Patents by Inventor Ramnik Xavier

Ramnik Xavier 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: 20240174662
    Abstract: Small molecule inhibitors of salt inducible kinases (SIKs) are provided. In particular, compounds of formula (II) and compounds of formula (III), and tautomers, stereoisomers, pharmaceutically acceptable salts and solvates thereof are provided. Also provided are pharmaceutical compositions containing the compounds, methods of preparing the compounds, and methods of using the compounds for inhibiting SIKs, such as SIK1 and SIK2, and methods of treating diseases mediated by SIKs.
    Type: Application
    Filed: January 31, 2022
    Publication date: May 30, 2024
    Inventors: Genesis M. BACANI, Wenying CHAI, De Michael CHUNG, Steven D. GOLDBERG, Gavin HIRST, Virendar KAUSHIK, Eduardo V. MERCADO-MARIN, Donald RAYMOND, Mark SEIERSTAD, Russel C. SMITH, Thomas SUNDBERG, Mark S. TICHENOR, Jennifer D. VENABLE, Jianmei WEI, Ramnik XAVIER
  • Publication number: 20240158392
    Abstract: Small molecule inhibitors of salt inducible kinases (SIKs) are provided. In particular, compounds of formula (I), and tautomers, stereoisomers, pharmaceutically acceptable salts and solvates thereof are provided. Also provided are pharmaceutical compositions containing the compounds, methods of preparing the compounds, and methods of using the compounds for inhibiting SIKs, such as SIK1 and SIK2, and methods of treating diseases mediated by SIKs.
    Type: Application
    Filed: January 31, 2022
    Publication date: May 16, 2024
    Inventors: Genesis M. BACANI, Wenying CHAI, De Michael CHUNG, Steven D. GOLDBERG, Gavin HIRST, Virnedar KAUSHIK, Eduardo V. MERCADO-MARIN, Donald RAYMOND, Mark SEIERSTAD, Russel C. SMITH, Thomas SUNDBERG, Mark S. TICHENOR, Jennifer D. VENABLE, Jianmei WEI, Ramnik XAVIER, Helena C. STEFFENS
  • Publication number: 20240108689
    Abstract: The subject matter disclosed herein is generally directed to pathogenic Th1 cells whose phenotype is dependent on IL-23R signaling. Th1 cell specific therapeutic targets and gene programs are disclosed herein. In particular, inhibition of CD160 reduces Th1 cell pathogenicity.
    Type: Application
    Filed: January 21, 2022
    Publication date: April 4, 2024
    Inventors: Vijay K. Kuchroo, Ramnik Xavier, Mathias Pawlak, David DeTomaso, Nir Yosef
  • Publication number: 20240024381
    Abstract: Microbes expressing cholesterol oxidoreductase (COR) proteins, methods of engineering the microbes expressing COR proteins, compositions and methods of using the microbes are provided.
    Type: Application
    Filed: March 6, 2023
    Publication date: January 25, 2024
    Inventors: Douglas Kenny, Hera Vlamakis, Ramnik Xavier, Emily Balskus, Damian Plichta
  • Patent number: 11806372
    Abstract: This application provides for methods of treatment for IBD, especially in subjects who have R. gnavus species or R. gnavus group IBD strains as a component of their microbiome. The application also provides for methods of diagnosing IBD, as well as kits for use in the claimed methods.
    Type: Grant
    Filed: April 20, 2018
    Date of Patent: November 7, 2023
    Assignees: The Broad Institute, Inc., The General Hospital Corporation, President and Fellows of Harvard College
    Inventors: Andrew Brantley Hall, Ramnik Xavier, Curtis Huttenhower, Moran Yassour, Hera Vlamakis
  • Patent number: 11725011
    Abstract: The present disclosure provides compounds of Formula (I), (II), and (III). The provided compounds are able to bind protein kinases (e.g., SIK) and may be useful in modulating (e.g., inhibiting) the activity of a protein kinase (e.g., SIK, (e.g., SIK1, SIK2, or SIK3)) in a subject or cell. The provided compounds may be useful in treating or preventing a disease (e.g., proliferative disease, musculoskeletal disease, genetic disease, hematological disease, neurological disease, painful condition, psychiatric disorder, or metabolic disorder) in a subject in need thereof. Also provided are pharmaceutical compositions, kits, methods, and uses that include or involve a compound described herein.
