Probing binding mechanism of interleukin-6 and olokizumab: in silico design of potential lead antibodies for autoimmune and inflammatory diseases

Computer-aided antibody engineering has been successful in the design of new biologics for disease diagnosis and therapeutic interventions. Interleukin-6 (IL-6), a well-recognized drug target for various autoimmune and inflammatory diseases such as rheumatoid arthritis, multiple sclerosis, and psoriasis, was investigated in silico to design potential lead antibodies. Here, crystal structure of IL-6 along with monoclonal antibody olokizumab was explored to predict antigen–antibody (Ag???Ab)-interacting residues using DiscoTope, Paratome, and PyMOL. Tyr56, Tyr103 in heavy chain and Gly30, Ile31 in light chain of olokizumab were mutated with residues Ser, Thr, Tyr, Trp, and Phe. A set of 899 mutant macromolecules were designed, and binding affinity of these macromolecules to IL-6 was evaluated through Ag???Ab docking (ZDOCK, ClusPro, and Rosetta server), binding free-energy calculations using Molecular Mechanics/Poisson Boltzman Surface Area (MM/PBSA) method, and interaction energy estimation. In comparison to olokizumab, eight newly designed theoretical antibodies demonstrated better result in all assessments. Therefore, these newly designed macromolecules were proposed as potential lead antibodies to serve as a therapeutics option for IL-6-mediated diseases.     

Quercetin-induced yeast apoptosis through mitochondrial dysfunction under the accumulation of magnesium in Candida albicans

Latterly, the upsurge in use of antifungal drugs has brought about the emergence of several drug-resistance strains, making it skeptical to continue relying on current therapeutic regime. In the necessity of resistance-free antifungal agent, flavonoids presented possibilities of replacing existing drugs, displaying antifungal activity against pathogenic fungi. Among them, quercetin, one of the most representative flavonoids, exhibited antifungal activity against Candida albicans. To inspect the further understanding regarding quercetin, the antifungal mode of action of quercetin was investigated. In the initial step, the apoptosis was monitored after quercetin treatment. Moreover, intracellular levels of Mg²⁺ was assessed and was determined that Mg²⁺ increase occurred under the influence of quercetin. In addition, several features of mitochondrial dysfunction were monitored. Mitochondrial dysfunction triggers decrease in mitochondrial redox levels and leads to disruption in mitochondrial antioxidant system. Increased intracellular ROS and decreased intracellular redox levels were also displayed, indicating the occurrence of overall disruption in antioxidant systems. Sequentially, DNA fragmentation was observed and this DNA damage in turn induces apoptosis. In analyses, hexaamminecobalt(III) chloride (Cohex) was applied to inhibit Mg²⁺ transport between cytosol and mitochondria. Cohex attenuated the effects induced by quercetin, which demonstrates that the presence of Mg²⁺ is essential in quercetin-induced apoptosis.     

Astrocyte Resilience to Oxidative Stress Induced by Insulin-like Growth Factor I (IGF-I) Involves Preserved AKT (Protein Kinase B) Activity

Disruption of insulin-like growth factor I (IGF-I) signaling is a key step in the development of cancer or neurodegeneration. For example, interference of the prosurvival IGF-I/AKT/FOXO3 pathway by redox activation of the stress kinases p38 and JNK is instrumental in neuronal death by oxidative stress. However, in astrocytes, IGF-I retains its protective action against oxidative stress. The molecular mechanisms underlying this cell-specific protection remain obscure but may be relevant to unveil new ways to combat IGF-I/insulin resistance. Here, we describe that, in astrocytes exposed to oxidative stress by hydrogen peroxide (H₂O₂), p38 activation did not inhibit AKT (protein kinase B) activation by IGF-I, which is in contrast to our previous observations in neurons. Rather, stimulation of AKT by IGF-I was significantly higher and more sustained in astrocytes than in neurons either under normal or oxidative conditions. This may be explained by phosphorylation of the phosphatase PTEN at the plasma membrane in response to IGF-I, inducing its cytosolic translocation and preserving in this way AKT activity. Stimulation of AKT by IGF-I, mimicked also by a constitutively active AKT mutant, reduced oxidative stress levels and cell death in H₂O₂-exposed astrocytes, boosting their neuroprotective action in co-cultured neurons. These results indicate that armoring of AKT activation by IGF-I is crucial to preserve its cytoprotective effect in astrocytes and may form part of the brain defense mechanism against oxidative stress injury.     

