Open Access. Powered by Scholars. Published by Universities.®
Articles 1 - 6 of 6
Full-Text Articles in Entire DC Network
Sars-Cov-2 Main Protease Targeting Potent Fluorescent Inhibitors: Repurposing Thioxanthones, Gönül Saadet Batibay, Eyüp Meti̇n
Sars-Cov-2 Main Protease Targeting Potent Fluorescent Inhibitors: Repurposing Thioxanthones, Gönül Saadet Batibay, Eyüp Meti̇n
Turkish Journal of Chemistry
The coronavirus disease, COVID-19, is the major focus of the whole world due to insufficient treatment options. It has spread all around the world and is responsible for the death of numerous human beings. The future consequences for the disease survivors are still unknown. Hence, all contributions to understand the disease and effectively inhibit the effects of the disease have great importance. In this study, different thioxanthone based molecules, which are known to be fluorescent compounds, were selectively chosen to study if they can inhibit the main protease of SARS-CoV-2 using various computational tools. All candidate ligands were optimized, molecular …
Virtual Screening, Drug-Likeness Analysis, And Molecular Docking Study Of Potentialsevere Acute Respiratory Syndrome Coronavirus 2 Main Protease Inhibitors, Nikola Nedeljkovic, Milos Nikolic, Ana Stankovic, Nevena Jeremic, Dusan Tomovic, Andriana Bukonjic, Gordana Radic, Marina Mijajlovic
Virtual Screening, Drug-Likeness Analysis, And Molecular Docking Study Of Potentialsevere Acute Respiratory Syndrome Coronavirus 2 Main Protease Inhibitors, Nikola Nedeljkovic, Milos Nikolic, Ana Stankovic, Nevena Jeremic, Dusan Tomovic, Andriana Bukonjic, Gordana Radic, Marina Mijajlovic
Turkish Journal of Chemistry
Due to the length of time required to develop specific antiviral agents, the World Health Organization adopted the strategy of repurposing existing medications to treat Coronavirus disease 2019 infection. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease is possible biological target for potential antiviral drugs. We selected various compounds from PubChem database based on the structure of main protease inhibitors in Protein Data Bank database. Ten compounds showed nontumorigenic and nonmutagenic potential and met Egan's and Lipinski's rules. Molecular docking analysis was performed using AutoDock Vina software. Based on number and type of key binding interactions, as well as …
Structural Rearrangement Of Neisseria Meningitidis Transferrin Binding Protein A (Tbpa) Prior To Human Transferrin Protein (Htf) Binding, Gi̇zem Nur Duran, Mehmet Özbi̇l
Structural Rearrangement Of Neisseria Meningitidis Transferrin Binding Protein A (Tbpa) Prior To Human Transferrin Protein (Htf) Binding, Gi̇zem Nur Duran, Mehmet Özbi̇l
Turkish Journal of Chemistry
Gram-negative bacterium Neisseria meningitidis, responsible for human infectious disease meningitis, acquires the iron (Fe3+) ion needed for its survival from human transferrin protein (hTf). For this transport, transferrin binding proteins TbpA and TbpB are facilitated by the bacterium. The transfer cannot occur without TbpA, while the absence of TbpB only slows down the transfer. Thus, understanding the TbpA-hTf binding at the atomic level is crucial for the fight against bacterial meningitis infections. In this study, atomistic level of mechanism for TbpA-hTf binding is elucidated through 100 ns long all-atom classical MD simulations on free (uncomplexed) TbpA. TbpA protein underwent conformational …
Why Protein Conformers In Molecular Dynamics Simulations Differ From Their Crystal Structures: A Thermodynamic Insight, Fi̇li̇ppo Pullara, Mao Wenzhi, Mert Gür
Why Protein Conformers In Molecular Dynamics Simulations Differ From Their Crystal Structures: A Thermodynamic Insight, Fi̇li̇ppo Pullara, Mao Wenzhi, Mert Gür
Turkish Journal of Chemistry
Conformers generally deviate structurally from their starting X-ray crystal structures early in molecular dynamics (MD) simulations. Studies have recognized such structural differences and attempted to provide an explanation for and justify the necessity of MD equilibrations. However, a detailed explanation based on fundamental physics and validation on a large ensemble of protein structures is still missing. Here we provide the first thermodynamic insights into the radically different thermodynamic conditions of crystallization solutions and conventional MD simulations. Crystallization solution conditions can lead to nonphysiologically high ion concentrations, low temperatures, and crystal packing with strong specific protein--protein interactions, not present under physiological …
Pore Length- And Ion Concentration-Dependent Ionic Current In Cylindrical Nanopores: An Atomistic Molecular Dynamics Study, Nazar İleri̇ Ercan
Pore Length- And Ion Concentration-Dependent Ionic Current In Cylindrical Nanopores: An Atomistic Molecular Dynamics Study, Nazar İleri̇ Ercan
Turkish Journal of Chemistry
The sensing of individual molecules as they pass through nanopores under an external field is a popular research field. The approach is simply based on the detectable temporary blockades in the ionic current as the molecules pass through the nanopores. These signatures of the current have been shown to be a function of nanoparticle and nanopore size and geometry as well as the external electric field. However, models developed in this context fail to predict the experimentally observed behavior in technologically important shorter nanopores. Here we present atomistic molecular dynamics simulation results from colloidal nanoparticle translocation through mid-to-low aspect ratio …
Exploring Distinct Binding Site Regions Of \Beta_2-Adrenergic Receptor Via Coarse-Grained Molecular Dynamics Simulations, Si̇bel Çakan, Ebru Demet Akdoğan
Exploring Distinct Binding Site Regions Of \Beta_2-Adrenergic Receptor Via Coarse-Grained Molecular Dynamics Simulations, Si̇bel Çakan, Ebru Demet Akdoğan
Turkish Journal of Chemistry
\beta_2-Adrenergic receptor (\beta_2AR) is a G protein- coupled receptor that is highly flexible and able to recognize a wide range of ligands through its conformational variations. Active and inactive conformations revealed by recent crystallographic experiments do not provide a complete dynamic picture of the receptor, especially in the binding site. In this study, molecular dynamics (MD) simulation through a residue-based coarse-grained model is used as an alternative and efficient method to explore a wider conformational search space. The system was composed of \beta_2AR embedded into a 1-palmitoyl-2-oleoyl-phosphatidylcholine membrane bilayer with surrounding water. A total of 6 \mu s of simulation …