Antibodies comprising site-specific non-natural amino acid residues, methods of their preparation and methods of their use

Abstract

Provided herein are antibodies comprising non-natural amino acid residues at site-specific positions, compositions comprising the antibodies, methods of their production and methods of their use. The antibodies are useful for methods of treatment and prevention, methods of detection and methods of diagnosis.

Description

ANTIBODIES COMPRISING SITE-SPECIFIC NON-NATURAL AMINO ACID RESIDUES, METHODS OF THEIR PREPARATION AND METHODS OF THEIR USE FIELD

[0001] Provided herein are antibodies comprising non-natural amino acid residues at site- specific positions, compositions comprising the antibodies, methods of their production and methods of their use. BACKGROUND

[0002] Antibodies are biological molecules with remarkable affinity for their target antigens. Nature provides antibodies as part of a defense system in certain vertebrates for the elimination or destruction of foreign proteins, cells and organisms. If a certain vertebrate is presented with a foreign protein on, for example, an infected cell or an infectious bacterium, an antibody can bind its target foreign protein to direct the foreign entity to its elimination or destruction.

[0003] The selective affinity of antibodies can be used by man to target nearly any antigen desired. The antigen can be a protein on an infected cell or infectious microorganism. It can also be, for example, a protein on a cancer cell, a protein on a cell of a target tissue, a protein in the bloodstream, a protein on an inflamed or inflammatory cell or any other protein whose selective binding is useful. Antibodies have thus found use in therapy for conditions such as cancer, inflammatory diseases, autoimmune diseases and transplant rejection. The antibody can signal the immune system to destroy or eliminate a diseased cell, or an engineered antibody can carry a molecular payload to destroy the target. In certain applications therapeutic antibodies are linked to molecular shields to increase their lifetime within an organism. Antibodies have also found use as diagnostics. These antibodies can carry a label to indicate the presence of a target antigen on a cell or in a tissue. These labels are typically linked to the antibodies by covalent bonds.

[0004] To date, techniques for linking antibodies molecular entities such as molecular payloads, molecular shields and labels have been limited by their heterogeneity in degree and location of linking to the antibodies, by their low yields and by losses in activity. Typical conjugation sites include random locations on antibody chains, e.g. random amines on amino acid side chains, and the N-terminus of certain antibody chains. In such techniques, some antibodies might be linked to the conjugate at one location while some antibodies are linked to the same conjugate at another location, and some antibodies might not be linked at all.

[0005] There is a need for antibodies modified at site-specific positions optimized for uniformity, yield and / or activity to further the promising use of antibodies in, for example, therapy and diagnostics. SUMMARY

[0006] Provided herein are antibodies modified at one or more site-specific positions with one or more non-natural amino acid residues. These site-specific positions are optimal for substitution of a natural amino acid residue with a non-natural amino acid residue. In certain embodiments, substitution at these site-specific positions yields antibodies that are uniform in substitution, i.e. that are substantially modified in the selected position. In certain embodiments, an antibody substituted at one or more of these site-specific positions has advantageous production yield, advantageous solubility, advantageous binding and / or advantageous activity. The properties of these antibodies are described in detail in the sections below.

[0007] In one aspect, provided herein are antibodies comprising a polypeptide chain having at least one non-natural amino acid residue at a position in the polypeptide chain that is optimally substitutable. The antibody can be any polypeptide or multimeric polypeptide recognized as an antibody to those of skill in the art. The polypeptide chain can be any polypeptide chain of the antibody, including any heavy chain and any light chain. The position in the polypeptide chain that is optimally substitutable is any position in the polypeptide chain that can provide a substitution with optimal yield, uniformity, solubility, binding and / or activity. The sections below describe in detail the optimally substitutable positions of such polypeptide chains. Also described below are useful antibodies useful non- natural amino acids.

[0008] In another aspect, provided herein are compositions comprising said antibodies. Advantageously, such compositions can have high uniformity because of the uniformity of the substitution of the antibodies provided herein. In certain embodiments, the compositions comprise a substantial amount of the antibody when measured by total weight of protein or when measured by total weight of antibody. In certain embodiments, the compositions comprise at least 80 % of the antibody, at least 85 % of the antibody, at least 90 % of the antibody or at least 95 % of the antibody by weight.

[0009] In another aspect, provided herein are methods of making the antibodies. The antibodies can be made by any technique apparent to those of skill in the art for incorporating non-natural amino acids into site-specific positions of antibody chains. In certain embodiments, the antibodies are made by solid phase synthesis, semi-synthesis, in vivo translation, in vitro translation or cell-free translation.

[0010] In another aspect, provided herein are methods of using the antibodies for therapy. Antibodies directed to a therapeutic target can incorporate one or more site-specific non- natural amino acids according to the description herein. These antibodies can be used for treating or preventing a disease or condition associated with the therapeutic target. Advantageously, a site-specific non-natural amino acid can be used to link the antibody to a therapeutic payload to facilitate efficacy. Exemplary antibodies, therapeutic targets and diseases or conditions are described herein.

[0011] In another aspect, provided herein are methods of using the antibodies for detection. Antibodies directed to a detection target can incorporate one or more site-specific non-natural amino acids according to the description herein. These antibodies can be used with a label to signal binding to the detection target. Advantageously, a site-specific non- natural amino acid can be used to link the antibody to a label to facilitate detection. Exemplary antibodies, detection targets and labels are described herein.

[0012] In another aspect, provided herein are methods of modifying the stability of antibodies. Antibodies can be modified with a non-natural amino acid as described herein to facilitate linking to a molecular entity that can modify the stability of the antibody. For instance, a site-specific non-natural amino acid can facilitate linking to a molecular shield, for example polyethylene glycol, to increase the stability of an antibody. Exemplary non-natural amino acids and linking moieties are described herein. BRIEF DESCRIPTION OF THE FIGURES

[0013] FIG. 1 provides the structure of exemplary cytotoxic reagent DBCO-MMAF.

[0014] FIG. 2 provides a single peak hydrophobic interaction chromatography (HIC) assay profile.

[0015] FIG. 3 provides a not-well-resolved (NWR) HIC assay profile.

[0016] FIG. 4 provides a well-resolved (WR) HIC assay profile.

[0017] FIGS. 5A and 5B depict exemplary HIC traces of two variants (HC T110 and HC S112), showing peaks corresponding to unconjugated, partially conjugated and fully conjugated IgGs.

[0018] FIGS. 6A-6E depict exemplary embodiments showing site-specific conjugation.

[0019] FIGS. 7A and 7B depict suppression efficiency and soluble yield comparison data of antibodies comprising different unnatural amino acids

[0020] FIG. 8 depicts cell killing of CD-30 positive cell lines by exemplary brentuximab antibody-drug conjugates.

[0021] FIG. 9 provides experimental results demonstrating that exemplary brentuximab antibody-drug conjugates do not kill cells that do not express CD-30.

[0022] FIG. 10 depicts binding to CD-30 positive cell lines by exemplary brentuximab (ADCETRIS®) antibody-drug conjugates.

[0023] FIGS. 11A, 11B, 11C, and 11D provide the structure of exemplary cytotoxic reagents DBCO-MMAF 2, DBCO-DM4, DBCO-DM4 2, and DBCO-MMAE, respectively.

[0024] FIG. 12 provides a graphical representation of the pharmacokinetics of an exemplary scFv-Fc site-specific antibody-drug conjugate.

[0025] FIGS. 13A and 13B depict a graphical representation of the in vivo effectiveness of exemplary site-specific antibody-drug conjugates to retard tumor growth and / or to regress tumor size in an animal model. DESCRIPTION OF EXEMPLARY EMBODIMENTS

[0026] Provided herein are antibodies having non-natural amino acids at one or more site- specific positions, compositions comprising the antibodies, methods of making the antibodies, and methods of their use. Definitions

[0027] When referring to the antibodies provided herein, the following terms have the following meanings unless indicated otherwise. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of ordinary skill in the art. In the event that there is a plurality of definitions for a term herein, those in this section prevail unless stated otherwise.

[0028] As used herein, the singular forms "a," "an," and "the" include the plural reference unless the context clearly indicates otherwise. Thus, for example, reference to an "antibody" is a reference to one or more such antibodies, etc.

[0029] The term "substantially pure" with respect to a composition comprising an antibody refers to a composition that includes at least 80, 85, 90 or 95 % by weight or, in certain embodiments, 95, 98, 99 or 100 % by weight, e.g. dry weight, of the antibody relative to the remaining portion of the composition. The weight percentage can be relative to the total weight of protein in the composition or relative to the total weight of antibodies in the composition. Purity can be determined by techniques apparent to those of skill in the art, for instance SDS-PAGE.

[0030] The term "isolated" refers to an antibody that is substantially or essentially free of components that normally accompany or interact with the antibody as found in its naturally occurring environment or in its production environment, or both. Isolated antibody preparations have less than about 30%, less than about 25%, less than about 20%, less than about 15%, less than about 10%, less than about 5%, less than about 4%, less than about 3%, less than about 2% or less than about 1% of contaminating protein by weight, e.g. dry weight.

[0031] The term "antibody" refers to any macromolecule that would be recognized as an antibody by those of skill in the art. Antibodies share common properties including binding and at least one polypeptide chain that is substantially identical to a polypeptide chain that can be encoded by any of the immunoglobulin genes recognized by those of skill in the art. The immunoglobulin genes include, but are not limited to, the <com:Math><semantics>κ<annotation encoding="application / x-tex">\kappa< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>λ<annotation encoding="application / x-tex">\lambda< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>α<annotation encoding="application / x-tex">\alpha< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>γ<annotation encoding="application / x-tex">\gamma< / annotation>< / semantics>< / com:Math> (IgG1, IgG2, IgG3, and IgG4), <com:Math><semantics>δ<annotation encoding="application / x-tex">\delta< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>ϵ<annotation encoding="application / x-tex">\epsilon< / annotation>< / semantics>< / com:Math> and <com:Math><semantics>μ<annotation encoding="application / x-tex">\mu< / annotation>< / semantics>< / com:Math> constant region genes, as well as the immunoglobulin variable region genes. The term includes full-length antibodies and antibody fragments recognized by those of skill in the art, and variants thereof. The term further includes glycosylated and aglycosylated antibodies.

[0032] The term "antibody fragment" refers to any form of an antibody other than the full-length form. Antibody fragments herein include antibodies that are smaller components that exist within full-length antibodies, and antibodies that have been engineered. Antibody fragments include but are not limited to Fv, Fc, Fab, and (Fab')2, single chain Fv (scFv), diabodies, triabodies, tetrabodies, bifunctional hybrid antibodies, CDR1, CDR2, CDR3, combinations of CDR's, variable regions, framework regions, constant regions, and the like (Maynard & Georgiou, 2000, Annu. Rev. Biomed. Eng. 2:339-76; Hudson, 1998, Curr. Opin. Biotechnol. 9:395-402).

[0033] The term "immunoglobulin (Ig)" refers to a protein consisting of one or more polypeptides substantially encoded by one of the immunoglobulin genes, or a protein substantially identical thereto in amino acid sequence. Immunoglobulins include but are not limited to antibodies. Immunoglobulins may have a number of structural forms, including but not limited to full-length antibodies, antibody fragments, and individual immunoglobulin domains including but not limited to <com:Math><semantics>VH<annotation encoding="application / x-tex">V_H< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>Cγ1<annotation encoding="application / x-tex">C\gamma 1< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>Cγ2<annotation encoding="application / x-tex">C\gamma 2< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>Cγ3<annotation encoding="application / x-tex">C\gamma 3< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>VL<annotation encoding="application / x-tex">V_L< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>CL<annotation encoding="application / x-tex">C_L< / annotation>< / semantics>< / com:Math>.

[0034] The term "immunoglobulin (Ig) domain" refers to a protein domain consisting of a polypeptide substantially encoded by an immunoglobulin gene. Ig domains include but are not limited to <com:Math><semantics>VH<annotation encoding="application / x-tex">V_H< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>Cγ1<annotation encoding="application / x-tex">C\gamma 1< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>Cγ2<annotation encoding="application / x-tex">C\gamma 2< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>Cγ3<annotation encoding="application / x-tex">C\gamma 3< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>VL<annotation encoding="application / x-tex">V_L< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>CL<annotation encoding="application / x-tex">C_L< / annotation>< / semantics>< / com:Math>.

[0035] The term "variable region" of an antibody refers to a polypeptide or polypeptides composed of the V<com:Sub>H< / com:Sub> immunoglobulin domain, the V<com:Sub>L< / com:Sub> immunoglobulin domains, or the V<com:Sub>H< / com:Sub> and V<com:Sub>L< / com:Sub> immunoglobulin domains. Variable region may refer to this or these polypeptides in isolation, as an Fv fragment, as a scFv fragment, as this region in the context of a larger antibody fragment, or as this region in the context of a full-length antibody or an alternative, non-antibody scaffold molecule.

[0036] The term "variable" refers to the fact that certain portions of the variable domains differ extensively in sequence among antibodies and are responsible for the binding specificity of each particular antibody for its particular antigen. However, the variability is not evenly distributed through the variable domains of antibodies. It is concentrated in three segments called Complementarity Determining Regions (CDRs) both in the light chain and the heavy chain variable domains. The more highly conserved portions of the variable domains are called the framework regions (FR). The variable domains of native heavy and light chains each comprise four FR regions, largely adopting a β-sheet configuration, connected by three or four CDRs, which form loops connecting, and in some cases forming part of, the β-sheet structure. The CDRs in each chain are held together in close proximity by the FR regions and, with the CDRs from the other chain, contribute to the formation of the antigen binding site of antibodies (see Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md. (1991)).

[0037] The constant domains are not typically involved directly in binding an antibody to an antigen, but exhibit various effector functions. Depending on the amino acid sequence of the constant region of their heavy chains, antibodies or immunoglobulins can be assigned to different classes. There are five major classes of immunoglobulins: IgA, IgD, IgE, IgG and IgM, and several of these may be further divided into subclasses (isotypes), e.g. IgG1, IgG2, IgG3, and IgG4; IgA1 and IgA2. The heavy chain constant regions that correspond to the different classes of immunoglobulins are called <com:Math><semantics>α<annotation encoding="application / x-tex">\alpha< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>δ<annotation encoding="application / x-tex">\delta< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>ϵ<annotation encoding="application / x-tex">\epsilon< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>γ<annotation encoding="application / x-tex">\gamma< / annotation>< / semantics>< / com:Math> and <com:Math><semantics>μ<annotation encoding="application / x-tex">\mu< / annotation>< / semantics>< / com:Math>, respectively. Of the various human immunoglobulin classes, only human IgG1, IgG2, IgG3 and IgM are known to activate complement.

[0038] The term "variant protein sequence" refers to a protein sequence that has one or more residues that differ in amino acid identity from another similar protein sequence. Said similar protein sequence may be the natural wild type protein sequence, or another variant of the wild type sequence. Variants include proteins that have one or more amino acid insertions, deletions or substitutions. Variants also include proteins that have one or more post-translationally modified amino acids.

[0039] The term "parent antibody" refers to an antibody known to those of skill in the art that is modified according to the description provided herein. The modification can be physical, i.e., chemically or biochemically replacing or modifying one or more amino acids of the parent antibody to yield an antibody within the scope of the present description. The modification can also be conceptual, i.e., using the sequence of one or more polypeptide chains of the parent antibody to design an antibody comprising one or more site-specific non- natural amino acids according to the present description. Parent antibodies can be naturally occurring antibodies or antibodies designed or developed in a laboratory. Parent antibodies can also be artificial or engineered antibodies, e.g., chimeric or humanized antibodies.

[0040] The term "conservatively modified variant" refers to an antibody that differs from a related antibody by conservative substitutions in amino acid sequence. One of skill will recognize that individual substitutions, deletions or additions to a peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a "conservatively modified variant" where the alteration results in the substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are well known in the art. Such conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homologs, and alleles of the invention.

[0041] The following eight groups each contain amino acids that are conservative substitutions for one another: 1) Alanine (A), Glycine (G); 2) Aspartic acid (D), Glutamic acid (E); 3) Asparagine (N), Glutamine (Q); 4) Arginine (R), Lysine (K), Histidine (H); 5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W); 7) Serine (S), Threonine (T); and 8) Cysteine (C), Methionine (M) (see, e.g., Creighton, Proteins: Structures and Molecular Properties (W H Freeman & Co.; 2nd edition (December 1993)

[0042] The terms "identical" or "identity," in the context of two or more polypeptide sequences, refer to two or more sequences or subsequences that are the same. Sequences are "substantially identical" if they have a percentage of amino acid residues or nucleotides that are the same (i.e., about 60% identity, optionally about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, or about 95% identity over a specified region), when compared and aligned for maximum correspondence over a comparison window, or designated region as measured using one of the following sequence comparison algorithms or by manual alignment and visual inspection. The identity can exist over a region that is at least about 50 amino acids or nucleotides in length, or over a region that is 75-100 amino acids or nucleotides in length, or, where not specified, across the entire sequence or a polypeptide. In the case of antibodies, identity can be measured outside the variable CDRs. Optimal alignment of sequences for comparison can be conducted, including but not limited to, by the local homology algorithm of Smith and Waterman (1970) Adv. Appl. Math. 2:482c, by the homology alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443, by the search for similarity method of Pearson and Lipman (1988) Proc. Nat'l. Acad. Sci. USA 85:2444, by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.); or by manual alignment and visual inspection (see, e.g., Ausubel et al., Current Protocols in Molecular Biology (1995 supplement)).

[0043] Examples of algorithms that are suitable for determining percent sequence identity and sequence similarity include the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al. (1977) Nuc. Acids Res. 25:3389-3402, and Altschul et al. (1990) J. Mol. Biol. 215:403-410, respectively. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) or 10, M=5, N=-4 and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength of 3, and expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff and Henikoff (1989) Proc. Natl. Acad. Sci. USA 89:10915) alignments (B) of 50, expectation (E) of 10, M=5, N=-4, and a comparison of both strands. The BLAST algorithm is typically performed with the "low complexity" filter turned off.

[0044] The BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-5787). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.2, more preferably less than about 0.01, and most preferably less than about 0.001.

[0045] The term "amino acid" refers to naturally occurring and non-naturally occurring amino acids, as well as imino acids such as proline, amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids.

[0046] Naturally encoded amino acids are the proteinogenic amino acids known to those of skill in the art. They include the 20 common amino acids (alanine, arginine, asparagine, aspartic acid, cysteine, glutamine, glutamic acid, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, and valine) and the less common pyrrolysine and selenocysteine. Naturally encoded amino acids include post-translational variants of the 22 naturally occurring amino acids such as prenylated amino acids, isoprenylated amino acids, myrisoylated amino acids, palmitoylated amino acids, N- linked glycosylated amino acids, O-linked glycosylated amino acids, phosphorylated amino acids and acylated amino acids.

[0047] The term "non-natural amino acid" refers to an amino acid that is not a proteinogenic amino acid, or a post-translationally modified variant thereof. In particular, the term refers to an amino acid that is not one of the 20 common amino acids or pyrrolysine or selenocysteine, or post-translationally modified variants thereof.

[0048] A "functional Releasing Factor 1 (RF1) protein" refers to RF1 that retains activity equal to or substantially similar to wild-type or unmodified RF1 protein. Functional RF1 activity can be tested, for example, by measuring the growth rate of bacteria expressing the modified RF1 protein, and comparing the growth rate to bacteria expressing wild-type or unmodified RF1. Functional RF1 activity can also be tested, for example, by the ability of the modified RF1 protein to reduce orthogonal tRNA incorporation of a nnAA at a specified position in an mRNA encoding a target protein, thereby increasing the amount of premature chain termination (i.e., increasing the amount of truncated protein).

[0049] An "attenuated Releasing Factor 1 (RF1) protein" refers to a modified RF1 that retains reduced activity relative to wild-type or unmodified RF1 protein. RF1 activity can be tested, for example, by measuring the growth rate of bacteria expressing the modified RF1 protein, and comparing the growth rate to bacteria expressing wild-type or unmodified RF1. RF1 activity can also be tested, for example, by the ability of the modified RF1 protein to reduce orthogonal tRNA incorporation of a nnAA at a specified position in an mRNA encoding a target protein, thereby increasing the amount of premature chain termination (i.e., increasing the amount of truncated protein). In some embodiments, the attenuated RF1 protein comprises transcriptional modifications; for example, the expression level of the RF1 protein (wild type or modified) can be reduced to achieve attenuation. The reduction can also achieved by using RNAi technologies. In some embodiments, the attenuated RF1 protein comprises translational modifications; for example, the amount of the synthesized RF1 protein (wild type or modified) can be reduced to achieve attenuation, e.g., by increasing the rate at which the protein is digested by protease via insertion of protease-specific sequence into the RF1 sequence. Antibodies

[0050] Provided herein are antibodies comprising one or more non-natural amino acid residues at site-specific positions in the amino acid sequence of at least one polypeptide chain.

[0051] The antibody can share high sequence identity with any antibody recognized by those of skill in the art, i.e. a parent antibody. In certain embodiments, the amino acid sequence of the antibody is identical to the amino acid sequence of the parent antibody, other than the non-natural amino acids at site-specific position. In further embodiments, the antibody provided herein can have one or more insertions, deletions or mutations relative to the parent antibody in addition to the one or more non-natural amino acids at the site-specific positions. In certain embodiments, the antibody provided herein can have a unique primary sequence, so long as it would be recognized as an antibody by those of skill in the art.

[0052] The antibody is typically a protein comprising multiple polypeptide chains. In certain embodiments, the antibody is a heterotetramer comprising two identical light (L) chains and two identical heavy (H) chains. Each light chain can be linked to a heavy chain by one covalent disulfide bond. Each heavy chain can be linked to the other heavy chain by one or more covalent disulfide bonds. Each heavy chain and each light chain can also have one or more intrachain disulfide bonds. As is known to those of skill in the art, each heavy chain typically comprises a variable domain (V<com:Sub>H< / com:Sub>) followed by a number of constant domains. Each light chain typically comprises a variable domain at one end (V<com:Sub>L< / com:Sub>) and a constant domain. As is known to those of skill in the art, antibodies typically have selective affinity for their target molecules, i.e. antigens.

[0053] The antibodies provided herein can have any antibody form known to those of skill in the art. They can be full-length, or fragments. Exemplary full length antibodies include IgA, IgA1, IgA2, IgD, IgE, IgG, IgG1, IgG2, IgG3, IgG4, IgM, etc. Exemplary fragments include Fv, Fab, Fc, sFv, etc.

[0054] The antibodies provided herein comprise at least one non-natural amino acid. The non-natural amino acid can be any non-natural amino acid known to those of skill in the art. Exemplary non-natural amino acids are described in the sections below.

[0055] The non-natural amino acids are positioned at select locations in a polypeptide chain of the antibody. These locations were identified as providing optimum sites for substitution with the non-natural amino acids. Each site is capable of bearing a non-natural amino acid with optimum structure, function and / or methods for producing the antibody.

[0056] In certain embodiments, a site-specific position for substitution provides an antibody that is stable. Stability can be measured by any technique apparent to those of skill in the art.

[0057] In certain embodiments, a site-specific position for substitution provides an antibody that is has optimal functional properties. For instance, the antibody can show little or no loss of binding affinity for its target antigen compared to an antibody without the site- specific non-natural amino acid. In certain embodiments, the antibody can show enhanced binding compared to an antibody without the site-specific non-natural amino acid.

[0058] In certain embodiments, a site-specific position for substitution provides an antibody that can be made advantageously. For instance, in certain embodiments, the antibody shows advantageous properties in its methods of synthesis, discussed below. In certain embodiments, the antibody can show little or no loss in yield in production compared to an antibody without the site-specific non-natural amino acid. In certain embodiments, the antibody can show enhanced yield in production compared to an antibody without the site- specific non-natural amino acid. In certain embodiments, the antibody can show little or no loss of tRNA suppression, described below, compared to an antibody without the site-specific non-natural amino acid. In certain embodiments, the antibody can show enhanced tRNA suppression, described below, in production compared to an antibody without the site- specific non-natural amino acid.

[0059] In certain embodiments, a site-specific position for substitution provides an antibody that has advantageous solubility. In certain embodiments, the antibody can show little or no loss in solubility compared to an antibody without the site-specific non-natural amino acid. In certain embodiments, the antibody can show enhanced solubility compared to an antibody without the site-specific non-natural amino acid.

[0060] In certain embodiments, a site-specific position for substitution provides an antibody that has advantageous expression. In certain embodiments, the antibody can show little or no loss in expression compared to an antibody without the site-specific non-natural amino acid. In certain embodiments, the antibody can show enhanced expression compared to an antibody without the site-specific non-natural amino acid.

[0061] In certain embodiments, a site-specific position for substitution provides an antibody that has advantageous folding. In certain embodiments, the antibody can show little or no loss in proper folding compared to an antibody without the site-specific non-natural amino acid. In certain embodiments, the antibody can show enhanced folding compared to an antibody without the site-specific non-natural amino acid. Venner Shipley 2014 / 04 / 07 CA 02875989 2014-12-05 15:25 PCT / US 2013 / 044 843 - 07-04-2014 Attorney Docket No. 108843.00008

[0062] In certain embodiments, a site-specific position for substitution provides an antibody that is capable of advantageous conjugation. As described below, several non- natural amino acids have side chains or functional groups that facilitate conjugation of the antibody to a second agent, either directly or via a linker. In certain embodiments, the antibody can show enhanced conjugation efficiency compared to an antibody without the same or other non-natural amino acids at other positions. In certain embodiments, the antibody can show enhanced conjugation yield compared to an antibody without the same or other non-natural amino acids at other positions. In certain embodiments, the antibody can show enhanced conjugation specificity compared to an antibody without the same or other non-natural amino acids at other positions.

[0063] The one or more non-natural amino acids are located at selected site-specific positions in at least one polypeptide chain of the antibody. The polypeptide chain can be any polypeptide chain of the antibody without limitation, including either light chain or either heavy chain. The site-specific position can be in any domain of the antibody, including any variable domain and any constant domain.

[0064] In certain embodiments, the antibodies provided herein comprise one non-natural amino acid at a site-specific position. In certain embodiments, the antibodies provided herein comprise two non-natural amino acids at sitc-specific positions. In certain embodiments, the antibodies provided herein comprise three non-natural amino acids at site-specific positions. In certain embodiments, the antibodies provided herein comprise more than three non-natural amino acids at site-specific positions.

[0065] The site-specific positions for substituting can be described with any antibody nomenclature system known to those of skill in the art. In the Kabat numbering system, these positions are at heavy chain residues H005, H023, H042, H065, H074, and H084. In the EU numbering system, these positions are at heavy chain residues H118, H119, H132, H134, H135, H136, H137, H138, H139, H155, H160, H162, H165, H172, H174, H176, H177, H191, H194, H219, H238, H239, H241, H243, H246, H262, H264, H265, H267, H268, H269, H270, H271, H272, H274, H275, H278, H280, H281, H282, H283, H286, H289, H292, H293, H294, H295, H296, H297, H298, H299, H300, H301, H303, H305, H317, H320, H324, H326, H327, H329, H330, H332, H333, H334, H335, H337, H339, H340, H342, II344, H355, H356, H358, H359, H360, H375, H383, H384, H386, H389, H392, H398, H404, H420, H421, H436, and H438. In other words, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from 540209 / 1 / SANFRANCISCO 15:25 Kabat residues H005, H023, H042, H065, H074, and H084; and EU residues H118, H119, H132, H134, H135, H136, H137, H138, H139, H155, H160, H162, H165, H172, H174, H176, H177, H191, H194, H219, H238, H239, H241, H243, H246, H262, H264, H265, H267, H268, H269, H270, H271, H272, H274, H275, H278, H280, H281, H282, H283, H286, H289, H292, H293, H294, H295, H296, H297, H298, H299, H300, H301, H303, H305, H317, H320, H324, H326, H327, H329, H330, H332, H333, H334, H335, H337, H339, H340, H342, H344, H355, H356, H358, H359, H360, H375, H383, H384, H386, H389, H392, H398, H404, H420, H421, H436, and H438.

[0066] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from Kabat residues H005, H023, H074, and H084; and EU residues H118, H119, H132, H134, H135, H136, H137, H139, H160, H162, H165, H172, H191, H194, H239, H241, H246, H267, H268, H269, H270, H271, H272, H274, H275, H280, H281, H282, H283, H286, H289, H292, H293, H294, H295, H296, H297, H298, H299, H300, H301, H303, H305, H317, H320, H324, H326, H327, H329, H330, H332, H333, H334, H335, H337, H339, H340, H342, H344, H355, H359, H375, H386, H389, H392, H398, H404, H420, H421, and H438.

