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Mutations of isocitrate dehydrogenase 1 (IDH1) are key biomarkers for glioma classification, but current methods for detection of mutated IDH1 (mIDH1) require invasive tissue sampling and cannot be used for longitudinal studies. Positron emission tomography (PET) imaging with mIDH1-selective radioligands is a promising alternative approach that could enable non-invasive assessment of the IDH status. In the present work, we developed efficient protocols for the preparation of four 18F-labeled derivatives of the mIDH1-selective inhibitor olutasidenib. All four probes were characterized by cellular uptake studies with U87 glioma cells harboring a heterozygous IDH1 mutation (U87-mIDH) and the corresponding wildtype cells (U87-WT). In addition, the most promising probe was evaluated by PET imaging in healthy mice and mice bearing subcutaneous U87-mIDH and U87-WT tumors. Although all four probes inhibited mIDH1 with variable potencies, only one of them ([18F]mIDH-138) showed significantly higher in vitro uptake into U87-mIDH compared to U87-WT cells. In addition, PET imaging with [18F]mIDH-138 in mice demonstrated good in vivo stability and low non-specific uptake of the probe, but also revealed significantly higher uptake into U87-WT compared to U87-mIDH tumors. Finally, application of a two-tissue compartment model (2TCM) to the PET data indicated that preferential tracer uptake into U87-WT tumors results from higher specific binding rather than from differences in tracer perfusion. In conclusion, these results corroborate recent findings that mIDH1-selective inhibition may not directly correlate with mIDH1-selective target engagement and indicate that in vivo engagement of wildtype and mutated IDH1 may be governed by factors that are not faithfully reproduced by in vitro assays, both of which could complicate development of PET probes. [ABSTRACT FROM AUTHOR]

Series of indole‐1,3,4‐thiadiazole compounds (IT 1–7) were synthesized and characterized by FT‐IR, 1H NMR, 13C NMR and ESI‐MS spectral data. Further, the compounds (IT 1–7) were screened for antidiabetic, antioxidant and anti‐inflammatory activities. Most of these compounds exhibited moderate to good antidiabetic, antioxidant and anti‐inflammatory activities against α‐amylase enzyme, ABTS and lipoxygenase enzyme, respectively. Among these, IT‐1 displayed the better activity compared to that of standard drugs. The mechanism of binding of IT‐1, IT‐5 and IT‐6 with a transporter protein, human serum albumin was investigated by fluorescence spectroscopic and circular dichroism studies. These compounds quenched the intrinsic fluorescence intensity of HSA and moderate binding was evident from the values of binding constants which are in the order of 105 M−1. The molecular docking studies of the compounds were performed against human pancreatic alpha‐amylase in complex with montbretin A (PDB ID: 4W93). The studied compounds interacted with amino acid residues (ASP197, GLU240 and TYR151) which were similar to that of the reference drug, acarbose. The ADME properties of designed compounds were studied using SwissADME software. All the compounds obeyed Lipinski's rule of five. All the compounds showed low or non‐toxicity towards different toxicity classes as analyzed using ProTox‐II online tool. [ABSTRACT FROM AUTHOR]

RNA-binding proteins are essential regulators of RNA processing and function. Translational repression assays can be used to study how they interact with specific RNA sequences by insertion of such a consensus sequence into the 5’ untranslated region of a reporter mRNA and measuring reporter protein translation. The straightforward set-up of these translational repression assays avoids the need for the isolation of the protein or the RNA providing speed, robustness and a low-cost method. Here, we report the optimization of the assay to function with linear RNA sequences instead of the previously reported hairpin type sequences to allow the study of a wider variety of RNA-binding proteins. Multiplication of a consensus sequence strongly improves the signal allowing analysis by both fluorescence intensity measurements and flow cytometry.

Mutations of isocitrate dehydrogenase 1 (IDH1) are key biomarkers for glioma classification, but current methods for detection of mutated IDH1 (mIDH1) require invasive tissue sampling and cannot be used for longitudinal studies. Positron emission tomography (PET) imaging with mIDH1-selective radioligands is a promising alternative approach that could enable non-invasive assessment of the IDH status. In the present work, we developed efficient protocols for the preparation of four 18F-labeled derivatives of the mIDH1-selective inhibitor olutasidenib. All four probes were characterized by cellular uptake studies with U87 glioma cells harboring a heterozygous IDH1 mutation (U87-mIDH) and the corresponding wildtype cells (U87-WT). In addition, the most promising probe was evaluated by PET imaging in healthy mice and mice bearing subcutaneous U87-mIDH and U87-WT tumors. Although all four probes inhibited mIDH1 with variable potencies, only one of them ([18F]mIDH-138) showed significantly higher in vitro uptake into U87-mIDH compared to U87-WT cells. In addition, PET imaging with [18F]mIDH-138 in mice demonstrated good in vivo stability and low non-specific uptake of the probe, but also revealed significantly higher uptake into U87-WT compared to U87-mIDH tumors. Finally, application of a two-tissue compartment model (2TCM) to the PET data indicated that preferential tracer uptake into U87-WT tumors results from higher specific binding rather than from differences in tracer perfusion. In conclusion, these results corroborate recent findings that mIDH1-selective inhibition may not directly correlate with mIDH1-selective target engagement and indicate that in vivo engagement of wildtype and mutated IDH1 may be governed by factors that are not faithfully reproduced by in vitro assays, both of which could complicate development of PET probes.

Abstract Qualitative NMR spectroscopic and quantitative calorimetric binding studies were performed to characterize the interaction of nontoxic mimics of the V-type nerve agent VX (O-ethyl S-[2-(diisopropylamino)ethyl] methylphosphonothioate) and the Novichok nerve agent A-234 (ethyl (1-(diethylamino)ethylidene)phosphoramidofluoridate) with a series of receptors in 100 mM aqueous phosphate buffer at pH 7.4 and 37 °C. These investigations provided information about the preferred geometry with which the nerve agent mimics are included into the receptor cavities and about the stability of the complexes formed. According to the results, the positively charged VX mimic prefers to bind to cation receptors such as sulfonated calixarenes and an acyclic cucurbituril but does not noticeably interact with cyclodextrins. While binding to the acyclic cucurbituril is stronger than that to calixarenes, the mode of inclusion into the sulfonatocalix[4]arene cavity is better suited for the development of scavengers that bind and detoxify V-type nerve agents. The neutral Novichok mimic, on the other hand, only interacts with the acyclic cucurbituril with a strength required for scavenger development. These binding studies thus provided guidelines for the further development of nerve agent scavengers.

