Table 2. Summary of the docking results and interface analysis for ligand-bound MD2.
| Comp | Ligand | Stability | Area (Hyd, A2) | Sol (kcal/mol) | Aff (kcal/mol) | H/Ar-bond | Hyd-bond |
|---|---|---|---|---|---|---|---|
| Analysis of the stability of MD2- or TLR4/MD2-bound opioids and their initial conformational, and of the hydrophobic pocket interface | |||||||
| MD2 | Morph(A) | No | 881 (11.8%) | −27.33 | −6.32 | Phe151 (Ar) | Ile32,52,153; Leu61; Phe121,151 |
| Morph(B) | No | 884 (11.8%) | −31.26 | −7.85 | Ile63, (Ar)Phe104 (Ar) | Ile44,63,117; Phe76,104,147; Leu149 | |
| M3G(A) | No | 840 (11.5%) | −34.70 | −7.60 | — | Ile32,52,153; Leu78; Phe151 | |
| M3G(B) | Yes | 870 (11.6%) | −38.17 | −8.6 | Phe76 (Ar) | Ile46,63,94,117; Leu61,78; Val135; Phe104,151 | |
| Nlx(B) | No | 873 (11.6%) | −34.60 | −8.22 | Phe104 (Ar) | Ile63,94,117; Leu71;Val113; Phe76,104,147 | |
| TLR4/MD2 | Morph(A) | Yes | 873 (11.6%) | −21.24 | −5.44 | Phe76 (Ar) | Phe76; Leu78; Ile94,117 |
| M3G(A) | No | 850 (11.5%) | −35.10 | −7.70 | Tyr102 (H), Phe151 (Ar) | Ile63; Leu61,78; Phe119,151; Val135 | |
| Nlx(A) | Yes | 872 (11.6%) | −27.52 | −6.64 | Phe151 (Ar) | Ile32,46,63; Leu61; Val24,48,135; Phe151 | |
| Investigation of the changes in pocket area and ligand and interfacial residue conformation, after 120 ns in stable complexes | |||||||
| MD2 | M3G(B) | Yes | 524 (6.6%) (5.1%↓) | −46.13 | −9.07 | Glu92 (H), Ser103 (H) | Ile94,117; Leu61,78; Val135; Phe76, 119 |
| TLR4/MD2 | Morph(A) | Yes | 480 (7.0%) (4.0%↓) | −31.40 | −7.20 | Thr81 (H), Phe121 (Ar) | Val82; Leu87; Ile80,124,153; Phe76,119,121 |
| Nlx(A) | Yes | 523 (7.4%) (4.2%↓) | −33.18 | −6.62 | Glu92 (H), Ser118 H), | Ile63,117; Leu61,78; Phe76 | |
↓: Decrease in area; Hyd: Hydrophobic; Sol: Solvation energy; Aff: Affinity; Nlx: Naloxone; Ar: Arene bonds.