Patent Publication Number: US-2022213447-A1

Title: AAV9 Affinity Agents

Description:
CROSS REFERENCE TO RELATED APPLICATIONS 
     This application claims the benefit of U.S. Provisional Application No. 62/852,717, filed on May 24, 2019 and U.S. Provisional Application No. 62/949,878, filed on Dec. 18, 2019, the contents of each of which are hereby incorporated by reference herein in their entirety. 
    
    
     BACKGROUND 
     The purity of biologically produced therapeutics is tightly scrutinized and regulated by authorities to ensure safety and efficacy. Thus, there remains a need for means to efficiently purify of biologically produced therapeutics to a high degree of purity. 
     SUMMARY 
     To support the clinical efforts for therapeutic proteins, compositions and methods to efficiently purify proteins from recombinant sources are needed. Affinity purification is a means to isolate and/or achieve desired purity of a protein in few steps, or a single step. However, the development of affinity agents (e.g., comprising an affinity ligand) can be a resource intensive and time consuming task and hence affinity agents exist for very few proteins. In the absence of an affinity agent, purification typically involves inefficient processes, such as a multi-column process. 
     Recombinant adeno-associated viruses (rAAV) are one of the most investigated viral vectors for the delivery of gene therapies in humans. AAV serotypes exhibit various cellular tropisms and interactions with cell receptors to allow entry into the cells and delivery of genetic cargo into the nucleus for expression. AAV9 is of particular interest to biopharmaceutical developers due to its reported ability to cross the blood brain barrier, which is of particular importance to potentially address an array of central nervous system (CNS) disorders. In addition to its application for CNS disorders, and due to a broad tropism towards liver, skeletal muscle and lung tissues, AAV9 is also being used to address non-CNS disorders. 
     The manufacturing of rAAV is difficult and expensive. Cell culture productivity is low and typically only achieves 10 13 -10 15  viral capsids per liter, which is equivalent to approximately 0.1-10 mg/L. Purification is mainly accomplished through the use of affinity chromatography. Currently, there are only 3 affinity resins available for the purification of AAV, POROS™ CaptureSelect™ AAV9, POROS™ CaptureSelect™ AAVX and AVB Sepharose. These resins have 2 major shortcomings, they cannot be cleaned with sodium hydroxide and can only be reused for a few cycles. This increases resin consumption and hence leads to high resin costs for the purification. 
     Affinity agents that bind AAV and are useful for isolation and/or affinity purification are described herein. 
     In some embodiments, provided herein are affinity agents comprising a ligand comprising the binding motif of SEQ ID Nos: 1-5, or an amino acid sequence that differs by no more than three, by no more than two, or by no more than one, substitutions, additions, or deletions. 
     In some embodiments, provided herein are affinity agents comprising a ligand, wherein the ligand comprises a polypeptide having an amino acid sequence according to SEQ ID NOs: 5-20, or an amino acid sequence that differs by no more than three, by no more than two, or by no more than one, substitutions, additions, or deletions. 
     In some embodiments, provided herein are affinity agents comprising a ligand, wherein the ligand comprises a polypeptide having an amino acid sequence according to SEQ ID NOs: 21-47, or an amino acid sequence that differs by no more than three, by no more than two, or by no more than one, substitutions, additions, or deletions. 
     In some embodiments, the N-terminus of the ligand is acetylated. In some embodiments, the ligand further comprises a C-terminal lysine. In some embodiments, the C-terminal lysine of the ligand is amidated. In some embodiments, the ligand further comprises at least one polyethylene glycol (PEG). In some embodiments, the at least one polyethylene glycol is PEG( 3 ). 
     In some embodiments, the ligand is attached to a solid surface. In some embodiments, the solid surface is a resin or bead. In some embodiments, the solid surface is a membrane. In some embodiments, the solid surface is a monolith. In some embodiments, the ligand is conjugated to the solid surface via a linker. In some embodiments, the linker comprises PEG and/or lysine. 
     In some embodiments, affinity agents and/or ligands provided by the present disclosure are or comprise cyclic peptides. In some embodiments, provided affinity agents and/or ligands comprise a cyclic portion. In some embodiments, provided herein are affinity agents comprising a ligand comprising a binding motif of SEQ ID No: 1, or an amino acid sequence that differs by no more than three, by no more than two, or by no more than one, substitutions, additions, or deletions within a cyclic peptide or cyclic portion of a peptide 
     In some embodiments, provided herein are affinity agents used for the purification of virus particles. In some embodiments, affinity agents and/or ligands provided by the present disclosure are or comprise cyclic peptides. In some embodiments, provided affinity agents and/or ligands comprise a cyclic portion. In some embodiments, provided herein are affinity agents comprising a ligand comprising a binding motif of SEQ ID Nos: 1-5, or an amino acid sequence that differs by no more than three, by no more than two, or by no more than one, substitutions, additions, or deletions within a cyclic peptide or cyclic portion of a peptide. 
     In some embodiments, provided herein are affinity agents used for the purification of virus particles. 
     In some embodiments, provided herein are affinity agents used for the purification of adeno associated virus particles. 
     In some embodiments, provided herein are methods of making an affinity agent comprising: conjugating a ligand according to any embodiment described herein to a solid surface. 
     Definitions 
     In order for the present disclosure to be more readily understood, certain terms are defined below. Unless defined otherwise herein, technical and scientific terms have the same meaning as commonly understood by one of ordinary skill in the art. 
     Approximately or about: As used herein, the term “approximately” or “about,” as applied to one or more values of interest, refers to a value that is similar to a stated reference value. In certain embodiments, the term “approximately” or “about” refers to a range of values that fall within 25%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, or less in either direction (greater than or less than) of the stated reference value unless otherwise stated or otherwise evident from the context (except where such number would exceed 100% of a possible value). 
     Biologically active: As used herein, the term “biologically active” refers to a characteristic of any agent that has activity in a biological system, and particularly in an organism. For instance, an agent that, when administered to an organism, has a biological effect on that organism, is considered to be biologically active. 
     Conservative and non-conservative substitution: A “conservative” amino acid substitution is one in which one amino acid residue is replaced with another amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined in the art, including basic side chains (e.g., lysine (K), arginine (R), histidine (H)); acidic side chains (e.g., aspartic acid (D), glutamic acid (E)); uncharged polar side chains (e.g., glycine (G); asparagine (N), glutamine (Q) , serine (S), threonine (T), tyrosine (Y), cysteine (C)); nonpolar side chains (e.g., alanine (A), valine (V), leucine (L), isoleucine (I), proline (P), phenylalanine (F), methionine (M), tryptophan (W), beta-branched side chains (e.g., threonine (T), valine (V), isoleucine (I)); and aromatic side chains (e.g., tyrosine (Y), phenylalanine (F), tryptophan (W), histidine (H)). For example, substitution of a phenylalanine for a tyrosine is a conservative substitution. In some embodiments, conservative amino acid substitutions in the sequence of a ligand confer or improve specific binding of the ligand a target of interest. In some embodiments, conservative amino acid substitutions in the sequences of a ligand do not reduce or abrogate the binding of the ligand to a target of interest. In some embodiments, conservative amino acid substitutions do not significantly affect specific binding of a ligand to a target of interest. Methods of identifying nucleotide and amino acid conservative substitutions and non-conservative substitutions which confer, alter or maintain selective binding affinity are known in the art (see, e.g., Brummell, Biochem. 32:1180-1187 (1993); Kobayashi,  Protein Eng.  12(10):879-884 (1999); and Burks, PNAS 94:412-417 (1997)). In some embodiments, non-conservative amino acid substitutions in the sequence of a ligand confer or improve specific binding of the ligand a target of interest. In some embodiments, non-conservative amino acid substitutions in the sequences of a ligand do not reduce or abrogate the binding of the ligand to a target of interest. In some embodiments, non-conservative amino acid substitutions do not significantly affect specific binding of a ligand to a target of interest. 
     Linker: As used herein a “linker” refers to a peptide or other chemical linkage that functions to link otherwise independent functional domains. In some embodiments, a linker is located between a ligand and another polypeptide component containing an otherwise independent functional domain. In some embodiments, a linker is a peptide or other chemical linkage located between a ligand and a surface. 
     Naturally occurring: The term “naturally occurring” when used in connection with biological materials such as a nucleic acid molecules, polypeptides, and host cells, refers to those which are found in nature and not modified by a human being. Conversely, “non-natural” or “synthetic” when used in connection with biological materials refers to those which are not found in nature and/or have been modified by a human being. 
     “Non-natural amino acids,” “amino acid analogs” and “non-standard amino acid residues” are used interchangeably herein. Non-natural amino acids that can be substituted in a ligand as provided herein are known in the art. In some embodiments, a non-natural amino acid is 4-hydroxyproline which can be substituted for proline; 5-hydroxylysine which can be substituted for lysine; 3-methylhistidine which can be substituted for histidine; homoserine which can be substituted for serine; and ornithine which can be substituted for lysine. Additional examples of non-natural amino acids that can be substituted in a polypeptide ligand include, but are not limited to molecules such as: D-isomers of the common amino acids, 2,4-diaminobutyric acid, alpha-amino isobutyric acid, A-aminobutyric acid, Abu, 2-amino butyric acid, gamma-Abu, epsilon-Ahx, 6-amino hexanoic acid, Aib, 2-amino isobutyric acid, 3-amino propionic acid, ornithine, norleucine, norvaline, hydroxyproline, sarcosine, citrulline, homocitrulline, cysteic acid, t-butylglycine, t-butylalanine, phenylglycine, cyclohexylalanine, beta-alanine, lanthionine, dehydroalanine, γ-aminobutyric acid, selenocysteine and pyrrolysine fluoro-amino acids, designer amino acids such as beta-methyl amino acids, C alpha-methyl amino acids, and N alpha-methyl amino acids. 
     “Polynucleotide” and “nucleic acid molecule”: As used interchangeably herein, polynucleotide and nucleic acid molecule refer to a polymeric form of nucleotides of any length, either ribonucleotides or deoxyribonucleotides. These terms include, but are not limited to, DNA, RNA, cDNA (complementary DNA), mRNA (messenger RNA), rRNA (ribosomal RNA), shRNA (small hairpin RNA), snRNA (small nuclear RNA), snoRNA (short nucleolar RNA), miRNA (microRNA), genomic DNA, synthetic DNA, synthetic RNA, and/or tRNA. 
     Operably linked: The term “operably linked,” as used herein, indicates that two molecules are attached so as to each retain functional activity. Two molecules are “operably linked” whether they are attached directly or indirectly. 
     Peptide tag: The term “peptide tag” as used herein refers to a peptide sequence that is part of or attached (for instance through genetic engineering) to another protein, to provide a function to the resultant fusion. Peptide tags are usually relatively short in comparison to a protein to which they are fused. In some embodiments, a peptide tag is four or more amino acids in length, such as, 5, 6, 7, 8, 9, 10, 15, 20, or 25 or more amino acids. In some embodiments, a ligand is a protein that contains a peptide tag. Numerous peptide tags that have uses as provided herein are known in the art. Examples of peptide tags that may be a component of a ligand fusion protein or a target bound by a ligand (e.g., a ligand fusion protein) include but are not limited to HA (hemagglutinin), c-myc, the Herpes Simplex virus glycoprotein D (gD), T7, GST, GFP, MBP, Strep-tags, His-tags, Myc-tags, TAP-tags and FLAG tag (Eastman Kodak, Rochester, N.Y.) Likewise, antibodies to the tag epitope allow detection and localization of the fusion protein in, for example, affinity purification, Western blots, ELISA assays, and immunostaining of cells. 
     Polypeptide: The term “polypeptide” as used herein refers to a sequential chain of amino acids linked together via peptide bonds. The term is used to refer to an amino acid chain of any length, but one of ordinary skill in the art will understand that the term is not limited to lengthy chains and can refer to a minimal chain comprising two amino acids linked together via a peptide bond. As is known to those skilled in the art, polypeptides may be processed and/or modified. 
     Protein: The term “protein” as used herein refers to one or more polypeptides that function as a discrete unit. If a single polypeptide is the discrete functioning unit and does not require permanent or temporary physical association with other polypeptides in order to form the discrete functioning unit, the terms “polypeptide” and “protein” may be used interchangeably. If the discrete functional unit is comprised of more than one polypeptide that physically associate with one another, the term “protein” refers to the multiple polypeptides that are physically coupled and function together as the discrete unit. 
     Specifically binds: As used herein in reference to ligands, the term “specifically binds” or “has selective affinity for” means a ligand reacts or associates more frequently, more rapidly, with greater duration, with greater affinity, or combinations of the above to a particular epitope, protein, or target molecule than with alternative substances, including unrelated proteins. Because of the sequence identity between homologous proteins in different species, specific binding can include a binding agent that recognizes a protein or target in more than one species. Likewise, because of homology within certain regions of polypeptide sequences of different proteins, specific binding can include a binding agent that recognizes more than one protein or target. It is understood that, in certain embodiments, a binding agent that specifically binds a first target may or may not specifically bind a second target. As such, “specific binding” does not necessarily require (although it can include) exclusive binding, i.e. binding to a single target. Thus, a ligand or affinity agent may, in certain embodiments, specifically bind more than one target. In certain embodiments, multiple targets may be bound by the same antigen-binding site on an affinity agent. 
     Substantially: As used herein, the term “substantially” refers to the qualitative condition of exhibiting total or near-total extent or degree of a characteristic or property of interest. One of ordinary skill in the biological arts will understand that biological and chemical phenomena rarely, if ever, go to completion and/or proceed to completeness or achieve or avoid an absolute result. The term “substantially” is therefore used herein to capture the potential lack of completeness inherent in many biological and chemical phenomena. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
         FIG. 1  shows the yield determined for each cycle of a column cycling study involving consecutive cycles of AAV purification that incorporated a 0.5 M NaOH clean for 30 minutes. 
         FIG. 2  shows the residual HCP determined throughout a column cycling study involving consecutive cycles of AAV purification that incorporated a 0.5 M NaOH clean for 30 minutes. The residual HCP of cycle 6 was not measured 
         FIG. 3  shows the residual HCDNA determined for each cycle of a column cycling study involving consecutive cycles of AAV purification that incorporated a 0.5 M NaOH clean for 30 minutes. 
         FIG. 4  shows the yield determined using different elution conditions. Elution buffers contained 0.25 M, 0.5 M or 1 M arginine at either at pH 4.5, 5 or 5.5. 
         FIG. 5  shows the biolayer interferometry sensorgrams for the binding of capsids to the ligands of SEQ ID NO:46 (full line) and SEQ ID NO:47. 
     
