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|HAI LALA AT TATUUS009758577B2 WIELU NA MAMA HATI (12 ) United States Patent ( 10 ) Patent No. : US 9 , 758 ,577 B2 Schurpf et al. (45 ) Date of Patent: * Sep . 12 , 2017 (54 ) COMPOSITIONS AND METHODS FOR (56 ) References Cited GROWTH FACTOR MODULATION U . S . PATENT DOCUMENTS @( 71 ) Applicant: SCHOLAR ROCK , INC ., Cambridge , 5 , 972 ,335 A 10 / 1999 Ferguson et al. MA (US ) 6 , 096 , 506 A 8 / 2000 Lee et al . 6 , 368 , 597 B14 / 2002 Strassmann et al. @( 72 ) Inventors : Thomas Schurpf , Cambridge , MA 6 , 468 , 535 B1 . 10 / 2002 Lee et al. ( US ) ; Nagesh K . Mahanthappa , 6 ,656 ,475 B1 12 / 2003 Lee et al. Cambridge , MA (US ) ; Michelle Marie 7 ,070 , 784 B1 7 / 2006 Halkier et al . 7 , 241 ,444 B2 7 / 2007 Goetsch et al . Straub , Brighton , MA (US ) 7 ,316 , 998 B2 1 /2008 Knopf et al. 7 ,320 ,789 B2 * 1 /2008 Aghajanian et al. C07K 16 / 22 @( 73 ) Assignee : Scholar Rock , Inc. , Cambridge , MA 424 / 130 . 1 (US ) 7 , 371 , 726 B2 5 / 2008 Junker et al. 7 , 432 , 079 B2 10 / 2008 Junker et al. @( * ) Notice : Subject to any disclaimer , the term of this 7 , 632, 499 B2 12 / 2009 Davies et al. patent is extended or adjusted under 35 7 , 635 , 760 B2 12 / 2009 Han et al. 7 , 750 , 128 B2 7 / 2010 Gegg et al . U . S . C . 154 ( b ) by 0 days . 7 , 785 , 587 B28 / 2010 Whittemore et al. 7 ,807 , 159 B2 10 /2010 Chin et al. This patent is subject to a terminal dis 7 , 888, 486 B2 2 / 2011 Walsh et al . claimer . 8 , 063 , 188 B2 11/ 2011 Sayers et al . 8 ,178 , 488 B2 5 /2012 Knopf et al. ( 21 ) Appl. No. : 15 / 187 ,278 8 , 420 , 082 B2 4 /2013 Veldman et al. 8 , 455 , 448 B2 6 / 2013 Jeanplong et al . (22 ) Filed : Jun . 20 , 2016 8 , 710, 016 B2 4 /2014 Seehra et al . 8 , 840, 894 B2 9 / 2014 Stitt et al . (65 ) Prior Publication Data 8 , 871 , 209 B2 10 / 2014 Stitt et al . 8 , 933 ,199 B2 1 /2015 Cload et al. US 2016 /0289318 A1 Oct. 6 , 2016 8 , 992, 913 B2 3 /2015 Mader et al . 8 , 999 ,343 B2 4 /2015 Han et al . 2003 /0129171 AL 7 /2003 Grobet et al . Related U . S . Application Data 2005 /0250936 A1 11/ 2005 Oppermann et al. 2006 / 0034831 A1 2 / 2006 Tobin ( 60 ) Division of application No . 14 /795 , 033 , filed on Jul. 2006 /0263354 A1 * 11/ 2006 Chin CO7K 16 / 22 9 , 2015 , now Pat . No. 9 , 399, 676 , which is a 424 / 133 . 1 continuation of application No . PCT/ US2014 /036933 , filed on May 6 , 2014 . (Continued ) FOREIGN PATENT DOCUMENTS ( 60 ) Provisional application No . 61/ 819 , 840 , filed on May EP 0404097 12 / 1990 6 , 2013 , provisional application No . 61/ 823 , 552 , filed EP 2422811 2 / 2012 on May 15 , 2013 , provisional application No . ( Continued ) 61/ 900 , 438 , filed on Nov . 6 , 2013 . (51 ) Int. Cl. OTHER PUBLICATIONS CO7K 16 / 00 ( 2006 .01 ) Stockis, J . et al. “ Membrane protein GARP is a receptor for latent CO7K 16 / 18 ( 2006 . 01 ) TGF -beta on the surface of activated human Treg. ” Eur J . Immunol. CO7K 16 / 22 ( 2006 .01 ) Dec . 2009; 39 ( 12 ) :3315 - 22 . CO7K 14 /495 ( 2006 . 01 ) (Continued ) COZK 16 / 28 ( 2006 .01 ) C12N 15 / 10 (2006 .01 ) A61K 38 /00 ( 2006 .01 ) Primary Examiner - Elizabeth C Kemmerer (52 ) U . S . CI. CPC . .. .. .. .. .. CO7K 16 / 22 ( 2013 .01 ) ; CO7K 14 /495 ( 74 ) Attorney , Agent, or Firm — McCarter & English , (2013 . 