[0067] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from Kabat residues H005, H023, and H084; and EU residues H118, H119, H132, H134, H136, H137, H160, H162, H172, H239, H241, H267, H269, H270, H271, H272, H282, H286, H292, H293, H296, H298, H329, H330, H334, H335, H340, H355, H359, H386, H389, H404, H420, H421, H438, and H342.

[0068] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from Kabat residues H005 and H084; and EU residues H118, H132, H136, H239, II293, H334, H355, H359, and H389.

[0069] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from Kabat residues H023 and H074; and EU residues H119, H134, H135, H137, H139, II160, H162, H165, H172, H191, H194, H241, H246, H267, H268, H269, H270, H271, H272, H274, H275, H280, H281, H282, II283, H286, H289, H292, II294, JI295, H296, H297, H298, H299, H300, H301, H303, H305, H317, H320, II324, H326, H327, H329, H330, H332, H333, H335, H337, H339, H342, H344, H355, H375, H386, H392, H398, H404, H420, H421, H340 and H438. RANDOOM IS AN ERANCISCO 15:25

[0070] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from Kabat residues H042 and H065; and EU residues H138, H155, H174, H176, H177, H219, H238, H243, H262, H264, H265, H278, H342, H356, H358, H360, H383, H384 H404, and H436.

[0071] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from EU residues corresponding to H292-H301, H303, and H305.

[0072] In the Chothia numbering system, these positions are at heavy chain residues H005, H023, H042, H065, H074, and H084. In the EU numbering system, these positions are at heavy chain residues H118, H119, H132, H134, H135, H136, H137, H138, H139, H155, H160, H162, H165, H172, H174, H176, H177, H191, H194, H219, H238, H239, H241, H243, H246, H262, H264, H265, H267, H268, H269, H270, H271, H272, H274, H275, H278, H280, H281, H282, H283, H286, H289, H292, H293, H294, H295, H296, H297, H298, H299, H300, H301, H303, H305, H317, H320, H324, H326, H327, H329, H330, H332, H333, H334, H335, H337, H339, H340, H342, H344, H355, H356, H358, H359, H360, H375, H383, H384, H386, H389, H392, H398, H404, H420, H421, H436, and H438. In other words, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from Chothia residues H005, H023, H042, H065, H074, and H084; and EU residues H118, H119, H132, H134, H135, H136, H137, H138, H139, H155, H160, H162, H165, H172, H174, H176, H177, H191, H194, H219, H238, H239, H241, H243, II246, H262, H264, H265, H267, H268, H269, H270, H271, H272, H274, H275, H278, H280, H281, H282, H283, H286, H289, H292, H293, H294, H295, H296, H297, H298, H299, H300, H301, H303, H305, H317, H320, H324, H326, H327, H329, H330, H332, H333, H334, H335, H337, H339, H340, H342, H344, H355, H356, H358, H359, H360, H375, H383, H384, H386, H389, H392, H398, H404, H420, H421, H436, and I1438.

[0073] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from Chothia residues H005, H023, H074, and H084; and EU residues H118, H119, H132, H134, H135, H136, H137, H139, H160, H162, H165, H172, H191, H194, H239, H241, H246, H267, H268, H269, H270, H271, H272, H274, H275, II280, H281, H282, H283, H286, H289, H292, H293, H294, H295, H296, H297, H298, H299, H300, II301, H303, H305, H317, H320, H324, 15:25 H326, H327, H329, H330, H332, H333, H334, H335, H337, H339, H340, H342, H344, H355, H359, H375, H386, H389, H392, H398, H404, H420, H421, and H438.

[0074] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from Chothia residues H005 and H084; and EU residues H118, H132, H136, H239, H293, H334, H342, H355, H359, H389 and H404.

[0075] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from EU residues corresponding to H292-H301, H303, and H305.

[0076] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from Chothia residues H023 and H074; and EU residues H119, H134, H135, H137, H139, H160, H162, H165, H172, H191, H194, H241, H246, H267, H268, H269, H270, H271, H272, H274, H275, H280, H281, H282, H283, H286, H289, H292, H294, H295, H296, H297, H298, H299, H300, H301, H303, H305, H317, H320, H324, H326, H327, H329, H330, H332, H333, H335, H337, H339, H342, H344, H355, H375, H386, H392, H398, H420, H421, H340, H404, and H438.

[0077] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from Chothia residues H042 and H065; and EU residues H138, H155, H174, H176, H177, H219, H238, H243, H262, H264, H265, H278, H342, H356, H358, H360, H383, H384, H404, and H436.

[0078] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from residues H005, H023, and H084 according to the Kabat or Chothia numbering scheme; and residues H118, H119, H132, H134, H136, H137, H160, H162, H172, H239, H241, H267, H269, II270, H271, H272, H282, H286, H292, H293, H296, H298, H329, H330, H334, H335, H340, H355, H359, H386, H389, H404, H420, H421, H438, and H342, according to the EU numbering scheme.

[0079] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from residues L043, L049, L056, L057, L060, L067, and L068, according to the Kabat or Chothia numbering scheme; and residues L109, L112, L114, L144, L153, L156, L157, L168, L184, L202, L203, and L206, according to the EU numbering scheme. In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected EXAMOND / 4 (CANICDANIC) 15:25 from residues L043, L049, L056, L057, L060, L067, and L068, according to the Kabat or Chothia numbering scheme; and residues L109, L112, L114, L144, L153, L156, L168, L184, L202, and L203, according to the EU numbering scheme. In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from residues L043, L049, L056, L057, L060, L067, and L068, according to the Kabat or Chothia numbering scheme; and residues L109, L144, L153, L156, L184, L202, and L203, according to the EU numbering scheme. In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from residues L049, L056, L057, L060, and L067, according to the Kabat or Chothia numbering scheme; and residues L109, L153, L202, and L203, according to the EU numbering scheme.

[0080] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from residues H023 and H084, according to the Kabat or Chothia numbering scheme; and residues H118, H119, H135, H136, H137, H160, H161, H162, H164, H195, H197, H219, H282, H289, H296, H330, H335, H361, H400, H404, H422, H440, H260, H267, H268, H272, H274, H292, H293, II297, H298, H303, H305, H332, H333, H334, H340, H341, H342, H343, H355, H362, H386, H392, H404, H424, H438, H442 and H443, according to the EU numbering scheme. In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from residues H023 and H084, according to the Kabat or Chothia numbering scheme; and residues H118, H119, H135, H136, H137, H160, H161, H162, H164, H195, H197, H219, H282, H296, H335, H361, H422, H440, H267, H272, H274, H293, H297, H298, H303, H305, H334, H340, H341, H342, H343, H355, H362, H392, H404, H424, H438, H442 and H443, according to the EU numbering scheme. In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from residues H023 and H084, according to the Kabat or Chothia numbering scheme; and residues H118, H119, H135, H136, H137, H160, H161, H162, H195, H197, H219, H282, H296, H422, H440, H267, H272, H293, H297, H298, H303, H305, H334, H340, H341, H342, H355, H392, H404, H424, H438, H442 and H443, according to the EU numbering scheme. In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from residues H023 and H084, according to the Kabat or Chothia numbering scheme; and H118, H119, H135, H136, H160, H162, H195, H219, H282, H296, H267, II293, H297, EURONAMIA JOAN COUNTRACTOR Attorney Docket No. 108843.00008 H298, H303, H305, H334, H340, H341, H392, and H438, H442, according to the EU numbering scheme.

[0081] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from residues H042, H003, H007, H014, H016, H019, H025, H040, H043, H051, H052, H053, H056, H070, H082A, H098, H100, H110, and H112, according to the Kabat or Chothia numbering scheme; and residues H121, H180, H184, H190, H192, H214, H216, H221, H222, H225, H227, H230, H231, H232, and H236, according to the EU numbering scheme. In certain embodiments, provided herein arc antibodies comprising one or more non-natural amino acids at one or more positions selected from residues H042, H003, H007, H014, H016, H019, H025, H040, H043, H052, H053, H056, H070, H082A, H100, H110, and H112, according to the Kabat or Chothia numbering scheme; and residues H121, H180, H190, H192, H214, H216, H221, H222, H225, H227, H230, H231, H232, and H236, according to the EU numbering scheme. In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from residues H042, H003, H007, H014, H016, H019, H025, H040, H043, H052, H070, H082A, H100, H110, and H112, according to the Kabat or Chothia numbering scheme; and residues H121, H180, H190, H192, H214, H216, H221, H222, H225, H227, H230, H231, H232, and H236, according to the EU numbering scheme. In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from residues H007, H014, H019, H025, H040, H043, H052, H070, H100, H110, and H112, according to the Kabat or Chothia numbering scheme; and residues H121, H180, H214, H216, H222, H227, H230, H231, H232, and H236, according to the EU numbering scheme.

[0082] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from residues (-)L001, L003, L005, L007, L008, L009, L010, L016, L017, L018, L020, L022, L026, L027, L045, L058, L063, L065, L066, L070, L077, L079, and L107, according to the Kabat or Chothia numbering scheme; and residues L138, L142, L143, L152, L171, L182, L188, L199, and L201, according to the EU numbering scheme. In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from residues minus 1, L003, L005, L007, L008, L009, L010, L016, L017, L018, L020, L022, L026, L027, L045, L058, L063, L065, L066, L070, L077, L079, and L107, according to the Kabat or Chothia numbering scheme; and residues L142, L143, L152, L171, L182, EVANABLE DARIOLOGICA Attorney Docket No. 108843.00008 L188, L199, and L201, according to the EU numbering scheme. In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from residues (-)L001, L003, L005, L007, L008, L009, L016, L017, L018, L020, L022, L026, L027, L045, L058, L063, L065, L066, L070, L077, L079, and L107, according to the Kabat or Chothia numbering scheme; and residues L142, L152, L171, L182, L188, and L199, according to the EU numbering scheme. In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from residues minus 1, L005, L007, L008, L016, L017, L018, L020, L022, L027, L045, L058, L063, L077, L079, and L107, according to the Kabat or Chothia numbering scheme; and residues L142, L152, L182, L188, and L199, according to the EU numbering scheme. In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from residues (-)L001, L016, and L063, according to the Kabat or Chothia numbering scheme; and residue L199, according to the EU numbering scheme.

[0083] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from residues H019, II025, H051, II070, H098, H110, and H112, according to the Kabat or Chothia numbering scheme; and residues H121, H136, H180, H187, H190, H214, H216, H221, and H222, according to the EU numbering scheme.

[0084] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from residues (-)L001, L007, L008, L016, L022, L063, L014, and L070, according to the Kabat or Chothia numbering scheme; and residues L138, L142, L143 and L152, according to the EU numbering scheme.

[0085] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from residues H019, H025, H051, H070, H077, H079, H098, H110, and H112, according to the Kabat or Chothia numbering scheme; and residues H121, H136, H180, H187, H190, H214, H216, H221, and H222, according to the EU numbering scheme.

[0086] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from residues (-)L001, L007, L008, L016, L022, L063, and L070, according to the Kabat or Chothia numbering scheme; and residues L138, L142, L143, L152 and L201, according to the EU numbering scheme. 15:25

[0087] The site-specific positions can also be identified relative to the amino acid sequences of the polypeptide chains of a reference antibody. For example, the amino acid sequence of a reference heavy chain is provided at SEQ ID NO:1. In the reference heavy chain, the site-specific positions are at residues 5, 23, 42, 66, 75, 88, 121, 122, 135, 137, 138, 139, 140, 141, 142, 158, 163, 165, 168, 175, 177, 179, 180, 194, 197, 222, 241, 242, 244, 246, 249, 265, 267, 268, 270, 271, 272, 273, 274, 275, 277, 278, 281, 283, 284, 285, 286, 289, 292, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 306, 308, 320, 323, 327, 329, 330, 332, 333, 335, 336, 337, 338, 340, 342, 343, 345, 347, 358, 359, 361, 362, 363, 378, 386, 387, 389, 392, 395, 401, 407, 423, 424, 439 and 441. In other words, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to 5, 23, 42, 66, 75, 88, 121, 122, 135, 137, 138, 139, 140, 141, 142, 158, 163, 165, 168, 175, 177, 179, 180, 194, 197, 222, 241, 242, 244, 246, 249, 265, 267, 268, 270, 271, 272, 273, 274, 275, 277, 278, 281, 283, 284, 285, 286, 289, 292, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 306, 308, 320, 323, 327, 329, 330, 332, 333, 335, 336, 337, 338, 340, 342, 343, 345, 347, 358, 359, 361, 362, 363, 378, 386, 387, 389, 392, 395, 401, 407, 423, 424, 439 and 441 of the representative heavy chain polypeptide according to SEQ ID NO:1.

[8800] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to 5, 23, 75, 88, 121, 122, 135, 137, 138, 139, 140, 142, 163, 165, 168, 175, 194, 197, 242, 244, 249, 270, 271, 272, 273, 274, 275, 277, 278, 283, 284, 285, 286, 289, 292, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 306, 308, 320, 323, 327, 329, 330, 332, 333, 335, 336, 337, 338, 340, 342, 343, 345, 347, 358, 362, 378, 389, 392, 395, 401, 407, 423, 424, and 441 of the representative heavy chain polypeptide according to SEQ ID NO:1.

[0089] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to 5, 23, 88, 121, 122, 135, 137, 138, 139, 140, 163, 165, 168, 175, 242, 244, 270, 273, 274, 275, 285, 289, 295, 296, 299, 300, 301, 332, 333, 337, 338, 343, 345, 358, 362, 389, 407, 423, 424, and 441 of the representative heavy chain polypeptide according to SEQ ID NO:1.

[0090] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to 5, 88, 121, 135, 139, 242, 296, 337, 358, 362, and 392 of the representative heavy chain polypeptide according to SEQ ID NO:1. 15:25

[0091] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to 23, 75, 122, 137, 138, 140, 142, 163, 165, 168, 175, 194, 197, 244, 249, 270, 271, 272, 273, 274, 275, 277, 278, 283, 284, 285, 286, 289, 292, 295, 297, 298, 299, 300, 301, 302, 303, 304, 306, 308, 320, 323, 327, 329, 330, 332, 333, 335, 336, 338, 340, 342, 343, 345, 347, 358, 378, 389, 395, 401, 407, 423, 424, and 441 of the representative heavy chain polypeptide according to SEQ ID NO:1.

[0092] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to 42, 66, 141, 158, 177, 179, 180, 222, 241, 246, 265, 267, 268, 281, 359, 361, 363, 386, 387, 407, and 439 of the representative heavy chain polypeptide according to SEQ ID NO:1.

[0093] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to 292- 301, 303, and 305 of the representative heavy chain polypeptide according to SEQ ID NO:1.

[0094] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to 23, 88, 121, 122, 138, 139, 140, 163, 164, 165, 167, 198, 200, 222, 285, 292, 299, 333, 338, 364, 403, 407, 425, 443, 263, 270, 271, 275, 277, 295, 296, 300, 301, 306, 308, 335, 336, 337, 343, 344, 345, 346, 358, 365, 389, 395, 407, 427, 441, 445, and 446 of the representative heavy chain polypeptide according to SEQ ID NO:1.

[0095] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to 23, 88, 121, 122, 138, 139, 140, 163, 164, 165, 167, 198, 200, 222, 285, 299, 338, 364, 425, 443, 270, 275, 277, 295, 296, 300, 301, 306, 308, 337, 343, 344, 345, 346, 358, 365, 395, 407, 427, 441, 445, and 446 of the representative heavy chain polypeptide according to SEQ ID NO:1.

[0096] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to 23, 88, 121, 122, 138, 139, 140, 163, 164, 165, 167, 198, 200, 222, 285, 299, 364, 425, 443, 270, 275, 296, 300, 301, 306, 308, 337, 343, 344, 345, 358, 365, 395, 407, 427, 441, 445, and 446 of the representative heavy chain polypeptide according to SEQ ID NO:1. AND INMADURACIONAL MARKET PARTY OF THE PROPERTY OF THE PROPERTY OF THE PROPERTY OF THE PROPERTY OF THE PROPERTY OF THE PROPERTY OF THE PROPERTY OF THE PROPERTY OF THE PROPERTY OF THE PROPERTY OF THE PROPERTY OF THE PROPERT 15:25

[0097] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to 23, 88, 121, 122, 138, 139, 140, 163, 164, 165, 198, 200, 222, 285, 299, 425, 443, 270, 275, 296, 300, 301, 306, 308, 337, 343, 344, 345, 358, 395, 407, 427, 441, 445, and 446 of the representative heavy chain polypeptide according to SEQ ID NO:1.

[0098] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to 23, 88, 121, 122, 138, 139, 163, 165, 198, 222, 285, 299, 270, 296, 300, 301, 306, 308, 337, 343, 344, 395, 407, and 441 of the representative heavy chain polypeptide according to SEQ ID NO:1.

[0099] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to 42, 3, 7, 14, 16, 19, 25, 40, 43, 51, 52, 54, 57, 71, 84, 102, 104, 114, 119, 124, 183, 187, 193, 195, 217, 219, 224, 225, 228, 230, 233, 234, 235 and 239 of the representative heavy chain polypeptide according to SEQ ID NO:1.

[00100] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to 42, 3, 7, 14, 16, 19, 25, 40, 43, 52, 54, 57, 71, 84, 104, 114, 119, 124, 183, 193, 195, 217, 219, 224, 225, 228, 230, 233, 234, 235 and 239 of the representative heavy chain polypeptide according to SEQ ID NO:1.

[00101] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to 7, 14, 19, 25, 40, 43, 52, 71, 104, 114, 119, 124, 183, 195, 217, 219, 230, 233, 234, 235, and 239 of the representative heavy chain polypeptide according to SEQ ID NO:1.

[00102] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to minus 1, 3, 5, 7, 8, 9, 10, 16, 17, 18, 20, 22, 26, 27, 45, 58, 63, 65, 66, 70, 77, 79, 107, 138, 142, 143, 152, 171, 182, 188, 199, and 201 of the representative light chain polypeptide according to SEQ ID NO:2.

[00103] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to minus 1, 3, 5, 7, 8, 9, 16, 17, 18, 20, 22, 26, 27, 45, 58, 63, 65, 66, 70, 77, 79, 107, 142, 143, 152, EXAMONO HIS AN ERANCISCO 15:25 171, 182, 188, 199, and 201 of the representative light chain polypeptide according to SEQ ID NO:2.

[00104] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to minus 1, 3, 5, 7, 8, 9, 16, 17, 18, 20, 22, 26, 27, 45, 58, 63, 65, 66, 70, 77, 79, 107, 142, 152, 171, 182, 188, and 199 of the representative light chain polypeptide according to SEQ ID NO:2.

[00105] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to minus 1, 5, 7, 8, 16, 17, 18, 20, 22, 27, 45, 58, 63, 77, 79, 107, 142, 152, 182, 188, and 199 of the representative light chain polypeptide according to SEQ ID NO:2.

[00106] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to minus 1, 16, 63, and 199 of the representative light chain polypeptide according to SEQ ID NO:2.

[00107] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to 19, 25, 51, 71, 102, 114, 119, 124, 139, 183, 187, 193, 217, 219, 224, and 225 of the representative heavy chain polypeptide according to SEQ ID NO:1.

[00108] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to minus 1, 7, 8, 16, 22, 63, 14, 70, 138, 142, 143 and 152 of the representative light chain polypeptide according to SEQ ID NO:2.

[00109] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to 19, 25, 51, 71, 78, 80, 102, 114, 119, 124, 139, 183, 187, 193, 217, 219, 224, and 225 of the representative heavy chain polypeptide according to SEQ ID NO:1.

[00110] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to minus 1, 7, 8, 16, 22, 63, 70, 138, 142, 143, 152, and 201of the representative light chain polypeptide according to SEQ ID NO:2.

[00111] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to 43, 49, 15:25 56, 57, 60, 67, 68, 109, 112, 114, 144, 153, 156, 157, 168, 184, 202, 203, and 206 of the representative light chain polypeptide according to SEQ ID NO:2.

[00112] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to 43, 49, 56, 57, 60, 67, 68, 109, 112, 144, 153, 156, 168, 184, 202, and 203 of the representative light chain polypeptide according to SEQ ID NO:2.

[00113] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to 43, 49, 56, 57, 60, 67, 68, 109, 144, 153, 156, 184, 202, and 203 of the representative light chain polypeptide according to SEQ ID NO:2.

[00114] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from those corresponding to 49, 56, 57, 60, 67, 109, 153, 202, and 203 of the representative light chain polypeptide according to SEQ ID NO:2.

[00115] In certain embodiments, the antibody comprises a polypeptide chain that can be described by the following formula (I): [Image disponible dans le document PDF, Image available in the PDF document] In Formula (I), each Xaa represents an amino acid in the polypeptide chain of any identity. In other words, each Xaa can be any amino acid, typically any naturally occurring amino acid, or a variant thereof. The superscript to the right of each Xaa represents the position of the amino acid within the primary sequence of the polypeptide chain. Xaa' represents the first, or N-terminal, amino acid in the polypeptide chain, and Xaa<com:Sup>q< / com:Sup> represents the last, or C- terminal, amino acid in the polypeptide chain. The variable q is an integer that is equal to the total number of amino acids in the polypeptide chain. Each Naa represents a non-natural amino acid within the polypeptide chain. Useful non-natural amino acids are described in the sections below. The integer n represents the number of non-natural amino acids in the polypeptide chain. In typical embodiments, n is an integer greater than 1. Each integer p(i) is greater than 1 and less than q, and the variable i is an integer that varies from 1 to n. Each integer p(i) represents a site-specific location in the amino acid sequence for the corresponding Naa. Each site specific location p(i) is optimal for substitution of a naturally occurring amino acid with a non-natural amino acid, such as Naa<com:Sup>p(i)< / com:Sup>, according to the techniques described herein. ANDOOR IS MARKED AND ROOM 15:25

[00116] Analysis of the data from TAG screening as presented in the Examples allowed selection of sites which are ideal candidates for making ADCs on the basis of cell killing, expression levels, drug-to-antibody ratio, solvent accessibility and (where available) thermal stability. The most preferred sites have lower solvent accessibility, and higher thermostability than the other tested variants. The preferred sites for nnAA incorporation are listed in Table I, below. Table I: Preferred Sites for nnAA Incorporation [Image disponible dans le document PDF, Image available in the PDF document]

[00117] Accordingly, in certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from the group consisting of heavy chain or light chain residues EU HC-F404, EU HC-K121, EU HC-Y180, EU HC-F241, Kabat or Chothia LC-T22, Kabat or Chothia LC-S7, EU LC-N152, EU HC- S136, Kabat or Chothia HC-S25, Kabat or Chothia HC-A40, EU HC-S119, EU HC-S190, EU HC-K222, Kabat or Chothia HC-R19, Kabat or Chothia HC-Y52, or Kabat or Chothia HC- S70, or a post-translationally modified variant thereof.

[00118] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from the group consisting of heavy chain or light chain residues EU IIC-F404, EU HC-K121, EU HC-Y180, EU HC-F241, Kabat or Chothia LC-T22, Kabat or Chothia LC-S7, EU LC-N152, EU HC-S136, Kabat or Chothia HC-S25, Kabat or Chothia HC-A40, EU HC-S119, EU HC-S190, and EU HC-K222, or a post-translationally modified variant thereof.

[00119] In certain embodiments, provided herein are antibodies comprising one or more non-natural amino acids at one or more positions selected from the group consisting of heavy chain or light chain residues EU HC-F404, EU HC-K121, EU HC-Y180, EU HC-F241, Kabat or Chothia LC-T22, Kabat or Chothia LC-S7, EU LC-N152, and EU HC-S136, or a post-translationally modified variant thereof.

[00120] In certain embodiments, further provided herein are conservatively modified variants of the above antibodies. Conservatively modified variants of an antibody include one or more insertions, deletions or substitutions that do not disrupt the structure and / or function of the antibody when evaluated by one of skill in the art. In certain embodiments, conservatively modified variants include 20 or fewer amino acid insertions, deletions or substitutions. In certain embodiments, conservatively modified variants include 15 or fewer amino acid insertions, deletions or substitutions. In certain embodiments, conservatively modified variants include 10 or fewer amino acid insertions, deletions or substitutions. In certain embodiments, conservatively modified variants include 9 or fewer amino acid insertions, deletions or substitutions. In certain embodiments, conservatively modified variants include 8 or fewer amino acid insertions, deletions or substitutions. In certain embodiments, conservatively modified variants include 7 or fewer amino acid insertions, deletions or substitutions. In certain embodiments, conservatively modified variants include 6 or fewer amino acid insertions, deletions or substitutions. In certain embodiments, conservatively modified variants include 5 or fewer amino acid insertions, deletions or substitutions. In certain embodiments, conservatively modified variants include 4 or fewer amino acid insertions, deletions or substitutions. In certain embodiments, conservatively modified variants include 3 or fewer amino acid insertions, deletions or substitutions. In certain embodiments, conservatively modified variants include 2 or fewer amino acid insertions, deletions or substitutions. In certain embodiments, conservatively modified variants include 1 amino acid insertion, deletion or substitution. In particular embodiments the substitutions are conservative, substituting an amino acid within the same class, as described above.

[00121] In certain embodiments, the antibodies can be modified to modulate structure, stability and / or activity. In such embodiments, the modifications can be conservative or other than conservative. The modifications need only be suitable to the practitioner carrying out the methods and using the compositions described herein. In certain embodiments, the modifications decrease but do not eliminate antigen binding affinity. In certain embodiments, the modifications increase antigen binding affinity. In certain embodiments, the modifications enhance structure or stability of the antibody. In certain embodiments, the modifications reduce but do not eliminate structure or stability of the antibody. In certain embodiments, modified variants include 20 or fewer amino acid insertions, deletions or substitutions. In certain embodiments, modified variants include 15 or fewer amino acid insertions, deletions or substitutions. In certain embodiments, modified variants include 10 or fewer amino acid insertions, deletions or substitutions. In certain embodiments, modified variants include 9 or fewer amino acid insertions, deletions or substitutions. In certain embodiments, modified variants include 8 or fewer amino acid insertions, deletions or substitutions. In certain embodiments, modified variants include 7 or fewer amino acid insertions, deletions or substitutions. In certain embodiments, modified variants include 6 or fewer amino acid insertions, deletions or substitutions. In certain embodiments, modified variants include 5 or fewer amino acid insertions, deletions or substitutions. In certain embodiments, modified variants include 4 or fewer amino acid insertions, deletions or substitutions. In certain embodiments, modified variants include 3 or fewer amino acid insertions, deletions or substitutions. In certain embodiments, modified variants include 2 or fewer amino acid insertions, deletions or substitutions. In certain embodiments, modified variants include 1 amino acid insertion, deletion or substitution.

[00122] Also within the scope are post-translationally modified variants. Any of the antibodies provided herein can be post-translationally modified in any manner recognized by those of skill in the art. Typical post-translational modifications for antibodies include interchain disulfide bonding, intrachain disulfide bonding, N-linked glycosylation and proteolysis. Also provided herein are other post-translationally modified antibodies having modifications such as phosphorylation, O-linked glycosylation, methylation, acetylation, lipidation, GPI anchoring, myristoylation and prenylation. The post-translational modification can occur during production, in vivo, in vitro or otherwise. In certain embodiments, the post-translational modification can be an intentional modification by a practitioner, for instance, using the methods provided herein.

[00123] Further included within the scope are antibodies fused to further peptides or polypeptides. Exemplary fusions include, but are not limited to, e.g., a methionyl antibody in which a methionine is linked to the N-terminus of the antibody resulting from the recombinant expression, fusions for the purpose of purification (including but not limited to, to poly-histidine or affinity epitopes), fusions for the purpose of linking to other biologically active molecules, fusions with serum albumin binding peptides, and fusions with serum proteins such as serum albumin. The antibodies may comprise protease cleavage sequences, reactive groups, antibody-binding domains (including but not limited to, FLAG or poly-His) or other affinity based sequences (including but not limited to, FLAG, poly-His, GST, etc.). The antibodies may also comprise linked molecules (including but not limited to, biotin) that improve detection (including but not limited to, GFP), purification or other features of the antibody. In certain embodiments, the antibodies comprise a C-terminal affinity sequence that facilitates purification of full length antibodies. In certain embodiments, such C-terminal affinity sequence is a poly-His sequence, e.g., a 6-His sequence.

