Lecture 4: Peptide-derived ligands Flashcards
(26 cards)
Can we already target all proteins with medication? Why yes or not?
No. There is only a portion of proteins related to diseases (~27%) - number will likely grow in the future
- from that only 3% are already targetted, and 7% seem to pose potential
- The “undruggable” ones usually lack a distinctive binding pocket (very often happens if there is protein to protein binding, but some interaction sites can be targetted) or they are located inside the cell
NOTE: when proteins bind to one another they often rely on specific organization of secondary structures -> even small alterations of those can disrupt the binding
Look at the Kinetics and Thermodynamics:
Research focuses on stabilizing the small peptide structure in the folded state (even though unfolded seems to be favoured)
Recap of protein states
Proteins usually exist in native states but have also other possible favoured states - often times tend to be unfolded
-> the larger structure gets the more likely it is to end up folded
- There are also global minima that cannot go back (usually aggregates)
What is the “easiest” way to stabilize small peptides?
- Adding a molecule that can bind to sides of the peptide that need to be kept in place for the secondary structure to fold = microcyclization
- E.g. at the ends of a loop
What is meant by Peptidomimetics?
= small peptide molecules that can mimic the natural peptides
A) Slightly modified - only focus on altering amino acids
- do NOT efficiently penetrate the cells, but have high affinity
B) More changes - more minor alterations e.g. side chains
= both still peptidic
C) Molecules with small molecular core and only few small residues in peptidic form
D) Molecules that mimics actions e.g. bind to similar regions
- easier to get them inside a cell, BUT lack specificity, affinity to target
=> try to find the golden route between affinity and efficiency
What kind of turns can we have?
Each of the turns has different position of H (they are defined by a hydrogen constrain)
E.g. H is placed in between carbonyl group at position i and NH group at position i+2
How can we mimic turns/loops?
- Microcyclization
- Induce a turn that wouldn’t have occured naturally
- Give preference to H that will form the desired bond
- Look for a scaffold that will bring the turns into correct position
Look at examples of structural mimetics:
How can beta-sheets look like?
Parallel X anti-parallel (more stable) -> this is what will be pursued
How can we stabilize the beta-sheets?
1) Find the turn to connect antiparallel ends
2) Include amino acids that will force a bond (and doesn’t occur normally)
3) Microcyclization between side-chains or between termini
4) Structural can mimic a single strand
NOTE: rarily do we use just one
Look at an example of turn mimetics of beta-sheets:
Look at an example of enforcing amino acids in beta-sheet.
Replace natural amino acid -> support beta-sheet arrangement along the sheet but also with the opposing beta-sheet
Look at the microcyclization in beta-sheets.
Look at the structural mimetics in beta-sheets.
Very difficult as beta-strands don’t usually exist alone -> they can onlt form in relation to alpha helix or another beta strand to form beta sheet
What determines the nomenclature of helices?
There are different types of helices - they differ based on the placement of H bonding
Nomenclature is determined by
- the number of residues participating in one turn e.g. 3
- the number of atoms within the turn e.g. 10
=> but more often we just use names e.g. alpha helix, pi-helix
How do the helix mimetics look?
1) Pick 2 residues of the helix that are close to another -> constrain them with another molecule
2) Foldamers - amino acids that promote helical fold
3) N-terminal cap
4) Structural mimetics
Look at example of class A helix mimetics.
Can also be switchable
Look at example of class B helix mimetics.
Look at example of class C (structural) helix mimetics.
What are pseudomonas aeruginosa?
- normally occuring bacterium
- BUT if our immunity is compromised (e.g. in the hospital) -> it can induce infections of burn wounds, pheumonia, eye infection
How does the bacterium function?
Bacterium injects ExoD enzyme into the host cell -> needs to associate to a human adaptor protein (14-3-3) -> only then can it, via internal pathway, change metabolic activity of the cell which could induce apoptosis
Look at a close-up of the interaction.
Research focused on mimicking the ExoS sequence
- wouldn’t look like this in solutions -> needs stabilization
-> testing of different combinations
What did they use in the end?
Utilized hydrophobic cross link - i.e. introduced non-natural amino acids -> close these and get rid of the double bonds
Look at the resulting molecule.
High affinity molecule
- orange = new, grey = original
- structure constraint
