Patents by Inventor Wilfred A. van der Donk

Wilfred A. van der Donk 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).

  • Publication number: 20240018501
    Abstract: An isolated nucleic acid that includes an open reading frame encoding a lanthipeptide protease polypeptide for scarless tag removal from a polypeptide is presented. Reagents, expression constructs and methods are also provided for preparing a scarless tag polypeptide product from a tagged polypeptide precursor containing a lanthipeptide protease cleavage site. The reagents are directed to novel lanthipeptide proteases and expression constructs and polypeptide precursors that include highly specific lanthipeptide protease substrate recognition sequence. Methods are provided that enable scarless tag removal from a cognate lanthipeptide, a non-cognate lanthipeptide or a heterologous polypeptide that includes extraneous amino acid sequences, such as leader peptides and tags.
    Type: Application
    Filed: November 29, 2022
    Publication date: January 18, 2024
    Inventors: Wilfred A. van der Donk, Weixin Tang
  • Patent number: 11149270
    Abstract: Platforms, systems and methods are provided for identifying engineered lanthipeptide display peptides expressed in vivo from biological organisms.
    Type: Grant
    Filed: September 28, 2015
    Date of Patent: October 19, 2021
    Assignee: The Board of Trustees of the University of Illinois
    Inventors: Wilfred A. van der Donk, Ayse Okesli, Xiao Yang, Mark Walker, Kenton J. Hetrick
  • Patent number: 9993490
    Abstract: The present invention relates to pharmaceutical compositions comprising a phosphonic acid compound, such as a natural product. Such compounds can include, such as an antibiotic or compound with other activity, derived from an Actinobacteria strain having a gene encoding pepM (phosphoenolpyruvate phosphomutase) or a pepM-dependent biosynthetic pathway. The present invention also relates to methods for treating or preventing or reducing the risk of a bacterial infection by administering a therapeutically effective or prophylactically effective amount of a phosphonic acid antibiotic, or a pharmaceutical composition containing such an antibiotic, to a patient or subject in need thereof. The present invention further relates to methods for isolating, purfying, and identifying such phosphonic acid compounds from Actinobacteria strains.
    Type: Grant
    Filed: July 21, 2015
    Date of Patent: June 12, 2018
    Assignee: The Board of Trustees of The University of Illinois
    Inventors: William W. Metcalf, Kou-San Ju, Jiangtao Gao, James R. Doroghazi, Wilfred A. van der Donk
  • Publication number: 20170240878
    Abstract: An isolated nucleic acid that includes an open reading frame encoding a lanthipeptide protease polypeptide for scarless tag removal from a polypeptide is presented. Reagents, expression constructs and methods are also provided for preparing a scarless tag polypeptide product from a tagged polypeptide precursor containing a lanthipeptide protease cleavage site. The reagents are directed to novel lanthipeptide proteases and expression constructs and polypeptide precursors that include highly specific lanthipeptide protease substrate recognition sequence. Methods are provided that enable scarless tag removal from a cognate lanthipeptide, a non-cognate lanthipeptide or a heterologous polypeptide that includes extraneous amino acid sequences, such as leader peptides and tags.
    Type: Application
    Filed: May 12, 2015
    Publication date: August 24, 2017
    Inventors: Wilfred A. van der Donk, Weixin Tang
  • Publication number: 20170204400
    Abstract: Platforms, systems and methods are provided for identifying engineered lanthipeptide display peptides expressed in vivo from biological organisms.
    Type: Application
    Filed: September 28, 2015
    Publication date: July 20, 2017
    Applicant: The Board of Trustees of the University of Illinois
    Inventors: Wilfred A. van der Donk, Ayse Okesli, Xiao Yang, Mark Walker, Kenton J. Hetrick
  • Publication number: 20170202863
    Abstract: The present invention relates to pharmaceutical compositions comprising a phosphonic acid compound, such as a natural product. Such compounds can include, such as an antibiotic or compound with other activity, derived from an Actinobacteria strain having a gene encoding pepM (phosphoenolpyruvate phosphomutase) or a pepM-dependent biosynthetic pathway. The present invention also relates to methods for treating or preventing or reducing the risk of a bacterial infection by administering a therapeutically effective or prophylactically effective amount of a phosphonic acid antibiotic, or a pharmaceutical composition containing such an antibiotic, to a patient or subject in need thereof. The present invention further relates to methods for isolating, purfying, and identifying such phosphonic acid compounds from Actinobacteria strains.
