Exploration of 3D activity cliffs on the basis of compound binding modes and comparison of 2D and 3D cliffs

Activity cliffs are formed by pairs or groups of structurally similar compounds having large differences in potency and are focal points of structure-activity relationship (SAR) analysis. The choice of molecular representations is a critically important aspect of activity cliffs analysis. Thus far, activity cliffs have predominantly been defined on the basis of molecular graph or fingerprint representations. Herein we introduce 3D activity cliffs derived from comparisons of experimentally determined compound binding modes. The analysis of 3D activity cliffs is generally applicable to target proteins for which structures of multiple ligand complexes are available. For two popular targets, β-secretase 1 (BACE1) and factor Xa (FXa), public domain X-ray structures with bound inhibitors were collected. Crystallographic binding modes of inhibitors were systematically compared using a 3D similarity method taking conformational, positional, and atomic property differences into account. In addition, standard 2D similarity relationships were also determined. SAR information associated with individual compounds substantially changed when either bioactive conformations or 2D molecular graphs were used for similarity evaluation. 3D activity cliffs were identified for BACE1 and FXa inhibitor sets and systematically compared to 2D cliffs. It was found that less than 40% of 3D activity cliffs were conserved when 2D similarity was applied. The limited conservation of 3D and 2D cliffs provides further evidence for the strong molecule representation dependence of activity cliffs. Moreover, 3D cliffs represent a new class of activity cliffs that convey SAR information in ways that differ from graph-based similarity measures. In cases where sufficient structural information is available, the comparison of 3D and 2D cliffs is expected to aid in SAR analysis and mapping of critical binding determinants.     

Enantioselective crystallization of D,L-amino acids induced by spontaneous asymmetric resolution of D,L-asparagine

Racemic D,L-asparagine induced spontaneous asymmetric resolution of co-existing D,L-phenylalanine or D,L-tryptophan by recrystallization from a homogeneous aqueous solution, and the enantiomeric excess of phenylalanine or tryptophan in the resulting crystals correlated linearly with that of asparagine crystallized with phenylalanine or tryptophan.     

Tunneling chemical reactions D + H2 --> DH + H and D + DH --> D2 + H in solid D2-H2 and HD-H2 mixtures: an electron-spin-resonance study

Tunneling chemical reactions D + H2 --> DH + H and D + DH --> D2 + H in solid HD-H2 and D2-H2 mixtures were studied in the temperature range between 4 and 8 K. These reactions were initiated by UV photolysis of DI molecules doped in these solids for 30 s and followed by measuring the time course of electron-spin-resonance (ESR) intensities of D and H atoms. ESR intensity of D atoms produced by the photolysis decreases but that of H atoms increases with time. Time course of the D and H intensities has the fast and slow processes. The fast process, which finishes within approximately 300 s after the photolysis, is assigned to the reaction of D atom with one of its nearest-neighboring H2 molecules, D(H2)n(HD)(12-n) --> H(H2)(n-1)(HD)(13-n) or D(H2)n(D2)(12-n) --> H(HD)(H2)(n-1)(D2)(12-n) for 12 > or = n > or = 1. Rate constant for the D + H2 reaction between neighboring D atom-H2 molecule pair is determined to be (7.5 +/- 0.7) x 10(-3) s(-1) in solid HD-H2 and (1.3+/-0.3) x 10(-2) s(-1) in D2-H2 at 4.1 K, which is very close to that calculated based on the theory of chemical reaction in gas phase by Hancock et al. [J. Chem. Phys. 91, 3492 (1989)] and Takayanagi and Sato [J. Chem. Phys. 92, 2862 (1990)]. This rate constant was found to be independent of temperature up to 7 K within experimental error of +/-30%. The slow process is assigned to the reaction of D atom produced in a cage fully surrounded by HD or D2 molecules, D(HD)12 or D(D2)12. This D atom undergoes the D + DH reaction with one of its nearest-neighboring HD molecules in solid HD-H2 or diffuses to the neighbor of H2 molecules to allow the D + H2 reaction in solid HD-H2 and D2-H2. The former is the main channel in solid HD-H2 below 6 K where D atoms diffuse very slowly, whereas the latter dominates over the former above 6 K. Rate for the reactions in the slow process is independent of temperature below 6 K but increases with the increase in temperature above 6 K. We found that the increase is due to the increase in hopping rate of D atoms to the neighbor of H2 molecules. Rate constant for the D + DH reaction was found to be independent of temperature up to 7 K as well.     

