Publications

Dervişoğlu Özdemir, C., Duran, G.N., Fındık, V., Özbil, M., Sağ Erdem, S. “Computational Insights into Iron Coordination Disruption in the Human Transferrin–Neisseria meningitidis Bacterial Protein Complex.” Inorganics, 13, 384, 2025. https://doi.org/10.3390/inorganics13120384

Eren, M.C., Güngör, G., De Jonghe, S., Jochmans, D., Özbil, M., Neyts, J., Kaptein, S., Şenol, H., Köse, A., Gezginci, M.H., Karalı, N. "Antiviral activities of phenylalanine derivatives carrying carboxylic acid bioisosteres against chikungunya and parainfluenza virus type 3" Bioorganic & Medicinal Chemistry, 130, 118343, 2025.
https://www.sciencedirect.com/science/article/pii/S0968089625002846

Özbil, M. "Molecular Dynamics Studies in the Pursuit of Excellent Artificial Metalloenzymes" In: Topics in Organometallic Chemistry. Springer, Berlin, Heidelberg. 2025. https://doi.org/10.1007/3418_2025_129

Ozbek, T., Demir, H., Dokuz, S., Tasdurmazli, S., Ozbey, U., Ozbil, M., Topuzogullari, M., Cinar, I., Karamese, M., Karamese, S.A., Acar, S., Bayrak, O.F., Cadirci, E. "Phage-inspired targeting of antibiotic-loaded polymeric micelles for enhanced therapeutic efficacy against monomicrobial sepsis" Journal of Controlled Release, 280, 773-786, 2025.  ​ www.sciencedirect.com/science/article/pii/S0168365925001488

Ozleyen, A., Duran, G.N., Donmez, S., Ozbil, M., Doveston, R.G., Tumer, T.B. “Identification and inhibition of PIN1-NRF2 protein–protein interactions through computational and biophysical approaches” Scientific Reports, 15, 8907, 2025. www.nature.com/articles/s41598-025-89342-0​  

Dönmez, S., Lapinskaite, R., Atalay, H.N., Tokay, E., Kockar, F., Rycek, L., Özbil, M., Tumer, T.B. “Selagibenzophenone B and Its Derivatives: SelB-1, a Dual Topoisomerase I/II Inhibitor Identified through In Vitro and In Silico Analyses”, ACS Bio & Med Chem Au, 4(4), 178-189, 2024. https://pubs.acs.org/doi/10.1021/acsbiomedchemau.4c00027​

Atiq, F., Rawley, O., O'Sullivan, J.M., Özbil, M., Doherty, D., Cooke, N., Terraube, V., Chion, A., Amin, A., Hulshof, A., Baci, B., Byrne, C., Aburawi, H., Lillicrap, D., O'DOnnell, J.S. "R1205H (Vicenza) causes conformational changes in the VWF-D’D3 domains and enhances VWF binding to clearance receptors LRP1 and SR-A1", Journal of Thrombosis and Haemostasis, 22(10), 2752-2760, 2024.  https://www.sciencedirect.com/science/article/pii/S1538783624003854?via%3Dihub​

Dokuz, S., Tasdurmazlı, S., Acar, T., Duran, G.N., Ozdemir, C., Ozbey, U., Ozbil, M., Karadayı, S., Bayrak, O.F., Derman, S., Chen, J.Y-S., Ozbek, T. "Evaluation of Bacteriophage ϕ11 host recognition protein and its host-binding peptides for diagnosing/targeting of Saphylococcus aureus infections", International Journal of Antimicrobial Agents,64(2), 107230, 2024.  www.sciencedirect.com/science/article/pii/S0924857924001481?via%3Dihub

Antika, G., Cinar,Z.Ö., Dönmez, S., Seçen, E., Özbil, M., Prandi, C., Tumer, T.B. “Effects of Strigolactones on NLRP3 Activation, Nitrosative Stress, and Antioxidant Mox Phenotype: In Vitro and In Silico Evidence” ACS Bio & Med Chem Au, 4(3), 131-136, 2024. pubs.acs.org/doi/10.1021/acsbiomedchemau.3c00063

​Soylu-Eter, Ö., Göktaş, F., Duran, G. N., Özbil, M., Karalı, N. L. "1H-Indole-2,3-dione 3-thiosemicarbazones carrying a 4-sulfamoylphenyl moiety with selective antiviral activity against Reovirus-1"  Acta. Chimica. Slov. ,71(2), 215-225, 2024.    https://acsi-journal.eu/index.php/ACSi/article/view/8589         

