycoconjugates containing Neu5Acα-2,6Galβ1,4Glc/GlcNAc trisaccharide sequences of asparagine-linked glycoproteins. Non-limiting exemplary lectins that may act as binding agents include SNA-1, SNA-1′, PSL1a, PSL1b, and polypeptides derived therefrom.
Amino acid sequences of exemplary lectins are provided below:








Sambucus Nigra Lectin 1 (Genbank Accession No. U27122):









(SEQ ID NO: 51)









MRLVAKLLYLAVLAICGLGIHGALTHPRVTPPVYPSVSFNLTGADTYEPFLRALQEKVIL



 


GNHTAFDLPVLNPESQVSDSNRFVLVPLTNPSGDTVTLAIDVVNLYVVAFSSNGKSYFFS


 


GSTAVQRDNLFVDTTQEELNFTGNYTSLERQVGFGRVYIPLGPKSLDQAISSLRTYTLTA


 


GDTKPLARGLLVVIQMVSEAARFRYIELRIRTSITDASEFTPDLLMLSMENNWSSMSSEIQ


 


QAQPGGIFAGVVQLRDERNNSIEVTNFRRLFELTYIAVLLYGCAPVTSSSYSNNAIDAQII


 


KMPVFRGGEYEKVCSVVEVTRRISGWDGLCVDVRYGHYIDGNPVQLRPCGNECNQLW


 


TFRTDGTIRWLGKCLTASSSVMIYDCNTVPPEATKWVVSIDGTITNPHSGLVLTAPQAAE


 


GTALSLENNIHAARQGWTVGDVEPLVTFIVGYKQMCLRENGENNFVWLEDCVLNRVQ


 


QEWALYGDGTIRVNSNRSLCVTSEDHEPSDLIVILKCEGSGNQRWVFNTNGTISNPNAKL


 


LMDVAQRDVSLRKIILYRPTGNPNQQWITTTHPA


 


Sambucus Nigra Lectin 1′ (Genbank Accession No. U66191):








(SEQ ID NO: 52)









MKVVATILYLVVLAICGLGIHGAHPTHSAPPTVYPSVSFNLTEANSNEYRHFLQELRGKV



 


ILGSHRAFDLPVLNPESKVSDSDRFVLVRLTNPSRKKVTLAIDVVTFYVVAFAQNDRSYF


 


FSGSSEVQRENLFVDTTQEDLNFKGDYTSLEHQVGFGRVYIPLGPKSLAQSISSLSTYKSS


 


AGDNKRLARSLLVVIQMVSEAARFRYIQLRIQASITDAKEFTPDLLMLSMENKWSSMSS


 


EIQQAQPGGAFAQVVKLLDQRNHPIDVTNFRRLFQLTSVAVLLHGCPTVTKMPAYIIKM


 


PVFNGGEDEERCSVVEEVTRRIGGRDGFCAEVKNGDEKDGTPVQLSSCGEQSNQQWTF


 


STDGTIQSLGKCLTTSSSVMIYNCKVVPPESTKWVVSIDGTITNPRSGLVLTAPKAAEGTL


 


VSLEKNVHAARQGWIVGNVEPLVTFIVGYEQMCLETNPGNNDVSLGDCSVKSASKVDQ


 


KWALYGDGTIRVNNDRSLCVTSEGKSSNEPIIILKCLGWANQRWVFNTDGTISNPDSKL


 


VMHVDQNDVPLRKIILSHPSGTSNQQWIASTHPA


 


Polyporous squamosus lectin 1a (UniProt Q75WT9)








(SEQ ID NO: 53)









MSFQGHGIYYIASAYVANTRLALSEDSSANKSPDVIISSDAVDPLNNLWLIEPVGEADTY



 


TVRNAFAGSYMDLAGHAATDGTAIIGYRPTGGDNQKWIISQINDVWKIKSKETGTFVTL


 


LNGDGGGTGTVVGWQNITNNTSQNWTFQKLSQTGANVHATLLACPALRQDFKSYLSD


 


GLYLVLTRDQISSIWQASGLGSTPWRSEIFDCDDFATVFKGAVAKWGNENFKANGFALL


 


CGLMFGSKSSGAHAYNWFVERGNFSTVTFFEPQNGTYSANAWDYKAYFGLF


 


Polyporous squamosus lectin 1b (UniProt Q75WT8)








(SEQ ID NO: 54)









MSFEGHGIYHIPHAHVANIRMALANRGSGQNGTPVIAWDSNNDAFDHMWLVEPTGEA



 


DTYTIHNVSTGTYMDVTASAVADNTPIIGYQRTGNDNQKWIIRQVQTDGGDRPWKIQC


 


KATGTFATLYSGGGSGTAIVGWRLVNSNGNQDWVFQKLSQTSVNVHATLLACGATVG


 


QDFKNYLYDGLYLVLPRDRISAIWKASGLGETARRDGIYDSDEFAMTFKSAAATWGKE


 


NFKADGFAILCGMMFGTKASTNRHAYNWVVERGSFSTVTFFEPQNGTYSDDAWGYKA


 