01 ) ; CO7K 16 /005 (2013 .01 ) ; CO7K LLP ; Marcie B . Clarke ; Maria Laccotripe Zacharakis 16 / 2863 ( 2013 . 01 ) ; C12N 15 / 1037 ( 2013 .01 ) ; A61K 38 / 00 ( 2013 .01 ) ; CO7K 2317 / 21 (57 ) ABSTRACT ( 2013 .01 ) ; COZK 2317 / 24 ( 2013 .01 ) ; COOK 2317 / 31 ( 2013 .01 ) ; CO7K 2317 /55 (2013 . 01 ) ; Provided herein are proteins, antibodies, assays and methods CO7K 2317 / 565 ( 2013 . 01 ) ; CO7K 2317 / 76 useful for modulating growth factor levels and /or activities . ( 2013 .01 ) ; CO7K 2317 /92 ( 2013 .01 ) ; CO7K In some embodiments , such growth factors are members of 2317 / 94 ( 2013 .01 ) ; GOIN 2333/ 71 (2013 .01 ) the TGF- B superfamily of proteins . ( 58 ) Field of Classification Search None See application file for complete search history . 16 Claims, 23 Drawing Sheets US 9 , 758 , 577 B2 Page 2 ( 56 ) References Cited European Search Report for EP application No . 13853885. 5 dated May 13 , 2016 . U . S . PATENT DOCUMENTS Japanese Office Action for JP application No . 2015 - 540878 dated Apr . 26 , 2016 . 2007 /0178095 A18 / 2007 Smith et al . 2008 /0206219 AL 8 / 2008 Coussens et al. Notification of Transmittal of the International Search Report and 2008 / 0279834 AL 11/ 2008 Garaczi et al . the Written Opinion of the International Searching Authority , or the 2009 /0136481 AL 5 / 2009 Kambadur et al. Declaration , from International Application No . PCT /US2013 / 2010 /0322925 Al 12 / 2010 Knopf et al . 68613 , dated May 7 , 2014 . 2011/ 0129469 A1 6 / 2011 Koncarevic et al . Battaglia et al. The Tregs ' world according to GARP. Eur J 2011/ 0250198 A 10 / 2011 Wolfman et al. Immunol. Dec . 2009 ; 39 ( 12 ) : 3296 - 300 . 2011/ 0256132 Al 10 / 2011 Ashman et al. Tran DQ . TGF - B : the sword , the wand , and the shield of FOXP3 ( = ) regulatory T cells . J Mol Cell Biol. 2012 (Feb ; 4 ( 1 ) : 29 -37 . FOREIGN PATENT DOCUMENTS Cuende , Julia et al . “ Monoclonal antibodies against GARP / TGF -B1 complexes inhibit the immunosuppresive activity of human regu ?? 2832747 2 / 2015 WO 92 / 00330 AL 1 / 1992 latory T cells in vivo ” , Sci . Transl. Med ., Apr . 22 , 2015 , vol. 7 , Issue WO 94 /09812 A1 5 / 1994 284 , pp . 1 - 12 . WO 00 / 43781 7 / 2000 Cuende, Julia et al . “ Supplemental Materials for Monoclonal anti WO 00 /66620 11 / 2000 bodies against GARP / TGF -B1 complexes inhibit the immunosup WO 01/ 12777 2 / 2001 presive activity of human regulatory T cells in vivo ” , Sci . Transl. WO 02 / 09641 2 / 2002 Med ., Apr. 22 , 2015 , vol . 7 , Issue 284 , pp . 1 - 10 . WO 2005 /010049 2 / 2005 International Preliminary Report on Patentability , International WO 2006 / 106599 Al 10 / 2006 WO 2006 / 116002 11/ 2006 Application No. PCT/ US2014 / 036933 , dated Nov . 19 , 2015 . WO 2007 /050793 A2 3 / 2007 Taylor , R . G . et al ., 1985 . Histopathologic features of phorbol WO 2007 /050793 A2 5 / 2007 myristate acetate - induced lung injury . Lab Invest. 52 ( 1 ) :61 - 70 . WO 2008 /060371 5 / 2008 Studnicka , G . M . et al .