WO 2015/054658 Al 16 April 2015 (16.04.2015) P O P C T
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(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2015/054658 Al 16 April 2015 (16.04.2015) P O P C T (51) International Patent Classification: (74) Agents: PATHAK, Rahul et al; Squire Patton Boggs C07D 401/12 (2006.01) A61K 39/395 (2006.01) (US) LLP, 275 Battery Street, Suite 2600, San Francisco, C07D 409/12 (2006.01) A61K 47/48 (2006.01) California 941 11 (US). C07D 257/08 (2006.01) (81) Designated States (unless otherwise indicated, for every (21) International Application Number: kind of national protection available): AE, AG, AL, AM, PCT/US20 14/060 169 AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, (22) International Filing Date: DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, 10 October 2014 (10.10.2014) HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (25) Filing Language: English KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, (26) Publication Language: English PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, (30) Priority Data: SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 61/890,1 18 11 October 2013 ( 11. 10.2013) US TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (71) Applicant: SUTRO BIOPHARMA, INC. [US/US]; 310 (84) Designated States (unless otherwise indicated, for every Utah Avenue, Suite 150, South San Francisco, California kind of regional protection available): ARIPO (BW, GH, 94080 (US). GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, (72) Inventors: YANG, Wenjin; 383 Bodega Street, Foster TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, City, California 94404 (US). YIN, Qun; 747 Coastland DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, Drive, Palo Alto, California 94303 (US). LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, [Continued on nextpage] (54) Title: MODIFIED AMINO ACIDS COMPRISING TETRAZINE FUNCTIONAL GROUPS, METHODS OF PREPARA TION, AND METHODS OF THEIR USE (57) Abstract: Provided herein are modified amino acids comprising a tetrazine groups according to Formula I: poly FIG. 3 peptides, antibodies, payloads and conjugates comprising these modified amino acid residues derived from the modi fied amino acids, and methods of producing the poly peptides, antibodies, payloads and conjugates comprising the modified amino acid residues. The polypeptides, antibodies, payloads and conjugates are useful in methods of treatment and prevention, methods of detection and methods of dia- 00 (I) NH N R w o 2015/054658 Ai II 1111 1111II I II I II 11 11II I I I 1111 II I II SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, Published: GW, KM, ML, MR, NE, SN, TD, TG). — with international search report (Art. 21(3)) Declarations under Rule 4.17: — before the expiration of the time limit for amending the — as to applicant's entitlement to apply for and be granted claims and to be republished in the event of receipt of a patent (Rule 4.1 7(H)) amendments (Rule 48.2(h)) — as to the applicant's entitlement to claim the priority of the earlier application (Rule 4. 17(Hi)) MODIFIED AMINO ACIDS COMPRISING TETRAZINE FUNCTIONAL GROUPS, METHODS OF PREPARATION, AND METHODS OF THEIR USE CROSS-REFERENCE TO RELATED APPLICATIONS [0001] This application claims the benefit of U.S. Provisional Patent Application No. 61/890,1 18, filed October 11, 2013, the contents of which are hereby incorporated by reference in their entirety. FIELD [0002] Provided herein are modified amino acids comprising a tetrazine functional group, polypeptides, antibodies, payloads and conjugates comprising modified amino acid residues derived from the modified amino acids, and methods of producing the polypeptides, antibodies, payloads and conjugates comprising the modified amino acid residues. The polypeptides, antibodies, payloads and conjugates are useful in methods of treatment and prevention, methods of detection and methods of diagnosis. BACKGROUND [0003] Engineered polypeptides are used widely in therapeutic and diagnostic applications. Therapeutic antibodies have been used for many years in, for example, treatment of cancer and inflammatory conditions. Therapeutic polypeptides are also used to treat and prevent blood conditions and viral infections. Diagnostic polypeptides have been used successfully to identify healthy and diseased cells and tissues in vivo. [0004] Many polypeptides can provide targeting functionality to specific cells. The selective affinity of certain polypeptides can be used to target nearly any cell or tissue desired, for example a cell expressing an antigen. A polypeptide can carry a payload to destroy the target cell or tissue, or to slow its growth. Polypeptides have thus found use in therapy for conditions such as cancer, inflammatory diseases, autoimmune