Table 3.
Summary of top seven ranked ligands screened against RBD of Spike 2019 n-cov2, with their respective classification, chemical formula, binding affinity, hydrogen, and hydrophobic interacting residues
| Ligand name | Open state | Closed state | ||||
|---|---|---|---|---|---|---|
| Binding affinity (kcal/mol) | Hydrogen bond | Hydrophobic bond | Binding affinity (kcal/mol) | Hydrogen bond | Hydrophobic bond | |
| Rossicaside A | −7.5 |
Gln238 Val239 Ser247 Thr249 Trp251 Asn252 Arg253 Ser297 |
Lys249 Ala250 Tyr347 Asn348 Tyr349 Leu350 | −6.8 |
Ala257 Ser284 Ser286 Asn353 Asn350 |
Phe255 Leu354 |
| Etravirine | −7.4 | Ser271 |
Phe240 Asn241 Trp334 Leu339 |
−6.7 | Gly409 | Phe377 Glu429 |
| 1,2-Ethanediol,1,2-bis(4-fluorophenyl) | −6.7 | Gly394 |
Asn319 Tyr393 Tyr403 |
−6.7 | – |
Tyr408 Asn414 Tyr418 |
| 1,2-Propanediol,3,3,3-trifluoro-2-phenyl-(2R) | −6.7 | Gly394 |
Tyr393 Asn399 Tyr403 |
−6.7 | Asn414 |
Tyr408 Asn414 |
| 1,1-bis(3-Fluorophenyl)-2-methoxyethanol | −6.6 | Gly394 Gln396 Asn399 Gly400 | Tyr393 Tyr403 | −6.6 |
Gly409 Gln411 Asn414 Gly415 |
Tyr408 Asn414 Tyr418 |
| 1,1-Diphenyl propane-1,2-diol | −6.4 |
Gly394 Asn399 |
Arg301 Tyr393 TYR403 |
−6.4 |
Gln411 Asn414 |
Arg316 Tyr408 Tyr418 |
| (S)-1,1-Diphenylpropane-1,2-diol | −6.2 |
Gly394 Gln396 Asn399 |
Tyr393 Tyr403 |
−6.4 |
Gly409 Asn414 |
Arg316 Tyr408 Tyr418 |