Drug Design - Finding A Lead

Question 1

If you wanted to know the structure of a compound via NMR, how would you do this?

Answer 1

Prepare NMR sample of protein with bound ligand.
Record high resolution 2D NMR spectra
Identify NMR signals and any inter-nuclear interactions to reconstruct the 3D structure

Question 2

How are lead candidates found?

Answer 2

Found by design, or by screening existing compounds.

One needs to design a suitable test in order to identify lead compound(s)

Question 3

Name 3 main groups of compounds where leads can be discovered from the natural world

Answer 3

Plant extracts
Venoms and toxins
Endogenous compounds

Question 4

How does one undergo receptor-based virtual screening? What does it involve?

Answer 4

Receptor-based virtual screening involves docking of ligands from a large structural database into the active (or allosteric) binding site of the target, provided the 3D structure of that target is known via X-ray crystallography or NMR analysis.

Question 5

What is Kd?

Answer 5

Dissociation constant
I.e.
The concentration of drug that can respond when 50% is bound.
The lower Kd is, the more potent the drug is.

Question 6

Describe the procedure of fragment based NMR screening

Name one advantage of this procedure

Answer 6

A range of low molecular weight compounds are screened against the target.
Binding ca be detected by observing a shift in the 15N or 13C NMR signals.
This shift can only be induced by the interaction of the fragment with the target. This will also reveal which part of the binding site is occupied by the fragment.
Once two fragments have been identified, the structure of each can be further optimised to enhance binding affinity.
Then the new ligand can be designed where the 2 fragments are linked together.
This approach offers a high level of structural diversity for drug leads.

Question 7

In structure-based drug design, what would you do after you’ve obtained the target structure?

Answer 7

Step 2-
Download the obtained structure to computer for molecular modelling studies.
Identify where the ligand is, and thus identify the binding site.
Identify the binding interactions and target by measuring the distances between the ligand and the neighbouring atoms in the binding site

Question 8

What is the drug lead for salbutamol

Answer 8

Salbutamol is a Beta-2-agonist which originates from adrenaline

Question 9

Name a drug made from/inspired by 5-hydroxytryptamine (serotonin)
What does this drug treat?

Answer 9

Sumatriptan (agonist)

Treats headaches and migraines

Question 10

What drug can histamine be used as a drug lead for?

Answer 10

Cimetidine (antagonist)

H2-receptor antagonist that is used to treat heartburn and peptic ulcers

Question 11

Name 3 ways/techniques of finding a lead compound chemically

Answer 11

Molecular modelling
X ray crystallography
NMR

Question 12

Where was the drug lead for Saquinavir?

Answer 12

Phenyalaline + proline (dipeptide) was the drug lead for saquinavir (HIV drug)

Question 13

Briefly state the three steps of structure-based drug design?

Answer 13

Step 1 - either X-ray based or NMR based
Step 2 - Download the structure, identify where the ligand is and identify the binding interactions
Step 3 - Identify vacant regions in the compound for extra interactions and remove the ligand from the binding site. Fit other compounds into it to test binding capabilities

Question 14

How does NMR aid virtual world drug design?

Answer 14

NMR allows one to determine the protein structures in solutions

Question 15

Define “Lead Candidate”

Answer 15

A compound used as a starting point of drug development, that demonstrates a property likely to be therapeutically useful.
Note: The lead activity and target selectivity are not crucial at this stage

Question 16

What is structure-based drug design?

Answer 16

A strategy used to carry out drug design based on the identified interactions between the lead compound and the target binding site

Question 17

How can the virtual world assist with drug leads?

Answer 17

Detailed knowledge of target binding sites may significantly assist drug design

Question 18

Name two natural substances for enzymes that are drug leads for pharmaceutical products

Answer 18

Enkephalins have been used as a drug lead for enkephalinase inhibitors
Peptides have been used as drug leads for protease inhibitors

Question 19

Give 2 examples of venoms/toxins that has acted as a drug lead, and what drug(s) it has formed

Answer 19

1-Curare is a toxin which South Americans once used for hunting. This was used as a drug lead to form the neuromuscular blocker, Atracurium, which is used in surgery for broncho-ventilations
2-Teprotide is an oligopeptide that was isolated from the venom of the Brazillian viper and was one of the leas compounds for the antihypertensive Captopril

Question 20

What is the fragment based NMR strategy screening based upon?

Answer 20

Based on identification of small molecules (fragments) which will find to specific but different regions of a protein binding site.
The separate fragment structure bind to only one part of the binding site.
However, linking the 2 separate fragments with an appropriate spacer may lead to a larger molecule that binds to the whole binding site. This may considerably increase binding affinity (and thus activity) of the resulting lead compound towards the protein active site.

Question 21

Give 2 examples of plant extracts that have been turned into commonly used drugs

Answer 21

Salicylic acid from willow tree has acetic anhydride added to it. This is how it is made into aspirin.
Another example is the coca bush, which is a drug lead for cocaine. Cocaine is then used as a drug lead for Procaine.

Question 22

What would you do if you had to assess known compounds from a large database that may go on to be lead compounds?

Answer 22

Virtual screening helps to access whether known compounds from a large database are likely to be lead candidates for a particular target

Question 23

How does X-ray crystallography specifically aid drug design?

Answer 23

Preferably it does this with the ligand bound to the binding site

Question 24

How does one obtain the structure of an enzyme or receptor binding site via the virtual world?

Answer 24

X-ray crystallography

NMR

Question 25

If you wanted to know the structure of a compound via X ray crystallography, how would you do this?

Answer 25

Crystallise target protein with bound ligand.

Acquire structure via x ray crystallography

Question 26

What is the drug lead for Propranolol?

Answer 26

Adrenaline (a hormone and neurotransmitter)

Propranolol s a non-selective beta-blocker

Question 27

In structure-based drug design, what would you do once you know where the binding site is and what the binding interactions between the ligand and target are?

Answer 27

Step 3
Identify vacant regions for extra binding interactions
Remove the ligand from the binding site in silico.
Using receptor-based virtual screening, ‘fit’ analogues into the binding site in silico to test their binding capabilities.
Alternative approach involves rational de novo design of lead molecules

Question 28

In structure-based drug design, once you have a few analogues fitted into the binding site (by using receptor-based virtual screening), what is the next step?

Answer 28

Step 4
Identify the most promising analogues
Synthesise and test for activity
Crystallise a promising analogue with the target protein

Alternatively, prepare a sample of a selected ligand with the target protein and record high-resolution 2D NMR spectra.

Repeat the whole process