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Natural products are widely used for treating mitochondrial dysfunction-related diseases and cancers. Curcumin, a well-known natural product, can be potentially used to treat cancer. Human salt-induced kinase 3 (SIK3) is one of the target proteins for curcumin. However, the interactions between curcumin and human SIK3 have not yet been investigated in detail. In this study, we studied the binding models for the interactions between curcumin and human SIK3 using computational tools such as homology modeling, molecular docking, molecular dynamics simulations, and binding free energy calculations. The open activity loop conformation of SIK3 with the ketoenol form of curcumin was the optimal binding model. The I72, V80, A93, Y144, A145, and L195 residues played a key role for curcumin binding with human SIK3. The interactions between curcumin and human SIK3 were also investigated using the kinase assay. Moreover, curcumin exhibited an IC50 (half-maximal inhibitory concentration) value of 131 nM, and it showed significant antiproliferative activities of 9.62 ± 0.33 µM and 72.37 ± 0.37 µM against the MCF-7 and MDA-MB-23 cell lines, respectively. This study provides detailed information on the binding of curcumin with human SIK3 and may facilitate the design of novel saltinducible kinases inhibitors. [ABSTRACT FROM AUTHOR]

DestruxinA(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. [ABSTRACT FROM AUTHOR]

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 I50 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.

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. [ABSTRACT FROM AUTHOR]

The skeletal muscle ryanodine receptor (RyR1) proteins are intracellular calcium (Ca2+) release channels on the membrane of the sarcoplasmic reticulum (SR) and required for skeletal muscle excitation-contraction coupling. Homer (Vesl) is a family of scaffolding proteins that modulate target proteins including RyRs (ryanodine receptors), mGluRs (group 1 metabotropic glutamate receptors) and IP 3 Rs (inositol-1,4,5-trisphosphate receptors) through a conserved EVH1 (Ena/VASP homology 1) domain. Here, we examined the interaction between Homer1 EVH1 domain and RyR1 by co-immunoprecipitation, continuous sucrose density-gradient centrifugation, and bio-layer interferometry binding assay at different Ca2+ concentrations. Our results show that there exists a high-affinity binding between the Homer1 EVH1 domain and RyR1, especially at 1 mM of Ca2+. Based on our data and the known structures of Homer1 EVH1 domain and RyR1, we found two consensus proline-rich sequences in the structure of RyR1, PPHHF and FLPPP, and proposed two corresponding binding models to show mechanisms of recognition different from those used by other proline-rich motifs. The side proline residues of two proline-rich motifs from RyR1 are away from the hydrophobic surface of Homer1 EVH1, rather than buried in this hydrophobic surface. Our results provide evidence that Homer1 regulates RyR1 by direct interaction. • Homer1 EVH1 domain directly interacts with RyR1 at different Ca2+ concentrations. • There exists high-affinity binding between Homer1 EVH1 domain and RyR1 (K D ∼10 nM). • Homer regulates RyR1 with diverse binding affinities at diverse Ca2+ concentrations. • Ca2+ might change the conformation and the affinity of RyR1 to Homer1 EVH1. • Homer1 EVH1 domain recognizes proline-rich motifs of RyR1 specifically. [ABSTRACT FROM AUTHOR]

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.

Lysophosphatidylserine (LysoPS) is an endogenous pan-agonist of three G-protein coupled receptors (GPCRs): LPS 1 /GPR34, LPS 2 /P2Y 10 , and LPS 3 /GPR174, and we previously reported a series of LysoPS-based agonists of these receptors. Interestingly, we found that LPS 1 agonist activity was very sensitive to structural change at the hydrophobic fatty acid moiety, whereas LPS 2 agonist activity was not. Here, to probe the molecular basis of LPS 2 agonist binding, we developed a new class of hydrophobic fatty acid surrogates having a biphenyl-ether scaffold. The LPS 2 agonist activity of these compounds proved sensitive to molecular modification of the hydrophobic skeleton. Thus, we next constructed an LPS 2 model by homology modeling and docking/molecular dynamics (MD) simulation, and validated it by means of SAR studies together with point mutations of selected receptor amino-acid residues. The putative ligand-binding site of LPS 2 is Γ-shaped, with a hydrophilic site horizontally embedded in the receptor transmembrane helix bundles and a perpendicular hydrophobic groove adjoining transmembrane domains 4 and 5 that is open to the membrane bilayer. The binding poses of LPS 2 agonists to this site are consistent with easy incorporation of various kinds of fatty acid surrogates. Structural development based on this model afforded a series of potent and selective LPS 2 full agonists, which showed enhanced in vitro actin stress fiber formation effect. [Display omitted] • A biphenyl-ether skeleton of LPS 2 -selective agonist was found to amplify the activity change upon structural modifications of the hydrophobic moiety. • Docking studies and point mutation of the receptor elucidated LPS 2 agonist binding mode as representing a hydrophilic site parallel to membrane bilayer and a perpendicular hydrophobic groove between transmembrane helices 4 & 5. • Binding model-guided-ligand design led to the development of potent and selective LPS 2 agonists with improved actin stress fiber formation activity. [ABSTRACT FROM AUTHOR]

