IP Library Granted Patent US 12,258,362
Granted Patent B2
US 12,258,362 · App. 17/169,611 · Granted Mar 25, 2025

Processes for preparing phosphorodiamidate morpholino oligomers

Inventors: Baozhong Cai (Cambridge, MA); Mitchell Martini (Cambridge, MA); Ross Shimabuku (Cambridge, MA); Katie Thomas (Cambridge, MA)
C07F9/062C07F9/65583C07F9/65616
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Quick Facts
Patent No.
US 12,258,362
App. No.
17/169,611
Granted
Mar 25, 2025
Kind
B2
Abstract

Provided herein are processes for preparing an oligomer (e.g., a morpholino oligomer). The synthetic processes described herein may be advantageous to scaling up oligomersynthesis while maintaining overall yield and purity of a synthesized oligomer.

Claims (216)

1. A compound of Formula (A9):

or a pharmaceutically acceptable salt thereof, wherein:

n is an integer from 10 to 40;

R 1 is a support-medium;

R 3 is selected from the group consisting of hydrogen, trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl; and

R 4 is, independently at each occurrence, selected from the group consisting of:

2. The compound of claim 1 , wherein the compound of Formula (A9) is a compound of Formula (A9a):

wherein:

n is an integer from 10 to 40,

R 1 is a support-medium

R 3 is selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl, and

R 4 is, independently for each occurrence, selected from the group consisting of:

3. The compound of claim 1 , wherein the compound of Formula (A9) is a compound of Formula (IX):

or a pharmaceutically acceptable salt thereof, wherein:

R 1 is a support-medium, and

R 2 is, independently at each occurrence, selected from the group consisting of:

and

wherein R 2 is at each position from 1 to 30 and 5′ to 3′:

Position No. 5′ to 3′

R 2

 1

PC

 2

T

 3

PC

 4

PC

 5

PA

 6

PA

 7

PC

 8

PA

 9

T

10

PC

11

PA

12

PA

13

DPG

14

DPG

15

PA

16

PA

17

DPG

18

PA

19

T

20

DPG

21

DPG

22

PC

23

PA

24

T

25

T

26

T

27

PC

28

T

29

PA

30

DPG.

4. The compound of claim 3 , wherein the compound of Formula (IX) is a compound of Formula (IXa):

or a pharmaceutically acceptable salt thereof, wherein

R 1 is a support-medium, and

R 2 is, independently at each occurrence, selected from the group consisting of:

and

wherein R 2 is at each position from 1 to 30 and 5′ to 3′:

Position No. 5′ to 3′

R 2

 1

PC

 2

T

 3

PC

 4

PC

 5

PA

 6

PA

 7

PC

 8

PA

 9

T

10

PC

11

PA

12

PA

13

DPG

14

DPG

15

PA

16

PA

17

DPG

18

PA

19

T

20

DPG

21

DPG

22

PC

23

PA

24

T

25

T

26

T

27

PC

28

T

29

PA

30

DPG.

5. The compound of claim 1 , wherein the compound of Formula (A9) is a compound of Formula (Xa):

or a pharmaceutically acceptable salt thereof, wherein

R 1 is a support-medium, and

R 2 is, independently at each occurrence, selected from the group consisting of:

and

wherein R 2 is at each position from 1 to 30 and 5′ to 3′:

Position No. 5′ to 3′

R 2

 1

PC

 2

T

 3

PC

 4

PC

 5

PA

 6

PA

 7

PC

 8

PA

 9

T

10

PC

11

PA

12

PA

13

DPG

14

DPG

15

PA

16

PA

17

DPG

18

PA

19

T

20

DPG

21

DPG

22

PC

23

PA

24

T

25

T

26

T

27

PC

28

T

29

PA

30

DPG.

