In-silico analysis of Calcium Dependent Protein Kinase 6 of Cryptosporidium parvum through molecular modeling, docking, and dynamics simulation study.

Calcium Dependent Protein Kinases are found in the Apicomplexan, algae, and plants; however, they are not reported in vertebrates and are regarded as excellent drug targets for pharmaceutical interventions. Calcium Dependent Protein Kinases of Cryptosporidium are probably involved in the regulation of invasion and egress process during the infection of the host cells. The previous study reported that after the Calcium Dependent Protein Kinase 1 gene, Calcium Dependent Protein Kinase 6 of Cryptosporidium parvum is expressed in all stages of the parasite (merozoites/schizonts as well as sexual stages) at a comparable level and makes it as a valid drug target. In this study, an attempt is made to address the similarity in sequences and phylogenetic study of Calcium Dependent Protein Kinase 6 (CDPK6) among Calcium Dependent Protein Kinases of Apicomplexans. Further, the three-dimensional structure determination of CDPK6 of C. parvum was performed through a molecular modeling approach followed by virtual screening of small-molecule inhibitors from different datasets. The best inhibitor from Tres Cantos Antimalarial Set with ID 11730 reported a binding affinity of -8.2 kcal/mol against CDPK6 of C. parvum. Furthermore, the reliability of the binding mode of the inhibitor is validated through a complex molecular dynamics simulation study for a time interval of 100 ns. The simulation study advocates that the inhibitor Tres Cantos Antimalarial Set_11730 formed a stable interaction with the predicted active site residues and can be considered for industrial pharmaceutical research in future.Communicated by Ramaswamy H. Sarma.

An immunoinformatics approach for design and validation of multi-subunit vaccine against Cryptosporidium parvum.

An immunoinformatics-based approach is explored for potential multi-subunit vaccine candidates against Cryptosporidium parvum. We performed protein structure based systematic methodology for the development of a proficient multi-subunit vaccine candidate against C. parvum based on their probability of antigenicity, allergenicity and transmembrane helices as the screening criteria. The best-screened epitopes like B-cell epitopes (BCL), Helper T-lymphocytes (HTL) and cytotoxic T- lymphocytes (CTL) were joined by using the appropriate linkers to intensify and develop the presentation and processing of the antigenic molecules. Modeller software was used to generate the best 3D model of the subunit protein. RAMPAGE and other web servers were employed for the validation of the modeled protein. Furthermore, the predicted modeled structure was docked with the two known receptors like TLR2 and TLR4 through ClusPro web server. Based on the docking score, the multi-subunit vaccine docked with TLR2 was subjected to energy minimization by molecular dynamics (MD) simulation to examine their stability within a solvent system. From the simulation study, we found that the residue Glu-107 of subunit vaccine formed a hydrogen bond interaction with Arg-299 of the TLR2 receptor throughout the time frame of the MD simulation. The overall results showed that the multi-subunit vaccine could be an efficient vaccine candidate against C. parvum.

In-silico screening of small molecule inhibitors against Lactate Dehydrogenase (LDH) of Cryptosporidium parvum.

Cryptosporidium parvum is a protozoan parasite which causes waterborne diseases known as Cryptosporidiosis. It is an acute enteric diarrheal disease being severe in the case of immunocompromised individuals and children. C. parvum mainly depends on the glycolysis process for energy production and LDH (Lactate Dehydrogenase) is a key controller of this process. In this study from different in-silico approaches such as structure-based, ligand-based and de novo drug design; a total of 40 compounds were selected for docking studies against LDH. The study reported a compound CHEMBL1784973 from Pathogen Box as the best inhibitor in terms of docking score and pharmacophoric features. Furthermore, the binding mode of the best-reported inhibitor was validated through molecular dynamics simulation for a time interval of 70 ns in water environment. The findings resulted in the stable conformation of the inhibitor in the active site of the protein. This study will be helpful for experimental validation.

Peanut skin extract mediated synthesis of gold nanoparticles, silver nanoparticles and gold-silver bionanocomposites for electrochemical Sudan IV sensing.

