Patents by Inventor Mark A. Murcko

Mark A. Murcko 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: 9965597
    Abstract: Methods and systems for drug discovery collaboration provide collaborative drug discovery electronic workplaces simultaneously accessible by multiple user computing devices. In certain embodiments, a server computer running a server side application communicates with multiple user computing devices. The server side application communicates with electronic databases that define the parameters of each electronic workplace. Each workplace includes an indication of one or more items, such as compounds, and data pertaining to such items, such as computational and experimental data. Updates to a workplace made by one user may be saved to the workplace definition and propagated and displayed to other users. New items of interest may be added to a workplace. A new item added to a workplace may also be saved to the database and registered with the system for use by other users and in connection with other workplaces.
    Type: Grant
    Filed: April 29, 2015
    Date of Patent: May 8, 2018
    Assignee: Schrödinger, Inc.
    Inventors: Scott Becker, Brian Schoolman, William C. Jordan, Mark Murcko, Richard C. Friesner
  • Publication number: 20150310006
    Abstract: Methods and systems for drug discovery collaboration provide collaborative drug discovery electronic workplaces simultaneously accessible by multiple user computing devices. In certain embodiments, a server computer running a server side application communicates with multiple user computing devices. The server side application communicates with electronic databases that define the parameters of each electronic workplace. Each workplace includes an indication of one or more items, such as compounds, and data pertaining to such items, such as computational and experimental data. Updates to a workplace made by one user may be saved to the workplace definition and propagated and displayed to other users. New items of interest may be added to a workplace. A new item added to a workplace may also be saved to the database and registered with the system for use by other users and in connection with other workplaces.
    Type: Application
    Filed: April 29, 2015
    Publication date: October 29, 2015
    Inventors: Scott Becker, Brian Schoolman, William C. Jordan, Mark Murcko, Richard C. Friesner
  • Patent number: 8691848
    Abstract: The present invention relates to novel classes of compounds which are caspase inhibitors, in particular interleukin-1? converting enzyme (“ICE”) inhibitors. This invention also relates to pharmaceutical compositions comprising these compounds. The compounds and pharmaceutical compositions of this invention are particularly well suited for inhibiting caspase activity and consequently, may be advantageously used as agents against interleukin-1-(“IL-1”), apoptosis-, interferon-? inducing factor-(IGIF), or interferon-?-(“IFN-?”) mediated diseases, including inflammatory diseases, autoimmune diseases, destructive bone disorders, proliferative disorders, infectious diseases, and degenerative diseases. This invention also relates to methods for inhibiting caspase activity and decreasing IGIF production and IFN-? production and methods for treating interleukin-1, apoptosis-, and interferon-?-mediated diseases using the compounds and compositions of this invention.
    Type: Grant
    Filed: January 22, 2008
    Date of Patent: April 8, 2014
    Assignee: Vertex Pharmaceuticals Incorporated
    Inventors: Marion W. Wannamaker, Guy W. Bemis, Paul S. Charifson, David J. Lauffer, Michael D. Mullican, Mark A. Murcko, Keith P. Wilson, James W. Janetka, Robert J. Davies, Anne-Laure Grillot, Zhan Shi, Cornelia J. Forster
  • Publication number: 20130012430
    Abstract: The present invention relates to compounds, methods and pharmaceutical compositions for inhibiting proteases, particularly serine proteases, and more particularly HCV NS3 proteases. The compounds, and the compositions and methods that utilize them, can be used, either alone or in combination to inhibit viruses, particularly HCV virus.
    Type: Application
    Filed: June 27, 2012
    Publication date: January 10, 2013
    Applicant: Vertex Pharmaceuticals Incorporated
    Inventors: Roger D. Tung, Scott L. Harbeson, David D. Deininger, Mark A. Murcko, Govinda R. Bhisetti, Luc J. Farmer
  • Patent number: 8338412
    Abstract: The present invention relates to inhibitors of p38, a mammalian protein kinase involved cell proliferation, cell death and response to extracellular stimuli. The invention also relates to methods for producing these inhibitors. The invention also provides pharmaceutical compositions comprising the inhibitors of the invention and methods of utilizing those compositions in the treatment and prevention of various disorders.