[00124] The antibody can have any antibody form recognized by those of skill in the art. The antibody can comprise a single polypeptide chain – a single heavy chain or a single light chain. The antibody can also form multimers that will be recognized by those of skill in the art including homodimers, heterodimers, homomultimers, and heteromultimers. These multimers can be linked or unlinked. Useful linkages include interchain disulfide bonds typical for antibody molecules. The multimers can also be linked by other amino acids, including the non-natural amino acids introduced according to the present description. The antibody can be an immunoglobulin such as of any class or subclass including IgA, IgA1, IgA2, IgD, IgE, IgG, IgG1, IgG2, IgG3, IgG4 and IgM. The antibody can be of the form of any antibody fragment including Fv, Fc, Fab, and (Fab')<com:Sub>2< / com:Sub> and scFv.

[00125] The antibody may further be glycosylated or aglycosylated. Accordingly, in certain embodiments, the antibody is glycosylated. In certain embodiments, the antibody is aglycosylated. Agylcosylated antibodies comprising a non-natural amino acid may be made, for example, as described in the Examples provided herein or through bacterial expression systems known to those skilled in the art. Glycosylated antibodies comprising a non-natural amino acid may be made, for example, as described by Axup et al., 2012, Proc. Nat. Acad. Sci. USA 109(40):16101-16106.

[00126] Also provided herein are antibodies that are conjugated to one or more conjugation moieties. The conjugation moiety can be any conjugation moiety deemed useful to one of skill in the art. For instance, the conjugation moiety can be a polymer, such as polyethylene glycol, that can improve the stability of the antibody in vitro or in vivo. The conjugation moiety can have therapeutic activity, thereby yielding an antibody-drug conjugate. The conjugation moiety can be a molecular payload that is harmful to target cells. The conjugation moiety can be a label useful for detection or diagnosis. In certain embodiments, the conjugation moiety is linked to the antibody via a direct covalent bond. In certain embodiments, the conjugation moiety is linked to the antibody via a linker. In advantageous embodiments, the conjugation moiety or the linker is attached via one of the non-natural amino acids of the antibody. Exemplary conjugation moieties and linkers are discussed in the sections below. Non-natural amino acids

[00127] The non-natural amino acid can be any non-natural amino acid known to those of skill in the art. In some embodiments, the non-naturally encoded amino acid comprises a functional group. The functional group can be any functional group known to those of skill in the art. In certain embodiments the functional group is a label, a polar group, a non-polar group or a reactive group.

[00128] Reactive groups are particularly advantageous for linking further functional groups to the antibody at the site-specific position of the antibody chain. In certain embodiments, the reactive group is selected from the group consisting of amino, carboxy, acetyl, hydrazino, hydrazido, semicarbazido, sulfanyl, azido and alkynyl.

[00129] In certain embodiments, the amino acid residue is according to any of the following formulas: [Image disponible dans le document PDF, Image available in the PDF document] Those of skill in the art will recognize that antibodies are generally comprised of L-amino acids. However, with non-natural amino acids, the present methods and compositions provide the practitioner with the ability to use L-, D- or racemic non-natural amino acids at the site-specific positions. In certain embodiments, the non-natural amino acids described herein include D- versions of the natural amino acids and racemic versions of the natural amino acids.

[00130] In the above formulas, the wavy lines indicate bonds that connect to the remainder of the polypeptide chains of the antibodies. These non-natural amino acids can be incorporated into polypeptide chains just as natural amino acids are incorporated into the same polypeptide chains. In certain embodiments, the non-natural amino acids are incorporated into the polypeptide chain via amide bonds as indicated in the formulas.

[00131] In the above formulas R designates any functional group without limitation, so long as the amino acid residue is not identical to a natural amino acid residue. In certain embodiments, R can be a hydrophobic group, a hydrophilic group, a polar group, an acidic group, a basic group, a chelating group, a reactive group, a therapeutic moiety or a labeling moiety. In certain embodiments, R is selected from the group consisting of R<com:Sup>1< / com:Sup>NR<com:Sup>2< / com:Sup>R<com:Sup>3< / com:Sup>, <com:Math><semantics>R1C(=O)R2<annotation encoding="application / x-tex">R^{1}C(=O)R^{2}< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>R1C(=O)OR2<annotation encoding="application / x-tex">R^{1}C(=O)OR^{2}< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>R1N3<annotation encoding="application / x-tex">R^{1}N_{3}< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>R1C(≡CH)<annotation encoding="application / x-tex">R^{1}C(\equiv CH)< / annotation>< / semantics>< / com:Math>. In these embodiments, <com:Math><semantics>R1<annotation encoding="application / x-tex">R^{1}< / annotation>< / semantics>< / com:Math> is selected from the group consisting of a bond, alkylene, heteroalkylene, arylene, heteroarylene. R<com:Sup>2< / com:Sup> and R<com:Sup>3< / com:Sup> are each independently selected from the group consisting of hydrogen, alkyl and heteroalklyl.

[00132] In some embodiments, the non-naturally encoded amino acids include side chain functional groups that react efficiently and selectively with functional groups not found in the 20 common amino acids (including but not limited to, azido, ketone, aldehyde and aminooxy groups) to form stable conjugates. For example, antigen-binding polypeptide that includes a non-naturally encoded amino acid containing an azido functional group can be reacted with a polymer (including but not limited to, poly(ethylene glycol) or, alternatively, a second polypeptide containing an alkyne moiety to form a stable conjugate resulting for the selective reaction of the azide and the alkyne functional groups to form a Huisgen [3+2] cycloaddition product.

[00133] Exemplary non-naturally encoded amino acids that may be suitable for use in the present invention and that are useful for reactions with water soluble polymers include, but are not limited to, those with carbonyl, aminooxy, hydrazine, hydrazide, semicarbazide, azide and alkyne reactive groups. In some embodiments, non-naturally encoded amino acids comprise a saccharide moiety. Examples of such amino acids include N-acetyl-L- glucosaminyl-L-serine, N-acetyl-L-galactosaminyl-L-serine, N-acetyl-L-glucosaminyl-L- threonine, N-acetyl-L-glucosaminyl-L-asparagine and O-mannosaminyl-L-serine. Examples of such amino acids also include examples where the naturally-occurring N- or O-linkage between the amino acid and the saccharide is replaced by a covalent linkage not commonly found in nature—including but not limited to, an alkene, an oxime, a thioether, an amide and the like. Examples of such amino acids also include saccharides that are not commonly found in naturally-occurring proteins such as 2-deoxy-glucose, 2-deoxygalactose and the like.

[00134] Many of the non-naturally encoded amino acids provided herein are commercially available, e.g., from Sigma-Aldrich (St. Louis, Mo., USA), Novabiochem (a division of EMD Biosciences, Darmstadt, Germany), or Peptech (Burlington, Mass., USA). Those that are not commercially available are optionally synthesized as provided herein or using standard methods known to those of skill in the art. For organic synthesis techniques, see, e.g., Organic Chemistry by Fessendon and Fessendon, (1982, Second Edition, Willard Grant Press, Boston Mass.); Advanced Organic Chemistry by March (Third Edition, 1985, Wiley and Sons, New York); and Advanced Organic Chemistry by Carey and Sundberg (Third Edition, Parts A and B, 1990, Plenum Press, New York). See, also, U.S. Patent Application Publications 2003 / 0082575 and 2003 / 0108885. In addition to unnatural amino acids that contain novel side chains, unnatural amino acids that may be suitable for use in the present invention also optionally comprise modified backbone structures, including but not limited to, as illustrated by the structures of Formula II and III: [Image disponible dans le document PDF, Image available in the PDF document] [Image disponible dans le document PDF, Image available in the PDF document] CA wherein Z typically comprises OH, NH<com:Sub>2< / com:Sub>, SH, NH–R', or S–R'; X and Y, which can be the same or different, typically comprise S or O, and R and R', which are optionally the same or different, are typically selected from the same list of constituents for the R group described above for the unnatural amino acids having Formula I as well as hydrogen. For example, unnatural amino acids of the invention optionally comprise substitutions in the amino or carboxyl group as illustrated by Formulas II and III. Unnatural amino acids of this type include, but are not limited to, <com:Math><semantics>α<annotation encoding="application / x-tex">\alpha< / annotation>< / semantics>< / com:Math>-hydroxy acids, <com:Math><semantics>α<annotation encoding="application / x-tex">\alpha< / annotation>< / semantics>< / com:Math>-thioacids, <com:Math><semantics>α<annotation encoding="application / x-tex">\alpha< / annotation>< / semantics>< / com:Math>-aminothiocarboxylates, including but not limited to, with side chains corresponding to the common twenty natural amino acids or unnatural side chains. In addition, substitutions at the <com:Math><semantics>α<annotation encoding="application / x-tex">\alpha< / annotation>< / semantics>< / com:Math>-carbon optionally include, but are not limited to, L, D, or <com:Math><semantics>α<annotation encoding="application / x-tex">\alpha< / annotation>< / semantics>< / com:Math>-<com:Math><semantics>α<annotation encoding="application / x-tex">\alpha< / annotation>< / semantics>< / com:Math>-disubstituted amino acids such as D-glutamate, D- alanine, D-methyl-O-tyrosine, aminobutyric acid, and the like. Other structural alternatives include cyclic amino acids, such as proline analogues as well as 3, 4, 6, 7, 8, and 9 membered ring proline analogues, P and y amino acids such as substituted <com:Math><semantics>β<annotation encoding="application / x-tex">\beta< / annotation>< / semantics>< / com:Math>-alanine and <com:Math><semantics>γ<annotation encoding="application / x-tex">\gamma< / annotation>< / semantics>< / com:Math>-amino butyric acid.

[00135] Many unnatural amino acids are based on natural amino acids, such as tyrosine, glutamine, phenylalanine, and the like, and are suitable for use in the present invention. Tyrosine analogs include, but are not limited to, para-substituted tyrosines, ortho-substituted tyrosines, and meta substituted tyrosines, where the substituted tyrosine comprises, including but not limited to, a keto group (including but not limited to, an acetyl group), a benzoyl group, an amino group, a hydrazine, an hydroxyamine, a thiol group, a carboxy group, an isopropyl group, a methyl group, a <com:Math><semantics>C6<annotation encoding="application / x-tex">C_6< / annotation>< / semantics>< / com:Math>-<com:Math><semantics>C20<annotation encoding="application / x-tex">C_{20}< / annotation>< / semantics>< / com:Math> straight chain or branched hydrocarbon, a saturated or unsaturated hydrocarbon, an O-methyl group, a polyether group, a nitro group, an alkynyl group or the like. In addition, multiply substituted aryl rings are also contemplated. Glutamine analogs that may be suitable for use in the present invention include, but are not limited to, <com:Math><semantics>α<annotation encoding="application / x-tex">\alpha< / annotation>< / semantics>< / com:Math>-hydroxy derivatives, <com:Math><semantics>γ<annotation encoding="application / x-tex">\gamma< / annotation>< / semantics>< / com:Math>-substituted derivatives, cyclic derivatives, and amide substituted glutamine derivatives. Example phenylalanine analogs that may be suitable for use in the present invention include, but are not limited to, para-substituted phenylalanines, ortho-substituted phenyalanines, and meta-substituted phenylalanines, where the substituent comprises, including but not limited to, a hydroxy group, a methoxy group, a methyl group, an allyl group, an aldehyde, an azido, an iodo, a bromo, a keto group (including but not limited to, an acetyl group), a benzoyl, an alkynyl group, or the like. Specific examples of unnatural amino acids that may be suitable for use in the present invention include, but are not limited to, a p-acetyl-L-phenylalanine, an O-methyl-L-tyrosine, an L-3-(2- naphthyl)alanine, a 3-methyl-phenylalanine, an O-4-allyl-L-tyrosine, a 4-propyl-L-tyrosine, a tri-O-acetyl-GlcNAcβ-serine, an L-Dopa, a fluorinated phenylalanine, an isopropyl-L- phenylalanine, a p-azido-L-phenylalanine, a p-acyl-L-phenylalanine, a p-benzoyl-L- phenylalanine, an L-phosphoserine, a phosphonoserine, a phosphonotyrosine, a p-iodo- phenylalanine, a p-bromophenylalanine, a p-amino-L-phenylalanine, an isopropyl-L- phenylalanine, and a p-propargyloxy-phenylalanine, and the like. Examples of structures of a variety of unnatural amino acids that may be suitable for use in the present invention are provided in, for example, WO 2002 / 085923 entitled "In vivo incorporation of unnatural amino acids." See also Kiick et al., (2002) Incorporation of azides into recombinant proteins for chemoselective modification by the Staudinger ligation, PNAS 99:19-24, for additional methionine analogs.

[00136] Many of the unnatural amino acids suitable for use in the present invention are commercially available, e.g., from Sigma (USA) or Aldrich (Milwaukee, Wis., USA). Those that are not commercially available are optionally synthesized as provided herein or as provided in various publications or using standard methods known to those of skill in the art. For organic synthesis techniques, see, e.g., Organic Chemistry by Fessendon and Fessendon, (1982, Second Edition, Willard Grant Press, Boston Mass.); Advanced Organic Chemistry by March (Third Edition, 1985, Wiley and Sons, New York); and Advanced Organic Chemistry by Carey and Sundberg (Third Edition, Parts A and B, 1990, Plenum Press, New York). Additional publications describing the synthesis of unnatural amino acids include, e.g., WO 2002 / 085923 entitled "In vivo incorporation of Unnatural Amino Acids;" Matsoukas et al., (1995) J. Med. Chem., 38, 4660-4669; King, F. E. & Kidd, D. A. A. (1949) A New Synthesis of Glutamine and of γ-Dipeptides of Glutamic Acid from Phthylated Intermediates. J. Chem. Soc., 3315-3319; Friedman, O. M. & Chatterrji, R. (1959) Synthesis of Derivatives of Glutamine as Model Substrates for Anti-Tumor Agents. J. Am. Chem. Soc. 81, 3750-3752; Craig, J. C. et al. (1988) Absolute Configuration of the Enantiomers of 7-Chloro-4 [[4- (diethylamino)-1-methylbutyl]amino]quinoline (Chloroquine). J. Org. Chem. 53, 1167-1170; Azoulay, M., Vilmont, M. & Frappier, F. (1991) Glutamine analogues as Potential Antimalarials, Eur. J. Med. Chem. 26, 201-5; Koskinen, A. M. P. & Rapoport, H. (1989) Synthesis of 4-Substituted Prolines as Conformationally Constrained Amino Acid Analogues. J. Org. Chem. 54, 1859-1866; Christie, B. D. & Rapoport, H. (1985) Synthesis of Optically Pure Pipecolates from L-Asparagine. Application to the Total Synthesis of (+)-Apovincamine through Amino Acid Decarbonylation and Iminium Ion Cyclization. J. Org. Chem. 1989:1859-1866; Barton et al., (1987) Synthesis of Novel a-Amino-Acids and Derivatives Using Radical Chemistry: Synthesis of L- and D-a-Amino-Adipic Acids, L-a-aminopimelic Acid and Appropriate Unsaturated Derivatives. Tetrahedron Lett. 43:4297-4308; and, Subasinghe et al., (1992) Quisqualic acid analogues: synthesis of beta-heterocyclic 2- aminopropanoic acid derivatives and their activity at a novel quisqualate-sensitized site. J. Med. Chem. 35:4602-7. See also, patent applications entitled "Protein Arrays," filed Dec. 22, 2003, Ser. No. 10 / 744,899 and Ser. No. 60 / 435,821 filed on Dec. 22, 2002.

[00137] Amino acids with a carbonyl reactive group allow for a variety of reactions to link molecules (including but not limited to, PEG or other water soluble molecules) via nucleophilic addition or aldol condensation reactions among others.

[00138] Exemplary carbonyl-containing amino acids can be represented as follows: [Image disponible dans le document PDF, Image available in the PDF document] wherein n is 0-10; R<com:Sub>1< / com:Sub> is an alkyl, aryl, substituted alkyl, or substituted aryl; R<com:Sub>2< / com:Sub> is H, alkyl, aryl, substituted alkyl, and substituted aryl; and R<com:Sub>3< / com:Sub> is H, an amino acid, a polypeptide, or an amino terminus modification group, and R<com:Sub>4< / com:Sub> is H, an amino acid, a polypeptide, or a carboxy terminus modification group. In some embodiments, n is 1, R<com:Sub>1< / com:Sub> is phenyl and R<com:Sub>2< / com:Sub> is a simple alkyl (i.e., methyl, ethyl, or propyl) and the ketone moiety is positioned in the para position relative to the alkyl side chain. In some embodiments, n is 1, R<com:Sub>1< / com:Sub> is phenyl and R<com:Sub>2< / com:Sub> is a simple alkyl (i.e., methyl, ethyl, or propyl) and the ketone moiety is positioned in the meta position relative to the alkyl side chain.

[00139] In the present invention, a non-naturally encoded amino acid bearing adjacent hydroxyl and amino groups can be incorporated into the polypeptide as a "masked" aldehyde functionality. For example, 5-hydroxylysine bears a hydroxyl group adjacent to the epsilon amine. Reaction conditions for generating the aldehyde typically involve addition of molar excess of sodium metaperiodate under mild conditions to avoid oxidation at other sites within the polypeptide. The pH of the oxidation reaction is typically about 7.0. A typical reaction involves the addition of about 1.5 molar excess of sodium meta periodate to a buffered solution of the polypeptide, followed by incubation for about 10 minutes in the dark. See, e.g. U.S. Pat. No. 6,423,685.

[00140] The carbonyl functionality can be reacted selectively with a hydrazine-, hydrazide-, hydroxylamine-, or semicarbazide-containing reagent under mild conditions in aqueous solution to form the corresponding hydrazone, oxime, or semicarbazone linkages, respectively, that are stable under physiological conditions. See, e.g., Jencks, W. P., J. Am. Chem. Soc. 81, 475-481 (1959); Shao, J. and Tam, J. P., J. Am. Chem. Soc. 117:3893-3899 (1995). Moreover, the unique reactivity of the carbonyl group allows for selective modification in the presence of the other amino acid side chains. See, e.g., Cornish, V. W., et al., J. Am. Chem. Soc. 118:8150-8151 (1996); Geoghegan, K. F. & Stroh, J. G., Bioconjug. Chem. 3:138-146 (1992); Mahal, L. K., et al., Science 276:1125-1128 (1997).

[00141] Non-naturally encoded amino acids containing a nucleophilic group, such as a hydrazine, hydrazide or semicarbazide, allow for reaction with a variety of electrophilic groups to form conjugates (including but not limited to, with PEG or other water soluble polymers). 00142] Exemplary hydrazine, hydrazide or semicarbazide -containing amino acids can be represented as follows: [Image disponible dans le document PDF, Image available in the PDF document] wherein n is 0-10; R<com:Sub>1< / com:Sub> is an alkyl, aryl, substituted alkyl, or substituted aryl or not present; X, is O, N, or S or not present; R<com:Sub>2< / com:Sub> is H, an amino acid, a polypeptide, or an amino terminus modification group, and R<com:Sub>3< / com:Sub> is H, an amino acid, a polypeptide, or a carboxy terminus modification group.

[00143] In some embodiments, n is 4, <com:Math><semantics>R1<annotation encoding="application / x-tex">R_1< / annotation>< / semantics>< / com:Math> is not present, and X is N. In some embodiments, n is 2, R<com:Sub>1< / com:Sub> is not present, and X is not present. In some embodiments, n is 1, R<com:Sub>1< / com:Sub> is phenyl, X is O, and the oxygen atom is positioned para to the aliphatic group on the aryl ring.

[00144] Hydrazide-, hydrazine-, and semicarbazide-containing amino acids are available from commercial sources. For instance, L-glutamate-γ-hydrazide is available from Sigma Chemical (St. Louis, Mo.). Other amino acids not available commercially can be prepared by one skilled in the art. See, e.g., U.S. Pat. No. 6,281,211.

[00145] Polypeptides containing non-naturally encoded amino acids that bear hydrazide, hydrazine or semicarbazide functionalities can be reacted efficiently and selectively with a variety of molecules that contain aldehydes or other functional groups with similar chemical reactivity. See, e.g., Shao, J. and Tam, J., J. Am. Chem. Soc. 117:3893-3899 (1995). The unique reactivity of hydrazide, hydrazine and semicarbazide functional groups makes them significantly more reactive toward aldehydes, ketones and other electrophilic groups as compared to the nucleophilic groups present on the 20 common amino acids (including but not limited to, the hydroxyl group of serine or threonine or the amino groups of lysine and the N-terminus).

[00146] Non-naturally encoded amino acids containing an aminooxy (also called a hydroxylamine) group allow for reaction with a variety of electrophilic groups to form conjugates (including but not limited to, with PEG or other water soluble polymers). Like hydrazines, hydrazides and semicarbazides, the enhanced nucleophilicity of the aminooxy group permits it to react efficiently and selectively with a variety of molecules that contain aldehydes or other functional groups with similar chemical reactivity. See, e.g., Shao, J. and Tam, J., J. Am. Chem. Soc. 117:3893-3899 (1995); H. Hang and C. Bertozzi, Acc. Chem. Res. 34: 727-736 (2001). Whereas the result of reaction with a hydrazine group is the corresponding hydrazone, however, an oxime results generally from the reaction of an aminooxy group with a carbonyl-containing group such as a ketone.

[00147] Exemplary amino acids containing aminooxy groups can be represented as follows: [Image disponible dans le document PDF, Image available in the PDF document] wherein n is 0-10; R<com:Sub>1< / com:Sub> is an alkyl, aryl, substituted alkyl, or substituted aryl or not present; X is O, N, S or not present; m is 0-10; <com:Math><semantics>Y=C(O)<annotation encoding="application / x-tex">Y=C(O)< / annotation>< / semantics>< / com:Math> or not present; <com:Math><semantics>R2<annotation encoding="application / x-tex">R_2< / annotation>< / semantics>< / com:Math> is H, an amino acid, a polypeptide, or an amino terminus modification group, and R<com:Sub>3< / com:Sub> is H, an amino acid, a polypeptide, or a carboxy terminus modification group. In some embodiments, n is 1, R<com:Sub>1< / com:Sub> is phenyl, X is O, m is 1, and Y is present. In some embodiments, n is 2, R<com:Sub>1< / com:Sub> and X are not present, m is 0, and Y is not present.

[00148] Aminooxy-containing amino acids can be prepared from readily available amino acid precursors (homoserine, serine and threonine). See, e.g., M. Carrasco and R. Brown, J. Org. Chem. 68: 8853-8858 (2003). Certain aminooxy-containing amino acids, such as L-2- amino-4-(aminooxy)butyric acid), have been isolated from natural sources (Rosenthal, G. et al., Life Sci. 60: 1635-1641 (1997). Other aminooxy-containing amino acids can be prepared by one skilled in the art.

[00149] The unique reactivity of azide and alkyne functional groups makes them extremely useful for the selective modification of polypeptides and other biological molecules. Organic azides, particularly alphatic azides, and alkynes are generally stable toward common reactive chemical conditions. In particular, both the azide and the alkyne functional groups are inert toward the side chains (i.e., R groups) of the 20 common amino acids found in naturally-occurring polypeptides. When brought into close proximity, however, the "spring-loaded" nature of the azide and alkyne groups is revealed and they react selectively and efficiently via Huisgen [3+2] cycloaddition reaction to generate the corresponding triazole. See, e.g., Chin J., et al., Science 301:964-7 (2003); Wang, Q., et al., J. Am. Chem. Soc. 125, 3192-3193 (2003); Chin, J. W., et al., J. Am. Chem. Soc. 124:9026- 9027 (2002).

[00150] Because the Huisgen cycloaddition reaction involves a selective cycloaddition reaction (see, e.g., Padwa, A., in COMPREHENSIVE ORGANIC SYNTHESIS, Vol. 4, (ed. Trost, B. M., 1991), p. 1069-1109; Huisgen, R. in 1,3-DIPOLAR CYCLOADDITION CHEMISTRY, (ed. Padwa, A., 1984), p. 1-176) rather than a nucleophilic substitution, the incorporation of non-naturally encoded amino acids bearing azide and alkyne-containing side chains permits the resultant polypeptides to be modified selectively at the position of the non- naturally encoded amino acid. Cycloaddition reaction involving azide or alkyne-containing antibody can be carried out at room temperature under aqueous conditions by the addition of Cu(II) (including but not limited to, in the form of a catalytic amount of CuSO<com:Sub>4< / com:Sub>) in the presence of a reducing agent for reducing Cu(II) to Cu(I), in situ, in catalytic amount. See, e.g., Wang, Q., et al., J. Am. Chem. Soc. 125, 3192-3193 (2003); Tornoe, C. W., et al., J. Org. Chem. 67:3057-3064 (2002); Rostovtsev, et al., Angew. Chem. Int. Ed. 41:2596-2599 (2002). Exemplary reducing agents include, including but not limited to, ascorbate, metallic copper, quinine, hydroquinone, vitamin K, glutathione, cysteine, Fe<com:Sup>2+< / com:Sup>, Co<com:Sup>2+< / com:Sup>, and an applied electric potential.

[00151] In some cases, where a Huisgen [3+2] cycloaddition reaction between an azide and an alkyne is desired, the antigen-binding polypeptide comprises a non-naturally encoded amino acid comprising an alkyne moiety and the water soluble polymer to be attached to the amino acid comprises an azide moiety. Alternatively, the converse reaction (i.e., with the azide moiety on the amino acid and the alkyne moiety present on the water soluble polymer) can also be performed.

[00152] The azide functional group can also be reacted selectively with a water soluble polymer containing an aryl ester and appropriately functionalized with an aryl phosphine moiety to generate an amide linkage. The aryl phosphine group reduces the azide in situ and the resulting amine then reacts efficiently with a proximal ester linkage to generate the corresponding amide. See, e.g., E. Saxon and C. Bertozzi, Science 287, 2007-2010 (2000). The azide-containing amino acid can be either an alkyl azide (including but not limited to, 2- amino-6-azido-1-hexanoic acid) or an aryl azide (p-azido-phenylalanine).

[00153] Exemplary water soluble polymers containing an aryl ester and a phosphine moiety can be represented as follows: [Image disponible dans le document PDF, Image available in the PDF document] wherein X can be O, N, S or not present, Ph is phenyl, W is a water soluble polymer and R can be H, alkyl, aryl, substituted alkyl and substituted aryl groups. Exemplary R groups include but are not limited to <com:Math><semantics>−CH2<annotation encoding="application / x-tex">-CH_2< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(CH3)3<annotation encoding="application / x-tex">-C(CH_3)_3< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−OR′<annotation encoding="application / x-tex">-OR'< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−NR′R″<annotation encoding="application / x-tex">-NR'R''< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−SR′<annotation encoding="application / x-tex">-SR'< / annotation>< / semantics>< / com:Math>, -halogen, <com:Math><semantics>−C(O)R′<annotation encoding="application / x-tex">-C(O)R'< / annotation>< / semantics>< / com:Math>, - CONR'R", -S(O)<com:Sub>2< / com:Sub>R', -S(O)<com:Sub>2< / com:Sub>NR'R", -CN and -NO<com:Sub>2< / com:Sub>. R', R", R" and R"" each independently refer to hydrogen, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, including but not limited to, aryl substituted with 1-3 halogens, substituted or unsubstituted alkyl, alkoxy or thioalkoxy groups, or arylalkyl groups. When a compound of the invention includes more than one R group, for example, each of the R groups is independently selected as are each R', R", R" and R" groups when more than one of these groups is present. When R' and R" are attached to the same nitrogen atom, they can be combined with the nitrogen atom to form a 5-, 6-, or 7-membered ring. For example, -NR'R" is meant to include, but not be limited to, 1-pyrrolidinyl and 4-morpholinyl. From the above discussion of substituents, one of skill in the art will understand that the term "alkyl" is meant to include groups including carbon atoms bound to groups other than hydrogen groups, such as haloalkyl (including but not limited to, -CF<com:Sub>3< / com:Sub> and -CH<com:Sub>2< / com:Sub>CF<com:Sub>3< / com:Sub>) and acyl (including but not limited to, - <com:Math><semantics>C(O)CH3<annotation encoding="application / x-tex">C(O)CH_3< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(O)CF3<annotation encoding="application / x-tex">-C(O)CF_3< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(O)CH2OCH3<annotation encoding="application / x-tex">-C(O)CH_2OCH_3< / annotation>< / semantics>< / com:Math>, and the like).

[00154] The azide functional group can also be reacted selectively with a water soluble polymer containing a thioester and appropriately functionalized with an aryl phosphine moiety to generate an amide linkage. The aryl phosphine group reduces the azide in situ and the resulting amine then reacts efficiently with the thioester linkage to generate the corresponding amide. Exemplary water soluble polymers containing a thioester and a phosphine moiety can be represented as follows: [Image disponible dans le document PDF, Image available in the PDF document] wherein n is 1-10; X can be O, N, S or not present, Ph is phenyl, and W is a water soluble polymer.