FtsZ, an essential cytokinesis protein, was a highly promising target for antibacterial agents. Following up the identification of trisubstituted benzimidazoles targeting Mycobacterium tuberculosis FtsZ ( Mtb FtsZ) in previous studies and in order to explore the possible binding mode of these analogues, in silico methodologies such as 3D-QSAR, ProFunc analysis, molecular docking and molecular dynamic simulation were performed. They corroborated well with each other and gave credence to the proposed binding mechanism of trisubstituted benzimidazoles in the interdomain cleft region of Mtb FtsZ. The benzimidazole scaffold and cyclohexyl group of trisubstituted benzimidazoles were orthogonal to each other in low energy state and inclosed in a most hydrophobic environment formed by residues from the C-terminal β sheets and H7 helix. The carbamate groups at the 5-position extended outward form the cleft cavity to the hydrophilic surface. The substituents at the 6-position fitted into the top portion of the cleft by directly interacting with the T7 loop. It was believed that the hydrophobic interactions and the polar contacts were major contributors to the stabilization of the ligand binding in the interdomain cleft. The binding mechanism provided useful clues to design new trisubstituted benzimidazoles inhibitors of Mtb FisZ with promising activity. The work presented here may even be expanded tremendously to screen novel Mtb FtsZ inhibitors with different scaffolds by using the molecular dynamic refined Mtb FtsZ structure and docking based 3D QSAR CoMFA. Graphical Abstract: [ABSTRACT FROM AUTHOR]

Ligand binding dynamics and the concept of drug-target residence time are essential factors in the development of novel drugs. Conventional ligand binding assays, which usually collect end-point data, do not provide abundant information regarding the ligand binding kinetics. Therefore, novel methods that allow on-line monitoring of ligand binding processes have to be developed and implemented for drug discovery studies. In this study, we provide a short overview of novel possibilities to characterize ligand binding dynamics to different G protein-coupled receptors (GPCRs). Special attention has been paid to the ligand binding to melanocortin 4 receptors and to the development of a fluorescence anisotropy-based assay system using receptors in budded baculovirus particles. It has been shown that ligand binding to melanocortin 4 receptors occurs to tandemly arranged interconnecting ligand binding sites and that the conventional equilibrium usually cannot be achieved in this system. Therefore, the apparent potencies of the same ligand may differ by up to four orders of magnitude, depending on the experimental conditions and the reporter ligand used. [ABSTRACT FROM AUTHOR]

Hypericin (Hyp) is one of the principal active constituents of a traditional folk medicine, Hypericum (Saint John’s wort), and possesses variety biological activities. The interaction of Hyp with DNA may play an important role in biological activity, however only a few investigations were reported on this issue. In this paper, we studied the interaction of Hyp with different DNA forms. Hyp was found to selectively bind parallel DNA G-Quadruplexes (G4) over other DNA forms, such as ss-/ds-DNA, antiparallel G4s and mix-type G4s. Binding studies suggest that Hyp bind on G-quartet surface of G4s through end-stacking interaction. These results provide new information for the investigation of action mechanism of Hyp. [ABSTRACT FROM AUTHOR]

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 %. [ABSTRACT FROM AUTHOR]

Determining the energetics of the unfolded state of a protein is essential for understanding the folding mechanics of ordered proteins and the structure-function relation of intrinsically disordered proteins. Here, we adopt a coil-globule transition theory to develop a general scheme to extract interaction and free energy information from single-molecule fluorescence resonance energy transfer spectroscopy. By combining protein stability data, we have determined the free energy difference between the native state and the maximally collapsed denatured state in a number of systems, providing insight on the specific/nonspecific interactions in protein folding. Both the transfer and binding models of the denaturant effects are demonstrated to account for the revealed linear dependence of inter-residue interactions on the denaturant concentration, and are thus compatible under the coil-globule transition theory to further determine the dimension and free energy of the conformational ensemble of the unfolded state. The scaling behaviors and the effective θ-state are also discussed. [ABSTRACT FROM AUTHOR]

All-trans-retinoic acid (ATRA) as a physiological metabolite of vitamin A is widely applied in the treatment of cancer, skin, neurodegenerative and autoimmune diseases. CYP26A1 enzyme, induced by ATRA in liver and target tissues, metabolizes ATRA into 4-hydroxyl-RA. Inhibition of CYP26A1 metabolic enzyme represents a promising strategy for discovery of new specific anticancer agents. Herein, we describe the design, synthesis and biological evaluation of a series of new amide imidazole derivatives as retinoic acid metabolism blocking agents (RAMBAs) toward CYP26A1 enzyme. First, based on the recent theoretical models (Sun et al., J. Mol. Graph. Model. , 2015 , 56 , 10–19) a series of RAMBAs with novel scaffolds were designed using fragment-based drug discovery approach. Subsequently, the new RAMBAs were synthesized and evaluated for their biological activities. All the compounds demonstrated appropriate enzyme activities and cell activities. The promising inhibitors 20 and 23 with IC 50 value of 0.22 μM and 0.46 μM toward CYP26A1, respectively, were further evaluated for CYP selectivity and the metabolic profile of ATRA. Both compounds 20 and 23 showed higher selectivity for CYP26A1 over other CYPs (CYP2D6, CYP3A4) when compared to liarozole. They also showed better inhibitory activities for the metabolism of ATRA when also compared to liarozole. These studies further validated the pharmacophore and structure–activity relationship models obtained about CYP26A1 inhibitors and highlighted the promising activities of the new series of CYP26A1 inhibitors designed from such models. They also paved the way for future development of those candidates as potential drugs. [ABSTRACT FROM AUTHOR]