    
    
     DETAILED DESCRIPTION 
     Affinity agents prepared from identified and characterized peptide ligands are shown to generate highly purified preparations of virus particles. Affinity resins described herein are useful for removal protein product related impurities as well as the host cell derived contaminants. 
     Ligand Binding to Targets of Interest for Use in an Affinity Agent 
     The characteristics of ligand binding to a target can be determined using known or modified assays, bioassays, and/or animal models known in the art for evaluating such activity. 
     As used herein, terms such as “binding affinity for a target”, “binding to a target” and the like refer to a property of a ligand which may be directly measured, for example, through the determination of affinity constants (e.g., the amount of ligand that associates and dissociates at a given antigen concentration). Several methods are available to characterize such molecular interactions, for example, competition analysis, equilibrium analysis and microcalorimetric analysis, and real-time interaction analysis based on surface plasmon resonance interaction (for example using a BIACORE instrument). These methods are well-known to those of skill in the art and are discussed in publications such as Neri D et al. (1996)  Tibtech  14:465-470 and Jansson M et al. (1997)  J Biol Chem  272:8189-8197. 
     Affinity requirements for a given ligand binding event are contingent on a variety of factors including, but not limited to: the composition and complexity of the binding matrix, the valency and density of both the ligand and target molecules, and the functional application of the ligand. In some embodiments, a ligand binds a target of interest with a dissociation constant (K D ) of less than or equal to 5×10 −3  M, 10 −3  M, 5×10 −4  M, 10 −5  M, 5×10 −5  M, or 10 −5  M. In some embodiments, a ligand binds a target of interest with a K D  of less than or equal to 5×10 −6  M, 10 −6  M, 5×10 −7  M, 10 −7 M, 5×10 −8  M, or 10 −8  M. In some embodiments, a ligand binds a target of interest with a K D  less than or equal to 5×10 −9  M, 10 −9  M, 5×10 −10  M, 10 −10  M, 5×10 −11 M, 10 −11  M, 5×10 −12  M, 10 −12  M, 5×10 −13  M, 10 −13  M, 5×10 −14  M, 10 −14  M, 5×10 −15  M, or 10 −15  M. some embodiments, a ligand generated by methods disclosed herein has a dissociation constant of from about 10 −4  M to about 10 −5  M, from about 10 −5  M to about 10 −6  M, from about 10 −6  M to about 10 −7  M, from about 10 −7  M to about 10 −8  M, from about 10 −8  M to about 10 −9  M, from about 10 −9  M to about 10 −10  M, from about 10 −10  M to about 10 −11  M, or from about 10 −11  M to about 10 12  M. 
     Binding experiments to determine K D  and off-rates can be performed in a number of conditions including, but not limited to, [pH 6.0, 0.01% Tween 20], [pH 6.0, 0.1% gelatin], [pH 5.0, 0.01% Tween 20], [pH9.0, 0.1% Tween 20], [pH 6.0, 15% ethylene glycol, 0.01% Tween 20], [pH 5.0, 15% ethylene glycol, 0.01% Tween 20], and [pH 9.0, 15% ethylene glycol, 0.01% Tween 20]. The buffers in which to make these solutions can readily be determined by one of skill in the art, and depend largely on the desired pH of the final solution. Low pH solutions (&lt;pH 5.5) can be made, for example, in citrate buffer, glycine-HCl buffer, or in succinic acid buffer. High pH solutions can be made, for example, in Tris-HCl, phosphate buffers, or sodium bicarbonate buffers. A number of conditions may be used to determine K D  and off-rates for the purpose of determining, for example, optimal pH and/or salt concentrations. 
     In some embodiments, a ligand specifically binds a target of interest with a k off  ranging from 0.1 to 10 −7  sec −1 , 10 −2  to 10 −7  sec −1 , or 0.5×10 −2  to 10 −7  sec −1 . In some embodiments, a ligand binds a target of interest with an off rate (k off ) of less than 5×10 −2  sec −1 , 10 −2  sec −1 , 5×10 −3  sec −1 , or 10 −3  sec −1 . In some embodiments a ligand binds a target of interest with an off rate (k off ) of less than 5×10 −4  sec −1 , 10 −4  sec −1 , 5×10 −5  sec −1 , or 10 −5  sec −1 , 5×10 −6  sec −1 , 10 −6  sec −1 , 5×10 −7  sec −1 , or 10 −7  sec −1 . 
     In some embodiments, a ligand specifically binds a target of interest with a k on  ranging from about 10 3  to 10 7  M −1 sec −1 , 10 3  to 10 6  M −1 sec −1 , or 10 3  to 10 5 M −1 sec −1 . In some embodiments, a ligand (e.g., a ligand fusion protein) binds the target of interest with an on rate (k on ) of greater than 10 3  M −1 sec −1 , 5×10 3  M −1 sec −1 , 10 4  M −1 sec −1 , or 5×10 4  M −l sec −1 . In an additional embodiment, a ligand, binds a target of interest with a k on  of greater than 10 5  M −1 sec −1 , 5×10 5 M −l sec −1 , 10 6  M −1  sec −1 , 5×10 6  M −1  sec −1 , or 10 7  M −1  sec −1 . 
     Targets of Interest 
     A target of interest specifically bound by a ligand can be any molecule for which it is desirable for a ligand of an affinity agent to bind. For example, a target specifically bound by ligand can be any target of purification, manufacturing, formulation, therapeutic, diagnostic, or prognostic relevance or value. A number of exemplary targets are provided herein, by way of example, and are intended to be illustrative and not limiting. A target of interest can be naturally occurring or synthetic. In some embodiments, a target is a biologically active protein. In some embodiments, a target of interest is an extracellular component or an intracellular component, a soluble factor (e.g., an enzyme, hormone, cytokine, growth factor, antibody, and the like), or a transmembrane protein (e.g., a cell surface receptor). In some embodiments, a target of interest specifically bound by a ligand is itself a ligand having a different sequence. 
     Linkers 
     The terms “linker” and “spacer” are used interchangeably herein to refer to a peptide or other chemical linkage that functions to link otherwise independent functional domains. In some embodiments, a linker is located between a ligand and another polypeptide component containing an otherwise independent functional domain. Suitable linkers for coupling two or more linked ligands may generally be any linker used in the art to link peptides, proteins or other organic molecules. In some embodiments, such a linker is suitable for constructing proteins or polypeptides that are intended for pharmaceutical use. 
     Suitable linkers for operably linking a ligand and an additional component of a ligand fusion protein in a single-chain amino acid sequence include but are not limited to, polypeptide linkers such as glycine linkers, serine linkers, mixed glycine/serine linkers, glycine- and serine-rich linkers or linkers composed of largely polar polypeptide fragments. 
     In some embodiments, a linker comprises a majority of amino acids selected from glycine, alanine, proline, asparagine, glutamine, and lysine. In some embodiments, a linker comprises a majority of amino acids selected from glycine, alanine, proline, asparagine, aspartic acid, threonine, glutamine, and lysine. In some embodiments, a ligand linker is made up of a majority of amino acids that are sterically unhindered. In some embodiments, a linker comprises a majority of amino acids selected from glycine, serine, and/or alanine. In some embodiments, a peptide linker is selected from polyglycines (such as (Gly) 5 , and (Gly) 8 , poly(Gly-Ala), and polyalanines. 
     Linkers can be of any size or composition so long as they are able to operably link a ligand in a manner that permits the ligand to bind a target of interest. In some embodiments, linkers are from about 1 to 50 amino acids, from about 1 to 20 amino acids, from about 1 to 15 amino acids, from about 1 to 10 amino acids, from about 1 to 5 amino acids, from about 2 to 20 amino acids, from about 2 to 15 amino acids, from about 2 to 10 amino acids, or from about 2 to 5 amino acids. It should be clear that the length, the degree of flexibility and/or other properties of the linker(s) may influence certain properties of a ligand for use in an affinity agent, such as affinity, specificity or avidity for a target of interest, or for one or more other target proteins of interest, or for proteins not of interest (i.e., non-target proteins). In some embodiments, two or more linkers are utilized. In some embodiments, two or more linkers are the same. In some embodiments, two or more linkers are different. 
     In some embodiments, a linker is a non-peptide linker such as an alkyl linker, or a PEG linker. For example, alkyl linkers such as —NH—(CH2)s—C(0)—, wherein s=2-20 can be used. These alkyl linkers may further be substituted by any non-sterically hindering group such as lower alkyl e.g., C1 C6) lower acyl, halogen (e.g., CI, Br), CN, NH2, phenyl, etc. An exemplary non- peptide linker is a PEG linker. In some embodiments, a PEG linker has a molecular weight of from about 100 to 5000 kDa, or from about 100 to 500 kDa. 
     Linkers can be evaluated using techniques described herein and/or otherwise known in the art. In some embodiments, linkers do not alter (e.g., do not disrupt) the ability of a ligand to bind a target molecule. 
     Affinity Agents Comprising Conjugated Ligands 
     Ligands that promote specific binding to targets of interest can be chemically conjugated with a variety of chromatography compositions (e.g., beads, resins, gels, membrane, monoliths, etc.) to prepare an affinity agent. Affinity agents comprising ligands are particularly useful for purification and manufacturing applications. 
