Table 4.
Details of the synthesized derivatives
| Drug name or derivative code | 6LU7 |
6VSB |
|||||
|---|---|---|---|---|---|---|---|
| Binding affinity (kcal/mol) | Hydrogen bonds (n) | Active aminoacid residues | Binding affinity (kcal/mol) | Hydrogen bonds (n) | Active amino acid residues | ||
| Native ligand | − 9 | 7 | Leu141, Phe140, Glu166, Gln192, Pro168, Gln189, Met49, His41, Arg188, Met165, Asp187, His164, Leu27, Thr25, Thr26, Thr24 | − | − | − | |
| Approved drugs for the treatment of SARS-CoV-2 infection | Nelfinavir | − 8 | 3 | Leu27, Cys145, Asn142, Glu166, His164, His41, Tyr54, Asp187, Met165, Gln189, His163, His172, Phe140, Leu141, Ser144, Gly143, Thr26, Thr25 | − 8.7 | 1 | Gly-A:232, Arg-C:355, Phe-C:464 |
| Lopinavir | − 7.3 | 2 | Pro168, Glu166, Asn142, Ser46, Thr25, Thr26, Leu27, Cys145, Met49, His164, Asp187, His41, Arg188, Tyr54, Met165, Gln189 | − 8.5 | 0 | Arg-B:995, Asp-C:994, Thr-B:998, Arg-A:995, Thr-A:998, Tyr-B:756, Thr-C:998 | |
| Ivermectin | − 7.3 | 3 | Asn85, Val186, Arg40, Asn53, Met82 | − 9.1 | 4 | Cys-C:379, Glu-A:988, Val-C:382, Pro-A:987, Val-A:991, Val-B:991, Lys-C:378 | |
| Approved drugs for the treatment of SARS-CoV-2 infection | Remdesivir | − 7 | 8 | Pro168, Leu167, Thr190, His172, Met165,Phe140, His163, Leu141, Ser144, His164, Cys145, Gly143, Met49, Asn142, Glu166, Gln189, Ala191 | − 6.3 | 5 | Asn-B:542, Thr-B:547, Asp-C:745, Leu-C:981, Thr-B:549, Lys-B:386, Leu-C:981 |
| Favipiravir | − 5.7 | 4 | Gln127, Asp295, Phe08, Asn151, Phe112, Phe294, Thr292, Thr111, Gln110, Ile106 | − 5.2 | 4 | Asp-A:994, Phe-C:970, Arg-C:995, Thr-C:998, Gly-C:999 | |
| Novel pyrimidine-linked benzimidazole hybrids | 2a | − 6.6 | 1 | Thr190, Met165, His41, Glu166, His164, Met49, Cys145, Thr26, Gly143, Leu27, Thr25, Ser144, Leu141, Gln189 | − 7.2 | 3 | Thr-B:998, Thr-A:998, Asp-B:994, Tyr-B:756 |
| 2b | − 7.1 | 2 | Pro168, Asn142, His41, Met49, Asp187, Arg188, Tyr54, Met165, Gln189, Cys145, Leu167 | − 7.9 | 2 | Asp-B:994, Thr-B:998 | |
| 2c | − 7.8 | 4 | His163, Asn142, His164, His41, Met165, Asp187, Arg188, Val186, Gln192, Thr190, Pro168, Gln189, Cys145, Met49, Thr25, Thr26, Leu27, Gly143, Leu141, Ser144 | − 8.5 | 3 | Asn-B:978, Leu-B:977, Thr-A:547, Val-B:976, Leu-A:546 | |
| 2d | − 7.6 | 3 | Thr25, Leu27, Thr26, Gly143, Leu141, Gln189, Thr190, Met165, Glu166, His164, Arg188, Asp187, Met49 | − 8.4 | 3 | Thr-C:998, Asp-B:994, Arg-A:995, Thr-B:998, Tyr-C:756 | |
| 2e | − 7.4 | 4 | Tyr54, Asp187, Met49, His164, Asn142, Leu167, Pro168, Thr190, Gln192, Glu166, Gln189, Met165, Arg188, His41 | − 8.8 | 1 | Thr-C:998, Tyr-C:756, Thr-B:998, Arg-A:995, Asp-B:994, Arg-C:995, Arg-B:995 | |
| Novel pyrimidine-linked benzimidazole hybrids | 2f | − 8.1 | 1 | His41, His164, Met165, Met49, Tyr54, Asp187, Arg188, Gln189, Thr190, Gln192, Leu167, Pro168, Leu141, Asn142, Cys145, Ser144, Gly143, Leu27 | − 8.2 | 3 | Thr-B:415, Gly-B:416, Gln-B:414, Pro-C:384, Glu-A:988, Asp-A:985, Thr-C:385 |
| 2g | − 7.2 | 4 | Cys145, His41, Met165, His164, Met49, Gln189, Glu166, Leu167, Pro168, Asn142, Leu141, Phe140, Arg188, Tyr54, His163, Asp187 | − 8.3 | 4 | Thr-A:998, Arg-A:995, Thr-C:998, Tyr-C:756, Thr-B:998, Thr-C:998 | |
| 2h | − 8.0 | 2 | Met165, Cys145, Ser144, Met49 | − 8.3 | 1 | Tyr-B:756, Thr-C:998, Thr-B:998. Tyr-C:756 | |