Drug Discovery and Development

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Drug Discovery and Development

• How are drugs discovered and developed?

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• Choose a disease
• Choose a drug target
• Identify a bioassay
• bioassay A test used to determine
  biological activity.

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• Find a lead compound
• lead compound structure that has some
  activity against the chosen target, but not yet
  good enough to be the drug itself.
• If not known, determine the structure of the
  lead compound

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• Synthesize analogs of the lead
• Identify Structure-Activity-Relationships (SARs)
• Synthesize analogs of the lead
• Identify Structure-Activity-Relationships (SARs)

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• Identify the pharmacophore
• pharmacophore the structural features directly
  responsible for activity
• Optimize structure to improve interactions with
  target

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• Determine toxicity and efficacy in animal models.

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• Determine pharmacodynamics and pharmacokinetics
  of the drug.
• Pharmacodynamics explores what a drug does to the
  body, whereas pharmacokinetics explores what the
  body does to the drug.

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• Patent the drug
• Continue to study drug metabolism
• Continue to test for toxicity

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• Design a manufacturing process
• Carry out clinical trials
• Market the drug

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Choosing a Disease

• Pharmaceutical companies are commercial
  enterprises
• Pharmaceutical companies will, therefore, tend to
  avoid products with a small market (i.e. a
  disease which only affects a small subset of the
  population)

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Choosing a Disease

• Pharmaceutical companies will also avoid products
  that would be consumed by individuals of lower
  economic status (i.e. a disease which only
  affects third world countries)

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Choosing a Disease (cont.)

• Most research is carried out on diseases which
  afflict first world countries (e.g. cancer,
  cardiovascular diseases, depression, diabetes,
  flu, migraine, obesity).

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The Orphan Drug Act

• The Orphan Drug Act of 1983 was passed to
  encourage pharmaceutical companies to develop
  drugs to treat diseases which affect fewer than
  200,000 people in the US

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• Under this law, companies who develop such a drug
  are entitled to market it without competition for
  seven years.
• This is considered a significant benefit, since
  the standards for patent protection are much more
  stringent.

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Identifying a Drug Target

• Drug Target specific macromolecule, or
  biological system, which the drug will interact
  with
• Sometimes this can happen through incidental
  observation

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Identifying a Drug Target (cont.)

• Example In addition to their being able to
  inhibit the uptake of noradrenaline, the older
  tricyclic antidepressants were observed to
  incidentally inhibit serotonin uptake. Thus,
  it was decided to prepare molecules which could
  specifically inhibit serotonin uptake. It wasnt
  clear that this would work, but it eventually
  resulted in the production of fluoxetine
  (Prozac).

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The mapping of the human genome should help!

• In the past, many medicines (and lead compounds)
  were isolated from plant sources.
• Since plants did not evolve with human beings in
  mind, the fact that they posses chemicals which
  results in effects on humans is incidental.

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• Having the genetic code for the production of an
  enzyme or a receptor may enable us to
  over-express that protein and determine its
  structure and biological function. If it is
  deemed important to the disease process,
  inhibitors (of enzymes), or antagonists or
  agonists of the receptors can be prepared through
  a process called rational drug design.

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Simultaneously, Chemistry is Improving!

• This is necessary, since, ultimately, plants and
  natural sources are not likely to provide the
  cures to all diseases.
• In a process called combinatorial chemistry
  large numbers of compounds can be prepared at one
  time.
• The efficiency of synthetic chemical
  transformations is improving.

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Selectivity is Important!

• e.g. targeting a bacterial enzyme, which is not
  present in mammals, or which has significant
  structural differences from the corresponding
  enzyme in mammals

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The Standards are Being Raised

• More is known about the biological chemistry of
  living systems
• For example Targeting one subtype of receptor
  may enable the pharmaceutical chemist to avoid
  potentially troublesome side effects.

