Computer-assisted anti-AIDS drug development: cyclophilin B against the HIV-1 subtype A V3 loop

Abstract

Aim: The objects of this study originated from the experimental observations, whereby the HIV -1 gp120 V3 loop is a high-affinity ligand for immunophilins, and consisted in generating the structural complex of cyclophilin (Cyc) B belonging to immunophilins family with the virus subtype A V3 loop (SA-V3 loop) as well as in specifying the Cyc B segment forming the binding site for V3 synthetic copy of which, on the assumption of keeping the 3D peptide structure in the free state, may present a forwardlooking basic structure for anti-AIDS drug development. Methods: To reach the objects of view, molecular docking of the HIV-1 SA-V3 loop structure determined previously with the X-ray conformation of Cyc B was put into practice by Hex 4.5 program (http://www.loria.fr/~ritchied/ hex/) and the immunophilin stretch responsible for binding to V3 (Cyc B peptide) was identified followed by examination of its 3D structure and dynamic behavior in the unbound status. To design the Cyc B peptide, the X-ray conformation for the identical site of the native protein was involved in the calculations as a starting model to find its best energy structural variant. The search for this most preferable structure was carried out by consecutive use of the molecular mechanics and simulated annealing methods. The molecular dynamics computations were implemented for the Cyc B peptide by the GROMACS computer package (http:// www.gromacs.org/). Results: The overmolecular structure of Cyc B with V3 was built by computer modeling tools and the immunophilinderived peptide able to mask effectively the structurally invariant V3 segments embracing the functionally crucial amino acids of the HIV-1 gp120 envelope protein was constructed and analyzed. Conclusions: Starting from the joint analysis of the results derived with those of the literature, the generated peptide was suggested to offer a promising basic structure for making a reality of the protein engineering projects aimed at developing the anti-AIDS drugs able to stop the HIV's spread.

Determination of the invariant structural elements for the third variable domain of the HIV-1 gp120 protein by molecular modeling

“…Впоследствии этим методом были расшифрованы еще две структурные модели белка gp120 в комплексах с нейтрализующим антителом 412d и молекулой CD4 [5] и с CD4-связывающим участком антитела F105 [6]. Кроме того, в литературе описан ряд структурных комплексов пептидов петли V3 с Fab-фрагментами различных антител в кристалле [7][8][9][10][11][12][13][14][15][16][17][18], а также предложены модели V3-домена и его пептидов, построенные на основе данных спектроскопии ЯМР [19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36] и компьютерного моделирования [37][38][39].…”