Portakal, Hüseyin Saygın
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Portakal, Saygin Huseyin
Portakal, Huseyin Saygin
Portakal, Huseyin S.
Portakal, Huseyin Saygin
Portakal, Huseyin S.
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saygin.portakal@ieu.edu.tr
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05.08. Genetics and Bioengineering
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Current Staff
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Sustainable Development Goals
8
DECENT WORK AND ECONOMIC GROWTH
0
Research Products
9
INDUSTRY, INNOVATION AND INFRASTRUCTURE
1
Research Products
10
REDUCED INEQUALITIES
0
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17
PARTNERSHIPS FOR THE GOALS
0
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12
RESPONSIBLE CONSUMPTION AND PRODUCTION
0
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7
AFFORDABLE AND CLEAN ENERGY
0
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1
NO POVERTY
0
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5
GENDER EQUALITY
0
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13
CLIMATE ACTION
0
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4
QUALITY EDUCATION
0
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14
LIFE BELOW WATER
0
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2
ZERO HUNGER
0
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15
LIFE ON LAND
0
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16
PEACE, JUSTICE AND STRONG INSTITUTIONS
0
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6
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0
Research Products
3
GOOD HEALTH AND WELL-BEING
1
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11
SUSTAINABLE CITIES AND COMMUNITIES
0
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Documents
9
Citations
19
h-index
3
Documents
9
Citations
34
Scholarly Output
12
Articles
10
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32/111
Supervised MSc Theses
1
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0
WoS Citation Count
14
Scopus Citation Count
17
WoS h-index
2
Scopus h-index
3
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0
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0
WoS Citations per Publication
1.17
Scopus Citations per Publication
1.42
Open Access Source
8
Supervised Theses
1
| Journal | Count |
|---|---|
| Turkish Computational and Theoretical Chemistry | 3 |
| Istanbul Journal of Pharmacy | 2 |
| Journal of Research in Pharmacy | 1 |
| Bıoorganıc & Medıcınal Chemıstry Letters | 1 |
| Naunyn-Schmiedeberg's Archives of Pharmacology | 1 |
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12 results
Scholarly Output Search Results
Now showing 1 - 10 of 12
Master Thesis Investigation the Functions of Novel G-Quadruplex Structures in E. Coli Genome(İzmir Ekonomi Üniversitesi, 2021) Portakal, Hüseyin Saygın; Doluca, OsmanG-dörtlüleri nükleik asit moleküllerinin özel üçüncül yapılardan biri olup kanonik olmayan topolojilerdir. Yıllar boyunca birçok organizmadaki G-dörtlülerinin biyolojik rolleri incelenmiş ve ortaya çıkarılmıştır. Özellikle insan genomunun düzenleyici bölgelerinde bulunması G-dörtlülerinin düzenleyici rollerini ve hücre metabolizmasındaki önemini göstermektedir. Escherichia coli (E. coli) proteomik ve genomik yapılarının detaylıca ortaya çıkarılması ile laboratuvar uygulamalarında model organizma haline gelerek günümüzde en popüler bakteriyel organizmalardan birisidir. Bu zamana kadar E. coli genomunda çeşitli genlerin yakınında bulunan 52 G-dörtlüsü oluşturan sekans hesaplama araçları ile analiz edilmiştir. Ancak biyolojik fonksiyonları henüz keşfedilmemiştir. Bu bağlamda bu çalışmada G-dörtlülerinin biyolojik rolleri G-dörtlüsüne bağlanan proteinlerin MALDI-TOF-TOF tekniği ve CRISPR/Cas9 tekniğiyle G-dörtlüsü nakavtının civarındaki genlerin ekspresyon seviyesine olan etkisinin araştırılmasıyla incelenmiştir. MALDI-TOF-TOF sonuçları uyumlu moleküler ağırlıkları ve eşleşme skorları göz önünde bulundurularak asetaldehit alkol dehidrogenaz (adh) ve DNA bağımlı RNA polimeraz beta altbirimi olarak iki farklı proteinin G-dörtlüsüne bağlanan protein olmak üzere yüksek olasılığa sahip olduğunu göstermiştir. Bu doğrultuda G-dörtlülerinin alkol fermentasyonu işleminde ve yakın genlerin transkripsiyonunda rol oynadığı tahmin edilmektedir. Ancak maalesef ki bu çalışma doğrultusunda geliştirilen ve G-dörtlülerinin yüksek stabilite sahip olmasından dolayı G-dörtlülerini düzenleyemeyen CRISPR/Cas9 yaklaşımının iyileştirilmesi gerekmektedir. G-dörtlülerinin biyolojik fonksiyonlarının ortaya çıkarılması bakteri metabolizmasındaki önemine ışık tutacak ve gelecek çalışmalar için bir mihenk taşı olacaktır.Article Exploring the Potential of Lavandula stoechas in Smoking Cessation: A Molecular Docking Study of α4β2 Nicotinic Acetylcholine Receptor Interactions(Istanbul