Research

Yuce, M., Koman, E., Sungur, F., Yazgan-Karatas, A., & Kurkcuoglu, O. (2026). A multi-stage computational pipeline and in vitro validation for the discovery of small-molecule translation inhibitors targeting the bacterial ribosome. RSC Advances, 16, 18359–18373. https://doi.org/10.1039/D6RA01785A

Yuce, M., Sungur, F., & Kurkcuoglu, O. (2026). Multiscale Modeling of the Bacterial Ribosome to Identify Potential Peptide Modulators and Their Allosteric Effects. Biochemistry. https://doi.org/10.1021/acs.biochem.5c00832

Sarica, Z., Sungur, F., & Kurkcuoglu, O. (2026). RinPy, a Python Package for Residue Interaction Network Model to Analyze Protein Structures and Predict Ligand Binding Sites. Journal of Chemical Information and Modeling. https://doi.org/10.1021/acs.jcim.6c00004

Tok, F., Özer, F., Kuzu, Z., Sıcak, Y., Kemaloğu, F., Baday, S., … Öztürk, M. (2026). Synthesis, biological evaluation and molecular docking of novel 2-pyrazoline-1-carboxamides as anti-Alzheimer agents. Future Medicinal Chemistry, 18, 1–17. https://doi.org/10.1080/17568919.2025.2594970

Doğan, M., Polat, Y., Göksu, S., Baltaş, N., Kemaloğlu, F., Baday, S., … Tok, F. (2026). Synthesis, Molecular Docking, Molecular Dynamics and DFT Studies of New Thiazole Derivatives as Dual Cholinesterase Inhibitors Against Alzheimer’s Disease. Polycyclic Aromatic Compounds, 1–25. https://doi.org/10.1080/10406638.2026.2677663

Çiçek, E., Munar, İ., Çınar, S., Başçeken, S., Monard, G., Aviyente, V., & Sungur, F. (2025). Computational insights into substrate-assisted citrullination mechanisms of PAD2 isozyme: A comparative analysis of reaction pathways. Journal of Molecular Graphics and Modelling, 140, 109107. https://doi.org/10.1016/j.jmgm.2025.109107

Güner-Yılmaz, Z. Ö., Kocaaga, B., Yılmaz, A., Balcik, M., Kurkcuoglu, O., Sungur, F., … Güner, S. F. (2025). Graphene oxide-based and porous nanocarriers for drug delivery developed with computational and experimental approaches. Surfaces and Interfaces, 76, 107860. https://doi.org/10.1016/j.surfin.2025.107860

Sarica, Z., Kurkcuoglu, O., & Sungur, F. (2025). In Silico Identification of Putative Allosteric Pockets and Inhibitors for the KRASG13D-SOS1 Complex in Cancer Therapy. International Journal of Molecular Sciences, 26, 3293. https://doi.org/10.3390/ijms26073293

Yuce, M., Ates, B., Yasar, N., Sungur, F., & Kurkcuoglu, O. (2024). A computational workflow to determine drug candidates alternative to aminoglycosides targeting the decoding center of E. coli ribosome. Journal of Molecular Graphics and Modelling, 131, 108817. https://doi.org/10.1016/j.jmgm.2024.108817

Kocaaga, B., Inan, T., Yasar, N., Yalcin, C., Sungur, F., Kurkcuoglu, O., … Arslan, H. (2024). Innovative Use of an Injectable, Self-Healing Drug-Loaded Pectin-Based Hydrogel for Micro- and Supermicro-Vascular Anastomoses. Biomacromolecules, 25, 3959–3975. https://doi.org/10.1021/acs.biomac.4c00102

Tataroğlu, M., & Sungur, F. (2023). Mechanistic insights into the challenges of organocatalytic Beckmann rearrangement reactions. Org. Biomol. Chem., 21, 1254–1263. https://doi.org/10.1039/D2OB01641A

Cicek, E., Monard, G., & Sungur, F. (2022). Molecular Mechanism of Protein Arginine Deiminase 2: A Study Involving Multiple Microsecond Long Molecular Dynamics Simulations. Biochemistry, 61, 1286–1297. https://doi.org/10.1021/acs.biochem.2c00158

Koroglu, M., Kurkcuoglu, O., & Sungur, F. (2021). Monte Carlo and Molecular Dynamics Simulations suggest controlled release of corticosteroids from mesoporous host MIL-101 (Cr). Molecular Simulation, 47, 1530–1539. https://doi.org/10.1080/08927022.2021.1991579

Yuce, M., Cicek, E., Inan, T., Dag, A., Kurkcuoglu, O., & Sungur, F. (2021). Repurposing of FDA-approved drugs against active site and potential allosteric drug-binding sites of COVID-19 main protease. Proteins: Structure, Function, and Bioinformatics, 89, 1425–1441. https://doi.org/10.1002/prot.26164

