Patents by Inventor Zihni Basar Bilgicer

Zihni Basar Bilgicer 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: 20240343835
    Abstract: A strategy for site specific covalent modification of antibodies using a specialized targeting covalent heterobivalent ligand (cHBL), and corresponding design for a covalent heterobivalent inhibitor (cHBI) that can be used to prevent Immunoglobulin E (IgE) mediated allergic reactions triggered by drug molecules, according to one embodiment. These molecules contain four important components: (1) an IgE antigen binding site (ABS) ligand that can be a mimotope for the allergen protein, a small molecule, or a peptidomimetic, (2) an appropriate linker, which can be any flexible or rigid chemical linker, providing spacing between the ABS binder and the other moieties, (3) a nucleotide binding site (NBS) ligand, and (4) a reactive moiety to form a covalent link with an amino acid side chain of target IgE antibodies.
    Type: Application
    Filed: June 6, 2024
    Publication date: October 17, 2024
    Applicant: UNIVERSITY OF NOTRE DAME DU LAC
    Inventors: Zihni Basar BILGICER, Peter Edward DEAK, Tanyel KIZILTEPE BILGICER, Michael William HANDLOGTEN, Jonathan Darryl ASHLEY
  • Patent number: 12018092
    Abstract: The invention provides a strategy for site specific covalent modification of antibodies using a specialized targeting covalent heterobivalent ligand (cHBL), and corresponding design for a covalent heterobivalent inhibitor (cHBI) that can be used to prevent Immunoglobulin E (IgE) mediated allergic reactions triggered by drug molecules, according to one embodiment. These molecules contain four important components: (1) an IgE antigen binding site (ABS) ligand that can be a mimotope for the allergen protein, a small molecule, or a peptidomimetic, (2) an appropriate linker, which can be any flexible or rigid chemical linker, providing spacing between the ABS binder and the other moieties, (3) a nucleotide binding site (NBS) ligand, and (4) a reactive moiety to form a covalent link with an amino acid side chain of target IgE antibodies.
    Type: Grant
    Filed: December 18, 2020
    Date of Patent: June 25, 2024
    Assignee: University of Notre Dame Du Lac
    Inventors: Zihni Basar Bilgicer, Peter Edward Deak, Tanyel Kiziltepe Bilgicer, Michael William Handlogten, Jonathan Darryl Ashley
  • Patent number: 11638763
    Abstract: Embodiments of the present disclosure provide a nanoparticle based platform, and nanoallergens for identifying, evaluating and studying allergen mimotopes as multiple copies of a single mimotope or various combinations on the same particle. The nanoparticle is extremely versatile and allows multivalent binding to IgEs specific to a variety of mimotopes, simulating allergen proteins. Nanoparticles can include various molecular ratios of components. For example, the nanoallergens can include about 0.1-40% mimotope-lipid conjugate and about 60-99.9% lipid. The mimotope-lipid conjugate includes a mimotope, a first linker, and lipid molecule. Nanoallergens can be used in in vitro and in vivo applications to identify a specific patient's sensitivity to a set of epitopes and predict a symptomatic clinical response, identify allergen epitopes through blind screening peptide sequences from allergen protein, and in a clinical application similar to a scratch test.
    Type: Grant
    Filed: December 18, 2020
    Date of Patent: May 2, 2023
    Assignee: University of Notre Dame du Lac
    Inventors: Zihni Basar Bilgicer, Peter Edward Deak, Tanyel Kiziltepe Bilgicer, Jared Francis Stefanick, Jonathan Darryl Ashley
  • Publication number: 20220218839
    Abstract: A method of crosslinking a hetero-bifunctional photo crosslinking compound to an immunoglobulin having at least one heterocyclic photo reactive group and at least one non-photo reactive group where the non-photo reactive group is coupled to an effector molecule and the photo reactive group is coupled to the nucleotide binding site of an immunoglobulin. Alternatively, the photo crosslinker contains an orthogonal reactive group such as a thiol, which can be coupled to an effector molecule or functionalized ligand.
