Patents Examined by Christopher M. Gross
  • Patent number: 12258371
    Abstract: The invention relates autonomous VH domains (aVH) with cysteines in positions 52a and 71 or in positions 33 and 52 in order to stabilize the autonomous VH domains. Said cysteines are capable of forming a disulfide bond and/or form a disulfide bond under suitable conditions. The invention further relates to aVH libraries.
    Type: Grant
    Filed: July 30, 2020
    Date of Patent: March 25, 2025
    Assignee: Hoffman-La Roche Inc.
    Inventors: Laura Deak Codarri, Stefan Dengl, Jens Fischer, Thomas Hofer, Laurent Lariviere, Ekkehard Moessner, Stefan Seeber, Pablo Umana, Anne-Claire Zagdoun
  • Patent number: 12252690
    Abstract: According to a first aspect of the invention, a method for the generation of a cell line is provided, comprising the steps of (a) providing a plurality of mammalian B cells, wherein each of the plurality of B cells comprises a transgenic genomic DNA sequence encoding a marker protein inserted into an endogenous immunoglobulin locus comprised in said B cell, and wherein the transgenic genomic DNA sequence is amenable to cleavage by a site directed nuclease, particularly Cas9; (b) replacing the transgenic genomic DNA sequence encoding a marker protein with a second transgenic DNA sequence encoding a protein of interest; (c) sorting B cells based on the presence or absence of the marker protein; and (d) collecting B cells in which the marker protein is absent.
    Type: Grant
    Filed: June 5, 2023
    Date of Patent: March 18, 2025
    Assignee: ETH ZURICH
    Inventors: Sai Reddy, William Kelton, Cristina Parola, Derek Mason, Mark Pogson
  • Patent number: 12240882
    Abstract: The present disclosure presents a general approach to engineering existing protein-protein interactions through domain addition and evolution. The disclosure teaches the creation of novel fusion proteins that include knottin peptides where a portion of the knottin peptide is replaced with a sequence that has been created for binding to a particular target. Such fusion proteins can also be bispecific or multi specific in that they can bind to and/or inhibit two or more receptors or receptor ligands. Knottins may be fused with an existing ligand (or receptor) as a general platform tor increasing the affinity of a ligand-receptor interaction or for creating a multi specific protein. In addition, the fusion proteins may comprise a knottin peptide fused to another protein where the other protein facilitates proper expression and folding of the knottin.
    Type: Grant
    Filed: November 14, 2022
    Date of Patent: March 4, 2025
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Jennifer R. Cochran, Douglas S. Jones, Mihalis S. Kariolis, Ping-Chuan Tsai
  • Patent number: 12241060
    Abstract: Provided herein are methods for capturing a connected probe and/or a capture handle sequence to a capture domain of a capture probe.
    Type: Grant
    Filed: March 3, 2023
    Date of Patent: March 4, 2025
    Assignee: 10x Genomics, Inc.
    Inventors: Hanyoup Kim, David Sukovich, Layla Katiraee, Augusto Manuel Tentori
  • Patent number: 12241062
    Abstract: The present disclosure provides mammalian cell lines for expression of viral vectors, and methods of making and using the same. Provided methods employ use of identifiers that are capable of being packaged into a viral vector to select and/or identify mammalian cell lines with engineered sequences associated with beneficial characteristics for viral vectors production. Exemplary viral vectors include AAV vectors.
    Type: Grant
    Filed: October 23, 2023
    Date of Patent: March 4, 2025
    Assignee: 64-X, Inc.
    Inventors: Alexis Rovner, Gaurab Chakrabarti, David Thompson, Gregory Sieczkiewicz
  • Patent number: 12237054
    Abstract: The present invention provides a model for high-throughput screening of endocrine disruptors and a method for screening the same. In the present invention, primary structural alerts, secondary structural alerts and tertiary structural alerts of compounds are extracted according to a nuclear receptor, and then the primary structural alerts, the secondary structural alerts and the tertiary structural alerts form a nuclear receptor high-throughput screening model; hierarchical structural alert matching is carried out on target compounds through the nuclear receptor high-throughput screening model, and ligand-receptor binding mode analysis and semi-quantitative prediction of binding activity and disrupting activity are performed.
