Chemistry Reference
In-Depth Information
Figure 4.5
Left: crystal structure of the ligand-binding site of human A-FABP. The structure
of one of the primary hits from the NMR screen (BVT.1960 shown in thin black lines) was
used to design a higher affinity ligand (BVT.1961 shown in thicker lines) with a similar binding
mode and retained selectivity against H-FABP. There are three amino acid residues (Ile104,
Val115 and Cys117) in the vicinity of these ligands that are different between A-FABP and
H-FABP. The bulkier leucine side-chains of H-FABP in the corresponding positions could
account for its lower affinity for these ligands. Adapted with permission from van Dongen
et al
.,
J. Am. Chem. Soc.,
124
, 11874. Copyright 2002 American Chemical Society. Right: a
compounded figure of several ligands in complex with humanA-FABP. The ligands all cluster in
one region of the binding pocket, leaving most of the solvent molecules (spheres) unperturbed.
Approximately 10 water molecules in the binding pocket are conserved in all structures of the
ligand-target complexes.
theAvailable Chemicals Directory (ACD-3D, MDL Information Systems) and the in-house
compound collection were conducted to find compounds with the BVT.1960 scaffold and
small extensions at different positions. Eleven compounds were identified and tested in
the fluorescence polarization assay against both A-FABP and H-FABP. As illustrated in
Figure 4.6, it was discovered that substitutions at the ethylene linker carbons resulted in a
loss of selectivity, whereas replacing the
p
-hydroxyl group on the aromatic ring resulted in
decreased potency. Substitutions at the
ortho
and
meta
positions with respect to the ethylene
linker, on the other hand, appeared to have the capacity to combine improved potency with
retained selectivity.
On the basis of these findings, 12 additional analogues to BVT.1960, mainly differing in
substitutions on the phenyl ring, were synthesized. Binding studies by NMR and potency
ranking using the fluorescence polarization assay for these compounds distinctly pointed
to a beneficial effect of substitutions at the
meta
(R
2
) position. As is shown in Figure 4.7,
an isopropyl substitution to produce BVT.1961 combined a potency of 10 M with a
completely retained selectivity for A-FABP over H-FABP. An X-ray structure confirmed
that BVT.1961 adopts an equivalent binding mode as BVT.1960 (Figure 4.5). In addition,
two compounds, with a benzyl or phenone group at the
meta
position, showed potencies in
the low M range.
