1. Drug Discovery and Development
How are drugs discovered and developed?

2. Choose a disease
Choose a drug target
Identify a “bioassay”
bioassay = A test used to determine biological activity.

3. 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”

4. Synthesize analogs of the lead
Identify Structure-Activity-Relationships (SAR’s)

5. Identify the “pharmacophore”
pharmacophore = the structural features directly responsible for activity
Optimize structure to improve interactions with target

6. Determine toxicity and efficacy in animal models.

7. 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.

8. Patent the drug
Continue to study drug metabolism
Continue to test for toxicity

9. Design a manufacturing process
Carry out clinical trials
Market the drug

10. 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)

11. 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)

12. 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).

13. 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

14. 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.

15. Identifying a Drug Target
Drug Target = specific macromolecule, or biological system, which the drug will interact with
Sometimes this can happen through incidental observation…

16. 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 wasn’t clear that this would work, but it eventually resulted in the production of fluoxetine (Prozac).

17. 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.

18. 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.

19. 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.

20. 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

21. 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.

22. 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.

23. 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.

24. 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

25. Choosing the Bioassay (cont.)
In vivo tests
More expensive
May cause suffering to animals
Results may be clouded by interference with other biological systems

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

27. 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

28. 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

29. Finding the Lead (cont.)
Using Someone Else’s 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).

30. Finding the Lead (cont.)
Enhance a side effect

31. Use structural similarity to a natural ligand

32. 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.

33. 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

34. 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.

35. 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 1999–2001 exceeded $1 billion.

36. Finding a Lead (cont.)

38. Structure-Activity-Relationships (SAR’s)
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”)

40. The pharmacophore is the precise section of the molecule that is responsible for biological activity

41. 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

42. Link

43. Next step: Improve Pharmacokinetic Properties
Improve pharmacokinetic properties. pharmacokinetic = The study of absorption, distribution, metabolism and excretion of a drug (ADME).
Video
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44. 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.

45. 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

46. Mechanism of Cytochrome P450

47. 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

50. The Liver
Oral administration frequently brings the drugs (via the portal system) to the liver

51. Metabolism of Drugs (cont.)
Phase II metabolism links the drug to still more polar molecules to render them even more easy to excrete

52. Metabolism of Drugs (cont.)
Another Phase II reaction is sulfation (shown below)

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

54. 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

55. 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.

56. 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

57. 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

59. caused by use of thalidomide
Birth defects
caused by use of thalidomide

60. 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.

61. 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

62. 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.

63. Clinical Trials
Phase I: Drug is tested on healthy volunteers to determine toxicity relative to dose and to screen for unexpected side effects

64. 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.

65. Clinical Trials
Phase III: Drug is tested on much larger group of patients and compared with existing treatments and with a placebo

66. Clinical Trials
Phase IV: Drug is placed on the market and patients are monitored for side effects

67. Assigned Reading
Haffner Marlene E; Whitley Janet; Moses Marie Two decades of orphan product development. Nature reviews. Drug discovery (2002), 1(10), Link
Franks Michael E; Macpherson Gordon R; Figg William D Thalidomide. Lancet (2004), 363(9423), Link
Abou-Gharbia, Magid. Discovery of innovative small molecule therapeutics. Journal of Medicinal Chemistry (2009), 52(1), Link
Paul, S. M. et al. How to improve R&D productivity: the pharmaceutical industry’s grand challenge. Nature Reviews Drug Discovery (2010), 9:
Jorgensen, W. L. The many roles of computation in drug discovery. Science (2004) 303:
Butcher, E. C. et al. Systems biology in drug discovery. Nature biotechnology (2004) 22(10):

68. 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), Link
Cragg, G. M.; Newman, D. J. Nature: a vital source of leads for anticancer drug development. Phytochemistry Reviews (2009), 8(2), Link
Betz, U. A. K. et al. Genomics: success or failure to deliver drug targets? Current Opinion in Chemical Biology (2005), 9:
Sams-Dodd, F. Target-based drug discovery: is something wrong? Drug Discovery Today (2005) 10:

69. 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?