Çapan, Ö.Y., Yapıcı, Z., Özbil, M., Çağlayan, H.S. “Exome data of developmental and epileptic encephalopathy patients reveals de novo and inherited pathologic variants in epilepsy-associated genes” Seizure-Eur. J. Epilep., 116, 51-64, 2024.   www.sciencedirect.com/science/article/pii/S1059131123001620 

Soylu-Eter, Ö., Duran, G.N., Özbil, M., Göktaş, F., Cihan-Üstündağ, G., Karalı, N. “Antiviral activity and molecular modeling studies on 1H-indole-2,3-diones carrying a naphthalene moiety” J. Mol. Struc., 1281, 135100, 2023.     www.sciencedirect.com/science/article/abs/pii/S0022286023002016?via%3Dihub

Çubuk, H., Özbil, M., “In silico analysis of SARS-CoV-2 spike protein N501Y and N501T mutation effects on human ACE2 binding” J. Mol. Graph. Model., 116, 108260, 2022. ​www.sciencedirect.com/science/article/pii/S1093326322001395?dgcid=author

Antika, G., Cinar, Z.Ö., Seçen, E., Özbil, M., Tokay, E., Köçkar, F., Prandi, C., Tumer, T.B. “Strigolactone Analogs: Two New Potential Bioactiphores For Gliblastoma” ACS Chem. Neurosci., 13, 5, 572–580, 2022.  ​pubs.acs.org/doi/abs/10.1021/acschemneuro.1c00702

Duran, G.N., Özbil, M. “Structural rearrangement of Neisseria meningitidis transferrin binding protein A (TbpA) prior to human transferrin protein (hTf) binding” Turk. J. Chem, 45, 1146-1154, 2021.     journals.tubitak.gov.tr/cgi/viewcontent.cgi?article=1073&context=chem

Cubuk, H., Ozbil, M., Hatir, P.C. “Computational analysis of functional monomers used in molecular imprinting for promising COVID-19 detection” Comput. Theor. Chem., 11325, 2021.      www.sciencedirect.com/science/article/pii/S2210271X21000748 

Çubuk, H., Özbil, M. “Comparison of Clinically Approved Molecules on SARS-CoV-2 Drug Target Proteins: A Molecular Docking Study” Turk. J. Chem, 45, 35-41, 2021.   journals.tubitak.gov.tr/cgi/viewcontent.cgi?article=1146&context=chem

Fareed, F.M.A, Korulu, S., Özbil, M., Çapan, Ö.Y. “HNF1A-MODY Mutations in Nuclear Localization Signal Impair HNF1A-Import Receptor KPNA6 Interactions” Protein J., 40, 512-521, 2021.  ​link.springer.com/article/10.1007/s10930-020-09959-0

Turk‐Erbul, B., Karaman E.F., Duran, G.N., Ozbil, M., Ozden, S., Goktas, F. “Synthesis, in vitro cytotoxic and apoptotic effects, and molecular docking study of novel adamantane derivatives” Arch Pharm. e2000256, 2021.  https://onlinelibrary.wiley.com/doi/full/10.1002/ardp.202000256 

​Sevinçli, Z.Ş., Duran, G.N., Özbil, M., Karalı, N. “Synthesis, molecular modeling and antiviral activity of novel 5-fluoro-1H-indole-2,3-dione 3-thiosemicarbazones ”  Bioorg. Chem., 2068, 31499, 2020.   https://onlinelibrary.wiley.com/doi/full/10.1002/ardp.201900028​ 

Göktaş, F., Özbil, M., Cesur, N., Vanderlinden, E., Naesens, L., Cesur, Z.  “Novel N‐(1‐thia‐4‐azaspiro[4.5]decan‐4‐yl)carboxamide derivatives as potent and selective influenza virus fusion inhibitors” Arch. Pharm. Chem. Life Sci., e1900028, 2019.      https://onlinelibrary.wiley.com/doi/full/10.1002/ardp.201900028

Özbil, M. “Computational investigation of influenza A virus M2 protein inhibition mechanism by ion channel blockers” Turk. J. Chem., 43, 335-351, 2019.  journals.tubitak.gov.tr/chem/vol43/iss1/27/

Ozalp, L., Erdem, S.S., Yüce-Dursun, B., Mutlu, Ö., Özbil, M. “Computational insight into the phthalocyanine-DNA binding via docking and molecular dynamics simulations” Comp. Biol. Chem., 77, 87-96, 2018.   https://www.sciencedirect.com/science/article/pii/S1476927118303785

