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).
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Publication number: 20120289686Abstract: 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: ApplicationFiled: January 23, 2012Publication date: November 15, 2012Applicant: 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
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Patent number: 8241851Abstract: 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: GrantFiled: May 24, 2010Date of Patent: August 14, 2012Assignee: The Penn State Research FoundationInventors: Stephen J. Benkovic, Frank Salinas
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Patent number: 8137913Abstract: 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: GrantFiled: May 24, 2010Date of Patent: March 20, 2012Assignee: The Penn State Research FoundationInventors: Stephen J. Benkovic, Frank Salinas
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Patent number: 8129116Abstract: 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: GrantFiled: May 24, 2010Date of Patent: March 6, 2012Assignee: The Penn State Research FoundationInventors: Stephen J. Benkovic, Frank Salinas
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Patent number: 8124342Abstract: 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: GrantFiled: May 24, 2010Date of Patent: February 28, 2012Assignee: The Pann State Research FoundationInventors: Stephen J. Benkovic, Frank Salinas
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Patent number: 8106031Abstract: 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: GrantFiled: May 2, 2007Date of Patent: January 31, 2012Assignee: 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
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Publication number: 20110288008Abstract: 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: ApplicationFiled: June 6, 2007Publication date: November 24, 2011Applicant: THE PENN STATE RESEARCH FOUNDATIONInventors: Kenneth C. Keiler, Stephen J. Benkovic
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Patent number: 7968752Abstract: 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: GrantFiled: November 13, 2008Date of Patent: June 28, 2011Assignee: 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
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Patent number: 7906279Abstract: 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: GrantFiled: June 15, 2005Date of Patent: March 15, 2011Assignee: The Penn State Research FoundationInventors: Stephen J. Benkovic, Frank Salinas
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Patent number: 7888356Abstract: 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: GrantFiled: January 9, 2008Date of Patent: February 15, 2011Assignee: 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
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Patent number: 7846710Abstract: 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: GrantFiled: February 1, 2007Date of Patent: December 7, 2010Assignee: The Penn State Research FoundationInventors: Stephen J. Benkovic, Charles P. Scott, Ernesto V. Abel-Santos
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Publication number: 20100285482Abstract: 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: ApplicationFiled: May 24, 2010Publication date: November 11, 2010Inventors: Stephen J. Benkovic, Frank Salinas
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Publication number: 20100285538Abstract: 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: ApplicationFiled: May 24, 2010Publication date: November 11, 2010Inventors: STEPHEN J. BENKOVIC, FRANK SALINAS
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Publication number: 20100285481Abstract: 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: ApplicationFiled: May 24, 2010Publication date: November 11, 2010Inventors: Stephen J. Benkovic, Frank Salinas
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Publication number: 20100279358Abstract: 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: ApplicationFiled: May 24, 2010Publication date: November 4, 2010Inventors: Stephen J. Benkovic, Frank Salinas
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Publication number: 20100279379Abstract: 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: ApplicationFiled: May 24, 2010Publication date: November 4, 2010Inventors: Stephen J. Benkovic, Frank Salinas
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Publication number: 20100279357Abstract: 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: ApplicationFiled: May 24, 2010Publication date: November 4, 2010Inventors: Stephen J. Benkovic, Frank Salinas
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Patent number: 7820413Abstract: 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: GrantFiled: February 19, 2008Date of Patent: October 26, 2010Assignee: The Penn State Research FoundationInventors: Stephen J. Benkovic, Marc Ostermeier, Stefan Lutz, Andrew E. Nixon
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Patent number: 7723031Abstract: 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: GrantFiled: August 15, 2005Date of Patent: May 25, 2010Assignee: ThePenn State Research FoundationInventors: Stephen J. Benkovic, Frank Salinas
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Publication number: 20090239824Abstract: 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: ApplicationFiled: November 13, 2008Publication date: September 24, 2009Applicant: 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