Dehydroabietic acid (DAA) is a naturally occurring diterpene resin acid of confers, such as pinus species ( P. densiflora , P. sylvestris ) and grand fir ( Abies grandis ), and it induces various biological actions including antimicrobial, antiulcer, and cardiovascular activities. The cellular targets that mediate these actions are largely unknown yet. In this report, we suggest that DAA is an anti-aging reagent. DAA has lifespan extension effects in Caenorhabditis elegans , prevents lipofuscin accumulation, and prevents collagen secretion in human dermal fibroblasts. We found that these anti-aging effects are primarily mediated by SIRT1 activation. Lifespan extension effects by DAA were ameliorated in sir-2.1 mutants and SIRT1 protein expression was increased, resulting in the deacetylation of SIRT1 target protein PGC-1α. Moreover, DAA binds directly to the SIRT1 protein independent of the SIRT1 substrate NAD + levels. Through a molecular docking study, we also propose a binding model for DAA-SIRT1. Taken together, our results demonstrate that the anti-aging effects are the first identified biological property of DAA and that the direct activation of SIRT1 enzymatic activity suggests the potential use of this natural diterpene, or related compounds, in age-related diseases or as a preventive reagent against the aging process. [ABSTRACT FROM AUTHOR]

Rhamnetin is a flavonoid found in cloves and vegetables. Previously, we found that rhamnetin showed anti-inflammatory activity in lipopolysaccharide-stimulated RAW264.7 cells, mediated by actions on mitogen-activated protein kinases pathways. Here, we investigated interactions between extracellular signal-regulated kinase 1 ( ERK1) and rhamnetin. Based on docking study, we propose a binding model of rhamnetin and ERK1, where the 4′-hydroxyl groups of the B-ring and the 5-hydroxyl group of the A-ring of rhamnetin play key roles. In a fluorescence quenching experiment, rhamnetin exhibited high binding affinity to ERK1. We found that rhamnetin has an IC50 value similar to that of the ERK1 inhibitor U0126 in ERK1 kinase assays, as well as to that of the JNK1 inhibitor SP600125 in JNK1 kinase assays. These results imply that rhamnetin may be a candidate inhibitor of ERK1 and JNK1, with potent anti-inflammatory activity. [ABSTRACT FROM AUTHOR]

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 this disease 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. [ABSTRACT FROM AUTHOR]

Long-span air supported membrane structures are typical wind sensitive buildings, wind load is often their control load. The existing analysis of air supported membrane structures basically assumes that the nodes of the cable net and membrane are bound together, the slide or separation between the cable net and the membrane under wind load is not considered. The lack of cable–membrane​ contact model causes hidden danger to the safety of wind resistance performance of long-span air supported membrane structures. In this paper, ANSYS software is adopted for structural analysis, the cable net of air supported membrane structure is divided into many small cable segments, and nodes of all cable segments form point-surface contact pairs with the membrane surface, the joints of all cable segments may bond, slide or separate from the membrane surface. The cable–membrane contact model is used to analyze the wind-induced response of an air supported membrane structure with orthogonal cable net, and the results are compared with the wind-induced response of the cable–membrane binding model. The analysis results of the two models show that: when the cable–membrane contact model is adopted, the displacement and stress responses of the membrane are greatly increased under strong wind load due to the separation of the membrane and the cable net, the axial force distribution of the cable is more uniform due to the sliding between the cable net and membrane. The cable–membrane binding model overestimates the restraint effect of cable net on membrane, in order to better optimize the design of long-span air supported membrane structures, it is necessary to consider adopting cable–membrane contact model. • Cable–membrane contact model was established for air-supported membrane structures. • Pressure distribution of an air-supported structure was obtained by wind tunnel test. • Wind vibration responses analysis was solved adopting slow dynamic method. • The results using cable–membrane contact model were compared with those using cable–membrane binding model. • Displacement response of membrane increases significantly adopting cablemembrane contact model. [ABSTRACT FROM AUTHOR]

