Eşsiz, Şebnem
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Eşsiz, Şebnem
Eşsiz, Sebnem
E., Sebnem
Sebnem Eşsiz
Eşsiz, Ş.
Essiz, Sebnem
Essiz,Sebnem
Şebnem Eşsiz
S. Eşsiz
Essiz,Ş.
E., Şebnem
Eşsiz, S.
DAVUTYAN N.
Eşsiz, ŞEBNEM
Ş. Eşsiz
Şebnem EŞSIZ
Eşsiz,Ş.
EŞSIZ, Şebnem
E.,Sebnem
Essiz,S.
ŞEBNEM EŞSIZ
Sebnem, Essiz
Davutyan N.
EŞSIZ, ŞEBNEM
Gökhan, Şebnem Eşsiz
Eşsiz, Şebnem
Eşsiz Gökhan, Şebnem
Gökhan Eşsiz, Şebnem
Gökhan, Şebnem Eşsiz
Essız, Sebnem
Eşsiz, Şebnem
Essız, Sebnem
Eşsiz Gökhan, Şebnem
Eşsiz, Sebnem
E., Sebnem
Sebnem Eşsiz
Eşsiz, Ş.
Essiz, Sebnem
Essiz,Sebnem
Şebnem Eşsiz
S. Eşsiz
Essiz,Ş.
E., Şebnem
Eşsiz, S.
DAVUTYAN N.
Eşsiz, ŞEBNEM
Ş. Eşsiz
Şebnem EŞSIZ
Eşsiz,Ş.
EŞSIZ, Şebnem
E.,Sebnem
Essiz,S.
ŞEBNEM EŞSIZ
Sebnem, Essiz
Davutyan N.
EŞSIZ, ŞEBNEM
Gökhan, Şebnem Eşsiz
Eşsiz, Şebnem
Eşsiz Gökhan, Şebnem
Gökhan Eşsiz, Şebnem
Gökhan, Şebnem Eşsiz
Essız, Sebnem
Eşsiz, Şebnem
Essız, Sebnem
Eşsiz Gökhan, Şebnem
Job Title
Dr. Öğr. Üyesi
Email Address
Main Affiliation
Molecular Biology and Genetics
Status
Current Staff
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ORCID ID
Scopus Author ID
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Sustainable Development Goals
15
LIFE ON LAND
0
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16
PEACE, JUSTICE AND STRONG INSTITUTIONS
0
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14
LIFE BELOW WATER
0
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6
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0
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3
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8
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17
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0
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4
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2
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10
REDUCED INEQUALITIES
0
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7
AFFORDABLE AND CLEAN ENERGY
3
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13
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0
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1
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0
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9
INDUSTRY, INNOVATION AND INFRASTRUCTURE
1
Research Products
12
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1
Research Products
8
DECENT WORK AND ECONOMIC GROWTH
0
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11
SUSTAINABLE CITIES AND COMMUNITIES
0
Research Products
5
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0
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Documents
23
Citations
270
h-index
9
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0
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0
Scholarly Output
28
Articles
15
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218/2280
Supervised MSc Theses
9
Supervised PhD Theses
2
WoS Citation Count
202
Scopus Citation Count
237
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5
Scopus h-index
7
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0
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0
WoS Citations per Publication
7.21
Scopus Citations per Publication
8.46
Open Access Source
17
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11
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| Journal | Count |
|---|---|
| Journal of Molecular Modeling | 2 |
| European Journal of Medicinal Chemistry | 2 |
| Turkish Journal of Biology | 2 |
| Chemical Biology & Drug Design | 1 |
| ChemistrySelect | 1 |
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28 results
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Now showing 1 - 10 of 28
