US 5,965,352 A · Methods for identifying pathways of drug action

Abstract

The present invention provides methods for identifying and representing the biological pathways of drug action on a cell by: (i) measuring responses of cellular constituents to graded exposures of the cell to a drug of interest; (ii) measuring the responses of cellular constituents to perturbations in one or more biological pathways of the cell; and (iii) scaling a combination of the measured pathway responses to fit the measured drug responses best according to an objective measure. In alternative embodiments, the present invention also provides for assessing the significance of the identified representation and for verifying that the identified pathways are actual pathway of drug action. In various embodiments, the effects on the cell can be determined by measuring gene expression, protein abundances, protein activities, or a combination of such measurements. In various embodiments, perturbation to a biological pathway in the cell can be made by use of titratable expression systems, use of transfection systems, modification to abundances of pathway RNAs, modifications to abundances of pathway proteins, or modifications to activities of the pathway proteins. The present invention also provides methods for drug development based on the methods for identifying biological pathways of drug action, and methods for representing the biological pathways involved in the effect of an environmental change upon a cell.

Claims45

Dependent claims

A method of identifying biological pathways involved in the action of a drug in a cell type comprising:

(a) providing a drug response of said drug in said cell type, said drug response having been obtained by a method comprising measuring a plurality of cellular constituents in a cell of said cell type at a plurality of levels of exposure to said drug;
(b) representing a model drug response as a combination of one or more biological pathway responses in said cell type, wherein a biological pathway response in said cell type is the product of a method comprising measuring cellular constituents of a biological pathway in a cell of said cell type at a plurality of levels of a perturbation to said biological pathway, and wherein each of said one or more biological pathway responses in said combination are subject to an independent scaling transformation;
and
(c) determining best scaling transformations of said one or more biological pathway responses which minimize the value of an objective function of the difference between said provided drug response and said model drug response,
wherein said combination of said one or more biological pathway responses subject to said best scaling transformations identifies the biological pathways involved in the action of said drug in said cell type.

2 more elements

A method of identifying biological pathways involved in the action of a drug in a cell type, said method comprising determining best scaling transformations of one or more biological pathway responses which minimize the value of an objective function of the difference between a provided drug response and a model drug response, wherein:

(a) said one or more biological pathway responses are the product of a method comprising measuring cellular constituents of one or more biological pathways in a cell of said cell type at a plurality of levels of perturbation to said biological pathways;
(b) said provided drug response is provided by a method comprising measuring a plurality of cellular constituents in a cell of the cell type at a plurality of levels of exposure to said drug;
and
(c) said model drug response is represented as a combination of said one or more biological pathway responses, each of said one or more biological pathway responses in said combination being subject to an independent scaling transformation,
wherein the combination of said one or more biological pathway responses subject to said best scaling transformations identifies the biological pathways involved in the action of said drug in said cell type.

2 more elements

A method of determining a more pathway-specific drug candidate from an initial drug candidate comprising:

(a) identifying the biological pathways involved in the action of an initial drug candidate by a method comprising determining best scaling transformations of one or more biological pathway responses which are the product of a method comprising measuring cellular constituents of one or more biological pathways in a cell of a cell type at a plurality of levels of perturbation to said biological pathways, wherein
(i) said best scaling transformations minimize the value of an objective function of the difference between a provided drug response for said initial drug candidate and a model drug response for said initial drug candidate,
(ii) said provided drug response for said initial drug candidate is provided by a method comprising measuring a plurality of cellular constituents in a cell of the cell type at a plurality of levels of exposure to said initial drug candidate, and
(iii) said model drug response for said initial drug candidate is represented as a combination of said one or more biological pathway responses, each of said one or more biological pathway responses in said combination being subject to an independent scaling transformation;
(b) modifying the structure of said initial drug candidate to produce a modified drug candidate;
and
(c) identifying the biological pathways involved in the action of said modified drug candidate by a method comprising determining best scaling transformations of said one or more biological pathway responses, wherein
(i) said best scaling transformations minimize the value of an objective function of the difference between a provided drug response for said modified drug candidate, and a model drug response for said modified drug candidate,
(ii) said provided drug response for said modified drug candidate is provided by a method comprising measuring a plurality of cellular constituents in a cell of the cell type at a plurality of levels of exposure to said modified drug candidate, and
(iii) said model drug response for said modified drug candidate is represented as a combination of said one or more biological pathway responses, each of said one or more biological pathway responses in said combination being subject to an independent scaling transformation;
wherein said modified drug candidate is a more pathway-specific drug candidate than said initial drug candidate if fewer biological pathways are identified in the action of said modified drug candidate than in the action of said initial drug candidate.

