Classifications

• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K1/00—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
  • C07K1/14—Extraction; Separation; Purification
  • C07K1/16—Extraction; Separation; Purification by chromatography
  • C07K1/22—Affinity chromatography or related techniques based upon selective absorption processes
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K1/00—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
  • C07K1/14—Extraction; Separation; Purification
  • C07K1/36—Extraction; Separation; Purification by a combination of two or more processes of different types
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01D—SEPARATION
  • B01D15/00—Separating processes involving the treatment of liquids with solid sorbents; Apparatus therefor
  • B01D15/08—Selective adsorption, e.g. chromatography
  • B01D15/26—Selective adsorption, e.g. chromatography characterised by the separation mechanism
  • B01D15/38—Selective adsorption, e.g. chromatography characterised by the separation mechanism involving specific interaction not covered by one or more of groups B01D15/265 and B01D15/30 - B01D15/36, e.g. affinity, ligand exchange or chiral chromatography
  • B01D15/3804—Affinity chromatography
  • B01D15/3809—Affinity chromatography of the antigen-antibody type, e.g. protein A, G or L chromatography
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
  • B01J20/00—Solid sorbent compositions or filter aid compositions; Sorbents for chromatography; Processes for preparing, regenerating or reactivating thereof
  • B01J20/30—Processes for preparing, regenerating, or reactivating
  • B01J20/32—Impregnating or coating ; Solid sorbent compositions obtained from processes involving impregnating or coating
  • B01J20/3231—Impregnating or coating ; Solid sorbent compositions obtained from processes involving impregnating or coating characterised by the coating or impregnating layer
  • B01J20/3242—Layers with a functional group, e.g. an affinity material, a ligand, a reactant or a complexing group
  • B01J20/3268—Macromolecular compounds
  • B01J20/3272—Polymers obtained by reactions otherwise than involving only carbon to carbon unsaturated bonds
  • B01J20/3274—Proteins, nucleic acids, polysaccharides, antibodies or antigens
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K1/00—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
  • C07K1/107—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length by chemical modification of precursor peptides
  • C07K1/1072—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length by chemical modification of precursor peptides by covalent attachment of residues or functional groups
  • C07K1/1077—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length by chemical modification of precursor peptides by covalent attachment of residues or functional groups by covalent attachment of residues other than amino acids or peptide residues, e.g. sugars, polyols, fatty acids
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K1/00—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
  • C07K1/14—Extraction; Separation; Purification
  • C07K1/30—Extraction; Separation; Purification by precipitation
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K1/00—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
  • C07K1/14—Extraction; Separation; Purification
  • C07K1/30—Extraction; Separation; Purification by precipitation
  • C07K1/32—Extraction; Separation; Purification by precipitation as complexes
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
  • C07K14/305—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Micrococcaceae (F)
  • C07K14/31—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Micrococcaceae (F) from Staphylococcus (G)
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
  • C07K14/315—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Streptococcus (G), e.g. Enterococci
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K17/00—Carrier-bound or immobilised peptides; Preparation thereof
  • C07K17/02—Peptides being immobilised on, or in, an organic carrier
  • C07K17/08—Peptides being immobilised on, or in, an organic carrier the carrier being a synthetic polymer
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
  • C07K16/06—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies from serum

