Journal of Pharmaceutical Sciences & Emerging Drugs 2380-9477

Research Article, J Pharm Sci Emerg Drugs Vol: 4 Issue: 2

Structure Based Docking of Small Hirudin like Peptides with Thrombin

Aparna Jadhav1*, RadhaCharan Dash2, Raj Hirwani1 and Mailk Abdin3
1Council of Scientific and Industrial Research-Unit for Research and Development of Information Products, “Tapovan” NCL Campus, S.No.113, 114, Pashan, Pune 411 008, India
2School of Pharmacy, University of Connecticut, 69 N Eagleville Rd Storrs, CT 06269, USA
3Department of Biotechnology, Faculty of Science, Jamia Hamdard, New Delhi- 110062, India
Corresponding author : Aparna Jadhav
Council of Scientific and Industrial Research- Unit for Research and Development of Information Products, “Tapovan” NCL Campus, S.No.113,114, Pashan, Pune 411008, India
Tel: 020 32676541
Fax: 43/20251324
E-mail: [email protected], [email protected]
Received: November 02 , 2016 Accepted: November 15, 2016 Published: November 23, 2016
Citation: Jadhav A, Dash RC, Hirwani R, Abdin M (2016) Structure Based Docking of Small Hirudin like Peptides with Thrombin. J Pharm Sci Emerg Drugs 4:2. doi: 10.4172/2380-9477.1000116

Abstract

Hirudin variant like small peptide or peptidomemitic compounds are known to inhibit thrombin. These 10 to 20 amino acid long molecules are reported to primarily bind at exosite 1 of thrombin. To know more about their interaction with thrombin, initially we docked 5 different hirudin variant peptides having 10 to 13 aa sequences. It helped to identify single best docking peptide (12 aa sequence) i.e. GDFEEIPEEYLQ (pdb: 1FPH _I chain) with docking score -3.42 kcal/Mol, amongst the set of peptides. This peptide was further truncated to form a series of peptides having 7 to 12 aa sequence range. The truncated peptides were further docked at thrombin exosite 1 binding site. Amongst these the best docking 7 aa peptide i.e. GDFEEIP, with docking score -4.43 kcal/Mol was identified. This experiment helped to predict the best possible peptide sequence, much needed for strong thrombin docking and can be competent peptide based antithrombin lead.

Keywords: Hirudin variant; Thrombin; Docking

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