The novel coronavirus disease 2019 (COVID‐19) caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) still has serious negative effects on health, social life, and economics. Recently, vaccines from various companies have been urgently approved to control SARS‐CoV‐2 infections. However, any specific antiviral drug has not been confirmed so far for regular treatment. An important target is the main protease (M pro ), which plays a major role in replication of the virus. In this study, Gaussian and residue network models are employed to reveal two distinct potential allosteric sites on M pro that can be evaluated as drug targets besides the active site. Then, Food and Drug Administration (FDA)‐approved drugs are docked to three distinct sites with flexible docking using AutoDock Vina to identify potential drug candidates. Fourteen best molecule hits for the active site of M pro are determined. Six of these also exhibit high docking scores for the potential allosteric regions. Full‐atom molecular dynamics simulations with MM‐GBSA method indicate that compounds docked to active and potential allosteric sites form stable interactions with high binding free energy (∆ G bind ) values. ∆ G bind values reach −52.06 kcal/mol for the active site, −51.08 kcal/mol for the potential allosteric site 1, and − 42.93 kcal/mol for the potential allosteric site 2. Energy decomposition calculations per residue elucidate key binding residues stabilizing the ligands that can further serve to design pharmacophores. This systematic and efficient computational analysis successfully determines ivermectine, diosmin, and selinexor currently subjected to clinical trials, and further proposes bromocriptine, elbasvir as M pro inhibitor candidates to be evaluated against SARS‐CoV‐2 infections.
The novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) still has serious negative effects on health, social life, and economics. Recently, vaccines from various companies have been urgently approved to control SARS-CoV-2 infections. However, any specific antiviral drug has not been confirmed so far for regular treatment. An important target is the main protease (Mpro), which plays a major role in replication of the virus. In this study, Gaussian and residue network models are employed to reveal two distinct potential allosteric sites on Mpro that can be evaluated as drug targets besides the active site. Then, FDA-approved drugs are docked to three distinct sites with flexible docking using AutoDock Vina to identify potential drug candidates. 14 best molecule hits for the active site of Mpro are determined. 6 of these also exhibit high docking scores for the potential allosteric regions. Full-atom molecular dynamics simulations with MM-GBSA method indicate that compounds docked to active and potential allosteric sites form stable interactions with high binding free energy (∆Gbind) values. ∆Gbind values reach -52.06 kcal/mol for the active site, -51.08 kcal/mol for the potential allosteric site 1, and -42.93 kcal/mol for the potential allosteric site 2. Energy decomposition calculations per residue elucidate key binding residues stabilizing the ligands that can further serve to design pharmacophores. This systematic and efficient computational analysis successfully determines ivermectine, diosmin and selinexor currently subjected to clinical trials, and further proposes bromocriptine, elbasvir as Mpro inhibitor candidates to be evaluated against SARS-CoV-2 infection
Photopolymerization kinetics of doxycycline hyclate (DOX)-imprinted hydrogels were monitored by real-time Fourier transform infrared spectroscopy and differential photocalorimetry. 2-Hydroxyethyl methacrylate-based hydrogels were synthesized by using ethylene glycol dimethacrylate as a cross-linker, acrylic acid (AA) as a functional monomer, and 2,2-dimethyl-2-hydroxy acetophenone as a photoinitiator. For imprinting DOX in hydrogels, the molar ratio of template to functional monomer (DOX:AA) was chosen as 1:8 and 1:16. The polymerization was achieved at two different initiator concentrations. The conversion and reaction rate were calculated as a function of the molar ratio of template, and the results were compared to those of nonimprinted ones. In order to reveal the effect of DOX on the photoinduced radical polymerization, thermal polymerization was also performed for imprinted and nonimprinted hydrogels by using 2,2 ′ -azobis(2,4-dimethyl-pentanenitrile) as a thermal initiator. All results showed that there is a significant effect of DOX concentration on the conversion and reaction rate of the photopolymerization reaction. The conversion and reaction rate decreased during photopolymerization when the template concentration increased in the monomer mixture.
The aim of this study is to develop doxycycline imprinted contact lenses that will be used in the treatment of corneal neovascularization, which can eventually cause blindness. For this purpose, doxycycline imprinted contact lenses were first prepared in two different diameters, 5.7 and 5.8 mm, then they were loaded with doxycycline and their in vitro and in vivo performances were determined. In the synthesis of the contact lenses, 2-hydroxyethyl methacrylate was used as a backbone monomer. The functional monomer was selected as itaconic acid using molecular simulations. Doxycycline release profile of the lenses was determined in NaCl solution at 37 °C. Their doxycycline release was reached about 3 µg/mg contact lenses in 6 hours. Higuchi model was fitted better than the others as a kinetic model. Swelling degrees of the contact lenses were determined as 38.8 %. Cytotoxic response of the lenses was investigated on retinal pigment epithelium cells. According to the results the lenses were not cytotoxic to RPE cell line. In vivo experiments in rat models were performed to study the treatment patterns. The rats were sacrificed fifteen days after treatment, and clinical examination under optical microscope was performed to evaluate neovascularization, infiltration of inflammatory cells, and corneal epithelial changes. In conclusion; doxycycline imprinted contact lenses promise as an effective treatment method for corneal neovascularization.
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