Definitions

• Supramolecular assembly is a bottom-up approach to construct hierarchical and functional nanostructures.
• peptide- based materials are notably appealing because of their biocompatibility, biodegradability, and low toxicity.
• the presentation of bioactive epitopes on a supramolecular substrate enables the active-targeting of the nanostructures for efficient molecular/cellular recognition and signaling, as well as the precise delivery and accumulation of therapeutics at desired sites.
• the epitope spatial arrangement plays an important role in regulating their functionality.
• Co-assembly of bioactive building units with an inert molecule has been shown to effectively modulate the epitope density and achieve enhanced bioactivities. Meanwhile, the use of flexible linkers for spacing out the epitope in the radial direction of the resultant nanostructures is equally essential to improve the epitope accessibility and their interactions with target biomolecules.
• Affinity precipitation has been increasingly explored as a promising alternative to protein A chromatography for the purification of monoclonal antibodies (mAbs) and other therapeutic proteins, as the conventional protein A-based affinity chromatography method suffers from limited production capacities and high media cost.
• the use of salt to trigger or aid in the precipitation of antibodies is prevalent during the purification process.
• high salt concentration is known to increase the risks of protein instability and the non specific precipitation of impurities present in the solution.
• the disclosure provides a system comprising: (a) one or more filler molecules comprising a linear hydrocarbon chain conjugated to an amino acid sequence of 2-5 amino acids; (b) one or more ligand molecules comprising a linear hydrocarbon chain, an amino acid sequence of 2-5 amino acids, a linker, and a Z33 peptide of Staphylococcus aureus Protein A, or an antibody-binding fragment thereof, conjugated to the linker, wherein the one or more filler molecules and one or more ligand molecules have the ability to self-assemble into immunofibers (IFs) under physiological conditions. Also provided are methods of purifying an antibody and/or fusion Fc protein using the aforementioned system.
• Figures 1A-1C include schematic diagrams illustrating the molecular design of the immunofiber (IF) building units with OEG (or PEG) linkers and the formation of IFs for monoclonal antibody (mAh) capture.
• Figure 1 A shows the chemical structures of the filler molecule, C12-VVEE, and the ligand molecules, C12-VVKK[Linker]Z33.
• Figure IB is a schematic illustrating the ligand molecule design with various linkers and the effect of linker length on the presentation of Z33 peptide on co-assembled IFs.
• Figure 1C illustrates co assembly of filler and ligand molecules into supramolecular IFs and four possible states of mAbs in an IF solution: (1) two Fc-portions of a mAh bound to two ligands from two different IFs; (2) two Fc-portions of a mAh bound to two adjacent ligands from the same IF; (3) one Fc-portion of a mAh bound to one ligand on an IF; (4) free mAbs in the solution bound to zero, one, or two monomer ligands that are not assembled into IFs.
• Figures 2A-2H show the characterization of filler and ligand molecules.
• Figure 2H is a graph illustrating normalized CD spectra of self-assembled ligand molecules with different OEG (or PEG) linkers, suggesting the formation and retention of a-helix secondary structures.
• Figures 3A-3D are graphs illustrating ITC profiles and binding curves for the stepwise injection of 100 mM mAbl into 40 pM 04 (3A), 08 (3B), 012 (3C), 016 (3D) at 25 °C in PBS, pH 7.4.
• Figures 4A-4E show comparisons of mAh precipitation performance of IFs with different ligand molecules.
• Figures 4A and 4B are graphs illustrating mAh precipitation yields for 20 pM and 40 pM mAbl, respectively, incubated with various co-assembled IFs (2.5 mM filler, 100 pM ligand) under 1 M salt or no salt conditions. The data point for G2 with 1 M salt in Figure 4A was replotted from reference.
• Figures 4C and 4D are graphs illustrating precipitated mAh mass from 100 pL samples of 20 pM (0.3 mg) (4C) and 40 pM (0.6 mg) (4D) mAbl incubated with various 100 IFs (2.5 mM filler, 100 pM ligand) under 1 M salt or no salt conditions.
• Figure 4E includes photographs of co-assembled IFs (2.5 mM filler, 100 pM ligand) after mixing with 40 pM mAh for 5 minutes under 1 M salt or no salt conditions. All experiments were performed in triplicate and the data is shown as mean ⁇ standard deviation.
• Figures 5A-5F show optimization of mAh precipitation yield.
• Figures 5A and 5B are graphs illustrating the yield and mass, respectively, of mAh precipitation for 100 pL mAbl at 40 pM (0.6 mg), 80 pM (1.2 mg), and 133 pM (2 mg) incubated with IFs at various 016 concentrations.
• Figure 5C is a graph illustrating a comparison of mAh precipitation yield for 40 pM mAbl incubated with optimized IFs (2.5 mM filler, 250 pM 016) under 1 M salt and no salt conditions.
• Figure 5D is a schematic diagram showing a proposed mechanism of mAb-IF agglomeration as the ligand concentration increases for a fixed mAh concentration.
• FIG. 5E is a graph showing turbidity of 40 pM mAh with optimized IFs (2.5 mM filler, 250 pM 016) in 2 hours.
• Figure 5F is a graph showing the effect of binding time on the mAh precipitation yield for 40 pM mAbl incubated with optimized IFs (2.5 mM filler, 250 pM 016). All experiments were performed in triplicate and the data is shown as mean ⁇ standard deviation.
• Figures 6A-6F show purification of mAh from clarified bulk cell culture harvest (abbreviated as “mAh CB”) and separation of mAbs at high titers.
• Figure 6A is a schematic illustration of the mAh purification process using IFs in PBS solution.
• Figure 6B is a graph showing mAh precipitation yield, yield loss at wash step, and elution yield for 40 pM and 80 mM pure mAbl after two sequential precipitations under no salt conditions.
• Figure 6C is a graph showing mAb precipitation yields for 40 mM and 80 mM mAbl CB after two sequential precipitations with IF solutions under no salt conditions.
• Figure 6D is a schematic illustration of the high titer mAb purification process using solid IFs in lyophilized powder form.
• Figures 6E and 6F are graphs showing precipitation yields for 21 mg/mL (6E) and 31 mg/mL (6F) pure mAbl using sequential precipitation with lyophilized IFs under no salt conditions. All experiments were performed in triplicate and the data is shown as mean ⁇ standard deviation.
• Figure 7 is a graph illustrating mAb precipitation yields for 100 pL mAbl at 10 mM and 20 pM after an incubation with 100 pL IFs at various 016 concentrations. IFs with 200 pM 016 gave the best mAb precipitation yield for both mAb concentrations.
• nucleic acid refers to a polymer or oligomer of pyrimidine and/or purine bases, preferably cytosine, thymine, and uracil, and adenine and guanine, respectively (See Albert L. Lehninger, Principles of Biochemistry, at 793-800 (Worth Pub. 1982)).
