Table 2.
The binding energies and molecular interaction profiles of the control drug and the active compounds from Azadirachta indica, Mangifera indica, and Moringa oleifera leaves against the main protease of SARS-CoV-2.
| Ligands | Plant Source | Binding Energy kcal/mol | No. of H-Bond | Residues involved in Hydrogen bond | Residues involved in hydrophobic interaction | Residues involved in π-stacking | Residues involved in Salt Bridge |
|---|---|---|---|---|---|---|---|
| Caffeic acid | M. oleifera | −5.6 | 3 | Leu141,Ser144 and His163 | Phe140,Leu141,Asn142,Gly143,Ser144,Cys145,His163,Met165,Glu166 and Gln189 | – | – |
| Catechin | M. indica and M. oleifera | −7.2 | 4 | Glu166,Asp187,Thr190 and Gln192 | His41,His164,Met165,Pro168,Asp187,Arg188,Gln189,Thr190 and Gln192 | His41 | – |
| Chlorogenic acid | M. oleifera | −7.2 | 5 | Cys145,His163,Arg188,Thr190 and Gln192 | Leu141,Asn142,Gly143,His163,His164,Met165,Glu166,His172,Arg188,Gln189 and Thr190 | – | His41, His163 and His172 |
| Ellagic acid | M. indica and M. oleifera | −7.3 | 3 | His41,Arg188 and Thr190 | His41,Cys145,His164,Met165,Glu166,Asp187 and Arg188 | – | – |
| Epicatechin | M. indica and M. oleifera | −7.0 | 3 | Ser144,His163 and Gln189 | His41,Met49,Phe140,Leu141,His163,His164,Met165,Glu166,Asp187,Arg188 and Gln189 | – | – |
| Gallic acid | M. indica and M. oleifera | −5.5 | 6 | Leu141,Gly143,Ser144,Cys145,His163 and Glu166 | Phe140,Leu141,Asn142,Gly143,Ser144,His163,Met165 and Glu166 | – | – |
| Gedunin | A. indica | −7.3 | 1 | Asn142 | His41,Asn142,Gly143,Cys145,His164,Met165,Glu166,Pro168,Gln189 and Thr190 | – | – |
| Hydroxychloroquine | Control ligand | −6.4 | 4 | Ser144,Cys145,Gln189 and Thr190 | Phe140,Leu141,Asn142,Gly143,Ser144,Met165,Glu166,Arg188 and Gln189 | – | – |
| Kaempferol | M. indica and M. oleifera | −7.8 | 3 | Leu141,Ser144 and Gln189 | Met49,Leu141,Cys145,His163,Met164,His165,Glu166,Asp187,Arg188 and Gln189 | – | – |
| Lupeol | M. indica | −7.6 | – | – | His41,Asn142,Gly143,Cys145,His164,Met165,Glu166,Leu167,Pro168,Gln189 and Thr190 | – | – |
| Mangiferin | M. indica | −8.4 | 9 | His41,Leu141,Asn142,Gly143,Ser144,Cys145,Arg188,Thr190 and Gln192 | His41,Met49,Leu141,Asn142Gly143,Ser144,Cys145,Met165,Glu166,Arg188,Gln189,Thr190 and Gln192 | – | – |
| Myrecitin | M. oleifera | −7.7 | – | – | Thr26,Leu27,His41,Met49,Tyr54,Gly143,Cys145,His164,Met165,Asp187,Arg188 and Gln189 | – | – |
| Nimbandiol | A. indica | −7.1 | 2 | Thr26 and Gly143 | Thr25,Leu27,His41,Met49,Phe140,Leu141,Asn142,Gly143,Cys145,Gln166 and Gln189 | – | – |
| Nimbin | A. indica | −6.2 | 2 | Arg40 and Arg188 | Arg40,Tyr54,Glu55,Met82,Asn84,Cys85,Gly179,Asn180,Phe181,Val186,Asp187 and Arg188 | – | Arg41 and Arg188 |
| Nimbinene | A. indica | −6.5 | 2 | Asn142 and Gly143 | Thr25,Thr26,Leu27,Met49,Phe140,Leu141,Asn142,Gly143,Cys145 and Gln189 | – | – |
| Nimbolide | A. indica | −7.6 | 3 | Glu55,Phe181 and Arg188 | Arg40,Asn53,Tyr54,Glu55,Met82,Cys85,Asn180,Phe181,Val186 and Arg188 | – | Arg40 and Arg188 |
| Nimbolinin | A. indica | −6.2 | 1 | Arg40 | Arg40,Tyr54,Glu55,Met82,Asn84,Cys85,Asn180,Phe181,Phe185,Val186 and Arg188 | – | Arg40 and Arg188 |
| Quercetin | A. indica, M. indica and M. oleifera | −7.5 | 4 | Leu141,Ser144,His163 and Gln189 | His41,Met49,Phe140,Leu141,His163,Met165,Glu166,Asp187,Arg188 and Gln189 | – | – |