New Cu(II), Mn(II) and Mn(III) Schiff base complexes cause noncovalent interactions: X-ray crystallography survey, Hirshfeld surface analysis and molecular simulation investigation against SARS-CoV-2

Sepehrfar, Soraya; Salehi, Mehdi; Parvarinezhad, Sakineh; Grześkiewicz, Anita M.; Kubicki, Maciej

doi:10.1016/j.molstruc.2022.134857

Cited by 11 publications

(12 citation statements)

References 49 publications

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“…The biological activity studies of these complexes were conducted against the SARS‐CoV‐2 (PDB ID: 6 M03) and SARS‐CoV‐2 (PDB ID: 6Y2F) viruses. The molecular docking results of this complex (6Y2F) with more negative binding energy showed better performance than synthesized nickel complexes ( 1a and 1b ) shows 41 . Nickel (II) and copper (II) complexes were synthesized using Schiff base ligands from the condensation reaction of 5‐bromo‐salicylaldehyde with 3‐picoyl amine/ethylenediamine.…”

Section: Resultsmentioning

confidence: 99%

“…The enrichment ratio index has been calculated to study and understand more accurately the intermolecular contacts in the molecular structure of nickel (II) complexes by means of the contribution of intermolecular exchanges achieved from the FPs diagram for all complexes. In addition, Table 5 shows the enrichment ratio (E XY ) calculations 41 . For combinations of 2 with more than one independent molecule in an asymmetric unit, due to the different results for these molecules, the data for each molecule are presented and discussed separately.…”

Section: Resultsmentioning

confidence: 99%

“…To further assay the inhibitory potential of the three Ni (II) complexes by their binds targeting proteins 6Y2F and 6M0J, that are among the greatest proteins included in the mechanism of action of SARS‐CoV‐2 and human ACE‐2, and the most favorable position of the ligand is calculated with the most negative values of the binding energy. In this study, affinity with the selected receptors was analyzed 41,67 . The connection models of nickel complexes are shown in Figures 13–15.…”

Section: Resultsmentioning

confidence: 99%

“…The results showed that these compounds have effective biological activity against organisms such as Enterococcus faecile, Salmonella typhi, and Escherichia coli 40 . Soraya Sepehrfar et al studied new Schiff base 2‐amino 2‐methyl‐1‐propanol derivate complexes and investigated by Hirshfeld surface analysis and molecular simulation against SARS‐CoV‐2 41 . Considering the importance of the synthesis of new compounds with new biological properties in the development of biological drugs, we have focused on the synthesis and properties of new compounds.…”

Section: Introductionmentioning

confidence: 99%

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Novel dinuclear Ni (II) Schiff base complexes induced noncovalent exchanges: Crystal structure investigation, electrochemical assessment, Hirshfeld surface analysis and SARS‐CoV‐2 docking study

Roozbahani,

Malekshah,

Salehi

et al. 2023

Applied Organom Chemis

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In this work, novel Ni (II) complexes, namely, [Ni2(L)2(OAc)2(EtOH)2] (1a), [Ni2(L)2(OAc)2(H2O)2] (1b‐1) and [Ni2(L)2(OAc)2(EtOH)2] (1b‐2) as co‐crystal were synthesized by the 1:1 condensation (https://www.sciencedirect.com/topics/chemistry/condensation) of Ni (CH3COO)2·4H2O and Schiff base ligand (H2L) (2‐hydroxy‐4‐methoxybenzaldehyde and 2‐amino‐2‐methylpropanol). The ligand based on Schiff base and fabricated complexes (1a) and (1b‐1 and 1b‐2) were successfully identified by CHN assessment, FT‐IR, UV–Vis spectra, melting point and CV voltammogram. The electrochemical behavior investigation shows that the nickel complexes exhibited irreversible oxidation processes in methanol solution. Additionally, the crystal structures of complexes (1a) and (1b) have been recognized by single‐crystal X‐ray diffraction investigation. It turned out that the complexes (1b‐1) and (1b‐2) crystallize together, making a co‐crystal 1b with an additional EtOH solvent molecule in the crystal structure. A detailed study of intermolecular exchanges was performed using attractive graphical analysis tools such as three‐dimensional Hirshfeld surfaces analysis, two‐dimensional fingerprint plots (FPs), and enrichment ratios (E), which make C‐H … C, C‐H … O hydrogen bond, C … O, H … H, and O … O short contacts on Hirshfeld surfaces with color code are observed. Moreover, an appraisement of the inhibitory trace against coronavirus (main protease SARS‐CoV‐2, PDB ID: 6Y2F) and molecular targets of human angiotensin‐converting enzyme‐2 (ACE‐2) was performed by a molecular docking study in which two nickel complexes performed best for PDB protein ID: 6M0J and all three complexes for PDB protein ID: 6Y2F.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Novel dinuclear Ni (II) Schiff base complexes induced noncovalent exchanges: Crystal structure investigation, electrochemical assessment, Hirshfeld surface analysis and SARS‐CoV‐2 docking study