Article Citation - WoS: 54Citation - Scopus: 65Synthesis, Biological Evaluation and Molecular Docking Studies of Bis-Chalcone Derivatives as Xanthine Oxidase Inhibitors and Anticancer Agents(Elsevier, 2019) Burmaoğlu, Serdar; Özcan, Şeyda; Balcıoğlu, Sevgi; Gencel, Melis; Noma, Samir Abbas Ali; Eşsiz, Şebnem; Ateş, Burhan; Algül, ÖztekinIn this study, a series of B-ring fluoro substituted bis-chalcone derivatives were synthesized by Claisen-Schmidt condensation reactions and evaluated for their ability to inhibit xanthine oxidase (XO) and growth inhibitory activity against MCF-7 and Caco-2 human cancer cell lines, in vitro. According to the results obtained, the bis-chalcone with fluoro group at the 2 (4b) or 2,5-position (4g) of B-ring were found to be potent inhibitors of the enzyme with IC50 values in the low micromolar range. The effects of these compounds were about 7 fold higher than allopurinol. The binding modes of the bis-chalcone derivatives in the active site of xanthine oxidase were explained using molecular docking calculations. Also, compound 4g and 4h showed in vitro growth inhibitory activity against a panel of two human cancer cell lines 1.9 and 6.8 μM of IC50 values, respectively.Article Protein Homology Modeling in the Low Sequence Similarity Regime(2024) Essız, SebnemPredicting the 3-D structure of a protein from its sequence based on a template protein structure is still one of the most exact modeling techniques present today. However, template-based modeling is heavily dependent on the selection of a single template structure and the sequence alignment between target and template. Mainly when the target and template sequence identity is low, the error from the alignment introduces larger errors to the model structure. An iterative method to correct such alignment mistakes is used in this study with a benchmark set from CASP in the extremely low sequence-identity regime. This is a protocol developed and tested before and it evaluates the alignment quality by building rough 3-D models for each alignment. Then by using a genetic algorithm it iteratively creates a new set of alignments. Since the method evaluates models, not sequence alignments, structural features are automatically incorporated into the alignment protocol. In the current study, models from structural alignment have been built by Modeller program to show the maximum possible quality of the model that can be obtained from that template structure with the iterative modeling protocol. Then the results and correctly aligned segments from the iterative modeling protocol are analyzed. Finally, it has been shown that if a good local fragment assessment scoring function is developed, the correctly aligned segments exist in the pool of alignments created by the protocol. Thus, the improvement of modeling in the low sequence identity regime is conceivable.Article Modelling of C-Terminal Tail of Human Sting and Its Interaction With\rtank-Binding Kinase 1(2022) Masrı, Rahaf Ata Ouda Al; Bıda, Hajara Audu; Eşsiz, ŞebnemStimulator of interferon genes (STING) plays a significant role in a cell’s intracellular defense against pathogens or selfDNA by inducing inflammation or apoptosis through a pathway known as cGAS-cGAMP-STING. STING uses one of its domains, the\rC-terminal tail (CTT) to recruit the members of the pathway. However, the structure of this domain has not been solved experimentally.\rSTING conformation is open and more flexible when inactive. When STING gets activated by cGAMP, its conformation changes to a\rclosed state covered by 4 beta-sheets over the binding site. This conformational change leads to its binding to Tank-binding kinase 1\r(TBK1). TBK1 then phosphorylates STING aiding its entry to the cell’s nucleus.