Homology modeling, molecular dynamics, and docking studies of pattern-recognition transmembrane protein-lipopolysaccharide and β-1,3 glucan-binding protein fromFenneropenaeus indicus

Elucidating the mutational impact in causing Niemann-Pick disease type C: an in silico approach

Niemann-Pick disease type C is a rare autosomal recessive of lysosomal storage disorder characterized by impaired intracellular lipid transport and has a tendency to accumulate the fatty acids and glycosphingolipids in a variety of neurovisceral tissues. This work includes computational tools to deciphere the mutational effect in NPC protein. The study initiated with the collection of 471 missense mutations from various databases, which were then analyzed using computational tools. The mutations (G549V, F703S, Q775P and L1244P) were said to be disease associated, altering the biophysical properties, in highly conserved regions and reduces the stability using several in silico methods and were subjected to molecular docking analysis. To analyze the ligand (Itraconazole: a small molecule of antifungal drug class, which is known to inhibit cholesterol export from lysosomes) activity Molecular docking study was performed for all the complex proteins. The average binding affinity was taken and found to be -10.76 kcal/mol (native) and -11.06 kcal/mol (Q775P was located in transmembrane region IV which impacts the sterol-sensing domain of the NPC1 protein and associated with a severe infantile neurological form). Finally, molecular dynamic simulation was performed in duplicate and trajectories were built for the backbone of the RMSD, RMSF, the number of intramolecular hydrogen bonds, the radius of gyration and the SSE percent for both the complex proteins. This work contributes to understand the effectiveness and may provide an insight on the stability of the drug with the complex variant structures.Communicated by Ramaswamy H. Sarma.

Determination of the efficacy of using a serine protease gene as a DNA vaccine to protect against Vibrio parahaemolyticus infection in Litopenaeus vannamei

Serine proteases are proteolytic enzymes that exhibit biological roles in many biological systems. Previously, a Vibrio parahaemolyticus serine protease was reported to be a virulence factor. Here, the serine protease gene of V. parahaemolyticus was investigated as a DNA vaccine against V. parahaemolyticus in Litopenaeus vannamei. The serine protease gene was mutated to replace the conserved residues His82, Asp131 and Ser231 with Gly, Asp and Pro, respectively. Then, a pcDNA3.1 vector to express mutVpSP (mutant serine protease) was constructed for in vitro and in vivo DNA vaccine investigation. In vivo mutVpSP transcriptional analysis revealed expression in various immunized white shrimp tissues, such as hemocytes, hepatopancreas, stomach, intestine, gills, and muscle. The efficiency of prevention of V. parahaemolyticus infection was investigated in vaccinated shrimp, and the lowest cumulative mortality percentage was 30%, while the control shrimp had a 60% cumulative mortality rate. The immune system was stimulated in shrimp vaccinated with the DNA vaccine. The mRNA expression of the shrimp immune-responsive genes phenoloxidase, peroxinectin and C-type lectin was significantly upregulated. Additionally, the humoral and cellular immune responses, including the PO, phagocytic, and encapsulation activities and nodule formation, were elevated. These results suggested that the serine protease could be a V. parahaemolyticus virulence determinant and that this DNA vaccine could be applied as an effective vaccine candidate for control of acute hepatopancreatic necrosis disease syndrome (AHPND) in shrimp.

Identification and characterization of a novel PRR of fibrinogen-related protein in Apostichopus japonicus

Fibrinogen-related proteins (FREPs) play important roles in innate immunity by recognizing pathogen associated molecular patterns on pathogenic bacteria surfaces via conserved fibrinogen-like domain (FBG). In this paper, the full-length cDNA of Apostichopus japonicus FREP (designated as AjFREP) was cloned combined with rapid amplification of cDNA ends (RACE) and transcriptome sequencing. The full-length cDNA of AjFREP was of 2110 bp with an open reading frame (ORF) of 1659 bp. SMART analysis revealed that the AjFREP contained a typical signal peptide of 19 amino acid residues, a FBG and two unusual epidermal growth factor-like domains (EGFs). Multiple sequence alignments suggested that FBG domain shared a remarkably high structural conservation in polypeptide binding site and Ca²⁺ binding site. Tissue distribution analysis revealed that AjFREP was constitutively expressed in all examined tissues with the largest magnitude in coelomocytes, indicating AjFREP might play an important role in immune defense. The mRNA level of AjFREP in coelomocytes was sharply up-regulated by Vibrio splendidus challenge, and reached its peak expression at 48 h. Knock-down AjFREP by specific siRNA could significantly repress the coelomocyte phagocytosis rate. Meantime, the survival number of V. splendidus in the coelomic fluid was promoted. All these current results indicated that AjFREP might be involved in pathogen clearance through mediating coelomocytes phagocytosis activity.

