Patents by Inventor Luca Monfregola
Luca Monfregola 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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Patent number: 11782062Abstract: Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information.Type: GrantFiled: February 8, 2023Date of Patent: October 10, 2023Assignee: Encodia, Inc.Inventors: Mark S. Chee, John M. Beierle, Norihito Muranaka, Kevin L. Gunderson, Michael Phillip Weiner, Lei Shi, Robert C. James, Luca Monfregola
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Publication number: 20230236198Abstract: Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information.Type: ApplicationFiled: February 8, 2023Publication date: July 27, 2023Applicant: Encodia, Inc.Inventors: Mark S. CHEE, John M. BEIERLE, Norihito MURANAKA, Kevin L. GUNDERSON, Michael Phillip WEINER, Lei SHI, Robert C. JAMES, Luca MONFREGOLA
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Publication number: 20230168254Abstract: Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information.Type: ApplicationFiled: August 11, 2022Publication date: June 1, 2023Applicant: Encodia, Inc.Inventors: Mark S. Chee, John M. BEIERLE, Norihito MURANAKA, Kevin L. GUNDERSON, Michael Phillip WEINER, Lei SHI, Robert C. JAMES, Luca MONFREGOLA
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Patent number: 11584773Abstract: Aspects of the present disclosure include compositions that make use of phosphorus and/or nucleobase protecting groups which find use in the synthesis of long polynucleotides. Phosphorus protecting groups are provided that help increase the stepwise coupling yield and/or phosphorous protecting groups that can be removed during the oxidation step. Amidine nucleobase protecting groups are provided that find use in the subject compositions and methods which provides for e.g., increased resistance to depurination during polynucleotide synthesis. In some instances, the methods and compositions disclosed herein utilize a combination of the phosphorus and amidine nucleobase protecting groups in the synthesis of polynucleotides having a sequence of 200 or more monomeric units in length. Also provided are methods for synthesizing a polynucleotide (e.g., a DNA) using one or more compounds disclosed herein.Type: GrantFiled: July 19, 2021Date of Patent: February 21, 2023Assignee: Agilent Technologies, Inc.Inventors: Douglas J. Dellinger, Luca Monfregola, Marvin Caruthers, Mithun Roy
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Publication number: 20220409641Abstract: Compositions involving a modified egg yolk extract for use as an effective anti-cancer agent are described. The modified egg yolk extract involves specific fractions of phosphatidylcholines and sphingomyelins modified and produced from a chemical synthesis applied to the extract that produce a beneficial effect on the inhibition of cancerous cell growth. Methods of administering these compositions are also described.Type: ApplicationFiled: August 22, 2022Publication date: December 29, 2022Applicant: MACHAVERT PHARMACEUTICALS LLCInventors: Jakub D. STASZAK-JIRKOVSKY, Lukas KOBR, Gregory MIKNIS, Colleen HUDSON, Luca MONFREGOLA, Pavel JIRKOVSKY, Zboncáková MILADA, Jason DUEX, Pitchaimani KANDASAMY
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Patent number: 11513126Abstract: Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information.Type: GrantFiled: October 31, 2018Date of Patent: November 29, 2022Assignee: Encodia, Inc.Inventors: Mark S. Chee, John M. Beierle, Norihito Muranaka, Kevin L. Gunderson, Michael Phillip Weiner, Lei Shi, Robert C. James, Luca Monfregola
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Patent number: 11433085Abstract: Compositions involving a modified egg yolk extract for use as an effective anti-cancer agent are described. The modified egg yolk extract involves specific fractions of phosphatidylcholines and sphingomyelins modified and produced from a chemical synthesis applied to the extract that produce a beneficial effect on the inhibition of cancerous cell growth. Methods of administering these compositions are also described.Type: GrantFiled: October 15, 2019Date of Patent: September 6, 2022Assignee: MACHAVERT PHARMACEUTICALS, LLCInventors: Jakub Staszak-Jirkovsky, Lukas Kobr, Gregory Miknis, Colleen Hudson, Luca Monfregola, Pavel Jirkovsky, Zbon{hacek over (c)}áková Milada, Jason Duex, Pitchaimani Kandasamy
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Publication number: 20220227889Abstract: The present invention relates to methods of cleaving the N-terminal amino acid from a polypeptide, which may be in free form or conjugated to a carrier or surface, such as a bead. It provides methods to activate the N-terminal amine of a polypeptide to promote formation of a cyclic adduct of the N-terminal amino acid, resulting in cleavage of the N-terminal amino acid from the polypeptide. The method can be used to sequence and/or analyze a polypeptide. For example, the methods can be combined with methods described herein for sequencing and/or analysis that employ barcoding and nucleic acid encoding of molecular recognition events, and/or detectable labels. The invention also provides compounds and kits useful for practicing these methods.Type: ApplicationFiled: April 24, 2020Publication date: July 21, 2022Applicant: Encodia, Inc.Inventors: Kevin L. GUNDERSON, Fei HUANG, Robert C. JAMES, Luca MONFREGOLA, Stephen VERESPY, III, Eric Cunyu ZHOU
