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The rate of drug delivery to cells and the subsequent rate of drug metabolism are dependent on the cell membrane permeability to the drug. In some cases, tissue may be composed of different types of cells that exhibit order of magnitude differences in their membrane permeabilities. This paper presents a brief review of the components of the tissue scale three-compartment pharmacokinetic model of drug delivery to single−cell−type populations. The existing model is extended to consider tissue composed of two different cell types. A case study is presented of infusion mediated delivery of doxorubicin to a tumor that is composed a drug reactive cell type and of a drug resistive cell type. The membrane permeabilities of the two cell types differ by an order of magnitude. A parametric investigation of the population composition is conducted and it is shown that the drug metabolism of the low permeability cells are negatively influenced by the fraction of the tissue composed of the permeable drug reactive cells. This is because when the population is composed mostly of drug permeable cells, the extracellular space is rapidly depleted of the drug. This has two compounding effects: (i) locally there is simply less drug available to the neighboring drug resistant cells, and (ii) the depletion of the drug from the extracellular space near the vessel-tissue interface leaves less drug to be transported to booth cell types farther away from the vessel.

Destruxin A (DA), a hexa-cyclodepsipeptidic mycotoxin produced by the entomopathogenic fungus Metarhizium anisopliae, exhibits insecticidal activities in a wide range of pests and is known as an innate immunity inhibitor. However, its mechanism of action requires further investigation. In this research, the interactions of DA with the six aminoacyl tRNA synthetases (ARSs) of Bombyx mori, BmAlaRS, BmCysRS, BmMetRS, BmValRS, BmIleRS, and BmGluProRS, were analyzed. The six ARSs were expressed and purified. The BLI (biolayer interferometry) results indicated that DA binds these ARSs with the affinity indices (KD) of 10−4 to 10−5 M. The molecular docking suggested a similar interaction mode of DA with ARSs, whereby DA settled into a pocket through hydrogen bonds with Asn, Arg, His, Lys, and Tyr of ARSs. Furthermore, DA treatments decreased the contents of soluble protein and free amino acids in Bm12 cells, which suggested that DA impedes protein synthesis. Lastly, the ARSs in Bm12 cells were all downregulated by DA stress. This study sheds light on exploring and answering the molecular target of DA against target insects.

