Molecular Docking of Spike Protein of COVID-19 Using Selective Ligands

Authors:

Mayana Ibtisam Khan

Pages: 41-45

Abstract:

The latest coronavirus outbreak poses an unprecedented threat to health of human beings and society around the world. The

development of appropriate therapies is critical in this situation. The viral spike protein and the cognate host cell receptor ACE2

can be used as therapeutic targets. The current computational study shows that fisetin not only has a high affinity for the viral s

protein and the host receptor ACE2, but also for their complex RBD of the spike protein of SARS-CoV-2 and ACE2; RBD/ACE2-

complex. AutoDock Vina was used for docking fisetin with ACE2 receptor and S protein of SARS-CoV-2. The binding affinities

values are -2.56 and -1.9 kcal/mol for the S protein and ACE2, respectively. Fisetin binds directly to the viral S protein RBD.

Fisetin binds to the interface of the RBD/ACE2-complex, causing the alpha helices and beta strands of the protein complex to

fluctuate. The results of the docking showed that the binding pocket involves the amino acid residues Thr24, Thr25, Thr26,

Leu27, His41, Thr45, Ser46, Met49, Phe140, Leu141, Asn142, Gly143, Ser144, Cys145, His163, Met165, Glu143, Ser144,

Cys145, His163, Met165, Glu166, His172, Val3, Leu4, Leu167,Pro168,Ala2. Protein- protein interactions in the presence of

fisetin corroborate the above findings, indicating that this flavonoid is effective in preventing the formation of the S protein-

ACE2 complex. Finally, for the first time, this computational study predicts the possibility of flavonoid as a therapeutic strategy

against SARS-CoV-2.