Section 5

Question 1

What is lead optimisation?

Answer 1

An iterative process where the initial biological lead is chemically modified to produce new analogues.

Question 2

What are the 5 characteristics of an ideal clinical candidate?

Answer 2

Potency
Selectivity
Efficacy
Physical and pharmaceutical properties.
Optimal safety profile.

Question 3

What does lead optimisation cover?

Answer 3

Optimisation of drug-target interactions (via testing the biological activity of synthesised compounds in primary/secondary assays).

Optimisation of drug-like properties and pharmacokinetics.

In vivo testing for toxicity and safety prior to preclinical studies.

Question 4

What is the effect of drug-target binding on enthalpy and entropy?

Answer 4

Enthalpy - enthalpic gains (more negative) from favourable interactions e.g., ionic bonds, H-bonds, vdWs

Entropy - Reduced rotational and translational freedom in bound form than unbound form (entropic penalty). However, the reduction in exposed non-polar surface area increases the amount of disordered water (entropic gain).

Question 5

What does thermodynamics refer to in drug discovery?

Answer 5

The heat changes that occur when biomolecules interact.

Question 6

What is enthalpy-entropy compensation?

Answer 6

When a ligand binds to a target protein, there is a disruption of interactions of each free partner with the solvent, and the formation of new interactions with each other.

During lead optimisation, the ligand is modified to increase bonding interactions with the binding site. This causes enthalpy (H) to become more negative (favourable enthalpy). However, the increased interactions increase the order of the complex and therefore reduce entropy (S) (unfavourable entropy).

Since these two parameters oppose
each other, the overall ∆G° of binding often is relatively unchanged, confounding the
aim to improve affinity.

Question 7

How do enthalpy, entropy, and Gibbs free energy relate to drug-binding affinity?

Answer 7

Higher affinity is a result of a more negative Gibbs free energy (delta G), a more negative enthalpy (delta H), and a more positive entropy (delta S).

Question 8

What are the 7 common types of non-covalent interactions in order of strength?

Answer 8

1. Ionic bonding
2. Dipole-dipole interactions
3. Hydrogen bonding
4. Ion-dipole interactions
5. Cation-pi interactions
6. Pi-pi interactions
7. Van der Waals interactions

Question 9

What do ionic/electrostatic interactions take place between?

Answer 9

Cationic (+) and anionic (-) species.

Question 10

What do dipole-dipole interactions take place between?

Answer 10

Areas of high electron density (partially negative) and low electron density (partially positive)

Question 11

What do hydrogen bonding interactions take place between?

Answer 11

A hydrogen bond donor (strongly electronegative atom e.g., NH, OH) and a hydrogen bond acceptor (electronegative atom with a lone pair available e.g., N, O, F)

Question 12

What do ion-dipole interactions take place between?

Answer 12

A formally charged species (e.g., Mg or Zn in the catalytic site of an enzyme) and a polar functionality.

Question 13

What do cation-pi interactions take place between?

Answer 13

A positively charged ion (e.g., quarternary/positive nitrogen or a metal cation) and an electron-rich pi system (e.g., aromatic rings of phenylalanine, tryptophan, tyrosine).

Question 14

What do pi-pi interactions take place between?

Answer 14

2 aromatic partners, dependent on the differential electron density around each system.

Question 15

How do Van der Waals interactions take place?

Answer 15

Formation of temporary dipoles generated through fluctuations in electron density around the ligand or area of the protein target.

Question 16

How are covalent bonds most commonly formed in ligand binding?

Answer 16

Nucleophilic attack by a protein residue on target upon an electrophilic centre on the drug.

Either due to an nucleophilic substitution or Michael addition reaction.

Question 17

What is a Michael addition reaction?

Answer 17

Nucleophilic addition of a nucleophile to an alpha, beta - unsaturated carbonyl compound at the beta-carbon.

An alpha-beta unsaturated carbonyl compound:

R2-C=C(R)=O

(alpha carbon is one bound to oxygen aka carbonyl carbon, beta carbon is the other one).

Question 18

Give an example of a Michael addition reaction.

Answer 18

Binding of tyrosine kinase inhibitor Neratinib to HER2.

