Exploring the Distinct Binding and Activation Mechanisms for Different CagA Oncoproteins and SHP2 by Molecular Dynamics Simulations

CagA is a major virulence factor of Helicobacter pylori. H. pylori CagA is geographically subclassified into East Asian CagA and Western CagA, which are characterized by the presence of a EPIYA-D or EPIYA-C segment. The East Asian CagA is more closely associated with gastric cancer than the Western CagA. In this study, molecular dynamic (MD) simulations were performed to investigate the binding details of SHP2 and EPIYA segments, and to explore the allosteric regulation mechanism of SHP2. Our results show that the EPIYA-D has a stronger binding affinity to the N-SH2 domain of SHP2 than EPIYA-C. In addition, a single EPIYA-D binding to N-SH2 domain of SHP2 can cause a deflection of the key helix B, and the deflected helix B could squeeze the N-SH2 and PTP domains to break the autoinhibition pocket of SHP2. However, a single EPIYA-C binding to the N-SH2 domain of SHP2 cannot break the autoinhibition of SHP2 because the secondary structure of the key helix B is destroyed. However, the tandem EPIYA-C not only increases its binding affinity to SHP2, but also does not significantly break the secondary structure of the key helix B. Our study can help us better understand the mechanism of gastric cancer caused by Helicobacter pylori infection.     

A Computational Approach Applied to the Study of Potential Allosteric Inhibitors Protease NS2B/NS3 from Dengue Virus

Dengue virus (DENV) is a danger to more than 400 million people in the world, and there is no specific treatment. Thus, there is an urgent need to develop an effective method to combat this pathology. NS2B/NS3 protease is an important biological target due it being necessary for viral replication and the fact that it promotes the spread of the infection. Thus, this study aimed to design DENV NS2B/NS3pro allosteric inhibitors from a matrix compound. The search was conducted using the Swiss Similarity tool. The compounds were subjected to molecular docking calculations, molecular dynamics simulations (MD) and free energy calculations. The molecular docking results showed that two compounds, ZINC000001680989 and ZINC000001679427, were promising and performed important hydrogen interactions with the Asn152, Leu149 and Ala164 residues, showing the same interactions obtained in the literature. In the MD, the results indicated that five residues, Lys74, Leu76, Asn152, Leu149 and Ala166, contribute to the stability of the ligand at the allosteric site for all of the simulated systems. Hydrophobic, electrostatic and van der Waals interactions had significant effects on binding affinity. Physicochemical properties, lipophilicity, water solubility, pharmacokinetics, druglikeness and medicinal chemistry were evaluated for four compounds that were more promising, showed negative indices for the potential penetration of the Blood Brain Barrier and expressed high human intestinal absorption, indicating a low risk of central nervous system depression or drowsiness as the the side effects. The compound ZINC000006694490 exhibited an alert with a plausible level of toxicity for the purine base chemical moiety, indicating hepatotoxicity and chromosome damage in vivo in mouse, rat and human organisms. All of the compounds selected in this study showed a synthetic accessibility (SA) score lower than 4, suggesting the ease of new syntheses. The results corroborate with other studies in the literature, and the computational approach used here can contribute to the discovery of new and potent anti-dengue agents.     

Surfactants Used in Food Industry: A Review

The understanding of the formation, structures, and properties of emulsions is essential to the creation and stabilization of structures in food. The increasing use of surfactants, the identification of compounds with low toxicity and good surface activity properties is of great interest. The relevance of the major end points specified in the Organisation for Economic Co-operation and Development (OECD) guidelines for the hazard assessment of food chemicals is critically analyzed and main parameters are acute toxicity, subacute repeated studies, allergy, reproductive toxicity, long-term studies, and mutagenicity tests. We focus this article on surfactant association structures and food colloids. There is almost infinite number of combinations are organized and arranged in very complex internal microstructures with various types of assemblies such as dispersions, emulsions, foams, gels, etc. Low-mass surfactants are very mobile at the interface and they are particularly efficient reducing the interfacial tension. As a result, they rapidly coat the freshly created oil-water interface during emulsification. In this category, we mainly mentioned monoglycerides, lecithins, glycolipids, fatty alcohols and fatty acids. High-mass surfactants cover protein and polysacharide groups. The protein molecule may interpenetrate in the lipid phase to various degrees. The specific binding is predominantly electrostatic: The headgroups of the surfactants bind to groups of opposite charge on the protein. The saturation binding for anionic surfactants is pH-independent and seems to be controlled by the cooperative hydrophobic interactions. Polysaccharides and smallmolecule surfactants are two of the predominant groups of amphiphilic materials that have been explored for the stabilization of emulsions. One of the most important aspects of polymer-surfactant systems is their ability to control stability and rheology over a wide range of composition. Biocompatible, biodegradable, and/or nontoxic emulsion-based formulations have great potential for applications in the food. The combination of particular characteristics such as emulsifying, anti-adhesive and antimicrobial activities presented by biosurfactants suggests potential application as multipurpose ingredients or additives.     

Positive Allosteric Control of Guests Encapsulation by Metal Binding to Covalent Porphyrin Cages

The allosteric control of the receptor properties of two flexible covalent cages is reported. These receptors consist of two zinc(II) porphyrins connected by four linkers of two different sizes, each incorporating two 1,2,3-triazolyl ligands. Silver(I) ions act as effectors, responsible for an on/off encapsulation mechanism of neutral guest molecules. Binding silver(I) ions to the triazoles opens the cages and triggers the coordination of pyrazine or the encapsulation of N,N′-dibutyl-1,4,5,8-naphthalene diimide. The X-ray structure of the silver(I)-complexed receptor with short connectors is reported, revealing the hollow structure with a cavity well-defined by two eclipsed porphyrins. Rather unexpectedly, the crystallographic structure of this receptor with pyrazine as a guest molecule showed that the cavity is occupied by two pyrazines, each binding to the zinc(II) porphyrin in a monotopic fashion.     

