Patents by Inventor Stephen J. Benkovic

Stephen J. Benkovic 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: 10973835
    Abstract: A method is disclosed for altering the redox equilibrium of a transmembrane receptor-like protein tyrosine phosphatase (RPTP), particularly a type IIa RPTP, by chemically modulating the activity through contact of such an enzyme with a diaryl boron compound that preferentially reacts with an RPTP in an oxidized state (CyS-OH). This redox modulation is most readily observed and put to use by assaying the inhibition of the phosphatase activity of the RPTP. Such an assay can be carried out on an enzyme in vitro or by contacting the enzyme in a living organism (in vivo). A useful diaryl boron compound corresponds in structure to Formula I in which Ar-1, Ar-2, R1, R2, R3 and R4 are defined within. A pharmaceutical composition containing a useful diaryl boron compound is also disclosed, as are particularly preferred diaryl boron compounds.
    Type: Grant
    Filed: March 2, 2018
    Date of Patent: April 13, 2021
    Assignees: The Penn State Research Foundation, Cold Spring Harbor Laboratory
    Inventors: Stephen J. Benkovic, Nicholas K. Tonks, Chun Yu Liu, Navasona Krishnan, Chunliang Liu
  • Publication number: 20210052614
    Abstract: A method is disclosed for altering the redox equilibrium of a transmembrane receptor-like protein tyrosine phosphatase (RPTP), particularly a type IIa RPTP, by chemically modulating the activity through contact of such an enzyme with a diaryl boron compound that preferentially reacts with an RPTP in an oxidized state (CyS-OH). This redox modulation is most readily observed and put to use by assaying the inhibition of the phosphatase activity of the RPTP. Such an assay can be carried out on an enzyme in vitro or by contacting the enzyme in a living organism (in vivo). A useful diaryl boron compound corresponds in structure to Formula I in which Ar-1, Ar-2, R1, R2, R3 and R4 are defined within. A pharmaceutical composition containing a useful diaryl boron compound is also disclosed, as are particularly preferred diaryl boron compounds.
    Type: Application
    Filed: November 3, 2020
    Publication date: February 25, 2021
    Inventors: Stephen J. Benkovic, Nicholas K. Tonks, Chun Yu Liu, Navasona Krishnan, Chunliang Liu
  • Patent number: 10597735
    Abstract: Inhibitors of the tmRNA pathway have antibacterial activity with broad species specificity, including B. anthracis and other pathogens of military and civilian interest. Identified cyclic or linear peptides are further selected by in vivo selection methods, kill bacterial pathogens when added exogenously, and/or eliminate plasmids carrying antibiotic resistance or virulence genes. The molecular target of each cyclic peptide is in the tmRNA pathway and the tmRNA pathway is inhibited in vitro and in vive by the addition of the peptides.
    Type: Grant
    Filed: December 20, 2016
    Date of Patent: March 24, 2020
    Assignee: The Penn State Research Foundation
    Inventors: Kenneth C Keiler, Stephen J Benkovic
  • Patent number: 10160867
    Abstract: A latex paint composition that contains a film-forming binder and pigment dispersed in an aqueous vehicle and also contains an effective amount of one or more cellulose-supportable fungus growth-inhibiting benzoxaborole compounds of Formula C is disclosed. A method of using that latex paint to inhibit the growth of a cellulose-supportable fungus on a cellulosic surface is also disclosed, as is a method of inhibiting such growth by painting over an fungus-infected surface with a contemplated latex paint.
    Type: Grant
    Filed: August 3, 2016
    Date of Patent: December 25, 2018
    Assignee: THE PENN STATE RESEARCH FOUNDATION
    Inventors: Stephen J. Benkovic, Chunyu Liu, Edward Q. Kaiser
  • Publication number: 20180265906
    Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.
    Type: Application
    Filed: May 31, 2018
    Publication date: September 20, 2018
    Applicant: The Penn State Research Foundation
    Inventors: Stephen J. Benkovic, Frank Salinas
  • Publication number: 20180258106
    Abstract: A method is disclosed for altering the redox equilibrium of a transmembrane receptor-like protein tyrosine phosphatase (RPTP), particularly a type IIa RPTP, by chemically modulating the activity through contact of such an enzyme with a diaryl boron compound that preferentially reacts with an RPTP in an oxidized state (CyS-OH). This redox modulation is most readily observed and put to use by assaying the inhibition of the phosphatase activity of the RPTP. Such an assay can be carried out on an enzyme in vitro or by contacting the enzyme in a living organism (in vivo). A useful diaryl boron compound corresponds in structure to Formula I in which Ar-1, Ar-2, R1, R2, R3 and R4 are defined within. A pharmaceutical composition containing a useful diaryl boron compound is also disclosed, as are particularly preferred diaryl boron compounds.
    Type: Application
    Filed: March 2, 2018
    Publication date: September 13, 2018
    Inventors: Stephen J. Benkovic, Nicholas K. Tonks, Chun Yu Liu, Navasona Krishnan, Chunliang Liu
  • Patent number: 10017803
    Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.
    Type: Grant
    Filed: March 15, 2016
    Date of Patent: July 10, 2018
    Assignee: The Penn State Research Foundation
    Inventors: Stephen J Benkovic, Frank Salinas
  • Patent number: 10000781
    Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.
