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.     

Generalizations of the Nikodym boundedness and Vitali–Hahn–Saks theorems

Generalizations of the Nikodym boundedness and Vitali–Hahn–Saks theorems for scalar-valued measures on rings of sets that are in general not σ-rings are presented. As a consequence, the rings of subsets of N with density zero and uniform density zero are shown to have the Nikodym property. In addition, vector measure generalizations of the Vitali–Hahn–Saks theorem are given.     

Synthesis of molecular imprinted organic-inorganic hybrid polymer binding caffeine

Random copolymers of poly{(methacrylamide)-co-(vinyl trimethoxysilane)} and poly{(methacrylic acid)-co-(vinyl trimethoxysilane)} were synthesized via a free radical polymerization reaction. Acid catalyzed sol-gel process of tetraethylorthosilicate (TEOS) with aforementioned polymers in the presence of methyl xanthine class of alkaloid like caffeine resulted in the formation of highly transparent monoliths. Solvent extraction of the template leaves behind the recognition sites intact with high selectivity towards the print molecule. The ionic and non-specific adsorptions, which are considered to be the main disadvantages of the molecularly imprinted polymers (MIP), are prevented to a considerable extent by the end capping of surface silanol groups. The template binding efficiencies of MIP were determined by HPLC analysis.     

Comparative behavior of polybutadiene and polynorbornene‐based latices prepared by dispersion ring‐opening metathesis polymerization with a poly(ethylene oxide) macromonomer

This study critically examines the similarities and differences between poly(ethylene oxide) (PEO) stabilized latices of polynorbornene and polybutadiene. Features such as the kinetics of copolymerization of norbornene and cyclooctadiene with a macromonomer of PEO, the particles' size and morphology, the type of copolymer formed, and the stability of these latices were investigated and the results obtained are considered. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 2705–2716, 2004     

The exponential power law: partial wetting kinetics and dynamic contact angles

An equation for the kinetics of partial drop spreading is proposed. This equation was empirically derived from experimental data for the spreading kinetics of partially wetting liquids in terms of the wet area versus time. The equation has the form of an exponential power law (EPL), and transforms into the well-known power law for complete wetting, when the equilibrium contact angle approaches zero. The EPL fits very well available experimental data. To lend additional support to the validity of this generalized equation, it will be demonstrated that when it is transformed to present the dynamic contact angle (DCA), it fits very well DCA experimental data for other wetting processes, such as capillary flow and tape coating.     

The diameter of randomly perturbed digraphs and some applications

The central observation of this paper is that if εn random arcs are added to any n‐node strongly connected digraph with bounded degree then the resulting graph has diameter 𝒪(lnn) with high probability. We apply this to smoothed analysis of algorithms and property testing. Smoothed Analysis: Recognizing strongly connected digraphs is a basic computational task in graph theory. Even for digraphs with bounded degree, it is NL‐complete. By XORing an arbitrary bounded degree digraph with a sparse random digraph R ∼ 𝔻_n,ε/n we obtain a “smoothed” instance. We show that, with high probability, a log‐space algorithm will correctly determine if a smoothed instance is strongly connected. We also show that if NL ⫅̸ almost‐L then no heuristic can recognize similarly perturbed instances of (s,t)‐connectivity. Property Testing: A digraph is called k‐linked if, for every choice of 2k distinct vertices s₁,…,s_k,t₁,…,t_k, the graph contains k vertex disjoint paths joining s_r to t_r for r = 1,…,k. Recognizing k‐linked digraphs is NP‐complete for k ≥ 2. We describe a polynomial time algorithm for bounded degree digraphs, which accepts k‐linked graphs with high probability, and rejects all graphs that are at least εn arcs away from being k‐linked. © 2007 Wiley Periodicals, Inc. Random Struct. Alg., 2007     

Corner spontaneous magnetization

Details are given of a new method allowing an exact calculation of the spontaneous magnetization in the corner as well as along the edge at an arbitrary distance of the corner for a rectangular planar Ising ferromagnet.