     In some embodiments, a ligand (e.g., a ligand fusion protein) contains at least one reactive residue. Reactive residues are useful, for example, as sites for the attachment of conjugates such as chemotherapeutic drugs. An exemplary reactive amino acid residue is lysine. A reactive residue (e.g., lysine) can be added to a ligand at either end, or within the ligand sequence and/or can be substituted for another amino acid in the sequence of a ligand. A suitable reactive residue (e.g., lysine, etc.,) can also be located within the sequence of an identified ligand without need for addition or substitution. 
     Attachment to Solid Surface 
     “Solid surface,” “support,” or “matrix” are used interchangeably herein and refer to, without limitation, any column (or column material), bead, test tube, microtiter dish, solid particle (for example, agarose or sepharose), microchip (for example, silicon, silicon-glass, or gold chip), or membrane (synthetic (e.g. a filter) or biological (e.g. liposome or vesicle) in origin) to which a ligand, antibody, or other protein may be attached (i.e., coupled, linked, or adhered), either directly or indirectly (for example, through other binding partner intermediates such as other antibodies or Protein A), or in which an ligand or antibody may be embedded (for example, through a receptor or channel). Reagents and techniques for attaching polypeptides to solid supports (e.g, matrices, resins, plastic, etc.) are well-known in the art. Suitable solid supports include, but are not limited to, a chromatographic resin or matrix (e.g., SEPHAROSE-4 FF agarose beads), the wall or floor of a well in a plastic microtiter dish, a silica based biochip, polyacrylamide, agarose, silica, nitrocellulose, paper, plastic, nylon, metal, and combinations thereof. Ligands and other compositions may be attached on a support material by a non-covalent association or by covalent bonding, using reagents and techniques known in the art. In some embodiments, a ligand is coupled to a chromatography material using a linker. 
     Production of Ligands 
     The production of a ligand, useful in practicing the provided methods, may be carried out using a variety of standard techniques for chemical synthesis, semi-synthetic methods, and recombinant DNA methodologies known in the art. Also provided are methods for producing a ligand, individually or as part of multi-domain fusion protein, as soluble agents and cell associated proteins. In some embodiments, the overall production scheme for a ligand comprises obtaining a reference protein scaffold and identifying a plurality of residues within the scaffold for modification. Depending on the embodiment, the reference scaffold may comprise a protein structure with one or more alpha-helical regions, or other tertiary structure. Once identified, the plurality of residues can be modified, for example by substitution of one or more amino acids. In some embodiments, one or more conservative substitutions are made. In some embodiments, one or more non-conservative substitutions are made. In some embodiments a natural amino acid (e.g., one of alanine, arginine, asparagine, aspartic acid, cysteine, glutamine, glutamic acid, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, or valine) is substituted into a reference scaffold at targeted positions for modification. In some embodiments, modifications do not include substituting in either a cysteine or a proline. After modifications have been made at identified positions desired in a particular embodiment, the resulting modified polypeptides (e.g., candidate ligands) can be recombinantly expressed, for example in a plasmid, bacteria, phage, or other vector (e.g. to increase the number of each of the modified polypeptides). The modified polypeptides can then be purified and screened to identify those modified polypeptides that have specific binding to a particular target of interest. Modified polypeptides may show enhanced binding specificity for a target of interest as compared to a reference scaffold, or may exhibit little or no binding to a given target of interest (or to a non-target protein). In some embodiments, depending on the target of interest, the reference scaffold may show some interaction (e.g. nonspecific interaction) with a target of interest, while certain modified polypeptides will exhibit at least about two fold, at least about five fold, at least about 10 fold, at least about 20 fold, at least about 50 fold, or at least about 100 fold (or more) increased binding specificity for the target of interest. Additional details regarding production, selection, and isolation of ligand are provided in more detail below. 
     Recombinant Expression of Ligands 
     In some embodiments, a ligand such as a ligand fusion protein is “recombinantly produced,” (i.e., produced using recombinant DNA technology). Exemplary recombinant methods available for synthesizing ligand fusion proteins, include, but are not limited to polymerase chain reaction (PCR) based synthesis, concatemerization, seamless cloning, and recursive directional ligation (RDL) (see, e.g., Meyer et al.,  Biomacromolecules  3:357-367 (2002), Kurihara et al.,  Biotechnol. Lett.  27:665-670 (2005), Haider et al.,  Mol. Pharm.  2:139-150 (2005); and McMillan et al.,  Macromolecules  32(11):3643-3646 (1999). 
     Nucleic acids comprising a polynucleotide sequence encoding a ligand are also provided. Such polynucleotides optionally further comprise one or more expression control elements. For example, a polynucleotide can comprise one or more promoters or transcriptional enhancers, ribosomal binding sites, transcription termination signals, and polyadenylation signals, as expression control elements. A polynucleotide can be inserted within any suitable vector, which can be contained within any suitable host cell for expression. 
     The expression of nucleic acids encoding ligands is typically achieved by operably linking a nucleic acid encoding the ligand to a promoter in an expression vector. Typical expression vectors contain transcription and translation terminators, initiation sequences, and promoters useful for regulation of the expression of the desired nucleic acid sequence. Exemplary promoters useful for expression in  E. coli  include, for example, the T7 promoter. 
     Methods known in the art can be used to construct expression vectors containing the nucleic acid sequence encoding a ligand along with appropriate transcriptional/ translational control signals. These methods include, but are not limited to in vitro recombinant DNA techniques, synthetic techniques and in vivo recombination/genetic recombination. The expression of the polynucleotide can be performed in any suitable expression host known in the art including, but not limited to, bacterial cells, yeast cells, insect cells, plant cells or mammalian cells. In some embodiments, a nucleic acid sequence encoding a ligand is operably linked to a suitable promoter sequence such that the nucleic acid sequence is transcribed and/or translated into ligand in a host. 
     A variety of host-expression vector systems can be utilized to express a nucleic acid encoding a ligand. Vectors containing the nucleic acids encoding a ligand (e.g., individual ligand subunits or ligand fusions) or portions or fragments thereof, include plasmid vectors, a single and double-stranded phage vectors, as well as single and double-stranded RNA or DNA viral vectors. Phage and viral vectors may also be introduced into host cells in the form of packaged or encapsulated virus using known techniques for infection and transduction. Moreover, viral vectors may be replication competent or alternatively, replication defective. Alternatively, cell-free translation systems may also be used to produce the protein using RNAs derived from the DNA expression constructs (see, e.g., WO86/05807 and WO89/01036; and U.S. Pat. No. 5,122,464). 
     Generally, any type of cell or cultured cell line can be used to express a ligand provided herein. In some embodiments a background cell line used to generate an engineered host cell is a phage, a bacterial cell, a yeast cell or a mammalian cell. A variety of host-expression vector systems may be used to express the coding sequence a ligand fusion protein. Mammalian cells can be used as host cell systems transfected with recombinant plasmid DNA or cosmid DNA expression vectors containing the coding sequence of the target of interest and the coding sequence of the fusion polypeptide. The cells can be primary isolates from organisms, cultures, or cell lines of transformed or transgenic nature. 
     Suitable host cells include but are not limited to microorganisms such as, bacteria (e.g.,  E. coli, B. subtilis ) transformed with recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vectors containing ligand coding sequences; yeast (e.g.,  Saccharomyces, Pichia ) transformed with recombinant yeast expression vectors containing ligand coding sequences; insect cell systems infected with recombinant virus expression vectors (e.g., Baculovirus) containing ligand coding sequences; plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors (e.g., Ti plasmid) containing ligand coding sequences. 
     Prokaryotes useful as host cells in producing a ligand include gram negative or gram positive organisms such as,  E. coli  and  B. subtilis.  Expression vectors for use in prokaryotic host cells generally contain one or more phenotypic selectable marker genes (e.g., genes encoding proteins that confer antibiotic resistance or that supply an autotrophic requirement). Examples of useful prokaryotic host expression vectors include the pKK223-3 (Pharmacia, Uppsala, Sweden), pGEM1 (Promega, Wis., USA), pET (Novagen, Wis., USA) and pRSET (Invitrogen, Calif., USA) series of vectors (see, e.g., Studier, J. Mol. Biol. 219:37 (1991) and Schoepfer,  Gene  124:83 (1993)). Exemplary promoter sequences frequently used in prokaryotic host cell expression vectors include T7, (Rosenberg et al.,  Gene  56:125-135 (1987)), beta-lactamase (penicillinase), lactose promoter system (Chang et al.,  Nature  275:615 (1978)); and Goeddel et al.,  Nature  281 :544 (1979)), tryptophan (trp) promoter system (Goeddel et al.,  Nucl. Acids Res.  8:4057, (1980)), and tac promoter (Sambrook et al., 1990, Molecular Cloning, A Laboratory Manual, 2d Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.). 
