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Rewritable paper has recently become prevalent in both academic research and marketplace due to the potential environmental advantages, including forest conservation, pollution reduction, energy saving and resource sustainability. However, its real-life applications are limited by a lack of effective strategy to realize multicolour and water-jet printing on rewritable paper with long legible image-lasting times. Herein, we report an effective strategy to construct rewritable paper based on colour or luminescence switching induced by dynamic metal-ligand coordination. This type of rewritable paper can be conveniently utilized for multicolour water-jet printing by using aqueous solutions containing different metal salts as ink. In addition, the printed images on the water-jet rewritable paper can be retained for a long time (> 6 months), which shows great progress compared to previous work. We believe that this type of rewritable paper could be considered as a prototype for multicolour water-jet printing to meet the practical needs. [ABSTRACT FROM AUTHOR]

Paper-based point-of-care (POC) devices exhibit the advantages of simplicity, rapidity, trim sizes, and low cost, which are of particular importance for food safety, biological analysis, and medical diagnosis. However, the materials utilized to make paper-based POC rarely produce multiple signals, hampering further applications in diverse situations. Herein, we present an appealing approach, namely Colorimetric-Temperature Dual-Signal Output Sensor (CTDSS), and construct a CTDSS based on coordinative self-assembly biomimetic nanozymes Fe-GMP-L-His CPNs as a proof of concept. These CPNs mimic the structure of horseradish peroxidase (HRP), in which Fe (II) is the center, nucleotide GMP and histidine are chosen as ligands to simulate metal coordination of the pyrrole ring and protein function in HRP, respectively. This strategy allows CPNs to show an excellent peroxidase-like activity, efficiently converting H 2 O 2 into •OH and oxidizing TMB to generate colorimetric-temperature dual-signal. As a proof-of-concept application, we exploited cholesterol as the target and successfully applied this CTDSS to detect cholesterol, displaying extraordinary features of rapidity, dramatic specificity, and high sensitivity. By utilizing the colorimetric test strip and temperature discoloration sticker, the paper-based POC tools were constructed to visualize the target. Meanwhile, two proposed test strip POC devices generating different signal outputs exhibited remarkable feasibility and were further employed to detect cholesterol in human serum. We anticipate that this CTDSS platform will inspire innovative concepts for future portable detection tools. [ABSTRACT FROM AUTHOR]

Introduction and aim. Opioids have pain-relieving and anti- inflammatory properties, as demonstrated in animal models of colitis and abdominal pain. Kappa opioid receptors (KOP) are not well characterized, but KOP ligands influence the progression or inhibition of cancer growth. In this study we focused on the level of expression of prodynorphin and kappa opioid receptors in experimental colorectal cancer. Material and methods. The effects of U50488H, a selective KOP agonist, and Nor-binaltorphimine (nor-BNI), a selective KOP antagonist, were tested in in vitro and in vivo models. Colitis-associated colorectal cancer was induced in mice using azoxymethane and dextran sodium sulfate, and U50488H was injected intraperitoneally twice a week at the dose of 1 mg/kg. MC-38 cell line was used to verify the impact of KOP ligands on the cell viability. Gene and protein expression was assessed using real time RT-PCR and western blot. Results. U50488H decreased cell viability after 24 hours in MC-38 cells. Nor-Bni had no effect on the cell viability, but counteracted U50488H. The mixture of U50488H and Nor-Bni had a worse effect than U50488H alone. In vivo, the colonic length did not differ between AOM/DSS and U50488H-treated groups. In mice trated with AOM/DSS we observed a thicker submucosal and muscle layer with increased immune cell infiltration as compared to U50488H-treated mice. Conclusion. U50488H shown the ability to influence the development of the colonic cancer in mice. [ABSTRACT FROM AUTHOR]

Background: The discovery of bioactive compounds in traditional Chinese medicine (TCM) has become an important field in TCM modernization. Ligand fishing is a suitable method for discovery of bioactive compounds in complex mixtures such as TCM with high selectivity. Because of unique advantage of low cost and convenience, paper-based microdevices can be good carriers for enzyme immobilized ligand fishing. Methods: As an important enzyme for glucose metabolism, α-glucosidase was immobilized on polycaprolactone–chitosan-modified paper to prepare the microdevice with unique microfluid structure generated by 3D printing technology, which can be easily applied to screen active compounds in herbal extracts. The preparation conditions of the paper microarray were optimized. The activity of immobilized α-glucosidase was verified by colorimetric reactions which can be easily monitored by cellphone. The paper microarray with α-glucosidase immobilized was used to screen active compounds in the water extracts of mulberry leaves and lotus leaves. Results: Several key parameters including Na2CO3 solution concentration, Na2CO3 solution volume, glutaraldehyde concentration, crosslinking time of glutaraldehyde and time of α-glucosidase immobilization were optimized. The proposed paper-based microarray was successfully applied in screening active compounds in two herbal extracts. Four compounds including chlorogenic acid, quercetin-3-O-glucuronide, isoquercetin, and quercetin were identified as α-glucosidase inhibitors. The compounds with significant non-specific adsorption caused by chitosan, such as isoquercitrin, astragalin, quercetin, were also found to be active compounds. Conclusions: An enzyme immobilized paper microarray was designed and fabricated in this work. Polycaprolactone and chitosan were used to modify filter paper to prepare paper microarrays. Parameters of paper device preparation were optimized. Our findings suggested that 3D-printing paper-based microarrays can be a simple and low-cost approach for discovery of active compounds of TCM. [ABSTRACT FROM AUTHOR]

This document is a summary of a special issue of the journal Inorganics that focuses on the chemistry of metal complexes with N-donor ligands. The articles cover a wide range of topics, including the coordination chemistry of these complexes, their reactivity, and their applications in various fields such as chemistry, biochemistry, material science, and the chemical industry. The papers discuss the synthesis, characterization, and properties of different types of metal complexes with N-donor ligands, including pyridine, pyrazoles, Schiff bases, and N-heterocyclic compounds. The special issue also includes two review papers that provide an overview of the chemistry of transition metal salts with ammonia-ligand complexes and the NMR spectroscopic and structural features of gold(III) cyclometallated compounds. Overall, these articles contribute to the understanding of the diverse and rapidly developing field of inorganic complex chemistry. [Extracted from the article]

The International Journal of High Performance Computing Applications has published a special issue featuring the papers of the three finalists for the 2022 ACM Gordon Bell Special Prize for High Performance Computing-Based COVID-19 Research. The winning paper, titled "GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics," focuses on training large language models for long genomic sequences to generate potential SARS-CoV-2 variants of concern. The other two finalist papers include "Running ahead of evolution," which uses AI-based screening to identify advantageous variants of the SARS-CoV-2 spike receptor binding domain, and "TwoFold," which predicts the structure of protein-ligand complexes to aid drug discovery for SARS-CoV-2. The ACM Gordon Bell Prize committee judged the nominations for the special prize. [Extracted from the article]

