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Drug Discovery and Development. How are drugs discovered and developed?. Basic Steps. Choose a disease Choose a drug target Identify a “bioassay” bioassay = A test used to determine biological activity. Find a “lead compound”

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Drug Discovery and Development

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Drug Discovery and Development

How are drugs discovered and developed?


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Basic Steps

  • Choose a disease

  • Choose a drug target

  • Identify a “bioassay”

    bioassay = A test used to determine biological activity.

  • 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”

  • Synthesize analogs of the lead

  • Identify Structure-Activity-Relationships (SAR’s)


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Basic Steps (cont.)

  • Structure-Activity-Relationship (SAR) = How does the activity change as structure is systematically altered?

  • Identify the “pharmacophore”

    pharmacophore = the structural features directly responsible for activity

  • Vary structure to improve interactions with target

  • Improve pharmacokinetic properties.

    pharmacokinetic = The study of absorption, distribution, metabolism and excretion of a drug (ADME).


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Basic steps (cont.)

  • Patent the drug

  • Study drug metabolism

  • Test for toxicity

  • Design a manufacturing process

  • Carry out clinical trials

  • Market the drug


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Choosing a Disease

  • Pharmaceutical companies must make a profit to exist

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

  • 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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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 wasn’t 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.

  • 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.

  • 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 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).


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Finding the Lead (cont.)

Enhance a side effect


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Finding the Lead (cont.)

Use structural similarity to a natural ligand


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Finding the Lead (cont.)

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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Finding a Lead (cont.)

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. 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.

Wikipedia


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Finding a Lead (cont.)


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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”)

  • 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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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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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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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

  • 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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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. 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.

Teratogenic = Causing malformations in a fetus


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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

  • 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.

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

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


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