WO2024258949A2 - Immunosorbent nanoparticles and methods of using thereof - Google Patents
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- WO2024258949A2 WO2024258949A2 PCT/US2024/033583 US2024033583W WO2024258949A2 WO 2024258949 A2 WO2024258949 A2 WO 2024258949A2 US 2024033583 W US2024033583 W US 2024033583W WO 2024258949 A2 WO2024258949 A2 WO 2024258949A2
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
- C07K16/18—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans
- C07K16/28—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
- C07K16/2803—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily
- C07K16/2833—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily against MHC-molecules, e.g. HLA-molecules
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K2317/00—Immunoglobulins specific features
- C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
- C07K2317/22—Immunoglobulins specific features characterized by taxonomic origin from camelids, e.g. camel, llama or dromedary
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K2317/00—Immunoglobulins specific features
- C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
- C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
- C07K2317/569—Single domain, e.g. dAb, sdAb, VHH, VNAR or nanobody®
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K2317/00—Immunoglobulins specific features
- C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
- C07K2317/92—Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value
Definitions
- Whole blood may be characterized as comprising three size classes of molecules: (i) small molecules having a size less than 1.5 nm such as water, electrolytes, glucose, urea, and small compounds, etc.; (ii) medium sized molecules having a mass of about 0.5 ⁇ 50 kDa or a size of about 1.5 ⁇ 4 nm (which are often referred to as “middle molecules”); and (iii) large molecules having a mass over 50 kDa or a size over 4 nm.
- hemodialysis is a lifesaving therapy wherein a hemodialyzer instrument fulfils the blood filtering function of healthy kidneys.
- B2M beta-2 microglobulin
- DRA dialysis related amyloidosis
- B2M In patients with reduced renal function, who must undergo long-term dialysis, B2M can accumulate at concentrations more than 60 times higher than normal. This can lead to the aggregation of B2M into insoluble amyloid fibrils throughout the body, causing painful disorders of the bones and joints, including carpal tunnel syndrome and, in extreme cases, paraplegia. Thus, control B2M concentrations in subjects is of considerable medical importance.
- Albumin is also a medium sized molecule (having a diameter of about 2.5 nm). Albumin, however, is an essential component in blood as it functions to maintain plasma oncotic pressure.
- the present invention is directed to an immunosorbent nanoparticle comprising or consisting of (a) a plurality of one or more subunit proteins which form a protein cage having an exterior surface, and (b) a binder against beta-2 microglobulin (B2M), said binder is recombinantly linked, directly or indirectly, to at least one of the one or more subunit proteins, wherein the binder is presented on the exterior surface.
- B2M beta-2 microglobulin
- the binder is (a) a nanobody comprising the following CDR sequences: SEQ ID NO: 25, SEQ ID NO: 26, and SEQ ID NO: 27, or (b) a DARPin comprising SEQ ID NO: 29 or SEQ ID NO: 30.
- the binder is a nanobody having a sequence that (a) contains CDR sequences: SEQ ID NO: 25, SEQ ID NO: 26, and SEQ ID NO: 27, and (b) at least 90% sequence identity to SEQ ID NO: 28.
- the one or more subunit proteins are selected from the group consisting of: a subunit protein having 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 1, and a subunit protein having 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 2; a subunit protein having 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 3, and a subunit protein having 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 4; a subunit protein having 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 5,
- the immunosorbent nanoparticle comprises or consists of: a plurality of protein chains having SEQ ID NO: 42 and SEQ ID NO: 43; a plurality of protein chains having SEQ ID NO: 44 and SEQ ID NO: 45; a plurality of protein chains having SEQ ID NO: 46 and SEQ ID NO: 47; a plurality of protein chains having SEQ ID NO: 48 and SEQ ID NO: 49; or a plurality of protein chains having SEQ ID NO: 50 and SEQ ID NO: 51.
- the one or more subunit proteins are selected from the group consisting of a subunit protein having 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 1, and a subunit protein having 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 2; a subunit protein having 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 3, and a subunit protein having 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 4; a subunit protein having 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 5,
- the binder comprises or consists of SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, or SEQ ID NO: 33.
- the immunosorbent nanoparticle is immobilized on solid substrate.
- the present invention is directed to an article comprising (a) a housing having at least one outlet, and (b) a plurality of immunosorbent nanoparticles, as described herein, contained within the housing.
- the article comprising immunosorbent nanoparticles as described herein is in fluidic communication with a dialyzer.
- the present invention is directed to a kit comprising (1) a plurality of immunosorbent nanoparticles, as described herein, or (2) an article comprising a housing having at least one outlet and the plurality of immunosorbent nanoparticles.
- the present invention is directed to a hemodialysis device comprising (a) a dialyzer, and (b) an article comprising a housing having at least one outlet and a plurality of immunosorbent nanoparticles, as described herein.
- the article comprising immunosorbent nanoparticles as described herein is in fluidic communication with the dialyzer.
- the present invention is directed to a hemodialysis device comprising (a) a dialyzer, and (b) an article comprising a housing having at least one outlet, and (b) a plurality of self-assembling protein cages contained within the housing.
- the plurality of self-assembling protein cages comprise one or more subunit proteins are selected from the group consisting of: a subunit protein having 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 1, and a subunit protein having 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 2; a subunit protein having 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 3, and a subunit protein having 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 4; a subunit protein having 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to
- the article comprising immunosorbent nanoparticles as described herein is in fluidic communication with the dialyzer.
- the present invention is directed to a method of removing beta-2 microglobulin (B2M) from a liquid, which comprises (a) contacting the liquid with a plurality of immunosorbent nanoparticles, which are BACs as described herein, or flowing the liquid through an article or a hemodialysis device comprising the BACs, thereby binding the B2M to the plurality of BACs, and then (b) separating the liquid from the BACs having B2M bound thereto.