A 3D QSAR study on a set of dopamine D4 receptor antagonists

The molecular alignments obtained from a previously reported pharmacophore model have been employed in a three-dimensional quantitative structure-activity relationship (3D QSAR) study, to obtain a more detailed insight into the structure-activity relationships for D(2) and D(4) receptor antagonists. The frequently applied CoMFA method and the related CoMSIA method were used. Statistically significant models have been derived with these two methods, based on a set of 32 structurally diverse D(2) and D(4) receptor antagonists. The CoMSIA and the CoMFA methods produced equally good models expressed in terms of q(2) values. The predictive power of the derived models were demonstrated to be high. Graphical interpretation of the results, provided by the CoMSIA method, brings to light important structural features of the compounds related to either low- or high-affinity D(2) or D(4) antagonism. The results of the 3D QSAR studies indicate that bulky N-substituents decrease D(2) binding, whereas D(4) binding is enhanced. Electrostatically favorable and unfavorable regions exclusive to D(2) receptor binding were identified. Likewise, certain hydrogen-bond acceptors can be used to lower D(2) affinity. These observations may be exploited for the design of novel dopamine D(4) selective antagonists.     

Dimension Engineering of Stimuli-Responsive 1D Molecular Crystals into Unusual 2D and 3D Zigzag Waveguides

We demonstrate an innovative technique to achieve organic 2D and 3D waveguides with peculiar shapes from an acicular, stimuli-responsive molecular crystal, (2Z,2′Z)-3,3′-(anthracene-9,10-diyl)bis(2-(3,5-bis(trifluoromethyl)phenylacrylonitrile), Ant-CF₃. The greenish-yellow fluorescent (FL) Ant-CF₃ molecular crystals exhibit laser power-dependent permanent mechanical bending in 2D and 3D. Investigation of a single-crystal using spatially-resolved Raman/FL/electron microscopy, and theoretical calculations revealed photothermal (Z,E)/(E,E) isomerization-assisted transition from crystalline to amorphous phase at the laser-exposed regions. This phenomenon facilitates the dimension engineering of a 1D crystal waveguide into 2D waveguide on a substrate or a 3D waveguide in free space. The bends can be used as interconnection points to couple different optical elements. The presented technique has broader implications in organic photonics and other crystal-related photonic technologies.     

食品中维生素D与25-羟基维生素D检测技术及含量分布研究进展

维生素D是一种对于维持人体健康具有重要作用的脂溶性维生素,25-羟基维生素D是其在人体内循环和存储的主要形式。食品中维生素D和25-羟基维生素D前处理的通常采用碱皂化、有机溶剂提取、固相萃取或者半制备色谱净化;其测定方法多为放射免疫法和液相色谱法。液相色谱串联质谱凭借高灵敏度和高准确度,目前在食品中维生素D和25-羟基维生素D测定中发挥重要作用。近年来二维液相色谱和超高效超临界流体色谱由于其强大的分离能力,在食品中维生素D和25-羟基维生素D的分析中表现出强大的潜力。该文综述了近年来食品中维生素D和25-羟基维生素D的检测方法及二者在动物食品和植物食品中的含量分布研究,以期为建立适合不同食物样品的测定方法,指导居民合理膳食,进行膳食摄入量评估等研究工作提供参考。     

Analysis of five rare alleles at the STR loci D1S1656, D12S391, D13S317, Penta D,and D2S441