Numerous studies have examined the role of flavonoids in modulating inflammatory responses in vitro. In this study, we found a novel flavonoid, 3,6,3'-trihydroxyflavone (1), with anti-inflammatory effects. Antiinflammatory activity and mechanism of action were examined in mouse macrophages stimulated with lipopolysaccharide (LPS). Our results showed that the anti-inflammatory effects of 1 are mediated via p38 mitogen-activated protein kinase (p38 MAPK), Jun-N terminal kinase (JNK), and the extracellularsignal- regulated kinase (ERK) pathway in lipopolysaccharide (LPS)-stimulated RAW264.7 cells. Binding studies revealed that 1 had a high binding affinity to JNK1 (1.568 x 108 M-1) and that the 3- and 6-hydroxyl groups of the C-ring and A-ring of 1 participated in hydrogen bonding interactions with the side chains of Asn114 and Lys55, respectively. The oxygen at the 3' position of the B-ring formed a hydrogen bond with side chain of Met111. Therefore, 1 could be a potential inhibitor of JNKs, with potent anti-inflammatory activity. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Quercetin is a major dietary flavonoid found in onions, apples, tea, and red wine, and potentially has beneficial effects on disease prevention. We carried out this study to investigate the effect of quercetin on UVB-induced matrix metalloproteinase-1 (MMP-1) expression in human keratinocyte HaCaT cells and to further understand the mechanisms of its action. The anti-inflammatory activity of quercetin was investigated and quercetin significantly suppressed the NO production in LPS-stimulated RAW264.7 mouse macrophages. Post treatment of quercetin decreased UV irradiation-induced phosphorylation of JNK, p38 MAPK, and ERK by 91%, 21%, and 17%, respectively. MMP-1 is mainly responsible for the degradation of dermal collagen during the aging process of human skin and quercetin suppressed the UVB-induced MMP-1 by 94%. Binding studies revealed that quercetin binds to p38 with high binding affinity (1.85 x 106 M-1). The binding model showed that the 4'- hydroxy groups of the B-ring of quercetin participated in hydrogen bonding interactions with the side chains of Lys53, Glu71, and Asp168 and the 5-hydroxy group of the A-ring formed a hydrogen bond with the backbone amide of Met109. The major finding of this study shows that quercetin inhibits phosphorylation of JNK, p38 MAPK, and ERK pathway leading to the prevention of MMP-1 expression in human keratinocyte HaCaT cells. Therefore, our findings suggested the potentials of quercetin as a skin anti-photoaging agent. [ABSTRACT FROM AUTHOR]

Abstract: In this study, a copolymer, poly (vinyl amino-N, N′-bis-propane diol-co-DADMAC) (GPVA-co-DADMAC) was synthesized in three comonomer ratios (2%, 5% and 10%) and efficiently exploited for boron removal via polymer enhanced ultrafiltration (PEUF). Boron concentration could be reduced from 10ppm down to 0.8ppm by the employment of novel copolymer in continuous PEUF at pH 9 and boron-to-polymer mass ratio (loading) of 0.001. Polymer precipitation was not observed even after complexation with boron. Boron retention was found to be highly pH dependent and boron concentration dependent at constant loading. Hence, efficient polymer regeneration can be expected due to high pH and concentration dependency of boron complexation. Moreover, permeate flux was not affected by the polymer concentration in the conditions studied (polymer concentration ≤10g/L; pressure drop: 2bar). Dynamic and static light scattering measurements showed that gyration radius of the polymers rises by dilution or by increasing pH of the solutions. Furthermore, a two-step equilibrium model was correlated with the experimental boron retention data. Having high boron binding affinity, hydrolytic stability and efficiency in boron removal, the synthesized copolymers possessing DADMAC segments seemed to be attractive and useful for large scale water treatment with PEUF systems. [Copyright &y& Elsevier]

Abstract: The protein tyrosine phosphatase 1B (PTP-1B) is acknowledged as an outstanding therapeutic target for the treatment of diabetes, obesity and cancer. In this work, six aryl diketoacid compounds have been studied on the basis of molecular dynamics simulations. Hydrogen bonds, binding energies and conformation changes of the WPD loop have been analyzed. The results indicated that their activation model falls into two parts: the target region of the monomeric aryl diketoacid compounds is the active site, whereas the target region of the dimeric aryl diketoacid compounds is the WPD loop or the R loop. The van der Waals interactions exhibit stronger effects than the short-range electrostatic interactions. The van der Waals interaction energy and the IC50 values exhibit an approximately exponential relationship. Furthermore, the van der Waals interactions cooperate with the hydrogen bond interactions. This study provides a more thorough understanding of the PTP-1B inhibitor binding processes. [Copyright &y& Elsevier]

Abstract: Novel types of PKCα activators based on isobenzofuranone bearing a myo-inositol moiety were designed and synthesized. The derivatives with bulky substituents on the myo-inositol moiety significantly activated PKCα, but their binding sites were not the same as that of phorbol ester. [Copyright &y& Elsevier]

Abstract: A series of 5-HT6 ligands derived from (R)-1-(amino)methyl-6-(phenyl)sulfonyltetralin was prepared that yielded several non-basic analogs having sub-nanomolar affinity. Ligand structure–activity relationships, receptor point mutation studies, and molecular modeling of these novel ligands all combined to reveal a new alternative binding mode to 5-HT6 for antagonism. [Copyright &y& Elsevier]