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Publication number: 20220002334Abstract: Aspects of the present disclosure include compositions that make use of phosphorus and/or nucleobase protecting groups which find use in the synthesis of long polynucleotides. Phosphorus protecting groups are provided that help increase the stepwise coupling yield and/or phosphorous protecting groups that can be removed during the oxidation step. Amidine nucleobase protecting groups are provided that find use in the subject compositions and methods which provides for e.g., increased resistance to depurination during polynucleotide synthesis. In some instances, the methods and compositions disclosed herein utilize a combination of the phosphorus and amidine nucleobase protecting groups in the synthesis of polynucleotides having a sequence of 200 or more monomeric units in length. Also provided are methods for synthesizing a polynucleotide (e.g., a DNA) using one or more compounds disclosed herein.Type: ApplicationFiled: July 19, 2021Publication date: January 6, 2022Inventors: Douglas J. Dellinger, Luca Monfregola, Marvin Caruthers, Mithun Roy
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Patent number: 11104699Abstract: Aspects of the present disclosure include compositions that make use of phosphorus and/or nucleobase protecting groups which find use in the synthesis of long polynucleotides. Phosphorus protecting groups are provided that help increase the stepwise coupling yield and/or phosphorous protecting groups that can be removed during the oxidation step. Amidine nucleobase protecting groups are provided that find use in the subject compositions and methods which provides for e.g., increased resistance to depurination during polynucleotide synthesis. In some instances, the methods and compositions disclosed herein utilize a combination of the phosphorus and amidine nucleobase protecting groups in the synthesis of polynucleotides having a sequence of 200 or more monomeric units in length. Also provided are methods for synthesizing a polynucleotide (e.g., a DNA) using one or more compounds disclosed herein.Type: GrantFiled: October 29, 2018Date of Patent: August 31, 2021Assignees: Agilent Technologies, Inc., University of Colorado BoulderInventors: Douglas J. Dellinger, Luca Monfregola, Marvin Caruthers, Mithun Roy
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Publication number: 20200348307Abstract: The present disclosure relates to methods and kits for analysis of polypeptides. In some embodiments, the present methods and kits employ barcoding and nucleic acid encoding of molecular recognition events, and/or detectable labels.Type: ApplicationFiled: October 31, 2018Publication date: November 5, 2020Applicant: Encodia, Inc.Inventors: John M. BEIERLE, Robert C. JAMES, Luca MONFREGOLA, Kevin GUNDERSON, Michael LEBL, Lei SHI
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Publication number: 20200348308Abstract: Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information.Type: ApplicationFiled: October 31, 2018Publication date: November 5, 2020Applicant: Encodia, Inc.Inventors: Mark S. CHEE, John M BEIERLE, Norihito MURANAKA, Kevin GUNDERSON, Michael Phillip WEINER, Lei SHI, Robert C. JAMES, Luca MONFREGOLA
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Publication number: 20200046744Abstract: Compositions involving a modified egg yolk extract for use as an effective anti-cancer agent are described. The modified egg yolk extract involves specific fractions of phosphatidylcholines and sphingomyelins modified and produced from a chemical synthesis applied to the extract that produce a beneficial effect on the inhibition of cancerous cell growth. Methods of administering these compositions are also described.Type: ApplicationFiled: October 15, 2019Publication date: February 13, 2020Inventors: Jakub STASZAK-JIRKOVSKY, Lukas KOBR, Gregory MIKNIS, Colleen HUDSON, Luca MONFREGOLA, Pavel JIRKOVSKY, Zboncáková MILADA, Jason DUEX, Pitchaimani KANDASAMY
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Patent number: 10493086Abstract: Compositions involving a modified egg yolk extract for use as an effective anti-cancer agent are described. The modified egg yolk extract involves specific fractions of phosphatidylcholines and sphingomyelins modified and produced from a chemical synthesis applied to the extract that produce a beneficial effect on the inhibition of cancerous cell growth. Methods of administering these compositions are also described.Type: GrantFiled: June 29, 2017Date of Patent: December 3, 2019Assignee: MACHAVERT PHARMACEUTICALS LLCInventors: Jakub Staszak-Jirkovsky, Lukas Kobr, Gregory F. Miknis, Colleen Hudson, Luca Monfregola, Pavel Jirkovsky, Zbon{hacek over (c)}áková Milada, Jason Duex, Pitchaimani Kandasamy
