ABSTRACT
The ongoing spillover of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) calls for expedited countermeasure through developing therapeutics from natural reservoirs and/or the use of less time-consuming drug discovery methodologies. This study aims to apply these approaches to identify potential blockers of the virus from the longstanding medicinal herb, Lagerstroemia speciosa, through comprehensive computational-based screening. Nineteen out of 22 L. speciosa phytochemicals were selected on the basis of their pharmacokinetic properties. SARS-CoV-2 Main protease (Mpro), RNA-directed RNA polymerase (RdRp), Envelope viroporin protein (Evp) and receptor-binding domain of Spike glycoprotein (S-RBD), as well as the human receptor Angiotensin-converting enzyme-2 (hACE2) were chosen as targets. The screening was performed by molecular docking, followed by 100-ns molecular dynamic simulations and free energy calculations. 24-Methylene cycloartanol acetate (24MCA) was found as the best inhibitor for both Evp and RdRp, and sitosterol acetate (SA) as the best hit for Mpro, S-RBD and hACE2. Dynamic simulations, binding mode analyses, free energy terms and share of key amino acids in protein-drug interactions confirmed the stable binding of these phytocompounds to the hotspot sites on the target proteins. With their possible multi-targeting capability, the introduced phytoligands might offer promising lead compounds for persistent fight with the rapidly evolving coronavirus. Therefore, experimental verification of their safety and efficacy is recommended.
ABSTRACT
New variants of SARS-CoV-2 are continuously being reported. To curtail the spread of this virus, it is essential to find an efficient and potent vaccine. Here, we report in silico designing of a protein (ferritin: FR) nanocage fused with multiple epitopes identified using the immuno-informatics approach and high-throughput screening. Employing computational approaches, we identified potential epitopes from membrane, nucleocapsid, and envelope proteins of SARS-CoV-2 and docked them on the selected human leukocyte antigen Class I and II receptors, then the stability of the complexes was assessed using molecular dynamics simulation studies. We have engineered chimeric ferritin nanocage, chm66FR, with the nested peptide of 10 epitopes by replacing the loop region at the 66th position of the nanocage, then its stability was confirmed using metadynamics simulation. Further, we used the homotrimeric '6-helical bundle' of the spike protein to engineer the chimeric 6HB (chm6HB). The chm6HB is, engineered with three epitope peptides, mounted on the N-terminal trimeric interface of the chm66FR to generate the chm6HB-chm66FR, which contains 15 epitope peptides. Chimeric FR nanocages and the chm6HB could be potential vaccine candidates against strains of SARS-CoV-2. These multivalent and multiple epitopes protein nanocages and scaffolds could mount both humoral and T-cell mediated immune responses against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.