The binding studies of DNA with small molecules have been an emerging field of research all the time since DNA as the genetic material is a major biological target for various drugs. Interpretation of small molecule-DNA binding helps in understanding their interactions with designing new drugs of greater medicinal activity. Posaconazole is an antifungal drug in the class of triazoles which are known to possess numerous pharmacological properties. In this work, the nature of the binding of posaconazole with calf-thymus DNA has been studied using spectroscopic techniques and molecular docking studies. A binding constant of the order of 103 M−1 was observed from UV–visible and fluorescence studies for the interaction between posaconazole and calf-thymus DNA. The fluorescence property of posaconazole was found to be quenched by calf-thymus DNA with a quenching constant of the order of 103 M−1. Competitive displacement of ethidium bromide and Hoechst 33258 by posaconazole using fluorescence technique suggested minor groove binding of posaconazole in calf-thymus DNA. Confirmation of the binding mode was further complemented by the viscosity measurement and DNA melting studies followed by KI quenching experiments. The studies on the effect of ionic strength on the binding suggested a possible role of electrostatic force in the interaction. Molecular docking studies reflected a crescent shape of the posaconazole within the minor groove of calf-thymus DNA validating the experimental findings showing the residues involved in the interaction. [ABSTRACT FROM AUTHOR]

RNA-binding proteins are essential regulators of RNA processing and function. Translational repression assays can be used to study how they interact with specific RNA sequences by insertion of such a consensus sequence into the 5' untranslated region of a reporter mRNA and measuring reporter protein translation. The straightforward set-up of these translational repression assays avoids the need for the isolation of the protein or the RNA providing speed, robustness and a low-cost method. Here, we report the optimization of the assay to function with linear RNA sequences instead of the previously reported hairpin type sequences to allow the study of a wider variety of RNA-binding proteins. Multiplication of a consensus sequence strongly improves the signal allowing analysis by both fluorescence intensity measurements and flow cytometry. [ABSTRACT FROM AUTHOR]

Au‐catalyzed hydroamination proceeds well for alkynes but not alkenes. We report gas‐phase binding energies of alkenes and alkynes to a cationic Au center, which indicate that differences in binding are not the origin of the disparate chemical behavior. We further report the synthesis and characterization of 2‐aminoalkylgold complexes, which would be the intermediates in a hypothetical Au‐catalyzed hydroamination of styrene. The reactivity of the well‐characterized and isolable complexes reveals that protonation or alkylation of the 2‐aminoalkylgold complexes results in amine elimination in solution, and in the gas phase, indicating that the failure of Au‐catalyzed alkene hydroamination derives from a non‐competitive protodeauration step. We analyze possible transition states for the protodeauration, and identify an insufficiently strong Au‐proton interaction as the reason that the transition states lie too high in energy to compete. [ABSTRACT FROM AUTHOR]

• The interactions of anamphiphilic drug(Propranolol Hydrochloride, PPL) with cationic surfactants was evaluated by the surface tension methods. • The non-ideal or synergistic behavior of the mixed systems studied were explored by using several physical models. • Several thermodynamic parameters of mixed micellization were measured. • The synergism between PPL and cationic surfactants was also confirmed by UV–visible spectroscopy. The interactions of amphiphilic drug(propranolol hydrochloride, PPL) with cationic surfactants, such as dodecyltrimethylammoniumbromide(DTAB), tetradecyltrimethylammonium bromide (TTAB), trimethyltetradecylammonium chloride(TTAC) and tetyltrimethylammonium bromide(CTAB), in an aqueous medium were evaluated. The surface tension measurement was used to examine the mixed micellization behavior and surface properties of drug-surfactant mixtures. The nonideal or synergistic behaviors of the mixed systems were explored by using several physical models, such as Clint, Rubingh, Rosen, and Motomura models, based on regular solution theory and pseudophase approximation. In addition, the synergism between PPL and cationic surfactants was also confirmed using ultraviolet–visible spectroscopy. The stoichiometric ratios, binding constants, and free energy changes of the drug–surfactant mixtures were computed using Benesi–Hildebrand (B–H) theory. [ABSTRACT FROM AUTHOR]

Enantioselective molecular recognition of chiral molecules that lack specific interaction sites for hydrogen bonding or Lewis acid–base interactions remains challenging. Here we introduce the concept of tailored chiral π‐surfaces toward the maximization of shape complementarity. As we demonstrate for helicenes it is indeed possible by pure van‐der‐Waals interactions (π–π interactions and CH–π interactions) to accomplish enantioselective binding. This is shown for a novel benzo[ghi]perylene trisimide (BPTI) receptor whose π‐scaffold is contorted into a chiral plane by functionalization with 1,1′‐bi‐2‐naphthol (BINOL). Complexation experiments of enantiopure (P)‐BPTI with (P)‐ and (M)‐[6]helicene afforded binding constants of 10 700 M−1 and 550 M−1, respectively, thereby demonstrating the pronounced enantiodifferentiation by the homochiral π‐scaffold of the BPTI host. The enantioselective recognition is even observable by the naked eye due to a specific exciplex‐type emission originating from the interacting homochiral π‐scaffolds of electron‐rich [6]helicene and electron‐poor BPTI. [ABSTRACT FROM AUTHOR]

There are many fluorescence-based applications that can be used to characterize molecular interactions. However, available methods often depend on site-specific labeling techniques or binding-induced changes in conformation or size of the probed target molecule. To overcome these limitations, we applied a ratiometric dual-emission approach that quantifies ligand-induced spectral shifts with sub-nanometer sensitivity. The use of environment-sensitive near-infrared dyes with the method we describe enables affinity measurements and thermodynamic characterization without the explicit need for site-specific labeling or ligand-induced conformational changes. We demonstrate that in-solution spectral shift measurements enable precise characterization of molecular interactions for a variety of biomolecules, including proteins, antibodies, and nucleic acids. Thereby, the described method is not limited to a subset of molecules since even the most challenging samples of research and drug discovery projects like membrane proteins and intrinsically disordered proteins can be analyzed. [ABSTRACT FROM AUTHOR]

