Table 2.
Molecular interaction analysis of SARS-CoV-2 RDRP with selected phytochemicals from selected plants.
| S. no. | Compound, PubChem ID, & source | H-bond | π–π/*π–π cation | Hydrophobic | Polar | Negative | Positive | Glycine |
|---|---|---|---|---|---|---|---|---|
| 1 |
Echinacoside (5281771) (E. angustifolia) |
Asp452, Thr687, Asp760, Asp618, Lys551, Arg553, Ala554, Asp623 | – | Ala688, Tyr455, Cys622, Ala554, Pro620, Tyr619, Met794, Phe793, Val166 | Ser814, Ser795, Thr556, Ser682, Thr687, Asn691, Ser759 | Asp452, Asp623, Asp618, Asp164, Glu167, Asp761, Asp760 | Arg624, Arg555, Lys621, Arg553, Lys551, Lys798 | – |
| 2 |
Rutin (5280805) (E. angustifolia) |
Asp760, Asp452, Arg555, Arg553, Lys551, Asp618 | *Arg555, *Lys551 | Cys622, Pro620, Tyr619, Ala550, Ala554 | Ser549, Thr556 | Asp760, Asp623, Asp618, Asp452 | Arg624, Lys621, Lys798, Lys551, Arg553, Arg555 | – |
| 3 |
Kaempferol-3-O-rutinoside (5318767) (E. purpurea) |
Asp452, Lys551, Asp623, Lys621, Tyr619, Asp618, Asp760, | – | Ala554, Ala550, Cys622, Pro620, Tyr619, Trp617, Ala762, Cys813, Tyr455 | Ser814, Ser549, Thr556 | Asp452, Glu811, Asp761, Asp760, Asp618, Asp623 | Arg555, Arg553, Lys551, Arg624, Lys621, Lys798 | |
| 4 |
Echinacoside (5281771) (E. purpurea) |
Ser795, Asp164, Asp760, Thr687, Asp623, Asp452, Arg555, Ala554, Arg553 | – | Val166, Phe793, Ala554, Tyr619, Pro620, Tyr455, Cys622, Ala688 | Ser795, Ser814, Ser759, Asn691, Ser682, Thr687, Thr556 | Asp618, Asp164, Asp623, Asp452, Asp761, Asp760 | Lys798, Lys551, Arg553, Arg555, Lys621, Arg624 | – |
| 5 |
Rutin (5280805) (H. perforatum) |
Asp760, Asp452, Arg555, Arg553, Lys551, Asp618 | *Arg555, *Lys551 | Cys622, Pro620, Tyr619, Ala550, Ala554 | Ser549, Thr556 | Asp760, Asp623, Asp618, Asp452 | Arg624, Lys621, Lys798, Lys551, Arg553, Arg555 | – |
| 6 |
Quercetin-3-O-xyloside (5320863) (H. perforatum) |
Asn497, Arg569, Gly683, Asn543 | *Lys500 | Ala502, Val557, Ala558, Val560, Ile562, Leu498, Val495, Ala512, Tyr516, Ala685 | Asn543, Ser501, Asn497, Thr565 | Asp684 | Arg569, Lys500 | Gly683, Gly559 |
| 7 | Mpro-remdesivir (control) | Arg553, Thr556, Cys622, Asp623, Asn691,Ser759 | – | Tyr455, Ala554, Val557, Tyr619, Pro620, Cys622, Ala688 | Ser549, Thr556, Thr680, Ser682, Thr687, Asn691, Ser759 | Asp618, Asp623, Asp760 |
Lys545, Lys551 Arg553, Arg555, Lys621, Arg624 |
– |