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(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) CORRECTED VERSION (19) World Intellectual Property Organization I International Bureau (10) International Publication Number (43) International Publication Date WO 2017/123676 A9 20 July 2017 (20.07.2017) P O P C T (51) International Patent Classification: 16 November 2016 (16. 11.2016) US C12N 9/78 (2006.0 1) C12N 1/00 (2006.0 1) 15/379,445 14 December 20 16 ( 14. 12.20 16) us A61K 35/74 (2015.01) C12N 15/52 (2006.01) 62/434,406 14 December 2016 (14. 12.2016) us A61K 35/741 (2015.01) C12N 15/74 (2006.01) 62/439,820 28 December 2016 (28. 12.2016) us C07K 14/195 (2006.01) 62/439,871 28 December 2016 (28. 12.2016) us PCT/US201 6/069052 (21) International Application Number: 28 December 2016 (28. 12.2016) us PCT/US20 17/0 13074 62/443,639 6 January 2017 (06.01.2017) us (22) International Filing Date: PCT/US201 7/013072 11 January 2017 ( 11.01 .2017) 11 January 2017 ( 11.01 .2017) us (25) Filing Language: English Applicant: SYNLOGIC, INC. [US/US]; 130 Brookline Street, #201, Cambridge, MA 02139 (US). (26) Publication Language: English (72) Inventors: FALB, Dean; 180 Lake Street, Sherborn, MA (30) Priority Data: 01770 (US). KOTULA, Jonathan, W.; 345 Washington 62/277,413 11 January 2016 ( 11.01.2016) US Street, Somerville, MA 02143 (US). ISABELLA, Vin¬ 62/277,450 11 January 2016 ( 11.01.2016) us cent, M.; 465 Putnam Avenue, Unit 1, Cambridge, MA 62/277,455 11 January 2016 ( 11.01.2016) us 02139 (US). MILLER, Paul, F.; 39 Emerald Glen Lane, 62/291,461 4 February 2016 (04.02.2016) us Salem, CT 06420 (US). TUCKER, Alex; 19 Wyatt Street, 62/291,468 4 February 2016 (04.02.2016) us Somerville, MA 02143 (US). MILLET, Yves; 15 Freder 62/291,470 4 February 2016 (04.02.2016) us ick Street, Newton, MA 02460 (US). FISHER, Adam B.; 62/297,778 19 February 2016 (19.02.2016) us 240 Sidney Street, #306, Cambridge, MA 02139 (US). PCT/US2016/020530 2 March 20 16 (02.03.2016) us 62/305,462 8 March 2016 (08.03.2016) us (74) Agents: HANLEY, Elizabeth, A. et al; McCarter & Eng 62/3 13,691 25 March 2016 (25.03.2016) us lish, LLP, 265 Franklin Street, Boston, MA 021 10 (US). 62/3 14,322 28 March 2016 (28.03.2016) us (81) Designated States (unless otherwise indicated, for every 62/335,780 13 May 2016 (13.05.2016) us kind of national protection available): AE, AG, AL, AM, 62/335,940 13 May 2016 (13.05.2016) us AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, 62/336,338 13 May 2016 (13.05.2016) us BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, PCT/US2016/032562 13 May 201 6 (13.05.2016) us DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, PCT/US2016/032565 13 May 201 6 (13.05.2016) us HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KH, KN, 15/154,934 13 May 2016 (13.05.2016) us KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, 62/345,242 3 June 2016 (03.06.2016) us MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, 62/347,508 8 June 2016 (08.06.2016) us NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, 62/347,576 8 June 2016 (08.06.2016) us RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, 62/348,360 10 June 2016 (10.06.2016) us TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, 62/348,620 10 June 2016 (10.06.2016) us ZA, ZM, ZW. PCT/US2016/037098 10 June 201 6 (10.06.2016) us 62/354,682 24 June 2016 (24.06.2016) us (84) Designated States (unless otherwise indicated, for every PCT/US20 16/039444 24 June 201 6 (24.06.2016) us kind of regional protection available): ARIPO (BW, GH, 62/362,954 15 July 2016 (15.07.2016) us GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, 62/385,235 8 September 2016 (08.09.2016) us TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, PCT/US2016/050836 TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, 8 September 2016 (08.09.2016) us DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, 15/260,3 19 8 September 2016 (08.09.2016) us LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, 62/423,170 16 November 2016 (16. 