Short tandem repeat (STR) automatic typing technology is extensively used in forensic laboratories with commercial kits, in rare cases genotyping misinterpretations or mislabeling may occur due to unexpected rare alleles. This study refers to the investigation of several rare alleles observed from routine cases. Besides cross-kit verification with Goldeneye 25A (Beijing PeopleSpot Inc, China) and Huaxia platinum (Thermo Fisher Scientific, USA) kits, the next-generation sequencing technology by MiSeq FGx System (Illumina, USA) was applied to further validation. To solve the inconsistent outcomes reached by the above mentioned approaches at D2S441 locus, single gene amplification, gene cloning, and genetic sequencing was also performed. As a result, five rare alleles were detected. Two novel alleles of allele 3 at the D13S317 locus and allele 5 at the D2S441 locus were found; three previously reported alleles of allele 9 at D1S1656 locus, allele 19 at Penta D locus, and allele 28 at D12S391 locus in STRBase were initially supplemented with sequence information. We, therefore, propose that such uncommon observations with rare events should be carefully investigated and interpreted.     

Measurement of Monomer Reactivity Ratios of D,L-3-Methylglycolide with Glycolide or D,L-Lactide

Polylactides, polyglycolide and copolymers based on them, are still gaining interestbecause of the numerous applications in the biomedical and pharmaceutical fieldsl. Theyare usually prepared by bulk homo- and co-polymerizations of lactides, glycolideinitiated with stannous octoate (Snoot,) because Snoot, is a highly efficient commercialcatalyst and a permitted food additive in numerous countriesl-2. However, the propertiesof poly(D,L-lactic acid-co-glycolic acid) (D,L-PLGA) have widely va…     

Chitosan and Whey Protein Bio-Inks for 3D and 4D Printing Applications with Particular Focus on Food Industry

The application of chitosan (CS) and whey protein (WP) alone or in combination in 3D/4D printing has been well considered in previous studies. Although several excellent reviews on additive manufacturing discussed the properties and biomedical applications of CS and WP, there is a lack of a systemic review about CS and WP bio-inks for 3D/4D printing applications. Easily modified bio-ink with optimal printability is a key for additive manufacturing. CS, WP, and WP–CS complex hydrogel possess great potential in making bio-ink that can be broadly used for future 3D/4D printing, because CS is a functional polysaccharide with good biodegradability, biocompatibility, non-immunogenicity, and non-carcinogenicity, while CS–WP complex hydrogel has better printability and drug-delivery effectivity than WP hydrogel. The review summarizes the current advances of bio-ink preparation employing CS and/or WP to satisfy the requirements of 3D/4D printing and post-treatment of materials. The applications of CS/WP bio-ink mainly focus on 3D food printing with a few applications in cosmetics. The review also highlights the trends of CS/WP bio-inks as potential candidates in 4D printing. Some promising strategies for developing novel bio-inks based on CS and/or WP are introduced, aiming to provide new insights into the value-added development and commercial CS and WP utilization.     

Assembly of one dimensional inorganic nanostructures into functional 2D and 3D architectures. Synthesis, arrangement and functionality

This review will focus on the synthesis, arrangement, structural assembly, for current and future applications, of 1D nanomaterials (tubes, wires, rods) in 2D and 3D ordered arrangements. The ability to synthesize and arrange one dimensional nanomaterials into ordered 2D or 3D micro or macro sized structures is of utmost importance in developing new devices and applications of these materials. Micro and macro sized architectures based on such 1D nanomaterials (e.g. tubes, wires, rods) provide a platform to integrate nanostructures at a larger and thus manageable scale into high performance electronic devices like field effect transistors, as chemo- and biosensors, catalysts, or in energy material applications. Carbon based, metal oxide and metal based 1D arranged materials as well as hybrid or composite 1D materials of the latter provide a broad materials platform, offering a perspective for new entries into fascinating structures and future applications of such assembled architectures. These architectures allow bridging the gap between 1D nanostructures and the micro and macro world and are the basis for an assembly of 1D materials into higher hierarchy domains. This critical review is intended to provide an interesting starting point to view the current state of the art and show perspectives for future developments in this field. The emphasis is on selected nanomaterials and the possibilities for building three dimensional arrays starting from one dimensional building blocks. Carbon nanotubes, metal oxide nanotubes and nanowires (e.g. ZnO, TiO(2), V(2)O(5), Cu(2)O, NiO, Fe(2)O(3)), silicon and germanium nanowires, and group III-V or II-VI based 1D semiconductor nanostructures like GaS and GaN, pure metals as well as 1D hybrid materials and their higher organized architectures (foremost in 3D) will be focussed. These materials have been the most intensively studied within the last 5-10 years with respect to nano-micro integration aspects and their functional and application oriented properties. The critical review should be interesting for a broader scientific community (chemists, physicists, material scientists) interested in synthetic and functional material aspects of 1D materials as well as their integration into next higher organized architectures.     

