Chemistry Reference
In-Depth Information
(such as genomics targets) are interrogated by a binding assay. The molecules that bind are
then used in cellular assays to investigate the possible role of the target. Reverse chemical
genomics can be defined as screening a target for a ligand, akin to the typical drug discovery
paradigm. Both of these approaches have obvious advantages for novel pathways/targets
and are imminently tractable to FBDD.
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The information that should be put into a complete target dossier on the target is as
follows. Can the protein be produced in sufficient quantities and purity for biochemical
and/or biophysical assay (microgram versus milligram quantities)? Is the protein soluble,
monodisperse and stable under typical working conditions? Has it been a target of drug
discovery before? If so, how was it done and what was the outcome? Are there structural
data? If not, are there suitable surrogates? Questions of this type (not to be considered an
exhaustive list) are important for designing an appropriate process and will be discussed
in more detail under assay assessment. The more that is known about the target, the better
the decision can be made on assembling the process. For example, if the protein cannot
be produced in the amount and purity needed for biophysical screening,
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this affects
decisions in assay and compound assessment. If the target has stability issues, it may be
more amenable to one screening method over an other. If the target was previously the
focus of drug discovery, it is important to ascertain whether those efforts were successful,
what methods were applied, etc.
Another important component of the protein dossier is structural information. Do high-
resolution structures (either NMR
o
r X-ray) exist that can be used for library generation and
hypothesis testing/generation
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? Are these structures with bound ligands? In many
medicinal chemists' eyes, this is the most important of the criteria; in fact, to many it
is so important that hit follow-up will not be pursued until suitable structures are in
hand. Several companies' entire business model is based upon X-ray-based screening of
fragment libraries.
If structures of the target do not exist, structures of isoforms or surrogates may exist.
There are many reasons for using surrogates: the target cannot be produced in sufficient
quantities for screening, no assay is developed for the target, there is no structure for the
target, etc.
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Surrogates can also be used as the first filter in the screening process, thereby
reducing the need for protein for later follow-up screening. This can be especially useful if
the target is in limited supply. One important caveat is that it is possible that something may
be missed. However, as mentioned later in this chapter and in other chapters in this topic,
the hit rate for fragments is high relative to other screening methods, so although a real
possibility, it is typically worth the risk. In many cases, particularly membrane proteins,
there is a very small likelihood of ever having structural information, so this is a moot
point. FBDD, like lead-like discovery, can progress just as efficiently without structural
information as with it.
2.2.2 Assay Assessment
The decision on what type of screen to use in FBDD is affected by many different factors:
availability of protein for screening, compound selection, throughput, turnaround and rate
of false positives and negatives. The resolution of these questions from target assessment
directly impact the possibilities in this section. If there is not sufficient protein for a bio-
physical screen, a biochemical screen is the only choice. Protein that is not stable for
