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Title

 

 

 

 

Designing cyclic peptide inhibitor of dengue virus NS3-NS2B protease by using molecular docking approach 

Authors

Usman Sumo Friend Tambunan*& Samira Alamudi

Affiliation

Department of Chemistry, Faculty of Mathematics and Natural Science, University of Indonesia, Depok Campus, Depok 16424, Indonesia

Email

usman@ui.ac.id

Article Type

Hypothesis

 

Date

Received December 01, 2009; Accepted November 09, 2010; Published November 27, 2010
 

Abstract

Peptides are preferred for designing inhibitors because of their high activity and specificity. Seven cyclopentapeptide inhibitors were designed in this study against dengue virus type 2 (DEN-2) NS3-NS2B protease: CKRRC, CGRRC, CRGRC, CRTRC, CTRRC, CKRKC and CRRKC. Docking analysis was performed to study the enzyme-inhibitor binding interactions. The free energy binding and estimated Ki values for all the inhibitors were found to be small (within micromolar range), indicating that the inhibitors bind considerably well to the binding site. The results showed that the cyclopentapeptide CKRKC was the best peptide inhibitor candidate with estimated free binding energy of -8.39 kcal/mol and Ki of 0.707 ÁM when compared to the standard inhibitor Bz-Nle-Lys-Arg-Arg-H that has been experimentally tested and shown to exhibit Ki value of 5.8 ÁM. Several modes of weak interactions were observed between the cyclopentapeptide CKRKC and the active site of DEN-2 NS3-NS2B protease. Thus, the cyclopentapeptide is proposed as a potential inhibitor to the NS3-NS2B protease activities of DEN-2. While these preliminary results are promising, further experimental investigation is necessary to validate the results. 

Keywords

 

Dengue virus, DEN-2 NS3-NS2B protease, docking, inhibitor, peptide

Citation

Tambunan & Alamudi. Bioinformation, 5(6): 250-254, 2010

Edited by

Tan Tin Wee

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.