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.     

Dynamics and modulation studies of human voltage gated Kv1.5 channel

The voltage gated Kv1.5 channels conduct the ultrarapid delayed rectifier current (IK_ur) and play critical role in repolarization of action potential duration. It is the most rapidly activated channel and has very little or no inactivated states. In human cardiac cells, these channels are expressed more extensively in atrial myocytes than ventricle. From the evidences of its localization and functions, Kv1.5 has been declared a selective drug target for the treatment of atrial fibrillation (AF). In this present study, we have tried to identify the rapidly activating property of Kv1.5 and studied its mode of inhibition using molecular modeling, docking, and simulation techniques. Channel in open conformation is found to be stabilized quickly within the dipalmitoylphosphatidylcholine membrane, whereas most of the secondary structure elements were lost in closed state conformation. The obvious reason behind its ultra-rapid property is possibly due to the amino acid alteration in S4–S5 linker; the replacement of Lysine by Glutamine and vice versa. The popular published drugs as well as newly identified lead molecules were able to inhibit the Kv1.5 in a very similar pattern, mainly through the nonpolar interactions, and formed sable complexes. V512 is found as the main contributor for the interaction along with the other important residues such as V505, I508, A509, V512, P513, and V516. Furthermore, two screened novel compounds show surprisingly better inhibitory potency and can be considered for the future perspective of antiarrhythmic survey.     

Comparison of different methods of determining cell viability after exposure to cytotoxic compounds

Cell-survival (of DON and L1210 cells) after treatment with cytotoxic compounds was assessed by measuring cloning efficiency, exclusion of trypan blue and erythrosin B, [⁵¹Cr] release, and attachment of DON cells to glass. Cell survival as measured by cloning efficiency did not correlate with survival measured by any of the other methods. We found that the stainability of cells after drug exposure depended on the cell line used. For example, after 3 h exposure to tubercidin although 100% of both DON and L1210 cells were killed (on basis of cloning efficiency), only 11% of DON cells and 68% of L1210 cells were dead as indicated by staining with erythrosin B. The stainability of cells also depended on the particular drug used. For example, after 24 h exposure of L1210 cells to adriamycin and tubercidin (both killed >99% of cells on basis of cloning efficiency) 21% of cells exposed to adriamycin and 99% of cells exposed to tubercidin were stained. The results obtained with several other cytotoxic compounds are discussed.     

Critical micelle concentration and hemolytic activity--a correlation suggested by the marine sterol, halistanol trisulfate.

The marine natural product, halistanol trisulfate, has a relatively low critical micelle concentration of 0.001% m/v (14.5 microM) and strong hemolytic potency with an EC50 of 0.00046% m/v (6.67 microM). As expected of a detergent, it inhibits the growth of gram-positive but not gram-negative bacteria. The hemolytic activity of halistanol trisulfate and other detergents has been shown to correlate with critical micelle concentration. This correlation may have important implications in the mechanism of membranolytic bioactivity.     

Larval rearing of fringe-lipped carp,Labeo fimbriatus (Bloch) with low cost diets including green bottle fly Lucilia sericata (Meigen) larvae meal incorporated diet

