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Graffinity's Fragment Based
Drug Discovery Process
– RAISE
Graffinity has pioneered RAISE (Rapid Array Informed Structure
Evolution), an efficient fragment based drug discovery paradigm that
enables the rapid identification of small molecules and the development
of diverse novel quality leads.
Our Technology team has developed this unique drug fragment based
discovery platform which is in routine use since 2003 for both external
clients as well as In-house programs.
To date, this unique fragment screening process has been successfully
applied for more than 60 targets.
Our partners as well as our in house projects hereby enjoy a highly
professional project management. |
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| RAISE
Process – Rapid Array Informed Structure Evolution |
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1. Design & Synthesis
By virtue of the design process, fragments and leadlike compounds
comprise excellent starting points for drug discovery.
Design
Primary fragment screening is an attractive and efficient
paradigm in the quest for new lead molecules. Compounds of low
complexity are more likely to match a given binding site and also make
better use of their chemical functionalities resulting in more
efficient binders than those found in traditional screening libraries.
Due to the higher hit probability, fewer compounds need to be screened
to identify starting points for chemical optimization. Although being
expected to be weak binders, small diverse and information-rich
fragments leave more room for optimization without risking to leave
leadlike or druglike chemical space. Low-affinity screening using
tethered drug-fragments on chemical microarrays is a highly promising
approach for fragment screening and the rapid discovery and
optimization of such small
molecules.
Synthesis
The preparation of high density chemical microarrays for drug discovery
requires a highly parallel and controlled process for the synthesis of
fragment and leadlike compounds. Compound production is achieved by
nanoscale solid phase organic synthesis (40 nmoles/ compound). All
compounds are linked to the same proprietary spacer molecule
(ChemTag®), which serves as an attachment point for the
covalent immobilization on the array surface.
After synthesis compounds are cleaved from the solid phase and stored
as stock solutions in microtiter plates. Each compound is quality
controlled by LC-MS to guarantee highest quality standards. Aliquots of
this stock solutions are further diluted and used in the subsequent
spotting step to generate chemical microarrays. Graffinity’s
libraries contain about 23,000 fragments and 90,000 leadlike compounds.
The array content is key to the success of the drug discovery process
and is continously upgraded.
2.
Array Production
Nanoliter amount of compounds are transferred from daugther library
plates onto the surfaces of microarrays in a highly reproducible,
parallel array production process using customized spotting technology.
The result of the array production process is a chemical microarray
carrying about 10.000 compounds displayed on top of a self assembled
monolayer (SAM). A thin gold layer provides basis for SAM formation and
SPR detection.
The SAM serves two purposes:
(1) it prevents unspecific protein binding to the array surface and (2)
it presents anchor molecules that allow covalent binding of the
compounds on the array surface via the ChemTag®. The number of
displayed compounds is controlled and can be varied by ratio of
diluent/anchor molecules of the SAM.
3.
Fingerprinting / Fragment Screening
High-throughput, label-free fragment screening and
screening of displayed-fragment microarrays on its proprietary SPR
platform, allows
Graffinity to rapidly identify novel drug fragments and leadlike
molecules as ligands for a biomolecular target.
The Plasmon Imager® is based on the phenomenon of surface
plasmon resonance (SPR) which requires the presence of a thin gold
metal film on the array´s glass carrier. Changes of
refractive index at the gold/liquid interface effect the resonance
condition of electron energy states in the metal. In
Graffinity´s set up, a wavelength shift that corresponds to
the increase of mass concentration on the chip surface during binding
between the solubilized protein and the immobilized chemical substances
is recorded. Currently, Graffinity's Plasmon Imager® devices
are capable of routinely processing about 10,000 measuring points
simultaneously in a fourfold parallel fashion.
4.
Data Analysis
The evaluation of protein-ligand affinity fingerprints is aided by
proprietary, Javabased software. Chemical microarray content is
visualized in a point-and-click fashion, individual spots refer to
chemical structures and associated read-out information. During the
process, a specific pattern or "fingerprint" emerges for each target
protein, reflecting the protein´s chemical binding
preferences. Chemical proximity display, statistic functions and
database cross-queries provide powerful insight into affinity
relationships.
Structure-activity relationship (SAR) patterns can be mapped from the
microarray fingerprints and supported by protein X-ray crystallography
the process allows the unambiguous determination of binding mode for
multiple ligands.
5.
Hit Evolution
The RAISE® Hit Evolution program uses array "fingerprint" data
for rapid compound optimization by high throughput chemistry, secondary
assays and SAR building. Starting point for the RAISE®-process
is the synthesis of array compounds as soluble untagged analogs by
removal of the Chemtag spacer subunit. Biochemical and micoarray data
allow the rapid analoging of the first generation compounds and the
building of SAR models. These models are confirmed and refined by
focussed libraries and further optimization.
The RAISE®-process enables the rapid optimization of chemical
compounds to generate lead candidates. The wealth of information
produced by the RAISE®-process supports the further development
of compounds by medicinal chemistry programs. |
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