Thiol on cysteine 805 on HER2 acts as a Michael donor and attacks a carbon Neratinib to form a carbon-sulphur bond.

Question 19

How does stereochemistry affect binding in the case of adrenaline?

Answer 19

The secondary alcohol in adrenaline is attached to a chiral centre.

R-(-)-adrenaline has a combination of pi-pi, H-bond, and ionic interactions. This is the more active enantiomer (eutomer).

S-(+)-adrenaline has pi-pi and ionic interactions, but no H-bonding due to the conformation of the alcohol. This results in a 100-fold decrease in overall binding affinity. This is the less active enantiomer (distomer).

Question 20

What are congeners?

Answer 20

Compounds with the same core structure but varying functional group apendages.

Question 21

How can congeners be used to determine SARs?

Answer 21

By altering functional groups, you can determine which aspects of the lead structure are necessary for activity and which can be altered to improve activity.

Question 22

What does the Hammett equation do?

Answer 22

Quantifies the electronic properties of functional groups as a constant (sigma) in relation to their location on the ring (para, meta, ortho). A positive sigma value indicates an electron drawing effect and vice versa.

Question 23

What does logP indicate in terms of membrane permeability?

Answer 23

Measure of lipophilicity.

Low/negative logP = hydrophilic = high drug concentration required for membrane permeability.

High/positive logP = lipophilic = low drug concentration required for membrane permeability but drug can get trapped in the membranes.

Ideal level is in the middle where a drug can permeate easily but still reach site of action.

Question 24

What is the Hansch-Fujita constant?

Answer 24

The Hansch-Fujita constant (pi) describes the lipophilic contribution of a substituent.

It is calculated as the difference between logP of the substituent and logP of the unsubstituted parent compound which has hydrogen in the equivalent position.

Question 25

What is the difference between logP and logD?

Answer 25

LogP is used for neutral molecules.

LogD is used for ionisable molecules and considers the effects of the ionisation of the molecule and changes in evironmental pH.

Question 26

Name 2 methods to quantify molecular substituents for SAR studies.

Answer 26

Steric parameter (Es) = measure of steric bulk of the R group based on their effect on the rate of ester hydrolysis, relative to that of the parent ester.

Molar refractivity (MR) = measure of molecular volume and polarisability.

Question 27

What is the STERIMOL programme used for?

Answer 27

Determines the length of a substituent from the parent molecule (L) and the width from the plane in 4 directions (B1-4).

Question 28

How can the results of the STERIMOL be related to biological activity?

Answer 28

Hansch equation - uses linear multiple regression analysis considering size, lipophilicty, and electron characteristics to determine which congeners have impact on a target of interest.

Free-Wilson (additivity) equation - assess additive substituent effects on the overall molecule, rather than component functional groups. It attempts to directly relate changes in structure to changes in activity, rather than in correlation to the physicochemical properties.

Question 29

What is a pharmacophore?

Answer 29

The ensemble of steric and electronic features that are necessary to ensure the optimal supramolecular interactions with a specific biological target structure and to trigger (or to block) its biological response.

Question 30

What is the receptor-excluded volume and receptor-essential area of a drug?

Answer 30

Receptor-excluded volume - the combined 3D volume of all active analogues which fit the pharmacophore model.

Receptor-essential area - the combined extra volume of compounds which adhere to the pharmacophore but are inactive. Often these areas extend the boundaries of the binding pocket and sterically clash with the receptor.

Question 31

What are CoMFA and CoMSIA?

Answer 31

Comparative Molecular Field Analysis.
Comparative Molecular Similarity Index Analysis.

Generate and superimpose low energy conformers of molecules with similar biological activity, with pharmacophoric element matching.
For each conformer, the electrostatic and steric field is determined.

Question 32

What is a conformer?

Answer 32

A stereoisomer produced by rotation about a sigma (σ) bond.

Question 33

What is the relationship between the distance between 2 atoms and the potential energy?

Answer 33

At distance sigma (the size of the atom), the potential energy is 0v.
As they come closer, dipole-dipole interactions occur resulting in a slightly negative potential energy.
As they get even closer, the attraction increases, resulting in more negative potential energy, until an optimum energy minimum value is reached (epsilon).
If the atoms get any closer, the potential energy will start to increase back towards 0v as the overlap in atomic orbitals results in repulsive forces which forces them apart.

