Table 2.
The binding affinity, RMSD, and interacting residues of the screened phytocompounds against RBD domain of omicron B.1.1.529. spike protein with the resolution of 2.79Å.
| Seaweeds | Chemical Compound | Binding Affinity | RMSD (Å) |
H/C-H Bond Interaction | Interaction Distances | Hydrophobic Interaction | Alkyl Interaction | Pi-Sigma /Cation Stacked Interaction |
|---|---|---|---|---|---|---|---|---|
| Standard drug | Ceftriaxone | −7.1 | 43.189 | ARG403, ASN417, TYR453, SER494, SER496, TYR501 | 5.36, 4.21, 6.03, 3.24, 3.59, 6.23 | ASP405, GLU406, ARG408, GLN409, LEU455, ARG493 | - | ARG403, HIS505 |
| Cefuroxime | −5.3 | 2.483 | THR376, GLY404 *, ARG408, TYR508 | 4.52, 5.06, 4.71, 5.71 | PHE375, ASN437 | ARG408, VAL503 | - | |
| C. officinalis | 3’,8,8’-Trimethoxy-3-piperidin-1-yl2,2’-binaphthyl-1,1’,4,4’-tetrone | −6.9 | 1.897 | - | - | ARG355, TYR396, ASP428, PHE429, THR430, SER514, PHE515, LEU517, LEU518 | PRO426, PRO463 | PHE464, GLU516 |
| Cholestan-3-ol, 2-methylene-, (3beta, 5 alpha) | −6.0 | 3.074 | SER494 | 4.22 | GLY482, THR470 | LEU452, TYR449, ILE472, ALA484, PHE490 | PHE490 | |
| C. racemosa | Glucobrassicin | −6.8 | 1.521 | ARG457, ARG466, ASP467, ASP467 * | 4.45, 6.50, 3.18, 5.49 | ARG454, PHE456, SER459, GLU465, ILE468, SER469, TYR473, PRO491 | ARG457, LYS458 | ARG457, ASP467, GLU471 |
| G. corticata | Bicyclo[3.2.1]oct-3-en-2-one, 3,8-dihydroxy-1-methoxy-7-(7-methoxy-1,3-benzodioxol-5-yl)-6-methyl-5 | −6.3 | 20.322 | THR430 | 4.16 | ARG355, ASP428, SER514, PHE515, GLU516, LEU517 | TYR396, PRO426, PHE429, PRO463, PHE464 | - |
| Cholesta-8,24-dien-3-ol, 4-methyl-, (3.beta.,4.alpha.)- | −6.8 | 1.544 | - | - | TYR396, ASP428, THR430, GLU465, SER514, PHE515, GLU516 | PRO426, LYS462, PRO463, PHE464 | - | |
| P. boergesenii | Glucobrassicin | −6.8 | 1.521 | ARG454, LYS458, SER459, SER469 | 5.00, 4.44, 2.38, 3.25 | PHE456, ARG457, TYR473, PRO491 | - | ASP467, GLU471 |
| Glycitein | −6.1 | 11.668 | THR376, ASP405 * | 4.71, 4.5 | GLY404, ARG408, VAL503, GLY504 | VAL407 | TYR508, PHE375 | |
| Matairesinol | −6.0 | 1.707 | ARG355, PHE464 *, SER514 | 6.65, 4.98, 3.72 | TYR396, ASP428, PHE429, THR430, PRO463, PHE515, GLU516, LEU517 | PRO426 | - | |
| Naringenin | −6.4 | 20.209 | ASN437, LYS440, LEU441 | 4.09, 4.44, 4.14 | ASN343, PHE374, PHE375, SER438, ASN439 | PRO373, LYS440 | TRP436 | |
| Pyrano [4,3-b] benzopyran-1,9-dione, 5a-methoxy-9a-methyl-3-(1-propenyl) perhydro | −6.1 | 29.617 | SER496, TYR501 | 3.39, 5.24 | ARG403, TYR453, TYR495, GLY502 | HIS505 | TYR501, HIS505 | |
| Syringaresinol | −6.4 | 0.44 | ARG355, ASP427 *, PRO463 *, PHE515 *, GLU516 | 6.88, 4.19, 4.81, 7.35, 3.78 | ASP428, THR430, SER514 | TYR396, PRO426, LYS462, PRO463 | PHE464 | |
| S. wightii | 5-p-coumaroylquinic acid | −6.0 | 4.96 | ARG403, ASN417, TYR453, SER496 | 5.43, [2.96, 4.87], 5.62, 3.42 | GLN409, GLY416, ILE418, LEU455, SER494, TYR495, TYR501, HIS505 | - | - |
| Caffeic acid hexoside | −6.4 | 2.82 | ARG403, GLU406, ASN417, TYR453, SER496 | [5.38, 6.24], 3.95, 4.96, 5.76, [3.34, 3.36] | ASP405, ARG408, GLN409, ILE418, LEU455, TYR495, SER494, TYR501, HIS505 | - | - | |
| Phloretin | −6.3 | 0.061 | TYR501, SER496, TYR453 | 5.37, 1.49, 5.90 | ARG403, TYR495, PHE497, THR500, GLY502 | - | TYR501, HIS505 | |
| Quercetin-3-O-arabinoglucoside | −6.1 | 2.248 | ASN331, THR333, GLY526, PRO527 *, LYS528C | 5.09, [3.47, 3.38], [3.93, 4.29], 4.60, 5.10 | PRO330, ILE332, CYS361, THR523 | VAL362, CYS525 | ASN360 |
Note: * = Carbon–hydrogen bond.