Tataroğlu, M., & Sungur, F. (2017). A computational insight into cyclopropenone activated dehydration reaction of alcohols. J Mol Graph Model, 77, 106–114. https://doi.org/10.1016/j.jmgm.2017.08.009

Kilic, H., Bayindir, S., Erdogan, E., Cinar, A. S., Konuklar, F., Bali, S., … Aviyente, V. (2017). Bismuth nitrate-promoted disproportionative condensation of indoles with cyclohexanone: a new-type azafulvenium reactivity of indole. New J. Chem., 41, 9674–9687. https://doi.org/10.1039/C7NJ01987D

Gökcan, H., Monard, G., & Konuklar, A. F. (2016). Molecular dynamics simulations of apo, holo, and inactivator bound GABA-at reveal the role of active site residues in PLP dependent enzymes. Proteins, 84, 875–91. https://doi.org/10.1002/prot.24991

Ince, H., Konuklar, A. F., Ugur, I., Ozcan, A. Ö., Sayadi, M., Feig, M., & Aviyente, V. (2015). Role of the n+1 amino acid residue on the deamidation of asparagine in pentapeptides. Molecular Physics, 113, 3839–3848. https://doi.org/10.1080/00268976.2015.1068394

Boz, E., Haşlak, P. Z., Tüzün, N., & Konuklar, A. F. (2014). A Theoretical Study On Rh(I) Catalyzed Enantioselective Conjugate Addition Reactions of Fluoroalkylated Olefins. Organometallics, 33, 5111–5119. https://doi.org/10.1021/om401112f

Gökcan, H., & Konuklar, A. F. (2014). Stereoelectronic explanations for the mechanistic details of transimination and HF elimination reactions. J Mol Graph Model, 51, 173–83. https://doi.org/10.1016/j.jmgm.2014.05.006

Yildirim, A., Konuklar, F., Catak, S., Van Speybroeck, V., Waroquier, M., Dogan, I., & Aviyente, V. (2012). Solvent-catalyzed ring-chain-ring tautomerization in axially chiral compounds. Chemistry, 18, 12725–32. https://doi.org/10.1002/chem.201200363

Gökcan, H., & Konuklar, A. F. (2012). Theoretical study on HF elimination and aromatization mechanisms: a case of pyridoxal 5’ phosphate-dependent enzyme. J Org Chem, 77, 5533–43. https://doi.org/10.1021/jo3005815

Çoban, M., & Konuklar, A. F. (2011). A computational study on the mechanism and the kinetics of urethane formation. Computational and Theoretical Chemistry, 963, 168–175. https://doi.org/10.1016/j.comptc.2010.10.017

Durak, A., Gökcan, H., & Konuklar, F. (2011). Theoretical studies on the inactivation mechanism of γ-aminobutyric acid aminotransferase. Org Biomol Chem, 9, 5162–71. https://doi.org/10.1039/c1ob05146f

Özen, C., Konuklar, A. F., & Tu?zu?n, N. (2009). Mechanistic Study on [3+2] Cycloaddition and Cyclopropanation Reactions of 1,3-Dioxepine Derivatives in the Presence of Copper(I) Catalyst. Organometallics, 28, 4964–4973. https://doi.org/10.1021/om900235a

Konuklar, F., Aviyente, V., & Haliloğlu, T. (2006). Coupling of structural fluctuations to deamidation reaction in triosephosphate isomerase by Gaussian network model. Proteins, 62, 715–27. https://doi.org/10.1002/prot.20668

Aydeniz, Y., Oguz, F., Yaman, A., Konuklar, A., Dogan, I., Aviyente, V., & Klein, R. (2004). Barriers to internal rotation around the C-N bond in 3-(o-aryl)-5-methyl-rhodanines using NMR spectroscopy and computational studies. Electron density topological analysis of the transition states. Org Biomol Chem, 2, 2426–36. https://doi.org/10.1039/B406556E

Konuklar, F., Aviyente, V., Monard, G., & Lopez, M. (2004). Theoretical Approach to the Wear and Tear Mechanism in Triosephoshate Isomerase: A QM/MM Study. The Journal of Physical Chemistry B, 108, 3925–3934. https://doi.org/10.1021/jp037791m

Aylin, F., Konuklar, S., & Aviyente, V. (2003). Modelling the hydrolysis of succinimide: formation of aspartate and reversible isomerization of aspartic acid via succinimide. Org Biomol Chem, 1, 2290–7. https://doi.org/10.1039/b211936f

Konuklar, A. F., Aviyente, V., Sen, T., & Bahar, I. (2001). Modeling the deamidation of asparagine residues via succinimide intermediates. 7, 147–160. https://doi.org/10.1007/s008940100025

Resat, H., Sungur, F., Baginski, M., Borowski, E., & Aviyente, V. (2000). Conformational properties of amphotericin B amide derivatives–impact on selective toxicity. J Comput Aided Mol Des, 14, 689–703. https://doi.org/10.1023/a:1008144208706