    Type: Grant
    Filed: May 13, 2011
    Date of Patent: December 25, 2012
    Assignee: Vertex Pharmaceuticals Incorporated
    Inventors: Guy W. Bemis, Francesco G. Salituro, John P. Duffy, John E. Cochran, Edmund M. Harrington, Mark A. Murcko, Keith P. Wilson, Michael Su, Vincent P. Galullo
  • Patent number: 8314141
    Abstract: The present invention relates to Formula (II) compounds having the structure as well as to their use in methods and pharmaceutical compositions for inhibiting proteases, particularly serine proteases, and more particularly HCV NS3 proteases.
    Type: Grant
    Filed: February 14, 2008
    Date of Patent: November 20, 2012
    Assignee: Vertex Pharmaceuticals Incorporated
    Inventors: Roger D. Tung, Scott L. Harbeson, David D. Deininger, Mark A. Murcko, Govinda R. Bhisetti, Luc J. Farmer
  • Publication number: 20120238749
    Abstract: The present invention relates to novel classes of compounds which are inhibitors of interleukin-1? converting enzyme. The ICE inhibitors of this invention are characterized by specific structural and physicochemical features. This invention also relates to pharmaceutical compositions comprising these compounds. The compounds and pharmaceutical compositions of this invention are particularly well suited for inhibiting ICE activity and consequently, may be advantageously used as agents against interleukin-1 mediated diseases, including inflammatory diseases, autoimmune diseases and neurodegenerative diseases. This invention also relates to methods for inhibiting ICE activity and methods for treating interleukin-1 mediated diseases using the compounds and compositions of this invention.
    Type: Application
    Filed: October 12, 2011
    Publication date: September 20, 2012
    Applicant: VERTEX PHARMACEUTICALS INCORPORATED
    Inventors: Guy W. Bemis, Julian M. C. Golec, David J. Lauffer, Michael D. Mullican, Mark A. Murcko, David J. Livingston
  • Publication number: 20120165319
    Abstract: The present invention relates to novel classes of compounds which are inhibitors of interleukin-1? converting enzyme. The ICE inhibitors of this invention are characterized by specific structural and physicochemical features. This invention also relates to pharmaceutical compositions comprising these compounds. The compounds and pharmaceutical compositions of this invention are particularly well suited for inhibiting ICE activity and consequently, may be advantageously used as agents against IL-1-, apoptosis-, IGIF-, and IFN-?-mediated diseases, inflammatory diseases, autoimmune diseases, destructive bone disorders, proliferative disorders, infectious diseases, degenerative diseases, and necrotic diseases. This invention also relates to methods for inhibiting ICE activity, for treating interleukin-1-, apoptosis-, IGIF- and IFN-?-mediated diseases and decreasing IGIF and IFN-? production using the compounds and compositions of this invention.
    Type: Application
    Filed: November 10, 2011
    Publication date: June 28, 2012
    Applicant: VERTEX PHARMACEUTICALS INCORPORATED
    Inventors: Mark James Batchelor, David Bebbington, Guy W. Bemis, Wolf Herman Fridman, Roger John Gillespie, Julian M.C. Golec, Yong Gu, David J. Lauffer, David J. Livingston, Saroop Singh Matharu, Michael D. Mullican, Mark A. Murcko, Robert Murdoch, Philip Nyce, Andrea L.C. Robidoux, Michael Su, M. Woods Wannamaker, Keith P. Wilson, Robert E. Zelle
  • Patent number: 8119631
    Abstract: The present invention relates to novel classes of compounds which are inhibitors of interleukin-1? converting enzyme. The ICE inhibitors of this invention are characterized by specific structural and physicochemical features. This invention also relates to pharmaceutical compositions comprising these compounds. The compounds and pharmaceutical compositions of this invention are particularly well suited for inhibiting ICE activity and consequently, may be advantageously used as agents against IL-1-, apoptosis-, IGIF-, and IFN-?-mediated diseases, inflammatory diseases, autoimmune diseases, destructive bone disorders, proliferative disorders, infectious diseases, degenerative diseases, and necrotic diseases. This invention also relates to methods for inhibiting ICE activity, for treating interleukin-1-, apoptosis-, IGIF- and IFN-?-mediated diseases and decreasing IGIF and IFN-? production using the compounds and compositions of this invention.