- B2M beta-2 microglobulin
- FIG.1 Assembled BACs bind to and coelute with B2M cargo.
- A nbBAC-1-SL mixed with B2M elutes in size-exclusion chromatography (SEC) at a volume consistent with proper cage assembly (denoted with asterisk). SDS-PAGE analysis of the cage peak fraction indicates B2M co-elutes with BAC.
- B nbBAC-2 mixed with B2M elutes in SEC at a volume consistent with proper cage assembly (denoted with asterisk).
- FIG.2 Purification and B2M binding of an improved B2M-binding nanoparticle, nbBAC-1-LL.
- SDS-PAGE analysis (right) of the cage peak fraction indicates B2M co-elutes with BAC.
- FIG.3 Binding of B2M by nbBAC-1-LL in a B2M retention assay.
- nbBAC-1- LL binds to soluble B2M and retains it in the supernatant of a concentrator column with a molecular weight cutoff of 100 kDa (right).
- B2M flows through the membrane unimpeded (left).
- B2M has a MW of 13.8 kDa and nbBAC has a MW of 662 kDa.
- An SDS-PAGE gel shows the composition of the flow through in each experiment. B2M is only present in the gel run on the flow through of the experiment without nbBAC added, showing that B2M is fully retarded by the interaction between nbBAC-1-LL and B2M.
- FIG.4 Immunoblot analysis of flowthrough from the B2M retention assay. Serial dilutions of flow through from the size-filtration retention assay either with (top) or without (bottom) nbBAC-1-LL added to supernatant were analyzed for B2M via immunoblot. a positive control (1 ⁇ M B2M) is depicted in top right.
- FIG.5 Measurement of binding affinity of B2M to nbBAC-1-LL.
- FIG.6 Nanoparticle nbBAC-1-LL bound to a stationary matrix fully removes B2M from human serum. SDS-PAGE gels are analyzed by Western blotting with an anti-B2M antibody. A: Analysis of flow through of serum supplemented with B2M flowed over resin, either with nbBAC-1-LL bound to the column (lanes 5-7) or without (lanes 2-4). Lane 1 is 20X diluted serum supplemented with B2M.
- TACs target adsorbent cages
- TACs may be used to remove small proteins and other molecules from a liquid phase via size-based separation methods in the art, (e.g., size-based filtration) or adsorption chromatography (e.g., polyvalent binding to a stationary matrix). As such, TACs may be used to remove abnormal or unwanted molecules from, e.g., the blood of, subjects.
- TACs that comprise either nanobodies or DARPins against beta-2 microglobulin (B2M).
- B2M adsorbent cages BACs
- BACs comprising nanobodies as the binder are referred to as “nbBACs”
- DARPBACs BACs comprising DARPins as the binder
- the BACs specifically bind B2M with nanomolar binding affinity ( ⁇ 64 nM).
- B2M molecules complexed with BACs may be readily removed from a liquid phase (e.g., plasma) using size-based separation methods in the art, (e.g., size- based filtration) or adsorption chromatography (e.g., polyvalent binding to a stationary matrix). Therefore, BACs may be employed in combination with hemodialysis to reduce the risk of and/or treat dialysis-related amyloidosis, existing methods for treating dialysis-related amyloidosis.
- Self-assembling protein cages are known in the art. See, for example, US8969521, US9066870, US9630994, US10248758, US10501733, US20200397886, US20210163540, and WO2020/220044.
- Self-assembling protein cages comprise a plurality of polypeptide subunits that are held together via intermolecular forces to form a protein nanoparticle having a “shell”, i.e., an exterior surface.
- a “protein cage” refers to a plurality of polypeptides (“subunits” or “oligomeric protein units”) which collectively self-assemble to form a three-dimensional structure whereby some of the amino acids of a subunit are exterior residues that form part of the “shell”, and the remainder of the amino acids of the subunit are interior residues which may form an interior cavity.
- the amino acid sequences of the subunits may be the same or different.
- protein cages are formed with (a) subunits having the same amino acid sequence, or (b) 2 ⁇ 3 different of subunits, e.g., some subunits have a first amino acid sequence and some protein cage subunits have a second amino acid sequence.
- Each subunit of a protein cage typically occurs in multiple copies (e.g., 12, 24, or 60 copies), and at least one of the subunits has one or more amino acids at or near a terminal end that is exposed on the exterior surface of the protein cage.
- the subunits of the protein cages self-assemble into a symmetric geometric shapes that mimic the 3D shape of any one of the Platonic solids: tetrahedron, cube, octahedron, icosahedron, and dodecahedron.
- BACs exemplified herein are based on a tetrahedral protein cage known as “T33-51” (see Cannon (2020)) and an icosahedral protein cage known as “I53-50” (see Bale (2016)).
- T33-51 tetrahedral protein cage
- I53-50 icosahedral protein cage
- nbBAC-1 and DARPBAC-1 to -3 have a tetrahedral protein cage based on T33-51
- nbBAC-2 has a protein cage based on I53-50.
- sequences of the subunits of nbBAC-1 and DARPBAC-1 to -3 comprise SEQ ID NO: 1 (“subunit A”) and SEQ ID NO: 2 (“subunit B”, which is a truncation of SEQ ID NO: 6).
- the binder is covalently linked to subunit B and subunit A comprises SEQ ID NO: 5.
- the binder is covalently linked to subunit A, i.e., SEQ ID NO: 1 , which is a truncation of SEQ ID NO: 5.
- SEQ ID NO: 1 has about 90% sequence identity to SEQ ID NO: 5.
- sequences of the subunits of nbBAC-2 comprise SEQ ID NO: 3 (“subunit A”) and SEQ ID NO: 4 (“subunit B”).