Vitamin D and Skin Cancer

Vitamin D signaling plays a key role in many important processes, including cellular proliferation, differentiation and apoptosis, immune regulation, hormone secretion and skeletal health. Furthermore, vitamin D production and supplementation have been shown to exert protective effects via an unknown signaling mechanism involving the vitamin D receptor (VDR) in several diseases and cancer types, including skin cancer. With over 3.5 million new diagnoses in 2 million patients annually, skin cancer is the most common cancer type in the United States. While ultraviolet B (UVB) radiation is the main etiologic factor for nonmelanoma skin cancer (NMSC), UVB also induces cutaneous vitamin D production. This paradox has been the subject of contradictory findings in the literature in regards to amount of sun exposure necessary for appropriate vitamin D production, as well as any beneficial or detrimental effects of vitamin D supplementation for disease prevention. Further clinical and epidemiological studies are necessary to elucidate the role of vitamin D in skin carcinogenesis.     

Performance evaluation of 2D fingerprint and 3D shape similarity methods in virtual screening

Virtual screening (VS) can be accomplished in either ligand- or structure-based methods. In recent times, an increasing number of 2D fingerprint and 3D shape similarity methods have been used in ligand-based VS. To evaluate the performance of these ligand-based methods, retrospective VS was performed on a tailored directory of useful decoys (DUD). The VS performances of 14 2D fingerprints and four 3D shape similarity methods were compared. The results revealed that 2D fingerprints ECFP_2 and FCFP_4 yielded better performance than the 3D Phase Shape methods. These ligand-based methods were also compared with structure-based methods, such as Glide docking and Prime molecular mechanics generalized Born surface area rescoring, which demonstrated that both 2D fingerprint and 3D shape similarity methods could yield higher enrichment during early retrieval of active compounds. The results demonstrated the superiority of ligand-based methods over the docking-based screening in terms of both speed and hit enrichment. Therefore, considering ligand-based methods first in any VS workflow would be a wise option.     

Polar discontinuities and 1D interfaces in monolayered materials

Interfaces are the birthplace of a multitude of fascinating discoveries in fundamental science, and have enabled modern electronic devices, from transistors, to lasers, capacitors or solar cells. These interfaces between bulk materials are always bi-dimensional (2D) ‘surfaces’. However the advent of graphene and other 2D crystals opened up a world of possibilities, as in this case the interfaces become one-dimensional (1D) lines. Although the properties of 1D nanoribbons have been extensively discussed in the last few years, 1D interfaces within infinite 2D systems had remained mostly unexplored until very recently. These include grain boundaries in polycrystalline samples, or interfaces in hybrid 2D sheets composed by segregated domains of different materials (as for example graphene/BN hybrids, or chemically different transition metal dichalcogenides). As for their 2D counterparts, some of these 1D interfaces exhibit polar characteristics, and can give rise to fascinating new physical properties. Here, recent experimental discoveries and theoretical predictions on the polar discontinuities that arise at these 1D interfaces will be reviewed, and the perspectives of this new research topic, discussed.     