• the terms encompass any deoxyribonucleotide, ribonucleotide, or peptide nucleic acid component, and any chemical variants thereof, such as methylated, hydroxymethylated, or glycosylated forms of these bases.
• the polymers or oligomers may be heterogenous or homogenous in composition, may be isolated from naturally occurring sources, or may be artificially or synthetically produced.
• nucleic acids may be DNA or RNA, or a mixture thereof, and may exist permanently or transitionally in single- stranded or double-stranded form, including homoduplex, heteroduplex, and hybrid states.
• a nucleic acid or nucleic acid sequence comprises other kinds of nucleic acid structures such as, for instance, a DNA/RNA helix, peptide nucleic acid (PNA), morpholino nucleic acid (see, e.g., Braasch and Corey, Biochemistry, 47(14): 4503-4510 (2002) and U.S. Patent 5,034,506), locked nucleic acid (LNA; see Wahlestedt et ak, Proc. Natl. Acad. Sci. U.S.A., 97: 5633-5638 (2000)), cyclohexenyl nucleic acids (see Wang, J. Am. Chem.
• nucleic acid and “nucleic acid sequence” may also encompass a chain comprising non-natural nucleotides, modified nucleotides, and/or non-nucleotide building blocks that can exhibit the same function as natural nucleotides (e.g., “nucleotide analogs”).
• amino acid refers to natural amino acids, unnatural amino acids, and amino acid analogs, all in their D and L stereoisomers, unless otherwise indicated, if their structures allow such stereoisomeric forms.
• Natural amino acids include alanine (Ala or A), arginine (Arg or R), asparagine (Asn or N), aspartic acid (Asp or D), cysteine (Cys or C), glutamine (Gin or Q), glutamic acid (Glu or E), glycine (Gly or G), histidine (His or H), isoleucine (lie or I), leucine (Leu or L), Lysine (Lys or K), methionine (Met or M), phenylalanine (Phe or F), proline (Pro or P), serine (Ser or S), threonine (Thr or T), tryptophan (Trp or W), tyrosine (Tyr or Y), and valine (Val or V).
• Unnatural amino acids include, but are not limited to, azetidinecarboxylic acid, 2- aminoadipic acid, 3-aminoadipic acid, beta-alanine, naphthylalanine (“naph”), aminopropionic acid, 2-aminobutyric acid, 4-aminobutyric acid, 6-aminocaproic acid, 2- aminoheptanoic acid, 2-aminoisobutyric acid, 3-aminoisbutyric acid, 2-aminopimelic acid, tertiary-butylglycine (“tBuG”), 2,4-diaminoisobutyric acid, desmosine, 2,2'-diaminopimelic acid, 2,3-diaminopropionic acid, N-ethylglycine, N-ethylasparagine, homoproline (“hPro” or “homoP”), hydroxylysine, allo-hydroxylysine, 3 -hydroxy proline (“3Hyp”),
• Other unnatural amino acids that may be employed are disclosed in, e.g., International Patent Application Publication WO 2018/106937.
• polypeptide and “protein” are used interchangeably herein and refer to a polymeric form of amino acids of any length, which can include coded and non-coded amino acids, chemically or biochemically modified or derivatized amino acids, and polypeptides having modified peptide backbones.
• peptide includes a sequence of from four to 100 amino acid residues in length, preferably about 10 to 80 residues in length, more preferably, 15 to 65 residues in length, and in which the a-carboxyl group of one amino acid is joined by an amide bond to the main chain (a- or b-) amino group of the adjacent amino acid.
• a peptide may comprise natural amino acids, non-natural amino acids, amino acid analogs, and/or modified amino acids.
• a peptide may be a subsequence of naturally occurring protein or a non-natural (synthetic) sequence.
• the term “immuno-amphiphiles” means a molecule that can spontaneously associate into discrete, stable supramolecular nanostructures termed “immunofibers.”
• the IFs can assemble in a pH range between about 2.8 to about 7.5.
• the binding properties are also pH dependent. Those IFs which are more positively charged are easier to associate with higher pH solutions, and conversely, negatively charged IFs will associate easier in lower pH solutions.
• the term “antibody” refers to an immunoglobulin molecule that is typically composed of two identical pairs of polypeptide chains, each pair having one “light” (L) chain and one “heavy” (H) chain.
• Human light chains are classified as kappa and lambda light chains.
• Heavy chains are classified as mu, delta, gamma, alpha, or epsilon, and define the antibody's isotype as IgM, IgD, IgG, IgA, and IgE, respectively.
• the variable and constant regions are joined by a “J” region of about 12 or more amino acids, with the heavy chain also including a “D” region of about 3 or more amino acids.
• Each heavy chain is comprised of a heavy chain variable region (abbreviated herein as HCVR or VH) and a heavy chain constant region.
• the heavy chain constant region is comprised of three domains, CHI, CH2 and Cm.
• Each light chain is comprised of a light chain variable region (abbreviated herein as LCVR or VL) and a light chain constant region.
• the light chain constant region is comprised of one domain, CL.
• the constant regions of the antibodies may mediate the binding of the immunoglobulin to host tissues or factors, including various cells of the immune system (e.g., effector cells) and the first component (Clq) of the classical complement system.
• VH and VL regions can be further subdivided into regions of hypervariability, termed complementarity determining regions (CDR), interspersed with regions that are more conserved, termed framework regions (FR).
• CDR complementarity determining regions
• FR framework regions
• Each VH and VL is composed of three CDRs and four FRs, arranged from amino-terminus to carboxy- terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4.
• the term “antibody” encompasses an antibody that is part of an antibody multimer (a multimeric form of antibodies), such as dimers, trimers, or higher-order multimers of monomeric antibodies.
• antibody that is linked or attached to, or otherwise physically or functionally associated with, anon-antibody moiety.
• antibody is not limited by any particular method of producing the antibody. For example, it includes, inter alia, recombinant antibodies, synthetic antibodies, monoclonal antibodies, polyclonal antibodies, bi-specific antibodies, and multi-specific antibodies.
• the term “monoclonal antibody,” as used herein, refers to an antibody produced by a single clone of B lymphocytes that is directed against a single epitope on an antigen.
• Monoclonal antibodies typically are produced using hybridoma technology, as first described in Kohler and Milstein, Eur. J. Immunol., 5: 511-519 (1976).
• Monoclonal antibodies may also be produced using recombinant DNA methods (see, e.g., U.S. Patent 4,816,567), isolated from phage display antibody libraries (see, e.g., Clackson et al. Nature, 352 : 624- 628 (1991)); and Marks et al., J. Mol.
• polyclonal antibodies are antibodies that are secreted by different B cell lineages within an animal. Polyclonal antibodies are a collection of immunoglobulin molecules that recognize multiple epitopes on the same antigen.