Assignments (2)
SECURITY INTEREST Recorded May 7, 2025
From: SAREPTA THERAPEUTICS, INC.
To: JPMORGAN CHASE BANK, N.A. AS ADMINISTRATIVE AGENT
Reel/Frame 071218/0445 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded May 26, 2021
From: CAI, BAOZHONG; MARTINI, MITCHELL; SHIMABUKU, ROSS; THOMAS, KATIE
To: SAREPTA THERAPEUTICS, INC.
Reel/Frame 056355/0521 →
Continuity (4)
Continuation 16302443
Provisional Application 62357134 · Jun 30, 2016
Provisional Application 62340953 · May 24, 2016
Related Publication 20220340605A1 · Oct 27, 2022
References Cited (135)
US 5034506A · Summerton et al. · 1991 [cited by applicant]
US 5142047A · Summerton et al. · 1992 [cited by applicant]
US 5166315A · Summerton et al. · 1992 [cited by applicant]
US 5185444A · Summerton et al. · 1993 [cited by applicant]
US 5217866A · Summerton et al. · 1993 [cited by applicant]
US 5506337A · Summerton et al. · 1996 [cited by applicant]
US 5521063A · Summerton et al. · 1996 [cited by applicant]
US 5698685A · Summerton et al. · 1997 [cited by applicant]
US 6355640B1 · Akahane et al. · 2002 [cited by applicant]
US 6670461B1 · Wengel et al. · 2003 [cited by applicant]
US 6794499B2 · Wengel et al. · 2004 [cited by applicant]
US 7034133B2 · Wengel et al. · 2006 [cited by applicant]
US 7053207B2 · Wengel · 2006 [cited by applicant]
US 7060809B2 · Wengel et al. · 2006 [cited by applicant]
US 7084125B2 · Wengel · 2006 [cited by applicant]
US 7569575B2 · Sorensen et al. · 2009 [cited by applicant]
US 7572582B2 · Wengel et al. · 2009 [cited by applicant]
US 7807816B2 · Wilton et al. · 2010 [cited by applicant]
US 7960541B2 · Wilton et al. · 2011 [cited by applicant]
US 8067571B2 · Weller et al. · 2011 [cited by applicant]
US 8076476B2 · Reeves et al. · 2011 [cited by applicant]
US 8232384B2 · Wilton et al. · 2012 [cited by applicant]
US 8299206B2 · Fox et al. · 2012 [cited by applicant]
US 8450474B2 · Wilton et al. · 2013 [cited by applicant]
US 8455634B2 · Wilton et al. · 2013 [cited by applicant]
US 8455635B2 · Wilton et al. · 2013 [cited by applicant]
US 8455636B2 · Wilton et al. · 2013 [cited by applicant]
US 8476423B2 · Wilton et al. · 2013 [cited by applicant]
US 8486907B2 · Wilton et al. · 2013 [cited by applicant]
US 8524880B2 · Wilton et al. · 2013 [cited by applicant]
US 8637483B2 · Wilton et al. · 2014 [cited by applicant]
US 8969551B2 · Ueda · 2015 [cited by applicant]
US 9018368B2 · Wilton et al. · 2015 [cited by applicant]
US 9024007B2 · Wilton et al. · 2015 [cited by applicant]
US 9035040B2 · Wilton et al. · 2015 [cited by applicant]
US 9175286B2 · Wilton et al. · 2015 [cited by applicant]
US 9228187B2 · Wilton et al. · 2016 [cited by applicant]
US 9249416B2 · Wilton et al. · 2016 [cited by applicant]
US 9416361B2 · Iversen et al. · 2016 [cited by applicant]
US 9422555B2 · Wilton et al. · 2016 [cited by applicant]
US 9441229B2 · Wilton et al. · 2016 [cited by applicant]
US 9447415B2 · Wilton et al. · 2016 [cited by applicant]
US 9506058B2 · Kaye · 2016 [cited by applicant]
US 9605262B2 · Wilton et al. · 2017 [cited by applicant]
US 9758783B2 · Wilton et al. · 2017 [cited by applicant]
US 9944926B2 · Linsley et al. · 2018 [cited by applicant]
US 9994851B2 · Wilton et al. · 2018 [cited by applicant]
US 10227590B2 · Wilton et al. · 2019 [cited by applicant]
US 10266827B2 · Wilton et al. · 2019 [cited by applicant]
US 10287586B2 · Wilson et al. · 2019 [cited by applicant]
US 10337003B2 · Kaye · 2019 [cited by applicant]
US 10364431B2 · Kaye · 2019 [cited by applicant]
US 10421966B2 · Wilton et al. · 2019 [cited by applicant]
