Drug-design Study Targeting HIV-1 Gp41 And CCR5

Since AIDS was recognized in June, 1981, 25 million people have died of HIV-related causes. On a global scale, although the HIV epidemic has stabilized since 2000, unacceptable high levels of new HIV infections and AIDS deaths still occur each year. According to UNAIDS report, in 2007, there were an estimated 33 million people living with HIV, 2.0 million people died due to AIDS. After over 20 years of research, HIV remains a difficult target for a vaccine. Thus the AIDS treatment continues to focus on the search for chemical anti-HIV agents. The highly active antiretroviral therapy (HAART) which combines several such drugs, typically three or four, has achieved significant success in clinical treatment. However, the therapeutic effect is limited by adverse effects and toxicities due to long-term use and the emergence of drug-resistant. The multiple steps of HIV replication cycle present several therapeutic targets. In recent years, HIV entry inhibitors which block the viral entry process have gained wide attention of medical research. One of the entry inhibitors, T-20 (Fuzeon), has been approved by FDA for clinical treatment in 2003.Computer-aided drug design (CADD) is a rapidly evolving field that leverages new data and techniques to provide approaches for tackling the needs of drug discovery. The applications of CADD now span the whole drug discovery process and contribute significantly to improve the low overall productivity of the pharmaceutical industry. The use of computational methods has not only enabled more efficient drug discovery and leads optimization but also provided insights into target-drug interactions. With the assistance of CADD approaches, the work of this thesis is implemented on two primary purposes: first, to investigate the binding mechanism and structural features of HIV-1 entry inhibitors; second, to further design, synthesize and test novel compounds as potential HIV-1 entry inhibitors. The research work in this thesis is summarized as the following:(1) Study on binding mode for NB-2 and NB-64 with HIV-1 transmembrane protein gp41NB-2 and NB-64 are two newly discovered N-substituted pyrrole derivations which inhibit the virus-cell membrane fusion by interfering with the formation of six-helical bundle of HIV-1 gp41. Revealing the binding mode of these two inhibitors with gp41 may provide important information for designing HIV-1 fusion inhibitors. Molecular docking, molecular dynamics (MD) simulation and molecular mechanics Poisson–Boltzmann surface area (MM-PBSA)/ molecular mechanics Generalized Born surface area (MM-GBSA) analysis were applied to predict the binding mode and interacting mechanism of NB-2 and NB-64 with the hydrophobic pocket in gp41. Multiple receptor conformations were used in docking and several possible binding modes were selected for MD simulations. The most favorable binding mode was identified through MM-PBSA binding energy calculations. MM-PBSA results indicate that binding is mainly driven by van der Waals interactions while polar interactions determine the orientation of the ligands upon binding. Further binding energy decomposition reveals that the carboxylate group in the ligands contributes significantly to the binding affinity through electrostatic interactions with Arg579 of gp41. This study helps establish a good starting point for further refinement of N-Substituted pyrrole derivatives as HIV-1 fusion inhibitors.(2) Rational design and synthesis of novel HIV-1 fusion inhibitorsBased on the predicted binding mode of NB-2 with gp41 hydrophobic pocket, a de novo drug design method (LeapFrog) was used to optimize the structure of NB-2 in order to design novel, potent, and selective inhibitors of gp41. 103 compounds were designed and the binding modes and activities of these compounds were then evaluated by using molecular docking. These compounds possess structural features not seen in known HIV-1 gp41 inhibitors and most of them have lower binding free energy than NB-2. Inspired by the de novo design results, we designed a set of novel compounds that target gp41 and have synthesized and tested seven of them. The seven novel compounds are able to inhibit the formation of six-helical bundle of gp41 in in vitro assays. Synthesis of the other compounds is processing. Hopefully, compounds with high inhibital activities will be discovered and used as leads for further study.(3) 3D-QSAR analysis on pyrrolidine-derivate CCR5 antagonistsAiming to investigate the structure-activity relationship of CCR5 antagonist, a series of 1,3,4-trisubstituted pyrrolidine derivate CCR5 antagonists were taken to construct CoMFA (Comparative Molecular Field Analysis) models. 72 of the compounds with diversified structures and activities were selected as training set molecules for building the CoMFA models. First, two alignment rules were adopted to align the molecules: common-structure alignment and force-field alignment. Partial Least Square (PLS) regression analysis was then used to construct the CoMFA model for each of the two alignment results. Region focusing was applied to eliminate noise of the two models, resulting in another two models. A testing set of another 39 compounds of this family were selected to test the four models. The region focusing CoMFA model based on common-structure alignment exhibits the best statistical properties and predicting ability: the conventional correlation coefficient r2 = 0.952, the cross-validated coefficient q2 = 0.637, and the correlation factor on the test set prediction R = 0.785. The contour map of this model visualizes key steric and electrostatic features for these antagonists binding to CCR5, demonstrating the potential receptor-ligand interactions. This study could provide useful clues for structural optimization of this type of CCR5 antagonists.In this thesis, structure-based and ligand-based CADD methods were used to attain detailed information for drug design targeting to HIV-1 protein gp41 and CCR5 chemokine co-receptor which are crucial for viral entry. The new compounds designed as gp41 inhibitors were proved to be active. This work may help to further develop drug candidates that block the HIV entry process.