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: 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
  • Patent number: 12286648
    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: March 8, 2023
    Date of Patent: April 29, 2025
    Assignee: Codexis, Inc.
    Inventors: Jovana Nazor, Robert Osborne, Jack Liang, Jonathan Vroom, Xiyun Zhang, David Entwistle, Rama Voladri, Ravi David Garcia, Jeffrey C. Moore, Shane Grosser, Birgit Kosjek, Matthew Truppo
  • Publication number: 20250122488
    Abstract: The present disclosure provides engineered adenylate kinases, and recombinant polynucleotides encoding the engineered adenylate kinases. The present disclosure further provides uses of the engineered adenylate kinases for converting NMP to NDP.
    Type: Application
    Filed: October 11, 2024
    Publication date: April 17, 2025
    Inventors: Stephanie Marie Forget, Anders Matthew Knight, Marissa Greene MacAvoy, Simon Ng, Nicholas Porter, Jonathan Vroom
  • Publication number: 20250122487
    Abstract: The present disclosure relates to engineered acetate kinase enzymes and compositions thereof, recombinant polynucleotides encoding the engineered acetate kinase enzymes, and method of using the engineered acetate kinase enzymes.
    Type: Application
    Filed: October 11, 2024
    Publication date: April 17, 2025
    Inventors: Stephanie Marie Forget, Marissa Greene MacAvoy, Simon Ng, Nicholas Porter, Jonathan Vroom
  • Publication number: 20250122486
    Abstract: The present disclosure provides engineered adenosine kinase polypeptides, and recombinant polynucleotides encoding the engineered adenosine kinases. The present disclosure further provides method of using the engineered adenosine kinases.
    Type: Application
    Filed: October 11, 2024
    Publication date: April 17, 2025
    Inventors: Stephanie Marie Forget, Marissa Greene MacAvoy, Simon Ng, Nicholas Porter, Leann Quertinmont Teadt, Jonathan Vroom
  • Patent number: 12275962
    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: Grant
    Filed: June 30, 2020
    Date of Patent: April 15, 2025
    Assignee: Codexis, Inc.
    Inventors: Jonathan Vroom, Alberto Ortega Guerra, Jovana Nazor, Mikayla Jianghongxia Krawczyk
  • Publication number: 20240318152
    Abstract: The present invention provides improved P450-BM3 variants with improved activity. In some embodiments, the P450-BM3 variants exhibit improved activity on a 1-tert-Butoxycarbonylaminocyclopentanoic acid substrate.
    Type: Application
    Filed: November 21, 2023
    Publication date: September 26, 2024
    Inventors: David Entwistle, Jason Fell, Stephan Jenne, Anders Matthew Knight, Simon Ng, Ryan D. Reeves, Zara Maxine Seibel, Jonathan Vroom
  • Publication number: 20240309353
    Abstract: The present disclosure relates to engineered DNA ligase polypeptides and compositions thereof, as well as polynucleotides encoding the engineered DNA ligase polypeptides. The present disclosure also provides methods of using the engineered DNA ligase polypeptides or compositions thereof in diagnostics and as a molecular biological tool.
    Type: Application
    Filed: January 23, 2024
    Publication date: September 19, 2024
    Inventors: Jacob Hansen Artz, Rachelle Copeland, Jason Fell, Anders Matthew Knight, Mikayla Jianghongxia Krawczyk, Mathew G. Miller, Jovana Nazor, Amani Shoubber, Jonathan Vroom
  • Publication number: 20240263154
    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: April 5, 2024
    Publication date: August 8, 2024
    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: 20240228997
    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: Application
    Filed: March 20, 2024
    Publication date: July 11, 2024
    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
  • Publication number: 20240209406
    Abstract: The present disclosure provides enzymatic methods for the production of 3?-phosphate-nucleoside-5?-triphosphate (NQP). The present disclosure further provides enzymatic methods for the production of nucleotide-5?-triphosphates.
    Type: Application
    Filed: October 12, 2023
    Publication date: June 27, 2024
    Inventors: David Entwistle, Stephanie Marie Forget, Anders Matthew Knight, Mikayla Jianghongxia Krawczyk, Marissa Greene MacAvoy, Simon Ng, Nicholas Porter, Philip Provencher, Amani Shoubber, Leann Quertinmont Teadt, Jonathan Vroom, David Watts, Leland Ken Wong
  • Publication number: 20240209408
    Abstract: The present invention provides engineered 3?O-kinase polypeptides useful for construction of materials used in template-independent polynucleotide synthesis, as well as compositions and methods of utilizing these engineered polypeptides. The present disclosure also describes one-pot methods for conversion of a natural or modified nucleoside to a nucleoside tetraphosphate or NQP.
    Type: Application
    Filed: October 12, 2023
    Publication date: June 27, 2024
    Applicant: Codexis, Inc.
    Inventors: David Entwistle, Stephanie Marie Forgel, Anders Matthew Knight, Mikayla Krawczyk, Philip Provencher, Amani Shoubber, Jonathan Vroom, David Watts, Leland Wong
  • Patent number: 12018295
    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: Grant
    Filed: June 11, 2021
    Date of Patent: June 25, 2024
    Assignee: Codexis, Inc.
    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: 20240190926
    Abstract: The present invention provides improved P450-BM3 variants with improved activity. In some embodiments, the P450-BM3 variants exhibit improved activity on indanone substrates.
    Type: Application
    Filed: November 21, 2023
    Publication date: June 13, 2024
    Inventors: Margie Tabuga Borra-Garske, Jessica Anna Hurtak, Anders Matthew Knight, Kalyanaraman Krishnamoorthy, Jovana Nazor, James Nicholas Riggins, Nandhitha Subramanian, Jonathan Vroom
  • Publication number: 20240182876
    Abstract: The present invention provides engineered terminal deoxynucleotidyl transferase (TdT) polypeptides useful in template-independent polynucleotide synthesis, as well as compositions, methods of utilizing these engineered polypeptides, and polynucleotides encoding the engineered terminal deoxynucleotidyl transferases.
    Type: Application
    Filed: October 12, 2023
    Publication date: June 6, 2024
    Applicant: Codexis, Inc.
    Inventors: David Entwistle, Stephanie Forget, Michelle Li, Niusha Mahmoodi, Ryan Reeves, Ljubica Vojcic, Jonathan Vroom, David Watts, Leland Ken Wong
  • Patent number: 11970722
    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: December 18, 2020
    Date of Patent: April 30, 2024
    Assignee: Codexis, 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
  • Publication number: 20240132858
    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: Application
    Filed: January 3, 2024
    Publication date: April 25, 2024
    Inventors: Jonathan Vroom, Jessica Anna Hurtak, Anders Matthew Knight
  • Publication number: 20240076647
    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: Application
    Filed: November 7, 2023
    Publication date: March 7, 2024
    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: 11920167
    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: March 5, 2024
    Assignee: TATE & LYLE SOLUTIONS USA LLC
    Inventors: Jonathan Vroom, Stephanie Sue Galanie, Nikki Dellas, Jack Liang, Joyce Liu, David Entwistle, Courtney Dianne Moffett
  • Patent number: 11913045
    Abstract: The present invention provides engineered phenylalanine ammonia-lyase (PAL) polypeptides and compositions thereof, as well as polynucleotides encoding the engineered phenylalanine ammonia-lyase (PAL) polypeptides.
    Type: Grant
    Filed: September 2, 2020
    Date of Patent: February 27, 2024
    Assignee: Codexis, Inc.
    Inventors: Gjalt W. Huisman, Nicholas J. Agard, Benjamin Mijts, Jonathan Vroom, Xiyun Zhang