Small-Molecule Library Screening: Hit Identification & Optimization

Hit Identification: Optimizing the Compound Library

As mentioned in the introduction to this chapter, compound library screening is used to identify an organic molecule that will serve as a starting point for designing an efficient and safe molecule to use in disease treatment. Since the space of small organic molecules is enormous and contains an endless number of compounds, we need rules to help limit the number of molecules in the libraries used for screening. Below, we’d like to discuss some basic compound filtering techniques used in the process. There are, of course, many other rules that can be applied to various cases. However, they are not discussed in this context.

Library Filtering: Analyzing Protein-Ligand Interactions

At the initial filtering step, perhaps the most significant factors to consider are the shape and physicochemical complementarity between the ligand and the binding site. This includes the molecular interactions that contribute to stabilizing ligand binding:

• Hydrophobic interactions
• Hydrogen bonds
• Electrostatic forces (salt bridges)
• Helix dipoles
• Aromatic-aromatic interactions
• Entropic effects
• Water molecules

The relative importance of these interactions depends on the energy involved. For example, hydrogen bond energy ranges from 2 to 10 kcal/mol, while electrostatic interaction energy varies from 3 to 5 kcal/mol, depending on the distance and polarity of the environment. By analyzing the nature of amino acid residues within the protein’s binding site, we can create a so-called pharmacophore model that can help select compounds that satisfy the interactions. This significantly reduces the total number of compounds to include in the library. A pharmacophore model can also be applied in other contexts, such as virtual screening of a compound library and ligand-based drug design.

Library Filtering: Lipinski’s Rule of 5

To limit the chemical space when preparing suitable screening libraries, empirical rules have been developed from analyzing existing small-molecule drug molecules, in addition to physical interactions described above. Lipinski and his colleagues defined the so-called Lipinski’s rule of 5. These rules state that an orally active drug should not have more than one violation of the following criteria:

• Mw < 500 g/mol
• Hydrogen bond acceptors < 10 (N and O)
• hydrogen bond donors < 5 (OH and NH)
• logP < 5 (logP=log ([C-octanol]/[C-water])

logP describes the distribution of the compound in an octanol-water system, where [C-octanol] and [C-water] represent the concentrations of the compound in the octanol and water phases, respectively.

When combined with a pharmacophore model, these rules will significantly reduce chemical space, making the screening task much easier to manage. Of course, other methods are also employed to limit the size of a compound library. One such method involves the use of fragment libraries.