[00155] Exemplary alkyne-containing amino acids can be represented as follows: [Image disponible dans le document PDF, Image available in the PDF document] wherein n is 0-10; R<com:Sub>1< / com:Sub> is an alkyl, aryl, substituted alkyl, or substituted aryl or not present; X is O, N, S or not present; m is 0-10, R<com:Sub>2< / com:Sub> is H, an amino acid, a polypeptide, or an amino terminus modification group, and R<com:Sub>3< / com:Sub> is H, an amino acid, a polypeptide, or a carboxy terminus modification group. In some embodiments, n is 1, R<com:Sub>1< / com:Sub> is phenyl, X is not present, m is 0 and the acetylene moiety is positioned in the para position relative to the alkyl side chain. In some embodiments, n is 1, R<com:Sub>1< / com:Sub> is phenyl, X is O, m is 1 and the propargyloxy group is positioned in the para position relative to the alkyl side chain (i.e., O-propargyl-tyrosine). In some embodiments, n is 1, R<com:Sub>1< / com:Sub> and X are not present and m is 0 (i.e., proparylglycine).

[00156] Alkyne-containing amino acids are commercially available. For example, propargylglycine is commercially available from Peptech (Burlington, Mass.). Alternatively, alkyne-containing amino acids can be prepared according to standard methods. For instance, p-propargyloxyphenylalanine can be synthesized, for example, as described in Deiters, A., et al., J. Am. Chem. Soc. 125: 11782-11783 (2003), and 4-alkynyl-L-phenylalanine can be synthesized as described in Kayser, B., et al., Tetrahedron 53(7): 2475-2484 (1997). Other alkyne-containing amino acids can be prepared by one skilled in the art.

[00157] Exemplary azide-containing amino acids can be represented as follows: [Image disponible dans le document PDF, Image available in the PDF document] wherein n is <com:Math><semantics>0−10<annotation encoding="application / x-tex">0-10< / annotation>< / semantics>< / com:Math>; <com:Math><semantics>R1<annotation encoding="application / x-tex">R_1< / annotation>< / semantics>< / com:Math> is an alkyl, aryl, substituted alkyl, substituted aryl or not present; X is O, N, S or not present; m is 0-10; R<com:Sub>2< / com:Sub> is H, an amino acid, a polypeptide, or an amino terminus modification group, and R<com:Sub>3< / com:Sub> is H, an amino acid, a polypeptide, or a carboxy terminus modification group. In some embodiments, n is 1, R<com:Sub>1< / com:Sub> is phenyl, X is not present, m is 0 and the azide moiety is positioned para to the alkyl side chain. In some embodiments, n is 0-4 and <com:Math><semantics>R1<annotation encoding="application / x-tex">R_1< / annotation>< / semantics>< / com:Math> and X are not present, and m=0. In some embodiments, n is 1, <com:Math><semantics>R1<annotation encoding="application / x-tex">R_1< / annotation>< / semantics>< / com:Math> is phenyl, X is O, m is 2 and the P-azidoethoxy moiety is positioned in the para position relative to the alkyl side chain.

[00158] Azide-containing amino acids are available from commercial sources. For instance, 4-azidophenylalanine can be obtained from Chem-Impex International, Inc. (Wood Dale, Ill.). For those azide-containing amino acids that are not commercially available, the azide group can be prepared relatively readily using standard methods known to those of skill in the art, including but not limited to, via displacement of a suitable leaving group (including but not limited to, halide, mesylate, tosylate) or via opening of a suitably protected lactone. See, e.g., Advanced Organic Chemistry by March (Third Edition, 1985, Wiley and Sons, New York).

[00159] The unique reactivity of beta-substituted aminothiol functional groups makes them extremely useful for the selective modification of polypeptides and other biological molecules that contain aldehyde groups via formation of the thiazolidine. See, e.g., J. Shao and J. Tam, J. Am. Chem. Soc. 1995, 117 (14) 3893-3899. In some embodiments, beta- substituted aminothiol amino acids can be incorporated into antibodies and then reacted with water soluble polymers comprising an aldehyde functionality. In some embodiments, a water soluble polymer, drug conjugate or other payload can be coupled to an antibody polypeptide comprising a beta-substituted aminothiol amino acid via formation of the thiazolidine.

[00160] Particular examples of useful non-natural amino acids include, but are not limited to, p-acetyl-L-phenylalanine, O-methyl-L-tyrosine, L-3-(2-naphthyl)alanine, 3-methyl- phenylalanine, O-4-allyl-L-tyrosine, 4-propyl-L-tyrosine, tri-O-acetyl-GlcNAc b-serine, L- Dopa, fluorinated phenylalanine, isopropyl-L-phenylalanine, p-azido-L-phenylalanine, p- acyl-L-phenylalanine, p-benzoyl-L-phenylalanine, L-phosphoserine, phosphonoserine, phosphonotyrosine, p-iodo-phenylalanine, p-bromophenylalanine, p-amino-L-phenylalanine, isopropyl-L-phenylalanine, and p-propargyloxy-phenylalanine. Further useful examples include N-acetyl-L-glucosaminyl-L-serine, N-acetyl-L-galactosaminyl-L-serine, N-acetyl-L- glucosaminyl-L-threonine, N-acetyl-L-glucosaminyl-L-asparagine and O-mannosaminyl-L- serine.

[00161] In particular embodiments, the non-natural amino acids are selected from p- acetyl- phenylalanine, p-ethynyl-phenylalanine, p-propargyloxyphenylalanine, and p-azido- phenylalanine. One particularly useful non-natural amino acid is p-azido phenylalanine. This amino acid residue is known to those of skill in the art to facilitate Huisgen [3+2] cyloaddition reactions (so-called "click" chemistry reactions) with, for example, compounds bearing alkynyl groups. This reaction enables one of skill in the art to readily and rapidly conjugate to the antibody at the site-specific location of the non-natural amino acid.

[00162] In certain embodiments, the first reactive group is an alkynyl moiety (including but not limited to, in the unnatural amino acid p-propargyloxyphenylalanine, where the propargyl group is also sometimes referred to as an acetylene moiety) and the second reactive group is an azido moiety, and [3+2] cycloaddition chemistry can be used. In certain embodiments, the first reactive group is the azido moiety (including but not limited to, in the unnatural amino acid p-azido-L-phenylalanine) and the second reactive group is the alkynyl moiety.

[00163] In the above formulas, each L represents a divalent linker. The divalent linker can be any divalent linker known to those of skill in the art. Generally, the divalent linker is capable of forming covalent bonds to the functional moiety R and the alpha carbon of the non-natural amino acid. Useful divalent linkers a bond, alkylene, substituted alkylene, heteroalkylene, substituted heteroalkylene, arylene, substituted arylene, heteroarlyene and substituted heteroarylene. In certain embodiments, L is <com:Math><semantics>C1−10<annotation encoding="application / x-tex">C_{1-10}< / annotation>< / semantics>< / com:Math> alkylene or <com:Math><semantics>C1−10<annotation encoding="application / x-tex">C_{1-10}< / annotation>< / semantics>< / com:Math> heteroalkylene.

[00164] The non-natural amino acids used in the methods and compositions described herein have at least one of the following four properties: (1) at least one functional group on the sidechain of the non-natural amino acid has at least one characteristics and / or activity and / or reactivity orthogonal to the chemical reactivity of the 20 common, genetically- encoded amino acids (i.e., alanine, arginine, asparagine, aspartic acid, cysteine, glutamine, glutamic acid, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, and valine), or at least orthogonal to the chemical reactivity of the naturally occurring amino acids present in the polypeptide that includes the non-natural amino acid; (2) the introduced non-natural amino acids are substantially chemically inert toward the 20 common, genetically-encoded amino acids; (3) the non-natural amino acid can be stably incorporated into a polypeptide, preferably with the stability commensurate with the naturally-occurring amino acids or under typical physiological conditions, and further preferably such incorporation can occur via an in vivo system; and (4) the non-natural amino acid includes an oxime functional group or a functional group that can be transformed into an oxime group by reacting with a reagent, preferably under conditions that do not destroy the biological properties of the polypeptide that includes the non-natural amino acid (unless of course such a destruction of biological properties is the purpose of the modification / transformation), or where the transformation can occur under aqueous conditions at a pH between about 4 and about 8, or where the reactive site on the non-natural amino acid is an electrophilic site. Illustrative, non-limiting examples of amino acids that satisfy these four properties for non-natural amino acids that can be used with the compositions and methods described herein are presented in FIGS. 2, 3, 35 and 40- 43. Any number of non-natural amino acids can be introduced into the polypeptide. Non- natural amino acids may also include protected or masked oximes or protected or masked groups that can be transformed into an oxime group after deprotection of the protected group or unmasking of the masked group. Non-natural amino acids may also include protected or masked carbonyl or dicarbonyl groups, which can be transformed into a carbonyl or dicarbonyl group after deprotection of the protected group or unmasking of the masked group and thereby are available to react with hydroxylamines or oximes to form oxime groups.

[00165] In further embodiments, non-natural amino acids that may be used in the methods and compositions described herein include, but are not limited to, amino acids comprising a photoactivatable cross-linker, spin-labeled amino acids, fluorescent amino acids, metal binding amino acids, metal-containing amino acids, radioactive amino acids, amino acids with novel functional groups, amino acids that covalently or non-covalently interact with other molecules, photocaged and / or photoisomerizable amino acids, amino acids comprising biotin or a biotin analogue, glycosylated amino acids such as a sugar substituted serine, other carbohydrate modified amino acids, keto-containing amino acids, aldehyde-containing amino acids, amino acids comprising polyethylene glycol or other polyethers, heavy atom substituted amino acids, chemically cleavable and / or photocleavable amino acids, amino acids with an elongated side chains as compared to natural amino acids, including but not limited to, polyethers or long chain hydrocarbons, including but not limited to, greater than about 5 or greater than about 10 carbons, carbon-linked sugar-containing amino acids, redox- active amino acids, amino thioacid containing amino acids, and amino acids comprising one or more toxic moiety.

[00166] In some embodiments, non-natural amino acids comprise a saccharide moiety. Examples of such amino acids include N-acetyl-L-glucosaminyl-L-serine, N-acetyl-L- galactosaminyl-L-serine, N-acetyl-L-glucosaminyl-L-threonine, N-acetyl-L-glucosaminyl-L- asparagine and O-mannosaminyl-L-serine. Examples of such amino acids also include examples where the naturally-occurring N- or O-linkage between the amino acid and the saccharide is replaced by a covalent linkage not commonly found in nature—including but not limited to, an alkene, an oxime, a thioether, an amide and the like. Examples of such amino acids also include saccharides that are not commonly found in naturally-occurring proteins such as 2-deoxy-glucose, 2-deoxygalactose and the like.

[00167] The chemical moieties incorporated into antibodies via incorporation of non- natural amino acids offer a variety of advantages and manipulations of polypeptides. For example, the unique reactivity of a carbonyl or dicarbonyl functional group (including a keto- or aldehyde-functional group) allows selective modification of antibodies with any of a number of hydrazine- or hydroxylamine-containing reagents in vivo and in vitro. A heavy atom non-natural amino acid, for example, can be useful for phasing x-ray structure data. The site-specific introduction of heavy atoms using non-natural amino acids also provides selectivity and flexibility in choosing positions for heavy atoms. Photoreactive non-natural amino acids (including but not limited to, amino acids with benzophenone and arylazides (including but not limited to, phenylazide) side chains), for example, allow for efficient in vivo and in vitro photocrosslinking of polypeptides. Examples of photoreactive non-natural amino acids include, but are not limited to, p-azido-phenylalanine and p-benzoyl- phenylalanine. The antibodies with the photoreactive non-natural amino acids may then be crosslinked at will by excitation of the photoreactive group-providing temporal control. In a non-limiting example, the methyl group of a non-natural amino can be substituted with an isotopically labeled, including but not limited to, with a methyl group, as a probe of local structure and dynamics, including but not limited to, with the use of nuclear magnetic resonance and vibrational spectroscopy.

[00168] Amino acids with an electrophilic reactive group allow for a variety of reactions to link molecules via various chemical reactions, including, but not limited to, nucleophilic addition reactions. Such electrophilic reactive groups include a carbonyl- or dicarbonyl-group (including a keto- or aldehyde group), a carbonyl-like- or dicarbonyl-like-group (which has reactivity similar to a carbonyl- or dicarbonyl-group and is structurally similar to a carbonyl- or dicarbonyl-group), a masked carbonyl- or masked dicarbonyl-group (which can be readily converted into a carbonyl- or dicarbonyl-group), or a protected carbonyl- or protected dicarbonyl-group (which has reactivity similar to a carbonyl- or dicarbonyl-group upon deprotection). Such amino acids include amino acids having the structure of Formula (I): [Image disponible dans le document PDF, Image available in the PDF document] wherein: A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene; B is optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -O-, -O-(alkylene or substituted alkylene)—, <com:Math><semantics>−S<annotation encoding="application / x-tex">-S< / annotation>< / semantics>< / com:Math>—, <com:Math><semantics>−S<annotation encoding="application / x-tex">-S< / annotation>< / semantics>< / com:Math>—(alkylene or substituted alkylene)—, <com:Math><semantics>−S(O)k<annotation encoding="application / x-tex">-S(O)_k< / annotation>< / semantics>< / com:Math>— where k is 1, 2, or 3, <com:Math><semantics>−S(O)k<annotation encoding="application / x-tex">-S(O)_k< / annotation>< / semantics>< / com:Math>(alkylene or substituted alkylene)-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−NS(O)2<annotation encoding="application / x-tex">-NS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−OS(O)2<annotation encoding="application / x-tex">-OS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>- (alkylene or substituted alkylene)-, -C(S)-, -C(S)-(alkylene or substituted alkylene)-, - N(R')-, -NR'-(alkylene or substituted alkylene)-, -C(O)N(R')-, -CON(R')-(alkylene or substituted alkylene)-, -CSN(R')-, -CSN(R')-(alkylene or substituted alkylene)-, - <com:Math><semantics>N(R′)CO<annotation encoding="application / x-tex">N(R')CO< / annotation>< / semantics>< / com:Math>—(alkylene or substituted alkylene)—, <com:Math><semantics>−N(R′)C(O)O<annotation encoding="application / x-tex">-N(R')C(O)O< / annotation>< / semantics>< / com:Math>—, <com:Math><semantics>−S(O)kN(R′)<annotation encoding="application / x-tex">-S(O)_kN(R')< / annotation>< / semantics>< / com:Math>—, — <com:Math><semantics>N(R′)C(O)N(R′)−,−N(R′)C(S)N(R′)−,−N(R′)S(O)kN(R′)−,−N(R′)−N=,−C(R′)=N−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,<annotation encoding="application / x-tex">N(R')C(O)N(R')-, -N(R')C(S)N(R')-, -N(R')S(O)_kN(R')-, -N(R')-N=, -C(R')=N-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-,< / annotation>< / semantics>< / com:Math> <com:Math><semantics>C(R′)=N−N(R′)−<annotation encoding="application / x-tex">C(R')=N-N(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)=N−N=<annotation encoding="application / x-tex">-C(R')=N-N=< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)2−N=N−<annotation encoding="application / x-tex">-C(R')_2-N=N-< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−C(R′)2−N(R′)−N(R′)−<annotation encoding="application / x-tex">-C(R')_2-N(R')-N(R')-< / annotation>< / semantics>< / com:Math>, where each R' is independently H, alkyl, or substituted alkyl; J is [Image disponible dans le document PDF, Image available in the PDF document] R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; each R" is independently H, alkyl, substituted alkyl, or a protecting group, or when more than one R" group is present, two R" optionally form a heterocycloalkyl; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; each of R<com:Sub>3< / com:Sub> and R<com:Sub>4< / com:Sub> is independently H, halogen, lower alkyl, or substituted lower alkyl, or R<com:Sub>3< / com:Sub> and R<com:Sub>4< / com:Sub> or two R<com:Sub>3< / com:Sub> groups optionally form a cycloalkyl or a heterocycloalkyl; or the -A-B-J-R groups together form a bicyclic or tricyclic cycloalkyl or heterocycloalkyl comprising at least one carbonyl group, including a dicarbonyl group, protected carbonyl group, including a protected dicarbonyl group, or masked carbonyl group, including a masked dicarbonyl group; or the -J-R group together forms a monocyclic or bicyclic cycloalkyl or heterocycloalkyl comprising at least one carbonyl group, including a dicarbonyl group, protected carbonyl group, including a protected dicarbonyl group, or masked carbonyl group, including a masked dicarbonyl group; with a proviso that when A is phenylene and each R<com:Sub>3< / com:Sub> is H, B is present; and that when A is –(CH<com:Sub>2< / com:Sub>)<com:Sub>4< / com:Sub>– and each R<com:Sub>3< / com:Sub> is H, B is not –NHC(O)(CH<com:Sub>2< / com:Sub>CH<com:Sub>2< / com:Sub>)–; and that when A and B are absent and each R<com:Sub>3< / com:Sub> is H, R is not methyl. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00169] In certain embodiments, compounds of Formula (I) are stable in aqueous solution for at least 1 month under mildly acidic conditions. In certain embodiments, compounds of Formula (I) are stable for at least 2 weeks under mildly acidic conditions. In certain embodiments, compound of Formula (I) are stable for at least 5 days under mildly acidic conditions. In certain embodiments, such acidic conditions are pH 2 to 8.

[00170] In certain embodiments of compounds of Formula (I), B is lower alkylene, substituted lower alkylene, -O-(alkylene or substituted alkylene)-, -C(R')=N-N(R')-, - <com:Math><semantics>N(R′)CO−,−C(O)−,−C(R′)=N−,−C(O)−(alkyleneorsubstitutedalkylene)−,−CON(R′)−<annotation encoding="application / x-tex">N(R')CO-, -C(O)-, -C(R')=N-, -C(O)-(alkylene or substituted alkylene)-, -CON(R')-< / annotation>< / semantics>< / com:Math> (alkylene or substituted alkylene)—, —S(alkylene or substituted alkylene)—, —S(O)(alkylene or substituted alkylene)—, or –S(O)<com:Sub>2< / com:Sub>(alkylene or substituted alkylene)—. In certain embodiments of compounds of Formula (I), B is -O(CH<com:Sub>2< / com:Sub>)-, -CH=N-, -CH=N-NH-, -NHCH<com:Sub>2< / com:Sub>-, - <com:Math><semantics>NHCO−,−C(O)−,−C(O)−(CH2)−,−CONH−(CH2)−,−SCH2−,−S(=O)CH2−,or−S(O)2CH2−.<annotation encoding="application / x-tex">NHCO-, -C(O)-, -C(O)-(CH_2)-, -CONH-(CH_2)-, -SCH_2-, -S(=O)CH_2-, or -S(O)_2CH_2-.< / annotation>< / semantics>< / com:Math> In certain embodiments of compounds of Formula (I), R is C<com:Sub>1< / com:Sub>-6 alkyl or cycloalkyl. In certain embodiments of compounds of Formula (I) R is -CH<com:Sub>3< / com:Sub>, -CH(CH<com:Sub>3< / com:Sub>)<com:Sub>2< / com:Sub>, or cyclopropyl. In certain embodiments of compounds of Formula (I), R<com:Sub>1< / com:Sub> is H, tert-butyloxycarbonyl (Boc), 9- Fluorenylmethoxycarbonyl (Fmoc), N-acetyl, tetrafluoroacetyl (TFA), or benzyloxycarbonyl (Cbz). In certain embodiments of compounds of Formula (I), <com:Math><semantics>R1<annotation encoding="application / x-tex">R_1< / annotation>< / semantics>< / com:Math> is a resin, amino acid, polypeptide, or polynucleotide. In certain embodiments of compounds of Formula (I), R<com:Sub>2< / com:Sub> is OH, O-methyl, O-ethyl, or O-t-butyl. In certain embodiments of compounds of Formula (I), R<com:Sub>2< / com:Sub> is a resin, amino acid, polypeptide, or polynucleotide. In certain embodiments of compounds of Formula (I), R<com:Sub>2< / com:Sub> is a polynucleotide. In certain embodiments of compounds of Formula (I), R<com:Sub>2< / com:Sub> is ribonucleic acid (RNA). In certain embodiments of compounds of Formula (I), R<com:Sub>2< / com:Sub> is tRNA. In certain embodiments of compounds of Formula (I), the tRNA specifically recognizes a selector codon. In certain embodiments of compounds of Formula (I) the selector codon is selected from the group consisting of an amber codon, ochre codon, opal codon, a unique codon, a rare codon, an unnatural codon, a five-base codon, and a four-base codon. In certain embodiments of compounds of Formula (I), R<com:Sub>2< / com:Sub> is a suppressor tRNA.

[00171] In certain embodiments of compounds of Formula (I), [Image disponible dans le document PDF, Image available in the PDF document] is selected from the group consisting of: (i) A is substituted lower alkylene, C<com:Sub>4< / com:Sub>-arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene; B is optional, and when present is a divalent linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, -O-, -O-(alkylene or substituted alkylene)-, -S-, <com:Math><semantics>−S(O)<annotation encoding="application / x-tex">-S(O)< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−S(O)<annotation encoding="application / x-tex">-S(O)< / annotation>< / semantics>< / com:Math><com:Sub>2< / com:Sub>, <com:Math><semantics>−NS(O)<annotation encoding="application / x-tex">-NS(O)< / annotation>< / semantics>< / com:Math><com:Sub>2< / com:Sub>, <com:Math><semantics>−OS(O)<annotation encoding="application / x-tex">-OS(O)< / annotation>< / semantics>< / com:Math><com:Sub>2< / com:Sub>, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-(alkylene or substituted alkylene), <com:Math><semantics>−C(S)<annotation encoding="application / x-tex">-C(S)< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)<annotation encoding="application / x-tex">-N(R')< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(O)N(R′)<annotation encoding="application / x-tex">-C(O)N(R')< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−CON(R′)<annotation encoding="application / x-tex">-CON(R')< / annotation>< / semantics>< / com:Math>-(alkylene or substituted alkylene)-, <com:Math><semantics>−CSN(R′)<annotation encoding="application / x-tex">-CSN(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−CSN(R′)<annotation encoding="application / x-tex">-CSN(R')< / annotation>< / semantics>< / com:Math> N(R')CO-(alkylene or substituted alkylene)-, -N(R')C(O)O-, -N(R')C(S)-, -S(O)N(R'), - <com:Math><semantics>S(O)2N(R′)<annotation encoding="application / x-tex">S(O)_2N(R')< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)C(O)N(R′)<annotation encoding="application / x-tex">-N(R')C(O)N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)C(S)N(R′)<annotation encoding="application / x-tex">-N(R')C(S)N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)S(O)N(R′)<annotation encoding="application / x-tex">-N(R')S(O)N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)S(O)2N(R′)<annotation encoding="application / x-tex">-N(R')S(O)_2N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)S(O)2N(R′)<annotation encoding="application / x-tex">-N(R')S(O)_2N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)S(O)2N(R′)<annotation encoding="application / x-tex">-N(R')S(O)_2N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)S(O)2N(R′)<annotation encoding="application / x-tex">-N(R')S(O)_2N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)S(O)2N(R′)<annotation encoding="application / x-tex">-N(R')S(O)_2N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)S(O)2N(R′)<annotation encoding="application / x-tex">-N(R')S(O)_2N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)S(O)2N<annotation encoding="application / x-tex">-N(R')S(O)_2N< / annotation>< / semantics>< / com:Math> [Image disponible dans le document PDF, Image available in the PDF document] (ii) A is optional, and when present is substituted lower alkylene, C<com:Sub>4< / com:Sub>—arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene; B is a divalent linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, <com:Math><semantics>−O<annotation encoding="application / x-tex">-O< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−O<annotation encoding="application / x-tex">-O< / annotation>< / semantics>< / com:Math>-(alkylene or substituted alkylene)-, <com:Math><semantics>−S<annotation encoding="application / x-tex">-S< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−S(O)<annotation encoding="application / x-tex">-S(O)< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−S(O)<annotation encoding="application / x-tex">-S(O)< / annotation>< / semantics>< / com:Math>2-, <com:Math><semantics>−NS(O)<annotation encoding="application / x-tex">-NS(O)< / annotation>< / semantics>< / com:Math>2-, <com:Math><semantics>−OS(O)<annotation encoding="application / x-tex">-OS(O)< / annotation>< / semantics>< / com:Math>2-, <com:Math><semantics>−OS(O)<annotation encoding="application / x-tex">-OS(O)< / annotation>< / semantics>< / com:Math>2-, <com:Math><semantics>−OS(O)<annotation encoding="application / x-tex">-OS(O)< / annotation>< / semantics>< / com:Math>2-, <com:Math><semantics>−OS(O)<annotation encoding="application / x-tex">-OS(O)< / annotation>< / semantics>< / com:Math>2-, <com:Math><semantics>−OS(O)<annotation encoding="application / x-tex">-OS(O)< / annotation>< / semantics>< / com:Math>2-, <com:Math><semantics>−OS(O)<annotation encoding="application / x-tex">-OS(O)< / annotation>< / semantics>< / com:Math>2-, <com:Math><semantics>−OS(O)<annotation encoding="application / x-tex">-OS(O)< / annotation>< / semantics>< / com:Math>2-, <com:Math><semantics>−OS(O)<annotation encoding="application / x-tex">-OS(O)< / annotation>< / semantics>< / com:Math>2-, <com:Math><semantics>−OS(O)<annotation encoding="application / x-tex">-OS(O)< / annotation>< / semantics>< / com:Math>2-, <com:Math><semantics>−OS(O)<annotation encoding="application / x-tex">-OS(O)< / annotation>< / semantics>< / com:Math>2-, <com:Math><semantics>−OS(O)<annotation encoding="application / x-tex">-OS(O)< / annotation>< / semantics>< / com:Math>2-, C(O)-, -C(O)-(alkylene or substituted alkylene)-, -C(S)-, -N(R')-, -C(O)N(R')-, - CON(R')–(alkylene or substituted alkylene)–, –CSN(R')–, –N(R')CO–(alkylene or substituted alkylene)-, <com:Math><semantics>−N(R′)C(O)O<annotation encoding="application / x-tex">-N(R')C(O)O< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)C(S)<annotation encoding="application / x-tex">-N(R')C(S)< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−S(O)N(R′)<annotation encoding="application / x-tex">-S(O)N(R')< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−S(O)2N(R′)<annotation encoding="application / x-tex">-S(O)_2N(R')< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)C(O)N(R′)<annotation encoding="application / x-tex">-N(R')C(O)N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−<annotation encoding="application / x-tex">-< / annotation>< / semantics>< / com:Math> <com:Math><semantics>N(R′)C(S)N(R′)−,−N(R′)S(O)N(R′)−,−N(R′)S(O)2N(R′)−,−N(R′)−N=,−C(R′)=N−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N<annotation encoding="application / x-tex">N(R')C(S)N(R')-, -N(R')S(O)N(R')-, -N(R')S(O)_2N(R')-, -N(R')-N=, -C(R')=N-N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N< / annotation>< / semantics>< / com:Math> <com:Math><semantics>C(R′)=N−N=<annotation encoding="application / x-tex">C(R')=N-N=< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)2−N=N−<annotation encoding="application / x-tex">-C(R')_2-N=N-< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−C(R′)2−N(R′)−N(R′)−<annotation encoding="application / x-tex">-C(R')_2-N(R')-N(R')-< / annotation>< / semantics>< / com:Math>; (iii) A is lower alkylene; B is optional, and when present is a divalent linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, <com:Math><semantics>−O−<annotation encoding="application / x-tex">-O_{-}< / annotation>< / semantics>< / com:Math>, – O-(alkylene or substituted alkylene)-, <com:Math><semantics>−S<annotation encoding="application / x-tex">-S< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−S<annotation encoding="application / x-tex">-S< / annotation>< / semantics>< / com:Math>(O)-, <com:Math><semantics>−S<annotation encoding="application / x-tex">-S< / annotation>< / semantics>< / com:Math>(O)<com:Sub>2< / com:Sub>-, <com:Math><semantics>−NS<annotation encoding="application / x-tex">-NS< / annotation>< / semantics>< / com:Math>(O)<com:Sub>2< / com:Sub>-, <com:Math><semantics>−OS<annotation encoding="application / x-tex">-OS< / annotation>< / semantics>< / com:Math>(O)<com:Sub>2< / com:Sub>-, <com:Math><semantics>−C<annotation encoding="application / x-tex">-C< / annotation>< / semantics>< / com:Math>(O)-, -C(O)-(alkylene or substituted alkylene)-, -C(S)-, -N(R')-, -C(O)N(R')-, -CSN(R')-, - CON(R')-(alkylene or substituted alkylene)-, -N(R')C(O)O-, -N(R')C(S)-, -S(O)N(R'), - <com:Math><semantics>S(O)2N(R′),−N(R′)C(O)N(R′)−,−N(R′)C(S)N(R′)−,−N(R′)S(O)N(R′)−,−N(R′)S(O)2N(R′)−,−N(R′)S(O)2N(R′)−,−N(R′)S(O)2N(R′)−,−N(R′)S(O)2N(R′)−,−N(R′)S(O)2N(R′)−,−N(R′)S(O)2N(R′)−,−N(R′)S(O)2N(R′)−,−N(R′)S(O)2N<annotation encoding="application / x-tex">S(O)_2N(R'), -N(R')C(O)N(R')-, -N(R')C(S)N(R')-, -N(R')S(O)N(R')-, -N(R')S(O)_2N(R')-, -N(R')S(O)_2N(R')-, -N(R')S(O)_2N(R')-, -N(R')S(O)_2N(R')-, -N(R')S(O)_2N(R')-, -N(R')S(O)_2N(R')-, -N(R')S(O)_2N(R')-, -N(R')S(O)_2N< / annotation>< / semantics>< / com:Math> <com:Math><semantics>N(R′)−N=<annotation encoding="application / x-tex">N(R')-N=< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)=N−N(R′)−<annotation encoding="application / x-tex">-C(R')=N-N(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)=N−N=<annotation encoding="application / x-tex">-C(R')=N-N=< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)2−N=N−<annotation encoding="application / x-tex">-C(R')_2-N=N-< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−C(R′)2−N(R′)−N(R′)−<annotation encoding="application / x-tex">-C(R')_2-N(R')-N(R')-< / annotation>< / semantics>< / com:Math>; and (iv) A is phenylene; B is a divalent linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, -O-, - O-(alkylene or substituted alkylene)-, <com:Math><semantics>−S<annotation encoding="application / x-tex">-S< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−S<annotation encoding="application / x-tex">-S< / annotation>< / semantics>< / com:Math>(O)-, <com:Math><semantics>−S<annotation encoding="application / x-tex">-S< / annotation>< / semantics>< / com:Math>(O)<com:Sub>2< / com:Sub>-, <com:Math><semantics>−NS<annotation encoding="application / x-tex">-NS< / annotation>< / semantics>< / com:Math>(O)<com:Sub>2< / com:Sub>-, <com:Math><semantics>−OS<annotation encoding="application / x-tex">-OS< / annotation>< / semantics>< / com:Math>(O)<com:Sub>2< / com:Sub>-, <com:Math><semantics>−C<annotation encoding="application / x-tex">-C< / annotation>< / semantics>< / com:Math>(O)-, -C(O)-(alkylene or substituted alkylene)-, -C(S)-, -N(R')-, -C(O)N(R')-, -CON(R')- (alkylene or substituted alkylene)—, -CSN(R')—, -N(R')CO—(alkylene or substituted alkylene)-, <com:Math><semantics>−N(R′)C(O)O<annotation encoding="application / x-tex">-N(R')C(O)O< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)C(S)<annotation encoding="application / x-tex">-N(R')C(S)< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−S(O)N(R′)<annotation encoding="application / x-tex">-S(O)N(R')< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−S(O)2N(R′)<annotation encoding="application / x-tex">-S(O)_2N(R')< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)C(O)N(R′)<annotation encoding="application / x-tex">-N(R')C(O)N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−<annotation encoding="application / x-tex">-< / annotation>< / semantics>< / com:Math> <com:Math><semantics>N(R′)C(S)N(R′)−,−N(R′)S(O)N(R′)−,−N(R′)S(O)2N(R′)−,−N(R′)−N=,−C(R′)′N−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N<annotation encoding="application / x-tex">N(R')C(S)N(R')-, -N(R')S(O)N(R')-, -N(R')S(O)_2N(R')-, -N(R')-N=, -C(R')'N-N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N< / annotation>< / semantics>< / com:Math> <com:Math><semantics>C(R′)=N−N=,−C(R′)2−N=N−, and −C(R′)2−N(R′)−N(R′)−;J is <annotation encoding="application / x-tex">C(R')=N-N=, -C(R')_2-N=N-, \text{ and } -C(R')_2-N(R')-N(R')-; J \text{ is }< / annotation>< / semantics>< / com:Math> [Image disponible dans le document PDF, Image available in the PDF document] each R' is independently H, alkyl, or substituted alkyl; R<com:Sub>1< / com:Sub> is optional, and when present, is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is optional, and when present, is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; and each R<com:Sub>3< / com:Sub> and R<com:Sub>4< / com:Sub> is independently H, halogen, lower alkyl, or substituted lower alkyl; and R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl.