• Fc region can be used interchangeably herein to refer to the region of a monoclonal antibody comprising the hinge and constant heavy-chain domains (CH2 and CH3).
• the Fc region mediates downstream effector functions via its interaction with Fc-receptors on (innate) immune cells or with Clq, the recognition molecule of the complement system.
• the interaction with Fc- receptors can exert a broad range of immunomodulatory functions, such as antibody- dependent cell-mediated cytotoxicity (ADCC) and antibody-dependent cellular phagocytosis (ADCP), in response to infectious agents.
• ADCC antibody- dependent cell-mediated cytotoxicity
• ADCP antibody-dependent cellular phagocytosis
• fragment of an antibody refers to mean one or more fragments of an antibody that retain the ability to specifically bind to an antigen (see, generally, Holliger et al., Nat. Biotech., 23(9): 1126-1129 (2005)).
• An antibody fragment desirably comprises, for example, one or more CDRs, the variable region (or portions thereof), the constant region (or portions thereof), or combinations thereof.
• antibody fragments include, but are not limited to, (i) a Fab fragment, which is a monovalent fragment consisting of the VL, VH, CL, and CHI domains, (ii) a F(a’)2 fragment, which is a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region, (iii) a Fv fragment consisting of the VL and VH domains of a single arm of an antibody, (iv) a Fab’ fragment, which results from breaking the disulfide bridge of an F(ab’)2 fragment using mild reducing conditions, (v) a disulfide-stabilized Fv fragment (dsFv), and (vi) a domain antibody (dAb), which is an antibody single variable region domain (VH or VL) polypeptide that specifically binds antigen.
• a Fab fragment which is a monovalent fragment consisting of the VL, VH, CL, and CHI domains
• F(a’)2 fragment which
• antibody binding peptide means a peptide that has the ability to bind an antibody, or a specific portion of an antibody molecule, for example, the Fc portion, with high specificity, such as having a Kd of between about 10 6 M to about 10 10 M.
• sample means any sample, solution, fluid, or mixture containing an antibody of interest or an Fc region-containing protein of interest (e.g., an Fc fusion protein) which can be bound using the immunofibers of the present invention.
• the sample can be a biological sample.
• the sample includes, for example, cell cultures, cell lysates, and/or clarified bulk (e.g., clarified cell culture supernatant).
• the sample is produced from a host cell or organism that expresses the antibody or Fc region-containing protein of interest (either naturally or recombinantly).
• the cells in a cell culture include host cells transfected with an expression construct containing a nucleic acid that encodes an antibody or Fc fusion protein of interest. These host cells can be bacterial cells, fungal cells, insect cells or, preferably, animal cells grown in culture.
• biological sample and “biological fluid,” as used herein, refers to any quantity of a substance from a living or formerly living patient or mammal or from cultured cells.
• substances include, but are not limited to, blood, serum, plasma, urine, cells, organs, tissues, bone, bone marrow, lymph, lymph nodes, synovial tissue, chondrocytes, synovial macrophages, endothelial cells, skin, cell cultures, cell lysates, and clarified bulk (e.g., clarified cell culture supernatant).
• oligomer is a molecule possessing from about 1 to about 30 monomers.
• the architecture of an oligomer can be, e.g., linear, branched, or forked.
• An oligomer is a type of polymer.
• polymer refers to a substance or material containing large molecules, or macromolecules, composed of many monomers (e.g., hundreds or thousands).
• the present disclosure is predicated, at least in part, on the construction of a supramolecular immunofiber (IF) system by co-assembling rationally-designed filler and ligand molecules for the affinity precipitation and purification of monoclonal antibodies (mAbs).
• the ligand molecule comprises a protein A mimicking peptide that binds to the Fc-portion of immunoglobulin G (IgG) from most mammalian species in a pH-specific manner.
• IgG immunoglobulin G
• a series of linkers may be incorporated into the ligand design to increase flexibility and accessibility of the protein A mimicking peptide.
• the resulting enhanced multivalent mAb- IF binding could potentially result in IF crossbnking into large complexes and facilitate monoclonal antibody precipitation under low salt or no salt conditions.
• the disclosure provides a system comprising one or more filler molecules and one or more ligand molecules that have the ability to self-assemble into immunofibers (IFs) under physiological conditions.
• IFs immunofibers
• filler or “filler molecule,” as used herein, refer to a molecule, particle, or compound that is added to a composition that can improve specific properties of the composition.
• the one or more filler molecules are designed to modulate the distribution of the ligand molecule in the co-assembled immunofibers.
• ligand or “ligand molecule,” as used herein, refer to a substance that forms a complex with a biomolecule to produce a biological effect.
• a ligand produces a signal by binding to a site on a target protein (e.g., a receptor).
• a ligand may be a small molecule, ion, or protein which binds to a nucleic acid molecule, such as a DNA double helix.
• Other types of ligands include, but are not limited to, steroid hormones, growth factors, neurotransmitters, and other peptides.
• each of the one or more filler molecules and each of the one or more ligand molecules comprises a linear hydrocarbon chain conjugated to an amino acid sequence.
• a “hydrocarbon” is an organic compound consisting entirely of hydrogen and carbon.
• the linear hydrocarbon chain may be of any suitable length.
• a linear hydrocarbon chain comprises from 1 to 24 carbon atoms, for example, 1 to 16 carbon atoms, 1 to 14 carbon atoms, 1 to 12 carbon atoms, 1 to 10 carbon atoms, 1 to 8 carbon atoms, 1 to 6 carbon atoms, or 1 to 4 carbon atoms.
• the linear hydrocarbon chain comprises 10-15 carbon atoms (e.g., 10, 11, 12, 13, 14, or 15 carbon atoms). Ideally, the linear hydrocarbon chain comprises 12 carbon atoms.
• One of ordinary skill in the art will appreciate that there is an upper limit to the number of carbons included in the linear hydrocarbon chain to maintain solubility in an aqueous solution.
• Each of the one or more filler molecules and each of the one or more ligand molecules also comprises an amino acid sequence conjugated to the linear hydrocarbon chain.
• the amino acid sequence present in the one or more filler molecules may be the same as or different than the amino acid sequence present in the one or more ligand molecules.
• the amino acid sequences present in the filler and ligand molecules are designed to promote interaction among the molecules during co-assembly.
