The drug discovery process

Question 1

True/False? It is easy and trivial to discover a drug

Answer 1

FALSE

Question 2

What are the two strategies in drug discovery and how do they differ?

Answer 2

Target-Based discovery: you know what target (protein/enzyme) you want to hit

Phenotype-based discovery: You know the disease phenotype you want to treat

Question 3

What is the difference between a first in class and a follower drug?

Answer 3

A first in class drug is a drug newly discovered through eg genomics or proteomics

A follower drug is one based off a follower drug with a slight modification

Question 4

Which screening method has the highest rate of follower drugs? What does this imply?

Answer 4

Target-based approach

Suggests that once a MMOA has been established, target-based optimization does in fact work

Question 5

What is the best method for lead discovery?

Answer 5

It depends

Question 6

What is the difference between a hit and a lead?

Answer 6

A hit is just something that responded during a High Throughput Screening,
A lead is a hit that has been optimized and is of likely therapeutic value

Question 7

Empirical data has shown that what types of molecules make good drug targets? Which don’t?

Answer 7

Enzymes, receptors and channels are good targets

Protein:protein interactions are not as good

Question 8

Why can’t simple competitive inhibitors be readily developed despite many MMOAs being reported?

Answer 8

Because simple equilibrium binding of a drug at its active site is often times not sufficient for biological activity

Question 9

What are two components that are required for efficient drug action?

Answer 9

Mass-action binding (concentration dependent)

Biochemical/structural rearrangements that shift the target away from mass-action binding, effectively locking the target in an inactive state

Question 10

What are the 5 basic steps for structure-based drug design?

Answer 10

Target-selection
Structure determination of target
Pharmacophore identification or screening
Structure development of lead compound(s)
Lead candidate for biological assays and clinical trials

Question 11

Define the biochemical approach of identifying targets

Answer 11

Basic research that leads to the elucidation of biochemical mechanisms of diseases

eg thalidomide’s target was discovered by fixing the drug to a column and running cell lysate over it to see what sticks

Question 12

Describe the genetic approach of identifying targets

Answer 12

Mutations that predispose people to certain diseases

eg PARP + repair inhibitor leads to selective death in BRCA-deficient (breast cancer) cells

Question 13

What is the point of target validation?

Answer 13

To prove that targeting a given protein will result in the desired biological outcome

Question 14

What does target validation usually entail?

Answer 14

Establishment of biochemical mechanisms, hot spots (active sites), and CRISPR-KO/KIs to determine loss/gain of function

Question 15

What are the two ways to identify hits?

Answer 15

High Throughput Screening

Structure-based approaches

Question 16

Describe the HTS method of hit identification

Answer 16

“Brute force” method
A compound library is scanned for “primaries” based on properties, followed by more stringent “secondaries” to narrow down the list and eliminate false positives

Primaries are screened with a single high concentration of compound, whereas secondaries can be calculated over a range of concentrations, to identify hits that give rise to a IC50 curve

Question 17

Define the structure-based approaches to identify hits

Answer 17

De novo/rational design: based on pharmacophore identification. Locate 3D position of key hydrogen bonds, electrostatic and hydrophobic interactions

Fragment-based discovery: Ligand that binds strongly is made of smaller, weakly-binding components that are joined together

Virtual screening: Computational research based on virtual screening of compounds deemed viable (Many false positives)

Question 18

Define the pharmacophore of a drug

Answer 18

The part of the drug that actually causes a biological response

Question 19

How can the pharmacophore be determined?

Answer 19

By inspection of a series of compounds with different activities towards the target

Question 20

How is the pharmacophore defined?

Answer 20

By a number of features such as H-Bond donor/acceptors, hydrophobic groups, etc (defined in 3D with distances)

Question 21

Define the Quantitative Structure-Activity Relationship model

Answer 21

A large number of similarly related drugs are split into two groups

One group is used to build a predictive model, and the other group is compared to the predictions of the first

Question 22

Describe the process of lead optimization

Answer 22

Once a hit’s pharmacophore has been discovered, modifications are made to the molecule to effect its other properties (ADMET and DMPK)

Question 23

What are the steps involved in lead optimization?

Answer 23

Start from one series of hits
Determine the molecular mechanism of action of hits through biochemical assays and structural studies
Increase potency by performind structure-activity studies (requires the generation of a series of analogs) - typically need to reach Kd in nanomolar range for efficacy
WHILE this is happening, optimize ADMET and DMPK

Question 24

Why does the Kd of a lead need to be in the nanomolar range for efficacy?

Answer 24

Nanomolar Kd = residence time in seconds = stronger drug

Question 25

Why do you optimize ADMET and DMPK at the same time as the Kd?

Answer 25

Because if you do it after you waste time and money

No sense in spending all this time on a drug with a great Kd only to figure out that eg it doesn’t cross BBB

Question 26

How can you make a good rough compound for an enzyme?

Answer 26

By mimicking the natural substrate

Question 27

How did they test anti-HIV protease drugs using isatin?

Answer 27

Isatin binds proline and forms a compound that absorbs yellow light very well

Treated HIV with isatin and inhibitor, if inhibitor did not work HIV protease would cleave protein leaving prolines which would bind isatin (yellow light still absorbed)

If inhibitor did work it would inhibit protease from binding isatin, yellow light would no longer be absorbed

Question 28

What is a property of HIV (and many viruses) in terms of replication? What does this lead to? What does THAT lead to? How was this dealt with?

Answer 28

Very fast replication rate, very low fidelity (high error rate)

This leads to many daughter cells of HIV to have mutations, and those mutations can alter the active site, causing drugs to lose their efficacy

A drug (Darunavir) was developed to bind the amino acid backbone (which cannot mutate) to inhibit HIV protease activity