Question 34

What is the difference between CoMFA and CoMSIA models?

Answer 34

CoMFA models generate 2 maps: a steric plot, showing where steric bulk is desirable and undesirable, and an electronic plot, showing where electron rich and poor areas are optimal.

CoMSIA considers size, electrostatic potential, hydrophobic properties, and H-bond donor/acceptor capability. There are maps: a steric plot, showing where steric bulk is desirable and undesirable, an electronic plot, showing where electron rich and poor areas are optimal, and a hydrophobic map, where hydrophobic and hydrophilic areas are optimal.

Question 35

How would CB1R antagonists be used as anti-obesity drugs?

Answer 35

Cannabinoid receptor 1 (CB1R) is a G-coupled protein receptor activated by endogenous cannabinoids such as anandamine and 2-AG. Agonist binding results in signalling through a Gi cascade which causes inhibition of intracelullar adenylate and subsequent reduction in cAMP.
In central CB1Rs (found in hypothalamus and nucleus accumbens), this drives feeding behaviour. In peripheral CB1Rs (adipose tissue, liver, GIT, muscle), this causes insulin resistance and increased triglycerides.

Basically causes increased food intake and fat storage and weight gain, so inhibition would prevent it.

Question 36

What does the pharmacophore of CB1R ligands include?

Answer 36

H-bond acceptors
Aromatic rings
Hydrophobic groups

Question 37

Describe the hydrolysis of cyclic guanine monophosphate (cGMP) by phosphodiesterase.

Answer 37

1. Zinc acts as Lewis acid to activate phosphorous oxygen bond in phosphate of cGMP, make the phosphorous more electrophilic.
2. Lone pair on incoming water attacks electrophilic phosphorous atom.
3. Phosphorous-oxygen double bond opens up and then reforms as it pushes out the alkoxy (O-R) leaving group at the 3’ position of the ribose ring, breaking this cyclic structure.
4. Outgoing alkoxy group picks up proton from adjacent His613 residue on enzyme.
5. This produces guanine monophosphate (GMP)

Question 38

How do PDE inhibitors work?

Answer 38

PDE inhibitors prevent degradation of intracellular messengers cAMP and cGMP, thus improving intracellular signalling.

The result depends on which PDE isoform is targeted.

Question 39

Briefly describe the development of Mardepodect for treatment of schizophrenia.

Answer 39

1. Excessive dopamine signaling in the striatum may directly lead to psychotic symptoms in schizophrenia. PDE10A found in striatum area of the brain and, due to impacts on cyclic nucleotides, impacts dopamine signalling.
2. Compound library screened in PDE10A affinity assay. Triaylimidazole 10 was identified.
3. Co-crystallisation of triaylimidazole 10 with PDE10A revealed interactions which explained its good affinity and high selectivity.
4. A second round of screening was performed to find compounds which: fit the selectivity pocket, could form H-bonds with Tyr-693, and obeyed certain physicochemical parameters which promote BBB permeability. Compound 11 identified.
5. Removal of a methylene group from compound 11 produced compound 12 which had a different orientation in the binding pocket resulting in an additional H-bond. This improved binding affinity, ligand efficiency, and reduced molecular weight.
6. Compound 12 undergoes in vivo conditioned avoidance response (CAR) test and does not perform well unless at extremely high concentrations.
7. Compound 12 optimised to produce Mardepodect.

Question 40

What is a conditioned avoidance response (CAR) test?

Answer 40

1. Animal is conditioned by simultaneous exposure to the conditioning stimulus (e.g., a sound) and an unconditional stimulus (e.g., mild electric shock).
2. In response to unconditioned stimulus, the animal will try to escape/avoid it. In doing so, it will begin to associate the conditioning stimulus with this.
3. After this, exposure to only the conditioned stimulus will result in the same avoidance behaviour.

Question 41

What does the pharmacophore of PDE10A inhibitors include?

Answer 41

4-pyridine moiety.
Methylation of pyrazole.
Quinoline ring system.