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(2) Patent Application Publication (10) Pub. No.: US 2016/0213702 A1 Von Maltzahn Et Al

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(2) Patent Application Publication (10) Pub. No.: US 2016/0213702 A1 Von Maltzahn Et Al US 201602.13702A1 (19) United States (2) Patent Application Publication (10) Pub. No.: US 2016/0213702 A1 von Maltzahn et al. (43) Pub. Date: Jul. 28, 2016 (54) GLYCAN THERAPEUTICS AND RELATED 2015, provisional application No. 62/152,005, filed on METHODS THEREOF Apr. 23, 2015, provisional application No. 62/108,039, filed on Jan. 26, 2015. (71) Applicant: KALEIDO BIOSCIENCES, INC., Cambridge, MA (US) Publication Classification (72) Inventors: Geoffrey A. von Maltzahn, Somerville, (51) Int. Cl. MA (US); Jared Silverman, Brookline, A61R 31/715 (2006.01) MA (US); Yvonne J. Yamanaka, A61 K. 3 1/12 (2006.01) Cambridge, MA (US); John Miles A61 K. 3 1/7034 (2006.01) Milwid, Winchester, MA (US); John M. A61 K. 3 1/353 (2006.01) Geremia, Watertown, MA (US) A61 K. 3 1/165 (2006.01) A61 K. 3 1/34 (2006.01) (73) Assignee: KALEIDO BIOSCIENCES, INC., A61 K. 3 1/365 (2006.01) Cambridge, MA (US) A61 K. 3 I/II (2006.01) A61 K. 3 1/366 (2006.01) A61 K. 3 1/706 (2006.01) (21) Appl. No.: 15/017,396 A61 K. 3 1/7048 (2006.01) A61 K. 3 1/09 (2006.01) (22) Filed: Feb. 5, 2016 (52) U.S. CI. CPC ........... A61K3I/715 (2013.01); A61K3I/7048 Related U.S. Application Data (2013.01); A61K31/12 (2013.01); A61 K (63) Continuation of application No. PCT/US2016/ 31/7034 (2013.01); A61K 31/353 (2013.01); 0.13305, filed on Jan. 13, 2016. A61K3I/09 (2013.01); A61K3I/34 (2013.01); A61K 31/365 (2013.01); A61K3I/II (60) Provisional application No. 62/238,110, filed on Oct. (2013.01); A61K3I/366 (2013.01); A61 K 6, 2015, provisional application No. 62/238,112, filed 31/706 (2013.01); A61K 31/165 (2013.01); on Oct. 6, 2015, provisional application No. 62/216, A61K 2035/115 (2013.01) 993, filed on Sep. 10, 2015, provisional application No. 62/216,995, filed on Sep. 10, 2015, provisional (57) ABSTRACT application No. 62/216,997, filed on Sep. 10, 2015, Preparations of glycan therapeutics, pharmaceutical compo provisional application No. 62/217,002, filed on Sep. sitions and medical foods thereof, optionally comprising 10, 2015, provisional application No. 62/152,017, micronutrients, polyphenols, prebiotics, probiotics, or other filed on Apr. 23, 2015, provisional application No. agents are provided and methods of making same. Also pro 62/152,016, filed on Apr. 23, 2015, provisional appli vided are methods of using said glycan therapeutics, e.g. for cation No. 62/152,011, filed on Apr. 23, 2015, provi the modulation of human gastrointestinal microbiota and to sional application No. 62/152,007, filed on Apr. 23, treat dysbioses. Patent Application Publication Jul. 28, 2016 Sheet 1 of 21 US 2016/0213702 A1 | FIG. 1 Patent Application Publication Jul. 28, 2016 Sheet 2 of 21 US 2016/0213702 A1 ******* 5.5 5.4 5.3 5.2 5. i. 5.0 4.9 4.8 4.7 4.6 4.5 4.4 4.3 4.2 f2 (ppm) FIG. 2 Patent Application Publication Jul. 28, 2016 Sheet 3 of 21 US 2016/0213702 A1 f FIG. 3A Patent Application Publication Jul. 28, 2016 Sheet 4 of 21 US 2016/0213702 A1 f FIG. 3B Patent Application Publication Jul. 28, 2016 Sheet 5 of 21 US 2016/0213702 A1 FIG. 3C Patent Application Publication Jul. 28, 2016 Sheet 6 of 21 US 2016/0213702 A1 ******* ? ** «; f *********:: Patent Application Publication Jul. 28, 2016 Sheet 7 of 21 US 2016/0213702 A1 FIG. 5 Patent Application Publication Jul. 28, 2016 Sheet 8 of 21 US 2016/0213702 A1 polymeric backbone side chains FIG. 6A linker cationic group acidic group side chain : FIG. 6B Patent Application Publication Jul. 28, 2016 Sheet 9 of 21 US 2016/0213702 A1 p = 0.0043 0. 5 - - - - 00 3 12 O OO 0. 0 Water Xylose FIG. 7 Patent Application Publication Jul. 28, 2016 Sheet 10 of 21 US 2016/0213702 A1 p = 0.0313 4. 0 s. it 3.5 O to | | | O GD O .P. O 3.0 s (0. -- FIG. 8 Patent Application Publication Jul. 28, 2016 Sheet 11 of 21 US 2016/0213702 A1 | FIG. 9A FIG. 9B Patent Application Publication Jul. 28, 2016 Sheet 13 of 21 US 2016/0213702 A1 § • -- - - - - 3:33:33 3. ; : * ~ * ~ * * * * ~ 2:3 3. : - - - - - $33333333;&# & . §§x:3:3: § ¥3&#y s. ~~~~~~~~ & FIG. 11 Patent Application Publication Jul. 28, 2016 Sheet 14 of 21 US 2016/0213702 A1 $33. g?ó3333333333 $38xxxx:#; 33333 * ****** gºgº §§§ f assermance : & : - aggregaºce: —s &xxxxx's : FIG. 12 Patent Application Publication Jul. 28, 2016 Sheet 15 of 21 US 2016/0213702 A1 25 20 | 5 : - {} • & Sººgut Ö0 gig.23ga:33fuc33 s' . glu?