US RE47691E · Wilton et al. · 2019 [cited by applicant]
US RE47751E · Wilton et al. · 2019 [cited by applicant]
US RE47769E · Wilton et al. · 2019 [cited by applicant]
US 10875880B2 · Cai · 2020 [cited by examiner]
US 10961262B2 · Cai · 2021 [cited by examiner]
US 11384105B2 · Cai · 2022 [cited by examiner]
US 20080227742A1 · Dmochowski et al. · 2008 [cited by applicant]
US 20100292458A1 · Buhler et al. · 2010 [cited by applicant]
US 20110263686A1 · Wilton et al. · 2011 [cited by applicant]
US 20130211062A1 · Watanabe et al. · 2013 [cited by applicant]
US 20140256926A1 · Damha et al. · 2014 [cited by applicant]
US 20140330006A1 · Hanson et al. · 2014 [cited by applicant]
US 20150197786A1 · Osborne et al. · 2015 [cited by applicant]
US 20160076033A1 · Torii et al. · 2016 [cited by applicant]
US 20180163205A1 · Wilton et al. · 2018 [cited by applicant]
US 20180177814A1 · Passini et al. · 2018 [cited by applicant]
US 20190270994A1 · Wilton et al. · 2019 [cited by applicant]
US 20190292208A1 · Cai et al. · 2019 [cited by applicant]
US 20190323010A1 · Wilton et al. · 2019 [cited by applicant]
US 20190359982A1 · Kaye · 2019 [cited by applicant]
US 20200040337A1 · Kaye · 2020 [cited by applicant]
US 20200080079A1 · Cai · 2020 [cited by applicant]
WO WO9002749A1 · 1990 [cited by applicant]
WO WO2004043977A2 · 2004 [cited by applicant]
WO WO2006000057A1 · 2006 [cited by applicant]
WO WO2009064471A1 · 2009 [cited by applicant]
WO WO2010115993A1 · 2010 [cited by applicant]
WO WO2011150408A2 · 2011 [cited by applicant]
WO WO2012043730A1 · 2012 [cited by applicant]
WO WO2013053928A1 · 2013 [cited by applicant]
WO WO2013082551A1 · 2013 [cited by applicant]
WO WO2014153240A2 · 2014 [cited by applicant]
WO WO2017205496A1 · 2017 [cited by applicant]
WO WO2017205513A1 · 2017 [cited by applicant]
WO WO2017205880A1 · 2017 [cited by applicant]
Alul, R.H., et al., “Oxalyl-CPG: A Labile Support for Synthesis of Sensitive Oligonucleotide Derivatives,” Nucleic Acids Research 19(7):1527-1532, Oxford University Press, England (Apr. 1991). [cited by applicant]
Bayer, E., et al., “A New Support for Polypeptide Synthesis in Columns,” Tetrahedron Letters 51:4503-4505, Elsevier, England (Nov. 1970). [cited by applicant]
Berg, R.H., et al., “Long-chain polystrene-grafted polyethylene film matrix: A new support for solid phase peptide synthesis,” Journal of the American Chemical Society 111:8024, (1989). [cited by applicant]
Bonora, G.M., et al., “A Liquid-Phase Process Suitable for Large-Scale Synthesis of Phosphorothioate Oligonucleotides,” Organic Process Research & Development 4 (3):225-231, American Chemical Society (2000). [cited by applicant]
Cirak, S., et al., “Exon Skipping and Dystrophin Restoration in Patients With Duchenne Muscular Dystrophy After Systemic Phosphorodiamidate Morpholino Oligomer Treatment: An Open-label, Phase 2, Dose-escalation Study,” … [cited by applicant]
Daniels, S.B., et al., “Membranes as Solid Supporters for Peptide Synthesis,” Tetrahedron Letters 30:4345-4348, (1989). [cited by applicant]
Wright, P., et al., “Large Scale Synthesis of Oligonucleotides via Phosphoramidite Nucleosides and a High-loaded Polystyrene Support,” Tetrahedron Letters 34:3373, (1993). [cited by applicant]
Geysen, H.M., et al., “Use of Peptide Synthesis to Probe Viral Antigens for Epitopes to a Resolution of a Single Amino Acid,” Proceedings of the National Academy of Sciences of the United States of America 81(13):3998-4… [cited by applicant]