    Type: Grant
    Filed: May 24, 2010
    Date of Patent: February 21, 2012
    Assignee: Vertex Pharmaceuticals Incorporated
    Inventors: Mark James Batchelor, David Bebbington, Guy W. Bemis, Wolf Herman Fridman, Roger John Gillespie, Julian M. C. Golec, Yong Gu, David J. Lauffer, David J. Livingston, Saroop Singh Matharu, Michael D. Mullican, Mark A. Murcko, Robert Murdoch, Philip Nyce, Andrea L. C. Robidoux, Michael Su, M. Woods Wannamaker, Keith P. Wilson, Robert E. Zelle
  • Publication number: 20110178069
    Abstract: The present invention relates to novel classes of compounds which are inhibitors of interleukin-1? converting enzyme. The ICE inhibitors of this invention are characterized by specific structural and physicochemical features. This invention also relates to pharmaceutical compositions comprising these compounds. The compounds and pharmaceutical compositions of this invention are particularly well suited for inhibiting ICE activity and consequently, may be advantageously used as agents against IL-1-, apoptosis-, IGIF-, and IFN-?-mediated diseases, inflammatory diseases, autoimmune diseases, destructive bone disorders, proliferative disorders, infectious diseases, degenerative diseases, and necrotic diseases. This invention also relates to methods for inhibiting ICE activity, for treating interleukin-1-, apoptosis-, IGIF- and IFN-?-mediated diseases and decreasing IGIF and IFN-? production using the compounds and compositions of this invention.
    Type: Application
    Filed: May 24, 2010
    Publication date: July 21, 2011
    Applicant: VERTEX PHARMACEUTICALS INCORPORATED
    Inventors: Mark James Batchelor, David Bebbington, Guy W. Bemis, Wolf Herman Fridman, Roger John Gillespie, Julian M.C. Golec, Yong Gu, David J. Lauffer, David J. Livingston, Saroop Singh Matharu, Michael D. Mullican, Mark A. Murcko, Robert Murdoch, Philip Nyce, Andrea L.C. Robidoux, Michael Su, M. Woods Wannamaker, Keith P. Wilson, Robert E. Zelle
  • Patent number: 7951809
    Abstract: The present invention relates to inhibitors of p38, a mammalian protein kinase involved cell proliferation, cell death and response to extracellular stimuli. The invention also relates to methods for producing these inhibitors. The invention also provides pharmaceutical compositions comprising the inhibitors of the invention and methods of utilizing those compositions in the treatment and prevention of various disorders.
    Type: Grant
    Filed: April 3, 2008
    Date of Patent: May 31, 2011
    Assignee: Vertex Pharmaceuticals Incorporated
    Inventors: Guy W. Bemis, Francesco G. Salituro, John P. Duffy, John E. Cochran, Edmund M. Harrington, Mark A. Murcko, Keith P. Wilson, Michael Su, Vincent P. Galullo
  • Publication number: 20110015371
    Abstract: The present invention relates to novel classes of compounds which are inhibitors of interleukin-1? converting enzyme. The ICE inhibitors of this invention are characterized by specific structural and physicochemical features. This invention also relates to pharmaceutical compositions comprising these compounds. The compounds and pharmaceutical compositions of this invention are particularly well suited for inhibiting ICE activity and consequently, may be advantageously used as agents against interleukin-1 mediated diseases, including inflammatory diseases, autoimmune diseases and neurodegenerative diseases. This invention also relates to methods for inhibiting ICE activity and methods for treating interleukin-1 mediated diseases using the compounds and compositions of this invention.
