Identification of prodigious and under-privileged structural features for RG7834 analogs as Hepatitis B virus expression inhibitor

Masand, Vijay H.; El-Sayed, Nahed N. E.; Rastija, Vesna; Rathore, Mithilesh M.; Karnaš, Maja

doi:10.1007/s00044-019-02455-w

Cited by 4 publications

(3 citation statements)

References 29 publications

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“…To test the multicollinearity of the descriptors involved in the model and avoid “apparent” prediction, a power matrix of correlation (1) was generated. Low collinearity was confirmed by the values of the correlation coefficient ( R ≤ 0.7) and verified with the value of the multivariate correlation index ( Kxx ) and the difference between global correlation among descriptors (Δ K ≥ 0.05) [ 37 , 40 ] ( Table 4 and Table 5 ). The stability and robustness of a model were confirmed by parameters of internal validation employing leave-one-out (LOO) cross-validation.…”

Section: Resultsmentioning

confidence: 63%

“…The obtained model satisfied the suggested threshold values of fitting criteria: coefficient of determination ( R 2 tr ) greater than 0.60, as well as higher or equal to the adjusted coefficient of determination ( R 2 adj ). Also, the concordance correlation coefficient of the training set ( CCC tr ) is higher than 0.80 [ 37 , 38 , 39 ]. To test the multicollinearity of the descriptors involved in the model and avoid “apparent” prediction, a power matrix of correlation (1) was generated.…”

Section: Resultsmentioning

confidence: 99%

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Biological Activities Related to Plant Protection and Environmental Effects of Coumarin Derivatives: QSAR and Molecular Docking Studies

Rastija

Vrandečić

Ćosić

et al. 2021

IJMS

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The aim was to study the inhibitory effects of coumarin derivatives on the plant pathogenic fungi, as well as beneficial bacteria and nematodes. The antifungal assay was performed on four cultures of phytopathogenic fungi by measuring the radial growth of the fungal colonies. Antibacterial activity was determined by the broth microdilution method performed on two beneficial soil organisms. Nematicidal activity was tested on two entomopathogenic nematodes. The quantitative structure-activity relationship (QSAR) model was generated by genetic algorithm, and toxicity was estimated by T.E.S.T. software. The mode of inhibition of enzymes related to the antifungal activity is elucidated by molecular docking. Coumarin derivatives were most effective against Macrophomina phaseolina and Sclerotinia sclerotiorum, but were not harmful against beneficial nematodes and bacteria. A predictive QSAR model was obtained for the activity against M. phaseolina (R2tr = 0.78; R2ext= 0.67; Q2loo = 0.67). A QSAR study showed that multiple electron-withdrawal groups, especially at position C-3, enhanced activities against M. phaseolina, while the hydrophobic benzoyl group at the pyrone ring, and –Br, –OH, -OCH3, at the benzene ring, may increase inhibition of S. sclerotiourum. Tested compounds possibly act inhibitory against plant wall-degrading enzymes, proteinase K. Coumarin derivatives are the potentially active ingredient of environmentally friendly plant-protection products.

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Section: Resultsmentioning

confidence: 63%

Section: Resultsmentioning

confidence: 99%

Biological Activities Related to Plant Protection and Environmental Effects of Coumarin Derivatives: QSAR and Molecular Docking Studies

Rastija

Vrandečić

Ćosić

et al. 2021

IJMS

Self Cite

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show abstract

“…The model demonstrates a satisfactory stability in internal validation ( Q 2 LOO ≥ 0.5; Q 2 LMO ≥ 0.6; RMSE tr < RMSE cv ; r 2 m ≥ 0.6) ( Kiralj and Ferreira, 2009 ; Veerasamy et al, 2011 ). Parameters of Y-scrambling ( R 2 Yscr < 0.2; Q 2 Yscr < 0.2) highlight that the model is robust and not obtained by chance correlation ( Masand et al, 2019 ). The only failed parameter is the concordance correlation coefficient obtained by cross-validation ( CCC cv ) that is higher than 0.85.…”

Section: Resultsmentioning

confidence: 99%

Green Synthesis of Thiazolidine-2,4-dione Derivatives and Their Lipoxygenase Inhibition Activity With QSAR and Molecular Docking Studies

et al. 2022

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Thiazolidinediones are five-membered, heterocyclic compounds that possess a number of pharmacological activities such as antihyperglycemic, antitumor, antiarthritic, anti-inflammatory, and antimicrobial. Conventional methods for their synthesis are often environmentally unacceptable due to the utilization of various catalysts and organic solvents. In this study, deep eutectic solvents were used in the synthesis of thiazolidinedione derivatives that acted as both solvents and catalysts. Initially, a screening of 20 choline chloride-based deep eutectic solvents for thiazolidinedione synthesis, via Knoevenagel condensation, was performed in order to find the most suitable solvent. Deep eutectic solvent, choline chloride, N-methylurea, was proven to be the best for further synthesis of 19 thiazolidinedione derivatives. Synthesized thiazolidinediones are obtained in yields from 21.49% to 90.90%. The synthesized compounds were tested for the inhibition of lipid peroxidation as well as for the inhibition of soy lipoxygenase enzyme activity. The antioxidant activity of the compounds was also determined by the ABTS and DPPH methods. Compounds showed lipoxygenase inhibition in the range from 7.7% to 76.3%. Quantitative structure–activity relationship model (R2 = 0.88; Q2loo = 0.77; F = 33.69) for the inhibition of soybean lipoxygenase was obtained with descriptors Mor29m, G2u, and MAXDP. The molecular docking confirms experimentally obtained results, finding the binding affinity and interactions with the active sites of soybean LOX-3.

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e-QSAR (Explainable AI-QSAR), molecular docking, and ADMET analysis of structurally diverse GSK3-beta modulators to identify concealed modulatory features vindicated by X-ray

Masand,

Al-Hussain,

Masand

et al. 2024

Computational Biology and Chemistry

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Identification of prodigious and under-privileged structural features for RG7834 analogs as Hepatitis B virus expression inhibitor

Cited by 4 publications

References 29 publications

Biological Activities Related to Plant Protection and Environmental Effects of Coumarin Derivatives: QSAR and Molecular Docking Studies

Biological Activities Related to Plant Protection and Environmental Effects of Coumarin Derivatives: QSAR and Molecular Docking Studies

Green Synthesis of Thiazolidine-2,4-dione Derivatives and Their Lipoxygenase Inhibition Activity With QSAR and Molecular Docking Studies

e-QSAR (Explainable AI-QSAR), molecular docking, and ADMET analysis of structurally diverse GSK3-beta modulators to identify concealed modulatory features vindicated by X-ray

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