    Type: Grant
    Filed: December 15, 2019
    Date of Patent: February 25, 2025
    Assignee: Nanjing University
    Inventors: Wei Shi, Haoyue Tan, Qinchang Chen, Hongxia Yu
  • Patent number: 12235276
    Abstract: A method for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding is disclosed.
    Type: Grant
    Filed: August 12, 2024
    Date of Patent: February 25, 2025
    Assignee: Encodia, Inc.
    Inventors: Mark S. Chee, Kevin L. Gunderson, Michael Phillip Weiner
  • Patent number: 12230363
    Abstract: The present disclosure provides methods for improving libraries for screening protein-protein interactions (PPI) by excluding amino acid substitutions that are predicted to have a redundant or minimal effect on binding between protein binding partners.
    Type: Grant
    Filed: July 5, 2024
    Date of Patent: February 18, 2025
    Assignee: A-Alpha Bio
    Inventors: Ryan Emerson, Randolph Lopez, David Younger
  • Patent number: 12224040
    Abstract: Disclosed herein is a method of estimating the pose of a ligand in a receptor comprising identifying all possible atom pairs of protein-ligand complexes in a given configuration space for a system that comprises proteins; creating a first database and a second database; where the first database comprises associated pairwise distant dependent energies and where the second database comprises all probabilities that include how the atom pairs can combine; combining the first database with the second database via statistical mechanics to accurately estimate binding free energies as well as a pose of a ligand in a receptor; and selecting a protein-ligand complex for further study.
    Type: Grant
    Filed: April 16, 2019
    Date of Patent: February 11, 2025
    Assignees: Board of Trustees of Michigan State University, University of Florida Research Foundation, Inc.
    Inventors: Zheng Zheng, Kenneth M. Merz, Jr.
  • Patent number: 12195730
    Abstract: Provided herein are methods for identifying pairs of protein binding partners, mutations of which may inform the discovery of pharmaceutically useful small molecules. The methods disclosed herein may allow for the adaptation of the native protein degradation system to modulate specific disease targets at the protein level, in particular, for targets that have long been considered undruggable.
    Type: Grant
    Filed: August 31, 2022
    Date of Patent: January 14, 2025
    Assignee: A-Alpha Bio, Inc.
    Inventors: David Younger, Randolph Lopez, Arpita Sen, Ryan Emerson
  • Patent number: 12168210
    Abstract: A method of synthesis of a nucleotide chain, the nucleotide chain including an ordered plurality of nucleotides, the method including: identifying a first nucleotide of the ordered plurality of nucleotides; controlling a polymerase enzyme to assemble the first nucleotide onto the nucleotide chain by electrically modulating an electrode; identifying a subsequent nucleotide in the ordered plurality of nucleotides as a current nucleotide; and controlling the polymerase enzyme to assemble the current nucleotide onto an end of the nucleotide chain by electrically modulating the electrode.
    Type: Grant
    Filed: May 17, 2019
    Date of Patent: December 17, 2024
    Assignee: Georgia Tech Research Corporation
    Inventors: Hua Wang, Andrew Hessel
  • Patent number: 12158445
    Abstract: A method of synthesizing an oligonucleotide using a nanofluidic device including a plurality of nanopore channels, a plurality of electrodes, and an electrolyte solution, includes coupling a primer to an inner wall of a nanopore channel of the plurality of nanopore channels, the primer having a protecting group. The method also includes applying a voltage to an electrode of the plurality of electrodes that corresponds to the nanopore channel to produce an acid from the electrolyte solution at the electrode. The electrode includes an anode and a cathode disposed at opposite sides of the nanopore channel. The method further includes the acid removing the protecting group from the primer. Moreover, the method includes coupling a nucleotide to the primer with the protecting group removed to form an intermediate product. In addition, the method includes repeating the steps on the intermediate product until the oligonucleotide is synthesized.
    Type: Grant
    Filed: March 27, 2023
    Date of Patent: December 3, 2024
    Assignee: PALOGEN, INC.