Razlog za nastanek mnogih bolezni je nenormalna ekspresija proteinov oziroma motnja v prenosu signalov, zato je ena izmed obetavnih metod zdravljenja nadzorovanje teh mehanizmov. Protein toplotnega šoka 90 (Hsp90) je pomemben in evolucijsko ohranjen šaperon, ki se v evkariontih izraža v povečani meri med celičnim stresom z namenom zmanjšanja celičnih poškodb. V celici je Hsp90 regulator genskega izražanja, proliferacije in celičnega cikla ter sodeluje pri dozorevanju več kot 300 proteinov, zato lahko opazimo, da motnje izražanja Hsp90 lahko povzročijo povečano izražanje proteinov, ki so induktorji patoloških stanj. S tem razlogom je Hsp90 postal pomembna tarča za razvoj zaviralcev, ki lahko s svojim delovanjem ustavijo zvijanje in dozorevanje številnih patoloških proteinov. Do danes so kar nekaj zaviralcev N-končne domene Hsp90 vrednotili v kliničnih študijah, vendar so razvoj večine, predvsem zaradi toksičnosti in aktivacije odziva toplotnega šoka, ustavili. V zadnjih dvajsetih letih se je po odkritju alosteričnega vezavnega mesta v C-končni domeni proteina veliko skupin usmerilo v razvoj alosteričnih zaviralcev, ki pa za razliko od N-končnih zaviralcev ne povzročajo aktivacije odziva toplotnega šoka in so v splošnem manj toksični. Ker še ni bilo eksperimentalno določene strukture Hsp90, ki bi imela kokristaliziran alosterični zaviralec C-končne domene, smo se odločili, da z računalniškimi metodami raziščemo model vezave, kar bi izboljšalo nadaljnje načrtovanje zaviralcev. Z uporabo računalniškega sidranja, simulacijami molekulske dinamike in uporabo zaviralcev, katerih aktivnost je poznana, smo predlagali model vezave nekaterih najaktivnejših učinkovin, kar da globlji vpogled v vezavni žep in interakcije, ki so pomembne za zaviralno aktivnost. Ker je vezavni žep v C-končnem delu zelo voluminozen, je raziskava potekala v dveh delih. Najprej smo se posvetili iskanju vezavnega mesta, v katerega se veže referenčna spojina TVS-21 in njeni analogi. Drugi del raziskav je bilo odkrivanje odnosa med strukturo in delovanjem spojin. Izbrali smo več spojin, tako aktivnih kot neaktivnih, ki smo jih sidrali v izbran vezavni žep. S tem smo želeli razložiti, kako posamezna modifikacija vpliva na model vezave sorodnih spojin. Spoznanja, ki smo jih pridobili z raziskovanjem vezav alosteričnih zaviralcev, nam bodo v prihodnje olajšala načrtovanje novih zaviralcev z močnejšim delovanjem na Hsp90. Zavedati se moramo, da so predlagani modeli le hipotetični in bi za podporo le teh potrebovali še rezultate eksperimentalnih metod, kot so testi mutageneze in/ali raziskave STD-NMR. Za nadaljnje raziskave in modifikacije bi bilo smiselno uporabiti spojino 8 kot referenčno spojino in referenčni model vezave. Many diseases are caused by abnormal protein expression or impaired signal transduction. Therefore, one of the promising targets for treatment of various diseases is to control these mechanisms. Heat shock protein 90 (Hsp90) is an important and evolutionarily conserved chaperone whose expression in eukaryotes increases during cellular stress in order to reduce cellular damage. Hsp90 is a cellular regulator of gene expression, proliferation, cell cycle and is responsible for maturation of over 300 proteins. It can be observed that dysregulation of Hsp90 expression can cause increased expression of proteins, which in turn are inducers of pathological conditions. For this reason, the protein has become an important target for the development of inhibitors that can, by acting on Hsp90, stop the folding of a wide range of pathological proteins. To date, quite a few inhibitors of the Hsp90 N-terminal domain have entered clinical trials, but most have been discontinued due to toxicity and heat shock response activation. In the last twenty years, following the identification of an allosteric binding site in the C-terminal domain of Hsp90, many groups have focused their research on the development of allosteric inhibitors, which unlike N-terminal inhibitors, do not activate the heat shock response and are generally less toxic. Since there has been no experimentally determined structure of Hsp90 co-crystallized with allosteric C-terminal domain inhibitor, we decided to use computational methods to determine the binding mode, which would improve further design of allosteric inhibitors. Using computational docking, molecular dynamics simulations, and a library of active compounds with known activities, we proposed a binding model of some of the most potent compounds that gives us a deeper insight into the binding pocket and interactions relevant to the inhibitory activity. Because the binding pocket in the C-terminal domain is very voluminous, the research was conducted in two parts, where we initially focused on locating the binding site where the reference active compound TVS-21 and its derivatives bind. The second part of the research was to establish structure-activity relationship of the previously prepared Hsp90 inhibitors. We selected several active and inactive compounds, which we docked in the selected binding pocket. With this, we wanted to explain how an individual modification affects the binding of related active compounds. The lessons learned from the research of the binding of allosteric inhibitors will enable the design of new compounds with improved activity in the future. However, we must be aware that the proposed models are only hypothetical and the results of experimental methods, such as site-directed mutagenesis and/or STD-NMR experiments, would be needed to support our findings. Compound 8 should be used as the reference compound and reference binding model for further research and optimisation.

