A novel identification approach for discovery of 5-HydroxyTriptamine 2A antagonists: combination of 2D/3D similarity screening,molecular docking and molecular dynamics

5-HydroxyTriptamine 2A antagonists are potential targets for treatment of various cerebrovascular and cardiovascular disorders. In this study, we have developed and performed a unique screening pipeline for filtering ZINC database compounds on the basis of similarities to known antagonists to determine novel small molecule antagonists of 5-HydroxyTriptamine 2A. The screening pipeline is based on 2D similarity, 3D dissimilarity and a combination of 2D/3D similarity. The shortlisted compounds were docked to a 5-HydroxyTriptamine 2A homology-based model, and complexes with low binding energies (287 complexes) were selected for molecular dynamics (MD) simulations in a lipid bilayer. The MD simulations of the shortlisted compounds in complex with 5-HydroxyTriptamine 2A confirmed the stability of the complexes and revealed novel interaction insights. The receptor residues S239, N343, S242, S159, Y370 and D155 predominantly participate in hydrogen bonding. π–π stacking is observed in F339, F340, F234, W151 and W336, whereas hydrophobic interactions are observed amongst V156, F339, F234, V362, V366, F340, V235, I152 and W151. The known and potential antagonists shortlisted by us have similar overlapping molecular interaction patterns. The 287 potential 5-HydroxyTriptamine 2A antagonists may be experimentally verified.     

Insights into the structure–function relationship of brown plant hopper resistance protein,Bph14 of rice plant: a computational structural biology approach

Brown plant hopper (BPH) is one of the major destructive insect pests of rice, causing severe yield loss. Thirty-two BPH resistance genes have been identified in cultivated and wild species of rice Although, molecular mechanism of rice plant resistance against BPH studied through map-based cloning, due to non-existence of NMR/crystal structures of Bph14 protein, recognition of leucine-rich repeat (LRR) domain and its interaction with different ligands are poorly understood. Thus, in the present study, in silico approach was adopted to predict three-dimensional structure of LRR domain of Bph14 using comparative modelling approach followed by interaction study with jasmonic and salicylic acids. LRR domain along with LRR-jasmonic and salicylic acid complexes were subjected to dynamic simulation using GROMACS, individually, for energy minimisation and refinement of the structure. Final binding energy of jasmonic and salicylic acid with LRR domain was calculated using MM/PBSA. Free-energy landscape analysis revealed that overall stability of LRR domain of Bph14 is not much affected after forming complex with jasmonic and salicylic acid. MM/PBSA analysis revealed that binding affinities of LRR domain towards salicylic acid is higher as compared to jasmonic acid. Interaction study of LRR domain with salicylic acid and jasmonic acid reveals that THR987 of LRR form hydrogen bond with both complexes. Thus, THR987 plays active role in the Bph14 and phytochemical interaction for inducing resistance in rice plant against BPH. In future, Bph14 gene and phytochemicals could be used in BPH management and development of novel resistant varieties for increasing rice yield.     

HHV-5 epitope: A potential vaccine candidate with high antigenicity and large coverage

Outbreak of Human Herpes virus-5 (HHV-5) infection in emerging countries has raised worldwide health concern owing to prevalence of congenital impairments and life threatening consequences in immunocompromised individuals. Thus, there lies an impending need to develop vaccine against HHV-5. HHV-5 enters into host cells with the help of necessary components glycoprotein B (gB) and H/L. In this study, the conformational linear B-cell and T-cell epitopes for gB of HHV-5 have been predicted using conformational approaches, for their possible collective use as vaccine candidates. We examined epitope’s interactions with major histocompatibility complexes using molecular docking and also investigated their stable binding with specific toll like receptor-2 (TLR2), present on host cells during HHV-5 infection. Predicted MHC-I epitope ‘LVAIAVVII’ with high antigenicity and large coverage of HLA alleles was found to superimpose on MHC-II epitope (Rank 1) and was also identified to be the core sequence of putative B cell epitope ‘ILVAIAVVIITYLI’. Resulting epitope was found to have consistent interaction with TLR2 during long term (100?ns) MD run. We also validated this nonamer epitope for its dissimilarity with human genome and high population coverage, suggesting it to be a potential vaccine candidate with higher coverage for both the MHC alleles of Indian population.

