Natural Product Sources

Question 0

What extracts are best seen as sources of chemically diverse libraries of compounds?

Answer 0

Natural product extracts

Question 1

What percentage of currently used medicines are from microbial or plant sources?

Answer 1

Approximately 60%

Question 2

What are the sources used to screen natural products?

Answer 2

Fermentation/microbial sources
Plant/herbal sources (parts of plant e.g. Bark, root, leaves, fungi)
Marine sources (like sponges)

Question 3

What is the process of progressing form a natural product to a hit?

Answer 3

The whole natural product extract is screened for activity.
If it is found to be active. The active constituents undergo bioassay directed purification which involves fractionating an extract (using chromatography) into a range of fractions that contain different natural products in each fraction.

Subsequent bioassays of each fraction will reveal which ones contain the active compounds. This is repeated until compounds are obtained in the pure form.

Structure of active compound is then determined, usually by spectroscopic techniques like NMR.

Once pure, active compound is classified as a hit and progressed to further testing

Question 4

What are examples of compounds that have been discovered and extracted from natural sources?

Answer 4

Statins: Zocor, Xenical,

Anticancer agents: Daunomycin and taxol

Asntibtiocs: vancomycin

Question 5

What is particular about drug discovery from natural plant sources?

Answer 5

Often the active compounds have amazingly complex structures that no one would ever have envisaged or attempted to synthesise

Question 6

What is analogue synthesis?

Answer 6

A structure activity relationship is usually developed in this process. This is a model which allows us to predict what features of the active compound are helpful for bioactivity and which features are not.

Question 7

Why are analogues synthesised?

Answer 7

To optimise the structure and activity of the compound.

All analogues are then evaluated for bioavailability, ultimately leading to a most active analogue

Question 8

What are huge main critical factors which must be determined for an experimental drug?

Answer 8

Its absorption, distribution, metabolism and elimination

Question 9

What are one of the most common factors which causes most lead compounds to fail in clinical trials?

Answer 9

Its lack of efficacy, side effects or toxicity

Question 10

How are the problems of leS compound failure due to lack of efficacy, side effects or toxicity overcome?

Answer 10

Many companies are now undertaking ADME studies earlier in the drug development process

Also utilising computational methods more to try and predict mde properties (known as chemoinformatics)

Question 11

What is absorption and bioavailability?

Answer 11

How well the drug is absorbed into bloodstream when given orally or intravaneously.

Is it unchanged by metabolism

Question 12

What physical parameter can be determined and used to predict absorption and bioavailability?

Answer 12

Log P. This can be correlated to how well a drug may be absorbed

Question 13

What is distribution and elimination?

Answer 13

Drugs are distributed about various fluid compartments of the body and are eventually eliminated as the drug or it’s metabolised products.

Tissue distribution studies in animals can determine if the drug reaches the target organ and whether or not it accumulates at various sites

Question 14

What sort of markers are used in tissue distribution studies?

Answer 14

Radiolabelled 3H or 14C.

This labelled drug is also used to determine the routes and time course of elimination

Question 15

What is metabolism?

Answer 15

This typically leads to inactivation of a drug where body uses enzymes to derivatise the molecule to make it more amenable to excretion.
The main processes include oxidation, reduction or hydrolysis followed by coupling to carbohydrates,

Question 16

What is metabolite identification important for?

Answer 16

FDA registration

Question 17

Where does metabolism predominantly take place in the body?

Answer 17

The liver, so liver homogenates can be used to assess the metabolic fate of isotopically labelled drugs

Question 18

Why is a patent needed?

Answer 18

Patient in provides the basis for exclusivity of the manufacture, use and sale of pharmaceuticals, and thus allows the return on the development costs of drug development

Question 19

What are the three main types of patents?

Answer 19

Composition of matter
Use
Process

Question 20

What is a composition of matter patent?

Answer 20

The most valuable type. This includes a description and claim to some chemical entity or structurally related series.

Patent discloses physical properties, method of preparation and some designated utility.

The basic requirements of this patent is that the subject must be novel and un obvious i.e. Not easily produced from someone else’s material

Question 21

What is a use patent?

Answer 21

These can be filed on known compounds with the claim being that there is a previously unreported and un obvious pharmacological activity.

Companies can claim new uses for their own drugs or they can claim a new use for competitor’s drugs

Question 22

What is a process patent?

Answer 22

These describe a novel or improved method of synthesising a previously described compound
I.e. A different or better way of a asking something e.g. Omeprazole

Question 23

How long does a patent last?

Answer 23

20 years from the date of issue.

Question 24

What happens after the patent has expired?

Answer 24

The patented drug comes out of patent protection and it typically leads to the production of the rug as generics- produced by some other company e.g. Zovirax (aciclovir), Zantac (ranitidine), Prozac (fluoxetine)

The loss of market can be very dramatic

Question 25

What kind of a financial threat do generic drugs pose on branded drugs?

Answer 25

Once the patent has expired, generic drugs quickly overtake the sales of branded drugs.

Sales data suggest it takes only 6 months before generic drugs pick up 80% of the share of sales.

Question 26

What are the ways of defending a brand drug name?