    Inventors: Bita Karimirad, Kyung Joon Han
  • Patent number: 12135300
    Abstract: A method of analyzing a population of cells is disclosed. In certain embodiments, the method includes i) obtaining an array of cells on a substrate, wherein the cells are labeled with one or more mass tags and are separated from one another, ii) measuring, using secondary ion mass spectrometry (SIMS), the abundance of the one or more mass tags at a plurality of locations occupied by the cells, thereby generating, for each individual cell measured, a set of data, and iii) outputting the set of data for each of the cells analyzed. Also provided herein are systems that find use in performing the subject method. In some embodiments, the system is an automated system for analyzing a population of cells using SIMS.
    Type: Grant
    Filed: October 6, 2020
    Date of Patent: November 5, 2024
    Assignee: THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIVERSITY
    Inventors: Garry P. Nolan, Sean C. Bendall, Robert M. Angelo
  • Patent number: 12130291
    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: August 11, 2022
    Date of Patent: October 29, 2024
    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: 12123878
    Abstract: A method for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding is disclosed.
    Type: Grant
    Filed: May 2, 2017
    Date of Patent: October 22, 2024
    Assignee: Encodia, Inc.
    Inventors: Mark Chee, Kevin Gunderson, Michael Phillip Weiner
  • Patent number: 12122996
    Abstract: A device for allowing compartmentalized reactions with minimized cross-contamination between the compartments, utilizing a delivery of material by loading wells to pooling wells, such that the pooling wells can be additively provided with reactants while maintaining isolation between the pooling wells. The use of geometric properties is used to facilitate transmission of fluids/droplets without the need for hydrophilic surfaces.
    Type: Grant
    Filed: September 25, 2018
    Date of Patent: October 22, 2024
    Assignee: CALIFORNIA INSTITUTE OF TECHNOLOGY
    Inventors: Rustem F. Ismagilov, Eugenia Khorosheva, Dmitriy V. Zhukov
  • Patent number: 12117442
    Abstract: Disclosed herein are methods of screening candidate binding compounds to a plurality of target nucleic acids either of the same sequence or of different sequences utilizing a device configured to detect changes in the folding and unfolding force of the target nucleic acid upon binding to various candidate binding compounds. In the presence of a plurality of nucleic acid sequences, the methods described herein also can rapidly determine the specificity of the small molecule or polypeptide to a nucleic acid structure. Also, disclosed herein are methods of measuring binding kinetics of binding compounds to a target nucleic acid using a device configured to detect changes in the folding and unfolding force of the target nucleic acid upon binding to varying concentrations of the candidate binding compound.
    Type: Grant
    Filed: June 22, 2023
    Date of Patent: October 15, 2024
    Assignee: Depixus SAS
    Inventors: Gordon Hamilton, Jimmy Ouellet, Zhen Wang, Henning Labuhn
  • Patent number: 12116572
    Abstract: Provided herein are compositions and methods to identify a binding element (e.g., peptide, peptoid, or protein) that can be bound by an immunoreceptor (e.g., antibody). The binding element can be provided in a target binding unit comprising two binding elements separated by a spacer such that the two binding elements simultaneously bind to a single molecule comprising an antigen binding domain of an antibody. The present disclosure provides various methods to construct the spacer. The identified binding elements can be further used to manufacture an array which can be used to profile antibodies obtained from a blood sample.
    Type: Grant
    Filed: December 15, 2022
    Date of Patent: October 15, 2024
    Assignee: Guangzhou Chengyuan Bioimmunology Technology Co., Ltd.
    Inventors: Xi Chen, Ely Porter
  • Patent number: 12098366
    Abstract: Disclosed herein is a subgenomic promoter library derived from alphavirus. Also provided herein are methods of using the subgenomic promoters to produce antibodies and other molecules.
    Type: Grant
    Filed: February 7, 2020
    Date of Patent: September 24, 2024
    Assignee: Massachusetts Institute of Technology
    Inventors: Ron Weiss, Jin Huh
  • Patent number: 12092642
    Abstract: Systems and methods for obtaining qualitative or quantitative measurements of proteoforms of polypeptides are described. The described methods include measurements of affinity reagent binding on single-molecule polypeptide arrays to distinguish between polypeptide isoforms. The described methods may provide high resolution quantitative comparisons of proteoforms with very low copy numbers.
    Type: Grant
    Filed: January 19, 2022
    Date of Patent: September 17, 2024
    Assignee: NAUTILUS SUBSIDIARY, INC.
    Inventors: Parag Mallick, Jarrett D. Egertson, Gregory Kapp