Roozbahani,

Malekshah,

Salehi

et al. 2023

Applied Organom Chemis

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“…Hirshfeld surface analysis (HSA) [20][21][22][23] is a useful tool to gain quantitative descriptions of the intermolecular interactions in molecules. Crystal Explorer 17 software [24] was used to reveal the noncovalent interactions in the studied complexes.…”

Section: Hirshfeld Surface Analysismentioning

confidence: 99%

Synthesis, spectra, crystal structure, Hirshfeld surface analysis, DFT calculations and molecular docking evaluation on novel mononuclearZn(II), Mn(III) and Co(III) Schiff base complexes derived from 2- hydroxy-1-naphthaldehyde

Parvarinezhad

Ramezanipoor

Kubicki

et al. 2023

Preprint

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four novel complexes of bidentate Schiff base ligand derived from 2-hydroxy-1-(2-methoxyethylimino)-naphthalen (HL) were synthesized and characterized using elemental analysis, FTIR, and UV–Vis spectroscopies. X-ray single crystal structures of Zn(II), Mn(III) and Co(III) complexes (1–4) have also been determined, and it was indicated that these Zn(II) and Co(III) complexes (1, 4) are in an octahedral geometry. Whereas, it was found that the Zn complex (2) in quite a regular tetrahedral environment. Also, Mn center in complex (3), is ligated by two azomethine nitrogen atom, two ligand oxygen atoms and one Cl atom of metal salt forming five coordinated tetragonal pyramid geometry around of the Mn atoms. The cyclic voltammetry (CV) of the complexes specifies an irreversible redox behavior for all complexes (1–4). Next, the molecular electrostatic potential (MEP) was studied for all complexes to better understand and predict the reaction sites of electrophilic and nucleophilic attacks. Also, density functional theory (DFT) calculations were performed to determine the optimal geometrical configurations, and comparison between experimental and theoretical data, and non-covalent interactions were determined by Hirshfeld surface analysis (HSA) using CrystalExplorer program. Also, finding binding affinity of complexes with protein (PDB ID: 4LXD) was also done using molecular docking.

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The effect of structural variations of heteroleptic Cu(II) complexes of tri‐dentate unsymmetrical Schiff‐base main ligands with pyridine or bithiazole co‐ligands on molecular docking against SARS‐CoV‐2 and its Omicron variant main proteases

Ghasemi,

Behzad,

Abedi

et al. 2023

Applied Organom Chemis

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Meso‐1,2‐diphenyl‐1,2‐ethylenediamine was reacted with salicylaldehyde derivatives, copper(II) perchlorate, and pyridine to produce various four‐coordinated heteroleptic [Cu (SBn)(py)]ClO4 (n = 1–4) complexes. Ligand exchange of the monodentate pyridine with bidentate 2,2′‐dimethyl‐4,4′‐bithiazole (BTZ) produced other new series of five‐coordinated [Cu (SBna)(BTZ)]ClO4 complexes. Elemental analysis, Fourier‐transform infrared spectroscopy (FT‐IR), and ultraviolet–visible (UV–Vis) spectroscopy were used to identify the complexes. The crystal structures of 1a and 2a were also determined by single‐crystal X‐ray crystallography (SCXRC). The inhibitory potential of these complexes against SARS‐CoV‐2 and its omicron variant main proteases (PDB IDs: 6LU7 and 7TLL, respectively) was investigated by means of molecular‐docking modeling. According to the estimated free binding energy (EFBE), the order of binding energies were (3) > (3a) > (1a) > (1) > (2a) > (4a) > (4) > (2) for 6LU7 and (1a) > (3) > (1) > (4) > (2) > (4a) > (2a) > (3a) for 7TLL. The complexes (1a) for 6LU7 and (3) for 7TLL with electronegative Br substituents were at the top of the series and had the most negative ΔGbinding. The EFBE of four conventional corona‐virus medicines, that is, remdesivir, hydroxychloroquine, dexamethasone, and AstraZeneca were also obtained and compared with the synthesized complexes. The EFBE of the complexes were comparable to standard drugs.

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New Cu(II), Mn(II) and Mn(III) Schiff base complexes cause noncovalent interactions: X-ray crystallography survey, Hirshfeld surface analysis and molecular simulation investigation against SARS-CoV-2

Cited by 11 publications

References 49 publications

Novel dinuclear Ni (II) Schiff base complexes induced noncovalent exchanges: Crystal structure investigation, electrochemical assessment, Hirshfeld surface analysis and SARS‐CoV‐2 docking study

Novel dinuclear Ni (II) Schiff base complexes induced noncovalent exchanges: Crystal structure investigation, electrochemical assessment, Hirshfeld surface analysis and SARS‐CoV‐2 docking study

Synthesis, spectra, crystal structure, Hirshfeld surface analysis, DFT calculations and molecular docking evaluation on novel mononuclearZn(II), Mn(III) and Co(III) Schiff base complexes derived from 2- hydroxy-1-naphthaldehyde

The effect of structural variations of heteroleptic Cu(II) complexes of tri‐dentate unsymmetrical Schiff‐base main ligands with pyridine or bithiazole co‐ligands on molecular docking against SARS‐CoV‐2 and its Omicron variant main proteases

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