Patents by Inventor Xiyun Zhang

Xiyun Zhang 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).

  • Transaminase polypeptides
    Patent number: 11939602
    Abstract: The present disclosure provides engineered transaminase enzymes having improved properties as compared to a naturally occurring wild-type transaminase enzyme. Also provided are polynucleotides encoding the engineered transaminase enzymes, host cells capable of expressing the engineered transaminase enzymes, and methods of using the engineered transaminase enzymes to synthesize a variety of chiral compounds.
    Type: Grant
    Filed: November 30, 2022
    Date of Patent: March 26, 2024
    Inventors: Ish K. Dhawan, Gregory Miller, Xiyun Zhang
  • Engineered phenylalanine ammonia lyase polypeptides
    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
  • NOVEL P450-BM3 VARIANTS WITH IMPROVED ACTIVITY
    Publication number: 20240026313
    Abstract: The present invention provides improved P450-BM3 variants with improved activity. In some embodiments, the P450-BM3 variants exhibit improved activity over a wide range of substrates.
    Type: Application
    Filed: September 28, 2023
    Publication date: January 25, 2024
    Inventors: Robert Osborne, Vesna Mitchell, Khin Yu Naing Htwe, Xiyun Zhang, Erika M. Milczek, Jeffrey C. Moore
  • P450-BM3 variants with improved activity
    Patent number: 11807874
    Abstract: The present invention provides improved P450-BM3 variants with improved activity. In some embodiments, the P450-BM3 variants exhibit improved activity over a wide range of substrates.
    Type: Grant
    Filed: February 15, 2022
    Date of Patent: November 7, 2023
    Assignee: Codexis, Inc.
    Inventors: Robert Osborne, Vesna Mitchell, Khin Yu Naing Htwe, Xiyun Zhang, Erika M. Milczek, Jeffrey C. Moore
  • BIOCATALYSTS AND METHODS FOR HYDROXYLATION OF CHEMICAL COMPOUNDS
    Publication number: 20230272354
    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: March 8, 2023
    Publication date: August 31, 2023
    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
  • NOVEL P450-BM3 VARIANTS WITH IMPROVED ACTIVITY
    Publication number: 20230250403
    Abstract: The present invention provides improved P450-BM3 variants with improved activity. In some embodiments, the P450-BM3 variants exhibit improved activity over a wide range of substrates.
    Type: Application
    Filed: January 12, 2023
    Publication date: August 10, 2023
    Inventors: Robert Osborne, Vesna Mitchell, Khin Yu Naing Htwe, Xiyun Zhang, Erika M. Milczek, Jeffrey C. Moore
  • Second Additional Phytase Variants and Methods
    Publication number: 20230250405
    Abstract: The present invention relates to variant phytase enzymes and their use thereof.
    Type: Application
    Filed: February 9, 2022
    Publication date: August 10, 2023
    Applicant: Fornia BioSolutions, Inc.
    Inventors: Jie Yang, Xiyun Zhang, Yangyuan Li, Jiang Huang
  • Vectors for expression of biocatalysts
    Patent number: 11634695
    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: October 16, 2020
    Date of Patent: April 25, 2023
    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
  • TRANSAMINASE POLYPEPTIDES
    Publication number: 20230120624
    Abstract: The present disclosure provides engineered transaminase enzymes having improved properties as compared to a naturally occurring wild-type transaminase enzyme. Also provided are polynucleotides encoding the engineered transaminase enzymes, host cells capable of expressing the engineered transaminase enzymes, and methods of using the engineered transaminase enzymes to synthesize a variety of chiral compounds.
    Type: Application
    Filed: November 30, 2022
    Publication date: April 20, 2023
    Inventors: Ish K. Dhawan, Gregory Miller, Xiyun Zhang
  • VARIANT G6P G7P GLUCOAMYLASE COMPOSITIONS AND METHODS
    Publication number: 20230108132
    Abstract: The invention is directed to novel variant glucoamylases.
    Type: Application
    Filed: July 22, 2022
    Publication date: April 6, 2023
    Applicant: Fornia BioSolutions, Inc.
    Inventors: Xiyun ZHANG, Jie YANG, Goutami BANERJEE, Khin OO, Marielle De Jesus PALATINO, Eric Lin HU, Imad N. SAWAYA, Tatsuya FUKUSHIMA, Jijiao ZENG, Wenhua LU
  • P450-BM3 variants with improved activity
    Patent number: 11591578
    Abstract: The present invention provides improved P450-BM3 variants with improved activity. In some embodiments, the P450-BM3 variants exhibit improved activity over a wide range of substrates.
    Type: Grant
    Filed: March 16, 2021
    Date of Patent: February 28, 2023
    Assignee: Codexis, Inc.
    Inventors: Robert Osborne, Vesna Mitchell, Khin Yu Naing Htwe, Xiyun Zhang, Erika M. Milczek, Jeffrey C. Moore
  • AUTOMATED SCREENING OF ENZYME VARIANTS
    Publication number: 20230048421
    Abstract: Disclosed are methods for identifying bio-molecules with desired properties (or which are most suitable for a round of directed evolution) from complex bio-molecule libraries or sets of such libraries. Some embodiments of the present disclosure provide methods for virtually screening proteins for beneficial properties. Some embodiments of the present disclosure provide methods for virtually screening enzymes for desired activity and/or selectivity for catalytic reactions involving particular substrates. Some embodiments combine screening and directed evolution to design and develop proteins and enzymes having desired properties. Systems and computer program products implementing the methods are also provided.