11.2016) us SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, PCT/US2016/062369 GW, KM, ML, MR, NE, SN, TD, TG). [Continued on nextpage] (54) Title: RECOMBINANT BACTERIA ENGINEERED TO TREAT DISEASES AND DISORDERS ASSOCIATED WITH AMINO ACID METABOLISM AND METHODS OF USE THEREOF (57) Abstract: The present disclosure provides recombinant bacterial cells that have been engineered with genetic circuitry which al low the recombinant bacterial cells to sense a patient's internal environment and respond by turning an engineered metabolic path - way on or off. When turned on, the recombinant bacterial cells complete all of the steps in a metabolic pathway to achieve a thera - peutic effect in a host subject. These recombinant bacterial cells are designed to drive therapeutic effects throughout the body of a host from a point of origin of the microbiome. Specifically, the present disclosure provides recombinant bacterial cells that comprise an amino acid catabolism enzyme for the treatment of diseases and disorders associated with amino acid metabolism, including can cer, in a subject. The disclosure further provides pharmaceutical compositions and methods of treating disorders associated with amino acid metabolism, such as cancer. w o 2017/123676 1lllll II Hill lllll Hill llll III III Hill Hill Hill lllll lllll llll llll llll llll Declarations under Rule 4.17: (48) Date of publication of this corrected version: — as to applicant's entitlement to apply for and be granted 1 4 September 2017 apatent (Rule 4.1 7(H)) (15) Information about Correction: — as to the applicant's entitlement to claim the priority of see Notice o f 1 4 September 2017 the earlier application (Rule 4.17(Hi)) Published: RECOMBINANT BACTERIA ENGINEERED TO TREAT DISEASES AND DISORDERS ASSOCIATED WITH AMINO ACID METABOLISM AND METHODS OF USE THEREOF Related Applications [01] This application claims priority to U.S. Provisional Application No. 62/277,413, filed on January 11, 2016; U.S. Provisional Application No. 62/335,780, filed on May 13, 2016; and U.S. Provisional Application No. 62/345,242, filed on June 3, 2016, the entire contents of each of which are expressly incorporated herein by reference. Background [02] It has recently been discovered that the microbiome in mammals plays a large role in health and disease (see Cho and Blaser, Nature Rev. Genet., 13:260-270, 2012 and Owyang and Wu, Gastroenterol., 146(6):1433-1436, 2014). Indeed, bacteria-free animals have abnormal gut epithelial and immune function, suggesting that the microbiome in the gut plays a critical role in the mammalian immune system. Specifically, the gut microbiome has been shown to be involved in diseases, including, for example, diseases associated with amino acid metabolism, cancer, immune diseases (such as Inflammatory Bowel Disease), autism, liver disease, food allergy, metabolic diseases (such as urea cycle disorder, phenylketonuria, and maple syrup urine disease), obesity, and infection, among many others. [03] With respect to cancers, it is known that many tumors depend on certain amino acids for survival. For example, it is known that melanomas depend on leucine for survival, and that leucine deprivation causes the apoptotic death of melanoma cells through inhibiting mTORCl, the main repressor of autophagy (Shee et al., Cancer Cell, 19:613-628, 201 1). Furthermore, it is known that arginine is also necessary for mTORCl activation. Other groups have demonstrated that deprivation of the amino acids serine and glycine improve survival in cancer based mouse models, and studies have recommended serine-free diets in cancer patients in order to improve their survival odds (Locasale, Nature Reviews, 13:572-583, 2013). Other tumors have been shown to have a dependence on asparagine, such as leukemia (Amylon et al., Leukemia, 13:335-342, 1999). [04] Moreover, therapeutic administration of isolated recombinant bacterial proteins which catabolize amino acids, such as asparagine, have been approved by the FDA and shown to be therapeutically beneficial and to increase survival for cancer patients (Amylon et al, Leukemia, 13:335-342, 1999). However, patients treated with the isolated amino acid catabolism enzymes have also been shown to develop severe side effects, including an immune response (hypersensitivity) against the asparaginase enzyme (Vrooman et al, Pediatr. Blood Cancer, 54(2):199-205, 2010 and Wetzler, Blood, 124(8): 1206-1207, 2014), and other severe side effects such as coagulopathy, bone marrow suppression, and stroke (Muller, Critical Reviews in Oncology/Hematology, 28(2):97-ll, 1998). Accordingly, a need remains for the development of more effective therapeutic options with fewer side effects for treating diseases associated with amino acid metabolism, such as cancer. Summary [05] The present disclosure provides recombinant bacterial cells that have been engineered with genetic circuitry which allow the recombinant bacterial cells to sense a patient' s internal environment and respond by turning an engineered metabolic pathway on or off.