     In some embodiments, a eukaryotic host cell system is used, including yeast cells transformed with recombinant yeast expression vectors containing the coding sequence of a ligand. Exemplary yeast that can be used to produce compositions of the invention, include yeast from the genus  Saccharomyces, Pichia, Actinomycetes  and  Kluyveromyces.  Yeast vectors typically contain an origin of replication sequence from a 2mu yeast plasmid, an autonomously replicating sequence (ARS), a promoter region, sequences for polyadenylation, sequences for transcription termination, and a selectable marker gene. Examples of promoter sequences in yeast expression constructs include, promoters from metallothionein, 3-phosphoglycerate kinase (Hitzeman,  J. Biol. Chem.  255:2073 (1980)) and other glycolytic enzymes, such as, enolase, glyceraldehyde-3-phosphate dehydrogenase, hexokinase, pyruvate decarboxylase, phosphofructokinase, glucose-6-phosphate isomerase, 3-phospho glycerate mutase, pyruvate kinase, triosephosphate isomerase, phosphoglucose isomerase, and glucokinase. Additional suitable vectors and promoters for use in yeast expression as well as yeast transformation protocols are known in the art. See, e.g., Fleer,  Gene  107:285-195 (1991) and Hinnen,  PNAS  75:1929 (1978). 
     Insect and plant host cell culture systems are also useful for producing the compositions of the invention. Such host cell systems include for example, insect cell systems infected with recombinant virus expression vectors (e.g., baculovirus) containing the coding sequence of a ligand; plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors (e.g., Ti plasmid) containing the coding sequence of a ligand, including, but not limited to, the expression systems taught in U.S. Pat. No. 6,815,184; U.S. Publ. Nos. 60/365,769, and 60/368,047; and WO2004/057002, WO2004/024927, and WO2003/078614. 
     In some embodiments, host cell systems may be used, including animal cell systems infected with recombinant virus expression vectors (e.g., adenoviruses, retroviruses, adeno-associated viruses, herpes viruses, lentiviruses) including cell lines engineered to contain multiple copies of the DNA encoding a ligand either stably amplified (CHO/dhfr) or unstably amplified in double-minute chromosomes (e.g., murine cell lines). In some embodiments, a vector comprising a polynucleotide(s) encoding a ligand is polycistronic. Exemplary mammalian cells useful for producing these compositions include 293 cells (e.g., 293T and 293F), CHO cells, BHK cells, NS0 cells, SP2/0 cells, YO myeloma cells, P3X63 mouse myeloma cells, PER cells, PER.C6 (Crucell, Netherlands) cells VERY, Hela cells, COS cells, MDCK cells, 3T3 cells, W138 cells, BT483 cells, Hs578T cells, HTB2 cells, BT20 cells, T47D cells, CRL7O30 cells, HsS78Bst cells, hybridoma cells, and other mammalian cells. Additional exemplary mammalian host cells that are useful in practicing the invention include but are not limited, to T cells. Exemplary expression systems and selection methods are known in the art and, including those described in the following references and references cited therein: Borth et al.,  Biotechnol. Bioen.  71(4):266-73 (2000), in Werner et al.,  Arzneimittelforschung/Drug Res.  48(8):870-80 (1998), Andersen et al.,  Curr. Op. Biotechnol.  13:117-123 (2002), Chadd et al.,  Curr. Op, Biotechnol.  12:188-194 (2001), and Giddings, Curr. Op. Biotechnol. 12:450-454 (2001). Additional examples of expression systems and selection methods are described in Logan et al.,  PNAS  81:355-359 (1984), Birtner et al.  Methods Enzymol.  153:51-544 (1987)). Transcriptional and translational control sequences for mammalian host cell expression vectors are frequently derived from viral genomes. Commonly used promoter sequences and enhancer sequences in mammalian expression vectors include, sequences derived from Polyoma virus, Adenovirus 2, Simian Virus 40 (SV40), and human cytomegalovirus (CMV). Exemplary commercially available expression vectors for use in mammalian host cells include pCEP4 (Invitrogen) and pcDNA3 (Invitrogen). 
     Physical methods for introducing a nucleic acid into a host cell (e.g., a mammalian host cell) include calcium phosphate precipitation, lipofection, particle bombardment, microinjection, electroporation, and the like. Methods for producing cells comprising vectors and/or exogenous nucleic acids are well-known in the art. See, for example, Sambrook et al. (2001, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York). 
     Biological methods for introducing a polynucleotide of interest into a host cell include the use of DNA and RNA vectors. Viral vectors, and especially retroviral vectors, have become the most widely used method for inserting genes into mammalian (e.g., human) cells. Other viral vectors can be derived from lentivirus, poxviruses, herpes simplex virus I, adenoviruses and adeno-associated viruses, and the like. See, for example, U.S. Pat. Nos. 5,350,674 and 5,585,362. 
     Methods for introducing a DNA and RNA polynucleotides of interest into a host cell include electroporation of cells, in which an electrical field is applied to cells in order to increase the permeability of the cell membrane, allowing chemicals, drugs, or polynucleotides to be introduced into the cell. Ligand containing DNA or RNA constructs may be introduced into mammalian or prokaryotic cells using electroporation. 
     In some embodiments, electroporation of cells results in the expression of a ligand-CAR on the surface of T cells, NK cells, NKT cells. Such expression may be transient or stable over the life of the cell. Electroporation may be accomplished with methods known in the art including MaxCyte GT® and STX® Transfection Systems (MaxCyte, Gaithersburg, Md., USA). 
     Chemical means for introducing a polynucleotide into a host cell include colloidal dispersion systems, such as macromolecule complexes, nanocapsules, microspheres, beads, and lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposomes. An exemplary colloidal system for use as a delivery vehicle in vitro and in vivo is a liposome (e.g., an artificial membrane vesicle). In the case where a non-viral delivery system is utilized, an exemplary delivery vehicle is a liposome. The use of lipid formulations is contemplated for the introduction of the nucleic acids into a host cell (in vitro, ex vivo or in vivo). In some embodiments, the nucleic acid is associated with a lipid. A nucleic acid associated with a lipid can be encapsulated in the aqueous interior of a liposome, interspersed within the lipid bilayer of a liposome, attached to a liposome via a linking molecule that is associated with both the liposome and the oligonucleotide, entrapped in a liposome, complexed with a liposome, dispersed in a solution containing a lipid, mixed with a lipid, combined with a lipid, contained as a suspension in a lipid, contained or complexed with a micelle, or otherwise associated with a lipid. Lipid, lipid/DNA or lipid/expression vector associated compositions are not limited to any particular structure in solution. For example, they can be present in a bilayer structure, as micelles, or with a “collapsed” structure. They can also simply be interspersed in a solution, possibly forming aggregates that are not uniform in size or shape. Lipids are fatty substances which can be naturally occurring or synthetic lipids. For example, lipids include the fatty droplets that naturally occur in the cytoplasm as well as the class of compounds which contain long-chain aliphatic hydrocarbons and their derivatives, such as fatty acids, alcohols, amines, amino alcohols, and aldehydes. 
     Lipids suitable for use can be obtained from commercial sources. For example, dimyristyi phosphatidylcholine (“DMPC”) can be obtained from Sigma, St. Louis, Mo.; dicetyl phosphate (“DCP”) can be obtained from K &amp; K Laboratories (Plainview, N.Y.); cholesterol (“Choi”) can be obtained from Calbiochem-Behring; dimyristyi phosphatidylglycerol (“DMPG”) and other lipids may be obtained from Avanti Polar Lipids, Inc. (Birmingham, Ala.). Stock solutions of lipids in chloroform or chloroform/methanol can be stored at about −20° C. Chloroform may be used as the only solvent since it is more readily evaporated than methanol. “Liposome” is a generic term encompassing a variety of single and multilamellar lipid vehicles formed by the generation of enclosed lipid bilayers or aggregates. Liposomes can be characterized as having vesicular structures with a phospholipid bilayer membrane and an inner aqueous medium. Multilamellar liposomes have multiple lipid layers separated by aqueous medium. They form spontaneously when phospholipids are suspended in an excess of aqueous solution. The lipid components undergo self-rearrangement before the formation of closed structures and entrap water and dissolved solutes between the lipid bilayers (Ghosh et al.,  Glycobiology  5:505-510 (1991)). However, compositions that have different structures in solution than the normal vesicular structure are also encompassed. For example, the lipids can assume a micellar structure or merely exist as non-uniform aggregates of lipid molecules. Also contemplated are lipofectamine-nucleic acid complexes. 
