Section 5 Flashcards
What is lead optimisation?
An iterative process where the initial biological lead is chemically modified to produce new analogues.
What are the 5 characteristics of an ideal clinical candidate?
Potency
Selectivity
Efficacy
Physical and pharmaceutical properties.
Optimal safety profile.
What does lead optimisation cover?
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.
What is the effect of drug-target binding on enthalpy and entropy?
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).
What does thermodynamics refer to in drug discovery?
The heat changes that occur when biomolecules interact.
What is enthalpy-entropy compensation?
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.
How do enthalpy, entropy, and Gibbs free energy relate to drug-binding affinity?
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).
What are the 7 common types of non-covalent interactions in order of strength?
- Ionic bonding
- Dipole-dipole interactions
- Hydrogen bonding
- Ion-dipole interactions
- Cation-pi interactions
- Pi-pi interactions
- Van der Waals interactions
What do ionic/electrostatic interactions take place between?
Cationic (+) and anionic (-) species.
What do dipole-dipole interactions take place between?
Areas of high electron density (partially negative) and low electron density (partially positive)
What do hydrogen bonding interactions take place between?
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)
What do ion-dipole interactions take place between?
A formally charged species (e.g., Mg or Zn in the catalytic site of an enzyme) and a polar functionality.
What do cation-pi interactions take place between?
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).
What do pi-pi interactions take place between?
2 aromatic partners, dependent on the differential electron density around each system.
How do Van der Waals interactions take place?
Formation of temporary dipoles generated through fluctuations in electron density around the ligand or area of the protein target.
How are covalent bonds most commonly formed in ligand binding?
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.
What is a Michael addition reaction?
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).
Give an example of a Michael addition reaction.
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.
How does stereochemistry affect binding in the case of adrenaline?
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).
What are congeners?
Compounds with the same core structure but varying functional group apendages.
How can congeners be used to determine SARs?
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.
What does the Hammett equation do?
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.
What does logP indicate in terms of membrane permeability?
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.
What is the Hansch-Fujita constant?
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.
What is the difference between logP and logD?
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.
Name 2 methods to quantify molecular substituents for SAR studies.
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.
What is the STERIMOL programme used for?
Determines the length of a substituent from the parent molecule (L) and the width from the plane in 4 directions (B1-4).
How can the results of the STERIMOL be related to biological activity?
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.
What is a pharmacophore?
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.
What is the receptor-excluded volume and receptor-essential area of a drug?
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.
What are CoMFA and CoMSIA?
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.
What is a conformer?
A stereoisomer produced by rotation about a sigma (σ) bond.
What is the relationship between the distance between 2 atoms and the potential energy?
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.
What is the difference between CoMFA and CoMSIA models?
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.
How would CB1R antagonists be used as anti-obesity drugs?
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.
What does the pharmacophore of CB1R ligands include?
H-bond acceptors
Aromatic rings
Hydrophobic groups
Describe the hydrolysis of cyclic guanine monophosphate (cGMP) by phosphodiesterase.
- Zinc acts as Lewis acid to activate phosphorous oxygen bond in phosphate of cGMP, make the phosphorous more electrophilic.
- Lone pair on incoming water attacks electrophilic phosphorous atom.
- 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.
- Outgoing alkoxy group picks up proton from adjacent His613 residue on enzyme.
- This produces guanine monophosphate (GMP)
How do PDE inhibitors work?
PDE inhibitors prevent degradation of intracellular messengers cAMP and cGMP, thus improving intracellular signalling.
The result depends on which PDE isoform is targeted.
Briefly describe the development of Mardepodect for treatment of schizophrenia.
- 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.
- Compound library screened in PDE10A affinity assay. Triaylimidazole 10 was identified.
- Co-crystallisation of triaylimidazole 10 with PDE10A revealed interactions which explained its good affinity and high selectivity.
- 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.
- 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.
- Compound 12 undergoes in vivo conditioned avoidance response (CAR) test and does not perform well unless at extremely high concentrations.
- Compound 12 optimised to produce Mardepodect.
What is a conditioned avoidance response (CAR) test?
- Animal is conditioned by simultaneous exposure to the conditioning stimulus (e.g., a sound) and an unconditional stimulus (e.g., mild electric shock).
- 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.
- After this, exposure to only the conditioned stimulus will result in the same avoidance behaviour.
What does the pharmacophore of PDE10A inhibitors include?
4-pyridine moiety.
Methylation of pyrazole.
Quinoline ring system.
