Patents by Inventor Chris M. Farnet
Chris M. Farnet 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: 20100016170Abstract: A method for identifying gene cluster is disclosed. The method may be used for identifying gene clusters involved in the biosynthesis of natural products. A small insert library of DNA fragments of genomic DNA and a large insert library of DNA fragments of genomic DNA are prepared. Fragments in the small insert library are sequenced and compared by homology comparison under computer control to a database containing genes, gene fragments or proteins known to be involved in the biosynthesis of microbial natural products. Fragments having similar structure to genes, gene fragments or proteins known to be involved in the biosynthesis of naturally occurring metabolites are used as probes to screen the large insert library of genomic DNA to detect gene clusters involved in the biosynthesis of microbial natural products.Type: ApplicationFiled: May 14, 2007Publication date: January 21, 2010Applicant: Thallion Pharmaceuticals, Inc.Inventors: Chris M. Farnet, Alfredo Staffa, Emmanuel Zazopoulos
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Patent number: 7635765Abstract: The present invention relates to isolated genetic sequences encoding nonribosomal peptide synthetase (NRPS) proteins which direct the biosynthesis of the antibiotic ramoplanin in microorganisms such as Actinoplanes sp. The isolated gene sequences serve as substrates for bioengineering of antibiotic structures.Type: GrantFiled: August 17, 2005Date of Patent: December 22, 2009Assignee: Thallion Pharmaceuticals, Inc.Inventors: Chris M. Farnet, Emmanuel Zazopoulos, Alfredo Staffa
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Publication number: 20090263886Abstract: This invention relates to a novel farnesylated dibenzodiazepinone, named ECO-04601, its pharmaceutically acceptable salts and derivatives, and to methods for obtaining such compounds. One method of obtaining the ECO-04601 compound is by cultivation of a novel strain of Micromonospora sp., 046-ECO11; another method involves expression of biosynthetic pathway genes in transformed host cells. The present invention further relates to Micromonospora sp. strain 046-ECO11, to the use of and its pharmaceutically acceptable salts and derivatives as pharmaceuticals, in particular to their use as inhibitors of cancer cell growth, bacterial cell growth, mammalian lipoxygenase, and to pharmaceutical compositions comprising ECO-04601 or a pharmaceutically acceptable salt or derivative thereof. Finally, the invention relates to novel polynucleotide sequences and their encoded proteins, which are involved in the biosynthesis of ECO-04601.Type: ApplicationFiled: March 9, 2009Publication date: October 22, 2009Inventors: Emmanuel ZAZOPOULOS, Chris M. FARNET
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Patent number: 7521222Abstract: This invention relates to a novel farnesylated dibenzodiazepinone, named ECO-04601, its pharmaceutically acceptable salts and derivatives, and to methods for obtaining such compounds. One method of obtaining the ECO-04601 compound is by cultivation of a novel strain of Micromonospora sp., 046-ECO11; another method involves expression of biosynthetic pathway genes in transformed host cells. The present invention further relates to Micromonospora sp. strain 046-ECO11, to the use of ECO-04601 and its pharmaceutically acceptable salts and derivatives as pharmaceuticals, in particular to their use as inhibitors of cancer cell growth, bacterial cell growth, mammalian lipoxygenase, and to pharmaceutical compositions comprising ECO-04601 or a pharmaceutically acceptable salt or derivative thereof. Finally, the invention relates to novel polynucleotide sequences and their encoded proteins, which are involved in the biosynthesis of ECO-04601.Type: GrantFiled: August 28, 2006Date of Patent: April 21, 2009Assignee: Thallion Pharmaceuticals, Inc.Inventors: Emmanuel Zazopoulos, Chris M. Farnet
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Publication number: 20090069396Abstract: This invention relates to novel biologically active polyene oxazoles, their pharmaceutically acceptable salts and derivatives, and to methods of obtaining them. One method for obtaining the compounds is by cultivation of Streptomyces sparsogenes NRRL 2940 or a mutant or variant thereof.Type: ApplicationFiled: November 2, 2007Publication date: March 12, 2009Applicant: THALLION PHARMACEUTICALS, INC.Inventors: James B. McAlpine, Chris M. Farnet, Emmanuel Zazopoulos, Nargis Ismail, Brian O. Bachmann
