Molecular docking analysis of Clostridium perfringens beta toxin model with potential inhibitors from the ZINC database

Beta toxin from Clostridium perfringens after being secreted in gut is capable of causing necrotic enteritis in humans and several other animal species and does not respond to routinely used antibiotics. Therefore, there is a need to design an effective inhibitor for the Clostridium perfringens beta toxin (CPB) using cutting edge drug discovery technologies. Hence, potential CPB inhibitors were identified using computer aided screening of compounds from the ZINC database. Further, we document the molecular docking analysis of Clostridium perfringens beta toxin model (that revealed 4 binding pockets, A-D) with the identified potential inhibitors. We show that ZINC291192 [N-[(1-methylindol-3-yl) methyl eneamino]-7,10-dioxabicyclo[4.4.0]deca-2,4,11-triene-8- carboxamide] has optimal binding features with calculated binding energy of -10.38 kcal/mol and inhibition constant of 24.76 nM for further consideration.     

Human erythrocyte flickering: temperature,ATP concentration,water transport,and cell aging,plus a computer simulation

Images of human erythrocytes from a healthy donor were recorded under differential interference contrast (DIC) microscopy; they were acquired rapidly (~336 Hz) and the intensity of the centermost pixel of each cell was recorded for ~60 s (20,000 values). Various techniques were used to analyze the data, including detrended fluctuation analysis (DFA) and multiscale entropy (MSE); however, power spectrum analysis was deemed the most appropriate for metrifying and comparing results. This analysis was used to compare cells from young and old populations, and after perturbing normal conditions, with changes in temperature, adenosine triphosphate (ATP) concentration (using NaF, an inhibitor of glycolysis, and α-toxin, a pore-forming molecule used to permeabilize red cells to ATP), and water transport rates [using glycerol, and p-chloromercuriphenylsulfonic acid (pCMBS) to inhibit aquaporins, AQPs]. There were measurable differences in the membrane fluctuation characteristics in populations of young and old cells, but there was no significant change in the flickering time series on changing the temperature of an individual cell, by depleting it of ATP, or by competing with the minor water exchange pathway via AQP3 using glycerol. However, pCMBS, which inhibits AQP1, the major water exchange pathway, inhibited flickering in all cells, and yet it was restored by the membrane intercalating species dibutyl phthalate (DBP). We developed a computer model to simulate acquired displacement spectral time courses and to evaluate various methods of data analysis, and showed how the flexibility of the membrane, as defined in the model, affects the flickering time course.     

New imidazoquinoxaline derivatives: Synthesis,biological evaluation on melanoma,effect on tubulin polymerization and structure–activity relationships

Microtubules are considered as important targets of anticancer therapy. EAPB0503 and its structural imidazo[1,2-a]quinoxaline derivatives are major microtubule-interfering agents with potent anticancer activity. In this study, the synthesis of several new derivatives of EAPB0503 is described, and the anticancer efficacy of 13 novel derivatives on A375 human melanoma cell line is reported. All new compounds show significant antiproliferative activity with IC₅₀ in the range of 0.077–122 μM against human melanoma cell line (A375). Direct inhibition of tubulin polymerization assay in vitro is also assessed. Results show that compounds 6b, 6e, 6g, and EAPB0503 highly inhibit tubulin polymerization with percentages of inhibition of 99%, 98%, 90%, and 84% respectively. Structure–activity relationship studies within the series are also discussed in line with molecular docking studies into the colchicine-binding site of tubulin.     

The mechanism of the converter domain rotation in the recovery stroke of myosin motor protein

Upon ATP binding, myosin motor protein is found in two alternative conformations, prerecovery state M* and postrecovery state M**. The transition from one state to the other, known as the recovery stroke, plays a key role in the myosin functional cycle. Despite much recent research, the microscopic details of this transition remain elusive. A critical step in the recovery stroke is the rotation of the converter domain from “up” position in prerecovery state to “down” position in postrecovery state that leads to the swing of the lever arm attached to it. In this work, we demonstrate that the two rotational states of the converter domain are determined by the interactions within a small structural motif in the force‐generating region of the protein that can be accurately modeled on computers using atomic representation and explicit solvent. Our simulations show that the transition between the two states is controlled by a small helix (SH1) located next to the relay helix and relay loop. A small translation in the position of SH1 away from the relay helix is seen to trigger the transition from “up” state to “down” state. The transition is driven by a cluster of hydrophobic residues I687, F487, and F506 that make significant contributions to the stability of both states. The proposed mechanism agrees well with the available structural and mutational studies. Proteins 2012; © 2012 Wiley Periodicals, Inc.     

Effect of filaments within the synaptic cleft on the response of excitatory synapses simulated by computer experiments

Mathematical models of the excitatory synapse are furnishing valuable information about the synaptic response. Based on Brownian-diffusion of glutamate molecules, a synapse model was utilized to investigate the synaptic response on a femto-second time scale by the use of a parallel computer. In particular, the presence of fibrils crossing the synaptic cleft was simulated, which could have a role in shaping the brain activity. To this aim the model of synapse was modified by considering trans-synaptic filaments with diameters ranging from 7 nm to 3 nm, disposed on a grid with spacing of 14 nm or 8 nm. The simulation demonstrated that the presence of filaments induced an increase in the synaptic response, most likely linked to an increment in the probability of encounter between glutamate molecules and receptors. The increase was small - from 5 to 20%, but metabolic and functional considerations provide substantive hints about the importance of these small changes for brain activity. Moreover, it was shown that the presence of filaments made more stable the response of the synapse to random variations of pre-synaptic elements. Originated by these computational results, some inferences about the biological bases of mind diseases such as autism, mental retardation and schizophrenia, are reported in the Discussion.     

