Potent γ-secretase inhibitors/modulators interact with amyloid-β fibrils but do not inhibit fibrillation: A high-resolution NMR study

Recently, γ-secretase modulators (GSM) have been shown to interact directly with the amyloid precursor protein (APP) and simultaneously inhibit the activity of the Presenilin domain of γ-secretase. A clear understanding of the molecular recognition pathways by which GSM can target both γ-secretase and Aβ precursor protein can lead to the development of more effective inhibitors. To examine whether this direct interaction with APP affects the downstream Aβ fibril formation, we chose to investigate three different molecules in this study: Sulindac sulfide, Semagacestat and E2012 from the class of generation I GSMs, γ-secretase inhibitors (GSI), and generation II GSM molecules, respectively. Firstly, through NMR based ligand titration, we identified that Sulindac sulfide and Semagacestat interact strongly with Aβ40 monomers, whereas E2012 does not. Secondly, using saturation transfer difference (STD) NMR experiments, we found that all three molecules bind equally well with Aβ40 fibrils. To determine if these interactions with the monomer/fibril lead to a viable inhibition of the fibrillation process, we designed an NMR based time-dependent assay and accurately distinguished the inhibitors from the non-inhibitors within a short period of 12 h. Based on this pre-seeded fibril assay, we conclude that none of these molecules inhibit the ongoing fibrillation, rather ligands such as Semagacestat and E2012 accelerated the rate of aggregation.     

Auto-FACE: An NMR Based Binding Site Mapping Program for Fast Chemical Exchange Protein-Ligand Systems

Background

Nuclear Magnetic Resonance (NMR) spectroscopy offers a variety of experiments to study protein-ligand interactions at atomic resolution. Among these experiments, N Heteronuclear Single Quantum Correlation (HSQC) experiment is simple, less time consuming and highly informative in mapping the binding site of the ligand. The interpretation of N HSQC becomes ambiguous when the chemical shift perturbations are caused by non-specific interactions like allosteric changes and local structural rearrangement. Under such cases, detailed chemical exchange analysis based on chemical shift perturbation will assist in locating the binding site accurately.

Methodology/Principal Findings

We have automated the mapping of binding sites for fast chemical exchange systems using information obtained from N HSQC spectra of protein serially titrated with ligand of increasing concentrations. The automated program Auto-FACE (Auto-FAst Chemical Exchange analyzer) determines the parameters, e.g. rate of change of perturbation, binding equilibrium constant and magnitude of chemical shift perturbation to map the binding site residues. Interestingly, the rate of change of perturbation at lower ligand concentration is highly sensitive in differentiating the binding site residues from the non-binding site residues. To validate this program, the interaction between the protein and the ligand BH3I-1 was studied. Residues in the hydrophobic BH3 binding groove of were easily identified to be crucial for interaction with BH3I-1 from other residues that also exhibited perturbation. The geometrically averaged equilibrium constant () calculated for the residues present at the identified binding site is consistent with the values obtained by other techniques like isothermal calorimetry and fluorescence polarization assays (). Adjacent to the primary site, an additional binding site was identified which had an affinity of 3.8 times weaker than the former one. Further NMR based model fitting for individual residues suggest single site model for residues present at these binding sites and two site model for residues present between these sites. This implies that chemical shift perturbation can represent the local binding event much more accurately than the global binding event.

Conclusion/Significance

Detail NMR chemical shift perturbation analysis enabled binding site residues to be distinguished from non-binding site residues for accurate mapping of interaction site in complex fast exchange system between small molecule and protein. The methodology is automated and implemented in a program called “Auto-FACE”, which also allowed quantitative information of each interaction site and elucidation of binding mechanism.     

Nutritional and hormonal effects on storage proteins in the silkworm,Bombyx mori L.

Starvation of 48 h old fifth instar larvae depressed storage protein titres initially for 48 h but retained the levels comparable to control thereafter, possibly due to nutrients obtained during the 48 h feeding after fourth ecdysis. After an initial decline ligated larvae accumulated maximum storage proteins in haemolymph. This is because of inhibitory juvenile hormone titre at the basal level besides the appropriate release of 20-hydroxyecdysone from the ectopic source(s). Injection of methoprene (10 Μg/larva) repressed accumulation of storage proteins while 20-hydroxyecdysone (10 Μg/larva) increased the same. P-soyatose injection to starved and ligated larvae accelerated storage protein accumulation in haemolymph, signalling nutrient indispensability for initiation of storage protein synthesis at the appropriate time of last instar development inBombyx mori.     

Detection of genetic polymorphism in the populations of brinjal shoot and fruit borer, Leucinodes orbonalis (Guenee)

In the present study six different populations of L. orbonalis were collected and subjected to analysis of genetic variability in terms of carboxylesterase isozyme pattern and DNA polymorphism using RAPD-PCR. Pattern of carboxylesterase revealed a similar isozyme cluster in the populations namely, sivaganga (population-3), dindigal (population-4), virudhunagar (population-5) and coimbatore (population-6). Similarly, the populations of L. orbonalis recorded 3 distinct randomly amplified polymorphic DNA markers in all populations grouped above. This pattern of genetic variability in the populations was also supported by the analysis of the similarity indices and UPGMA dendrogram.     