Univ, Fac Pharmacy, 2025) Barış, Elif; Portakal, Hüseyin SaygınBackground: Lavandula stoechas, commonly known as lavender, has traditionally been used in various therapeutic applications, including smoking cessation. The molecular interaction of Lavandula stoechas compounds with the α4β2 nicotinic acetylcholine receptors, which are crucial for smoking cessation, is not well understood. This study aims to analyze these interactions and compare them with the known smoking cessation drug varenicline tartrate. Methods: Molecular docking analysis was performed on essential compounds of Lavandula stoechas to assess their binding affinities to the α4β2 nicotinic acetylcholine receptors. The study utilized the crystal structure of the receptor and conducted virtual drug screening using AutoDock Vina in the PyRx Virtual Screening Tool. ADME (Absorption, Distribution, Metabolism, and Excretion) and toxicity profiles were also predicted using in silico methods. Results: The molecular docking revealed that several Lavandula stoechas compounds exhibited signif7 icant binding affinities to the α4β2 receptor. Compounds with the highest binding affinities were identified and compared with varenicline. The ADME and toxicity profiles indicated that these compounds had more favorable properties than varenicline, suggesting their potential as alternative smoking cessation agents. Discussion: The findings demonstrate that Lavandula stoechas contains compounds with significant binding affinities to the α4β2 nicotinic acetylcholine receptors, similar to varenicline. This indicates a potential role for Lavandula stoechas in smoking cessation therapy. The favorable ADME and toxicity profiles of these compounds further support their potential as alternatives to current smoking cessation drugs. This study paves the way for further research into the therapeutic applications of Lavandula stoechas in smoking cessation.Article Citation - WoS: 8Citation - Scopus: 8Fluorene/Fluorenone Carboxamide Derivatives as Selective Light-Up Fluorophores for C-Myc G-Quadruplex(Pergamon-Elsevier Science Ltd, 2021) Duyar, Halil; Portakal, Hüseyin Saygın; Yalcin, Ergin; Kanat, Beyza; Doluca, Osman; Seferoglu, ZeynelThe development of fluorescent dyes capable of selective recognition of G-quadruplexes is essential for studying its localization and biological functions. However, considering the G-quadruplex topologies may vary significantly, the synthesis of compounds showing both selectivity and strong fluorescence properties still remains a great challenge. Recently we have developed fluorene/fluorenone derivatives with structure-specific binding towards dsRNA, indicating its potential for structure-selective ligands. Herein, we report the synthesis of novel fluorene/fluorenone derivatives and their selectivity towards various DNA structures, particularly G-quadruplexes, two of which showed strong affinity to the proto-oncogene c-myc promoter G-quadruplex.Article Citation - WoS: 2Citation - Scopus: 2Liraglutide Modulates Cyclooxygenase and α7 Acetylcholine Receptors: in Vitro and in Silico Insights Into Its Anti-Inflammatory Role in LPS-Induced Inflammation in Raw 264.7 Macrophages(Springer, 2025) Baris, Elif; Portakal, Huseyin Saygin; Aslan, Arda; Karagonlar, Zeynep Firtina; Tosun, MetinerLiraglutide, a glucagon-like peptide-1 (GLP-1) receptor agonist, is well-established for its metabolic benefits, including glycemic control and weight loss. Beyond these roles, it exhibits significant anti-inflammatory properties, though the mechanisms remain underexplored. This study investigates the anti-inflammatory effects of liraglutide in lipopolysaccharide (LPS)-stimulated RAW 264.7 murine macrophages. Results demonstrate that increasing concentrations of liraglutide suppresses LPS-elevated prostaglandin E2 (PGE2), 6-keto prostaglandin F1 alpha (6-keto-PGF1 alpha, a stable prostacyclin metabolite) and thromboxane A2 (TXA2), similar to that observed with conventional anti-inflammatory agents, ibuprofen and celecoxib. Mechanistic exploration reveals that liraglutide's anti-inflammatory action is dually-modulated by cyclooxygenase (COX) and nicotinic acetylcholine receptor (nAChR) signaling. The application of non-selective, non-competitive nAChR antagonist or selective and potent alpha 7-nAChR antagonist, mecamylamine (MEC) and methyllycaconitine (MLA), respectively, highlights the involvement of cholinergic pathways in liraglutide's activity. Based on in silico molecular docking analyses, liraglutide exhibits favorable binding affinities to COX-1, COX-2, prostacyclin synthase (PGIS), and alpha 7nAChRs, supporting its potential multi-target anti-inflammatory effects. These findings suggest that the therapeutic potential of liraglutide may go beyond metabolic regulation and may be promising for conditions in which metabolic and inflammatory pathways