Sepsis, characterized with high risk of life‐threatening organ dysfunction, represents a major cause of health loss and the World Health Organization (WHO) labelled sepsis as the most urgent unmet medical need in 2017. The emerging biological understanding of the role of RIPK1 in sepsis has opened up an exciting opportunity to explore potent and selective RIPK1 inhibitors as an effective therapeutic strategy for SIRS and sepsis therapy. Herein, we have synthesized a class of highly potent dual‐mode RIPK1 inhibitors occupying both the allosteric and the ATP binding pockets, exemplified by compound 21 (ZB‐R‐55) which is about 10‐fold more potent than GSK2982772, and exhibits excellent kinase selectivity, good oral pharmacokinetics and good therapeutic effects in the LPS‐induced sepsis model, suggesting that compound ZB‐R‐55 is a highly promising preclinical candidate. [ABSTRACT FROM AUTHOR]

Although some progress has been achieved in understanding certain aspects of the allergenic mechanism of animal lipocalins, they still remain largely enigmatic. One possibility to unravel this property is to investigate their interaction with components of the immune system. Since these components are highly complex we intended to use a high-throughput technology for this purpose. Therefore, we used phage-display of a random peptide library for panning against the dog allergen Can f 1. By this method we identified a Can f 1 binding peptide corresponding to the antigen-binding site of a putative γδT-cell receptor. Additional biochemical investigations confirmed this interaction. [ABSTRACT FROM AUTHOR]

[Display omitted] • 1,3,4-oxadiazole-thiazolidine-2,4-dione hybrid compounds (TOT-1 to 15) were synthesized, characterized and screened for various biological activities. • Single-crystal X-ray diffraction data was collected for the intermediate compound, TOT and its structure was proposed. • The compounds, TOT 12–15 exhibited significant anti-cancer activity. • Molecular docking studies were carried out. Two synthetic methods were proposed for the preparation of a new series of thiophene-1,3,4-oxadiazole-thiazolidine-2,4-dione hybrids (TOT-1 to 15) and their structures were elucidated based on spectral data. Studies on cytotoxicity, ROS, cellular uptake and interactions of TOT-14 with calf thymus DNA were carried out. Anticancer activity of compounds, TOT-1 to 15 on breast cancer (MCF-7) cell lines was investigated. The IC 50 values for the standard, epirubicin hydrochloride and TOT-12, 13, 14 and 15 were found to be 6.78, 5.52, 6.53, 4.83 and 5.57 µg/mL, respectively. Notably, TOT-14 exhibited a remarkable antiproliferative activity with a strikingly selective inhibitory effect compared to standard. This specific selectivity could be attributed to the synergistic effect of increased cellular uptake and generation of higher ROS in cancer cells after irradiation. The binding constant of 4.25 x 103 M−1 indicated the moderate interaction between TOT-14 and ct-DNA. The docking score of TOT derivatives was substantially identical to the docking score of epirubicin hydrochloride. The designed molecules complied with the requirements for drug-likeness and ADME. [ABSTRACT FROM AUTHOR]

In the fields of pharmacology and life sciences, it is essential to study how prescribed drugs interact with carrier proteins in human serum albumin. The current study has evaluated the binding properties of rhodanine derivative; (z)-2-(4-(5-((3-(3-chlorophenyl)-1-phenyl-1H-pyrazol-4-oxo-2-thioxothiazolidin-3-yl)benzamido)acetic acid (P3CL) on bovine serum albumin (BSA) by biophysical approach. BSA is a homology model of Human serum albumin. Due to the cost-effectiveness of Human Serum Albumin (HSA) we have studied the binding properties of rhodanine derivative (P3CL) on BSA. The BSA-P3CL interactions were investigated by fluorescence spectroscopy and revealed the presence of a static quenching mechanism. P3CL possesses good binding affinity on BSA with binding constant K P3CL = 5.36330 × 10 13 M -1 binding free energy. We have calculated the binding free energy, the number of binding sites, and the binding constants. The establishment of hydrogen bonds and the active participation of amino acids in drug binding were confirmed by molecular docking studies. As conventional processes for the investigation of pharmacological drugs, therapeutic combinations, and coordinated drug intake, the offered strategies are simple to comprehend, accurate, and rapid to put into practice. Our findings will support an additional investigation into ligand's pharmacological activity.Communicated by Ramaswamy H. Sarma.

