Chemistry Reference
In-Depth Information
a cell lysate. However, more recently, Cravatt and co-workers have started to use these
techniques to identify ligands also, including previously uncharacterized ligands. [ 54 ]
10.5 Opportunities with Fragment Capture Methods
The fragment capture methods described above provide some of the benefits of other
fragment-based screening methods, but go beyond these in two important ways. First,
covalent capture allows a site-directed screening approach based on homology models
and in the absence of direct structural information, and therefore is applicable to proteins
that are not amenable to NMR or crystallography. Second, covalent capture methods permit
target-directed fragment assembly, whereby the target protein guides the covalent assembly
of fragments with compatible binding modes (this method is described in Section 10.3.4).
The ability to explore chemical diversity space effectively remains a formidable challenge
in small-molecule drug discovery. It has been estimated that the number of possible small
molecules suitable for drug discovery exceeds 10 60 , but only a fraction of these, at most
a few million, can possibly be synthesized and screened at one time. [ 55 ] A combinatorial
fragment-based approach has the potential to probe a larger fraction of the chemical diversity
space. In fragment-based lead discovery, small drug fragments are screened against a target
protein and only fragments with binding affinity for the target are actually expanded or
linked with other fragments to generate new starting points for lead discovery. Using this
approach, a collection of 10 4 fragments can theoretically probe a chemical diversity space
of 10 8 molecules, still a small fraction of total diversity space, but a significant increase
relative to traditional HTS (Figure 10.5). Most importantly, a chemical diversity space of
10 8 molecules can be explored by screening and synthesizing as few as 10 4 molecules,
representing tremendous savings of cost and time.
Although a combinatorial fragment-based approach provides some great advantages,
implementation of effective screening methods has presented a new set of challenges. One
Screen
site A
10 hits
Screen
Link
100 molecules
Hits
10 hits
Screen
site B
10,100 molecules
20,100 screens
Probed 10 8 virtual
compounds
Synthesize 10 4
drug fragments
Figure 10.5 Fragment-based capture methods permit a combinatorial approach to lead dis-
covery; 10 4 fragments can be combined to create 10 8 two-fragment molecules. Rather than
synthesizing and screening 10 8 compounds, the 10 4 fragments can be screened individually
and only the fragments that hit will be converted into two-fragment molecules. Compared with
HTS, the fragment-based approach can be accomplished with far less synthetic and screening
effort.
 
Search WWH ::




Custom Search