DFT, ADMET, molecular docking and molecular dynamics studies of pyridoxal

Garkusha, Nadezhda A.; Anikeeva, Oksana P.; Bayıl, İmren; Taşkın‐Tok, Tuğba; Safin, Damir A.

doi:10.1016/j.jics.2023.100926

Cited by 19 publications

(2 citation statements)

References 61 publications

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“…The Avogadro software 59 was utilized to create and analyze the synthesized compounds. The global DFT parameters 60–63 defined as ionization potential (I), electron affinity (A), global softness (S), absolute softness (σ), additional electronic charge (ΔN max ), electrophilicity index (ω), absolute electronegativity (χ), global hardness (η) and chemical potential (Pi) for the compounds are calculated using the magnitude of HOMO and LUMO. The ionization potential (I), electron affinity (A) and energy gap (ΔE) are evaluated via Equations :

normalI goodbreak= - E_{HOMO}

normalA goodbreak= - E_{LUMO}

ΔE goodbreak= E_{LUMO} goodbreak- E_{HOMO}

…”

Section: Methodsmentioning

confidence: 99%

Exploring the antimicrobial, antioxidant and cytotoxic activities of organyltellurium (IV) complexes incorporating 2‐hydroxy‐1‐naphthaldehyde schiff base ligand: Synthesis, spectroscopic investigations and theoretical studies

Dalal,

Devi,

Antil

et al. 2023

Applied Organom Chemis

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In this study, Schiff base ligand 1,1′‐((propane‐1,3‐diylbis [azaneylylidene]) bis (methaneylylidene))bis (naphthalen‐2‐ol) based Organyltellurium (IV) complexes were synthesized with formulae C32H27ClN2O3Te (5a)\C31H25ClN2O3Te (5b)\C32H27ClN2O3Te (5c)\ C39H34N2O4Te (5d)\ C37H30N2O4Te (5e)\ C39H34N2O4Te (5f) for acquiring a potential therapeutic agent. The synthesized compounds were characterized by ultraviolet–visible (UV–Vis), FT‐IR, 1H‐NMR, 13C‐NMR, mass spectrometry, molar conductance, elemental analysis, powder X‐ray diffraction and EDAX, which states that the tetradentate Schiff base ligand (HNDP) coordinated via oxygen and nitrogen atom with tellurium giving hexa‐coordinated tellurium (IV) complexes. The thermal features of the ligand and complexes were studied using thermal (TGA and DTG) technique. The biochemical behavior of the Schiff base and its complexes was assessed by examining their reactivity against various microbial strains, DPPH free radicals as well as normal and cancer cells. The complex 5c exhibited the highest inhibition activity against bacterial strains while complex 5f showed the strongest inhibition activity against fungal strains. Complexes 5e and 5f displayed the most effective suppression of DPPH free radicals. The results of in vitro cytotoxicity study revealed that complex 5a demonstrated moderate cytotoxic effect on the L929 cell lines. Complex 5c displayed a significant cytotoxic effect on the PC3 cell line. Moreover, complex 5a, 5c and 5e exhibited the best cytotoxic activity against the Saos‐2 cell line. Additionally, the structural forms of synthesized compounds were elucidated by DFT study. Furthermore, pharmacokinetic ADMET properties were estimated for their drug similarity behavior. The results advocate that complexes can be utilized as biological drugs.

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normalI goodbreak= - E_{HOMO}

normalA goodbreak= - E_{LUMO}

ΔE goodbreak= E_{LUMO} goodbreak- E_{HOMO}

…”

Section: Methodsmentioning

confidence: 99%

Exploring the antimicrobial, antioxidant and cytotoxic activities of organyltellurium (IV) complexes incorporating 2‐hydroxy‐1‐naphthaldehyde schiff base ligand: Synthesis, spectroscopic investigations and theoretical studies

Dalal,

Devi,

Antil

et al. 2023

Applied Organom Chemis

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“…Furthermore, the novel 1,2,3,4-tetrahydropyrimidine derivative as inhibitor of SARS-CoV-2 was reported recently [31]. Thus, 1,2,3,4-tetrahydroquinazoline derivatives are of potential interest for the therapy of COVID- 19. With all this in mind, as well as in continuation of our ongoing interest in the chemistry of nitrogen-containing six-membered rings [32][33][34][35][36][37][38][39] and in in silico studies of bioactive compounds [40][41][42][43][44][45][46][47][48][49][50][51][52][53][54][55], we have directed our attention to a novel 1,2,3,4tetrahydroquinazoline derivative, named 2-(6,8-dibromo-3-(4-hydroxycyclohexyl)-1,2,3,4-tetrahydroquinazolin-2-yl)phenol (1), which was obtained from the hydrochloride of 4-((2-amino-3,5-dibromobenzyl)amino)cyclohexan-1-ol, which is commonly known under its trademark ambroxol, and salicylaldehyde and is constructed from the tetrahydroquinazoline, phenylene, and cyclohexylene rings (Figure 1). Theoretical density-functional-theory (DFT)-based calculations were applied to 1 to reveal its electronic and optical properties.…”