- SEQ ID NO: 3 has 97.1% sequence identity to SEQ ID NO: 7
- SEQ ID NO: 4 has 95% sequence identity to SEQ ID NO: 8.
- the binder is covalently linked to subunit B.
- the protein cages based on T33-51 have 12 pairs of subunit chains A and B (i.e., a stoichiometry of A 12 B 12 ) and protein cages based on I53-50 have 60 pairs of subunit chains A and B (i.e., a stoichiometry of A60B60).
- nbBAC-1 and DARPBAC-1 to -3 have 12 copies and single molecules of nbBAC-2 have on their surface 60 copies of the given binder against B2M on their surfaces.
- the exemplified BACs comprise the given binder against B2M covalently linked to an amino acid residue of one of the subunit chains that is presented at the outer surface of the protein cage, which allows the given binder to interact with and bind B2M.
- Any protein cage known in the art may be employed as the scaffold to which a binder against B2M is covalently linked thereto to give a BAC as contemplated herein.
- Suitable protein cages include: T33-51, I53-50, T33-31, T33-21, T33-28, I53-47, I53-40, I52-32, I32-28, ferritin, and sulfur oxygenase reductase, which are composed of subunits having the following amino acid sequences: [0040] T33-51 protein cage ( ⁇ 130 nm dia.): Subunit A: mftrrgdqgetdlanrarvgkdspvvevqgtidelnsfigyalvLSRWDdiRNdlFRiqNdlfVl gEdvsTgGKGRTVTmDmiiYlikRsvEmkAEigKIELfvvpGGSVEsaslhmaravsrrlerrik aaselteinanvllyanmlsnilfmhalisnkRLNIPEKIWSIHRVSLE (SEQ ID NO: 5)
- Subunit B mrittkv
- a given binder against B2M is preferably covalently linked to any one of the exterior residues of one of the subunit chains of a protein cage above to result in a BAC as contemplated herein.
- the given binder is recombinantly fused to one of the exterior residues of one of the subunit chains of a protein cage.
- the given binder is covalently attached to one of the exterior residues of one of the subunit chains of a protein cage using chemical protein synthesis techniques in the art.
- the exterior residue to which the binder is covalently linked to is one of the last exterior residues at or near the C-terminus of the subunit chain.
- a subunit chain may be truncated to remove 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 16 residues at the N-terminus and/or the C-terminus and the binder is covalently linked to the N- or C-terminus of the truncated subunit chain.
- a subunit chain may be truncated to remove any interior residues at the C-terminus and the binder is covalently linked to the C-terminus of the truncated subunit chain.
- a subunit chain may be truncated to remove any interior residues at the N-terminus and the binder is covalently linked to the N-terminus of the truncated subunit chain.
- a subunit chain is modified by adding to its N- or C-terminus one or more amino acid residues, which will be presented on the exterior of the protein cage, and the binder is covalently linked to the one or more amino acid residues that were added.
- the binder of the nbBAC constructs is a nanobody having the following CDR sequences: SEQ ID NO: 25, SEQ ID NO: 26, and SEQ ID NO: 27.
- the binder is a nanobody comprising the following CDR sequences: SEQ ID NO: 25, SEQ ID NO: 26, and SEQ ID NO: 27.
- the nanobody sequence comprises CDR sequences: SEQ ID NO: 25, SEQ ID NO: 26, and SEQ ID NO: 27, and at least 90% sequence identity to SEQ ID NO: 28.
- the binder of the DARPBAC constructs is a DARPin.
- sequences of the exemplified DARPins comprise at least about 80% sequence identity to each other and have the following consensus sequence: K-K-X1-L-D-A-A-S-A-G-X2-D-D-X3-V-X4-X5-L-X6-A-X7-G-A-D-V-N-A-S-X8-X9- X10-G-X11-T-P-L-H-X12-A-A-X13-X14-G-H-L-E-I-V-X15-V-L-L-X16-X17-G-A-D- X18-N-A-S-D-X19-Y-G-W-T-P-L-H-X20-A-A-X21-X22-G-H-L-E-I-V-X23-X24-L-L- X25-X26-G-A-D-V-N-A-Q-D-K-F-
- the binder is a DARPin comprising SEQ ID NO: 29, wherein each X is independently any amino acid.
- the binder is a DARPin comprising SEQ ID NO: 30, wherein X1 is Q or L; X2 is Y or Q; X3 is Q or E; X4 is A or R; X5 is A or I; X6 is L or M; X7 is K or N; X8 is D or N; X9 is W or N; X10 is N or W; X11 is W or Y; X12 is S or A; X13 is Q or Y; X14 is W, R or D; X15 is E or D; X16 is K or A; X17 is R, N or Y; X18 is I or V; X19 is W or Y; X20 is V or S; X21 is T or R; X22 is W, N or Q; X23 is E or D
- the BACs exemplified herein indicate that subunit proteins forming a protein cage of BAC (excluding the binder and any linkers and tags) need only have at least about 90% sequence identity to the parental sequences, i.e., the sequences of the subunits of the known protein cages from which the BACs are based. Therefore, in some embodiments, the sequences of subunits forming the protein cage of a BAC are at least 90% identical to the parental sequences of the protein cages described herein. Thus, where the BAC is based on the T33-51 protein cage, then the sequences of the subunits forming the protein cage of the BAC have at least 90% sequence identity to SEQ ID NO: 5 and at least 90% sequence identity to SEQ ID NO: 6.
- BACs comprise: (1) a protein cage formed of: ⁇ a subunit protein having 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 1, and a subunit protein having 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 2; ⁇ a subunit protein having 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 3, and a subunit protein having 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 3, and a subunit protein having 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%,
- BAC Design [0056] The subunit proteins of the BACs exemplified herein were over-expressed in E. coli cells. The BACs self-assemble and to therefore appear in their assembled forms upon expression and purification. The BACs were purified by affinity chromatography. For binding tests, the BACs were mixed with purified B2M protein and assessed for binding using size exclusion chromatography (SEC). In the event of a stable interaction between the BAC and B2M, co-elution of proteins would be expected. If no interaction occurs, B2M would be expected to elute much later due to its significantly smaller size relative to the BAC assembly. nbBAC-1-SL and nbBAC-2 co-eluted with B2M. See FIG.1.