Gliotoxin (GT) is a fungal secondary metabolite that has attracted great interest due to its high biological activity since it was discovered by the 1930s. It exhibits a unique structure that contains a N-C = O group as the characteristics of the classical PSII inhibitor. However, GT’s phytotoxicity, herbicidal activity and primary action targets in plants remain hidden. Here, it is found that GT can cause brown or white leaf spot of various monocotyledonous and dicotyledonous plants, being regarded as a potential herbicidal agent. The multiple sites of GT action are located in two photosystems. GT decreases the rate of oxygen evolution of PSII with an I 50 value of 60 µM. Chlorophyll fluorescence data from Chlamydomonas reinhardtii cells and spinach thylakoids implicate that GT affects both PSII electron transport at the acceptor side and the reduction rate of PSI end electron acceptors’ pool. The major direct action target of GT is the plastoquinone QB-site of the D1 protein in PSII, where GT inserts in the QB binding niche by replacing native plastoquinone (PQ) and then interrupts electron flow beyond plastoquinone QA. This leads to severe inactivation of PSII RCs and a significant decrease of PSII overall photosynthetic activity. Based on the simulated modeling of GT docking to the D1 protein of spinach, it is proposed that GT binds to the-QB-site through two hydrogen bonds between GT and D1-Ser264 and D1-His252. A hydrogen bond is formed between the aromatic hydroxyl oxygen of GT and the residue Ser264 in the D1 protein. The 4-carbonyl group of GT provides another hydrogen bond to the residue D1-His252. So, it is concluded that GT is a novel natural PSII inhibitor. In the future, GT may have the potential for development into a bioherbicide or being utilized as a lead compound to design more new derivatives.

The interaction of a ligand with a macromolecule has been modeled following different theories. The tenants of the induced fit model consider that upon ligand binding, the protein–ligand complex undergoes a conformational change. In contrast, the allosteric model assumes that only one among different coexisting conformers of a given protein is suitable to bind the ligand optimally. In the present paper, we propose a general framework to model the binding of ligands to a macromolecule. Such framework built on the binding polynomial allows opening new ways to teach in a unified manner ligand binding, enzymology and receptor binding in pharmacology. Moreover, we have developed simple software that allows building the binding polynomial from the schematic description of the biological system under study. Taking calmodulin as a canonical example, we show here that the proposed tool allows the easy retrieval of previously experimental and computational reports. This article is part of a Special Issue entitled: Calcium Signaling in Health and Disease. Guest Editors: Geert Bultynck, Jacques Haiech, Claus W. Heizmann, Joachim Krebs, and Marc Moreau.

Previously we have shown that 3,6-dihydroxyflavone (3,6-DHF) is a potent agonist of the human peroxisome proliferator-activated receptor (hPPAR) with cytotoxic effects on human cervical cancer cells. To date, the mechanisms by which 3,6-DHF exerts its antitumor effects on cervical cells have not been clearly defined. Here, we demonstrated that 3,6-DHF exhibits a novel antitumor activity against HeLa cells with IC50 values of 25 μM and 9.8 μM after 24 h and 48 h, respectively. We also showed that the anticancer effects of 3,6-DHF are mediated via the toll-like receptor (TLR) 4/CD14, p38 mitogen-activated protein kinase (MAPK), Jun-N terminal kinase (JNK), extracellular-signaling regulated kinase (ERK), and cyclooxygenase (COX)-2 pathways in lipopolysaccharide (LPS)-stimulated RAW264.7 cells. We found that 3,6-DHF showed a similar IC50 (113 nM) value to that of the JNK inhibitor, SP600125 (IC50 = 118 nM) in a JNK1 kinase assay. Binding studies revealed that 3,6-DHF had a strong binding affinity to JNK1 (1.996 × 105 M−1) and that the 6-OH and the carbonyl oxygen of the C ring of 3,6-DHF participated in hydrogen bonding interactions with the carbonyl oxygen and the amide proton of Met111, respectively. Therefore, 3,6-DHF may be a candidate inhibitor of JNKs, with potent anticancer effects.