Sustainable methods are needed for rapid and efficient detection of environmental and food pollutants. The Sudan group of dyes has been used extensively as adulterants in food and also are found to be polluting the soil and water bodies. There have been several methods for detection of Sudan dyes, but most of them are not practical enough for common use. In this study, the electrochemical detection efficiency and stability of gold nanoparticle (AuNPs), silver NPs and Au-Ag bionanocomposites, synthesised by peanut skin extract, modified glassy carbon electrode has been investigated. The synthesised nanomaterial samples were characterised, for their quality and quantity, using ultra-visible spectroscopy, inductive coupled plasma mass spectrophotometer, Fourier transform infrared spectroscopy, energy-dispersive X-ray spectroscopy, high-resolution transmission electron microscope and field emission scanning electron microscope. The nanomaterial hybrid electrodes showed great efficiency and stability in the detection of Sudan IV compared with the other previous electrodes. The peak current of the Sudan IV oxidation and reduction was found to be proportional to its concentration, in the range of 10-80 µM, with a detection limit of 4 µM. The hybrid electrodes showed 90% stability in detection for 20 cycles.

Autoclave mediated one-pot-one-minute synthesis of AgNPs and Au-Ag nanocomposite from Melia azedarach bark extract with antimicrobial activity against food pathogens.

BACKGROUND: The increasing use of nanoparticles and nanocomposite in pharmaceutical and processed food industry have increased the demand for nontoxic and inert metallic nanostructures. Chemical and physical method of synthesis of nanostructures is most popular in industrial production, despite the fact that these methods are labor intensive and/or generate toxic effluents. There has been an increasing demand for rapid, ecofriendly and relatively cheaper synthesis of nanostructures. METHODS: Here, we propose a strategy, for one-minute green synthesis of AgNPs and a one-pot one-minute green synthesis of Au-Ag nanocomposite, using Melia azedarach bark aqueous extract as reducing agent. The hydrothermal mechanism of the autoclave technology has been successfully used in this study to accelerate the nucleation and growth of nano-crystals. RESULTS: The study also presents high antimicrobial potential of the synthesized nano solutions against common food and water born pathogens. The multistep characterization and analysis of the synthesized nanomaterial samples, using UV-visible spectroscopy, ICP-MS, FT-IR, EDX, XRD, HR-TEM and FE-SEM, also reveal the reaction dynamics of AgNO3, AuCl3 and plant extract in synthesis of the nanoparticles and nanocomposite. CONCLUSIONS: The antimicrobial effectiveness of the synthesized Au-Ag nanocomposite, with high gold to silver ratio, reduces the dependency on the AgNPs, which is considered to be environmentally more toxic than the gold counterpart. We hope that this new strategy will change the present course of green synthesis. The rapidity of synthesis will also help in industrial scale green production of nanostructures using Melia azedarach.

Computational identification of microRNAs and their targets in Catharanthus roseus expressed sequence tags.

No study has been performed on identifying microRNAs (miRNAs) and their targets in the medicinal plant, Catharanthus roseus. In the present study, using the comparative genomics approach, we have predicted two potential C. roseus miRNAs. Furthermore, twelve potential mRNA targets were identified in C. roseus genome based on the characteristics that miRNAs exhibit perfect or nearly perfect complementarity with their targeted mRNA sequences. Among them many of the targets were predicted to encode enzymes that regulate the biosynthesis of terpenoid indole alkaloids (TIA). In addition, most of the predicted targets were the gene coding for transcription factors which are mainly involved in cell growth and development, signaling and metabolism. This is the first in silico study to indicate that miRNA target gene encoding enzymes involved in vinblastine and vincristine biosynthesis, which may help to understand the miRNA-mediated regulation of TIA alkaloid biosynthesis in C. roseus.

Computational identification of sweet wormwood (Artemisia annua) microRNA and their mRNA targets.

Despite its efficacy against malaria, the relatively low yield (0.01%-0.8%) of artemisinin in Artemisia annua is a serious limitation to the commercialization of the drug. A better understanding of the biosynthetic pathway of artemisinin and its regulation by both exogenous and endogenous factors is essential to improve artemisinin yield. Increasing evidence has shown that microRNAs (miRNAs) play multiple roles in various biological processes. In this study, we used previously known miRNAs from Arabidopsis and rice against expressed sequence tag (EST) database of A. annua to search for potential miRNAs and their targets in A. annua. A total of six potential miRNAs were predicted, which belong to the miR414 and miR1310 families. Furthermore, eight potential target genes were identified in this species. Among them, seven genes encode proteins that play important roles in artemisinin biosynthesis, including HMG-CoA reductase (HMGR), amorpha-4,11-diene synthase (ADS), farnesyl pyrophosphate synthase (FPS) and cytochrome P450. In addition, a gene coding for putative AINTEGUMENTA, which is involved in signal transduction and development, was also predicted as one of the targets. This is the first in silico study to indicate that miRNAs target genes encoding enzymes involved in artemisinin biosynthesis, which may help to understand the miRNA-mediated regulation of artemisinin biosynthesis in A. annua.