Influence of latitude, water depth, day v. night and wet v. dry periods on the species composition of reef fish communities in tropical Western Australia

Trap sampling over reefs in deep (mean = 20 m) and shallow (mean = 10 m) waters along c. 1500 km of coastline in tropical north‐western Australia during both day and night and in wet and dry periods yielded 23 377 fishes, representing 32 families, 58 genera and 119 species. Individuals of the Serranidae, Lutjanidae, Lethrinidae and Carangidae contributed 88·9% to the total catch. The ichthyofaunal compositions of the Kimberley, Canning and Pilbara bioregions were relatively discrete. Species composition was influenced far more by location (latitude) than by water depth, period and time of day, and underwent a gradational change southwards. The latter change reflected differences in the trends exhibited by the relative abundances of certain species with increasing latitude and the confinement of other species largely to particular regions. The three most abundant species, i.e. Lethrinus sp. 3, Lutjanus carponotatus and Lethrinus laticaudis contributed 34·8, 20·8 and 11·6% to the total catch, respectively. The first species was rarely recorded in the two most northern locations and was abundant in the four most southern locations, whereas the last two species were relatively more abundant in northern than in southern locations. Lutjanus bitaeniatus and Lutjanus johnii were found exclusively at the two locations in the Kimberley region, whereas Abalistes stellatus, Pentapodus emeryii and Lethrinus nebulosus were not caught in this region but were found in both locations of the Canning and Pilbara regions. The species composition in deep and shallow waters at each location almost invariably differed significantly between day and night and between dry and wet periods, with species such as L. bitaeniatus, L. johnii, Lutjanus sebae and A. stellatus being more abundant over deep reefs, whereas L. carponotatus, L. laticaudis, Siganus fuscescens and Lethrinus lentjan were more numerous over shallow reefs. Species such as L. johnii and Lethrinus atkinsoni were relatively more important in night‐time than daytime catches, whereas the reverse applied to Lethrinus lentjan, L. laticaudis and Choerodon cyanodus. Lethrinus sp. 3 and L. laticaudis were relatively more important in catches during the dry than wet period.     

Correlation between the parameters of contingent negative variation and characteristics of variational pulsometry in Parkinsonian patients

In patients suffering from Parkinson's disease (PD), we analyzed correlations between the parameters of contingent negative variation (CNV) and data of variational pulsometry (according to the measurements of R-R ECG intervals). Studies were carried out on 35 patients (group PD), 49 to 74 years old, with the stage of disease of 1.5 to 3.0 according to the Hoehn-Yahr international classification. In the course of CNV recording (i.e., in the state of a certain functional loading), we observed significant negative correlations between the integral magnitude (area) of this potential and indices of variational pulsometry (RMSSD, SDNN, C. var, and HF) that characterize the intensity of parasympathetic (respiratory) influences on the cardiovascular system. In the control group, such correlations were absent. We found significant correlations between the autonomic balance, CNV magnitude, and stage of PD reflecting the level of generalization of the pathological process. In the subgroup of patients with the PD stage 1.5 to 2.0, significant changes in the mean values of indices of parasympathetic influences during recording of the CNV were not observed, while in another subgroup (the PD stage 2.5 to 3.0), these values increased significantly (P < 0.05 and P < 0.01). If the estimates of the PD stage were low, the CNV area demonstrated greater values (P < 0.01). The disturbance of coordination of muscle-to-muscle interactions in the PD group is, probably, an important factor responsible for parasympathetic dysregulation and suppression of the CNV generation. We found positive correlation between the intensity of parasympathetic influences in the course of CNV recording and the level of postural disorders (r = 0.37, P < 0.05). On the contrary, the CNV magnitude demonstrated a negative correlation with the intensity of these disorders (r = −0.36, P < 0.05), as well as with the level of postural instability (r = −0.55, P < 0.001). We hypothesize that alterations of the autonomic balance and the activity of those cerebral structures, which are responsible for the motor readiness, result, to a significant extent, from weakening of the activity of the noradrenergic system due to degenerative processes developing in cells of the locus coeruleus. The impairment of the latter structure, together with degeneration of neurons of the substantia nigra and a decrease in the level of nigro-striatal dopamine, underlies the pathomorphological pattern of PD. Neirofiziologiya/Neurophysiology, Vol. 40, No. 3, pp. 242–253, May–June, 2008.     