     Regardless of the method used to introduce exogenous nucleic acids into a host cell, the presence of the recombinant nucleic acid sequence in the host cell can routinely be confirmed through a variety of assays known in the art. Such assays include, for example, “molecular biological” assays known in the art, such as Southern and Northern blotting, RT-PCR and PCR; “biochemical” assays, such as detecting the presence or absence of a particular peptide, e.g., by immunological means (ELISAs and Western blots) or by assays described herein to identify agents falling within the scope of the invention. 
     Reporter genes are used for identifying potentially transfected cells and for evaluating the functionality of regulatory sequences. In general, a reporter gene is a gene that is not present in or expressed by the recipient organism, tissue, or cell and that encodes a polypeptide whose expression is manifested by some easily detectable property, e.g., enzymatic activity. Expression of the reporter gene is assayed at a suitable time after the DNA has been introduced into the recipient cells. Suitable reporter genes include, but are not limited to, genes encoding luciferase, beta-galactosidase, chloramphenicol acetyl transferase, secreted alkaline phosphatase, or the green fluorescent protein gene (e.g., Ui-Tei et al.,  FEBS Lett.  479:79-82 (2000)). Suitable expression systems are known in the art and can be prepared using known techniques or obtained commercially. In general, the construct with the minimal 5′ flanking region showing the highest level of expression of reporter gene is identified as the promoter. Such promoter regions can routinely be linked to a reporter gene and used to evaluate agents for the ability to modulate promoter-driven transcription. 
     A number of selection systems can be used in mammalian host-vector expression systems, including, but not limited to, the herpes simplex virus thymidine kinase, hypoxanthine-guanine phosphoribosyltransferase and adenine phosphoribosyltransferase (Lowy et al.,  Cell  22:817 (1980)) genes. Additionally, antimetabolite resistance can be used as the basis of selection for e.g., dhfr, gpt, neo, hygro, trpB, hisD, ODC (ornithine decarboxylase), and the glutamine synthase system. 
     Ligand Purification 
     Once a ligand or a ligand fusion protein has been produced by recombinant expression, it can be purified by methods known in the art for purification of a recombinant protein, for example, by chromatography (e.g., ion exchange, affinity, and sizing column chromatography), centrifugation, differential solubility, or by any other standard technique for the purification of proteins. In some embodiments, a ligand is optionally fused to heterologous polypeptide sequences specifically disclosed herein or otherwise known in the art to facilitate purification. In some embodiments, ligands (e.g., antibodies and other affinity matrices) for ligand affinity columns for affinity purification and that optionally, the ligand or other components of the ligand fusion composition that are bound by these ligands are removed from the composition prior to final preparation of the ligand using techniques known in the art. 
     Chemical Synthesis of Ligand 
     In addition to recombinant methods, ligand production may also be carried out using organic chemical synthesis of the desired polypeptide using a variety of liquid and solid phase chemical processes known in the art. Various automatic synthesizers are commercially available and can be used in accordance with known protocols. See, for example, Tam et al.,  J. Am. Chem. Soc.,  105:6442 (1983); Merrifield,  Science,  232:341-347 (1986); Barany and Merrifield, The Peptides, Gross and Meienhofer, eds, Academic Press, New York, 1-284; Barany et al.,  Int. J. Pep. Protein Res.,  30:705 739 (1987); Kelley et al. in Genetic Engineering Principles and Methods, Setlow, J. K., ed. Plenum Press, NY. 1990, vol. 12, pp. 1-19; Stewart et al., Solid-Phase Peptide Synthesis, W.H. Freeman Co., San Francisco, 1989. One advantage of these methodologies is that they allow for the incorporation of non-natural amino acid residues into the sequence of the ligand. 
     The ligand that are used in the methods of the present invention may be modified during or after synthesis or translation, e.g., by glycosylation, acetylation, benzylation, phosphorylation, amidation, pegylation, formylation, derivatization by known protecting/blocking groups, proteolytic cleavage, linkage to an antibody molecule, hydroxylation, iodination, methylation, myristoylation, oxidation, pegylation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, ubiquitination, etc. (See, e.g., Creighton, Proteins: Structures and Molecular Properties, 2d Ed. (W.H. Freeman and Co., N.Y., 1992); Postranslational Covalent Modification of Proteins, Johnson, ed. (Academic Press, New York, 1983), pp. 1-12; Seifter,  Meth. Enzymol.,  182:626-646 (1990); Rattan,  Ann. NY Acad. Sci.,  663:48-62 (1992).) In some embodiments, the peptides are acetylated at the N-terminus and/or amidated at the C-terminus. 
     Any of numerous chemical modifications may be carried out by known techniques, including, but not limited to acetylation, formylation, etc. Additionally, derivatives may contain one or more non-classical amino acids. 
     In some embodiments cyclization, or macrocyclization of the peptide backbone is achieved by sidechain to sidechain linkage formation. Methods for achieving this are well known in the art and may involve natural as well as unnatural amino acids. Approaches includes disulfide formation, lanthionine formation or thiol alkylations (e.g. Michael addition), amidation between amino and carboxylate sidechains, click chemistry (e.g. azide-alkyne condensation), peptide stapling, ring closing metathesis and the use of enzymes. 
     Affinity Agents for Purification 
     In purification based on affinity chromatography, a target of interest (e.g. protein or molecule) are selectively isolated according to their ability to specifically and reversibly bind to a ligand that has typically been covalently coupled to a chromatographic matrix. In some embodiments, ligands can be used as reagents for affinity purification of targets of interest from either recombinant sources or natural sources such as biological samples (e.g., serum). 
     In some embodiments, a ligand that specifically binds a target of interest is immobilized on beads and then used to affinity purify the target. 
     Methods of covalently coupling proteins to a surface are known by those of skill in the art, and peptide tags that can be used to attach ligand to a solid surface are known to those of skill in the art. Further, ligand can be attached (i.e., coupled, linked, or adhered) to a solid surface using any reagents or techniques known in the art. In some embodiments, a solid support comprises beads, glass, slides, chips and/or gelatin. Thus, a series of ligands can be used to make an array on a solid surface using techniques known in the art. For example, U.S. Publ. No. 2004/0009530 discloses methods for preparing arrays. 
     In some embodiments, a ligand is used to isolate a target of interest by affinity chromatography. In some embodiments, a ligand is immobilized on a solid support. The ligand can be immobilized on the solid support using techniques and reagents described herein or otherwise known in the art. Suitable solid supports are described herein or otherwise known in the art and in specific embodiments are suitable for packing a chromatography column. The immobilized ligand can then be loaded or contacted with a solution under conditions favorable to form a complex between the ligand and the target of interest. Non-binding materials can be washed away. Suitable wash conditions can readily be determined by one of skill in the art. Examples of suitable wash conditions are described in Shukla and Hinckley,  Biotechnol Prog.  2008 September-October; 24(5):1115-21. doi: 10.1002/btpr.50. 
     In some embodiments, chromatography is carried out by mixing a solution containing the target of interest and the ligand, then isolating complexes of the target of interest and ligand. For example, a ligand is immobilized on a solid support such as beads, then separated from a solution along with the target of interest by filtration. In some embodiments, a ligand is a fusion protein that contains a peptide tag, such as a poly-HIS tail or streptavidin binding region, which can be used to isolate the ligand after complexes have formed using an immobilized metal affinity chromatographic resin or streptavidin-coated substrate. Once separated, the target of interest can be released from the ligand under elution conditions and recovered in a purified form. 
     EXAMPLES 
     Peptides were synthesized by standard Fmoc solid phase peptide synthesis techniques and purified by preparative reverse phase HPLC. The purity of peptides was assessed by RP HPLC with both UV and quadrupole time-of-flight mass spectrometric detection. 
     Example 1 
     This example demonstrates the production and characterization of affinity agents comprising ligands identified and described herein. Affinity resins were prepared by conjugating ligands to agarose beads. RAPID RUN 6% Agarose beads (ABT, Madrid, Spain) were activated with disuccinimidyl carbonate and coupled with peptide ligands at ligand densities 1-8 mg/mL resin. The actual ligand density for all resins was measured using a subtractive RP-HPLC method according to the following formula: 
       Actual Ligand Density=(Measured [ligand] in feed−Measured [ligand] in effluent).
 