Molecular characterization of a pattern recognition protein LGBP highly expressed in the early stages of mud crab Scylla paramamosain

The early developmental stages of the mud crab Scylla paramamosain suffer from high mortality caused by pathogen infections; however, few immune associated factors are known. Lipopolysaccharide and β-1,3-glucan-binding protein (LGBP) functions as a typical pathogen recognition receptor and plays an important role in the innate immune system of invertebrates. In this study we characterized a LGBP gene (SpLGBP) which was highly expressed in the late embryonic, zoea I larval stage and hepatopancreas of S. paramamosain.. It encodes 364 amino acids, composed of several conserved domains like the bacterial glucanase motif. The recombinant SpLGBP protein (rSpLGBP) was obtained through the E.coli expression system, in which two 6◊His-tags were added to both C and N terminals during vector construction for the improvement of purification efficiency. In vivo the study showed that the SpLGBP mRNA was significantly up-regulated under Vibrio parahaemolyticus and a lipopolysaccharide (LPS) challenge in the hemocytes and hepatopancreas. The ELISA binding assay in vitro indicated that the rSpLGBP was capable of binding to LPSs and peptidoglycan (PGN). The rSpLGBP could agglutinate both G+ and G- bacteria in the presence of Ca²⁺. Our results suggest that SpLGBP may play an immunological role against pathogenic infection in the early developmental stages of S. paramamosain.

Atom-based 3D-QSAR, induced fit docking, and molecular dynamics simulations study of thieno[2,3-b]pyridines negative allosteric modulators of mGluR5

Atom-based three dimensional-quantitative structure-activity relationship (3D-QSAR) model was developed on the basis of 5-point pharmacophore hypothesis (AARRR) with two hydrogen bond acceptors (A) and three aromatic rings for the derivatives of thieno[2,3-b]pyridine, which modulates the activity to inhibit the mGluR5 receptor. Generation of a highly predictive 3D-QSAR model was performed using the alignment of predicted pharmacophore hypothesis for the training set (R² = 0.84, SD = 0.26, F = 45.8, N = 29) and test set (Q² = 0.74, RMSE = 0.235, Pearson-R = 0.94, N = 9). The best pharmacophore hypothesis AARRR was selected, and developed three dimensional-quantitative structure activity relationship (3D-QSAR) model also supported the outcome of this study by means of favorable and unfavorable electron withdrawing group and hydrophobic regions of most active compound 42d and least active compound 18b. Following, induced fit docking and binding free energy calculations reveals the reliable binding orientation of the compounds. Finally, molecular dynamics simulations for 100 ns were performed to depict the protein-ligand stability. We anticipate that the resulted outcome could be supportive to discover potent negative allosteric modulators for metabotropic glutamate receptor 5 (mGluR5).

Lipopolysaccharide- and β-1,3-glucan-binding protein from Litopenaeus vannamei: Purification, cloning and contribution in shrimp defense immunity via phenoloxidase activation