Communicated by Ramaswamy H. Sarma     

Exploratory algorithm to devise multi-epitope subunit vaccine by investigating Leishmania donovani membrane proteins

Visceral leishmaniasis (VL) is a deadly parasitic infection which affects poorest to poor population living in the endemic countries. Increasing resistant to existing drugs, disease burden and a significant number of deaths, necessitates the need for an effective vaccine to prevent the VL infection. This study employed a combinatorial approach to develop a multi-epitope subunit vaccine by exploiting Leishmania donovani membrane proteins. Cytotoxic T- and helper T-lymphocyte binding epitopes along with suitable adjuvant and linkers were joined together in a sequential manner to design the subunit vaccine. The occurrence of B-cell and IFN-γ inducing epitopes approves the ability of subunit vaccine to develop humoral and cell-mediated immune response. Physiochemical parameters of vaccine protein were also assessed followed by homology modeling, model refinement and validation. Moreover, disulfide engineering was performed for the increasing stability of the designed vaccine and molecular dynamics simulation was performed for the comparative stability purposes and to conform the geometric conformations. Further, molecular docking and molecular dynamics simulation study of a mutated and non-mutated subunit vaccine against TLR-4 immune receptor were performed and respective complex stability was determined. In silico cloning ensures the expression of designed vaccine in pET28a(+) expression vector. This study offers a cost-effective and time-saving way to design a novel immunogenic vaccine that could be used to prevent VL infection.

Communicated by Ramaswamy H. Sarma     

Seed Priming with Iron Oxide Nanoparticles Triggers Iron Acquisition and Biofortification in Wheat (Triticum aestivum L.) Grains

Iron deficiency anaemia is a major challenge among consumers in developing countries. Given the deficiency of iron in the diet, there is an urgent need to devise a strategy for providing the required iron in the daily diet to counter the iron deficiency anaemia. We propose that iron biofortification of wheat (Triticum aestivum L.) through seed priming would be an innovative strategy to address this issue. This investigation attempts to find the interaction of iron oxide nanoparticles on germination, growth parameters and accumulation of grain iron in two contrasting wheat genotypes WL711 (low-iron genotype) and IITR26 (high-iron genotype). Wheat seeds were primed with different concentrations of iron oxide nanoparticles in the range of 25–600 ppm, resulting in differential accumulation of grain iron contents. We observed a pronounced increase in germination percentage and shoot length at 400 and 200 ppm treatment concentrations in IITR26 and WL711 genotypes, respectively. Intriguingly, the treatment concentration of 25 ppm demonstrated higher accumulation with a significant increase in grain iron contents to 45.7% in IITR26 and 26.8% in WL711 genotypes, respectively. Seed priming represents an innovative and user-friendly approach for wheat biofortification which triggers iron acquisition and accumulation in grains.

     

Endophytic Bacteria in Plant Salt Stress Tolerance: Current and Future Prospects

Soil salinity is a major limiting factor for crop productivity worldwide and is continuously increasing owing to climate change. A wide range of studies and practices have been performed to induce salt tolerance mechanisms in plants, but their result in crop improvement has been limited due to lack of time and money. In the current scenario, there is increasing attention towards habitat-imposed plant stress tolerance driven by plant-associated microbes, either rhizospheric and/or endophytic. These microbes play a key role in protecting plants against various environmental stresses. Therefore, the use of plant growth-promoting microbes in agriculture is a low-cost and eco-friendly technology to enhance crop productivity in saline areas. In the present review, the authors describe the functionality of endophytic bacteria and their modes of action to enhance salinity tolerance in plants, with special reference to osmotic and ionic stress management. There is concrete evidence that endophytic bacteria serve host functions, such as improving osmolytes, anti-oxidant and phytohormonal signaling and enhancing plant nutrient uptake efficiency. More research on endophytes has enabled us to gain insights into the mechanism of colonization and their interactions with plants. With this information in mind, the authors tried to solve the following questions: (1) how do benign endophytes ameliorate salt stress in plants? (2) What type of physiological changes incur in plants under salt stress conditions? And (3), what type of determinants produced by endophytes will be helpful in plant growth promotion under salt stress?

