Lecture 2: Rational design, new modalities Flashcards
The Drug Development Process
Research
Development
Commercialisation
Flow Chart of Drug Discovery
- Identify and define medical needs
- Research on disease mechanism:
Identify and validate targets (receptors) involved in disease processes - Search for lead compounds that interact with the targets
- Optimize the properties of the lead
compounds to generate potential drug molecules - Perform drug development and pre-clinical studies (in vitro and in vivo studies)
Structure Based Drug Design
Ligand Based: Knowledge of structures of ligands allows development of a
“pharmacophore”
Receptor Based: Knowledge of structures of receptors allows in silico screening and modelling/prediction of interactions.
Complex Based: Knowledge of structures of complexes allows very detailed analysis of interactions and structure based design.
Methods available for high resolution
structure determination:
X-ray crystallography,
NMR spectroscopy,
Cryo-Electron Microscopy
X-ray crystallography advantages and disadvantages
Advantages:
Very high resolution and accuracy. Ideal for complexes. Ideal for large proteins. Fast to generate data for different ligands.
Disadvantages:
Requires crystals. Packing artefacts. Not ideal for dynamics.
NMR spectroscopy advantages and disadvantages
Advantages:
In solution – as in real life! Good for dynamic systems. Allows monitoring of binding events – screening.
Disadvantages:
Lower resolution, can be time consuming. Requires solubility of analytes. Limited to smaller proteins.
Cryo-EM
- Collect 2D images of different
orientations via electron beams - Reconstruct a 3D map
- Model protein within map
Ads
- Easier sample prep and low amounts
- Excellent for big proteins and complexes
Nuclear Magnetic Resonance
(NMR) in Drug Design
- A technique for determining molecular
structures (Ligands, Receptors, Complexes) - Based on magnetic properties of nuclei
- Certain nuclei have a ‘spin’ and a ‘magnetic moment’ (e.g. 1H, 13C, 15N, but not 12C)
- Applications in drug design often involve isotope labelling strategies to utilize these nuclei.
Resonance Frequency
-Chemical Shift
- Reflects the local environment at each
individual nucleus. - Electrons surrounding a nucleus provides shielding from the magnetic field.
- Affected by neighboring atoms.
- Range: 10 ppm for 1H and a couple of
hundred ppm for 15N and 13C. - Spectrometers are 500 MHz-1.2 GHz for 1H
- Higher field spectrometer -better sensitivity and dispersion of signals!
Pharmacophore
- Map of key features based on knowledge of structures of several ligands
- Can be used to predict binding to a
receptor and guide exploration of
modifications to increase binding and
selectivity.
In silico screening
- Take known structure of target protein
- Use computers to “dock” potential ligands into active sites on protein surface
- Rank potential ligands
– Quality of fit
– Drug-like properties
– Ease of synthesis - Test hypothesis by making compounds
SAR by NMR
structure-activity relationships (SAR) are obtained from NMR. With this technique, compounds with nanomolar affinities for the FK506 binding protein were rapidly discovered by tethering two ligands with micromolar affinities
- Find molecules that bind
- Optimise
- Discover 2nd ligand
- Optimize 2nd ligand
- Link fragments
Thermodynamic principles of
linked fragment approach
Free energies of binding are (roughly) additive, so effects on binding constants are multiplicative
SAR-BY NMR:
development of FKBP inhibitors
FKBR binds calcineurin and a floating thing (?lol)
Biological effect:
* Stops activity of calcineurin and
inhibits T-cell proliferation
SAR by NMR: disadvantages
- Requires the NMR data of the target
protein to be assigned - Relatively large library
– Large number of samples to be screened
– Large amounts of 15N protein (a few
hundred milligram) - Not easy to find two compounds that can bind in a way they can be linked –
fragment expansion may be easier
What makes a good drug?
Lipinski’s Rule of Five
The “rule of 5” states that: good absorption/permeation and oral
availability is more likely when:
A. There are no more than 5 H-bond donors (expressed as the sum
of OHs and NHs);
B. There are no more than 10 H-bond acceptors (expressed as the
sum of Ns and Os).
C. The MWT is less than 500;
D. The LogP is less than 5;
The Rule of 5 got its name from the cut-off values for each of the four parameters that define the “drug-likeness” of potential drug candidates: all of these values are close to five or a multiple of five.
“We found that the sum of Ns and Os in the molecular formula was greater than 10 in 12% of the compounds. Eleven percent of compounds had a MWT of over 500. Ten percent of compounds
had a CLogP larger than 5 and in 8% of compounds the sum of OHs and NHs in the chemical structure was larger than 5.”