- nbBAC-1-SL displayed limited stability in its assembled state, precipitating out of solution over time, and exhibited a propensity to disassemble into smaller subunits; and nbBAC-2 displayed sub-stoichiometric binding to B2M when visualized on SDS-PAGE.
- a BAC comprising a longer 12-residue (GS) 6 linker i.e., nbBAC-1- LL
- GS 12-residue
- nbBAC-1-LL was designed and tested.
- nbBAC-1-LL exhibited better stability and a higher yield of protein eluting at the expected elution volume compared nbBAC-1-SL. See FIG.2.
- nbBAC-2 exhibited a limited capacity for B2M binding compared to the nbBAC-1 constructs.
- BACs based on T33-51 protein cages are preferred over BACs based on I53-50 protein cages.
- B2M Removal To characterize the ability of the BACs to bind and sequester B2M, size-based retention assays utilizing a centrifugal filter with a molecular weight cutoff of 100 kDa, which falls between the size of B2M and the BACs, were employed. When centrifuged, a stable interaction between B2M and BAC should prevent B2M from passing through the filter, whereas B2M alone should pass through the filter unimpeded. See FIG.3.
- adding the BAC to a solution of B2M should prevent any protein material from passing through the size filter, and this was confirmed experimentally.
- the protein concentration was measured in the flow through of both experiments, testing 100 nM B2M plus or minus addition of nbBAC-1-LL at 1 ⁇ M. The resulting protein concentration in the flow through was determined to be at least 5 times lower when nbBAC-1-LL was added (above the centrifugal filter) compared to when it was absent.
- the BAC effectively sequesters the B2M by forming a complex therewith, which complex is unable to pass through the filter membrane.
- nbBAC-1-LL was incubated at 37°C in human serum for 4 hours and then assayed for its oligomeric state. After pulling down nbBAC-1-LL based on its poly-histidine tag using Ni-NTA resin, and then eluting with imidazole, SEC analysis indicates that the major species had a size that corresponded to that of the assembled protein cage thereby indicating that BACs are structurally stable under hemodialysis conditions.
- nbBAC-1-LL was immobilized on a metal affinity (His-trap) column and then human serum supplemented with 50 ug/ml B2M was flowed therethrough and the amount of B2M in the flow-through (after resulting serum had passed through the column) was assayed. The amount of B2M in the column eluate after washing off the BAC from the column using imidazole was also assayed. Western blot was used to analyze samples for B2M and B2M was observed in the BAC elution fraction only. No detectable amounts of B2M were present in the flow-through. See FIG.6.
- BACs as described herein are capable of removing B2M from serum and blood and can therefore be used to effectively remove B2M in the in the serum and blood of subjects, who may have elevated levels of B2M as a result of hemodialysis.
- the BACs may be used to remove B2M from the blood or serum of subjects.
- BACs are immobilized on a solid substrate, e.g., beads or other solid phase media, and B2M is removed from blood or plasma by contacting the blood or plasma with the BACs immobilized on the solid substrate and then separating the blood or plasma from the solid substrate.
- BACs may be immobilized on the stationary matrix of a purification column, then the B2M in blood or plasma is removed by flowing the blood or plasma through the purification column; or (b) BACs may be immobilized on magnetic beads, then the B2M in blood or plasma is removed by contacting the blood or plasma with the magnetic beads and then the magnetic beads having B2M bound thereto are removed from the blood or plasma via magnetic fields.
- size-exclusion methods in the art may be used to remove B2M from blood or plasma.
- BACs may be added to the blood or plasma and then the BACs and BACs having B2M complexed therewith are separated from the blood or plasma using, e.g., membrane filtration or size exclusion chromatography.
- membrane filtration or size exclusion chromatography For example, if the protein cage of the BAC, excluding any bound B2M has a diameter of 130 nm, then the pore size of the membrane used for membrane filtration should be ⁇ 130 nm. Similarly, if the protein cage of the BAC has a diameter of 230 nm, then the pore size of the filtration membrane should be ⁇ 230 nm.
- size- based exclusion media should have a channel size or pore size smaller than the diameter of the protein cage of the given BAC being employed. Because suitable protein cages have a protein size that is typically between 500 kDa and 2 MDa in size, in some embodiments, the size exclusion media employed has a channel or pore size that prevents proteins of 500 kDa or larger from passing therethrough. In some embodiments, the pore size of the membrane or size-based media may be considerably smaller, while retaining the property that proteins of 500 kDa are prevented from passing through.
- the use of BACs to remove B2M from blood or plasma may be employed in combination with existing hemodialysis methods in the art.
- BACs may be used to remove B2M concurrently with hemodialysis, e.g., at the same time a subject’s blood is passed through the dialyzer of a hemodialysis machine.
- the BACs are added to the blood or plasma to be dialyzed, i.e., added upstream of the dialyzer of a hemodialysis machine.
- the dialyzer will then remove the BACs and any B2M complexed thereto at the same time the dialyzer removes other unwanted molecules from the subject’s blood or plasma.
- BACs are used to remove B2M in a step that is “in series” with the step where the blood or plasma is passed through the dialyzer.
- the blood or plasma is contacted with the BACs and the BACs and any B2M complexed thereto are removed before the blood or plasma is passed through the dialyzer.
- the dialyzed blood or plasma is contacted with the BACs and then the BACs and any B2M complexed thereto are removed therefrom before the blood or plasma is returned to the subject’s body.
