Molecular docking based screening of compounds against VP40 from Ebola virus


Hanaa M Alam El-Din1*, Samah A. Loutfy1, Nasra Fathy1, Mostafa H Elberry1, Ahmed M Mayla1, Sara Kassem2, Asif Naqvi3


1Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, 1stKasr El Aini St., Fom El-Khalig, Cairo, Egypt, PO Box 11796; 2Chemistry of natural microbial products Department, National Research Center, Giza, Egypt City, State, Country; 3BioDiscovery Group, Agra, India;


Hanaa M Alam El-Din E-mail:; *Corresponding author

Article Type



Received May 2, 2016; Revised May 27, 2016; Accepted May 27, 2016; Published June 15, 2016


Ebola virus causes severe and often fatal hemorrhagic fevers in humans. The 2014 Ebola epidemic affected multiple countries. The virus matrix protein (VP40) plays a central role in virus assembly and budding. Since there is no FDA-approved vaccine or medicine against Ebola viral infection, discovering new compounds with different binding patterns against it is required. Therefore, we aim to identify small molecules that target the Arg 134 RNA binding and active site of VP40 protein. 1800 molecules were retrieved from PubChem compound database based on Structure Similarity and Conformers of pyrimidine-2, 4-dione. Molecular docking approach using Lamarckian Genetic Algorithm was carried out to find the potent inhibitors for VP40 based on calculated ligand-protein pairwise interaction energies. The grid maps representing the protein were calculated using auto grid and grid size was set to 60*60*60 points with grid spacing of 0.375 Ǻ. Ten independent docking runs were carried out for each ligand and results were clustered according to the 1.0 Ǻ RMSD criteria. The post-docking analysis showed that binding energies ranged from -8.87 to 0.6 Kcal/mol. We
report 7 molecules, which showed promising ADMET results, LD-50, as well as H-bond interaction in the binding pocket. The small molecules discovered could act as potential inhibitors for VP40 and could interfere with virus assembly and budding process.


Ebola VP40, molecular docking, virtual screening, anti-PV40 agents, proteomics, Lamarcking GA


Alam El-Din et al. Bioinformation 12(3): 192-196 (2016)

Edited by

P Kangueane




Biomedical Informatics


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