The resolution of inflammation is the primary domain of specialised pro-resolving mediators (SPMs), which include resolvins, protectins, and their forms synthesised under the influence of aspirin and the maresins. The role of these SPMs has been discussed by many authors in the literature, with particular reference to neuroinflammation and significant neurological disorders. This review discusses the role of G protein-coupled receptor 18 (GPR18), resolvin D2 (RvD2) activity, and the GPR18-RvD2 signalling axis, as well as the role of small molecule ligands of GPR18 in inflammation in various health disorders (brain injuries, neuropathic pain, neurodegenerative/cardiometabolic/cardiovascular/gastrointestinal diseases, peritonitis, periodontitis, asthma and lung inflammation, Duchenne muscular dystrophy, SARS-CoV-2-induced inflammation, and placenta disorders. The idea of biological intervention through modulating GPR18 signalling is attracting growing attention because of its great therapeutic potential. With this paper, we aimed to present a comprehensive review of the most recent literature, perform a constructive view of data, and point out research gaps. [ABSTRACT FROM AUTHOR]

This review thoroughly covers aspects of synthetic chemistry, reactivity, and the properties of dinuclear and oligonuclear actinoid complexes based on Schiff base ligands within the last 20 years in an extensive way and with clear presentation. 10.3390/molecules181012264 6 Liu X., Hamon J.-R. Recent Developments in Penta-, Hexa- and Heptadentate Schiff Base Ligands and Their Metal Complexes. As stated by two of the seven papers [[1]] published in the Special Issue entitled "Oligonuclear Metal Complexes with Schiff Base Ligands" that I guest edited, the chemistry of Schiff bases began in 1864 due to the discovery made by Hugo Schiff [[3]], but even more than one and a half centuries after their first synthesis, Schiff bases continue to surprise inorganic chemists. C=N is usually incorporated into more articulated architectures in addition to other donor atoms, the so-called polydentate ligands [[6]], since metal complexes with macrocyclic and acyclic polydentate Schiff bases [[7]] show enhanced thermodynamic stability due to the chelating effect [[9]]. [Extracted from the article]

Organometallic drug development is still in its early stage, but recent studies show that organometallics having iron as the central atom have the possibility of becoming good drug candidates because iron is an important micro-nutrient, and it is compatible with many biological systems, including the human body. Being an eco-friendly Lewis acid, iron can accept the lone pair of electrons from imino(sp2)-nitrogen, and the resultant iron–imine complexes with iron as a central atom have the possibility of interacting with several proteins and enzymes in humans. Iron–imine complexes have demonstrated significant potential with anticancer, bactericidal, fungicidal, and other medicinal activities in recent years. This article systematically discusses major synthetic methods and pharmacological potentials of iron–imine complexes having in vitro activity to significant clinical performance from 2016 to date. In a nutshell, this manuscript offers a simplistic view of iron complexes in medicinal inorganic chemistry: for instance, iron is presented as an "eco-friendly non-toxic" metal (as opposed to platinum) that will lead to non-toxic pharmaceuticals. The abundant literature on iron chelators shows that many iron complexes, particularly if redox-active in cells, can be quite cytotoxic, which can be beneficial for future targeted therapies. While we made every effort to include all the related papers, any omission is purely unintentional. [ABSTRACT FROM AUTHOR]

In the process of systematically studying the methylhydroxyiminoethaneamide bis-chelate ligands with polymethylene spacers of different lengths, L1–L3, and their transition metal complexes, a number of new Ni(II) and Cu(II) species have been isolated, and their molecular and crystal structures were determined using single-crystal X-ray diffraction. In all of these compounds, the divalent metal is coordinated by the ligand donor atoms in a square-planar arrangement. In addition, a serendipitously discovered new type of neutral Ni(II) complex, where the propane spacer of ligand L2 underwent oxidation to the propene spacer, and one of the amide groups was oxidised to the ketoimine, is also reported. The resulting ligand L2′ affords the formation of neutral planar Ni(II) complexes, which are assembled in the solid state on top of each other, and yield two polymorphic structures. In both structures, the resulting infinite, exclusively parallel metal ion columns in ligand insulation may serve as precursor materials for sub-nano-conducting connectors. Overall, this paper reports the synthesis and characterisation of seven new anionic, cationic, and neutral Ni(II) and Cu(II) complexes, their crystal structures, as well as experimental and computed UV–Vis absorption spectra for two structurally similar Ni(II) complexes, yellow and red. [ABSTRACT FROM AUTHOR]

Simple Summary: Colon cancer is a solid tumor that is a prominent contributor to global mortality. Immune cells genetically engineered with a chimeric antigen receptor (CAR) that can recognize cancer-specific targets is a new innovative therapy approach that has had success in treating blood cancers but is still in development for treating solid tumors such as colon cancer. Part of the reason for the added difficulty in targeting solid tumors is the tumor microenvironment that acts as a protective barrier around a solid tumor. In this research paper, we have developed a new cellular approach for the targeted treatment of colon cancer that is designed to overcome the tumor microenvironment. We tested this new CAR cell therapy against multiple solid colon cancer models, and confirmed its efficacy and functionality in finding and eliminating solid tumors. Colorectal carcinoma (CRC) presents a formidable medical challenge, demanding innovative therapeutic strategies. Chimeric antigen receptor (CAR) natural killer (NK) cell therapy has emerged as a promising alternative to CAR T-cell therapy for cancer. A suitable tumor antigen target on CRC is carcinoembryonic antigen (CEA), given its widespread expression and role in tumorigenesis and metastasis. CEA is known to be prolifically shed from tumor cells in a soluble form, thus hindering CAR recognition of tumors and migration through the TME. We have developed a next-generation CAR construct exclusively targeting cell-associated CEA, incorporating a PD1-checkpoint inhibitor and a CCR4 chemokine receptor to enhance homing and infiltration of the CAR-NK-92 cell line through the TME, and which does not induce fratricidal killing of CAR-NK-92-cells. To evaluate this therapeutic approach, we harnessed intricate 3D multicellular tumor spheroid models (MCTS), which emulate key elements of the TME. Our results demonstrate the effective cytotoxicity of CEA-CAR-NK-92 cells against CRC in colorectal cell lines and MCTS models. Importantly, minimal off-target activity against non-cancerous cell lines underscores the precision of this therapy. Furthermore, the integration of the CCR4 migration receptor augments homing by recognizing target ligands, CCL17 and CCL22. Notably, our CAR design results in no significant trogocytosis-induced fratricide. In summary, the proposed CEA-targeting CAR-NK cell therapy could offer a promising solution for CRC treatment, combining precision and efficacy in a tailored approach. [ABSTRACT FROM AUTHOR]