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Patent number: 7462705Abstract: Five protein families cooperate to form the warhead structure that characterizes enediyne compounds, both chromoprotein enediynes and non-chromoprotein enediynes. The protein families include a polyketide synthase and thioesterase protein which form a polyketide synthase catalytic complex involved in warhead formation in enediynes. Genes encoding a member of each of the five protein families are found in all enediyne biosynthetic loci. The genes and proteins may be used in genetic engineering applications to design new enediyne compounds and in methods to identify new enediyne biosynthetic loci.Type: GrantFiled: February 8, 2005Date of Patent: December 9, 2008Assignee: Thallion Pharmaceuticals Inc.Inventors: Chris M. Farnet, Alfredo Staffa, Emmanuel Zazopoulos
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Patent number: 7416868Abstract: This invention relates to a new class of polyene polyketides, their pharmaceutically acceptable salts and derivatives, and to methods for obtaining the compounds. One method of obtaining these compounds is by cultivation of novel strains of Streptomyces aizunensis; another method involves expression of biosynthetic pathway genes in transformed host cells. The present invention further relates to the novel strains of Streptomyces aizunensis used to produce these compounds, to the use of these compounds and their pharmaceutically acceptable salts and derivatives as pharmaceuticals, in particular to their use as inhibitors of fungal cell growth and cancer cell growth. The invention also relates to pharmaceutical compositions comprising these novel polyketides or a pharmaceutically acceptable salts or derivatives thereof. Finally, the invention relates to novel polynucleotide sequences and their encoded proteins, which are involved in the biosynthesis of these novel polyketides.Type: GrantFiled: January 21, 2004Date of Patent: August 26, 2008Assignee: Thallion Pharmaceuticals, Inc.Inventors: Emmanuel Zazopoulos, Chris M. Farnet
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Publication number: 20080199940Abstract: This invention relates to a novel farnesylated dibenzodiazepinone, named ECO-04601, its pharmaceutically acceptable salts and derivatives, and to methods for obtaining such compounds. One method of obtaining the ECO-04601 compound is by cultivation of a novel strain of Micromonospora sp., 046-ECO11; another method involves expression of biosynthetic pathway genes in transformed host cells. The present invention further relates to Micromonospora sp. strain 046-ECO11, to the use of ECO-04601 and its pharmaceutically acceptable salts and derivatives as pharmaceuticals, in particular to their use as inhibitors of cancer cell growth, bacterial cell growth, mammalian lipoxygenase, and to pharmaceutical compositions comprising ECO-04601 or a pharmaceutically acceptable salt or derivative thereof. Finally, the invention relates to novel polynucleotide sequences and their encoded proteins, which are involved in the biosynthesis of ECO-04601.Type: ApplicationFiled: August 28, 2006Publication date: August 21, 2008Applicant: Ecopia BioSciences, Inc.Inventors: James B. McAlpine, Emmanuel Zazopoulos, Chris M. Farnet, Mahmood Piraee
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Publication number: 20080131943Abstract: This invention provides genes and their encoded proteins, involved in the biosynthesis of farnesyl dibenzodiazepinones, including ECO-04601. The invention relates to expression vectors comprising the genes and to host cells transformed with these vectors. The invention further relates to methods of producing farnesyl dibenzodiazepinone compounds using the genes and proteins of the invention, for example, involving expression of biosynthetic pathway genes in transformed host cells.Type: ApplicationFiled: October 22, 2007Publication date: June 5, 2008Applicant: Thallion Pharmaceuticals Inc.Inventors: Chris M. Farnet, Emmanuel Zazopoulos
