Yet the p38 project was a failure as it was shown that isoform
selective p38 inhibitor was less effective in treating rheumatoid
arthritis than methotrexate [66]. Finally, Locus felt that not more
than one order of magnitude in potency must be lost when going
from a protein inhibition assay to cell assay and addition of blood to
the cell assay must lead to only an additional loss of one order of
magnitude in potency.4.3 Computational
Study for Structure-
Based Designing
of Novel Hepatitis C
Virus Helicase
Inhibitor
Hepatitis C virus (HCV) causes hepatitis C infection that could lead
to hepatic disorders such as cirrhosis subsequently progressing to
hepatocellular carcinoma. Current therapy includes direct antiviral
agents, which is associated with several side effects and are
expensive.
The case study is a pragmatic methodology for de novo based
ligand drug discovery to design potential inhibitors for HCV NS3
helicase [67]. The crystal structure PDB 1A1V that was cocrystal-
lized with DNA strand attached to the helicase domain was chosen
for the study.
The first step involved finding the binding site for ligand.
Therefore, the amino acids involved in the enzyme activity were
explored and Arg393 was found conserved. Arg393 plays a signifi-
cant role in enzymatic activity as mutation of this particular amino
acid caused unfavorable impact on the enzyme activity. The nucleic
acid was detached from the structure, due to which the neighbor-
ing residues came in direct contact to the solvent. Furthermore it
was found that at a distance of nearly 10 A ̊ the sulfur atom of
Cys431 is in synergy with mercaptoethanol molecule of crystallized
H 2 O. This made it clear that Cys431 can covalently bond with a
suitable small molecule. By these observations it was proposed that
a molecule can be a potential inhibitor of helicase if it is interacting
with Arg393 in addition to making covalent bond with Cys431.
The Ligbuilder software was used to design the ligand. The first
step is to look for the binding site in the protein structure. Design
of ligand involves identification of seed molecule for generation of
lead compound. After which it constructs number of molecules by
linking the most suitable fragments to the growing structures. The
resultant series of structures were complex and difficult to obtain
synthetically. To solve this problem, screening of fragment library
was performed to select residues with least possibility to generate
chiral centers after the combining process. For lead molecule to
interact with the desired residue an atomic wall with no physical
properties was formed. This reduced the complexity of the resultant
structure, and it was able to interact with Arg393. Additionally
there was an interaction with A481 with no functional group
attached and in close proximity with Cys431. This represented a
suitable basic scaffold for further functionalization.
The in silico design process was optimized by employing a
different approach. A series of virtual libraries was created usingFragment-Based Ligand Designing 139