Theme 7: Developing a Drug from an Optimised Lead

Question 1

What are the 4 points the disclosure patent must be?

Answer 1

1. Novel
2. Inventive (i.e. not obvious to one skilled in the art)
3. It must not have been disclosed anywhere in the world prior
   to filing (except in the US)
4. It must have a utility

Question 2

How many years the patent is protected? When you start to generate profit? What happen after the patent expires?

Answer 2

There is 20 years for patent protection. After the 13 year you have profit. After the patent expires, The inventor- lost 20 years of exclusivity due to the companies s can make drug and lower prices in the market.

Question 3

How long does a patent take to be published?

Answer 3

18 months

Question 4

Which are the elements of patent ? Patent Composition

Answer 4

• Bibliography
• Summary (US only)
• Scope - a representation of the invention
• Description - prior art, full technical details and
  examples
• Claims - most important since this details the components of the invention as briefly and clearly
  as possible

Question 5

What are the aims and characteristics for the patent introduction?

Answer 5

The introduction Has to inform reader of the technical field and background art.

• Technical field crucial to direct Patent Office
  Searcher to the correct area to carry out their search.
• Background does not need to be a literature review and does not need to explain how
  the invention came about. (very different from a research paper)

Question 6

Explain the stament of invention in a patent.

Answer 6

• This re-states the main patent claim(s).
  “The invention provides compounds of
  formula (X)”
• Followed by statements setting out what is
  new and useful regarding the invention
  “The compounds have high activity at
  receptor Y and they thus have use in treatment
  of disease Z”.

Question 7

What are the different routes for drug administration ? which is the favorite route?

Answer 7

1. Oral dose
2. Intravenous dose
3. Skin/nasal dose
4. Sublingual (under the tongue) (mucosa mouth)
5. Intraperitoneal injection or IP injection is the injection of a substance into the peritoneum (body cavity)
   -Renal
   -Buccal (mucosa mouth)

Question 8

What are the differences between oral dose and intravenous dose/Nasal/Skin dose?

Answer 8

Intravenous dose/Nasal/Skin dose ge direct into the intestine and live without passing intestine and liver.

Question 9

Why high bioavailability for
oral drugs is so important?

Answer 9

• Safe
  -Cost
• Compliance (Small tablets will be prefered by patients)

Question 10

Provided the ADME route for Oral, intravenous, Nasal/ Skin dose.

Answer 10

Question 11

Indicate which is the compartment 1 and compartment 2 in the following image. Explain the differences

Answer 11

Question 12

How can we measure the plasma protein binding?

Answer 12

Plasma protein binding can be measure with equilibrium dialysis.

Drug molecule allowed to equilibrate between a protein-containing compartment from a protein-free compartment.

• Know concentration of drug in plasma then Wait equilibrium around 4-5 hours then use LCMS to calculate concentration of the drug into the two compartments.

Other way to know binding plasma protein is include Serum in the original invitro- look for differences in potency of binding with serum and without

Question 13

Transport proteins can pump drug molecules
both into and out of certain cell types, P-Glycoprotein (P-gp) can be a significant
problem for drug absorption from the GI tract. However can be taken advantage off. One example is Loperamide. Explain it.

Answer 13

Loperamide is use to treat diarrhoea, Bind also to opio receptor. This is transported out to the brain by P-gp making safe and no addictive in contrasted of morphine.

Question 14

Describe three types of patents that are used to protect drug and drug candidates.

Answer 14

1. A composition of matter patent covers novel compounds with a proven utility that is not obvious to one skilled in the art. These can cover a specific chemical entity and/or structurally related series with specified modifications.
2. A method of use patent can protect known compounds for which a new, non-obvious use has been discovered.
3. A process patent can protect a process or synthesis that is used to manufacture a drug and prevents others from using that same process or synthesis

Question 15

What are some of the properties and characteristics of a molecule that can affect its distribution in the body?

Answer 15

*Lipophilicity: highly lipophilic compounds accumulate in fatty tissue
* pKa: pH differences in tissues and organs can affect where the drug accumulates.
* Permeability: how permeable a compound is will affect where and how well it is absorbed
* Ability to bind to plasma proteins: affects diffusion across membranes and into target organs
* Ability to be recognised by transporter proteins: compounds that are recognised by transporters can reach high concentrations in specific organs and cells. Conversely, compounds recognised by
efflux pumps can be prevented from accumulating in certain cells or organs

Question 16

Explain several reasons why a drug might have excellent potency in in vitro assays but poor activity in in vivo animal models.

Answer 16

A drug might have excellent potency in in vitro assays but poor activity in in vivo animal models due to unfavourable PK properties.

Specifically, poor absorption of the compound would prevent it from being absorbed into the bloodstream or into cells. Rapid metabolism and elimination would cause the compound to be
degraded or eliminated before it could reach its biological target. Unfavourable distribution properties, due to high plasma protein binding, efflux by transporters, or other mechanisms, would

prevent the compound from reaching its target in vivo

Question 17

Which organ is the central axis for metabolism?