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Patent number: 7375088Abstract: This invention relates to a new class of polyene polyketides, their pharmaceutically acceptable salts and derivatives, and to methods for obtaining the compounds. One method of obtaining these compounds is by cultivation of novel strains of Streptomyces aizunensis; another method involves expression of biosynthetic pathway genes in transformed host cells. The present invention further relates to the novel strains of Streptomyces aizunensis used to produce these compounds, to the use of these compounds and their pharmaceutically acceptable salts and derivatives as pharmaceuticals, in particular to their use as inhibitors of fungal cell growth and cancer cell growth. The invention also relates to pharmaceutical compositions comprising these novel polyketides or a pharmaceutically acceptable salts or derivatives thereof. Finally, the invention relates to novel polynucleotide sequences and their encoded proteins, which are involved in the biosynthesis of these novel polyketides.Type: GrantFiled: January 21, 2004Date of Patent: May 20, 2008Assignee: Thallion Pharmaceuticals Inc.Inventors: Brian O. Bachmann, James B. McAlpine, Emmanuel Zazopoulos, Chris M. Farnet
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Patent number: 7358241Abstract: This invention relates to methods of inhibiting growth and/or proliferation of a neoplastic cell, and methods of treating neoplasms using the farnesylated dibenzodiazepinone compound of Formula I.Type: GrantFiled: May 16, 2005Date of Patent: April 15, 2008Assignee: Thallion Pharmaceuticals, Inc.Inventors: Pierre Falardeau, Francois Berger, Henriette Gourdeau, James B. McAlpine, Chris M. Farnet, Violetta Dimitriadou
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Patent number: 7312339Abstract: Polyene oxazoles of the following formula wherein R3 is selected from H and methyl, are disclosed. Such compounds, and pharmaceutically acceptable salts thereof, may be used in the inhibition of tumor cell growth. The polyene oxazoles and their pharmaceutically acceptable salts may be formulated as pharmaceutical compositions with pharmaceutically acceptable carriers for use in the inhibition of tumor cells. The polyene oxazoles may be obtained from strains of Streptomyces sparsogenes, such as strain 022 having deposit number IDAC 270504-04.Type: GrantFiled: June 14, 2004Date of Patent: December 25, 2007Assignee: Thallion Pharmaceuticals Inc.Inventors: James B. McAlpine, Chris M. Farnet, Emmanuel Zazopoulos, Nargis Ismail, Brian O. Bachmann
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Patent number: 7300921Abstract: Novel polyene polyketides, their pharmaceutically acceptable salts, prodrugs and derivatives have been found to have antibiotic activity. One method for obtaining the compounds is by cultivation of Amycolatopsis orientalis ATCCâ„¢ 43491 or a mutant or variant such as the strain IDAC-220604-1. Another method for obtaining the compounds is post-biosynthesis chemical modification of the compounds obtained by cultivation. Novel polynucleotide sequences and encoded proteins for the biosynthesis of the polyene polyketides are also presented.Type: GrantFiled: September 10, 2004Date of Patent: November 27, 2007Assignee: Ecopia Biosciences, Inc.Inventors: James B. McAlpine, Chris M. Farnet, Emmanuel Zazopoulos, Dan Sorensen
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Patent number: 7297524Abstract: This invention provides genes and their encoded proteins, involved in the biosynthesis of farnesyl dibenzodiazepinones, including ECO-04601. The invention relates to expression vectors comprising the genes and to host cell transformed with these vectors. The invention further relates to methods of producing farnesyl dibenzodiazepinone compounds using the genes and proteins of the invention, for example, involving expression of biosynthetic pathway genes in transformed host cells.Type: GrantFiled: January 12, 2006Date of Patent: November 20, 2007Assignee: Thallion Pharmceuticals Inc.Inventors: Chris M. Farnet, Emmanuel Zazopoulos
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Patent number: 7291490Abstract: Genes and proteins involved in the biosynthesis of benzodiazepines by microorganisms, including the genes and proteins forming the biosynthetic loci for the benzodiazepine anthramycin from Streptomyces refuineus subsp. thermotolerans. The genes and proteins allow direct manipulation of benzodiazepines and related chemical structures via chemical engineering of the enzymes involved in the biosynthesis of anthramycin.Type: GrantFiled: July 7, 2006Date of Patent: November 6, 2007Assignee: Ecopia Biosciences Inc.Inventors: Chris M. Farnet, Alfredo Staffa