For the structure and functioning of bio-molecules, metals are important. The main focus of research remains the design and synthesis of novel metal-based complexes and metal ion binding to substances in search of novel medicines. Studies have established the well-defined geometry, thermodynamic stability and excellent coordination power of vanadium in different oxidation states. This paper summarizes the biological activities of vanadium complexes, particularly their anticancer activity. Future multidisciplinary research and analysis focused on comprehending the biochemistry of vanadium complexes with different ligands is required. [ABSTRACT FROM AUTHOR]

Maintaining life (respiration), cell death (apoptosis), oxygen transport and immunity are main biological functions of heme containing proteins. These functions are controlled by the axial ligands and the redox status of the iron ion (oscillations between Fe2+ and Fe3+) in the heme group. This paper aims to evaluate the current state of knowledge on oxidation and oxygenation effects in heme proteins. We determined the redox status of the iron ion in whole blood (without and with anticoagulant), hemoglobin in erythrocytes, in isolated cytochrome c and cytochrome c in mitochondria of the human lung cancer cells using UV–VIS electronic absorption spectroscopy, Raman spectroscopy and Raman imaging. Here we discussed the mechanism responsible for the Q electronic absorption band spectral behavior, i.e., its splitting, and its change in extinction coefficient, as well as vibrational modifications upon oxygenation and oxidation. We compared the redox status of heme in hemoglobin of human erythrocytes and cytochrome c in mitochondria of human lung cancer cells. Presented results allow simultaneous identification of oxy- and deoxy-Hb, where 1547 and 1604 cm−1 vibrations correspond to deoxygenated hemoglobin, while 1585 and 1638 cm−1 correspond to oxyhemoglobin, respectively. Our results extend knowledge of oxidation and oxygenation effects in heme proteins. We demonstrated experimentally the mechanism of electronic-vibrational coupling for the Q band splitting. Presented results extend knowledge on oxidation and oxygenation effects in heme proteins and provide evidence that both processes are strongly coupled. We showed that retinoic acid affects the redox state of heme in cytochrome c in mitochondria. The change of the redox status of cytochrome c in mitochondria from the oxidized form to the reduced form has very serious consequences in dysfunction of mitochondria resulting in inhibition of respiration, apoptosis and cytokine induction. [ABSTRACT FROM AUTHOR]

An amendment to this paper has been published and can be accessed via a link at the top of the paper. [ABSTRACT FROM AUTHOR]

The catalytic (CAT) domain is a key region of poly (ADP-ribose) polymerase 1 (PARP1), which has crucial interactions with inhibitors, DNA, and other domains of PARP1. To facilitate the development of potential inhibitors of PARP1, it is of great significance to clarify the differences in structural dynamics and key residues between CAT/inhibitors and DNA/PARP1/inhibitors through structure-based computational design. In this paper, conformational changes in PAPR1 and differences in key residue interactions induced by inhibitors were revealed at the molecular level by comparative molecular dynamics (MD) simulations and energy decomposition. On one hand, PARP1 inhibitors indirectly change some residues of the CAT domain which interact with DNA and other domains. Furthermore, the interaction between ligands and catalytic binding sites can be transferred to the DNA recognition domain of PARP1 by a strong negative correlation movement among multi-domains of PARP1. On the other hand, it is not reliable to use the binding energy of CAT/ligand as a measure of ligand activity, because it may in some cases differs greatly from the that of PARP1/DNA/ligand. For PARP1/DNA/ligand, the stronger the binding stability between the ligand and PARP1, the stronger the binding stability between PARP1 and DNA. The findings of this work can guide further novel inhibitor design and the structural modification of PARP1 through structure-based computational design. [ABSTRACT FROM AUTHOR]

In this Special Issue, "Featured Papers in Organometallic Chemistry", we report on the synthesis and characterization of [IPr#–PEPPSI], a new, well-defined, highly hindered Pd(II)–NHC precatalyst for cross-coupling reactions. This catalyst was commercialized in collaboration with MilliporeSigma, Burlington, ON, Canada (no. 925489) to provide academic and industrial researchers with broad access to reaction screening and optimization. The broad activity of [IPr#–PEPPSI] in cross-coupling reactions in a range of bond activations with C–N, C–O, C–Cl, C–Br, C–S and C–H cleavage is presented. A comprehensive evaluation of the steric and electronic properties is provided. Easy access to the [IPr#–PEPPSI] class of precatalysts based on modular pyridine ligands, together with the steric impact of the IPr# peralkylation framework, will facilitate the implementation of well-defined, air- and moisture-stable Pd(II)–NHC precatalysts in chemistry research. [ABSTRACT FROM AUTHOR]

Combretastatin derivatives is a promising class of antitumor agents, tubulin assembly inhibitors. However, due to poor solubility and insufficient selectivity to tumor cells, we believe, their therapeutic potential has not been fully realized yet. This paper describes polymeric micelles based on chitosan (a polycation that causes pH and thermosensitivity of micelles) and fatty acids (stearic, lipoic, oleic and mercaptoundecanoic), which were used as a carrier for a range of combretastatin derivatives and reference organic compounds, demonstrating otherwise impossible delivery to tumor cells, at the same time substantially reduced penetration into normal cells. Polymers containing sulfur atoms in hydrophobic tails form micelles with a zeta potential of about 30 mV, which increases to 40–45 mV when cytostatics are loaded. Polymers with tails of oleic and stearic acids form poorly charged micelles. The use of polymeric 400 nm micelles provides the dissolution of hydrophobic potential drug molecules. Micelles could significantly increase the selectivity of cytostatics against tumors, which has been shown using MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay, Fourier transform infrared (FTIR) spectroscopy, flow cytometry and fluorescence microscopy. Atomic force microscopy presented the difference between the unloaded micelles and those loaded with the drug: the size of the former was 30 nm on average, while the latter had a "disc-like" shape and a size of about 450 nm. The loading of drugs into the core of micelles was confirmed by UV and fluorescence spectroscopy methods; shifts of absorption and emission maxima into the long-wavelength region by tens of nm was observed. With FTIR spectroscopy, a high interaction efficiency of micelles with the drug on cells was demonstrated, but at the same time, selective absorption was observed: micellar cytostatics penetrate into A549 cancer cells 1.5–2 times better than the simple form of the drugs. Moreover, in normal HEK293T, the penetration of the drug is reduced. The proposed mechanism for reducing the accumulation of drugs in normal cells is the adsorption of micelles on the cell surface and the preservation of cytostatics to penetrate inside the cells. At the same time, in cancer cells, due to the structural features of the micelles, they penetrate inside, merging with the membrane and releasing the drug by pH- and glutathione-sensitive mechanisms. From a methodological point of view, we have proposed a powerful approach to the observation of micelles using a flow cytometer, which, in addition, allows us to quantify the cells that have absorbed/adsorbed cytostatic fluorophore and distinguish between specific and non-specific binding. Thus, we present polymeric micelles as drug delivery systems in tumors using the example of combretastatin derivatives and model fluorophore-cytostatic rhodamine 6G. [ABSTRACT FROM AUTHOR]

