How to Choose A Library for Screening?

In this article in our series on structural biology and structure-based drug discovery, we further discuss methods and benefits of fragment screening and how to select a fragment library. As I mentioned in the previous post, screening is central to any drug design strategy we may choose. Screening aims to identify a molecule (hit identification) or a series of compounds that bind to the drug target and modify its activity. Before the start, we need to define two essential factors: the type of library (fragment or drug-like compounds) we want to use and the screening method.

How do I choose the library? We know that the chemical space is endless. However, the good news is that there is no need for a library with billions of molecules. We can limit the number of compounds to be screened in many ways. One of the best-known is Lipinski’s rule of five, which can be used in the choice of a library of orally available drug candidates (Lipinsky et al., 2001). This is an empirical rule based on the analysis of known drug molecules. The rule states 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 ([Coctanol]/[Cwater])

logP is needed to ensure the molecules’ solubility is at a certain level. It describes the distribution of the compound in an octanol-water system, where [Coctanol] and [Cwater] represent the concentrations of the compound in the octanol and water phases, respectively. These conditions will limit the potential number of compounds in the library. We could further narrow our choice by selecting compounds similar to known lead compounds (lead-like compounds) or targeting a particular target class by defining shape complementarity to fit a specific binding site. Another essential factor, of course, is the chemistry of the compounds. They should be easy to modify chemically and should not contain atomic groups known to trigger a toxic response or unwanted reactions. Limiting the number of rotatable bonds (a maximum of seven) is also considered to be an essential parameter (Veber et al., 2002).

Fragment-based lead discovery is an alternative to drug-like or lead-like compounds. A clear benefit of a fragment library is that it can be constructed to sample a much larger chemical space than lead-like or drug-like libraries. It has gained considerable popularity due to its benefits and efficiency in identifying a pharmacophore. A pharmacophore describes the interactions that contribute to ligand binding and can be used to design new compounds during hit-to-lead optimization. Another benefit of fragment-based screening is that it uses a relatively small library with compounds having molecular weights in the 100-300 Da range. The small size of the fragments will minimize unfavorable interactions, such as steric repulsion, thereby increasing the probability of binding to the target protein and the hit rate. This will identify weakly potent and biologically active molecules. Complexes of these molecules with the target can be studied with X-ray crystallography or NMR spectroscopy. The three-dimensional structure will guide the expansion and optimization of affinities and specificities into potent leads.

For constructing a fragment library, the rule of three has been suggested (Congreve et al., 2003):
MW 100-300
LogP ≤ 3.0
H-Bond Acceptors ≤ 3
H-Bond Donors ≤ 3
Rotatable bonds ≤ 3
Polar Surface Area ≤ 60 Å2

Crystallography fragment screening and NMR spectroscopy can be used for hit identification and studying compound binding. Generally, in fragment screening, biophysical methods quickly became the first choice because they provide a rapid, efficient assessment of the binding of weak hits, which can be challenging to identify in biochemical assays. Other methods used in fragment screening include:

Surface plasmon resonance (SPR)
Thermal shift assay (differential scanning fluorimetry, DSF)
Weak affinity chromatography (WAC™)

SARomics Biostructures’ integrated structural biology services include fragment screening and hit identification using crystallography and NMR spectroscopy, as well as WAC™ screening techniques. WAC™ is a proprietary method jointly owned by SARomics Biostructures and our partner, RG Discovery. The method uses a chromatography column to inject a solution of fragments or lead-like compounds. During elution, the fragments with a higher affinity for the protein will stay on the column longer than those with a low affinity. Mass spectrometry can conveniently detect and identify the fragments, thus establishing a direct ranking of hits. WAC™ is an efficient, high-throughput, and lower-cost alternative to other biophysical screening methods. In addition, we offer our proprietary library of MedChem-friendly, low-molecular-weight fragments, designed to be general-purpose (non-target-directed), covering a diverse range of chemical space. Of course, customers’ libraries may also be used for screening. Please refer to our blog article for more information on the WAC method.

Another popular approach involves creating DNA-encoded libraries (DELs). DELs offer the advantage of enabling even greater chemical space coverage (see our blog post on our collaboration with Vipergen).

We will continue this series of posts on structural biology and structure-based drug discovery and design. Follow us on LinkedIn to ensure you do not miss our future posts!