Design of (quinolin-4-ylthio)carboxylic acids as new Escherichia coli DNA gyrase B inhibitors: machine learning studies, molecular docking, synthesis and biological testing

Metelytsia, Larysa; Hodyna, Diana; Dobrodub, Inga; Semenyuta, Ivan; Zavhorodnii, Mikhail; Blagodatny, Volodymyr; Kovalishyn, Vasyl; Brazhko, Oleksandr

doi:10.1016/j.compbiolchem.2020.107224

Cited by 15 publications

(14 citation statements)

References 20 publications

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“…The HL 2 bonded to GLY 119 and VAL 120 amino acid residues of 4WUB proteins with O19 and O20 atoms and binding lengths were observed as 2.252 Å and 2.404 Å. In another study conducted by Metelytsia et al (2020), the binding of ligands to the regions of amino acid residues were reported as GLY 119 and His 116. This finding is similar to the results of docking investigations in the current study in terms of attachment regions.…”

Section: Molecular Docking Studiesmentioning

confidence: 93%

“…4 With the discovery of new compounds, several studies were performed in the last decade to inhibit antibacterial drug resistance and reduce associated adverse effects on human health. 5 It is clear that new types of viruses and bacteria affect the lives of humans worldwide in a variety of ways. Accordingly, this places immense responsibility on researchers and chemists who work to develop new materials to decrease the effects of viruses and bacteria as well as biologists and physicians who test the new compounds on animals and humans.…”

Section: Introductionmentioning

confidence: 99%

“…12 The reason for the investigation of E. coli pathogens in molecular-docking studies is this bacterium's resistance against some medications and its high binding capacity. 5 Furthermore, E. coli, also known as the most-common human pathogen, causes different types of infections, such as kidney, gallbladder, skin, and respiratory infections in addition to meningitis in neonates. 13,14 The physicochemical properties of compounds affect bioavailability, including electrostatic potential, molar absorptivity, stability, solubility, structure, intracellular absorption, hydrogen bonds, and bonding energy.…”

Section: Introductionmentioning

confidence: 99%

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Synthesis, Crystallographic Structure, Hirshfeld Surface Analysis, Drug-likeness Properties and Molecular Docking Studies of New Oxime-pyridine Compounds

Topal

2021

ACSi

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A detailed description of the two new pyridine ligands, (2E,3Z)-3-[2-(3-chloropyridin-2-yl)hydrazinylidene]-N-hydroxybutan-2-imine and 3-chloro-2-{(2Z)-2-[1-(4 nitrophenyl)ethylidene]hydrazinyl}, is reported. The synthesized compounds were characterized by spectroscopic studies, spectral features were performed by TD-DFT calculations. New-generation pyridine ligand of HL2 was also determinate by single-crystal X-ray diffraction and Hirshfeld surface analysis with two-dimensional fingerprint plots was used to analyze intermolecular interactions in crystals. Molecular-docking was performed to investigate the binding areas of chemical compounds, and the results showed the inhibitory activity of the studied HL1 and HL2 against E. coli. The results of the current study revealed the drug-likeness and bioactive properties of the ligands.

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Section: Molecular Docking Studiesmentioning

confidence: 93%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Synthesis, Crystallographic Structure, Hirshfeld Surface Analysis, Drug-likeness Properties and Molecular Docking Studies of New Oxime-pyridine Compounds

Topal

2021

ACSi

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“…Hodyna and co-workers designed (quinolin-4-ylthio)carboxylic acid derivatives by using machine learning methods to develop new E. coli DNA gyrase B inhibitors and investigated in vitro biological studies of these compounds [27]. In this research, www.…”

Section: Supervised Learningmentioning

confidence: 99%

The role of machine learning method in the synthesis and biological ınvestigation of heterocyclic compounds

Mermer

2021

Mol Divers

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Machine learning (ML) methods have attracted increasing interest in chemistry as in all fields of science in recent years. This method is of great importance for the design of targeted bioactive compounds, especially by avoiding loss of time, money, and chemicals. There are lots of online web-based platforms such as LibSVM and OCHEM for the application of ML methods. In this paper, it has been examined the literature data on the activity predictions of heterocyclic compounds, biological activity results such as antiurease, HIV-1 Integrase, E. Coli DNA Gyrase B, and antifungal, pharmacophore-based studies, synthesis, and finding possible inhibitors using different machine learning methods.

