Drug Discovery and Development Notes

Drug Discovery and Drug Development

Topic Learning Outcomes

Describe drug development in the past and present.
Describe how to identify disease, drug target, pharmacophore, bioassays, and find a lead compound.
Explain the isolation, purification, and determining the structure of a lead compound.
Describe ways to improve target interaction and pharmacokinetic properties.
Describe the physicochemical factors affecting drug absorption and biological action.
Describe how to improve molecule properties through synthesis.
Describe better late-stage functionalization, mimicking nature, isosteres, fragment-based drug discovery in drug development.

What is Drug Development?

A process.
A long, multifaceted process.
To develop a product intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease; or intended to affect the structure or function of the body.
Drug development is the multi-disciplinary process of bringing a new drug or device to market, encompassing drug discovery, preclinical research, clinical trials, and regulatory submissions.

Drug Development Process

The drug development process includes the following stages:

Research
- Discovery & Chemical Synthesis
- Non-Clinical Research in Laboratory and Animals
- 30-day Safety Review
Clinical Trials & IND (Investigational New Drug Application)
- Pre-IND Meeting
- Phase 1 Trials: Clinical Pharmacology Studies
- End of Phase 1 Meeting
- Phase 2 Trials: Controlled Studies
- End of Phase 2 Meeting
- Phase 3 Trials: Confirmatory Studies
NDA/BLA (New Drug Application/Biologics License Application)
- Pre-NDA Meeting
Post-Market Activities

Drug Discovery and Development - Past

The earlier historical method of drug discovery was either by:
- 'Trial-and-error' testing of chemical substances on cultured cells or animals
- Matching the apparent effects to treatments.

Examples of Past Drug Discovery

Opium plant (Papaver somniferum) was used in ancient civilizations (4000-1000 BC) for various medicinal purposes and in religious ceremonies.
Rhubarb root has been used as a purgative.
Cinchona bark has been used as a malaria treatment.
Atropa belladonna used for medicinal purposes like pain relief and to dilate pupils.
Snake root plant used as a cure for snakebite, earaches, toothaches, sore throats, croup and colds. Its main use today is as an expectorant in cough syrups, teas and lozenges, and as a gargle for sore throats.
Rauwolfia serpentina (Reserpine) used as a treatment for high blood pressure and psychotic episodes.
Ipecacuanha root used in the treatment of dysentery.

Serendipity in Drug Discovery

Cisplatin: Accidental discovery of its cytotoxic agent properties from the effect of electric fields on bacterial growth using platinum electrodes.
Viagra: Discovered by chance from a project aimed at developing a new heart drug; initially intended as an anti-impotence drug.
Clonidine: Originally designed as a nasal vasoconstrictor for nasal drops and shaving soaps but found to be an important antihypertensive agent after clinical trials.
Vincrystine and Vinblastine: Searched as lowering blood glucose agents but they proved to be cytotoxic agents.
Cyclosporine: Investigated as an antibacterial but found to suppress the immune system and used during organ and bone marrow transplant.

Drug Discovery and Development – Present

Targeted screening partially leverages the concept of rational drug design.
Utilizing an understanding of the structure-activity and structure-toxicity relationships of various compounds.
Mechanisms of interaction with potential targets leading to a higher probability of exhibiting biological activity.

Rational Drug Design

Designing candidate compounds and (3D) three-dimensional structures to interact with a specific target, receptor, or biological pathway known to mediate a given pathology.
The subsequent design is then tested.
Rational drug design requires advanced understanding of the target, modeling, and simulation techniques.

Classification of Drugs Based Upon Their Discovery

The way drugs are classified or grouped can be confusing.

1. By Pharmacological Effect

Drugs are grouped depending upon the biological effect they have, e.g., analgesics, anti-psychotics, anti-hypertensives, anti-asthmatics, antibiotics, etc.
There are many biological mechanisms which the medicinal chemist can target to get the desired results.
Many drugs do not fit purely into one category or another, and some drugs may have more uses than just one.
- A sedative drug might also have uses as an anticonvulsant.