Stirling et al., (10.1371/journal.pone.0108482) presented an analysis on some of our publications on the formation of stripe-like domains on mixed-ligand coated gold nanoparticles. The authors shed doubts on some of our results however no valid argument is provided against what we have shown since our first publication: scanning tunneling microscopy (STM) images of striped nanoparticles show stripe-like domains that are independent of imaging parameters and in particular of imaging speed. We have consistently ruled out the presence of artifacts by comparing sets of images acquired at different tip speeds, finding invariance of the stipe-like domains. Stirling and co-workers incorrectly analyzed this key control, using a different microscope and imaging conditions that do not compare to ours. We show here data proving that our approach is rigorous. Furthermore, we never solely relied on image analysis to draw our conclusions; we have always used the chemical nature of the particles to assess the veracity of our images. Stirling et al. do not provide any justification for the spacing of the features that we find on nanoparticles: ~1 nm for mixed ligand particles and ~ 0.5 nm for homoligand particles. Hence our two central arguments remain unmodified: independence from imaging parameters and dependence on ligand shell chemical composition. The paper report observations on our STM images; none is a sufficient condition to prove that our images are artifacts. We thoroughly addressed issues related to STM artifacts throughout our microscopy work. Stirling et al. provide guidelines for what they consider good STM images of nanoparticles, such images are indeed present in our literature. They conclude that the evidences we provided to date are insufficient, this is a departure from one of the authors’ previous article which concluded that our images were composed of artifacts. Given that four independent laboratories have reproduced our measurements and that no scientifically rigorous argument is presented to invalidate our STM images, and also given that Stirling et al. do not contest the quality of our recent STM images, we re-affirm that specific binary mixture of ligands spontaneously form features in their ligand shell that we describe as stripe-like domains ~1 nm in width. [ABSTRACT FROM AUTHOR]

Combined treatments employing lower concentrations of different drugs are used and studied to develop new and more effective anticancer therapeutic approaches. The combination therapy could be of great interest in the controlling of cancer. Regarding this, our research group has recently shown that peptide nucleic acids (PNAs) that target miR-221 are very effective and functional in inducing apoptosis of many tumor cells, including glioblastoma and colon cancer cells. Moreover, in a recent paper, we described a series of new palladium allyl complexes showing a strong antiproliferative activity on different tumor cell lines. The present study was aimed to analyze and validate the biological effects of the most active compounds tested, in combination with antagomiRNA molecules targeting two miRNAs, miR-221-3p and miR-222-3p. The obtained results show that a "combination therapy", produced by combining the antagomiRNAs targeting miR-221-3p, miR-222-3p and the palladium allyl complex 4d, is very effective in inducing apoptosis, supporting the concept that the combination treatment of cancer cells with antagomiRNAs targeting a specific upregulated oncomiRNAs (in this study miR-221-3p and miR-222-3p) and metal-based compounds represents a promising therapeutic strategy to increase the efficacy of the antitumor protocol, reducing side effects at the same time. [ABSTRACT FROM AUTHOR]

In this paper, two benzimidazole derivative ligands were obtained using o-phenylenediamine and n-pyridine formaldehyde (n = 3, 4) by amine–aldol condensation reactions, which were reacted with selected inorganic metal salts by ambient temperature volatilization method to give compounds 1–4: {[(L1)6]·[Cu8I8]} (1), {[L1]·[CuBr]·H2O} (2), {[L2]·[CuBr]}n (3), and {[(L2)4]·[Cu4I4]} (4). They were characterized by IR, UV-Vis absorption spectroscopy, thermogravimetric analysis, and single crystal X-ray analysis. Simultaneously, compounds 1–4 were found to possess photocatalytic degradation of ciprofloxacin (CIP) by preliminary experimental investigations. [ABSTRACT FROM AUTHOR]

Iron is one of the essential metals required by almost all living organisms. However, nature has certain constraints in distributing this element among tissues. Since polymeric oxide-bridged Fe (III) is the prominent source of Fe (III) ions, the insolubility of Fe (III) ions in aqueous systems reduces the direct uptake by cells. Secondly, the free-Fe entities which generate .OH radicals pave the way to the destruction of the cells. Hence, a protective coordination environment via sophisticated chemical systems is required for the acquisition of Fe, its successive transport, storage, and effective utilization in various tissues. Siderophores are polydentate ligands used by bacterial cells for Fe acquisition, with a relatively high affinity for Fe (III) ions. Secreted from the bacterial cells into the external aqueous medium, they sequester Fe to give a soluble complex which re-enters the organism at a specific receptor. Once it gets inside the cell, the Fe is released from the complex and utilized for essential biochemical reactions. The medicinal applications of these natural ligands, developing progressively in various research groups, necessitate the theoretical aspects of their coordination chemistry. This research paper deals with the coordination chemistry of one of the siderophores, cepabactin (Cep). The chemical computations confirm that the FeIII(Cep)3 complex is octahedral and high spin. The oxygen atoms of Cep, which are hard and negatively charged, thus act as electron donors in the FeIII(Cep)3 complex formation. This in turn makes the siderophores relatively less attractive towards Fe (II) ions. [ABSTRACT FROM AUTHOR]

The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor, classically associated with the regulation of xenobiotic metabolism in response to environmental toxins. In recent years, transgenic rodent models have implicated AhR in aging and longevity. Moreover, several AhR ligands, such as resveratrol and quercetin, are compounds proven to extend the lifespan of model organisms. In this paper, we first review AhR biology with a focus on aging and highlight several AhR ligands with potential anti-aging properties. We outline how AhR-driven expression of xenobiotic metabolism genes into old age may be a key mechanism through which moderate induction of AhR elicits positive benefits on longevity and healthspan. Furthermore, via integration of publicly available datasets, we show that liver-specific AhR target genes are enriched among genes subject to epigenetic aging. Changes to epigenetic states can profoundly affect transcription factor binding and are a hallmark of the aging process. We suggest that the interplay between AhR and epigenetic aging should be the subject of future research and outline several key gaps in the current literature. Finally, we recommend that a broad range of non-toxic AhR ligands should be investigated for their potential to promote healthspan and longevity. [ABSTRACT FROM AUTHOR]