Changes of haemolymph protein profile in the larva of Pericallia ricini (Fabricius) parasitised by the Braconid Wasp, Apanteles taragamae Viereck (Hymenoptera: Braconidae)

Parasitism by the braconid wasp, A. taragamae caused alterations in the haemolymph polypeptides of woolly bear larvae of P. ricini. Analysis of haemolymph proteins by SDS-PAGE and densitometry showed that the quantities of haemolymph proteins were reduced dramatically in the parasitised larvae. Simultaneously, parasitism induced large amount of 95 kDa polypeptides in the haemolymph of the parasitised larvae. Also, a remarkable induction of 43 and 45 kDa polypeptides which are not detectable in non-parasitised larvae appeared in the parasitised larvae.     

Phagodeterrence and insecticidal activity of Hyptis suaveolens (Poit.) against four important lepidopteran pests

This study was carried out to evaluate the antifeedant and larvicidal activities of Hyptis suaveolens Poit. (Lamiaceae) leaves crude extracts and their fractions against four lepidopteran pests namely Helicoverpa armigera (Hbn.), Spodoptera litura (Fab.), Earias vittella (Fab.) and Leucinodes orbonalis (G.). Hexane, chloroform and ethyl acetate extracts were tested by leaf disc and fruit disc no-choice methods at 1% and 1,000?ppm concentrations for crude and fractions, respectively. Ethyl acetate extract of H. suaveolens exhibited the maximum antifeedant and insecticidal activity at 1% concentration against all the tested insects. It was subjected to fractionation using silica column chromatography with different combinations of hexane and ethyl acetate used as mobile phase. Among the 15 fractions obtained, fraction 2 showed the maximum antifeedant and insecticidal activity against all tested insects at 1000?ppm concentration. Preliminary phytochemical analysis of fraction 2 showed the presence of terpenoids and alkaloids. H. suaveolens could be considered as a safe and eco-friendly insecticide for lepidopteron pest management.     

Diversity and analysis of sequences encoded by arcelin genes from Indian wild pulses resistant to bruchids

Wild pulse accessions are considered a vital source of genes for insect resistance for crop improvement programmes. Wild pulses resistant to infestation towards the bruchid insect pest, Callosobruchus maculatus from South India were chosen to screen the existence of potent insecticidal protein, arcelin from APA locus (Arcelin/Phytohemagglutinin/α-Amylase inhibitor) to ascertain their nature and functional diversity without any specific indication for insect resistant factors. The DNA sequence coding for arcelin from various species of wild pulses were amplified, sequenced and deduced to their protein sequences. These protein sequences were examined physico-chemically using several bioinformatics tools and docked with various sugars to resolve the nature of arcelin molecules. Results indicated the presence of significant differences in the properties of arcelin molecules from various species of Indian wild pulses with their amino acid sequences, several physico-chemical properties and binding ability with sugars. The differences observed on these arcelin molecules from diverse wild pulses are predicted to provide a prospective insect pest control factors.     

Phosphoramidate and phosphate prodrugs of (-)-beta-D-(2R,4R)-dioxolane-thymine: synthesis, anti-HIV activity and stability studies

A series of phosphoramidate and phosphate prodrugs of DOT were synthesized via dichlorophosphate or H-phosphonate chemistry and evaluated for their anti-HIV activity against LAI M184V mutants in PBM cells as well as for their cytotoxicity. The antiviral and cytotoxic profiles of the prodrugs were compared with that of the parent compound (DOT), and it was found that four aryl phosphoramidates 5, 18, 20, and 26 showed a significant enhancement (8- to 12-fold) in anti-HIV activity without cytotoxicity. Chemical stability of these prodrugs was evaluated in phosphate buffer at pH values of biological relevance (i.e., pH 2.0 and 7.4). Enzymatic hydrolysis was also studied in esterase or lipase in buffer solution. Chemical stability studies indicate that the phosphoramidates have good chemical stability at pH 2.0 and at pH 7.4 phosphate buffer. Phosphoramidate prodrugs were hydrolyzed in vitro by esterase or lipase and found to be better substrates for lipases than for esterases. 1,3-Diol cyclic phosphates showed potent anti-HIV activity without increasing the cytotoxicity compared with that of DOT and have good chemical and enzymatic stability. Long-chain lipid phosphates, although showed potent anti-HIV activity, exhibited increased cytotoxicity.     

Recycling spent larval food of Corcyra cephalonica stainton as a broiler feed ingredient

In commercial insectaries, large-scale production of rice moth, Corcyra cephalonica Stainton in pearl millet grain medium leads to an extensive accumulation of spent C. cephalonica larval medium (CLM). Experiments were conducted to determine whether inclusion of CLM for corn in the standard broiler diet (SBD) could ensure normal growth and development of broilers. Chemical analysis revealed that CLM diets met the nutritional requirements as of SBD. CLM diet contained no aflatoxin as well. Biological experiments were conducted to study the suitability of CLM diet in different combinations with SBD at 100% + 0%, 75% + 25%, 50% + 50%, 25% + 75% and 0% + 100% w/w without any nutritional change, and after nutritional modification with corn starch. CLM replacement was based on the corn content of the basal diet. Birds preferred SBD 100% and SBD 75% + CLM 25% nutritionally unchanged diets, and showed higher growth rate and weight gain. These parameters were significantly lower in other diet combinations. Modified isoenergetic CLM based diets in all the combinations, however, contributed higher feed intake and resulted in more weight gain as of SBD. Furthermore, none of treatments in both experiments yielded bird mortalities. The experimental CLM diets except SBD 75% + CLM 25% in both experiments were cost effective and contributed lower diet cost/kg weight gain.