Answer 26

Re formulate
Rebrand
New indications

Question 27

What is reformulation?

Answer 27

Allows a company to develop better products, build a franchise, limit the impact of generics e.g. Prozac Weekly was approved by the FDA Two years after the original patent ended, for the same continual treatment phase of major depressive disorder.

PW contains 90mg of fluoxetine with an enteric coating which delays the release into the bloodstream. This formulation takes advantage of the protective effects provided by fluoxetines naturally long half life, requiring PW only to be administered once a week.

The new formulation was patented as an improved method of delivery which is safer and improved patient compliance. This stops other companies selling selling PW until 2017

Question 28

What is rebranding?

Answer 28

Where pharmaceutical companies give a new brand name to a molecule and introduces it into a new market.

E.g. July 2000: the FDA approved Eli Lilly’s sarafem for the treatment of premenstural dysphoric disorder. It contains the same active ingredient found in Prozac.
The additional patent protection also helps with educational efforts for the largely under recognised disorder. Is also reduces confusion about the differences between depression and PMDD

Sarafem became the first prescription medicine indicted for the treatment of PMDD in the US

Question 29

What are new indications?

Answer 29

Where companies sell the product too treat a wider range of diseases, so the overall volume is not as heavily affected.

E.g. New indications for antidepressants like Prozac include treating for OCD, panic disorders and other anxiety/stress conditions.

These new indications are often heavily pushed by sales reps of the pharmaceutical companies, ensuring doctors remember their products and reminding doctors of all the conditions that their drugs can be used to treat.

Question 30

When is the best time to file a patent?

Answer 30

Companies will want to patent its new drug as late in the development as possible to allow more time for it to live when the drug is on the market so that the company can gain its return of the development costs.

However, they risk another company patenting the drug.

Question 31

What does a provisional patent mean?

Answer 31

The applicants have one year to file a full patent.
These are useful as the date of the filing (priority date) will help define who patented first, but the year of the provisional patent does not count against the term of the issued patent.

Question 33

What happens during the lead optimisation phase?

Answer 33

The companies chemical process development group undertakes the synthesis of bulk quantities of the raw drug substance .

The drug is then formulated providing suitable dosage forms for clinical purposes

Toxicity studies are also initiated in several animal species, investigating the metabolic disposition and pharmacokinetic properties of the drug.

Question 34

What happens if findings in the lead optimisation phase are untoward?

Answer 34

Further development of the drug may stop.

Question 35

What happens if the drug survives all the studies in the lead optimisation phase?

Answer 35

Company will file an investigational new drug application with the US FDA. This is a formal request to begin the clinical trials of the drug

Question 36

Why are clinical trials undertaken?

Answer 36

To finally evaluate the ability of the compound to provide benefit to humans

Question 37

How many phases of clinical trials are there?

Answer 37

Four phases:

1) clinical pharmacology and toxicity
2) initial clinical investigation for treatment effect
3) full scale evaluation of treatment
4) post marketing surveillance

Question 38

What is clinical pharmacology and toxicity?

Answer 38

This is the first phase of clinical trials.
The studies conducted in this phase are concerned with the safety of the compound.
Studies are performed on ~20-100 health volunteers

Question 39

What are the three small studies undertaken in the clinical pharmacology and toxicity phase (phase1) of the clinical trials

Answer 39

1) single dose (often low dose) on health males
2) rising dose studies to determine an acceptable single dose via route of interest, on health males/females. This helps to establish the therapeutic range
3) food interaction studies in both health male/females

Question 40

What other studies are undertaken simultaneously in the clinical pharmacology and toxicity phase (phase 1) of the clinical trials?

Answer 40

Drug metabolism and bioavailability studies

Question 41

When would drugs be given to unhealthy volunteers in the clinical pharmacology and toxicity phase (phase 1) of the clinical trials?

Answer 41

When drugs that will most likely have toxic effects e.g. New anticancer drugs.
Any serious adverse effect will usually result in trials being aborted

Question 42

What is the probability of the drug making it into the market once it has surpassed the clinical pharmacology and toxicity phase (phase 1) of the clinical trials?

Answer 42

15%.

The cost of trials to this point is ~$5.4M NZD

Question 43

What does the initial clinical investigation for treatment effect phase (phase 2) of the clinical trials test for?

Answer 43

Safety of the new compound and beings to monitor efficacy in the selected patient population.

Typically divided into 2 stages

Question 44

What are the 2 stages of the initial clinical investigation for treatment effect phase (phase2) of the clinical trials?

Answer 44

1) proof of concept trial- where a limited trial is conducted in selected patients to ascertain the drug has some degree of efficacy
2) more broad range trial - which involves a larger number of patients often trial lying two different dose strengths. Required to refine the optimal dosage and determine the best way to administer the drug

Question 45

How are trials in the initial clinical investigation for treatment effect phase (phase2) conducted ?

Answer 45

Typically on a double blind bias.

Many Regulatory agencies also require a positive control group where patients are given a known drug

Question 46

Why is a positive control group required in the initial clinical investigation for treatment effect phase (phase2) of the clinical trial?