Section: Introductionmentioning

confidence: 99%

A Novel Ambroxol-Derived Tetrahydroquinazoline with a Potency against SARS-CoV-2 Proteins

Krysantieva

Voronina

Safin

2023

IJMS

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We report synthesis of a novel 1,2,3,4-tetrahydroquinazoline derivative, named 2-(6,8-dibromo-3-(4-hydroxycyclohexyl)-1,2,3,4-tetrahydroquinazolin-2-yl)phenol (1), which was obtained from the hydrochloride of 4-((2-amino-3,5-dibromobenzyl)amino)cyclohexan-1-ol (ambroxol hydrochloride) and salicylaldehyde in EtOH. The resulting compound was produced in the form of colorless crystals of the composition 1∙0.5EtOH. The formation of the single product was confirmed by the IR and 1H spectroscopy, single-crystal and powder X-ray diffraction, and elemental analysis. The molecule of 1 contains a chiral tertiary carbon of the 1,2,3,4-tetrahydropyrimidine fragment and the crystal structure of 1∙0.5EtOH is a racemate. Optical properties of 1∙0.5EtOH were revealed by UV-vis spectroscopy in MeOH and it was established that the compound absorbs exclusively in the UV region up to about 350 nm. 1∙0.5EtOH in MeOH exhibits dual emission and the emission spectra contains bands at about 340 and 446 nm upon excitation at 300 and 360 nm, respectively. The DFT calculations were performed to verify the structure as well as electronic and optical properties of 1. ADMET properties of the R-isomer of 1 were evaluated using the SwissADME, BOILED-Egg, and ProTox-II tools. As evidenced from the blue dot position in the BOILED-Egg plot, both human blood–brain barrier penetration and gastrointestinal absorption properties are positive with the positive PGP effect on the molecule. Molecular docking was applied to examine the influence of the structures of both R-isomer and S-isomer of 1 on a series of the SARS-CoV-2 proteins. According to the docking analysis results, both isomers of 1 were found to be active against all the applied SARS-CoV-2 proteins with the best binding affinities with Papain-like protease (PLpro) and nonstructural protein 3 (Nsp3_range 207–379-AMP). Ligand efficiency scores for both isomers of 1 inside the binding sites of the applied proteins were also revealed and compared with the initial ligands. Molecular dynamics simulations were also applied to evaluate the stability of complexes of both isomers with Papain-like protease (PLpro) and nonstructural protein 3 (Nsp3_range 207–379-AMP). The complex of the S-isomer with Papain-like protease (PLpro) was found to be highly unstable, while the other complexes are stable.

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Interaction of Hydrazonophenylacetaldehyde Oxime with Acetone: Nitrone versus Oxime

Panova,

Safin

2024

ChemistrySelect

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Detailed experimental and computational studies of the nitrone 3,3‐dimethyl‐6‐phenyl‐2,3‐dihydro‐1,2,4‐triazin‐4‐oxide (2), which is a cyclized product of an open‐chain isomer 2‐phenyl‐2‐(propan‐2‐ylidenehydrazono)acetaldehyde oxime (1), are reported. The isolated compound 2 was characterized by elemental analysis, powder X‐ray diffraction, IR and UV‐vis spectroscopy, and spectrofluorometry. Electronic properties of 1 and 2 were elucidated by the DFT‐based calculations in water, which revealed that both compounds are pronounced electrophiles. The ADMET properties of the oxime 1 and nitrone 2 were predicted using the SwissADME, which includes the BOILED‐Egg method, and ProTox‐II online tools. Using a molecular docking approach, the discussed compounds were also predicted to actively interact with all the studied herein SARS‐CoV‐2 proteins. The most pronounced activity for both discussed compounds was established with Nonstructural protein 14 (Nsp14_N7‐MTase). Complex Nsp14_N7‐MTase‐1 is characterized by the calculated ligand efficiency scores being close for a Hit.

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DFT, ADMET, molecular docking and molecular dynamics studies of pyridoxal

Cited by 19 publications

References 61 publications

Exploring the antimicrobial, antioxidant and cytotoxic activities of organyltellurium (IV) complexes incorporating 2‐hydroxy‐1‐naphthaldehyde schiff base ligand: Synthesis, spectroscopic investigations and theoretical studies

Exploring the antimicrobial, antioxidant and cytotoxic activities of organyltellurium (IV) complexes incorporating 2‐hydroxy‐1‐naphthaldehyde schiff base ligand: Synthesis, spectroscopic investigations and theoretical studies

A Novel Ambroxol-Derived Tetrahydroquinazoline with a Potency against SARS-CoV-2 Proteins

Interaction of Hydrazonophenylacetaldehyde Oxime with Acetone: Nitrone versus Oxime

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