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Publication number: 20190194242Abstract: Aspects of the present disclosure include compositions that make use of phosphorus and/or nucleobase protecting groups which find use in the synthesis of long polynucleotides. Phosphorus protecting groups are provided that help increase the stepwise coupling yield and/or phosphorous protecting groups that can be removed during the oxidation step. Amidine nucleobase protecting groups are provided that find use in the subject compositions and methods which provides for e.g., increased resistance to depurination during polynucleotide synthesis. In some instances, the methods and compositions disclosed herein utilize a combination of the phosphorus and amidine nucleobase protecting groups in the synthesis of polynucleotides having a sequence of 200 or more monomeric units in length. Also provided are methods for synthesizing a polynucleotide (e.g., a DNA) using one or more compounds disclosed herein.Type: ApplicationFiled: October 29, 2018Publication date: June 27, 2019Inventors: Douglas J. Dellinger, Luca Monfregola, Marvin Caruthers, Mithun Roy
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Patent number: 10196418Abstract: Aspects of the present disclosure include compositions that make use of phosphorus and/or nucleobase protecting groups which find use in the synthesis of long polynucleotides. Phosphorus protecting groups are provided that help increase the stepwise coupling yield and/or phosphorous protecting groups that can be removed during the oxidation step. Amidine nucleobase protecting groups are provided that find use in the subject compositions and methods which provides for e.g., increased resistance to depurination during polynucleotide synthesis. In some instances, the methods and compositions disclosed herein utilize a combination of the phosphorus and amidine nucleobase protecting groups in the synthesis of polynucleotides having a sequence of 200 or more monomeric units in length. Also provided are methods for synthesizing a polynucleotide (e.g., a DNA) using one or more compounds disclosed herein.Type: GrantFiled: April 30, 2015Date of Patent: February 5, 2019Assignee: Agilent Technologies, Inc.Inventors: Douglas J. Dellinger, Luca Monfregola, Marvin Caruthers, Mithun Roy
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Publication number: 20180028545Abstract: Compositions involving a modified egg yolk extract for use as an effective anti-cancer agent are described. The modified egg yolk extract involves specific fractions of phosphatidylcholines and sphingomyelins modified and produced from a chemical synthesis applied to the extract that produce a beneficial effect on the inhibition of cancerous cell growth. Methods of administering these compositions are also described.Type: ApplicationFiled: October 6, 2017Publication date: February 1, 2018Inventors: Jakub STASZAK-JIRKOVSKY, Lukas KOBR, Gregory F. MIKNIS, Colleen HUDSON, Luca MONFREGOLA,, Pavel JIRKOVSKY, Zboncáková MILADA, Jason DUEX, Pitchaimani KANDASAMY
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Publication number: 20180000850Abstract: Compositions involving a modified egg yolk extract for use as an effective anti-cancer agent are described. The modified egg yolk extract involves specific fractions of phosphatidylcholines and sphingomyelins modified and produced from a chemical synthesis applied to the extract that produce a beneficial effect on the inhibition of cancerous cell growth. Methods of administering these compositions are also described.Type: ApplicationFiled: June 29, 2017Publication date: January 4, 2018Inventors: Jakub STASZAK-JIRKOVSKY, Lukas KOBR, Gregory F. MIKNIS, Colleen HUDSON, Luca MONFREGOLA,, Pavel JIRKOVSKY, Zboncåkovå MILADA, Jason DUEX, Pitchaimani KANDASAMY
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Publication number: 20150315227Abstract: Aspects of the present disclosure include compositions that make use of phosphorus and/or nucleobase protecting groups which find use in the synthesis of long polynucleotides. Phosphorus protecting groups are provided that help increase the stepwise coupling yield and/or phosphorous protecting groups that can be removed during the oxidation step. Amidine nucleobase protecting groups are provided that find use in the subject compositions and methods which provides for e.g., increased resistance to depurination during polynucleotide synthesis. In some instances, the methods and compositions disclosed herein utilize a combination of the phosphorus and amidine nucleobase protecting groups in the synthesis of polynucleotides having a sequence of 200 or more monomeric units in length. Also provided are methods for synthesizing a polynucleotide (e.g., a DNA) using one or more compounds disclosed herein.Type: ApplicationFiled: April 30, 2015Publication date: November 5, 2015Inventors: Douglas J. Dellinger, Luca Monfregola, Marvin Caruthers, Mithum Roy