öga??0. : . &#3:00. * . .FCS . .. .Vancomycin . * . Water. ; : . .: Treatmen: FIG. 13 Patent Application Publication Jul. 28, 2016 Sheet 17 of 21 US 2016/0213702 A1 (C. Control Acacia {} man52gu29gattg FIG. 15 Patent Application Publication Jul. 28, 2016 Sheet 18 of 21 US 2016/0213702 A1 92 O > g tº . ºf § ii; - {} & t 3. ~ + ºr £ontro; Acacia Fiber FOS glui Q0 man52giu29gal19 FIG. 16 Patent Application Publication Jul. 28, 2016 Sheet 19 of 21 US 2016/0213702 A1 FIG. H.7A FIG. 17B Patent Application Publication Jul. 28, 2016 Sheet 20 of 21 US 2016/0213702 A1 280° 160: FIG. 18 Patent Application Publication Jul. 28, 2016 Sheet 21 of 21 US 2016/0213702 A1 : FIG. 19 US 2016/0213702 A1 Jul. 28, 2016 GLYCAN THERAPEUTICS AND RELATED cosidic bond, a 1->4 glycosidic bond, or a 1->6 glycosidic METHODS THEREOF bond. In some embodiments, one or more, two or more, or three or more glycosidic bonds are present in both alpha and CLAIM OF PRIORITY beta configuration. [0001] This application claims priority to International [0006] In some embodiments, a glycan unit comprises at Application No. PCT/US2016/013305, filed Jan. 13, 2016, least one, at least two, at least three, or more of a monosac which claims priority to U.S. Application No. 62/108,309, charide selected from the group of a tetrose, a pentose, a filed Jan. 26, 2015; U.S. Application No. 62/152,016, filed hexose, and a heptose. In some embodiments, a glycan unit Apr. 23, 2015; U.S. Application No. 62/152,005, filed Apr. comprises at least one, at least two, at least three, or more of 23, 2015; U.S. Application No. 62/152,007, filed Apr. 23, a monosaccharide selected from the group of glucose, galac 2015; U.S. Application No. 62/152,011, filed Apr. 23, 2015; tose, arabinose, mannose, fructose, xylose, fucose, and rham U.S. Application No. 62/152,017, filed Apr. 23, 2015; U.S. In OSe. Application No. 62/216,995, filed Sep. 10, 2015; U.S. Appli [0007] In some embodiments, at least a plurality of the cation No. 62/216,997, filed Sep. 10, 2015; U.S. Application glycans, e.g., at least 10, 20, 3040, 50, 60, 70, 80, 90, 95, or No. 62/217,002, filed Sep. 10, 2015; U.S. Application No. 99% (by weight or number), or substantially all, of the gly 62/216,993, filed Sep.10, 2015; U.S. Application No. 62/238, cans in the preparation, do not comprise more than a prese 112, filed Oct. 6, 2015; and U.S. Application No. 62/238,110, lected reference level, of a repeating unit of glycan units, e.g., filed Oct. 6, 2015, the disclosure of each of which is incorpo a repeating unit of 2, 3, 4 or more glycan units. In an embodi rated herein by reference in its entirety. ment, the preselected reference level is 10, 20, 30, 40, 50, or 60% of the total glycan units in a glycan. By way of example, BACKGROUND in an embodiment, a glycan made up of 20 saccharide mono mers, less than 50% of those 20 monomers are repeating units [0002] The microbiota of humans is complex, and varies by of a 2 or 3 glycan repeat. individual depending on genetics, age, sex, stress, nutrition [0008] In some embodiments, the glycan therapeutic and diet. The microbiota perform many activities and may preparation is synthetic and not isolated from a natural oli influence the physiology of the host. Changing the numbers gosaccharide or polysaccharide source. and species of gut microbiota can alter community function [0009] In some embodiments, the abundance of the bacte and interaction with the host. A limited number of probiotic rial taxa (e.g., of each of a first and a second bacterial taxa) in bacteria is known in the art, and some association with health the human subject’s gastrointestinal microbiota is modulated benefits documented when taken by humans. Some foods are by at least about 5%, 10%, 25% 50%, 75%, 100%, 250%, considered ‘prebiotic’ foods that contain substances that may 500%, 750%, or by at least 1000%. In some embodiments, the promote the growth of certain bacteria that are thought to be modulation comprises an increase or a decrease in the abun beneficial to the human host. The results of clinical tests with dance of the bacterial taxa (e.g., of each of a first and a second these substances are conflicted with respect to their efficacy, bacterial taxa) in the human subject’s gastrointestinal micro and their influence on human health is generally described as biota. being modest. Thus, there is a need for novel therapeutic [0010] In some embodiments, the bacterial taxa (e.g., a first inputs that can stimulate beneficial microbiota shifts and and a second bacterial taxa) comprises a commensal bacterial improve human health.
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