2. By Chemical Structure

In some cases (penicillins), this is a useful classification since the biological activity (antibiotic activity for penicillins) is the same.
For example, barbiturates may look much alike and yet have completely different uses in medicine.
The same holds true for steroids. It is also important to consider that most drugs can act at several sites of the body and have several pharmacological effects.
The opiates are a group of drugs with similar chemical structures.

3. By Target System

These are compounds that are classified according to whether they affect a target system in the body – usually involving a chemical messenger, e.g., antihistamines, etc.
This classification is a bit more specific than the first since it is identifying a system with which a drug interacts.
All antihistamines are to be similar compounds since the system by which “histamine” is synthesized, released, interacts with its receptor, and is finally removed can be attacked at all these stages.

4. By Site of Action

These are compounds grouped according to the enzyme or a receptor with which they interact.
Anticholinesterases are a group of drugs that act through inhibition of the enzyme ‘acetylcholinesterase’.
This is a more specific classification of drugs since we now identify the precise target at which the drug acts.

Stages Involved in the Drug Discovery and Drug Development

Choose a disease and a drug target.
Identify a bioassay
Find a lead compound “isolate and purify”.
Determine the structure of a lead compound.
Identify the structure – activity relationship (SAR) the pharmacophore.
Improve target interactions and pharmacokinetic properties.
Study drug metabolism / toxicity.
Design a manufacturing process.
Carry out clinical trials.
Identify and patent the drug.
Market the drug and make profits.

A) Choosing a Disease

Pharmaceutical companies decide which disease to target when designing a new drug.
It would make sense to concentrate on diseases where there is a need for new/improved drugs.
Pharmaceutical companies have to consider economic factors as well as medical ones.
A huge investment has to be made toward the research and development of a new drug.
Therefore, companies must ensure that they get a good financial return for their investment.

Factors Influencing Disease Targeting

Research projects tend to be biased towards ‘first world’ diseases since this is the market best able to afford new drugs.
- A great deal of research is carried out on ailments such as migraine, depression, ulcers, obesity, flu, cancers, cardiovascular diseases, and antibiotics.
- Less research is carried out on the tropical diseases – diseases which can reduce life expectancies.
Only when such diseases start to make an impact on western society do the pharmaceutical companies sit up and take notice (e.g., anti-malarials, anti-aids, etc.) because of the increase of tourism to most exotic countries.
Choosing which disease to tackle is usually a matter for a company’s market strategists.

B) Choosing a Drug Target

Drug target, receptor, enzyme, or nucleic acid.
- An understanding of which enzymes or receptors are involved in a particular disease state is clearly important.
- To identify whether agonists/antagonists for a particular receptor.
- To target activator/inhibitors for particular enzymes.

Discovering Drug Targets

Recently discovered novel targets are the “caspases”.
These are a family of enzymes that catalyze the hydrolysis of important cellular proteins and have been found to play a role in inflammation and cell death.
The cell death is a normal occurrence in the body, and cells are regularly recycled. Therefore, the caspases should not necessarily be seen as bad or undesirable enzymes.
Without them, cells could be more prone to unregulated growth, resulting in diseases such as cancer.

Target Specificity and Selectivity

Between Species:
- In the field of antimicrobial agents, the best targets to choose are those which are unique to the microbes and which are not present in humans.
- Penicillin targets an enzyme involved in bacterial cell wall biosynthesis.
- Since mammalian cells do not have a cell wall, this enzyme is absent in human cells, and penicillin has few side effects.
It is still possible to design drugs against targets which are present both in humans and microbes.
- The antifungal agent “fluconazole” inhibits a fungal demethylase enzyme involved in steroidal biosynthesis.
- This enzyme is also present in humans, BUT the structural differences between the two enzymes are significantly different.
Within the Body:
- Target selectivity on our own receptors or enzymes.
- Enzyme inhibitors should only inhibit the target enzyme and not some other enzyme.
- Receptor agonists/antagonists should ideally interact with a specific kind of receptor rather than a variety of receptors.

