Engineering SimulaTOr) suite was used to calculate SA (synthetic
accessibility) score. SA score of 4.680 and 5.036 was obtained for
C_773 and C_997 respectively, indicating feasibility of their chem-
ical synthesis. This in silico study reported two de novo designed
potential anti-inflammatory drug molecules, which can be further
explored to check whether they have potential to overcome limita-
tions posed by clinically available drug molecules.4.2 Computational
Fragment Based
Designing of p38
Inhibitor
With the discovery of p38 MAPK as the key factor in the produc-
tion of various pro-inflammatory molecules, numerous efforts were
focused toward designing p38 inhibitors. It became the focal point
for drug discovery as blocking of p38 exhibited the potential to
downregulate the pro-inflammatory mediators TNF-alpha,
IL-beta, and COX-2.Locus Pharmaceuticalstried to explore the
opportunity of regulating signal transduction process by targeting
p38 by fragment-based drug discovery method. The approach was
mainly aimed at creating a small molecule which was orally available
and nontoxic, and did not bind at the ATP site of p38.
The initial study results from two groups; Bayer and Boehrin-
ger Ingelheim (BI) intensely led to conflicting views atLocuson
whether to target the ATP site or not. The molecules discovered at
Bayer exemplified allosteric inhibitors that instead of binding at the
ATP site, were binding at the conserved DFG (Asp-Phe-Gly) motif.
Yet the compounds had poor in vivo profile due to planar hydro-
phobic nature. Subsequently the BI group reported increase in
solubility of DFG-binding molecules with the addition of
morpholino-ATP binding moiety to these compounds. In addition
to this BIRB-796 was shown to have low affinity for 11 other
kinases [64]. Thus, to work this out,Locusdecided to test BIRB-
796 after synthesizing it. They ran point assays against panel of
kinases and the four isoforms of p38. Inhibition of all p38 isoforms
was observed and the other significant finding was that a key
hydrogen bond was formed between BIRB-796 and ATP-site.
This led to the proposal of a hypothesis that the lack of selectivity
might be resulting from this specific interaction. The idea was to
make a superior derivative of BIRB-796 with high affinity for ATP
site, but did not participate in the specific hydrogen bond
formation.
The technology that was used to discover fragments, which did
not make hydrogen bond with methionine in the ATP site but still
had high affinity for it, was called simulated annealing of chemical
potential (SACP). The technology was run on BI crystal structure
(PDB ID: 1KV2). SACP method involves Monte Carlo procedure
which ranks the binding affinity of different fragments in relative
order for a specific site in the protein. It is possible to generalize the
procedure as an automated protocol to identify hotspots in protein
that can make nonbonded interactions of high affinity. For the
algorithm, the only input is the structure of the protein and theFragment-Based Ligand Designing 137