    Type: Application
    Filed: September 2, 2021
    Publication date: July 14, 2022
    Applicant: University of Notre Dame du Lac
    Inventors: Zihni Basar BILGICER, Nathan J. ALVES
  • Patent number: 11116848
    Abstract: A method of crosslinking a hetero-bifunctional photo crosslinking compound to an immunoglobulin having at least one heterocyclic photo reactive group and at least one non-photo reactive group where the non-photo reactive group is coupled to an effector molecule and the photo reactive group is coupled to the nucleotide binding site of an immunoglobulin. Alternatively, the photo crosslinker contains an orthogonal reactive group such as a thiol, which can be coupled to an effector molecule or functionalized ligand.
    Type: Grant
    Filed: June 24, 2019
    Date of Patent: September 14, 2021
    Assignee: University of Notre Dame du Lac
    Inventors: Zihni Basar Bilgicer, Nathan J. Alves
  • Publication number: 20210138089
    Abstract: Embodiments of the present disclosure provide a nanoparticle based platform, and nanoallergens for identifying, evaluating and studying allergen mimotopes as multiple copies of a single mimotope or various combinations on the same particle. The nanoparticle is extremely versatile and allows multivalent binding to IgEs specific to a variety of mimotopes, simulating allergen proteins. Nanoparticles can include various molecular ratios of components. For example, the nanoallergens can include about 0.1-40% mimotope-lipid conjugate and about 60-99.9% lipid. The mimotope-lipid conjugate includes a mimotope, a first linker, and lipid molecule. Nanoallergens can be used in in vitro and in vivo applications to identify a specific patient's sensitivity to a set of epitopes and predict a symptomatic clinical response, identify allergen epitopes through blind screening peptide sequences from allergen protein, and in a clinical application similar to a scratch test.
    Type: Application
    Filed: December 18, 2020
    Publication date: May 13, 2021
    Applicant: University of Notre Dame du Lac
    Inventors: Zihni Basar BILGICER, Peter Edward DEAK, Tanyel KIZILTEPE BILGICER, Jared Francis STEFANICK, Jonathan Darryl ASHLEY
  • Publication number: 20210115157
    Abstract: The invention provides a strategy for site specific covalent modification of antibodies using a specialized targeting covalent heterobivalent ligand (cHBL), and corresponding design for a covalent heterobivalent inhibitor (cHBI) that can be used to prevent Immunoglobulin E (IgE) mediated allergic reactions triggered by drug molecules, according to one embodiment. These molecules contain four important components: (1) an IgE antigen binding site (ABS) ligand that can be a mimotope for the allergen protein, a small molecule, or a peptidomimetic, (2) an appropriate linker, which can be any flexible or rigid chemical linker, providing spacing between the ABS binder and the other moieties, (3) a nucleotide binding site (NBS) ligand, and (4) a reactive moiety to form a covalent link with an amino acid side chain of target IgE antibodies.
    Type: Application
    Filed: December 18, 2020
    Publication date: April 22, 2021
    Applicant: University of Notre Dame du Lac
    Inventors: Zihni Basar BILGICER, Peter Edward DEAK, Tanyel KIZILTEPE BILGICER, Michael William HANDLOGTEN, Jonathan Darryl ASHLEY
  • Patent number: 10947320
    Abstract: The invention provides a strategy for site specific covalent modification of antibodies using a specialized targeting covalent heterobivalent ligand (cHBL), and corresponding design for a covalent heterobivalent inhibitor (cHBI) that can be used to prevent Immunoglobulin E (IgE) mediated allergic reactions triggered by drug molecules, according to one embodiment. These molecules contain four important components: (1) an IgE antigen binding site (ABS) ligand that can be a mimotope for the allergen protein, a small molecule, or a peptidomimetic, (2) an appropriate linker, which can be any flexible or rigid chemical linker, providing spacing between the ABS binder and the other moieties, (3) a nucleotide binding site (NBS) ligand, and (4) a reactive moiety to form a covalent link with an amino acid side chain of target IgE antibodies.
