A computational overview of integrase strand transfer inhibitors (INSTIs) against emerging and evolving drug-resistant HIV-1 integrase mutants.

AIDS (Acquired immunodeficiency syndrome) is one of the chronic and potentially life-threatening epidemics across the world. Hitherto, the non-existence of definitive drugs that could completely cure the Human immunodeficiency virus (HIV) implies an urgent necessity for the discovery of novel anti-HIV agents. Since integration is the most crucial stage in retroviral replication, hindering it can inhibit overall viral transmission. The 5 FDA-approved integrase inhibitors were computationally investigated, especially owing to the rising multiple mutations against their susceptibility. This comparative study will open new possibilities to guide the rational design of novel lead compounds for antiretroviral therapies (ARTs), more specifically the structure-based design of novel Integrase strand transfer inhibitors (INSTIs) that may possess a better resistance profile than present drugs. Further, we have discussed potent anti-HIV natural compounds and their interactions as an alternative approach, recommending the urgent need to tap into the rich vein of indigenous knowledge for reverse pharmacology. Moreover, herein, we discuss existing evidence that might change in the near future.

Biologically Synthesized Silver Nanoparticles and Their Diverse Applications.

Nanotechnology has become the most effective and rapidly developing field in the area of material science, and silver nanoparticles (AgNPs) are of leading interest because of their smaller size, larger surface area, and multiple applications. The use of plant sources as reducing agents in the fabrication of silver nanoparticles is most attractive due to the cheaper and less time-consuming process for synthesis. Furthermore, the tremendous attention of AgNPs in scientific fields is due to their multiple biomedical applications such as antibacterial, anticancer, and anti-inflammatory activities, and they could be used for clean environment applications. In this review, we briefly describe the types of nanoparticle syntheses and various applications of AgNPs, including antibacterial, anticancer, and larvicidal applications and photocatalytic dye degradation. It will be helpful to the extent of a better understanding of the studies of biological synthesis of AgNPs and their multiple uses.

Computational approach to explore the inhibitory potential of biologically derived compounds against Spodoptera litura vitellogenin receptor (VgR) using structure based virtual screening and molecular dynamics.

In the everlasting combat against the pests of agricultural importance, it is essential to come up with a novel strategy for pest control. This can be achieved through understanding the insect pest at cellular and molecular levels. Vitellogenin (Vg) and vitellogenin receptor (VgR) are essential for successful reproduction in insect. The N-terminal Ligand Binding Domain (LBD) of VgR is responsible for the transportation of vital protein (Vg) to the developing oocyte through receptor mediated endocytosis pathway. This can be implemented to various predicaments and betterments for exploitation in pest management, in a target specific and eco-friendly manner. For this, natural metabolites isolated from various biological sources were used as ligand. The purpose of this study was to analyze the inhibitory potential of 14 biologically derived compounds against N-terminal (Ligand Binding Repeats) LBRs of S. litura by computational docking. 3 D structure of LBRs of S. litura was generated by Raptor X software and the structure was refined and validated. The validated structure was docked using autodock vina. Docking results revealed that spinosyn A and milbemycin A4 have inhibitory activity against VgR. Molecular dynamics (MD) simulation confirms the stable binding of the ligand. From the above results, spinosyn A and milbemycin A4 may be exploited for the pest management.Communicated by Ramaswamy H. Sarma.

Immunoglobulin interface redesigning to enhance lebrikizumab mediated immunomodulation of IL-13 hyper-response.

The overexpression of interleukin-13 (IL-13) leads to autoimmune and inflammatory diseases. These adverse responses can be neutralized by using lebrikizumab as a therapeutic monoclonal antibody (mAb). Herein, we have attempted to modulate the lebrikizumab mAb to enhance its binding affinity towards IL-13. The interface residues of the lebrikizumab-IL-13 complex were determined by the PyMOL and verified by the artificial neural network-based B-cell epitope prediction server (ABCpred server) and the Paratome web server. The Cologne University Protein Stability Analysis Tool (CUPSAT) web server based mutational approach was used to identify the stable and favorable interface mutations in the lebrikizumab. Only 40 mutations were selected to generate a single mutant library, and their binding affinity for IL-13 was analyzed by using the Z-Dock server. Based on high Z-score, mutants having a better affinity with IL-13 were selected to create a multi-mutant library. The multi-mutant library was again subjected to the Z-Dock server, and their binding affinity was determined. The highest-scoring ten mAb mutants were validated by using PatchDock and ClusPro servers. The best two potential mAb mutants were identified and subjected to molecular dynamics (MD) simulations to ensure its structural stability at the microscopic level. The changes in the different bonds as the effect of mutation were assessed by LigPlot + v2.1. The AllerTOP and ToxinPred web servers were used to analyze the non-allergic and nontoxic nature of the selected mutants. Therefore, these redesigned mAb could be used for potential treatment against IL-13 associated diseased conditions.Communicated by Ramaswamy H. Sarma.

