title: Prediction of HIV-1 entry inhibitors neomycin-arginine conjugates interaction with the CD4-gp120 binding site by molecular modeling and multistep docking procedure.
abstract: Developing of multi-target HIV-1 entry inhibitors represents an important avenue of drug therapy. Two such inhibitors are hexa-arginine-neomycin-conjugate (NeoR6) and nona-d-arginine-neomycin-conjugate (Neo-r9). Our findings that NeoR6-resistant mutations appear in the gp120 constant regions; and NeoR6 is not CCR5 antagonist, but inhibits CXCR4 and CCR5 HIV-1 using isolates, led us to suggest that NeoR6 may inhibit HIV-1 entry by interfering with the CD4-gp120 binding. To support this notion, we constructed a homology model of unliganded HIV-1(IIIB) gp120 and docked NeoR6 and Neo-r9 to it, using a multistep docking procedure: geometric-electrostatic docking by MolFit; flexible ligand docking by Autodock3 and final refinement of the obtained complexes by Discover3. Binding free energies were calculated by MM-PBSA methodology. The model predicts competitive inhibition of CD4-gp120 binding by NeoR6 and Neo-r9. We determined plausible binding sites between constructed CD4-bound gp120 trimer and homology modeled membranal CXCR4, and tested NeoR6 and Neo-r9 interfering with this interaction. These models support our notion that another mechanism of anti-HIV-1 activity of NeoR6 is inhibition of gp120-CXCR4 binding. These structural models and interaction of NeoR6 and Neo-r9 with gp120 and CXCR4 provide a powerful approach for structural based drug design for selective targeting of HIV-1 entry and/or for inhibition of other retroviruses with similar mechanism of entry.
authors.affiliation: Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot, 76100, Israel.
authors.forename: Alexander
authors.initials: A
authors.lastname: Berchanski
authors.forename: Aviva
authors.initials: A
authors.lastname: Lapidot
mesh_terms: D019380:Anti-HIV Agents / Q000737:chemistry*; D001120:Arginine / Q000737:chemistry*; D001665:Binding Sites; D015704:CD4 Antigens / Q000737:chemistry* / Q000648:ultrastructure; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D009355:Neomycin / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D053586:Virus Internalization
chemical_list: D019380:Anti-HIV Agents; D015704:CD4 Antigens; D001120:Arginine; D009355:Neomycin