    Type: Grant
    Filed: December 19, 2016
    Date of Patent: March 16, 2021
    Assignee: University of Notre Dame du Lac
    Inventors: Zihni Basar Bilgicer, Peter Edward Deak, Tanyel Kiziltepe Bilgicer, Michael William Handlogten, Jonathan Darryl Ashley
  • Patent number: 10874751
    Abstract: Embodiments of the present disclosure provide a nanoparticle based platform, and nanoallergens for identifying, evaluating and studying allergen mimotopes as multiple copies of a single mimotope or various combinations on the same particle. The nanoparticle is extremely versatile and allows multivalent binding to IgEs specific to a variety of mimotopes, simulating allergen proteins. Nanoparticles can include various molecular ratios of components. For example, the nanoallergens can include about 0.1-40% mimotope-lipid conjugate and about 60-99.9% lipid. The mimotope-lipid conjugate includes a mimotope, a first linker, and lipid molecule. Nanoallergens can be used in in vitro and in vivo applications to identify a specific patient's sensitivity to a set of epitopes and predict a symptomatic clinical response, identify allergen epitopes through blind screening peptide sequences from allergen protein, and in a clinical application similar to a scratch test.
    Type: Grant
    Filed: September 26, 2016
    Date of Patent: December 29, 2020
    Assignee: University of Notre Dame du Lac
    Inventors: Zihni Basar Bilgicer, Peter Edward Deak, Tanyel Kiziltepe Bilgicer, Jared Francis Stefanick, Jonathan Darryl Ashley
  • Publication number: 20190375857
    Abstract: The invention provides a strategy for site specific covalent modification of antibodies using a specialized targeting covalent heterobivalent ligand (cHBL), and corresponding design for a covalent heterobivalent inhibitor (cHBI) that can be used to prevent Immunoglobulin E (IgE) mediated allergic reactions triggered by drug molecules, according to one embodiment. These molecules contain four important components: (1) an IgE antigen binding site (ABS) ligand that can be a mimotope for the allergen protein, a small molecule, or a peptidomimetic, (2) an appropriate linker, which can be any flexible or rigid chemical linker, providing spacing between the ABS binder and the other moieties, (3) a nucleotide binding site (NBS) ligand, and (4) a reactive moiety to form a covalent link with an amino acid side chain of target IgE antibodies.
    Type: Application
    Filed: December 19, 2016
    Publication date: December 12, 2019
    Applicant: University of Notre Dame du Lac
    Inventors: Zihni Basar BILGICER, Peter Edward DEAK, Tanyel KIZILTEPE BILGICER, Michael William HANDLOGTEN, Jonathan Darryl ASHLEY
  • Publication number: 20190328896
    Abstract: A method of crosslinking a hetero-bifunctional photo crosslinking compound to an immunoglobulin having at least one heterocyclic photo reactive group and at least one non-photo reactive group where the non-photo reactive group is coupled to an effector molecule and the photo reactive group is coupled to the nucleotide binding site of an immunoglobulin. Alternatively, the photo crosslinker contains an orthogonal reactive group such as a thiol, which can be coupled to an effector molecule or functionalized ligand.
    Type: Application
    Filed: June 24, 2019
    Publication date: October 31, 2019
    Applicant: University of Notre Dame du Lac
    Inventors: Zihni Basar BILGICER, Nathan J. ALVES
  • Patent number: 10342846
    Abstract: The invention provides pharmaceutical compositions and method of using the compositions, wherein the compositions comprise liposomes or micelles that contain one or more targeting peptides and/or anticancer drugs. In various embodiments, the components of the liposomes can include a) a phospholipid and optionally a lipid that is not a phospholipid; b) a pegylated lipid; c) a peptide-ethylene glycol (EG)-lipid conjugate wherein the peptide is a targeting ligand, and d) one or more drug-conjugated lipid, encapsulated drugs, or a combination thereof. The peptide-EG-lipid conjugate can be, for example, a compound of Formula (I) or Formula (II). The ethylene glycol (EG) segments of the peptide-EG-lipid conjugate can be, for example, EG6 to about EG36; and the EG segment can be conjugated to one or more lysine moieties.
