A QSPR Study of Association Constants of Macrocycles toward Sodium Cation

Ahmadi, Shahin

doi:10.6060/mhc2012.110734a

Cited by 13 publications

(2 citation statements)

References 40 publications

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“…The applicability domain (AD) is another key guideline that should be included in a built QSPR/QSAR model. It was defined by the OECD as "the response and chemical structure space in which the model produces predictions with a specified reliability" [ 48 , 49 ]. The CORAL-based QSAR model computes AD based on the dispersion of SMILES features in the training and calibration sets [ 50 ].…”

Section: Methodsmentioning

confidence: 99%

In-silico activity prediction and docking studies of some flavonol derivatives as anti-prostate cancer agents based on Monte Carlo optimization

Tajiani,

Ahmadi,

Lotfi

et al. 2023

BMC Chemistry

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The QSAR models are employed to predict the anti-proliferative activity of 81 derivatives of flavonol against prostate cancer using the Monte Carlo algorithm based on the index of ideality of correlation (IIC) criterion. CORAL software is employed to design the QSAR models. The molecular structures of flavonols are demonstrated using the simplified molecular input line entry system (SMILES) notation. The models are developed with the hybrid optimal descriptors i.e. using both SMILES and hydrogen-suppressed molecular graph (HSG). The QSAR model developed for split 3 is selected as a prominent model ($${R}_{Validation}^{2}$$ R Validation 2 = 0.727, $${IIC}_{validation}$$ IIC validation = 0.628, $${Q}_{Validation}^{2}$$ Q Validation 2 = 0.642, and $${\overline{r} }_{m}^{2}$$ r ¯ m 2 =0.615). The model is interpreted mechanistically by identifying the characteristics responsible for the promoter of the increase or decrease. The structural attributes as promoters of increase of pIC50 were aliphatic carbon atom connected to double-bound (C…=…, aliphatic oxygen atom connected to aliphatic carbon (O…C…), branching on aromatic ring (c…(…), and aliphatic nitrogen (N…). The pIC50 of eight natural flavonols with pIC50 more than 4.0, were predicted by the best model. The molecular docking is also performed for natural flavonols on the PC-3 cell line using the protein (PDB: 3RUK).

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Section: Methodsmentioning

confidence: 99%

In-silico activity prediction and docking studies of some flavonol derivatives as anti-prostate cancer agents based on Monte Carlo optimization

Tajiani,

Ahmadi,

Lotfi

et al. 2023

BMC Chemistry

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“…41 It consists of four descriptors of topological (IC5, LP1) and steric (E1v, RDF125m) nature, which were used to predict logarithm of the association constant (logK) of 53 macrocycles with sodium cation, via an MLR model with rudimentary validation. Data set J is the only one in this work as an example in which the reference data set i.e., the data set obtained from variable selection, has been obtained after data splitting of an essential descriptor pool subset.…”

Section: Data Set Imentioning

confidence: 99%

Integral Sign Change Problem Check in Quantitative Structure-Activity/Property Relationships: A Tutorial

Kiralj¹

2014

Croat. Chem. Acta

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Abstract. Sign change problem (SCP) in multivariate Quantitative Structure-Activity/Property Relationships (QSAR/QSPR) is the inconsistency in the direction of association between molecular descriptors and the dependent variable. Sign change is observed when the signs of the elements of the reference vector (correlation vector for the data set obtained from variable selection) are compared to the signs of the elements of all correlation and regression vectors related to a model. SCP check in this work, named Integral SCP (ISCP) check, is established to be a general effective anti-SCP procedure, consisting of five check levels. Twelve diverse QSAR/QSPR data sets from literature were tested, and performance of data sets, models and descriptors was assessed by qualitative labeling systems. Most data sets and models did not have satisfactory performance, what is discussed in terms possible data and model remedy.

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Molecular Descriptors in QSPR/QSAR Modeling

Ahmadi

Ketabi

Javan

2023

Challenges and Advances in Computational Chemistry and Physics

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A QSPR Study of Association Constants of Macrocycles toward Sodium Cation

Abstract: The association constant (logK) of 53 chelates of new macrocycles (hemispherands, cryptahemispherands, and bridged calix-4)

Cited by 13 publications

References 40 publications

In-silico activity prediction and docking studies of some flavonol derivatives as anti-prostate cancer agents based on Monte Carlo optimization

In-silico activity prediction and docking studies of some flavonol derivatives as anti-prostate cancer agents based on Monte Carlo optimization

Integral Sign Change Problem Check in Quantitative Structure-Activity/Property Relationships: A Tutorial

Molecular Descriptors in QSPR/QSAR Modeling

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