The Theoretical Calculation Study Involved Interaction Between HIV-1 Protease And Inhibitors

With insights into the function of Human Genome Project (HGP), the post-genomic era based on the functional genomics and proteomics researches has already come. Studies on the structure-affinity relationship and its actual application are important parts of the proteomics research. Some viral protein molecules play crucial roles in the life activities through recognition and interactions with inhibitors molecules.Therefore, the studies of these interactions between protein receptor and inhibitors are important for understanding interaction mechanism of inhibitors with protein receptor,which will also provide the theory foundation for designing and discovering new drug targets.The prevalence of AIDS dramatically threatens human life health, which makes the drug design against AIDS as a hot field and many countries are spending huge money on it. Over years, the human immunodeficiency virus type ? aspartic protease has become an important target for the development of new anti-AIDS virus inhibitors. Because HIV-1 protease is responsible for the cleavage of the gag and pol nonfunctional polypeptides into mature and functional HIV viral particles that can infect a host cell in the life cycle of the HIV virus, it is significant to investigate the interaction mechanism of HIV protease with inhibitors for the design of inhibitors targeting HIV protease.It is difficult to determine a protein complex structure through experimental methods. Recently, with the continuous progress of computers'processing ability, as well as the rapid development and extensive application of theoretical simulation and molecular modeling methods, such as molecular dynamics (MD) simulation, molecular docking and free energy computation, have become important tools for exploring protein with receptor. The interaction mechanisms of HIV protease with inhibitors are investigated and explained by using the decomposition of binding free energy based on inhibitor-residue pair at atomic level, which may provide theoretical hint for the design of HIV-1 protease.Owing to strong electrostatic repulsion between two residues Asp25 and Asp25′in HIV protease-inhibitor complex, correct protonations of Asp25 and Asp25′have strong influence on the stabilities for the binding of inhibitor to HIV-1 protease. Different protonation states of Asp25/Asp25′were found depending on the structure of the PIs and the local environment in which the PI-PR complex locates. However, the hydrogen position in the X-ray structural data is missing and the information about the protonation cannot be directly gained from the X-ray data, which makes studies of the protonation states of Asp25 and Asp25′indispensable. In this work, molecular dynamics simulations combined with the calculation of free energy are carried out to investigate the protonations of Asp25 and Asp25′in HIV protease-BEA369 complex, and the result suggests that the monoprotonation of Asp25 may be the most applicable to the current complex. Our data are helpful to the design of potent HIV-1 protease inhibitors.Due to drug-resistant mutations and side effects in clinical treatment, the development of improved inhibitors combating HIV virus is required. MD simulation, the decomposition of binding free energy and dynamics analysis of hydrogen bond are applied to investigate the functions of the fluoro-substituted inhibitors. Our results suggest that van der Waals interactions drive the binding of current studied inhibitors to HIV-1 protease and the the fluoro-substitution leads to the increase in van der Waals interaction. The decomposition of free energy and dynamics analysis of hydrogen bond based on the MD simulation show that the fluoro-substituted inhibitors can interact with the conserved residue in the protease, which suggests that the fluoro-substitution assist in the development of potent inhibitors.Because of drug-resistant mutations and side effect of drugs, the therapeutic success and efficacy of the current inhibitors are highly limited. It is significantly helpful to elucidate the drug-resistant mechanism of mutation for the development new inhibitors that can remove the drug resistance. 3-ns MD simulations combined with the calculation of binding free energy by using the MM-PB/SA method were carried out to analyze the drug resistance of D30N and I50V to TMC-114, and also investigate the binding mechanisms of TMC-114 to the WT, PRD30N and PRI50V. The results suggest that the decrease in the van der Waals energy and electrostatic energy in the gas phase definitively produce the drug resistance of D30N to TMC-114, while for I50V, the decrease in the electrostatic energy mainly drive its drug resistance to TMC-114. The separate MD simulations of the complex, the protein and the inhibitor were performed to investigate the effects of the conformational changes on the binding. The computed strain energies show that mutants D30N and I50V result in more rigid structure of the PR/TMC-114 complex than the WT.The analyses of the structure-affinity relationship were applied to investigate the binding mode of TMC-114 to the PR and the drug-resistance mechanisms of D30N and I50V to TMC-114. Among three complexes, the favorable interactions come from Gly27, Ala28/Ala28′, Asp30′(Asn30′), Ile50/Ile50′or Val50/Val50′and Ile84/Ile84′. The favorable interactions mainly were produced by four type interaction: the hydrogen bond interaction, the C-H…πinteractions, the C-H…O interactions and the C-H…H-C interactions. The comparisons of the structure-affinity relationship between the PR and mutant PR expose the resistant mechanisms of two mutations to TMC-114. The loss of the hydrogen bond between TMC-114 and the side chain of Asn30′is the main driving force of the resistance of D30N to TMC-114, additionally, the reduction in the van der Waals energy between Ile84 and TMC-114, also contributes slightly to the resistance of D30N to TMC-114. For I50V, the increase in the polar solvation energies between TMC-114 and two residues Val50′and Asp30′definitively drives the resistance of I50V to TMC-114. The analyses of the hydrogen bonds concerning the water molecule Wat301 were done to investigate the effect of Wat301 on the resistance, and the data show that Wat301 hardly contribute the resistance of D30N and I50V to TMC-114. This study provides a quantitative and mechanistic explanation of mutational effect from detailed analyses of the structure-affinity relationship. We expect that this work can provide some helpful insights into the nature of mutational effect and aid the future design of more potent inhibitors.This thesis consists of seven chapters. In the first chapter, the structure and function of HIV-1 protease and inhibitors used in clinical treatment are introduced. The classes of the interactions between proteins and inhibitors are described in the second chapter. Theories and methods used in the study, including quantum theory, molecular mechanics method, MD simulation and the calculations of free energy, are introduced in the third chapter. From the fourth chapter to the sixth chapter, the computational work and the main computational results are presented. The fourth chapter analyzes the functional role of the protonation in HIV-1 protease. In the fifth chapter, MD simulation and the dynamical analyses of hydrogen bonds are applied to study the functional roles of the fluoro-substituted inhibitors. The drug-resistant mechanisms of D30N and I50V to TMC-114 are explored by using MM-PBSA method of separate trajectory in the sixth chapter. The seventh chapter draws a conclusion for the whole work and views the future development of the study concerning HIV-1 protease and MD simulation.