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Online Journal of Bioinformatics


Volume 19 (1):13-19, 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




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 ( 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.