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Table 1 Binding free energies of solvation and its components for the PCU-based ligands complexed with the HIV protease in in kcal/mol (the 3D structures of these compounds are provided with the supporting information)

From: Pentacycloundecane lactam vs lactone norstatine type protease HIV inhibitors: binding energy calculations and DFT study

Ligand a ΔE Ele ΔE VDW ΔE Sol (PB) ΔE Sol (GB) ΔG Bind (PBSA) b ΔG Bind (GBSA) b
PCU-lactam-NH-EAIS(a) −22.45 −69.26 55.49 48.12 −45.36 −52.63
PCU-lactone-NH-EAIS(a) c −22.36 −62.33 49.97 48.90 −41.28 −43.39
PCU-lactam-NH-EAIS(b) −22.25 −63.76 55.16 46.05 −40.31 −47.06
PCU-lactone-NH-EAIS(b) c −22.67 −59.18 50.16 45.94 −39.36 −42.95
PCU-lactam-CO-EAIS(a) c −23.82 −64.47 47.35 43.28 −45.89 −49.18
PCU-lactone-CO-EAIS(a) −11.47 −57.01 39.23 34.16 −41.77 −46.36
PCU- lactam-CO-EAIS(b) c −23.82 −64.47 46.58 43.28 −45.89 −49.18
PCU-lactone-CO-EAIS(b) −20.95 −62.08 50.62 46.85 −41.35 −44.01
PCU-lactam(a) −1.48 −34.13 12.73 12.39 −29.52 −27.63
PCU-lactone(a) −2.51 −25.61 14.05 13.34 −28.19 −17.37
PCU-lactam(b) −1.88 −30.14 14.94 14.99 −29.69 −19.99
PCU-lactone(b) −5.30 −27.26 17.60 17.53 −23.39 −17.92
  1. a(a) and (b) refer to the enantiomers of the models and the diasteromeric peptides, respectively.
  2. bNote that the total free energy of solvation values in AMBER were used and not the Quasi-harmonic Entropy Approximation energies.
  3. cTheoretically designed PCU-lactone-peptide inhibitors analogous to the previously synthesised PCU-lactam-peptides.