    Type: Grant
    Filed: November 20, 2020
    Date of Patent: August 15, 2023
    Assignees: THE GENERAL HOSPITAL CORPORATION, DANA-FARBER CANCER INSTITUTE, INC., THE BROAD INSTITUTE, INC.
    Inventors: Nathanael S. Gray, Yanke Liang, Hwan Geun Choi, Thomas Sundberg, Alykhan Shamji, Ramnik Xavier, David E. Fisher, Nisma Mujahid
  • Publication number: 20230234959
    Abstract: The present disclosure provides compounds of Formula (I), (II), and (III). The provided compounds are able to bind protein kinases (e.g., SIK) and may be useful in modulating (e.g., inhibiting) the activity of a protein kinase (e.g., SIK, (e.g., SIK1, SIK2, or SIK3)) in a subject or cell. The provided compounds may be useful in treating or preventing a disease (e.g., proliferative disease, musculoskeletal disease, genetic disease, hematological disease, neurological disease, painful condition, psychiatric disorder, or metabolic disorder) in a subject in need thereof. Also provided are pharmaceutical compositions, kits, methods, and uses that include or involve a compound described herein.
    Type: Application
    Filed: March 27, 2023
    Publication date: July 27, 2023
    Applicants: THE BROAD INSTITUTE, INC., DANA-FARBER CANCER INSTITUTE, INC., THE GENERAL HOSPITAL CORPORATION
    Inventors: Nathanael S. Gray, Yanke Liang, Hwan Geun Choi, Thomas Sundberg, Alykhan Shamji, Ramnik Xavier, David E. Fisher, Nisma Mujahid
  • Patent number: 11633436
    Abstract: Microbes expressing cholesterol oxidoreductase (COR) proteins, methods of engineering the microbes expressing COR proteins, compositions and methods of using the microbes are provided.
    Type: Grant
    Filed: September 18, 2020
    Date of Patent: April 25, 2023
    Assignees: The Broad Institute, Inc., The General Hospital Corporation, President and Fellows of Harvard College
    Inventors: Douglas Kenny, Hera Vlamakis, Ramnik Xavier, Emily Balskus, Damian Plichta
  • Publication number: 20220305016
    Abstract: The present disclosure provides methods of treating and/or preventing osteoporosis using salt-inducible kinase (SIK) inhibitors. Also provided are methods of using SIK inhibitors for increasing the function of osteocytes, increasing the number of osteoblasts, increasing the activity of osteoblasts, inhibiting the resorption of a bone, decreasing the number of osteoclasts, inhibiting the activity of osteoclasts, increasing the mass of a bone, down-regulating the expression of the gene SOST, and/or inhibiting the activity of sclerostin. The SIK inhibitors may be combined with Src inhibitors or CSF I R inhibitors. Exemplary SIK inhibitors include the compounds of the formula: (I), (II), (III), (IV), (V) or (VI).
    Type: Application
    Filed: January 21, 2022
    Publication date: September 29, 2022
    Applicants: The General Hospital Corporation, The Broad Institute, Inc., Dana-Farber Cancer Institute, Inc.
    Inventors: Marc Wein, Henry Kronenberg, Thomas Sundberg, Ramnik Xavier, Nathanael S. Gray, Yanke Liang, Hwan Geun Choi, Alykhan Shamji
  • Publication number: 20220293215
    Abstract: A system and method for prediction of immunodominant epitopes is provided herein. MHCII peptidomics was used to discover complex bacterial epitopes and host antigen processing pathways. Novel insights into the features of antigenicity are leveraged to build an algorithm for prediction of immunodominant epitopes. Use of immunodominant epitopes is described.
    Type: Application
    Filed: June 27, 2018
    Publication date: September 15, 2022
    Inventors: Ramnik Xavier, Daniel B. Graham, Chengwei Luo
  • Patent number: 11382908
    Abstract: Disclosed herein are compounds for the treatment of inflammatory bowel disease. Additionally, provided herein are compositions and methods for using these compounds and compositions in the treatment of inflammatory bowel disease in a subject.