Abstract: In this work, a novel (patent pending) orifice die design for precise extensional viscosity data determination from entrance pressure drop measurements has been developed and tested both theoretically (through Finite Element Analysis) and experimentally. It has been demonstrated that the proposed novel orifice die allows much more precise extensional viscosity measurements for polymer melts in comparison with conventional orifice dies. Moreover, it has been found that, for extensional strain hardening and extensional strain thinning polymer melts, the corrected Cogswell model and Binding/Gibson model should be preferred, respectively. Otherwise, the extensional viscosity determination can be rather erroneous. [Copyright &y& Elsevier]

Two tiny hairpin DNAs, CORE (dAGGCTTCGGCCT) and AP2 (dAGGCTXCGGCCT; X: abasic nucleotide), fold into almost the same tetraloop hairpin structure with one exception, that is, the sixth thymine (T6) of CORE is exposed to the solvent water (Kawakami, J. et al., Chem. Lett. 2001, 258-259). In the present study, we selected small peptides that bind to CORE or AP2 from a combinatorial pentapeptide library with 2.5 × 106 variants. On the basis of the structural information, the selected peptide sequences should indicate the essential qualifications for recognition of the hairpin loop DNA with and without a flipped base. In the selected DNA binding peptides, aromatic amino acids such as histidine for CORE and glutamine/aspartic acid for AP2 were found to be abundant amino acids. This amino acid preference suggests that CORE-binding peptides use π-π stacking to recognize the target while hydrogen bonding is dominant for AP2-binding peptides. To investigate the binding properties of the selected peptide to the target, surface plasmon resonance was used. The binding constant of the interaction between CORE and a CORE-binding peptide (HWHHE) was about 1.1 × 106 M-1 at 25°C and the resulting binding free energy change at 25°C (ΔG°25) was -8.2 kcal mol-1. The binding of the peptide to AP2 was also analyzed and the resulting binding constant and ΔG°25 were about 4.2 × 104 M-1 and -6.3 kcal mol-1, respectively. The difference in the binding free energy changes (ΔΔG°25) of 1.9 kcal mol-1 was comparable to the values reported in other systems and was considered a consequence of the loss of π-π stacking. Moreover, the stabilization effect by stacking affected the dissociation step as well as the association step. Our results suggest that the existence of an aromatic ring (T6 base) produces new dominant interactions between peptides and nucleic acids, although hydrogen bonding is the preferable mode of interaction in the absence of the flipping base. These findings regarding CORE and AP2 recognition are expected to give useful information in the design of novel artificial DNA binding peptides. [ABSTRACT FROM AUTHOR]

The current model for insulin binding to the insulin receptor proposes that there are two binding sites, referred to as sites 1 and 2, on each monomer in the receptor homodimer and two binding surfaces on insulin, one involving residues predominantly from the dimerization face of insulin (the classical binding surface) and the other residues from the hexamerization face. High-affinity binding involves one insulin molecule using its two surfaces to make bridging contacts with site 1 from one receptor monomer and site 2 from the other. Whilst the receptor dimer has two identical site 1-site 2 pairs, insulin molecules cannot bridge both pairs simultaneously. Our structures of the insulin receptor (IR) ectodomain dimer and the L1-CR-L2 fragments of IR and insulin-like growth factor receptor (IGF-1R) explain many of the features of ligand-receptor binding and allow the two binding sites on the receptor to be described. The IR dimer has an unexpected folded-over conformation which places the C-terminal surface of the first fibronectin-III domain in close juxtaposition to the known L1 domain ligand-binding surface suggesting that the C-terminal surface of FnIII-1 is the second binding site involved in high-affinity binding. This is very different from previous models based on three-dimensional reconstruction from scanning transmission electron micrographs. Our single-molecule images indicate that IGF-1R has a morphology similar to that of IR. In addition, the structures of the first three domains (L1-CR-L2) of the IR and IGF-1R show that there are major differences in the two regions governing ligand specificity. The implications of these findings for ligand-induced receptor activation will be discussed. This review summarizes the key findings regarding the discovery and characterization of the insulin receptor, the identification and arrangement of its structural domains in the sequence and the key features associated with ligand binding. The remainder of the review deals with a description of the receptor structure and how it explains much of the large body of biochemical data in the literature on insulin binding and receptor activation. [ABSTRACT FROM AUTHOR]

Abstract: Isothermal titration calorimetry (ITC) is a well established technique for the study of biological interactions. The strength of ITC is that it directly measures enthalpy changes associated with interactions. Experiments can also yield binding isotherms allowing quantification of equilibrium binding constants, hence an almost complete thermodynamic profile can be established. Principles and application of ITC have been well documented over recent years, experimentally the technique is simple to use and in ideal scenarios data analysis is trivial. However, ITC experiments can be designed such that previously inaccessible parameters can be evaluated. We outline some of these advances, including (1) exploiting different experimental conditions; (2) low affinity systems; (3) high affinity systems and displacement assays. In addition we ask the question: What if data cannot be fit using the fitting functions incorporated in the data-analysis software that came with your ITC? Examples where such data might be generated include systems following non 1:n binding patterns and systems where binding is coupled to other events such as ligand dissociation. Models dealing with such data are now appearing in literature and we summarise examples relevant for the study of ligand–DNA interactions. [Copyright &y& Elsevier]