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“…Thus, Patel S. R. et al published results of 3D QSAR study by Comparative Molecular Field Analysis of three series of anti-tuberculosis quinolines, including 4-R-quinoline-2-carboxamides[27], Wang J. et al built 3D QSAR models for quinoline-aminopiperidine inhibitors which acted on DNA gyrase B subunit of M. tuberculosis[28]. QSAR analysis of 2,4-disubstituted quino-lines with antimalarial activity (Jiménez Villalobos T. P. et al[29]), antiproliferative activity (Karnik S. K. et al[30]), and E. coli inhibitors (Metelytsia L. et al[31]) was performed recently as well. But, no relationships were analyzed for derivatives that have diuretic activity.…”

mentioning

confidence: 99%

QSAR analysis and molecular docking study of pyrrolo- and pyridoquinolinecarboxamides with diuretic activity

Golik

Titko

Shaposhnyk

et al. 2021

SR: PS

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The aim. The aim of the study was to reveal QSAR and ascertain the possible mechanism of action via docking study in the row of tricyclic quinoline derivatives with diuretic activity. Materials and methods. Pyrrolo- and pyridoquinolinecarboxamides with proven diuretic activity were involved in the study. Molecular descriptors were calculated using HyperChem and GRAGON software, and QSAR models were built using BuildQSAR software. For receptor-oriented flexible docking, the Autodock 4.2 software package was used. Results. Multivariate linear QSAR models were built on two datasets of quinolinecarboxamides: Vol = a∙X1 + b∙X2 + c∙X3 + d, where Vol – volume of the daily produced urine in rats, Xi – molecular descriptor. QSAR analysis showed that the diuretic activity is determined by the geometric and spatial structure of molecules, logP, the energy values, RDF- and 3D-MoRSE-descriptors. Based upon internal and external validation of the models, the most informative two-parameter linear QSAR model 3а was proposed. Docking data showed the high affinity of two lead compounds to the carbonic anhydrase II. Conclusions. QSAR analysis of tricyclic quinoline derivatives revealed that the diuretic activity increases with the increase of value of logP, refractivity, and dipole moment and with the decrease of volume, surface area, and polarization of the molecules. Increase of values of such energy descriptors as bonds energy, core-core interaction, and energy of the highest occupied molecular orbital results in higher diuresis; decrease in hydration energy leads to higher diuretic activity. Based upon molecular docking calculation, the mechanism of diuretic action is proposed to be carbonic anhydrase inhibition. QSAR models and docking data are useful for in-depth study of diuretic activity of tricyclic quinolines and could be a theoretical basis for de novo-design of new diuretics

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Design of (quinolin-4-ylthio)carboxylic acids as new Escherichia coli DNA gyrase B inhibitors: machine learning studies, molecular docking, synthesis and biological testing

Cited by 15 publications

References 20 publications

Synthesis, Crystallographic Structure, Hirshfeld Surface Analysis, Drug-likeness Properties and Molecular Docking Studies of New Oxime-pyridine Compounds

Synthesis, Crystallographic Structure, Hirshfeld Surface Analysis, Drug-likeness Properties and Molecular Docking Studies of New Oxime-pyridine Compounds

The role of machine learning method in the synthesis and biological ınvestigation of heterocyclic compounds

QSAR analysis and molecular docking study of pyrrolo- and pyridoquinolinecarboxamides with diuretic activity

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