Patents by Inventor Jonathan Vroom
Jonathan Vroom has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Patent number: 12565641Abstract: The present invention provides engineered terminal deoxynucleotidyl transferase (TdT) polypeptides useful in template-independent polynucleotide synthesis using a nucleoside triphosphate-3?-O-removable blocking group (NTP-3?-O-RBG), as well as compositions, methods of utilizing these engineered polypeptides, and polynucleotides encoding the engineered terminal deoxynucleotidyl transferases.Type: GrantFiled: October 13, 2022Date of Patent: March 3, 2026Assignee: Codexis, Inc.Inventors: Charlene Ching, Stephanie Marie Forget, Anders Matthew Knight, Mikayla Jianghongxia Krawczyk, Niusha Mahmoodi, Melissa Ann Mayo, Mathew G. Miller, Jonathan Vroom
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Publication number: 20260035675Abstract: The present invention provides engineered sucrose phosphorylase (SP) enzymes, polypeptides having SP activity, and polynucleotides encoding these enzymes, as well as vectors and host cells comprising these polynucleotides and polypeptides. Methods for producing SP enzymes are also provided. The present invention further provides compositions comprising the SP enzymes and methods of using the engineered SP enzymes. The present invention finds particular use in the production of pharmaceutical compounds.Type: ApplicationFiled: October 21, 2025Publication date: February 5, 2026Applicant: Codexis, Inc.Inventors: Jonathan Vroom, Santhosh Sivaramakrishnan, Nandhitha Subramanian
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Publication number: 20260015595Abstract: The present invention provides engineered glycosyltransferase (GT) enzymes, polypeptides having GT activity, and polynucleotides encoding these enzymes, as well as vectors and host cells comprising these polynucleotides and polypeptides. The present invention provides engineered sucrose synthase (SuS) enzymes, polypeptides having SuS activity, and polynucleotides encoding these enzymes, as well as vectors and host cells comprising these polynucleotides and polypeptides. The present invention also provides compositions comprising the GT enzymes and methods of using the engineered GT enzymes to make products with ?-glucose linkages. The present invention further provides compositions and methods for the production of rebaudiosides (e.g., rebaudioside M, rebaudioside A, rebaudioside I, and rebaudioside D). The present invention also provides compositions comprising the SuS enzymes and methods of using them. Methods for producing GT and SuS enzymes are also provided.Type: ApplicationFiled: September 16, 2025Publication date: January 15, 2026Inventors: Jonathan VROOM, Stephanie Sue GALANIE, Jack LIANG, Joyce LIU, Nikki DELLAS, Melissa Ann MAYO, David ENTWISTLE
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Publication number: 20260009012Abstract: The present invention provides engineered phosphopentomutase (PPM) enzymes, polypeptides having PPM activity, and polynucleotides encoding these enzymes, as well as vectors and host cells comprising these polynucleotides and polypeptides. Methods for producing PPM enzymes are also provided. The present invention further provides compositions comprising the PPM enzymes and methods of using the engineered PPM enzymes. The present invention finds particular use in the production of pharmaceutical compounds.Type: ApplicationFiled: September 15, 2025Publication date: January 8, 2026Applicant: Codexis, Inc.Inventors: Scott J. Novick, Xiang Yi, Nikki Dellas, Oscar Alvizo, Jovana Nazor, Da Duan, Vesna Mitchell, Jonathan Vroom, Santhosh Sivaramakrishnan, Nandhitha Subramanian, Jeffrey C. Moore, Mark Huffman, Agustina Rodriguez-Granillo, Deeptak Verma, Grant S. Murphy, Nicholas Marshall, Jay Russell, Keith A. Canada
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Publication number: 20260002136Abstract: The present invention provides engineered glycosyltransferase (GT) enzymes, polypeptides having GT activity, and polynucleotides encoding these enzymes, as well as vectors and host cells comprising these polynucleotides and polypeptides. The present invention provides engineered sucrose synthase (SuS) enzymes, polypeptides having SuS activity, and polynucleotides encoding these enzymes, as well as vectors and host cells comprising these polynucleotides and polypeptides. The present invention also provides compositions comprising the GT enzymes and methods of using the engineered GT enzymes to make products with ?-glucose linkages. The present invention further provides compositions and methods for the production of rebaudiosides (e.g., rebaudioside M, rebaudioside A, rebaudioside I, and rebaudioside D). The present invention also provides compositions comprising the SuS enzymes and methods of using them. Methods for producing GT and SuS enzymes are also provided.Type: ApplicationFiled: July 1, 2025Publication date: January 1, 2026Inventors: Jonathan VROOM, Stephanie Sue GALANIE, Nikki DELLAS, Jack LIANG, Joyce LIU, David ENTWISTLE, Courtney Dianne MOFFETT
