Estimation of Binding Sites of Efavirenz with 3EO9 Receptor: In Silico Molecular Docking and Molecular Dynamics Studies

Abstract

The compound (2H-3, 1-benzoxazin-2-one,6-chloro-4-(cyclopropylethynyl)-1,4- dihydro-4-(trifluoromethyl)-,(4S)), commonly known as efavirenz, is an anti-HIV drug. It is used in combination with antiretroviral agents for the treatment of HIV-1 infection. In this work, the geometry of efavirenz has been optimized by density functional method at B3LYP level. Also, the electronic structure and molecular properties of efavirenz have been investigated. Further, the optimized structure is used for molecular docking study that has been carried out by SwissDock web server in order to check the binding affinity of efavirenz with 3EO9 receptor. The binding energies between efavirenz and the residues of the 3EO9 receptor demonstrate that there exist various attractive binding sites between efavirenz and residue positions of the target protein. The best binding site is further taken for the molecular dynamics simulation which also validates the result of molecular docking. Results have been discussed in order to elucidate the binding mechanism of efavirenz with protein receptor along with various physico-chemical properties of the drug molecule.

Keywords:

• Anti-HIV drug
• binding affinity
• DFT
• molecular docking
• molecular dynamics

Acknowledgement

D. Sharma is thankful to UGC, New Delhi, India for providing Start-Up Project [F.30-505/2020(BSR)].

Disclosure statement

No potential conflict of interest was reported by the authors.