    Type: Application
    Filed: July 21, 2015
    Publication date: July 20, 2017
    Inventors: William W. Metcalf, Kou-San Ju, Jiangtao Gao, James R. Doroghazi, David P. Labeda, Wilfred A. van der Donk
  • Patent number: 9326523
    Abstract: The disclosure provides lantibiotics geobacillin I and geobacillin II from Geobacillus thermodenitrificans, compositions comprising the lantibiotics, and methods of use of the lantibiotics. Further disclosed are the sequences of lantibiotics geobacillin I and geobacillin I, and alternative structures of geobacillin I and geobacillin II comprising amino acid substitutions. Antimicrobial compositions comprising one or more isolated geobacillins and a pharmaceutically acceptable carrier, and methods of reducing reproduction of bacteria comprising administering to a subject a therapeutically effective amount of the antimicrobial composition are also provided.
    Type: Grant
    Filed: February 7, 2013
    Date of Patent: May 3, 2016
    Assignee: The Board of Trustees of the University of Illinois
    Inventors: Wilfred A. van der Donk, Neha Garg, Yuki Goto, Weixin Tang
  • Publication number: 20150050256
    Abstract: The invention provides lantibiotics geobacillin I and geobacillin II from Geobacillus thermodenitrificans, compositions comprising the lantibiotics, and methods of use of the lantibiotics.
    Type: Application
    Filed: February 7, 2013
    Publication date: February 19, 2015
    Applicant: The Board of Trustees of the University of Illinois
    Inventors: Wilfred A. van der Donk, Neha Garg, Yuki Goto, Weixin Tang
  • Publication number: 20140113874
    Abstract: Compounds comprising peptides capable of binding C3 protein and inhibiting complement activation are disclosed. These cyclic compounds are modified to improve stability while maintaining substantially equivalent complement activation-inhibitory activity as compared with currently available compounds. The compounds comprise compstatin analogs in which the disulfide bond between C2 and C12 is modified via a thioether bond to form a cystathionine.
    Type: Application
    Filed: September 21, 2011
    Publication date: April 24, 2014
    Applicant: THE TRUSTEES OF THE UNIVERSITY OF PENNSYLVANIA
    Inventors: John D. Lambris, Wilfred A. Van Der Donk
  • Patent number: 8372601
    Abstract: The disclosure of the present application provides polypeptide sequences and nucleotide sequences coding for the polypeptide sequences of proteins used in the production of APPA-containing peptides. In at least one embodiment of the present disclosure, an isolated nucleic acid is disclosed which comprises a nucleotide sequence encoding a polypeptide having a sequence identity of 60 percent or greater to an amino acid sequence selected from the group consisting of SEQ ID NOS: 2-13, and 15-23.
    Type: Grant
    Filed: January 21, 2011
    Date of Patent: February 12, 2013
    Assignee: University of Illinois at Urbana-Champaign
    Inventors: William W. Metcalf, Wilfred A. van der Donk, Junkal Zhang, Benjamin T. Circello, Svetlana A. Borisova
  • Publication number: 20110217734
    Abstract: The disclosure of the present application provides polypeptide sequences and nucleotide sequences coding for the polypeptide sequences of proteins used in the production of APPA-containing peptides. In at least one embodiment of the present disclosure, an isolated nucleic acid is disclosed which comprises a nucleotide sequence encoding a polypeptide having a sequence identity of 60 percent or greater to an amino acid sequence selected from the group consisting of SEQ ID NOS: 2-13, and 15-23.
    Type: Application
    Filed: January 21, 2011
    Publication date: September 8, 2011
    Inventors: William W. Metcalf, Wilfred A. van der Donk, Junkal Zhang, Benajmin T. Circello, Svetlana A. Borisova
  • Patent number: 7985837
    Abstract: The present invention relates to two-component lantibiotics isolated from Bacillus sp. Methods for producing said lantibiotics are provided, wherein dehydration and cyclization of the peptides is carried out by two substrate-specific modifying enzymes. Given the antimicrobial activity of the instant lantibiotics, methods for preventing or treating bacterial infections are also provided.
    Type: Grant
    Filed: October 31, 2007
    Date of Patent: July 26, 2011
    Assignee: The Board of Trustees of the University of Illinois
    Inventors: Wilfred A. van der Donk, Lisa E. Cooper, Amanda L. McClerren
  • Publication number: 20090325254
    Abstract: A new xylose reductase encoding gene from Neurspora crassa was heterologously expressed in E. coli as a His-tag fusion protein and subsequently purified in high yield. This xylose reductase was shown to have a high turnover rate and catalytic efficiency, high stability at room temperature, broad pH profile, and a preference of NADPH over NADH. This enzyme is utilized in production of xylitol and other sugar alcohols such as sorbitol and also in the metabolic enhancement of organisms used for fermentation of plant biomass into ethanol.