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Problems can arise

• Example The chosen target, may over time, lose
  its sensitivity to the drug
• Example The penicillin-binding-protein (PBP)
  known to the the primary target of penicillin in
  the bacterial species Staphylococcus aureus has
  evolved a mutant form that no longer recognizes
  penicillin.

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Choosing the Bioassay

• Definitions
• In vitro In an artificial environment, as in a
  test tube or culture media
• In vivo In the living body, referring to tests
  conductedin living animals
• Ex vivo Usually refers to doing the test on a
  tissue taken from a living organism.

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Choosing the Bioassay (cont.)

• In vitro testing
• Has advantages in terms of speed and requires
  relatively small amounts of compound
• Speed may be increased to the point where it is
  possible to analyze several hundred compounds in
  a single day (high throughput screening)
• Results may not translate to living animals

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Choosing the Bioassay (cont.)

• In vivo tests
• More expensive
• May cause suffering to animals
• Results may be clouded by interference with other
  biological systems

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Finding the Lead

• Screening Natural Products
• Plants, microbes, the marine world, and animals,
  all provide a rich source of structurally complex
  natural products.

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• It is necessary to have a quick assay for the
  desired biological activity and to be able to
  separate the bioactive compound from the other
  inactive substances
• Lastly, a structural determination will need to
  be made

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Finding the Lead (cont.)

• Screening synthetic banks
• Pharmaceutical companies have prepared thousands
  of compounds
• These are stored (in the freezer!), cataloged and
  screened on new targets as these new targets are
  identified

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Finding the Lead (cont.)

• Using Someone Elses Lead
• Design structure which is similar to existing
  lead, but different enough to avoid patent
  restrictions.
• Sometimes this can lead to dramatic improvements
  in biological activity and pharmacokinetic
  profile. (e.g. modern penicillins are much
  better drugs than original discovery).

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Finding the Lead (cont.)

• Enhance a side effect

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• Use structural similarity to a natural ligand

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• Computer-Assisted Drug Design
• If one knows the precise molecular structure of
  the target (enzyme or receptor), then one can use
  a computer to design a perfectly-fitting ligand.
• Drawbacks Most commercially available programs
  do not allow conformational movement in the
  target (as the ligand is being designed and/or
  docked into the active site). Thus, most
  programs are somewhat inaccurate representations
  of reality.

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• Serendipity a chance occurrence
• Must be accompanied by an experimentalist who
  understands the big picture (and is not solely
  focused on his/her immediate research goal), who
  has an open mind toward unexpected results, and
  who has the ability to use deductive logic in the
  explanation of such results.
• Example Penicillin discovery
• Example development of Viagra to treat erectile
  dysfunction

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Finding a Lead (cont.)

• Sildenafil (compound UK-92,480) was synthesized
  by a group of pharmaceutical chemists working at
  Pfizer's Sandwich, Kent research facility in
  England.
• It was initially studied for use in hypertension
  (high blood pressure) and angina pectoris (a form
  of ischaemic cardiovascular disease).
• Phase I clinical trials under the direction of
  Ian Osterloh suggested that the drug had little
  effect on angina, but that it could induce marked
  penile erections.

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• Pfizer therefore decided to market it for
  erectile dysfunction, rather than for angina.
• The drug was patented in 1996, approved for use
  in erectile dysfunction by the Food and Drug
  Administration on March 27, 1998, becoming the
  first pill approved to treat erectile dysfunction
  in the United States, and offered for sale in the
  United States later that year.
• It soon became a great success annual sales of
  Viagra in the period 19992001 exceeded 1
  billion.