Fibrinogen C domain-containing protein 1 (FIBCD1) is an immune protein proposed to be involved in host recognition of chitin on the surface of pathogens. As FIBCD1 readily binds acetylated molecules, we have determined the high-resolution crystal structures of a recombinant fragment of the FIBCD1 C-terminal domain complexed with small N-acetyl-containing ligands to determine the mode of recognition. All ligands bind at the conserved N-acetyl-binding site (S1) with galactose and glucose-derived ligands rotated 180° relative to each other. One subunit of a native structure derived from protein expressed in mammalian cells binds glycosylation from a neighboring subunit, in an extended binding site. Across the various structures, the primary S1 binding pocket is occupied by N-acetyl-containing ligands or acetate, with N-acetyl, acetate, or sulfate ion in an adjacent pocket S1(2). Inhibition binding studies of N-acetylglucosamine oligomers, (GlcNAc) n , n = 1, 2, 3, 5, 11, via ELISA along with microscale thermophoresis affinity assays indicate a strong preference of FIBCD1 for longer N-acetylchitooligosaccharides. Binding studies of mutant H396A, located beyond the S1(2) site, showed no significant difference from wildtype, but K381L, within the S1(2) pocket, blocked binding to the model ligand acetylated bovine serum albumin, suggesting that S1(2) may have functional importance in ligand binding. The binding studies, alongside structural definition of diverse N-acetyl monosaccharide binding in the primary S1 pocket and of additional, adjacent binding pockets, able to accommodate both carbohydrate and sulfate functional groups, suggest a versatility in FIBCD1 to recognize chitin oligomers and other pathogen-associated carbohydrate motifs across an extended surface., Competing Interests: Conflict of interest The authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Phosphopantetheine adenylyltransferase (PPAT, EC. 2.7.7.3) catalyzes an essential step in the reaction that transfers an adenylyl group from adenosine tri phosphate (ATP) to 4′-phosphopantetheine (pPant) yielding 3′- dephospho-coenzyme A (dPCoA) and pyrophosphate (PP) in the coenzyme A (CoA) biosynthesis pathway. The enzyme PPAT from Acinetobacter baumannii (Ab PPAT) was cloned, expressed and purified. The binding studies of Ab PPAT were carried out with two compounds, tri‑sodium citrate (TSC) and l -ascorbic acid (LAA, vitamin-C) using fluorescence spectroscopic (FS) and surface Plasmon resonance (SPR) methods. Both methods provided similar values of dissociation constants for TSC and LAA which were of the order of 10−8 M and 10−5 M respectively. The computer aided docking studies indicated fewer interactions of LAA with Ab PPAT as compared to those of TSC. The freshly purified samples of Ab PPAT were crystallized. The crystals of Ab PPAT were soaked in the solutions containing TSC and LAA. However, the crystals of the complex of Ab PPAT with LAA did not diffract well and hence the structure of the complex of Ab PPAT with LAA could not be determined. On the other hand, the crystals of the complex of Ab PPAT with TSC diffracted well and the structure was determined at 1.76 Å resolution. It showed that TSC bound to Ab PPAT at the ATP binding site and formed several intermolecular contacts including 12 hydrogen bonds. The results of binding studies for both TSC and LAA and the structure of the complex of Ab PPAT with TSC clearly indicated a potential role of TSC and LAA as antibacterial agents. • Ascorbic acid and Citric acid bind to Ab PPAT with high affinities. • Structure of Ab PPAT with citric acid was determined at 1.76 Å resolution. • Structure of Ab PPAT with citric acid shows that it binds at substrate binding site. • Both compounds show antibacterial effects against sensitive and resistant isolate. [ABSTRACT FROM AUTHOR]

Abstract Cucumber mosaic virus coat protein (CMV CP) plays a key role in cell-to-cell movement in host organisms. 1,4-Pentadien-3-one derivatives have excellent antiviral activities. In this study, we cloned, expressed and purified a CP recombinant protein. Then, we studied the binding interactions of CMV CP and 1, 4-pentadien-3-one derivatives N1–N20. Microscale thermophoresis experiments showed that N12 and N16 bound to CMV CP with dissociation constants of 0.071 and 0.11 μM, respectively. Docking and site-directed mutagenesis studies provided further insights into the interactions of N12 and N16 with Ile210, Thr69 and Ser213of CMV CP. Thus, these CMV CP residues may be important binding sites for the 1,4-pentadien-3-one derivatives N12 and N16. The data are important for designing and synthesizing new pentadienone derivatives. Graphical abstract Unlabelled Image Highlights • CMV CP proteins was overexpressed and identified as a target for antiviral compounds. • Compounds N12 and N16 directly interacts with CMV CP via hydrogen bonding with the Ile210, Thr69 and Ser213, respectively. • The Ile210, Thr69 and Ser213 of CMV CP are important for designing and synthesizing new pentadienone derivatives. [ABSTRACT FROM AUTHOR]

Legionella pneumophila is a freshwater bacterium that replicates in predatory amoeba and alveolar macrophage. The ability of L. pneumophila to thrive in eukaryotic host cells is conferred by the Legionella containing vacuole (LCV). Formation and intracellular trafficking of the LCV are governed by an arsenal of effector proteins, many of which are secreted by the Icm/Dot Type 4 Secretion System. One such effector, known as LpnE (L. pneumophila Entry), has been implicated in facilitating bacterial entry into host cells, LCV trafficking, and substrate translocation. LpnE belongs to a subfamily of tetratricopeptide repeat proteins known as Sel1‐like repeats (SLRs). All eight of the predicted SLRs in LpnE are required to promote host cell invasion. Herein, we report that LpnE(1‐375) localizes to cis‐Golgi in HEK293 cells via its signal peptide (aa 1–22). We further verify the interaction of LpnE(73‐375) and LpnE(22‐375) with Oculocerebrorenal syndrome of Lowe protein (OCRL) residues 10–208, restricting the known interacting residues for both proteins. To further characterize the SLR region of LpnE, we solved the crystal structure of LpnE(73‐375) to 1.75Å resolution. This construct comprises all SLRs, which are arranged in a superhelical fold. The α‐helices forming the inner concave surface of the LpnE superhelix suggest a potential protein–protein interaction interface. Database: Coordinates and structure factors were deposited in the Protein Data Bank with the accession number 6DEH. The effector protein LpnE from Legionella pneumophila contains eight Sel1‐like repeats that bind the Oculocerebrorenal syndrome of Lowe (OCRL) protein. The N‐terminal two‐and‐a‐half Sel1s (lighter shade) are not involved in OCRL binding but removing the entire third Sel1 abrogates this interaction. The 'handshake' of the His‐tags cemented by the Ni2+ ions is essential for the formation of this crystal form. [ABSTRACT FROM AUTHOR]

Progranulin (PGRN) is a secreted anti-inflammatory protein which can be processed by neutrophil proteases to various granulins. It has been reported that at least a significant portion of the anti-inflammatory effects of PGRN is due to direct high affinity binding to tumor necrosis factor receptor-1 (TNFR1) and TNFR2 and inhibition of tumor necrosis factor (TNF)-induced TNFR1/2 signaling. Two studies failed to reproduce the interaction of TNFR1 and TNFR2 with PGRN, but follow up reports speculated that this was due to varying experimental circumstances and/or the use of PGRN from different sources. However, even under consideration of these speculations, there is still a striking discrepancy in the literature between the concentrations of PGRN needed to inhibit TNF signaling and the concentrations required to block TNF binding to TNFR1 and TNFR2. While signaling events induced by 0.2–2 nM of TNF have been efficiently inhibited by low, near to equimolar concentrations (0.5–2.5 nM) of PGRN in various studies, the reported inhibitory effects of PGRN on TNF-binding to TNFR1/2 required a huge excess of PGRN (100–1,000-fold). Therefore, we investigated the effect of PGRN on TNF binding to TNFR1 and TNFR2 in highly sensitive cellular binding studies. Unlabeled TNF inhibited >95% of the specific binding of a Gaussia princeps luciferase (GpL) fusion protein of TNF to TNFR1 and TNFR2 and blocked binding of soluble GpL fusion proteins of TNFR1 and TNFR2 to membrane TNF expressing cells to >95%, too. Purified PGRN, however, showed in both assays no effect on TNF–TNFR1/2 interaction even when applied in huge excess. To rule out that tags and purification- or storage-related effects compromise the potential ability of PGRN to bind TNF receptors, we directly co-expressed PGRN, and as control TNF, in TNFR1- and TNFR2-expressing cells and looked for binding of GpL-TNF. While expression of TNF strongly inhibited binding of GpL-TNF to TNFR1/2, co-expression of PGRN had not effect on the ability of the TNFR1/2-expressing cells to bind TNF.