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Patent number: 7257562Abstract: A method for identifying gene cluster is disclosed. The method may be used for identifying gene clusters involved in the biosynthesis of natural products. A small insert library of DNA fragments of genomic DNA and a large insert library of DNA fragments of genomic DNA are prepared. Fragments in the small insert library are sequenced and compared by homology comparison under computer control to a database containing genes, gene fragments or proteins known to be involved in the biosynthesis of microbial natural products. Fragments having similar structure to genes, gene fragments or proteins known to be involved in the biosynthesis of naturally occurring metabolites are used as probes to screen the large insert library of genomic DNA to detect gene clusters involved in the biosynthesis of microbial natural products.Type: GrantFiled: September 3, 2002Date of Patent: August 14, 2007Assignee: Thallion Pharmaceuticals Inc.Inventors: Chris M. Farnet, Alfredo Staffa, Emmanuel Zazopoulos
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Patent number: 7235651Abstract: Genes and proteins involved in the biosynthesis of lipopeptides by microorganisms, in particular the nucleic acids forming the biosynthetic locus for the A54145 lipopeptide from Streptomyces fradiae and the A54145-like lipopeptide from Streptomyces refuineus. These nucleic acids can be used to make expression constructs and transformed host cells for the production of lipopeptides. The genes and proteins allow direct manipulation of lipopeptides and related chemical structures via chemical engineering of the proteins involved in the biosynthesis of A54145.Type: GrantFiled: December 24, 2002Date of Patent: June 26, 2007Assignee: Cubist Pharmaceuticals, Inc.Inventors: Chris M. Farnet, Alfredo Staffa, Emmanuel Zazopoulos
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Patent number: 7186713Abstract: This invention relates to methods of inhibiting growth of a cancer cell and methods of treating cancer using a novel farnesylated dibenzodiazepinone.Type: GrantFiled: September 27, 2004Date of Patent: March 6, 2007Assignee: Ecopia BioSciences, Inc.Inventors: Chris M. Farnet, Violetta Dimitriadou, Brian O. Bachmann
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Patent number: 7101872Abstract: This invention relates to a novel farnesylated dibenzodiazepinone, named ECO-04601, its pharmaceutically acceptable salts and derivatives, and to methods for obtaining such compounds. One method of obtaining the ECO-04601 compound is by cultivation of a novel strain of Micromonospora sp., 046-ECO11; another method involves expression of biosynthetic pathway genes in transformed host cells. The present invention further relates to Micromonospora sp. strain 046-ECO11, to the use of ECO-04601 and its pharmaceutically acceptable salts and derivatives as pharmaceuticals, in particular to their use as inhibitors of cancer cell growth, bacterial cell growth, mammalian lipoxygenase, and to pharmaceutical compositions comprising ECO-04601 or a pharmaceutically acceptable salt or derivative thereof. Finally, the invention relates to novel polynucleotide sequences and their encoded proteins, which are involved in the biosynthesis of ECO-04601.Type: GrantFiled: January 21, 2004Date of Patent: September 5, 2006Assignee: Ecopia BioSciences, Inc.Inventors: Brian O. Bachmann, James B. McAlpine, Emmanuel Zazopoulos, Chris M. Farnet, Mahmood Piraee
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Patent number: 7078185Abstract: The present invention relates to an isolated genetic sequence encoding a nonribosomal peptide synthetase (NRPS) protein which directs the biosynthesis of the antibiotic ramoplanin in microorganisms such as Actinoplanes sp. The isolated gene sequence serves as a substrate for bioengineering of antibiotic structures.Type: GrantFiled: October 15, 2001Date of Patent: July 18, 2006Assignee: Ecopia BioSciences Inc.Inventors: Chris M. Farnet, Emmanuel Zazopoulos, Alfredo Staffa