drug design lecture 1

8/6/2019 Drug Design Lecture 1

1/35

Modern Methods of Drug Discovery

Lecture 1: An Introduction


2/35

The Top 10 Pharmaceutical Companies

19.4Bristol-Myers Squibb

19.7Abbott Labs

20.4Aventis-Sanofi

21.4AstraZeneca

22.9Merck

24.5Hoffman LaRoche

28.2Novartis

39.0GlaxoSmithKline

45.2Pfizer

47.4Johnson & Johnson

2004 sales figures(billions)

15.3Bristol-Myers Squibb

16.6Hoffman LaRoche

20.3Novartis

24.0AstraZeneca

34.0Aventis-Sanofi


19.7Abbott Labs

21.9Merck

34.0GlaxoSmithKline

44.2Pfizer


14.8Eli Lilly

26.6Hoffman LaRoche

28.9Novartis

25.7AstraZeneca

35.6Aventis-Sanofi


15.7Wyeth

22.6Merck

37.0GlaxoSmithKline

45.1Pfizer



3/35

Research based pharmaceutical companies, on average, spend

about 20% of their sales on research and development (R&D).

This percentage is significantly higher than in most other

industries, including electronics, aerospace, automobiles, and

computers.

Since 1980 US pharmaceutical companies have practically doubled

spending on R&D every 5 yrs.


4/35

Despite these enormous expenditures, there has been a steady

decline in the number of drugs introduced each year into human

therapy.

70-100 in the 60s

60-70 in the 70s~50 in the 80s

~40 in the 90s

Innovation Deficit - coined in 1996 by Jurgen Drews, president

of research at Hoffmann-LaRoche.

- the gap between the number of new chemicalentities (NCEs) required to be launched in

order to accomplish an annual 10% revenue

increase and the actual number of NCEsintroduced in the market by the top 10

pharmaceutical companies.


5/35

Reasons for the innovation deficit:

a) increased demand on safety for drugs.

- the average number of clinical trials per new drug application

(NDA) increased from 30 in the 70s to 40 in the 80s, to 70 in the

90s.- the increased demand on safety is also reflected in a prolonged

duration of the drug development process.

In the 60s, total development time was 8.1 yrs



In the 90s, total development time was 14.9 yrsCurrently, total development time is ~16 yrs

b) low hanging fruit have been picked.


6/35

A new drug today costs ~$880 million and takes ~15-16 yrs to

develop.

Allocation of R&D funds

Allocation of R&D time


7/35

About 75% of this cost ($660 million) is attributable to failure

during development.

90% of all drug development candidates fail to make it to market.

Methods that enhance the drug discovery process and reduce

failure rates are highly desirable!


8/35

This course (Modern Methods of Drug Discovery) will focus on

some of the key methods used in the first 4 steps.

The Drug Discovery Process

Target

Validation

Drug

Target

Identification

Lead

Compound

Identification

Lead

Optimization

Preclinical and

Clinical

Development


9/35

1) Drug Target Identification

The identification of new, clinically relevant, molecular targets

is of utmost importance to the discovery of innovative drugs.

It has been estimated that up to 10 genes contribute to

multifactoral diseases.

Science 287:1960-1964 (2000)

Typically these disease genes are linked to another 5 to 10

gene products in physiological circuits which are also suitable

for pharmaceutical intervention.

If these numbers are multiplied with the number of diseases

that pose a major medical problem in the industrial world,

then there are ~5000 to 10000 potential drug targets.


10/35

Current therapy is based upon less than 500 molecular targets

45% of which are G-protein coupled receptors

28% are enzymes11% are hormones and factors

5% ion channels

2% nuclear receptors

Therefore, many more drug targets exist! How to identify them?

Besides classical methods of cellular and molecular biology, newtechniques of target identification are becoming increasingly

important. These include:

a) genomics (Biotechniques 31: 626-630 2001)

b) bioinformatics (Drug Discovery Today 7:315-323 2002)

c) proteomics (J. Pharmacol. Toxicol. Methods 44:291-300

2000; Biopolymers 60:206-211 2001)


11/35

a) genomics

term was coined in the mid 80s.

evolved from 2 independent advances:

1) Automation resulting in a significant increase in the

number of experiments that could be constructed

in a given time. (eg. DNA sequencing)

$22.5 MillionUS $300,000 each


12/35

2) Informatics- the ability to transform raw data into meaningful

information by applying computerized techniques for managing,

analyzing, and interpreting data.

the identification of new biological targets has benefited from the

genomics approach:

eg. The sequencing of the human genome

Nature 409:860-921 2001;

Science 291:1304-1351 2001 blueprint of all proteins

bioinformatics methods are used to transform the raw

sequence into meaningful information (eg. genes and theirencoded proteins) and to compare whole genomes (disease vs.

not).

