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).

  • Patent number: 11782062
    Abstract: 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: Grant
    Filed: February 8, 2023
    Date of Patent: October 10, 2023
    Assignee: Encodia, Inc.
    Inventors: Mark S. Chee, John M. Beierle, Norihito Muranaka, Kevin L. Gunderson, Michael Phillip Weiner, Lei Shi, Robert C. James, Luca Monfregola
  • Publication number: 20230236198
    Abstract: 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: Application
    Filed: February 8, 2023
    Publication date: July 27, 2023
    Applicant: Encodia, Inc.
    Inventors: Mark S. CHEE, John M. BEIERLE, Norihito MURANAKA, Kevin L. GUNDERSON, Michael Phillip WEINER, Lei SHI, Robert C. JAMES, Luca MONFREGOLA
  • Publication number: 20230168254
    Abstract: 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: Application
    Filed: August 11, 2022
    Publication date: June 1, 2023
    Applicant: Encodia, Inc.
    Inventors: Mark S. Chee, John M. BEIERLE, Norihito MURANAKA, Kevin L. GUNDERSON, Michael Phillip WEINER, Lei SHI, Robert C. JAMES, Luca MONFREGOLA
  • Patent number: 11584773
    Abstract: 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: Grant
    Filed: July 19, 2021
    Date of Patent: February 21, 2023
    Assignee: Agilent Technologies, Inc.
    Inventors: Douglas J. Dellinger, Luca Monfregola, Marvin Caruthers, Mithun Roy
  • Publication number: 20220409641
    Abstract: 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: Application
    Filed: August 22, 2022
    Publication date: December 29, 2022
    Applicant: MACHAVERT PHARMACEUTICALS LLC
    Inventors: Jakub D. STASZAK-JIRKOVSKY, Lukas KOBR, Gregory MIKNIS, Colleen HUDSON, Luca MONFREGOLA, Pavel JIRKOVSKY, Zboncáková MILADA, Jason DUEX, Pitchaimani KANDASAMY
  • Patent number: 11513126
    Abstract: 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: Grant
    Filed: October 31, 2018
    Date of Patent: November 29, 2022
    Assignee: Encodia, Inc.
    Inventors: Mark S. Chee, John M. Beierle, Norihito Muranaka, Kevin L. Gunderson, Michael Phillip Weiner, Lei Shi, Robert C. James, Luca Monfregola
  • Patent number: 11433085
    Abstract: 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: Grant
    Filed: October 15, 2019
    Date of Patent: September 6, 2022
    Assignee: MACHAVERT PHARMACEUTICALS, LLC
    Inventors: Jakub Staszak-Jirkovsky, Lukas Kobr, Gregory Miknis, Colleen Hudson, Luca Monfregola, Pavel Jirkovsky, Zbon{hacek over (c)}áková Milada, Jason Duex, Pitchaimani Kandasamy
  • Publication number: 20220227889
    Abstract: 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: Application
    Filed: April 24, 2020
    Publication date: July 21, 2022
    Applicant: Encodia, Inc.
    Inventors: Kevin L. GUNDERSON, Fei HUANG, Robert C. JAMES, Luca MONFREGOLA, Stephen VERESPY, III, Eric Cunyu ZHOU
  • Publication number: 20220002334
    Abstract: 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: Application
    Filed: July 19, 2021
    Publication date: January 6, 2022
    Inventors: Douglas J. Dellinger, Luca Monfregola, Marvin Caruthers, Mithun Roy
  • Patent number: 11104699
    Abstract: 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: Grant
    Filed: October 29, 2018
    Date of Patent: August 31, 2021
    Assignees: Agilent Technologies, Inc., University of Colorado Boulder
    Inventors: Douglas J. Dellinger, Luca Monfregola, Marvin Caruthers, Mithun Roy
  • Publication number: 20200348307
    Abstract: 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: Application
    Filed: October 31, 2018
    Publication date: November 5, 2020
    Applicant: Encodia, Inc.
    Inventors: John M. BEIERLE, Robert C. JAMES, Luca MONFREGOLA, Kevin GUNDERSON, Michael LEBL, Lei SHI
  • Publication number: 20200348308
    Abstract: 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: Application
    Filed: October 31, 2018
    Publication date: November 5, 2020
    Applicant: Encodia, Inc.
    Inventors: Mark S. CHEE, John M BEIERLE, Norihito MURANAKA, Kevin GUNDERSON, Michael Phillip WEINER, Lei SHI, Robert C. JAMES, Luca MONFREGOLA
  • Publication number: 20200046744
    Abstract: 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: Application
    Filed: October 15, 2019
    Publication date: February 13, 2020
    Inventors: Jakub STASZAK-JIRKOVSKY, Lukas KOBR, Gregory MIKNIS, Colleen HUDSON, Luca MONFREGOLA, Pavel JIRKOVSKY, Zboncáková MILADA, Jason DUEX, Pitchaimani KANDASAMY
  • Patent number: 10493086
    Abstract: 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: Grant
    Filed: June 29, 2017
    Date of Patent: December 3, 2019
    Assignee: MACHAVERT PHARMACEUTICALS LLC
    Inventors: Jakub Staszak-Jirkovsky, Lukas Kobr, Gregory F. Miknis, Colleen Hudson, Luca Monfregola, Pavel Jirkovsky, Zbon{hacek over (c)}áková Milada, Jason Duex, Pitchaimani Kandasamy
  • Publication number: 20190194242
    Abstract: 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: Application
    Filed: October 29, 2018
    Publication date: June 27, 2019
    Inventors: Douglas J. Dellinger, Luca Monfregola, Marvin Caruthers, Mithun Roy
  • Patent number: 10196418
    Abstract: 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: Grant
    Filed: April 30, 2015
    Date of Patent: February 5, 2019
    Assignee: Agilent Technologies, Inc.
    Inventors: Douglas J. Dellinger, Luca Monfregola, Marvin Caruthers, Mithun Roy
  • Publication number: 20180028545
    Abstract: 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: Application
    Filed: October 6, 2017
    Publication date: February 1, 2018
    Inventors: Jakub STASZAK-JIRKOVSKY, Lukas KOBR, Gregory F. MIKNIS, Colleen HUDSON, Luca MONFREGOLA,, Pavel JIRKOVSKY, Zboncáková MILADA, Jason DUEX, Pitchaimani KANDASAMY
  • Publication number: 20180000850
    Abstract: 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: Application
    Filed: June 29, 2017
    Publication date: January 4, 2018
    Inventors: Jakub STASZAK-JIRKOVSKY, Lukas KOBR, Gregory F. MIKNIS, Colleen HUDSON, Luca MONFREGOLA,, Pavel JIRKOVSKY, Zboncåkovå MILADA, Jason DUEX, Pitchaimani KANDASAMY
  • Publication number: 20150315227
    Abstract: 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: Application
    Filed: April 30, 2015
    Publication date: November 5, 2015
    Inventors: Douglas J. Dellinger, Luca Monfregola, Marvin Caruthers, Mithum Roy