Abstract: Neonicotinoid insecticides show selective actions on insect nicotinic acetylcholine receptor (nAChR). Two key residues (Trp and Arg/Lys) have been identified as contributing to the neonicotinois binding. To investigate the selective mechanism, a computational model was set up to simulate the interaction between residues (Trp and Arg) of insect nAChR and neonicotinoids by quantum chemistry method. Three analogues of neonicotinoid derivatives without the chloropyridinyl moiety and 3-methyl-indole (3MI), guanidinium (Gua) were used to mimic the neonicotinoids and the side chain of key residues Trp and Arg accordingly. Interaction features of 3MI-analogues, analogues-Gua and 3MI-analogues -Gua complexes were analyzed comparatively. Hydrogen bonding between the nitro group of analogues and Gua was found to be the most important for binding. Moreover, the cooperative π–π interaction between analogues and the indole ring, which is strengthened by the existence of Gua, also contributes to the binding. The alternative binding model of neonicotinoids proposed here, although slightly different from others, might be close to the actual. [Copyright &y& Elsevier]

Abstract: 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. [Copyright &y& Elsevier]

Abstract: Evolution of resistance by pests is the greatest threat to the continuous success of theBacillus thuringiensis (Bt) toxins used in conventional sprays or in transgenic plants. The most common mechanism of insect resistance to Bt is reduced binding of toxins to target sites in the brush border membrane of the larval mid-gut. In this paper, binding experiments were performed with three 125I-Cry1A toxins and the brush border membrane vesicles from Cry1Ac resistant or susceptible strains of Helicoverpa armigera. The homologous competition test showed that there was no significant difference in Cry1Ac-binding affinity, but the concentration of Cry1Ac-binding sites dramatically decreased in the resistant strain (R t decreased from 5.87±1.40 to 2.23±0.80). The heterologous competition test showed that there were three Cry1Ac-binding sites in the susceptible strain. Among them, site 1 bound with all three Cry1A toxins, site 2 bound with both Cry1Ab and Cry1Ac, and site 3 only bound with Cry1Ac. In the Cry1Ac resistant strain, the binding capability of site 1 with Cry1Ab decreased and site 2 did not bind with Cry1Ac. It is suggested that the absence of one binding site is responsible for H. armigera resistance to Cry1Ac. This result also showed that the resistance fitted the “mode 1” pattern of Bt resistance described previously. [Copyright &y& Elsevier]

Circular dichroism (CD) spectra of complexes of 4-benzylaminopyrimido[4′,5′ :4,5]selenolo(2,3-b)quinoline (BAPSQ) with octanucleotide I (d(TGACGTCA)), which is the cAMPresponsive element (CRE) in gene promoters, and its inverse d(ACTGCAGT) (octanucleotide II) have been measured over a range of drug/DNA ratios. It was demonstrated that the anticancer polyaromatic drug BAPSQ intercalates into DNA basepairs with its long direction perpendicular to both the DNA helix axis and the base pair long axis and induces larger conformational changes in CpG containing octanucleotide I CRE than in its reverse sequence, octanucleotide II. It was concluded that CD is a powerful and sensitive technique to discriminate between drug-binding modes of DNA and to define the geometry of the chromophore inserted into base pairs. [ABSTRACT FROM AUTHOR]

The interaction between double-stranded (ds) DNA and the 4-butylamino pyrimido[4′,5′:4,5]selenolo(2,3-b)quinoline (BPSQ) has been studied with spectral luminescence methods. Binding constant values determined by absorption and fluorescence titration indicated a binding constant of 4.24 × 104 and 5.9 × 104 M−1, respectively. The interaction was markedly suppressed by increasing the salt concentration. BPSQ exhibited a strong specificity for the guanine–cytosine (GC) sequence in total DNA at an ionic strength of 0.01 (5.54 × 106 M−1). BPSQ increased the viscosity of sonicated rod-like DNA fragments, producing a calculated increment in length of 2.4 Å per bound drug molecule. A circular dichroism experiment showed that BPSQ might interact with DNA according to two possible binding modes depending on its structure and concentration. The first mode concerned intercalation of BPSQ with its long axis perpendicular to the long axis of the DNA helix. The same drug was able to bind to external sites, second mode, once the intercalation sites were saturated at high concentration. The results from cytotoxicity assays indicate that BPSQ was found to be toxic to all cell lines tested with IC50 values ranging from 2.8 to ≥ 20 µM. It was concluded that the binding of BPSQ to DNA occurs by a mechanism of intercalation, which probably accounts for its reported antitumor activity. [ABSTRACT FROM AUTHOR]