Wireless communication plays a critical role in determining the lifetime of Internet-of-Things (IoT) systems. Data aggregation approaches have been widely used to enhance the performance of IoT applications. Such approaches reduce the number of packets that are transmitted by combining multiple packets into one transmission unit, thereby minimising energy consumption, collisions and congestion. However, current data aggregation schemes restrict developers to a specific network structure or cannot handle multi-hop data aggregation. In this paper, we propose Hitch Hiker 2.0, a component binding model that provides support for multi-hop data aggregation. Hitch Hiker uses component meta-data to discover remote component bindings and to construct a multi-hop overlay network within the free payload space of existing traffic flows. Hitch Hiker 2.0 provides end-to-end routing of low-priority traffic while using only a small fraction of the energy of standard communication. This paper extends upon our previous work by incorporating new mechanisms for decentralised route discovery and providing additional application case studies and evaluation. We have developed a prototype implementation of Hitch Hiker for the LooCI component model. Our evaluation shows that Hitch Hiker consumes minimal resources and that using Hitch Hiker to deliver low-priority traffic reduces energy consumption by up to 32 %.

The mean intrinsic thermodynamic quantity can be defined by considering the relative population of complex species in the solution and the value of intrinsic thermodynamic quantity corresponds to each step of ligation. In the present study a new method is introduced for analysis of experimental ligand binding data on basis of mean intrinsic thermodynamic quantities. In this regard, a deviation parameter was defined by comparing the non-interacting system with the cooperative interactive one. This parameter can be calculated just by estimation of the first binding constant. A set of relations between this deviation parameter and other binding characteristics, such as mean intrinsic Gibbs free energy of binding and mean Gibbs free energy of site-site interaction, have been developed. This model presents binding mechanism in a unified way that is simple, yet stringent, more straightforward, more reliable and informative. This analyzing method has been successfully applied for evaluation of various systems such as oxygen binding to hemoglobin, laurate and warfarin binding to human serum albumin, and reveals some new biological features of these binding systems.

Parkinson’s disease is characterised pathologically by a relatively selective death of dopaminergic neurons in the substantia nigra of the brain. The vulnerability of these neurons appears to be linked to the pigment neuromelanin. However, as yet there is limited understanding behind the mechanisms of thisdisease process. Complications arise due to the difficulty in obtaining appreciable quantities of neuromelanin. Furthermore, an appropriate model for studying neuromelanin has not been identified.To date there has been many studies looking at the binding and chemical characteristics of neuromelanin. However, a range of different synthetic and organic melanins have been used as models and leading to many varied conclusions being drawn. Therefore, the aim of this review is to present Sepia melanin as the most appropriate study model for the binding characteristics of neuromelanin. Considerations included chemical structure, surface characteristics and structural features of both synthetic and organic melanins. Refereed/Peer-reviewed

Uranium(VI), which is often elevated in granitoidic groundwaters, is known to adsorb strongly to Fe (hydr)oxides under certain conditions. This process can be used in water treatment to remove U(VI). To develop a consistent geochemical model for U(VI) adsorption to ferrihydrite, batch experiments were performed and previous data sets reviewed to optimize a set of surface complexation constants using the 3-plane CD-MUSIC model. To consider the effect of dissolved organic matter (DOM) on U(VI) speciation, new parameters for the Stockholm Humic Model (SHM) were optimized using previously published data. The model, which was constrained from available X-ray absorption fine structure (EXAFS) spectroscopy evidence, fitted the data well when the surface sites were divided into low- and high-affinity binding sites. Application of the model concept to other published data sets revealed differences in the reactivity of different ferrihydrites towards U(VI). Use of the optimized SHM parameters for U(VI)-DOM complexation showed that this process is important for U(VI) speciation at low pH. However in neutral to alkaline waters with substantial carbonate present, Ca-U-CO3 complexes predominate. The calibrated geochemical model was used to simulate U(VI) adsorption to ferrihydrite for a hypothetical groundwater in the presence of several competitive ions. The results showed that U(VI) adsorption was strong between pH 5 and 8. Also near the calcite saturation limit, where U(VI) adsorption was weakest according to the model, the adsorption percentage was predicted to be >80%. Hence U(VI) adsorption to ferrihydrite-containing sorbents may be used as a method to bring down U(VI) concentrations to acceptable levels in groundwater. QC 20100525

