TOPICS IN (NANO) BIOTECHNOLOGY

Drug DiscoveryLecture 10

14th May, 2003

PhD Course

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)

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.

The Original Approach to Drug Discovery- Pharmacology-to-Protein -

Defined BiologicalEndpoint(e.g., bacterialgrowth)

Screening of VeryCrude Extracts forBiological Activity

Extract Fractionation/Purification to IdentifyActive Entity(“Pharmacophore”)

MolecularDeterminationof ActivePharmacophore

Chemical Structure -Activity Analysis•Therapeutic Index•Pharmacokinetics

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.

The Semi-Original Approach to Drug Discovery- Protein-to-Gene -

Enzyme/Receptorof Interest

Isolation/Characterization/Purification ofTarget Molecule

ProteinMicrosequencing

High-ThroughputScreening AssaysEstablished againstTarget Protein

Identify LeadInhibitor.Confirm Role inDisease Process.

Gene Cloning/Sequencing. TargetProtein Expressedat High Levels.

Chemical Structure-Activity Analysis•Therapeutic Index•Pharmacokinetics

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.

A New Paradigm for Drug Discovery- Gene-to-Function -

Gene ofUnknownFunction

Determination of Cellular Function

Validation as anAttractive DrugTarget

High-ThroughputScreening AssaysEstablished againstTarget Protein

Identify LeadInhibitor

Expression/ProteinPurification

Chemical Structure-Activity Analysis•Therapeutic Index•Pharmacokinetics

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.

Productivity Gaps Facing Drug Discovery Programs

- Why do Drugs Fail? -

Other Failures(10%)

Toxicity Failures(10%)

PhamacokineticFailures(10%)Metabolism

Failures(10%)

SuccessfulNCE

(25%)

Target-RelatedFailures(35%)

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

Drug Discovery in the Genomic Age- Changing Bottlenecks -

Target Discovery

Target Validation& Selection

Small MoleculeDrug Discovery

High-ThroughputScreening/CombinatorialChemistry

GenomeProjectCompletions

?

TimeEarly OldMillenium

Late OldMillenium

NewMillenium

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.

Target Validation Approaches

Gene ProteinTargetValidation

Correlative Approaches•Comparative Genomics

•Transcriptional Profiling

•Proteomics

Drug Identification

ClinicalDevelopment

Causative Approaches

•Overexpression Systems

•Gene Knockouts

•Small Molecules

•Antibody Approaches

•Antisense

•Interference RNA

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.

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.

Advances in RNA Analytics has Resulted in Marked Increases in Information Obtained Per Experiment

Northern blot RPA DNA Arrays ?