Targeting Drugs to Specific Organs and Tissues

For example, the β-adrenergic receptors in the heart are predominantly β1, while those in the lungs are β2.
This makes it feasible to design drugs that will work on the lungs with minimal side effects on the heart, and vice versa.

C. Identification of Pharmacophore

The pharmacophore summarizes the important functional groups required for biological activity and their relative positions in space with respect to each other.

Definition

“The atoms and functional groups required for a specific pharmacological activity, and their relative positions in space.”
For example, if it is discovered that the important binding groups for the drug “GLIPINE” are:
- the two phenol groups,
- the aromatic ring,
- the nitrogen atom
  then the pharmacophore is as shown below, where the nitrogen atom is $5.063$ Å from the Center of the phenolic ring and lies at an angle of $18$ ° degree from the plane of the ring.

Functional Groups in Pharmacophore

The phenol groups can act as hydrogen bond donors or acceptors.
The aromatic ring can participate in van der Waals interactions.
The amine can act as a hydrogen bond acceptor or an ionic center if it is protonated.

Identifying Essential Functional Groups

By synthesizing compounds (glipine) where one particular functional group of the molecule is removed or altered.
This involves testing all the analogs for biological activity and comparing them with the original compound.
If an analog shows a significantly lowered activity, then the group that has been modified must have been important.
If the activity remains similar, then the group is not essential.

D. Identifying a Bioassay

Choosing the right bioassay or test system which should be simple, quick, and relevant.
Human testing is not possible at such an early stage, and so the test has to be done by:
- in vitro (i.e., on isolated cells, tissues, enzymes, or receptors)
- in vivo (on animals).

In Vitro vs. In Vivo Tests

In general, in vitro tests are preferred over in vivo tests.

i) In Vivo Tests

In vivo tests on animals often involve inducing a clinical condition in an animal to produce observable symptoms.
The animal is then treated to see whether the drug alleviates the problem by eliminating the observable symptoms.

Transgenic Animals

“These are the animals whose genetic code has been altered.”
The mouse produces the human receptor or enzyme, and this allows in vivo testing against that target.
Alternatively, the mouse genes could be altered such that the mouse became susceptible to a particular disease (e.g., breast cancer).

Problems with In Vivo Testing

Such testing is slow and causing animal suffering.
Problems of pharmacokinetics and the results obtained may not be rationalized; observed symptoms might be caused by some other physiological mechanism.

Prodrugs

Prodrugs: Are inactive precursors of a drug, converted into its active form in the body by normal metabolic processes.
Precursor: A biochemical substance, as an intermediate compound in a chain of enzymatic reactions, from which a more stable product is formed.

ii) In Vitro Tests

“In vitro tests” Instead specific tissues, cells, or enzymes are used.
- Enzyme inhibitors can be tested on the pure enzyme in solution.
- Receptor agonists and antagonists can be tested on isolated tissues or cells that express the target receptor on their surface.
HIV protease has been cloned and expressed in the bacterium “Escherichia coli”.

iii) Test Validity

An antibacterial agent can be tested in vitro by measuring how effectively it kills bacterial cells.
A local anesthetic can be tested in vitro on how well it blocks action potentials in isolated nerve tissue.

iv) High Throughput Screening (HTS)

Robotics and the miniaturization of in vitro tests on genetically modified cells have led to a process called HTS.
This involves automated testing of large numbers of compounds against a large number of targets.
Receptor antagonists can be studied using modified cells by this method.

v) Screening by Nuclear Magnetic Resonance (NMR)

NMR spectroscopy can be used to detect whether a compound bounds to a protein target.
In an NMR spectrum, a compound is radiated with a short pulse of energy, and its nuclei are promoted to an excited state. The nuclei then slowly relax to the ground state, giving off energy as they do so. This energy can be measured to produce a spectrum.