Repositioning Old Drugs For New Indications Using Computational Approaches

Yannick Pouliot, PhDKhatri Laboratory

4/7/2014

Discovering New Drugs Is Getting Much Harder

One Approach: Finding Unrecognized Indications For Existing Drugs

• Most drugs have more than one activity beyond their approved indication(s)– usually unrecognized– example: thalidomide now approved for treatment of myeloma

• Focus of existing drugs because already FDA-approved…– “known” safety profile– increasingly off-patent

• But, how to identify unrecognized indications?– “wet lab” approaches– computational approaches

Target: Inflammatory Bowel Diseases

Approach Is A Sausage Machine:

Inflammatory Bowel Diseases - Overview

• IBD = Ulcerative colitis, Crohn’s disease• Inflammation of intestinal tract• Chronic, progressive, episodic

– North America: >1M patients

• High heritability• No cure; poor treatment options

– surgery– drugs with serious adverse effects (e.g., corticosteroids)

Players In Computational Drug Repositioning

functional genomics data repository with >1M samples

integration of medical terminologies, classification, and coding standards

free relational database server; dominant in life sciences

free statistical analysis and plotting language; dominant in life sciences

WARNING

If You Go Fishing And Don’t Know What Fish Look Like, You Will Definitely Find Something.

It Just Won’t Be A Fish.

The False Discovery Rate: A Key Concept Of Data Mining

“The q-value of a test measures the proportion of false positives incurred … when that particular test is called significant” Dabney, A., Storey, J. & Warnes, G., R Package "qvalue". (2011).

• When evaluating many significance test results, you must have an a priori expectation of what you will consider to be a “true” result across many tests, as well as for individual significance tests

• A significance test whose value results in rejecting the null hypothesis can still be a false positive because “too many” tests were performed.

• Controlled by multiple hypothesis testing, and the resulting q-value threshold.• Relies on “bootstrapping” permutation to generate a distribution of scores based

on observed values

Hypothesis

Drugs that increase gene expression in the reverse direction to what is observed in IBD vs. normal tissues should decrease symptoms

Assessment Method: 1. Characterize the effect of drugs on human gene transcript

levels2. Characterize the difference in human gene transcript levels

between disease and normal tissue pairs3. Find drugs that induce the reciprocal signature observed in

disease

Source Data

Disease data• Assemble MySQL database of 176 gene expression microarray

datasets from GEO– diseased vs. normal tissue pairs– 100 specific diseases manually reviewed and encoded using UMLS

identifiers

Drug data (“Connectivity Map”)Gene expression microarray profiles of effects of 164 drugs in:

– breast cancer: MCF7 epithelial cell line – prostate cancer: PC3 epithelial cell line– leukemia: HL60 – melanoma: SKMEL5

Finding Drug Candidates Using Rank-Ordered, Drug-Disease Anti-Correlation Scores

1. Compute an anti-similarity score for each drug-disease pairs (anti-correlation score)

2. Compute P-values of anti-correlation scores (significance testing) using distance between observed score vs. scores of 100 randomly-generated comparisons

3. Retain correlation that have FDR values better than 0.05

Selected Drug: Topiramate (Candidate #2)

• Anticonvulsant drug whose activity “may be due to a combination of potential mechanisms: Blocks neuronal voltage-dependent sodium channels, enhances GABA(A) activity, antagonizes AMPA/kainate glutamate receptors, and weakly inhibits carbonic anhydrase” -- UpToDate

• Off-patent since 2009!

Validation In Rat Model of IBD - 1

• Sprague-Dawley rats treated with TNBS to induce colitis

• Video endoscopy at days 3 and 7 post-induction

• Readout is fraction of animals with diarrhea

• Result: treatment with topiramate decreases diarrhea (one-way ANOVA p<0.005)

pos control

topiramate

prednisolone

neg control

Validation In Rat Model of IBD - 2

Evaluation of Eight Randomly-Selected Counter-Expressed Genes

qPCRmicroarrayEvaluation of Eight Randomly-Selected Counter-Expressed

Genes

Since Then…

• Upcoming case report to be published of topiramate working in a patient refractory to steroids.

Summary

• Proof of principle that drugs that affect gene transcript levels in an anti-correlated manner to the normal/disease pattern can ameliorate symptoms

• Everything from public domain– data– algorithm– software

• In principle, applicable to any domain where data exist