YFGLF






Interfering Agents that Bind to HA Polypeptides
In some embodiments, interfering agents are entities that bind to HA polypeptides (and/or to variants, fragments, and/or characteristic portions thereof), such as any of the HA polypeptides described herein. In some embodiments, interfering agents are entities that bind to H1 HA polypeptides (and/or to variants, fragments, and/or characteristic portions thereof). In some embodiments, interfering agents bind to H1 HA polypeptides with greater affinity than they bind to non-H1 HA polypeptides. In some embodiments, interfering agents bind to H1 HA polypeptides with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than they bind to non-H1 HA polypeptides. In some embodiments, interfering agents bind to H1 HA polypeptides having one or more of the following mutations: Ile219Lys, Ser186Pro, Ala189Thr, and/or Glu227Ala with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than they bind to H1 HA polypeptides not having one or more of those mutations. In some embodiments, interfering agents bind to H1 HA polypeptides having a Ile219Lys mutation with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than they bind to H1 HA polypeptides not having that mutation. In some embodiments, interfering agents bind to H1 HA polypeptides having Ser186Pro, Ala189Thr, and Glu227Ala mutations with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than they bind to H1 HA polypeptides not having those mutations. In some embodiments, interfering agents bind to H1 HA polypeptides having Lys145Ser or Lys145Asn mutations with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than they bind to H1 HA polypeptides not having those mutations. In some embodiments, interfering agents bind to H1 HA polypeptides having Lys145Ser/Lys145Asn, Ser186Pro, Ala189Thr, and Glu227Ala mutations with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than they bind to H1 HA polypeptides not having those mutations. In some embodiments, interfering agents bind to H1 HA polypeptides having Lys145Ser/Lys145Asn and Ile219Lys mutations with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than they bind to H1 HA polypeptides not having those mutations.
In some embodiments, an interfering agent binds to influenza virus expressing an H1 HA polypeptide with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than it binds to an influenza virus expressing a non-H1 HA polypeptide. In some embodiments, interfering agents bind to influenza virus expressing H1 HA polypeptides having one or more of the following mutations: Ile219Lys, Ser186Pro, Ala189Thr, and/or Glu227Ala with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than they bind to influenza virus expressing H1 HA polypeptides not having one or more of those mutations. In some embodiments, interfering agents bind to influenza virus expressing H1 HA polypeptides having a Ile219Lys mutation with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than they bind to influenza virus expressing H1 HA polypeptides not having that mutation. In some embodiments, interfering agents bind to influenza virus expressing H1 HA polypeptides having Ser186Pro, Ala189Thr, and Glu227Ala mutations with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than they bind to influenza virus expressing H1 HA polypeptides not having those mutations. In some embodiments, interfering agents bind to influenza virus expressing H1 HA polypeptides having Lys145Ser or Lys145Asn mutations with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than they bind to influenza virus expressing H1 HA polypeptides not having those mutations. In some embodiments, interfering agents bind to influenza virus expressing H1 HA polypeptides having Lys145Ser/Lys145Asn, Ser186Pro, Ala189Thr, and Glu227Ala mutations with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than they bind to influenza virus expressing H1 HA polypeptides not having those mutations. In some embodiments, interfering agents bind to influenza virus expressing H1 HA polypeptides having Lys145Ser/Lys145Asn and Ile219Lys mutations with a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold, or more than 1000-fold greater affinity than they bind to influenza virus expressing H1 HA polypeptides not having those mutations.
Interfering agents having one or more of the binding preferences described herein may be useful as therapeutic agents for treatment and/or prevention of influenza, e.g., H1 HA influenza. In some embodiments, interfering agents having one or more of the binding preferences described herein may be useful as therapeutic agents for treatment and/or prevention of influenza expressing H1 HA polypeptides having one or more of Lys145Ser, Lys145Asn, Ile219Lys, Ser186Pro, Ala189Thr, and/or Glu227Ala mutations. In some embodiments, interfering agents having one or more of the binding preferences described herein may be useful as therapeutic agents for treatment and/or prevention of influenza expressing H1 HA polypeptides having an Ile219Lys mutation. In some embodiments, interfering agents having one or more of the binding preferences described herein may be useful as therapeutic agents for treatment and/or prevention of influenza expressing H1 HA polypeptides having Ile219Lys, Ser186Pro, Ala189Thr, and Glu227Ala mutations. In some embodiments, interfering agents having one or more of the binding preferences described herein may be useful as therapeutic agents for treatment and/or prevention of influenza expressing H1 HA polypeptides having Lys145Ser or Lys145Asn mutations. In some embodiments, interfering agents having one or more of the binding preferences described herein may be useful as therapeutic agents for treatment and/or prevention of influenza expressing H1 HA polypeptides having Lys145Ser/Lys145Asn, Ser186Pro, Ala189Thr, and Glu227Ala mutations. In some embodiments, interfering agents having one or more of the binding preferences described herein may be useful as therapeutic agents for treatment and/or prevention of influenza expressing H1 HA polypeptides having Lys145Ser/Lys145Asn and Ile219Lys mutations.
In some embodiments, when administered to a subject, interfering agents bind to at least about 10%, about 15%, about 20%, about 25%, about 30% about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or more of the HA polypeptides (e.g., of the H1 polypeptides and/or of the H1 polypeptide variants with enhanced human binding and/or infectivity) present with the subject (e.g., present within a subject's blood, mucosal tissues, etc.).
Aptamers
In some embodiments, binding agents provided in accordance with the present invention are aptamers. Aptamer interfering agents can function by binding to umbrella topology glycans and/or HA polypeptides, e.g., H1 HA polypeptides (and/or to variants, fragments, and/or characteristic portions thereof).
Aptamers are macromolecules composed of nucleic acid (e.g., RNA, DNA) that bind tightly to a specific molecular target (e.g., an umbrella topology glycan and/or an HA polypeptide, variant, fragment, and/or characteristic portion thereof). A particular aptamer may be described by a linear nucleotide sequence and is typically about 15-60 nucleotides in length. Without wishing to be bound by any theory, it is contemplated that the chain of nucleotides in an aptamer form intramolecular interactions that fold the molecule into a complex three-dimensional shape, and this three-dimensional shape allows the aptamer to bind tightly to the surface of its target molecule. Given the extraordinary diversity of molecular shapes that exist within the universe of all possible nucleotide sequences, aptamers may be obtained for a wide array of molecular targets, including proteins and small molecules. In addition to high specificity, aptamers have very high affinities for their targets (e.g., affinities in the picomolar to low nanomolar range for proteins). Aptamers are chemically stable and can be boiled or frozen without loss of activity. Because they are synthetic molecules, they are amenable to a variety of modifications, which can optimize their function for particular applications. For example, aptamers can be modified to dramatically reduce their sensitivity to degradation by enzymes in the blood for use in in vivo applications. In addition, aptamers can be modified to alter their biodistribution or plasma residence time.
Selection of aptamers that can bind umbrella topology glycans (and/or to umbrella topology glycan mimics) can be achieved through methods known in the art. For example, aptamers can be selected using the SELEX (Systematic Evolution of Ligands by Exponential Enrichment) method (Tuerk, C., and Gold, L., Science 249:505-510 (1990); incorporated herein by reference). In the SELEX method, a large library of nucleic acid molecules (e.g., 1015 different molecules) is produced and/or screened with a target molecule (e.g., an umbrella topology glycan and/or an HA polypeptide, variant, fragment, and/or characteristic portion thereof). A target molecule is allowed to incubate with the library of nucleotide sequences for a period of time. Several methods, known in the art, can then be used to physically isolate the aptamer target molecules from the unbound molecules in the mixture, which can be discarded. Aptamers with the highest affinity for the target molecule can then be purified away from the target molecule and amplified enzymatically to produce a new library of molecules that is substantially enriched for aptamers that can bind the target molecule. The enriched library can then be used to initiate a new cycle of selection, partitioning, and amplification. After 5-15 cycles of this iterative selection, partitioning and amplification process, the library is reduced to a small number of aptamers that bind tightly to the target molecule. Individual molecules in the mixture can then be isolated, their nucleotide sequences determined, and their properties with respect to binding affinity and specificity measured and compared. Isolated aptamers can then be further refined to eliminate any nucleotides that do not contribute to target binding and/or aptamer structure, thereby producing aptamers truncated to their core binding domain. See Jayasena, S. D. Clin. Chem. 45:1628-1650 (1999) for review of aptamer technology; the entire teachings of which are incorporated herein by reference.
Antibodies
In some embodiments, interfering agents are antibodies that recognize umbrella-topology glycans and/or HA polypeptides, e.g., H1 HA polypeptides (and/or to variants, fragments, and/or characteristic portions thereof).
Antibodies may be monoclonal or polyclonal and may be prepared by any of a variety of techniques known to those of ordinary skill in the art (e.g., see Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988; incorporated herein by reference). For example, antibodies can be produced by cell culture techniques, including the generation of monoclonal antibodies, or via transfection of antibody genes into suitable bacterial or mammalian cell hosts, in order to allow for the production of recombinant antibodies.
Antibodies suitable for the invention include antibodies or fragments of antibodies that bind immunospecifically to any umbrella topology glycan epitope. As used herein, the term “antibodies” is intended to include immunoglobulins and fragments thereof which are specifically reactive to the designated protein or peptide, or fragments thereof. Suitable antibodies include, but are not limited to, human antibodies, primatized antibodies, chimeric antibodies, bi-specific antibodies, humanized antibodies, conjugated antibodies (i.e., antibodies conjugated or fused to other proteins, radiolabels, cytotoxins), Small Modular ImmunoPharmaceuticals (“SMIPsTM”), single chain antibodies, cameloid antibodies, and antibody fragments. As used herein, the term “antibodies” also includes intact monoclonal antibodies, polyclonal antibodies, single domain antibodies (e.g., shark single domain antibodies (e.g., IgNAR or fragments thereof)), multispecific antibodies (e.g., bi-specific antibodies) formed from at least two intact antibodies, and antibody fragments so long as they exhibit the desired biological activity. Antibody polypeptides for use herein may be of any type (e.g., IgA, IgD, IgE, IgG, IgM).
As used herein, an “antibody fragment” includes a portion of an intact antibody, such as, for example, the antigen-binding or variable region of an antibody. Examples of antibody fragments include Fab, Fab′, F(ab′)2, and Fv fragments; triabodies; tetrabodies; linear antibodies; single-chain antibody molecules; and multi specific antibodies formed from antibody fragments. The term “antibody fragment” also includes any synthetic or genetically engineered protein that acts like an antibody by binding to a specific antigen to form a complex. For example, antibody fragments include isolated fragments, “Fv” fragments, consisting of the variable regions of the heavy and light chains, recombinant single chain polypeptide molecules in which light and heavy chain variable regions are connected by a peptide linker (“ScFv proteins”), and minimal recognition units consisting of the amino acid residues that mimic the hypervariable region.
Antibodies can be generated using methods well known in the art. For example, protocols for antibody production are described by Harlow and Lane, Antibodies: A Laboratory Manual, (1988). Typically, antibodies can be generated in mouse, rat, guinea pig, hamster, camel, llama, shark, or other appropriate host. Alternatively, antibodies may be made in chickens, producing IgY molecules (Schade et al., (1996) ALTEX 13(5):80-85; incorporated herein by reference). In some embodiments, antibodies suitable for the present invention are subhuman primate antibodies. For example, general techniques for raising therapeutically useful antibodies in baboons may be found, for example, in Goldenberg et al., international patent publication No. WO 91/11465 (1991; incorporated herein by reference), and in Losman et al., Int. J. Cancer 46: 310 (1990; incorporated herein by reference). In some embodiments, monoclonal antibodies may be prepared using hybridoma methods (Milstein and Cuello, (1983) Nature 305(5934):537-40; incorporated herein by reference). In some embodiments, monoclonal antibodies may also be made by recombinant methods (U.S. Pat. No. 4,166,452, 1979; incorporated herein by reference).
In some embodiments, antibodies suitable for the invention may include humanized or human antibodies. Humanized forms of non-human antibodies are chimeric Igs, Ig chains or fragments (such as Fv, Fab, Fab′, F(ab′)2 or other antigen-binding subsequences of Abs) that contain minimal sequence derived from non-human Ig. Generally, a humanized antibody has one or more amino acid residues introduced from a non-human source. These non-human amino acid residues are often referred to as “import” residues, which are typically taken from an “import” variable domain. Humanization is accomplished by substituting rodent complementarity determining regions (CDRs) or CDR sequences for the corresponding sequences of a human antibody (Riechmann et al., Nature 332(6162):323-7, 1988; Verhoeyen et al., Science. 239(4847):1534-6, 1988; incorporated herein by reference). Such “humanized” antibodies are chimeric Abs (U.S. Pat. No. 4,816,567, 1989; incorporated herein by reference), wherein substantially less than an intact human variable domain has been substituted by the corresponding sequence from a non-human species. In some embodiments, humanized antibodies are typically human antibodies in which some CDR residues and possibly some FR residues are substituted by residues from analogous sites in rodent Abs. Humanized antibodies include human Igs (recipient antibody) in which residues from a CDR of the recipient are replaced by residues from a CDR of a non-human species (donor antibody) such as mouse, rat or rabbit, having the desired specificity, affinity and capacity. In some instances, corresponding non-human residues replace Fv framework residues of the human Ig. Humanized antibodies may comprise residues that are found neither in the recipient antibody nor in the imported CDR or framework sequences. In general, the humanized antibody comprises substantially all of at least one, and typically two, variable domains, in which most if not all of the CDR regions correspond to those of a non-human Ig and most if not all of the FR regions are those of a human Ig consensus sequence. The humanized antibody optimally also comprises at least a portion of an Ig constant region (Fc), typically that of a human Ig (Riechmann et al., Nature 332(6162):323-7, 1988; Verhoeyen et al., Science. 239(4847):1534-6, 1988; all of which are incorporated herein by reference).
Human antibodies can also be produced using various techniques, including phage display libraries (Hoogenboom et al., Mol Immunol. (1991) 28(9):1027-37; Marks et al., J Mol Biol. (1991) 222(3):581-97; all of which are incorporated herein by reference) and the preparation of human monoclonal antibodies (Reisfeld and Sell, 1985, Cancer Surv. 4(1):271-90; incorporated herein by reference). Similarly, introducing human Ig genes into transgenic animals in which the endogenous Ig genes have been partially or completely inactivated can be exploited to synthesize human antibodies. Upon challenge, human antibody production is observed, which closely resembles that seen in humans in all respects, including gene rearrangement, assembly, and antibody repertoire (Fishwild et al., High-avidity human IgG kappa monoclonal antibodies from a novel strain of minilocus transgenic mice, Nat. Biotechnol. 1996 July; 14(7):845-51; Lonberg et al., Antigen-specific human antibodies from mice comprising four distinct genetic modifications, Nature 1994 Apr. 28; 368(6474):856-9; Lonberg and Huszar, Human antibodies from transgenic mice, Int. Rev. Immunol. 1995; 13(1):65-93; Marks et al., By-passing immunization: building high affinity human antibodies by chain shuffling. Biotechnology (N Y). 1992 July; 10(7):779-83; all of which are incorporated herein by reference).
Testing Interfering Agents in Animal Models
The present invention provides methods for testing an interfering agent (e.g., HA polypeptides, LSBAs, USBAs, UTSBAs, umbrella-topology glycans, etc.) in an animal host. As used herein, an “animal host” includes any animal model suitable for influenza research. For example, animal hosts suitable for the invention can be any mammalian hosts, including primates, ferrets, cats, dogs, cows, horses, rodents such as, mice, hamsters, rabbits, and rats. In certain embodiments, an animal host used for the invention is a ferret. In particular, in some embodiments, an animal host is naïve to viral exposure or infection prior to administration of an interfering agent (optionally in a composition). In some embodiments, the animal host is inoculated with, infected with, or otherwise exposed to virus prior to or concurrent with administration of an interfering agent. An animal host used in the practice of the present invention can be inoculated with, infected with, or otherwise exposed to virus by any method known in the art. In some embodiments, an animal host may be inoculated with, infected with, or exposed to virus intranasally.
In some embodiments, a suitable animal host may have a similar distribution of umbrella vs. cone topology glycans and/or α2-6 glycans vs. α2-3 glycans to the distribution found in the human respiratory tract. For example, it is contemplated that a ferret as an animal host may be more representative than a mouse when used as model of disease caused by influenza viruses in humans (Tumpey, et al. Science (2007) 315; 655-659; incorporated herein by reference). Without wishing to be bound any theories, the present invention encompasses the idea that ferrets may have a more similar distribution of glycans in the respiratory tract to those in the human respiratory tract than mouse does to human.
Naïve and/or inoculated animals may be used for any of a variety of studies. For example, such animal models may be used for virus transmission studies as in known in the art. It is contemplated that the use of ferrets in virus transmission studies may serve as a reliable predictor for virus transmission in humans. For example, air transmission of viral influenza from inoculated animals (e.g., ferrets) to naïve animals is known in the art (Tumpey, et al. Science (2007) 315; 655-659; incorporated herein by reference). Virus transmission studies may be used to test interfering agent polypeptides (e.g., HA polypeptides). For example, interfering agents may be administered to a suitable animal host before, during or after virus transmission studies in order to determine the efficacy of said interfering agent in blocking virus binding and/or infectivity in the animal host. Using information gathered from virus transmission studies in an animal host, one may predict the efficacy of an interfering agent in blocking virus binding and/or infectivity in a human host.
Detection of H1-Containing Influenzas
The present invention provides systems, compositions, and methods for detection of influenza. In some embodiments, the invention provides binding agents that preferentially bind to a particular HA polypeptide (and/or to variants, fragments, and/or characteristic portions thereof). For example, in some embodiments, a binding agent preferentially binds to H1 HA polypeptides as compared with non-H1 HA polypeptides, as described in further detail in the section above entitled “HA Polypeptide Binding Agents.” In some embodiments, a binding agent preferentially binds to an H1 HA polypeptide having enhanced human binding and/or infectivity as compared with a parent H1 HA polypeptide (e.g., a parent H1 HA influenza strain found on Table 1).