• the amino acid sequences may be of any suitable length.
• the amino acid sequence present in a filler molecule and/or a ligand molecules comprises 1-20 amino acids, such as 1-5 amino acids, 5-10 amino acids, 1-10 amino acids, 10-15 amino acids, or 15-20 amino acids.
• each of the one or more filler molecules comprises an amino acid sequence of 2-5 amino acids (e.g., 2, 3, 4, or 5 amino acids), and, in some aspects, 4 amino acids.
• each of the one or more ligand molecules comprises an amino acid sequence of 2-5 amino acids (e.g., 2, 3, 4, or 5 amino acids), and, in some aspects, 4 amino acids.
• An exemplary amino acid sequence for inclusion in the one or more filler molecules and/or the one or more ligand molecules comprises VVXX (SEQ ID NO: 2, with “X” indicating any amino acid).
• each of the one or more filler molecules comprises the amino acid sequence WEE (SEQ ID NO: 3), and each of the one or more ligand molecules comprises the amino acid sequence VVKK (SEQ ID NO: 4).
• WEE amino acid sequence WEE
• VVKK amino acid sequence VVKK
• each of the one or more ligand molecules further comprises a linker and a Z33 peptide of Staphylococcus aureus Protein A, or an antibody -binding fragment thereof, conjugated to the linker.
• a “linker” is any chemical moiety that is capable of linking one compound to another compound (e.g., a cell-binding agent such as a peptide ligand or antibody) in a stable, covalent manner. Linkers can be susceptible to, or be substantially resistant to, acid-induced cleavage, light-induced cleavage, peptidase-induced cleavage, esterase-induced cleavage, and/or disulfide bond cleavage.
• the linker can be any amino acid with a side chain having a free amino, carboxyl or disulfide group.
• exemplary amino acids useful as amino acid linkers in the one or more filler molecules and/or one or more ligand molecules of the present invention include lysine (K), glutamic acid (E), arginine (R) and cysteine (C).
• Other suitable linkers are well known in the art and include, for example, disulfide groups, thioether groups, acid labile groups, photolabile groups, peptidase labile groups, and esterase labile groups. Linkers also include charged linkers and hydrophilic forms thereof as described herein and known in the art.
• the linker may be a cleavable linker, a non-cleavable linker, a hydrophilic linker, and a dicarboxylic acid-based linker.
• the linker is a hydrophilic linker comprising one or more poly(ethylene glycol) (PEG) molecules or one or more oligo(ethylene glycol) (OEG) molecules.
• PEG poly(ethylene glycol)
• OEG oligo(ethylene glycol)
• a “PEG oligomer” or an oligoethylene glycol (OEG) is one in which all of the monomer subunits are ethylene oxide subunits.
• substantially all, or all, monomeric subunits are ethylene oxide subunits, though the oligomer may contain distinct end capping moieties or functional groups, e.g., for conjugation.
• PEG oligomers for use in the present disclosure will comprise one of the two following structures: “ — (CEECEhO) — ” or “ — (CEECEhC n-iCEhCEh — ,” depending upon whether or not the terminal oxygen(s) has been displaced, e.g., during a synthetic transformation.
• the variable (n) ranges from 1 to 30, and the terminal groups and architecture of the overall PEG or OEG can vary.
• PEGylation is a process through which polyethylene glycol chains are conjugated to proteins (e.g., therapeutic proteins), peptides, aptamers, enzymes, small molecule drugs, antibodies, and other molecules.
• proteins e.g., therapeutic proteins
• peptides e.g., peptides, aptamers
• enzymes e.g., enzymes, small molecule drugs, antibodies, and other molecules.
• PEGylation also reduces the immunogenicity of the protein to which it is conjugated.
• PEG and OEG linkers and related conjugation methods are described in, e.g., U.S. Patent 6,716,821; U.S. Patent 9,388,104; U.S. Patent Application Publication 2009/0285780; and Harris, J.M. and Chess, R.B., Nature Reviews Drug Discovery, 2: 214-221 (2003).
• the linker may comprise any suitable number of PEG or OEG molecules, units, or monomers.
• the linker comprises 2-50 (e.g., 5, 10, 15, 20, 25, 30, 35, 40, or 45) PEG or OEG molecules.
• the linker comprises 10-20 (e.g., 10, 11, 13, 14, 15, 16, 17, 18, 19, or 20) PEG or OEG molecules, or 30-40 (e.g., 31, 32, 33,
• the linker may comprise 16 OEG or PEG molecules, or 36 OEG or PEG molecules.
• the ligand molecule disclosed herein further comprises a Z33 peptide of Staphylococcus aureus Protein A, or an antibody-binding fragment thereof, conjugated to the linker.
• Staphylococcal protein A (SPA) is a protein originally found in the cell wall of Staphylococcus aureus. It is composed of five homologous domains that fold into a three- helix bundle. Protein A plays an important role in immunology due to its specific binding to the Fc-portion of immunoglobulin G (IgG) from most mammalian species, including human. Extensive structural and biochemical studies of protein A have been conducted.
• the Z-58 domain of protein A was the first protein A domain widely used in affinity chromatography and affinity precipitation.
• the minimized binding domain Z-33 was later developed without significantly changing the function of the molecule.
• the Z33 peptide is a Protein A mimic having the amino acid sequence FNMQQQRRFYEALHDPNLNEEQRNAKIKSIRDD (SEQ ID NO: 1), and contains a motif of two a-helices.
• the disclosure also encompasses a ligand molecule comprising any antigen-binding fragment of a Z33 peptide, or a peptide having an amino acid sequence that is at least 95% (e.g., 95%, 96%, 97%, 98%, or 99%) identical to SEQ ID NO: 1.
• the degree of nucleic acid and/or amino acid identity can be determined using any method known in the art, such as the BLAST sequence database.
• the disclosure further provides a method for purifying an antibody or an Fc fusion protein, which comprises (a) dissolving the above-described system in an aqueous solution at physiological pH and aging overnight, whereby the one or more filler molecules and one or more ligand molecules self-assemble into immunofibers (IFs); (b) mixing a sample containing a protein comprising an Fc region with the IFs under conditions whereby the IFs bind to the Fc region to form an immunofiber-protein complex in solution; (c) separating the immunofiber-protein complex from the solution by adding salt and/or centrifugation; and (d) dissociating the protein comprising an Fc region from the IFs.
• IFs immunofibers
• any suitable protein that contains an Fc region may be purified using the methods disclosed herein.
• the Fc region-containing protein may be an antibody, such as a monoclonal antibody.
• the Fc region-containing protein may be an Fc fusion protein.
• An “Fc fusion protein” is a bioengineered polypeptide that joins the crystallizable fragment (Fc) domain of an antibody with another biologically active protein domain or peptide to generate a molecule with unique structure-function properties and, in some cases, therapeutic potential.