A new black fly species of Simulium (Nevermannia) (Simuliidae: Diptera) from the Southern Eastern Ghats, India.

A new black fly species, Simulium (Nevermannia) karavalliense sp. nov. is described from Southern Eastern Ghats of South India. This new species is placed in the Simulium ruficorne species-group of the subgenus Nevermannia. S. (N.) karavalliense sp. nov. is characterized by female with a long sensory vesicle, male upper eye with 14 vertical columns and 16 horizontal rows of large facets, pupal gill with 8 filaments and larval hypostoma with 6 hypostomal bristles lying parallel to lateral margin. Taxonomic keys are provided to distinguish this new species from related species in India.

A new mayfly species of Choroterpes (Euthraulus) (Ephemeroptera: Leptophlebiidae) from South India.

A new mayfly species, Choroterpes (Euthraulus) kalladaensis sp. n. is described based on nymphs and subimagoes from South India. The nymph of Choroterpes (Euthraulus) kalladaensis sp. n. is characterized by a labrum with antero-median emargination well broad and 'V' shaped, femora with two black spots on median and basal region, claw with 2 sections of 13 denticles with 3 smaller serrations, posteriolateral spines present on segment 2-9, paraprocts smooth with pores and their inner margin with small triangular spines and outer margin with long setae and in the subimago the fore wing has four intercalary veins between costa and subcosta, penis lobes are short, membranous, separated apically and covered with minute setae. Taxonomic notes are given to distinguish this new species from closely related species.

In Vivo Anti Cancer Potential of Pyrogallol in Murine Model of Colon Cancer.

Background: Colon cancer is aggressive and it causes 0.5 million deaths per year. Practicing natural medicines for cancer treatment is safer than conventional drugs. World health organization emphasizes on the importance of practicing natural medicines and developing natural product based drugs for cancer treatment. Recently we reported an anti colon cancer activity associated with pyrogallol isolated from medicinal plant Acacia nilotica in HT-29 cells in vitro. To extend our observation in this study we evaluated in vivo colon tumor remission property of acetone extract of A. nilotica (ACE) and pyrogallol. Materials and Methods: In vivo toxicity of ACE and pyrogallol was assessed and In vivo tumor remission activity of ACE and pyrogallol was determined in murine model. Results: Mice were tolerated different doses of ACE and pyrogallol. Tumor size was considerably reduced in pyrogallol treated mice similar to doxorubicin. Tumor bearing mice treated with ACE and pyrogallol showed mild decline in body weight. Conclusion: Pyrogallol was found to be an effective anti colon cancer agent with less toxicity.

A new species of Simulium (Gomphostilbia) (Diptera: Simuliidae) from South India.

Simulium (Gomphostilbia) kumbakkaraiense sp. n. is described based on adults, pupae and mature larvae from Kumbakkarai stream, in the Palani Hills of Western Ghats, South India. This new species is placed in the Simulium batoense species-group of the subgenus Gomphostilbia Enderlein. This new species is characterized by a scutum with three brownish-black longitudinal vittae and hind basitarsus in the female 5.3 times as long as wide, and in male the large facets of the upper eye in 13 vertical columns and 14 horizontal rows, the respiratory gill with short common basal in the pupa and postgenal cleft arrow-head-shaped in the larva. Taxonomic notes are provided to distinguish this new species from related species. [Zoobank register: http://zoobank.org/urn:lsid:zoobank.org:act:C575FB25-B6B2-414B-AE11-0468A1871DFA].

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.

Induction of HT-29 Colon Cancer Cells Apoptosis by Pyrogallol with Growth Inhibiting Efficacy Against Drug-Resistant Helicobacter pylori.