The effect of temperature on bacterial degradation of EDTA in pH-auxostat

The effect of temperature on the maximum specific growth rate and the cell yield was studied during cultivation of two bacterial strains (LPM-4 and Pseudomonas sp. LPM-410) on EDTA under unlimited cell growth conditions in a pH-auxostat. Both strains displayed linear dependence of reciprocal biomass yield against reciprocal specific growth rate, from which the values of rate of substrate expenditure for cell maintenance and the “maximum” yield (i.e., hypothetical yield without cell maintenance processes) were estimated. Analysis of the maximum yield values based on mass–energy balance theory suggested that oxidation of the carboxylic acid side chains of EDTA by a monooxygenase had zero or low energetic efficiency. An Arrhenius equation with different values of Arrhenius parameters within different temperature ranges gave a good fit with the temperature dependence of both growth rate and biomass yield. Specific growth rates of both strains showed a more pronounced temperature dependence than did the cell yields. A possible kinetic mechanism was suggested which might be responsible for the modes of the temperature dependences of specific growth rate and yield that were found. The mechanism is based on a hypothetical key substance governing the metabolic flows, which is formed in a zero-order reaction and destroyed in a first-order reaction, both rate constants depending on temperature according to the Arrhenius law.     

Sexual dimorphism in scales of marbled flounder Pseudopleuronectes yokohamae (Pleuronectiformes: Pleuronectidae), with comments on the relevance to their spawning behaviour

Variation of scales on the blind side of Pseudopleuronectes yokohamae in relation to sex, maturity and body size was examined. Immature males often have cycloid scales, while mature males have mostly ctenoid scales. Large females also often have ctenoid scales (but with fewer spines compared with males), and small females have mostly cycloid scales. The number of spines (ctenii) on the blind‐side scale increases with body size in both sexes, indicating an ontogenetic change in scale morphology. As P. yokohamae spawn demersal eggs with males positioning themselves above the females on the ocular side, it is hypothesized that ctenoid scales on the blind side in mature males function for maintaining contact with females during spawning.     

Calcium-dependent binding of EDTA-extractable proteins to calf lens fiber membrane structures

Calf lens fiber membranes and fractions enriched in junction-like structures have been isolated in the absence and presence of EDTA. Their biochemical features have been studied. Sodium dodecyl sulfate polyacrylamide gel electrophoresis and immunoblotting experiments have provided evidence that a distinct group of EDTA-extractable proteins, being one of the main protein components of calf lens fiber membranes and very likely also of junction-like structures, is bound to these membranes via calcium ions. In addition to these proteins, four polypeptides with apparent molecular weights between 14 000 and 17 000 are characteristic for detergent-insoluble lens fiber structures prepared in calcium-rich medium. The absence of EDTA-extractable proteins in the urea-soluble calcium-containing fraction implies that they are not components of the cytoskeleton and that the calcium-dependent binding of these proteins to the membrane is urea-resistant. The use of EDTA throughout the whole membrane isolation procedure results in their complete removal from the membranes which already starts during buffer washing. This indicates that EDTA-extractable proteins exclusively consist of extrinsic membrane proteins which probably are not involved in cytoskeleton binding.