Binding of poly(amido amine) dendrimer to sodium hyaluronate (NaHA) in aqueous 0.25 M NaCl solution has been investigated by static light scattering. It was observed that the apparent weight-average molecular weight and the radius of gyration increase with the ratio of NH2 terminal groups in the dendrimer to the carboxylate groups in the NaHA, [NH2]/[COO−]. Up to [NH2]/[COO−]=31, the observed variation of molecular weight was reproduced by the “average binding” model, where an average number of dendrimers binds to each NaHA chain. Based on the “critical binding” model, the maximum number, nmax, of dendrimers which can bind to a NaHA chain was calculated to be nmax=300 for a solution of [NH2]/[COO−]=56. The obtained value corresponds to the binding of one dendrimer per 1.5 repeating units on a NaHA chain. It is suggested from the observed radius of gyration that, while the dendrimer–NaHA complexes of [NH2]/[COO−] up to 5 maintain a wormlike character similar to NaHA without bound dendrimers, those of [NH2]/[COO−] above 10 behave like rigid rods. It is concluded that the hydrogen-bonding interaction, besides the electrostatic interaction, should play an important role in the formation of the NaHA–dendrimer complexes. [Copyright &y& Elsevier]

Complexes of DNA with actinocin derivatives containing benzocrown groups at positions 1 and/or 9 of the chromophore were studied by spectrophotometric titration and circular dichroism. The actinocin chromophore and the crown fragments are the DNA-binding sites of the ligands. The mode of ligand–DNA binding is shown to depend on the size of the crown group, its distance to the actinocin chromophore, and the ionic strength of the medium. Na+-selective benzocrown fragments combine with DNA phosphate groups. The simultaneous interaction of the actinocin chromophore with the DNA bases is possible only at an optimal distance between the two binding sites of ligand molecule. [ABSTRACT FROM AUTHOR]

• The three compartment PK model is extended to delivery to two cell types. • The model is applied to mixed cell populations (drug resistant and drug responsive) • High proportions of responsive cells can deplete extracellular drug concentrations. • High proportions of responsive cells can lower drug metabolized in resistant cells. 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 of 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 both cell types farther away from the vessel. [ABSTRACT FROM AUTHOR]

Denaturation with guanidine hydrochloride (GdnHCl) or urea is one of the primary ways of measuring the conformational stability of proteins and comparing the stability of mutant proteins. Despite the widespread use of these two denaturants to provide quantitative data for the free energies of unfolding, the mode of action of these agents is not well understood. We are not even certain whether the action of these agents on proteins is direct and can be regarded as ligand binding, or indirect and involves a change in the properties of solvent (water) in the presence of GdnHCl and urea. In this paper, an extensive kinetic study of the inhibition of ribonuclease A and papain by urea has been performed. The results suggest that the effect of urea on activities of these enzymes can be well described by the denaturant binding model. The binding constants of urea determined by the present method are nearly identical to that determined from a variety of different studies on model compounds and proteins. [ABSTRACT FROM PUBLISHER]

The inhibition in the rate of hydrolysis of four esters, by the anionic micelles of sodium laurylsulphate has been explained by a binding model. It provides the critical micelle concentration under reaction conditions. Kinetic data suggest that more than 90% of the substrate is micelle-bound at 0.010 M concentration of the anionic micelle and the binding constants obtained agree with those of other systems studied elsewhere. The marked inhibition in the comicellar phase and the cationic micellar phase of sodium Iaurylsulphate, cetyldimethylbenzylammonium chloride or cetyltrimethylammonium bromide, has been explained by using the same pseudo model and the binding constant, K and the fraction of substrate held at the comicellar surface, F , indicates greater binding at the comicellar surface. The cooperativity treatment has been extended to micelle-inhibited reactions and the proposed model has been tested with literature data as well as in the present work. The cooperativity index value ranges from 0.59 to 1.51, and a value less than unity indicates negative cooperativity. [ABSTRACT FROM AUTHOR]

We recently presented evidence showing that the visible CD spectrum of the purple membrane from Halobacterium halobium consists of two contributions: a broad positive band centered at the absorption maximum due to the interaction of the chromophore with the protein to which it is bound, and an exciton coupling band due to the interaction between chromophores of adjacent bacteriorhodopsin molecules in the hexagonal surface lattice (Heyn et al., 1975). This interpretation receives strong support from the present experiments in which the chromophore-free membrane is reconstituted by the addition of retinal. Since the coupling signal arises from the interaction between pairs of neighboring chromophores, its contribution to the spectrum would be expected to be very small in the initial stages of the titration experiment, but increasing quadratically with the percentage reconstitution. The broad positive band, on the other hand, is expected to increase linearly with the percentage reconstitution. On the basis of these considerations a satisfactory explanation of the CD reconstitution experiments could be given. Since it appears to be impossible to explain the titration experiments without the quadratic term, we conclude that chromophore-chromophore interactions play an important role. No significant changes in secondary structure upon reconstitution could be detected consistent with our binding model which neglects cooperativity. [ABSTRACT FROM AUTHOR]