Goemans, N.M., et al., “Systemic Administration of PRO051 in Duchenne's Muscular Dystrophy,” The New England Journal of Medicine 364(16):1513-1522, Massachusetts Medical Society, United States (Apr. 2011). [cited by applicant]
Gravert, D.J and Janda, K.D, “Organic Synthesis on Soluble Polymer Supports: Liquid-Phase Methodologies,” Chemical Reviews 97(2):489-510, American Chemical Society, United States (Apr. 1997). [cited by applicant]
Houghten, R.A, “General Method for the Rapid Solid-phase Synthesis of Large Numbers of Peptides: Specificity of Antigen-antibody Interaction at the Level of Individual Amino Acids,” Proceedings of the National Academy o… [cited by applicant]
Kent, S.B.H and Merrifield, R.B, “Preparation and Properties of Tert-butyloxycarbonylaminoacy1-4-(Oxymethyl) Phenylacetamidomethyl-(Kel F-g-styrene) Resin, an Insoluble, Noncrosslinked Support for Solid Phase Peptide Sy… [cited by applicant]
Kinali, M., et al., “Local Restoration of Dystrophin Expression With the Morpholino Oligomer AVI-4658 in Duchenne Muscular Dystrophy: a Single-blind, Placebo-controlled, Dose-escalation, Proof-of-concept Study,” The Lan… [cited by applicant]
Parr, W and Grohmann, K, “Solid-phase Peptide Synthesis on an Inorganic Matrix Having Organic Groups on the Surface,” Angewandte Chemie (International ed. in English) 11(4):314-315, Wiley-VCH, Germany (Apr. 1972). [cited by applicant]
International Preliminary Report on Patentability for Application No. PCT/US2017/034284, mailed on Nov. 27, 2018, 6 pages. [cited by applicant]
Atherton, E., et al., “Letter: Polyamide Supports for Polypeptide Synthesis,” Journal of the American Chemical Society, 97(22):6584-6585, American Chemical Society, United States (Oct. 1975). [cited by applicant]
Atherton, E., et al., “The Polyamide Method of Solid Phase Peptide and Oligonucleotide Synthesis,” Bioorganic Chemistry, 8(3):351-370, Elsevier Inc (Sep. 1979). [cited by applicant]
International Search Report and Written opinion for International Application No. PCT/US2017/034284, European Patent Office, HV Rijswijk, mailed on Jul. 27, 2017. [cited by applicant]
Summerton, J. and Weller, D., “Morpholino Antisense Oligomers: Design, Preparation, and Properties,” Antisense & Nucleic Acid Drug Development 7(3):187-195, Mary Ann Liebert, Inc., United States (Jun. 1997). [cited by applicant]
Van Deutekom, J.C., et al., “Local Dystrophin Restoration with Antisense Oligonucleotide PRO051,” The New England Journal of Medicine 357(26):2677-2686, Massachusetts Medical Society, United States (Dec. 2007). [cited by applicant]
Van Rietschoten, Peptides 1974, “Simultaneous Synthesis of Two Peptide Analogs on Different Insoluble Supports”, Y. Wolman, Ed., Wiley and Sons, New York, 1975, pp. 113-116. [cited by applicant]
Virta, P., et al., “Solid-Supported Synthesis of Oligomeric Bioconjugates,” Tetrahedron, 34(38):5137-5174, Elsevier Science Publishers, Amsterdam, NL (Jul. 2003). [cited by applicant]
International Search Report and Written Opinion for International Application No. PCT/US2017/034235, European Patent Office, Netherlands, mailed Jul. 31, 2017, 9 pages. [cited by applicant]
International Preliminary Report on Patentability for International Application No. PCT/US2017/034235, European Patent Office, Netherlands, mailed Nov. 27, 2018, 6 pages. [cited by applicant]
Atherton, E., et al., “Peptide synthesis. Part 2. Procedures for Solid-phase Synthesis using N [cited by applicant]
Scott, R.P., et al., “The Use of Resin Coated Glass Beads in the form of a Packed Bed for the Solid Phase Synthesis of Peptides,” [cited by applicant]
