Rational design of inhibitors against LpxA protein of Acinetobacter baumannii using a virtual screening method

BackgroundAcinetobacter baumannii is a highly antimicrobial resistant nosocomial pathogen. Resistance to currently used antibiotics has limited effective drugs against this bacterium. This study aimed to propose a rational inhibitor design against the LpxA protein of A. baumannii using a virtual screening method based on a similar structure of ligands.MethodsIn this study, we targeted LpxA protein, which is involved in the early stage of LPS biosynthesis. In the next step, we used Peptide920 and 1,2- Ethanediol as templates to find similar compounds using Drugbank and Zinc15 webservers, respectively. Subsequently, molecular dynamics (MD) simulations were carried out for LpxA protein and two complexes of ZINC895081 and Macrolactam-1 which represented the highest binding affinity and best conformation. Finally, ADMET properties, water solubility and drug-likeness of the desired compounds were evaluated using SwissADME and DruLiTo softwares.ResultsAccording to considered criteria, Drugbank suggested 5 compunds including Ilomastat, Macrolactam-1, Macrolactam-2, Macimorelin, and Oglufanide. On the other hand, Zinc15 webserver suggested 4 compunds including ZINC895048, ZINC895081, ZINC901061 and ZINC1531008. The result of the HDOCK server and Molegro virtual docker (MVD) showed that Macrolactam-1 and ZINC895081 (Citrate) had the highest docking score. In addition, MD simulations showed that ZINC895081 and Macrolactam-1 ligands have the stable binding to the LpxA protein. According to Lipinski's rule, these two compounds are non-carcinogenic, non-toxic and promising inhibitors against LpxA of A. baumannii.ConclusionIt seems that Macrolactam-1 and ZINC895081 (Citrate) are two valuable promising inhibitors against the LpxA protein of A. baumannii. Further in vitro and in vivo experiments are needed to confirm the capabilities of these proposed compounds against A. baumannii.     

DOX delivery based on chitosan-capped graphene oxide-mesoporous silica nanohybride as pH-responsive nanocarriers

Journal of Sol-Gel Science and Technology - pH-responsive chitosan-coated graphene oxide-mesoporous silica nanoparticles (GMSN-Cs) was synthesized as a core–shell nanosheets to be used as DOX...     

An evaluation of british columbian beetle-killed hybrid spruce for bioethanol production

The development of bioconversion technologies for production of fuels, chemicals, and power from renewable resources is currently a high priority for developed nations such as the United States, Canada, and the European Union as a way to improve national energy security and reduce greenhouse gas emissions. The widespread implementation of such technologies will require a sustainable supply of biomass from forestry and agriculture. Forests are a major source of feedstocks for biofuels production in Canada. Woody biomass includes residues from logging and forest thinning, and from wood processing and pulp production. More recently, damaged wood caused by beetle infestations has become available on a large scale in Western Canada. This study evaluates beetle-killed British Columbian hybrid spruce (HS) (Picea glauca x P. engelmannii) as a feedstock for the production of bioethanol. In the past 30 yr, attack by the beetle Dendroctonus rufipennis and associated fungi has resulted in estimated losses of more than three billion board feet in British Columbia alone. Here we describe the chemical and some physical characteristics of both healthy (HHS) and beetle-killed (BKHS) British Columbian HS and evaluate the technical feasibility of using these feedstocks as a source of biomass for bioethanol production. Untreated HHS and BKHS did not differ significantly in chemical composition except for the moisture content, which was significantly lower in BKHS (approx 10%) compared with HHS (approx 18%). However, the yields of carbohydrates in hydrolyzable and fermentable forms were higher at mild pretreatment conditions (H-Factor <1000) for BKHS compared with HHS. At medium (H-Factor 1000-2000) and severe (H-Factor >2000) pretreatment conditions HHS and BKHS behaved similarly. Organosolv pretreated HHS and BKHS demonstrated good ethanol theoretical yields, approx 70 and 80%, respectively.     

Optical Toffoli and Feynman reversible gates designing using DNA transmission lines

Optical gates based on switchable material have become a focus of investigation. The present study designs an optical gate that uses DNA transmission lines and developed for Feynman and Toffoli reversible gates. It is shown that the implementation of a transmission line such as Ag/DNA/Ag produces a structure with high-quality switching. The switching characteristics of DNA were considered when designing the basic transmission line. The “On” mode is assumed for DNA with low conductivity. As conductivity increases, the line switches to the “Off” mode. A conceptual design is proposed in the present study for Feynman and Toffoli reversible gates for an optical regime at 300 THz based on DNA switching. A conceptual model is developed with an Ag/DNA/Ag transmission line controlled by changing the DNA bias. This transmission line provides a “Yes” gate, which is necessary for a reversible gate. The full wave time domain method was used to model the optical gates. The current work discusses how a DNA memristor can be used to design a compact reversible gate having a simple structure and high switching quality for use in optical systems.     

Theoretical Study of the Interactions between Isolated DNA Bases and Various Groups IA and IIA Metal Ions by Ab Initio Calculations

Interactions of the DNA bases adenine (A), guanine (G), cytosine (C), and thymine (T) with various metal ions (M) of groups IA and IIA of the periodic table of the elements were studied at the HF, MP2, and DFT levels of theory. The structures and thermodynamic stabilities of these species were studied at the gas phase. The calculations uphold that there exist two active sites in G and one in A, C, and T. The calculations also show that the O² atom in T is a more active site for metal ion bindings than that in C. The stability energies for G … M complexes are larger than those for A … M complexes and the stability energies for T … M complexes are larger than those for C … M complexes. As z/r ratio for the metal ion increases, the interaction energy for the complex increases systematically. Thermodynamic quantities such as ΔH, ΔG, ΔS, and ln K were determined for each complexation reaction, [Base+M ⁿ⁺ →(Base … M) ⁿ⁺]. A, G, and C complexation reactions except for C … Rb⁺ are exothermic. The situation is quite different for T complexation reactions and all except for T … Be²⁺ and T … Mg²⁺ are endothermic.     

Chelation of a proton by an aliphatic tertiary diamine

A series of monoprotonated aliphatic diamines has been examined, which crystallize in three general motifs: salt-bridged, cyclic, or clustered. The monoprotonated triflic acid salt of Me2N(CH2)4NMe2 forms a proton-bridged cyclic cation. The internal N-N distance is 2.66 A, with the bridging proton in the middle, having an NHN angle >/=172 degrees. The triflate oxygens lie more than 4 A away from the midpoint between the nitrogen atoms, indicating that a salt bridge does not form. The average NH distance in a solid sample was determined by measuring the 15N-H dipolar coupling in the triflic acid salt of the completely deuterated diamine (CD3)2N(CD2)4N(CD3)2. The value of the dipolar coupling constant, 5250 +/- 90 Hz, corresponds to an average NH distance of 1.32 A, nearly half-the NN distance. That result agrees with DFT calculations, which give a double-well potential minimum for proton transit between the two amino groups, having a zero-point vibrational level close to the barrier top. Theory predicts that the maximum value of the zero point vibrational wave function is almost coincident with a local potential energy maximum, consistent with the experimental findings.