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    US 201203 01950A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2012/0301950 A1 Baynes et al. (43) Pub. Date: Nov. 29, 2012 (54) BOLOGICAL SYNTHESIS OF Publication Classification DIFUNCTIONAL HEXANES AND PENTANES FROM CARBOHYDRATE FEEDSTOCKS (51) Int. Cl. CI2N I/2 (2006.01) (76) Inventors: Brian M. Baynes, Cambridge, MA CI2N I/19 (2006.01) (US); John Michael Geremia, (52) U.S. Cl. ................................... 435/252.3; 435/254.2 Somerville, MA (US); Shaun M. Lippow, Somerville, MA (US) (57) ABSTRACT (21) Appl. No.: 12/661,125 Provided herein are methods for the production of difunc tional alkanes in microorganisms. Also provided are enzymes (22) Filed: Mar. 11, 2010 and nucleic acids encoding Such enzymes, associated with the difunctional alkane production from carbohydrates feed Related U.S. Application Data stocks in microorganisms. The invention also provides (60) Provisional application No. 61/209,917, filed on Mar. recombinant microorganisms and metabolic pathways for the 11, 2009. production of difunctional alkanes. Patent Application Publication Nov. 29, 2012 Sheet 1 of 10 US 2012/030 1950 A1 g f Patent Application Publication Nov. 29, 2012 Sheet 2 of 10 US 2012/030 1950 A1 O m D v Patent Application Publication Nov. 29, 2012 Sheet 3 of 10 US 2012/030 1950 A1 Patent Application Publication Nov. 29, 2012 Sheet 4 of 10 US 2012/030 1950 A1 O O O<—OSSHD (~~~~(~~~~D HDD(~~~ GS?un61– Patent Application Publication Nov. 29, 2012 Sheet 5 of 10 US 2012/030 1950 A1 Eas sa O [] HQ-H0HN H0 N?HH0U0 D?HN sanºººº} Patent Application Publication Nov.
  • Pygal Application No. 61/209.917, Filed on Mar. CNENEEEN", ON."

    Pygal Application No. 61/209.917, Filed on Mar. CNENEEEN", ON."

    USOO8404465B2 (12) UnitedO States Patent (10) Patent No.: US 8.404,465 B2 Baynes et al. (45) Date of Patent: *Mar. 26, 2013 (54) BIOLOGICAL SYNTHESIS OF 2006.01601 38 A1 7, 2006 Church 6-AMINOCAPROCACID FROM 3.28 2. A 3.92 ElaC CARBOHYDRATE FEEDSTOCKS 2007/025.4341 A1 11/2007 Raemakers-Franken 2007,0269870 A1 11/2007 Church (75) Inventors: Brian M. Baynes, Cambridge, MA 2008, OO6461.0 A1 3/2008 Lipovsek (US); John Michael Geremia, 2008/0287320 A1 1 1/2008 Baynes Somerville, MA (US); Shaun M. 2009,008784.0 A1 4/2009 Baynes Lippow, Somerville, MA (US) 2009,0246838 A1 10, 2009 Zelder FOREIGN PATENT DOCUMENTS (73) Assignee: Celexion, LLC, Cambridge, MA (US) JP 2002223 770 8, 2008 c WO WO9507996 3, 1995 (*) Notice: Subject to any disclaimer, the term of this WO WOO166573 9, 2001 patent is extended or adjusted under 35 WO WOO3106691 12/2003 U.S.C. 154(b) by 225 days. WO WO2004O13341 2, 2004 WO WO2007099029 9, 2007 This patent is Subject to a terminal dis- WO WO2007101867 9, 2007 claimer. WO WO2O08092.720 9, 2008 WO WO2008127283 10, 2008 WO WO2009/046375 4/2009 (21) Appl. No.: 12/661,125 WO WO2009.113853 9, 2009 WO WO2009.113855 9, 2009 (22) Filed: Mar 11, 2010 WO WO2009,151728 12/2009 (65) Prior Publication Data OTHER PUBLICATIONS US 2012/O3O1950 A1 Nov. 29, 2012 Chica et al. Curr Opin Biotechnol. Aug. 2005:16(4):378-84.* Sen et al. Appl Biochem Biotechnol. Dec. 2007: 143(3):212-23.* Related U.S.