1- Summary of the 2025 Publication Outputs of Prof. Dr. İsmail YILMAZ’s Research Group
In line with our university's strategic goals aimed at strengthening research capacity, Prof. Dr. İsmail YILMAZ and his research team have recently exhibited remarkable academic performance through their scientific studies. High-quality publications in international, high-impact, peer-reviewed journals and successfully completed research projects reinforce the team's leading position in the field of sensor chemistry. These studies, grounded in interdisciplinary collaborations, not only provide original contributions to the relevant research field but also significantly increase our university's scientific visibility and impact. Prof. Dr. Nurcan Şenyurt Tüzün, with her work in computational chemistry, and Asst. Prof. Dr. Abdulhalim Kılıç, with his work in intracellular imaging, along with their respective research teams, have made significant contributions to these research outputs. The publication outputs for the year 2025 are as follows:
M.I. Gunduz, E. Ozdemir, Y. Alcay, E. Yilmaz, O. Yavuz, N. Ejder, B. Kura, N.Ş. Tuzun, I. Yilmaz, Innovative molecular architecture of a new Hg2+/Cu2+-dual chemosensor based on functionalizable chromenylium-cyanine framework, Microchemical Journal, 220 (2026) 116340. https://doi.org/10.1016/J.MICROC.2025.116340.
In this study, a novel NIR chromenylium-cyanine sensor (NIR9) capable of detecting Hg2+ and Cu2+ ions with high selectivity was developed. The sensor, which exhibits a turn-on fluorescence signal and color change for Hg2+, and a decrease in absorbance for Cu2+, yielded successful results in real, environmental, and biological samples and enabled detection via smartphone.
O. Yavuz, B. Yıldız, E. Ahmetali, H. Aribuga, U. Ertugral, B. Kura, N.Ş. Tuzun, M.K. Şener, I. Yilmaz, A new asymmetric phthalocyanine-based chemosensor for the detection of ultra trace amount of copper (II) ions in environmental samples: comprehensive complex characterization and DFT analysis, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 346 (2026) 126935. https://doi.org/10.1016/J.SAA.2025.126935.
In this publication, the asymmetric phthalocyanine-based PCA-ZnPc-5 sensor was developed, which selectively determines Cu2+ ions at nanomolar levels. The sensor exhibited a remarkably short response time to Cu2+ ions and a high binding constant, providing analysis with high recovery in environmental samples.
M. Kaplan, O. Yavuz, Y. Alcay, I. Yilmaz, Development of a new aminophenol-extended naphthoquinone-based chemical sensor with superior performance and easy accessibility for on-site and instantaneous determination of Cu2+ ions in selected environmental and food samples, Food Chemistry, 491 (2025) 145182. https://doi.org/10.1016/J.FOODCHEM.2025.145182.
In this study, a novel aminophenol-derived naphthoquinone-based colorimetric sensor (APNQ) was synthesized. The sensor detected Cu2+ ions rapidly with a very low detection limit, provided high-accuracy analysis in water and fruit samples, and enabled on-site measurement using a smartphone.
V. Basan, Y. Alcay, E. Ozdemir, M.I. Gunduz, B. Kura, N.Ş. Tuzun, C. Cil, A. Kilic, I. Yilmaz, Architecture of a novel NIR and switch-on fluorescent chemosensor based on mercapto propanehydrazide-functionalized chromenylium-cyanine for the quantification of mercury(II) in environment and living cells, Spectrochimica Acta Part A: Molecular and BiomolecularSpectroscopy, 329 (2025) 125589. https://doi.org/10.1016/J.SAA.2024.125589.
In this study, a new chromenylium-cyanine derivative Hg2+ sensor named NIR8 was developed. The sensor exhibited a rapid response, a low detection limit, and a distinct color change; it was successfully applied for the determination of Hg2+ in water samples and cells.
O. Yavuz, M. Kaplan, E. Ozdemir, Y. Alcay, N.Ş. Tuzun, I. Yilmaz, A new phthalocyanine probe with superior analytical performance for visual and fluorometric detection of thiosulfate in real samples, Microchemical Journal, 210 (2025) 112975. https://doi.org/10.1016/J.MICROC.2025.112975.
