Helen R W Yu

7935493, May 3, 2011

Jun 12, 2006

11/450379

Stephen William Watson Michnick - Westmount, CA
Ingrid Remy - Montreal, CA
Marnie MacDonald - Pleasanton CA, US
Jane Lamerdin - Livermore CA, US
Helen Yu - Mountain View CA, US
John K. Westwick - San Ramon CA, US

Odyssey Thera Inc. - San Ramon CA

G01N 33/53
G01N 33/532
G01N 33/533
G01N 33/573
G01N 21/00
G01N 21/76
C07K 14/00

435 72, 435 4, 435 74, 435 17, 435 21, 436164, 436172, 530350

The present invention provides protein fragment complementation assays for drug discovery, in particular to identify compounds that activate or inhibit cellular pathways. Based on the selection of an interacting protein pair combined with an appropriate PCA reporter, the assays may be run in high-throughput or high-content mode and may be used in automated screening of libraries of compounds. The interacting pair may be selected by cDNA library screening; by gene-by-gene interaction mapping; or by prior knowledge of a pathway. Fluorescent and luminescent assays can be constructed using the methods provided herein. The selection of suitable PCA reporters for high-throughput or high-content (high-context) assay formats is described for a diversity of reporters, with particular detail provided for examples of monomeric enzymes and fluorescent proteins. Methods are described for constructing such assays for one or more steps in a biochemical pathway; testing the effects of compounds from combinatorial, natural product, peptide, antibody, nucleic acid or other diverse libraries on the protein or pathway(s) of interest; and using the results of the screening to identify specific compounds that activate or inhibit the protein or pathway(s) of interest. Single-color and multi-color assays are disclosed.

20040161787, Aug 19, 2004

Feb 5, 2004

10/772021

Stephen Michnick - Westmount, CA
Ingrid Remy - Montreal, CA
Marnie MacDonald - Pleasanton CA, US
Jane Lamerdin - Livermore CA, US
Helen Yu - Mountain View CA, US
John Westwick - San Ramon CA, US

Odyssey Thera, Inc. - San Ramon CA

C12Q001/68
G01N033/53
G01N033/567
G01N033/543

435/006000, 435/007200, 436/518000

The present invention provides protein fragment complementation assays for drug discovery, in particular to identify compounds that activate or inhibit cellular pathways. Based on the selection of an interacting protein pair combined with an appropriate PCA reporter, the assays may be run in high-throughput or high-content mode and may be used in automated screening of libraries of compounds. The interacting pair may be selected by cDNA library screening; by gene-by-gene interaction mapping; or by prior knowledge of a pathway. Fluorescent and luminescent assays can be constructed using the methods provided herein. The selection of suitable PCA reporters for high-throughput or high-content (high-context) assay formats is described for a diversity of reporters, with particular detail provided for examples of monomeric enzymes and fluorescent proteins. Methods are described for constructing such assays for one or more steps in a biochemical pathway; testing the effects of compounds from combinatorial, natural product, peptide, antibody, nucleic acid or other diverse libraries on the protein or pathway(s) of interest; and using the results of the screening to identify specific compounds that activate or inhibit the protein or pathway(s) of interest. Single-color and multi-color assays are disclosed. Further disclosed are universal expression vectors with cassettes that allow the rapid construction of assays for a large and diverse number of gene/reporter combinations. The development of such assays is shown to be straightforward, providing for a broad, flexible and biologically relevant platform for drug discovery.

20060009506, Jan 12, 2006

Jul 6, 2005

11/174630

John Westwick - San Ramon CA, US
Helen Yu - Mountain View CA, US
Stephen Owens - Martinez CA, US
Marnie MacDonald - Pleasnaton CA, US

Odyssey Thera, Inc. - San Ramon CA

A61K 31/4172

514395000

The invention features a method for treating a patient having a cancer or other neoplasm, by administering to the patient one of the following drugs or a metabolite or analog thereof: cinnarizine; desipramine; fenofibrate; flunarizine; isoreserpine; nicardipine; promazine; promethazine; suloctidil; terfenadine; atorvastatin; mebeverine; sertraline; albendazole; bepridil; bergaptene; clomiphene; dichlorophene; droperidol; mebendazole; meclocycline; metergoline; ramiphenazone; sanguinarine; dipyrone; nicardipine; or 4-dimethylaminoantipyrine.

20060040338, Feb 23, 2006

Aug 17, 2005

11/205021

John Westwick - San Ramon CA, US
Helen Yu - Mountain View CA, US
Marnie MacDonald - Pleasanton CA, US

Odyssey Thera, Inc. - San Ramon CA

C12Q 1/02
C12M 1/34

435029000, 435287100

The instant invention provides a method for establishing safety profiles for chemical compounds, as well as pharmacological profiling said method comprising (A) testing the effects of said chemical compounds on the amount and/or post-translational modifications of two or more macromolecules in intact cells; (B) constructing a pharmacological profile based on the results of said tests; and (C) comparing said profile to the profile(s) of drugs with established safety characteristics. Additionally, the invention is also directed to a composition comprising an assay panel, said panel comprising at least one high-content assay for the amount and/or post-translational modification of a protein and at least one high-content assay for the amount and/or subcellular location of a protein-protein interaction.

