Patents Assigned to Codexis, Inc.
  • 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
  • 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
  • Engineered ketoreductase polypeptides
    Patent number: 11512332
    Abstract: The present disclosure provides engineered ketoreductase enzymes having improved properties as compared to a naturally occurring wild-type ketoreductase enzyme. Also provided are polynucleotides encoding the engineered ketoreductase enzymes, host cells capable of expressing the engineered ketoreductase enzymes, and methods of using the engineered ketoreductase enzymes to synthesize a variety of chiral compounds. The engineered ketoreductase polypeptides are optimized for catalyzing the conversion of N-methyl-3-keto-3-(2-thienyl)-1-propanamine to (S)—N-methyl-3-hydroxy-3-(2-thienyl)-1-propanamine.
    Type: Grant
    Filed: July 17, 2020
    Date of Patent: November 29, 2022
    Assignee: Codexis, Inc.
    Inventors: Christopher Savile, John M. Gruber, Emily Mundorff, Gjalt W. Huisman, Steven J. Collier
  • 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
  • Ketoreductase polypeptides for the reduction of acetophenones
    Patent number: 11479756
    Abstract: The present disclosure provides engineered ketoreductase enzymes having improved properties as compared to a naturally occurring wild-type ketoreductase enzyme. Also provided are polynucleotides encoding the engineered ketoreductase enzymes, host cells capable of expressing the engineered ketoreductase enzymes, and methods of using the engineered ketoreductase enzymes to synthesize a variety of chiral compounds.
    Type: Grant
    Filed: January 14, 2021
    Date of Patent: October 25, 2022
    Assignee: Codexis, Inc.
    Inventors: Jack Liang, Stephane J. Jenne, Emily Mundorff, Charlene Ching, John M. Gruber, Anke Krebber, Gjalt W. Huisman
  • Engineered tyrosine ammonia lyase
    Patent number: 11473077
    Abstract: The present invention provides engineered tyrosine ammonia-lyase (TAL) polypeptides and compositions thereof. In some embodiments, the engineered TAL polypeptides have been optimized to provide enhanced catalytic activity while reducing sensitivity to proteolysis and increasing tolerance to acidic pH levels. The invention also provides methods for utilization of the compositions comprising the engineered TAL polypeptides for therapeutic and industrial purposes.
    Type: Grant
    Filed: December 6, 2019
    Date of Patent: October 18, 2022
    Assignee: Codexis, Inc.
    Inventors: Joyce Liu, Nikki Dellas, Stephan Jenne
  • Engineered galactose oxidase variant enzymes
    Patent number: 11466259
    Abstract: The present invention provides engineered galactose oxidase (GOase) enzymes, polypeptides having GOase activity, and polynucleotides encoding these enzymes, as well as vectors and host cells comprising these polynucleotides and polypeptides. Methods for producing GOase enzymes are also provided. The present invention further provides compositions comprising the GOase enzymes and methods of using the engineered GOase enzymes. The present invention finds particular use in the production of pharmaceutical and other compounds.
    Type: Grant
    Filed: July 2, 2019
    Date of Patent: October 11, 2022
    Assignee: Codexis, Inc.
    Inventors: Christopher Michael Micklitsch, Oscar Alvizo, Jovana Nazor, Harvinder Chagger Maniar, Mikayla Jianghongxia Krawczyk, Margie Tabuga Borra-Garske, Nandhitha Subramanian, Anna Fryszkowska, Nicholas M. Marshall, Agustina Rodriguez-Granillo, Deeptak Verma, Dewan Andrews
  • Ketoreductase polypeptides for the production of (R)-3-hydroxythiolane
    Patent number: 11427841
    Abstract: The present disclosure provides engineered ketoreductase enzymes having improved properties as compared to a naturally occurring wild-type ketoreductase enzyme. Also provided are polynucleotides encoding the engineered ketoreductase enzymes, host cells capable of expressing the engineered ketoreductase enzymes, and methods of using the engineered ketoreductase enzymes to synthesize chiral compounds.
    Type: Grant
    Filed: October 26, 2020
    Date of Patent: August 30, 2022
    Assignee: Codexis, Inc.
    Inventors: Jack S Liang, Stephan Jenne, Emily Mundorff, Rama Voladri, James J. Lalonde, Gjalt W. Huisman
  • Human alpha-galactosidase variants
    Patent number: 11427813
    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 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 invention also relates to the use of the compositions comprising the engineered human alpha-galactosidase polypeptides for therapeutic purposes.
    Type: Grant
    Filed: December 19, 2019
    Date of Patent: August 30, 2022
    Assignee: Codexis, Inc.
    Inventors: William Casey Hallows, Kristen Jean Vallieu, Nikki Dellas, Yu Zhu, Judy Victoria Antonio Viduya, Chinping Chng, Antoinette Sero, Gjalt W. Huisman, Rachel Cathleen Botham, Moulay Hicham Alaoui Ismaili
  • Engineered tyrosine ammonia lyase
    Patent number: 11421253
    Abstract: The present invention provides engineered tyrosine ammonia-lyase (TAL) polypeptides and compositions thereof. In some embodiments, the engineered TAL polypeptides have been optimized to provide enhanced catalytic activity and enhanced acid stability, while reducing sensitivity to proteolysis and increasing tolerance to acidic pH levels. The invention also provides methods for utilization of the compositions comprising the engineered TAL polypeptides for therapeutic and industrial purposes.
    Type: Grant
    Filed: January 14, 2021
    Date of Patent: August 23, 2022
    Assignee: Codexis, Inc.