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Finding a Lead (cont.)
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Structure-Activity-Relationships (SARs)

• Once a lead has been discovered, it is important
  to understand precisely which structural features
  are responsible for its biological activity (i.e.
  to identify the pharmacophore)

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The pharmacophore is the precise section of the
molecule that is responsible for biological
activity
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• This may enable one to prepare a more active
  molecule
• This may allow the elimination of excessive
  functionality, thus reducing the toxicity and
  cost of production of the active material
• This can be done through synthetic modifications
• Example R-OH can be converted to R-OCH3 to see
  if O-H is involved in an important interaction
• Example R-NH2 can be converted to R-NH-COR to
  see if interaction with positive charge on
  protonated amine is an important interaction

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Link
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Next step Improve Pharmacokinetic Properties

• Improve pharmacokinetic properties.pharmacokineti
  c The study of absorption, distribution,
  metabolism and excretion of a drug (ADME).
• Video
• exerciseMedicationDistributiontitleMedication2
  0Absorption,20Distribution,20Metabolism20and20
  Excretion20Animationpublication_ID2450

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Metabolism of Drugs

• The body regards drugs as foreign substances, not
  produced naturally.
• Sometimes such substances are referred to as
  xenobiotics

• Body has goal of removing such xenobiotics from
  system by excretion in the urine
• The kidney is set up to allow polar substances to
  escape in the urine, so the body tries to
  chemically transform the drugs into more polar
  structures.

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Metabolism of Drugs (cont.)

• Phase 1 Metabolism involves the conversion of
  nonpolar bonds (eg C-H bonds) to more polar bonds
  (eg C-OH bonds).
• A key enzyme is the cytochrome P450 system, which
  catalyzes this reaction

RH O2 2H 2e ? ROH H2O
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Mechanism of Cytochrome P450
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Phase I metabolism may either detoxify or toxify.

• Phase I reactions produce a more polar molecule
  that is easier to eliminate.
• Phase I reactions can sometimes result in a
  substance more toxic than the originally ingested
  substance.
• An example is the Phase I metabolism of
  acetonitrile

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The Liver

• Oral administration frequently brings the drugs
  (via the portal system) to the liver

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Metabolism of Drugs (cont.)

• Phase II metabolism links the drug to still more
  polar molecules to render them even more easy to
  excrete

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Metabolism of Drugs (cont.)

• Another Phase II reaction is sulfation (shown
  below)

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Phase II Metabolism

• Phase II reactions most commonly detoxify
• Phase II reactions usually occur at polar sites,
  like COOH, OH, etc.

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Manufacture of Drugs

• Pharmaceutical companies must make a profit to
  continue to exist
• Therefore, drugs must be sold at a profit
• One must have readily available, inexpensive
  starting materials
• One must have an efficient synthetic route to the
  compound
• As few steps as possible
• Inexpensive reagents

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• The route must be suitable to the scale up
  needed for the production of at least tens of
  kilograms of final product
• This may limit the structural complexity and/or
  ultimate size (i.e. mw) of the final product
• In some cases, it may be useful to design
  microbial processes which produce highly
  functional, advanced intermediates. This type of
  process usually is more efficient than trying to
  prepare the same intermediate using synthetic
  methodology.

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Toxicity

• Toxicity standards are continually becoming
  tougher
• Must use in vivo (i.e. animal) testing to screen
  for toxicity
• Each animal is slightly different, with different
  metabolic systems, etc.
• Thus a drug may be toxic to one species and not
  to another

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Example Thalidomide

• Thalidomide was developed by German
  pharmaceutical company Grünenthal. It was sold
  from 1957 to 1961 in almost 50 countries under at
  least 40 names. Thalidomide was chiefly sold and
  prescribed during the late 1950s and early 1960s
  to pregnant women, as an antiemetic to combat
  morning sickness and as an aid to help them
  sleep. Before its release, inadequate tests were
  performed to assess the drug's safety, with
  catastrophic results for the children of women
  who had taken thalidomide during their
  pregnancies.

Antiemetic a medication that helps prevent and
control nausea and vomiting
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Birth defects caused by use of thalidomide
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Example Thalidomide

• From 1956 to 1962, approximately 10,000 children
  were born with severe malformities, including
  phocomelia, because their mothers had taken
  thalidomide during pregnancy. In 1962, in
  reaction to the tragedy, the United States
  Congress enacted laws requiring tests for safety
  during pregnancy before a drug can receive
  approval for sale in the U.S.

