Double Variational Binding—(SMILES) Conformational Analysis by Docking Mechanisms for Anti-HIV Pyrimidine Ligands

International Journal of Molecular Sciences

Mihai V. Putz²  Nicoleta A. Dudaș²  Adriana Isvoran¹ 

[1] Environmental Advanced Researches Laboratories, Biology-Chemistry Department, West University of Timisoara, Str. Pestalozzi No. 16, 300115 Timisoara, Romania;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; E-Mail:

关键词: anti-HIV;    1;    3-disubstituted uracil derivative;    SMILES;    ligand-receptor docking;    chemical binding affinity;    interacting amino acid;   

DOI  :  10.3390/ijms160819553

来源: mdpi

【 摘 要 】

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.

【 授权许可】

CC BY   
© 2015 by the authors; licensee MDPI, Basel, Switzerland.