Fragment-based screening: enabling technology for early lead generation
Modern drug discovery is difficult, expensive and inefficient. In today's pharmaceutical research arena there is an overall need to increase the success-rate of drug candidates, decrease the timeline of drug development and minimize the cost of overall development. The methodology of fragment-based screening (FBS) has been shown to address these basic problems of the drug discovery pipeline (Nienaber et al., Nature Biotechnology 2000 18, 1105). Rigaku is uniquely positioned to satisfy the needs of users of the FBS technique.
The concept of fragment-based screening
FBS is a validated method of searching for novel leads in the drug
discovery process, the goal of which is to rapidly convert the identified
leads into clinical candidates. In its simplest incarnation, this method
involves soaking small (100-300 Da), drug-like, organic compounds into
pre-formed protein crystals. As protein crystals are highly porous, fragments
that have an affinity for a protein will bind at its active site, while those
that do not will remain in the solvent channels. Binding at the active site is
determined using X-ray crystallography to detect difference density in the
active site. Using high-throughput crystallographic methods, a large number of
fragments can be assessed in a relatively short time; typically 10-100
compounds can be scanned in a day. The method can detect fragments with
relatively low affinity, 100 μM-10 mM. FBS is well suited to take advantage
of the improvements in automation, software and brighter X-ray sources that
have become available in recent years.
Time frames from target identification to Investigational New Drug Application (IND) have been reported to be as short as two years using FBS, significantly shorter than for traditional methods such as high-throughput screening (HTS). The leads produced from FBS are, by definition, higher quality than from HTS because they are tailored to the target active site, have lower molecular weights, and bind more efficiently.
First,
crystals (right) of an interesting drug-target protein are grown that have
only water in the active site. The crystals are soaked in a solution
containing a mixture of small, drug-like fragments (below left). Fragments that
bind are identified by determining an X-ray structure (below right). The advantage of the method is that the experiment identifies the fragments
that bind to the protein, along with the three-dimensional detailed structure of the fragments bound to the site.
Using the structures, you can rapidly develop new,
novel inhibitors of the protein target.
X-ray
crystallography is integral to the successful discovery of fragment-derived lead
compounds. Crystallographic screening is a fully validated method of fragment
screening and has been routinely applied by companies such as Abbott
Laboratories, ASTEX and SGX Pharmaceuticals. Co-crystal structures with
fragments are also required for the successful optimization of fragments
detected by other techniques.
A
high-speed crystallography system is great but for the FBS technique to really
be successful, automated sample changing is essential.