BACKGROUND: Colon cancer is the most aggressive form of cancers, that causes 0.5 million deaths per year around the globe. Targeting colon cancer by conventional therapeutic options elicits toxicity. Traditional medicines take a lead to alleviate the existing clinical challenges. OBJECTIVE: To investigate antibacterial activity against Helicobacter Pylori and in vitro anti-colon cancer activity by Acacia nilotica extract (ACE) and its active constituent pyrogallol. METHODS: Pyrogallol isolated from A. nilotica by column chromatography and HPLC and structure was elucidated by spectral analysis. Antibacterial activity was done by flow cytometry. Cytotoxicity was measured by MTT assay. Apoptotic morphology and nuclear fragmentation were assessed with AO/ethidium bromide and DAPI staining. DNA fragmentation was done by electrophoresis. Western blot used to analyze the molecular mechanism of apoptosis. Cell cycle arrest was determined using flow cytometry of propidium iodide stained cells. Cell migration was determined by wound healing assay. RESULTS: ACE (20 µg/ml) and pyrogallol (10 µg/ml) treatment reduced the survival of H.pylori at 61% and 62%, respectively. MTT results show that HT-29 cells are more sensitive to pyrogallol with an IC50 value of 35µg/ml compared to ACE. Pyrogallol treated HT-29 cells reached dead state i.e. late apoptotic state with severe nuclear fragmentation. Pyrogallol elicits dose dependent DNA fragmentation in HT-29 cells. Pyrogallol induced apoptosis by simultaneous down-regulation of Bcl-2 and up-regulation of BAX and cytochrome c. Pyrogallol arrested HT-29 cells in S and G2/M phase of cell cycle. Further pyrogallol exhibited marked antimetastatic potential by inhibiting the migration of HT-29 cells dose dependently. CONCLUSION: Both ACE and pyrogallol repressed the growth of H.pylori and as significant anti-colon cancer agent.

Encapsulation and Systemic Delivery of 5-Fluorouracil Conjugated with Silkworm Pupa Derived Protein Nanoparticles for Experimental Lymphoma Cancer.

Protein-based drug delivery systems have an edge over conventional drug delivery systems due to their biodegradability, non-antigenicity, and excellent biocompatibility to improve the therapeutic properties of anticancer drugs. This study describes the increased anticancer efficacy of 5-fluorouracil (5-FU) conjugated with silkworm Bombyx mori pupal biowaste derived nanoparticles. Here, we have checked the toxicity of pupa-protein nanoparticles (PpNps) and their potential as a carrier for anticancer drugs. PpNps were prepared by a desolvation method which resulted in a uniform particle size of 162.7 ± 2.9 nm. The 5-FU loaded PpNps were formulated and characterized. The drug content of the developed 5-FU conjugated nanoparticles was evaluated by HPLC analysis. The entrapment efficiency and loading capacity of 5-FU were analyzed by HPLC and determined to be 93% and 88.6%, respectively. The release studies showed the biphasic release of 5-FU at pH 7.4 where rapid drug release was achieved for first 30 min, followed by a sustained release of 5-FU from the developed Nps achieved for the next 8 h. Mice with developed ascites tumors were intraperitoneally treated with 5-FU-PpNps and sacrificed. There was a significant increase in total red blood cells and hemoglobulin in 5-FU-PpNps treated mice, whereas a significant decrease in white blood cells which indicated the reduced inflammation of cancer. Subsequently, 5-FU-PpNps decreased the tumor volume and tumor cell viability, which proved its cytotoxic property to cancer cells. This study presents a novel approach to derive B. mori pupal protein nanoparticles, which can be safely used for cancer drug delivery.

Investigation of immunogenic properties of Hemolin from silkworm, Bombyx mori as carrier protein: an immunoinformatic approach.

Infectious diseases are the major cause of high mortality among infants and geriatric patients. Vaccines are the only weapon in our arsenal to defend us ourselves against innumerable infectious diseases. Though myriad of vaccines are available, still countless people die due to microbial infections. Subunit vaccine is an effective strategy of vaccine development, combining a highly immunogenic carrier protein with highly antigenic but non-immunogenic antigen (haptens). In this study we have made an attempt to utilize the immunoinformatic tool for carrier protein development. Immunogenic mediators (T-cell, B-cell, IFN-γ epitopes) and physiochemical properties of hemolin protein of silkworm, Bombyx mori were studied. Hemolin was found to be non-allergic and highly antigenic in nature. The refined tertiary structure of modelled hemolin was docked against TLR3 and TLR4-MD2 complex. Molecular dynamics study emphasized the stable microscopic interaction between hemolin and TLRs. In-silico cloning and codon optimization was carried out for effective expression of hemolin in E. coli expression system. The overall presence of Cytotoxic T Lymphocytes (CTL), Humoral T Lymphocytes (HTL), and IFN-γ epitopes with high antigenicity depicts the potential of hemolin as a good candidate for carrier protein.

Immunoinformatics approaches to design a novel multi-epitope subunit vaccine against HIV infection.

