Table 2.
Docking interactions of active components of N. sativa with N-terminal RNA binding domain (NRBD) of SARS-CoV-2 nucleocapsid protein (PDB ID: 6M3M) versus standard drugs hydroxychloroquine and ivermectin.
| AutoDock v4.2.6 |
AutoDock Vina |
iGEMDOCK v2.1 |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| S.No | Ligands | BE (kcal/mol) | Kd | Interacting amino acids | BE (kcal/mol) | Kd | Interacting amino acids | T.E. (kcal/mol) |
VDW | HB | EI | Interacting amino acids |
| 1. | 24-methylene- cycloartanol | −8.29 | 842.64 nM | Ala126,Ala135,Asn49, Asp129, Asp64,Gly125, Gly130, IIe131,IIe132, Lys128,Phe67, Trp109, Trp133,Tyr124, | −9.8 | 76.87 nM | Gln161,Gln84,Glu137 Gly164,Gly70,Ile75,Leu160, Leu162,Leu168, Pro163,Pro81,Ser79,Thr136, Thr161,Thr166,Thr167 |
−96.16 | −91.43 | −4.72 | 0 | Arg69,Gln161,Gln84, Glu137,Glu165,Gly70,Leu160, Leu162,Leu16,Pro163,Pro81,Ser79, Ser80,Thr136,Thr166,Tyr173 |
| 2. | Alpha-spinasterol | −9.54 | 101.42 nM | Ala126,Ala135,Arg69,Asp64,Gln71, Gly130,Gly70,IIe131,IIe132, Leu65,Lys128,Lys66,Phe67,Pro68, Th136,Trp133,Tyr124Val134 | −9.6 | 101.42 nM | Ala107,Asp108,Asp164,Glu161, Glu167,Gly163His89, Leu162,Lys157,Lys92,Pro248,Thr301, Trp108,Trp93,Tyr264,Tyr264,Tyr273 | −91.33 | −84.04 | −7.29 | 0 | Asn109,Gln269,Glu161,Gly160, His89Leu162,Thr158,Val159 |
| 3. | Beta-sitosterol | −8.69 | 426.43 nM | Ala35,Arg69,Asp64,Gln71,Gly130, Gly70,IIe132,Leu65,Lys128, Lys66,Phe67,Pro68,Thr136, Trp109,Trp133,Tyr124,Val134 | −10.4 | 76.87 nM |
Asn76,Gln161,Gln71,Gln84, Gly70Leu160,Leu162, Leu168,Leu57,Pro163,Pro81,Ser79, Thr136,Thr166,THr167,Tyr173 | −88.19 | −84.69 | −3.5 | 0 | Ala126,Arg69,Asn127,Asn155, Gly125,Gly70Ile131,Ile132, Lys128,Phe67,Pro68, Trp133,Tyr124 |
| 4. | Campesterol | −8.57 | 522.64 nM | Ala126,Ala135Arg69, Asn127Asp129, Gln71,Gly70,IIe131 ,Lys128,Lys66,Phe67,Pro68,Trp133, Tyr124,Val134 |
−9.8 | 76.87 nM | Asn76,Gln161,Gln71,Gln84, Glu137,Gly165,Gly70,Leu160, Leu162,Leu168,Pro163Pro81,Ser79, Thr136,Thr166,THr167Thr77,Tyr173 | −93.83 | −90.33 | −3.5 | 0 | Gln161,Gln164,Gln84,Glu137, Gly165,Gly70,Leu162,Pro81,Ser79, Thr136,Thr166,Thr167 |
| 5. | Citrostadienol | −8.43 | 663.45 nM | Ala126,Arg69Asn127,Asn49, Asp129,Gly125,IIe131,IIe132, Lys128,Phe67,Pro152, Thr50,Trp133,Tyr124 | −8.9 | 259.96 nM |
Ala156,Asn127Asn155,Asn76, Asn78,Asp145,Gln161, Ile158,Thr149,Thr50,Trp53,Val159 | −80.13 | −75.88 | −4.24 | 0 | Ala156,Ala157,Asn155Asp145, Glm161,Gly148,His146, Ile158,Thr149,Val159 |
| 6. | Taraxerol | −8.5 | 588.67 nM | Asn49,Asp129,Asp64, Gly130,IIe131IIe132, Leu65,Lys128Lys656Trp133,Tyr124 | −12.1 | 76.87 nM |
Gln161,Gln71Gln84,Glu137, Gly165,Gly70,Ile75,Leu160, Leu162,Leu168,Pro163,Pro74Thr136, Thr166,Thr167,Thr173 | −96.11 | −93.61 | −2.5 | 0 | Gln161,Gln71,Gln84,Glu137, Gly165,Gly70,Ile75Leu160, Leu162,Leu168,Pro163,Pro74, Thr136,Thr166,Tyr173 |
| 7. | Hydroxychloroquine | −3.96 | 1.25 mM | Ala126,Arg69,Asn49,IIe131,IIe132, Lys66Phe67,Thr50,Trp133,Tyr124 | −6.7 | 588.67 nM |
Arg150,Asn151,Asn155, Asn76Gly148,Ile147,Ile158, Ile75,The77,Thr149,Thr50,Trp53 | −78.61 | −75.11 | −3.5 | 0 | Ala156,Asn76,Asp145,Gln161, Gly148,His146,IIe147,IIe158, IIe75,Thr149,Thr77,Val159 |
| 8. | Ivermectin | −9.08 | 220.28 nM | Ala126,Arg89,Arg89,Asn127,Asn154, Asn155,Asn49,Asn76,Asn78,Asp64, Gly117,Gly125,IIe131, IIe132,Leu65Lys128, Lys66,Pro118,Thr50,Trp133,Trp53 | −9.8 | 76.87 nM |
Ala157,Ala174,Ala56,Arg108, Arg150,His60,Pro152, Thr55,Thr58,Tyr110Tyr173,Val159 | −114.23 | −96.98 | −17.28 | 0 | Ala126,Ala51,Arg89,Asn127, Asn154,Asn155,Asn49,Asp129, Asp129,Asp64,Gly130,Ile131, Ile132,Leu65,Lys128,Lys66, Pro118,Thr50,Trp133, Tyr110,Tyr112 |