[00172] In addition, amino acids having the structure of Formula (II) are included: [Image disponible dans le document PDF, Image available in the PDF document] wherein: A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene; B is optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -O-, -O-(alkylene or substituted alkylene)-, -S-, -S-(alkylene or substituted alkylene)-, -S(O)<com:Sub>k< / com:Sub>- where k is 1, 2, or 3, -S(O)<com:Sub>k< / com:Sub>(alkylene or substituted alkylene)-, -C(O)-, -NS(O)<com:Sub>2< / com:Sub>-, -OS(O)<com:Sub>2< / com:Sub>-, -C(O)- (alkylene or substituted alkylene)-, -C(S)-, -C(S)-(alkylene or substituted alkylene)-, - N(R')-, -NR'-(alkylene or substituted alkylene)-, -C(O)N(R')-, -CON(R')-(alkylene or substituted alkylene)-, -CSN(R')-, -CSN(R')-(alkylene or substituted alkylene)-, - <com:Math><semantics>N(R′)CO<annotation encoding="application / x-tex">N(R')CO< / annotation>< / semantics>< / com:Math>—(alkylene or substituted alkylene)—, <com:Math><semantics>−N(R′)C(O)O<annotation encoding="application / x-tex">-N(R')C(O)O< / annotation>< / semantics>< / com:Math>—, <com:Math><semantics>−S(O)kN(R′)<annotation encoding="application / x-tex">-S(O)_kN(R')< / annotation>< / semantics>< / com:Math>—, <com:Math><semantics>−<annotation encoding="application / x-tex">-< / annotation>< / semantics>< / com:Math> <com:Math><semantics>N(R′)C(O)N(R′)−,−N(R′)C(S)N(R′)−,−N(R′)S(O)kN(R′)−,−N(R′)−N=,−C(R′)=N−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,<annotation encoding="application / x-tex">N(R')C(O)N(R')-, -N(R')C(S)N(R')-, -N(R')S(O)_kN(R')-, -N(R')-N=, -C(R')=N-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-,< / annotation>< / semantics>< / com:Math> <com:Math><semantics>C(R′)=N−N(R′)−,−C(R′)=N−N=,−C(R′)2−N=N−, and −C(R′)2−N(R′)−N(R′)−, where each R′<annotation encoding="application / x-tex">C(R')=N-N(R')-, -C(R')=N-N=, -C(R')_2-N=N-, \text{ and } -C(R')_2-N(R')-N(R')-, \text{ where each } R'< / annotation>< / semantics>< / com:Math> is independently H, alkyl, or substituted alkyl; R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide. In certain embodiments, when A is phenylene, B is present; and that when A is <com:Math><semantics>−(CH2)4<annotation encoding="application / x-tex">-(CH_2)_4< / annotation>< / semantics>< / com:Math>, B is not <com:Math><semantics>−NHC(O)(CH2CH2)<annotation encoding="application / x-tex">-NHC(O)(CH_2CH_2)< / annotation>< / semantics>< / com:Math>; and that when A and B are absent, R is not methyl. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00173] In addition, amino acids having the structure of Formula (III) are included: [Image disponible dans le document PDF, Image available in the PDF document] wherein: B is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -O-, -O-(alkylene or substituted alkylene)-, -S-, -S-(alkylene or substituted alkylene)–, <com:Math><semantics>−S(O)k<annotation encoding="application / x-tex">-S(O)_k< / annotation>< / semantics>< / com:Math>– where k is 1, 2, or 3, <com:Math><semantics>−S(O)k<annotation encoding="application / x-tex">-S(O)_k< / annotation>< / semantics>< / com:Math>(alkylene or substituted alkylene)-, -C(O)-, -NS(O)<com:Sub>2< / com:Sub>-, -OS(O)<com:Sub>2< / com:Sub>-, -C(O)-(alkylene or substituted alkylene)-, -C(S)- , –C(S)–(alkylene or substituted alkylene)–, –N(R')–, –NR'–(alkylene or substituted alkylene)-, -C(O)N(R')-, -CON(R')-(alkylene or substituted alkylene)-, -CSN(R')-, - CSN(R')-(alkylene or substituted alkylene)-, -N(R')CO-(alkylene or substituted alkylene)-, <com:Math><semantics>−N(R′)C(O)O−<annotation encoding="application / x-tex">-N(R')C(O)O-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−S(O)kN(R′)−<annotation encoding="application / x-tex">-S(O)_kN(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)C(O)N(R′)−<annotation encoding="application / x-tex">-N(R')C(O)N(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)C(S)N(R′)−<annotation encoding="application / x-tex">-N(R')C(S)N(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)S(O)kN(R′)−<annotation encoding="application / x-tex">-N(R')S(O)_kN(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)C(O)N(R′)−<annotation encoding="application / x-tex">-N(R')C(O)N(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)N(R′)−<annotation encoding="application / x-tex">-N(R')N(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)N(R′)−<annotation encoding="application / x-tex">-N(R')N(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)N(R′)−<annotation encoding="application / x-tex">-N(R')N(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)N(R′)−<annotation encoding="application / x-tex">-N(R')N(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)N(R′)−<annotation encoding="application / x-tex">-N(R')N(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)N(R′)−<annotation encoding="application / x-tex">-N(R')N(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)N(R<annotation encoding="application / x-tex">-N(R')N(R< / annotation>< / semantics>< / com:Math> <com:Math><semantics>N(R′)−N=<annotation encoding="application / x-tex">N(R')-N=< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)=N−<annotation encoding="application / x-tex">-C(R')=N-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)=N−N(R′)−<annotation encoding="application / x-tex">-C(R')=N-N(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)=N−N=<annotation encoding="application / x-tex">-C(R')=N-N=< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)2−N=N−<annotation encoding="application / x-tex">-C(R')_2-N=N-< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−C(R′)2−N=N−<annotation encoding="application / x-tex">-C(R')_2-N=N-< / annotation>< / semantics>< / com:Math> N(R')-N(R')-, where each R' is independently H, alkyl, or substituted alkyl; R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; each Ra is independently selected from the group consisting of H, halogen, alkyl, substituted alkyl, <com:Math><semantics>−N(R′)2<annotation encoding="application / x-tex">-N(R')_2< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(O)k<annotation encoding="application / x-tex">-C(O)_k< / annotation>< / semantics>< / com:Math> R'where k is 1, 2, or 3, <com:Math><semantics>−C(O)N(R′)2<annotation encoding="application / x-tex">-C(O)N(R')_2< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−OR′<annotation encoding="application / x-tex">-OR'< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−S(O)kR′<annotation encoding="application / x-tex">-S(O)_kR'< / annotation>< / semantics>< / com:Math>, where each R' is independently H, alkyl, or substituted alkyl. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00174] In addition, the following amino acids are included: [Image disponible dans le document PDF, Image available in the PDF document] [Image disponible dans le document PDF, Image available in the PDF document] Such non-natural amino acids may be are optionally amino protected group, carboxyl protected and / or in the form of a salt, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00175] In addition, the following amino acids having the structure of Formula (IV) are included: [Image disponible dans le document PDF, Image available in the PDF document] wherein <com:Math><semantics>−NS(O)2<annotation encoding="application / x-tex">-NS(O)_2< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−OS(O)2<annotation encoding="application / x-tex">-OS(O)_2< / annotation>< / semantics>< / com:Math>, optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -O-, -O-(alkylene or substituted alkylene)-, -S-, -S-(alkylene or substituted alkylene)-, -S(O)<com:Math><semantics>k<annotation encoding="application / x-tex">_k< / annotation>< / semantics>< / com:Math>- where k is 1, 2, or 3, <com:Math><semantics>−S(O)k<annotation encoding="application / x-tex">-S(O)_k< / annotation>< / semantics>< / com:Math>(alkylene or substituted alkylene)-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-(alkylene or substituted alkylene)-, -C(S)-, -C(S)-(alkylene or substituted alkylene)-, -N(R')-, -NR'-(alkylene or substituted alkylene)-, -C(O)N(R')-, -CON(R')-(alkylene or substituted alkylene)-, - CSN(R')-, -CSN(R')-(alkylene or substituted alkylene)-, -N(R')CO-(alkylene or substituted alkylene)-, <com:Math><semantics>−N(R′)C(O)O<annotation encoding="application / x-tex">-N(R')C(O)O< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−S(O)kN(R′)<annotation encoding="application / x-tex">-S(O)_kN(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)C(O)N(R′)<annotation encoding="application / x-tex">-N(R')C(O)N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)C(S)N(R′)<annotation encoding="application / x-tex">-N(R')C(S)N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)C(S)N(R′)<annotation encoding="application / x-tex">-N(R')C(S)N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)C(S)N(R′)<annotation encoding="application / x-tex">-N(R')C(S)N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)C(S)N(R′)<annotation encoding="application / x-tex">-N(R')C(S)N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)C(S)N(R′)<annotation encoding="application / x-tex">-N(R')C(S)N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)C(S)N(R′)<annotation encoding="application / x-tex">-N(R')C(S)N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)C(S)N(R′)<annotation encoding="application / x-tex">-N(R')C(S)N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)C(S)N(R′)<annotation encoding="application / x-tex">-N(R')C(S)N(R')< / annotation>< / semantics>< / com:Math> <com:Math><semantics>N(R′)S(O)kN(R′)−,−N(R′)−N=,−C(R′)=N−,−C(R′)=N−N(R′)−,−C(R′)=N−N=,−C(R′)2−<annotation encoding="application / x-tex">N(R')S(O)_kN(R')-, -N(R')-N=, -C(R')=N-, -C(R')=N-N(R')-, -C(R')=N-N=, -C(R')_2-< / annotation>< / semantics>< / com:Math> <com:Math><semantics>N=N−<annotation encoding="application / x-tex">N=N-< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−C(R′)2−N(R′)−N(R′)−<annotation encoding="application / x-tex">-C(R')_2-N(R')-N(R')-< / annotation>< / semantics>< / com:Math>, where each R' is independently H, alkyl, or substituted alkyl; R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; each R<com:Sub>a< / com:Sub> is independently selected from the group consisting of H, halogen, alkyl, substituted alkyl, <com:Math><semantics>−N(R′)2<annotation encoding="application / x-tex">-N(R')_2< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(O)kR′<annotation encoding="application / x-tex">-C(O)_kR'< / annotation>< / semantics>< / com:Math> where k is 1, 2, or 3, <com:Math><semantics>−C(O)N(R′)2<annotation encoding="application / x-tex">-C(O)N(R')_2< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−OR′<annotation encoding="application / x-tex">-OR'< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−S(O)kR′<annotation encoding="application / x-tex">-S(O)_kR'< / annotation>< / semantics>< / com:Math>, where each R' is independently H, alkyl, or substituted alkyl; and n is 0 to 8. In certain embodiments, when A is <com:Math><semantics>−(CH2)4<annotation encoding="application / x-tex">-(CH_2)_4< / annotation>< / semantics>< / com:Math>, B is not -NHC(O)(CH<com:Sub>2< / com:Sub>CH<com:Sub>2< / com:Sub>)-. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00176] In addition, the following amino acids are included: [Image disponible dans le document PDF, Image available in the PDF document] wherein such compounds are optionally amino protected, optionally carboxyl protected, optionally amino protected and carboxyl protected, or a salt thereof, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00177] In addition, the following amino acids having the structure of Formula (VIII) are included: [Image disponible dans le document PDF, Image available in the PDF document] wherein, A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene; B is optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -O-, -O-(alkylene or substituted alkylene)–, –S–, –S–(alkylene or substituted alkylene)–, –S(O)<com:Sub>k< / com:Sub>– where k is 1, 2, or 3, <com:Math><semantics>−S(O)k<annotation encoding="application / x-tex">-S(O)_k< / annotation>< / semantics>< / com:Math> (alkylene or substituted alkylene)-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−NS(O)2<annotation encoding="application / x-tex">-NS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−OS(O)2<annotation encoding="application / x-tex">-OS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>- (alkylene or substituted alkylene)—, —C(S)—, —C(S)—(alkylene or substituted alkylene)—, — N(R')-, -NR'-(alkylene or substituted alkylene)-, -C(O)N(R')-, -CON(R')-(alkylene or substituted alkylene)—, -CSN(R')—, -CSN(R')—(alkylene or substituted alkylene)—, - <com:Math><semantics>N(R′)CO<annotation encoding="application / x-tex">N(R')CO< / annotation>< / semantics>< / com:Math>—(alkylene or substituted alkylene)—, <com:Math><semantics>−N(R′)C(O)O<annotation encoding="application / x-tex">-N(R')C(O)O< / annotation>< / semantics>< / com:Math>—, <com:Math><semantics>−S(O)kN(R′)<annotation encoding="application / x-tex">-S(O)_kN(R')< / annotation>< / semantics>< / com:Math>—, <com:Math><semantics>−<annotation encoding="application / x-tex">-< / annotation>< / semantics>< / com:Math> <com:Math><semantics>N(R′)C(O)N(R′)−,−N(R′)C(S)N(R′)−,−N(R′)S(O)kN(R′)−,−N(R′)−N=,−C(R′)=N−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,<annotation encoding="application / x-tex">N(R')C(O)N(R')-, -N(R')C(S)N(R')-, -N(R')S(O)_kN(R')-, -N(R')-N=, -C(R')=N-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-,< / annotation>< / semantics>< / com:Math> <com:Math><semantics>C(R′)=N−N(R′)−<annotation encoding="application / x-tex">C(R')=N-N(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)=N−N=<annotation encoding="application / x-tex">-C(R')=N-N=< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)2−N=N−<annotation encoding="application / x-tex">-C(R')_2-N=N-< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−C(R′)2−N(R′)−N(R′)−<annotation encoding="application / x-tex">-C(R')_2-N(R')-N(R')-< / annotation>< / semantics>< / com:Math>, where each R' is independently H, alkyl, or substituted alkyl; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00178] In addition, the following amino acids having the structure of Formula (IX) are included: [Image disponible dans le document PDF, Image available in the PDF document] wherein, B is optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -O-, -O-(alkylene or substituted alkylene)-, -S-, -S-(alkylene or substituted alkylene)-, -S(O)<com:Sub>k< / com:Sub>- where k is 1, 2, or 3, - <com:Math><semantics>S(O)k<annotation encoding="application / x-tex">S(O)_k< / annotation>< / semantics>< / com:Math>(alkylene or substituted alkylene)-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−NS(O)2<annotation encoding="application / x-tex">-NS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−OS(O)2<annotation encoding="application / x-tex">-OS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-(alkylene or substituted alkylene)-, -C(S)-, -C(S)-(alkylene or substituted alkylene)-, -N(R')-, -NR'- (alkylene or substituted alkylene)—, —C(O)N(R')—, —CON(R')—(alkylene or substituted alkylene)-, -CSN(R')-, -CSN(R')-(alkylene or substituted alkylene)-, -N(R')CO-(alkylene or substituted alkylene)-, <com:Math><semantics>−N(R′)C(O)O<annotation encoding="application / x-tex">-N(R')C(O)O< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−S(O)kN(R′)<annotation encoding="application / x-tex">-S(O)_kN(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)C(O)N(R′)<annotation encoding="application / x-tex">-N(R')C(O)N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−<annotation encoding="application / x-tex">-< / annotation>< / semantics>< / com:Math> <com:Math><semantics>N(R′)C(S)N(R′)−,−N(R′)S(O)kN(R′)−,−N(R′)−N=,−C(R′)=N−,−C(R′)=N−N(R′)−,−N(R′)−,−N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−<annotation encoding="application / x-tex">N(R')C(S)N(R')-, -N(R')S(O)_kN(R')-, -N(R')-N=, -C(R')=N-, -C(R')=N-N(R')-, -N(R')-, -N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-< / annotation>< / semantics>< / com:Math> <com:Math><semantics>C(R′)=N−N=<annotation encoding="application / x-tex">C(R')=N-N=< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)2−N=N−<annotation encoding="application / x-tex">-C(R')_2-N=N-< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−C(R′)2−N(R′)−N(R′)−<annotation encoding="application / x-tex">-C(R')_2-N(R')-N(R')-< / annotation>< / semantics>< / com:Math>, where each R' is independently H, alkyl, or substituted alkyl; R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; wherein each R<com:Sub>a< / com:Sub> is independently selected from the group consisting of H, halogen, alkyl, substituted alkyl, <com:Math><semantics>−N(R′)2<annotation encoding="application / x-tex">-N(R')_2< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(O)kR′<annotation encoding="application / x-tex">-C(O)_kR'< / annotation>< / semantics>< / com:Math> where k is 1, 2, or 3, <com:Math><semantics>−C(O)N(R′)2<annotation encoding="application / x-tex">-C(O)N(R')_2< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−OR′<annotation encoding="application / x-tex">-OR'< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−S(O)k<annotation encoding="application / x-tex">-S(O)_k< / annotation>< / semantics>< / com:Math> R', where each R' is independently H, alkyl, or substituted alkyl. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00179] In addition, the following amino acids are included: [Image disponible dans le document PDF, Image available in the PDF document] [Image disponible dans le document PDF, Image available in the PDF document] wherein such compounds are optionally amino protected, optionally carboxyl protected, optionally amino protected and carboxyl protected, or a salt thereof, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00180] In addition, the following amino acids having the structure of Formula (X) are included: [Image disponible dans le document PDF, Image available in the PDF document] wherein, B is optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -O-, -O-(alkylene or substituted alkylene)-, -S-, -S-(alkylene or substituted alkylene)-, -S(O)<com:Sub>k< / com:Sub>- where k is 1, 2, or 3, - <com:Math><semantics>S(O)k<annotation encoding="application / x-tex">S(O)_k< / annotation>< / semantics>< / com:Math>(alkylene or substituted alkylene)-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−NS(O)2<annotation encoding="application / x-tex">-NS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−OS(O)2<annotation encoding="application / x-tex">-OS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-(alkylene or substituted alkylene)-, -C(S)-, -C(S)-(alkylene or substituted alkylene)-, -N(R')-, -NR'- (alkylene or substituted alkylene)-, -C(O)N(R')-, -CON(R')-(alkylene or substituted alkylene)-, -CSN(R')-, -CSN(R')-(alkylene or substituted alkylene)-, -N(R')CO-(alkylene or substituted alkylene)-, <com:Math><semantics>−N(R′)C(O)O<annotation encoding="application / x-tex">-N(R')C(O)O< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−S(O)kN(R′)<annotation encoding="application / x-tex">-S(O)_kN(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)C(O)N(R′)<annotation encoding="application / x-tex">-N(R')C(O)N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−<annotation encoding="application / x-tex">-< / annotation>< / semantics>< / com:Math> <com:Math><semantics>N(R′)C(S)N(R′)−,−N(R′)S(O)kN(R′)−,−N(R′)−N=,−C(R′)=N−,−C(R′)=N−N(R′)−,−N(R′)−,−N(R′)−N=,−C(R′)=N−N(R′)−,−N(R′)−,−N(R′)−N=,−C(R′)=N−N(R′)−,−N(R′)−,−N(R′)−N=,−C(R′)=N−N(R′)−,−N(R′)−N=,−C(R′)=N−N(R′)−,−N(R′<annotation encoding="application / x-tex">N(R')C(S)N(R')-, -N(R')S(O)_kN(R')-, -N(R')-N=, -C(R')=N-, -C(R')=N-N(R')-, -N(R')-, -N(R')-N=, -C(R')=N-N(R')-, -N(R')-, -N(R')-N=, -C(R')=N-N(R')-, -N(R')-, -N(R')-N=, -C(R')=N-N(R')-, -N(R')-N=, -C(R')=N-N(R')-, -N(R'< / annotation>< / semantics>< / com:Math> <com:Math><semantics>C(R′)=N−N=<annotation encoding="application / x-tex">C(R')=N-N=< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)2−N=N−<annotation encoding="application / x-tex">-C(R')_2-N=N-< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−C(R′)2−N(R′)−N(R′)−<annotation encoding="application / x-tex">-C(R')_2-N(R')-N(R')-< / annotation>< / semantics>< / com:Math>, where each R' is independently H, alkyl, or substituted alkyl; R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; each R<com:Sub>a< / com:Sub> is independently selected from the group consisting of H, halogen, alkyl, substituted alkyl, <com:Math><semantics>−N(R′)2<annotation encoding="application / x-tex">-N(R')_2< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(O)kR′<annotation encoding="application / x-tex">-C(O)_kR'< / annotation>< / semantics>< / com:Math> where k is 1, 2, or 3, <com:Math><semantics>−C(O)N(R′)2<annotation encoding="application / x-tex">-C(O)N(R')_2< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−OR′<annotation encoding="application / x-tex">-OR'< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−<annotation encoding="application / x-tex">-< / annotation>< / semantics>< / com:Math> S(O)<com:Sub>k< / com:Sub>R', where each R' is independently H, alkyl, or substituted alkyl; and n is 0 to 8. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non- natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00181] In addition, the following amino acids are included: [Image disponible dans le document PDF, Image available in the PDF document] wherein such compounds are optionally amino protected, optionally carboxyl protected, optionally amino protected and carboxyl protected, or a salt thereof, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00182] In addition to monocarbonyl structures, the non-natural amino acids described herein may include groups such as dicarbonyl, dicarbonyl like, masked dicarbonyl and protected dicarbonyl groups. For example, the following amino acids having the structure of Formula (V) are included: [Image disponible dans le document PDF, Image available in the PDF document] wherein, A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene; B is optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -O-, -O-(alkylene or substituted alkylene)—, <com:Math><semantics>−S<annotation encoding="application / x-tex">-S< / annotation>< / semantics>< / com:Math>—, <com:Math><semantics>−S<annotation encoding="application / x-tex">-S< / annotation>< / semantics>< / com:Math>—(alkylene or substituted alkylene)—, <com:Math><semantics>−S(O)k<annotation encoding="application / x-tex">-S(O)_k< / annotation>< / semantics>< / com:Math>— where k is 1, 2, or 3, <com:Math><semantics>−S(O)k<annotation encoding="application / x-tex">-S(O)_k< / annotation>< / semantics>< / com:Math> (alkylene or substituted alkylene)-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−NS(O)2<annotation encoding="application / x-tex">-NS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−OS(O)2<annotation encoding="application / x-tex">-OS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>- (alkylene or substituted alkylene)—, –C(S)—, –C(S)—(alkylene or substituted alkylene)—, – N(R')-, -NR'-(alkylene or substituted alkylene)-, -C(O)N(R')-, -CON(R')-(alkylene or substituted alkylene)-, -CSN(R')-, -CSN(R')-(alkylene or substituted alkylene)-, - <com:Math><semantics>N(R′)CO<annotation encoding="application / x-tex">N(R')CO< / annotation>< / semantics>< / com:Math>—(alkylene or substituted alkylene)—, <com:Math><semantics>−N(R′)C(O)O<annotation encoding="application / x-tex">-N(R')C(O)O< / annotation>< / semantics>< / com:Math>—, <com:Math><semantics>−S(O)kN(R′)<annotation encoding="application / x-tex">-S(O)_kN(R')< / annotation>< / semantics>< / com:Math>—, — <com:Math><semantics>N(R′)C(O)N(R′)−,−N(R′)C(S)N(R′)−,−N(R′)S(O)kN(R′)−,−N(R′)−N=,−C(R′)=N−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,<annotation encoding="application / x-tex">N(R')C(O)N(R')-, -N(R')C(S)N(R')-, -N(R')S(O)_kN(R')-, -N(R')-N=, -C(R')=N-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-,< / annotation>< / semantics>< / com:Math> <com:Math><semantics>C(R′)=N−N(R′)−<annotation encoding="application / x-tex">C(R')=N-N(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)=N−N=<annotation encoding="application / x-tex">-C(R')=N-N=< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)2−N=N−<annotation encoding="application / x-tex">-C(R')_2-N=N-< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−C(R′)2−N(R′)−N(R′)−<annotation encoding="application / x-tex">-C(R')_2-N(R')-N(R')-< / annotation>< / semantics>< / com:Math>, where each R' is independently H, alkyl, or substituted alkyl; R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00183] In addition, the following amino acids having the structure of Formula (VI) are included: [Image disponible dans le document PDF, Image available in the PDF document] wherein, B is optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -O-, -O-(alkylene or substituted alkylene)-, -S-, -S-(alkylene or substituted alkylene)-, -S(O)<com:Sub>k< / com:Sub>- where k is 1, 2, or 3, - <com:Math><semantics>S(O)k(alkylene or substituted alkylene)−,−C(O)−,−NS(O)2−,−OS(O)2−,−C(O)−(alkylene or substituted alkylene)<annotation encoding="application / x-tex">S(O)_k(alkylene \text{ or substituted alkylene})-, -C(O)-, -NS(O)_2-, -OS(O)_2-, -C(O)-(alkylene \text{ or substituted alkylene})< / annotation>< / semantics>< / com:Math> substituted alkylene)-, -C(S)-, -C(S)-(alkylene or substituted alkylene)-, -N(R')-, -NR'- (alkylene or substituted alkylene)-, -C(O)N(R')-, -CON(R')-(alkylene or substituted alkylene)—, -CSN(R')—, -CSN(R')—(alkylene or substituted alkylene)—, -N(R')CO–(alkylene or substituted alkylene)-, <com:Math><semantics>−N(R′)C(O)O<annotation encoding="application / x-tex">-N(R')C(O)O< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−S(O)kN(R′)<annotation encoding="application / x-tex">-S(O)_kN(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)C(O)N(R′)<annotation encoding="application / x-tex">-N(R')C(O)N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−<annotation encoding="application / x-tex">-< / annotation>< / semantics>< / com:Math> <com:Math><semantics>N(R′)C(S)N(R′)−,−N(R′)S(O)kN(R′)−,−N(R′)−N=,−C(R′)=N−,−C(R′)=N−N(R′)−,−N(R′)−,−N(R′)−N=,−C(R′)=N−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,−N(R′)−,<annotation encoding="application / x-tex">N(R')C(S)N(R')-, -N(R')S(O)_kN(R')-, -N(R')-N=, -C(R')=N-, -C(R')=N-N(R')-, -N(R')-, -N(R')-N=, -C(R')=N-N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-, -N(R')-,< / annotation>< / semantics>< / com:Math> <com:Math><semantics>C(R′)=N−N=<annotation encoding="application / x-tex">C(R')=N-N=< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)2−N=N−<annotation encoding="application / x-tex">-C(R')_2-N=N-< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−C(R′)2−N(R′)−N(R′)−<annotation encoding="application / x-tex">-C(R')_2-N(R')-N(R')-< / annotation>< / semantics>< / com:Math>, where each R' is independently H, alkyl, or substituted alkyl; R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; R<com:Sub>1< / com:Sub> is II, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; wherein each R<com:Sub>a< / com:Sub> is independently selected from the group consisting of H, halogen, alkyl, substituted alkyl, <com:Math><semantics>−N(R′)2<annotation encoding="application / x-tex">-N(R')_2< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(O)kR′<annotation encoding="application / x-tex">-C(O)_kR'< / annotation>< / semantics>< / com:Math> where k is 1, 2, or 3, <com:Math><semantics>−C(O)N(R′)2<annotation encoding="application / x-tex">-C(O)N(R')_2< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−OR′<annotation encoding="application / x-tex">-OR'< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−S(O)kR′<annotation encoding="application / x-tex">-S(O)_kR'< / annotation>< / semantics>< / com:Math>, where each R' is independently H, alkyl, or substituted alkyl. Such non–natural amino acids may be in the form of a salt, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00184] In addition, the following amino acids are included: [Image disponible dans le document PDF, Image available in the PDF document] [Image disponible dans le document PDF, Image available in the PDF document] [Image disponible dans le document PDF, Image available in the PDF document] wherein such compounds are optionally amino protected and carboxyl protected, or a salt thereof. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00185] In addition, the following amino acids having the structure of Formula (VII) are included: [Image disponible dans le document PDF, Image available in the PDF document] wherein, B is optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -O-, -O-(alkylene or substituted alkylene)-, -S-, -S-(alkylene or substituted alkylene)-, -S(O)<com:Sub>k< / com:Sub>- where k is 1, 2, or 3, - <com:Math><semantics>S(O)k<annotation encoding="application / x-tex">S(O)_k< / annotation>< / semantics>< / com:Math>(alkylene or substituted alkylene)-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−NS(O)2<annotation encoding="application / x-tex">-NS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−OS(O)2<annotation encoding="application / x-tex">-OS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-(alkylene or substituted alkylene)-, -C(S)-, -C(S)-(alkylene or substituted alkylene)-, -N(R')-, -NR'- (alkylene or substituted alkylene)-, -C(O)N(R')-, -CON(R')-(alkylene or substituted alkylene)--, -CSN(R')--, alkylene or substituted alkylene)--, -N(R')CO-(alkylene or substituted alkylene)-, <com:Math><semantics>−N(R′)C(O)O<annotation encoding="application / x-tex">-N(R')C(O)O< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−S(O)kN(R′)<annotation encoding="application / x-tex">-S(O)_kN(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)C(O)N(R′)<annotation encoding="application / x-tex">-N(R')C(O)N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−<annotation encoding="application / x-tex">-< / annotation>< / semantics>< / com:Math> <com:Math><semantics>N(R′)C(S)N(R′)−,−N(R′)S(O)kN(R′)−,−N(R′)−N=,−C(R′)=N−,−C(R′)=N−N(R′)−,−N(R′)−,−N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−<annotation encoding="application / x-tex">N(R')C(S)N(R')-, -N(R')S(O)_kN(R')-, -N(R')-N=, -C(R')=N-, -C(R')=N-N(R')-, -N(R')-, -N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-< / annotation>< / semantics>< / com:Math> <com:Math><semantics>C(R′)=N−N=<annotation encoding="application / x-tex">C(R')=N-N=< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)2−N=N−<annotation encoding="application / x-tex">-C(R')_2-N=N-< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−C(R′)2−N(R′)−N(R′)−<annotation encoding="application / x-tex">-C(R')_2-N(R')-N(R')-< / annotation>< / semantics>< / com:Math>, where each R' is independently H, alkyl, or substituted alkyl; R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; each Ra is independently selected from the group consisting of H, halogen, alkyl, substituted alkyl, <com:Math><semantics>−N(R′)2<annotation encoding="application / x-tex">-N(R')_2< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(O)kR′<annotation encoding="application / x-tex">-C(O)_kR'< / annotation>< / semantics>< / com:Math> where k is 1, 2, or 3, <com:Math><semantics>−C(O)N(R′)2<annotation encoding="application / x-tex">-C(O)N(R')_2< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−OR′<annotation encoding="application / x-tex">-OR'< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−<annotation encoding="application / x-tex">-< / annotation>< / semantics>< / com:Math> S(O)<com:Sub>k< / com:Sub>R', where each R' is independently H, alkyl, or substituted alkyl; and n is 0 to 8. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non- natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00186] In addition, the following amino acids are included: [Image disponible dans le document PDF, Image available in the PDF document] wherein such compounds are optionally amino protected and carboxyl protected, or a salt thereof, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00187] In addition, the following amino acids having the structure of Formula (XXX) are included: [Image disponible dans le document PDF, Image available in the PDF document] wherein: A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene; R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; <com:Math><semantics>X1<annotation encoding="application / x-tex">X_1< / annotation>< / semantics>< / com:Math> is C, S, or S(O); and L is alkylene, substituted alkylene, N(R')(alkylene) or N(R')(substituted alkylene), where R' is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non- natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00188] In addition, the following amino acids having the structure of Formula (XXX-A) are included: [Image disponible dans le document PDF, Image available in the PDF document] wherein: A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene; R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; L is alkylene, substituted alkylene, N(R')(alkylene) or N(R')(substituted alkylene), where R' is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00189] In addition, the following amino acids having the structure of Formula (XXX-B) are included: [Image disponible dans le document PDF, Image available in the PDF document] wherein: A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene; R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; L is alkylene, substituted alkylene, N(R')(alkylene) or N(R')(substituted alkylene), where R' is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00190] In addition, the following amino acids having the structure of Formula (XXXI) are included: [Image disponible dans le document PDF, Image available in the PDF document] wherein: A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene; R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; <com:Math><semantics>X1<annotation encoding="application / x-tex">X_1< / annotation>< / semantics>< / com:Math> is C, S, or S(O); and n is 0, 1, 2, 3, 4, or 5; and each R<com:Sup>8< / com:Sup> and R<com:Sup>9< / com:Sup> on each CR<com:Sup>8< / com:Sup>R<com:Sup>9< / com:Sup> group is independently selected from the group consisting of H, alkoxy, alkylamine, halogen, alkyl, aryl, or any <com:Math><semantics>R8<annotation encoding="application / x-tex">R^8< / annotation>< / semantics>< / com:Math> and <com:Math><semantics>R9<annotation encoding="application / x-tex">R^9< / annotation>< / semantics>< / com:Math> can together form =0 or a cycloalkyl, or any to adjacent <com:Math><semantics>R8<annotation encoding="application / x-tex">R^8< / annotation>< / semantics>< / com:Math> groups can together form a cycloalkyl. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00191] In addition, the following amino acids having the structure of Formula (XXXI-A) are included: [Image disponible dans le document PDF, Image available in the PDF document] wherein: A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene; R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; n is 0, 1, 2, 3, 4, or 5; and each R<com:Sup>8< / com:Sup> and R<com:Sup>9< / com:Sup> on each CR<com:Sup>8< / com:Sup>R<com:Sup>9< / com:Sup> group is independently selected from the group consisting of H, alkoxy, alkylamine, halogen, alkyl, aryl, or any R<com:Sup>8< / com:Sup> and R<com:Sup>9< / com:Sup> can together form <com:Math><semantics>=<annotation encoding="application / x-tex">=< / annotation>< / semantics>< / com:Math>O or a cycloalkyl, or any to adjacent <com:Math><semantics>R8<annotation encoding="application / x-tex">R^8< / annotation>< / semantics>< / com:Math> groups can together form a cycloalkyl. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non- natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00192] In addition, the following amino acids having the structure of Formula (XXXI-B) are included: [Image disponible dans le document PDF, Image available in the PDF document] wherein: A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene; R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; n is 0, 1, 2, 3, 4, or 5; and each R<com:Sup>8< / com:Sup> and R<com:Sup>9< / com:Sup> on each CR<com:Sup>8< / com:Sup>R<com:Sup>9< / com:Sup> group is independently selected from the group consisting of H, alkoxy, alkylamine, halogen, alkyl, aryl, or any R<com:Sup>8< / com:Sup> and R<com:Sup>9< / com:Sup> can together form =O or a cycloalkyl, or any to adjacent R<com:Sup>8< / com:Sup> groups can together form a cycloalkyl. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non- natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00193] In addition, the following amino acids having the structure of Formula (XXXII) are included: [Image disponible dans le document PDF, Image available in the PDF document] wherein: A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene; R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; X1 is C, S, or S(O); and L is alkylene, substituted alkylene, N(R')(alkylene) or N(R')(substituted alkylene), where R' is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non- natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00194] The In addition, the following amino acids having the structure of Formula (XXXII-A) are included: [Image disponible dans le document PDF, Image available in the PDF document] wherein: A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene; R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; L is alkylene, substituted alkylene, N(R')(alkylene) or N(R')(substituted alkylene), where R' is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00195] In addition, the following amino acids having the structure of Formula (XXXII-B) are included: [Image disponible dans le document PDF, Image available in the PDF document] wherein: A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene; R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; L is alkylene, substituted alkylene, N(R')(alkylene) or N(R')(substituted alkylene), where R' is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00196] In addition, amino acids having the structure of Formula (XXXX) are included: [Image disponible dans le document PDF, Image available in the PDF document] wherein: A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene; [Image disponible dans le document PDF, Image available in the PDF document] <com:Math><semantics>−C(R3)−<annotation encoding="application / x-tex">-C(R_3)-< / annotation>< / semantics>< / com:Math> [Image disponible dans le document PDF, Image available in the PDF document] [Image disponible dans le document PDF, Image available in the PDF document] (b) [Image disponible dans le document PDF, Image available in the PDF document] [Image disponible dans le document PDF, Image available in the PDF document] (b) [Image disponible dans le document PDF, Image available in the PDF document] [Image disponible dans le document PDF, Image available in the PDF document] [Image disponible dans le document PDF, Image available in the PDF document] (a) (a) where (a) indicates bonding to the A group and (b) indicates bonding to respective carbonyl groups, R<com:Sub>3< / com:Sub> and R<com:Sub>4< / com:Sub> are independently chosen from H, halogen, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl, or R<com:Sub>3< / com:Sub> and R<com:Sub>4< / com:Sub> or two R<com:Sub>3< / com:Sub> groups or two R<com:Sub>4< / com:Sub> groups optionally form a cycloalkyl or a heterocycloalkyl; R is H, halogen, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; T<com:Sub>3< / com:Sub> is a bond, C(R)(R), O, or S, and R is H, halogen, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00197] In addition, amino acids having the structure of Formula (XXXXI) are included: [Image disponible dans le document PDF, Image available in the PDF document] wherein: [Image disponible dans le document PDF, Image available in the PDF document] <com:Math><semantics>−C(R3)−<annotation encoding="application / x-tex">-C(R_3)-< / annotation>< / semantics>< / com:Math> [Image disponible dans le document PDF, Image available in the PDF document] [Image disponible dans le document PDF, Image available in the PDF document] (b) [Image disponible dans le document PDF, Image available in the PDF document] [Image disponible dans le document PDF, Image available in the PDF document] (b) [Image disponible dans le document PDF, Image available in the PDF document] [Image disponible dans le document PDF, Image available in the PDF document] [Image disponible dans le document PDF, Image available in the PDF document] (a) (a) where (a) indicates bonding to the A group and (b) indicates bonding to respective carbonyl groups, R<com:Sub>3< / com:Sub> and R<com:Sub>4< / com:Sub> are independently chosen from H, halogen, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl, or R<com:Sub>3< / com:Sub> and R<com:Sub>4< / com:Sub> or two R<com:Sub>3< / com:Sub> groups or two R<com:Sub>4< / com:Sub> groups optionally form a cycloalkyl or a heterocycloalkyl; R is H, halogen, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; T<com:Sub>3< / com:Sub> is a bond, C(R)(R), O, or S, and R is H, halogen, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; each R<com:Sub>a< / com:Sub> is independently selected from the group consisting of H, halogen, alkyl, substituted alkyl, <com:Math><semantics>−N(R′)2<annotation encoding="application / x-tex">-N(R')_2< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(O)kR′<annotation encoding="application / x-tex">-C(O)_kR'< / annotation>< / semantics>< / com:Math> where k is 1, 2, or 3, <com:Math><semantics>−C(O)N(R′)2<annotation encoding="application / x-tex">-C(O)N(R')_2< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−OR′<annotation encoding="application / x-tex">-OR'< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−S(O)kR′<annotation encoding="application / x-tex">-S(O)_kR'< / annotation>< / semantics>< / com:Math>, where each R' is independently H, alkyl, or substituted alkyl. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00198] In addition, amino acids having the structure of Formula (XXXXII) are included: [Image disponible dans le document PDF, Image available in the PDF document] wherein: R is H, halogen, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; and T<com:Sub>3< / com:Sub> is O, or S. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00199] In addition, amino acids having the structure of Formula (XXXXIII) are included: [Image disponible dans le document PDF, Image available in the PDF document] wherein: R is H, halogen, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl.

