Chemistry Reference
In-Depth Information
medicinal chemistry represents a first-generation extension of fragment-based drug dis-
covery towards the direction of target-guided fragment optimization. The
in situ
linking of
fragments was articulated in a proof-of-concept format for DCC in 1997 by Huc and Lehn
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and for Click chemistry in 2002 by Sharpless, Finn and co-workers.
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These novel synthetic
approaches have since flourished as elegant and vibrant research disciplines in their own
right, each with broadly scoped potential applications of which drug discovery is just one.
Performing synthetic chemistry to link fragments covalently within the reaction envir-
onment dictated by a target biomolecule in its native state is demanding, but this is now
reasonably well established for both DCC and Click chemistry. The introductory mater-
ial of this chapter will provide an overview into the principles of both
in situ
DCC and
Click chemistry approaches as they apply to fragment-based drug discovery. A discussion
on the practical considerations that are key to translating these synthetic approaches from
proof-of-concept investigations to outcomes-focused applications that may then be con-
sidered as useful tools by the pharmaceutical industry for the purpose of drug discovery
will follow. Critical to this translational capacity is the ability to identify rapidly and accur-
ately the linked fragments of interest. An account of how mass spectrometry is emerging
as the key analytical methodology to fulfil the analytical demands associated with
in situ
medicinal chemistry will be presented. Griffey and Swayze
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have previously described
the principles of electrospray ionization mass spectrometry (ESI-MS) and demonstrated its
immense value as a primary screen for fragment-based drug discovery. Here we will focus
our discussion on 'practical aspects', including the optimization of experimental conditions
that allow mass spectrometry to detect specific target-ligand binding interactions. By way
of published examples, we will demonstrate that mass spectrometry is an invaluable tool as
a primary screen particularly in the case of
in situ
medicinal chemistry applications where
synthesis and screening are integrated into a single step.
7.2 Target-guided
In Situ
Medicinal Chemistry - the Principles
Biomolecular targets exist as an ensemble of equilibrating conformers, and these conform-
ational changes are associated with dynamic disorder, i.e. distributions and fluctuations
over time-scales of 1 ms to 100 s.
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Structural variations can range from subtle to extreme
and invariably compromise the outcome of structure-based drug design efforts that are
typically guided by a static and/or ensemble-averaged conformation. Even so, applying the
principles of molecular recognition may sometimes effectively guide the design of small
molecules and the level of success with structure-based drug design is in many respects
very good. This approach is plagued, however, by the difficulty of appropriately interrogat-
ing the subtleties and complexities of molecular recognition between a dynamic target and
a small molecule within the biological context. Structure-based drug design is imperfect
and necessarily a resource-intensive approach to drug discovery, requiring many iterative
cycles between small-molecule synthesis and biological assay results, intervened by inter-
pretation of structure-activity relationships and refinement of the 'rational' structure-based
drug design model.
Target-guided
in situ
medicinal chemistry is a novel means of synthesizing small-
molecule ligands for medically relevant biomolecular targets, whereby the target bio-
molecule directs the outcome of the synthetic efforts. Target-guided synthesis (TGS) has