Evaluation of Bioremediation Treatments in a Shoreline-Simulating Microcosm

A microcosm test was designed to study the efficiency of bioremediation treatments at oil contaminated shorelines. The biodegradation in the hermetically closed microcosm was monitored by measuring the total cumulative inorganic carbon evolved during the bioremediation process. The effects of three different additives, medium-release methylene urea (MU) + apatite, fast-release MU + superphosphate, and a biosorbent, on the biodegradation of weathered crude oil (North Sea Brent) were evaluated at +10°C. All the additives significantly increased mineralization. The total amount of inorganic carbon evolved during the 10-week study was measured in the microcosm treated with oil, and with oil and medium-release MU + apatite, fast-release MU + superphosphate, and biosorbent. The amounts were 40,670,490, and 580 mg, respectively. The respirometric measurements were supported by microbiological determinations, ATP content in the sand, number of heterotrophic bacteria, and amount of biomass-C determined by the substrate-induced respiration method. Nutrient analysis indicated that biodegradation was nitrogen limited. The microcosm test proved to be suitable for comparing the effectiveness of different treatments in enhancing the biodegradation of crude oil-contaminated shores.     

Simulating control strategies for a spatially structured weed invasion: <Emphasis Type="Italic">Spartina alterniflora</Emphasis> (Loisel) in Pacific Coast estuaries

Patterns in the spatial arrangement of invasive plant populations can provide opportunity for strategic placement of control efforts. Smooth cordgrass (Spartina alterniflora) is rapidly invading the intertidal mudflats of Pacific Coast estuaries. Its pattern of spread is distinctive. Seedlings establish in open mud and then grow vegetatively to form expanding circular patches, which dot the mudflats and eventually coalesce into a contiguous monospecific meadow. The invasion typically begins in the upper tide zone and then moves down the tidal gradient. A spatially explicit model was used to simulate the spread of S. alterniflora and compare various strategies for control in a situation where only a fraction of the total infestation could be controlled each year. A strategy of killing outlying patches first and then attacking the dense meadows (moving up the tidal gradient) led to eradication with up to 44% less time and effort than a strategy of attacking the dense meadows first and outlying patches second (moving down the tidal gradient). In the control of contiguous meadows located adjacent to the shoreline, the best strategy was to approach one end of the infestation, moving across the meadow to the other end. Suppression of seeds was not an effective control strategy. In general, effective control strategies were those that first eliminate the plant in areas where current or future vegetative growth is greatest. Application of these results in control programs for S. alterniflora and similar invasive species could greatly reduce the costs of control work and improve the likelihood of local or complete eradication.     

Docking of Antizyme to Ornithine Decarboxylase and Antizyme Inhibitor using Experimental Mutant and Double-Mutant Cycle Data

Antizyme (Az) is a highly conserved key regulatory protein bearing a major role in regulating polyamine levels in the cell. It has the ability to bind and inhibit ornithine decarboxylase (ODC), targeting it for degradation. Az inhibitor (AzI) impairs the activity of Az. In this study, we mapped the binding sites of ODC and AzI on Az using Ala scan mutagenesis and generated models of the two complexes by constrained computational docking. In order to scan a large number of mutants in a short time, we developed a workflow combining high-throughput mutagenesis, small-scale parallel partial purification of His-tagged proteins and their immobilization on a tris-nitrilotriacetic-acid-coated surface plasmon resonance chip. This combination of techniques resulted in a significant reduction in time for production and measurement of large numbers of mutant proteins. The data-driven docking results suggest that both proteins occupy the same binding site on Az, with Az binding within a large groove in AzI and ODC. However, single-mutant data provide information concerning the location of the binding sites only, not on their relative orientations. Therefore, we generated a large number of double-mutant cycles between residues on Az and ODC and used the resulting interaction energies to restrict docking. The model of the complex is well defined and accounts for the mutant data generated here, and previously determined biochemical data for this system. Insights on the structure and function of the complexes, as well as general aspects of the method, are discussed.     

Solvent-induced lid opening in lipases: A molecular dynamics study

In most lipases, a mobile lid covers the substrate binding site. In this closed structure, the lipase is assumed to be inactive. Upon activation of the lipase by contact with a hydrophobic solvent or at a hydrophobic interface, the lid opens. In its open structure, the substrate binding site is accessible and the lipase is active. The molecular mechanism of this interfacial activation was studied for three lipases (from Candida rugosa, Rhizomucor miehei, and Thermomyces lanuginosa) by multiple molecular dynamics simulations for 25 ns without applying restraints or external forces. As initial structures of the simulations, the closed and open structures of the lipases were used. Both the closed and the open structure were simulated in water and in an organic solvent, toluene. In simulations of the closed lipases in water, no conformational transition was observed. However, in three independent simulations of the closed lipases in toluene the lid gradually opened. Thus, pathways of the conformational transitions were investigated and possible kinetic bottlenecks were suggested. The open structures in toluene were stable, but in water the lid of all three lipases moved towards the closed structure and partially unfolded. Thus, in all three lipases opening and closing was driven by the solvent and independent of a bound substrate molecule.