Drug Discovery Today 5:135-143 2000


13/35

Sequencing of microbial genomes will enable the identification of

novel drug targets, especially when comparing to the human genome

(eg MEP pathway).

b) Bioinformatics the in silico identification of novel drug targets

is now feasible by systematically searching for paralogs (related

proteins within an organism) of known drug targets (eg. may be

able to modify an existing drug to bind to the paralog).

Can compare the entire genome of pathogenic and non-

pathogenic strains of a microbe and identify genes/proteinsassociated with pathogenism.

Current Opin. Microbiol 1:572-579 1998


14/35

Using gene expression microarrays and gene chip technologies,

a single device can be used to evaluate and compare the expression

of up to 20000 genes of healthy and diseased individuals at once.Trends Biotechnol 19:412-415 2001

c) Proteomics concerning expression analysis, it has been shown

that the correlation between RNA and protein expression is weak

and ranges in yeast from 10-40% for lower abundance proteins to

up to 94% for higher abundance proteins.

Molecular Cell Biol 19:1720-1730 1999

It is becoming increasingly evident that the complexity of biological

systems lies at the level of the proteins, and that genomics alone will

not suffice to understand these systems.

It is also at the protein level that disease processes become

manifest, and at which most (91%) drugs act.


15/35

Therefore, the analysis of proteins (including protein-protein,

protein-nucleic acid, and protein-ligand interactions) will beutmost importance to target discovery.

Proteomics is the systematic high-throughput separation and

characterization of proteins within biological systems.

Target identification with proteomics is performed by comparing

the protein expression levels in normal and diseased tissues.

2D PAGE is used to separate the proteins, which are subsequently

identified and fully characterized with LC-MS/MS.


16/35

Target

Validation

Drug

Target

Identification

Lead

Compound

Identification

Lead

Optimization

Preclinical and

Clinical

Development


2) Target Validation

Involves demonstrating the relevance of the target protein in a

disease process/pathogenicity and ideally requires both gain and

loss of function studies.

This is accomplished primarily with knock-out or knock-in animal

models, small molecule inhibitors/agonists/antagonists, antisense

nucleic acid constructs, ribozymes, and neutralizing antibodies.


17/35

Since strong interactions between a protein and its ligand are

characterized by a high degree of complementarity, knowledge ofthe protein three dimensional structure will enable the prediction of

druggability of the protein.


18/35

Target

Validation

Drug

Target

Identification

Lead

Compound

Identification

Lead

Optimization

Preclinical and

Clinical

Development


3) Lead Compound Identification

Compounds are identified which interact with the target protein

and modulate its activity.

Compounds are mainly identified using random (screening) or

rational (design) approaches.


19/35

A) High-throughput Screening

Used to test large numbers of compounds for their ability to affect

the activity of target proteins.

Natural product and synthetic compound libraries with millions

of compounds are screened using a test assay.Curr Opin Chem Biol 4:445-451 2000

There are concerns with the numbers approach to screening for

a lead molecule. In theory generating the entire chemical space

for drug molecules and testing them would be an elegant approach

to drug discovery.

In practice, this isnt feasible.



20/35

Therefore, concepts are needed to synthesize and select biologically

relevant compounds.

One solution may be to accumulate as much knowledge as possible

on biological targets (eg. structure, function, interactions, ligands)

and choose targeted approaches to chemical synthesis.

Another crucial point for reliable high-throughput screening

results is the robustness and quality of the biological test assays.


21/35

B) Structure Based Drug Design

Three dimensional structures of compounds from virtual or

physically existing libraries are docked into binding sites oftarget proteins with known or predicted structure.

Scoring functions evaluate the steric and electrostatic

complementarity between compounds and the target protein.

The highest ranked compounds are then suggested for

biological testing.



22/35

Once hits (compounds that elicit a positive response in an assay)

have been identified via the screening approach, these are validated

by re-testing them and checking the purity and structure of thecompounds.

Only if the hits fulfill certain criteria are they regarded as leads.

The criteria can originate from:

1) Pharmacodynamic properties - efficacy, potency, selectivity

2) Physiochemical properties - water solubility, chemicalstability, Lipinskis rule-of-five.

3) Pharmacokinetic properties - metabolic stability and

toxological aspects.4) Chemical optimization potential - ease of chemical synthesis

and derivatization.

5) Patentability


23/35

Target

Validation

Drug

Target

Identification

Lead

Compound

Identification

Lead

Optimization

Preclinical and

Clinical

Development


4) Lead Optimization

Molecules are chemically modified and subsequently characterized

in order to obtain compounds with suitable properties to become a

drug.

Leads are characterized with respect to pharmacodynamic

properties such as efficacy and potency in vitro and in vivo,

physiochemical properties, pharmacokinetic properties, and

toxicological aspects.