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Patent number: 12497605Abstract: The present invention provides engineered acid alpha-glucosidase (GAA) polypeptides and compositions thereof. In some embodiments, the engineered GAA polypeptides have been optimized to provide increased expression, stability at neutral pH, and activity in cell lysates. The invention also provides methods for utilization of the compositions comprising the engineered GAA polypeptides for therapeutic and other purposes.Type: GrantFiled: March 20, 2024Date of Patent: December 16, 2025Assignee: Crosswalk Therapeutics, Inc.Inventors: William Casey Hallows, Rachel Cathleen Botham, Yu Zhu, Chinping Chng, Nikki Dellas, Gjalt W. Huisman, Moulay Hicham Alaoui Ismaili, David William Homan, Adam P. Silverman, Jonathan Vroom, Jessica P. Lao
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Patent number: 12480104Abstract: The present invention provides engineered sucrose phosphorylase (SP) enzymes, polypeptides having SP activity, and polynucleotides encoding these enzymes, as well as vectors and host cells comprising these polynucleotides and polypeptides. Methods for producing SP enzymes are also provided. The present invention further provides compositions comprising the SP enzymes and methods of using the engineered SP enzymes. The present invention finds particular use in the production of pharmaceutical compounds.Type: GrantFiled: June 30, 2020Date of Patent: November 25, 2025Assignee: Codexis, Inc.Inventors: Jonathan Vroom, Santhosh Sivaramakrishnan, Nandhitha Subramanian
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Patent number: 12460195Abstract: The present invention provides engineered deoxyribose-phosphate aldolase polypeptides useful under industrial process conditions for the production of pharmaceutical and fine chemical compounds.Type: GrantFiled: November 7, 2023Date of Patent: November 4, 2025Assignee: Codexis, Inc.Inventors: Da Duan, Oscar Alvizo, Jovana Nazor, Harvinder Chagger Maniar, James Nicholas Riggins, Jonathan Vroom, Santhosh Sivaramakrishnan, Hao Yang, Anna Fryszkowska, Mark A. Huffman, Joshua N. Kolev, Iman Farasat, Agustina Rodriguez-Granillo, Deeptak Verma
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Patent number: 12454682Abstract: The present invention provides engineered glycosyltransferase (GT) enzymes, polypeptides having GT activity, and polynucleotides encoding these enzymes, as well as vectors and host cells comprising these polynucleotides and polypeptides. The present invention provides engineered sucrose synthase (SuS) enzymes, polypeptides having SuS activity, and polynucleotides encoding these enzymes, as well as vectors and host cells comprising these polynucleotides and polypeptides. The present invention also provides compositions comprising the GT enzymes and methods of using the engineered GT enzymes to make products with ?-glucose linkages. The present invention further provides compositions and methods for the production of rebaudiosides (e.g., rebaudioside M, rebaudioside A, rebaudioside I, and rebaudioside D). The present invention also provides compositions comprising the SuS enzymes and methods of using them. Methods for producing GT and SuS enzymes are also provided.Type: GrantFiled: August 2, 2023Date of Patent: October 28, 2025Assignee: TATE & LYLE SOLUTIONS USA LLCInventors: Jonathan Vroom, Stephanie Sue Galanie, Jack Liang, Joyce Liu, Nikki Dellas, Melissa Ann Mayo, David Entwistle
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Patent number: 12428629Abstract: The present invention provides engineered uridine phosphorylase (UP) enzymes, polypeptides having UP activity, and polynucleotides encoding these enzymes, as well as vectors and host cells comprising these polynucleotides and polypeptides. Methods for producing UP enzymes are also provided. The present invention further provides compositions comprising the UP enzymes and methods of using the engineered UP enzymes. The present invention finds particular use in the production of pharmaceutical compounds.Type: GrantFiled: January 3, 2024Date of Patent: September 30, 2025Assignee: Codexis, Inc.Inventors: Jonathan Vroom, Jessica Anna Hurtak, Anders Matthew Knight