• the gamma immunoglobulin (IgG) isotype is often used as the basis for generating Fc-fusion proteins because of favorable characteristics such as recruitment of effector function and increased plasma half-life.
• the system described herein may be used to capture and purify other proteins that do not comprise and Fc region by incorporating customized binding pairs into the design of the filler and ligand molecules.
• “Physiologic” or “physiological” pH is the pH that typically occurs in human cells (e.g., human cells in vivo). In this regard, physiologic pH of the human body ranges between 7.35 to 7.45, with the average physiologic pH at 7.40.
• the incubation or “aging” of the filler and ligand molecules in solution may be for any suitable period of time.
• the dissolved system is aged for at least two hours, but not more than 48 hours.
• the dissolved system may be incubated or aged for 2-8 hours, 8-12 hours, 12-16 hours, 16-20 hours, 20-24 hours, 24-36 hours, or 36-48 hours.
• the dissolved system is aged overnight (e.g., about 6, 7, 8, 9, 10, 11, or 12 hours).
• the disclosed method comprises mixing a sample containing an antibody or an Fc fusion protein with the IFs under conditions whereby the IFs bind to the Fc region of the protein (e.g., an antibody or Fc fusion protein) to form an immunofiber-protein complex in solution.
• a sample containing an antibody or an Fc fusion protein binds to the Fc region of the protein (e.g., an antibody or Fc fusion protein) to form an immunofiber-protein complex in solution.
• Suitable conditions for affinity -based antibody purification methods are known in the art and may be employed in the disclosed method.
• reagents and conditions suitable for Protein A-based purification are known in the art and may be used in the context of the present disclosure (see, e.g., Proteus Protein A Antibody Purification Handbook, Bio-Rad (2016); and Fishman, J.B., and Berg, E.A., Cold Spring Harb Protoc; doi:10.1101/pdb.prot099143).
• the complexes formed can then be separated from the unbound immunofibers and Fc region- containing proteins (e.g., antibodies or Fc fusion proteins) and other components in the sample by many known separation means, including, for example, salt-induced precipitation and centrifugation.
• the separated complexes can then be introduced into another solution at an acidic pH, where the immunofibers lose their binding affinity for the Fc region-containing proteins (e.g., antibodies or Fc fusion proteins).
• the antibody or Fc fusion protein can then be dissociated from the immunofibers by filtration, such as diafiltration, microfiltration, or other means.
• the antibody or Fc fusion protein is dissociated from the IFs by lowering the pH to elution conditions (e.g., pH 2.5-4.0) and filtration or microfiltration.
• the antibody or Fc fusion protein may be dissociated from the IFs using sequential precipitation.
• a sample containing an Fc region-containing protein may be mixed with a first IF solution (prepared as described above), aged or incubated for any suitable amount of time (e.g., 2, 3, 4, 5, or 6 hours), and centrifuged (e.g., at 10,000-20,000 rpm).
• a first IF solution prepared as described above
• a second IF solution prepared as described above
• aged or incubated for any suitable amount of time e.g., 2, 3, 4, 5, or 6 hours
• centrifuged a second time e.g., at 10,000-20,000 rpm
• Fc region-containing protein e.g., antibody or Fc fusion protein
• the final precipitate is then washed and resuspended in elution buffer.
• the eluted antibodies or Fc fusion proteins may be fully recovered using membrane separation methods.
• the system and methods described herein have several advantages as compared to other protein purification methods known in the art, particularly protein A chromatography methods in which the capture step is one of the major downstream bottlenecks due to resin capacity limitation and high production cost.
• the IF system and methods described herein provide for high throughput purification of monoclonal antibodies, ease of handling, and reduced cost.
• the disclosed system and methods allow for rapid purification of proteins, in that antibody-IF binding and agglomeration can be completed in 30 minutes or less.
• Crude products were cleaved from the solid support using a mixture of trifluoroacetic acid (TFA)/ triisopropylsilane (TISyFEO in a ratio of 92.5:5:2.5 for 2.5 hours. Excess TFA was removed by evaporation and ice-cold diethyl ether was added to precipitate the crude products, followed by centrifugation.
• the crude products were purified by preparative RP-HPLC using a Varian Polymeric Column (PLRP-S, 100 A, 10 pm, 150x25 mm) at 25 °C on a Varian ProStar Model 325 preparative HPLC (Agilent Technologies, Santa Clara, CA, USA) monitored at 220 nm for the absorbance of peptide segments.
• CMC measurement The CMCs of the ligand molecules in PBS were determined using Nile Red, a hydrophobic dye that undergoes changes in both fluorescence intensity and emission wavelength (a blue-shift) upon partition into the hydrophobic domains of supramolecular assemblies.
• Nile Red was initially dissolved in acetone at 20 pM and 10 pi aliquots were loaded into several centrifuge tubes. After the acetone evaporated under room temperature, 500 pi fresh ligand solutions in PBS at various concentrations were added into the centrifuge tubes containing dry Nile Red and aged overnight for assembly. Fluorescent spectra of Nile Red were then monitored by a Fluorolog fluorometer (Jobin Yvon, Edison,
• CD Spectroscopy The CD spectra of self-assembled ligand molecules were collected on a Jasco J-710 spectropolarimeter (JASCO, Easton, MD, USA) using a 1 mm path length quartz UV-vis absorption cell (ThermoFisher Scientific, Pittsburgh, PA, USA) at 25 °C. A background spectrum of the solvent was acquired and subtracted from the sample spectrum. The collected data was averaged from three scans and normalized with respect to the ligand concentration.
• Jasco J-710 spectropolarimeter JASCO, Easton, MD, USA
• quartz UV-vis absorption cell ThermoFisher Scientific, Pittsburgh, PA, USA
• ITC Experiment ITC experiments were performed using a high precision VP- ITC titration calorimetric system (Microcal Inc.). 40 mM ligand solution was titrated with 100 mM mAbl in PBS (pH 7.4) at 25 °C. The heat evolved after each injection was obtained from the integral of the calorimetric signal. The heat associated with the binding between ligand molecule and mAbl was obtained by subtracting the heat of dilution. Analysis of the data was performed using MicroCal Origin package.
• mAb Precipitation IF stock solutions at desired filler and ligand concentrations were prepared one day before the precipitation experiment. In experimental groups, pure mAbl from a concentrated solution (448 mM, 64.5 g/L) was then added into 100 pL IF solutions to reach a desired final concentration and incubated for 30 minutes at room temperature. The solution was then centrifuged at 15000 rpm for 15 minutes. For the 1M salt group, ammonium sulfate was added to the mAb-IF mixtures to reach a final concentration of 1M and incubated for another 30 minutes before centrifugation.
