Hydrophobic amino acids in the hinge region of the 5A apolipoprotein mimetic peptide are essential for promoting cholesterol efflux by the ABCA1 transporter.

The bihelical apolipoprotein mimetic peptide 5A effluxes cholesterol from cells and reduces inflammation and atherosclerosis in animal models. We investigated how hydrophobic residues in the hinge region between the two helices are important in the structure and function of this peptide. By simulated annealing analysis and molecular dynamics modeling, two hydrophobic amino acids, F-18 and W-21, in the hinge region were predicted to be relatively surface-exposed and to interact with the aqueous solvent. Using a series of 5A peptide analogs in which F-18 or W-21 was changed to either F, W, A, or E, only peptides with hydrophobic amino acids in these two positions were able to readily bind and solubilize phospholipid vesicles. Compared with active peptides containing F or W, peptides containing E in either of these two positions were more than 10-fold less effective in effluxing cholesterol by the ABCA1 transporter. Intravenous injection of 5A in C57BL/6 mice increased plasma-free cholesterol (5A: 89.9 ± 13.6 mg/dl; control: 38.7 ± 4.3 mg/dl (mean ± S.D.); P < 0.05) and triglycerides (5A: 887.0 ± 172.0 mg/dl; control: 108.9 ± 9.9 mg/dl; P < 0.05), whereas the EE peptide containing E in both positions had no effect. Finally, 5A increased cholesterol efflux approximately 2.5-fold in vivo from radiolabeled macrophages, whereas the EE peptide was inactive. These results provide a rationale for future design of therapeutic apolipoprotein mimetic peptides and provide new insights into the interaction of hydrophobic residues on apolipoproteins with phospholipids in the lipid microdomain created by the ABCA1 transporter during the cholesterol efflux process.

Structural analysis of the envelope gp120 V3 loop for some HIV-1 variants circulating in the countries of Eastern Europe.

The V3 loop on gp120 from human immunodeficiency virus type 1 (HIV-1) is a focus of many research groups involved in anti-AIDS drug development because this region of the protein is a principal target for neutralizing antibodies and a major determinant for cell tropism and syncytium formation. In this study, the nucleotide sequences of the env gene region coding the V3 loop were determined by DNA sequencing methods for four novel HIV-1 strains that circulate in the countries of Eastern Europe, such as Russia, Belarus, Ukraine, etc. Based on the empirical data obtained, the 3D structures of the V3 loops associated with these viral modifications were generated by computer modeling and then compared to discover similarities in the spatial arrangement of this functionally important site of gp120. Despite the HIV-1 genetic variety, several regions of the V3 loop that contain residues critical for cell tropism were shown to be structurally invariant, which may explain its exceptional role in a co-receptor usage. These data together with those on the biological activity of the V3 individual residues clearly show that these conserved structural motifs of gp120 represent potential HIV-1 weak points most suitable for therapeutic intervention.

Discovery of novel promising targets for anti-AIDS drug developments by computer modeling: application to the HIV-1 gp120 V3 loop.

The V3 loop on gp120 from HIV-1 is a focus of many research groups involved in anti-AIDS drug studies, because this region of the protein determines the preference of the virus for T-lymphocytes or primary macrophages. Although the V3 loop governs cell tropism and, for this reason, exhibits one of the most attractive targets for anti-HIV-1 drug developments, its high sequence variability is a major complicating factor. Nevertheless, the data on the spatial arrangement of V3 obtained here for different HIV-1 subtypes by computer modeling clearly show that, despite a wide range of 3D folds, this functionally important site of gp120 forms at least three structurally invariant segments, which contain residues critical for cell tropism. It is evident that these conserved V3 segments represent potential HIV-1 vulnerable spots and, therefore, provide a blueprint for the design of novel, potent and broad antiviral agents able to stop the HIV's spread.

Computational model of the HIV-1 subtype A V3 loop: study on the conformational mobility for structure-based anti-AIDS drug design.

The V3 loop of the HIV-1gp120 glycoprotein presenting 35-residue-long, frequently glycosylated, highly variable, and disulfide bonded structure plays the central role in the virus biology and forms the principal target for neutralizing antibodies and the major viral determinant for co-receptor binding. Here we present the computer-aided studies on the 3D structure of the HIV-1 subtype A V3 loop (SA-V3 loop) in which its structurally inflexible regions and individual amino acids were identified and the structure-function analysis of V3 aimed at the informational support for anti-AIDS drug researches was put into practice. To this end, the following successive steps were carried out: (i) using the methods of comparative modeling and simulated annealing, the ensemble of the low-energy structures was generated for the consensus amino acid sequence of the SA-V3 loop and its most probable conformation was defined basing on the general criteria widely adopted as a measure of the quality of protein structures in terms of their 3D folds and local geometry; (ii) the elements of secondary V3 structures in the built conformations were characterized and careful analysis of the corresponding data arising from experimental observations for the V3 loops in various HIV-1 strains was made; (iii) to reveal common structural motifs in the HIV-1 V3 loops regardless of their sequence variability and medium inconstancy, the simulated structures were collated with each other as well as with those of V3 deciphered by NMR spectroscopy and X-ray studies for diverse virus isolates in different environments; (iv) with the object of delving into the conformational features of the SA-V3 loop, molecular dynamics trajectory was computed from its static 3D structure followed by determining the structurally rigid V3 segments and comparing the findings obtained with the ones derived hereinbefore; and (v) to evaluate the masking effect that can occur due to interaction of the SA-V3 loop with the two virtual molecules constructed previously by tools of computational modeling and named FKBP and CycA peptides, molecular docking of V3 with these molecules was implemented and inter-atomic contacts appearing in the simulated complexes were analyzed to specify the V3 stretches keeping in touch with the ligands. As a matter of record, V3 segments 3-7, 15-20, and 28-32 containing the highly conserved and biologically meaningful residues of gp120 were shown to retain their 3D main chain shapes in all the cases of interest presenting the forward-looking targets for anti-AIDS drug researches. From the data on molecular docking, synthetic analogs of the CycA and FKBP peptides were suggested being suitable frameworks for making a reality of the V3-based anti-HIV-1 drug projects.