THBF Bileşiğinin Insiliko Moleküler Yerleştirme Çalışmaları: TD-DFT Simülasyonları ve İlaç Tasarımı

Tekeş, Ahmet Turan; Ata, Ahmet Çağrı; Tanrıverdı, Aslıhan Aycan; Čakmak, İsmail

doi:10.21597/jist.953803

Cited by 6 publications

(3 citation statements)

References 26 publications

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“…The Maestro Molecular Modeling platform of the Schrödinger (version 11.8), LLC model was implemented via molecular insertion. [34][35][36][37] DNA polymerase beta substrate complex with templating cytosine and incoming Fapy-dGTP analog (DNA1) (PDB: 6DIA) [20], Human Aprataxin (APTX) bound to DNA, AMP, and Zn -product complex (DNA2) (PDB: 4NDH) [21] These DNA complexes, which are high resolution crystal structures, were Downloaded from http://www.rcsb.org/pdb. [37]…”

Section: Simulations Of the Theoretical Studiesmentioning

confidence: 99%

Synthesis of axially silicon phthalocyanine substituted with bis- (3,4-dimethoxyphenethoxy) groups and energy features, charge density analysis and molecular docking studies

Solğun

Tanrıverdı

Yıldıko

et al. 2022

Preprint

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Axially bis-substituted silicon phthalocyanine was synthesized from the reaction of 2-(3,4-dimethoxy phenyl) ethanol and SiPcCl2. The structure of the compound was justified by FT-IR, 1H NMR, 13C NMR, UV-Vis, and mass spectra. The conglomeration action of the phthalocyanine compound was determined by UV-visible spectra at different concentrations and in different solvents. Some parameters of this axial silicon phthalocyanine compound were investigated by computational chemistry. Structural optimization of axial silicon phthalocyanine substituted with compound, HOMO-LUMO energies and MEP maps was performed by density functional theory (DFT) studies. In addition, a chemical bond analysis of the molecule was performed with quantum theory atom in molecules (QTAIM). Finally, a molecular docking study was applied to this new phthalocyanine molecule in its binding mechanism.

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Section: Simulations Of the Theoretical Studiesmentioning

confidence: 99%

Synthesis of axially silicon phthalocyanine substituted with bis- (3,4-dimethoxyphenethoxy) groups and energy features, charge density analysis and molecular docking studies

Solğun

Tanrıverdı

Yıldıko

et al. 2022

Preprint

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“…Molecular docking study for ligand-enzyme interactions and the compound's potential to bind to protein as an inhibitor was performed with Schrödinger's Maestro Molecular Modeling (version 11.8) platform (Madhavi and et al, 2013). The crystal structures of human acetylcholinesterase (AChE) (PDB code:4M0E), butyrylcholinesterase (BChE) (PDB code:6SAM) and alpha-glucosidase (α-GLY) (PDB code:3A4A) enzymes were downloaded from PDB database (Altun and et al, 2021;Dong and et al, 2021;Tekes and et al, 2021). Preparation and ligand docking placement studies were carried out using ligprep module, protein prep, and receptor grid box modules.…”

Section: Molecular Quantum Chemical and Drug Potential Studiesmentioning

confidence: 99%

Structural and Spectral Properties of 4-(5-methyl-[1, 2, 4] triazolo [1, 5-a] pyrimidine-7-yloxy) phthalonitrile: Analysis by TD-DFT Method, ADME Analysis, and Molecular Docking Simulations

ALTUN

Yıldıko

Tanrıverdı

et al. 2022

Iğdır Üniversitesi Fen Bilimleri Enstitüsü Dergisi

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In this study, 4-(5-methyl-[1,2,4]triazolo[1,5-a]pyrimidine-7-yloxy) phthalonitrile (coded as MTPPN) was chosen as the phthalonitrile compound and the quantum chemical and in-silico studies have been done. First, the basis set of the time dependent density functional theory (TD-DFT) method was used and the boundary orbital energies and band gap calculations of the molecule were performed. Analysis of atoms in molecules (AIM) theoretical calculations is presented to learn about electron density and bond critical point. In addition, absorption, distribution, metabolism, and excretion analyzes (ADME) were performed for the drug potential of the compound. On some enzymes effect of MTPPN compound was examined. The docking score was obtained for AChE, BChE, α-GLY proteins -7.864, -6.848, and -5.511 kcal/mol, respectively. MTPPN gave a good inhibitory performance in an in-silico study as a drug candidate.

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“…Automated docking is frequently used in structure/function analysis and molecular design for the prediction of bimolecular complexes. The structure-based drug design process includes steps such as docking small molecule compounds into a receptor's binding site and determining the complex's binding affinity [27,35]. As a result of the TDOB -aldose reductase (PDB: 4ICC) docking study, Fig.…”

Section: Molecular Docking Studiesmentioning

confidence: 99%

Computational Investigation of 5.5'',7''-trihydroxy-3,7-dimethoxy-4'-4''-O-biflavone from Flavonoids Using DFT Calculations and Molecular Docking

2022

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The structural characterization of the 5.5",7"-trihydroxy-3,7-dimethoxy-4'-4"-O-biflavone (TDOB) molecule was done in this study. Based on the molecule's stable phase geometry, entire calculations were done by use of the detailed CAM-B3LYP and PBEPBE approach with SDD and LanL2DZ. In addition, a variety of HOMO-LUMO energy ranges, natural bond inter-orbital and inter-orbital interactions, and electro-static surface mapping operations were as well carried out. The specific binding location and mechanism of the ligand on the protein were studied using molecular docking. In the study, affinity scores for TDOB-AKR1B1 (Aldose Reductase) (PDB: 4ICC) and (PDB: 4IGS) were found to be -8.559 cal/mol and -5.461 cal/mol, respectively. 4ICC receptor binding score was found to be greater. The inhibitory properties of TDOB were investigated against the enzymes 4ICC and 4IGS, both of which showed effective inhibition.

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THBF Bileşiğinin Insiliko Moleküler Yerleştirme Çalışmaları: TD-DFT Simülasyonları ve İlaç Tasarımı

Cited by 6 publications

References 26 publications

Synthesis of axially silicon phthalocyanine substituted with bis- (3,4-dimethoxyphenethoxy) groups and energy features, charge density analysis and molecular docking studies

Synthesis of axially silicon phthalocyanine substituted with bis- (3,4-dimethoxyphenethoxy) groups and energy features, charge density analysis and molecular docking studies

Structural and Spectral Properties of 4-(5-methyl-[1, 2, 4] triazolo [1, 5-a] pyrimidine-7-yloxy) phthalonitrile: Analysis by TD-DFT Method, ADME Analysis, and Molecular Docking Simulations

Computational Investigation of 5.5'',7''-trihydroxy-3,7-dimethoxy-4'-4''-O-biflavone from Flavonoids Using DFT Calculations and Molecular Docking

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