title: Double Variational Binding--(SMILES) Conformational Analysis by Docking Mechanisms for Anti-HIV Pyrimidine Ligands.
abstract: Variational quantitative binding-conformational analysis for a series of anti-HIV pyrimidine-based ligands is advanced at the individual molecular level. This was achieved by employing ligand-receptor docking algorithms for each molecule in the 1,3-disubstituted uracil derivative series that was studied. Such computational algorithms were employed for analyzing both genuine molecular cases and their simplified molecular input line entry system (SMILES) transformations, which were created via the controlled breaking of chemical bonds, so as to generate the longest SMILES molecular chain (LoSMoC) and Branching SMILES (BraS) conformations. The study identified the most active anti-HIV molecules, and analyzed their special and relevant bonding fragments (chemical alerts), and the recorded energetic and geometric docking results (i.e., binding and affinity energies, and the surface area and volume of bonding, respectively). Clear computational evidence was also produced concerning the ligand-receptor pocket binding efficacies of the LoSMoc and BraS conformation types, thus confirming their earlier presence (as suggested by variational quantitative structure-activity relationship, variational-QSAR) as active intermediates for the molecule-to-cell transduction process.
authors: Laboratory of Structural and Computational Physical-Chemistry for Nanosciences and QSAR, Biology-Chemistry Department, West University of Timisoara, Str. Pestalozzi No. 16, 300115 Timisoara, Romania. mv_putz@yahoo.com.
authors: Mihai V
authors: MV
authors: Putz
authors: Laboratory of Structural and Computational Physical-Chemistry for Nanosciences and QSAR, Biology-Chemistry Department, West University of Timisoara, Str. Pestalozzi No. 16, 300115 Timisoara, Romania. nicole_suceveanu@yahoo.com.
authors: Nicoleta A
authors: NA
authors: Dudaș
authors: Environmental Advanced Researches Laboratories, Biology-Chemistry Department, West University of Timisoara, Str. Pestalozzi No. 16, 300115 Timisoara, Romania. aisvoran@yahoo.com.
authors: Adriana
authors: A
authors: Isvoran
mesh_terms: D000465:Algorithms; D019380:Anti-HIV Agents / Q000737:chemistry* / Q000627:therapeutic use; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D015195:Drug Design; D015658:HIV Infections / Q000188:drug therapy; D006801:Humans; D008958:Models, Molecular; D008968:Molecular Conformation; D062105:Molecular Docking Simulation; D011485:Protein Binding; D021281:Quantitative Structure-Activity Relationship; D014498:Uracil / Q000031:analogs & derivatives / Q000737:chemistry*
chemical_list: D019380:Anti-HIV Agents; D014498:Uracil
keywords: 1,3-disubstituted uracil derivative; SMILES; anti-HIV; chemical binding affinity; interacting amino acid; ligand-receptor docking