Chemical libraries have long been a mainstay in the search for new pharmaceutical compounds, and they have been created using many different paradigms. Vast diverse collections of unique compounds have been screened at high throughput to find appropriate effects on target proteins. Such large libraries continue to be used for drug discovery, but screening smaller, more focused libraries, can provide more efficient solutions with better overall hit rates.
Ten years ago, BioFocus®, a Galapagos company, launched a nonexclusive compound library specifically designed to target serine-threonine and tyrosine kinases. This library, SoftFocus® Kinase library one (SFK01), was designed to mimic the binding of ATP to the catalytic (hinge) region and had a rather simplistic design based around an aminopyrimidine core (Figure 1).
Protein kinases are enzymes that phosphorylate substrate proteins at specified residues such as serine, threonine, and tyrosine. The phosphorylation of the substrate protein initiates a cascade, that in turn, modulates the transcription of a gene or set of genes. Kinases play pivotal roles in modulating diverse cellular activities, including growth, differentiation, metabolism, adhesion, motility, and death, and have been implicated as important mediators of certain forms of cancer.
Kinases, therefore, represent key druggable target proteins. The initial realization that most kinases possess highly conserved catalytic domains initially made kinase targets ideally suited for compound screening via focused chemical libraries in which the library compounds were specifically created to bind to the catalytic (hinge) regions.
Despite the slightly higher costs generally associated with the design and synthesis of such focused libraries compared to large and diverse compound collections, true savings can be gained as a result of shortened project cycles coupled with the reduced costs of screening, storage, and quality control of a smaller screening library.
The increasing wealth of structural data available along with a number of new techniques such as in silico design has enabled the continual development of kinase-focused collections, providing increasingly more sophisticated chemical structures. One of the key benefits of this is that the current range of SoftFocus kinase libraries has been designed to target additional binding modes to those involving the hinge region; most notably the DFG-out binding mode and the novel binding mode first observed in the kinase PIM-1.
In Silico Design
Current in silico design processes enable automated docking and scoring of scaffold ideas into a variety of known x-ray structures that have been selected, not only for broad coverage of the kinome, but also different conformational states of individual kinase enzymes. The design premise is that, if the core of the molecule or scaffold contains the key recognition groups for binding into one of the known conformational states, it has the potential to target any kinase.
However, as different side chains or monomers are added, the potential to gain specificity for one target over another becomes reality. The various docking methods used in the design of the BioFocus libraries include hinge binding, the DFG-out model, and novel binding modes.