    Type: Application
    Filed: May 5, 2010
    Publication date: January 20, 2011
    Applicant: Vertex Pharmaceuticals Incorporated
    Inventors: Guy W. Bemis, Julian M. C. Golec, David J. Lauffer, Michael D. Mullican, Mark A. Murcko, David J. Livingston
  • Patent number: 7790713
    Abstract: The present invention relates to novel classes of compounds which are inhibitors of interleukin-1? converting enzyme. The ICE inhibitors of this invention are characterized by specific structural and physicochemical features. This invention also relates to pharmaceutical compositions comprising these compounds. The compounds and pharmaceutical compositions of this invention are particularly well suited for inhibiting ICE activity and consequently, may be advantageously used as agents against IL-1-, apoptosis-, IGIF-, and IFN-?-mediated diseases, inflammatory diseases, autoimmune diseases, destructive bone disorders, proliferative disorders, infectious diseases, degenerative diseases, and necrotic diseases. This invention also relates to methods for inhibiting ICE activity, for treating interleukin-1-, apoptosis-, IGIF- and IFN-?-mediated diseases and decreasing IGIF and IFN-? production using the compounds and compositions of this invention.
    Type: Grant
    Filed: January 18, 2007
    Date of Patent: September 7, 2010
    Assignee: Vertex Pharmaceuticals Incorporated
    Inventors: Mark James Batchelor, David Bebbington, Guy W. Bemis, Wolf Herman Fridman, Roger John Gillespie, Julian M. C. Golec, Yong Gu, David J. Lauffer, David J. Livingston, Saroop Singh Matharu, Michael D. Mullican, Mark A. Murcko, Robert Murdoch, Philip Nyce, Andrea L. C. Robidoux, Michael Su, M. Woods Wannamaker, Keith P. Wilson, Robert E. Zelle
  • Publication number: 20100210603
    Abstract: The present invention relates to a novel class of sulfonamides which are aspartyl protease inhibitors. In one embodiment, this invention relates to a novel class of HIV aspartyl protease inhibitors characterized by specific structural and physicochemical features. This invention also relates to pharmaceutical compositions comprising these compounds. The compounds and pharmaceutical compositions of this invention are particularly well suited for inhibiting HIV-1 and HIV-2 protease activity and consequently, may be advantageously used as anti-viral agents against the HIV-1 and HIV-2 viruses. This invention also relates to methods for inhibiting the activity of HIV aspartyl protease using the compounds of this invention and methods for screening compounds for anti-HIV activity.
    Type: Application
    Filed: September 11, 2009
    Publication date: August 19, 2010
    Inventors: Roger D. Tung, Mark A. Murcko, Govinda R. Bhisetti
  • Patent number: 7772366
    Abstract: The present invention relates to novel classes of compounds which are inhibitors of interleukin-1? converting enzyme. The ICE inhibitors of this invention are characterized by specific structural and physicochemical features. This invention also relates to pharmaceutical compositions comprising these compounds. The compounds and pharmaceutical compositions of this invention are particularly well suited for inhibiting ICE activity and consequently, may be advantageously used as agents against interleukin-1 mediated diseases, including inflammatory diseases, autoimmune diseases and neurodegenerative diseases. This invention also relates to methods for inhibiting ICE activity and methods for treating interleukin-1 mediated diseases using the compounds and compositions of this invention.
    Type: Grant
    Filed: September 18, 2007
    Date of Patent: August 10, 2010
    Assignee: Vertex Pharmaceuticals Incorporated
    Inventors: Guy W. Bemis, Julian M. Golec, David J. Lauffer, Michael D. Mullican, Mark A. Murcko, David J. Livingston
  • Publication number: 20100173851
    Abstract: The present invention relates to compounds that inhibit serine protease activity, particularly the activity of hepatitis C virus NS3-NS4A protease. As such, they act by interfering with the life cycle of the hepatitis C virus and are also useful as antiviral agents. The invention further relates to compositions comprising these compounds either for ex vivo use or for administration to a patient suffering from HCV infection. The invention also relates to methods of treating an HCV infection in a patient by administering a composition comprising a compound of this invention. The invention further relates to processes for preparing these compounds.
