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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 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]

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]

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]

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]

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]

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. [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]

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]

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]

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]

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]