Answer 17

The liver provides the central axis for metabolism but other organs and tissues are
involved

Question 18

How phases are involved in drug metabolism?

Answer 18

2 phases:
- Phase I
- Phase II

Question 19

Explain the Phase I in drug metabolism. ( reactions, organs involved..)

Answer 19

Phase I usually occurs in the liver
1. Modifies or adds a functional group to the parent drug. (On a particular position)

• Three of the most common phase I reactions are:
• oxidation (hydroxylation)
• reduction
• hydrolysis.

Question 20

Which type of enzymes carried out the oxidation?

Answer 20

Cytochrome P-450 enzymes
(CYPs). Also they are additional enzymes that play a role in oxidative metabolism include alcohol and aldehyde, dehydrogenases, aldehyde oxidase, amine oxidases,
and lipoxygenases.

Question 21

In drug metabolism phase I, for mono-substituted benzene compounds, what position (para-meta or ortho hydroxylation) will frequently predominate ?

Answer 21

for mono-substituted benzene compounds, para-hydroxylation frequently predominates.

Question 22

True or false, When more than one phenyl ring is present, only one
ring is typically hydroxylated

Answer 22

True

Question 23

Two metabolic pathways for cimetidine involve S-oxidation to the sulfoxide and hydroxylation of the 5-methyl group on the imidazole ring. Draw structures of these two metabolites.

Answer 23

Question 24

The metabolism of brompheniramine is shown below. Draw the reaction pathway of the first phase I
reactions to generate the carboxylic acid metabolite.

Answer 24

Question 25

Explain phase II or drug metabolism ( mentions the reactions and enzymes that are carried out)

Answer 25

Drug or metabolite is conjugated to a
small endogenous molecule in order
to expedite elimination or to reduce
reactivity.
* Glucuronidation
* Sulfation
* Amino acid conjugation
* Glutathione conjugation
* N-acetylation

• Phase II reactions are carried out by
  various transferase enzymes

Question 26

Explain the key parameters;
- Clearance (CL)
- Half-life (t½)
- Excretion routes

Answer 26

1. Clearance (CL)
   Volume of plasma cleared of the drug per unit time, reflecting both metabolism and excretion
2. Half-life (t½)
   Time taken to 50% of the drug to disappear from the circulation.
   - Favorable dosis schedule - Half live more than 24 hours side effects due accumulation.
3. Excretion routes
   Majority of drugs eliminated through the urine or the faeces
   * Other routes known, e.g. saliva, exhalatio
   - Elimination of xenobiotics as a metabolite- animal models (detecting concentration presence

Question 27

During your drug discovery program, you learn that the thiophene fragment of your lead (see below) is
extensively metabolized, resulting in very poor oral bioavailability. Unfortunately, thiophene contributes to
the potency of the molecule. On the basis of the concepts described in themes 6 & 7, design two new
replacements or changes to the thiophene that would address the metabolism issue but would likely
maintain potency

Answer 27

Two medicinal chemistry strategies frequently applied to limit the metabolism of a drug include introduction of steric
hindrance and isosteric replacement
* Introduction of an alkyl groups (such as methyl) α to the sulfur atom may help prevent oxidative metabolism by steric
hindrance.
* Three nonclassical bioisosteres for thiophenes provided in in the tables in your lecture notes are shown

• By use of an isostere, the compounds have similar size and characteristics and are likely to maintain their biological
  activity while having a different, and perhaps even improved, metabolic profile

Question 28

What can be include in toxic effects?

Answer 28

Toxic effects can include:

• Mechanism based pharmacology
• Formation of reactive metabolites
• Activation of other receptors, including hERG
• Interactions with other substances
• Idiosyncratic toxicity

Question 29

When mechanism-based pharmacology happen?

Answer 29

Mechanism-based pharmacology is caused when activation of the target
causes unwanted effects as well as the desired therapeutic effect.

Question 30

Why this functional groups should be avoid ?

Answer 30

These are all electrophiles, which means that they can
covalently bind to nucleophiles in the body, e.g. in proteins and DNA, which lead to toxic effects.

Question 31

for what is terfenadine used? What are the problems of its use?

Answer 31

Terfenadine – antihistamine drug on market for many years as an ‘OTC’ remedy for hayfever.
* Found to cause life threatening cardiac arrhythmias when co-administered with medicines such
as erythromycin (antibiotic) or ketoconazole (antifungal).
* Caused by inhibition of hepatic P450 enzymes.

Question 32

Explain the in-Vivo acute toxicity testing.

