Study On Design Of HIV Fusion Inhibitors

Until the end of 2005, twenty-seven drugs targeted to the HIV have been approved by the U.S. Food and Drug Administration (FDA). Although much progress has been obtained in the treatment of this infection by the introduction of highly active antiretroviral therapy (HAART), however, the high error rate of the reverse transcriptase leads to the emergence of drug resistant strains. Now, HIV infections represent a major medical problem in the world. Therefore, Development of safe and effective anti-HIV drugs is extremely urgent for the chemotherapy and/or prophylaxis of HIV infection. Blocking HIV-1 viral entry into the host cell offers a promising new strategy for interfering with the HIV-1 life cycle. Thus, it is pressing to develop more effective and less toxic HIV entry inhibitors for treatment and prevention of HIV infection.To bring a new drug to the market is very expensive, and the current price is about US$800 million. Therefore, it is not surprising that pharmaceutical companies are researching ways to decrease spending associated with R & D, with the goal of increasing profit margins. One of many methods quickly adopted by industry is the use of Computer-Aided Drug Design (CADD). It can abundantly save the expense and time spent on the long-run drug discovery process and has become effective tools in this area. CADD separates into two general categories: Mechanism-Based Drug Design and Structure-Based Drug Design. Now, the methods of CADD include: docking studies, where a ligand or drug is studied during the binding to an especial target; cheminformatics, where activity and structure are correlated using statistical means; and bioinformatics, where drug targets are derived from genomic data. In this thesis, the CADD methods were employed to study three projects, including interactions, binding free energies and the binding mode between gp41 and inhibitors; design of peptidomimetics; drug resistance of enfuvirtide. The thesis mainly includes three aspects as follows.1. Study on the fusion inhibitor of anti-HIV1.1 Molecular dynamics simulation on the complexes of N-terminal region of HIV-1 gp41 and its C-peptide inhibitors We report here 2 ns molecular dynamics simulation (MD) results on 14-residue C-peptides (C14wt and C14linkmid) which derived from the C-terminal region and complexes of C-peptides and N-terminal region. Both peptides were docked to the hydrophobic pocket of gp41 based on the structural information of N-terminal with AUTODOCK 3.0. The MD simulations were carried out in water by using GROMACS 3.0. The interaction energies were calculated with the linear interaction energy (LIE) method developed by ?qvist et al. The LIE method was used to estimate binding free energies. The calculated binding free energy for two models of C14linkmid-N45 and C14wt-N45 complexes are -25.17 and -20.99 kJ/mol, respectively, which are in very good agreement with the experimentally determined values (-25.42 and -18.83 kJ/mol). The analysis results show that there is a relationship between the inhibitory potency and the stability of corresponding helix. Three residues (Trp628, Glu630 and Ile635) from the C14wt insert into the hydrophobic pocket of gp41 and make extensive hydrophobic contacts. Four residues (Trp628, Gln629, Asp632, and Gln636) from the C14linkmid are deeply buried in the hydrophobic pocket of gp41 and make extensive hydrophobic contacts. Results provide strong evidence that the use of the crosslinker can improve the helix stabilization and the inhibitory potency.1.2 Design of the peptidomimetics of anti-HIV inhibitorSia et al. have suggested that a C14linkmid had the strong inhibitory potency of HIV-1. Based on the result of 1.1, in order to design a potent C14linkmid mimic, MD simulations were used to examine the interaction. We have also used the information from other and our studies to design several peptide mimics of C14linkmid. The results of MD simulations of those mimics reveal that the binding free energy of C14mimic3 and C14mimic4 (-26.29 and -26.55 kJ/mol, respectively) are less than that of C14linkmid. For the C14mimic4-N45 complex, the common binding hotspots could be Trp628, Trp631, Glu634, Ile635 and Tyr638.2 Studies on small molecular fusion inhibitors of anti-HIV2.1 The binding mode between gp41 and small moleculeA small inhibitor (TPL) is docked into the hydrophobic grooves of gp41 by using Autodock software, resulting in five alternative energetically favorable models. The molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) method was applied to calculate the binding free energies. The data from other studies were used to define our preferred models. We have found that only one binding mode is supported by the experimental evidence. The model could be used to design more effective HIV-1 inhibitors targeted to the HIV-1 gp41 core structure.2.2 Calculations of binding free energy between gp41 and small molecular inhibitorsIn order to understand the molecular mechanism of the small molecule inhibitors binding to gp41, we have carried out docking studies, explicit solvent MD simulations and binding free energy calculations. The results of calculated binding free energy are in agreement with the experimental data. The further analysis of the binding free energy components reveals the dominant contributions to hydrophobic interactions. These results could be used to design more effective HIV-1 inhibitors targeted to the hydrophobic pocket of HIV-1 gp41.3 Studies on drug resistance mechanism of anti-HIV fusion inhibitorEnfuvirtide is a 36-amino acid synthetic peptide whose sequence was derived from the gp41 HR-2 region of HIV-1. Enfuvirtide acts by binding to the HR1 domain of gp41 and prevents the interactions between the HR1 and HR2 domains of the viral gp41. Single and multiple mutations of gp41 at residue N42, N43, or S138 lead to degrees of resistance. Because the unavailability of the three-dimensional structure for the wild-type, we have constructed a 3D model of the gp41 ectodomain trimer by using the homology method. The stereo of gp41 parameters was checked using the PROCHECK program, and the result shows the structure is reasonable. We carried out a MD simulation of the HIV-1 gp41 N43D/S138A ectodomain domain and studied why these few mutations close to the active site cause resistance of Enfuvirtide. Four different conformations were chosen from the wild-type MD trajectories. The aim of our work is to understand the dynamics characteristics that play roles in the double mutant gp41 in the absence of any inhibitor. Moreover, we want to prove the influence of using different starting conformation on the MD trajectories. By comparison of the trajectories obtained from MD simulations, we have clarified that the starting structure does not affect the conformational space of this protein. It is found that the mutation MD behavior is similar to that of the wild-type MD properties.