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Patent number: 12421509Abstract: The present invention provides engineered phosphopentomutase (PPM) enzymes, polypeptides having PPM activity, and polynucleotides encoding these enzymes, as well as vectors and host cells comprising these polynucleotides and polypeptides. Methods for producing PPM enzymes are also provided. The present invention further provides compositions comprising the PPM enzymes and methods of using the engineered PPM enzymes. The present invention finds particular use in the production of pharmaceutical compounds.Type: GrantFiled: September 14, 2023Date of Patent: September 23, 2025Assignee: Codexis, Inc.Inventors: Scott J. Novick, Xiang Yi, Nikki Dellas, Oscar Alvizo, Jovana Nazor, Da Duan, Vesna Mitchell, Jonathan Vroom, Santhosh Sivaramakrishnan, Nandhitha Subramanian, Jeffrey C. Moore, Mark Huffman, Agustina Rodriguez-Granillo, Deeptak Verma, Grant S. Murphy, Nicholas Marshall, Jay Russell, Keith A. Canada
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Publication number: 20250290049Abstract: The present invention provides engineered proline hydroxylase polypeptides for the production of hydroxylated compounds, polynucleotides encoding the engineered proline hydroxylases, host cells capable of expressing the engineered proline hydroxylases, and methods of using the engineered proline hydroxylases to prepare compounds useful in the production of active pharmaceutical agents.Type: ApplicationFiled: June 4, 2025Publication date: September 18, 2025Inventors: Jonathan Vroom, Alberto Ortega Guerra, Jack Liang, Gregory A. Cope, Nikki Dellas, Christopher Keltie Prier
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Patent number: 12404499Abstract: The present invention provides engineered glycosyltransferase (GT) enzymes, polypeptides having GT activity, and polynucleotides encoding these enzymes, as well as vectors and host cells comprising these polynucleotides and polypeptides. The present invention provides engineered sucrose synthase (SuS) enzymes, polypeptides having SuS activity, and polynucleotides encoding these enzymes, as well as vectors and host cells comprising these polynucleotides and polypeptides. The present invention also provides compositions comprising the GT enzymes and methods of using the engineered GT enzymes to make products with ?-glucose linkages. The present invention further provides compositions and methods for the production of rebaudiosides (e.g., rebaudioside M, rebaudioside A, rebaudioside I, and rebaudioside D). The present invention also provides compositions comprising the SuS enzymes and methods of using them. Methods for producing GT and SuS enzymes are also provided.Type: GrantFiled: October 27, 2020Date of Patent: September 2, 2025Assignee: TATE & LYLE SOLUTIONS USA LLCInventors: Jonathan Vroom, Stephanie Sue Galanie, Nikki Dellas, Jack Liang, Joyce Liu, David Entwistle, Courtney Dianne Moffett
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Publication number: 20250250552Abstract: The present invention provides engineered DNA polymerase polypeptides and compositions thereof, as well as polynucleotides encoding the engineered DNA polymerase polypeptides. The invention also provides methods for use of the compositions comprising the engineered DNA polymerase polypeptides for diagnostic and other purposes.Type: ApplicationFiled: March 18, 2025Publication date: August 7, 2025Inventors: Mathew G. Miller, Vesna Mitchell, Jovana Nazor, Donald S. Baskerville, Nikki Dellas, David Elgart, Jonathan Vroom, Sandy M. Gomes, Nandhitha Subramanian, Ericka Bermudez
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Publication number: 20250236849Abstract: The present invention provides engineered proline hydroxylase polypeptides for the production of hydroxylated compounds, polynucleotides encoding the engineered proline hydroxylases, host cells capable of expressing the engineered proline hydroxylases, and methods of using the engineered proline hydroxylases to prepare compounds useful in the production of active pharmaceutical agents.Type: ApplicationFiled: April 7, 2025Publication date: July 24, 2025Inventors: Jovana Nazor, Robert Osbome, Jack Liang, Jonathan Vroom, Xiyun Zhang, David Entwistle, Rama Voladri, Ravi David Garcia, Jeffrey C. Moore, Shane Grosser, Birgit Kosjek, Matthew Truppo
