Lecture 9 - Fragment Based Approaches to Drug Discovery Flashcards
(17 cards)
What are fragments (what properties do they have)?
Low weight, small organic molecules with < 20 non-H (heavy) atoms
What is a fragment library? Give an example of a rule used to construct them. What factors should be considered constructing?
- Database containing fragments with good physicochemical properties
- Ro3 most commonly used
- Diversity, complexity, aq. solubility, lipohphilicity
What is the rule of three (Ro3)?
Fragments must:
- Have MW < 300 Da
- < 3 H bond donors/acceptors
- ClogP </= 3
What is bioassays screening method and what are advantages/disadvantages? (robust, false +ves, solubility, sensitivity)
- Testing against enzyme/protein
A:
- If robust in presence of high conc. ligand, rapid and quantitative method for detection
- Requires little protein
D:
- False +ves due to compound aggression/interference with assay endpoint/disruption of protein
- Compound solubility in assay buffers challenging
- Lack sensitivity to identify weakly binding fragments
What is capillary electrophoresis (CE) screening method? Advantages and disadvantages. (what it detects, protein, size, purity, immobilisation, aggregation, ic50, docked ligand)
- High-resolution technique, detects both high and low affinity molecular interactions
A:
- Low protein consumption, no size limit, don’t need high purity
- Solution based so don’t need immobilisation
- Insensitive to aggregation
- Generates iC50 data
D:
- Doesn’t offer insight info into docked ligand that X-Ray might
What is NMR screening method, types and advantages/disadvantages of each?
- Monitors changes in 1H/13C/15N correlation signals for labelled protein when binding to test compound
- If ligand based, relies on changes in ligand signals when binding to target
- 19F use recently has interest
Target based:
A:
- Generates binding affinities eben for weak ligands
- Detects nM –> mM interactions
- Provides structural info on binding site
D:
- Requires large amount of isotopically labelled protein
- Not all proteins required size/solubility
Ligand based:
A:
- Doesn’t require labelled protein
- Lower protein consumption
D:
- Issues detecting strong binders
19F NMR:
A:
- Faster/more robust than 1H in ligand based screening
D:
- Compounds must be 19F labelled
What is X-Ray screening method and advantages/disadvantages? (false +ves, use of techniques, ligands, resources, affinity, solubility)
- Uses X-ray crystallography as detection technique
A:
- Less false +ves as compound is seen via crystallography
- Assesses how to enhance binding by using modelling techniques/purchase of related analogues
- Different ligands may occupy different volumes of binding site, allows “linking” to enhance binding affinity
D:
- Time/resource intensive, large protein construct needed (requires 10-50 mg with > 95% purity)
- No affinity info
- Fragment ligands need to be soluble in medium
What does mass spectrometry screening method involve? Advantages/disadvantages. (immobilisation, conjugation, flase +ves, aggregation)
- Protein-small molecule complexes observed under careful conditions
A: - Requires v. small amounts of protein
- Don’t need to worry about effects of immobilisation/conjugation
D: - Can lead to false +ves due to aggregation
What does surface plasmon resonance (SPR) screening method involve? (A + D)(sensitivity, labels, libraries)
- Powerful tool for studying biomolecular interactions in sensitive, label-free format
A: - Can evaluate larger libraries of compounds
D: - Protein/ligand must be immobilised
What does thermal shift assay screening method involve? (protein stability, markers, ligands)
- Monitors changes in protein stability to identify fragments
- As T rises, protein unfolds and exposes hydrophobic core
- This can be measured by binding to fluorescent marker
- Ligands that bind to protein increase protein stability
What is virtual fragment screening and how does it work? Advantages?
- Computational technique for filtering fragments with desired bio. activities from fragment libraries
- Does this by docking fragments to particular targets and calculating binding affinity between them
- Reduces time, cost, expertise
What is a binding subpocket and how is it made?
- Smaller structural domain of active pocket that fragments bind to target protein through via steric, electrostatic, van der Waals and H bonding interactions
- Made by subdividing binding cavity of target protein
What is a pharmacophore?
- Molecular feature required for ligand to be recognised by target protein
- In FBDD, core fragment = pharmacophore structure
What is a core fragment? (properties: binding shape and affinity)
- Specific fragment with highly conserved binding pose and effective affinity contribution to binding
- In FBDD, core fragment = pharmacophore structure
How does fragment growing work? (Describe process) Why is it a good technique? (what is conserved, what can be monitored)
- Starts from core fragment placed at binding site
- Other suitable fragments linked to core fragment to improve binding affinity
- Newly assembled compound conserves binding mode of initial fragments
- Good strategy as every subtle change in binding mode can be monitored
What is scaffold hopping used for and how is it achieved? What is a scaffold? (novel compounds, ADMET)
- Used to discover novel compounds containing topologically different scaffolds but similar bioactivities from known parent compounds
- Scaffold consists of ring systems and linker moieties between rings, extracted by removing all other substituents from original compound
- To achieve scaffold hopping, heterocyclic ring replacement and ring closure/opening methods used
- Used to improve ADMET properties and to overcome patent limitations for current leads
What is bioisosterism? What are bioisosteres?
- Atoms/groups/whole molecules with similar shape/volume/electron distribution/physicochemical properties may produce broadly similar bio effects
- Bioisosteres = when 2 or more functional groups/molecules have similar physicochemical properties and share wide range of similar bio activities