Ahmed, L., Zhang, Y., Block, E., Buehl, M., Corr, M.J., Cormanich, R.A., Gundala, S., Matsunami, H., O’Hagan, D., Ozbil, M., et al. “Molecular mechanism of activation of human musk receptors OR5AN1 and OR1A1 by (R)-muscone and diverse other musk-smelling compounds”. Proc, Natl. Acad. Sci.,USA, 115 (17) E3950-E3958, 2018. www.pnas.org/doi/10.1073/pnas.1713026115

Lee, H.J., Korshavn, K.J., Nam, Y., Kang, J., Paul, T.J., Kerr, R.A., Youn, I.S., Ozbil, M., et al. “Structural and Mechanistic Insights into Development of Chemical Tools to Control Individual and Inter-Related Pathological Features in Alzheimer’s Disease”. Chem. Eur. J., 23, 2706 –2715, 2017. ​https://onlinelibrary.wiley.com/doi/abs/10.1002/chem.201605401

Berber, E., Ozbil, M., et al. “Functional Characterization of the Type 1 VWD candidate VWF gene variants: p.M771I, p.L881R , p.P1413L, and p.Q1475X”. Thrombosis and Haemostasis, doi: 10.2450/2016.0034-16, 2016. ashpublications.org/blood/article/120/21/97/87426/Functional-Characterization-of-the-Type-1-VWD

Paul, T.J., Barman, A., Ozbil, M., Bora, R.P., Zhang, T., Sharma, G., Hoffmann, Z. and Prabhakar, R. “Mechanisms of Peptide hydrolysis by Aspartyl and Metalloproteases”, Phys. Chem. Chem. Phys., 18, 24790-24801, 2016.    http://pubs.rsc.org/en/content/articlelanding/2016/cp/c6cp02097f#!divAbstract

Block, E., Jang, S., Matsunami, H., Batista, V.S., Dethier, B., Ertem. M.Z., Gundala, S., Jiang, H., Li, S., Li, Z., Lodge, S.N., Ozbil, M., Pan, Y., Penalba, S.F., Sekharan, S., and Zhuang, H. “Implausibility of the vibrational theory of olfaction”. Proc, Natl. Acad. Sci.,USA, 112, p: E2766–E2774, 2015. http://www.pnas.org/content/112/21/E2766.long

Derrick, J.S., Kerr, R.A., Nam, Y., Oh, S.B., Lee, H.J., Earnest, K.G., Suh, N., Peck, K.L., Ozbil, M., Korshavn, K.J., Ramamoorthy, A., Prabhakar, R., Merino, E.J., Shearer, J., Lee, J-Y., Ruotolo, B.T., and Lim, M.H. “A redox-active, compact tool for the crosslinking of amyloidogenic peptides into nontoxic, off-pathway aggregates: in vitro and in vivo efficacy and molecular mechanisms”. J. Am. Chem. Soc., 137(46), p: 14785-14797, 2015.   http://pubs.acs.org/doi/abs/10.1021/jacs.5b10043

Song, E.S., Ozbil, M., Zhang, T., Sheetz, M., Lee, D., Tran, D., Li, S., Prabhakar, R., Hersh, L.B., and Rodgers, D.W. “An Extended Polyanion Activation Surface in Insulun Degrading Enzyme”. PLOS One, 10(7):e0133114, 2015.   http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0133114

Zhang, T., Ozbil, M., Barman, A., Paul, T.J., Bora, R.P., Barman, A., and Prabhakar, R. “Theoretical Insights into the Functioning of Metallopeptidases andtheir Synthetic Analogues”. Acc. Chem. Res. (invited article), 48(2), p: 192-200, 2015. http://pubs.acs.org/doi/abs/10.1021/ar500301y

Cook, N.P., Ozbil, M., Katsampes, C., Prabhakar, R., and Martí, A.A. “Unraveling the Photoluminescence Response of Light-Switching Ruthenium(II) Complexes Bound to Amyloid-β”. J. Am. Chem. Soc., 135 (29), p: 10810–10816, 2013.  (Highlighted in C&EN NEWS, 90, 21, p:27, July 22 Issue, 2013). http://pubs.acs.org/doi/abs/10.1021/ja404850u

Liu, Y., Mukherjee, A., Nahumi, N., Ozbil, M., Brown, D., Angeles-Boza, A.M., Dooley, D.M.,   Prabhakar, R., and Roth, J.P. “Experimental and Computational Evidence of Metal-O2 Activation in a Copper Amine Oxidase”. J. Phys. Chem. B, 117 (1), p: 218–229, 2013. http://pubs.acs.org/doi/abs/10.1021/jp3121484