Phocomelia presents at birth very short or absent
long bones and flipper-like appearance of hands
and sometimes feet.
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Example Thalidomide

• Researchers, however, continued to work with the
  drug. Soon after its banishment, an Israeli
  doctor discovered anti-inflammatory effects of
  thalidomide and began to look for uses of the
  medication despite its teratogenic effects.
• He found that patients with erythema nodosum
  leprosum, a painful skin condition associated
  with leprosy, experienced relief of their pain by
  taking thalidomide.
• Teratogenic Causing malformations in a fetus

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Thalidomide

• Further work conducted in 1991 by Dr. Gilla
  Kaplan at Rockefeller University in New York City
  showed that thalidomide worked in leprosy by
  inhibiting tumor necrosis factor alpha. Kaplan
  partnered with Celgene Corporation to further
  develop the potential for thalidomide.
• Subsequent research has shown that it is
  effective in multiple myeloma, and it is now
  approved by the FDA for use in this malignancy.
  There are studies underway to determine the
  drug's effects on arachnoiditis, Crohn's disease,
  and several types of cancers.

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Clinical Trials

• Phase I Drug is tested on healthy volunteers to
  determine toxicity relative to dose and to screen
  for unexpected side effects

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Clinical Trials

• Phase II Drug is tested on small group of
  patients to see if drug has any beneficial effect
  and to determine the dose level needed for this
  effect.

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Clinical Trials

• Phase III Drug is tested on much larger group of
  patients and compared with existing treatments
  and with a placebo

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Clinical Trials

• Phase IV Drug is placed on the market and
  patients are monitored for side effects

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Assigned Reading

• Haffner Marlene E Whitley Janet Moses Marie
  Two decades of orphan product development.
  Nature reviews. Drug discovery (2002), 1(10),
  821-5. Link
• Franks Michael E Macpherson Gordon R Figg
  William D Thalidomide. Lancet (2004),
  363(9423), 1802-11. Link
• Abou-Gharbia, Magid. Discovery of innovative
  small molecule therapeutics. Journal of
  Medicinal Chemistry (2009), 52(1), 2-9. Link
• Paul, S. M. et al. How to improve RD
  productivity the pharmaceutical industrys grand
  challenge. Nature Reviews Drug Discovery (2010),
  9 203-214.
• Jorgensen, W. L. The many roles of computation in
  drug discovery. Science (2004) 303 1813-1818.
• Butcher, E. C. et al. Systems biology in drug
  discovery. Nature biotechnology (2004) 22(10)
  1253-1259.

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Optional Additional Reading

• Bartlett J Blake Dredge Keith Dalgleish Angus G
  The evolution of thalidomide and its IMiD
  derivatives as anticancer agents. Nature
  reviews. Cancer (2004), 4(4), 314-22. Link
• Cragg, G. M. Newman, D. J. Nature a vital
  source of leads for anticancer drug development.
  Phytochemistry Reviews (2009), 8(2),
  313-331. Link
• Betz, U. A. K. et al. Genomics success or
  failure to deliver drug targets? Current Opinion
  in Chemical Biology (2005), 9 387-391
• Sams-Dodd, F. Target-based drug discovery is
  something wrong? Drug Discovery Today (2005) 10
  139-147.

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Homework Questions

• What is an orphan drug. Why has the Orphan
  Drug Act been successful?
• Thalidomide is actually a mixture of two
  compounds. Draw their structures and list the
  physiological effects of each.
• What does ADMET stand for?
• List several possible reasons for poor efficacy
  of drug candidates in in vivo models.
• Explain how structure-based design was used to
  develop an inhibitor with improved selectivity
  for TACE over MMP-1 and MMP-9.
• How can the pharmaceutical industry increase the
  probability of technical success (p(TS))? What
  are the major causes of Phase II and III
  attrition?