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.     

Magnetic and martensitic transitions in Ni-Fe-Ga alloy

The ferromagnetic shape memory alloy with nominal composition Ni₅₄Fe₁₉Ga₂₇ is investigated by Ac susceptibility and resistivity measurements. The alloy shows long-range ferromagnetic order below 290 K. The anomaly due to the martensitic transition is observed in the susceptibility and resistivity data in the temperature range around 220 K, which is associated with clear thermal hysteresis. Minor hysteresis loop technique was used to investigate the phase coexistence across the martensitic transition, and our analysis indicate that both martensite and austenite phases mutually coexist in the region of hysteresis.     

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 decomposition of a generation 4.5 PAMAM dendrimer platinum drug conjugate

A nanoscale multivalent platinum drug based on a poly(amidoamine) [PAMAM] dendrimer (generation 4.5, carboxylate surface) has been synthesized and fully characterized using a variety of spectroscopic, chromatographic and thermal methods. Treatment of the dendrimer with an aqueous solution containing an excess diaquo(cis-1,2-diaminocyclohexane)platinum(II) produces a conjugate containing approximately forty (diaminocyclohexane)platinum(II) moieties at the surface of the dendrimer. This material undergoes smooth two-stage thermal decomposition to provide residual platinum oxide reflecting the platinum loading in the drug.     

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.     

High-rate vector quantization for detection

We investigate high-rate quantization for various detection and reconstruction loss criteria. A new distortion measure is introduced which accounts for global loss in best attainable binary hypothesis testing performance. The distortion criterion is related to the area under the receiver-operating-characteristic (ROC) curve. Specifically, motivated by Sanov's theorem, we define a performance curve as the trajectory of the pair of optimal asymptotic Type I and Type II error rates of the most powerful Neyman-Pearson test of the hypotheses. The distortion measure is then defined as the difference between the area-under-the-curve (AUC) of the optimal pre-encoded hypothesis test and the AUC of the optimal post-encoded hypothesis test. As compared to many previously introduced distortion measures for decision making, this distortion measure has the advantage of being independent of any detection thresholds or priors on the hypotheses, which are generally difficult to specify in the code design process. A high-resolution Zador-Gersho type of analysis is applied to characterize the point density and the inertial profile associated with the optimal high-rate vector quantizer. The analysis applies to a restricted class of high-rate quantizers that have bounded cells with vanishing volumes. The optimal point density is used to specify a Lloyd-type algorithm which allocates its finest resolution to regions where the gradient of the pre-encoded likelihood ratio has greatest magnitude.     

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.