Molecular modeling, simulation and docking study of ebola virus glycoprotein.
Ebola virus (EBOV) is a filamentous, enveloped, non-segmented, negative-strand ribonucleic acid (RNA) virus which belongs to family Filoviridae. Ebola virus includes different glycoproteins each of which plays their roles in different aspects of viral life cycle. In this study secreted glycoprotein (Q7T9E0) of Ebola virus was acquired from Uniprot. The formation of alpha helix and beta sheets of secondary structures were predicted through online servers. Higher flexibility and disordered regions of proteins were determined through RONN, GLOBPLOT and DISSEMBLE. Three dimensional (3D) structure of the protein was built through homology modeling techniques and MOE software. The validation and evaluation of the refined models were determined with two stereochemical tests i-e RAMPAGE and ERRAT servers. Further docking studies of given protein was performed with different derivatives of two antiviral drugs dronedarone and amiodarone through MOE. Docking score and binding affinity of respective derivatives demonstrate that these might be used as protein receptors.
Department of Chemistry, Islamia College University, Peshawar, Khyber Pakhtunkhwa, Pakistan.
Nasir
N
Ahmad
Department of Chemistry, Islamia College University, Peshawar, Khyber Pakhtunkhwa, Pakistan.
Aqsa
A
Farman
Department of Chemistry, Islamia College University, Peshawar, Khyber Pakhtunkhwa, Pakistan.
Syed Lal
SL
Badshah
Institute of Chemical Sciences, University of Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan.
Ata
A
Ur Rahman
Department of Chemistry, Sarhad University of Science & Information Technology, Peshawar, Khyber Pakhtunkhwa, Pakistan. Electronic address: haroongold@gmail.com.
Haroon
H
Ur Rashid
Department of Chemistry, Islamia College University, Peshawar, Khyber Pakhtunkhwa, Pakistan. Electronic address: drkhalidchem@yahoo.com.
Khalid
K
Khan
D000595:Amino Acid Sequence; D000638:Amiodarone / Q000031:analogs & derivatives / Q000737:chemistry; D000077764:Dronedarone; D029043:Ebolavirus / Q000737:chemistry*; D006023:Glycoproteins / Q000737:chemistry*; D064267:Intrinsically Disordered Proteins / Q000737:chemistry; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D017433:Protein Structure, Secondary; D014764:Viral Proteins / Q000737:chemistry*; D014771:Virion / Q000737:chemistry
D006023:Glycoproteins; D064267:Intrinsically Disordered Proteins; D014764:Viral Proteins; D000077764:Dronedarone; D000638:Amiodarone
3D structure simulation; Docking; Ebola virus; Secreted GP