    Type: Grant
    Filed: February 4, 2014
    Date of Patent: July 9, 2019
    Assignee: University of Notre Dame du Lac
    Inventors: Zihni Basar Bilgicer, Jonathan Ashley, Tanyel Kiziltepe Bilgicer, Jared Stefanick, Nathan J. Alves
  • Publication number: 20180272008
    Abstract: Embodiments of the present disclosure provide a nanoparticle based platform, and nanoallergens for identifying, evaluating and studying allergen mimotopes as multiple copies of a single mimotope or various combinations on the same particle. The nanoparticle is extremely versatile and allows multivalent binding to IgEs specific to a variety of mimotopes, simulating allergen proteins. Nanoparticles can include various molecular ratios of components. For example, the nanoallergens can include about 0.1-40% mimotope-lipid conjugate and about 60-99.9% lipid. The mimotope-lipid conjugate includes a mimotope, a first linker, and lipid molecule. Nanoallergens can be used in in vitro and in vivo applications to identify a specific patient's sensitivity to a set of epitopes and predict a symptomatic clinical response, identify allergen epitopes through blind screening peptide sequences from allergen protein, and in a clinical application similar to a scratch test.
    Type: Application
    Filed: September 26, 2016
    Publication date: September 27, 2018
    Applicant: University of Notre Dame du Lac
    Inventors: Zihni Basar BILGICER, Peter DEAK, Tanyel KIZILTEPE BILGICER, Jared Francis STEFANICK, Jonathan Darryl ASHLEY
  • Publication number: 20180263909
    Abstract: The disclosure provides pharmaceutical compositions and method of using the compositions, wherein the compositions comprise liposomes that contain two or more anticancer drugs. In various embodiments the components of the liposomes can include a) a phospholipid, b) a pegylated lipid, c) an aqueous core, and d) at least one covalently-linked drug-conjugated lipid, an encapsulated drug, or a combination thereof, wherein the drug of the lipid-drug conjugate, encapsulated drug, or both, are anticancer drugs.
    Type: Application
    Filed: September 15, 2016
    Publication date: September 20, 2018
    Applicant: University Of Notre Dame du Lac
    Inventors: Zihni Basar BILGICER, Tanyel KIZILTEPE BILGICER, Jonathan Darryl ASHLEY
  • Publication number: 20180177810
    Abstract: Embodiments provide systems, methods, and compositions for nanoparticle-based drug delivery to target cells or tissues. A drug delivery system may include a nanoparticle with a targeting component and a therapeutic component. The nanoparticle may have a predetermined number or valence of targeting molecules for multivalent interaction with a target cell or tissue. Binding of the targeting molecules to the target cell may result in receptor-mediated uptake of the nanoparticle by the target cell. The therapeutic component may be subsequently released within an endocytic vesicle of the target cell. Nanoparticle-based drug delivery systems as described herein may provide improved efficacy and/or reduced toxicity.
    Type: Application
    Filed: January 23, 2018
    Publication date: June 28, 2018
    Applicant: University of Notre Dame du Lac
    Inventors: Zihni Basar BILGICER, Tanyel KIZILTEPE BILGICER, Jonathan Darryl ASHLEY, Jared Francis STEFANICK, Nathan J. ALVES, Michael W. HANDLOGTEN
  • Patent number: 9872870
    Abstract: Embodiments provide systems, methods, and compositions for nanoparticle-based drug delivery to target cells or tissues. A drug delivery system may include a nanoparticle with a targeting component and a therapeutic component. The nanoparticle may have a predetermined number or valence of targeting molecules for multivalent interaction with a target cell or tissue. Binding of the targeting molecules to the target cell may result in receptor-mediated uptake of the nanoparticle by the target cell. The therapeutic component may be subsequently released within an endocytic vesicle of the target cell. Nanoparticle-based drug delivery systems as described herein may provide improved efficacy and/or reduced toxicity.
