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).

  • Patent number: 12565641
    Abstract: 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: Grant
    Filed: October 13, 2022
    Date of Patent: March 3, 2026
    Assignee: Codexis, Inc.
    Inventors: Charlene Ching, Stephanie Marie Forget, Anders Matthew Knight, Mikayla Jianghongxia Krawczyk, Niusha Mahmoodi, Melissa Ann Mayo, Mathew G. Miller, Jonathan Vroom
  • Publication number: 20260035675
    Abstract: 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: Application
    Filed: October 21, 2025
    Publication date: February 5, 2026
    Applicant: Codexis, Inc.
    Inventors: Jonathan Vroom, Santhosh Sivaramakrishnan, Nandhitha Subramanian
  • Publication number: 20260015595
    Abstract: 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: Application
    Filed: September 16, 2025
    Publication date: January 15, 2026
    Inventors: Jonathan VROOM, Stephanie Sue GALANIE, Jack LIANG, Joyce LIU, Nikki DELLAS, Melissa Ann MAYO, David ENTWISTLE
  • Publication number: 20260009012
    Abstract: 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: Application
    Filed: September 15, 2025
    Publication date: January 8, 2026
    Applicant: 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
  • Publication number: 20260002136
    Abstract: 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: Application
    Filed: July 1, 2025
    Publication date: January 1, 2026
    Inventors: Jonathan VROOM, Stephanie Sue GALANIE, Nikki DELLAS, Jack LIANG, Joyce LIU, David ENTWISTLE, Courtney Dianne MOFFETT
  • Patent number: 12497605
    Abstract: 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: Grant
    Filed: March 20, 2024
    Date of Patent: December 16, 2025
    Assignee: 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
  • Patent number: 12480104
    Abstract: 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: Grant
    Filed: June 30, 2020
    Date of Patent: November 25, 2025
    Assignee: Codexis, Inc.
    Inventors: Jonathan Vroom, Santhosh Sivaramakrishnan, Nandhitha Subramanian
  • Patent number: 12460195
    Abstract: The present invention provides engineered deoxyribose-phosphate aldolase polypeptides useful under industrial process conditions for the production of pharmaceutical and fine chemical compounds.
    Type: Grant
    Filed: November 7, 2023
    Date of Patent: November 4, 2025
    Assignee: 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
  • Patent number: 12454682
    Abstract: 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: Grant
    Filed: August 2, 2023
    Date of Patent: October 28, 2025
    Assignee: TATE & LYLE SOLUTIONS USA LLC
    Inventors: Jonathan Vroom, Stephanie Sue Galanie, Jack Liang, Joyce Liu, Nikki Dellas, Melissa Ann Mayo, David Entwistle
  • Patent number: 12428629
    Abstract: 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: Grant
    Filed: January 3, 2024
    Date of Patent: September 30, 2025
    Assignee: Codexis, Inc.
    Inventors: Jonathan Vroom, Jessica Anna Hurtak, Anders Matthew Knight
  • Patent number: 12421509
    Abstract: 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: Grant
    Filed: September 14, 2023
    Date of Patent: September 23, 2025
    Assignee: 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
  • Publication number: 20250290049
    Abstract: 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: Application
    Filed: June 4, 2025
    Publication date: September 18, 2025
    Inventors: Jonathan Vroom, Alberto Ortega Guerra, Jack Liang, Gregory A. Cope, Nikki Dellas, Christopher Keltie Prier
  • Patent number: 12404499
    Abstract: 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: Grant
    Filed: October 27, 2020
    Date of Patent: September 2, 2025
    Assignee: TATE & LYLE SOLUTIONS USA LLC
    Inventors: Jonathan Vroom, Stephanie Sue Galanie, Nikki Dellas, Jack Liang, Joyce Liu, David Entwistle, Courtney Dianne Moffett
  • Publication number: 20250250552
    Abstract: 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: Application
    Filed: March 18, 2025
    Publication date: August 7, 2025
    Inventors: Mathew G. Miller, Vesna Mitchell, Jovana Nazor, Donald S. Baskerville, Nikki Dellas, David Elgart, Jonathan Vroom, Sandy M. Gomes, Nandhitha Subramanian, Ericka Bermudez
  • Publication number: 20250236849
    Abstract: 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: Application
    Filed: April 7, 2025
    Publication date: July 24, 2025
    Inventors: 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
  • Publication number: 20250215404
    Abstract: 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: Application
    Filed: March 17, 2025
    Publication date: July 3, 2025
    Inventors: Jonathan Vroom, Alberto Ortega Guerra, Jovana Nazor, Mikayla Jianghongxia Krawczyk
  • Patent number: 12344865
    Abstract: 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: Grant
    Filed: November 19, 2020
    Date of Patent: July 1, 2025
    Assignee: Codexis, Inc.
    Inventors: Jonathan Vroom, Alberto Ortega Guerra, Jack Liang, Gregory A. Cope, Nikki Dellas, Christopher Keltie Prier
  • Patent number: 12344872
    Abstract: 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: Grant
    Filed: May 7, 2018
    Date of Patent: July 1, 2025
    Assignee: Codexis, Inc.
    Inventors: Mathew G. Miller, Jonathan Vroom, Nikki Dellas, Donald S. Baskerville, Sandy M. Gomes, David Elgart, Judy Victoria Antonio Viduya
  • Publication number: 20250179460
    Abstract: 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: Application
    Filed: October 3, 2024
    Publication date: June 5, 2025
    Inventors: 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
  • Patent number: 12291728
    Abstract: 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: Grant
    Filed: October 27, 2020
    Date of Patent: May 6, 2025
    Assignee: TATE & LYLE SOLUTIONS USA LLC
    Inventors: Jonathan Vroom, Stephanie Sue Galanie, Nikki Dellas, Jack Liang, Joyce Liu, David Entwistle, Courtney Dianne Moffett