In this paper, we successfully fabricated color conversion layers (CCLs) for full-color-mico-LED display using a perovskite quantum dot (PQD)/siloxane composite by ligand exchanged PQD with silane composite followed by surface activation by an addition of halide-anion containing salt. Due to this surface activation, it was possible to construct the PQD surface with a silane ligand using a non-polar organic solvent that does not damage the PQD. As a result, the ligand-exchanged PQD with a silane compound exhibited high dispersibility in the siloxane matrix and excellent atmospheric stability due to sol–gel condensation. Based on highly ambient stable PQD/siloxane composite based CCLs, full-color micro-LED display has a 1 mm pixel pitch, about 25.4 pixels per inch (PPI) resolution was achieved. In addition, due to the thin thickness of the black matrix to prevent blue light interference, the possibility of a flexible display that can be operated without damage even with a bending radius of 5 mm was demonstrated. [ABSTRACT FROM AUTHOR]

The exchange coupling, represented by the J parameter, is of tremendous importance in understanding the reactivity and magnetic behavior of open-shell molecular systems. In the past, it was the subject of theoretical investigations, but these studies are mostly limited to the interaction between metallic centers. The exchange coupling between paramagnetic metal ions and radical ligands has hitherto received scant attention in theoretical studies, and thus the understanding of the factors governing this interaction is lacking. In this paper, we use DFT, CASSCF, CASSCF/NEVPT2, and DDCI3 methods to provide insight into exchange interaction in semiquinonato copper(II) complexes. Our primary objective is to identify structural features that affect this magnetic interaction. We demonstrate that the magnetic character of Cu(II)-semiquinone complexes are mainly determined by the relative position of the semiquinone ligand to the Cu(II) ion. The results can support the experimental interpretation of magnetic data for similar systems and can be used for the in-silico design of magnetic complexes with radical ligands. [ABSTRACT FROM AUTHOR]

Supramolecular architectures, which are formed through the combination of inorganic metal cations and organic ligands by self-assembly, are one of the techniques in modern chemical science. This kind of multi-nuclear system in various dimensionalities can be implemented in various applications such as sensing, storage/cargo, display and molecular switching. Iron(II) mediated spin-crossover (SCO) supramolecular architectures with Schiff bases have attracted the attention of many investigators due to their structural novelty as well as their potential application possibilities. In this paper, we review a number of supramolecular SCO architectures of iron(II) with Schiff base ligands exhibiting varying geometrical possibilities. The structural and SCO behavior of these complexes are also discussed in detail. [ABSTRACT FROM AUTHOR]

The original published version of the paper contained labelling errors in Figures 1 and 5. The x-axis of Figure 1e was incorrectly labelled as "Receptors. μm2" instead of "Receptors. μm−2". The figure key in Figure 5b incorrectly labelled the blue circles as "Wild-type" and the purple circles as "+m-ephrinA1". The correct labels are blue: "Wild-type+m-ephrinA1" and purple: "Wild-type, no ligand." The original version also contained a typesetting error in Table 1. The values in the second row, rightmost column, were not all set in bold text as required. The errors do not impact the conclusions in the main text of the paper. These errors have been corrected in the PDF and HTML versions of the paper. [ABSTRACT FROM AUTHOR]

Simple Summary: The aryl hydrocarbon receptor (AhR) is expressed in breast cancer cells and tumors and in some studies, the AhR is a negative prognostic factor for patient survival. Structurally diverse AhR ligands have been extensively investigated as anticancer agents in breast cancer cells and tumors and show efficacy in both estrogen receptor (ER)-positive and ER -negative breast cancer cells. Moreover, synthetic AhR ligands are being developed and have been in clinical trials for treating breast cancer. In contrast, other reports show that AhR ligands enhance mammary carcinogenesis and in a few studies opposite results are observed for the same AhR ligands in comparable breast cancer cells lines. This paper attempts to provide an extensive, unbiased review of the contrasting effects of AhR ligands in breast cancer and points out that future research will be required to resolve these conflicting results. Breast cancer is a complex disease which is defined by numerous cellular and molecular markers that can be used to develop more targeted and successful therapies. The aryl hydrocarbon receptor (AhR) is overexpressed in many breast tumor sub-types, including estrogen receptor -positive (ER+) tumors; however, the prognostic value of the AhR for breast cancer patient survival is not consistent between studies. Moreover, the functional role of the AhR in various breast cancer cell lines is also variable and exhibits both tumor promoter- and tumor suppressor- like activity and the AhR is expressed in both ER-positive and ER-negative cells/tumors. There is strong evidence demonstrating inhibitory AhR-Rα crosstalk where various AhR ligands induce ER degradation. It has also been reported that different structural classes of AhR ligands, including halogenated aromatics, polynuclear aromatics, synthetic drugs and other pharmaceuticals, health promoting phytochemical-derived natural products and endogenous AhR-active compounds inhibit one or more of breast cancer cell proliferation, survival, migration/invasion, and metastasis. AhR–dependent mechanisms for the inhibition of breast cancer by AhR agonists are variable and include the downregulation of multiple genes/gene products such as CXCR4, MMPs, CXCL12, SOX4 and the modulation of microRNA levels. Some AhR ligands, such as aminoflavone, have been investigated in clinical trials for their anticancer activity against breast cancer. In contrast, several publications have reported that AhR agonists and antagonists enhance and inhibit mammary carcinogenesis, respectively, and differences between the anticancer activities of AhR agonists in breast cancer may be due in part to cell context and ligand structure. However, there are reports showing that the same AhR ligand in the same breast cancer cell line gives opposite results. These differences need to be resolved in order to further develop and take advantage of promising agents that inhibit mammary carcinogenesis by targeting the AhR. [ABSTRACT FROM AUTHOR]

This paper presents HBcompare, a method that classifies protein structures according to ligand binding preference categories by analyzing hydrogen bond topology. HBcompare excludes other characteristics of protein structure so that, in the event of accurate classification, it can implicate the involvement of hydrogen bonds in selective binding. This approach contrasts from methods that represent many aspects of protein structure because holistic representations cannot associate classification with just one characteristic. To our knowledge, HBcompare is the first technique with this capability. On five datasets of proteins that catalyze similar reactions with different preferred ligands, HBcompare correctly categorized proteins with similar ligand binding preferences 89.5% of the time. Using only hydrogen bond topology, classification accuracy with HBcompare surpassed standard structure-based comparison algorithms that use atomic coordinates. As a tool for implicating the role of hydrogen bonds in protein function categories, HBcompare represents a first step towards the automatic explanation of biochemical mechanisms. [ABSTRACT FROM AUTHOR]

