Fragment-based lead discovery

Library design

In analogy to the rule of five, it has been proposed that ideal fragments should follow the 'rule of three' (molecular weight

Library screening and quantification

In fragment-based drug discovery, the low binding affinities of the fragments pose significant challenges for screening. Many biophysical techniques have been applied to address this issue. In particular, ligand-observe nuclear magnetic resonance (NMR) methods such as water-ligand observed via gradient spectroscopy (waterLOGSY), saturation transfer difference spectroscopy (STD-NMR), 19F NMR spectroscopy and inter-ligand Overhauser effect (ILOE) spectroscopy, protein-observe NMR methods such as 1H-15N heteronuclear single quantum coherence (HSQC) that utilises isotopically labelled proteins, surface plasmon resonance (SPR), isothermal titration calorimetry (ITC) and Microscale Thermophoresis (MST) are routinely-used for ligand screening and for the quantification of fragment binding affinity to the target protein. At modern X-ray crystallography synchrotron beamlines, several hundred data sets of protein-ligand complex crystal structures can be obtained within 24 hours. This technology makes crystallographic fragment screening possible, i.e. the use of X-ray crystallography directly for the fragment screening step.

Once a fragment (or a combination of fragments) have been identified, protein X-ray crystallography is used to obtain structural models of the protein-fragment(s) complexes. Such information can then be used to guide organic synthesis for high-affinity protein ligands and enzyme inhibitors.

Advantages over traditional libraries

Advantages of screening low molecular weight fragment based libraries over traditional higher molecular weight chemical libraries are several. These include:

• More hydrophilic hits in which hydrogen bonding is more likely to contribute to affinity (enthalpically driven binding). It is generally much easier to increase affinity by adding hydrophobic groups (entropically driven binding); starting with a hydrophilic ligand increases the chances that the final optimized ligand will not be too hydrophobic (log P
• Higher ligand efficiency so that the final optimized ligand will more likely be relatively low in molecular weight (MW
• Since two to three fragments in theory can be combined to form an optimized ligand, screening a fragment library of N compounds is equivalent to screening N2 - N3 compounds in a traditional library.
• Fragments are less likely to contain sterically blocking groups that interfere with an otherwise favorable ligand-protein interaction, increasing the combinatorial advantage of a fragment library even further.

References

References

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