Theme 6- Lead Optimisation Flashcards
Which parameters are improve in the optimisation of a lead compound?
-Potency
-Selectivity
-Physicochemical Properties
-Pharmacokinetics
-Toxicity/safety
What are the differences between binding IC50 and functional IC50?
Binding IC50 is the binding with the purified form of the target protein while functional IC50 is the Cell based assay or potential in vivo approach- disease porfile in an animal
Explain How is primary assay work?
1st- The enzyme is purified and incubated with the substrate to make the normal role and produce the product.
(Measure the amount of product)
2nd- The molecule inhibitor is introduced which binds
allosteric or orthostatic
3rd The concentration of the product is mesuare
4rst. A Dose response curve can be obtain
Explain How is secondary assay work?
Generally measure potency and efficacy in a more complex testing system.
Which parameter primary assay measure?
Generally measure potency and sometimes selectivity towards a target
Which parameters secondary assay measure?
Generally measure potency and efficacy in a more complex testing system.
-With secondary assay we are able to know:
1. Metabolic activity
2. Diffusion cross membrane
3.Present of efflux pump (might pump molecule back out the cell)
4. Trapping
Diferences between primary and secondary assays?
Primary assay is carry out in an homogenous solution while secondary assay used a cell conditions.
What is potency? How is measure?
Potency is the concentration of compound required to
achieve desired effect. Potency usually measured as IC50 or EC50
What are the differences between IC50 and EC50?
IC50 is for antagonist and EC50 is for agonist.
Provide the usually potency values for the following assays:
- Primary assay
- Secondary assay
- In vivo assay
- <10 nM in isolated biochemical assay (primary assay)
- < 100 nM in cellular assay
(secondary assay) - ⩽ 50 mg/kg in animal model of disease (in vivo assay)
Define MED and MED50 ? Which assay you can do to measure this parameter?
MED (minimum effect dose) = lowest dose that
produce significant desirable effect.
MED50= dose that produce 50% of maximal responses
- MED can be calculated in an in Vivo assay
Define efficacy
Efficacy is a parameter that refers to the degree of effect of a compound. Usually measured as a percentage
compared to a standard (100%).
-Target efficacy is disease specific.
What is selectivity?
The ability of a compound to act on a specific target with minimal activity against
other biological targets.
Important: Primary, secondary and in vivo assays
used to monitor off-target effects with ratios >10-50 fold in favour of the disease t arget usually required
Bisoprolol is clinically established drug for the
treatment of numerous cardiovascular
diseases
- why would experimental compounds NDD-713 or NDD-825 be better suited for these conditions in patients with concomitant
respiratory conditions such as asthma or COPD? - Which of the two experimental compounds
would you progress first and why?
- The main driving factor here is the superior β1/β2 selectivity profile offered by NDD-713 and NDD-825 at the measured concentrations.
- Whilst both
compounds are good, I would select 825 as the compound to initially
progress further. It has a better overall off-target selectivity profile and whilst
it is does not display as high a % inhibition at the β1-AR, its value at the β2-
AR is very small and therefore provides a better β1/β2 selectivity profile
than 713.
Explain the concept of Lipophilicity. Which value provides infomation of this property?
Affinity of compound for lipophilic environment
- LogP most commonly reported value to
define this property
- For drug molecules containing an ionisable
group, LogD is a more useful
measurement
Which are the typical LogP values in orally available drugs and the drugs that needs BBB penetreation?
- 2-4 for orally available drugs
- 3-5 for drugs requiring BBB penetration
Why is solubility important in a drug design?
The drug need a passage through numerous aqueous compartments means acceptable solubility in this medium is critical.
- A compound must be in solution in order to be permeable
why permeability relies upon a compound’s solubility and lipophilicity?
To reach the desired molecular target a drug molecule needs to be
-Lipophilic enough to permeate a cell membrane
-Hydrophilic enough to be soluble
Solubility depends of some molecule characteristic. Which ones ?
*Functional groups
*Physical properties of the solid
What are the typical values of solubility at physiological pH?
At physiological pH solubility values are typically in the range 5-100 μM
Provide the name of a common primary assay and how it works.
primary assays such as a parallel artificial membrane permeability assay (PAMPA)
PAMPA: rate of passage through an artificial membrane.
This use an individual cell
Provide the name of a common secondary assay and how it works.