Microbial bioremediation is a very potent and eco-friendly approach to alleviate pesticide pollution in agricultural ecosystems, and hydrolase is an effective element for contaminant degradation. In the present study, a novel Mn 2+ -dependent esterase, PchA, that efficiently hydrolyzes carbamate pesticides with aromatic structures was identified from Pseudomonas sp. PS21. The hydrolytic activity was confirmed to be related closely to the core catalytic domain, which consists of six residues. The crucial residues indirectly stabilized the position of carbaryl via chelating Mn 2+ according to the binding model clarified by molecular simulations, and the additional hydrophobic interactions between carbaryl with several hydrophobic residues also stabilized the binding conformation. The residue Glu398, by serving as the general base, might activate a water molecule and facilitate PchA catalysis. This work offers valuable insights into the binding interaction and hydrolytic mechanism of carbaryl with the hydrolase PchA and will be crucial to designing strategies leading to the protein variants that are capable of degrading related contaminants.

The blockade of the PD-1/PD-L1 immune checkpoint pathway with small molecules is an emerging immunotherapeutic approach. A novel series of 4-phenylindoline derivatives were synthesized, and their inhibitory activity against the PD-1/PD-L1 protein-protein interaction (PPI) was evaluated through a homogenous time-resolved fluorescence (HTRF) assay. Among them, A20 and A22 exhibited potent activity with IC 50 values of 17 nM and 12 nM, respectively. Furthermore, A20 showed the promising inhibitory activity against the PD-1/PD-L1 interaction with the EC 50 value of 0.43 μM in a co-culture model of PD-L1/TCR Activator-expressing CHO cells and PD-1-expressing Jurkat cells. Besides, the structure−activity relationships (SAR) of the novel synthesized 4-phenylindoline derivatives was concluded, and the binding mode of A22 with the PD-L1 dimer was analyzed by molecular simulation and docking, demonstrating that the N-atom in the side chain of indoline fragment could interact with the amino acid residue of the PD-L1 protein to lead to the potent inhibitory activity. This study provided a new insight for further drug design. Image 1 • Several indoline derivatives targeting the PD-1/PD-L1 pathway were developed. • A22 inhibited the interaction of PD-1/PD-L1 potently (IC 50 = 12 nM). • A20 and A22 exhibited low toxicity in a co-culture model. • A20 inhibited the binding of PD-1/PD-L1 in a co-culture model (EC 50 = 0.43 μM). [ABSTRACT FROM AUTHOR]

Aberrant activation of the endosomal Toll-like receptor 7 (TLR7) has been implicated in myriad autoimmune diseases and is an established therapeutic target in such conditions. Development of diverse TLR7 antagonists is mainly accomplished through random screening. To correlate human TLR7 (hTLR7) antagonistic activity with the structural features in different chemotypes, we derived a hypothetical binding model based on molecular docking analysis along with molecular dynamics (MD) simulations study. The binding hypothesis revealed different pockets, grooves and a central cavity where ligand-receptor interaction with specific residues through hydrophobic and hydrogen bond interactions take place, which correlate with TLR7 antagonistic activity thus paving the way for rational design using varied chemotypes. Based on the structural insight thus gained, TLR7 antagonists with quinazoline were designed to understand the effect of engagement of these pockets as well as boundaries of the chemical space associated with them. The newly synthesized most potent hTLR7 antagonist, i.e. compound 63 , showed IC 50 value of 1.03 ± 0.05 μM and was validated by performing primary assay in human plasmacytoid dendritic cells (pDC) (IC 50 pDC: 1.42 μM). The biological validation of the synthesized molecules was performed in TLR7-reporter HEK293 cells as well as in human plasmacytoid dendritic cells (pDCs). Our study provides a rational design approach thus facilitating further development of novel small molecule hTLR7 antagonists based on different chemical scaffolds. Image 1 • hTLR7 antagonist binding hypothesis based on docking analysis of known antagonists. • Significance of engaging different pockets and grooves for hTLR7 antagonism. • MD simulation showed ligand binding stability and protein conformational change. • Newly designed ligands based on binding model showed potent hTLR7 antagonism. • Interaction pattern can correlate the structural change in molecule with the activity. [ABSTRACT FROM AUTHOR]

Determining the energetics of the unfolded state of a protein is essential for understanding the folding mechanics of ordered proteins and the structure-function relation of intrinsically disordered proteins. Here, we adopt a coil-globule transition theory to develop a general scheme to extract interaction and free energy information from single-molecule fluorescence resonance energy transfer spectroscopy. By combining protein stability data, we have determined the free energy difference between the native state and the maximally collapsed denatured state in a number of systems, providing insight on the specific/nonspecific interactions in protein folding. Both the transfer and binding models of the denaturant effects are demonstrated to account for the revealed linear dependence of inter-residue interactions on the denaturant concentration, and are thus compatible under the coil-globule transition theory to further determine the dimension and free energy of the conformational ensemble of the unfolded state. The scaling behaviors and the effective θ-state are also discussed., (© 2016 The Protein Society.)