A study was conducted with non-conventional ingredients to test their efficacy as fishmeal (FM) replacers in the diet of fringe- lipped carp. Labeo fimbriatus first feeding larvae and fry were reared for 30 and 60 days in indoor, 50 L, aerated, circular plastic tanks at 100 and 30 numbers tank⁻¹, respectively. In the first feeding larvae to fry rearing experiment (Exp. 1), the fish were fed with either of the following isonitrogenous and isocaloric diets – live plankton, FM diet, green bottle fly (Lucilia sericata) larvae meal (GBFLM) diet and silkworm pupa (SWP) diet. The fry to fingerling rearing (Exp. 2), was also conducted using the same diets described above except live plankton. All compounded diets were formulated to contain 40% crude protein for the experiment 1 and 35% for experiment 2 and were fed ad libitum. Triplicate tanks were maintained for each treatment in both the experiments. In Exp. 1, the mean final weight of fry was higher with plankton and FM diets, while no difference (p > .05) was observed between FM and GBFLM diets. Weight of fish fed SWP diets was not statistically different from those fed GBFLM diet. No difference (p > .05) in final length, survival and condition factor was recorded. Analysis of digestive enzyme activity of whole fish revealed lower (p < .05) activity of amylase in fish fed plankton. In Exp. 2, no difference (p > .05) was observed between the different diet groups in terms of mean final weight, length, survival and condition factor. Analysis of digestive enzyme activity of whole fish revealed no difference (p > .05) in the activity of digestive enzymes between the treatments except a lower (p < .05) activity of trypsin in FM diet and lipase in FM and GBFLM diets. Since the survival and condition factors of animals is the most important aspect during nursery rearing, similar (p > .05) values recorded in different treatments indicate the possibility of incorporation of these non-conventional protein sources in the diet of L. fimbriatus during first feeding larvae to fry and fry to fingerling rearing.     

Synthesis of Novel Quinoline–Benzoxazolinone Ester Hybrids: In Vitro Anti-Inflammatory Activity and Antibacterial Activity

Russian Journal of Bioorganic Chemistry - A series of novel quinoline-benzoxazolinone ester hybrids were synthesized characterized and assessed for their in vitro anti-inflammatory and...     

Modelling family 2 cystatins and their interaction with papain

Cystatins are extensively studied cysteine protease inhibitors, found in wide range of organisms with highly conserved structural folds. S-type of cystatins is well known for their abundance in saliva, high selectivity and poorer activity towards host cysteine proteases in comparison to their immediate ancestor cystatin C. Despite more than 90% sequence similarity, the members of this group show highly dissimilar binding affinity towards papain. Cystatin M/E is a potent inhibitor of legumain and papain like cysteine proteases and recognized for its involvement in skin barrier formation and potential role as a tumor suppressor gene. However, the structures of these proteins and their complexes with papain or legumain are still unknown. In the present study, we have employed computational methods to get insight into the interactions between papain and cystatins. Three-dimensional structures of the cystatins are generated by homology modelling, refined with molecular dynamics simulation, validated through numerous web servers and finally complexed with papain using ZDOCK algorithm in Discovery Studio. A high degree of shape complementarity is observed within the complexes, stabilized by numerous hydrogen bonds (HB) and hydrophobic interactions. Using interaction energy, HB and solvent accessible surface area analyses, we have identified a series of key residues that may be involved in papain–cystatin interaction. Differential approaches of cystatins towards papain are also noticed which are possibly responsible for diverse inhibitory activity within the group. These findings will improve our understanding of fundamental inhibitory mechanisms of cystatin and provide clues for further research.     

Lens-specific regulation of the thioredoxin-1 gene, but not thioredoxin-2, upon in vivo photochemical oxidative stress in the Emory mouse

The angiotensin II (Ang II) type 1 receptor mediates various actions of Ang II, whereas the function of the type 2 (AT2) receptor is not well understood. In the mice lacking the gene encoding the AT2 receptor, the pressor response to Ang II was increased although the underlying mechanism is unknown. We tested the hypothesis that vasoconstrictor response is exaggerated in the AT2 receptor null mice. We measured hemodynamic parameters and evaluated systemic vascular resistance (SVR) in the anesthetized open-chest wild-type and AT2 receptor null mice. Ang II infusion caused dose-dependent increases in SVR in both strains, while the response was significantly higher at 0.5 microgram/kg Ang II in the AT2 receptor null mice (305 +/- 53% of baseline) than in the wild-type mice (179 +/- 27% of baseline). To investigate further the vascular contractility, we examined contraction of aortic rings in vitro. The contraction induced by 1 microM Ang II was increased in the AT2 receptor null mice compared with that in the wild-type mice (0.82 +/- 0.11 vs. 0.54 +/- 0.12 g). Ang II-induced contraction was still greater in the AT2 receptor null mice when calibrated by the maximum tension induced by 90 mM KCl. These data suggest that the AT2 receptor modulates vascular contractility, which may influence blood pressure.