Title

Molecular docking analysis of zidovudine triphosphate with conserved residues from
NS3 protein

Authors

Ayesha Tazeen¹, Rafat Ali², Nida Jamil Khan², Anwar Ahmed³ & Shama Parveen^1,*

Affiliation

¹Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India; ²Department of Biosciences, Jamia Millia Islamia, New Delhi, India; ³Centre of Excellence in Biotechnology Research, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia; *Corresponding author

Email

Ayesha Tazeen - E-mail: ayesha133509@st.jmi.ac.in
Rafat Ali - E-mail: rs.rafat@jmi.ac.in
Nida Jamil Khan - E-mail: njkhan@jmi.ac.in
Anwar Ahmed - E-mail: anahmed@ksu.edu.sa

Shama Parveen - E-mail: sparveen2@jmi.ac.in

Article Type

Research Article

Date

Received August 1, 2025; Revised August 31, 2025; Accepted August 31, 2025, Published August 31, 2025

Abstract

Dengue fever poses a significant global health concern, yet despite extensive research there is no specific antiviral therapy against the infection. Therefore, it is of interest to study the interaction between the highly conserved N-terminal of NS3 protein of DENV-4 and an FDA approved antiviral, zidovudine triphosphate (ZDV-TP), using molecular docking and molecular dynamics (MD) simulation studies. Docking showed significant binding between NS3 protein and ZDV-TP with -7.7 kcal/mol of binding energy. ZDV-TP interacted with the conserved and active site residues of N-terminal NS3 protease including Gly133, Thr134, Ser135, Gly151 and Asn152. These residues are crucial for viral replication and are highly conserved in all the serotypes of DENV. MD simulation studies showed that the NS3-ZDV-TP complex had no major conformational instability with an approximately linear trajectory up to 200 ns simulation. ZDV-TP was well anchored at its binding position and minimized the compactness as compared to NS3 protein only, indicating high affinity for NS3.

Keywords

Dengue virus, NS3 protein, protein-ligand interaction, MD simulation

Citation

Tazeen et al. Bioinformation 21(8): 2550-2556 (2025)

Edited by

P Kangueane

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.