24/35

Efficacy vs PotencyPotency refers to the amount of drug required for its specific effect

to occur; it is measured simply as the inverse of the EC50 for thatdrug.

Efficacy measures the maximum strength of the effect itself, at

saturating drug concentrations.

Drug Red exceeds drug Black in potency, while the opposite istrue of the efficacy.


25/35

Pharmacokinetics - determining the fate of xenobiotics.- what the body does to the drug.

Often divided into areas examining the extent and rate

of adsorption, distribution, metabolism, and excretion(ADME).

Pharmacodynamics - determining the biochemical and physiological

effects of drugs, the mechanism of drug action,

and the relationship between drug

concentration and effect.

- what the drug does to the body


26/35

This is often the tightest bottleneck in drug discovery.

This process ideally requires the simultaneous optimization ofmultiple parameters and is thus a time consuming and costly step.

Hints on how to modify a lead compound can originate from

molecular modeling, quantitative structure-activity relationships,and from structural biology (structure-based drug design).


27/35

In parallel to compound characterization with respect to potencyand selectivity, in vitro assays for the prediction of pharmacokinetic

properties should be performed.

Curr Drug Metab 2:299-314 2001

Once compounds with desirable in vitro profiles have been

identified, these are characterized using in vivo models.

Compounds that do not fulfill the requirements for a successful

drug development candidate have to be optimized through the

synthesis of better suited derivatives.


28/35

It is vital to conceive lead optimization as a simultaneous

multidimensional process rather than a sequential one. Optimizingleads first with respect to pharmacodynamic properties (potency,

selectivity, etc) and looking at pharmacokinetic parameters of these

optimized compounds later guarantees frustration in the lateoptimization phase.


29/35

Target

Validation

Drug

Target

Identification

Lead

Compound

Identification

Lead

Optimization

Preclinical and

Clinical

Development


Preclinical studies involve in vitro studies and trials on animal

populations.

Wide ranging dosages of the compounds are introduced to the

cell line or animal in order to obtain preliminary efficacy and

pharmacokinetic information.


30/35

The NIH organizes clinical trials into 5 different types:

1) Treatment trials: test experimental treatments or a new

combination of drugs.

2) Prevention trials: look for ways to prevent a disease or prevent

it from returning.

3) Diagnostic trials: find better tests or procedures for diagnosinga disease.

4) Screening trials: test methods of detecting diseases.

5) Quality of Life trials: explore ways to improve comfort and

quality of life for individuals with a chronic illness.

Cli i l T i l


31/35

Clinical Trials

Phase 0 - a recent designation for exploratory, first-in-human trials.

Designed to expedite the development of promising

therapeutic agents by establishing early on whether the agent

behaves in human subjects as was anticipated from

preclinical studies.

Pharmaceutical clinical trials are commonly classified into 4 phases:

(as of 2006, there are now 5)

Phase I - a small group of healthy volunteers (20-80) are selected

to assess the safety, tolerability, pharmacokinetics, and

pharmacodynamics of a therapy.

- normally include dose ranging studies so that doses forclinical use can be set/adjusted.

New Scientist, March 2006,

Catastrophic immune response may have caused

drug trial horror


32/35

Phase I - there are 3 common kinds of phase I trials:

1) Single Ascending Dose (SAD) studies- a small group

of patients are given a single dose of the drug and thenare monitored over a period of time. If they do not exhibit

any adverse side effects, the dose is escalated and a new

group of patients is given the higher dose.

2) Multiple Ascending Dose (MAD) studies- a group of

patients receives multiple low doses of the drug, while

blood (and other fluids) are collected at various time

points and analyzed to understand how the drug is

processed within the body. The dose is subsequently

escalated for further groups.

3) Food effect- designed to investigate any differences in

absorption caused by eating before the dose is given.


33/35

80% of drugs fail the Phase I clinical trial.


34/35

Phase II - performed on larger groups (20-300) and are designed

to assess the activity of the therapy, and continue Phase I

safety assessments.

Phase III - randomized controlled trials on large patient groups

(hundreds to thousands) aimed at being the definitiveassessment of the efficacy of the new therapy, in comparison

with standard therapy. Side effects are also monitored.

-it is typically expected that there be at least two successfulphase III clinical trials to obtain approval from the FDA.

Once a drug has proven acceptable, the trial results are combined

into a large document which includes a comprehensive description

of manufacturing procedures, formulation details, shelf life, etc.

This document is submitted to the FDA for review.


35/35

Phase IV - post-launch safety monitoring and ongoing technical

support of a drug.

- may be mandated or initiated by the pharmaceuticalcompany.

- designed to detect rare or long term adverse effects over

a large patient population and timescale than was possibleduring clinical trials.

USA Today 10/12/2004 How did Vioxx debacle happen?

drug design lecture 1

Documents