     Example 2 
     This example demonstrates the use of affinity agents comprising binding ligands described herein for affinity purification of virus particles. Clarified cell culture feed stream (CCCF) containing viral capsids at a titer of approximately 1E12 total capsids/mL was used. A 0.66 cm ID×6 cm column was operated as shown in Table 1. 
     
       
         
           
               
             
               
                 TABLE 1 
               
             
            
               
                   
               
               
                 Column operating parameters 
               
            
           
           
               
               
               
               
            
               
                   
                   
                   
                 Linear 
               
               
                   
                   
                 Volume 
                 Velocity 
               
               
                 Step 
                 Solution ID 
                 (CV) 
                 (cm/hr) 
               
               
                   
               
            
           
           
               
               
               
               
            
               
                 Equilibration 
                 50 mM Sodium Phosphate/ 
                 3 
                 250 
               
               
                   
                 Sodium Citrate, pH 7.5, 
               
               
                   
                 0.1% Triton X-100 
               
               
                 Load Inject 
                 Production Harvest 
                 100 
                 88 
               
               
                 Wash (optional) 
                 50 mM Sodium Phosphate/ 
                 6 
                 88 
               
               
                   
                 Sodium Citrate, pH 7.5, 
               
               
                   
                 1M NaCl 
               
               
                 Elution 
                 50 mM Glycine, pH 2.5, 
                 5 
                 175 
               
               
                   
                 1M Arginine, 10% 
               
               
                   
                 Propylene glycol, 0.1% 
               
               
                   
                 Triton X-100 
               
               
                   
                 OR 
               
               
                   
                 Sodium Phosphate/Citrate 
               
               
                   
                 pH 4, +1M Arginine, +10% 
               
               
                   
                 Propylene Glycol 
               
               
                 Sani/Strip 
                 0.1M NaOH 
                 4 
                 175 
               
               
                 Pre-storage 
                 50 mM Sodium Phosphate/ 
                 8 
                 175 
               
               
                 equilibration 
                 Sodium Citrate, pH 7.5, 
               
               
                   
                 0.1% Triton X-100 
               
               
                   
               
            
           
         
       
     
     A total capsid ELISA was used to quantify capsid amounts. HCP was determined using an ELISA (Cygnus Technologies, Southport, N.C.). DNA was measured using a picogreen assay. Analysis of the purified viral capsids. Affinity resin performance metrics are shown in Table 2. 
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                 Performance parameters for the purification of viral capsids 
               
            
           
           
               
               
               
               
            
               
                 Parameter 
                 RES-1230 
                 RES-1233 
                 RES-1252 
               
               
                   
               
               
                 Ligand Seq ID 
                 21 
                 28 
                 23 
               
               
                 Dynamic Binding 
                 2.2E+14 
                 1.2E+14 
                 2.7E+14 
               
               
                 Capacity* (vp/mL*r) 
               
               
                 Elution Conditions 
                 Sodium 
                 Sodium 
                 Sodium 
               
               
                   
                 Phosphate/Citrate pH 
                 Phosphate/Citrate, pH 
                 Phosphate/Citrate, pH 
               
               
                   
                 4 +1M Arginine + 
                 4, +500 mM Arginine + 
                 4, +1M Arginine + 
               
               
                   
                 10% Propylene Glycol 
                 20% Propylene Glycol 
                 10% Propylene Glycol 
               
               
                 CIP conditions 
                 0.1N NaOH, 12 hour 
                 0.1N NaOH, 24 hour 
                 0.1N NaOH, 12 hour 
               
               
                   
                 stability 
                 stability 
                 stability 
               
               
                 Step Yield 
                 100% 
                 92% 
                 100% 
               
               
                 HCP Clearance - Log 
                 &gt;3.6 (&lt;800 ppm) 
                 &gt;3.6 (&lt;800 ppm) 
                 &gt;3.7 (&lt;600 ppm) 
               
               
                 reduction (ppm) 
               
               
                 DNA Clearance (log 
                  0.3 (1100 ppm) 
                 0.6 (400 ppm) 
                 1.0 (200 ppm) 
               
               
                 reduction) 
               
               
                   
               
            
           
         
       
     
     Example 3 
     This example demonstrates the stability of affinity agents under test conditions. The stability of resins prepared from ligand towards sodium hydroxide was determined using static binding experiments with resin slurry suspended in 0.1 M NaOH for predetermined times. For the purposes of calculating CIP lifetime, it was assumed one CIP cycle was equivalent to 15 minutes exposure to 0.1M NaOH. The data are shown in Table 3. 
     