    Type: Grant
    Filed: September 26, 2018
    Date of Patent: July 12, 2022
    Assignees: The Broad Institute, Inc., The General Hospital Corporation, President and Fellows of Harvard College
    Inventors: Elizaveta Leshchiner, Zhifang Cao, Jason Rush, Michael Durney, Alykhan Shamji, Daniel Graham, Stuart L. Schreiber, Ramnik Xavier
  • Publication number: 20220143148
    Abstract: The present invention provides novel compositions and methods based on the discovery of the mechanisms and gene expression programs associated with homeostatic ILC2s and proinflammatory ILC2s that drive tissue inflammation. Immune signaling abnormalities in the small intestine can trigger chronic type 2 inflammation. Applicants analyzed 58,067 immune cells from the mouse small intestine by single-cell RNA-seq at steady state and after induction of a type 2 inflammatory reaction to ovalbumin. Cell type composition and cell programs shifted in response to inflammation, especially in ILC2s. A key transcript in the inflammation-induced program in intestinal KLRG1+ILC2s was exon 5 of Calca, encoding the alpha-calcitonin gene-related peptide (a-CGRP). a-CGRP antagonized IL-25-induced activation of intestinal ILC2s and reduced their frequency in an ovalbumin reaction model. ?-CGRP activated a cAMP response, which suppressed ILC2 proliferation.
    Type: Application
    Filed: March 13, 2020
    Publication date: May 12, 2022
    Inventors: Aviv Regev, Heping Xu, Jiarui Ding, Ramnik Xavier
  • Patent number: 11285144
    Abstract: A method for treating inflammation and/or autoimmune diseases comprises administering to a subject in need thereof, a composition comprising a CDK8 inhibitor. In another aspect, a method for increasing IL-10 production comprises administering to a subject in need thereof a CDK8 inhibitor. In another aspect, a method for enhancing Treg cell differentiation, comprising administering a composition comprising a CDK8 inhibitor. In certain example embodiments, the subject suffers from an inflammatory bowel disease. In certain other example embodiments, the subject requires immunosuppression to prevent rejection following a transplantation procedure.
    Type: Grant
    Filed: August 3, 2017
    Date of Patent: March 29, 2022
    Assignees: The Broad Institute, Inc., The General Hospital Corporation, Dana-Farber Cancer Institute, Inc., President and Fellows of Harvard College
    Inventors: Thomas Sundberg, Alykhan Shamji, Ramnik Xavier, Liv Johannessen, Nathanael Gray, Bernard Khor, Jose Perez
  • Patent number: 11241435
    Abstract: The present disclosure provides methods of treating and/or preventing osteoporosis using salt-inducible kinase (SIK) inhibitors. Also provided are methods of using SIK inhibitors for increasing the function of osteocytes, increasing the number of osteoblasts, increasing the activity of osteoblasts, inhibiting the resorption of a bone, decreasing the number of osteoclasts, inhibiting the activity of osteoclasts, increasing the mass of a bone, down-regulating the expression of the gene SOST, and/or inhibiting the activity of sclerostin. The SIK inhibitors may be combined with Src inhibitors or CSF I R inhibitors. Exemplary SIK inhibitors include the compounds of the formula: (I), (II), (III), (IV), (V) or (VI).
    Type: Grant
    Filed: September 16, 2017
    Date of Patent: February 8, 2022
    Assignees: The General Hospital Corporation, The Broad Institute, Inc., Dana-Farber Cancer Institute, Inc.
    Inventors: Marc Wein, Henry Kronenberg, Thomas Sundberg, Ramnik Xavier, Nathanael S. Gray, Yanke Liang, Hwan Geun Choi, Alykhan Shamji
  • Publication number: 20210325387
    Abstract: The present invention provides for a human cell atlas of the colon from healthy and diseased subjects. The atlas was obtained by single sequencing of about 117,000 cells. The present invention discloses novel markers for cell types. Moreover, genes associated with disease are identified in the colon and colon specific cell types. The invention provides for diagnostic assays based on gene markers and cell composition, as well as target cell types that express genes associated with disease. Finally, disclosed are novel cell types and methods of quantitating, detecting and isolating the cell types.