Singh, Sanjay K., et al. “LNA (locked nucleic acids): synthesis and high-affinity nucleic acid recognition.” [cited by applicant]
Koshkin, Alexei A., et al. “LNA (Locked Nucleic Acids): Synthesis of the adenine, cytosine, guanine, 5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation, and unprecedented nucleic acid recog… [cited by applicant]
Wengel, Jesper. “Synthesis of 3 ′-C-and 4 ′-C-branched oligodeoxynucleotides and the development of locked nucleic acid (LNA).” [cited by applicant]
Obika, S., et al., “Synthesis of 2′-O, 4′-C-methylencuridine and-cytidine. Novel bicyclic nucleosides having a fixed C3,-endo sugar puckering.” [cited by applicant]
Obika, Satoshi, et al. “Stability and structural features of the duplexes containing nucleoside analogues with a fixed N-type conformation, 2′-O, 4′-C-methyleneribonucleosides.” [cited by applicant]
Obika, Satoshi, et al. “Synthesis and properties of 3′-amino-2′, 4′-BNA, a bridged nucleic acid with a N3′-→P5′ phosphoramidate linkage,” [cited by applicant]
Iyer, Radhakrishnan P., et al. “The automated synthesis of sulfur-containing oligodeoxyribonucleotides using 3H-1, 2-benzodithiol-3-one 1, 1-dioxide as a sulfur-transfer reagent.” [cited by applicant]
Yoo, B., et al., “2′-O-methyl-modified phosphorothioate antisense oligonucleotides have reduced non-specific effects in vitro,” [cited by applicant]
Martin, Pierre. “Ein neuer Zugang zu 2′-O-Alkylribonucleosiden und Eigenschaften deren Oligonucleotide.” [cited by applicant]
Yamada, T., et al., “Synthesis of 2′-O-[2-(N-methylcarbamoyl) ethyl] ribonucleosides using oxa-Michael reaction and chemical and biological properties of nucleotide derivatives incorporating these modified ribonucleosid… [cited by applicant]
Notice of Allowance mailed Apr. 29, 2020, in U.S. Appl. No. 16/303,356, Cai, B., filing date Nov. 20, 2018, 10 pages. [cited by applicant]
Eliel; E. L. and S. H. Wilen, Stereo-chemistry of Carbon Compounds, John Wiley & Sons, New York, 1994, pp. 1119-1190. [cited by applicant]
March, J., Advanced Organic Chemistry, 3d. Ed., Chap. 4, John Wiley & Sons, New York (1985)). [cited by applicant]
Office Action mailed Feb. 6, 2020, in U.S. Appl. No. 16/302,018, Cai, B., et al., filed Nov. 15, 2018, 15 pages. [cited by applicant]
International Search Report and Written Opinion for International Application No. PCT/US2017/040318, United States Patent and Trademark Office, United States, mailed Sep. 26, 2017, 10 pages. [cited by applicant]
International Preliminary Report on Patentability for Application No. PCT/US2017/040318, mailed on Nov. 27, 2018, 8 pages. [cited by applicant]
Johnsson, R., et al., “New Light Labile Linker For Solid Phase Synthesis Of 2′-O-Acetalester Oligonucleotides And Applications To Sirna Prodrug Development,” Bioorganic & Medicinal Chemistry Letters, 21(12): 3721-3725, … [cited by applicant]
International Search Report and Written opinion for International Application No. PCT/US17/40311, International Search Authority, United States, mailed Dec. 8, 2017, 10 pages. [cited by applicant]
International Preliminary Report on Patentability for Application No. PCT/US17/40311, International Search Authority, United States, mailed Nov. 27, 2018, 10 pages. [cited by applicant]
Office Action mailed Apr. 28, 2020, in U.S. Appl. No. 16/302,443, Cai, B. et al., filed Nov. 16, 2018. [cited by applicant]
Restriction Requirement mailed Jan. 27, 2020, in U.S. Appl. No. 16/302,443, Cai, B. et al., filed Nov. 16, 2018, 9 pages. [cited by applicant]