       
         
           
               
             
               
                 TABLE 3 
               
             
            
               
                   
               
               
                 Stability of the resins towards 0.1M NaOH 
               
            
           
           
               
               
               
               
            
               
                 Parameter 
                 RES-1230 
                 RES-1233 
                 RES-1252 
               
               
                   
               
               
                 NaOH incubation time before 
                 12 hour 
                 24 hour 
                 12 hour 
               
               
                 capture decreased by 10% 
               
               
                 Equivalent CIP cycles 
                 48 
                 96 
                 48 
               
               
                   
               
            
           
         
       
     
     Example 4 
     This example demonstrates the stability of affinity agents under use conditions and with exposure to 0.1 M NaOH. Columns were operated as described in example 2, except with the following 2 modifications. 
     1) between each cycle, the column was exposed to 0.1 M NaOH for 2 hours.
 
2) The elution buffer was 50 mM Glycine, pH 2.5, 1 M Arginine, 10% Propylene glycol, 0.1% Triton X-100.
 
Results demonstrating consistent performance throughout this study are shown in the following tables.
 
     
       
         
           
               
             
               
                 TABLE 4 
               
             
            
               
                   
               
               
                 Total capsid yield obtained during the cycling study 
               
            
           
           
               
               
               
               
               
            
               
                   
                 Cycle 
                 RES-1230 
                 RES-1233 
                 RES-1252 
               
               
                   
                   
               
               
                   
                 1 
                 101%  
                 130% 
                 92% 
               
               
                   
                 3 
                 90% 
                  92% 
                 111%  
               
               
                   
                 5 
                 91% 
                 104% 
                 84% 
               
               
                   
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 5 
               
             
            
               
                   
               
               
                 HCP reduction obtained during the cycling study. 
               
               
                 Residual HCP levels (ppm) are shown in brackets 
               
            
           
           
               
               
               
               
               
            
               
                   
                 Cycle 
                 RES-1230 
                 RES-1233 
                 RES-1252 
               
               
                   
                   
               
               
                   
                 1 
                 &gt;3.6 (&lt;700) 
                 &gt;3.8 (&lt;600) 
                 &gt;3.8 (&lt;600) 
               
               
                   
                 3 
                 &gt;3.6 (&lt;800) 
                 &gt;3.6 (&lt;800) 
                 &gt;3.8 (&lt;500) 
               
               
                   
                 5 
                 &gt;3.6 (&lt;800) 
                 &gt;3.7 (&lt;700) 
                 &gt;3.7 (&lt;600) 
               
               
                   
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 6 
               
             
            
               
                   
               
               
                 DNA reduction obtained during the cycling study. 
               
               
                 Residual DNA levels (ppm) are shown in brackets 
               
            
           
           
               
               
               
               
               
            
               
                   
                 Cycle 
                 RES-1230 
                 RES-1233 
                 RES-1252 
               
               
                   
                   
               
               
                   
                 1 
                  0.3 (1100) 
                 0.6 (400) 
                 1.0 (200) 
               
               
                   
                 3 
                 0.8 (300) 
                 1.0 (200) 
                 1.3 (100) 
               
               
                   
                 5 
                 0.9 (200) 
                 1.1 (200) 
                 1.2 (100) 
               
               
                   
                   
               
            
           
         
       
     
     Example 5 
     This example demonstrates the affinity agents comprising binding ligands described herein can be used for affinity purification of different variants of AAV9. Clarified cell culture feed streams (CCCF) from the production of different AAV9 capsids at titers of approximately 1E12-3E12 total capsids/mL were used. A 3 mm ID×100 mm column was operated as shown in Table 7. The resin comprised a ligand comprising SEQ ID 32 at 2 mg/mL ligand density. 
     
       
         
           
               
             
               
                 TABLE 7 
               
             
            
               
                   
               
               
                 Column operating parameters 
               
            
           
           
               
               
               
               
            
               
                   
                   
                   
                 Linear 
               
               
                   
                   
                 Volume 
                 Velocity 
               
               
                 Step 
                 Solution ID 
                 (CV) 
                 (cm/hr) 
               
               
                   
               
            
           
           
               
               
               
               
            
               
                 Equilibration 
                 50 mM Sodium Phosphate/ 
                 3 
                 250 
               
               
                   
                 Sodium Citrate, pH 7.5, 
               
               
                   
                 0.1% Triton X-100 
               
               
                 Sample load 
                 Clarified CCCF 
                 As 
                 88 
               
               
                   
                   
                 required 
               
               
                 Wash 
                 50 mM Sodium Phosphate/ 
                 6 
                 88 
               
               
                   
                 Sodium Citrate, pH 7.5, 
               
               
                   
                 0.1% Triton X-100 
               
               
                 Elution 
                 50 mM Glycine, 150 mM 
                 5 
                 175 
               
               
                   
                 NaCl, 0.1% Triton 
               
               
                   
                 X-100, pH 3 
               
               
                   
                 Or 
               
               
                   
                 50 mM Glycine, 1M Arg, 
               
               
                   
                 10% propyleneglycol, 0.1% 
               
               
                   
                 Triton X-100, pH 2.5 
               
               
                 Sani/Strip 
                 0.1M NaOH 
                 4 
                 175 
               
               
                 Pre-storage 
                 50 mM Sodium Phosphate/ 
                 8 
                 175 
               
               
                 equilibration 
                 Sodium Citrate, pH 7.5, 
               
               
                   
                 0.1% Triton X-100 
               
               
                   
               
            
           
         
       
     
     A total capsid ELISA was used to quantify capsid amounts. Residual HCP was determined using an ELISA (Cygnus Technologies, Southport, N.C.). Residual HCDNA was measured using the Quant-IT PicoGreen™ dsDNA Assay Kit. Affinity resin performance metrics are shown in Table 8. 
     
       
         
           
               
             
               
                 TABLE 8 
               
             
            
               
                   
               
               
                 Performance parameters for the purification of viral capsids 
               
            
           
           
               
               
               
               
            
               
                   
                 Parameter 
                 AAV9 capsid 1 
                 AAV9 capsid 2 
               
               
                   
                   
               
               
                   
                 Load Challenge 
                 1.0E+14 
                 1.5E+14 
               
               
                   
                 Step Yield 
                 100% 
                 87% 
               
               
                   
                 Elution buffer 
                 50 mM Glycine, 
                 50 mM Glycine, 
               
               
                   
                   
                 1M Arg, 10% 
                 150 mM NaCl, 
               
               
                   
                   
                 propyleneglycol, 
                 0.1% Tx-100, pH 3 
               
               
                   
                   
                 0.1% Triton 
               
               
                   
                   
                 x-100, pH 2.5 
               
               
                   
                 Residual HCP 
                 1.2E+03 
                 3.1E+03 
               
               
                   
                 Residual HCDNA 
                 2.0E+02 
                 Not determined 
               
               
                   
                   
               
            
           
         
       
     
     Example 6 
     This example demonstrates the stability of affinity agents under use conditions and with exposure to 0.5 M NaOH. The resin from example 5 was operated with repeated cycles of the method shown in Table 9 using a 6.6 mm ID×100 mm column. During each cycle the column was exposed to 0.5 M NaOH for a total of 30 minutes (Washed with 5 CVs then a static hold for 20 minutes). The AAV9 capsid was a 3 rd  variant. 
     
       
         
           
               
             
               
                 TABLE 9 
               
             
            
               
                   
               
               
                 Column operating parameters for each cycle 
               
            
           
           
               
               
               
               
            
               
                   
                   
                   
                 Linear 
               
               
                   
                   
                 Vol. 
                 Velocity 
               
               
                 Step 
                 Buffer 
                 (CV) 
                 (cm/hr) 
               
               
                   
               
            
           
           
               
               
               
               
            
               
                 Equilibration 
                 50 mM Tris, 250 mM NaCl pH 8.3 
                 1 
                 300 
               
               
                 Load Sample 
                 CCCF containing Capsid 3 @ 
                 22 
                 150 
               
               
                   
                 4.2E+12 vp/mL 
               
               
                 Chase 1 
                 50 mM Tris, 250 mM NaCl pH 8.3 
                 2 
                 150 
               
               
                 Chase 2 
                 50 mM Tris, 250 mM NaCl pH 8.3 
                 5 
                 300 
               
               
                 Wash 1 
                 50 mM Octanoic acid, 0.5M urea, 
                 5 
                 300 
               
               
                   
                 50 mM Tris, pH 8.0 
               
               
                 Wash 2 
                 50 mM Tris, 250 mM NaCl pH 8.3 
                 2 
                 300 
               
               
                 Elution 
                 50 mM Glycine, 150 mM NaCl, pH 3 
                 5 
                 300 
               
               
                 CIP 
                 0.5M NaOH 
                 5 
                 300 
               
               
                 Re- 
                 50 mM Tris, 250 mM NaCl pH 8.3 
                 8 
                 300 
               
               
                 equilibration 
               
               
                   
               
            
           
         