Simple Summary: Androgen receptor splice variant 7 (AR-V7) has always been considered a key driver for triggering enzalutamide resistance of castration-resistant prostate cancer (CRPC). In recent years, both the homeostasis of AR-V7 protein and AR-V7's relationship with LncRNAs have gained great attention with in-depth studies. Starting from protein stability and LncRNA, the paper discusses and summarizes the mechanisms and drugs that affect the CRPC patients' sensitivity to enzalutamide by regulating the protein or transcriptional stability of AR-V7, hoping to provide therapeutic ideas for subsequent research to break through the CRPC therapeutic bottleneck. Prostate cancer (PCa) has the second highest incidence of malignancies occurring in men worldwide. The first-line therapy of PCa is androgen deprivation therapy (ADT). Nonetheless, most patients progress to castration-resistant prostate cancer (CRPC) after being treated by ADT. As a second-generation androgen receptor (AR) antagonist, enzalutamide (ENZ) is the current mainstay of new endocrine therapies for CRPC in clinical use. However, almost all patients develop resistance during AR antagonist therapy due to various mechanisms. At present, ENZ resistance (ENZR) has become challenging in the clinical treatment of CRPC. AR splice variant 7 (AR-V7) refers to a ligand-independent and constitutively active variant of the AR and is considered a key driver of ENZR in CRPC. In this review, we summarize the mechanisms and biological behaviors of AR-V7 in ENZR of CRPC to contribute novel insights for CRPC therapy. [ABSTRACT FROM AUTHOR]

Background: The pandemic situation of the new coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-COV-2]) forces drug designers to formulate a new intelligent drug for this disease effective to treat all mutations of the virus. One way to control all mutations of virus is inhibition of spike protein (binding with angiotensin-converting enzyme 2 [ACE-2]) duo to inhibit the viral entry. Viral entry is the first step for virus to start infection. Methods: In this work, the interactions of SARS-COV-2 spike protein and ACE-2 are evaluated in silico by docking process and four different ligands are estimated to simulate those interactions to avoid bindings with ACE-2 needed for viral entry in reality. All ligand–receptor interactions are considered. Results: Results approve the suggested ligands in this work, have a definite inhibitory effect on SARS-COV-2 spike protein based on the interactions which they make with the receptor-binding domain. Docking process is done repeatedly to assure conclusions. Conclusion: All interactions were considered by docking of the receptor and ligands. All kinds of interactions contain Hydrogen bonds, steric bonds and etc approving the possibility of ligands to bind the receptor. These interactions approve the antiviral effects of ligands. As the result, ligands were approved to have an antiviral effect on SARS -COV -2. ligands 1 and 2 have higher affinity than other ligands which is completely compatible with the results invitro done by this paper authors. [ABSTRACT FROM AUTHOR]

Antibodies have become an important class of biological products in cancer treatments such as radiotherapy. The growing therapeutic applications have driven a demand for high-purity antibodies. Affinity chromatography with a high affinity and specificity has always been utilized to separate antibodies from complex mixtures. Quality chromatographic components (matrices and affinity ligands) have either been found or generated to increase the purity and yield of antibodies. More importantly, some matrices (mainly particles) and affinity ligands (including design protocols) for antibody purification can act as radiosensitizers or carriers for therapeutic radionuclides (or for radiosensitizers) either directly or indirectly to improve the therapeutic efficiency of radiotherapy. This paper provides a brief overview on the matrices and ligands used in affinity chromatography that are involved in antibody purification and emphasizes their applications in radiotherapy to enrich potential approaches for improving the efficacy of radiotherapy. [ABSTRACT FROM AUTHOR]

Ethylenediaminetetraacetic acid (EDTA) (E-385) as such and/or derivatized (salified) occupies a separate chapter, of wide interest in food sciences, because of its coordinating (sequestering) competences towards various organic and/or inorganic structures (especially metal cations) with small geometric dimensions. This paper aims to diversify the structural range of these hexadentate ligands, by accessing a synthetic protocol different from the classic one, the cyanoethylation of primary amine functional groups of ethylenediamine (ED). In this paper are considered the main dependences of the yields of nucleophilic addition of the amino groups to the activated double bond in acrylonitrile (AN) monomer, on the operating parameters (temperature, processing time, molar ratio of reactants), and finally the preliminary data on the coordinating (sequestering) competence of ethylenediaminetetrapropionic acid (EDTP). The conclusions drawn support further research to extend the area of hexadentate sequestering structures. [ABSTRACT FROM AUTHOR]

Immunotherapy is considered a promising approach for cancer treatment. An important strategy for cancer immunotherapy is the use of cancer vaccines, which have been widely used for cancer treatment. Despite the great potential of cancer vaccines for cancer treatment, their therapeutic effects in clinical settings have been limited. The main reason behind the lack of significant therapeutic outcomes for cancer vaccines is believed to be the immunosuppressive tumor microenvironment (TME). The TME counteracts the therapeutic effects of immunotherapy and provides a favorable environment for tumor growth and progression. Therefore, overcoming the immunosuppressive TME can potentially augment the therapeutic effects of cancer immunotherapy in general and therapeutic cancer vaccines in particular. Among the strategies developed for overcoming immunosuppression in TME, the use of toll-like receptor (TLR) agonists has been suggested as a promising approach to reverse immunosuppression. In this paper, we will review the application of the four most widely studied TLR agonists including agonists of TLR3, 4, 7, and 9 in cancer immunotherapy. [ABSTRACT FROM AUTHOR]

The adenosine A3 receptor is a promising target for treating and diagnosing inflammation and cancer. In this paper, a series of bicyclo[3.1.0]hexane-based nucleosides was synthesized and evaluated for their P1 receptor affinities in radioligand binding studies. The study focused on modifications at 1-, 2-, and 6-positions of the purine ring and variations of the 5′-position at the bicyclo[3.1.0]hexane moiety, closing existing gaps in the structure–affinity relationships. The most potent derivative 30 displayed moderate A3AR affinity (Ki of 0.38 μM) and high A3R selectivity. A subset of compounds varied at 5′-position was further evaluated in functional P2Y1R assays, displaying no off-target activity. [ABSTRACT FROM AUTHOR]

