Computational Design of Novel Allosteric Inhibitors for Plasmodium falciparum DegP

The serine protease, DegP exhibits proteolytic and chaperone activities, essential for cellular protein quality control and normal cell development in eukaryotes. The P. falciparum DegP is essential for the parasite survival and required to combat the oscillating thermal stress conditions during the infection, protein quality checks and protein homeostasis in the extra-cytoplasmic compartments, thereby establishing it as a potential target for drug development against malaria. Previous studies have shown that diisopropyl fluorophosphate (DFP) and the peptide SPMFKGV inhibit E. coli DegP protease activity. To identify novel potential inhibitors specific to PfDegP allosteric and the catalytic binding sites, we performed a high throughput in silico screening using Malaria Box, Pathogen Box, Maybridge library, ChEMBL library and the library of FDA approved compounds. The screening helped identify five best binders that showed high affinity to PfDegP allosteric (T0873, T2823, T2801, {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, CD00811) and the catalytic binding site (T0078L, T1524, T2328, BTB11534 and 552691). Further, molecular dynamics simulation analysis revealed {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, BTB11534 as the best hits forming a stable complex. WaterMap and electrostatic complementarity were used to evaluate the novel bio-isosteric chemotypes of {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, that led to the identification of 231 chemotypes that exhibited better binding affinity. Further analysis of the top 5 chemotypes, based on better binding affinity, revealed that the addition of electron donors like nitrogen and sulphur to the side chains of butanoate group are more favoured than the backbone of butanoate group. In a nutshell, the present study helps identify novel, potent and Plasmodium specific inhibitors, using high throughput in silico screening and bio-isosteric replacement, which may be experimentally validated.     

An efficient method for the synthesis of quinoxaline derivatives catalyzed by titanium silicate-1

Research on Chemical Intermediates - A series of quinoxaline derivatives were efficiently synthesized by convenient and simple procedure in excellent yields using 1 wt.% of titanium silicate (TS-1)...     

On c‐Bhaskar Rao designs with block size 4

Several new families of c‐Bhaskar Rao designs with block size 4 are constructed. The necessary conditions for the existence of a c‐BRD (υ,4,λ) are that: (1)λ_min=?λ/3 ≤ c ≤ λ and (2a) c≡λ (mod 2), if υ > 4 or (2b) c≡ λ (mod 4), if υ = 4 or (2c) c≠ λ ? 2, if υ = 5. It is proved that these conditions are necessary, and are sufficient for most pairs of c and λ; in particular, they are sufficient whenever λ?c ≠ 2 for c > 0 and whenever c ? λ_min≠ 2 for c < 0. For c < 0, the necessary conditions are sufficient for υ> 101; for the classic Bhaskar Rao designs, i.e., c = 0, we show the necessary conditions are sufficient with the possible exception of 0‐BRD (υ,4,2)'s for υ≡ 4 (mod 6). © 2002 Wiley Periodicals, Inc. J Combin Designs 10: 361–386, 2002; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jcd.10009     

Activity of microemulsion-based nanoparticles at the human bio-nano interface: concentration-dependent effects on thrombosis and hemolysis in whole blood