8 more elements

A method of identifying one or more specific biological pathways that are involved in the action of a drug and that mediate side-effects of the drug, said method comprising:

(a) identifying one or more biological pathways involved in the action of a first drug by determining best scaling transformations of one or more biological pathway responses which are the product of a method comprising measuring cellular constituents of one or more biological pathways in a cell of a cell type at a plurality of levels of perturbation to said biological pathways, wherein
(i) said best scaling transformations minimize the value of an objective function of the difference between a provided drug response for said first drug and a model drug response for said first drug,
(ii) said provided drug response for said first drug is provided by a method comprising measuring a plurality of cellular constituents in a cell of the cell type at a plurality of levels of exposure to said first drug, and
(iii) said model drug response for said first drug is represented as a combination of said one or more biological pathway responses, each of said one or more biological pathway responses in said combination being subject to an independent scaling transformation;
(b) identifying one or more biological pathways involved in the action of a second drug by determining best scaling transformations of said one or more biological pathway responses wherein said first and second drugs are different and exhibit therapeutic efficacy for the same disease or disorder, and wherein
(i) said best scaling transformations minimize the value of an objective function of the difference between a provided drug response for said second drug and a model drug response for said second drug,
(ii) said provided drug response for said second drug is provided by a method comprising measuring a plurality of cellular constituents in a cell of the cell type at a plurality of levels of exposure to said second drug, and
(iii) said model drug response for said second drug is represented as a combination of said one or more biological pathway responses, each of said one or more biological pathway responses in said combination being subject to an independent scaling transformation;
and
(c) identifying specific biological pathways involved in the action of said first drug that are different from those biological pathways involved in the action of said second drug, thereby identifying one or more specific biological pathways that are involved in the action of said first drug and that mediate side-effects of said first drug.

7 more elements

A method of identifying one or more specific biological pathways that are involved in mediating therapeutic efficacy for a disease or disorder, said method comprising:

(a) identifying one or more biological pathways involved in the action of a first drug by determining best scaling transformations of one or more biological pathway responses which are the product of a method comprising measuring cellular constituents of one or more biological pathways in a cell of a cell type at a plurality of levels of perturbation to said biological pathways, wherein
(i) said best scaling transformations minimize the value of an objective function of the difference between a provided drug response for said first drug and a model drug response for said first drug,
(ii) said provided drug response for said first drug is provided by a method comprising measuring a plurality of cellular constituents in a cell of the cell type at a plurality of levels of exposure to said first drug, and
(iii) said model drug response for said first drug is represented as a combination of said one or more biological pathway responses, each of said one or more biological pathway responses in said combination being subject to an independent scaling transformation;
(b) identifying the biological pathways involved in the action of a second drug by determining best scaling transformations of said one or more biological pathway responses, wherein said first and second drugs are different and exhibit therapeutic efficacy for the same disease or disorder, and wherein
(i) said best scaling transformations minimize the value of an objective function of the difference between a provided drug response for said second drug and a model drug response for said second drug,
(ii) said provided drug response for said second drug is provided by a method comprising measuring a plurality of cellular constituents in a cell of the cell type at a plurality of levels of exposure to said second drug, and
(iii) said model drug response for said second drug is represented as a combination of said one or more biological pathway responses, each of said one or more biological pathway responses in said combination being subject to an independent scaling transformation;
and
(c) identifying specific biological pathways involved in the action of both said first drug and said second drug, thereby identifying one or more specific biological pathways that are involved in the action of said first drug and that mediate therapeutic efficacy for said disease or disorder.

7 more elements

Dependencies are inferred from the claim text.

Methods for identifying pathways of drug action

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Methods for identifying pathways of drug action

Life of this patent

Abstract

Claims45