Several biochemical and biophysical methods are available to determine ligand binding affinities between a biological target and its ligands, most of which require purification, labelling or surface immobilisation. These measurements, however, remain challenging in regards to membrane proteins, as purification processes require their extraction from their native lipid environment, which may in turn impact receptor conformation and functionality. In this study, we have developed a novel experimental procedure using microscale thermophoresis (MST) directly from cell membrane fragments, to determine different ligand binding affinities to a membrane protein, the dopamine D2 receptor (D2R). In order to achieve this, two main challenges had to be overcome: determining the concentration of dopamine D2R in the crude sample; finding ways to minimize or account for non-specific binding of the ligand to cell fragments. Using MST, we were able to determine the D2R concentration in cell membrane fragments to approximately 36.8 ± 2.6 pmol/mg. Next, the doses-responses curves allowed for the determination of KD, to approximately 5.3 ± 1.7 nM, which is very close to the reported value. Important details of the experimental procedure have been detailed in this paper to allow the application of this novel method to various membrane proteins. [ABSTRACT FROM AUTHOR]

There is great interest to develop artificial intelligence-based protein–ligand binding affinity models due to their immense applications in drug discovery. In this paper, PointNet and PointTransformer, two pointwise multi-layer perceptrons have been applied for protein–ligand binding affinity prediction for the first time. Three-dimensional point clouds could be rapidly generated from PDBbind-2016 with 3772 and 11 327 individual point clouds derived from the refined or/and general sets, respectively. These point clouds (the refined or the extended set) were used to train PointNet or PointTransformer, resulting in protein–ligand binding affinity prediction models with Pearson correlation coefficients R  = 0.795 or 0.833 from the extended data set, respectively, based on the CASF-2016 benchmark test. The analysis of parameters suggests that the two deep learning models were capable to learn many interactions between proteins and their ligands, and some key atoms for the interactions could be visualized. The protein–ligand interaction features learned by PointTransformer could be further adapted for the XGBoost-based machine learning algorithm, resulting in prediction models with an average Rp of 0.827, which is on par with state-of-the-art machine learning models. These results suggest that the point clouds derived from PDBbind data sets are useful to evaluate the performance of 3D point clouds-centered deep learning algorithms, which could learn atomic features of protein–ligand interactions from natural evolution or medicinal chemistry and thus have wide applications in chemistry and biology. [ABSTRACT FROM AUTHOR]

Background: Although chronic periodontitis has previously been reported to be linked with Alzheimer's disease (AD), the pathogenesis between the two is unclear. The purpose of this study is to analyze and screen the relevant and promising molecular markers between chronic periodontitis and Alzheimer's disease (AD). Methods: In this paper, we analyzed three AD expression datasets and extracted differentially expressed genes (DEGs), then intersected them with chronic periodontitis genes obtained from text mining, and finally obtained integrated DEGs. We followed that by enriching the matching the matching cell signal cascade through DAVID analysis. Moreover, the MCODE of Cytoscape software was employed to uncover the protein–protein interaction (PPI) network and the matching hub gene. Finally, we verified our data using a different independent AD cohort. Results: The chronic periodontitis gene set acquired from text abstracting was intersected with the previously obtained three AD groups, and 12 common genes were obtained. Functional enrichment assessment uncovered 12 cross-genes, which were mainly linked to cell morphogenesis involved in neuron differentiation, leading edge membrane, and receptor ligand activity. After PPI network creation, the ten hub genes linked to AD were retrieved, consisting of SPP1, THY1, CD44, ITGB1, HSPB3, CREB1, SST, UCHL1, CCL5 and BMP7. Finally, the function terms in the new independent dataset were used to verify the previous dataset, and we found 22 GO terms and one pathway, "ECM-receptor interaction pathways", in the overlapping functional terms. Conclusions: The establishment of the above-mentioned candidate key genes, as well as the enriched signaling cascades, provides promising molecular markers for chronic periodontitis-related AD, which may help the diagnosis and treatment of AD patients in the future. [ABSTRACT FROM AUTHOR]

Protein flexibility remains a major challenge in library docking because of difficulties in sampling conformational ensembles with accurate probabilities. Here, we use the model cavity site of T4 lysozyme L99A to test flexible receptor docking with energy penalties from molecular dynamics (MD) simulations. Crystallography with larger and smaller ligands indicates that this cavity can adopt three major conformations: open, intermediate, and closed. Since smaller ligands typically bind better to the cavity site, we anticipate an energy penalty for the cavity opening. To estimate its magnitude, we calculate conformational preferences from MD simulations. We find that including a penalty term is essential for retrospective ligand enrichment; otherwise, high-energy states dominate the docking. We then prospectively docked a library of over 900,000 compounds for new molecules binding to each conformational state. Absent a penalty term, the open conformation dominated the docking results; inclusion of this term led to a balanced sampling of ligands against each state. High ranked molecules were experimentally tested by Tm upshift and X-ray crystallography. From 33 selected molecules, we identified 18 ligands and determined 13 crystal structures. Most interesting were those bound to the open cavity, where the buried site opens to bulk solvent. Here, highly unusual ligands for this cavity had been predicted, including large ligands with polar tails; these were confirmed both by binding and by crystallography. In docking, incorporating protein flexibility with thermodynamic weightings may thus access new ligand chemotypes. The MD approach to accessing and, crucially, weighting such alternative states may find general applicability. [ABSTRACT FROM AUTHOR]

An amendment to this paper has been published and can be accessed via a link at the top of the paper. [ABSTRACT FROM AUTHOR]

Riboswitches are key cis-regulatory elements, present at 5' UTRs of several prokaryotic mRNAs, involved in gene expression regulation by binding selectively to specific ligands followed by conformational changes. However, understanding of ligand-free riboswitch, conformational changes between the ligand-free and ligand-bound riboswitch and binding mechanism of ligand to the aptamer of riboswitch is limited. In the present paper we describe the structural and dynamical properties of ligand-free c-di-GMP I riboswitch aptamer and its possible binding mechanism with c-di-GMP by means of all-atom molecular dynamics (MD) simulations. Various analyses such as principal component analysis, cross correlation dynamics analysis, network analysis and trajectory analyses were carried out. The ligand-free structure shows stable conformation with folded P2, P3 and an unwind P1 helix with open binding pocket at helix-join-helix junction while the ligand-bound structure showed closed binding pocket structure compared to the ligand-free structure. The junction residues significantly showed anti-correlations with P1 helix and weak correlated motions with each other in the open conformation of the ligand-free aptamer of riboswitch. The networks analysis of binding pocket residues suggested interaction among the identified key residues of the binding pocket (G20, A47, C92) and P1 helix illustrating the role of P1 helix in binding of ligand. The structural insights, on c-di-GMP I riboswitch, presented in this paper can be useful for the development of therapeutics against V. cholerae. The understanding of the c-di-GMP I riboswitch at dynamic molecular level provides a potential solution for riboswitch drug design. [ABSTRACT FROM AUTHOR]

