Molecular modeling, simulation and docking study of ebola virus glycoprotein
Nasir Ahmad1, Aqsa Farman1, Syed Lal Badshah1
1Department of Chemistry, Islamia College University, Peshawar, Khyber Pakhtunkhwa, Pakistan.
Journal of Molecular Graphics & Modelling
|February 5, 2017
Summary
Researchers studied the Ebola virus (EBOV) secreted glycoprotein, predicting its structure and flexibility. Docking analysis suggests derivatives of dronedarone and amiodarone may act as effective protein receptors for EBOV.
Area of Science:
- Virology
- Structural Biology
- Drug Discovery
Background:
- Ebola virus (EBOV) is a negative-strand RNA virus from the Filoviridae family.
- Viral glycoproteins are crucial for the EBOV life cycle.
Purpose of the Study:
- To analyze the structural properties of the EBOV secreted glycoprotein (Q7T9E0).
- To investigate potential antiviral drug interactions with the EBOV glycoprotein.
Main Methods:
- Acquired EBOV glycoprotein sequence from UniProt.
- Predicted secondary structures (alpha-helix, beta-sheets) using online servers.
- Determined protein flexibility and disordered regions (RONN, GLOBPLOT, DISSEMBLE).
- Constructed a 3D protein model via homology modeling (MOE software).
- Validated the model using stereochemical tests (RAMPAGE, ERRAT).
- Performed molecular docking of glycoprotein with dronedarone and amiodarone derivatives (MOE).
Main Results:
- Secondary structure and flexibility of the EBOV glycoprotein were characterized.
- A validated 3D model of the glycoprotein was generated.
- Docking studies revealed potential binding interactions between EBOV glycoprotein and specific drug derivatives.
Conclusions:
- The structural and flexibility analysis provides insights into EBOV glycoprotein function.
- Dronedarone and amiodarone derivatives show promise as potential therapeutic agents targeting the EBOV glycoprotein.