UV-absorption and circular dichroism (CD) experiments showed that ellipticine derivatives may interact with DNA according to 3 possible binding modes depending on their structure and concentration. The first mode concerned intercalation of 1-methyl-9-hydroxyellipticine (1-Me-HE) with its long axis perpendicular to the long axis of base pairs. The same drug was able to bind to external sites (second mode) once the intercalation sites were saturated at high concentration. The third mode illustrated by 1,2-dimethyl-9-hydroxyisoellipticinium (1-Me-isoNMHE), concerned self-stacked molecules interacting at the surface of DNA. Biological significance of these different binding modes was then discussed in connection with in vitro cytotoxic activity of compounds.

The quantitative aspects of mitochondrial creatine kinase (mitCK) binding to mitochondrial membranes were investigated. A simple adsorption and binding model was used for data fitting, taking into account the influence of protein concentration, pH, ionic strength and substrate concentration on the enzyme adsorption. An analysis of our own data as well as of the data from the literature is consistent with the adsorption site of the octameric mitCK being composed of 4 amino acid residues with pK = 8.8 in the free enzyme. The pK value changes to 9.8 upon binding of the protein to the membrane. Lysine is is suggested as the main candidate to form the adsorption site of mitCK. Deprotonated octameric mitCK easily dissociated from the membrane ( K a = 0.39 mM at ionic strength I = 7.5 mM and 5°C); after protonation its affinity increased many times ( K ah = 39 nM ). Determination of mitCK adsorption capacity by another method at pH 7.4, when the enzyme is almost protonated, gave K ah = 15 nM . The effect of ionic strength on mitCK adsorption may be described in terms of Debye-Huckel's theory for activity coefficients assuming the charges of the interacting species to be + 4 and + 4. The dissociation constant for the mitCK-membrane complex at pH 7.4 and I = 0 was evaluated by different approaches as approx. 1 nM. Extramitochondrial ATP (or ADP) shifted greatly the equilibrium between the adsorbed and the free mitCK towards the solubilized state, since in the adsorbed protein the external ligands had access to four binding sites and in the free protein to eight sites.

A model is proposed describing multiple binding of multivalent antigen to specific receptors of immunocompetent cells. The rate at which these multiple bonds can dissociate and the effective valence of the antigen appear to be of the greatest importance in determining the degree of receptor occupancy at equilibrium. In particular, as antigen concentration decreases, only antigens with high number of determinants per molecule maintain the ability to form multiple bonds even if the dissociation rate is relatively high. Assuming that multiple binding is directly linked to lymphocyte activation, this may result in an inverse relation between antigen valence and ability to induce selection of clones with higher affinities.

The characteristics of hydrous zirconia gels obtained by hydrolysis of highly acidic ZrOCl₂· 8H₂O solutions at ∼100ºC are described. Under adequate conditions, monodisperse spherical hydrous zirconia is obtained. The role of sulphate and chloride ions is described. The gel has a large water content, indicating only modest crosslinking. Crystallization upon heating takes place with the formation of both monoclinic and tetragonal zirconia polymorphs; X-ray line widening studies do not indicate a particle size-crystal structure correlation. On the basis of this observation and using Stranki's rule, the crystallization sequence upon heating is rationalized. Surface properties of hydrous zirconia are discussed on the basis of electrophoretic measurements, and compared with those of baddeleyte. The site binding model is not very adequate to describe these systems, and the existence of a very thin gel-like region at the baddeleyte-water interface is postulated., Facultad de Ciencias Exactas