Table 5.
Interactions plots and interacting residues of fourteen potential hits with the SARS CoV-2 Mpro proteins are summarized with the number of hydrophobic interactions and the number of hydrogen bonds (where red spikes represent hydrophobic residues, green-colored residues represent hydrogen bonds).
| S. No. | Chemical Compound |
Functional Residues Involved in Hydrophobic Interactions | Total Hydrogen Bonds with Distance | Interaction plots | Binding affinity (kcal/mol) |
|---|---|---|---|---|---|
| 01 | Caeruleanone A | Thr111(A) | (1) |  |
−11.1 |
| Asn151(A) | Gln107(A) | ||||
| Phe294(A) | NE2-O3 = 2.89 Å | ||||
| Phe8(A) | |||||
| Asp153(A) | |||||
| Ile152(A) | |||||
| Arg105(A) | |||||
| Ile106(A) | |||||
| Gln107(A) | |||||
| 02 | 2′,4′-Dihydroxy-2″-(1-hydroxy-1-methylethyl) dihydrofuro [2,3-h] flavanone | Ile152(A) | (4) Ser158(A) |  |
−10.5 |
| Asn151(A) | OG-O5 = 3.24 Å | ||||
| Gln110(A) | Asp153(A) | ||||
| Phe294(A) | OD2-O5 = 3.07 Å | ||||
| Val104(A) | Thr111(A) | ||||
| OG1-O3 = 3.24 Å | |||||
| N-O3 = 3.20 Å | |||||
| 03 | Matairesinol | Gln110(A) | (1) |
|
−10.3 |
| Ile106(A) | Thr111(A) | ||||
| Asn151(A) | OG1-O2 = 3.17 Å | ||||
| Val104(A) | |||||
| Asp153(A) | |||||
| Phe294(A) | |||||
| Ile152(A) | |||||
| 04 | Vadimezan | Gln110(A) | (3) |
|
−9.6 |
| Thr292(A) | Thr111(A) | ||||
| Phe294(A) | O-O3 = 3.14 Å | ||||
| Asn151(A) | N-O3 = 2.93 Å | ||||
| Ile106(A) | OG1-O3 = 2.83 Å | ||||
| 05 | Tangeretin | Phe294(A) | NO hydrogen bonding |  |
−9.3 |
| Asn151(A) | |||||
| Arg105(A) | |||||
| Val104(A) | |||||
| Ile106(A) | |||||
| Thr111(A) | |||||
| Gln110(A) | |||||
| 06 | Imperatorin | Gln110(A) | (2) |  |
−9.2 |
| Gln107(A) | Thr111(A) | ||||
| Ile106(A) | OG1-O4 = 2.75 Å | ||||
| Asn151(A) | N-O4 = 3.08 Å | ||||
| Phe294(A) | |||||
| Thr292(A) | |||||
| 07 | Nobiletin | Thr111(A) | NO hydrogen bonding |
|
−9.2 |
| Asn151(A) | |||||
| Phe294(A) | |||||
| Gln110(A) | |||||
| Ile106(A) | |||||
| Arg105(A) | |||||
| Val104(A) | |||||
| 08 | Demethylnobiletin | Phe294(A) | (1) |  |
−9.2 |
| Asn151(A) | Thr111(A) | ||||
| Ile106(A) | O-O5 = 3.19 Å | ||||
| Gln110(A) | |||||
| Arg105(A) | |||||
| Val104(A) | |||||
| 09 | 2,6-Ditert-butyl-4-(1-hydroxyethyl) phenol | Asp295(A) | (3) |  |
−9.1 |
| Phe294(A) | Thr111(A) | ||||
| Asn151(A) | OG1-O2 = 3.18 Å | ||||
| Ile106(A) | N-O2 = 3.07 Å | ||||
| Gln110(A) | |||||
| NE2-O2 = 3.09 Å | |||||
| 10 | Zapotin | Gln107(A) | (1) |  |
−9.0 |
| Arg105(A) | Gln110(A) | ||||
| Ile106(A) | NE2-O6 = 2.96 Å | ||||
| Val104(A) | |||||
| Asn151(A) | |||||
| Asp153(A) | |||||
| Phe294(A) | |||||
| 11 | Calycosin | Val104(A) | (3) |
|
−8.7 |
| Ile106(A) | Asp295(A) | ||||
| Phe294(A) | OD1-O5 = 3.12 Å | ||||
| Asn151(A) | Thr292(A) | ||||
| Ser158(A) | OG1-O5 = 3.30 Å | ||||
| Gln110(A) | Thr111(A) | ||||
| OG1-O5 = 2.72 Å | |||||
| 12 | 2′-Hydroxy-3,4,4′,6′-tetramethoxychalcone | Ile106(A) | (2) |  |
−8.6 |
| Arg105(A) | Thr111(A) | ||||
| Val104(A) | O-O4 = 3.11 Å | ||||
| Asn151(A) | Gln110(A) | ||||
| Phe294(A) | NE2-O4 = 3.08 Å | ||||
| 13 | Pelubiprofen | Gln110(A) | (2) |  |
−8.5 |
| Ile106(A) | Thr111(A) | ||||
| Val104(A) | OG1-O2 = 2.90 Å | ||||
| Asn151(A) | N-O3 = 3.19 Å | ||||
| Phe294(A) | (2) | ||||
| 14 | Pterostilbene | Gln110(A) | (2) |  |
−7.7 |
| Arg105(A) | Asp295(A) | ||||
| Ile106(A) | OD1-O3 = 3.15 Å | ||||
| Val104(A) | Thr111(A) | ||||
| Asn151(A) | OG1-O3 = 2.92 Å | ||||
| Phe294(A) | |||||