In some embodiments, a binding agent preferentially binds to an H1 HA polypeptide having one or more of the following mutations: Lys145Ser, Lys145Asn, Ile219Lys, Ser186Pro, Ala189Thr, and/or Glu227Ala with as compared with an H1 HA polypeptide not having one or more of those mutations. In some embodiments, a binding agent preferentially binds to an H1 HA polypeptide having an Ile219Lys mutation as compared with an H1 HA polypeptide not having that mutation. In some embodiments, a binding agent preferentially binds to an H1 HA polypeptide having Ser186Pro, Ala189Thr, and Glu227Ala mutations as compared with an H1 HA polypeptide not having those mutations. In some embodiments, a binding agent preferentially binds to an H1 HA polypeptide having Lys145Ser or Lys145Asn mutations as compared with an H1 HA polypeptide not having those mutations. In some embodiments, a binding agent preferentially binds to an H1 HA polypeptide having Lys145Ser/Lys145Asn, Ser186Pro, Ala189Thr, and Glu227Ala mutations as compared with an H1 HA polypeptide not having those mutations. In some embodiments, a binding agent preferentially binds to an H1 HA polypeptide having Lys145Ser/Lys145Asn and Ile219Lys mutations as compared with an H1 HA polypeptide not having those mutations.
In some embodiments, binding agents that preferentially bind to H1 HA polypeptides (e.g., variants, fragments, and/or characteristic portions thereof) are useful for various diagnostic and/or surveillance methods. For example, binding agents that preferentially bind to particular HA polypeptides, such as H1 HA polypeptides, (and/or to variants, fragments, and/or characteristic portions thereof) can be used in assays to determine whether a patient is infected with and/or suffering from infection with an influenza virus. In some embodiments, binding agents that preferentially bind to H1 HA polypeptides (and/or to variants, fragments, and/or characteristic portions thereof) can be used in assays to determine whether a patient is infected with and/or suffering from infection with an H1 influenza virus. In some embodiments, binding agents that preferentially bind to H1 HA polypeptides (and/or to variants, fragments, and/or characteristic portions thereof) can be used in assays to determine whether a patient is infected with and/or suffering from infection with an H1 influenza virus characterized in that the H1 polypeptide shows enhanced human binding and/or infectivity. In some embodiments, binding agents that preferentially bind to particular H1 HA polypeptides (and/or to variants, fragments and/or characteristic portions thereof) can be used to determine whether a patient is infected with and/or suffering from infection with an H1 influenza virus characterized in that its H1 polypeptide has one or more of the following mutations: Lys145Ser, Lys145Asn, Ile219Lys, Ser186Pro, Ala189Thr, and/or Glu227Ala. In some embodiments, binding agents that preferentially bind to H1 HA polypeptides (and/or to variants, fragments, and/or characteristic portions thereof) can be used in assays to determine whether a patient is infected with and/or suffering from infection with an H1 influenza virus characterized in that the H1 polypeptide has an Ile219Lys mutation. In some embodiments, binding agents that preferentially bind to H1 HA polypeptides (and/or to variants, fragments, and/or characteristic portions thereof) can be used in assays to determine whether a patient is infected with and/or suffering from infection with an H1 influenza virus characterized in that the H1 polypeptide has Ser186Pro, Ala189Thr, and/or Glu227Ala mutations. In some embodiments, binding agents that preferentially bind to H1 HA polypeptides (and/or to variants, fragments, and/or characteristic portions thereof) can be used in assays to determine whether a patient is infected with and/or suffering from infection with an H1 influenza virus characterized in that the H1 polypeptide has Lys145Ser or Lys145Asn mutations. In some embodiments, binding agents that preferentially bind to H1 HA polypeptides (and/or to variants, fragments, and/or characteristic portions thereof) can be used in assays to determine whether a patient is infected with and/or suffering from infection with an H1 influenza virus characterized in that the H1 polypeptide has Lys145Ser/Lys145Asn, Ser186Pro, Ala189Thr, and Glu227Ala mutations. In some embodiments, binding agents that preferentially bind to H1 HA polypeptides (and/or to variants, fragments, and/or characteristic portions thereof) can be used in assays to determine whether a patient is infected with and/or suffering from infection with an H1 influenza virus characterized in that the H1 polypeptide has Lys145Ser/Lys145Asn and Ile219Lys mutations.
In some embodiments, binding agents that preferentially bind to HA polypeptides, such as H1 HA polypeptides, (and/or to variants, fragments, and/or characteristic portions thereof) can be used in assays to determine whether a sample contains influenza virus. In some embodiments, binding agents that preferentially bind to H1 HA polypeptides (and/or to variants, fragments, and/or characteristic portions thereof) can be used in assays to determine whether a sample contains an H1 influenza virus. In some embodiments, binding agents that preferentially bind to H1 HA polypeptides (and/or to variants, fragments, and/or characteristic portions thereof) can be used in assays to determine whether a sample contains an H1 influenza virus characterized in that the H1 polypeptide shows enhanced human binding and/or infectivity. In some embodiments, binding agents that preferentially bind to particular H1 HA polypeptides (and/or to variants, fragments and/or characteristic portions thereof) can be used to determine whether a sample contains an H1 influenza virus characterized in that its H1 polypeptide has one or more of the following mutations: Lys145Ser, Lys145Asn, Ile219Lys, Ser186Pro, Ala189Thr, and/or Glu227Ala. In some embodiments, binding agents that preferentially bind to H1 HA polypeptides (and/or to variants, fragments, and/or characteristic portions thereof) can be used in assays to determine whether a sample contains an H1 influenza virus characterized in that the H1 polypeptide has an Ile219Lys mutation. In some embodiments, binding agents that preferentially bind to H1 HA polypeptides (and/or to variants, fragments, and/or characteristic portions thereof) can be used in assays to determine whether a sample contains an H1 influenza virus characterized in that the H1 polypeptide has Ser186Pro, Ala189Thr, and/or Glu227Ala mutations. In some embodiments, binding agents that preferentially bind to H1 HA polypeptides (and/or to variants, fragments, and/or characteristic portions thereof) can be used in assays to determine whether a sample contains an H1 influenza virus characterized in that the H1 polypeptide has Lys145Ser or Lys145Asn mutations. In some embodiments, binding agents that preferentially bind to H1 HA polypeptides (and/or to variants, fragments, and/or characteristic portions thereof) can be used in assays to determine whether a sample contains an H1 influenza virus characterized in that the H1 polypeptide has Lys145Ser/Lys145Asn, Ser186Pro, Ala189Thr, and Glu227Ala mutations. In some embodiments, binding agents that preferentially bind to H1 HA polypeptides (and/or to variants, fragments, and/or characteristic portions thereof) can be used in assays to determine whether a sample contains an H1 influenza virus characterized in that the H1 polypeptide has Lys145Ser/Lys145Asn and Ile219Lys mutations.
The present invention provides systems, compositions, and methods utilizing HA polypeptide binding agents for detecting HA polypeptides (e.g., fragments and/or characteristic portions thereof) in pathological samples, including, but not limited to, blood, serum/plasma, peripheral blood mononuclear cells/peripheral blood lymphocytes (PBMC/PBL), sputum, urine, feces, throat swabs, dermal lesion swabs, cerebrospinal fluids, cervical smears, pus samples, food matrices, and tissues from various parts of the body such as brain, spleen, and liver. The present invention also provides systems, compositions, and methods for detecting HA polypeptides in environmental samples, including, but not limited to, soil, water, and flora. Other samples that have not been listed may also be applicable.
In some embodiments, methods for detecting HA polypeptides involve providing a pathological and/or environmental sample, contacting the sample with an HA polypeptide binding agent, and determining whether the HA polypeptide binding agent binds to the sample relative to a negative control binding agent. In some embodiments, such methods involve a step of processing the sample (e.g., subjecting the sample to one or more purification steps) prior to the step of contacting. In some embodiments, provided HA polypeptide binding agents are labeled with a detectable moiety (e.g., fluorescent, radioactive, chemiluminescent label, etc.). In some embodiments, HA polypeptide binding agents are detectable via immunological methods (e.g., western blotting, ELISA, immunofluorescence, etc.). In some embodiments, HA polypeptide binding agents are immobilized (e.g., to a bead, to a microtiter dish, to an array, to a glycan array, etc.) prior to the step of contacting.
In some embodiments, HA polypeptide binding agents are or comprise umbrella topology glycans (including umbrella topology glycan mimics). In such embodiments, glycans are immobilized to glycan arrays, and the step of contacting involves incubating the glycan array with the sample.
In some embodiments, HA polypeptide binding agents are or comprise antibodies (including antibody fragments, as described herein). In such embodiments, antibodies are immobilized to beads, and the step of contacting involves performing an immunoprecipitation.
Antibodies that bind to HA polypeptides can also be used in virus neutralization tests, in which a sample is treated with antibody specific to HA polypeptides of interest, and tested for its ability to infect cultured cells relative to untreated sample. If virus in that sample contains such HA polypeptides, the antibody will neutralize the virus and prevent it from infecting the cultured cells. Alternatively or additionally, such antibodies can also be used in HA-inhibition tests, in which the HA protein is isolated from a given sample, treated with antibody specific to a particular HA polypeptide or set of HA polypeptides, and tested for its ability to agglutinate erythrocytes relative to untreated sample. If virus in the sample contains such an HA polypeptide, the antibody will neutralize the activity of the HA polypeptide and prevent it from agglutinating erythrocytes (Harlow & Lane, Antibodies: A Laboratory Manual, CSHL Press, 1988; www.who.int/csr/resources/publications/influenza/WHO_CDS_CSR_NCS—2002—5/en/index.html; www.who.int/csr/disease/avian_influenza/guidelines/labtests/en/index.html).
In some embodiments, such agents may include nucleic acids that specifically bind to nucleotides that encode particular HA polypeptides and that can be used to specifically detect such HA polypeptides by RT-PCR or in situ hybridization (www.who.int/csr/resources/publications/influenza/WHO_CDS_CSR_NCS—2002—5/en/index.html; www.who.int/csr/disease/avian_influenza/guidelines/labtests/en/index.html). In certain embodiments, nucleic acids which have been isolated from a sample are amplified prior to detection. In certain embodiments, diagnostic reagents can be detectably labeled.
Kits
The present invention provides kits containing reagents useful for carrying out therapeutic, prophylactic, and/or diagnostic methods in accordance with the invention. Kits contents include, but are not limited to, HA polypeptides, HA polypeptide binding agents, HA polypeptide interfering agents, fragments thereof, variants thereof, and/or characteristic portions thereof. Kits may include nucleic acids (e.g., expression plasmids) encoding HA polypeptides, HA polypeptide binding agents, HA polypeptide interfering agents, fragments thereof, variants thereof, and/or characteristic portions thereof. Mammalian cell lines may also be included with the kits, including but not limited to, Vero and MDCK cell lines.
In certain embodiments, kits for use in accordance with the present invention may include, a reference sample, instructions for processing samples, performing the test, instructions for interpreting the results, buffers and/or other reagents necessary for performing the test. In certain embodiments the kit can comprise a panel of antibodies.
In some embodiments of the present invention, glycan arrays, as discussed below, may be utilized as diagnostics and/or kits.
In certain embodiments, glycan arrays and/or kits are used to perform dose response studies to assess binding of HA polypeptides to umbrella glycans at multiple doses (e.g., as described herein). Such studies give particularly valuable insight into the binding characteristics of tested HA polypeptides, and are particularly useful to assess specific binding. Dose response binding studies of this type find many useful applications. To give but one example, they can be helpful in tracking the evolution of binding characteristics in a related series of HA polypeptide variants, whether the series is generated through natural evolution, intentional engineering, or a combination of the two.
In certain embodiments, glycan arrays and/or kits are used to induce, identify, and/or select binding agents (e.g., HA polypeptides, and/or HA polypeptide variants) having desired binding characteristics. For instance, in some embodiments, glycan arrays and/or kits are used to exert evolutionary (e.g., screening and/or selection) pressure on a population of polypeptide binding agents (e.g., HA polypeptides).
In some embodiments, kits comprise instructions for use.
Glycan Arrays
To rapidly expand the current knowledge of known specific glycan-glycan binding protein (GBP) interactions, the Consortium for Functional Glycomics (CFG; www.functionalglycomics.org), an international collaborative research initiative, has developed glycan arrays comprising several glycan structures that have enabled high throughput screening of GBPs for novel glycan ligand specificities. The glycan arrays comprise both monovalent and polyvalent glycan motifs (i.e., attached to polyacrylamide backbone), and each array comprises 264 glycans with low (10 μM) and high (100 μM) concentrations, and six spots for each concentration (see http://www.functionalglycomics.org/static/consortium/resources/resourcecoreh5.shtml).
Arrays predominantly comprise synthetic glycans that capture the physiological diversity of N- and O-linked glycans. In addition to the synthetic glycans, N-linked glycan mixtures derived from different mammalian glycoproteins are also represented on the array.
As used herein, a glycan “array” refers to a set of one or more glycans, optionally immobilized on a solid support. In some embodiments, an “array” is a collection of glycans present as an organized arrangement or pattern at two or more locations that are physically separated in space. Typically, a glycan array will have at least 4, 8, 16, 24, 48, 96 or several hundred or thousand discrete locations. In general, glycan arrays may have any of a variety of formats. Various different array formats applicable to biomolecules are known in the art. For example, a huge number of protein and/or nucleic acid arrays are well known. Those of ordinary skill in the art will immediately appreciate standard array formats appropriate for glycan arrays of the present invention.
In some embodiments, glycan arrays are present in “microarray” formats. A microarray may typically have sample locations separated by a distance of 50-200 microns or less and immobilized sample in the nano to micromolar range or nano to picogram range. Array formats known in the art include, for example, those in which each discrete sample location has a scale of, for example, ten microns.
In some embodiments, glycan arrays comprise a plurality of glycans spatially immobilized on a support. The present invention provides glycan molecules arrayed on a support. As used herein, “support” refers to any material which is suitable to be used to array glycan molecules. As will be appreciated by those of ordinary skill in the art, any of a wide variety of materials may be employed. To give but a few examples, support materials which may be of use in the invention include hydrophobic membranes, for example, nitrocellulose, PVDF or nylon membranes. Such membranes are well known in the art and can be obtained from, for example, Bio-Rad, Hemel Hempstead, UK.
In some embodiments, the support on which glycans are arrayed may comprise a metal oxide. Suitable metal oxides include, but are not limited to, titanium oxide, tantalum oxide, and aluminum oxide. Examples of such materials may be obtained from Sigma-Aldrich Company Ltd, Fancy Road, Poole, Dorset. BH12 4QH UK. In some embodiments, such a support is or comprises a metal oxide gel. In some embodiments, such a support is or comprises silica gels or aluminum oxide gels (examples of such materials may be obtained from, for example, Merck KGaA, Darmstadt, Germany).
In some embodiments of the invention, glycan arrays are immobilized on a support that can resist change in size or shape during normal use. For example a support may be a glass slide coated with a component material suitable to be used to array glycans. Also, some composite materials can desirable provide solidity to a support.
As demonstrated herein, arrays are useful for the identification and/or characterization of different HA polypeptides and their binding characteristics. In certain embodiments, HA polypeptides are tested on such arrays to assess their ability to bind to umbrella topology glycans (e.g., to α2-6 sialylated glycans, and particularly to long α2-6 sialylated glycans arranged in an umbrella topology).
Indeed, the present invention provides arrays of HA polypeptide binding agents that are or comprise one or more of umbrella topology glycans, mimics of umbrella topology glycans, α2-6 sialylated glycans, and α2-3 sialylated glycans, that can be used to characterize HA polypeptide binding capabilities and/or as a diagnostic to detect, for example, human-binding HA polypeptides (e.g., H1 HA polypeptides, as described above). As will be clear to those of ordinary skill in the art, such arrays are useful for characterizing or detecting any HA polypeptides, including for example, those found in natural influenza isolates in addition to those designed and/or prepared by researchers.
In some embodiments, such arrays include glycans representative of about 10%, 15%, 20%, 25%, 30% 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90% 95%, or more of the glycans (e.g., the umbrella glycans, which will often be α2-6 sialylated glycans, particularly long α2-6 sialylated glycans) found on human HA receptors, and particularly on human upper respiratory tract HA receptors. In some embodiments, arrays include some or all of the glycan structures depicted in FIGS. 5-8. In some embodiments, arrays include at least about 10%, 15%, 20%, 25%, 30% 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90% 95%, or more of these depicted glycans.
The present invention provides methods for identifying or characterizing HA proteins using glycan arrays. In some embodiments, for example, such methods comprise steps of (1) providing a sample containing HA polypeptide, (2) contacting the sample with a glycan array comprising, and (3) detecting binding of HA polypeptide to one or more glycans on the array.
Suitable sources for samples containing HA polypeptides to be contacted with glycan arrays according to the present invention include, but are not limited to, pathological samples and/or environmental samples, such as those described above.
A wide variety of detection systems suitable for assaying HA polypeptide binding to glycan arrays are known in the art. For example, HA polypeptides can be detectably labeled (directly or indirectly) prior to or after being contacted with the array; binding can then be detected by detection of localized label. In some embodiments, scanning devices can be utilized to examine particular locations on an array.
Alternatively or additionally, binding to arrayed glycans can be measured using, for example, calorimetric, fluorescence, or radioactive detection systems, or other labeling methods, or other methods that do not require labeling. In general, fluorescent detection typically involves directly probing the array with a fluorescent molecule and monitoring fluorescent signals. Alternatively or additionally, arrays can be probed with a molecule that is tagged (for example, with biotin) for indirect fluorescence detection (in this case, by testing for binding of fluorescently-labeled streptavidin). Alternatively or additionally, fluorescence quenching methods can be utilized in which the arrayed glycans are fluorescently labeled and probed with a test molecule (which may or may not be labeled with a different fluorophore). In such embodiments, binding to the array acts to squelch the fluorescence emitted from the arrayed glycan, therefore binding is detected by loss of fluorescent emission. Alternatively or additionally, arrayed glycans can be probed with a live tissue sample that has been grown in the presence of a radioactive substance, yielding a radioactively labeled probe. Binding in such embodiments can be detected by measuring radioactive emission.
Such methods are useful to determine the fact of binding and/or the extent of binding by HA polypeptides to glycan arrays. In some embodiments of the invention, such methods can further be used to identify and/or characterize agents that interfere with or otherwise alter glycan-HA polypeptide interactions.
Methods described below may be useful for identifying whether a molecule thought to be capable of interacting with a carbohydrate can actually do so, or to identify whether a molecule unexpectedly has the capability of interacting with a carbohydrate.
The present invention provides methods of using arrays, for example, to detect a particular agent in a test sample. For instance, such methods may comprise steps of (1) contacting a glycan array with a test sample (e.g., with a sample thought to contain an HA polypeptide, e.g., an H1 HA polypeptide); and, (2) detecting the binding of any agent in the test sample to the array.
Binding to arrays may be utilized, for example, to determine kinetics of interaction between binding agent and glycan. For example, methods for determining interaction kinetics may include steps of (1) contacting a glycan array with the molecule being tested; and, (2) measuring kinetics of interaction between the binding agent and arrayed glycan(s).
