California Institute of Technology

University of California

The United States of America, as Represented by the Secretary, Department of Health and Human Services

Yale University

The Scripps Research Institute

University of Kansas

Cleave Biosciences, Inc.

Raymond J Deshaies

Svetlana A Lyapina

Rati Verma

Tsui-Fen Chou

Gregory Cope

Xavier Ambroggio

R M Renny Feldman

Craig C Correll

Brian M Stoltz

Han-Jie Zhou

Craig M Crews

Jeffrey Aube

Frank John Schoenen

Samuel Gerritz

Seth M Cohen

Hugh Rosen

Kevin Frankowski

Steven J Brown

Eugene Koonin

Kelin Li

Senthil Radhakrishnan

Jefferson Y Chan

Christian Perez

Kathleen M Sakamoto

Amanda C Jones

Gabriela Alexandru

Jing Li

Johannes Graumann

Lakshminarayanan Aravind

Yuyong Ma

Greg Cope

Candy S Lee

Candidate compounds for specific inhibition of Rpn11 are represented by Formula 1 where each of R, R, R, R, R, and Ris independently selected from hydrogen (H), substituted and unsubstituted alkyl groups, carboxyl groups, or substituted and unsubstituted carboxyamides.

Inhibitors of RPN11

Methods and compositions for inhibiting Nrf1 activity are provided for enhancing apoptosis in mammalian cells. Apoptosis is enhanced in mammalian cells by co-inhibiting Nrf1 activity and proteasome activity. Methods for identifying Nrf1 inhibitors are provided using an assay for screening Nrf1 inhibitors that enhance proteasome inhibition by preventing induced proteasome expression.

Methods for preventing induced synthesis of proteasomes in human cells

One aspect of the invention relates to compounds that inhibit the activity of p97, such as by binding covalently to a cysteine residue in the active site. In certain embodiments, the invention relates to the treatment of disease, such as cancer, comprising administering a compound of the invention.

Inhibitors of p97

Compounds of Formulas I-XLIII are identified as direct inhibitors of p97 ATPase or of the degradation of a p97-dependent ubiquitin-proteasome system (UPS) substrate. Methods and compositions are disclosed for inhibiting p97 ATPase and the degradation of a p97-dependent UPS substrate, and for identifying inhibitors thereof.

Methods and compositions for inhibition of the transitional endoplasmic reticulum ATPase

Hypoxia, a state of lower than normal tissue oxygen tension, has recently been implicated in a host of human diseases, including cancer, heart disease, and neurological disorders. Novel associations between p97 and other proteins, including UBX-domain-containing proteins (UBX-polypeptides), HIF1&#x3b1;, and a variety of E3 ligases are provided herein. The disclosure provides complexes comprising UBX-domain-containing polypeptides (UBX-polypeptides) and other polypeptides involved in the degradation of ubiquitinated proteins. In addition, the disclosure provides uses for active agents that modulate protein-protein complex formation between an UBX-polypeptide and its complementary-binding substrate. For example, the disclosure provides methods for treating or preventing hypoxia-related disorders or conditions in a patient or a cell by administration of an active agent that modulates the activity of an UBX-polypeptide and/or its complementary binding-substrate. Furthermore, the disclosure provides uses for active agents that modulate HIF1&#x3b1; activity; such agents may be used to modulate processes that are regulated by HIF1&#x3b1;. The disclosure also provides many screening assays to identify test agents that modulate complex formation between an UBX-polypeptide and its complementary-binding substrate or methods for evaluating modes of action and/or effects of active agents that have already been identified as modulators of an UBX-polypeptide and/or its complementary-binding substrate.

Compositions and method of treating hypoxia-associated diseases

The present invention is based on the discovery that a polypeptide containing the JAB subunit or the JAM domain has peptidase activity, e.g., isopeptidase activity. The present invention provides polypeptides and crystalline polypeptides containing the JAM domain and methods of using such polypeptides to screen for agents capable of affecting the peptidase activity of the polypeptides. The present invention also provides methods of using the JAM domain for rational drug design or identifying agents capable of affecting the peptidase activity of the JAM domain.

Regulation of target protein activity through modifier proteins

Methods for identifying agents that can increase or decrease the isopeptidase activity of a COP9 signalsome (CSN) are provided, as are agent identified using such screening assays. In addition, methods of ameliorating a pathologic condition such as a cancer or an autoimmune disease in a subject by modulating the CSN isopeptidase activity are provided, as are medicaments useful for treating a subject having such a condition.

Modulation of COP9 signalsome isopeptidase activity

The present invention is based on the discovery of a composition that provides targeted ubiquitination. Specifically the composition contains an ubiquitin pathway protein binding moiety which recognizes an ubiquitin pathway protein and a targeting moiety which recognizes a target protein. In addition, the present invention provides libraries of compositions, where each composition contains an ubiquitin pathway protein binding moiety and a member of a molecular library. The libraries of the present invention can be used to identify proteins involved in a predetermined function of cells.

Proteolysis targeting chimeric pharmaceutical

The present invention is based on the discovery of a simplified assay for identifying modulators of ubiquitin ligase activity. This assay allows detection of compounds that affect ubiquitination and thus, cell cycle regulation in cells. An increase in ubiquitination, in comparison to a test sample lacking a test compound, indicates a stimulation of activity, whereas a reduction in ubiquitination indicates an inhibitor of activity. Also disclosed herein are methods of identifying proteins having ubiquitin ligase activity, methods of identifying substrates for ubiquitination, methods for identifying an activity relationship between a particular ubiquitin ligase and a particular ubiquitin conjugating enzyme, and chimeric proteins comprising a ubiquitin conjugating enzyme and a ubiquitination substrate, which are useful in all of the disclosed methods.

Biochemical assay to monitor the ubiquitin ligase activities of cullins

A method is provided for identifying an compound that affects an activity of a polypeptide subunit of a SCF complex. The method includes contacting a sample comprising a chimeric SCF complex assembled from subunits derived from Saccharomyces cerevisiae or human and another species and a CDC34p polypeptide with the compound under conditions that allow the components to interact, and adding to these components an E1 enzyme, ubiquitin and ATP, and a SCF substrate. The ubiquitination of the SCF substrate is measured. A chimeric in vitro assay system is provided for measuring CDC53p or CUL1p activity, comprising a CDC4p, CDC34p, and a SKP1p polypeptide, and either a CDC53p or CUL1p polypeptide. In this assay the CDC4p, CDC34p, and SKP1p polypeptide are either a yeast polypeptide or a polypeptide from another species, and at least one of the CDC4p, CDC34p, and SKP1p polypeptides is a yeast polypeptide and at least one of the CDC4p, CDC34p, and SKP1p polypeptides is a polypeptide from another species. A method is further provided for identifying a compound that affects the ability of a CDC4p, a SKP1p, a CDC34p, and a CDC53p or a CUL1p to ubiquitinate a substrate. The method includes contacting a sample comprising a CDC4p, a SKP1p, a CDC34p, and a CDC53p or CUL1p, with the compound under conditions sufficient to allow the components to interact, and adding to these components an E1 enzyme, ubiquitin and ATP, and a substrate for ubiquitination. The ability of the CDC4p, the SKP1p, the CDC34p, and the CDC53p or CUL1p, to ubiquitinate the substrate is measured. A method is also provided of identifying a polypeptide having a function of a CDC4 subunit of SCF. A method is further provided for identifying a polypeptide as a substrate for a ubiquitination reaction.

Assay for the ubiquitination-promoting activity of human proteins

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Claremont, CA, United States of America

Raymond J Deshaies