converge, including inflammation and modulation of cholinergic signaling.Conference Object Citation - WoS: 1Citation - Scopus: 1Demonstration of G-Quadruplex Hybridization Chain Reaction for Nucleic Acid Detection(Institute of Electrical and Electronics Engineers Inc., 2020) Kanat B.; Portakal, Hüseyin Saygın; Doluca, OsmanIn recent years, the hybridization chain reaction (HCR) has been proposed as an alternative to polymerase chain reaction (PCR) for diagnosis. Unfortunately, the sensitivity of the HCR methods are still far below PCR and researchers focus on ways to improve it by investigating different HCR designs. While earlier designs exploit fluorescently labelled probes for detection, here we propose an HCR system that combines G-quadruplex formation and fluorescence for detection of single stranded DNA sequences with concentrations as low as 20 pM. We show that Gquadruplex-mediated oxidation of Amplex Red results in fluorescence increase and lowers the detection limit by about 10fold, in comparison to HCR using only fluorescently labelled HCR probes. © 2020 IEEE.Article Novel Tgase2 Allosteric Site Inhibitors: a Computational Study(DergiPark, 2024) Şahay, G.E.; Kızılkanat, N.; Sezgin, S.; Portakal, H.S.Tranglutaminase-2 (Tgase2) is one of the primary Transglutaminase enzyme family members having a significant role in Ca2+ -dependent and -independent post-translational modifications. It has been previously reported that Tgase2 has significant regulatory roles over metabolic functions such as signaling pathways, inflammatory response, and wound healing. In particular, many cancer types’ prognosis includes over Tgase2 activity since it might induce metastasis through regulating crosslinking of extracellular matrix (ECM) proteins, and tumor proliferation via leading spheroid formation. Considering these fundamentals, discovery of novel chemical compounds to inhibit Tgase2 activity might be a strong approach in cancer treatment. Furthermore, it’s known that Tgase2 activity might be inhibited through blocking its allosteric site with chemical compounds. As such, a drug library including 12,111 small compounds were virtually screened to allosteric site of Tgase2. The study has been validated by repetition the strategy with previously discovered inhibitors. Allosteric and active sites of Tgase2 have been demonstrated with protein-protein docking technique. Eventually, recently discovered ligands have been characterized according to their ADME and toxicity profiles. Results have demonstrated that Eltrombopag, Talniflumate, and Lumacaftor drugs might be repurposed in the inhibition of Tgase2 since that they exhibit high binding affinity, ADME, and toxicity properties comparing the known inhibitors. © (2024), (DergiPark). All Rights Reserved.Article Virtual Drug Screening Study to Discover Novel ERAP1 Allosteric Site Inhibitors for the Treatment of Ankylosing Spondylitis (AS)(Marmara Univ, Fac Pharmacy, 2025) Portakal, Hüseyin Saygın; Alp, Beste; Akyol, MertcanEndoplasmic reticulum aminopeptidase 1 (ERAP1) is one of the key molecules in the antigen presentation process. To date, associations of ERAP1 with Ankylosing Spondylitis (AS) have been revealed with strong data. As such, to target the allosteric site of ERAP1 exhibits a therapeutic potential in the treatment of AS. In this paper, 9,800 ligands from “FDA-Approved Drugs'', “World-not-FDA Approved Drugs'', and “Drugs in Clinical Trials'' datasets of ZINC15 database were screened to the allosteric site of ERAP1. The best scored drugs are filtered with ADME analysis, the toxicity and bioactivity profiles of the discovered drugs and the known inhibitors were investigated. Results revealed that ZINC000100052688 (Ventavis), ZINC000004217466, and ZINC000024760115 (Dactolicib) follow the Lipinski’s rule of five and have -10.0 kcal/mole, -9.8 kcal/mole, and -9.7 kcal/mole binding affinities to allosteric site of ERAP1, respectively. Furthermore, ZINC000004217466 is the most promising since it has high protease and enzyme inhibitory activity with no toxicity. Due to that to date, only few chemical ligands recognizing ERAP1 regulatory site have been synthesized, to reveal possible repurposable drugs is quite promising, and ZINC000004217466 is the best candidate among 9,800 drugs since it has rather binding affinity, proper chemical properties, no toxicity, and high bioactivity in the inhibition of ERAP1 regulatory site.Article Selective Binding Profiles of Curcumin Derivatives To G-Quadruplex (g4) Structures Found in Human Oncogene Promoters(DergiPark, 2024) Portakal, Hüseyin SaygınG-Quadruplex (G4) structures are special significant DNA topologies formed by accumulation of G-tetrads which are planar structures of four guanine residues interacting with hydrogen bonds through Hoogsten edges around monovalent cations such as potassium (K) or sodium (Na). While these