[00200] In addition, the following amino acids having structures of Formula (XXXXIII) are included: [Image disponible dans le document PDF, Image available in the PDF document] Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non- natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00201] Non-natural amino acids containing a hydroxylamine (also called an aminooxy) group allow for reaction with a variety of electrophilic groups to form conjugates (including but not limited to, with PEG or other water soluble polymers). Like hydrazines, hydrazides and semicarbazides, the enhanced nucleophilicity of the aminooxy group permits it to react efficiently and selectively with a variety of molecules that contain carbonyl- or dicarbonyl- groups, including but not limited to, ketones, aldehydes or other functional groups with similar chemical reactivity. See, e.g., Shao, J. and Tam, J., J. Am. Chem. Soc. 117:3893-3899 (1995); H. Hang and C. Bertozzi, Acc. Chem. Res. 34(9): 727-736 (2001). Whereas the result of reaction with a hydrazine group is the corresponding hydrazone, however, an oxime results generally from the reaction of an aminooxy group with a carbonyl- or dicarbonyl-containing group such as, by way of example, a ketones, aldehydes or other functional groups with similar chemical reactivity.

[00202] Thus, in certain embodiments described herein are non-natural amino acids with sidechains comprising a hydroxylamine group, a hydroxylamine-like group (which has reactivity similar to a hydroxylamine group and is structurally similar to a hydroxylamine group), a masked hydroxylamine group (which can be readily converted into a hydroxylamine group), or a protected hydroxylamine group (which has reactivity similar to a hydroxylamine group upon deprotection). Such amino acids include amino acids having the structure of Formula (XIV): [Image disponible dans le document PDF, Image available in the PDF document] wherein: A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene; B is optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -O-, -O-(alkylene or substituted alkylene)-, <com:Math><semantics>−S<annotation encoding="application / x-tex">-S< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−S<annotation encoding="application / x-tex">-S< / annotation>< / semantics>< / com:Math>-(alkylene or substituted alkylene)-, <com:Math><semantics>−S(O)k<annotation encoding="application / x-tex">-S(O)_k< / annotation>< / semantics>< / com:Math>- where k is 1, 2, or 3, <com:Math><semantics>−S(O)k<annotation encoding="application / x-tex">-S(O)_k< / annotation>< / semantics>< / com:Math>(alkylene or substituted alkylene)-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−NS(O)2<annotation encoding="application / x-tex">-NS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−OS(O)2<annotation encoding="application / x-tex">-OS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-(alkylene or substituted alkylene)-, <com:Math><semantics>−C(S)<annotation encoding="application / x-tex">-C(S)< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−C(S)<annotation encoding="application / x-tex">-C(S)< / annotation>< / semantics>< / com:Math>-(alkylene or substituted alkylene)-, <com:Math><semantics>−N(R′)<annotation encoding="application / x-tex">-N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−NR′<annotation encoding="application / x-tex">-NR'< / annotation>< / semantics>< / com:Math>- (alkylene or substituted alkylene)-, -C(O)N(R')-, -CON(R')-(alkylene or substituted alkylene)-, -CSN(R')-, -CSN(R')-(alkylene or substituted alkylene)-, -N(R')CO-(alkylene or substituted alkylene)-, <com:Math><semantics>−N(R′)C(O)O<annotation encoding="application / x-tex">-N(R')C(O)O< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−S(O)kN(R′)<annotation encoding="application / x-tex">-S(O)_kN(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)C(O)N(R′)<annotation encoding="application / x-tex">-N(R')C(O)N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)C(S)N(R′)<annotation encoding="application / x-tex">-N(R')C(S)N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)S(O)kN(R′)−<annotation encoding="application / x-tex">-N(R')S(O)_kN(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)−N=<annotation encoding="application / x-tex">-N(R')-N=< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)=N−<annotation encoding="application / x-tex">-C(R')=N-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)=N−<annotation encoding="application / x-tex">-C(R')=N-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)=N−<annotation encoding="application / x-tex">-C(R')=N-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)=N−<annotation encoding="application / x-tex">-C(R')=N-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)=N−<annotation encoding="application / x-tex">-C(R')=N-< / annotation>< / semantics>< / com:Math> <com:Math><semantics>N=N−<annotation encoding="application / x-tex">N=N-< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−C(R′)2−N(R′)−N(R′)−<annotation encoding="application / x-tex">-C(R')_2-N(R')-N(R')-< / annotation>< / semantics>< / com:Math>, where each R' is independently H, alkyl, or substituted alkyl; K is <com:Math><semantics>−NR6R7<annotation encoding="application / x-tex">-NR_6R_7< / annotation>< / semantics>< / com:Math> or <com:Math><semantics>−N=CR6R7<annotation encoding="application / x-tex">-N=CR_6R_7< / annotation>< / semantics>< / com:Math>; <com:Math><semantics>R1<annotation encoding="application / x-tex">R_1< / annotation>< / semantics>< / com:Math> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; each of R<com:Sub>3< / com:Sub> and R<com:Sub>4< / com:Sub> is independently H, halogen, lower alkyl, or substituted lower alkyl, or R<com:Sub>3< / com:Sub> and R<com:Sub>4< / com:Sub> or two R<com:Sub>3< / com:Sub> groups optionally form a cycloalkyl or a heterocycloalkyl; each of R<com:Sub>6< / com:Sub> and R<com:Sub>7< / com:Sub> is independently selected from the group consisting of H, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy, substituted alkoxy, polyalkylene oxide, substituted polyalkylene oxide, aryl, substituted aryl, heteroaryl, substituted heteroaryl, alkaryl, substituted alkaryl, aralkyl, and substituted aralkyl, -C(O)R", -C(O)<com:Sub>2< / com:Sub>R", - C(O)N(R")<com:Sub>2< / com:Sub>, wherein each R" is independently hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy, substituted alkoxy, aryl, substituted aryl, heteroaryl, alkaryl, substituted alkaryl, aralkyl, or substituted aralkyl; or R<com:Sub>6< / com:Sub> or R<com:Sub>7< / com:Sub> is L-X, where X is a selected from the group consisting of a label; a dye; a polymer; a water-soluble polymer; a derivative of polyethylene glycol; a photocrosslinker; a cytotoxic compound; a drug; an affinity label; a photoaffinity label; a reactive compound; a resin; a second protein or polypeptide or polypeptide analog; an antibody or antibody fragment; a metal chelator; a cofactor; a fatty acid; a carbohydrate; a polynucleotide; a DNA; a RNA; an antisense polynucleotide; a saccharide, a water-soluble dendrimer, a cyclodextrin, a biomaterial; a nanoparticle; a spin label; a fluorophore, a metal-containing moiety; a radioactive moiety; a novel functional group; a group that covalently or noncovalently interacts with other molecules; a photocaged moiety; a photoisomerizable moiety; biotin; a biotin analogue; a moiety incorporating a heavy atom; a chemically cleavable group; a photocleavable group; an elongated side chain; a carbon-linked sugar; a redox-active agent; an amino thioacid; a toxic moiety; an isotopically labeled moiety; a biophysical probe; a phosphorescent group; a chemiluminescent group; an electron dense group; a magnetic group; an intercalating group; a chromophore; an energy transfer agent; a biologically active agent; a detectable label; and any combination thereof; and L is optional, and when present is a linker selected from the group consisting of alkylene, substituted alkylene, alkenylene, substituted alkenylene, -O-, -O-(alkylene or substituted alkylene)-, <com:Math><semantics>−S<annotation encoding="application / x-tex">-S< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−S<annotation encoding="application / x-tex">-S< / annotation>< / semantics>< / com:Math>-(alkylene or substituted alkylene)-, <com:Math><semantics>−S(O)k<annotation encoding="application / x-tex">-S(O)_k< / annotation>< / semantics>< / com:Math>- where k is 1, 2, or 3, - <com:Math><semantics>S(O)k<annotation encoding="application / x-tex">S(O)_k< / annotation>< / semantics>< / com:Math>(alkylene or substituted alkylene)-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-(alkylene or substituted alkylene)-, <com:Math><semantics>−<annotation encoding="application / x-tex">-< / annotation>< / semantics>< / com:Math> <com:Math><semantics>C(S)<annotation encoding="application / x-tex">C(S)< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−C(S)<annotation encoding="application / x-tex">-C(S)< / annotation>< / semantics>< / com:Math>-(alkylene or substituted alkylene)-, <com:Math><semantics>−N(R′)<annotation encoding="application / x-tex">-N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−NR′<annotation encoding="application / x-tex">-NR'< / annotation>< / semantics>< / com:Math>-(alkylene or substituted alkylene)-, -C(O)N(R')-, -CON(R')-(alkylene or substituted alkylene)-, -CSN(R')-, - CSN(R')-(alkylene or substituted alkylene)-, -N(R')CO-(alkylene or substituted alkylene)-, - <com:Math><semantics>N(R′)C(O)O−,−S(O)kN(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(S)N(R′)−,−N(R′)S(O)kN(R′)−,−N(R′)S(O)kN(R′)−,−N(R′)S(O)kN(R′)−,−N(R′)S(O)kN(R′)−,−N(R′)S(O)kN(R′)−,−N(R′)S(O)kN(R′)−,−N(R′)S(O)kN(R′)−,−N(R′)S(O)kN(R′<annotation encoding="application / x-tex">N(R')C(O)O-, -S(O)_kN(R')-, -N(R')C(O)N(R')-, -N(R')C(S)N(R')-, -N(R')S(O)_kN(R')-, -N(R')S(O)_kN(R')-, -N(R')S(O)_kN(R')-, -N(R')S(O)_kN(R')-, -N(R')S(O)_kN(R')-, -N(R')S(O)_kN(R')-, -N(R')S(O)_kN(R')-, -N(R')S(O)_kN(R'< / annotation>< / semantics>< / com:Math> [Image disponible dans le document PDF, Image available in the PDF document] N(R')–N(R')–, where each R' is independently H, alkyl, or substituted alkyl. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00203] In certain embodiments of compounds of Formula (XIV), A is phenylene or substituted phenylene. In certain embodiments of compounds of Formula (XIV), B is - (alkylene or substituted alkylene)-, -O-(alkylene or substituted alkylene)-, -S-(alkylene or substituted alkylene)-, or -C(O)-(alkylene or substituted alkylene)-. In certain embodiments of compounds of Formula (XIV), B is <com:Math><semantics>−O(CH2)2<annotation encoding="application / x-tex">-O(CH_2)_2< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−S(CH2)2<annotation encoding="application / x-tex">-S(CH_2)_2< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−NH(CH2)2<annotation encoding="application / x-tex">-NH(CH_2)_2< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−CO(CH2)2<annotation encoding="application / x-tex">-CO(CH_2)_2< / annotation>< / semantics>< / com:Math>, or <com:Math><semantics>−(CH2)n<annotation encoding="application / x-tex">-(CH_2)_n< / annotation>< / semantics>< / com:Math> where n is 1 to 4. In certain embodiments of compounds of Formula (XIV), <com:Math><semantics>R1<annotation encoding="application / x-tex">R_1< / annotation>< / semantics>< / com:Math> is H, tert-butyloxycarbonyl (Boc), 9-Fluorenylmethoxycarbonyl (Fmoc), N-acetyl, tetrafluoroacetyl (TFA), or benzyloxycarbonyl (Cbz). In certain embodiments of compounds of Formula (XIV), R<com:Sub>1< / com:Sub> is a resin, amino acid, polypeptide, or polynucleotide. In certain embodiments of compounds of Formula (XIV), wherein R<com:Sub>2< / com:Sub> is OH, O-methyl, O-ethyl, or O-t- butyl. In certain embodiments of compounds of Formula (XIV), R<com:Sub>2< / com:Sub> is a resin, amino acid, polypeptide, or polynucleotide. In certain embodiments of compounds of Formula (XIV), R<com:Sub>2< / com:Sub> is a polynucleotide. In certain embodiments of compounds of Formula (XIV), R<com:Sub>2< / com:Sub> is ribonucleic acid (RNA). In certain embodiments of compounds of Formula (XIV), R2 is tRNA. In certain embodiments of compounds of Formula (XIV), the tRNA specifically recognizes a codon selected from the group consisting of an amber codon, ochre codon, opal codon, a unique codon, a rare codon, an unnatural codon, a five-base codon, and a four-base codon. In certain embodiments of compounds of Formula (XIV), R<com:Sub>2< / com:Sub> is a suppressor tRNA. In certain embodiments of compounds of Formula (XIV), each of R<com:Sub>6< / com:Sub> and R<com:Sub>7< / com:Sub> is independently selected from the group consisting of H, alkyl, substituted alkyl, alkoxy, substituted alkoxy, polyalkylene oxide, substituted polyalkylene oxide, aryl, substituted aryl, heteroaryl, substituted heteroaryl, alkaryl, substituted alkaryl, aralkyl, and substituted aralkyl. In certain embodiments of compounds of Formula (XIV), each of R<com:Sub>6< / com:Sub> and R<com:Sub>7< / com:Sub> is independently selected from the group consisting of H, methyl, phenyl, and -[(alkylene or substituted alkylene)-O- (hydrogen, alkyl, or substituted alkyl)<com:Math><semantics>x<annotation encoding="application / x-tex">_{x}< / annotation>< / semantics>< / com:Math>, wherein x is from 1-50. In certain embodiments of compounds of Formula (XIV), K is –NR<com:Sub>6< / com:Sub>R<com:Sub>7< / com:Sub>.

