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    Bio-nanomaterial formation via epitaxially guided assembly and its controlling factors
    (IEEE, 2017) Eryilmaz, Esma
    Macromolecular self-assembly is a promising way of fabricating ordered structures with interesting mechanical and optical properties. Learning how to produce highly organized structures and how to mediate the organization provide technological and application wise opportunities at both macroscale and nanoscale. In this study, we worked with an extracellular matrix protein collagen onto different substrates and try to control and to manipulate the assembly process externally. The most attractive benefit of producing biomaterial via self-assembly is the ability of controlling the mechanism by external parameters from nanometer scale to millimeter. Due to the prevalence of collagen fibril in human tissue and its self-assembly ability in vitro, Collagen becomes an important bio-macro molecule frequently used in biomedical materials and tissue engineering applications in recent decades. In this work, by using two different substrates, we observed a direct influence of the surface symmetry on the resulting fibrillar network. The unidirectional and the triangular orientation of collagen molecules at nanoscale in an organized manner give insights for using the network for different purposes of biomedical and biotechnological applications.
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    In Vitro Analysis of the Co-Assembly of Type-I and Type-III Collagen
    (SPRINGER, 2017) Eryilmaz, Esma; Teizer, Winfried; Hwang, Wonmuk
    An important step towards achieving functional diversity of biomimetic surfaces is to better understand the co-assembly of the extracellular matrix components. For this, we study type-I and type-III collagen, the two major collagen types in the extracellular matrix. By using atomic force microscopy, custom image analysis, and kinetic modeling, we study their homotypic and heterotypic assembly. We find that the growth rate and thickness of heterotypic fibrils decrease as the fraction of type-III collagen increases, but the fibril nucleation rate is maximal at an intermediate fraction of type-III. This is because the more hydrophobic type-I collagen nucleates fast and grows in both longitudinal and lateral directions, whereas more hydrophilic type-III limits lateral growth of fibrils, driving more monomers to nucleate additional fibrils. This demonstrates that subtle differences in physico-chemical properties of similar molecules can be used to fine-tune their assembly behavior.
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    Multi-targeted anti-leukemic drug design with the incorporation of silicon into Nelarabine: How silicon increases bioactivity
    (ELSEVIER, 2019) Eryilmaz, Esma
    Acute Lymphoblastic Leukemia (ALL) represents 30% of all childhood cancers and children younger than 5 years old have the highest risk for developing ALL. Existing ALL drugs do not respond in approximately 20% of treatment. Therefore, drug development studies against ALL must be continued with either developing existing drugs or discovering new ones. In this study, we evaluated the U.S Food and Drug Administration (FDA) approved ALL drugs according to their physicochemical and pharmaceutical properties, and Nelarabine was found to have the highest bioactivity score. Using the key strategy of bioisosterism commonly accepted by medicinal chemists, we investigated in silico ADME properties, drug-likeness, and biological activity of new designed twenty-four compounds including Nelarabine. The results were evaluated in terms of two classifications: broad spectrum biological activity and filtering of five different drug likeness criteria of the literature including Lipinski's rule of five. We interestingly observed that silicon incorporated compounds exhibited better performance on both criteria by targeting broader spectrum of drug receptors including G-protein coupled receptor (GPCR), ion channel modulator, kinase inhibitor, protease and enzyme inhibitor and by satisfying all of five different drug-likeness criteria reported in the literature. Design compound C19 appeared as a potential drug candidate for further pharmacological research.