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.     

Impedimetric Detection of DNA Damage with the Sensor Based on Silver Nanoparticles and Neutral Red

Novel electrochemical DNA‐sensor based on glassy carbon electrode (GCE) modified with Ag nanoparticles, Neutral red covalently attached to its surface and native DNA adsorbed on modifier coating was developed for the estimation of DNA damage on example of model system based on Fenton reagent. As was shown, the oxidation process resulted in synchronous increase of electron transfer resistance and capacitance measured by electrochemical impedance spectroscopy (EIS). The contribution of each sensor component on the signal was specified and sensitivity estimated against similar surface coatings. The shift of EIS parameters was found to be higher than that of similar biosensors reported. The DNA sensor was tested on the estimation of antioxidant capacity of green tea infusions again the results of coulometric titration with electrogenerated bromine.     

Soft Neutral Elastic Inhomogeneities with Membrane-type Interface Conditions

A foreign body, called an “inhomogeneity,” when introduced in a host solid disturbs the stress field which is present in it. One can explore the possibility of modifying the contact mechanism between the inhomogeneity and the host body so as to leave the stress field in the host solid undisturbed. If such a procedure succeeds, then the inhomogeneity is called “neutral.” Modification of the contact mechanism between the inhomogeneity and the host solid can be achieved, for example, by a suitably designed thick or thin interphase between them. When the interphase is thin, it can be represented by an “imperfect interface” model. In the present study we consider “soft” inhomogeneities which are more compliant than the host body. A “membrane-type interface” which models a thin and stiff interphase is used in rendering such inhomogeneities neutral. Illustrative examples are constructed for cylindrical neutral inhomogeneities of elliptical cross section under a triaxial loading, and for spheroidal inhomogeneities subjected to an axisymmetric loading.      

中性人乳寡糖的分离及结构鉴定

以脱脂、除蛋白后的人乳为原料,联合运用阴离子交换色谱(AEC)、凝胶渗透色谱(GPC)和多孔石墨化碳色谱(PGC)等多种分离纯化技术制备了18种中性人乳寡糖,并采用电喷雾碰撞诱导串联质谱(ESI-CIDMS/MS)技术对其结构进行了鉴定.结果表明,所制备的中性人乳寡糖主要为三至九糖,含有半乳糖(Gal)、葡萄糖(Glc)、N-乙酰葡萄糖胺(GlcNAc)和岩藻糖(Fuc).所有寡糖的还原端均含有乳糖核心(Galβ1-4Glc),非还原端均含有乳糖胺(Galβ1-3/4GlcNAc),并且Fuc以α1-2,α1-3和α1-4连接于主链的Gal,Glc和GlcNAc上.     

Limiting the Number of Potential Binding Modes by Introducing Symmetry into Ligands: Structure‐Based Design of Inhibitors for Trypsin‐Like Serine Proteases

In the absence of X‐ray data, the exploration of compound binding modes continues to be a challenging task. For structure‐based design, specific features of active sites in different targets play a major role in rationalizing ligand binding characteristics. For example, dibasic compounds have been reported as potent inhibitors of various trypsin‐like serine proteases, the active sites of which contain several binding pockets that can be targeted by cationic moieties. This results in several possible orientations within the active site, complicating the binding mode prediction of such compounds by docking tools. Therefore, we introduced symmetry in bi‐ and tribasic compounds to reduce conformational space in docking calculations and to simplify binding mode selection by limiting the number of possible pocket occupations. Asymmetric bisbenzamidines were used as starting points for a multistage and structure‐guided optimization. A series of 24 final compounds with either two or three benzamidine substructures was ultimately synthesized and evaluated as inhibitors of five serine proteases, leading to potent symmetric inhibitors for the pharmaceutical drug targets matriptase, matriptase‐2, thrombin and factor Xa. This study underlines the relevance of ligand symmetry for chemical biology.     

Phosphono Bisbenzguanidines as Irreversible Dipeptidomimetic Inhibitors and Activity‐Based Probes of Matriptase‐2

Matriptase‐2, a type II transmembrane serine protease, plays a key role in human iron homeostasis. Inhibition of matriptase‐2 is considered as an attractive strategy for the treatment of iron‐overload diseases, such as hemochromatosis and β‐thalassemia. In the present study, synthetic routes to nine dipeptidomimetic inactivators were developed. Five active compounds ( 41 – 45 ) were identified and characterized kinetically as irreversible inhibitors of matriptase‐2. In addition to a phosphonate warhead, these dipeptides possess two benzguanidine moieties as arginine mimetics to provide affinity for matriptase‐2 by binding to the S1 and S3/S4 subpockets, respectively. This binding mode was strongly supported by covalent docking analysis. Compounds 41 – 45 were obtained as mixtures of two diastereomers and were therefore separated into the single epimers. Compound 45 A , with S configuration at the N‐terminal amino acid and R configuration at the phosphonate carbon atom, was the most potent matriptase‐2 inactivator with a rate constant of inactivation of 2790 m ^?1 s^?1 and abolished the activity of membrane‐bound matriptase‐2 on the surface of intact cells. Based on the chemotyp of phosphono bisbenzguanidines, the design and synthesis of a fluorescent probe ( 51 A ) by insertion of a coumarin label is described. The in‐gel fluorescence detection of matriptase‐2 was demonstrated by applying 51 A as the first activity‐based probe for this enzyme.     

On nonexistence of Kneser solutions of third-order neutral delay differential equations

The aim of this paper is to complement existing oscillation results for third-order neutral delay differential equations by establishing sufficient conditions for nonexistence of so-called Kneser solutions. Combining newly obtained results with existing ones, we attain oscillation of all solutions of the studied equations.