occurring amino acids, it is possible to produce 8000 different tripeptides. If atypical
amino acids and amino acids in the unnatural D configuration are included, it is possible
to achieve 125,000 different compounds with relative ease. Peptide libraries are easy to
synthesize and, since amino acid side chains possess a wide variety of different func-
tional groups, it is possible to achieve a good measure of structural diversity. However,
in general, peptides are not drugs and a peptide lead would have to be modified into a
drug-like molecule. In addition to oligopeptides, other naturally occurring oligomeric
libraries are possible, including oligonucleotide libraries.
A step beyond the naturally occurring oligomeric libraries is to create libraries from
non-naturally occurring monomeric building blocks. The medicinal chemistry literature
contains a fair number of examples of such libraries, including oligocarbamates and
oligoureas. Although these libraries overcome the limitations of naturally occurring
oligomeric libraries, most drugs are not polymers.
To address this problem, new libraries emerged in which the central moiety was a
small organic molecule. The diversity library was then constructed by attaching many
different substituents to this central moiety. Some of these moieties were selected
because they were very simple to synthesize. For example, dioxapiperazines are cyclic
dipeptides and thus are relatively trivial to prepare. Other monomers were selected
because they had a good track record for being drug-like molecules. Benzodiazepines
are a good example of such libraries.
In preparing these various libraries, extensive use is made of solid phase synthetic
methods.These methods are all derived from the solid phase peptide synthesis (SPPS)
method developed by Merrifield in 1963. When performing a large number of synthe-
ses, it is preferable to perform the synthetic steps on a solid bead rather than complet-
ing the entire synthesis in the solution phase. The solid-phase technique makes byproduct
removal and final compound purification easier. The organic chemistry literature con-
tains a wealth of different types of solid-phase supports and novel linkers for attaching
the synthetic substrate to the bead.
3.2.6.4 High Throughput Screening and Drug Discovery
If a large, chemically diverse library is available, the next problem is to evaluate these
compounds in a time-efficient manner. If a 200,000 compound library is available, the
biological evaluation assay must be rapid and reliable. If the assay were capable of test-
ing five compounds per day, it would take 110 years to evaluate the entire library.
Clearly, this is not the time for elaborate in vivo testing. Fast, efficient in vitro assays
are required. The ability to inhibit an enzyme is a good example of a potentially useful
assay for high throughput screening.
A variety of high throughput assays have been developed and perfected over the past
10–20 years. These include the following basic types of assay:
- Microplate activity assays (assay is in solution in a well; the result of the assay, such
as enzyme inhibition, is linked to some observable, such as color change, to enable
identification of bioactivity) - Gel diffusion assays (biological target is mixed in soft agar and spread as a thin film;
the compound library is spread on the surface of the film; after allowing for compound
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