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Journal of Bioinformatics©
antiviral for non-structural protein NS3-4A of hepatitis C virus.
R Shanmugam1, K Mani1, B Vijay Kumar2
lab, Department of Botany, PSG college of Arts and science Coimbatore, 2Department
of Bioinformatics, Karpagam college of Arts and science, Coimbatore, India
Shanmugam R, Mani K, Vijay Kumar B., Fomecin –A antiviral for NS3-4A of Hepatitis C virus.
Onl J Bioinform., 19 (1):13-19, 2018. Non
structural proteins of Hepatitis C virus (HCV) NS3-4A are vital for viral
polyprotein processing and replication and could be targets for treatment of
hepatitis C. We modeled a NS3/4A complex
for docking with serine protease inhibitors from NCBI and QSAR serine
proteinase Benzamidine with fungal order Aphyllophorales. Hepatitis C
viral NS34A protein sequence 1a1r was retrieved from PDB (rcsb.org) as target
sequence. NS3-4A complex was extracted from Swiss PROT viewer and Deep Viewer
used to fit raw sequence with related template sequence for similarity.
Structure bond length, angles and restraints between angles were determined by
WHATCHECK validated by Ramachandran plot. Serine protease inhibitors extracted
from NCBI were docked with NS3-4A complex by Accelerys-dstudio
to generate acceptable docking scores. Several compounds in Aphyllophorales
fungi were compared with the previously docked Benzamidine
by Accelerys-TSAR. Based on
docking scores lead compounds were selected against NS3/4A. Adsorption and
distribution were tested by ADME/TOX. Query of serine protease generated 28
inhibitors for ligands by docking with Accelrys-dstudio)
and showed that Benzamidine generated a dock score of
52.184 at one site. Templates for modeling target sequence 1a1r
extracted from SWISS-PROT were 2f9v(PDB ID) an HCV NS3 protease domain with
NS34A peptide and a ketoamide inhibitor with P1 and
P2 cyclopropylalannines, 2gvf(PDB ID) an HCV NS3-4A
protease domain complexed with a macro cyclic ketoamide
inhibitor SCH419021 and 1rgq (PDB ID), and M9A HCV Protease complex with pentapeptide keto-amide inhibitor.
Hepatitis c virus,
Docking, TSAR, and ADME/TOX, serine protease inhibitors, WHATCHECK report, Fomecin A.
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