Abstract Nicotinic acetylcholine receptors (nAChRs) are the main target of neonicotinoid insecticides, which are widely used in crop protection against insect pests. Electrophysiological and molecular approaches have demonstrated the presence of several nAChR subtypes with different affinities for neonicotinoid insecticides. However, the precise mode of action of neonicotinoids on insect nAChRs remains to be elucidated. Radioligand binding studies with [3H]-α-bungarotoxin and [3H]-imidacloprid have proved instructive in understanding ligand binding interactions between insect nAChRs and neonicotinoid insecticides. The precise binding site interactions have been established using membranes from whole body and specific tissues. In this review, we discuss findings concerning the number of nAChR binding sites against neonicotinoid insecticides from radioligand binding studies on native tissues. We summarize the data available in the literature and compare the binding properties of the most commonly used neonicotinoid insecticides in several insect species. Finally, we demonstrate that neonicotinoid-nAChR binding sites are also linked to biological samples used and insect species. Graphical abstract Unlabelled Image Highlights • Affinity and number of α-Bgt binding sites vary with species, tissue, and isotope. • Majority of nAChRs are α-Bgt-sensitive and can bind neonicotinoids. • Diptera possess single IMI-binding site whereas hemiptera have several sites. • Neonicotinoids' affinity for IMI-binding sites depends on molecule and species. • Use of homogenate biological samples would increase binding assay quality. [ABSTRACT FROM AUTHOR]

Calixphyrins are hybrid macrocycles that contain both sp2- and sp3-hybridized carbon atoms and hence bear analogy to both porphyrins and calixpyrroles. Due to the presence of sp3-hybridized carbon atoms, π-conjugation is disrupted in calixphyrins, which leads to conformational flexibility. Hence, these molecules find a use in anion binding, host-guest chemistry and metal-coordination chemistry. During the last decade, studies on calixphyrins have been a topic of wide interest to researchers. Various functionalities have been introduced to the structure of calixphyrins, leading to the development of expanded calixphyrins, core-modified calixphyrins and N-confused calixphyrins with diverse applications. This review outlines the detailed historical origin of the synthesis of calixphyrins with emphasis on current research and development in this area. The modular syntheses of normal calixphyrins, expanded calixphyrins, core-modified calixphyrins and N-confused calixphyrins are also discussed, along with their applicative aspects. [ABSTRACT FROM AUTHOR]

Progranulin (PGRN) is a secreted anti-inflammatory protein which can be processed by neutrophil proteases to various granulins. It has been reported that at least a significant portion of the anti-inflammatory effects of PGRN is due to direct high affinity binding to tumor necrosis factor receptor-1 (TNFR1) and TNFR2 and inhibition of tumor necrosis factor (TNF)-induced TNFR1/2 signaling. Two studies failed to reproduce the interaction of TNFR1 and TNFR2 with PGRN, but follow up reports speculated that this was due to varying experimental circumstances and/or the use of PGRN from different sources. However, even under consideration of these speculations, there is still a striking discrepancy in the literature between the concentrations of PGRN needed to inhibit TNF signaling and the concentrations required to block TNF binding to TNFR1 and TNFR2. While signaling events induced by 0.2-2 nM of TNF have been efficiently inhibited by low, near to equimolar concentrations (0.5-2.5 nM) of PGRN in various studies, the reported inhibitory effects of PGRN on TNF-binding to TNFR1/2 required a huge excess of PGRN (100-1,000-fold). Therefore, we investigated the effect of PGRN on TNF binding to TNFR1 and TNFR2 in highly sensitive cellular binding studies. Unlabeled TNF inhibited >95% of the specific binding of a Gaussia princeps luciferase (GpL) fusion protein of TNF to TNFR1 and TNFR2 and blocked binding of soluble GpL fusion proteins of TNFR1 and TNFR2 to membrane TNF expressing cells to >95%, too. Purified PGRN, however, showed in both assays no effect on TNF-TNFR1/2 interaction even when applied in huge excess. To rule out that tags and purification- or storage-related effects compromise the potential ability of PGRN to bind TNF receptors, we directly co-expressed PGRN, and as control TNF, in TNFR1- and TNFR2-expressing cells and looked for binding of GpL-TNF. While expression of TNF strongly inhibited binding of GpL-TNF to TNFR1/2, co-expression of PGRN had not effect on the ability of the TNFR1/2-expressing cells to bind TNF. [ABSTRACT FROM AUTHOR]

The Tobamovirus helicase plays an important role in virus proliferation and host interaction. They can also be targets for antiviral drugs. Tobacco mosaic virus (TMV) is well controlled by ningnanmycin (NNM), but whether it acts on other virus helicases of Tobamovirus virus is not clear. In this study, we expressed and purified several Tobamovirus virus helicase proteins and analyzed the three–dimensional structures of several Tobamovirus virus helicases. In addition, the binding of Tobamovirus helicase to NNM was also studied. The docking study reveals the interaction between NNM and Tobamovirus virus helicase. Microscale Thermophoresis (MST) experiments have shown that NNM binds to Tobamovirus helicase with a dissociation constant of 4.64–12.63 μM. Therefore, these data are of great significance for the design and synthesis of new effective anti–plant virus drugs. [Display omitted] • Several Tobamovirus virus helicases were expressed in E. coli. • Predict the potential binding sites of multiple Tobamovirus virus helicases and small molecular compounds. • An in vitro drug screening model based on Tobamovirus virus helicases as potential targets was established. [ABSTRACT FROM AUTHOR]

