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.     

Dynamics of the periodic type-K competitive Kolmogorov systems

For time-periodic dissipative and irreducible type-K competitive Kolmogorov systems, it is proved that there is a canonically defined countable family F of unordered, disjoint invariant sets with the property that, for every persistent trajectory whose ω-limit set is not a cycle, there exists a unique trajectory in some element of F such that these two trajectories are asymptotic and the corresponding points in these two trajectories are K-related.     

Optimal inspection and perfect repair

Models are developed for decision making about monitoring andmaintenance of systems whose performance through time is describedby a general stochastic process. The system is monitored andpreventive and corrective maintenance actions are carried outin response to the observed system state. The decision processis simplified by using the maximum process as a decision variable.The models developed generalize age replacement models and othersimple maintenance strategies. The approach can deal with failuresthat prevent the system functioning further, and also failuresthat are defined by regulation or economic considerations. Attentionis restricted to perfect repair and inspection, but the structureprovides the framework for further developments.     

Highly Effective Phenol Hydroxylation over Ti-ZSM-5 Catalyst Prepared Using B-ZSM-5 as Precursor 以B-ZSM-5为母体合成Ti-ZSM-5高效苯酚羟基化催化剂

 以改进方法合成的B-ZSM-5为母体,采用气固相同晶取代法合成了较小晶粒的Ti-ZSM-5分子筛. 考察了样品的物化性能和催化苯酚羟基化性能. 结果表明: 所合成的小晶粒Ti-ZSM-5具有较高的结晶度,尺寸为100~200 nm,且不含锐钛矿型TiO2,对苯酚羟基化反应的催化性能优异.     

Preparation of Silica-Silk Fibroin-Polyurethane Composite Films via a Sol-Gel Route

A tetraethoxysilane (TEOS)-derived sol aged for 0 h–6 h at room temperature was mixed with a polyurethane (PU) matrix. A composite of silk fibroin (SF) powders and acrylamide (AAm) was dispersed in the sol-PU mixture and dried isothermally at temperatures between 25°C and 120°C to obtain composite films. Three competitive reactions take place, i.e., those between silica-silica, SF-PU and silica-organic phases, during formation of the composite films. These reactions determine the properties such as morphology and homogeneity of the composite films. IR absorption bands for amide groups (–CONH–), C=O (amide I, 1730 cm^–1) and N–H (amide II, 1530 cm^–1) become larger with decreasing aging time of TEOS-derived sol, or increasing drying temperature. DTA exothermic peak due to the thermal decomposition of SF-AAm composite, on the composite films prepared from the 0 h-aged sol or dried at more than 50°C, shifts toward higher temperature by 44 K or more than 63 K respectively, as compared to the SF-AAm composite. Shorter aging time of TEOS-derived sol and higher drying temperature increased the extent of dispersibility, among SF-AAm composite, PU and silica, to bring a composite film more homogeneous.     

Formation of N-cyclopropylhydrazones by azo coupling of cyclopropyldiazonium with aliphatic CH acids

Decomposition of N-cyclopropyl-N-nitrosourea under the action of K₂CO₃ or KOH containing 15—20% of H₂O at 0—7 °C gives rise to cyclopropyldiazonium, which reacts with some -diketones, methyl cyanoacetate, or malonodinitrile to form the corresponding cyclopropylhydrazones. The latter compounds are analogous to products of azo coupling and isomerization of aryldiazonium ions with the above-mentioned substrates. These transformations provide the first example of azo coupling of the cyclopropyldiazonium ion in the series of activated aliphatic CH acids.     

SINGLE AND BINARY ADSORPTION PERFORMANCE OF SALICYLIC ACID AND 5-SULFOSALICYLIC ACID ONTO HYPERCROSSLINKED POLYMERIC ADSORBENTS

Single and binary adsorption behaviors of salicylic acid and 5-sulfosalicylic acid onto hypercrosslinked polymeric adsorbents, i.e. NDA-101 and NDA-99 were investigated. The Freundlich model can successfully describe all the adsorption isotherms tested, which indicates a favorable and exothermic adsorption process. The adsorption of salicylic acid relies on π-π interaction, while the electrostatic interaction further influences the adsorption of 5-sulfosalicylic acid onto NDA-99. The adsorptive capacity of salicylic acid on NDA-99 decreases but increases on NDA-101 with 5-sulfosalicylic acid as the background component in a binary solute system. The amount of 5-sulfosalicylic acid adsorbed was decreased with the increase in initial concentration of salicylic acid on both adsorbents. The competition for the adsorption sites is considered to be predominant in the solid-to-liquid interaction process. The adsorption selectivity of salicylic acid onto NDA-101 is higher than onto NDA-99 by more than an order of magnitude. Thus, combination technique involving NDA-101 followed by NDA-99 can be effectively applied to separate and recover salicylic acid and 5-sulfosalicylic acid from wastewater.     

Molecular Replacement Studies of Cucurmosin from Cucurbita Moschata:Structure Homology with Trichosanthin

1 INTRODUCTION Many plants contain proteins that are capable of inactivating ribosomes and therefore are called ribosome-inactivating proteins or RIPs[1]. RIPs are RNA N-glycosidases that inactivate ribosomes through a site-specific deadenylation of the large ribosomal RNA[2, 3]. RIPs are also capable of inactivating many nonribosomal nucleic acid substrates and can be considered as polynucleotide: adenosine glycosidases[4～6]. There are two types of RIPs: type I, single chain pr…     

Competitive potentiometric determination of binding constants between α-cyclodextrin and 1-alkanols

The binding constants of 1-alkanols with α-cyclodextrin (α-CD) were determined by indirect competitive potentiometry, although potentiometry is usually inapplicable to nonionic compounds. This novel method utilizes competitive binding of 1-alkanol and octyltrimethylammonium bromide (OTAB) to α-CD in aqueous media, where the concentration of free OTAB depending on the competitive binding is monitored with an OTAB-selective electrode. Therefore, the concentration of 1-alkanol is indirectly estimated from the observed electromotive force. The binding constants of 1-propapnol, 1-butanol, 1-hexanol, and 1-octanol with α-CD, obtained by this method, are close to the literature values. The implications and limitations of this indirect competitive potentiometry were discussed.     

Inclusion complexes of proteins: Interaction of cyclodextrins with peptides containing aromatic amino acids studied by competitive spectrophotometry

The stability constants were measured of inclusion complexes formed from aromatic amino acids and their oligopeptides with - and-cyclodextrin, hydroxypropyl-cyclodextrin, and partially methylated-cyclodextrin. The method of competitive spectrophotometry withp-nitrophenol as a competing reagent was used, and measurements were made at pH 7.4-Cyclodextrin formed complexes of higher stability than the other hosts. The stability of complexes of oligopeptides containing L-phenylalanine was invariably higher than that of L-phenylalanine itself. A model for interaction of proteins with cyclodextrins is proposed, in which the most stable complexes are formed when the native functional form of proteins is unfolded and the nonpolar residues that are buried inside the structure are exposed to water. The complexation of the unfolded structure favors its formation; thus thermal denaturation of proteins is easier in the presence of cyclodextrins. On the other hand, this complexation prevents the intermolecular association of unfolded structures by noncovalent hydrophobic bonding between the exposed nonpolar residues; furthermore, the unfolded complexed forms may revert to the native functional form. This prevention of intermolecular association may explain the stabilizing effect of cyclodextrins on solutions of proteins: a return to the native form is achieved more easily from the complexed, unfolded form than from the unfolded, aggregated forms.Dedicated to Professor József Szejtli.