( 1994 ) , Human - engineered monoclonal anti WO 2009 / 114702 A2 9 / 2009 bodies retain full specific binding activity by preserving non -CDR WO 2009 / 144457 A2 12 / 2009 complementarity -modulating residues. Protein Eng . Jun . WO 2014 /093531 6 / 2014 1994 ; 7 (6 ): 805 - 14 . WO 2015 /015003 2 / 2015 McFarlane , Craig , et al . Proteolytic processing of myostatin is auto -regulated during myogensis , Developmental Biology , Mar . 23 , OTHER PUBLICATIONS 2005 , pp . 58 -69 , AgResearch , East Street , Hamilton , New Zealand , Department of Biological Sciences , University of Waikato , Hamil Shi, Minlong , et al . “ Latent TGF - B structure and activation ” , ton , New Zealand . Nature , vol. 474 , No . 7351, Jun . 15 , 2011 ( Jun . 15 , 2011 ) , pp . 343 - 349 . * cited by examiner U . S . Patent Sep. 12 , 2017 Sheet 1 of 23 US 9 ,758 ,577 B2 Figure 1 TGFB1 BMP , GDF10 TGFB2 BMPIS / / TGFB3 // myostatin (GOF8 ) wwwwwwwwwwwwwwwwwww BMP8A , 8 bin - 3A BMPO Inhibin -BB inhibin - BC BMPS murosawa Inhibin -BE BMP4 Lefty1 mm 1300 $ Lafty2 Nodalmumamman Anti BMPO (GDF2 ) ories Mullerian BMP10 homone GOFT GOES - UIQIYU- D GOFOGpF OF3 U . S . Patent Sep. 12 , 2017 Sheet 2 of 23 US 9 ,758 ,577 B2 Figure 2 Prodomain Stext ? C }eatae site signalpeptide Growth factor U . S . Patent Sep. 12 , 2017 Sheet 3 of 23 US 9 ,758 ,577 B2 Figure 3 Growth Factor- Prodomain Complex (GPC ) Free latency Associated Peptide (LAP ) Dimer Free Growth Factor Dimer 1 U . S . Patent Sep. 12 , 2017 Sheet 4 of 23 US 9 ,758 ,577 B2 Figure 4 Free latency Associated Peptide (LAP ) Dimer Trigger loop. man Bowtie region Alpha 2 helix mana Arm region Fastener region Latency loop ( also refer?d to as t?? latency lasso ) Amman Alpha 1 helix Residues for extracellular protein asscaths Free Growth Factor Dimer -~ ~ get egin U . S . Patent Sep. 12 , 2017 Sheet 5 of 23 US 9 ,758 ,577 B2 Figure 5 An embodiment of a recombinant GPC 34fde ??d C -terminus maeneo Growth factor domain Proprotein convertase cleavage site Latency - associated peptide (LAP ) Cys residue - HSM SH N - terminus Histidine tags U . S . Patent Sep. 12 , 2017 Sheet 6 of 23 US 9 ,758 ,577 B2 Figure 6 An embodiment of a proprotein convertase cleavage site mutant ( e . g . RXXR - RXG ; D2G ) HSG LSH An embodiment of an N -terminal cysteine mutant ( e . g . C45: Cys4 - Ser ) ????? U . S . Patent Sep. 12 , 2017 Sheet 7 of 23 US 9 ,758 ,577 B2 Figure 7 Embodiments of recombinantproteins Hobok LTBA GARDE prOTGF- B proprotein prOTGF - 6 proprotein proTGF- B proprotein convertase cleavage conv?rtaså c { e \ ????? convertase cleavage site mutant with N site mutant complexed site mutant complexed terminal cysteine with LTBP with GARP mutation H00M TGF- B LAP with N TGF- B LAP complexed terminal cysteine with GARP mutation U . S . Patent Sep. 12 , 2017 Sheet 8 of 23 US 9 ,758 ,577 B2 Figure 8A at Heix GFBIHU some generaltownWWWWWWWWxwwwwwwwwwwwwwwwwww * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Howto bietetsocialemediergenerelt W * * * * * * * * * ** * * * * * * * * * * * * * * * * * * * * * SUS X00 aime * AGPAAAAAAAAAARROVOCHOSSRBARSVAPOPO CHVCVXRON 46 ous * A8CPAAAAAAAAAAAGVOORRSSRPAPSAPDOPO CHVCVXROX $ point * * * * * * * * * * * * * * * * * * * * * * * * *XXSCOXUY * BXEGLCXICOXRON 2 in * * * * * * * * wwwww * * * * * www ENSBOKBW * XX10NACEYRON