Diabetes is a health condition associated with the elevated levels of glucose in the bloodstream and affects 366 million people worldwide. Type II diabetes is often treated with sulfonylurea drugs, which are known to bind tightly in the blood to the transport protein human serum albumin (HSA). One consequence of the elevated levels of glucose in diabetes is the nonenzymatic glycation of proteins such as HSA. Several areas of HSA are now known to be affected by glycation-related modifications, which may in turn affect the binding of sulfonylurea drugs and other solutes to this protein. This review discusses some recent studies that have examined these changes in drug-protein binding by employing high-performance affinity chromatography (HPAC). A description of the theoretical and experimental techniques that were used in these studies is given. The information on drug interactions with glycated HSA, as obtained through this method, is also summarized. In addition, the potential advantages of this approach in the areas of biointeraction analysis and personalized medicine are considered.

An efficient synthesis of 6,12-methanobenzo[d]pyrano[ 3,4-g][1,3]dioxocin-1(12H)-ones, a new class of 2,8-dioxabicyclo[ 3.3.1]nonanes, starting from 2-hydroxychalcones or their analogues and 4-hydroxy-6-methyl-2H-pyran-2-one has been achieved by use of amberlyst-15, a sulfonated polystyrene resin, as a recyclable heterogeneous catalyst. The methodology involves a domino sequence of Michael addition and two-stage heterocyclization. Among the synthesized products, two show significant ct-DNA-binding properties and all show strong binding with the carrier protein β-lactoglobulin (β-lg). A study of antibacterial properties conducted on two bacterial species by using four compounds showed that two of them are moderately active. [ABSTRACT FROM AUTHOR]

The purpose of the present study was to examine the analgesic activity of six novel hybrid molecules, which demonstrated in the previous research anticonvulsant activity in the maximal electroshock seizure (MES) and subcutaneous pentylenetetrazole seizure (scPTZ) tests in mice. The antinociceptive properties were estimated in three models of pain in mice-the hot plate test, the formalin test, and in the oxaliplatin-induced neuropathy. Moreover, extended anticonvulsant studies were carried out and the antiseizure activity was investigated in the 6-Hz test. Considering drug safety evaluation, the influence of compounds on locomotor activity and contextual memory were checked. Furthermore, chosen molecules were tested in vitro for potential hepatotoxicity. To explain the probable mechanism of action, the radioligand binding assays were performed. In both phases of formalin test, analgesic activity demonstrated compounds 4, 8, and 9. These agents relieved also mechanical allodynia in oxaliplatin-induced model of neuropathic pain. At active doses, they did not influence locomotor activity of mice. Moreover, for compounds 8 and 9, no deleterious effect on memory was observed, but compound 4 might induce memory deficits. All tested compounds ( 4, 5, 8, 9, 15, and 16) inhibited psychomotor seizures with the ED values = 24.66-47.21 mg/kg. The binding studies showed that compound 4 only at the high concentrations revealed the effective binding to the neuronal sodium channels and moderately binding to the L-type calcium (verapamil site) channels and NMDA receptors. The present preclinical results proved that novel hybrid molecules demonstrate very promising anticonvulsant and analgesic activity. [ABSTRACT FROM AUTHOR]

ABSTRACT A new method for the preparation of poly(oxyethylene phosphoramidate)s and glycopolymers is developed via modification of poly(oxyethylene H-phosphonate) which is a biodegradable, biocompatible and low toxic polymer. The phosphonate groups of the precursor are converted into tri-coordinated phosphorus species yielding poly(oxyethylene trimethylsilyl phosphite). The latter is then reacted with different azides, including sugar azides, via Staudinger reaction to furnish the desired poly(oxyethylene phosphoramidate)s and such containing sugar moieties in the side chains attached to the P-centers. 2002P NMR spectroscopy is applied as a powerful tool for determination of the conversion and structure of the reaction products. Studies on Concanavalin A binding to the obtained glycopolymers are performed using dynamic light scattering and analytical ultracentrifugation techniques. The viability of Human Embryonic Kidney 293 cell line is slightly affected when exposed to polyphosphoramidate glucoconjugate over a broad range of concentrations. The results obtained are encouraging for further investigations on the clustering and bio-recognition properties of the synthesized glycopolymers. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017, 55, 1730-1741 [ABSTRACT FROM AUTHOR]

In this study we report the in vitro activities of four cyclic opioid peptides with various sequence length/macrocycle size and N -methylamino acid residue content. N -Methylated amino acids were incorporated and cyclization was employed to enhance conformational rigidity to various extent. The effect of such modifications on ligand structure and binding properties were studied. The pentapeptide containing one endocyclic and one exocyclic N -methylated amino acid displayed the highest affinity to the mu-opioid receptor. This peptide was also shown to be a full agonist, while the other analogs failed to activate the mu opioid receptor. Results of molecular docking studies provided rationale for the explanation of binding properties on a structural basis. [ABSTRACT FROM AUTHOR]

The physicochemical properties of polybrominated diphenyl ethers are important for modeling their transport, but these data are often missing. Here, satisfactory bioactivity results were obtained using human serum albumin as the carrier, 2,2′,4,4′,5,6′-hexabromodiphenyl ether (BDE154) and 3-hydroxy-2,2′,4,4′, 5,6′-hexabromodiphenyl ether (3OH-BDE154) as the ligands, using UV–visible absorbance, fluorescence, circular dichroism, molecular docking, and molecular dynamics methods. The interactions between human serum albumin and BDE154 or 3OH-BDE154 were verified, consistent with the static quenching procedure. At pH 7.4, the binding constants of the complexes for site I were relatively comparable and increased in the order BDE154 < 3OH-BDE154. Then, the secondary structure and kinetic parameters of albumin were analyzed using the circular dichroism spectra and GROMACS software. The data obtained from these simulations indicate that hydrophobic attraction might be the key factor for the stability of complexes. The docking experiments provided further insight into the hydrophobic pocket and showed that 3OH-BDE154 has a stronger binding affinity to human serum albumin than BDE154. The experimental spectral data were obtained and compared with the simulation results, showing good agreement. A detailed analysis of PBDEs–HSA interactions would provide valuable information to better understand the interaction on this class of compounds. [ABSTRACT FROM AUTHOR]