- BACs are used to remove B2M from a subject’s blood or plasma in a procedure that is independent of any hemodialysis procedure that the subject may have undergone.
- nbBAC-1-LL complexes with B2M to produce an approximately 825 kDa assembly with a capacity to bind 12 copies of B2M on its exterior.
- BACs have the ability to remove B2M in a size-based separation, i.e., by employing a semi-permeable membrane filter that allows smaller proteins (e.g., albumin) to pass. While the experiments herein attached BACs to a nickelated substrate based on polyhistidine tails, other methods in the art may be used to immobilize the BACs on a given substrate.
- the BACs may be biotinylated and immobilized on a substrate via binding to streptavidin functional groups on the surface of the substrate.
- the substrate comprising BACs having B2M bound thereto may be reused by eluting the BACs, sterilizing the substrate, and then immobilizing fresh, unused BACs thereto.
- removal of B2M with BACs was achieved with only one passage of the serum over the solid phase medium, which is a striking improvement over existing size-based filtration methods that require multiple, e.g., up to 20, passages over filtration media.
- TACs may be used to selectively remove a target molecule of interest, which has a mass of about 50 kDa or less and/or or a diameter of 4 nm or less, from a liquid (e.g., plasma) using, e.g., size- based separation media and adsorption chromatography.
- the diameter of the pores of the size exclusion media used to separate the bound and unbound TACs from a given liquid is about 115 nm.
- the diameter of the pores of the size exclusion media used to separate the bound and unbound TACs from a given liquid is about 130 nm.
- the diameter of the pores of the size exclusion media used to separate the bound and unbound TACs from a given liquid is about 230 nm.
- the diameter of the pores of the size exclusion media used to separate the bound and unbound TACs from a given liquid is about 115 nm.
- the diameter of the pores of the size exclusion media used to separate the bound and unbound TACs from a given liquid is about 125 nm. In embodiments where the protein cage is T33-28, the diameter of the pores of the size exclusion media used to separate the bound and unbound TACs from a given liquid is about 125 nm. In embodiments where the protein cage is I53-47, the diameter of the pores of the size exclusion media used to separate the bound and unbound TACs from a given liquid is about 230 nm. In embodiments where the protein cage is I53-40, the diameter of the pores of the size exclusion media used to separate the bound and unbound TACs from a given liquid is about 240 nm.
- the diameter of the pores of the size exclusion media used to separate the bound and unbound TACs from a given liquid is about 260 nm. In embodiments where the protein cage is I32-28, the diameter of the pores of the size exclusion media used to separate the bound and unbound TACs from a given liquid is about 300 nm. In embodiments where the protein cage is Human H chain Ferritin, the diameter of the pores of the size exclusion media used to separate the bound and unbound TACs from a given liquid is about 125 nm. In embodiments where the protein cage is SOR, the diameter of the pores of the size exclusion media used to separate the bound and unbound TACs from a given liquid is about 150 nm.
- the TAC comprises or consists of a plurality of protein chains having SEQ ID NO: 42 and SEQ ID NO: 43 and the diameter of the pores of the size exclusion media used to separate the bound and unbound TACs from a given liquid is about 130 nm. In some embodiments, the TAC comprises or consists of a plurality of protein chains having SEQ ID NO: 44 and SEQ ID NO: 45 and the diameter of the pores of the size exclusion media used to separate the bound and unbound TACs from a given liquid is about 230 nm.
- the TAC comprises or consists of a plurality of protein chains having SEQ ID NO: 46 and SEQ ID NO: 47 and the diameter of the pores of the size exclusion media used to separate the bound and unbound TACs from a given liquid is about 130 nm. In some embodiments, the TAC comprises or consists of a plurality of protein chains having SEQ ID NO: 48 and SEQ ID NO: 49 and the diameter of the pores of the size exclusion media used to separate the bound and unbound TACs from a given liquid is about 130 nm.
- the TAC comprises or consists of a plurality of protein chains having SEQ ID NO: 50 and SEQ ID NO: 51 and the diameter of the pores of the size exclusion media used to separate the bound and unbound TACs from a given liquid is about 130 nm.
- Adsorption Chromatography In some embodiments, the TACs are immobilized on a solid substrate and the target molecule of interest is removed from a liquid by contacting the liquid with the TACs immobilized on the solid substrate.
- Exemplary solid substrate materials to which TACs may be immobilized include cellulose based materials (e.g., cellulose, cellulose acetate, and the like), polystyrene, nylon, polyethersulfone (PES), polypropelene, polyvinylidene fluoride (PVDF), polyamide, and biologically inert materials known in the art.
- cellulose based materials e.g., cellulose, cellulose acetate, and the like
- PES polyethersulfone
- PVDF polypropelene
- polyamide polyamide
- the proteins, i.e., subunits of TACs (including BACs) described herein may be made using methods in the art including chemical synthesis, biosynthesis or in vitro synthesis using recombinant DNA methods, and solid phase synthesis.
- Protein purification techniques in the art such as reverse phase high-performance liquid chromatography (HPLC), ion-exchange or immunoaffinity chromatography, filtration or size exclusion, or electrophoresis may be used to separate or remove TACs and complexes therewith from fluids and other molecules. See, e.g., Olsnes and Pihl (1973) Biochem 12(16):3121-3126; and Scopes (1982) Protein Purification, Springer-Verlag, NY, which are herein incorporated by reference. Polynucleotides that encode the TACs and BACs as described herein are also contemplated herein. In some embodiments, the proteins and polynucleotides are isolated.
- an “isolated” compound refers to a compound that is isolated from its native environment.
- an isolated polynucleotide is a one which does not have the bases normally flanking the 5’ end and/or the 3’ end of the polynucleotide as it is found in nature.
- an isolated polypeptide is a one which does not have its native amino acids, which correspond to the full-length polypeptide, flanking the N-terminus, C-terminus, or both.
