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Int. J. Mol. Sci. 2015, 16(8), 19553-19601; doi:10.3390/ijms160819553

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

1
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
2
Environmental Advanced Researches Laboratories, Biology-Chemistry Department, West University of Timisoara, Str. Pestalozzi No. 16, 300115 Timisoara, Romania
*
Authors to whom correspondence should be addressed.
Academic Editor: Christo Z. Christov
Received: 30 June 2015 / Revised: 30 July 2015 / Accepted: 11 August 2015 / Published: 18 August 2015
(This article belongs to the Special Issue Chemical Bond and Bonding 2015)
View Full-Text   |   Download PDF [4364 KB, uploaded 18 August 2015]   |  

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. View Full-Text
Keywords: anti-HIV; 1,3-disubstituted uracil derivative; SMILES; ligand-receptor docking; chemical binding affinity; interacting amino acid anti-HIV; 1,3-disubstituted uracil derivative; SMILES; ligand-receptor docking; chemical binding affinity; interacting amino acid
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Putz, M.V.; Dudaș, N.A.; Isvoran, A. Double Variational Binding—(SMILES) Conformational Analysis by Docking Mechanisms for Anti-HIV Pyrimidine Ligands. Int. J. Mol. Sci. 2015, 16, 19553-19601.

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