\rIn this study, we focused on the loop modeling of the CTT domain in both the active and inactive STING conformations. After the\rmodeling step, the active and inactive STING structures were docked to one of the cGAS-cGAMP-STING pathway members, TBK1,\rto observe the differences of binding modes. CTT loop stayed higher in the active structure, while all the best-scored models, active or\rinactive, ended up around the same position with respect to TBK1. However, when the STING poses are compared with the cryo-EM\rimage of the complex structure, the models in the active structure chain B displayed closer results to the complex structure.Article Citation - WoS: 49Citation - Scopus: 54New Azole Derivatives Showing Antimicrobial Effects and Their Mechanism of Antifungal Activity by Molecular Modeling Studies(Elsevier France-Editions Scientifiques Medicales Elsevier, 2017) Doğan, İnci Selin; Saraç, Selma; Sarı, Suat; Kart, Didem; Eşsiz, Şebnem; Vural, İmran; Dalkara, SevimAzole antifungals are potent inhibitors of fungal lanosterol 14 alpha demethylase (CYP51) and have been used for eradication of systemic candidiasis clinically. Herein we report the design synthesis and biological evaluation of a series of 1-phenyl/1-(4-chlorophenyl)-2-(1H-imidazol-1-yl) ethanol esters. Many of these derivatives showed fungal growth inhibition at very low concentrations. Minimal inhibition concentration (MIC) value of 15 was 0.125 mu g/mL against Candida albicans. Additionally some of our compounds such as 19 (MIC: 0.25 mu g/mL) were potent against resistant C. glabrata a fungal strain less susceptible to some first-line antifungal drugs. We confirmed their antifungal efficacy by antibiofilm test and their safety against human monocytes by cytotoxicity assay. To rationalize their mechanism of action we performed computational analysis utilizing molecular docking and dynamics simulations on the C. albicans and C. glabrata CYP51 (CACYP51 and CGCYP51) homology models we built. Leu130 and T131 emerged as possible key residues for inhibition of CGCYP51 by 19. (C) 2017 Elsevier Masson SAS. All rights reserved.Article Engineering of Geobacillus Kaustophilus Lipase for Enhanced Catalytic Efficiency and Methanol Tolerance in Biodiesel Production from Sunflower Oil(Elsevier, 2025) Tulek, Ahmet; Poyraz, Yagmur; Sukur, Gozde; Pacal, Nurettin; Ozdemir, F. Inci; Yildirim, Deniz; Essiz, SebnemLipase-mediated biodiesel production offers a sustainable and environmentally friendly alternative to conventional chemical methods. However, enzyme limitations such as low activity, poor thermal stability, and limited solvent tolerance remain challenges. In this study, a lipase from Geobacillus kaustophilus (Gklip) was engineered for improved biodiesel production using molecular docking, molecular dynamics (MD) simulations, and molecular mechanics/generalized born surface area (MM/GBSA) free energy calculations. Five mutants (Y29S, Q114T, F289D, Q184M, and Q114F) were generated via site-directed mutagenesis and expressed in Escherichia coli. Biochemical characterization revealed that all mutants retained the wild-type's optimal temperature (50 degrees C) and pH (8.0), while showing varying pH ranges, with the broadest observed in Q184M. Thermal stability increased significantly in Q184M (32.86-fold) and Q114F (5.93-fold). Catalytic efficiencies improved by 2.07-, 2.05-, and 2.63-fold in Q184M, F289D, and Y29S, respectively, compared to the wild-type (0.57). In the presence of 60 % methanol, the wild-type retained only 30.4 % activity, while Q184M maintained 67.5 %, highlighting superior solvent tolerance. Biodiesel conversion assays using sunflower oil showed no product formation by the wild-type, whereas Q184M, Q114F, and F289D achieved yields of 58.7 %, 56.3 %, and 49.2 %, respectively. These findings identify Q184M and Q114F as promising enzyme candidates for enzymatic biodiesel production.Master Thesis G. Kaustophilius Lipazinin Mutasyon Çalışmaları Kullanılarak Substrat Seçiciliğinin ve Aktivitesinin Geliştirilmesi(2025) Poyraz, Yağmur; Eşsiz, ŞebnemLipazlar, yağların hidrolizini katalize eden hidrolaz sınıfı enzimlerdir. Biyoteknolojide özellikle biyodizel üretimi alanında önemli bir yeri bulunmaktadır. Bu enzimler, yağların transesterifikasyon reaksiyonunu katalize ederek bitkisel veya hayvansal yağlardan biyodizel elde etmeye yardımcı olmaktadır. Fakat, biyodizel üretiminde lipaz