TABLE 6.
Bonds and binding sites of the identified best-binding compounds from C. gigantea and C. affinis against different targets, including DHFR, KOR, and COX-2.
| Receptor | Compound | Docking score (kcal/mol) | Bond type | Amino acids |
|---|---|---|---|---|
| DHFR (4M6J) | C1/C4 | −7.9 | Conventional hydrogen | Ser 59 and Ser 118 |
| Carbon-hydrogen | Thr 56 | |||
| Alkyl | Ile 16 and Lys 55 | |||
| Pi-alkyl | Ala 9 and Leu 22 | |||
| C2a | −8.8 | Carbon-hydrogen bond | Gly 20 | |
| Pi-sigma | Phe 34 | |||
| Alkyl | Ala 9, Ile 16, Leu 22, and Phe 31 | |||
| C2b | −8.8 | Alkyl | Ala 9, Leu 22, Phe 34, and Lys 55 | |
| C5 | −9.1 | Conventional hydrogen | Ala 9 and Ile 16 | |
| Pi-sigma | Leu 22 | |||
| Alkyl | Ile 60 | |||
| Pi-alkyl | Phe 34 | |||
| C6 | −8.1 | Conventional hydrogen | Ala 9 | |
| Unfavorable acceptor–acceptor | Glu 30 | |||
| Pi-alkyl | Ala 9, Ile 16, and Leu 22 | |||
| Ciprofloxacin | −8.1 | Carbon-hydrogen | Val 8, Thr 56, and Ser 118 | |
| Unfavorable donor-donor | Ala 9 | |||
| Pi-alkyl | Ile 16 and Leu 22 | |||
| KOR (6VI4) | C1/C4 | −7.7 | Carbon-hydrogen | Ser 192 |
| Pi-sigma | Ile 191 and Val 195 | |||
| Pi-pi stacked | Trp 183 | |||
| Alkyl | Leu 107 | |||
| Pi-alkyl | Ile 191 | |||
| C2a | −9.4 | Alkyl | Tyr 140, Ile 180, Trp 183, Leu 184, Ile 191, and Val 195 | |
| C2b | −10.5 | Alkyl | Tyr 140, Ile 180, Trp 183, Leu 184, and Ile 191 | |
| C5 | −9.7 | Pi-pi stacked | Tyr 140 and Trp 183 | |
| Alkyl | Leu 107, Leu 184, and Ile 191 | |||
| C6 | −8 | Conventional hydrogen | Ser 192 | |
| Unfavorable acceptor-acceptor | Ser 188 | |||
| Pi-sigma | Ile 191 and Val 195 | |||
| Pi-pi stacked | Trp 183 | |||
| Pi-alkyl | Ile 191 | |||
| Loperamide | −9.1 | Pi-sigma | Trp 183 | |
| Pi-pi stacked | Tyr 140 and Trp 183 | |||
| Alkyl | Ile 96, Phe 99, Leu 107, Leu 184, Trp 183, Ile 191, and Val 195 | |||
| COX-2 (1CX2) | C1/C4 | −7 | Pi-pi T-shaped | Gln 350 and His 351 |
| Pi-alkyl | His 356 | |||
| C2b | −8.7 | Conventional hydrogen | Asp 347 | |
| C3 | −7 | Conventional hydrogen | Leu 352, Ser 353, and Tyr 355 | |
| Carbon-hydrogen | Leu 352 and Ser 353 | |||
| Unfavorable acceptor-acceptor | Gln 192 | |||
| Alkyl | Val 349, Leu 359, Tyr 385, Trp 387, Phe 518, Met 522, Val 523, Ala 527, and Leu 531 | |||
| C5 | −7.2 | Van der Waals | Tyr 355 | |
| Conventional hydrogen | Ser 579 | |||
| Pi-pi T-shaped | Gly 354 and His 356 | |||
| C6 | −7.3 | Conventional hydrogen | Arg 120, Met 522, and Ser 530 | |
| Unfavorable donor-donor | Gly 526 and Ala 527 | |||
| Pi-sigma | Ala 527 | |||
| Pi-sulfur | Met 522 | |||
| Pi-alkyl | Val 349, Leu 352, Ala 527, and Leu 531 | |||
| Diclofenac sodium | −7.8 | Conventional hydrogen | Tyr 355 | |
| Pi-sigma | Val 349 and Ala 527 | |||
| Amide-pi stacked | Gly 526 | |||
| Pi-alkyl | Leu 352 and Leu 531 |