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Publication number: 20250215404Abstract: The present invention provides engineered acetate kinase (AcK) enzymes, polypeptides having AcK activity, and polynucleotides encoding these enzymes, as well as vectors and host cells comprising these polynucleotides and polypeptides. Methods for producing AcK enzymes are also provided. The present invention further provides compositions comprising the AcK enzymes and methods of using the engineered AcK enzymes. The present invention finds particular use in the production of pharmaceutical compounds.Type: ApplicationFiled: March 17, 2025Publication date: July 3, 2025Inventors: Jonathan Vroom, Alberto Ortega Guerra, Jovana Nazor, Mikayla Jianghongxia Krawczyk
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Patent number: 12344865Abstract: The present invention provides engineered proline hydroxylase polypeptides for the production of hydroxylated compounds, polynucleotides encoding the engineered proline hydroxylases, host cells capable of expressing the engineered proline hydroxylases, and methods of using the engineered proline hydroxylases to prepare compounds useful in the production of active pharmaceutical agents.Type: GrantFiled: November 19, 2020Date of Patent: July 1, 2025Assignee: Codexis, Inc.Inventors: Jonathan Vroom, Alberto Ortega Guerra, Jack Liang, Gregory A. Cope, Nikki Dellas, Christopher Keltie Prier
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Patent number: 12344872Abstract: The present invention provides engineered ligase polypeptides and compositions thereof, as well as polynucleotides encoding the engineered ligase polypeptides. The invention also provides methods for use of the compositions comprising the engineered ligase polypeptides for diagnostic and other purposes.Type: GrantFiled: May 7, 2018Date of Patent: July 1, 2025Assignee: Codexis, Inc.Inventors: Mathew G. Miller, Jonathan Vroom, Nikki Dellas, Donald S. Baskerville, Sandy M. Gomes, David Elgart, Judy Victoria Antonio Viduya
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Publication number: 20250179460Abstract: Engineered human alpha-galactosidase polypeptides and compositions thereof are provided. The engineered human alpha-galactosidase polypeptides have been optimized to provide improved thermostability, serum stability, improved cellular uptake, stability under both acidic (pH<4) and basic (pH>7) conditions, reduced immunogenicity, and improved globotriaosylceramide removal from cells. The use of the compositions comprising the engineered human alpha-galactosidase polypeptides for therapeutic purposes are described.Type: ApplicationFiled: October 3, 2024Publication date: June 5, 2025Inventors: William Casey Hallows, Nikki Dellas, Yu Zhu, Judy Victoria Antonio VIDUYA, Chinping Chng, Antoinette Sero, Rachel Cathleen Botham, David William Homan, Moulay Hicham Alaoui Ismaili, Jonathan Vroom, Adam P. Silverman, Kristen Jean Vallieu, Charu Shukla Reddy, Kerryn McCluskie
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Patent number: 12291728Abstract: The present invention provides engineered glycosyltransferase (GT) enzymes, polypeptides having GT activity, and polynucleotides encoding these enzymes, as well as vectors and host cells comprising these polynucleotides and polypeptides. The present invention provides engineered sucrose synthase (SuS) enzymes, polypeptides having SuS activity, and polynucleotides encoding these enzymes, as well as vectors and host cells comprising these polynucleotides and polypeptides. The present invention also provides compositions comprising the GT enzymes and methods of using the engineered GT enzymes to make products with ?-glucose linkages. The present invention further provides compositions and methods for the production of rebaudiosides (e.g., rebaudioside M, rebaudioside A, rebaudioside I, and rebaudioside D). The present invention also provides compositions comprising the SuS enzymes and methods of using them. Methods for producing GT and SuS enzymes are also provided.Type: GrantFiled: October 27, 2020Date of Patent: May 6, 2025Assignee: TATE & LYLE SOLUTIONS USA LLCInventors: Jonathan Vroom, Stephanie Sue Galanie, Nikki Dellas, Jack Liang, Joyce Liu, David Entwistle, Courtney Dianne Moffett