| The acquired immune deficiency syndrome (AIDS) which is induced by Human immunodeficiency virus (HIV) infection has become one of the major medical and humanitarian challenges. The HIV-1 protease (PR), as a member of the aspartyl proteases family, is one of the most important enzymes in drug discovery against AIDS, which cleaves the non-functional polypeptide into viral structural (gag) and functional protein (pol) essential for maturation of infectious HIV particles. Repression of the HIV-1 PR activity could prevent the production from maturing and infecting and hence block further HIV infection. Binding of the inhibitor to PR can lead to inactivation of the enzyme and hold back to infect the host cell at last. Thus the dimeric HIV-1 protease has been one of the most attractive targets for the development of antiviral therapeutics. Therefore, it is critically important to deeply research the mechanism of the interaction between PR and PI and the resistance induced by mutations for designing inhibitors.Since it is not convenient to measure the binding affinities of different PR and inhibitor experimentally, molecular dynamics (MD) simulation provide the opportunity to investigate the structural and functional characteristics of biochemical systems by computational simulation with techniques, especially for complicated biological systems, and it could be employed to investigate the mechanism of the drug-resistance for the HIV-1 protease-inhibitor complex.In the first study, a combination of computational alanine scanning mutagenesis and free energy decomposition methods was presented for the protein-inhibitor complex of HIV-1 protease complexed with the inhibitor to investigate the different contributions of residues to the binding of TMC-126. The calculated results demonstrate that the flap region (residues from 38 to 58) and the active site region (residues from 23 to 32) in HIV-1 protease provide 63.72% contribution of the protease to the binding of inhibitor. Especially, the detailed mechanism interactions of key residues were explored and discussed. Interestingly, the regression analyses between the computational alanine scanning method and the free energy decomposition method were performed with a correlation coefficient of 0.94, reflecting that both methods based on Generalized Born (GB) model agree with each other. Finally, our calculated results reveal that the binding free energy decomposition (BFED) is more efficient than the computational alanine scanning (CAS) for its faster calculation and decomposition into backbone and side-chain contributions on a per-residue basis. This work can provides some helpful insights into the interaction mechanism for HIV-1 protease binding to inhibitor and some guidance to choose the theoretical method.Because the rapid evolution of drug-resistant variants results in short-live drugs designed for clinical-care, there is an urgent need to develop antiretroviral drug with minimal side effects and broad-spectrum activity for current and future wild-type and mutant strains of HIV protease. Therefore, it is essential to deeply study the mechanism of the resistant interaction between the variants and inhibitors for designing drugs.In the following study, we adopt an atomistic molecular dynamics simulation approach to study the functional role of the G86 residue in the highly conserved triad G86-R87-D/N88 of the HIV-1 protease in the binding to the DRV. In our work, detailed binding free energies for the wile-type (WT) and mutated proteases binding to the TMC-114 are estimated to investigate the protein-inhibitor binding and drug resistance mechanism by molecule dynamic simulations and Molecular Mechanics Poisson Boltzmann surface area (MM-PBSA) method. The binding affinities between the mutants and the inhibitor are weaker than that in the wild-type complex and the major resistance to Darunavir (DRV) of G86A and G86S originate from the electrostatic energy and entropy, respectively. Furthermore, free energy decomposition analysis for the WT and the mutated complexes on the basis of per-residue indicates that the mutagenesis influences the energy contribution of the residue located at three regions: active site region (residue 24-32), the flap region and the region around the mutated residue G86 (residue 79-88), especially the flap region. Finally, further hydrogen bonds and structure analysis are carried out to detect the relationship between the energy and conformation. In all, the G86 mutations change the flap region's conformation and slightly pushed away from the active site loop region and hence weaken the binding affinities. The obtained results in this study should be helpful for studying the binding mechanism between receptor and ligand and designing potent inhibitors combating diseases. |
