Computational insight into the phthalocyanine-DNA binding via docking and molecular dynamics simulations

Özalp, Lalehan; Erdem, Safiye Sağ; Yüce‐Dursun, Başak; Mutlu, Özal; Özbi̇l, Mehmet

doi:10.1016/j.compbiolchem.2018.09.009

Cited by 32 publications

(19 citation statements)

References 37 publications

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“…A more positive value indicates a better binding, whereas a negative number indicates very weak binding, but not nonbinding. Similar data utilizing YASARA can also be found in the studies by Dulebo et al 37 and Ozalp et al 38 Thus, it is very similar to the MM/PBSA method, 39,40 except for the entropy term, which can be neglected in the context of the main goal of these calculations, where we compare ligand binding affinities for the same ligand in different binding sites and any error will be carried through all numbers.…”

Section: Binding Energysupporting

confidence: 61%

Computational investigation of influenza A virus M2 protein inhibitionmechanism by ion channel blockers

Özbi̇l¹

2019

Turk J Chem

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The M2 protein of the influenza A virus, responsible for flu, is a homotetramer transmembrane protein, forming a transmembrane ion channel, where His 37s act as pH sensors and Trp 41s and Asp 44s act as channel gates. Opening of this channel leads to transfer of virus RNA into the human host. Thus, blocking this transfer is an important pharmaceutical strategy to stop infection. As a result of viral drug resistance, commercially available channel inhibitors, rimantadine (RIM) and amantadine (AMA), are not as effective as they used to be. Understanding binding sites and outcomes of binding will lead to new inhibitor design studies. Here, utilizing molecular docking with classical and constant pH molecular dynamics simulations, two novel binding sites for RIM and AMA molecules were revealed. Both structural and chemical effects of inhibitors on M2 protein on the closed, inactive M2 channel structure were investigated. Upon binding of the inhibitor molecules, decrease in ion channel cross-distances was observed. Meanwhile, RIM binding did not alter protonation of His 37s and Asp 44s, whereas AMA binding drastically increased the protonation population of two residues from different monomers, creating a more basic channel at physiological pH.

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Section: Binding Energysupporting

confidence: 61%

Computational investigation of influenza A virus M2 protein inhibitionmechanism by ion channel blockers

Özbi̇l¹

2019

Turk J Chem

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“…The major reason for this is that the contact of compound ( 3–5 ) is very large; as the contact surface of the molecules increases, the biological activity value may increase. [ 55,56 ] Increased contact surface of molecules increases the interaction between molecules and proteins. These interactions are hydrogen bonds, polar and hydrophobic interactions, and π–π and halogen bonds.…”

Section: Resultsmentioning

confidence: 99%

Synthesis of (4R)‐2‐(3‐hydroxyphenyl)thiazolidine‐4‐carboxylic acid substituted phthalocyanines: Anticancer activity on different cancer cell lines and molecular docking studies

Bilgiçli

Hepokur

et al. 2021

Applied Organom Chemis

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In this study, firstly, (4R)‐2‐(3‐hydroxyphenyl)thiazolidine‐4‐carboxylic acid (1) and (4R)‐2‐(3‐(3,4‐dicyanophenoxy)phenyl)thiazolidine‐4‐carboxylic acid (2) were prepared. Then, the novel type metallophthalocyanines (ZnPc (3), CuPc (4), and CoPc (5)) bearing thiazolidine groups in peripheral positions were synthesized using by compound (2). The synthesized new compounds (1–5) were characterized by the combination of standard spectroscopic methods such as FT‐IR, 1H NMR, 13C NMR, UV–Vis spectral data, and MALDI‐TOF. Aggregation behaviors of peripheral tetra‐substituted metallophthalocyanines were investigated in dimethyl sulfoxide (DMSO) media. Fluorescence properties and fluorescence quantum yield of the new type zinc phthalocyanine (3) were performed in DMSO at room temperature. The anticancer activity of novel type metallophthalocyanines bearing thiazolidine groups in peripheral positions were investigated on rat glioma cancer (C6), human prostate carcinoma (DU‐145), and normal human lung fibroblast (WI‐38) cell lines. Finally, the biological and chemical activities of (4R)‐2‐(3‐(3,4‐dicyanophenoxy)phenyl)thiazolidine‐4‐carboxylic acid (2) and its novel type metallophthalocyanines (ZnPc (3), CuPc (4), and CoPc (5)) have been compared with many parameters obtained using theoretical methods that are the Gaussian software and molecular docking.