Lipopolysaccharide- and β-1,3-glucan-binding protein (LGBP) existed in diversity of invertebrates including shrimp plays a crucial role in an innate immunity via mediating the recognition of invading pathogens. In this study, LGBP was cloned and characterized from the hepatopancreas of Litopenaeus vannamei, named as LvLGBP. Its full-length cDNA of 1282 bp contained an open reading frame (1101 bp) encoding a peptide of 367 amino acids. The LGBP primary structure contained a glycosyl hydrolase domain, two integrin binding motifs, two kinase C phosphorylation sites, and two polysaccharide recognition motifs which were identified as a polysaccharide binding motif and a β-1,3-glucan recognition motif. The LvLGBP transcripts were expressed mainly in the hepatopancreas. Upon challenge with Vibrio parahaemolyticus or white spot syndrome virus (WSSV), the LvLGBP mRNA expression was significantly up-regulated to reach a maximum at 48 h post injection. Its expression was also induced by lipopolysaccharide (LPS) or β-1,3-glucan stimulation. RNAi-based silencing resulted in the critical suppression of LvLGBP expression. Knockdown of LvLGBP gene with co-inoculation by V. parahaemolyticus or WSSV led to increase in the cumulative mortality and reduce in the median lethal time. Native LGBP was detected only in the hepatopancreas as verified by Western blotting. Purified LGBP from the hepatopancreas exhibited the agglutinating and binding activity towards Gram-negative bacterium V. parahaemolyticus with calcium-dependence. Its agglutinating activity was dominantly inhibited by LPS with higher potential than β-1,3-glucan. Purified LvLGBP could significantly activate the hemocyte phenoloxidase activity in the presence of LPS (12.9 folds), while slight activation was detected with β-1,3-glucan (2.0 folds). It could enhance the encapsulation by hemocytes but did not have antibacterial activity. These results provided evidence that LvLGBP might act as a pathogenic recognition protein to activate shrimp immune defense against invading pathogens via the agglutination, binding and enhancing encapsulation and phenoloxidase activity of the hemocytes.

Advantages of Structure-Based Drug Design Approaches in Neurological Disorders

OBJECTIVE

The purpose of the review is to portray the theoretical concept on neurological disorders from research data.

BACKGROUND

The freak changes in chemical response of nerve impulse causes neurological disorders. The research evidence of the effort done in the older history suggests that the biological drug targets and their effective feature with responsive drugs could be valuable in promoting the future development of health statistics structure for improved treatment for curing the nervous disorders.

METHODS

In this review, we summarized the most iterative theoretical concept of structure based drug design approaches in various neurological disorders to unfathomable understanding of reported information for future drug design and development.

RESULTS

On the premise of reported information we analyzed the model of theoretical drug designing process for understanding the mechanism and pathology of the neurological diseases which covers the development of potentially effective inhibitors against the biological drug targets. Finally, it also suggests the management and implementation of the current treatment in improving the human health system behaviors.

CONCLUSION

With the survey of reported information we concluded the development strategies of diagnosis and treatment against neurological diseases which leads to supportive progress in the drug discovery.

Lipopolysaccharide- and β-1,3-glucan-binding protein from Fenneropenaeus merguiensis functions as a pattern recognition receptor with a broad specificity for diverse pathogens in the defense against microorganisms

In crustaceans, lipopolysaccharide- and β-1,3-glucan-binding protein (LGBP) plays an important role in innate immunity by mediating the recognition of pathogens to host cells. Hereby, LGBP was cloned from Fenneropenaeus merguiensis hepatopancreas. Its full-length cDNA (1280 bp) had an open reading frame of 1101 bp, encoding a peptide of 366 amino acids. The LGBP primary structure comprises a recognition motif for β-1,3-linkage of polysaccharides, two integrin binding motifs, a kinase C phosphorylation site and a bacterial glucanase motif. The LGBP mRNA was strongly expressed in hepatopancreas and significantly up-regulated to get the maximum at 12 h upon Vibrio harveyi challenge. Recombinant LGBP (rLGBP) could agglutinate Gram-negative and Gram-positive bacteria including yeast with Ca²⁺-dependence. V. harveyi agglutination induced by rLGBP was intensively inhibited by lipoteichoic acid, less in order were lipopolysaccharide, β-1,3-glucan and N-acetyl neuraminic acid. Western blotting revealed that rLGBP bound widely to Gram-negative and Gram-positive bacteria and also yeast. By ELISA quantification, rLGBP could bind to β-1,3-glucan better than to lipopolysaccharide and lipoteichoic acid. These findings suggest that LGBP may function as a receptor which recognizes invading diverse pathogens and contribute in F. merguiensis immune response.

Molecular Interactions of β-(1→3)-Glucans with Their Receptors

β-(1→3)-Glucans can be found as structural polysaccharides in cereals, in algae or as exo-polysaccharides secreted on the surfaces of mushrooms or fungi. Research has now established that β-(1→3)-glucans can trigger different immune responses and act as efficient immunostimulating agents. They constitute prevalent sources of carbons for microorganisms after subsequent recognition by digesting enzymes. Nevertheless, mechanisms associated with both roles are not yet clearly understood. This review focuses on the variety of elucidated molecular interactions that involve these natural or synthetic polysaccharides and their receptors, i.e., Dectin-1, CR3, glycolipids, langerin and carbohydrate-binding modules.