- isolated polynucleotides and polypeptides are made “by the hand of man”, e.g., using synthetic and/or recombinant techniques.
- a compound e.g., a binder as described herein “specifically binds” a given target (e.g., B2M) if it reacts or associates more frequently, more rapidly, with greater duration, and/or with greater binding affinity with the given target than it does with a given alternative, and/or indiscriminate binding that gives rise to non- specific binding and/or background binding.
- a given target e.g., B2M
- background binding refer to an interaction that is not dependent on the presence of a specific structure (e.g., a given epitope).
- binding affinity refers to the propensity of a compound to associate with (or alternatively dissociate from) a given target and may be expressed in terms of its dissociation constant, Kd. Binding affinity can be determined using methods in the art, such as equilibrium dialysis, equilibrium binding, gel filtration, immunoassays, surface plasmon resonance, and spectroscopy using experimental conditions that exemplify the conditions under which the compound and the given target may come into contact and/or interact. Dissociation constants may be used determine the binding affinity of a compound for a given target relative to a specified alternative.
- sample is used in its broadest sense and includes specimens and cultures obtained from any source, as well as biological samples and environmental samples. Biological samples may be obtained from animals (including humans) and encompass fluids, solids, tissues, and gases. Biological samples include blood products, such as plasma, serum, and the like. a biological sample can be obtained from a subject using methods in the art.
- a sample to be analyzed using one or more methods described herein can be either an initial unprocessed sample taken from a subject or a subsequently processed, e.g., partially purified, diluted, concentrated, fluidized, pretreated with a reagent (e.g., protease inhibitor, anti-coagulant, etc.), and the like.
- a reagent e.g., protease inhibitor, anti-coagulant, etc.
- the sample is a blood sample.
- the blood sample is a whole blood sample, a serum sample, or a plasma sample.
- the sample may be processed, e.g., condensed, diluted, partially purified, and the like.
- the sample is pretreated with a reagent, e.g., a protease inhibitor.
- TACs may comprise a detectable label attached thereto.
- BACs may comprise a detectable label so that they may be detected, measured, visualized, etc., in, e.g., a hemodialysis system.
- a “detectable label” is a compound or composition that produces or can be induced to produce a signal that is detectable by, e.g., visual, spectroscopic, photochemical, biochemical, immunochemical, or chemical means.
- a detectable label can be attached directly or indirectly by way of a linker (e.g., an amino acid linker or a chemical moiety).
- detectable labels include radioactive and non-radioactive isotopes (e.g., 125I, 18F, 13C, etc.), enzymes (e.g., ⁇ - galactosidase, peroxidase, etc.) and fragments thereof, enzyme substrates, enzyme inhibitors, coenzymes, catalysts, fluorophores (e.g., rhodamine, fluorescein isothiocyanate, etc.), dyes, chemiluminescers and luminescers (e.g., dioxetanes, luciferin, etc.), and sensitizers.
- radioactive and non-radioactive isotopes e.g., 125I, 18F, 13C, etc.
- enzymes e.g., ⁇ - galactosidase, peroxidase, etc.
- fragments thereof enzyme substrates
- enzyme inhibitors e.g., coenzymes, catalysts
- fluorophores
- kits for removing a given protein of interest e.g., B2M
- a fluid sample e.g., blood
- the kits comprise BACs as described herein packaged together with (a) reagents for immobilizing the BACs on a solid substrate, or (b) a device for delivering or contacting the BACs with the fluid sample to be treated.
- the device is a cassette, i.e., a housing, that contains the BACs packaged therein.
- the cassette comprises at least one connector whereby the cassette can be removably attached to a hemodialysis machine and placed in fluidic communication with the blood flow pathway of the hemodialysis machine.
- the cassette has an inlet connector and an outlet connector.
- the connectors may be luer connectors, quick connect couplings, dialysis connectors, and the like, which are known in the art.
- the cassette is connected in line with the venous blood line of a hemodialysis machine upstream of the dialyzer of the hemodialysis machine.
- the cassette via its outlet connector, is connected directly to and upstream of the dialyzer of a hemodialysis machine.
- the cassette is connected in line with the arterial blood line of a hemodialysis machine downstream of the dialyzer of the hemodialysis machine.
- the cassette via its inlet connector, is connected directly to and downstream of the dialyzer of a hemodialysis machine.
- the BACs in a cassette are immobilized on a solid substrate, e.g., solid phase media, contained within the cassette.
- the cassette is a reservoir from which BACs are dispensed therefrom into the venous blood upstream of the dialyzer of a hemodialysis machine.
- kits include a carrier, package, or container that may be compartmentalized to receive one or more containers, such as vials, tubes, and the like.
- the kits optionally include an identifying description or label or instructions relating to its use.
- the kits include information prescribed by a governmental agency that regulates the manufacture, use, or sale of compounds and compositions as contemplated herein.