kullanımının bir takım sorunları bulunmaktadır. Reaksiyon verimliliğinin yetersizliği, özellikle yüksek serbest yağ asidi içeriğine sahip ham yağların transesterifikasyonunda önemli bir sorundur. Ayrıca, lipazların reaksiyon hızı açısından yeterince hızlı olmama duumu söz konusudur. Bunlara ek olarak, bu enzimler çevre koşullarına duyarlıdır; uygun sıcaklık veya pH koşulları olmaması durumu enzim aktivitesini olumsuz etkileyebilirken, kararlılık sorunlarını da beraberinde getirebilmektedir. Araştırmacılar, lipazların performansını artırmak ve süreç verimliliğini iyileştirmek için sürekli olarak yenilikçi yöntemler ve teknolojiler araştırmaktadır. Enzim mutasyonu ve lipaz immobilizasyonu, bu çabada odaklanılan önemli alanlardır. Bu çalışma, Geobacillus kaustophilus termofilik lipazının yapısal ve dinamik özellikleri hakkındaki anlayışımızı geliştirmeyi ve aktivitesini, substrat seçiciliğini ve termal kararlılığını iyileştirmek için mutasyonları kullanmayı amaçlamaktadır. İdeal mutasyonları bulmak için Gklip lipazı modellenmiş ve hem yabani tip hem de mutasyonlu yapıların ligand seçiciliğini değerlendirmek için farklı uzunlukta karbon zincirli yağ asitleri ile dok çalışmaları yürütülmüştür. Daha sonra, tüm protein-ligand kompleksleri için 50 ns moleküler dinamik simülasyonları gerçekleştirilmiştir. Simülasyonların son 30 ns'si MM/GBS analizi için kullanılmıştır. 36 mutasyondan, en iyi 5 tanesi daha ileri deneysel çalışmalar için seçilmiştir.Article Citation - WoS: 41Citation - Scopus: 40Sustainable production of formic acid from CO2 by a novel immobilized mutant formate dehydrogenase(Elsevier, 2023) Tulek, Ahmet; Gunay, Elif; Servili, Burak; Essiz, Sebnem; Binay, Baris; Yildirim, DenizFormate dehydrogenase (NAD+-dependent FDH) is an enzyme that catalyzes the reversible oxidation of formate to CO2 while reducing NAD+ to NADH. The enzyme has been used in industrial and chemical applications for NADH regeneration for a long time. However, discovering the unique ability of FDHs, which is to reduce CO2 and produce formic acid, leads studies focusing on discovering or redesigning FDHs. Despite using various protein engineering techniques, these studies mostly target the same catalytic site amino acids of FDHs. Here, for the first time, the effect of an Asp188 mutation on a potential allosteric site in NAD+-dependent CtFDH around its subunit-subunit interface was studied by molecular modelling and simulation in the presence of bicarbonate and formate. Biochemical and kinetic characterization of this Asp188Arg mutant and wild type CtFDH enzymes were performed in detail. Both enzymes were also immobilized on newly synthesized MWCNT-Ni-O-Si/Ald and MWCNT-Ni-O-Si/Glu supports designed to overcome well-known CtFDH stability problems including thermostability and reuse resistance. Integrating mutation and immobilization provided about a 25-fold increase in catalytic efficiency for carbonate activity. The one-way ANOVA analysis also ensured significant effect of the mutation and immobilization on kinetic constants. After characterizing the immobilization of highly purified wild type and mutant enzyme with instrumental analysis techniques, the thermal stability of MWCNT-Ni-Si@wtCtFDH and MWCNT-Ni-Si@mt-CtFDH was found to increase about 11-and 18-fold, respectively, compared to their free counterparts at 50 degrees C. The mutant CtFDH and its immobilized counterpart produced around 2-fold more formic acid than those of wild type CtFDH and its immobilized counterpart under the same conditions. MWCNT-Ni-Si@wt-CtFDH and MWCNT-Ni-Si@mt-CtFDH remained around 82 % and 86 % of their initial activities respectively after lots of recycling. Integration of subunit interface amino acid position of NAD+ dependent FDHs engineering and immobilization provides a new insight can be scientifically and rationally employed for this current application FDHs as a solution to produce formic acids from renewable sources.Conference Object Soman as a Wrench in the Works of Human Acetylcholinesterase: Soman Induced Conformational Changes Revealed by Molecular Dynamics Simulations(Amer Chemical Soc, 2014) Bennion, Brian J.; Eşsiz, Şebnem; Lau, Edmond Y.; Fattebert, Jean-Luc; Emigh, Aiyana; Lightstone, Felice C.