     

Niacin deficiency modulates genes involved in cancer: Are smokers at higher risk?

The role of niacin’s metabolite, nicotinamide adenine dinucleotide (NAD), in DNA repair via base-excision repair pathway is well documented. We evaluated if niacin deficiency results in genetic instability in normal human fetal lung fibroblasts (MRC-5), and further, does it leads to enhanced accumulation of cigarette smoke–induced genetic damage? MRC-5 cells were grown discretely in niacin-proficient/deficient media, and exposed to nicotine-derived nitrosamine ketone (NNK, a cigarette smoke carcinogen). Niacin deficiency abated the NAD polymerization, augmented the spontaneous induction of micronuclei (MN) and chromosomal aberrations (CA) and raised the expression of 10 genes and suppressed 12 genes involved in different biological functions. NNK exposure resulted in genetic damage as measured by the induction of MN and CA in cells grown in niacin-proficient medium, but the damage became practically marked when niacin-deficient cells were exposed to NNK. NNK exposure raised the expression of 16 genes and suppressed the expression of 56 genes in cells grown in niacin-proficient medium. NNK exposure to niacin-deficient cells raised the expression of eight genes including genes crucial in promoting cancer such as FGFR3 and DUSP1 and suppressed the expression of 33 genes, including genes crucial in preventing the onset and progression of cancer like RASSF2, JUP, and IL24, in comparison with the cells grown in niacin-proficient medium. Overall, niacin deficiency interferes with the DNA damage repair process induced by chemical carcinogens like NNK, and niacin-deficient population are at the higher risk of genetic instability caused by cigarette smoke carcinogen NNK.     

Circular RNA hsa_circ_0076248 promotes oncogenesis of glioma by sponging miR-181a to modulate SIRT1 expression

Glioma is one of the most common primary malignancies of the central nervous system, which has aggressive clinical behavior and a poorer prognosis. MicroRNAs (miRs) are a class of small noncoding RNAs that function as mediators of gene expression, which can be sponged by circRNA provided with a closed circular structure. Dysregulations of circular RNAs (circRNAs) and miRs have been implicated in the development and progression of glioma. In the current study, we investigated the role of circular RNA hsa_circ_0076248 in mediating the oncogenesis of glioma by sponging miR-181a to modulate silent information regulator 1 (SIRT1) expression in vitro and in vivo. The quantitative real-time polymerase chain reaction results showed that the expression of miR-181a was significantly decreased in glioma tissues and cell lines compared with normal brain tissues and normal gliocyte, respectively, and the expression of hsa_circ_0076248 and SIRT1 demonstrated the opposite. Bioinformatics analysis identified hsa_circ_0076248 could sponge miR-181a, and miR-181a could target the mRNA of SIRT1. Our results verified that downregulating hsa_circ_0076248 or upregulating miR-181a could depress the proliferation and invasion of glioma in vitro and in vivo. The experiment also showed that downregulating hsa_circ_0076248 or upregulating miR-181a could remarkably promote the temozolomide chemotherapy sensitivity. Furthermore, Western blot analysis testified that downregulating hsa_circ_0076248 or upregulating miR-181a could promote the expression of p53 and SIRT1. In summary, our study sheds light on the regulatory mechanism of hsa_circ_0076248 in glioma growth and invasion via sponging miR-181a, which downregulates the SIRT1 expression and also suggests that hsa_circ_0076248, miR-181a, and SIRT1 may serve as potential therapeutic targets for glioma.