    Inventors: Gjalt W. Huisman, Joyce Liu, Nikki Dellas, Chinping Chng, William Casey Hallows
  • 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
  • Biocatalysts and methods for the synthesis of armodafinil
    Patent number: 11384343
    Abstract: The present invention relates to non-naturally occurring polypeptides useful for preparing armodafinil, polynucleotides encoding the polypeptides, and methods of using the polypeptides. The non-naturally occurring polypeptides of the present invention are effective in carrying out biocatalytic conversion of the (i) 2-(benzhydrylsulfinyl)acetamide to (?)-2-[(R)-(diphenylmethyl)sulfinyl]acetamide (armodafinil), or (ii) benzhydryl-thioacetic acid to (R)-2-(benzhydrylsulfinyl)acetic acid, which is a pivotal intermediate in the synthesis of armodafinil, in enantiomeric excess.
    Type: Grant
    Filed: February 24, 2021
    Date of Patent: July 12, 2022
    Assignee: Codexis, Inc.
    Inventors: Ee Lui Ang, Oscar Alvizo, Behnaz Behrouzian, Michael D. Clay, Steven J. Collier, Ellen D. Eberhard, Fu Fan, Shiwei Song, Derek J. Smith, Magnus Widegren, Robert Wilson, Junye Xu, Jun Zhu
  • Engineered imine reductases and methods for the reductive amination of ketone and amine compounds
    Patent number: 11377673
    Abstract: The present disclosure provides engineered polypeptides having imine reductase activity, polynucleotides encoding the engineered imine reductases, host cells capable of expressing the engineered imine reductases, and methods of using these engineered polypeptides with a range of ketone and amine substrate compounds to prepare secondary and tertiary amine product compounds.
    Type: Grant
    Filed: November 6, 2020
    Date of Patent: July 5, 2022
    Assignee: Codexis, Inc.
    Inventors: Haibin Chen, Steven J. Collier, Jovana Nazor, Joly Sukumaran, Derek Smith, Jeffrey C. Moore, Gregory Hughes, Jacob Janey, Gjalt W. Huisman, Scott J. Novick, Nicholas J. Agard, Oscar Alvizo, Gregory A. Cope, Wan Lin Yeo, Stefanie Ng Minor
  • Transaminase reactions
    Patent number: 11371067
    Abstract: The present disclosure relates to methods of using transaminase polypeptides in the synthesis of chiral amines from prochiral ketones.
    Type: Grant
    Filed: August 4, 2020
    Date of Patent: June 28, 2022
    Assignee: Codexis, Inc.
    Inventors: Gregory Hughes, Paul N. Devine, Fred J. Fleitz, Brendan T. Grau, John Limanto, Christopher Savile, Emily Mundorff
  • Engineered transaminase polypeptides for industrial biocatalysis
    Patent number: 11359183
    Abstract: The present invention provides engineered transaminase polypeptides useful for the synthesis of chiral amine compounds under industrially relevant conditions. The invention also provides polynucleotides encoding the engineered transaminase polypeptides, host cells capable of expressing the engineered transaminases, and methods of using the engineered transaminases for the production of chiral amine compounds.
    Type: Grant
    Filed: May 23, 2018
    Date of Patent: June 14, 2022
    Assignee: Codexis, Inc.
    Inventors: Scott J. Novick, Nikki Dellas, Oscar Alvizo, Ravi David Garcia, Charlene Ching, David Entwistle
  • Engineered imine reductases and methods for the reductive amination of ketone and amine compounds
    Patent number: 11352609
    Abstract: The present application provides engineered polypeptides having imine reductase activity, polynucleotides encoding the engineered imine reductases, host cells capable of expressing the engineered imine reductases, and methods of using these engineered polypeptides with a range of ketone and amine substrate compounds to prepare secondary and tertiary amine product compounds.
    Type: Grant
    Filed: September 2, 2020
    Date of Patent: June 7, 2022
    Assignee: Codexis, Inc.
    Inventors: Oscar Alvizo, Melissa Ann Mayo, Jeffrey C. Moore
  • Ketoreductase polypeptides for the preparation of phenylephrine
    Patent number: 11345898
    Abstract: The disclosure relates to engineered ketoreductase polypeptides and processes of using the polypeptides for production of phenylephrine.
    Type: Grant
    Filed: October 30, 2020
    Date of Patent: May 31, 2022
    Assignee: Codexis, Inc.
    Inventors: Oscar Alvizo, Steven J. Collier, Hans-Georg Joerg Hennemann, Seong Ho Oh, Wenjuan Zha
  • Methods and systems for engineering biomolecules
    Patent number: 11342046
    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: Grant
    Filed: June 6, 2019
    Date of Patent: May 24, 2022
    Assignee: Codexis, Inc.
    Inventors: Russell Javiniar Sarmiento, Donald Scott Baskerville, Xiyun Zhang
  • Transglutaminase variants
    Patent number: 11319531
    Abstract: The present invention provides engineered transglutamirase enzymes, polynucleotides encoding the enzymes, compositions comprising the enzymes, methods of producing these enzymes, and methods of using the engineered transglutaminase enzymes.
    Type: Grant
    Filed: November 2, 2018
    Date of Patent: May 3, 2022
    Assignee: Codexis, Inc.
    Inventors: Jovana Nazor, Jie Yang, Goutami Banerjee, Xiyun Zhang, James Nicholas Riggins, Erika M. Milczek, Jeffrey C. Moore
  • Engineered beta-glucosidases and glucosylation methods
    Patent number: 11299723
    Abstract: The present invention provides engineered ?-glucosidase (BGL) enzymes, polypeptides having BGL 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 enzymes, and methods of using the engineered BGL enzymes to make products with ?-glucose linkages.
    Type: Grant
    Filed: June 9, 2017
    Date of Patent: April 12, 2022
    Assignee: Codexis, Inc.
    Inventors: Jack Liang, Jonathan Vroom, Stephanie Sue Galanie, Nikki Dellas, Ravi David Garcia