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.     

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.     

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.     

Measurement of storage time, estimation of ion number and study of absorption line profile in a Paul trap

Europium (Eu⁺) ions were confined in a Paul trap and detected by non-destructive method. Storage time of Eu⁺ ions achieved in vacuum was improved by orders of magnitude employing buffer gas cooling. The experimentally detected signal was fitted to the ion response signal and the total number of ions trapped was estimated. It is found that the peak signal amplitude as well as the product of FWHM and the peak signal amplitude is proportional to the total number of trapped ions. The trapped ion secular frequency was swept at different rates and its effect on the absorption line profile was studied both experimentally and theoretically.     

Thermal desorption of interacting molecules from mixed adlayers

A Monte Carlo simulation method is used to study thermal desorption of gas molecules from mixed adlayers containing two species. The effects of lateral interactions among adatoms and initial surface coverage on the desorption spectra are examined. It is shown that attractive lateral interactions lead to sharper peaks and that desorption occurs at high temperatures, whereas repulsive interactions lead to multiple peak spectra. It is found that interactions between unlike molecules affect the spectra for species with lower desorption energy only, and that the two species desorb together only in certain cases. Lateral interactions also affect the desorption kinetics significantly and very different behavior for the two species may be obtained.     

A microspectroscopic study of the electronic homogeneity of ordered and disordered Sr2FeMoO6

Disordered Sr₂FeMoO₆ shows a drastic reduction in saturation magnetization compared to highly ordered samples, moreover magnetization as a function of the temperature for different disordered samples shows qualitatively different behaviours. We investigate the origin of such diversity by performing spatially resolved photoemission spectroscopy on various disordered samples. Our results establish that e_xtensive electronic inhomogeneity, arising most probably from an underlying chemical inhomogeneity in disordered samples, is responsible for the observed magnetic inhomogeneity. It is further pointed out that these inhomogeneities are connected with composition fluctuations of the type Sr₂Fe_1+x Mo_1-x O₆ with Fe-rich (x > 0) and Mo-rich (x < 0) regions. Dedicated to Prof J Gopalakrishnan on his 62nd birthday.     

Direct and inverse estimates for a new family of linear positive operators

In the present paper we introduce a new family of linear positive operators and study some direct and inverse results in simultaneous approximation.     

Modified Householder iterative method free from second derivatives for nonlinear equations

In this paper, we suggest and analyze a new two-step predictor–corrector type iterative method free from second derivatives for solving nonlinear equations of the type f(x)=0. This new method includes the two-step Newton method as a special case. We prove that the new iterative method is of fourth-order. Several examples are given to illustrate the efficiency of this new method and its comparison with other iterative methods. This method can be considered as a significant improvement of the Newton method and its variant forms.     

On the dispersion of a solute in oscillating flow of a non-Newtonian fluid in a channel

The paper presents an exact analysis of the dispersion of an immiscible solute in a non-Newtonian fluid (known as an incompressible second-order fluid which shows viscoelastic behaviour) flowing slowly in a parallel plate channel in the presence of a periodic pressure gradient. Using a generalized dispersion model which is valid for all times after the solute injection, the diffusion coefficients K _i (τ)(i=1,2,3,…) are obtained as functions of time τ in the case when the initial solute distribution is in the form of a slug of finite extent. The analysis leads to the novel result that K ₂(τ) (which is a measure of the longitudinal dispersion coefficient of the solute) has a steady part S in addition to a fluctuating part D ₂(τ) due to the pulsatility of the flow. It is found that S decreases with increase in the viscoelastic parameter M for given values of the amplitude λ and frequency ω of the pressure pulsation. On the other hand, it is found that at a fixed instant τ, the amplitude of D ₂(τ) increases with increase in M for given values of λ and ω. Further it is shown that at a given instant τ, the amplitude of D ₂(τ) decreases with increase in ω for given λ and M and the profile for D ₂(τ) becomes progressively flatter with increase in ω. Finally the axial distribution of the average concentration θ _m of the solute over the channel cross-section is determined at different instants after the solute injection for several values of M, λ and ω. The present study is likely to have important bearing on the problem of dispersion of tracers in blood flow through arteries.