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“…The best binding free energies obtained for each region were also used for the calculation of Boltzmann‐averaged binding energies (ΔG ba ) by means of the Boltzmann distribution equation (Equation ), where the number 5 represents each binding region of enzyme. [ 68 ] Δ G ba were utilized to calculate binding constants using the following Equation : K b = exp[−Δ G ba / RT ], where R is the gas constant and T = 298 K.

∆ G_{ba} goodbreak= \sum_{i = 1}^{5} \frac{e^{- ∆ G_{i} / kT}}{\sum_{i = 1}^{5} e^{- ∆ G_{i} / italickT}} ∆ G_{i}

…”

Section: Methodsmentioning

confidence: 99%

Some characteristics of new and innovative COX inhibitor derivatives: Potent hCA‐I and hCA‐II inhibitors supported by molecular docking studies

Karakılıç

Alım

Emirik

et al. 2021

Applied Organom Chemis

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In this study, two novel metallophthalocyanines (ZnPc and CoPc) were synthesized using the corresponding metal salts 4‐(4‐(4‐[4‐chlorophenyl]‐5‐methylisoxazol‐3‐yl)phenoxy)‐phthalonitrile (11), prepared from the reaction of 4‐nitrophthalonitrile and 4‐(4‐[4‐chlorophenyl]‐5‐methylisoxazol‐3‐yl)phenol (9). These metallophthalocyanines (MPcs) showed quite solubility in organic solvents such as dichloromethane (DCM), tetrahydrofuran (THF), dimethyl formamide (DMF), and dimethylsulfoxide (DMSO). The novel compounds 11a and 11b have been characterized using their UV–Vis, FT–IR, 1H NMR, 13C NMR, X‐Ray, and MALDI–TOF mass spectra. Supporting information cocerning with the study has been supplied. Photochemical, photophysical, and cyclic voltagram properties of these novel 4‐(4‐(4‐[4‐chlorophenyl]‐5‐methylisoxazol‐3‐yl)phenoxy substituted metallophthalocyanines (11a and 11b) were determined in DMF. DNA binding, metal chelating effect assay, and DPPH [2,2‐diphenyl‐1‐picrylhydrazyl hydrate] radical scavenging assay and electrochemical studies of MPcs were investigated. Further, the inhibitory effects of the COX‐inhibitor based novel metallophthalocyanines (11a and 11b) and their ligands (10 and 11) were examined on human erythrocyte carbonic anhydrase I (hCA‐I) and II (hCA‐II) isoenzymes, and the synthesized molecules exhibited very strong inhibitory effects on both isoforms. In addition, the hCA‐I and hCA‐II inhibition potential of Zn (II) and Co (II) Phthalocyanine complexes was supported by molecular docking studies. The binding interaction of metallophthalocyanines complexes 11a, 11b enzymes were analyzed in detail.

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Computational insight into the phthalocyanine-DNA binding via docking and molecular dynamics simulations

Cited by 32 publications

References 37 publications

Computational investigation of influenza A virus M2 protein inhibitionmechanism by ion channel blockers

Computational investigation of influenza A virus M2 protein inhibitionmechanism by ion channel blockers

Synthesis of (4R)‐2‐(3‐hydroxyphenyl)thiazolidine‐4‐carboxylic acid substituted phthalocyanines: Anticancer activity on different cancer cell lines and molecular docking studies

Some characteristics of new and innovative COX inhibitor derivatives: Potent hCA‐I and hCA‐II inhibitors supported by molecular docking studies

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