• the supernatant was taken out and analyzed by ProA-HPLC (POROSTM A 20 pm Column, Stainless Steel, 2.1 x 30 mm, 0.1 mL) to determine the protein concentrations.
• the precipitated amount of each species was calculated by subtracting the amount in the supernatant from the amount added.
• the precipitation yield was calculated by dividing the added amount by the precipitated amount.
• IF 1(2.5 mM filler, 250 mM 016), IF2 (2.5 mM filler, 750 pM 016), and IF3 (2.5 mM filler, 200 pM 016) were prepared one day before the precipitation experiment.
• Pure mAbl from a concentrated solution (448 pM, 64.5 g/L) was added into 100 uL IF1 and 100 uL IF2 to reach a desired final concentration of 40 pM and 80 pM, respectively.
• the resuspended solution was then dialyzed against 40 mM sodium acetate (1 L) at pH 3.7 for 24 hours with dialysis buffer replaced three times.
• the protein, filler, and ligand concentrations were determined by ProA- HPLC and RP-UPLC.
• An immunofiber system was formed by the co-assembly of filler and ligand molecules.
• the filler molecule, C12-VVEE was designed to modulate the distribution of the ligand molecule in the co-assembled IFs ( Figure 1 A).
• the Z33 peptide which possesses a two-helix motif, is conjugated on the C-terminus of the ligand molecule, 02- VVKK[Linker]Z33, for specific monoclonal antibody capture ( Figure 1A).
• a double glycine (GG) segment was inserted as a linker between the IF surface and Z33.
• a series of ligand molecules, 04, 08, 012, 016, 036, and P2000, with various OEG (or PEG) linkers were designed as summarized in Table 1.
• Figure 1C illustrates the spontaneous co-assembly process of filler and ligand molecules in aqueous solution, forming filamentous IFs with Z33 displayed on the IF surface.
• mAbs there were four possible states of mAbs in the IF solution.
• States 1 and 2 represent two Fc-portions of a mAh bound to two ligands from two different IFs or the same IF, respectively.
• State 3 only one Fc-portion of a mAh is bound to one ligand on an IF.
• This example describes the molecular assembly and characterization of immunofibers produced using the system and methods disclosed herein.
• TEM images revealed that each of the ligand molecules can self-assemble into filamentous structures with diameters of 11.1 ⁇ 0.9 nm (04), 12.6 ⁇ 1.2 nm (08), 13.6 ⁇ 1.2 nm (012), 14.9 ⁇ 1.3 nm (016), 18.5 ⁇ 1.8 nm (036), and 19.3 ⁇ 2.0 nm (P2000), respectively ( Figures 2B-2G).
• the IF diameter increased with the increase of the linker length.
• CD circular dichroism
• the supernatant was analyzed by ProA-HPLC to determine the remaining mAh concentration and calculate the mAh precipitation yield.
• the mAh precipitation yield showed significant improvement from 65% to higher than 88% when replacing the GG linker with 0(P)EG linkers in the ligand design. In particular, greater than 95% mAh precipitation yields were obtained for 04-036. Since there is no bias against the IF precipitation efficiency under 1M salt conditions, this mAh precipitation yield increase from G2 to the new ligand molecules with OEG (or PEG) linkers specifically reflects the significant improvement in the mAh binding efficiency as a result of the increased linker length and flexibility. A slight drop in the mAh precipitation yield was seen for P2000, likely due to the entanglement of long PEG chains that undermines the accessibility of the Z33 peptide for mAh capture.
• the mAh precipitation yields were generally lower than salt groups, while an upward trend was observed with an increase of the OEG linker length.
• the mAh precipitation yield under no salt conditions was determined by a combination of mAb binding efficiency and the precipitation efficiency of the mAb-IF complexes. From 04 to 036, there were no obvious differences in the mAh binding efficiency as indicated by the salt group data set.
• the increase in the mAb precipitation yield under no salt conditions represents an enhancement in the mAb precipitation efficiency, possibly caused by the improved crosslinking between IFs. More importantly, the yield difference between 1M salt and no salt groups was gradually diminished with increasing the linker length, leading to a less than 10% yield discrepancy for 036. This was considered very promising for mAb precipitation, in that the improved mAb-IF interactions achieved by using OEG or (PEG) linkers could potentially substitute for the salt contribution to mAb precipitation.
• Figure 4E shows the sample vials of 04-016 IFs after being mixed with 40 pM mAbl for 5 minutes under 1 M salt or no salt conditions.
• the cloudiness of the salt groups was relatively higher than the no salt groups, suggesting a higher mAb precipitation yield for the salt groups.
• the cloudiness increased from 04 to 016 in accordance with the yield trend shown in Figure 4B.
• Figures 5A and 5B show the plots of mAh precipitation yield and mass versus 016 concentration, respectively, and an optimal point was observed at a ligand: mAh molar ratio between 6: 1 to 9: 1 for all three mAh concentrations.
• the mAh precipitation yields for 40 and 80 pM mAh were around 85%, while only about 65% mAh was precipitated for 133 pM mAh, showing a decrease in the IF performance when scaling up for high mAh concentrations.
• This example describes sequential precipitation and elution of monoclonal antibodies.
• a two-step sequential precipitation was conducted to precipitate the remaining mAbs.
• the supernatant from the first precipitation step was added into fresh IF solution.
• a wash step was then carried out using PBS to remove the non-specifically bound impurities in the precipitates from the two precipitation steps.
• elution buffer 40 mM sodium acetate, pH 3.7
• the above Examples illustrate the design and construction of a series of supramolecular IF systems containing OEG (or PEG) linkers and demonstrate the impact of epitope topography in the radial direction of IFs on the IF bioactivity.
• the described results reveal that increasing the linker length to OEG16 can simultaneously improve monoclonal binding and precipitation efficiency under no salt conditions. Linkers that are too long, however, show an adverse impact on the function of the resultant supramolecular polymers.
• the mAh precipitation yield under no salt conditions may be efficiently optimized by tuning the ligand concentration to reach desired monoclonal antibody binding states.
• the strategy of engineering linkers for better epitope presentation sheds important light on the design of supramolecular polymers for specific molecular recognition and targeted drug delivery.
• the supramolecular IF system described herein can serve as an efficient alternative for the purification of monoclonal antibodies, and may be applied to the capture and purification of other molecules of interest by incorporating customized binding pairs into the system design.