       
     
     Results demonstrating consistent performance throughout this study are shown in the  FIGS. 1-3  demonstrating that the columns can withstand 0.5 M NaOH. 
     Example 7 
     This example demonstrates the affinity agents enable softer elution conditions. A 3 mm ID×25 mm column was challenged with 2E14 vp/mL of resin and eluted with buffers containing 0.25 M, 0.5 M or 1 M arginine at either at pH 4.5, 5 or 5.5. The measured yields are shown in  FIG. 4 . Yields decreased slightly at pH 5.5. 
     Example 8 
     This example demonstrates the binding of biotinylated ligands to AAV capsids using biolayer interferometry (ForteBio, Menlo Park, Calif.). Sensors containing immobilized ligands of SED ID NOs: 46-47 were incubated in 5 ug/mL AAV capsids. Sensorgrams are shown in  FIG. 5 . 
     It is contemplated that various combinations or sub-combinations of the specific features and aspects of the embodiments disclosed above may be made and still fall within the invention. Further, the disclosure herein of any particular feature, aspect, method, property, characteristic, quality, attribute, element, or the like in connection with an embodiment can be used in all other embodiments set forth herein. Accordingly, it should be understood that various features and aspects of the disclosed embodiments can be combined with or substituted for one another. Thus, it is intended that the scope of the invention described herein should not be limited by the particular disclosed embodiments described above. Moreover, while the invention is susceptible to various modifications, and alternative forms, specific examples thereof have been shown in the drawings and are herein described in detail. It should be understood, however, that the invention is not to be limited to the particular forms or methods disclosed, but to the contrary, the invention is to cover all modifications, equivalents, and alternatives falling within the spirit and scope of the various embodiments described. 
     Any methods disclosed herein need not be performed in the order recited. The methods disclosed herein include certain actions taken by a practitioner; however, they can also include any third-party instruction of those actions, either expressly or by implication. 
     SEQUENCES 
       
     
       
         
           
               
               
             
               
                   
               
               
                 Seq 
                   
               
               
                 ID 
                 Sequence 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
            
               
                 1 
                 KWDPQHQLVM 
               
               
                   
               
               
                 2 
                 QWEPMHQLVM 
               
               
                   
               
               
                 3 
                 PYHPLDLR 
               
               
                   
               
               
                 4 
                 AYHVLDLR 
               
               
                   
               
               
                 5 
                 TPTRX 1 PYHPLDLRX 2 YAGS 
               
               
                   
               
               
                 6 
                 CKWDPQHQLVMC 
               
               
                   
               
               
                 7 
                 CQWEPIVIHQLVMC 
               
               
                   
               
               
                 8 
                 TPTRCPYHPLDLRCYAGS 
               
               
                   
               
               
                 9 
                 CAYHVLDLRC 
               
               
                   
               
               
                 10 
                 TPTR$PYHPLDLR5YAGS 
               
               
                   
               
               
                 11 
                 TPTRJPYHPLDLR%YAGS 
               
               
                   
               
               
                 12 
                 TPTRJPYHPLDLR5YAGS 
               
               
                   
               
               
                 13 
                 TPTR5PYHPLDLRJYAGS 
               
               
                   
               
               
                 14 
                 D*AYHVLDLRJ 
               
               
                   
               
               
                 15 
                 A*YHVLDLRD** 
               
               
                   
               
               
                 16 
                 &amp;AYHVLDLRJ 
               
               
                   
               
               
                 17 
                 Acetyl-CAYHVLDLRC 
               
               
                   
               
               
                 18 
                 Acetyl-D*AYHVLDLRJ 
               
               
                   
               
               
                 19 
                 Acetyl-CAYHVLDLRCK-amide 
               
               
                   
               
               
                 20 
                 Acetyl-D*AYHVLDLRJK-amide 
               
               
                   
               
               
                 21 
                 Acetyl-CQWEPIVIHQLVMC-(Peg)3K-Amide 
               
               
                   
               
               
                 22 
                 Acetyl-CKWDPQHQLVMC-(Peg)3K-Amide 
               
               
                   
               
               
                 23 
                 Acetyl-CKWDPQHQLVMC(Peg)3(Peg)3K-Amide 
               
               
                   
               
               
                 24 
                 Acetyl-CKWDPHHQLVMC(Peg)3(Peg)3(Peg)3K-Amide 
               
               
                   
               
               
                 25 
                 Acetyl-CKWDPQHQLVMC-(Peg)3(Peg)3K-Amide 
               
               
                   
               
               
                 26 
                 Acetyl-TPTRCPYHPLDLRCYAGS-(Peg)3K-Amide 
               
               
                   
               
               
                 27 
                 Acetyl-CAYHVLDLRC(PEG)3K-Amide 
               
               
                   
               
               
                 28 
                 Acetyl-TPTR$PYHPLDLR5YAGS-(Peg)3K-Amide 
               
               
                   
               
               
                 29 
                 Acetyl-TPTRJPYHPLDLR%YAGS-(Peg)3K-Amide 
               
               
                   
               
               
                 30 
                 Acetyl-TPTRJPYHPLDLR5YAGS-(Peg)3K-Amide 
               
               
                   
               
               
                 31 
                 Acetyl-TPTR5PYHPLDLRJYAGS-(Peg)3K-Amide 
               
               
                   
               
               
                 32 
                 Acetyl-D*AYHVLDLRJ(PEG)3K-Amide 
               
               
                   
               
               
                 33 
                 &amp;AYHVLDLRJ-(Peg)3K-Amide 
               
               
                   
               
               
                 34 
                 Acetyl-CAYHVLDLRC(PEG)3(PEG)3K-Amide 
               
               
                   
               
               
                 35 
                 Acetyl-D*AYHVLDLRJ(PEG)3(PEG)3K-Amide 
               
               
                   
               
               
                 36 
                 Acetyl-CQWEPMHQLVMC-(Peg)3K(biotin)-Amide 
               
               
                   
               
               
                 37 
                 Acetyl-CKWDPQHQLVMC-(Peg)3K(biotin)-Amide 
               
               
                   
               
               
                 38 
                 Acetyl-CKWDPQHQLVMC(Peg)3(Peg)3K(biotin)- 
               
               
                   
                 Amide 
               
               
                   
               
               
                 39 
                 Acetyl-CKWDPHHQLVMC(Peg)3(Peg)3(Peg)3K 
               
               
                   
                 (biotin)-Amide 
               
               
                   
               
               
                 40 
                 Acetyl-CKWDPQHQLVMC-(Peg)3(Peg)3K(biotin)- 
               
               
                   
                 Amide 
               
               
                   
               
               
                 41 
                 Acetyl-TPTRCPYHPLDLRCYAGS-(Peg)3K(biotin)- 
               
               
                   
                 Amide 
               
               
                   
               
               
                 42 
                 Acetyl-TPTR$PYHPLDLR5YAGS-(Peg)3K(biotin)- 
               
               
                   
                 Amide 
               
               
                   
               
               
                 43 
                 Acetyl-TPTRJPYHPLDLR%YAGS-(Peg)3K(biotin)- 
               
               
                   
                 Amide 
               
               
                   
               
               
                 44 
                 Acetyl-TPTRJPYHPLDLR5YAGS-(Peg)3K(biotin)- 
               
               
                   
                 Amide 
               
               
                   
               
               
                 45 
                 Acetyl-TPTR5PYHPLDLRJYAGS-(Peg)3K(biotin)- 
               
               
                   
                 Amide 
               
               
                   
               
               
                 46 
                 Acetyl-D*AYHVLDLRJ(PEG)3K(biotin)-Amide 
               
               
                   
               
               
                 47 
                 &amp;AYHVLDLRJ-(Peg)3K(biotin)-Amide 
               
               
                   
               
            
           
         
       
         
         
           
             Ac-denotes N-terminal acetylation 
             Amide denotes C-terminal amidation 
             % or 5 denotes, respectively, a glutamic or aspartic acid residue in which the carboxyl sidechain is conjugated to either an épsilon amino group of a lysine residue that is denoted by $, or the beta amino group of a 2,3-diaminopropionic acid residue that is denoted by a J 
             (PEG) 3 -denotes 12-amino-4,7,10-trioxadodecanoic acid subunits 
             Cysteine residues may form intramolecular disulfide bonds 
             X n  denotes a cysteine, diaminopropionic, aspartic acid, lysine or glutamic acid and X 1  and X 2  may form intramolecular bonds 
             D* denotes an aspartic acid residue in which the carboxyl sidechain is conjugated to the beta amino group of a 2,3-diaminopropionic acid residue that is denoted by a J 
             (PEG) 3 -denotes 12-amino-4,7,10-trioxadodecanoic acid subunits 
             Cysteine residues may form intramolecular disulfide bonds 
             A* denotes an alanine residue with the alpha amino group bound to the carboxyl sidechain of an aspartate residue denoted by D** 
             &amp; denotes a succinyl group that is conjugated to the beta amino group of a 2,3-diaminopropionic acid residue that is denoted by a J