The kinetics of interaction of a binding agent with any of the glycans in an array can be measured by real time changes in, for example, colorimetric or fluorescent signals, as detailed above. Such methods may be of particular use in, for example, determining whether a particular binding agent is able to interact with a specific carbohydrate with a higher degree of binding than does a different binding agent interacting with the same carbohydrate.
It will be appreciated, of course, that glycan binding by HA polypeptides can be evaluated on glycan samples or sources not present in an array format per se. For example, HA polypeptides can be bound to tissue samples and/or cell lines to assess their glycan binding characteristics. Appropriate cell lines include, for example, any of a variety of mammalian cell lines, particularly those expressing HA receptors containing umbrella topology glycans (e.g., at least some of which may be α2-6 sialylated glycans, and particularly long α2-6 sialylated glycans). In some embodiments, utilized cell lines express individual glycans with umbrella topology. In some embodiments, utilized cell lines express a diversity of glycans. In some embodiments, cell lines are obtained from clinical isolates; in some they are maintained or manipulated to have a desired glycan distribution and/or prevalence. In some embodiments, tissue samples and/or cell lines express glycans characteristic of mammalian upper respiratory epithelial cells.
Treatment
The present invention provides systems, compositions, and methods to treat (e.g., alleviate, ameliorate, relieve, delay onset of, inhibit progression of, reduce severity of, and/or reduce incidence of one or more symptoms or features of) and/or prevent influenza infection. In some embodiments, interfering agents and/or binding agents such as those described herein may be used for a variety of therapeutic purposes, e.g., treating influenza infection and/or developing vaccines to immunize subjects against influenza infection.
The present invention encompasses the recognition that vaccines and/or therapeutics that successfully prevent, delay onset of, and/or treat infection with influenza strain A/South Carolina/1/1918 and/or A/Swine/Iowa/15/1930 may successfully prevent, delay onset of, and/or treat infection with influenza strain 2009 A/H1N1 (e.g., A/CA/4/2009). Vaccines and/or therapeutics that successfully prevent, delay onset of, and/or treat infection with influenza strain 2009 A/H1N1 (e.g., A/CA/4/2009) may successfully prevent, delay onset of, and/or treat infection with influenza strain A/South Carolina/1/1918 and/or A/Swine/Iowa/15/1930. Thus, in some embodiments, vaccine and/or therapeutic compositions (such as those described in the sections below) comprise one or more of influenza strains A/South Carolina/1/1918, A/Swine/Iowa/15/1930, and/or 2009 A/H1N1 (e.g., A/CA/4/2009). In some embodiments, vaccine and/or therapeutic compositions comprise influenza strains A/South Carolina/1/1918 and A/Swine/Iowa/15/1930. In some embodiments, vaccine and/or therapeutic compositions comprise influenza strains A/South Carolina/1/1918 and 2009 A/H1N1 (e.g., A/CA/4/2009). In some embodiments, vaccine and/or therapeutic compositions comprise influenza strains A/Swine/Iowa/15/1930 and 2009 A/H1N1 (e.g., A/CA/4/2009). In some embodiments, vaccine and/or therapeutic compositions comprise influenza strain A/South Carolina/1/1918. In some embodiments, vaccine and/or therapeutic compositions comprise influenza strain A/Swine/Iowa/15/1930. In some embodiments, vaccine and/or therapeutic compositions comprise influenza strain 2009 A/H1N1 (e.g., A/CA/4/2009).
In some embodiments, vaccine and/or therapeutic compositions (such as those described in the sections below) comprise one or more H1 HA polypeptides present in one or more of influenza strains A/South Carolina/1/1918, A/Swine/Iowa/15/1930, and/or 2009 A/H1N1 (e.g., A/CA/4/2009). In some embodiments, vaccine and/or therapeutic compositions comprise H1 HA polypeptides present in influenza strains A/South Carolina/1/1918 and A/Swine/Iowa/15/1930. In some embodiments, vaccine and/or therapeutic compositions comprise H1 HA polypeptides present in influenza strains A/South Carolina/1/1918 and 2009 A/H1N1 (e.g., A/CA/4/2009). In some embodiments, vaccine and/or therapeutic compositions comprise H1 HA polypeptides present in influenza strains A/Swine/Iowa/15/1930 and 2009 A/H1N1 (e.g., A/CA/4/2009). In some embodiments, vaccine and/or therapeutic compositions comprise H1 HA polypeptides present in influenza strain A/South Carolina/1/1918. In some embodiments, vaccine and/or therapeutic compositions comprise H1 HA polypeptides present in influenza strain A/Swine/Iowa/15/1930. In some embodiments, vaccine and/or therapeutic compositions comprise H1 HA polypeptides present in influenza strain 2009 A/H1N1 (e.g., A/CA/4/2009).
In some embodiments, methods of vaccination and/or treatment (such as those described in the sections below) involve stratification of a patient population based on prior exposure to influenza strains A/South Carolina/1/1918 and/or A/Swine/Iowa/15/1930. Such methods involve steps of determining whether a patient has been previously exposed to one or both of influenza strains A/South Carolina/1/1918 and/or A/Swine/Iowa/15/1930. Any of a variety of methods can be used to determine whether an individual has been previously exposed to one or both of influenza strains A/South Carolina/1/1918 and/or A/Swine/Iowa/15/1930. To give but a few examples, white blood cells can be isolated from a patient and analyzed to determine whether any 1918- and/or 1930-positive B cells are present. Alternatively or additionally, epidemiological methods can be utilized to determine a probability that a particular patient has or has not been exposed to 1918 and/or 1930 strains.
In some embodiments, if it is determined that a patient has been previously been exposed to one or both of influenza strains A/South Carolina/1/1918 and/or A/Swine/Iowa/15/1930, that patient may receive less concentrated, less potent, and/or less frequent doses of 2009 A/H1N1 (e.g., A/CA/4/2009) vaccines and/or therapeutics. If it is determined that a patient has not been previously been exposed to one or both of influenza strains A/South Carolina/1/1918 and/or A/Swine/Iowa/15/1930, that patient may receive more concentrated, more potent, and/or more frequent doses of 2009 A/H1N1 (e.g., A/CA/4/2009) vaccines and/or therapeutics.
In some embodiments, if it is determined that a patient has been previously been exposed to one or both of influenza strains A/South Carolina/1/1918 and/or A/Swine/Iowa/15/1930, that patient may be vaccinated using a vaccine composition which has demonstrated protection against A/South Carolina/1/1918 and/or A/Swine/Iowa/15/1930. In some embodiments, if it is determined that a patient has been previously been exposed to one or both of influenza strains A/South Carolina/1/1918 and/or A/Swine/Iowa/15/1930, that patient may be treated using a therapeutic composition which has demonstrated therapeutic effect against A/South Carolina/1/1918 and/or A/Swine/Iowa/15/1930.
A. Vaccination
In some embodiments, interfering agents and/or binding agents in accordance with the invention (e.g., entities that bind to HA polypeptides and/or fragments, variants, and/or characteristic portions thereof; entities that bind to umbrella-topology glycans) may be utilized for prophylactic applications. In some embodiments, prophylactic applications involve systems and methods for preventing, inhibiting progression of, and/or delaying the onset of influenza infection.
In some embodiments, influenza vaccines are used to prevent and/or delay onset of infection by influenza. In some embodiments, vaccination is tailored to a particular HA polypeptide. For example, vaccine compositions may comprise H1 HA polypeptides and/or variants, fragments, and/or characteristic portions thereof. In some embodiments, it is desirable for vaccine compositions to comprise antigens that have a native conformation, mediate a protective response (e.g., complement activation, virus neutralization, etc.), and/or can induce a strong antibody response.
In some embodiments, interfering agents may be utilized for passive immunization (i.e., immunization wherein antibodies are administered to a subject). In some embodiments, influenza vaccines for passive immunization may comprise antibody interfering agents, such as those described herein. In some embodiments, passive immunization occurs when antibodies are transferred from mother to fetus during pregnancy. In some embodiments, antibodies are administered directly to an individual (e.g., by injection, orally, etc.).
The present invention provides influenza vaccines for active immunization (i.e., immunization wherein microbes, proteins, peptides, epitopes, mimotopes, etc. are administered to a subject). In some embodiments, influenza vaccines may comprise one or more interfering agents and/or binding agents, as described herein.
In some embodiments, vaccines comprise at least one HA polypeptide (and/or to variants, fragments, and/or characteristic portions thereof), e.g., any of the HA polypeptides, variants, fragments, characteristic portions, and/or combinations thereof described herein (e.g., in the section entitled “HA Polypeptides”). In some embodiments, vaccines comprise H1 HA polypeptides (and/or to variants, fragments, and/or characteristic portions thereof). In some embodiments, vaccines comprise H1 HA polypeptides having one or more of the following mutations: Ile219Lys, Ser186Pro, Ala189Thr, and/or Glu227Ala. In some embodiments, vaccines comprise H1 HA polypeptides having an Ile219Lys mutation. In some embodiments, vaccines comprise H1 HA polypeptides having a mutation at amino acid position 219 (e.g., Ile219Lys) and at least one additional amino acid substitution at an amino acid position selected from the group consisting of a 98, 136, 137, 138, 145, 153, 155, 156, 159, 183, 186, 187, 189, 190, 192, 193, 194, 195, 196, 215, 219, 222, 225, 226, 227, and 228. In some embodiments, vaccines comprise H1 HA polypeptides having Ser186Pro, Ala189Thr, and Glu227Ala mutations. In some embodiments, vaccines comprise H1 HA polypeptides having mutations at amino acid positions 186, 189, and 227 (e.g., Ser186Pro, Ala189Thr, and Glu227Ala) and at least one additional amino acid substitution at an amino acid position selected from the group consisting of a 98, 136, 137, 138, 145, 153, 155, 156, 159, 183, 186, 187, 189, 190, 192, 193, 194, 195, 196, 215, 219, 222, 225, 226, 227, and 228. In some embodiments, vaccines comprise live active virus particles comprising one or more of any HA H1 polypeptide described herein, live attenuated virus particles comprising one or more of any HA H1 polypeptide described herein, virus-like particles (VLPs) comprising one or more of any HA H1 polypeptide described herein, subunit vaccines comprising one or more of any HA H1 polypeptide described herein, and/or combinations thereof.
In some embodiments, vaccines comprise at least one HA polypeptide (and/or to variants, fragments, and/or characteristic portions thereof) and at least one of influenza strains A/South Carolina/1/1918, A/Swine/Iowa/15/1930, and/or 2009 A/H1N1 (e.g., A/CA/4/2009). In some embodiments, vaccines comprise at least one HA polypeptide (and/or to variants, fragments, and/or characteristic portions thereof) and influenza strains A/South Carolina/1/1918 and A/Swine/Iowa/15/1930. In some embodiments, vaccines comprise at least one HA polypeptide (and/or to variants, fragments, and/or characteristic portions thereof) and influenza strains A/South Carolina/1/1918 and 2009 A/H1N1 (e.g., A/CA/4/2009). In some embodiments, vaccines comprise at least one HA polypeptide (and/or to variants, fragments, and/or characteristic portions thereof) and influenza strains A/Swine/Iowa/15/1930 and 2009 A/H1N1 (e.g., A/CA/4/2009). In some embodiments, vaccines comprise at least one HA polypeptide (and/or to variants, fragments, and/or characteristic portions thereof) and influenza strain A/South Carolina/1/1918. In some embodiments, vaccines comprise at least one HA polypeptide (and/or to variants, fragments, and/or characteristic portions thereof) and influenza strain A/Swine/Iowa/15/1930. In some embodiments, vaccines comprise at least one HA polypeptide (and/or to variants, fragments, and/or characteristic portions thereof) and influenza strain 2009 A/H1N1 (e.g., A/CA/4/2009).
In some embodiments, vaccines comprise at least one HA polypeptide (and/or to variants, fragments, and/or characteristic portions thereof) and at least one H1 HA polypeptide present in at least one of influenza strains A/South Carolina/1/1918, A/Swine/Iowa/15/1930, and/or 2009 A/H1N1 (e.g., A/CA/4/2009). In some embodiments, vaccines comprise at least one HA polypeptide (and/or to variants, fragments, and/or characteristic portions thereof) and H1 HA polypeptides present in influenza strains A/South Carolina/1/1918 and A/Swine/Iowa/15/1930. In some embodiments, vaccines comprise at least one HA polypeptide (and/or to variants, fragments, and/or characteristic portions thereof) and H1 HA polypeptides present in influenza strains A/South Carolina/1/1918 and 2009 A/H1N1 (e.g., A/CA/4/2009). In some embodiments, vaccines comprise at least one HA polypeptide (and/or to variants, fragments, and/or characteristic portions thereof) and H1 HA polypeptides present in influenza strains A/Swine/Iowa/15/1930 and 2009 A/H1N1 (e.g., A/CA/4/2009). In some embodiments, vaccines comprise at least one HA polypeptide (and/or to variants, fragments, and/or characteristic portions thereof) and H1 HA polypeptides present in influenza strain A/South Carolina/1/1918. In some embodiments, vaccines comprise at least one HA polypeptide (and/or to variants, fragments, and/or characteristic portions thereof) and H1 HA polypeptides present in influenza strain A/Swine/Iowa/15/1930. In some embodiments, vaccines comprise at least one HA polypeptide (and/or to variants, fragments, and/or characteristic portions thereof) and H1 HA polypeptides present in influenza strain 2009 A/H1N1 (e.g., A/CA/4/2009).
In some embodiments, a vaccine composition comprises at least one adjuvant. Any adjuvant may be used in accordance with the present invention. A large number of adjuvants are known; a useful compendium of many such compounds is prepared by the National Institutes of Health and can be found on the internet (www.niaid.nih.gov/daids/vaccine/pdf/compendium.pdf). See also Allison (1998, Dev. Biol. Stand., 92:3-11; incorporated herein by reference), Unkeless et al. (1998, Annu. Rev. Immunol., 6:251-281; incorporated herein by reference), and Phillips et al. (1992, Vaccine, 10:151-158; incorporated herein by reference). Hundreds of different adjuvants are known in the art and could be employed in the practice of the present invention. Exemplary adjuvants that can be utilized in accordance with the invention include, but are not limited to, cytokines, aluminum salts (e.g., aluminum hydroxide, aluminum phosphate, etc.; Baylor et al., Vaccine, 20:S18, 2002; incorporated herein by reference), gel-type adjuvants (e.g., calcium phosphate, etc.); microbial adjuvants (e.g., immunomodulatory DNA sequences that include CpG motifs; endotoxins such as monophosphoryl lipid A (Ribi et al., 1986, Immunology and Immunopharmacology of bacterial endotoxins, Plenum Publ. Corp., NY, p 407, 1986; incorporated herein by reference); exotoxins such as cholera toxin, E. coli heat labile toxin, and pertussis toxin; muramyl dipeptide, etc.); oil-emulsion and emulsifier-based adjuvants (e.g., Freund's Adjuvant, MF59 [Novartis], SAF, etc.); particulate adjuvants (e.g., liposomes, biodegradable microspheres, etc.); synthetic adjuvants (e.g., nonionic block copolymers, muramyl peptide analogues, polyphosphazene, synthetic polynucleotides, etc.); and/or combinations thereof. Other exemplary adjuvants include some polymers (e.g., polyphosphazenes; described in U.S. Pat. No. 5,500,161, which is incorporated herein by reference), Q57, saponins (e.g., QS21, Ghochikyan et al., Vaccine, 24:2275, 2006; incorporated herein by reference), squalene, tetrachlorodecaoxide, CPG 7909 (Cooper et al., Vaccine, 22:3136, 2004; incorporated herein by reference), poly[di(carboxylatophenoxy)phosphazene] (PCCP; Payne et al., Vaccine, 16:92, 1998; incorporated herein by reference), interferon-γ (Cao et al., Vaccine, 10:238, 1992; incorporated herein by reference), block copolymer P1205 (CRL1005; Katz et al., Vaccine, 18:2177, 2000; incorporated herein by reference), interleukin-2 (IL-2; Mbwuike et al., Vaccine, 8:347, 1990; incorporated herein by reference), polymethyl methacrylate (PMMA; Kreuter et al., J. Pharm. Sci., 70:367, 1981; incorporated herein by reference), etc.
B. Therapy
The present invention provides systems and methods for treating patients suffering from, susceptible to, and/or displaying symptoms of influenza infection. In some embodiments, the invention provides systems and methods useful for stratifying patients suffering from, susceptible to, and/or displaying symptoms of influenza infection.
In some embodiments, interfering agents and/or binding agents in accordance with the invention (e.g., entities that bind to HA polypeptides and/or fragments, variants, and/or characteristic portions thereof; entities that bind to umbrella-topology glycans) may be utilized for therapeutic applications.
In some embodiments, therapeutic applications comprise administering a therapeutically effective amount of at least one interfering agent and/or binding agent in accordance with the invention to a subject in need thereof. In some embodiments, administration of interfering agents and/or binding agents to a subject may alleviate, ameliorate, relieve, delay onset of, inhibit progression of, reduce severity of, and/or reduce incidence of one or more signs, symptoms, and/or features of influenza infection.
In some embodiments, administration of interfering agents and/or binding agents reduces the level of influenza virions circulating in a subject (e.g., influenza virions that are capable of infecting new cells). In some embodiments, administration of interfering agents and/or binding agents reduces the level of influenza virions circulating in a subject by about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, about 95%, about 99%, or about 100% relative to non-treated controls.
In some embodiments, interfering agents and/or binding agents may be used in vitro to reduce viral load in a subject. For reducing viral load of a body component, particularly a body component of a patient infected with influenza, a patient's blood is passed through a device comprising interfering agents and/or binding agents bound to a surface or solid support for capturing influenza virions (see, for example, U.S. Pat. Nos. 5,698,390 and 4,692,411; both of which are incorporated herein by reference). Various other devices found in the literature can be used with the subject antibodies to achieve a similar result. A body component can be a biological fluid (e.g., blood, serum, etc.), a tissue, an organ, such as the liver, and the like.
In some embodiments, the “level of influenza virions circulating in a subject” refers to an absolute number of virions circulating in a subject. In some embodiments, the “level of influenza virions circulating in a subject” refers to the number of virions per unit volume (e.g., milliliter, liter, etc.) of the subject's blood. In some embodiments, the “level of influenza virions circulating in a subject” refers to viral load.
In some embodiments, administration of interfering agents and/or binding agents inhibits binding of virus to HA receptors. In some embodiments, administration of interfering agents and/or binding agents inhibits binding of virus to at least one HA receptor by about 2-fold, about 3-fold, about 4-fold, about 5-fold, about 10-fold, about 50-fold, about 100-fold, about 500-fold, about 1000-fold, about 10,000-fold, or greater than about 10,000-fold relative to non-treated controls.
In some embodiments, administration of interfering agents and/or binding agents kills and/or inactivates influenza virions in a subject. In some embodiments, administration of influenza antibodies kills and/or inactivates about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, about 95%, about 99%, or about 100% of influenza virions in a subject relative to non-treated controls.
In some embodiments, administration of interfering agents and/or binding agents inhibits virus-mediated fusion with a target cell. In some embodiments, administration of interfering agents and/or binding agents inhibits virus-mediated fusion with a target cell by about 2-fold, about 3-fold, about 4-fold, about 5-fold, about 10-fold, about 50-fold, about 100-fold, about 500-fold, about 1000-fold, about 10,000-fold, or greater than about 10,000-fold relative to non-treated controls.
In some embodiments, administration of interfering agents and/or binding agents inhibits conformational changes of one or more proteins associated with virus entry. In some embodiments, administration of interfering agents and/or binding agents inhibits conformational changes of one or more proteins associated with virus entry by about 2-fold, about 3-fold, about 4-fold, about 5-fold, about 10-fold, about 50-fold, about 100-fold, about 500-fold, about 1000-fold, about 10,000-fold, or greater than about 10,000-fold relative to non-treated controls.
In some embodiments, administration of interfering agents and/or binding agents results in conformational changes in HA polypeptides and/or HA receptors. For example, administered interfering agents and/or binding agents may bind to HA polypeptides and/or HA receptors, thereby sterically blocking the HA polypeptide's and/or HA receptors' ability to recognize and/or interact with one another. In some embodiments, administered interfering agents and/or binding agents may bind to HA polypeptides and/or HA receptors, thereby changing the three-dimensional conformation of the HA polypeptides and/or HA receptors in such a way that renders HA polypeptides and/or HA receptors incapable of recognizing one another.