• The synthesized compounds displayed potent in vitro antidiabetic activity. • The single-crystal X-ray investigation validated the molecular structure. • The interaction of compounds with HSA has been studied. • Molecular docking studies were carried out. 2,4-thiazolidinedione-phenothiazine molecular hybrids, 9a–9t were synthesized, characterized and screened for antidiabetic activities viz., α -amylase inhibition and glucose uptake assay. The synthesized compounds were characterized by spectroscopic techniques. The molecule 9p was grown into single crystals, and its crystal structure and refinement data were deliberated. Most of the compounds displayed a significant to moderate α-amylase inhibition and glucose uptake activity. The compounds, 9m-9p showed a significant α-amylase inhibition with IC 50 values (83.7 ± 0.7 - 60.8 ± 0.8 µM), which are greater than that of the standard, acarbose (101.7 ± 2.0 µM). Most of the compounds showed good glucose uptake assay and compounds, 9a- 9 g showed IC 50 values in the range of 169.8 ± 1.2 - 213.3 ± 0.5 µM which are ∼2-fold greater compared to that of the standard, metronidazole (441.5 ± 2.1 µM). The compound, 9l showed acceptable values for both α-amylase inhibition (IC 50 = 130.6 ± 2.0 µM) and glucose uptake assay (IC 50 = 459.3 ± 2.2 µM) compared to those of the standard. Molecular docking studies confirmed interactions of the compounds with the human pancreatic α-amylase protein with PDB ID: 2QV4. Further, the interactions of 9o and 9p with human serum albumin were also investigated. [Display omitted] [ABSTRACT FROM AUTHOR]

Morphiceptin (Tyr-Pro-Phe-Pro-NH 2 ), a tetrapeptide amide, is a selective ligand of the μ-opioid receptor (MOR). This study reports the synthesis and biological evaluation of a series of novel morphiceptin analogs modified in positions 2 or/and 4 by introduction of 4,4-difluoroproline (F 2 Pro) in l or d configuration. Depending on the fluorinated amino acid configuration and its position in the sequence, new analogs behaved as selective full MOR agonists showing high, moderate, or relatively low potency. The most potent analog, Tyr-F 2 Pro-Phe- d -F 2 Pro-NH 2 , was also able to activate the κ-opioid receptor (KOR), although with low potency. Docking studies and the comparison of results with the high resolution crystallographic structure of a MOR-agonist complex revealed possible structure–activity relationships of this compound family. [ABSTRACT FROM AUTHOR]

Cyclic pentapeptide Tyr-c[D-Lys-Phe-Phe-Asp]NH 2, based on the structure of endomorphin-2 (EM-2), which shows high affinity to the μ-opioid receptor (MOR) and a very strong antinociceptive activity in mice was used as a parent compound for the structure–activity relationship studies. In this report we synthesized analogs of a general sequence Dmt-c[D-Lys-Xaa-Yaa-Asp]NH 2 , with D-1- or D-2-naphthyl-3-alanine (D-1-Nal or D-2-Nal) in positions 3 or 4. In our earlier papers we have indicated that replacing a phenylalanine residue by the more extended aromatic system of naphthylalanines may result in increased bioactivities of linear analogs. The data obtained here showed that only cyclopeptides modified in position 4 retained the sub-nanomolar MOR and nanomolar κ-opioid receptor (KOR) affinity, similar but not better than that of a parent cyclopeptide. In the in vivo mouse hot-plate test, the most potent analog, Dmt-c[D-Lys-Phe-D-1-Nal-Asp]NH 2 , exhibited higher than EM-2 but slightly lower than the cyclic parent peptide antinociceptive activity after peripheral (ip) and also central administration (icv). Conformational analyses in a biomimetic environment and molecular docking studies disclosed the structural determinants responsible for the different pharmacological profiles of position 3- versus position 4-modified analogs. [ABSTRACT FROM AUTHOR]

Preeclampsia (PE) is a complex illness of the human gestation. It is responsible for a high perinatal morbimortality.It is the illness of the multiple theories; in one environmentaland genetic factors are associated to explain it. To find genes candidates to be associated with PE, two methodology types are used: association and binding studies. In this paper we presented the foundation of both studies that explain the main genes candidates to involve in the genesis of this illness,like that ones that code for the methylenetetrahydrofolatereductase, lipoprotein lipase and endothelial nitric oxidesintase, Leiden‘s V factor, angiotensinogen, HLA-G, alphatumoral necrosis factor.

The oxovanadium(IV) Schiff base metal complex (ISNPV) have been synthesized as well as characterized by using micro analytical and traditional spectroscopic techniques. The spectral findings were utilized to validate the formation of ISNPV with structure exhibited square pyramidal geometry. The in vitro antibacterial activities of ISNPV were investigated to five different bacterial stains such as S. aureus , S. epidermidis , B. cereus , B. amyloliquefaciens and B. subtilis . The obtained result have suggested that the ISNPV has highest antibacterial activity against S. aureus than the other bacterial stains. The in vitro antioxidant activity like DPPH free radical scavenging assay method was studied by ISNPV in DMSO medium. Because it scavenges all free radicals, the ISNPV possesses higher antioxidant activity than the free ligand. UV-visible absorption and emission spectral techniques were used to investigate the binding of CT-DNA to the ISNPV. Both the spectral data indicate that the ISNPV binds the double helix structure of CT-DNA via an intercalation mode. Additionally, investigate the interactions of ISNPV with the protein molecules like BSA/HAS has been investigated using absorption and emission techniques. The absorption intensity of metal complex increases as well as the emission intensity of protein molecules ability decreases due to the binding nature of ISNPV with BSA/HSA protein molecules. The binding nature of ISNPV with bio molecules such as CT-DNA, BSA and HSA was also validated using molecular docking approach.

