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).

  • Publication number: 20120289686
    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: January 23, 2012
    Publication date: November 15, 2012
    Applicant: 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 R. Maples, Jacob J. Plattner, Fernando Rock, Virginia Sanders, Aaron M. Stemphoski, George Petros Yiannikouros, Siead Zagar, Yong-Kang Zhang, Huchen Zhou
  • Patent number: 8241851
    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 24, 2010
    Date of Patent: August 14, 2012
    Assignee: The Penn State Research Foundation
    Inventors: Stephen J. Benkovic, Frank Salinas
  • Patent number: 8137913
    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 24, 2010
    Date of Patent: March 20, 2012
    Assignee: The Penn State Research Foundation
    Inventors: Stephen J. Benkovic, Frank Salinas
  • Patent number: 8129116
    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 24, 2010
    Date of Patent: March 6, 2012
    Assignee: The Penn State Research Foundation
    Inventors: Stephen J. Benkovic, Frank Salinas
  • Patent number: 8124342
    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 24, 2010
    Date of Patent: February 28, 2012
    Assignee: The Pann State Research Foundation
    Inventors: Stephen J. Benkovic, Frank Salinas
  • Patent number: 8106031
    Abstract: Compositions and methods of use of boron derivatives, including benzoxaboroles, benzazaboroles and benzthiaboroles, as therapeutic agents for treatment of diseases caused by fungi, yeast, bacteria or viruses are disclosed, as well as methods for synthesis of said agents and compositions thereof.
    Type: Grant
    Filed: May 2, 2007
    Date of Patent: January 31, 2012
    Assignee: Anacor Pharmaceuticals, Inc.
    Inventors: Ving Lee, Jacob J. Plattner, Stephen J. Benkovic, Stephen J. Baker, Kirk R. Maples, Carolyn Bellinger-Kawahara, Tsutomu Akama, Yong-Kang Zhang, Rajeshwar Singh, Vittorio A. Sauro
  • Publication number: 20110288008
    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: Application
    Filed: June 6, 2007
    Publication date: November 24, 2011
    Applicant: THE PENN STATE RESEARCH FOUNDATION
    Inventors: Kenneth C. Keiler, Stephen J. Benkovic
  • Patent number: 7968752
    Abstract: Compositions and methods of use of borole derivatives, including benzoxaboroles, benzazaboroles and benzthiaboroles, as therapeutic agents for treatment of diseases caused by bacteria or viruses are disclosed, as well as methods for synthesis of said agents and compositions thereof.
    Type: Grant
    Filed: November 13, 2008
    Date of Patent: June 28, 2011
    Assignee: Anacor Pharmaceuticals, Inc.
    Inventors: Ving Lee, Jacob J. Plattner, Stephen J. Benkovic, Stephen J. Baker, Kirk R. Maples, Carolyn Bellinger-Kawahara, Tsutomu Akama, Yong-Kang Zhang, Rajeshwar Singh, Vittorio A. Sauro
  • Patent number: 7906279
    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 15, 2005
    Date of Patent: March 15, 2011
    Assignee: The Penn State Research Foundation
    Inventors: Stephen J. Benkovic, Frank Salinas
  • Patent number: 7888356
    Abstract: The structure and preparation of antibiotics incorporating borinic acid complexes are disclosed, especially hydroxyquinoline, imidazole and picolinic acid derivatives, along with compositions of these antibiotics and methods of using the antibiotics and compositions as bactericidal and fungicidal agents as well as therapeutic agents for the treatment of diseases caused by bacteria and fungi.
    Type: Grant
    Filed: January 9, 2008
    Date of Patent: February 15, 2011
    Assignee: Anacor Pharmaceuticals, Inc.
    Inventors: Ving Lee, Stephen J. Benkovic, Stephen J. Baker, Kirk R. Maples, Tsutomu Akama, Yong-Kang Zhang, Rajesjwar Singh, Vittorio A. Sauro, Chetan Pandit, Zhuoyi Su, Zhixiang Yang
  • Patent number: 7846710
    Abstract: Methods of producing cyclic peptides and splicing intermediates of peptides in a looped conformation are disclosed. The methods utilize the trans-splicing ability of split inteins to catalyze cyclization of peptides from a precursor peptide having a target peptide interposed between two portions of a split intein. The interaction of the two portions of the split intein creates a catalytically-active intein and also forces the target peptide into a loop configuration that stabilizes the ester isomer of the amino acid at the junction between one of the intein portions and the target peptide. A heteroatom from the other intein portion then reacts with the ester to form a cyclic ester intermediate. The active intein catalyzes the formation of an aminosuccinimide that liberates a cyclized form of the target peptide, which spontaneously rearranges to form the thermodynamically favored backbone cyclic peptide product.
    Type: Grant
    Filed: February 1, 2007
    Date of Patent: December 7, 2010
    Assignee: The Penn State Research Foundation
    Inventors: Stephen J. Benkovic, Charles P. Scott, Ernesto V. Abel-Santos
  • Publication number: 20100285482
    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 24, 2010
    Publication date: November 11, 2010
    Inventors: Stephen J. Benkovic, Frank Salinas
  • Publication number: 20100285538
    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 24, 2010
    Publication date: November 11, 2010
    Inventors: STEPHEN J. BENKOVIC, FRANK SALINAS
  • Publication number: 20100285481
    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 24, 2010
    Publication date: November 11, 2010
    Inventors: Stephen J. Benkovic, Frank Salinas
  • Publication number: 20100279358
    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 24, 2010
    Publication date: November 4, 2010
    Inventors: Stephen J. Benkovic, Frank Salinas
  • Publication number: 20100279379
    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 24, 2010
    Publication date: November 4, 2010
    Inventors: Stephen J. Benkovic, Frank Salinas
  • Publication number: 20100279357
    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 24, 2010
    Publication date: November 4, 2010
    Inventors: Stephen J. Benkovic, Frank Salinas
  • Patent number: 7820413
    Abstract: A series of methods that utilize the incremental truncation of nucleic acids are described to create a plurality of modified nucleic acids and hybrid polypeptides. A plurality of substantially all possible single base-pair deletions of a given nucleic acid sequence is created. A method of making shuffled incremental truncated nucleic acids, which is independent of nucleic acid sequence homology, is also described. These methods can be used in protein engineering, protein folding, protein evolution, and the chemical synthesis of novel hybrid proteins and polypeptides.
    Type: Grant
    Filed: February 19, 2008
    Date of Patent: October 26, 2010
    Assignee: The Penn State Research Foundation
    Inventors: Stephen J. Benkovic, Marc Ostermeier, Stefan Lutz, Andrew E. Nixon
  • Patent number: 7723031
    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: August 15, 2005
    Date of Patent: May 25, 2010
    Assignee: ThePenn State Research Foundation
    Inventors: Stephen J. Benkovic, Frank Salinas
  • Publication number: 20090239824
    Abstract: Compositions and methods of use of borole derivatives, including benzoxaboroles, benzazaboroles and benzthiaboroles, as therapeutic agents for treatment of diseases caused by bacteria or viruses are disclosed, as well as methods for synthesis of said agents and compositions thereof.
    Type: Application
    Filed: November 13, 2008
    Publication date: September 24, 2009
    Applicant: Anacor Pharmaceuticals, Inc.
    Inventors: Ving Lee, Jacob J. Plattner, Stephen J. Benkovic, Stephen J. Baker, Kirk R. Maples, Carolyn Bellinger-Kawahara, Tsutomu Akama, Yong-Kang Zhang, Rajeshwar Singh, Vittorio A. Sauro