    Type: Grant
    Filed: November 5, 2012
    Date of Patent: January 23, 2018
    Assignee: University of Notre Dame du Lac
    Inventors: Zihni Basar Bilgicer, Tanyel Kiziltepe Bilgicer, Jonathan Darryl Ashley, Jared Stefanick, Nathan J. Alves, Michael W. Handlogten
  • Publication number: 20170166607
    Abstract: Embodiments herein provide methods of purifying monoclonal and polyclonal anti-bodies (e.g., immunoglobulins) from biological fluids, such as cell lysates, cell supernatant and ascites fluids, using small molecule affinity chromatography. Various embodiments disclose a class of small molecules that selectively bind a nucleotide binding site that is inherent to all immunoglobulins, and in various embodiments, methods are disclosed that use one of these small molecules as a capture molecule in small molecule affinity chromatography. In some embodiments, the small molecule may be an indole, and in particular embodiments, the small molecule may be indole-3-butyric acid.
    Type: Application
    Filed: February 17, 2017
    Publication date: June 15, 2017
    Applicant: UNIVERSITY OF NOTRE DAME DU LAC
    Inventors: Zihni Basar Bilgicer, Tanyel Kiziltepe Bilgicer, Nathan Joseph Alves, Jonathan Darryl Ashley, Michael William Handlogten
  • Patent number: 9598460
    Abstract: Embodiments herein provide methods of purifying monoclonal and polyclonal antibodies (e.g., immunoglobulins) from biological fluids, such as cell lysates, cell supernatant and ascites fluids, using small molecule affinity chromatography. Various embodiments disclose a class of small molecules that selectively bind a nucleotide binding site that is inherent to all immunoglobulins, and in various embodiments, methods are disclosed that use one of these small molecules as a capture molecule in small molecule affinity chromatography. In some embodiments, the small molecule may be an indole, and in particular embodiments, the small molecule may be indole-3-butyric acid.
    Type: Grant
    Filed: January 18, 2012
    Date of Patent: March 21, 2017
    Assignee: UNIVERSITY OF NOTRE DAME DU LAC
    Inventors: Zihni Basar Bilgicer, Tanyel Kiziltepe Bilgicer, Nathan Joseph Alves, Jonathan Darryl Ashley, Michael William Handlogten
  • Publication number: 20160038607
    Abstract: The invention provides pharmaceutical compositions and method of using the compositions, wherein the compositions comprise liposomes or micelles that contain one or more targeting peptides and/or anticancer drugs. In various embodiments, the components of the liposomes can include a) a phospholipid and optionally a lipid that is not a phospholipid; b) a pegylated lipid; c) a peptide-ethylene glycol (EG)-lipid conjugate wherein the peptide is a targeting ligand, and d) one or more drug-conjugated lipid, encapsulated drugs, or a combination thereof. The peptide-EG-lipid conjugate can be, for example, a compound of Formula (I) or Formula (II). The ethylene glycol (EG) segments of the peptide-EG-lipid conjugate can be, for example, EG6 to about EG36; and the EG segment can be conjugated to one or more lysine moieties.
    Type: Application
    Filed: February 4, 2014
    Publication date: February 11, 2016
    Applicant: UNIVERSITY OF NOTRE DAME DU LAC
    Inventors: Zihni Basar BILGICER, Jonathan ASHLEY, Tanyel KIZILTEPE-BILGICER, Jared STEFANICK, Nathan J. ALVES
  • Publication number: 20160022834
    Abstract: The invention provides for a method of crosslinking a hetero-bifunctional photo crosslinking compound to an immunoglobulin having at least one heterocyclic photo reactive group and at least one non-photo reactive group where the non-photo reactive group is coupled to an effector molecule and the photo reactive group is coupled to the nucleotide binding site of an immunoglobulin. Alternatively, the photo crosslinker contains an orthogonal reactive group such as a thiol, which can be coupled to an effector molecule or functionalized ligand.
    Type: Application
    Filed: March 14, 2014
    Publication date: January 28, 2016
    Applicant: UNIVERSITY OF NOTRE DAME DU LAC
    Inventors: Zihni Basar Bilgicer, Nathan Alves