1. TOPICS IN (NANO) BIOTECHNOLOGY
Drug Discovery
Lecture 10
14th May, 2003
PhD Course

2. Functional Genomics and Pharmacology
Paradigm shifts in Drug Discovery resulting from the HGP and other Genome Projects.
Target Validation: The new unmet need for Drug Discovery
Correlative Approaches to Target Validation
Comparative Genomics
Microarrays
Proteomics
Causative Approaches to Target Validation
Overexpression systems
Knockout mice/Gene Ablation
Chemical Genomics
Antibodies
Antisense
Interference RNA (RNAi)

3. Paradigm Shifts in Drug Discovery - Product of the Genomics Revolution -
The original approach to Drug Discovery.
Drug Discovery had its origins in the late 1800’s with the identification and manufacture of natural products, and their derivatives.
Dye makers
Pharmacists
The original approach to Drug Discovery focused on the screening of natural products for biological activity in defined assay systems.
“Pharmacology-to-Protein” concept
Serendipitous Drug Discovery
Extremely laborious/time consuming
Limited areas of success (why?)
Antimicrobials*
Aspirin
…but, still practiced today.

4. The Original Approach to Drug Discovery - Pharmacology-to-Protein -
Defined Biological Endpoint (e.g., bacterial growth)
Extract Fractionation/ Purification to Identify Active Entity (“Pharmacophore”)
Screening of Very Crude Extracts for Biological Activity
Molecular Determination of Active Pharmacophore
Chemical Structure - Activity Analysis
Therapeutic Index
Pharmacokinetics

5. Paradigm Shifts in Drug Discovery - Product of the Genomics Revolution -
The semi-original approach to Drug Discovery
Major advancements in biochemistry and molecular biology began to produce changes in the way drugs were discovered.
“Protein-to-Gene” Concept
A protein implicated in disease was purified, monitored by functional assays, cloned, expressed and re-characterized.
Drug screening performed against expressed protein.
Still, very laborious/time consuming.

6. The Semi-Original Approach to Drug Discovery - Protein-to-Gene -
Isolation/
Characterization/
Purification of Target Molecule
Gene Cloning/
Sequencing. Target
Protein Expressed
at High Levels.
Enzyme/ Receptor of Interest
Protein
Microsequencing
High-Throughput Screening Assays
Established against
Target Protein
Identify Lead Inhibitor.
Confirm Role in Disease Process.
Chemical Structure- Activity Analysis
Therapeutic Index
Pharmacokinetics

7. Paradigm Shifts in Drug Discovery - Product of the Genomics Revolution -
The new paradigm for Drug Discovery: “Gene-to- Function”
The advent of high-throughput gene cloning and sequencing resulted in the rapid identification of thousands of novel genes, most without known function.
Mapping/sequencing of the human (and other) genomes.
Drug Discovery was presented with a new and very challenging task:
To identify functions for thousands of genes.
To determine which of the genes are the most attractive therapeutic targets.

8. A New Paradigm for Drug Discovery - Gene-to-Function -
Gene of
Unknown
Function
Validation as an
Attractive Drug
Target
Expression/
Protein
Purification
Determination of
Cellular Function
High-Throughput Screening Assays
Established against
Target Protein
Chemical Structure- Activity Analysis
Therapeutic Index
Pharmacokinetics
Identify Lead Inhibitor

9. Productivity Gaps Facing Drug Discovery Programs
A major deficit in productivity exists in the pharmaceutical industry.
Cost of drug discovery is very high.
To achieve a 10% annual growth rate, major companies need to bring 3-5 major new products to market per year.
Drug approvals have doubled; R&D costs have quintupled.
75% of drug discovery costs are ultimately on products that fail.
Failure costs increase astronomically at later stages of development.
Biggest gains in productivity will be made by eliminating failure sooner rather than later.
Good decisions early on in the drug discovery process are crucial.

10. Target-Related Failures Phamacokinetic Failures
Productivity Gaps Facing Drug Discovery Programs - Why do Drugs Fail? -
Target-Related Failures
(35%)
Other Failures
(10%)
Toxicity Failures
(10%)
Phamacokinetic Failures
(10%)
Successful NCE
(25%)
Metabolism Failures
(10%)

11. What are the new challenges for drug discovery as a result of the genomics revolution?
With genome closure pending, the industry is faced with a highly competitive target-rich environment.
The key next steps in creating therapeutic value from the “Genomics Revolution” are to determine:
The functions of the 35,000 human genes.
The role of these genes in human disease.
Which genes are the best targets for drug discovery.
Determining which genes are the best for drug discovery (“Target Validation”) is perceived as a major rate-limiting step for drug discovery.
Improved efficiency
Increased productivity/reduced failure
Intellectual property

12. Drug Discovery in the Genomic Age - Changing Bottlenecks -
Target Discovery ?
Target Validation & Selection
High-Throughput Screening/ Combinatorial Chemistry
Genome Project Completions
Small Molecule
Drug Discovery
Time
Early Old Millenium
Late Old Millenium
New Millenium

13. Productivity Gaps Facing Drug Discovery Programs - Genomics to the Rescue? -
Major investments in genomics by the pharmaceutical industry have been made in an effort to improve drug discovery productivity.
Identify the best targets early on in the drug discovery process (“Target Validation”).
Identify the best patient populations for a particular drug (“Pharmacogenomics”).
Be the first to obtain the intellectual property rights on a particular target (“Methods of Use Patents”).
These investments have resulted in major advancements in new technologies for the purpose of validating/invalidating potential drug targets on a very large scale.

14. Target Validation Approaches
Drug
Identification
Clinical
Development
Gene
Protein
Correlative Approaches
Causative Approaches
Comparative Genomics
Transcriptional Profiling
Proteomics
Overexpression Systems
Gene Knockouts
Small Molecules
Antibody Approaches
Antisense
Interference RNA

15. Comparative Genomics
Analysis of DNA sequence patterns between different organisms to help define protein function.
Orthologs
Provides “1st-Pass” information on the function of a putative protein based on the existence of conserved protein sequence motifs.
Advancements in computer software technologies (Bioinformatics) has made comparative analysis of genomes an extremely powerful approach for functional genomics.

16. DNA Microarrays
Numerous approaches have been developed over the years to measure the expression at the mRNA level of numerous genes simultaneously.
“Brute force” Northern Blot
RNase Protection
Differential display
Quantitative PCR
DNA micorarrays (also referred to as DNA chips, Gene Arrays) are a new technology that allows for the determination of mRNA abundance for a large number of genes simultaneously at high resolution.
Employ basic Watson-Crick hybridization principles.
Ultimate goal is to develop the ability to scan the mRNA expression state of all the genes for a particular genome simultaneously.

17. Advances in RNA Analytics has Resulted in Marked Increases in Information Obtained Per Experiment
Northern blot
RPA
DNA Arrays ?