In some embodiments, treatment and/or vaccination regimens are particularly tailored for the individual being treated and/or vaccinated. As described above, the present invention provides systems, compositions, and methods useful for determining whether a patient is infected with H1 HA influenza or non-H1 HA influenza. Such methods can be utilized to stratify patients into treatment and/or vaccination categories. In some embodiments, such methods may be advantageous because the treatment and/or vaccination is tailored to the particular individual being treated and/or vaccinated. To give but one particular example, if a patient is classified as being infected with H1 HA influenza, therapies that are useful for treatment of H1 HA influenza can be administered to the patient, and therapies that are not useful for treatment of H1 HA influenza will not be administered. This avoids or reduces the risk of adverse reactions from administering therapeutics that are not needed. Such methods eliminate the expense of treating and/or vaccinating patients who would not benefit from such treatment and/or vaccination.
C. Pharmaceutical Compositions
In some embodiments, the present invention provides for pharmaceutical compositions including interfering agents and/or binding agents, as described herein. For example, in some embodiments, interfering agent and/or binding agent polypeptides (e.g., HA polypeptides, polypeptides that bind to HA polypeptides, variants thereof, and/or fragments thereof), nucleic acids encoding such polypeptides, characteristic or biologically active fragments of such polypeptides or nucleic acids, antibodies that bind to and/or compete with such polypeptides or fragments, small molecules that interact with or compete with such polypeptides or with glycans that bind to them, etc. are included in pharmaceutical compositions. In some embodiments, interfering agents and/or binding agents that are not polypeptides, e.g., that are small molecules, umbrella topology glycans and mimics thereof, carbohydrates, aptamers, polymers, nucleic acids, etc., are included in pharmaceutical compositions.
The invention encompasses treatment and/or prophylaxis of influenza infections by administration of such pharmaceutical compositions. In some embodiments, pharmaceutical compositions are administered to a subject suffering from or susceptible to an influenza infection. In some embodiments, a subject is considered to be suffering from an influenza infection in the subject is displaying one or more symptoms commonly associated with influenza infection. In some embodiments, the subject is known or believed to have been exposed to the influenza virus. In some embodiments, a subject is considered to be susceptible to an influenza infection if the subject is known or believed to have been exposed to the influenza virus. In some embodiments, a subject is known or believed to have been exposed to the influenza virus if the subject has been in contact with other individuals known or suspected to have been infected with the influenza virus and/or if the subject is or has been present in a location in which influenza infection is known or thought to be prevalent.
In some embodiments, subjects suffering from or susceptible to influenza infection are tested for antibodies that recognize HA polypeptides prior to, during, or after administration of pharmaceutical compositions. In some embodiments, subjects having such antibodies are not administered pharmaceutical compositions comprising HA polypeptides. In some embodiments, an appropriate dose of pharmaceutical composition and/or binding agent is selected based on detection (or lack thereof) of such antibodies.
In some embodiments, selection of a particular subject for treatment and/or vaccination, particular binding agent or composition for administration, and/or particular dose or regimen for administration, is memorialized, for example in a written, printed, or electronic storage form.
Compositions provided herein may be administered prior to or after development of one or more symptoms of influenza infection.
The present invention encompasses treatment and/or prevention (e.g., vaccination) of influenza infections by administration of HA polypeptides, interfering agents, and/or binding agents described herein. In some embodiments, treatment of influenza infections according to the present invention is accomplished by administration of a vaccine. To date, although significant accomplishments have been made in the development of influenza vaccines, there is room for further improvement. The present invention provides vaccines comprising HA polypeptides, interfering agents, and/or binding agents. To give but a few examples, vaccines may comprise interfering agents that bind to umbrella glycans (e.g., α2-6 linked umbrella glycans such as, for example, long α2-6 sialylated glycans), binding agents that bind to HA polypeptides, and/or combinations thereof. In some embodiments, a composition is substantially free of agents that preferentially bind to non-umbrella topology glycans. In some such embodiments, pharmaceutical compositions contain not more than 50%, 40%, 30%, 20%, 10%, 5%, or 1% of an agent that binds to HA receptor glycans other than umbrella topology glycans.
In some embodiments, the present invention provides for vaccines and the administration of these vaccines to a human subject (e.g., to an individual suffering from or susceptible to influenza infection). In certain embodiments, vaccines are compositions comprising one or more of the following: (1) inactivated virus, (2) live attenuated influenza virus, for example, replication-defective virus, (3) interfering agent (e.g., HA polypeptides, LSBAs, UTBAs, UTBSAs, etc.), (4) nucleic acid encoding interfering agent polypeptides (e.g., HA polypeptides) and/or or characteristic or biologically active portions thereof, (5) DNA vector that encodes an interfering agent polypeptide (e.g., HA polypeptide) or characteristic or biologically active portion thereof, (6) binding agents (e.g., entities that bind to HA polypeptides), (7) nucleic acid encoding binding agent polypeptides and/or characteristic or biologically active portions thereof, (8) DNA vector that encodes a binding agent polypeptide and/or characteristic or biologically active portion thereof, (9) expression system, for example, cells expressing one or more HA polypeptides to be used as antigens, and/or (10) virus-like particles.
Thus, in some embodiments, the present invention provides inactivated flu vaccines. In certain embodiments, inactivated flu vaccines comprise one of three types of antigen preparation: inactivated whole virus, sub-virions where purified virus particles are disrupted with detergents or other reagents to solubilize the lipid envelope (“split” vaccine) or purified HA polypeptide (“subunit” vaccine). In certain embodiments, virus can be inactivated by treatment with formaldehyde, beta-propiolactone, ether, ether with detergent (such as TWEEN-80), cetyl trimethyl ammonium bromide (CTAB) and Triton N101, sodium deoxycholate and tri(n-butyl)phosphate. Inactivation can occur after or prior to clarification of allantoic fluid (from virus produced in eggs); the virions are isolated and purified by centrifugation (Nicholson et al., eds., Textbook of Influenza, Blackwell Science, Malden, Mass., 1998; incorporated herein by reference). To assess the potency of the vaccine, the single radial immunodiffusion (SRD) test can be used (Schild et al., Bull. World Health Organ., 52:43-50 & 223-31, 1975; Mostow et al., J. Clin. Microbiol., 2:531, 1975; incorporated herein by reference).
In some embodiments, the present invention provides virus-like particles (VLPs) that are useful for vaccines. In general, VLPs comprise multiple copies of a protein antigen that, when assembled together, mimic the conformation of a native virus. In some embodiments, VLPs contain repetitive high density displays of influenza virus surface proteins (e.g., HA polypeptides in accordance with the present invention) which present conformational epitopes that can elicit strong T cell and/or B cell immune responses. Since VLPs do not contain any viral genetic material, they may be safer than attenuated viruses in vaccine compositions. VLPs can be produced in a variety of cell culture systems including mammalian cell lines, insect cell lines, yeast, plant cells, etc. For a general discussion of VLPs, see, e.g., published PCT applications WO 02/000885, WO 05/020889, WO 06/108226, WO 07/130,327, WO 07/130,330, WO 08/005,777, WO 08/040,060, WO 08/054,535, WO 08/061,243, WO 08/094,197, WO 08/094,200, WO 08/148,104, WO 09/009,876, WO 09/012,489, WO 10/006,452, and US patent application publication 2005/0009008, all of which are incorporated herein by reference.
In some embodiments, a VLP in accordance with the invention is a specialized VLP called a lipoparticle. In general, lipoparticles are stable, highly purified, homogeneous VLPs that are engineered to contain high concentrations of a conformationally intact membrane protein of interest. In some embodiments, lipoparticles in accordance with the present invention contain influenza envelope proteins and/or other influenza antigens.
The present invention also provides live, attenuated flu vaccines, and methods for attenuation are well known in the art. In certain embodiments, attenuation is achieved through the use of reverse genetics, such as site-directed mutagenesis.
In some embodiments, influenza virus for use in vaccines is grown in eggs, for example, in embryonated hen eggs, in which case the harvested material is allantoic fluid. Alternatively or additionally, influenza virus may be derived from any method using tissue culture to grow the virus. Suitable cell substrates for growing the virus include, for example, dog kidney cells such as MDCK or cells from a clone of MDCK, MDCK-like cells, monkey kidney cells such as AGMK cells including Vero cells, cultured epithelial cells as continuous cell lines, 293T cells, BK-21 cells, CV-1 cells, or any other mammalian cell type suitable for the production of influenza virus (including upper airway epithelial cells) for vaccine purposes, readily available from commercial sources (e.g., ATCC, Rockville, Md.). Suitable cell substrates also include human cells such as MRC-5 cells. Suitable cell substrates are not limited to cell lines; for example primary cells such as chicken embryo fibroblasts are also included.
In some embodiments, vaccines further comprise one or more adjuvants. Any adjuvant may be used in accordance with the present invention. A large number of adjuvants are known; a useful compendium of many such compounds is prepared by the National Institutes of Health and can be found on the internet (www.niaid.nih.gov/daids/vaccine/pdf/compendium.pdf). See also Allison (1998, Dev. Biol. Stand., 92:3-11; incorporated herein by reference), Unkeless et al. (1998, Annu. Rev. Immunol., 6:251-281; incorporated herein by reference), and Phillips et al. (1992, Vaccine, 10:151-158; incorporated herein by reference). Hundreds of different adjuvants are known in the art and could be employed in the practice of the present invention. For example, aluminum salts (e.g., aluminum hydroxide, aluminum phosphate, etc., Baylor et al., Vaccine, 20:S18, 2002) and monophosphoryl lipid A (MPL; Ribi et al., (1986, Immunology and Immunopharmacology of bacterial endotoxins, Plenum Publ. Corp., NY, p 407, 1986) can be used as adjuvants in human vaccines. Alternatively or additionally, exemplary adjuvants that can be utilized in accordance with the invention include cytokines, calcium phosphate, microbial adjuvants (e.g., immunomodulatory DNA sequences that include CpG motifs; endotoxins such as monophosphoryl lipid A (Ribi et al., 1986, Immunology and Immunopharmacology of bacterial endotoxins, Plenum Publ. Corp., NY, p 407, 1986; incorporated herein by reference); exotoxins such as cholera toxin, E. coli heat labile toxin, and pertussis toxin; muramyl dipeptide, etc.); oil-emulsion and emulsifier-based adjuvants (e.g., Freund's Adjuvant, SAF, etc.); particulate adjuvants (e.g., liposomes, biodegradable microspheres, etc.); synthetic adjuvants (e.g., nonionic block copolymers, muramyl peptide analogues, polyphosphazene, synthetic polynucleotides, etc.); polymers (e.g., polyphosphazenes; described in U.S. Pat. No. 5,500,161, which is incorporated herein by reference), Q57, squalene, and/or tetrachlorodecaoxide.
Alternatively or additionally, new compounds are currently being tested as adjuvants in human vaccines, such as MF59 (Chiron Corp., http://www.chiron.com/investors/pressreleases/2005/051028.html), CPG 7909 (Cooper et al., Vaccine, 22:3136, 2004; incorporated herein by reference), and saponins, such as QS21 (Ghochikyan et al., Vaccine, 24:2275, 2006; incorporated herein by reference).
Additionally, some adjuvants are known in the art to enhance the immunogenicity of influenza vaccines, such as poly[di(carboxylatophenoxy)phosphazene] (PCCP; Payne et al., Vaccine, 16:92, 1998; incorporated herein by reference), interferon-γ (Cao et al., Vaccine, 10:238, 1992; incorporated herein by reference), block copolymer P1205 (CRL1005; Katz et al., Vaccine, 18:2177, 2000; incorporated herein by reference), interleukin-2 (IL-2; Mbwuike et al., Vaccine, 8:347, 1990; incorporated herein by reference), and polymethyl methacrylate (PMMA; Kreuter et al., J. Pharm. Sci., 70:367, 1981; incorporated herein by reference).
In some embodiments, pharmaceutical compositions do not include adjuvants (e.g., provided compositions are essentially free of adjuvants). In some embodiments, pharmaceutical compositions do not include an alum adjuvant (e.g., provided compositions are essentially free of alum).
The present invention provides other therapeutic compositions useful in the treatment and/or vaccination of viral infections. In some embodiments, treatment and/or vaccination is accomplished by administration of an agent that interferes with expression or activity of an HA polypeptide.
In some embodiments, the present invention provides pharmaceutical compositions comprising antibodies or other agents related to provided polypeptides, interfering agents, and/or binding agents. For example, the invention provides compositions containing antibodies recognize virus particles containing a particular HA polypeptide (e.g., an HA polypeptide that binds to umbrella glycans), nucleic acids (such as nucleic acid sequences complementary to HA sequences, which can be used for RNAi), glycans that compete for binding to HA receptors, small molecules or glycomometics that compete the glycan-HA polypeptide interaction, or any combination thereof. In some embodiments, collections of different agents, having diverse structures are utilized. In some embodiments, therapeutic compositions comprise one or more multivalent agents. In some embodiments, treatment comprises urgent administration shortly after exposure or suspicion of exposure.
In general, a pharmaceutical composition will include a therapeutic agent in addition to one or more inactive agents such as a sterile, biocompatible carrier including, but not limited to, sterile water, saline, buffered saline, or dextrose solution. Alternatively or additionally, a composition may comprise a pharmaceutically acceptable excipient, which, as used herein, includes any and all solvents, dispersion media, diluents, or other liquid vehicles, dispersion or suspension aids, disintegrating agents, surface active agents, isotonic agents, thickening or emulsifying agents, preservatives, buffering agents, solid binders, granulating agents, lubricants, coloring agents, sweetening agents, flavoring agents, perfuming agents, and the like, as suited to the particular dosage form desired. Remington's The Science and Practice of Pharmacy, 21st Edition, A. R. Gennaro, (Lippincott, Williams & Wilkins, Baltimore, Md., 2006; incorporated herein by reference) discloses various excipients used in formulating pharmaceutical compositions and known techniques for the preparation thereof. Except insofar as any conventional excipient medium is incompatible with a substance or its derivatives, such as by producing any undesirable biological effect or otherwise interacting in a deleterious manner with any other component of the pharmaceutical composition, its use is contemplated to be within the scope of this invention.
In certain embodiments, a pharmaceutical composition will include a therapeutic agent that is encapsulated, trapped, or bound within a lipid vesicle, a bioavailable and/or biocompatible and/or biodegradable matrix, or other microparticle.
In some embodiments, a provided pharmaceutical composition will include an HA polypeptide, interfering agent, and/or binding agent that is not aggregated. For example, in some embodiments, less than 1%, 2%, 5%, 10%, 20%, or 30%, by dry weight or number, of an HA polypeptide, interfering agent, and/or binding agent is present in an aggregate.
In some embodiments, a provided pharmaceutical composition will include an HA polypeptide, interfering agent, and/or binding agent that is not denatured. For example, in some embodiments, less than 1%, 2%, 5%, 10%, 20%, or 30%, by dry weight or number, of an HA polypeptide, interfering agent, and/or binding agent administered is denatured.
In some embodiments, a provided pharmaceutical composition will include an HA polypeptide, interfering agent, and/or binding agent that is not inactive. For example, in some embodiments, less than 1%, 2%, 5%, 10%, 20%, or 30%, by dry weight or number, of an HA polypeptide, interfering agent, and/or binding agent administered is inactive.
In some embodiments, pharmaceutical compositions are formulated to reduce immunogenicity of provided HA polypeptide, interfering agent, and/or binding agent. For example, in some embodiments, a provided HA polypeptide, interfering agent, and/or binding agent is associated with (e.g., bound to) an agent, such as polyethylene glycol and/or carboxymethyl cellulose, that masks its immunogenicity. In some embodiments, a provided HA polypeptide, interfering agent, and/or binding agent has additional glycosylation that reduces immunogenicity.
Liquid dosage forms for oral and parenteral administration include, but are not limited to, pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups, and/or elixirs. In addition to active ingredients, liquid dosage forms may comprise inert diluents commonly used in the art such as, for example, water or other solvents, solubilizing agents and emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, dimethylformamide, oils (in particular, cottonseed, groundnut, corn, germ, olive, castor, and sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof. Besides inert diluents, oral compositions can include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and/or perfuming agents. In certain embodiments for parenteral administration, compositions are mixed with solubilizing agents such a CREMOPHOR®, alcohols, oils, modified oils, glycols, polysorbates, cyclodextrins, polymers, and/or combinations thereof.
Compositions for rectal or vaginal administration are typically suppositories which can be prepared by mixing compositions with suitable non-irritating excipients such as cocoa butter, polyethylene glycol or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active ingredient.
Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules. In such solid dosage forms, the active ingredient is mixed with at least one inert, pharmaceutically acceptable excipient such as sodium citrate or dicalcium phosphate and/or fillers or extenders (e.g., starches, lactose, sucrose, glucose, mannitol, and silicic acid), binders (e.g., carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia), humectants (e.g., glycerol), disintegrating agents (e.g., agar, calcium carbonate, potato starch, tapioca starch, alginic acid, certain silicates, and sodium carbonate), solution retarding agents (e.g., paraffin), absorption accelerators (e.g., quaternary ammonium compounds), wetting agents (e.g., cetyl alcohol and glycerol monostearate), absorbents (e.g., kaolin and bentonite clay), and lubricants (e.g., talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate), and mixtures thereof. In the case of capsules, tablets and pills, the dosage form may comprise buffering agents.
Dosage forms for topical and/or transdermal administration of a compound in accordance with this invention may include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants and/or patches. Generally, the active ingredient is admixed under sterile conditions with a pharmaceutically acceptable excipient and/or any needed preservatives and/or buffers as may be required. Additionally, the present invention contemplates the use of transdermal patches, which often have the added advantage of providing controlled delivery of a compound to the body. Such dosage forms may be prepared, for example, by dissolving and/or dispensing the compound in the proper medium. Alternatively or additionally, the rate may be controlled by either providing a rate controlling membrane and/or by dispersing the compound in a polymer matrix and/or gel.
General considerations in the formulation and manufacture of pharmaceutical agents may be found, for example, in Remington's Pharmaceutical Sciences, 19th ed., Mack Publishing Co., Easton, Pa., 1995; incorporated herein by reference.
The present invention provides kits for administration of pharmaceutical compositions. For example, in some embodiments, the invention provides a kit comprising at least one dose of an HA polypeptide, HA polypeptide binding agent, HA polypeptide interfering agent, fragment thereof, variant thereof, and/or characteristic portion thereof. In some embodiments, the invention provides a kit comprising an initial unit dose and a subsequent unit dose of a binding agent. In some such embodiments, the initial unit dose is greater than the subsequent unit dose or wherein the two doses are equal.
In some embodiments, kits comprise at least one component of a delivery device, e.g., an inhaler. In some such embodiments, the invention provides a kit comprising at least one component of a delivery device, e.g., an inhaler and a dose of an HA polypeptide, HA polypeptide binding agent, HA polypeptide interfering agent, fragment thereof, variant thereof, and/or characteristic portion thereof. In some embodiments, kits comprise instructions for use.