In this research, a novel phthalocyanine probe (Q-DMAPZnPc) was developed that selectively and rapidly detects S2O32- ions. The study provided dual-channel (UV-Vis and fluorescence) detection and enabled on-site analysis via color change.
N. Ejder, K. Karaoglu, Z. Levent, Y. Alcay, E. Ozdemir, O. Yavuz, K. Kaya, M. Kopar, N.Ş. Tuzun, I. Yilmaz, Colorimetric and fluorimetric sensing of trace amount of Hg2+ in real samples by a new rhodamine B-based Schiff base probe: Smartphone, living cell applications and DFT calculation, Journal of Molecular Structure, 1321 (2025) 139687. https://doi.org/10.1016/J.MOLSTRUC.2024.139687.
In this study, a rhodamine B-based schiff base capable of detecting very low levels of Hg2+ ions was synthesized. The probe exhibited high sensitivity towards Hg2+ ions through both color change and fluorescence methods. Furthermore, it demonstrated successful results in Hg2+ analysis in real water samples and A549 cells.
2. A research team including Berna Dogan reported new findings in ACS Omega, presenting a pharmacophore- guided drug repurposing strategy to identify inhibitors of USP7, a key cancer-related enzyme. By screening 6,654 FDA-approved and investigational compounds using structure-based pharmacophore models and advanced molecular simulations, the team highlighted 12 promising drug candidates—such as carafiban, xantifibrate, etofylline clofibrate, and puromycin—with strong predicted binding affinities and potential anticancer activity. These results provide a valuable framework for accelerating the development of new USP7-targeted therapies and support future experimental validation.
3. Three active U.S. patents listing Berna Dogan as an inventor have been granted under the title “Physics-driven discovery of novel small therapeutic compounds for use as a BCL-2 inhibitor.” (US12435074B2, US12384746B2, US12398128B2). The patents cover newly designed small therapeutic molecules proposed as potent BCL-2 inhibitors, offering a novel approach to targeting apoptosis dysregulation—one of the central mechanisms driving cancer progression and treatment resistance. The inventions introduce physics-guided molecular design strategies that yield new BH3-mimetic scaffolds with the potential to overcome limitations associated with current BCL-2 inhibitors. These patents represent a significant contribution to anticancer drug discovery and provide a strong foundation for future preclinical development.
4. Bee bread-chitosan films for food packaging by Büşra İpek, Zeynep Kalaycıoğlu, Emrah Torlak, Gülşen Akın-Evingür, F. Bedia Erim
Researchers from Istanbul Technical University and collaborating institutions have developed a ground breaking biodegradable food packaging material by incorporating bee bread extract into chitosan films. This pioneering study highlights a nature-derived technology that strengthens food safety, minimizes waste, and reduces reliance on petroleum-based plastics—all while adding nutritional and antimicrobial value to packaged foods.
Each year, more than 400 million tons of plastic waste are generated worldwide, and nearly 40% comes from food packaging. Conventional plastics persist in the environment for centuries, contributing to severe ecological damage. Biopolymer-based films, such as chitosan derived from chitin in crustacean shells, offer a biodegradable and environmentally friendly alternative. Chitosan itself is already known for its biocompatibility and inherent antibacterial properties—but integrating bee-based bioactives unlocks new functional benefits.
Bee bread—a fermented bee product rich in phenolics, organic acids, amino acids, vitamins, and minerals—was selected as a natural active agent. When incorporated into chitosan films, the resulting material (BB-Chit) demonstrated notable structural and functional improvements compared to pure chitosan films. Results showed a 2.2-fold increase in mechanical stiffness (Young’s modulus), enhanced tensile strength, and strong microstructural compatibility confirmed by FTIR and SEM analyses.
Beyond durability, the films exhibited remarkable biological activity. In antibacterial tests, the BB-Chit films significantly reduced populations of Staphylococcus aureus and Escherichia coli—two common food-borne pathogens—outperforming both pure chitosan films and polypropylene controls.
Most importantly, real-food testing using fresh apple slices demonstrated superior shelf-life extension. While unprotected or purely chitosan-covered apples browned and shrank noticeably within days, samples sealed with the bee bread-enhanced film remained visually fresher, retaining both moisture and color after 10 days.
This study marks the first reported integration of bee bread into chitosan-based films, offering a promising step forward for next-generation sustainable packaging solutions.