Table 2.
Number of hydrogen bonds formed during the interaction between phytochemical structures with SARS-CoV-2 Proteins; S protein [PDB ID:6VSB,6VXX (closed), 6YVB (open)], 3 chymotrypsin like protease (3CLpro) (PDB ID:6LU7), papain like protease (PLpro) (PDB ID:4OVZ) and RNA-dependent RNA polymerase (RdRp) (PDB ID:6NUS). The interactions showing more binding affinity than remdesivir and SARS-CoV-2 are presented here
| Sl. No. | Compound with PubChem ID | Structural and chemical formula | No. of H bonds | Proteins of SARS-CoV-2 | Amino acid residues of viral receptor involved in hydrogen bonding with ligand |
|---|---|---|---|---|---|
| 1 |
Remdesivir 121,304,016 |
|
5 | S protein | GLN954, ARG1014, ARG1019 |
| 4 | 3CLpro | HIS41, AGR188, THR190 | |||
| 4 | PLpro | SER156, LEU163, TYR208, MET209 | |||
| 1 | RdRp | SER709 | |||
| 2 |
Astragalin 5,282,102 |
|
3 | S protein | PHE970, ASP994, THR998 |
| 2 | 3CLpro | SER144, ARG188 | |||
| 4 | PLpro | SER156, LYS158, ASP165, ARG167 | |||
| 3 |
Kaempferol 5,280,863 |
|
4 | S protein | TYR756, ARG995, THR756 |
| 5 | PLpro | THR75, ASP77, ARG83, ASN157 | |||
| 4 |
Quercetin 5,280,343 |
|
4 | S protein | THR549, ASP745, ASN978, ARG1000 |
| 2 | S protein (Closed) | TYR741 | |||
| 10 | S protein (Open) | TR549, ASN978, GLY744, ARG1000, THR573, MET740, TYR741 | |||
| 4 | RdRp | GLU350, PRO323, ASN628, VAL675 | |||
| 5 |
quercetin-3-O-glucoside 5,280,804 |
|
5 | S protein | PHE970, ARG995, THR998 |
| 1 | S protein (Closed) | THR998 | |||
| 4 | S protein (Open) | THR998, ARG995, ASP994 | |||
| 3 | 3CLpro | LEU141, HIS163, MET 165 | |||
| 8 | PLpro | HIS74, ARG83, TYR155,ASN157,HIS176 | |||
| 3 | RdRp | ALA125, HIS133 | |||
| 6 |
Quercitrin 5,280,459 |
|
8 | S protein | ASP994, AGR995, PHE970, THR998 |
| 1 | S protein (Closed) | THR998 | |||
| 3 | S protein (Open) | ASP994, VAL991 | |||
| 1 | 3CLpro | ASN142 | |||
| 1 | RdRp | TYR732 | |||
| 7 |
Hinokinin 442,879 |
|
4 | S protein | THR573, LEU977,ASN978, AGR1000 |
| 0 | RdRp | ||||
| 1 | PLpro | TYR269 | |||
| 8 |
Corilagin 73,568 |
|
5 | S protein | GLU773, LYS947, GLU1017, ASN1023 |
| 2 | S protein (Closed) | VAL991, THR998 | |||
| 4 | S protein (Open) | THR998, AGR995 | |||
| 6 | 3CLpro | GLY143, SER144, MET165, GLU166 | |||
| 5 | 6NUS | TYR129, HIS133, LEU207, ASN705, GLN724 | |||
| 9 |
Furosin 10,416,810 |
|
4 | S protein | ARG765, GLN954, AGG1014 |
| 2 | S protein (Closed) | LYS304, LEU754 | |||
| 7 | S protein (Open) | ASP40, ARG567, ASP571, SER967 | |||
| 4 | 3CLpro | THR24, THR26, ASN142, GLY143 | |||
| 6 | PLpro | ASP165, PRO249, GLN270, TYR274 | |||
| 7 | RdRp | ARG132, THR710, ASP711, GLY712, ASN713, TYR732 | |||
| 10 |
Geraniin 3,001,497 |
|
4 | S protein | THR302, ILE312, GLN314, ARG765 |
| 2 | S protein (Closed) | CYS291, SER750 | |||
| 5 | S protein (Open) | GLU988, ARG995, TYR756, THR998 | |||
| 5 | 3CLpro | LEU141, GLY143, SER144, CYS145, THR190 | |||
| 2 | PLpro | GLU251, TYR269 | |||
| 8 | RdRp | THR319, ASP390, LYS391, ARG349, PHE396, ARG457, ASN459 | |||
| 11 |
Isoandrographolide 343,585 |
|
2 | S protein | GLU773, ARG1019 |
| 1 | PLpro | TYR155 | |||
| 0 | RdRp | ||||
| 12 |
14-deoxy-14,15-didehydroandrographolide 6,473,762 |
|
1 | RdRp | SER236 |
| 13 |
14-Deoxyandrographolide 11,624,161 |
|
1 | RdRp | SER236 |
| 14 |
19-O-Acetyl-14-deoxy-11,12-didehydroandrographolide 46,179,874 |
|
4 | S protein | ARG319, LEU977, ARG1000 |
| 15 |
Neoandrographolide 9,848,024 |
|
2 | S protein | GLU748, ASN856 |
| 4 | RdRp | ALA125, ASP126, ARG132, HIS133 | |||
| 16 |
5-hydroxy-7,8,2′,5′-tetramethoxy flavone 16,215,023 |
|
4 | S protein | GLN314, GLN613, ILE666, LYS733 |
| 2 | RdRp | GLN728, TYR728 |