    Type: Grant
    Filed: March 15, 2016
    Date of Patent: June 19, 2018
    Assignee: The Penn State Research Foundation
    Inventors: Stephen J Benkovic, Frank Salinas
  • Publication number: 20170096717
    Abstract: Inhibitors of the tmRNA pathway have antibacterial activity with broad species specificity, including B. anthracis and other pathogens of military and civilian interest. Identified cyclic or linear peptides are further selected by in vivo selection methods, kill bacterial pathogens when added exogenously, and/or eliminate plasmids carrying antibiotic resistance or virulence genes. The molecular target of each cyclic peptide is in the tmRNA pathway and the tmRNA pathway is inhibited in vitro and in vive by the addition of the peptides.
    Type: Application
    Filed: December 20, 2016
    Publication date: April 6, 2017
    Inventors: KENNETH C. KEILER, Stephen J. Benkovic
  • Publication number: 20170037258
    Abstract: A latex paint composition that contains a film-forming binder and pigment dispersed in an aqueous vehicle and also contains an effective amount of one or more cellulose-supportable fungus growth-inhibiting benzoxaborole compounds of Formula C is disclosed. A method of using that latex paint to inhibit the growth of a cellulose-supportable fungus on a cellulosic surface is also disclosed, as is a method of inhibiting such growth by painting over an fungus-infected surface with a contemplated latex paint.
    Type: Application
    Filed: August 3, 2016
    Publication date: February 9, 2017
    Inventors: Stephen J. BENKOVIC, Chunyu LIU, Edward Q. KAISER
  • Patent number: 9562257
    Abstract: Inhibitors of the tmRNA pathway have antibacterial activity with broad species specificity, including B. anthracis and other pathogens of military and civilian interest. Identified cyclic or linear peptides are further selected by in vivo selection methods, kill bacterial pathogens when added exogenously, and/or eliminate plasmids carrying antibiotic resistance or virulence genes. The molecular target of each cyclic peptide is in the tmRNA pathway and the tmRNA pathway is inhibited in vitro and in vivo by the addition of the peptides.
    Type: Grant
    Filed: December 20, 2013
    Date of Patent: February 7, 2017
    Assignee: The Penn State Research Foundation
    Inventors: Kenneth C Keiler, Stephen J Benkovic
  • Patent number: 9562250
    Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.
    Type: Grant
    Filed: June 24, 2014
    Date of Patent: February 7, 2017
    Assignee: The Penn State Research Foundation
    Inventors: Stephen J Benkovic, Frank Salinas
  • Publication number: 20160265015
    Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.
    Type: Application
    Filed: March 15, 2016
    Publication date: September 15, 2016
    Inventors: Stephen J BENKOVIC, Frank SALINAS
  • Publication number: 20160237475
    Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.
    Type: Application
    Filed: March 15, 2016
    Publication date: August 18, 2016
    Inventors: Stephen J BENKOVIC, Frank Salinas
  • Patent number: 9353133
    Abstract: This invention relates to compounds useful for treating fungal infections, more specifically topical treatment of onychomycosis and/or cutaneous fungal infections. This invention is directed to compounds that are active against fungi and have properties that allow the compound, when placed in contact with a patient, to reach the particular part of the skin, nail, hair, claw or hoof infected by the fungus. In particular the present compounds have physiochemical properties that facilitate penetration of the nail plate.
    Type: Grant
    Filed: March 7, 2014
    Date of Patent: May 31, 2016
    Assignee: Anacor Pharmaceuticals, Inc.
    Inventors: Stephen J. Baker, Tsutomu Akama, Michael Richard Kevin Alley, Stephen J. Benkovic, Michael DiPierro, Vincent S. Hernandez, Karin M. Hold, Isaac Kennedy, Igor Likhotvorik, Weimin Mao, Kirk Maples, Jacob J. Plattner, Fernando Rock, Virginia Sanders, Aaron M. Stemphoski, George Petros Yiannikouros, Siead Zegar, Yong-Kang Zhang, Huchen Zhou
  • Patent number: 9322058
    Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.
    Type: Grant
    Filed: May 2, 2014
    Date of Patent: April 26, 2016
    Assignee: The Penn State Research Foundation
    Inventors: Stephen J Benkovic, Frank Salinas
  • Patent number: 9322057
    Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.
    Type: Grant
    Filed: December 16, 2013
    Date of Patent: April 26, 2016
    Assignee: The Penn State Research Foundation
    Inventors: Stephen J Benkovic, Frank Salinas
  • Patent number: 9322059
    Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.
    Type: Grant
    Filed: June 24, 2014
    Date of Patent: April 26, 2016
    Assignee: The Penn State Research Foundation
    Inventors: Stephen J Benkovic, Frank Salinas
  • Publication number: 20150119364
    Abstract: This invention relates to compounds useful for treating fungal infections, more specifically topical treatment of onychomycosis and/or cutaneous fungal infections. This invention is directed to compounds that are active against fungi and have properties that allow the compound, when placed in contact with a patient, to reach the particular part of the skin, nail, hair, claw or hoof infected by the fungus. In particular the present compounds have physiochemical properties that facilitate penetration of the nail plate.
    Type: Application
    Filed: November 10, 2014
    Publication date: April 30, 2015
    Inventors: Stephen J. BAKER, Tsutomu Akama, Michael Richard Kevin Alley, Stephen J. Benkovic, Michael DiPierro, Vincent S. Hernandez, Karin M. Hold, Isaac Kennedy, Igor Likhotvorik, Weimin Mao, Kirk Maples, Jacob J. Plattner, Fernando Rock, Virginia Sanders, Aaron M. Stemphoski, George Petros Yiannikouros, Siead Zegar, Yong-Kang Zhang, Huchen Zhou
  • Publication number: 20140356936
    Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.
    Type: Application
    Filed: June 24, 2014
    Publication date: December 4, 2014
    Inventors: Stephen J BENKOVIC, Frank Salinas