Molecular Docking of Curcumin and SARS-CoV-2

The molecular docking was conducted on the Lenovo ThinkPad T440p using the PyRx-Virtual Screening Tool. The structure of curcumin (sdf file format) was downloaded from the official website of the National Center for Biotechnology Information PubChem (https://pubchem.ncbi.nlm.nih.gov/, accessed on 3 January 2023). The energy minimization (optimization) was performed by a Universal Force Field (UFF). The 3D structure of curcumin–NLC constituents GMS, oleic acid, poloxamer 188, and tween 80 were obtained from drawing these chemical structures through ChemSchetch software and transferred from 2D to 3D and saved (as.mol file format). Then, they were converted to PDB format using the Discovery Studio visualizer 2019.
These structures were prepared for docking through PyRx software. The three host cell receptor structures of ACE2 (PDB ID: 7KMB, 7KNB, and 7KNH) were obtained from the RCSB PDB site (https://www.rcsb.org/, accessed on 3 January 2023). The receptor structures, with the aid of the Discovery Studio Visualizer 2021, were optimized, purified, and prepared for molecular docking. Autodock vina 1.1.2 in PyRx 0.8 was used to perform the molecular docking studies. A large number of glycosylated S proteins cover the surface of SARS-CoV-2 and bind to the host cell receptor angiotensin-converting enzyme 2 (ACE2), mediating a viral cell entry. Once the virus enters the cell, the viral RNA is released. Polyproteins are translated from the RNA genome, and the replication and transcription of the viral RNA genome occurs via the protein cleavage and assembly of the replicase–transcriptase complex. Viral RNA is replicated, and structural proteins are synthesized, assembled, and packaged in the host cell, after which viral particles are released [92 (link)]. For molecular docking, both ligands (PDBQT files), as well as the targets, were selected. The active binding receptors were examined and lightened using the BIOVIA Discovery Studio Visualizer (version-19.1.0.18287).