The end goal of HIV vaccine designing requires novel strategies to elicit a strong humoral and cell-mediated immune response. The emergence of drug resistance and the requirement of next line treatment necessitate the finding of the potential and immunogenic vaccine candidate. This study employed a novel immunoinformatics approach to design multi-epitope subunit vaccine against HIV infection. Here, we designed the subunit vaccine by the combination of CTL, HTL and BCL epitopes along with suitable adjuvant and linkers. Physiochemical characterization of subunit vaccine was assessed to ensure its thermostability, theoretical PI, and amphipathic behavior. In further assessment, subunit vaccine was found to be immunogenic with the capability to generate humoral and cell-mediated immune response. Further, homology modeling and refinement was performed and the refined modeled structure was used for molecular docking with the immune receptor (TLR-3) present on lymphocyte cells. Consequently, molecular dynamics simulation ensured the molecular interaction between TLR-3 and subunit vaccine candidate. Disulfide engineering was performed by placing the cysteine residues in the region of high mobility to enhance the vaccine stability. At last, in silico cloning was performed to warrant the translational efficiency and microbial expression of the designed vaccine.

Species diversity of black flies (Diptera: Simuliidae) in Oriental region and molecular phylogeny of the subgenus Gomphostilbia members.

BACKGROUND & OBJECTIVES: Black flies (Diptera: Simuliidae) are ecologically and medically important insects. Female adults of black flies are the solitary vectors of river blindness (onchocerciasis) and their larvae play a vital role in stream ecosystem. This study examined the distribution of black flies in the Oriental region and analyzed the phylogenetic relationship of the subgenus Gomphostilbia members based on two molecular loci. METHODS: The distribution data of black fly species in different countries of Oriental region were obtained from world black flies geographic inventory. The two gene sequences, COI and ITS1 were used to study the phylogenetic relationships of the members of subgenus Gomphostilbia members. RESULTS: The distribution analysis revealed that out of the 16 subgenera in the genus Simulium Latreille s., the species-level diversity of three subgenera (Gomphostilbia, Nevermannia and Simulium) contributes about thrice of total black fly species diversity. The highest diversity of species was found in the subgenus Simulium. The strict consensus of Tree analysis using New Technology (TNT) and Maximum Likelihood (ML) recovered similar topolo- gies for Gomphostilbia members and they formed as monophyly. The overall sequence identities of the 19 species of subgenus Gomphostilbia were high and shared 55-60% similarity. INTERPRETATION & CONCLUSION: Results of this study highlighted that eight subgenera of Simulium Latreille s. str are commonly distributed in different parts of Oriental region. Among these the subgenera of Simulium, Gomphostilbia and Nevermannia are most common with high diversity in China, Pakistan, Thailand and Vietnam. The phylogenetic analysis of Gomphostilbia members demonstrates the inter-specific divergence, indicating the centre of origin (India) or the recipient of ancestral migrant lineages in Oriental region.

Assessment of bacterial community composition in response to uranium levels in sediment samples of sacred Cauvery River.

Global industrialization is a major cause of effluent discharge from industries up to alarming concentrations. Especially, uranium concentrations in water bodies are of great concern, as its radioactivity significantly affects the persistent diversity of microbiota. Recently, continuous application of pesticides in the agricultural lands and accumulation of quartz that enter the Cauvery River has significantly increased the concentration of uranium (U) and other heavy metals. To perceive the impact of uranium on bacterial diversity in Cauvery River, sediment samples collected from polluted (UP) site with 32.4 Bq/K of U concentration and control (UNP) site were scrutinized for bacterial diversity through metagenomic analysis of the V3 region of 16S rDNA by Illumina sequencing. Taxonomic assignment revealed that the unpolluted sample was dominated by Bacteroidetes (27.7 %), and Firmicutes (25.9 %), while sediment sample from the highly polluted site revealed abundance of Proteobacteria (47.5 %) followed by Bacteroidetes (22.4 %) and Firmicutes (14.6 %). Among Proteobacteria, Gammaproteobacteria was the most prevalent group followed by alpha, delta, epsilon, and beta in the uranium-polluted sample. Rare and abundant species analysis revealed that species like Idiomarina loihiensis was abundant in the pollutant sample; however, it was rare (<0.1 %) in the sample from pristine environment. Similarly, the species distribution in both the samples varied, with the bacteria potentially active in redox activity and biosorption potential dominating in the polluted sample. Outcomes of the present study demonstrated the impact of uranium and metal accumulation on the bacterial communities and further confirmed the promising candidature of specific bacterial species as bioindicators of contamination.

A new species of Prosopistoma Latreille, 1833 (Ephemeroptera: Prosopistomatidae) from South India.