[00204] In certain embodiments of compounds of Formula (XIV), X is a biologically active agent selected from the group consisting of a peptide, protein, enzyme, antibody, drug, dye, lipid, nucleosides, oligonucleotide, cell, virus, liposome, microparticle, and micelle. In certain embodiments of compounds of Formula (XIV), X is a drug selected from the group consisting of an antibiotic, fungicide, anti-viral agent, anti-inflammatory agent, anti-tumor agent, cardiovascular agent, anti-anxiety agent, hormone, growth factor, and steroidal agent. In certain embodiments of compounds of Formula (XIV), X is an enzyme selected from the group consisting of horseradish peroxidase, alkaline phosphatase, β-galactosidase, and glucose oxidase. In certain embodiments of compounds of Formula (XIV), X is a detectable label selected from the group consisting of a fluorescent, phosphorescent, chemiluminescent, chelating, electron dense, magnetic, intercalating, radioactive, chromophoric, and energy transfer moiety.

[00205] In certain embodiments, compounds of Formula (XIV) are stable in aqueous solution for at least 1 month under mildly acidic conditions. In certain embodiments, compounds of Formula (XIV) are stable for at least 2 weeks under mildly acidic conditions. In certain embodiments, compound of Formula (XIV) are stable for at least 5 days under mildly acidic conditions. In certain embodiments, such acidic conditions are pH 2 to 8.

[00206] Such amino acids include amino acids having the structure of Formula (XV): [Image disponible dans le document PDF, Image available in the PDF document] wherein A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene; B is optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -O-, -O-(alkylene or substituted alkylene)-, <com:Math><semantics>−S<annotation encoding="application / x-tex">-S< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−S<annotation encoding="application / x-tex">-S< / annotation>< / semantics>< / com:Math>-(alkylene or substituted alkylene)-, <com:Math><semantics>−S(O)k<annotation encoding="application / x-tex">-S(O)_k< / annotation>< / semantics>< / com:Math>- where k is 1, 2, or 3, <com:Math><semantics>−S(O)k<annotation encoding="application / x-tex">-S(O)_k< / annotation>< / semantics>< / com:Math>(alkylene or substituted alkylene)-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−NS(O)2<annotation encoding="application / x-tex">-NS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−OS(O)2<annotation encoding="application / x-tex">-OS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-(alkylene or substituted alkylene)-, -C(S)-, -C(S)-(alkylene or substituted alkylene)-, -N(R')-, -NR'- (alkylene or substituted alkylene)-, -C(O)N(R')-, -CON(R')-(alkylene or substituted alkylene)-, -CSN(R')-, -CSN(R')-(alkylene or substituted alkylene)-, -N(R')CO-(alkylene or substituted alkylene)-, <com:Math><semantics>−N(R′)C(O)O−<annotation encoding="application / x-tex">-N(R')C(O)O-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−S(O)kN(R′)−<annotation encoding="application / x-tex">-S(O)_kN(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)C(O)N(R′)−<annotation encoding="application / x-tex">-N(R')C(O)N(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)C(S)N(R′)−<annotation encoding="application / x-tex">-N(R')C(S)N(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)S(O)kN(R′)−,−N(R′)−N=,−C(R′)=N−,−C(R′)=N−N(R′)−,−C(R′)=N−N=,−C(R′)2−<annotation encoding="application / x-tex">-N(R')S(O)_kN(R')-, -N(R')-N=, -C(R')=N-, -C(R')=N-N(R')-, -C(R')=N-N=, -C(R')_2-< / annotation>< / semantics>< / com:Math> <com:Math><semantics>N=N−<annotation encoding="application / x-tex">N=N-< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−C(R′)2−N(R′)−N(R′)−<annotation encoding="application / x-tex">-C(R')_2-N(R')-N(R')-< / annotation>< / semantics>< / com:Math>, where each R' is independently H, alkyl, or substituted alkyl; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; each of R<com:Sub>3< / com:Sub> and R<com:Sub>4< / com:Sub> is independently H, halogen, lower alkyl, or substituted lower alkyl, or R<com:Sub>3< / com:Sub> and R<com:Sub>4< / com:Sub> or two R<com:Sub>3< / com:Sub> groups optionally form a cycloalkyl or a heterocycloalkyl. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00207] A non-limiting, representative amino acid has the following structure: [Image disponible dans le document PDF, Image available in the PDF document] Such a non-natural amino acid may be in the form of a salt, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00208] Non-natural amino acids containing an oxime group allow for reaction with a variety of reagents that contain certain reactive carbonyl- or dicarbonyl-groups (including but not limited to, ketones, aldehydes, or other groups with similar reactivity) to form new non- natural amino acids comprising a new oxime group. Such an oxime exchange reaction allow for the further functionalization of non-natural amino acid polypeptides. Further, the original non-natural amino acids containing an oxime group may be useful in their own right as long as the oxime linkage is stable under conditions necessary to incorporate the amino acid into a polypeptide (e.g., the in vivo, in vitro and chemical synthetic methods described herein).

[00209] Thus, in certain embodiments described herein are non-natural amino acids with sidechains comprising an oxime group, an oxime-like group (which has reactivity similar to an oxime group and is structurally similar to an oxime group), a masked oxime group (which can be readily converted into an oxime group), or a protected oxime group (which has reactivity similar to an oxime group upon deprotection). Such amino acids include amino acids having the structure of Formula (XI): [Image disponible dans le document PDF, Image available in the PDF document] wherein: A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene; B is optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -O-, -O-(alkylene or substituted alkylene)-, -S-, -S-(alkylene or substituted alkylene)-, -S(O)<com:Sub>k< / com:Sub>- where k is 1, 2, or 3, <com:Math><semantics>−S(O)k<annotation encoding="application / x-tex">-S(O)_k< / annotation>< / semantics>< / com:Math>(alkylene or substituted alkylene)-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−NS(O)2<annotation encoding="application / x-tex">-NS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−OS(O)2<annotation encoding="application / x-tex">-OS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-(alkylene or substituted alkylene)-, -C(S)-, -C(S)-(alkylene or substituted alkylene)-, -N(R')-, -NR'- (alkylene or substituted alkylene)-, -C(O)N(R')-, -CON(R')-(alkylene or substituted alkylene)-, -CSN(R')-, -CSN(R')-(alkylene or substituted alkylene)-, -N(R')CO-(alkylene or substituted alkylene)-, <com:Math><semantics>−N(R′)C(O)O−<annotation encoding="application / x-tex">-N(R')C(O)O-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−S(O)kN(R′)−<annotation encoding="application / x-tex">-S(O)_kN(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)C(O)N(R′)−<annotation encoding="application / x-tex">-N(R')C(O)N(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)C(S)N(R′)−<annotation encoding="application / x-tex">-N(R')C(S)N(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)S(O)kN(R′)−,−N(R′)−N=,−C(R′)=N−,−C(R′)=N−N(R′)−,−C(R′)=N−N=,−C(R′)2−<annotation encoding="application / x-tex">-N(R')S(O)_kN(R')-, -N(R')-N=, -C(R')=N-, -C(R')=N-N(R')-, -C(R')=N-N=, -C(R')_2-< / annotation>< / semantics>< / com:Math> <com:Math><semantics>N=N−<annotation encoding="application / x-tex">N=N-< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−C(R′)2−N(R′)−N(R′)−<annotation encoding="application / x-tex">-C(R')_2-N(R')-N(R')-< / annotation>< / semantics>< / com:Math>, where each R' is independently H, alkyl, or substituted alkyl; R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; each of R<com:Sub>3< / com:Sub> and R<com:Sub>4< / com:Sub> is independently H, halogen, lower alkyl, or substituted lower alkyl, or R<com:Sub>3< / com:Sub> and R<com:Sub>4< / com:Sub> or two R<com:Sub>3< / com:Sub> optionally form a cycloalkyl or a heterocycloalkyl; R<com:Sub>5< / com:Sub> is H, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy, substituted alkylalkoxy, polyalkylene oxide, substituted polyalkylene oxide, aryl, substituted aryl, heteroaryl, substituted heteroaryl, alkaryl, substituted alkaryl, aralkyl, substituted aralkyl, -(alkylene or substituted alkylene)-ON(R")<com:Sub>2< / com:Sub>, -(alkylene or substituted alkylene)- C(O)SR", -(alkylene or substituted alkylene)-S-S-(aryl or substituted aryl), -C(O)R", - <com:Math><semantics>C(O)2R″<annotation encoding="application / x-tex">C(O)_2R''< / annotation>< / semantics>< / com:Math>, or <com:Math><semantics>−C(O)N(R″)2<annotation encoding="application / x-tex">-C(O)N(R'')_2< / annotation>< / semantics>< / com:Math>, wherein each R'' is independently hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy, substituted alkoxy, aryl, substituted aryl, heteroaryl, alkaryl, substituted alkaryl, aralkyl, or substituted aralkyl; or R<com:Sub>5< / com:Sub> is L-X, where X is a selected from the group consisting of a label; a dye; a polymer; a water-soluble polymer; a derivative of polyethylene glycol; a photocrosslinker; a cytotoxic compound; a drug; an affinity label; a photoaffinity label; a reactive compound; a resin; a second protein or polypeptide or polypeptide analog; an antibody or antibody fragment; a metal chelator; a cofactor; a fatty acid; a carbohydrate; a polynucleotide; a DNA; a RNA; an antisense polynucleotide; a saccharide, a water-soluble dendrimer, a cyclodextrin, a biomaterial; a nanoparticle; a spin label; a fluorophore, a metal-containing moiety; a radioactive moiety; a novel functional group; a group that covalently or noncovalently interacts with other molecules; a photocaged moiety; a photoisomerizable moiety; biotin; a biotin analogue; a moiety incorporating a heavy atom; a chemically cleavable group; a photocleavable group; an elongated side chain; a carbon-linked sugar; a redox-active agent; an amino thioacid; a toxic moiety; an isotopically labeled moiety; a biophysical probe; a phosphorescent group; a chemiluminescent group; an electron dense group; a magnetic group; an intercalating group; a chromophore; an energy transfer agent; a biologically active agent; a detectable label; and any combination thereof; and L is optional, and when present is a linker selected from the group consisting of alkylene, substituted alkylene, alkenylene, substituted alkenylene, -O-, - O-(alkylene or substituted alkylene)-, <com:Math><semantics>−S<annotation encoding="application / x-tex">-S< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−S<annotation encoding="application / x-tex">-S< / annotation>< / semantics>< / com:Math>-(alkylene or substituted alkylene)-, <com:Math><semantics>−S(O)k<annotation encoding="application / x-tex">-S(O)_k< / annotation>< / semantics>< / com:Math>- where k is 1, 2, or 3, <com:Math><semantics>−S(O)k<annotation encoding="application / x-tex">-S(O)_k< / annotation>< / semantics>< / com:Math> (alkylene or substituted alkylene)-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-(alkylene or substituted alkylene)-, <com:Math><semantics>−C(S)<annotation encoding="application / x-tex">-C(S)< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−C(S)<annotation encoding="application / x-tex">-C(S)< / annotation>< / semantics>< / com:Math>-(alkylene or substituted alkylene)-, <com:Math><semantics>−N(R′)<annotation encoding="application / x-tex">-N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−NR′<annotation encoding="application / x-tex">-NR'< / annotation>< / semantics>< / com:Math>- (alkylene or substituted alkylene)-, -C(O)N(R')-, -CON(R')-(alkylene or substituted alkylene)-, -CSN(R')-, -CSN(R')-(alkylene or substituted alkylene)-, -N(R')CO-(alkylene or substituted alkylene)-, -N(R')C(O)O-, -(alkylene or substituted alkylene)-O-N=CR'-, - (alkylene or substituted alkylene)—C(O)NR'—(alkylene or substituted alkylene)—, —(alkylene or substituted alkylene)–S(O)<com:Sub>k< / com:Sub>–(alkylene or substituted alkylene)–S–, –(alkylene or substituted alkylene)-S-S-, <com:Math><semantics>−S(O)kN(R′)<annotation encoding="application / x-tex">-S(O)_kN(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)C(O)N(R′)<annotation encoding="application / x-tex">-N(R')C(O)N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)C(S)N(R′)<annotation encoding="application / x-tex">-N(R')C(S)N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−<annotation encoding="application / x-tex">-< / annotation>< / semantics>< / com:Math> <com:Math><semantics>N(R′)S(O)kN(R′)−,−N(R′)−N=,−C(R′)=N−,−C(R′)=N−N(R′)−,−C(R′)=N−N=,−C(R′)2−<annotation encoding="application / x-tex">N(R')S(O)_kN(R')-, -N(R')-N=, -C(R')=N-, -C(R')=N-N(R')-, -C(R')=N-N=, -C(R')_2-< / annotation>< / semantics>< / com:Math> <com:Math><semantics>N=N−<annotation encoding="application / x-tex">N=N-< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−C(R′)2−N(R′)−N(R′)−<annotation encoding="application / x-tex">-C(R')_2-N(R')-N(R')-< / annotation>< / semantics>< / com:Math>, where each R' is independently H, alkyl, or substituted alkyl; with a proviso that when A and B are absent, R is not methyl. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00210] In certain embodiments of compounds of Formula (XI), B is -O-(alkylene or substituted alkylene)—. In certain embodiments of compounds of Formula (XI), B is – <com:Math><semantics>O(CH2)<annotation encoding="application / x-tex">O(CH_2)< / annotation>< / semantics>< / com:Math>—. In certain embodiments of compounds of Formula (XI), R is <com:Math><semantics>C1−4<annotation encoding="application / x-tex">C_{1-4}< / annotation>< / semantics>< / com:Math> alkyl. In certain embodiments of compounds of Formula (XI), R is -CH<com:Sub>3< / com:Sub>. In certain embodiments of compounds of Formula (XI), R<com:Sub>1< / com:Sub> is H, tert-butyloxycarbonyl (Boc), 9- fluorenylmethoxycarbonyl (Fmoc), N-acetyl, tetrafluoroacetyl (TFA), or benzyloxycarbonyl (Cbz). In certain embodiments of compounds of Formula (XI), R<com:Sub>1< / com:Sub> is a resin, amino acid, polypeptide, or polynucleotide. In certain embodiments of compounds of Formula (XI), R<com:Sub>2< / com:Sub> is OH, O-methyl, O-ethyl, or O-t-butyl. In certain embodiments of compounds of Formula (XI), R<com:Sub>2< / com:Sub> is a resin, amino acid, polypeptide, or polynucleotide. In certain embodiments of compounds of Formula (XI), R<com:Sub>2< / com:Sub> is a polynucleotide. In certain embodiments of compounds of Formula (XI), R<com:Sub>2< / com:Sub> is ribonucleic acid (RNA). In certain embodiments of compounds of Formula (XI), R<com:Sub>2< / com:Sub> is tRNA. In certain embodiments of compounds of Formula (XI), the tRNA specifically recognizes a selector codon. In certain embodiments of compounds of Formula (XI), the selector codon is selected from the group consisting of an amber codon, ochre codon, opal codon, a unique codon, a rare codon, an unnatural codon, a five-base codon, and a four-base codon. In certain embodiments of compounds of Formula (XI), R<com:Sub>2< / com:Sub> is a suppressor tRNA. In certain embodiments of compounds of Formula (XI), R<com:Sub>5< / com:Sub> is alkylalkoxy, substituted alkylalkoxy, polyalkylene oxide, substituted polyalkylene oxide, or <com:Math><semantics>−C(O)2R″<annotation encoding="application / x-tex">-C(O)_2R''< / annotation>< / semantics>< / com:Math>. In certain embodiments of compounds of Formula (XI), R<com:Sub>5< / com:Sub> is -[(alkylene or substituted alkylene)-O- (hydrogen, alkyl, or substituted alkyl)]<com:Sub>x< / com:Sub>, wherein x is from 1-50. In certain embodiments of compounds of Formula (XI), R<com:Sub>5< / com:Sub> is –(CH<com:Sub>2< / com:Sub>CH<com:Sub>2< / com:Sub>)–O–CH<com:Sub>3< / com:Sub> or –COOH.

[00211] In certain embodiments, compounds of Formula (XI) are stable in aqueous solution for at least 1 month under mildly acidic conditions. In certain embodiments, compounds of Formula (XI) are stable for at least 2 weeks under mildly acidic conditions. In certain embodiments, compound of Formula (XI) are stable for at least 5 days under mildly acidic conditions. In certain embodiments, such acidic conditions are pH 2 to 8.