Computational Investigation on the Allosteric Modulation of Androgen Receptor

Androgens have similar structures with different biological activities. To identify molecular determinants responsible for the activity difference, we have docked six steroidal androgens to the binding site or the surface of androgen receptor by using molecular docking with computational investigation. The energy was calculated respectively based on the QM (quantum mechanics) and MM (molecular mechanics) methods. The result shows that the allosteric modulation of androgen receptor plays an important role in the binding process between androgens and receptor. The open state receptor is less stable than the close state one, but the latter is more favorable for binding with androgens. It is worthy of note that when the androgen receptors binding or without binding with androgen are in close state, they are difficult to return to their open state. This phenomenon is an exception of the well known two-state model theory in which the two states are reversible. Whether the internal of close state androgen receptor has a combination of androgen or not, the androgen receptor surface can be combined with another androgen, and their surface binding energies could be very close. The result is consistent with the experimental observations, but this phenomenon of continuous combination from open state is also an exception of the two-state model theory.     

A model of the human M2 muscarinic acetylcholine receptor

The M₂ muscarinic acetylcholine receptor belongs to the family of rhodopsin like G-Protein Coupled Receptors. This subtype of muscarinic receptors is of special interest because it bears, aside from an orthosteric binding site, also an allosteric binding site. Based on the X-ray structure of bovine rhodopsin a complete homology model of the human M₂ receptor was developed. For the orthosteric binding site point mutations and binding studies with different agonists and antagonists are available. This knowledge was utilized for an initial verification of the M₂ model. Allosteric modulation of activity is mediated by structurally different ligands such as gallamine, caracurine V salts or W84 (a hexamethonium-derivative). Caracurine V derivatives with different affinities to M₂ were docked using GRID-fields. Subsequent molecular dynamics simulations yielded different binding energies based on diverse electrostatic and lipophilic interactions. The calculated affinities are in good agreement to experimentally determined affinities.     

Macrocyclization of the semiclathrochelate o -carboranylboronate and n -butylboronate iron(II ) oximehydrazonates: synthesis and structure of clathrochelate products and unexpected allosteric effect of the apical substituent

The template condensation of diacetylmonooxime hydrazone (HDXO) with n-butylboronic acid and dimethyl ester of o-carboranyldiboronic acid on the iron(II) ion matrix afforded the [Fe(DXO)₃(BBu)](BF₄) and [Fe(DXO)₃(Bo-carb)](BF₄) semiclathrochelates. The H⁺-ion-catalyzed macrocyclization of these precursors with an excess of formaldehyde and triethyl orthoformate (TOF) resulted in the corresponding macrobicyclic complexes. In the case of o-carboranylboronate semiclathrochelate, the macrocyclization with TOF gave the clathrochelate with the previously unknown syn,syn,anti-orientation of the ethoxy substituents relative to the 1,3,5-triazacyclohexane capping fragment. The complexes obtained were characterized using elemental analysis, IR, UV-Vis, MALDI-TOF mass, ¹H, ¹¹B, and ¹³C NMR, and ⁵⁷Fe M?ssbauer spectroscopies and X-ray crystallography. Dedicated to Academician G. A. Abakumov on the occasion of his 70th birthday. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1724–1731, September, 2007.     

Investigating Protein–Protein Allosteric Network using Current-Flow Scheme

Protein dynamic network analysis provides a powerful tool for investigating protein allosteric regulation. We recently developed a current-flow betweenness scheme for protein network analysis and demonstrated that this method, that is, using current-flow betweenness as edge weights, is more appropriate and more robust for investigating the signal transmission between two predefined protein residues or domains as compared with direct usage of correlation scores as edge weights. Here we seek to expand the current-flow scheme to study allosteric regulations involving protein–protein binding. Specifically, we investigated three gain-of-function mutations located at the binding interface of ALK2 (also known as ACVR1) kinase and its inhibitory protein FKBP12. We first searched for the optimal smoothing function for contact network construction and then calculated the subnetwork between FKBP12 protein and the kinase ATP binding site using current-flow betweenness. By comparing the networks between the wild-type and three mutants, we have identified statistically significant changes in the protein–protein networks that are common among all three mutants that allosterically shift the kinase toward a catalytically competent configuration. © 2019 Wiley Periodicals, Inc.     

Challenges in implementing clinical liquid chromatography‐tandem mass spectrometry methods ‐ seeing the light at the end of the tunnel

The use of liquid chromatography–tandem mass spectrometry (LC–MS/MS) in the clinical setting is a relatively new application. One of the significant barriers hampering the transition of LC–MS/MS from the research lab into a clinical setting is the uncertainty of how to successfully develop and validate a method that meets guidelines for clinical applications. Here, we have taken this seemingly overwhelming process and broken it into five general stages for consideration: assessing the clinical validity of a new LC–MS/MS assay, determination of feasibility, assay development, assay validation and post‐implementation monitoring. Although various publications are available and serve as resources for determining development processes and acceptability criteria for specific LC–MS/MS assays, many of them are general recommendations or are specific to research applications that may not translate either practically or clinically. In this perspective special feature article, a resource is compiled that describes key differences between LC–MS/MS methods for research use versus clinical use. In addition, the challenges facing the expanding role of this technique in the clinical setting are discussed, including instrumentation/automation challenges, potential regulation of laboratory developed tests by the US Food and Drug Administration and standardization and harmonization of MS methods through the use of traceable materials and availability of guidance documents. Copyright © 2013 John Wiley & Sons, Ltd.