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.     

Stereoselective synthesis of 3,4-trans-disubstituted pyrrolidines and cyclopentanes via intramolecular radical cyclizations mediated by CAN

The stereoselective intramolecular cyclizations of bis(cinnamyl)tosylamides and dimethyl bis(cinnamyl)malonates mediated by cerium(IV) ammonium nitrate leading to the synthesis of 3,4-trans-disubstituted pyrrolidines and cyclopentanes are described.     

An efficient synthesis of isothiazolidines via sulfonium ylides formed by the reaction of thietanes and nitrene

An efficient synthesis of isothiazolidines in good yields is described.     

Total electron scattering cross sections for carbon dioxide at low electron energies

Absolute total electron scattering cross sections for carbon dioxide have been measured at low electron energies using a photoelectron source. The measurements have been carried out at 27 electron energies varying from 0.91–9.14 eV with an accuracy of ±3%. The cross sections obtained in the present experiment have been compared with other measurements and theoretical computations.     

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.     

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.     

On composition of some general fractional integral operators

In the present paper we derive three interesting expressions for the composition of two most general fractional integral oprators whose kernels involve the product of a general class of polynomials and a multivariableH-function. By suitably specializing the coefficients and the parameters in these functions we can get a large number of (new and known) interesting expressions for the composition of fractional integral operators involving classical orthogonal polynomials and simpler special functions (involving one or more variables) which occur rather frequently in problems of mathematical physics. We have mentioned here two special cases of the first composition formula. The first involves product of a general class of polynomials and the Fox’sH-functions and is of interest in itself. The findings of Buschman [1] and Erdélyi [4] follow as simple special cases of this composition formula. The second special case involves product of the Jacobi polynomials, the Hermite polynomials and the product of two multivariableH-functions. The present study unifies and extends a large number of results lying scattered in the lierature. Its findings are general and deep.