    Type: Application
    Filed: November 2, 2022
    Publication date: February 16, 2023
    Applicant: Codexis, Inc.
    Inventors: Xiyun Zhang, Russell Javiniar Sarmiento, Donald Scott Baskerville, Gjalt W. Huisman
  • Transaminase polypeptides
    Patent number: 11542485
    Abstract: The present disclosure provides engineered transaminase enzymes having improved properties as compared to a naturally occurring wild-type transaminase enzyme. Also provided are polynucleotides encoding the engineered transaminase enzymes, host cells capable of expressing the engineered transaminase enzymes, and methods of using the engineered transaminase enzymes to synthesize a variety of chiral compounds.
    Type: Grant
    Filed: April 6, 2021
    Date of Patent: January 3, 2023
    Assignee: Codexis, Inc.
    Inventors: Ish K. Dhawan, Gregory Miller, Xiyun Zhang
  • Variant G6P G7P glucoamylase compositions and methods
    Patent number: 11535836
    Abstract: The invention is directed to novel variant glucoamylases.
    Type: Grant
    Filed: November 12, 2019
    Date of Patent: December 27, 2022
    Assignee: Fornia Biosolutions, Inc.
    Inventors: Xiyun Zhang, Jie Yang, Goutami Banerjee, Khin Oo, Marielle De Jesus Palatino, Eric Lin Hu, Imad N. Sawaya, Tatsuya Fukushima, Jijiao Zeng, Wenhua Lu
  • Automated screening of enzyme variants
    Patent number: 11535845
    Abstract: Disclosed are methods for identifying bio-molecules with desired properties (or which are most suitable for a round of directed evolution) from complex bio-molecule libraries or sets of such libraries. Some embodiments of the present disclosure provide methods for virtually screening proteins for beneficial properties. Some embodiments of the present disclosure provide methods for virtually screening enzymes for desired activity and/or selectivity for catalytic reactions involving particular substrates. Some embodiments combine screening and directed evolution to design and develop proteins and enzymes having desired properties. Systems and computer program products implementing the methods are also provided.
    Type: Grant
    Filed: May 15, 2020
    Date of Patent: December 27, 2022
    Assignee: Codexis, Inc.
    Inventors: Xiyun Zhang, Russell Javiniar Sarmiento, Donald Scott Baskerville, Gjalt W. Huisman
  • Human alpha-galactosidase variants
    Patent number: 11497798
    Abstract: The present invention provides engineered human alpha-galactosidase polypeptides and compositions thereof. The engineered human alpha-galactosidase polypeptides have been optimized to provide improved stability under both acidic (pH<4.5) and basic (pH>7) conditions. The invention also relates to the use of the compositions comprising the engineered human alpha-galactosidase polypeptides for therapeutic purposes.
    Type: Grant
    Filed: August 5, 2020
    Date of Patent: November 15, 2022
    Assignee: Codexis, Inc.
    Inventors: Nicholas J. Agard, Mathew G. Miller, Xiyun Zhang, Gjalt W. Huisman
  • Engineered phenylalanine ammonia lyase polypeptides
    Patent number: 11401515
    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: March 26, 2020
    Date of Patent: August 2, 2022
    Assignee: Codexis, Inc.
    Inventors: Gjalt W. Huisman, Nicholas J. Agard, Benjamin Mijts, Jonathan Vroom, Xiyun Zhang
  • METHODS AND SYSTEMS FOR ENGINEERING BIOMOLECULES
    Publication number: 20220238179
    Abstract: Disclosed are methods for building a sequence activity model with reference to structural data, which model can be used to guide directed evolution of proteins having beneficial properties. Some embodiments use genetic algorithms and structural data to filter out uninformative data. Some embodiments use a support vector machine to train the sequence activity model. The filtering and training methods can generate a sequence activity model having higher predictive power than conventional modeling methods. Systems and computer program products implementing the methods are also provided.
    Type: Application
    Filed: April 12, 2022
    Publication date: July 28, 2022
    Inventors: Russell Javiniar Sarmiento, Donald Scott Baskerville, Xiyun Zhang
  • TRANSGLUTAMINASE VARIANTS
    Publication number: 20220220456
    Abstract: The present invention provides engineered transglutaminase enzymes, polynucleotides encoding the enzymes, compositions comprising the enzymes, methods of producing these enzymes, and methods of using the engineered transglutaminase enzymes.
    Type: Application
    Filed: March 28, 2022
    Publication date: July 14, 2022
    Inventors: Jovana Nazor, Jie Yang, Goutami Banerjee, Xiyun Zhang, James Nicholas Riggins, Erika M. Milczek, Jeffrey C. Moore
  • Additional Endoglucanase Variants and Methods
    Publication number: 20220204956
    Abstract: The invention is directed to novel variant endoglucanases and their use thereof.
    Type: Application
    Filed: December 20, 2021
    Publication date: June 30, 2022
    Applicant: Fornia BioSolutions, Inc.
    Inventors: Jie Yang, Xiyun Zhang, William Buchanan Porterfield, Wenhua Lu, Khin Oo, Goutami Banerjee, Tatsuya Fukushima, Eric Lin Hu