Synthetic approaches to produce scaffolds that will act as efficient biosensors have been the subject of considerable research efforts in recent years. The preparation of host complexes which will specifically bind a given guest necessitates structural analysis of the potential complexes formed, as well as an assessment of the strength of the binding interaction. A challenge to the down-stream analytical scientist is to develop a rapid method that can probe the strength of binding, and the architecture of the complex. In this work we apply nano-ESI MS and Drift Tube ion mobility mass spectrometry (DT IM-MS) to examine host guest interactions. We present data on 5 cyclic peptide bis(Zn II -dipicolylamines) which have been systematically designed as potential molecular biosensors for pyrophosphate (PPi). The competition of the macrocycles for PPi compared with other small anions is investigated. Mass spectrometry provides the stoichiometry of the complex, and the proportion of complex preserved into the mass spectrometer correlates with solution phase data. We find the macrocycles have a higher affinity for PPi than for ATP or pyrocatechol violet (PV). The absolute scale of affinity from mass spectrometry is less (4–5 Log K a ) than that found in solution (4–9 Log K a ), but within the series of macrocycles trend in relative affinities are comparable. DT IM-MS shows that the collision cross sections ( DT CCS He ) of the macrocycles are unchanged on binding PPi, indicating that the anion is within the designed binding pocket. We also find that binding has tightened the conformation of the macrocycle, as revealed from analysis of the collision cross section distributions ( DT CCSD He ), where for 4/5 of the macrocycles there is a significant decrease in FWHM. Molecular mechanics (MMFF94) and semi empirical methods (ONIOM PM6:B3LYP/aug-cc-pvDZ) were used to generate candidate geometries for 4 to support our assertions on the nature of the binding pocket in the uncomplexed host, and to provide a route for improvement in the design. [ABSTRACT FROM AUTHOR]

In order to re-build Man 9 GlcNAc 2 clusters of the HIV gp120 glycoprotein, ∼2 nm gold glyconanoparticles (GNPs) were coated with the synthetic partial structures of Man 9, the tetramannoside Manα1–2Manα1–2Manα1–3Manα1– and the pentamannoside Manα1–2Manα1–3[Manα1–2Manα1–6]Manα1–. Their interactions with the anti-HIV broadly neutralizing antibody 2G12 were studied by surface plasmon resonance (SPR)-based biosensors and saturation transfer difference (STD)-NMR spectroscopy. A synergistic effect of the tetra- and pentamannosides multimerized on a same GNP was observed. The assembly of these antennas of the gp120 high-mannose type glycan on GNPs provided superior binding to the anti-HIV antibody 2G12 with respect to GNPs carrying only the individual oligomannosides. The results presented in this work provide new molecular information on the interactions between clusters of oligomannosides and 2G12 that could help in the design of a carbohydrate-based vaccine against HIV. [ABSTRACT FROM AUTHOR]

MicroScale Thermophoresis (MST) is a powerful technique to quantify biomolecular interactions. It is based on thermophoresis, the directed movement of molecules in a temperature gradient, which strongly depends on a variety of molecular properties such as size, charge, hydration shell or conformation. Thus, this technique is highly sensitive to virtually any change in molecular properties, allowing for a precise quantification of molecular events independent of the size or nature of the investigated specimen. During a MST experiment, a temperature gradient is induced by an infrared laser. The directed movement of molecules through the temperature gradient is detected and quantified using either covalently attached or intrinsic fluorophores. By combining the precision of fluorescence detection with the variability and sensitivity of thermophoresis, MST provides a flexible, robust and fast way to dissect molecular interactions. In this review, we present recent progress and developments in MST technology and focus on MST applications beyond standard biomolecular interaction studies. By using different model systems, we introduce alternative MST applications – such as determination of binding stoichiometries and binding modes, analysis of protein unfolding, thermodynamics and enzyme kinetics. In addition, wedemonstrate the capability of MST to quantify high-affinity interactions with dissociation constants ( K d s) in the low picomolar (pM) range as well as protein–protein interactions in pure mammalian cell lysates. [ABSTRACT FROM AUTHOR]

The human macrophage galactose-type lectin (MGL) is a key physiological receptor for the carcinoma-associated Tn antigen (GalNAc-α-1- O-Ser/Thr) in mucins. NMR and modeling-based data on the molecular recognition features of synthetic Tn-bearing glycopeptides by MGL are presented. Cognate epitopes on the sugar and matching key amino acids involved in the interaction were identified by saturation transfer difference (STD) NMR spectroscopy. Only the amino acids close to the glycosylation site in the peptides are involved in lectin contact. Moreover, control experiments with non-glycosylated MUC1 peptides unequivocally showed that the sugar residue is essential for MGL binding, as is Ca2+. NMR data were complemented with molecular dynamics simulations and Corcema-ST to establish a 3D view on the molecular recognition process between Gal, GalNAc, and the Tn-presenting glycopeptides and MGL. Gal and GalNAc have a dual binding mode with opposite trend of the main interaction pattern and the differences in affinity can be explained by additional hydrogen bonds and CH-π contacts involving exclusively the NHAc moiety. [ABSTRACT FROM AUTHOR]

During the course of protein synthesis in the cell, the translation process is often terminated due to various reasons. As a result, peptidyl-tRNA molecules are released which are toxic to the cell as well reducing the availability of free amino acid and tRNA molecules for the required protein synthesis in the cell. Such a situation is corrected by an enzyme, Pth (peptidyl-tRNA hydrolase), which catalyses the release of free tRNA and peptide moieties from peptidyl-tRNAs. This means that the active Pth is essential for the survival of bacteria. In order to design inhibitors of PaPth (Pth from Pseudomonas aeruginosa), we determined the structures of PaPth in its native and bound states with compounds amino acylate-tRNA analogue and 5-azacytidine. The structure determination of the native protein revealed that the substratebinding site was partially occupied by Glu161 from the neighbouring molecule. The structure of PaPth indicated that the substrate-binding site can be broadly divided into three distinct subsites. The structures of the two complexes showed that the amino acylate-tRNA analogue filled three subsites, whereas 5- azacytidine filled two subsites. The common sugar and the base moieties of the two compounds occupied identical positions in the cleft. Using surface plasmon resonance, the dissociation constants for the amino acylate-tRNA analogue and 5-azacytidine were found to be 3.53×10-8 M and 5.82×10-8 M respectively. [ABSTRACT FROM AUTHOR]