Almost all of the human immunodeficiency virus type I protease (HIV-1 PR) inhibitors contain a hydroxyl-ethylene moiety, which plays an essential role in recognition of the enzyme through the arpartic active sithe residues. Apparently, the affinity of the binding is associated with a proper ionization state of the sidechain of the inhibitor-bound residues. The protonation state of the active site residues is not clearly understood. We decided to carry out molecular dynamics simulations and conventional and modified free energy calculations to improve a prediction of the protonation state of the HIV-1 PR in complex with six HIV-1 PR drugs including Lopinavir (LPV), Ritonavir (RTV), Saquinavir (SQV), Indinavir (IDV), Amprenavir (APV), and Nelfinavir (NFV). All possible protonation states of the active site residues including monoprotonate at Asp25 (D25), monoprotonated at Asp25' (D25'), diprotonaition (D25,25'), and unprotonation (D-), were used to set up the system of HIV-1 PR-drug complexes for the simulations. The binding free energy (4Gbinding) was computed using a standard and hybrid methods of molecular mechanic Posisson Boltzmann or Generalized Born, and solvent accessible surface area (MMPB(GB)/SA), Inthis study, the 4Gbinding due to the protonation change at pH=7 was also taken into account. Comparison among the method used, the hybrid MMPB/SA approach offers a slightly advantage in reproducing absolute binding free energies whereas the use of Generalized Born approximation significantly affects the accuracy of the computed binding affinities.l Based on the 4Gbinding and the computational analysis, monoprotonation is the optimal state for the 6 drugs, D25 for LPV, SQV, and IDV and D25' for RTV, APV, and NFV. The stud y was extended to prodict molecular mutation due to the HIV-1 PR complexed with the 6 inhibitors and the influenza neuraminidase complexed with oseltamivir using the decomposition binding free energy as a critieria. The predicted mutation residues for both cases are in good agreement with the high and intermediate level of resistant reported clinically.