[00212] Amino acids of Formula (XI) include amino acids having the structure of Formula (XII): [Image disponible dans le document PDF, Image available in the PDF document] wherein, B is optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -O-, -O-(alkylene or substituted alkylene)-, -S-, -S-(alkylene or substituted alkylene)-, -S(O)<com:Sub>k< / com:Sub>- where k is 1, 2, or 3, - <com:Math><semantics>S(O)k<annotation encoding="application / x-tex">S(O)_k< / annotation>< / semantics>< / com:Math>(alkylene or substituted alkylene)-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−NS(O)2<annotation encoding="application / x-tex">-NS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−OS(O)2<annotation encoding="application / x-tex">-OS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-(alkylene or substituted alkylene)—, <com:Math><semantics>−C(S)<annotation encoding="application / x-tex">-C(S)< / annotation>< / semantics>< / com:Math>—, <com:Math><semantics>−C(S)<annotation encoding="application / x-tex">-C(S)< / annotation>< / semantics>< / com:Math>—(alkylene or substituted alkylene)—, <com:Math><semantics>−N(R′)<annotation encoding="application / x-tex">-N(R')< / annotation>< / semantics>< / com:Math>—, <com:Math><semantics>−NR′<annotation encoding="application / x-tex">-NR'< / annotation>< / semantics>< / com:Math>— (alkylene or substituted alkylene)—, -C(O)N(R')—, -CON(R')—(alkylene or substituted alkylene)—, -CSN(R')—, -CSN(R')—(alkylene or substituted alkylene)—, -N(R')CO—(alkylene or substituted alkylene)-, <com:Math><semantics>−N(R′)C(O)O<annotation encoding="application / x-tex">-N(R')C(O)O< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−S(O)kN(R′)<annotation encoding="application / x-tex">-S(O)_kN(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)C(O)N(R′)<annotation encoding="application / x-tex">-N(R')C(O)N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−<annotation encoding="application / x-tex">-< / annotation>< / semantics>< / com:Math> <com:Math><semantics>N(R′)C(S)N(R′)−,−N(R′)S(O)kN(R′)−,−N(R′)−N=,−C(R′)=N−,−C(R′)=N−N(R′)−,−N(R′)−,−N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−<annotation encoding="application / x-tex">N(R')C(S)N(R')-, -N(R')S(O)_kN(R')-, -N(R')-N=, -C(R')=N-, -C(R')=N-N(R')-, -N(R')-, -N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-< / annotation>< / semantics>< / com:Math> <com:Math><semantics>C(R′)=N−N=<annotation encoding="application / x-tex">C(R')=N-N=< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)2−N=N−<annotation encoding="application / x-tex">-C(R')_2-N=N-< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−C(R′)2−N(R′)−N(R′)−<annotation encoding="application / x-tex">-C(R')_2-N(R')-N(R')-< / annotation>< / semantics>< / com:Math>, where each R' is independently H, alkyl, or substituted alkyl; R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; R<com:Sub>5< / com:Sub> is H, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy, substituted alkylalkoxy, polyalkylene oxide, substituted polyalkylene oxide, aryl, substituted aryl, heteroaryl, substituted heteroaryl, alkaryl, substituted alkaryl, aralkyl, substituted aralkyl, –(alkylene or substituted alkylene)—ON(R")<com:Sub>2< / com:Sub>, –(alkylene or substituted alkylene)—C(O)SR", –(alkylene or substituted alkylene)–S–S–(aryl or substituted aryl), <com:Math><semantics>−C(O)R″<annotation encoding="application / x-tex">-C(O)R''< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(O)2R″<annotation encoding="application / x-tex">-C(O)_2R''< / annotation>< / semantics>< / com:Math>, or <com:Math><semantics>−C(O)N(R″)2<annotation encoding="application / x-tex">-C(O)N(R'')_2< / annotation>< / semantics>< / com:Math>, wherein each R" is independently hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy, substituted alkoxy, aryl, substituted aryl, heteroaryl, alkaryl, substituted alkaryl, aralkyl, or substituted aralkyl; or R<com:Sub>5< / com:Sub> is L–X, where X is a selected from the group consisting of a label; a dye; a polymer; a water-soluble polymer; a derivative of polyethylene glycol; a photocrosslinker; a cytotoxic compound; a drug; an affinity label; a photoaffinity label; a reactive compound; a resin; a second protein or polypeptide or polypeptide analog; an antibody or antibody fragment; a metal chelator; a cofactor; a fatty acid; a carbohydrate; a polynucleotide; a DNA; a RNA; an antisense polynucleotide; a saccharide, a water-soluble dendrimer, a cyclodextrin, a biomaterial; a nanoparticle; a spin label; a fluorophore, a metal- containing moiety; a radioactive moiety; a novel functional group; a group that covalently or noncovalently interacts with other molecules; a photocaged moiety; a photoisomerizable moiety; biotin; a biotin analogue; a moiety incorporating a heavy atom; a chemically cleavable group; a photocleavable group; an elongated side chain; a carbon-linked sugar; a redox-active agent; an amino thioacid; a toxic moiety; an isotopically labeled moiety; a biophysical probe; a phosphorescent group; a chemiluminescent group; an electron dense group; a magnetic group; an intercalating group; a chromophore; an energy transfer agent; a biologically active agent; a detectable label; and any combination thereof; and L is optional, and when present is a linker selected from the group consisting of alkylene, substituted alkylene, alkenylene, substituted alkenylene, -O-, -O-(alkylene or substituted alkylene)--, - S-, -S-(alkylene or substituted alkylene)-, -S(O)<com:Sub>k< / com:Sub>- where k is 1, 2, or 3, -S(O)<com:Sub>k< / com:Sub>(alkylene or substituted alkylene)-, -C(O)-, -C(O)-(alkylene or substituted alkylene)-, -C(S)-, -C(S)- (alkylene or substituted alkylene)—, –N(R')—, –NR'—(alkylene or substituted alkylene)—, – C(O)N(R')-, -CON(R')-(alkylene or substituted alkylene)-, -CSN(R')-, -CSN(R')-(alkylene or substituted alkylene)-, -N(R')CO-(alkylene or substituted alkylene)-, -N(R')C(O)O-, - (alkylene or substituted alkylene)—O—N=CR'—, —(alkylene or substituted alkylene)—C(O)NR'— (alkylene or substituted alkylene)—, –(alkylene or substituted alkylene)—<com:Math><semantics>S(O)k<annotation encoding="application / x-tex">S(O)_k< / annotation>< / semantics>< / com:Math>–(alkylene or substituted alkylene)—S-, –(alkylene or substituted alkylene)—S-S-, –S(O)<com:Sub>k< / com:Sub>N(R')-, – <com:Math><semantics>N(R′)C(O)N(R′)−,−N(R′)C(S)N(R′)−,−N(R′)S(O)kN(R′)−,−N(R′)−N=,−C(R′)=N−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,<annotation encoding="application / x-tex">N(R')C(O)N(R')-, -N(R')C(S)N(R')-, -N(R')S(O)_kN(R')-, -N(R')-N=, -C(R')=N-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-,< / annotation>< / semantics>< / com:Math> <com:Math><semantics>C(R′)=N−N(R′)−<annotation encoding="application / x-tex">C(R')=N-N(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)=N−N=<annotation encoding="application / x-tex">-C(R')=N-N=< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)2−N=N−<annotation encoding="application / x-tex">-C(R')_2-N=N-< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−C(R′)2−N(R′)−N(R′)−<annotation encoding="application / x-tex">-C(R')_2-N(R')-N(R')-< / annotation>< / semantics>< / com:Math>, where each R' is independently H, alkyl, or substituted alkyl. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00213] Such amino acids include amino acids having the structure of Formula (XIII): [Image disponible dans le document PDF, Image available in the PDF document] wherein, R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; R<com:Sub>5< / com:Sub> is H, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy, substituted alkylalkoxy, polyalkylene oxide, substituted polyalkylene oxide, aryl, substituted aryl, heteroaryl, substituted heteroaryl, alkaryl, substituted alkaryl, aralkyl, substituted aralkyl, –(alkylene or substituted alkylene)–ON(R")<com:Sub>2< / com:Sub>, -(alkylene or substituted alkylene)-C(O)SR", -(alkylene or substituted alkylene)-S-S-(aryl or substituted aryl), <com:Math><semantics>−C(O)R″<annotation encoding="application / x-tex">-C(O)R''< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(O)2R″<annotation encoding="application / x-tex">-C(O)_2R''< / annotation>< / semantics>< / com:Math>, or <com:Math><semantics>−C(O)N(R″)2<annotation encoding="application / x-tex">-C(O)N(R'')_2< / annotation>< / semantics>< / com:Math>, wherein each R'' is independently hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy, substituted alkoxy, aryl, substituted aryl, heteroaryl, alkaryl, substituted alkaryl, aralkyl, or substituted aralkyl; or R<com:Sub>5< / com:Sub> is L-X, where X is a selected from the group consisting of a label; a dye; a polymer; a water-soluble polymer; a derivative of polyethylene glycol; a photocrosslinker; a cytotoxic compound; a drug; an affinity label; a photoaffinity label; a reactive compound; a resin; a second protein or polypeptide or polypeptide analog; an antibody or antibody fragment; a metal chelator; a cofactor; a fatty acid; a carbohydrate; a polynucleotide; a DNA; a RNA; an antisense polynucleotide; a saccharide, a water-soluble dendrimer, a cyclodextrin, a biomaterial; a nanoparticle; a spin label; a fluorophore, a metal-containing moiety; a radioactive moiety; a novel functional group; a group that covalently or noncovalently interacts with other molecules; a photocaged moiety; a photoisomerizable moiety; biotin; a biotin analogue; a moiety incorporating a heavy atom; a chemically cleavable group; a photocleavable group; an elongated side chain; a carbon-linked sugar; a redox-active agent; an amino thioacid; a toxic moiety; an isotopically labeled moiety; a biophysical probe; a phosphorescent group; a chemiluminescent group; an electron dense group; a magnetic group; an intercalating group; a chromophore; an energy transfer agent; a biologically active agent; a detectable label; and any combination thereof; and L is optional, and when present is a linker selected from the group consisting of alkylene, substituted alkylene, alkenylene, substituted alkenylene, -O-, -O-(alkylene or substituted alkylene)-, -S-, -S-(alkylene or substituted alkylene)–, <com:Math><semantics>−S(O)k<annotation encoding="application / x-tex">-S(O)_k< / annotation>< / semantics>< / com:Math>– where k is 1, 2, or 3, <com:Math><semantics>−S(O)k<annotation encoding="application / x-tex">-S(O)_k< / annotation>< / semantics>< / com:Math>(alkylene or substituted alkylene)-, -C(O)-, -C(O)-(alkylene or substituted alkylene)-, -C(S)-, -C(S)-(alkylene or substituted alkylene)-, -N(R')-, -NR'-(alkylene or substituted alkylene)-, -C(O)N(R')-, - CON(R')-(alkylene or substituted alkylene)-, -CSN(R')-, -CSN(R')-(alkylene or substituted alkylene)-, -N(R')CO-(alkylene or substituted alkylene)-, -N(R')C(O)O-, -(alkylene or substituted alkylene)-O-N=CR'-, -(alkylene or substituted alkylene)-C(O)NR'-(alkylene or substituted alkylene)—, –(alkylene or substituted alkylene)—<com:Math><semantics>S(O)k<annotation encoding="application / x-tex">S(O)_k< / annotation>< / semantics>< / com:Math>–(alkylene or substituted alkylene)-S-, -(alkylene or substituted alkylene)-S-S-, -S(O)<com:Sub>k< / com:Sub>N(R')-, -N(R')C(O)N(R')-, - <com:Math><semantics>N(R′)C(S)N(R′)−,−N(R′)S(O)kN(R′)−,−N(R′)−N=,−C(R′)=N−,−C(R′)=N−N(R′)−,−N(R′)−,−N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−<annotation encoding="application / x-tex">N(R')C(S)N(R')-, -N(R')S(O)_kN(R')-, -N(R')-N=, -C(R')=N-, -C(R')=N-N(R')-, -N(R')-, -N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-< / annotation>< / semantics>< / com:Math> <com:Math><semantics>C(R′)=N−N=<annotation encoding="application / x-tex">C(R')=N-N=< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)2−N=N−<annotation encoding="application / x-tex">-C(R')_2-N=N-< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−C(R′)2−N(R′)−N(R′)−<annotation encoding="application / x-tex">-C(R')_2-N(R')-N(R')-< / annotation>< / semantics>< / com:Math>, where each R' is independently H, alkyl, or substituted alkyl. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00214] Further non-limiting examples of such amino acids include amino acids having the following structures: [Image disponible dans le document PDF, Image available in the PDF document] [Image disponible dans le document PDF, Image available in the PDF document] Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non- natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00215] In addition, such amino acids include amino acids having the structure of Formula (XIV): [Image disponible dans le document PDF, Image available in the PDF document] wherein: A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene; B is optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -O-, -O-(alkylene or substituted alkylene)-, -S-, -S-(alkylene or substituted alkylene)-, -S(O)<com:Sub>k< / com:Sub>- where k is 1, 2, or 3, <com:Math><semantics>−S(O)k<annotation encoding="application / x-tex">-S(O)_k< / annotation>< / semantics>< / com:Math>(alkylene or substituted alkylene)-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−NS(O)2<annotation encoding="application / x-tex">-NS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−OS(O)2<annotation encoding="application / x-tex">-OS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>- (alkylene or substituted alkylene)-, -C(S)-, -C(S)-(alkylene or substituted alkylene)-, - N(R')-, -NR'-(alkylene or substituted alkylene)-, -C(O)N(R')-, -CON(R')-(alkylene or substituted alkylene)-, -CSN(R')-, -CSN(R')-(alkylene or substituted alkylene)-, - <com:Math><semantics>N(R′)CO<annotation encoding="application / x-tex">N(R')CO< / annotation>< / semantics>< / com:Math>—(alkylene or substituted alkylene)—, <com:Math><semantics>−N(R′)C(O)O<annotation encoding="application / x-tex">-N(R')C(O)O< / annotation>< / semantics>< / com:Math>—, <com:Math><semantics>−S(O)kN(R′)<annotation encoding="application / x-tex">-S(O)_kN(R')< / annotation>< / semantics>< / com:Math>—, <com:Math><semantics>−<annotation encoding="application / x-tex">-< / annotation>< / semantics>< / com:Math> <com:Math><semantics>N(R′)C(O)N(R′)−,−N(R′)C(S)N(R′)−,−N(R′)S(O)kN(R′)−,−N(R′)−N=,−C(R′)=N−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,<annotation encoding="application / x-tex">N(R')C(O)N(R')-, -N(R')C(S)N(R')-, -N(R')S(O)_kN(R')-, -N(R')-N=, -C(R')=N-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-,< / annotation>< / semantics>< / com:Math> <com:Math><semantics>C(R′)=N−N(R′)−<annotation encoding="application / x-tex">C(R')=N-N(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)=N−N=<annotation encoding="application / x-tex">-C(R')=N-N=< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)2−N=N−<annotation encoding="application / x-tex">-C(R')_2-N=N-< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−C(R′)2−N(R′)−N(R′)−<annotation encoding="application / x-tex">-C(R')_2-N(R')-N(R')-< / annotation>< / semantics>< / com:Math>, where each R' is independently H, alkyl, or substituted alkyl; K is -NR<com:Sub>6< / com:Sub>R<com:Sub>7< / com:Sub> or -N=CR<com:Sub>6< / com:Sub>R<com:Sub>7< / com:Sub>; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; each of R<com:Sub>3< / com:Sub> and R<com:Sub>4< / com:Sub> is independently H, halogen, lower alkyl, or substituted lower alkyl, or R<com:Sub>3< / com:Sub> and R<com:Sub>4< / com:Sub> or two R<com:Sub>3< / com:Sub> groups optionally form a cycloalkyl or a heterocycloalkyl; each of R<com:Sub>6< / com:Sub> and R<com:Sub>7< / com:Sub> is independently selected from the group consisting of H, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy, substituted alkoxy, polyalkylene oxide, substituted polyalkylene oxide, aryl, substituted aryl, heteroaryl, substituted heteroaryl, alkaryl, substituted alkaryl, aralkyl, and substituted aralkyl, <com:Math><semantics>−C(O)R″<annotation encoding="application / x-tex">-C(O)R''< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(O)2R″<annotation encoding="application / x-tex">-C(O)_2R''< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(O)N(R″)2<annotation encoding="application / x-tex">-C(O)N(R'')_2< / annotation>< / semantics>< / com:Math>, wherein each R'' is independently hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy, substituted alkoxy, aryl, substituted aryl, heteroaryl, alkaryl, substituted alkaryl, aralkyl, or substituted aralkyl; or R<com:Sub>6< / com:Sub> or R<com:Sub>7< / com:Sub> is L–X, where X is a selected from the group consisting of a label; a dye; a polymer; a water-soluble polymer; a derivative of polyethylene glycol; a photocrosslinker; a cytotoxic compound; a drug; an affinity label; a photoaffinity label; a reactive compound; a resin; a second protein or polypeptide or polypeptide analog; an antibody or antibody fragment; a metal chelator; a cofactor; a fatty acid; a carbohydrate; a polynucleotide; a DNA; a RNA; an antisense polynucleotide; a saccharide, a water-soluble dendrimer, a cyclodextrin, a biomaterial; a nanoparticle; a spin label; a fluorophore, a metal-containing moiety; a radioactive moiety; a novel functional group; a group that covalently or noncovalently interacts with other molecules; a photocaged moiety; a photoisomerizable moiety; biotin; a biotin analogue; a moiety incorporating a heavy atom; a chemically cleavable group; a photocleavable group; an elongated side chain; a carbon-linked sugar; a redox-active agent; an amino thioacid; a toxic moiety; an isotopically labeled moiety; a biophysical probe; a phosphorescent group; a chemiluminescent group; an electron dense group; a magnetic group; an intercalating group; a chromophore; an energy transfer agent; a biologically active agent; a detectable label; and any combination thereof; and L is optional, and when present is a linker selected from the group consisting of alkylene, substituted alkylene, alkenylene, substituted alkenylene, -O-, -O-(alkylene or substituted alkylene)-, -S-, -S-(alkylene or substituted alkylene)–, <com:Math><semantics>−S(O)k<annotation encoding="application / x-tex">-S(O)_k< / annotation>< / semantics>< / com:Math>– where k is 1, 2, or 3, <com:Math><semantics>−S(O)k<annotation encoding="application / x-tex">-S(O)_k< / annotation>< / semantics>< / com:Math>(alkylene or substituted alkylene)-, -C(O)-, -C(O)-(alkylene or substituted alkylene)-, -C(S)-, -C(S)-(alkylene or substituted alkylene)-, -N(R')-, -NR'-(alkylene or substituted alkylene)-, -C(O)N(R')-, - CON(R')-(alkylene or substituted alkylene)-, -CSN(R')-, -CSN(R')-(alkylene or substituted alkylene)-, -N(R')CO-(alkylene or substituted alkylene)-, -N(R')C(O)O-, -S(O)<com:Sub>k< / com:Sub>N(R')-, - <com:Math><semantics>N(R′)C(O)N(R′)−,−N(R′)C(S)N(R′)−,−N(R′)S(O)kN(R′)−,−N(R′)−N=,−C(R′)=N−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,<annotation encoding="application / x-tex">N(R')C(O)N(R')-, -N(R')C(S)N(R')-, -N(R')S(O)_kN(R')-, -N(R')-N=, -C(R')=N-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-,< / annotation>< / semantics>< / com:Math> <com:Math><semantics>C(R′)=N−N(R′)−<annotation encoding="application / x-tex">C(R')=N-N(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)=N−N=<annotation encoding="application / x-tex">-C(R')=N-N=< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)2−N=N−<annotation encoding="application / x-tex">-C(R')_2-N=N-< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−C(R′)2−N(R′)−N(R′)−<annotation encoding="application / x-tex">-C(R')_2-N(R')-N(R')-< / annotation>< / semantics>< / com:Math>, where each R' is independently H, alkyl, or substituted alkyl. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00216] Such amino acids further include amino acids having the structure of Formula (XVI): [Image disponible dans le document PDF, Image available in the PDF document] wherein: A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene; B is optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -O-, -O-(alkylene or substituted alkylene)—, <com:Math><semantics>−S<annotation encoding="application / x-tex">-S< / annotation>< / semantics>< / com:Math>—, <com:Math><semantics>−S<annotation encoding="application / x-tex">-S< / annotation>< / semantics>< / com:Math>—(alkylene or substituted alkylene)—, <com:Math><semantics>−S(O)k<annotation encoding="application / x-tex">-S(O)_k< / annotation>< / semantics>< / com:Math>— where k is 1, 2, or 3, <com:Math><semantics>−S(O)k<annotation encoding="application / x-tex">-S(O)_k< / annotation>< / semantics>< / com:Math>(alkylene or substituted alkylene)-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−NS(O)2<annotation encoding="application / x-tex">-NS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−OS(O)2<annotation encoding="application / x-tex">-OS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>- (alkylene or substituted alkylene)-, -C(S)-, -C(S)-(alkylene or substituted alkylene)-, - N(R')-, -NR'-(alkylene or substituted alkylene)-, -C(O)N(R')-, -CON(R')-(alkylene or substituted alkylene)—, -CSN(R')—, -CSN(R')—(alkylene or substituted alkylene)—, - <com:Math><semantics>N(R′)CO<annotation encoding="application / x-tex">N(R')CO< / annotation>< / semantics>< / com:Math>—(alkylene or substituted alkylene)—, <com:Math><semantics>−N(R′)C(O)O<annotation encoding="application / x-tex">-N(R')C(O)O< / annotation>< / semantics>< / com:Math>—, <com:Math><semantics>−S(O)kN(R′)<annotation encoding="application / x-tex">-S(O)_kN(R')< / annotation>< / semantics>< / com:Math>—, — <com:Math><semantics>N(R′)C(O)N(R′)−,−N(R′)C(S)N(R′)−,−N(R′)S(O)kN(R′)−,−N(R′)−N=,−C(R′)=N−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,−N(R′)C(O)N(R′)−,<annotation encoding="application / x-tex">N(R')C(O)N(R')-, -N(R')C(S)N(R')-, -N(R')S(O)_kN(R')-, -N(R')-N=, -C(R')=N-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)N(R')-,< / annotation>< / semantics>< / com:Math> <com:Math><semantics>C(R′)=N−N(R′)−<annotation encoding="application / x-tex">C(R')=N-N(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)=N−N=<annotation encoding="application / x-tex">-C(R')=N-N=< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)2−N=N−<annotation encoding="application / x-tex">-C(R')_2-N=N-< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−C(R′)2−N(R′)−N(R′)−<annotation encoding="application / x-tex">-C(R')_2-N(R')-N(R')-< / annotation>< / semantics>< / com:Math>, where each R' is independently H, alkyl, or substituted alkyl; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; each of R<com:Sub>3< / com:Sub> and R<com:Sub>4< / com:Sub> is independently H, halogen, lower alkyl, or substituted lower alkyl, or R<com:Sub>3< / com:Sub> and R<com:Sub>4< / com:Sub> or two R<com:Sub>3< / com:Sub> optionally form a cycloalkyl or a heterocycloalkyl; each of R<com:Sub>6< / com:Sub> and R<com:Sub>7< / com:Sub> is independently selected from the group consisting of H, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy, substituted alkoxy, polyalkylene oxide, substituted polyalkylene oxide, aryl, substituted aryl, heteroaryl, substituted heteroaryl, alkaryl, substituted alkaryl, aralkyl, and substituted aralkyl, -C(O)R", <com:Math><semantics>−C(O)2R″<annotation encoding="application / x-tex">-C(O)_2R''< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(O)N(R″)2<annotation encoding="application / x-tex">-C(O)N(R'')_2< / annotation>< / semantics>< / com:Math>, wherein each R'' is independently hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy, substituted alkoxy, aryl, substituted aryl, heteroaryl, alkaryl, substituted alkaryl, aralkyl, or substituted aralkyl; or R<com:Sub>6< / com:Sub> or R<com:Sub>7< / com:Sub> is L-X, where X is a selected from the group consisting of a label; a dye; a polymer; a water-soluble polymer; a derivative of polyethylene glycol; a photocrosslinker; a cytotoxic compound; a drug; an affinity label; a photoaffinity label; a reactive compound; a resin; a second protein or polypeptide or polypeptide analog; an antibody or antibody fragment; a metal chelator; a cofactor; a fatty acid; a carbohydrate; a polynucleotide; a DNA; a RNA; an antisense polynucleotide; a saccharide, a water-soluble dendrimer, a cyclodextrin, a biomaterial; a nanoparticle; a spin label; a fluorophore, a metal-containing moiety; a radioactive moiety; a novel functional group; a group that covalently or noncovalently interacts with other molecules; a photocaged moiety; a photoisomerizable moiety; biotin; a biotin analogue; a moiety incorporating a heavy atom; a chemically cleavable group; a photocleavable group; an elongated side chain; a carbon-linked sugar; a redox-active agent; an amino thioacid; a toxic moiety; an isotopically labeled moiety; a biophysical probe; a phosphorescent group; a chemiluminescent group; an electron dense group; a magnetic group; an intercalating group; a chromophore; an energy transfer agent; a biologically active agent; a detectable label; and any combination thereof; and L is optional, and when present is a linker selected from the group consisting of alkylene, substituted alkylene, alkenylene, substituted alkenylene, -O-, - O-(alkylene or substituted alkylene)-, <com:Math><semantics>−S<annotation encoding="application / x-tex">-S< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−S<annotation encoding="application / x-tex">-S< / annotation>< / semantics>< / com:Math>-(alkylene or substituted alkylene)-, <com:Math><semantics>−S<annotation encoding="application / x-tex">-S< / annotation>< / semantics>< / com:Math>(O)<com:Sub>k< / com:Sub>- where k is 1, 2, or 3, <com:Math><semantics>−S(O)k<annotation encoding="application / x-tex">-S(O)_k< / annotation>< / semantics>< / com:Math> (alkylene or substituted alkylene)-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-(alkylene or substituted alkylene)-, -C(S)-, -C(S)-(alkylene or substituted alkylene)-, -N(R')-, -NR'- (alkylene or substituted alkylene)-, -C(O)N(R')-, -CON(R')-(alkylene or substituted alkylene)—, -CSN(R')—, -CSN(R')—(alkylene or substituted alkylene)—, -N(R')CO–(alkylene or substituted alkylene)-, <com:Math><semantics>−N(R′)C(O)O<annotation encoding="application / x-tex">-N(R')C(O)O< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−S(O)kN(R′)<annotation encoding="application / x-tex">-S(O)_kN(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)C(O)N(R′)<annotation encoding="application / x-tex">-N(R')C(O)N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−<annotation encoding="application / x-tex">-< / annotation>< / semantics>< / com:Math> <com:Math><semantics>N(R′)C(S)N(R′)−,−N(R′)S(O)kN(R′)−,−N(R′)−N=,−C(R′)=N−,−C(R′)=N−N(R′)−,−N(R′)−,−N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−<annotation encoding="application / x-tex">N(R')C(S)N(R')-, -N(R')S(O)_kN(R')-, -N(R')-N=, -C(R')=N-, -C(R')=N-N(R')-, -N(R')-, -N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-< / annotation>< / semantics>< / com:Math> <com:Math><semantics>C(R′)=N−N=<annotation encoding="application / x-tex">C(R')=N-N=< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)2−N=N−<annotation encoding="application / x-tex">-C(R')_2-N=N-< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−C(R′)2−N(R′)−N(R′)−<annotation encoding="application / x-tex">-C(R')_2-N(R')-N(R')-< / annotation>< / semantics>< / com:Math>, where each R' is independently H, alkyl, or substituted alkyl. Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non-natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00217] Further, such amino acids include amino acids having the structure of Formula (XVII): [Image disponible dans le document PDF, Image available in the PDF document] wherein: B is optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -O-, -O-(alkylene or substituted alkylene)-, -S-, -S-(alkylene or substituted alkylene)-, -S(O)<com:Sub>k< / com:Sub>- where k is 1, 2, or 3, - <com:Math><semantics>S(O)k<annotation encoding="application / x-tex">S(O)_k< / annotation>< / semantics>< / com:Math>(alkylene or substituted alkylene)-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−NS(O)2<annotation encoding="application / x-tex">-NS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−OS(O)2<annotation encoding="application / x-tex">-OS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-(alkylene or substituted alkylene)-, -C(S)-, -C(S)-(alkylene or substituted alkylene)-, -N(R')-, -NR'- (alkylene or substituted alkylene)—, —C(O)N(R')—, —CON(R')—(alkylene or substituted alkylene)—, -CSN(R')—, -CSN(R')—(alkylene or substituted alkylene)—, -N(R')CO–(alkylene or substituted alkylene)-, <com:Math><semantics>−N(R′)C(O)O<annotation encoding="application / x-tex">-N(R')C(O)O< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−S(O)kN(R′)<annotation encoding="application / x-tex">-S(O)_kN(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)C(O)N(R′)<annotation encoding="application / x-tex">-N(R')C(O)N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−<annotation encoding="application / x-tex">-< / annotation>< / semantics>< / com:Math> <com:Math><semantics>N(R′)C(S)N(R′)−,−N(R′)S(O)kN(R′)−,−N(R′)−N=,−C(R′)=N−,−C(R′)=N−N(R′)−,−N(R′)−,−N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−N=N(R′)−<annotation encoding="application / x-tex">N(R')C(S)N(R')-, -N(R')S(O)_kN(R')-, -N(R')-N=, -C(R')=N-, -C(R')=N-N(R')-, -N(R')-, -N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-N=N(R')-< / annotation>< / semantics>< / com:Math> <com:Math><semantics>C(R′)=N−N=<annotation encoding="application / x-tex">C(R')=N-N=< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)2−N=N−<annotation encoding="application / x-tex">-C(R')_2-N=N-< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−C(R′)2−N(R′)−N(R′)−<annotation encoding="application / x-tex">-C(R')_2-N(R')-N(R')-< / annotation>< / semantics>< / com:Math>, where each R' is independently H, alkyl, or substituted alkyl; R<com:Sub>1< / com:Sub> is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and R<com:Sub>2< / com:Sub> is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; each of R<com:Sub>6< / com:Sub> and R<com:Sub>7< / com:Sub> is independently selected from the group consisting of H, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy, substituted alkoxy, polyalkylene oxide, substituted polyalkylene oxide, aryl, substituted aryl, heteroaryl, substituted heteroaryl, alkaryl, substituted alkaryl, aralkyl, and substituted aralkyl, -C(O)R", -C(O)<com:Sub>2< / com:Sub>R", - C(O)N(R")<com:Sub>2< / com:Sub>, wherein each R" is independently hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy, substituted alkoxy, aryl, substituted aryl, heteroaryl, alkaryl, substituted alkaryl, aralkyl, or substituted aralkyl; or R<com:Sub>6< / com:Sub> or R<com:Sub>7< / com:Sub> is L-X, where X is a selected from the group consisting of a label; a dye; a polymer; a water-soluble polymer; a derivative of polyethylene glycol; a photocrosslinker; a cytotoxic compound; a drug; an affinity label; a photoaffinity label; a reactive compound; a resin; a second protein or polypeptide or polypeptide analog; an antibody or antibody fragment; a metal chelator; a cofactor; a fatty acid; a carbohydrate; a polynucleotide; a DNA; a RNA; an antisense polynucleotide; a saccharide, a water-soluble dendrimer, a cyclodextrin, a biomaterial; a nanoparticle; a spin label; a fluorophore, a metal-containing moiety; a radioactive moiety; a novel functional group; a group that covalently or noncovalently interacts with other molecules; a photocaged moiety; a photoisomerizable moiety; biotin; a biotin analogue; a moiety incorporating a heavy atom; a chemically cleavable group; a photocleavable group; an elongated side chain; a carbon-linked sugar; a redox-active agent; an amino thioacid; a toxic moiety; an isotopically labeled moiety; a biophysical probe; a phosphorescent group; a chemiluminescent group; an electron dense group; a magnetic group; an intercalating group; a chromophore; an energy transfer agent; a biologically active agent; a detectable label; and any combination thereof; and L is optional, and when present is a linker selected from the group consisting of alkylene, substituted alkylene, alkenylene, substituted alkenylene, -O-, -O-(alkylene or substituted alkylene)-, -S-, -S-(alkylene or substituted alkylene)-, -S(O)<com:Sub>k< / com:Sub>- where k is 1, 2, or 3, - <com:Math><semantics>S(O)k<annotation encoding="application / x-tex">S(O)_k< / annotation>< / semantics>< / com:Math>(alkylene or substituted alkylene)—, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>—(alkylene or substituted alkylene)—, -C(S)-, -C(S)-(alkylene or substituted alkylene)-, -N(R')-, -NR'-(alkylene or substituted alkylene)-, -C(O)N(R')-, -CON(R')-(alkylene or substituted alkylene)-, -CSN(R')-, - CSN(R')-(alkylene or substituted alkylene)-, -N(R')CO-(alkylene or substituted alkylene)-, <com:Math><semantics>−N(R′)C(O)O−<annotation encoding="application / x-tex">-N(R')C(O)O-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−S(O)kN(R′)−<annotation encoding="application / x-tex">-S(O)_kN(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)C(O)N(R′)−<annotation encoding="application / x-tex">-N(R')C(O)N(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)C(S)N(R′)−<annotation encoding="application / x-tex">-N(R')C(S)N(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)S(O)kN(R′)−<annotation encoding="application / x-tex">-N(R')S(O)_kN(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)S(O)kN(R′)−<annotation encoding="application / x-tex">-N(R')S(O)_kN(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)S(O)kN(R′)−<annotation encoding="application / x-tex">-N(R')S(O)_kN(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)S(O)kN(R′)−<annotation encoding="application / x-tex">-N(R')S(O)_kN(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)S(O)kN(R′)−<annotation encoding="application / x-tex">-N(R')S(O)_kN(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)S(O)kN(R′)−<annotation encoding="application / x-tex">-N(R')S(O)_kN(R')-< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−N(R′)S(O)kN(R<annotation encoding="application / x-tex">-N(R')S(O)_kN(R< / annotation>< / semantics>< / com:Math> <com:Math><semantics>N(R′)−N=,−C(R′)=N−,−C(R′)=N−N(R′)−,−C(R′)=N−N=,−C(R′)2−N=N−, and −C(R′)2−N=N−<annotation encoding="application / x-tex">N(R')-N=, -C(R')=N-, -C(R')=N-N(R')-, -C(R')=N-N=, -C(R')_2-N=N-, \text{ and } -C(R')_2-N=N-< / annotation>< / semantics>< / com:Math> N(R')–N(R')–, where each R' is independently H, alkyl, or substituted alkyl.

[00218] Non-limiting examples of such amino acids include amino acids having the following structures: [Image disponible dans le document PDF, Image available in the PDF document] Such non-natural amino acids may be in the form of a salt, or may be incorporated into a non- natural amino acid polypeptide, polymer, polysaccharide, or a polynucleotide and optionally post translationally modified.

[00219] Additionally, such amino acids include amino acids having the structure of Formula (XVIII): [Image disponible dans le document PDF, Image available in the PDF document] wherein: B is optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -O-, -O-(alkylene or substituted alkylene)-, -S-, -S-(alkylene or substituted alkylene)-, -S(O)<com:Sub>k< / com:Sub>- where k is 1, 2, or 3, - <com:Math><semantics>S(O)k<annotation encoding="application / x-tex">S(O)_k< / annotation>< / semantics>< / com:Math>(alkylene or substituted alkylene)-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−NS(O)2<annotation encoding="application / x-tex">-NS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−OS(O)2<annotation encoding="application / x-tex">-OS(O)_2< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−C(O)<annotation encoding="application / x-tex">-C(O)< / annotation>< / semantics>< / com:Math>-(alkylene or substituted alkylene)-, -C(S)-, -C(S)-(alkylene or substituted alkylene)-, -N(R')-, -NR'- (alkylene or substituted alkylene)—, —C(O)N(R')—, —CON(R')—(alkylene or substituted alkylene)-, -CSN(R')-, -CSN(R')-(alkylene or substituted alkylene)-, -N(R')CO-(alkylene or substituted alkylene)-, <com:Math><semantics>−N(R′)C(O)O<annotation encoding="application / x-tex">-N(R')C(O)O< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−S(O)kN(R′)<annotation encoding="application / x-tex">-S(O)_kN(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−N(R′)C(O)N(R′)<annotation encoding="application / x-tex">-N(R')C(O)N(R')< / annotation>< / semantics>< / com:Math>-, <com:Math><semantics>−<annotation encoding="application / x-tex">-< / annotation>< / semantics>< / com:Math> [Image disponible dans le document PDF, Image available in the PDF document] <com:Math><semantics>C(R′)=N−N=<annotation encoding="application / x-tex">C(R')=N-N=< / annotation>< / semantics>< / com:Math>, <com:Math><semantics>−C(R′)2−N=N−<annotation encoding="application / x-tex">-C(R')_2-N=N-< / annotation>< / semantics>< / com:Math>, and <com:Math><semantics>−C(R′)2−N(R′)−N(R′)−<annotation encoding="application / x-tex">-C(R')_2-N(R')-N(R')-< / annotation>< / semantics>< / com:Math>, where each R' is independently H, alkyl, or substituted alkyl; R<...

Claims

1. An antibody of the IgG class comprising a polypeptide chain having one or more non-natural amino acid residues at specific sites selected from the group consisting of light chain residue L7 according to the Kabat or Chothia numbering scheme, heavy chain residues H404, H121, H180, and H136 according to the EU numbering scheme, or a post- translationally modified variant thereof, wherein the one or more non-natural amino acid residues are not one of the 20 common amino acids or pyrrolysine or selenocysteine, or post- translationally modified variants thereof.

2. The antibody of claim 1 comprising a polypeptide chain having the three CDRs comprised in SEQ ID NO:1 and at least 95% identity to SEQ ID NO:1 and having one or more non-natural amino acid residues at specific sites selected from the group consisting of sites corresponding to residues 407, 124, 183, and 139 of the representative heavy chain polypeptide according to SEQ ID NO:1, or a post-translationally modified variant thereof, and a polypeptide chain having the three CDRs comprised in SEQ ID NO:2 and at least 95% identity to SEQ ID NO:2 and having one or more non-natural amino acid residues at residue 7 of the representative light chain polypeptide according to SEQ ID NO:2, or a post- translationally modified variant thereof.

3. The antibody of claim 1 or claim 2 wherein said polypeptide chain is a light chain of a type selected from λ \lambda and κ \kappa .

4. The antibody of any one of claims 1 to 3 that is of a subclass selected from the group consisting of IgG1, IgG2, IgG3, and IgG4.

5. The antibody of any one of claims 1 to 4 wherein said non-natural amino acid residue comprises a moiety selected from the group consisting of amino, carboxy, acetyl, hydrazino, hydrazido, semicarbazido, sulfanyl, azido and alkynyl.

6. The antibody of any one of claims 1 to 5 wherein each non-natural amino acid residue is according to the formula CA 2875989 [Image disponible dans le document PDF, Image available in the PDF document] wherein each L is independently a divalent linker; and each R is independently a functional group.

7. The antibody of claim 6 wherein R is a reactive group, a therapeutic moiety or a labeling moiety.

8. The antibody of claim 7 wherein the reactive group is selected from the group consisting of amino, carboxy, acetyl, hydrazino, hydrazido, semicarbazido, sulfanyl, azido, and alkynyl.

9. The antibody of any one of claims 6 to 8 wherein each L is a divalent linker selected from the group consisting of a bond, alkylene, substituted alkylene, heteroalkylene, substituted heteroalkylene, arylene, substituted arylene, heteroarlyene and substituted heteroarylene.

10. An antibody conjugate comprising the antibody of any one of claims 1 to 9 linked to one or more therapeutic moieties or labeling moieties.

11. The antibody conjugate of claim 10 that comprises said antibody linked to one or more drugs or polymers.

12. The antibody conjugate of claim 10 that comprises said antibody linked to one or more labeling moieties.

13. The antibody conjugate of claim 10 that comprises said antibody linked to one or more single chain binding domains (scFv).

14. The antibody conjugate of any one of claims 10 to 13 wherein said antibody is linked to said one or more therapeutic moieties or labeling moieties via one or more linkers.

15. A composition comprising the antibody of any one of claims 1 to 9 and a pharmaceutically acceptable carrier, wherein said composition is substantially pure.

16. A composition comprising the antibody of any one of claims 1 to 9 and a pharmaceutically acceptable carrier, wherein said antibody is at least 95% by weight of the total antibody weight of said composition.