Answer 46

to validate both the trial and to demonstrate the new drug has comparable or superior efficacy and an equivalent or superior safety profile

Question 47

When is a placebo not given in the initial clinical investigation for treatment effect phase (phase2) of the clinical trial?

Answer 47

In the case of life threatening diseases such as cancer,

The new drug is compared to a known medication

Question 48

How long do phase II trials take?

Answer 48

2 years, often involving 200-500 patients

Question 49

How likely is the drug to succeed in the market if it has surpassed phase II clinical trials?

Answer 49

nearly 50%.

Phase II requires $80M NZD

Question 50

What is the full scale evaluation of treatment phase (phase3) of the clinical trials?

Answer 50

This consists of two global trials at 2 dose strengths with ~2000 people per trial

The dosages used are important as these are the doses to be used if the drug is marketed,
Testing is always conducted as double blind vs. Placebo/currently use drug

Different racial groups will often be included to investigate a possible difference between ethnicities

Question 51

How long to phase III clinical trials last?

Answer 51

Usually 2 years, but can take as long as 8 years if a patient numbers are low.
The trial will run as long as needed to obtain sufficient info for the application to be made to the US FDA for a new drug application

The FDA then takes 18 months to decide

Question 52

What percentage of the drug gets into the market once it has surpassed phase III clinical trials?

Answer 52

More than 90%. This has costed $1.1Billion NZD

Question 53

What is phase IV of the clinical trials?

Answer 53

Post marketing surveillance

Occurs after drug approval
Involves monitoring of adverse effects and additional long term, large scale studies of drug efficacy. These studies can also help identify additional new uses for the drug

Question 54

What is a clinical example of post marketing surveillance?

Answer 54

Merck has recently reduced its top selling arthritis and acute pain medication, Vioxx.
A study conducted in huge use if Vioxx in treating colorectal polyps discovered patients had an increased probability of CVD events beginning after 18 months of treatment compared to those taking placebo.

Merck has another drug, Arcoxia which treats arthritis and pain they are hoping to transfer patients onto without any overall loss of income.
Vioxx has already easily made back the money spent on its research and development, so they can afford to let it go, still having made an overall profit

Question 55

If we knew the molecular structure of the desired target, what would drug discovery then require?

Answer 55

Experimental structure determination,
3D protein structures as templates for model building,
Comparative modelling, 
Sequence of novel therapeutic targets
Virtual libraries
3D models of therapeutic targets
High throughput docking (in silico screening of compounds on 3D targets) 
Structure based library design
Hits,
Structure based analogue design
Less

Question 56

What is virtually screening?

Answer 56

The process of using computational methods to design molecules which fit into the binding pockets on the protein

This involves high level docking calculations that require powerful computers.

Question 57

What happens after virtual screening?

Answer 57

Chemists then synthesise the molecules and perform bioassays,
The programmes will usually design molecules than bind extremely efficiently

Question 58

What is a limitation of virtual screening?

Answer 58

The computer doesn’t always design molecules that are easy to make.

It also takes a lot of time to generate these structures for assay. They may be too complicated

Question 59

What is an example of structure based design?

Answer 59

Relenza (anti influenza medication)
Inhibits salidase on the virus which mediates the hydrolysis of a polysaccharide. This is an important step in the release of new virus particles from an infected cell.

To design new inhibitors of the enzyme, they crystallised the enzyme with a compound related to the normal sialic acid substrate.
Resultant X-ray crystallography 3d structure allowed visualisation of the active site of enzyme.
By modelling this active site, they could design molecules that would fit into it very tightly due to close interactions of opposite charged functional groups and close alignment of hydrophobic groups.
After modelling, target compounds were prepared and screened against the enzyme, leading to the discovery of Relenza.

Question 60

What is the result of tighter interactions with the active site of the enzyme in the case of Relenza ?

Answer 60

Lowers the substrate turn over capacity of the enzyme,

The result of enzyme inhibition is the inability of the virus to replicate and move about the body

Question 61

What is a limitation of Relenza?

Answer 61

They found their drug had no oral bioavailability and was only active when taken directly into lungs using an inhaler device.
This limited their sales and opened up the market to its competitors. Tamiflu (sold by Roche) was then developed using “me-too” philosophy as an oral alternative to Relenza.

Question 62

How was Tamiflu a better drug than Relenza?

Answer 62

Tamiflu took the design of Relenza and adapted it to fit lipski’s rulers with the sole aim of making a good oral drug.

Tamiflu currently outsells Relenza on a 100:1 ratio

Question 71

Why did the pharmaceutical company AstraZeneca encourage all doctors to convert patients taking their anti ulcer treatment Losec to the newer drug Nexium?

Answer 71

Losec = omeprazole, sold as a racemic mixture. Only one isomer is active. The other isomer is inactive and completely safe

Nexium = esomperazole. Name is derived from s isomer of the racemic drug.

40mg of Losec has the same effect as 20mg of Nexium and to date, no clinical trial has shown any valid reason for taking Nexium over Losec.
AstraZeneca’s composition of matter patent had elapsed on Losec so by converting patients to Nexium, the company still has the financial advantage over their competition.