special topologies are mostly observed in telomere regions, they might be found over regulatory regions of the genes such as promoter, enhancer etc. In addition, since that various oncogenes carry G4 structures over their promoters, it’s highlighted that G4s have significant role over cancer prognosis through regulation of expression level. To date, binding profiles of curcumin having great antioxidant and anti-inflammatory properties and its derivatives to G4s found in telomere regions and promoter of c-Myc were discovered. As such, to discover selective binding profiles of curcumin derivatives to G4s found in promoters of various oncogenes such as c-Myc, c-KIT, hTERT, RET, VEGF, and PARP1 have quite potential in the drug design for several cancer types. In light of these information, 18 curcumin derivatives from ZINC15 database were docked to related G4 structures. ADME and toxicity properties of all derivatives were analyzed and biological reactivity as well as molecular electrostatic surface potential (MESP) features of totally 4 derivatives (C11, C13, C14, and C15) exhibiting selective binding pattern to certain G4s were analyzed with density functional theory (DFT) method. © (2024), (DergiPark). All rights reserved.Article Citation - Scopus: 3Discovery of Repurposable Drugs in the Combination Therapy of Breast Cancer: a Virtual Drug Screening Study(DergiPark, 2024) Kırmızıay, E.; Demir, R.; Öğütçü, C.; Portakal, H.S.Cathepsin D (Cat D) is a lysosomal aspartic acid protease encoded by CTSD gene and has significant biological roles such as degradation of extracellular and intracellular proteins, regulation of apoptosis, hormone processing, antigen processing etc. Furthermore, it is overexpressed by breast cancer cells and it acts a role in many processes affecting the cancer prognosis such as metastasis, angiogenesis, invasion, and drug resistance through regulation of the metabolic pathways and digesting the extracellular matrix (ECM) proteins. Due to that there is no drug targeting Cat D in clinical trial phases, a virtual drug screening in order to reveal possible drugs with high Cat D inhibitory activity from a library composed of 12, 111 ligands is carried out with this study. Results have demonstrated that ZINC000003922429 (Adozelesin), ZINC000012358610 (Phthalocyanine), ZINC000051951669 (Bemcentinib), ZINC000003786250 (YM022), and ZINC000150338819 (Ledipasvir) have high binding affinity to Cat D. Among these chemical ligands, YM022 from Drugs in Clinical Trials dataset has been evaluated as most promising one that might be repurposed in the treatment of breast cancer due to its high affinity, convenient ADME and Toxicity properties, and highest bioactivity profiles. However, the possible activity of YM022 should be analyzed with further molecular dynamics (MD) simulations, in vitro and in vivo studies. © (2024), (DergiPark). All rights reserved.Article Virtual Drug Screening for P65/Rela Subunit of Nf-Κb: Promising Repurposable Drugs in the Treatment of Stress-Based Diseases(Istanbul Univ, Fac Pharmacy, 2023) Portakal, Hüseyin SaygınBackground and Aims: Although NF-kappa B is composed of five subunits, RelA receives much more attention due to fact that its expression level is regulated under various stress conditions, such as exposure to radiation, reactive oxygen species (ROS), hypoxia, pathogens, and inflammatory cytokines, as well as regulating many inflammatory, proliferation, and apoptosis genes. To date, many pieces of evidence have demonstrated that RelA plays a significant role in in the prognosis of various proliferative and inflammatory diseases. Therefore, the design of novel inhibitors and the discovery of repurposable drugs are considered promising approaches in the treatment of RelA-based diseases.Methods: A drug library including a total of 12,111 ligands has been screened for the RelA subunit of NF-kappa B. The sufficiency of the study's strategy has been revealed by analysis of commercially available inhibitors and re-docking applications.Results: Findings demonstrate that ZINC000096928979 (Deleobuvir), ZINC000012503187 (Conivaptan), and ZINC000003974230 ligands have the highest binding affinity to RelA. Furthermore, many ligands with structural similarities to Valstar, Ergotamine drugs and Benzo[a]pyrene-7,8-Diol metabolite have been discovered.Conclusion: While the ligands with the highest binding affinities could be repurposed in the treatment of RelA-based diseases, the structures of the ligands exhibiting similarity with Valstar, Ergotamine, and Benzo[a]pyrene-7, 8-D may be used as a scaffold in structure-based drug design studies. The stability of the interactions between the ligands and the receptor should be analyzed with further Molecular Dynamics Simulations (MD) studies and the possible ligands should be investigated by both in vitro and in vivo applications.