20060094059, May 4, 2006

Sep 21, 2005

11/230569

John Westwick - San Ramon CA, US
Marnie MacDonald - Pleasanton CA, US
Helen Yu - Mountain View CA, US
Stephen Owens - Martinez CA, US
Stephen Michnick - Montreal, CA

Odyssey Thera, Inc. - San Ramon CA

C40B 40/10
G01N 33/53

435007100

The screening system utilizes dynamic measurements of pathway activity to detect the activities of drugs within cellular pathways. The methods of the invention can be used to identify previously unknown drug activities and therapeutic uses, even for drugs that have been well characterized with standard biochemical assays. We demonstrated the utility of the invention by screening a portion of the known pharmacopeia. We identified dozens of drugs, previously or currently marked for a variety of indications, with surprising and previously-unsuspected activity against ‘hallmark’ cancer pathways. We also showed that over 20 of these drugs indeed have anti-proliferative activity in human tumor cells, underscoring the utility and predictability of the screening system. The methodology will extend the utility of the current pharmacopeia and provide the basis for de novo discovery of drugs with a broad range of therapeutic indications.

20070212677, Sep 13, 2007

Aug 31, 2006

11/513068

Marnie MacDonald - Pleasanton CA, US
Jane Lamerdin - Livermore CA, US
Stephen Owens - Martinez CA, US
Brigitte Keon - Castro Valley CA, US
Graham Bilter - Pleasanton CA, US
Zhidi Shang - Fremont CA, US
Zhengping Huang - Pleasanton CA, US
Helen Yu - Mountain View CA, US
Jennifer Dias - Dublin CA, US
Tomoe Minami - Dublin CA, US
Stephen Michnick - Montreal, CA
John Westwick - San Ramon CA, US

Odyssey Thera, Inc. - San Ramon CA

C12Q 1/00
C12Q 1/68
G01N 33/53
G06F 19/00

435004000, 435006000, 435007100, 702019000

This invention provides principles, methods and compositions for ascertaining the mechanism of action of pharmacologically important compounds in the context of network biology, across the entire scope of the complex pathways of living cells. Importantly, the principles, methods and compositions provided allow a rapid assessment of the on-pathway and off-pathway effects of lead compounds and drug candidates in living cells, and comparisons of lead compounds with well-characterized drugs and toxicants to identify patterns associated with efficacy and toxicity. The invention will be useful in improving the drug discovery process, in particular by identifying drug leads with desired safety and efficacy and in effecting early attrition of compounds with potential adverse effects in man.

20120149597, Jun 14, 2012

May 2, 2011

13/067007

Stephen William Watson Michnick - Quebec, CA
Ingrid Remy - Montreal, CA
Marnie MacDonald - Pleasanton CA, US
Jane Lamerdin - Livermore CA, US
Helen Yu - Mountain View CA, US
John K. Westwick - San Ramon CA, US

Odyssey Thera, Inc. - San Ramon CA

C40B 30/06
C40B 40/10

506 10, 506 18

The present invention provides protein fragment complementation assays for drug discovery, in particular to identify compounds that activate or inhibit cellular pathways. Based on the selection of an interacting protein pair combined with an appropriate PCA reporter, the assays may be run in high-throughput or high-content mode and may be used in automated screening of libraries of compounds. The interacting pair may be selected by cDNA library screening; by gene-by-gene interaction mapping; or by prior knowledge of a pathway. Fluorescent and luminescent assays can be constructed using the methods provided herein. The selection of suitable PCA reporters for high-throughput or high-content (high-context) assay formats is described for a diversity of reporters, with particular detail provided for examples of monomeric enzymes and fluorescent proteins. Methods are described for constructing such assays for one or more steps in a biochemical pathway; testing the effects of compounds from combinatorial, natural product, peptide, antibody, nucleic acid or other diverse libraries on the protein or pathway(s) of interest; and using the results of the screening to identify specific compounds that activate or inhibit the protein or pathway(s) of interest. Single-color and multi-color assays are disclosed. Further disclosed are universal expression vectors with cassettes that allow the rapid construction of assays for a large and diverse number of gene/reporter combinations. The development of such assays is shown to be straightforward, providing for a broad, flexible and biologically relevant platform for drug discovery.

20200223907, Jul 16, 2020

Jul 2, 2019

16/460094

- Foster City CA, US
Brian A. Carr - Foster City CA, US
Magdeleine S. Hung - Mountain View CA, US
Manu Kanwar - San Marcos CA, US
Craig S. Pace - Belmont CA, US
Doug Rehder - Bonsall CA, US
Matthew Robert Schenauer - Dana Point CA, US
Loredana Serafini - Orinda CA, US
Heather Theresa Stephenson - San Jose CA, US
Nathan D. Thomsen - Castro Valley CA, US
Helen Yu - Mountain View CA, US
Xue Zhang - San Diego CA, US

Gilead Sciences, Inc. - Foster City CA

C07K 16/10
A61P 31/18

Antibodies that bind to HIV gp120 and neutralize HIV are disclosed. Also disclosed are methods of using such antibodies alone or in combination with other therapeutic agents to treat or prevent HIV infection.