An amendment to this paper has been published and can be accessed via a link at the top of the paper. [ABSTRACT FROM AUTHOR]

In virtual drug screening, the chemical diversity of hits is an important factor, along with their predicted activity. Moreover, interim results are of interest for directing the further research, and their diversity is also desirable. In this paper, we consider a problem of obtaining a diverse set of virtual screening hits in a short time. To this end, we propose a mathematical model of task scheduling for virtual drug screening in high-performance computational systems as a congestion game between computational nodes to find the equilibrium solutions for best balancing the number of interim hits with their chemical diversity. The model considers the heterogeneous environment with workload uncertainty, processing time uncertainty, and limited knowledge about the input dataset structure. We perform computational experiments and evaluate the performance of the developed approach considering organic molecules database GDB-9. The used set of molecules is rich enough to demonstrate the feasibility and practicability of proposed solutions. We compare the algorithm with two known heuristics used in practice and observe that game-based scheduling outperforms them by the hit discovery rate and chemical diversity at earlier steps. Based on these results, we use a social utility metric for assessing the efficiency of our equilibrium solutions and show that they reach greatest values. [ABSTRACT FROM AUTHOR]

Gu-tong formula (GTF) has achieved good curative effects in the treatment of cancer-related pain. However, its potential mechanisms have not been explored. We used network pharmacology and molecular docking to investigate the molecular mechanism and the effective compounds of the prescription. Through the analysis and research in this paper, we obtained 74 effective compounds and 125 drug-disease intersection targets to construct a network, indicating that quercetin, kaempferol, and β-sitosterol were possibly the most important compounds in GTF. The key targets of GTF for cancer-related pain were Jun proto-oncogene (JUN), mitogen-activated protein kinase 1 (MAPK1), and RELA proto-oncogene (RELA). 2204 GO entries and 148 pathways were obtained by GO and KEGG enrichment, respectively, which proved that chemokine, MAPK, and transient receptor potential (TRP) channels can be regulated by GTF. The results of molecular docking showed that stigmasterol had strong binding activity with arginine vasopressin receptor 2 (AVPR2) and C-X3-C motif chemokine ligand 1 (CX3CL1) and cholesterol was more stable with p38 MAPK, prostaglandin-endoperoxide synthase 2 (PTGS2), and transient receptor potential vanilloid-1 (TRPV1). In conclusion, the therapeutic effect of GTF on cancer-related pain is based on the comprehensive pharmacological effect of multicomponent, multitarget, and multichannel pathways. This study provides a theoretical basis for further experimental research in the future. [ABSTRACT FROM AUTHOR]

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An amendment to this paper has been published and can be accessed via a link at the top of the paper. [ABSTRACT FROM AUTHOR]

The recent literature is replete with papers evaluating computational tools (often those operating on 3D structures) for their performance in a certain set of tasks. Most commonly these papers compare a number of docking tools for their performance in cognate re-docking (pose prediction) and/or virtual screening. Related papers have been published on ligand-based tools: pose prediction by conformer generators and virtual screening using a variety of ligand-based approaches. The reliability of these comparisons is critically affected by a number of factors usually ignored by the authors, including bias in the datasets used in virtual screening, the metrics used to assess performance in virtual screening and pose prediction and errors in crystal structures used. [ABSTRACT FROM AUTHOR]

In this paper we describe our approaches to predict the binding mode of twenty BACE1 ligands as part of Grand Challenge 4 (GC4), organized by the Drug Design Data Resource. Calculations for all submissions (except for one, which used AutoDock4.2) were performed using AutoDock-GPU, the new GPU-accelerated version of AutoDock4 implemented in OpenCL, which features a gradient-based local search. The pose prediction challenge was organized in two stages. In Stage 1a, the protein conformations associated with each of the ligands were undisclosed, so we docked each ligand to a set of eleven receptor conformations, chosen to maximize the diversity of binding pocket topography. Protein conformations were made available in Stage 1b, making it a re-docking task. For all calculations, macrocyclic conformations were sampled on the fly during docking, taking the target structure into account. To leverage information from existing structures containing BACE1 bound to ligands available in the PDB, we tested biased docking and pose filter protocols to facilitate poses resembling those experimentally determined. Both pose filters and biased docking resulted in more accurate docked poses, enabling us to predict for both Stages 1a and 1b ligand poses within 2 Å RMSD from the crystallographic pose. Nevertheless, many of the ligands could be correctly docked without using existing structural information, demonstrating the usefulness of physics-based scoring functions, such as the one used in AutoDock4, for structure based drug design. [ABSTRACT FROM AUTHOR]

Synaptic cell adhesion molecules are well established to exhibit synaptogenic activity when overexpressed in target cells, indicating that they are involved in formation and functional maturation of synapses. The postsynaptic adhesion proteins Neuroligin1 and LRRTM2 both induce synaptic vesicle clusters in presynaptic axons in vitro by transsynaptically interacting with neurexins. In neurons, this is accompanied by the induction of glutamatergic, but not GABAergic synapses. Although the synaptogenic activity of Neuroligin1 has been well characterized, the properties of the synaptogenic activities of other synaptic adhesion molecules are largely unknown. In this paper, we now compared characteristics of the synaptogenic activities of Neuroligin1 and LRRTM2 upon overexpression in cultured mouse cortical neurons. Individual cortical neurons were transfected with Neuroligin1 and LRRTM2 expression plasmids, respectively, and synaptic vesicle clustering in contacting axons was examined by immunostaining for the vesicle membrane protein VAMP2. In immature neurons at 6–7 days in vitro (DIV) both Neuroligin1 and LRRTM2 exhibited strong synaptogenic activity. However, upon further neuronal differentiation only LRRTM2 retained significant synaptogenic activity at 12–13 DIV. A similar differential developmental maturation of the synaptogenic activities of Neuroligin1 and LRRTM2 was observed for the induction of glutamatergic synapses, which were detected by co-immunostaining for VGLUT1 and Homer1. Most interestingly, the synaptogenic activity of Neuroligin1 was strongly dependent on the expression and function of the synaptic adhesion molecule N-cadherin in immature neurons. In contrast, the synaptogenic activity of LRRTM2 was independent of N-cadherin expression and function in both immature (6–7 DIV) and more mature neurons (14–15 DIV). Taken together, our results with overexpression in cultured cortical neurons revealed striking differences in the properties of the synaptogenic activities of Neuroligin1 and LRRTM2, although both transsynaptically interact with presynaptic neurexins. [ABSTRACT FROM AUTHOR]

An amendment to this paper has been published and can be accessed via a link at the top of the paper. [ABSTRACT FROM AUTHOR]