Landscapes

• Chemical & Material Sciences (AREA)
• Organic Chemistry (AREA)
• Health & Medical Sciences (AREA)
• Life Sciences & Earth Sciences (AREA)
• Molecular Biology (AREA)
• Biochemistry (AREA)
• General Health & Medical Sciences (AREA)
• Genetics & Genomics (AREA)
• Biophysics (AREA)
• Medicinal Chemistry (AREA)
• Proteomics, Peptides & Aminoacids (AREA)
• Analytical Chemistry (AREA)
• Gastroenterology & Hepatology (AREA)
• Chemical Kinetics & Catalysis (AREA)
• Immunology (AREA)
• General Chemical & Material Sciences (AREA)
• Peptides Or Proteins (AREA)

Priority Applications (5)

Applications Claiming Priority (2)

Publications (1)

Family

ID=84979716

Family Applications (1)

Country Status (6)

Citations (2)

• 2022
  • 2022-07-18 KR KR1020247004948A patent/KR20240038740A/ko active Pending
  • 2022-07-18 WO PCT/US2022/073822 patent/WO2023004273A1/en not_active Ceased
  • 2022-07-18 JP JP2024501249A patent/JP2024526704A/ja active Pending
  • 2022-07-18 US US18/579,578 patent/US20240327455A1/en active Pending
  • 2022-07-18 EP EP22846765.0A patent/EP4373839A4/en active Pending
  • 2022-07-18 CN CN202280051543.9A patent/CN117769562A/zh active Pending

Patent Citations (2)

Non-Patent Citations (1)

Also Published As

Similar Documents

Legal Events