Background: Although microemulsion-based nanoparticles (MEs) may be useful for drug delivery or scavenging, these benefits must be balanced against potential nanotoxicological effects in biological tissue (bio-nano interface). We investigated the actions of assembled MEs and their individual components at the bio-nano interface of thrombosis and hemolysis in human blood. Methods: Oil-in-water MEs were synthesized using ethylbutyrate, sodium caprylate, and pluronic F-68 (ME4) or F-127 (ME6) in 0.9% NaCl_w/v. The effects of MEs or components on thrombosis were determined using thrombo-elastography, platelet contractile force, clot elastic modulus, and platelet counting. For hemolysis, ME or components were incubated with erythrocytes, centrifuged, and washed for measurement of free hemoglobin by spectroscopy. Results and conclusions: The mean particle diameters (polydispersity index) for ME6 and ME4 were 23.6 ± 2.5 nm (0.362) and 14.0 ± 1.0 nm (0.008), respectively. MEs (0, 0.03, 0.3, 3 mM) markedly reduced the thromboelastograph maximal amplitude in a concentration-dependent manner (49.0 ± 4.2, 39.0 ± 5.6, 15.0 ± 8.7, 3.8 ± 1.3 mm, respectively), an effect highly correlated (r2 = 0.94) with similar changes caused by pluronic surfactants (48.7 ± 10.9, 30.7 ± 15.8, 20.0 ± 11.3, 2.0 ± 0.5) alone. Neither oil nor sodium caprylate alone affected the thromboelastograph. The clot contractile force was reduced by ME (27.3 ± 11.1–6.7 ± 3.4 kdynes/cm², P = 0.02, n = 5) whereas the platelet population not affected (175 ± 28–182 ± 23 10⁶/ml, P = 0.12, n = 6). This data suggests that MEs reduced platelet activity due to associated pluronic surfactants, but caused minimal changes in protein function necessary for coagulation. Although pharmacological concentrations of sodium caprylate caused hemolysis (EC₅₀ = 213 mM), MEs and pluronic surfactants did not disrupt erythrocytes. Knowledge of nanoparticle activity and potential associated nanotoxicity at this bio-nano interface enables rational ME design for in vivo applications.     

Magnetic poly(N‐isopropylacrylamide) microspheres by dispersion and inverse emulsion polymerization

The aim of this study was to develop novel thermally responsive polymer microspheres with magnetic properties. Dispersion and inverse emulsion copolymerization of N‐isopropylacrylamide (NIPAAm) and N,N′‐methylenebisacrylamide (MBAAm) was investigated in the presence of γ‐Fe₂O₃ nanoparticles. The resulting microspheres were characterized in terms of morphology, size, polydispersity, iron content, and temperature‐dependent swelling using optical microscopy, transmission electron microscopy, scanning electron microscopy, QELS, and AAS. The effects of several variables, such as the concentration of γ‐Fe₂O₃, MBAAm crosslinking agent, Span 80 surfactant, 2,2′‐azobis(2‐methyloctanenitrile) (AMON) initiator, and polymerization temperature on the properties of the microspheres were studied. Swelling and thermoresponsive behavior of the microspheres containing γ‐Fe₂O₃ nanoparticles were also investigated. The microspheres contained about 8 wt % of iron. The presence of magnetic nanoparticles and their concentration changes did not have any significant effect on the temperature sensitivity of the composites. The particles gradually shrink into an increasingly collapsed state when the temperature is raised to 40 °C since the increase in temperature weakens the hydration and PNIPAAm chains gradually become more hydrophobic, which leads to the collapse of the particles. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 5884–5898, 2007     

Time structure of iodine laser pulse in the free running mode of operation

Time structure of iodine laser pulse in the free running mode of operation was studied using the power amplifier of laser system PERUN as the laser oscillator. Two characteristic shapes of laser pulse correspond to different regimes of laser operation, the existence of which is ascribed to the critical concentration of I₂ molecules. Simultaneously an additional chemical pumping was proved at least in the initial phase of photodissociation and in a late-time lasing after the end of flashlamps pumping light.     

Oxidation of isoniazid by quinolinium dichromate in an aqueous acid medium and kinetic determination of isoniazid in pure and pharmaceutical formulations.

The kinetics of oxidation of isoniazid in acidic medium was studied spectrophotometrically. The reaction between QDC and isoniazid in acid medium exhibits (4:1) stoichiometry (QDC:isoniazid). The reaction showed first order kinetics in quinolinium dichromate (QDC) concentration and an order of less than unity in isoniazid (INH) and acid concentrations. The oxidation reaction proceeds via a protonated QDC species, which forms a complex with isoniazid. The latter decomposes in a slow step to give a free radical derived from isoniazid and an intermediate chromium(V), which is followed, by subsequent fast steps to give the products. The reaction constants involved in the mechanism are evaluated. Isoniazid was analyzed by kinetic methods in pure and pharmaceutical formulations.