A new species of Prosopistoma (Ephemeroptera: Prosopistomatidae) is described on the basis of mature nymphs from Coorg, Karnataka, South India. Prosopistoma coorgum, new species can be readily distinguished from the other members of Prosopistoma by the following combination of characters: inner margin of outer canine near apex with 2-3 short spines, the length ratio of maxillary palp segments (3.3:4.8:1), ventral margin of fore tibia with 6-8 pectinate setae, and gill II leaf-like and cleft.

A new species of Simulium (Gomphostilbia) (Diptera: Simuliidae) from South India, with keys to Indian members of the subgenus Gomphostilbia.

A new black fly species, Simulium (Gomphostilbia) cauveryense sp. n., is described based on adult female, adult male, pupal and larval specimens collected from Kushalanagar, Karnataka, South India. This new species is placed in the decuplum subgroup of the batoense species-group within the subgenus Gomphostilbia. Keys to the species of the subgenus Gomphostilbia reported from India are provided for females, males, pupae and mature larvae.

Antiapoptotic activity of 30 kDa lipoproteins family from fat body tissue of silkworm, Bombyx mori.

The family of 30 kDa lipoproteins (LP1-5) is abundant in silkworm pupa fat body (FB) and hemolymph. One of its members, the 29 kDa protein decreased in concentration from peripheral (PP) FB tissue but was sustained in perivisceral (PV) FB tissue at the time of apoptosis. This study investigated the correlation of the 30 kDa proteins with FB apoptosis. Two protein fractions were purified, a 29 and a 30/31 kDa protein fraction, and they were used to test for activity against actinomycin D-induced apoptosis in the FB tissues. Concentrations as little as 50 µg/mL of the 29 kDa protein fraction efficiently inhibited apoptosis. Less antiapoptotic activity was detected for the higher MW fraction; DNA fragmentation was observed in FB tissue treated with 50 µg/mL of the 30/31 kDa fraction. The viability of the cells in the 29 kDa protein-supplemented culture was 40% higher than in the 31 kDa protein-supplemented culture. However, the 30 kDa lipoproteins were not able to prevent scheduled FB degeneration during silkworm metamorphosis. Thus, it is hypothesized that the antiapoptotic 29 kDa protein needs to be proteolytically degraded by a regulatory mechanism to allow programmed cell death of FB tissue.

Hsp70 is an independent stress marker among frequent users of mobile phones.

The aim of this study was to measure the serum concentrations of heat shock protein (HSP) 70 and C-reactive protein (CRP) and the expression levels of the hsp70 gene among frequent users of mobile phones (FUMPs). We enrolled 120 employees of information technology (IT)/IT enabled service companies (FUMPs; IT professionals) and 102 infrequent users of mobile phones (IFUMPs; people from non-IT professions) as controls. The serum concentrations of HSP70 and CRP were measured by enzyme-linked immunosorbant assay and hsp70 gene expression by reverse transcription polymerase chain reaction. Significantly higher concentrations of serum HSP70 (P < 0.00012) and CRP (P < 0.04) were observed among FUMPs than IFUMPs. A higher level of hsp70 gene expression (fold induction) was observed among FUMPs than IFUMPs (P < 7.06 × 10-13). In contrast to the duration of exposure-dependent increase of serum concentration of CRP, the serum HSP70 concentration was found to be independent of the duration of exposure to mobile phones. Thus, the study convincingly demonstrated the role of serum HSP and CRP as systemic inflammatory biomarkers for mobile phone-induced radiation.

Two new species of Simulium (Gomphostilbia) (Diptera: Simuliidae) from Peninsular India with keys to Peninsular Indian members of the genus Simulium.

Two new species of black flies, Simulium (Gomphostilbia) peteri sp. nov. and S. (G.) takaokai sp. nov., are described on the basis of reared adult, pupal and larval specimens collected from Peninsular India. These two new species are placed in the batoense species group within the subgenus Gomphostilbia. S. (G.) peteri sp. nov. is distinguished in the female by having a medium-sized round opening of the sensory vesicle and a large basal tooth on the claw, in the male by 12 vertical columns in the upper eye large facets, in the pupa by a ventral pair of 2 gill filaments somewhat thicker than the other filaments and in the larva by 5 hypostomal bristles per side lying parallel to the lateral margin. S. (G.) takaokai sp. nov. is characterized in the pupa by having the eight gill filaments with a medium-long common basal stalk and in the larva by the labral fan with 38 main rays and 4 hypostomal bristles on each side. Keys to 13 black fly species reported from Peninsular India are provided for females, males and pupae.