D. Administration
Pharmaceutical compositions can be administered to any subject (e.g., any animal) in need thereof, including humans. Pharmaceutical compositions may be administered either alone or in combination with one or more other therapeutic agents including, but not limited to, vaccines and/or antibodies. By “in combination with,” it is not intended to imply that the agents must be administered at the same time or formulated for delivery together, although these methods of delivery are within the scope of the invention. In general, each agent will be administered at a dose and on a time schedule determined for that agent. Additionally, the invention encompasses the delivery of the pharmaceutical compositions in combination with agents that may improve their bioavailability, reduce or modify their metabolism, inhibit their excretion, or modify their distribution within the body. Although the pharmaceutical compositions of the present invention can be used for treatment and/or vaccination of any subject (e.g., any animal) in need thereof, they are most preferably used in the treatment and/or vaccination of humans. In some embodiments, pharmaceutical compositions and/or binding agents are administered in combination with one or more of an anti-viral agent (e.g., Oseltamivir [tamiflu], Zanamavir [Releza], etc.) and/or a sialidase.
Pharmaceutical compositions may be administered using any amount and any route of administration effective for treatment and/or vaccination. The exact amount required will vary from subject to subject, depending on the species, age, and general condition of the subject, the severity of the infection, the particular composition, its mode of administration, its mode of activity, and the like. Pharmaceutical compositions are typically formulated in dosage unit form for ease of administration and uniformity of dosage. It will be understood, however, that the total daily usage of the compositions of the present invention will be decided by the attending physician within the scope of sound medical judgment. The specific therapeutically effective dose level for any particular subject or organism will depend upon a variety of factors including the disorder being treated and/or vaccinated and the severity of the disorder; the activity of the specific vaccine composition employed; the half-life of the composition after administration; the age, body weight, general health, sex, and diet of the subject; the time of administration, route of administration, and rate of excretion of the specific compound employed; the duration of the treatment; drugs used in combination or coincidental with the specific compound employed; and like factors, well known in the medical arts.
Pharmaceutical compositions of the present invention may be administered by any route. In some embodiments, pharmaceutical compositions of the present invention are administered by a variety of routes, including oral (PO), intravenous (IV), intramuscular (IM), intra-arterial, intramedullary, intrathecal, subcutaneous (SQ), intraventricular, transdermal, interdermal, intradermal, rectal (PR), vaginal, intraperitoneal (IP), intragastric (IG), topical (e.g., by powders, ointments, creams, gels, lotions, and/or drops), mucosal, intranasal, buccal, enteral, vitreal, sublingual; by intratracheal instillation, bronchial instillation, and/or inhalation; as an oral spray, nasal spray, and/or aerosol, and/or through a portal vein catheter.
In general, the most appropriate route of administration will depend upon a variety of factors including the nature of the agent being administered (e.g., its stability upon administration), the condition of the subject (e.g., whether the subject is able to tolerate a particular mode of administration), etc. In specific embodiments, pharmaceutical compositions may be administered intranasally. In specific embodiments, pharmaceutical compositions may be administered by intratracheal instillation. In specific embodiments, pharmaceutical compositions may be administered by bronchial instillation. In specific embodiments, pharmaceutical compositions may be administered by inhalation. In specific embodiments, pharmaceutical compositions may be administered as a nasal spray. In specific embodiments, pharmaceutical compositions may be administered mucosally. In specific embodiments, pharmaceutical compositions may be administered orally. In specific embodiments, pharmaceutical compositions may be administered by intravenous injection. In specific embodiments, pharmaceutical compositions may be administered by intramuscular injection. In specific embodiments, pharmaceutical compositions may be administered by subcutaneous injection. At present the oral or nasal spray or aerosol route (e.g., by inhalation) is most commonly used to deliver therapeutic agents directly to the lungs and respiratory system. However, the invention encompasses the delivery of a pharmaceutical composition by any appropriate route taking into consideration likely advances in the sciences of drug delivery.
In some embodiments, preparations for inhaled or aerosol delivery comprise a plurality of particles. In some embodiments, such preparations have a mean particle size of 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13 microns. In some embodiments, preparations for inhaled or aerosol delivery are formulated as a dry powder. In some embodiments, preparations for inhaled or aerosol delivery are formulated as a wet powder, for example through inclusion of a wetting agent. In some embodiments, the wetting agent is selected from the group consisting of water, saline, or other liquid of physiological pH.
In some embodiments, compositions are administered as drops to the nasal or buccal cavity. In some embodiments, a dose may comprise a plurality of drops (e.g., 1-100, 1-50, 1-20, 1-10, 1-5, etc.).
In some embodiments, compositions are administered using a device that delivers a metered dosage of a pharmaceutical composition.
Pharmaceutical compositions may be administered in any dose appropriate to achieve a desired outcome. In some embodiments, the desired outcome is reduction in intensity, severity, and/or frequency, and/or delay of onset of one or more symptoms of influenza infection.
In some embodiments, pharmaceutical compositions are formulated to administer a dose of an HA polypeptide (e.g., variant, fragment, and/or characteristic portion thereof) effective to compete with influenza HA for binding to umbrella topology glycans. In some embodiments, such binding by influenza HA is reduced after administration of one or more doses of a composition as compared with its level absent such administration. In some embodiments, pharmaceutical compositions are formulated to administer a dose of HA polypeptide effective to saturate at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or more than 99% of HA binding sites (e.g., HA binding sites containing umbrella topology glycans) present in the subject (e.g., in the respiratory tract of the subject) receiving the composition.
In some embodiments, pharmaceutical compositions are formulated to administer a dose of an interfering agent (e.g., umbrella topology glycan mimic) effective to compete with HA receptors for binding to HA polypeptides (e.g., on the surface of influenza virus particles). In some embodiments, binding of influenza HA polypeptides to HA receptors is reduced after administration of one or more doses of a composition as compared with its level absent such administration. In some embodiments, pharmaceutical compositions are formulated to administer a dose of an interfering agent effective to saturate at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or more than 99% of HA binding sites (e.g., HA binding sites containing umbrella topology glycans) present in the subject (e.g., in the respiratory tract of the subject) receiving the composition.
In certain embodiments, pharmaceutical compositions may be administered at dosage levels sufficient to deliver from about 0.001 mg/kg to about 100 mg/kg, from about 0.01 mg/kg to about 50 mg/kg, from about 0.1 mg/kg to about 40 mg/kg, from about 0.5 mg/kg to about 30 mg/kg, from about 0.01 mg/kg to about 10 mg/kg, from about 0.1 mg/kg to about 10 mg/kg, or from about 1 mg/kg to about 25 mg/kg of a therapeutic agent per subject body weight per day to obtain a desired therapeutic effect. A desired dosage may be delivered to a subject only once. A desired dosage may be delivered more than three times per day, three times per day, two times per day, once per day, every other day, every third day, every week, every two weeks, every three weeks, every four weeks, every two months, every six months, every twelve months, every two years, every three years, every four years, every five years, every 10 years, or every 20 years. In certain embodiments, the desired dosage may be delivered using multiple administrations (e.g., two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, or more administrations).
It will be appreciated that compositions in accordance with the present invention can be employed in combination therapies. The particular combination of therapies (e.g., therapeutics or procedures) to employ in a combination regimen will take into account compatibility of the desired therapeutics and/or procedures and the desired therapeutic effect to be achieved. It will be appreciated that the therapies employed may achieve a desired effect for the same purpose (for example, an agent useful for treating, preventing, and/or delaying the onset of influenza infection may be administered concurrently with another agent useful for treating, preventing, and/or delaying the onset of influenza infection), or they may achieve different effects (e.g., control of any adverse effects). The invention encompasses delivery of pharmaceutical compositions in combination with agents that may improve their bioavailability, reduce and/or modify their metabolism, inhibit their excretion, and/or modify their distribution within the body.
Pharmaceutical compositions in accordance with the present invention may be administered either alone or in combination with one or more other therapeutic agents. By “in combination with,” it is not intended to imply that the agents must be administered at the same time and/or formulated for delivery together, although these methods of delivery are within the scope of the invention. Compositions can be administered concurrently with, prior to, or subsequent to, one or more other desired therapeutics or medical procedures. In will be appreciated that therapeutically active agents utilized in combination may be administered together in a single composition or administered separately in different compositions. In general, each agent will be administered at a dose and/or on a time schedule determined for that agent.
In general, it is expected that agents utilized in combination with be utilized at levels that do not exceed the levels at which they are utilized individually. In some embodiments, the levels utilized in combination will be lower than those utilized individually.
In some embodiments, pharmaceutical compositions are administered in combination with one or more of an anti-viral agent (e.g., Oseltamivir [tamiflu], Zanamavir [Releza], etc.) and/or a sialidase.
EXEMPLIFICATION
Example 1
Glycan Binding Specificity of 2009 A/H1N1 HA
The present inventors have characterized glycan binding specificity of 2009 A/H1N1 HA, which infects primarily swine, and identified mutant forms of H1 HA that would lead to its human adaptation for efficient airborne human-to-human transmission that is characteristic of HAs from both the seasonal and pandemic influenza A H1N1 viruses. Although several 2009 A/H1N1 strains have been isolated and sequenced, there are few intragenic variations among these. Thus, the present inventors utilized HA from a representative 2009 A/H1N1 virus, i.e., A/California/0409 (henceforth referred to as CA/04).
Materials and Methods
Binding of CA/04 Hemagglutinin to Human Respiratory Tissues
Formalin-fixed and paraffin-embedded normal human tracheal tissue sections and human alveolar tissue sections were purchased from US Biological and US Biomax respectively. Tissue sections were deparaffinized, rehydrated and pre-blocked with 1% BSA in PBS for 30 minutes at room temperature (RT). HA-antibody pre-complexes were generated by incubating 20 μg/ml of recombinant CA/04 HA protein with primary (mouse anti 6×His tag, Abcam) and secondary (Alexa Fluor 488 goat anti mouse IgG, Molecular Probes) antibodies in a ratio of 4:2:1, respectively, for 20 minutes on ice. Tissue binding studies were performed by incubating tissue sections with the diluted HA-antibody complexes for 3 hours at RT. To visualize cell nuclei, sections were counterstained with propidium iodide (Invitrogen; 1:100 in TBST) for 20 minutes at RT. In the case of sialidase pretreatment, tissue sections were incubated with 0.2 units of Sialidase A (recombinant from Arthrobacter ureafaciens, Prozyme) for 3 hours at 37° C. prior to incubation with the proteins. Sections were then washed and viewed under a Zeiss LSM510 laser scanning confocal microscope.
Dose Dependent Direct Receptor Binding of CA/04 HA
The receptor specificity of recombinantly expressed Ca/04 HA was investigated using a panel of glycans comprising of both α2-3 and α2-6 sialylated glycans. The wells of streptavidin-coated high binding capacity 384-well plates (Pierce) were incubated with 50 μl of 2.4 μM biotinylated glycans overnight at 4° C. The glycans included were 3′-SLN, 3′-SLN-LN, 3′SLN-LN-LN, 6′-SLN and 6′SLN-LN (LN corresponds to lactosamine (Galβ1-4GlcNAc) and 3′SLN and 6′SLN respectively correspond to Neu5Acα2-3 and Neu5Acα2-6 linked to LN) and were obtained from the Consortium of Functional Glycomics (www.functionalglycomics.org) through their resource request program. A stock solution of HA complex was prepared by incubating appropriate amounts of HA protein, primary antibody (mouse anti 6×His tag IgG, Abcam) and secondary antibody (HRP conjugated goat anti mouse IgG, Santacruz Biotechnology) in the ratio 4:2:1, respectively, on ice for 20 minutes. Appropriate amounts of precomplexed stock HA were diluted to 250 μl with 1% BSA in PBS. 50 μl of precomplexed HA was added to each of the glycan-coated wells and incubated at room temperature for 2 hours followed by three washes with PBST (PBS+0.1% Tween-20) and three washes with PBS. The binding signal was determined based on HRP activity using Amplex Red Peroxidase Assay (Invitrogen) according to the manufacturer's instructions. Appropriate negative controls were included.
Results
Glycan Binding Properties of 2009 A/H1N1 HA
A dose-dependent binding of HA to representative human and avian receptors on a biotin-strepatividin based glycan array platform permitted quantification using an apparent binding constant Kd′ (Srinivasan et al., 2008, Proc. Natl. Acad. Sci. U.S.A., 105:2800-05; incorporated herein by reference). The parameter Kd′ can be calculated by fitting the binding data (over a range of HA concentrations) using the Hill equation for multivalent binding (Srinivasan et al., 2008, Proc. Natl. Acad. Sci. U.S.A., 105:2800-05; incorporated herein by reference). The trimeric HA unit comprises of three HA monomers (with one RBS per monomer). The spatial arrangement of the biotinylated glycans in the wells of the streptavidin plate array favors binding to only one of the three HA monomers in the trimeric HA unit. Therefore in order to specifically enhance the multivalency in the HA-glycan interactions, the recombinant HA is pre-complexed with the primary and secondary antibodies in the ratio of 4:2:1 (HA:primary:secondary) as described previously (Srinivasan et al., 2008, Proc. Natl. Acad. Sci. U.S.A., 105:2800-05; and Stevens et al., 2006, Nat. Rev. Microbiol., 4:857-64; both of which are incorporated herein by reference). The identical spatial arrangement of 4 trimeric HA units in the precomplex relative to the glycans on the array platform, homogenizes the avidity effects across different HAs and hence permits quantitative comparison between glycan binding strengths of different HAs.
Glycan binding properties of the 2009 A/H1N1 HA were examined using dose-dependent direct receptor binding (Srinivasan et al., 2008, Proc Natl Acad Sci USA, 105:2800-5; incorporated herein by reference) and human lung tissue binding (Chandrasekaran et al., 2008, Nat Biotechnol, 26:107-13; incorporated herein by reference) assays. These assays were performed with CA/04 HA that was recombinantly expressed using a construct that was designed to produce a soluble protein as described previously (Chandrasekaran et al., 2008, Nat Biotechnol, 26:107-13; incorporated herein by reference). In a direct glycan receptor-binding assay, CA/04 HA exhibited a dose-dependent binding to only a single α2-6 glycan (6′SLN-LN) and only minimal binding to α2-3 glycans (FIG. 9A). While the binding pattern of Cal/04 HA is similar to that of HA from the 1918 pandemic influenza A virus (A/South Carolina/1/1918; or SC18), the binding affinity of CA/04 HA is lower than that of SC18 HA (FIG. 9B).
Examining the tissue binding of CA/04 HA indicates that it binds uniformly to the apical surface of the human tracheal (representative upper respiratory) tissue sections (FIG. 10). This binding pattern correlates with the predominant distribution of α2-6 sialylated glycans on the apical surface of the tracheal tissue (Chandrasekaran et al., 2008, Nat Biotechnol, 26:107-13; incorporated herein by reference) and the α2-6 binding of CA/04 HA in the direct binding assay. Although CA/04 shows some binding to alveolus, it is not as extensive as the tracheal binding consistent with the minimal α2-3 binding observed in the direct binding assay.
Based on the above data, it is clear that while the A/2009H1N1 HA has a similar binding selectivity of the pandemic SC18 HA, its α2-6 binding affinity is substantially lower than that of SC18 HA. It was demonstrated previously (Tumpey et al., 2007, Science, 315:655-59; incorporated herein by reference) that the efficiency of airborne transmission (e.g., using a ferret animal model, which is an established animal model for influenza A virus transmission in humans) correlates with the α2-6 binding affinity of the viral HA. In fact, a single amino acid mutation in HA of the efficiently transmitting SC18 virus led to a virus (NY18) that transmitted inefficiently. The α2-6 binding affinity of NY18 HA was substantially lower than that of SC18 HA (Srinivasan et al., 2008, Proc Natl Acad Sci USA, 105:2800-5; incorporated herein by reference). In a similar fashion the substantially lower α2-6 binding affinity of CA/04 HA than that of SC18 HA indicates that this virus has not yet fully adapted to the human host for efficient airborne human-to-human transmission. Consistent with this conclusion, the lower human receptor-binding strength of CA04 HA correlated with the lower observed efficiency of transmission of the CA04 virus in ferrets, as compared with highly transmissible SC18 (see, e.g., Tumpey et al., 2007, Science, 315:655-59; and Maines et al., 2009, Science, 325:484-87; both of which are incorporated herein by reference). Similar results were also obtained in mice (Maines et al., 2009, Science, 325:484-87; incorporated herein by reference).
Structural Analysis of 2009 A/H1N1 HA
The receptor-binding site (RBS) of the 2009 A (H1N1) HAs (Soundararajan et al., 2009, Nat Biotechnol, 27:510-3; incorporated herein by reference), used in this study and those from SC18 and the recent seasonal influenza H1N1 viruses was compared (FIG. 11). The similarity in the binding pattern between CA/04 HA and SC18 HA could potentially arise from the majority of “similar or analogous” RBS residues between these HAs including Asp190 and Asp225, which are “hallmark” amino acids of human adapted H1N1 HAs that make optimal contacts with the α2-6 glycans. Differences in RBS between SC18 and CA/04 HA occur at positions 145, 186, 189, 219 and 227. CA/04 HA has a unique Lys145 which provides an additional anchoring contact for the sialic acid (Soundararajan et al., 2009, Nat Biotechnol, 27:510-3; incorporated herein by reference). Residues at 186, 187 189 are positioned to form an interaction network with Asp190 (Soundararajan et al., 2009, Nat Biotechnol, 27:510-3; incorporated herein by reference). In the case of SC18 HA, this network involves oxygen atoms of Thr187, Thr189 and Asp190 (Srinivasan et al., 2008, Proc Natl Acad Sci USA, 105:2800-5; and Gamblin et al., 2004, Science, 303, 1838-42; both of which are incorporated herein by reference). In a similar fashion, in the case of CA/04 HA, the oxygen atoms of Ser186, Thr187 and Asp190 could potentially form this network. Residues 219 and 227 in turn influence the orientation of residue 186. Comparison of residues 219 and 227 (FIG. 11) reveals that either both amino acids are hydrophobic such as Ala219 and Ala227 (as observed in SC18 HA) or they are charged residues such as Lys219 and Glu227 (as observed in the seasonal influenza HAs). The present invention encompasses the recognition that 2009 A(H1N1) HAs have a unique combination of Ile219 and Glu227 that results in a set of interactions that is neither fully hydrophobic nor fully charged. This combination could destabilize the hydrophobic or ionic network of residues at 186, 219 and 227 thereby disrupting optimal contacts with α2-6 sialylated glycans (FIG. 12). Analysis of the RBS of the 2009 A(H1N1) HA offers an explanation for the lower α2-6 binding affinity of CA/04 HA as compared to SC18 HA despite the similar binding pattern (FIG. 9).
Structural analysis (FIG. 12) offers an explanation for the lower affinity due to a combination of amino acids in the RBS that is unique to 2009 A/H1N1 HAs. The present invention encompasses the recognition that mutations in the RBS might fix the issue of positioning the Asp190 for optimal contact with α2-6 glycans and hence increase the affinity for α2-6 binding. According to the present invention, possible combinations of mutations that would fix this issue include:

    
    
        Ile219→Lys: This would make the network of interactions between the residue positions 219, 222, 225, 227 substantially (if not entirely) ionic which in turn would permit positioning of Ser186 for making interactions with Asp190 that in turn would position Asp190 for making contact with α2-6. This part of the network of interactions in the mutant HA is similar to that observed in recent seasonal influenza H1N1 HAs.
        Ser186→Pro/Ala189Thr/Glu227Ala: This would make the network of interactions between residue positions 186, 219 and 227 hydrophobic and the Thr189 in the mutant HA along with Thr187 would be positioned for making interactions with Asp190 which in turn would position Asp190 for making contacts with α2-6. This part of the network of interactions in the mutant HA is similar to that observed for SC18.
    
    


Both combinations of mutations listed above lead to a unique HA that is unlike any of the recent seasonal influenza H1N1 HAs as well as unlike SC18 HA.
Discussion
In early 2009, a novel strain of a H1N1 influenza virus (referred to as 2009H1N1) originated from a North American triple reassortant swine H1 virus. The global health threat posed by this virus subsequently led the WHO to categorize this strain as a pandemic (WHO, 2009, Weekly Epid. Rec., 84:249-57; incorporated herein by reference). Based on extensive sequence and structural analysis of the key 2009H1N1 influenza viral proteins, the present inventors investigated properties of the virus including glycan-receptor binding of the viral hemagglutinin (HA), drug resistance, virulence and transmissibility (see, e.g., Results above Soundararajan et al., 2009, Nat. Biotechnol., 27:510-13; incorporated herein by reference). In contrast to the results presented above in Example 1, which demonstrated that CA/04 HA binds preferentially to α2-6 glycans (as opposed to α2-3 glycans), Childs et al. (2009, Nat. Biotechnol., 27:797-99; incorporated herein by reference) subsequently reported that the 2009H1N1 virus bound to both α2→3-(avian receptors) and α2→6-(human receptors) linked sialylated glycans in the context of a lipid-based glycan array platform.
Analysis of whole viruses on glycan array platforms, as reported by Childs et al., presents several challenges in understanding subtle differences in binding arising from amino acid substitutions in the glycan receptor-binding site (RBS) of HA. For example, one commonly used method to measure viral titer is based on the ability of the virus to agglutinate red blood cells (RBCs), a property mediated by the binding of viral HA to sialylated glycan receptors on the RBC surface. However, use of this method to compare mutant strains with altered glycan-receptor binding properties to one another or to a reference wild type (WT) strain is complicated by the fact that the same hemagglutination titer of the WT and mutant form of a virus may not correspond to the same number of viral particles. This issue can be circumvented to an extent by using directly labeled viruses (Kumari et al., 2007, Virol. J., 4:42; incorporated herein by reference) or by adjusting the viral titer based on equivalent concentrations of viral protein (e.g., using gel electrophoresis), as reported by Childs et al.
Studies that have been published after the data and conclusions presented in Example 1 focus on qualitative characterization (typically at a high virus or HA concentration). These studies have been designed such that binding signals can be observed for the maximum number of glycans on the array (see, e.g., Childs et al., 2009, Nat. Biotechnol., 27:797-99; and Hua et al., 2010, PLoS Currents: Influenza; both of which are incorporated herein by reference). These studies, while offering a vague idea of the number of avian and human receptors that bind to a given HA or virus, are not suitable to quantify and compare binding strength (or affinity) of HA-glycan interactions. In contrast, the present inventors obtained quantitative information by designing assays that analyze binding over a range of HA concentrations and measuring the approach to saturation by taking into account avidity and/or cooperativity effects.
In summary, the present inventors have characterized HA-glycan receptor binding properties of 2009H1N1. The inventors demonstrated that HA from a representative 2009H1N1 virus (A/California/04/09 or “CA04”) bound specifically to human receptors on a glycan array platform and on human upper respiratory epithelia and showed no observable binding to avian receptors (see Results above and Maines et al., 2009, Science, 325:484-87; incorporated herein by reference). The binding strength of CA04 HA to the human receptor, however, was substantially lower than that of HA from the prototypic 1918H1N1 pandemic, A/South Carolina/1/1918 (“SC18”) (see Results above and Maines et al., 2009, Science, 325:484-87; incorporated herein by reference). The lower human receptor-binding strength of CA04 HA correlated with the lower observed efficiency of transmission of the CA04 virus (see Results above and Maines et al., 2009, Science, 325:484-87; incorporated herein by reference), as compared with highly transmissible SC18) in ferrets (see Tumpey et al., 2007, Science, 315:655-59; incorporated herein by reference). The lack of observable binding by CA04 HA to avian receptors is consistent with recent glycan microarray analysis of 2009H1N1 HAs (Hua et al., 2010, PLoS Currents: Influenza; incorporated herein by reference) but is in contrast to the observations in the report by Childs et al. using whole viruses. Without wishing to be bound by any particular theory, these differences may be attributed to differences in the presentation of HA (e.g., as a recombinant protein as against on a whole virus) and glycan receptors in the different array platforms (see Childs et al.).
Example 2
Comparison of 2009 A/H1N1 Isolates with 1918 and 1930 Pandemic Strain Isolates
In 1918 and 1930, strains of H1 influenza viruses emerged that showed enhanced human infectivity as compared with their parent strains. Each of these strains led to a pandemic of influenza infections in humans.
The present inventors have compared binding and/or sequence characteristics of the A/South Carolina/1/1918 and A/Swine/Iowa/15/1930 strains with a representative 2009 A/H1N1 strain, A/California/0409 (CA/04). The present invention encompasses the recognition that similar results would be obtained for other 2009 A/H1N1 strains. The present invention demonstrates that 2009 A/H1N1 shares significant similarities with both the A/South Carolina/1/1918 and A/Swine/Iowa/15/1930 strains, and particularly with the 1918 strain (FIG. 4A-C). This finding implies, among other things, that (1) immunization against the A/South Carolina/1/1918 and A/Swine/Iowa/15/1930 strains, and particularly against the 1918 strain, might provide some cross-reactive protection against 2009 A/H1N1; and/or (2) individuals previously exposed to the A/South Carolina/1/1918 and A/Swine/Iowa/15/1930 strains, and particularly to the 1918 strain, (a) might be less susceptible to infection, and therefore, might demonstrate a lesser need of vaccination and/or treatment than individuals not previously exposed; (b) might require less concentrated, less potent, and/or less frequent dosage of vaccine and/or therapeutic compositions; and/or (c) might be primed due to the previous exposure and likely to achieve successful vaccination.
Example 3
Binding Characteristics of H1 HA Polypeptides
Those of ordinary skill in the art, after reading the present specification, will appreciate that techniques described herein may be used to analyze or determine binding characteristics of H1 polypeptides from any source. Table 4 below provides sequences of various H1 HA polypeptides from a variety of strains. Some of the sequences presented in Table 4 correspond to the HA1 region (e.g., which contains all or part of the glycan receptor binding site). Any number of additional H1 HA polypeptide sequences can be accessed from public databases, including, but not limited to, the GISAID Influenza portal database (http://platform.gisaid.org/dante-cms/live/struktur.jdante?aid=1131) and/or the NCBI Flu database (http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html).







TABLE 4







Sequences of Exemplary H1 HA Polypeptides








Strain
H1 HA Sequence












A/Aichi/8/09 (HA1 only)
DTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLENSHNG




KLCLLKGIAPLQLGNCSVAGWILGNPECELLISKESWSYI



VEKPNPENGTCYPGHFAEYEELREQLSSVSSFERFEIFPKE



SSWPNHTVTGVSASCSHNGESSFYRNLLWLTGKNGLYP



NLSKSYANNKEKEVLVLWGVHHPPNIAAQKTLYHTENA



YVSVVSSHYSRKFTPEIAKRPKVRDQEGRINYYWTLLEP



GDTIIFEANGNLIAPRYAFALSRGFGSGIINSNAPMDKCD



AKCQTPQGAINSSLPFQNVHPVTIGECPKYVRSAKLRMV



TGLRNIPSIQSR (SEQ ID NO: 55)


 


A/Aichi/9/2009 (HA1 only)
DTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLENSHNG



KLCLLKGIAPLQLGNCSVAGWILGNPECELLISKESWSYI



VEKPNPENGTCYPGHFADYEELREQLSSVSSFERFEIFPK



ESSWPNHTVTGVSASCSHNGENSFYRNLLWLTGKNGLY



PNLSKSYANNKEKEVLVLWGVHHPPNIADQKALYHTEN



AYVSVVSSHYSRKFTPEIAKRPKVRDQEGRINYYWTLLE



PGDTIIFEANGNLIAPRYAFALSRGFGSGIINSNAPMDKCD



AKCQTPQGAINSSLPFQNVHPVTIGECPKYVRSAKLRMV



TGLRNIPSIQSR (SEQ ID NO: 56)


 


A/Aichi/37/09 (HA1 only)
DTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLENSHNG



KLCLLKGIAPLQLGNCSVAGWILGNPECELLISKESWSYI



VEKPNPENGTCYPGHFADYEELREQLSSVSSFERFEIFPK



ESSWPNHTVTGVSASCSHNGENSFYRNLLWLTGKNGLY



PNLSKSYANNKEKEVLVLWGVHHPPNIADQKTLYHTEN



AYVSVVSSHYSRKFTPEIAKRPKVRDQEGRINYYWPLLE



PGDTIIFEANGNLIAPRYAFALSRGFGSGIINSNAPMDKCD



AKCQTPQGAINSSLPFQNVHPVTIGECPKYVRSAKLRMV



TGLRNIPSIQSR (SEQ ID NO: 57)


 


A/Brisbane/59/2007 (HA1
DTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLENSHNG


only)
KLCLLKGIAPLQLGNCSVAGWILGNPECELLISKESWSYI



VEKPNPENGTCYPGHFADYEELREQLSSVSSFERFEIFPK



ESSWPNHTVTGVSASCSHNGESSFYRNLLWLTGKNGLY



PNLSKSYANNKEKEVLVLWGVHHPPNIGDQKALYHTEN



AYVSVVSSHYSRKFTPEIAKRPKVRDQEGRINYYWTLLE



PGDTIIFEANGNLIAPRYAFALSRGFGSGIINSNAPMDKCD



AKCQTPQGAINSSLPFQNVHPVTIGECPKYVRSAKLRMV



TGLRNIPSIQSR (SEQ ID NO: 58)


 


A/Washington/1/09
MKVKLLVLLCTFTATYADTICIGYHANNSTDTVDTVLEK



NVTVTHSVNLLENSHNGKLCLLKGIAPLQLGNCSVAGWI



LGNPECELLISKESWSYIVEKPNPENGTCYPGHFADYEEL



REQLSSVSSFERFEIFPKESSWPNHTVTGVSASCSHNGESS



FYRNLLWLTGKNGLYPNLSKSYANNKEKEVLVLWGVH



HPPNIVXQKTLYRTENAYVSVVSSHYSRKFTPEIAKRPK



VRDQEGRINYYWTLLEPGDTIIFEANGNLIAPRYAFALSR



GFGSGIINSNAPMDKCDAKCQTPQGAINSSLPFQNVHPV



TIGECPKYVRSAKLRMVTGLRNIPSIQSRGLFGAIAGFIEG



GWTGMVDGWYGYHHQNEQGSGYAADQKSTQNAINGI



TNKVNSVIEKMNTQFTAVGKEFNKLERRMENLNKKVD



DGFIDIWTYNAELLVLLENERTLDFHDSNVKNLYEKVKS



QLKNNAKEIGNGCFEFYHKCNDECMESVKNGTY (SEQ



ID NO: 59)


 


A/Canterbury/106/2004
MKVKLLVLLCTFTATYADTICIGYHANNSTDTVDTVLEK



NVTVTHSVNLLEDSHNGKLCLLKGIAPLQLGNCSVAGWI



LGNPECELLISKESWSYIVEKPNPENGTCYPGHFADYEEL



REQLSSVSSFERFEIFPKESSWPNHTVTGVSASCSHNGKS



SFYKNLLWLTGKNGLYPNLSKSYANNKEKEVLVLWGV



HHPPNIGDQKALYHTENAYVSVVSSHYSRKFTPEIAKRP



KVRDQEGRINYYWTLLEPGDTIIFEANGNLIAPRYAFALS



RGFGSGIINSNAPMDECDAKCQTPQGAINSSLPFQNVHPV



TIGECPKYVRSAKLRMVTGLRNIPSIQSRGLFGAIAGFIEG



GWTGMVDGWYGYHHQNEQGSGYAADQKSTQNAINGI



TNKVNSVIEKMNTQFTAVGKEFNKLERRMENLNKKVD



DGFIDIWTYNAELLVLLENERTLDFHDSNVKNLYEKVKS



QLKNNAKEIGNGCFEFYHKCNDECMESVKNGTYDYPKY



SEESKLNREKIDGVKLESMGVYQILAIYSTVASSLVLLVS



LGAISFWMCSNGSLQCRICI (SEQ ID NO: 60)


 


A/New_York/212/2001
MKAKLLVLLCTFTATYADTICIGYHANNSTDTVDTVLEK



NVTVTHSVNLLEDSHNGKLCLLKGIAPLQLGNCSVAGWI



LGNPECELLISKESWSYIVETPNPENGTCYPGYFADYEEL



REQLSSVSSFERFEIFPKGSSWPNHTVTGVSASCSHNGKS



SFYRNLLWLTGKNGLYPNLSMSYVNNKEKEVLVLWGV



HHPPNIGDQRALYHTENAYVSVVSSHYSRRFTPEIAKRP



KVRDQEGRINYYWTLLEPGDTIIFEANGNLIAPWYAFAL



SRGFGSGIITSNAPMDECDAKCQTPQGAINSSLPFQNVHP



VTIGECPKYVRSAKLRMVTGLRNIPSIQSRGLFGAIAGFIE



GGWTGMVDGWYGYHHQNEQGSGYAADQKSTQNAING



ITNKVNSVIEKMNTQFTAVGKEFNKLERRMENLNKKVD



DGFLDIWTYNAELLVLLENERTLDFHDSNVKNLYEKVK



SQLKNNAKEIGNGCFEFYHKCDNECMESVKNGTYDYPK



YSEESKLNREKIDGVKLESMGVYQILAIYSTVASSLVLLV



SLGAISFWMCSNGSLQCRICI (SEQ ID NO: 61)


 


A/New_York/307/2001
KAKLLVLLCTFTATYADTICIGYHANNSTDTVDTVLEKN



VTVTHSVNLLEDSHNGKLCRLKGTAPLQLGNCSIAGWIL



GNPECESLFSKESWSYIAETPNPKNGTCYPGYFADYEEL



REQLSSVSSFERFEIFPKDSSWPNHTVTKGVTASCSHNGK



SSFYKNLLWLTEKNGLYPNLSKSYVNKKGKEVLVLWG



VHHPSNMGDQRAIYHKENAYVSVLSSHYSRRFTPEIAKR



PKVRDQEGRINYYWTLLEPGDTIIFEANGNLIAPWYAFA



LSRGFGSGIIISNASMGECDAKCQTPQGAINSSLPFQNVH



PVTIGECPKYVRSTKLRMVTGLRNVPSIQSRGLFGAIAGF



IEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAIN



GITNKVNSIIEKMNTQFTAVGKEFNRLERRMENLNKKVD



DGFLDIWTYNAELLVLLENERTLDFHDSNVKDLYEKVK



TQLKNNAKEIGNGCFEFYHKCNNECMESVKNGTYDYPK



YSKESKLNREKIDGVKLESMGVYQILAIYSTVASSLVLLV



SLGAISFWMCSNGSLQCRICI (SEQ ID NO: 62)


 


A/Taiwan/117/1996
MKAKLLVLLCAFTATYADTICIGHHANNSTDTVDTVLE



KNVTVTHSVNLLEDSHNGKLCRLKGTAPLQLGNCSVAG



WILGNPECESLFSKESWSYIAETPNPENGTCYPGYFADYE



ELREQLSSVSSFERFEIFPKESSWPNHTVTKGVTASCSHN



GKSSFYKNLLWLTGKNGLYPNLSKSYVNHKEKEVLVL



WGVHHPSNIRDQRAIYHTENAYVSVVSSHYSRRFTPEIA



KRPKVRDQEGRINYYWTLLEPGDTIIFEANGNLIAPWYA



FALSRGFGSGIITSNASMGECDAKCQTPQGAINSSLPFQN



VHPVTIGECPKYVRSTKLRMVTGLRNIPSIQSRGLFGAIA



GFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNA



INGI (SEQ ID NO: 63)


 


A/Brazil/099/01
DTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNG



KLCLLKGIAPLQLGNCSVAGWILGNPECELLISKESWSYI



VETPNPENGTCYPGYFADYEELREQLSSVSSFERFEIFPKE



SSWPNHTVTGVSASCSHNGKSSFYRNLLWLTGKNGLYP



NLSKSYANNKEKEVLVLWGVHHPPNIGDQRALYHTENA



YVSVVSSHYSRRFTPEIAKRPKVRDQEGRINYYWTLLEP



GDTIIFEANGNLIAPRYAFALSRGFGSGIITSNAPMDECDA



KCQTPQGAINSSLPFQNVHPITIGECPKYVRSAKLRMVTG



LRNIPSIQS (SEQ ID NO: 64)









