Publications
- 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., in press, 2023.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. doi:10.3906/kim-2102 25 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. https://doi.org/10.1016/j.comptc.2021.113215. 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. doi:10.3906/kim-2008-35 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., 2021. doi:10.1007/s10930-020-09959-0 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., doi: 10.1039/C6CP02097F, 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
Conference Presentations
- Özbil, M. “Computational Construction of Neisseria Meningiditis Fe3+ Transfer Triple Complex”, 2nd Euroasia Biochemical Approaches & Technologies Congress, Antalya, Turkey, October 26-30, 2019.2. 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.