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Journal of Bioinformatics©
Volume 19 (1):8-13, 2018...
Fomecin-A antiviral
for non-structural protein NS3-4A of hepatitis C virus.
R Shanmugam1, K Mani1, B Vijay Kumar2
1BRT lab, Department of Botany, PSG college of Arts and science Coimbatore, 2Department of Bioinformatics, Karpagam college of Arts and
science, Coimbatore, India
ABSTRACT
Shanmugam R, Mani K, Vijay Kumar B., Fomecin –A antiviral for NS3-4A of
Hepatitis C virus. Onl J Bioinform.,
19
(1):8-13, 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.
Key words:
Hepatitis c virus,
Docking, TSAR, and ADME/TOX, serine protease inhibitors, WHATCHECK report, Fomecin A.
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