Ozbil, M., Barman, A., Bora, R.P., and Prabhakar, R. “Perspective: Computational Insights into Dynamics of Protein Aggregation and Enzyme-Substrate Interactions”. J. Phys. Chem. Lett., 3, p: 3460-3469, 2012.http://pubs.acs.org/doi/abs/10.1021/jz301597k

Kurouski, D., Washington, J., Ozbil, M., Prabhakar, R., Shekhtman, A., and Lednev, I., “Disulfide Bridges Remain Intact While Native Insulin Converts into Amyloid Fibrils”. PLoS ONE, 7(6), e36989, 2012.http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0036989

Zhu, X., Barman, A., Ozbil, M., Zhang, T., Li, S. and Prabhakar, R., “Mechanism of Peptide Hydrolysis by Co-catalytic Metal Centers Containing Leucine Aminopeptidase Enzyme: A DFT Approach”. J. Biol. Inorg. Chem., 17(2), p: 209-222, 2011. http://link.springer.com/article/10.1007%2Fs00775-011-0843-2

Bora, R.P., Barman, A., Zhu, X., Ozbil, M., and Prabhakar, R., “Which One Among Aspartyl Protease, Metallopeptidase, and Artificial Metallopeptidase is the Most Efficient Catalyst in Peptide Hydrolysis?”. J. Phys. Chem. B, 114, p: 10860-10875, 2010. http://pubs.acs.org/doi/abs/10.1021/jp104294x

Bora, R.P., Ozbil, M., and Prabhakar, R., “Elucidation of Insulin Degrading Enzyme Catalyzed Site Specific Hydrolytic Cleavage of Amyloid β-Peptide: A Comparative DFT Study”. J. Biol. Inorg. Chem., 15(40), p: 485-495, 2010.http://link.springer.com/article/10.1007%2Fs00775-009-0617-2​​

Özbil, M., Duran G, Dervişoğlu, C., Erdem, S. “Understanding Fe3+ Theft by Neisseria Meningiditis: A Comprehensive Computational Study”, EuChem SCompChem 2023, Thessaloniki, Greece, August 27-31, 2023.

Özbil, M. “The applications of computational techniques in biotechnological research”, 1st International Advances in Molecular Biology, İstanbul, Turkey, September 19-22, 2022. 

Özbil, M. “Neisseria meningitidis Transferrin Binding Protein A (TbpA) Rearranges Itself For Binding Human Transferrin Protein (hTf)”, 3rd Euroasia Biochemical Approaches & Technologies Congress, Antalya, Turkey, November 4-7, 2021.

​Özbil, M. “Computational Construction of Neisseria Meningiditis Fe3+ Transfer Triple Complex”, 2nd Euroasia Biochemical Approaches & Technologies Congress, Antalya, Turkey, October 26-30, 2019.     

Özbil, M. “Antiviral Bileşiklerin Herpes simpleks Virüslerine Bağlanmalarının in silico Analizi”, 31. Ulusal Kimya Kongresi, Istanbul, Turkey, September 10-14, 2019.

Özbil, M. “Computational Investigation on Influenza A Virus M2 Protein Inhibition”, 1st Euroasia Biochemical Approaches & Technologies Congress, Antalya, Turkey, October 27-30, 2018.

Özbil, M. “Chemical and Structural Effects of Inhibitor Moleules on Influenza A Virus M2 Proton Channel” 11th European Conference of Theoretical and Computational Chemistry, Barcelona, Spain, September 4-7, 2017. 

Özbil, M. “Investigating Inhibitor Binding Sites on Influenza A Virus M2 Protein” 4th International BAU Drug Design Congress, Istanbul, Turkey, October 13-15, 2016.

Ozbil, M. and Prabhakar, R. “Mechanisms of Stimulation of Insulin Degrading Enzyme (IDE) and Substrate Specificity of Neprilysin (NEP)” ACS National Meeting, New Orleans, LA, April 7-11, 2013. (selected for Chairs` Prime Choices Section)

Ozbil, M. and Prabhakar, R., “Investigating The Activation of Insulin Degrading Enzyme (IDE) and Selectivity of Neprilysin (NEP)” FAME-ACS Florida Section Meeting,Tampa, FL, May 17-20, 2012. 

Ozbil, M. and Prabhakar, R., “Investigating The Peptide Bond Hydrolysis by Neprilysin (NEP)” FAME-ACS Florida Section Meeting, Tampa, FL, May 15-18, 2011. 

Ozbil, M. and Prabhakar, R., “Computational Study of Neprilysin (NEP) and The Full Length Alzheimer`s Amyloid Beta (Aβ)” FAME-ACS Florida Section Meeting, Tampa, FL, May 13-16, 2010.