- BACs Sequences [0082] nbBAC-1-SL: [0083] Subunit A MFTRRGDQGETDLANRARVGKDSPVVEVQGTIDELNSFIGYALVLSRWDDIRNDLFRIQNDLFVL GEDVSTGGKGRTVTMDMIIYLIKRSVEMKAEIGKIELFVVPGGSVESASLHMARAVSRRLERRIK AASELTEINANVLLYANMLSNILFMHALISNKRLNIPEKIWSIHRVSLE (SEQ ID NO: 40) [0084] Subunit B MRITTKVGDKGSTRLFGGEEVWKDDPIIEANGTLDELTSFIGEAKHYVDEEMKGILEEIQNDIYK IMGEIGSKGKIEGISEERIKWLAGLIERYSEMVNKLSFVLPGGTLESAKLDVCRTIARRAERKVA TVLREFGIGTLAAIYLALLSRLLFLLARVIEIEKNKLKEVRSGGSQVQLQES
- nbBAC-1-LL [0086] Subunit A MFTRRGDQGETDLANRARVGKDSPVVEVQGTIDELNSFIGYALVLSRWDDIRNDLFRIQNDLFVL GEDVSTGGKGRTVTMDMIIYLIKRSVEMKAEIGKIELFVVPGGSVESASLHMARAVSRRLERRIK AASELTEINANVLLYANMLSNILFMHALISNKRLNIPEKIWSIHRVSLE (SEQ ID NO: 42) [0087] Subunit B MRITTKVGDKGSTRLFGGEEVWKDDPIIEANGTLDELTSFIGEAKHYVDEEMKGILEEIQNDIYK IMGEIGSKGKIEGISEERIKWLAGLIERYSEMVNKLSFVLPGGTLESAKLDVCRTIARRAERKVA TVLREFGIGTLAAIYLALLSRLLFLLARVIEIEKNKLKEVRSGGSGGGSGGGGSQVQLQESGGGS VQAGGSLRLSCAASGYTDSRY
- nbBAC-2 [0089] Subunit A MKMEELFKKHKIVAVLRANSVEEAIEKAVAVFAGGVHLIEITFTVPDADTVIKALSVLKEKGAII GAGTVTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGVMTPTELVKAMKLGHDILKL FPGEVVGPQFVKAMKGPFPNVKFVPTGGVNLDNVCKWFKAGVLAVGVGKALVKGKPDEVREKAKK FVKKIRGCTE (SEQ ID NO: 44) [0090] Subunit B MNQHSHKDHETVRIAVVRARWHAEIVDACVSAFEAAMRDIGGDRFAVDVFDVPGAYEIPLHARTL AETGRYGAVLGTAFVVNGGIYRHEFVASAVINGMMNVQLNTGVPVLSAVLTPHNYDKSKAHTLLF LALFAVKGMEAARACVEILAAREKIAAGSGGSGGSGGSQVQLQESGGGSVQAGGSLRL
- DARPBAC-1 [0092] Subunit A MFTRRGDQGETDLANRARVGKDSPVVEVQGTIDELNSFIGYALVLSRWDDIRNDLFRIQNDLFVL GEDVSTGGKGRTVTMDMIIYLIKRSVEMKAEIGKIELFVVPGGSVESASLHMARAVSRRLERRIK AASELTEINANVLLYANMLSNILFMHALISNKRKEELDKKQLDAASAGYDDQVAALLAKGADVNA SDWNGWTPLHSAAQWGHLEIVEVLLKRGADINASDWYGWTPLHVAATWGHLEIVELLLRWGADVN AQDKFGKTPFDLAIDNGNEDIAEVLQKAA (SEQ ID NO: 46)
- the binder (DARPin) sequence (underlined) is SEQ ID NO: 31, and the linker sequence is SEQ ID NO: 37.
- the tag (italicized) is SEQ ID NO: 38.
- DARPBAC-2 [0095] Subunit A MFTRRGDQGETDLANRARVGKDSPVVEVQGTIDELNSFIGYALVLSRWDDIRNDLFRIQNDLFVL GEDVSTGGKGRTVTMDMIIYLIKRSVEMKAEIGKIELFVVPGGSVESASLHMARAVSRRLERRIK AASELTEINANVLLYANMLSNILFMHALISNKRKEELDKKLLDAASAGQDDEVRILMANGADVNA SDNWGYTPLHAAAYRGHLEIVDVLLANGADVNASDYYGWTPLHVAARNGHLEIVDVLLAHGADVN AQDKFGKTPFDLAIDNGNEDIAEVLQKAAKLN (SEQ ID NO: 48)
- the binder (DARPin) sequence (underlined) is SEQ ID NO: 32, and the linker sequence is SEQ ID NO: 37.
- Subunit B MRITTKVGDKGSTRLFGGEEVWKDDPIIEANGTLDELTSFIGEAKHYVDEEMKGILEEIQNDIYK IMGEIGSKGKIEGISEERIKWLAGLIERYSEMVNKLSFVLPGGTLESAKLDVCRTIARRAERKVA TVLREFGIGTLAAIYLALLSRLLFLLARVIEIEKNKLKEVRSHHHHHH (SEQ ID NO: 49)
- the tag is SEQ ID NO: 38.
- DARPBAC-3 [0098] Subunit A MFTRRGDQGETDLANRARVGKDSPVVEVQGTIDELNSFIGYALVLSRWDDIRNDLFRIQNDLFVL GEDVSTGGKGRTVTMDMIIYLIKRSVEMKAEIGKIELFVVPGGSVESASLHMARAVSRRLERRIK AASELTEINANVLLYANMLSNILFMHALISNKRKEELDKKLLDAASAGQDDEVRILMANGADVNA SNWWGYTPLHAAAQDGHLEIVDVLLAYGADVNASDWYGWTPLHSAATQGHLEIVDVLLAHGADVN AQDKFGKTPFDLAIDNGNEDIAEVLQKAAKLN (SEQ ID NO: 50)
- the binder (DARPin) sequence (underlined) is SEQ ID NO: 33, and the linker sequence is SEQ ID NO: 37.
- BACs were performed by cloning sequence-verified BAC-encoding expression vectors into Shuffle T7 Express lysY cells (New England Biolabs) to allow for proper folding of disulfide bond-containing nanobodies. Cells were grown in autoinduction media (see Studier (2005)) at 25°C for 48 hours. Cells were harvested at 4000 x g and stored at ⁇ 20°C until purification. [0102] BAC Purification [0103] Frozen pelleted cells were solubilized in lysis buffer containing 50 mM TRIS pH 8.0, 250 mM NaCl, and protease inhibitor tablets (Pierce). Cells were lysed using a C3 Emulsiflex with 4 passages through the instrument.