[Abstract Not Available]Article Citation - WoS: 3Citation - Scopus: 1Newly Synthesized 6-Substituted Piperazine/Phenyl-9-cyclopentyl Containing Purine Nucleobase Analogs Act as Potent Anticancer Agents and Induce Apoptosis via Inhibiting Src in Hepatocellular Carcinoma Cells(Royal Soc Chemistry, 2023) Bilget Guven, Ebru; Durmaz Sahin, Irem; Altiparmak, Duygu; Servili, Burak; Essiz, Sebnem; Cetin-Atalay, Rengul; Tuncbilek, MeralNewly synthesized 6-substituted piperazine/phenyl-9-cyclopentyl-containing purine nucleobase analogs were tested for their in vitro anticancer activity against human cancer cells. Compounds 15, 17-24, 49, and 56 with IC50 values less than 10 mu M were selected for further examination on an enlarged panel of liver cancer cell lines. Experiments revealed that compound 19 utilizes its high cytotoxic potential (IC50 < 5 mu M) to induce apoptosis in vitro. Compound 19 displayed a KINOMEscan selectivity score S35 of 0.02 and S10 of 0.01 and demonstrated a significant selectivity against anaplastic lymphoma kinase (ALK) and Bruton's tyrosine kinase (BTK) over other kinases. Compounds 19, 21, 22, 23, and 56 complexed with ALK, BTK, and (discoidin domain-containing receptor 2) DDR2 were analyzed structurally for binding site interactions and binding affinities via molecular docking and molecular dynamics simulations. Compounds 19 and 56 displayed similar interactions with the activation loop of the kinases, while only compound 19 reached toward the multiple subsites of the active site. Cell cycle and signaling pathway analyses exhibited that compound 19 decreases phosho-Src, phospho-Rb, cyclin E, and cdk2 levels in liver cancer cells, eventually inducing apoptosis.Master Thesis G. Kaustophilius Lipazinin Mutasyon Çalışmaları Kullanılarak Substrat Seçiciliğinin ve Aktivitesinin Geliştirilmesi(2025) Poyraz, Yağmur; Eşsiz, ŞebnemLipazlar, yağların hidrolizini katalize eden hidrolaz sınıfı enzimlerdir. Biyoteknolojide özellikle biyodizel üretimi alanında önemli bir yeri bulunmaktadır. Bu enzimler, yağların transesterifikasyon reaksiyonunu katalize ederek bitkisel veya hayvansal yağlardan biyodizel elde etmeye yardımcı olmaktadır. Fakat, biyodizel üretiminde lipaz kullanımının bir takım sorunları bulunmaktadır. Reaksiyon verimliliğinin yetersizliği, özellikle yüksek serbest yağ asidi içeriğine sahip ham yağların transesterifikasyonunda önemli bir sorundur. Ayrıca, lipazların reaksiyon hızı açısından yeterince hızlı olmama duumu söz konusudur. Bunlara ek olarak, bu enzimler çevre koşullarına duyarlıdır; uygun sıcaklık veya pH koşulları olmaması durumu enzim aktivitesini olumsuz etkileyebilirken, kararlılık sorunlarını da beraberinde getirebilmektedir. Araştırmacılar, lipazların performansını artırmak ve süreç verimliliğini iyileştirmek için sürekli olarak yenilikçi yöntemler ve teknolojiler araştırmaktadır. Enzim mutasyonu ve lipaz immobilizasyonu, bu çabada odaklanılan önemli alanlardır. Bu çalışma, Geobacillus kaustophilus termofilik lipazının yapısal ve dinamik özellikleri hakkındaki anlayışımızı geliştirmeyi ve aktivitesini, substrat seçiciliğini ve termal kararlılığını iyileştirmek için mutasyonları kullanmayı amaçlamaktadır. İdeal mutasyonları bulmak için Gklip lipazı modellenmiş ve hem yabani tip hem de mutasyonlu yapıların ligand seçiciliğini değerlendirmek için farklı uzunlukta karbon zincirli yağ asitleri ile dok çalışmaları yürütülmüştür. Daha sonra, tüm protein-ligand kompleksleri için 50 ns moleküler dinamik simülasyonları gerçekleştirilmiştir. Simülasyonların son 30 ns'si MM/GBS analizi için kullanılmıştır. 36 mutasyondan, en iyi 5 tanesi daha ileri deneysel çalışmalar için seçilmiştir.
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