diseases and transplant rejection. [0005] In certain applications therapeutic polypeptides are linked to molecular shields (e.g., macromolecules) to increase their half-life within an organism. For example, the attachment of polyethylene glycol (PEG) to a polypeptide can render the polypeptide non- detectable or less detectable by a patient's immune system, thereby reducing immunogenicity. [0006] Polypeptides have also found use as diagnostics. These polypeptides can carry a label whose detection indicates the presence of a target receptor or antigen on a cell or in a tissue. These labels are typically linked to the polypeptides by covalent bonds. [0007] To date, techniques for linking polypeptides to payloads such as molecular shields, labels, diagnostic compounds, and therapeutic compounds have been limited by their heterogeneity in degree and location of linking to the polypeptides, by their low yields and by losses in activity. These problems are particularly acute when attempting to conjugate more than one payload to a single polypeptide in a controlled manner, to produce a homogeneous product. Typical conjugation sites include random locations on polypeptide chains, e.g. random amines on amino acid residue side chains, and the N-terminus of certain polypeptide chains. In such cases, some polypeptides might be linked to a payload at one location while some polypeptides are linked to the same payload at another location, and some polypeptides might not be linked at all. If more than one payload is used, some polypeptides may be linked to a single payload, some polypeptides may be linked to all payloads, and some polypeptides may be linked to fewer than all payloads. [0008] There is a need, therefore, for polypeptides modified at site-specific positions optimized for uniformity, yield and/or activity to further the promising use of polypeptides in, for example, therapy and diagnostics. SUMMARY [0009] Provided herein are modified amino acids comprising a tetrazine group, polypeptides, antibodies, payloads and conjugates comprising the modified amino acid residues derived from the modified amino acids, and methods of producing the polypeptides, antibodies, payloads and conjugates comprising modified amino acid residues. The polypeptides, antibodies, payloads and conjugates are useful in methods of treatment and prevention, methods of detection and methods of diagnosis. [0010] In one aspect a compound according to formula I is provided: Formula I; or a salt thereof, wherein: Ar is V is a single bond, lower alkylene, or - W1- W2- ; one of Wi and W2 is absent or lower alkylene, and the other is -NH-, -0-, or -S-; each Xi is independently -NH-, -0-, or -S-; one of Zi, Z2, and Z is -CH- or -N- and the others of Zi, Z2, and Z are each independently - CH-; and R is lower alkyl. In certain embodiments, when Ar is and V is -NH-, then one of Zi, Z2, and Z is -N-. [001 1] In a further aspect, polypeptides and antibodies comprising an amino acid residue corresponding to a compound of formula I are provided. In particular embodiments, conjugates of the polypeptides and payloads are provided. In further embodiments, conjugates of the antibodies and payloads are provided. [0012] In another aspect, an orthogonal tRNA is provided aminoacylated with an amino acid residue corresponding to a compound of formula I. In a related aspect, a method of producing a polypeptide is provided, comprising contacting a polypeptide with an orthogonal tRNA aminoacylated with an amino acid residue corresponding to a compound of formula I. [0013] The compounds of formula I described herein can be incorporated into any polypeptide known to those of skill in the art. Such polypeptides include, but are not limited to, proteins, antibodies, antibody fragments, and enzymes. BRIEF DESCRIPTION OF THE FIGURES [0014] FIG. 1 provides results demonstrating that tRNA synthetase 2A2 incorporates a compound of formula 9 into a GFP polypeptide, as described in Example 4. In FIG. 1, the y- axis shows fluorescence, in relative fluorescence units (RFU); "aaRS" is 2A2; "GFP" is native GFP (without K49TAG); and "negative control" is a cell-free protein synthesis reaction without a DNA template. [0015] FIG. 2 provides results demonstrating that tRNA synthetase 2A9 incorporates a compound of formula 6 into a GFP polypeptide, as described in Example 4. In FIG. 2, the y- axis shows fluorescence, in relative fluorescence units (RFU); "aaRS" is 2A9; "GFP" is native GFP (without K49TAG); and "negative control" is a cell-free protein synthesis reaction without a DNA template. [0016] FIG. 3 provides an autoradiogram of an antibody incorporating para-azido methyl phenylalanine (pAMF) at position S7 of the light chain and a tetrazine-containing non-natural amino acid (AB 4091) at position F404 of the heavy chain.