    Type: Application
    Filed: June 3, 2009
    Publication date: July 8, 2010
    Inventors: Janos Pitlik, Kevin M. Cottrell, Luc J. Farmer, Robert B. Perni, Lawrence F. Courtney, John H. van Drie, Mark A. Murcko
  • Patent number: 7608632
    Abstract: The present invention relates to a novel class of sulfonamides which are aspartyl protease inhibitors. In one embodiment, this invention relates to a novel class of HIV aspartyl protease inhibitors characterized by specific structural and physicochemical features. This invention also relates to pharmaceutical compositions comprising these compounds. The compounds and pharmaceutical compositions of this invention are particularly well suited for inhibiting HIV-1 and HIV-2 protease activity and consequently, may be advantageously used as anti-viral agents against the HIV-1 and HIV-2 viruses. This invention also relates to methods for inhibiting the activity of HIV aspartyl protease using the compounds of this invention and methods for screening compounds for anti-HIV activity.
    Type: Grant
    Filed: April 19, 2006
    Date of Patent: October 27, 2009
    Assignee: Vertex Pharmaceuticals Incorporated
    Inventors: Roger D. Tung, Mark A. Murcko, Govinda R. Bhisetti
  • Publication number: 20090203702
    Abstract: The present invention relates to inhibitors of p38, a mammalian protein kinase involved cell proliferation, cell death and response to extracellular stimuli. The invention also relates to methods for producing these inhibitors. The invention also provides pharmaceutical compositions comprising the inhibitors of the invention and methods of utilizing those compositions in the treatment and prevention of various disorders.
    Type: Application
    Filed: April 3, 2008
    Publication date: August 13, 2009
    Applicant: VERTEX PHARMACEUTICALS INCORPORATED
    Inventors: Guy W. Bemis, Francesco Gerald Salituro, John Patrick Duffy, John E. Cochran, Edmund Martin Harrington, Mark A. Murcko, Keith P. Wilson, Michael Su, Vincent P. Galullo
  • Publication number: 20090143312
    Abstract: The present invention relates to compounds, methods and pharmaceutical compositions for inhibiting proteases, particularly serine proteases, and more particularly HCV NS3 proteases. The compounds, and the compositions and methods that utilize them, can be used, either alone or in combination to inhibit viruses, particularly HCV virus.
    Type: Application
    Filed: February 14, 2008
    Publication date: June 4, 2009
    Applicant: VERTEX PHARMACEUTICALS INCORPORATED
    Inventors: Roger D. Tung, Scott L. Harbeson, David D. Deininger, Mark A. Murcko, Govinda R. Bhisetti, Luc J. Farmer
  • Publication number: 20090048226
    Abstract: The present invention relates to novel classes of compounds which are caspase inhibitors, in particular interleukin-1? converting enzyme (“ICE”) inhibitors. This invention also relates to pharmaceutical compositions comprising these compounds. The compounds and pharmaceutical compositions of this invention are particularly well suited for inhibiting caspase activity and consequently, may be advantageously used as agents against interleukin-1-(“IL-1”), apoptosis-, interferon-? inducing factor-(IGIF), or interferon-?-(“IFN-?”) mediated diseases, including inflammatory diseases, autoimmune diseases, destructive bone disorders, proliferative disorders, infectious diseases, and degenerative diseases. This invention also relates to methods for inhibiting caspase activity and decreasing IGIF production and IFN-? production and methods for treating interleukin-1, apoptosis-, and interferon-?-mediated diseases using the compounds and compositions of this invention.
    Type: Application
    Filed: January 22, 2008
    Publication date: February 19, 2009
    Inventors: Marion W. Wannamaker, Guy W. Bemis, Paul S. Charifson, David J. Lauffer, Michael D. Mullican, Mark A. Murcko, Keith P. Wilson, James W. Janetka, Robert J. Davies, Anne-Laure Grillot, Zhan Shi, Cornelia J. Forster