    Type: Application
    Filed: September 1, 2009
    Publication date: December 31, 2009
    Applicants: BIOTECHNOLOGY RESEARCH AND DEVELOPMENT CORPORATION, THE BOARD OF TRUSTEES OF THE UNIVERSITY OF ILLINOIS
    Inventors: Huimin Zhao, Ryan Woodyer, Michael Simurdiak, Wilfred A. van der Donk
  • Patent number: 7592163
    Abstract: A new xylose reductase encoding gene from Neurspora crassa was heterologously expressed in E. coli as a His-tag fusion protein and subsequently purified in high yield. This xylose reductase was shown to have a high turnover rate and catalytic efficiency, high stability at room temperature, broad pH profile, and a preference of NADPH over NADH. This enzyme is utilized in production of xylitol and other sugar alcohols such as sorbitol and also in the metabolic enhancement of organisms used for fermentation of plant biomass into ethanol.
    Type: Grant
    Filed: May 19, 2008
    Date of Patent: September 22, 2009
    Assignees: The Board of Trustees of the University of Illinois, Biotechnology Research and Development Corporation
    Inventors: Huimin Zhao, Ryan Woodyer, Michael Simurdiak, Wilfred A. van der Donk
  • Publication number: 20080241900
    Abstract: A new xylose reductase encoding gene from Neurspora crassa was heterologously expressed in E. coli as a His-tag fusion protein and subsequently purified in high yield. This xylose reductase was shown to have a high turnover rate and catalytic efficiency, high stability at room temperature, broad pH profile, and a preference of NADPH over NADH. This enzyme is utilized in production of xylitol and other sugar alcohols such as sorbitol and also in the metabolic enhancement of organisms used for fermentation of plant biomass into ethanol.
    Type: Application
    Filed: May 19, 2008
    Publication date: October 2, 2008
    Applicants: THE BOARD OF TRUSTEES OF THE UNIVERSITY OF ILLINOIS, BIOTECHNOLOGY RESEARCH AND DEVELOPMENT CORPORATION
    Inventors: Huimin Zhao, Ryan Woodyer, Michael Simurdiak, Wilfred A. van der Donk
  • Publication number: 20080242617
    Abstract: The present invention relates to two-component lantibiotics isolated from Bacillus sp. Methods for producing said lantibiotics are provided, wherein dehydration and cyclization of the peptides is carried out by two substrate-specific modifying enzymes. Given the antimicrobial activity of the instant lantibiotics, methods for preventing or treating bacterial infections are also provided.
    Type: Application
    Filed: October 31, 2007
    Publication date: October 2, 2008
    Inventors: Wilfred A. van der Donk, Lisa E. Cooper, Amanda L. McClerren
  • Patent number: 7402419
    Abstract: Phosphite dehydrogenase mutant enzymes were generated that provide relaxed cofactor specificity and increased thermostability over the wild type enzyme. The mutant enzymes are useful for nicotinamide cofactor regeneration.
    Type: Grant
    Filed: June 10, 2004
    Date of Patent: July 22, 2008
    Assignees: Biotechnology Research and Development Corporation, Board of Trustees of the University of Illinois
    Inventors: Huimin Zhao, William W. Metcalf, Wilfred A. van der Donk, Tyler Johnannes, Ryan Woodyer
  • Patent number: 7381553
    Abstract: A new xylose reductase encoding gene from Neurspora crassa was heterologously expressed in E. coli as a His-tag fusion protein and subsequently purified in high yield. This xylose reductase was shown to have a high turnover rate and catalytic efficiency, high stability at room temperature, broad pH profile, and a preference of NADPH over NADH. This enzyme is utilized in production of xylitol and other sugar alcohols such as sorbitol and also in the metabolic enhancement of organisms used for fermentation of plant biomass into ethanol.
    Type: Grant
    Filed: June 14, 2005
    Date of Patent: June 3, 2008
    Assignee: The Board of Trustees of the Universtiy of Illinois
    Inventors: Huimin Zhao, Ryan Woodyer, Michael Simurdiak, Wilfred A. van der Donk
  • Publication number: 20080026999
    Abstract: The present invention relates to two-component lantibiotics isolated from Bacillus sp. Methods for producing said lantibiotics are provided, wherein dehydration and cyclization of the peptides is carried out by two substrate-specific modifying enzymes. Given the antimicrobial activity of the instant lantibiotics, methods for preventing or treating bacterial infections are also provided.
    Type: Application
    Filed: June 26, 2007
    Publication date: January 31, 2008
    Inventor: Wilfred A. van der Donk
  • Publication number: 20060035353
    Abstract: A new xylose reductase encoding gene from Neurspora crassa was heterologously expressed in E. coli as a His-tag fusion protein and subsequently purified in high yield. This xylose reductase was shown to have a high turnover rate and catalytic efficiency, high stability at room temperature, broad pH profile, and a preference of NADPH over NADH. This enzyme is utilized in production of xylitol and other sugar alcohols such as sorbitol and also in the metabolic enhancement of organisms used for fermentation of plant biomass into ethanol.
    Type: Application
    Filed: June 14, 2005
    Publication date: February 16, 2006
    Inventors: Huimin Zhao, Ryan Woodyer, Michael Simurdiak, Wilfred van der Donk