Answer 32

• Studies done in animals at increasing doses until toxicity is observed. Generally begun in rodents and progress to dogs or rabbits.
  *Acute testing begins with a single dose, and the animal is observed for signs of
  toxicity e.g. vomiting, diarrhoea, weight loss, lethargy or death over a 7–14 day period after the dose.
  *Blood levels of the drug are also monitored to determine at what drug concentration toxicity is observed.

Question 33

Define Toxicokinetics (TK)

Answer 33

The relationship between toxicity and concentration of drug in the blood is termed toxicokinetics (TK).

Question 34

Explain Range-Finding Studies testing.

Answer 34

Carried out such that several different doses (usually a high, medium and lose
dose) are administered daily over 2–4 weeks.
* These studies establish the range of doses that can be administered without significant toxicity, as well as the maximum tolerated dose (MTD)
* Dictate the doses that will be used in subsequent sub-chronic and chronic toxicity testing.

Question 35

Explain Sub-chronic Testing

Answer 35

Comprise next level of in vivo toxicity testing
* Involves much longer duration of dosing.
* During sub-chronic testing animals (either rodents or non-rodents) are dosed daily for three months and monitored for signs of toxicity, including weight loss or gain.
* After study completion, tissues are harvested and examined for histological
changes compared to control animals.

Question 36

Explain Chronic Testing

Answer 36

Lasts for longer than three months
*Should have at least the same duration as the proposed
clinical trials
*Carried out in at least one rodent and at least one non-rodent
species
*Animals monitored after dosing stops to identify effects that
appear after long-term dosing

Question 37

What are the two main components in the Chronic Testing?

Answer 37

Chronic testing has two components:
*First is 6–12 months of observation, looking for signs of toxicity.
*second is 12–24 months of observation for signs of
carcinogenicity.

Question 38

What no observed adverse
effect level (NOAEL) of the drug means?

Answer 38

This value is the highest dose of the drug that can be administered without serious
toxicity, and helps define the tolerable dose for clinical trials.

Question 39

Reproductive Toxicity Testing, determines whether the investigational drug will exert any effect on:
*Fertility
*Ability to maintain a pregnancy
*Health of the progeny of patients

Completed in 3 parts, explain the 3 different segments.

Answer 39

Segment I testing

• Looks at fertility and reproductive performance in
  both male and female animals that are administered the drug.

Segment II testing

• Evaluates embryonic toxicity (teratogenicity) during early pregnancy of mothers being dosed
  with the drug.

Segment III testing

-Determines if there are any effects of the drug on final stage of pregnancy alongside delivery and lactation, when administered to a pregnant female.
Determines if there are any effects
of the drug on final stage of
pregnancy alongside delivery and lactation, when administered to a pregnant female.

Note: SEGMENT III IS MAKING IN PARALEL WITH SEGMENT 1 AND 2 MAKE IT SAGE FOR PREGNACY WOMEN

Question 40

Explain the Phase I clinical trial. Characteristics-cost.

Answer 40

First introduction of candidate drug into humans:

• Determines safety & tolerance of the drug
• Uses healthy ‘volunteers’ (usually paid) (20-80 subjects)
• Blood levels monitored to determine t½ and metabolism
• Whilst Phase I trial subjects are healthy, it is possible to gain early clues on effectiveness of the drug.
• Regardless of activity, Phase I trial must establish
  the drug is safe before progression to Phase II
• Estimated that ~US$17m per year spent on
  drugs in Phase I

Question 41

Explain the phase II clinical trials. ( Main purpose, number of patients, cost..)

Answer 41

Marks the first time the candidate drug is used on
diseased patients

• Patients closely monitored to determine; Effectiveness, Proper dosing.
• Whilst most serious side effects/safety issues should
  have been highlighted in Phase I, Phase II patients still
  monitored for unwanted drug effects
• Trials involve several hundred patients
• Cost per patient estimated to be ~ US$25,000
• Estimated that ~US$34m per year spent on drugs in
  Phase II
• Plans for Phase III trials presented and, depending on
  the data, the FDA may recommend specific clinical tests or additional animal trials to clarify any issues.

Question 42

Explain Phase III of clinical trials

Answer 42

Trials involve hundreds to thousands of patients
* Cost per patient often less than Phase II
* Larger patient sample size allows demographic representation with regards to age, race & gender
* Differences (if any) can be monitored to determine more accurate prescribing & dosing information
* Estimated that ~US$27m per year spent on drugs
in Phase III
* Effectiveness and long-term safety are the primary
goals of Phase III trials
* Late on in the trial, the company again meets with
the FDA to ensure data collected to-date is adequate for the IND to be considered for full approval.

Note: phase trails should be conducted in a controlled, double-blind fashion.

Question 43

What are the differences between single and double blind?

Answer 43

Single Blind

• Patients do not know whether they are receiving drug or placebo.

Double Blind

• Neither the patient or the
  healthcare staff know who is or isn’t receiving drug or placebo (all encoded).
• Only clinical staff members
  unassociated with administering the drug and collecting data know who is receiving what-