Common secondary assay is the Caco-2 assay
-Measures rate of transit through a monolayer of epithelial cells
- Helps to quantify if the drug is back out if there is pump molecules that are again absorption.
Complete
How apparent permeability coefficient Papp is calculate?
Explain the permability if the permeability coefficient Papp have the next values:
- Papp < 5 x 10^-6 cm/s
- Papp > 20 x 10^-6 cm/s
So compounds with Papp < 5 x 10^-6 cm/s display poor Caco-2 permeability and those with Papp > 20 x 10
^-6 cm/s display high Caco-2 permeability.
How to measure in vivo metabolic stability?**
In vivo metabolic
stability may come from an in vitro assay based on incubation of the compound
with liver microsomes that contain active metabolic enzymes.
How liver microsomes are obtained?
Liver microsomes are obtain with 3 homogenize and then centrifugation steps to collect in a pellet- re-homogenization (make the process again).
Equation of oral bioavailability.
Measures the conc. of dug in the blood following oral
dosing, as compared to the conc. following intravenous dosing
What is a ligand efficiency? provived the equation.
-Assesses and compares compounds on the basis of how efficiently they bind (affinity).
Which is the ligand efficiency of two compounds A & B that have the following properties ?
- Both compound have identical IC50
values of 10 nM
- Compound A HAC = 30 -Compound B HAC = 40
How Lipophilic Ligand Efficiency is calculated?
Name the Lipinski rules: rule of five.
Name the variation of lipinski rules:rule of three
Name the veber rules.
Name the veber rules.
Explain the image.
The HIV drug maraviroc was developed by lead optimisation of a hit found by high-throughput screening.
Compare the structure of maraviroc to that of the original hit and identify three strategies that were applied
during lead optimisation and incorporated into the drug molecule
The compound below, Daltroban, is a thromboxane antagonist.
Design two new compounds, each containing one fluorine atom.
Explain what changes the incorporation of the fluorine atom should impart onto the new analogue
compared to Daltroban.
In compound A, addition of a fluorine atom meta to the aryl sulfonamide may decrease
metabolism, increase lipophilicity and gain additional interactions with the target, such as a
hydrogen-bonding interaction. In compound B, introduction of a fluorine atom at the α
position to the carboxylic acid would reduce the pKa of the acidic hydrogen. (A second
fluorine atom at the α position would further decrease the pKa). It may also change
lipophilicity, and make additional binding interactions with the target.
There are plenty of other suggestions you could make so please do think the detail above is
exhaustive
AVPI is a tetrapeptide that mimics activity of the protein Smac. The Smac protein binds and inhibits the protein XIAP. Therefore AVPI is a potential starting point (hit) for a drug discovery effort targeting inhibitors of the protein XIAP.
Identify two groups that could be replaced with isosteres and design two different molecules that incorporate two isosteric replacements.
Using the same AVPI peptide, assume that the pharmacophoric elements are those in red.
Design two different molecules that incorporate conformational constraints. The molecule is drawn in a way that is suggestive of the active conformation.
** A literature search for “conformational constraint” in the Journal of Medicinal Chemistry gives over 30
examples for the years 2016–2017. One article describes a series of conformationally restricted gamma secretase inhibitors that were evaluated as potential Alzheimer’s drugs (J. Med. Chem. 2017, 60, 2383–2400). Identify the two different conformational constraints that were introduced to the lead compound. These
compounds will need to penetrate the blood-brain barrier, so describe the effect of modifications on the cLogP.
The lead compound was first modified to maintain the key hydrogen-bond acceptor, and introduce a conformational constraint to afford a series of oxadiazines (19–25).
Further modification introduced a second constraint in the aryl ether linkage to give heterocyclic oxadiazines.
An excellent example of rational drug design is seen in the development of the histamine H2 receptor antagonists.
Burimamide was identified as the first selective H2 receptor antagonist. However, Burimamide did not translate well due to poor bioavailability in humans. The pKa of imidazole in burimamide is 7.3 which increase [dication] in GI tract and decrease permeability and absorption. Also, lack of 4-methyl group favours Nπ -tautomer.
Indicate how the addition of the red groups in the chemical structure optimised the molecule.
- EW effect of the sulfur atom
helps balance the electron donating effect of the
4-methyl group - Metiamide was both bioavailable and possessed
excellent in vivo activity, eliminating gastric ulcers
within 3 weeks of dosing
Note: Inserting a methyl group into the 4-position of the imidazole ↑pKa and further diminish oral bioavailability