    Type: Application
    Filed: July 17, 2018
    Publication date: October 21, 2021
    Inventors: Alexander K. Shalek, Christopher Smillie, Rebecca H. Herbst, Moshe Biton, Aviv Regev, Jose Ordovas-Montanes, Ramnik Xavier
  • Publication number: 20210147425
    Abstract: The present disclosure provides compounds of Formula (I), (II), and (III). The provided compounds are able to bind C protein kinases (e.g., SIK) and may be useful in modulating (e.g., inhibiting) the activity of a protein kinase (e.g., SIK, (e.g., SIK1, SIK2, or SIK3)) in a subject or cell. The provided compounds may be useful in treating or preventing a disease (e.g., proliferative disease, musculoskeletal disease, genetic disease, hematological disease, neurological disease, painful condition, psychiatric disorder, or metabolic disorder) in a subject in need thereof. Also provided are pharmaceutical compositions, kits, methods, and uses that include or involve a compound described herein.
    Type: Application
    Filed: November 20, 2020
    Publication date: May 20, 2021
    Applicants: The Broad Institute, Inc., Dana-Farber Cancer Institute, Inc., The General Hospital Corporation
    Inventors: Nathanael S. Gray, Yanke Liang, Hwan Geun Choi, Thomas Sundberg, Alykhan Shamji, Ramnik Xavier, David E. Fisher, Nisma Mujahid
  • Publication number: 20210128642
    Abstract: Microbes expressing cholesterol oxidoreductase (COR) proteins, methods of engineering the microbes expressing COR proteins, compositions and methods of using the microbes are provided.
    Type: Application
    Filed: September 18, 2020
    Publication date: May 6, 2021
    Inventors: Douglas KENNY, Hera VLAMAKIS, Ramnik XAVIER, Emily BALSKUS, Damian PLICHTA
  • Patent number: 10954242
    Abstract: The present disclosure provides compounds of Formula (I), (II), and (III). The provided compounds are able to bind protein kinases (e.g., SIK) and may be useful in modulating (e.g., inhibiting) the activity of a protein kinase (e.g., SIK, (e.g., SIK1, SIK2, or SIK3)) in a subject or cell. The provided compounds may be useful in treating or preventing a disease (e.g., proliferative disease, musculoskeletal disease, genetic disease, hematological disease, neurological disease, painful condition, psychiatric disorder, or metabolic disorder) in a subject in need thereof. Also provided are pharmaceutical compositions, kits, methods, and uses that include or involve a compound described herein.
    Type: Grant
    Filed: July 5, 2017
    Date of Patent: March 23, 2021
    Assignees: The Broad Institute, Inc., Dana-Farber Cancer Institute, Inc., The General Hospital Corporation
    Inventors: Nathanael S. Gray, Yanke Liang, Hwan Geun Choi, Thomas Sundberg, Alykhan Shamji, Ramnik Xavier, David E. Fisher, Nisma Mujahid
  • Publication number: 20210071255
    Abstract: The present invention is generally directed to using a single cell atlas for identifying genes and gene programs that are associated with a phenotype (e.g., disease phenotypes or traits). The present invention is also generally directed to identifying interacting genetic variants using a single cell atlas as a prior for selecting variants for testing. The single cell atlas is used for constructing gene modules. Interactions are tested within and between modules. Applicants identified genetic variants that can be used to identify pathways and cell types important for IBD risk. Moreover, genetic variants were identified that can be used as therapeutic targets.
    Type: Application
    Filed: September 8, 2020
    Publication date: March 11, 2021
    Inventors: Aviv Regev, Karthik Jagadeesh, Ramnik Xavier, Christopher Smillie
  • Publication number: 20210040442
    Abstract: An atlas of intestinal epithelial cells, intestinal epithelial stem cells and intestinal immune cells identifies new cell populations, markers, networks, and responses to stimuli. Intestinal epithelial cell sub-types are also found in the trachea. Accordingly, disclosed are methods of modulating epithelial cell differentiation, maintenance and/or function, related methods for the treatment of disease, including IBD and asthma. Also disclosed are methods and kits for identifying cell types, their differentiation, homeostasis and activation.
    Type: Application
    Filed: April 12, 2018
    Publication date: February 11, 2021
    Inventors: Jayaraj Rajagopal, Aviv Regev, Moshe Biton, Adam Haber, Daniel Montoro, Ramnik Xavier