Variational principles for mechanistic quantitative structure–activity relationship (QSAR) studies: application on uracil derivatives’ anti-HIV action

Putz, Mihai V.; Dudaş, Nicoleta A.

doi:10.1007/s11224-013-0249-6

Cited by 28 publications

(25 citation statements)

References 66 publications

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“…Worth noting is that the QSAR analysis performed by some of the present authors already revealed the general mechanism of action for the Genuine-LoSMoC-BraS related configuration for the actual pyrimidines’ anti-HIV ligands of Table 1 [ 97 , 98 , 99 ]. Yet, assessing of the highest propensity of anti-HIV binding for the individual molecule in the actual set of working compounds remains the aim of this work.…”

Section: Smiles Of Anti-hiv Pyrimidinesmentioning

confidence: 92%

“…From this point onward, one employs the working molecules under those actually most likely to form, targeting the considered end-point, namely the anti-HIV activity, as produced by uracil-based pyrimidines [ 87 , 96 ]. They are represented by the (gas-phase) genuine molecular structure alongside the two forms of their simplified molecular input line entry system (SMILES) structure, as presented in Table 1 , respectively [ 9 , 96 , 97 , 98 , 99 ].…”

Section: Smiles Of Anti-hiv Pyrimidinesmentioning

confidence: 99%

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

Putz

Dudaş

Isvoran

2015

IJMS

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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.

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Section: Smiles Of Anti-hiv Pyrimidinesmentioning

confidence: 92%

Section: Smiles Of Anti-hiv Pyrimidinesmentioning

confidence: 99%

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

Putz

Dudaş

Isvoran

2015

IJMS

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“…Next, Putz and Dudaş [137] reported a study of anti-HIV pyrimidinic 1,3-disubstituted uracil derivatives in which QSAR was used. Such 1,3-dialkylated uracils have been shown to react with suitable carbenes to form the corresponding methano derivative, a 2,4-diazanorcaradiene [138].…”

Section: Issuementioning

confidence: 99%

Interplay of thermochemistry and structural chemistry, the journal (volume 24, 2013, issues 5–6) and the discipline

2014

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“…The cut method turned out to be very useful in the investigation of molecular structure-descriptors, called topological indices. These indices are used in theoretical chemistry for the design of quantitative structure-property relations (QSPR) and quantitative structure-activity relations (QSAR), see the books [1,2,3], the recent book chapter [4], and articles [5,6,7]. For the role of distance-sum-based molecular descriptors in a drug discovery process we refer to [8].…”

Section: Introductionmentioning

confidence: 99%

Cut Method: Update on Recent Developments and Equivalence of Independent Approaches

Nadjafi-Arani

2015

COC

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The cut method is a powerful tool for the investigation of distance-based (and some other) molecular structure-descriptors. In this paper a survey on the recent developments of the method is given. The instances of the standard cut method for the Wiener index, the Szeged index, the PI index, the generalized terminal Wiener index, the Gutman index, the edge-Wiener index, and the edge-Szeged index are described, where a standard cut method is a method that applies to partial cubes. It is pointed out that the standard cut method was recently independently discovered a couple of times. Numerous proper extensions of the standard cut method are presented. The method extends to 1-graphs, graphs with a non-trivial canonical metric representation, graphs with transitive relation Θ, and partial Hamming graphs. The instances of these extended cut methods include the Wiener index, the degree distance, distance moments, and the colored Wiener index.

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Variational principles for mechanistic quantitative structure–activity relationship (QSAR) studies: application on uracil derivatives’ anti-HIV action

Cited by 28 publications

References 66 publications

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

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

Interplay of thermochemistry and structural chemistry, the journal (volume 24, 2013, issues 5–6) and the discipline

Cut Method: Update on Recent Developments and Equivalence of Independent Approaches

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