Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection

Permanent URI for this collectionhttps://hdl.handle.net/11147/7148

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Access type: Open accessSubject: search.filters.subject.Docking

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  • Article
    Synthesis, Characterization, Crystal Structure, Electrochemical and Photoluminescence Properties, Dft and Molecular Docking Studies, and Antimicrobial Activities of Two Mononuclear Nickel (II) Complexes With Pyrazole-Derived Ligands
    (Elsevier, 2025) Amin, Mina A.; Diker, Halide; Sahin, Onur; Varlikli, Canan; Soliman, Ahmed A.
    Two octahedral nickel complexes; [Ni(fdtp)2(DMF)2] (1) and [Ni(dcdtp)2(DMF)2] (2), based on 4-((3-fluorophenyl)diazenyl)-3-(trifluoromethyl)-1H-pyrazol-5-ol (fdtp) and 4-((2,4-dichlorophenyl)diazenyl)-3-(trifluoromethyl)-1H-pyrazol-5-ol (dcdtp) were synthesized. The complexes were characterized spectroscopically (FTIR, UV-Vis, Photoluminescence), Mass spectrometry, elemental analyses, electrochemically, thermally, and through Single-crystal X-ray investigations. The formation of the complexes was confirmed by the existence of Ni-O and Ni-N vibrations at bonds were observed as weak bands at 526-497 and 470-438 cm-1. According to the thermogravimetric analyses, the complexes were thermally stable and had relatively high activation energies (585.81 and 730.07 kJ mol-1 for 1, and 2, respectively). Cyclic voltammograms showed that the anodic potential region of 1 and 2 exhibited two irreversible oxidation peaks at 1.34 V &1.55 V and 1.41 V & 1.63 V, respectively, attributed to metal-localized oxidation. The complexes showed enhanced antibacterial activities compared to free ligands and comparable to the standard. The inhibition zones exhibited via 1 were about 21.7, 19.3, and 26.7 mm versus Escherichia coli (E. coli), Staphylococcus aureus (S. Aureus), and Bacillus Subtits (B. Subtits), respectively. Docking studies supported the antibacterial investigations; the binding energies of the complexes were -8.81 and -9.69 kcal/mol for 1 and 2 respectively, against E. coli (PDB ID: 6F86).
  • Article
    Citation - WoS: 5
    Citation - Scopus: 6
    Sequence Identification and in Silico Characterization of Novel Thermophilic Lipases From Geobacillus Species
    (WILEY, 2023) Sürmeli, Yusuf; Tekedar, Hasan Cihad; Sanli-Mohamed, Gulsah
    Microbial lipases are utilized in various biotechnological areas, including pharmaceuticals, food, biodiesel, and detergents. In this study, we cloned and sequenced Lip21 and Lip33 genes from Geobacillus sp. GS21 and Geobacillus sp. GS33, then we in silico and experimentally analyzed the encoded lipases. For this purpose, Lip21 and Lip33 were cloned, sequenced, and their amino acid sequences were investigated for determination of biophysicochemical characteristics, evolutionary relationships, and sequence similarities. 3D models were built and computationally affirmed by various bioinformatics tools, and enzyme-ligand interactions were investigated by docking analysis using six ligands. Biophysicochemical property of Lip21 and Lip33 was also determined experimentally and the results demonstrated that they had similar isoelectric point (pI) (6.21) and T-m (75.5(degrees)C) values as T-m was revealed by denatured protein analysis of the circular dichroism spectrum and pI was obtained by isoelectric focusing. Phylogeny analysis indicated that Lip21 and Lip33 were the closest to lipases from Geobacillus sp. SBS-4S and Geobacillus thermoleovorans, respectively. Alignment analysis demonstrated that S144-D348-H389 was catalytic triad residues in Lip21 and Lip33, and enzymes possessed a conserved Gly-X-Ser-X-Gly motif containing catalytic serine. 3D structure analysis indicated that Lip21 and Lip33 highly resembled each other and they were alpha/beta hydrolase-fold enzymes with large lid domains. BAN Delta IT analysis results showed that Lip21 and Lip33 had higher thermal stability, compared to other thermostable Geobacillus lipases. Docking results revealed that Lip21- and Lip33-docked complexes possessed common residues (H112, K115, Q162, E163, and S141) that interacted with the substrates, except paranitrophenyl (pNP)-C10 and pNP-C12, indicating that these residues might have a significant action on medium and short-chain fatty acid esters. Thus, Lip21 and Lip33 can be potential candidates for different industrial applications.