Binding characteristics of these strains may be assessed, for example with respect to umbrella-topology glycans and/or with respect to cone-topology glycans. Binding characteristics may be assessed with respect to, for example, α2-6 sialylated glycans and/or with respect to α2-3 sialylated glycans. In some embodiments, binding characteristics are assessed with respect to at least long α2-6 sialylated glycans (e.g., 6′SLN-LN glycans).
Those of ordinary skill in the art, after reading the present specification, will appreciate that any H1 polypeptide listed in Table 4 that shows appropriate glycan binding characteristics and/or appropriate human infectivity (e.g., not human pandemic infectivity) may be used as a reference against which “enhanced” human binding H1 HA polypeptides are compared. Comparably, any H1 polypeptide listed in Table 4 that shows appropriate glycan binding characteristics (e.g., extensive binding to umbrella-topology glycans and/or preference for umbrella-topology glycans as compared with cone-topology glycans) and/or appropriate human infectivity (e.g., human pandemic infectivity) may be used as a comparator to confirm “enhanced” human binding of a particular H1 HA polypeptide (e.g., a particular H1 HA polypeptide variant).
Example 4
Receptor Binding Properties of Mutated 2009H1N1 Influenza A Virus HA
Materials and Methods
Cloning, Baculovirus Synthesis, Expression and Purification of HA
Briefly, recombinant baculoviruses with WT or mutant HA genes, respectively, were used to infect (MOI=1) suspension cultures of Sf9 cells (Invitrogen, Carlsbad, Calif.) cultured in BD Baculogold Max-XP SFM (BD Biosciences, San Jose, Calif.). Infection was monitored and the conditioned media was harvested 3-4 days post-infection. Soluble HA from the harvested conditioned media was purified using Nickel affinity chromatography (HisTrap HP columns, GE Healthcare, Piscataway, N.J.). Eluting fractions containing HA were pooled, concentrated and buffer exchanged into 1×PBS pH 8.0 (Gibco) using 100K MWCO spin columns (Millipore, Billerica, Mass.). Purified protein was quantified using BCA method (Pierce).
Homology Based Structural Modeling of CA/04 and Mutants
Using the SWISS-MODEL web-based automated homology modeling platform (http://swissmodel.expasy.org/), homology structural models of CA04, CA04M1 and CA04M2 were constructed. The template structure chosen by SWISS-MODEL was that of a recently solved crystal structure of 2009H1N1 HA (PDB ID: 3LZG). The starting pose of the HA-human receptor complex was obtained by superimposing the modeled HA structure with the co-crystal structure of 1918H1N1 HA with human receptor (PDB ID: 2WRG). The starting structural complex was subject to energy minimization (500 steps of steepest descent followed by 500 steps of conjugate gradient). The AMBER force-field was used to assign potentials and charges. The default version of AMBER was that provided with the Discover module of InsightII molecular modeling suite (Accelrys, San Diego, Calif.).
Binding of Recombinant WT and Mutant CA04 HAs to Human Tracheal Tissue Sections
Paraffinized human tracheal (US Biological) tissue sections were deparaffinized, rehydrated and incubated with 1% BSA in PBS for 30 minutes to prevent non-specific binding. HA was pre-complexed with primary antibody (mouse anti 6×His tag, Abcam) and secondary antibody (Alexa fluor 488 goat anti mouse, Invitrogen) in a molar ratio of 4:2:1, respectively, for 20 minutes on ice. Tissue binding was performed over different HA concentrations by diluting the pre-complexed HA in 1% BSA-PBS. Tissue sections were then incubated with the HA-antibody complexes for 3 hours at room temperature (RT). Tissue sections were counterstained by propidium iodide (Invitrogen; 1:100 in TBST). Tissue sections were mounted and then viewed under a confocal microscope (Zeiss LSM510 laser scanning confocal microscopy). In the case of sialidase pretreatment, tissue sections were incubated with 0.2 units of Sialidase A (recombinant from Arthrobacter ureafaciens, Prozyme) for 3 hours at 37° C. prior to incubation with the proteins. This enzyme has been demonstrated to cleave the terminal Neu5Ac from both Neu5Acα2→3Gal and Neu5Acα2→6Gal motifs.
Dose Dependent Direct Binding of WT and Mutant CA04 HAs
To investigate the multivalent HA-glycan interactions a streptavidin plate array comprising representative biotinylated α2→3 and α2→6 sialylated glycans as described previously (Srinivasan et al., 2008, Proc. Natl. Acad. Sci. U.S.A., 105:2800-05; incorporated herein by reference) (FIG. 14). 3′SLN, 3′SLN-LN, 3′SLN-LN-LN are representative avian receptors. 6′SLN and 6′SLN-LN are representative human receptors. Biotinylated glycans were obtained from the Consortium of Functional Glycomics through their resource request program. Streptavidin-coated High Binding Capacity 384-well plates (Pierce) were loaded to the full capacity of each well by incubating the well with 50 μl of 2.4 μM of biotinylated glycans overnight at 4° C. Excess glycans were removed through extensive washing with PBS. The trimeric HA unit comprises of three HA monomers (and hence three RBS, one for each monomer). The spatial arrangement of the biotinylated glycans in the wells of the streptavidin plate array favors binding to only one of the three HA monomers in the trimeric HA unit. Therefore in order to specifically enhance the multivalency in the HA-glycan interactions, the recombinant HA proteins were pre-complexed with the primary and secondary antibodies in the ratio of 4:2:1 (HA:primary:secondary). The identical arrangement of 4 trimeric HA units in the precomplex for all the HAs permits comparison between their glycan binding affinities.
A stock solution containing appropriate amounts of histidine-tagged HA protein, primary antibody (Mouse anti 6×His tag IgG) and secondary antibody (HRP conjugated goat anti Mouse IgG (Santacruz Biotechnology) in the ratio 4:2:1, respectively, and incubated on ice for 20 minutes. Appropriate amounts of precomplexed stock HA were diluted to 250 μl with 1% BSA in PBS. 50 μl of precomplexed HA was added to each of the glycan-coated wells and incubated at room temperature for 2 hours followed by the above wash steps. The binding signal was determined based on HRP activity using Amplex Red Peroxidase Assay (Invitrogen, CA) according to the manufacturer's instructions. The experiments were done in triplicate. Minimal binding signals were observed in the negative controls including binding of precomplexed unit to wells without glycans and binding of the antibodies alone to the wells with glycans. The binding parameters, cooperativity (n) and apparent binding constant (Kd′), for H2 HA-glycan binding were calculated by fitting the average signal value (from the triplicate analysis) and the HA concentration to the linearized form of the Hill equation:




  
    log
    ⁡
    
      (
      
        y
        
          1
          -
          y
        
      
      )
    
  
  =
  
    
      n
      *
      
        log
        ⁡
        
          (
          
            [
            HA
            ]
          
          )
        
      
    
    -
    
      log
      ⁡
      
        (
        
          K
          d
          ′
        
        )
      
    
  




where y is the fractional saturation (average binding signal/maximum observed binding signal). The theoretical y values calculated using the Hill equation:




  y
  =
  
    
      
        [
        HA
        ]
      
      n
    
    
      
        
          [
          HA
          ]
        
        n
      
      +
      
        K
        d
        ′
      
    
  




(for the set of n and Kd′ parameters) were plotted against the varying concentration of HA to obtain the binding curves for the representative human receptor (6′SLN-LN) in FIG. 15D and FIG. 16.
Results
CA04M1 (Ile219Lys) and CA04M2 (Ser186→Pro+Ala189→Thr+Glu227→Ala)
In Example 1, the sequence and structure of the RBS of CA04 was compared with that of highly transmissible human-adapted H1N1 HAs. In Example 1, the inventors predicted that a mismatch in the inter-residue interaction between Ile219 (hydrophobic) and Glu227 (ionic) in CA04 HA potentially disrupts its optimal contact with the human receptors which is in turn responsible for lowering the binding strength (FIG. 13A) (see Maines et al., 2009, Science, 325:484-87; incorporated herein by reference). Without wishing to be bound by any one particular theory, this mismatch may explain the inability of the natural variants to substantially improve human receptor-binding strength despite acquiring mutations at Asp225 in the RBS. As explained in Example 1, the present inventors provided the insight that fixing this mismatched combination would improve the human receptor binding strength of 2009H1N1 HA. As presented in Example 1, structural analysis of the RBS of CA04 HA indicated two possible ways of fixing this mismatch. The first possibility involved a single Ile219→Lys mutation (CA04M1) that would make the Lys219-Glu227 interaction ionic (FIG. 13B) similar to that observed in RBS of seasonal H1N1 influenza viruses (Maines et al., 2009, Science, 325:484-87; incorporated herein by reference). The second possibility involved three amino acid changes, Ser186Pro/Ala189→Thr/Glu227→Ala (CA04M2) (FIG. 13C) that would make the interactions hydrophobic similar to that observed in the RBS of SC18 HA (FIG. 13D). The present inventors confirmed that the prediction described in Example 1 was accurate by recombinantly expressing the CA04M1 and CA04M2 mutants and quantifying their respective glycan receptor binding strengths by analyzing them (in their pre-complexed state) using the dose-dependent glycan array analysis.
CA04M1 and CA04M2 showed specific binding to both the representative human receptors (6′SLN and 6′SLN-LN; FIG. 14) on the array (only minimal binding signals to avian receptors were observed at the higher concentrations of 20-40 μg/ml) (FIG. 15A,B). The binding strength of CA04M1 (Kd′ ̃50 picomolar (pM)) and CA04M2 (Kd′ ̃6 pM) to 6′SLN-LN is significantly higher than that of CA04 HA (and the natural variants at the 225 position) and is in the same range as that of SC18 HA (FIG. 15C). The differences in the human receptor binding strengths of CA04, CA04M1 and CA04M2 HAs were also reflected in their staining of the apical surface of the human tracheal tissue section, which predominantly expresses human receptors and is a target for efficient viral transmission by respiratory droplets (see, e.g., Srinivasan et al., 2008, Proc. Natl. Acad. Sci. U.S.A., 105:2800-05; and Chandrasekaran et al., 2008, Nat. Biotechnol., 26:107-13; both of which are incorporated herein by reference). In comparison to CA04 HA, both CA04M1 and CA04M2 HAs show more intense staining of the apical surface of the human tracheal tissue sections (FIG. 15D). Thus, as predicted in Example 1, both of CA04M1 and CA04M2 HAs improved human HA receptor binding strength.
In contrast to the qualitative binding assays described by Childs et al., the present inventors performed dose-dependent binding assays with recombinant HAs which are able to quantify the differences in the relative glycan receptor-binding strengths of WT and mutant HAs. Using such assays, the present inventors have demonstrated mutants of CA04 HA (CA04M1 and CA04M2) that have significantly higher human receptor binding strength as compared to WT HA. These results validated the prediction presented in Example 1, i.e., that fixing mismatched molecular interactions in the RBS of 2009H1N1 HA substantially increases its human receptor binding strength. The present invention encompasses the recognition that qualitative binding assays would have likely missed identification of these mutants.
The present invention encompasses the recognition that mutant 2009H1N1 HAs that exhibit increased human receptor binding strength would be likely to promote enhanced human transmission of 2009H1N1 strains. Indeed, human receptor-binding strength has been shown to correlate with human-to-human transmissibility of the 1918 pandemic H1N1 virus (Srinivasan et al., 2008, Proc. Natl. Acad. Sci. U.S.A., 105:2800-05; and Tumpey et al., 2007, Science, 315:655-59; both of which are incorporated herein by reference). In addition, the present invention encompasses the recognition that such mutant HAs can be useful for the production of vaccines and/or therapeutics as described herein.
CA04M3 (Asp225→Glu), CA04M4 (Asp225→Asn), and CA04M5 (Asp225→Gly)
Recent isolates of the 2009H1N1 viruses have acquired mutations in the RBS of HA thereby raising concern regarding the potential evolution of a more virulent and transmissible strain (Melidou et al., May 20, 2010, Virus Res.; incorporated herein by reference). Notably, Asp225, which is involved in human receptor binding (Srinivasan et al., 2008, Proc. Natl. Acad. Sci. U.S.A., 105:2800-05; incorporated herein by reference), has mutated into Glu, Asn or Gly. Monitoring such mutations in the glycan receptor-binding site (RBS) of hemagglutinin (HA) may be useful to assess their impact on the human-to-human transmissibility of the 2009H1N1 viruses. Qualitative assessment of the binding specificity of at the 225 mutants showed that their binding properties are similar to the WT HA (Hua et al., 2010, PLoS Currents: Influenza; incorporated herein by reference). In contrast, the present inventors have carried out quantitative analyses of the effect of Asp225 mutations generated in the context of CA04 HA on the human receptor-binding strength using a dose-dependent glycan array binding analysis (FIG. 16).
The present inventors' analysis demonstrates that the binding specificity to the representative human receptor (6′SLN-LN; FIG. 14) is the same between Asp225→Glu (CA04M3) and Asp225→Asn (CA04M4) mutants, consistent with the results obtained in the previous study (Hua et al., 2010, PLoS Currents: Influenza; incorporated herein by reference). However there were differences in their human receptor binding strengths where CA04M4 (Kd′ ̃0.7 nanomolar (nM))>CA04 (Kd′ ̃1 nM)>>CA04M3 (Kd′ ̃7 nM). The Asp225→Gly (CA04M5) mutant showed a dramatically reduced dose-dependent binding to human receptors and also bound to avian receptors. The binding of CA04M5 mutant to representative avian receptors is in agreement with the previous studies (Hua et al., 2010, PLoS Currents: Influenza; incorporated herein by reference). Transmission studies are carried out in ferret and mouse essentially as described in Example 1 and in Maines et al. (2009, Science, 325:484-87; both of which are incorporated herein by reference) to confirm these results. Taken together, none of the mutants with the natural amino acid substitutions at the 225 position show substantially improved human receptor binding strength over the WT HA.
EQUIVALENTS
Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. The scope of the present invention is not intended to be limited to the above Description, but rather is as set forth in the following claims:

## Claims

1. An H1 HA influenza hemagglutinin (“HA”) polypeptide variant whose amino acid sequence:
i) shows at least 90% identity with a reference wild type H1 HA polypeptide that is the HA from A/California/04/2009 strain (SEQ ID NO: 46);
ii) includes a sequence substitution relative to the reference at each of the following positions:















Position
Amino 



(corresponding to
acid residue



wild type H3 HA)
in reference









186
Ser



189
Ala



219
Ile



227
Glu









and iii) differs from that of each of ADA76, A/duck/Alberta/35/76 (H1N1) (SEQ ID NO: 23); ASI30, A/Swine/Iowa/30 (H1N1) (SEQ ID NO: 24); APR34, A/Puerto Rico/8/34 (H1N1) (SEQ ID NO: 25); ASC18, A/South Carolina/1/18 (H1N1) (SEQ ID NO: 26); AT91, A/Texas/36/91 (H1N1) (SEQ ID NO: 27); ANY18, A/New York/1/18 (H1N1) (SEQ ID NO: 28); ADU63, A/Duck/Ukraine/1/63 (H3N8) (SEQ ID NO: 29); AAI68, A/Aichi/2/68 (H3N2) (SEQ ID NO: 30); AM99, A/Moscow/10/99 (H3N2) (SEQ ID NO: 31); ADS97, A/Duck/Singapore/3/97 (H5N3) (SEQ ID NO: 32); Viet04, A/Vietnam/1203/2004 (H5N1) (SEQ ID NO: 33).

2. A pharmaceutical composition comprising the H1 HA polypeptide variant of claim 1.

3. A method of treating influenza infection by administering a composition comprising the H1 HA polypeptide variant of claim 1 to a subject.

4. A vaccine composition comprising the H1 HA polypeptide variant of claim 1.

5. A method comprising administering the vaccine composition of claim 4 to an individual suffering from or susceptible to influenza virus infection.

6. The H1 HA polypeptide variant of claim 1, wherein the variant residue at position 219 is Lys.

7. The H1 HA polypeptide variant of claim 1, wherein the variant residue at position 186 is Pro.

8. The H1 HA polypeptide variant of claim 1, wherein the variant residue at position 189 is Thr.

9. The H1 HA polypeptide variant of claim 1, wherein the variant residue at position 227 is Ala.

10. The H1 HA polypeptide variant of claim 1, whose amino acid sequence further includes one or more sequence substitutions relative to the reference at positions selected from the group consisting of: 98, 136, 137, 138, 145, 153, 155, 156, 159, 183, 187, 190, 192, 193, 194, 195, 196, 215, 222, 225, 226, 228, and combinations thereof, corresponding to positions in wild type H3 HA sequence.

11. The H1 HA polypeptide variant of claim 10, wherein the variant residue at position 225 is selected from the group consisting of Asn, Gly, and Glu.

12. The H1 HA polypeptide variant of claim 10, wherein the variant residue at position 145 is selected from the group consisting of Ser and Asn.