- Lysate was clarified by centrifugation at 18000 x g for 35 minutes after which the supernatant fraction was passed over a gravity-flow column containing Ni-NTA functionalized agarose beads (Thermo Fisher). The column was washed with lysis buffer containing imidazole of sequential concentrations: 50 mM, 75 mM, and 100 mM. BACs were eluted from the column using lysis buffer supplemented with 500 mM imidazole. BAC proteins were then buffer-exchanged using dialysis into assay buffer containing: 50 mM TRIS, 150 mM NaCl, and 0.02% Tween-20.
- Biosensors functionalized with streptavidin were used to bind biotinylated B2M at a concentration of 2.5 ⁇ g/ml and tested for binding with soluble BACs.
- Buffer used for experiments was 50 mM TRIS pH 8.0, 150 mM NaCl, 0.02% Tween-20.
- Immunoblots [0109] 3 ⁇ l aliquots of flow through samples from spin columns were applied to nitrocellulose paper, allowed to dry then repeated at the same location once. Established methods for western blotting were then used develop and image the blot. Anti-biotin antibodies were used to recognize biotinylated B2M (Invitrogen).
- Serum mixture was then flowed over a column containing HisPur Ni-NTA resin (Thermo Fisher Scientific), and washed and eluted with buffers identical to those used in IMAC purification. Elution fraction was analyzed by SDS-PAGE and concentrated and injected into a Superose 6 gel filtration column (Cytiva Life Sciences) for oligomeric state determination.
- B2M Removal Experiment [0115] 1 ml His-Trap columns (Cytiva life sciences) were used as a stationary matrix to immobilize BACs. Following incubation with SEC-purified BACs, human serum supplemented with 50 ⁇ g/ml of B2M was flowed over the column and the flow-through was collected.
- non-human animal and “animal” refer to all non-human vertebrates, e.g., non-human mammals and non-mammals, such as non-human primates, horses, sheep, dogs, cows, pigs, chickens, and other veterinary subjects and test animals.
- the subject is a mammal.
- the subject is a human.
- diagnosis refers to the physical and active step of informing, i.e., communicating verbally or by writing (on, e.g., paper or electronic media), another party, e.g., a patient, of the diagnosis.
- prognosis refers to the physical and active step of informing, i.e., communicating verbally or by writing (on, e.g., paper or electronic media), another party, e.g., a patient, of the prognosis.
- a and/or B means “A, B, or both A and B” and “A, B, C, and/or D” means “A, B, C, D, or a combination thereof” and said “A, B, C, D, or a combination thereof” means any subset of A, B, C, and D, for example, a single member subset (e.g., A or B or C or D), a two-member subset (e.g., A and B; A and C; etc.), or a three-member subset (e.g., A, B, and C; or A, B, and D; etc.), or all four members (e.g., A, B, C, and D).
- a single member subset e.g., A or B or C or D
- a two-member subset e.g., A and B; A and C; etc.
- a three-member subset e.g., A, B, and C; or A, B, and D; etc.
- the phrase “one or more of”, e.g., “one or more of A, B, and/or C” means “one or more of A”, “one or more of B”, “one or more of C”, “one or more of A and one or more of B”, “one or more of B and one or more of C”, “one or more of A and one or more of C” and “one or more of A, one or more of B, and one or more of C”.
- the phrase “comprises or consists of A” is used as a tool to avoid excess page and translation fees and means that in some embodiments the given thing at issue: comprises A or consists of A.
- the sentence “In some embodiments, the composition comprises or consists of A” is to be interpreted as if written as the following two separate sentences: “In some embodiments, the composition comprises A. In some embodiments, the composition consists of A.” [0125]
- a sentence reciting a string of alternates is to be interpreted as if a string of sentences were provided such that each given alternate was provided in a sentence by itself.
- the sentence “In some embodiments, the composition comprises A, B, or C” is to be interpreted as if written as the following three separate sentences: “In some embodiments, the composition comprises A. In some embodiments, the composition comprises B.
- the composition comprises C.”
- the sentence “In some embodiments, the composition comprises at least A, B, or C” is to be interpreted as if written as the following three separate sentences: “In some embodiments, the composition comprises at least A. In some embodiments, the composition comprises at least B. In some embodiments, the composition comprises at least C.”
- the terms “protein”, “polypeptide” and “peptide” are used interchangeably to refer to two or more amino acids linked together. Groups or strings of amino acid abbreviations are used to represent peptides. Except when specifically indicated, peptides are indicated with the N-terminus on the left and the sequence is written from the N-terminus to the C-terminus.
- sequence identity refers to the percentage of nucleotides or amino acid residues that are the same between sequences, when compared and optimally aligned for maximum correspondence over a given comparison window, as measured by visual inspection or by a sequence comparison algorithm in the art, such as the BLAST algorithm, which is described in Altschul et al., (1990) J Mol Biol 215:403-410.
- the comparison window can exist over a given portion, e.g., a functional domain, or an arbitrarily selection a given number of contiguous nucleotides or amino acid residues of one or both sequences. Alternatively, the comparison window can exist over the full length of the sequences being compared. For purposes herein, where a given comparison window (e.g., over 80% of the given sequence) is not provided, the recited sequence identity is over 100% of the given sequence.
- the percentages of sequence identity of the proteins provided herein are determined using BLASTP 2.8.0+, scoring matrix BLOSUM62, and the default parameters available at blast.ncbi.nlm.nih.gov/Blast.cgi. See also Altschul, et al., (1997) Nucleic Acids Res 25:3389-3402; and Altschul, et al., (2005) FEBS J 272:5101- 5109.
- Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv Appl Math 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J Mol Biol 48:443 (1970), by the search for similarity method of Pearson & Lipman, PNAS USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, WI), or by visual inspection.
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