基于一维和二维纳米材料的神经界面构筑

Neural interfaces have contributed significantly to our understanding of brain functions as well as the development of neural prosthetics. An ideal neural interface should create a seamless and reliable link between the nervous system and external electronics for long periods of time. Implantable electronics that are capable of recording and stimulating neuronal activities have been widely applied for the study of neural circuits or the treatment of neurodegenerative diseases. However, the relatively large cross-sectional footprints of conventional electronics can cause acute tissue damage during implantation. In addition, the mechanical mismatch between conventional rigid electronics and soft brain tissue has been shown to induce chronic tissue inflammatory responses, leading to signal degradation during long-term studies. Thus, it is essential to develop new strategies to overcome these existing challenges and construct more stable neural interfaces. Owing to their unique physical and chemical properties, one-dimensional (1D) and two-dimensional (2D) nanomaterials constitute promising candidates for next-generation neural interfaces. In particular, novel electronics based on 1D and 2D nanomaterials, including carbon nanotubes (CNTs), silicon nanowires (SiNWs), and graphene (GR), have been demonstrated for neural interfaces with improved performance. This review discusses recent developments in neural interfaces enabled by 1D and 2D nanomaterials and their electronics. The ability of CNTs to promote neuronal growth and electrical activity has been proven, demonstrating the feasibility of using CNTs as conducting layers or as modifying layers for electronics. Owing to their good mechanical, electrical and biological properties, CNTs-based electronics have been demonstrated for neural recording and stimulation, neurotransmitter detection, and controlled drug release. Different from CNTs-based electronics, SiNWs-based field effect transistors (FETs) and microelectrode arrays have been successfully demonstrated for intracellular recording of action potentials through penetration into neural cells. Significantly, SiNWs FETs can detect neural activity at the level of individual axons and dendrites with a high signal-to-noise ratio. Their ability to record multiplexed intracellular signals renders SiNWs-based electronics superior to traditional intracellular recording techniques such as patch-clamp recording. Besides, SiNWs have been explored for optically controlled nongenetic neuromodulation due to their tunable electrical and optical properties. As the star of the 2D nanomaterials family, GR has been applied as biomimetic substrates for neural regeneration. Transparent GR-based electronics combining electrophysiological measurements, optogenetics, two-photon microscopy with multicellular calcium imaging have been applied for the construction of multimodal neural interfaces. Finally, we provide an overview of the challenges and future perspectives of nanomaterial-based neural interfaces.     

Comparison of 2D similarity and 3D superposition. Application to searching a conformational drug database

In a database of about 2000 approved drugs, represented by 10(5) structural conformers, we have performed 2D comparisons (Tanimoto coefficients) and 3D superpositions. For one class of drugs the correlation between structural resemblance and similar action was analyzed in detail. In general Tanimoto coefficients and 3D scores give similar results, but we find that 2D similarity measures neglect important structural/funtional features. Examples for both over- and underestimation of similarity by 2D metrics are discussed. The required additional effort for 3D superpositions is assessed by implementation of a fast algorithm with a processing time below 0.01 s and a more sophisticated approach (0.5 s per superposition). According to the improvement of similarity detection compared to 2D screening and the pleasant rapidity on a desktop PC, full-atom 3D superposition will be an upcoming method of choice for library prioritization or similarity screening approaches.     

Collaborative annotation of 3D crystallographic models

This paper describes the AnnoCryst system-a tool that was designed to enable authenticated collaborators to share online discussions about 3D crystallographic structures through the asynchronous attachment, storage, and retrieval of annotations. Annotations are personal comments, interpretations, questions, assessments, or references that can be attached to files, data, digital objects, or Web pages. The AnnoCryst system enables annotations to be attached to 3D crystallographic models retrieved from either private local repositories (e.g., Fedora) or public online databases (e.g., Protein Data Bank or Inorganic Crystal Structure Database) via a Web browser. The system uses the Jmol plugin for viewing and manipulating the 3D crystal structures but extends Jmol by providing an additional interface through which annotations can be created, attached, stored, searched, browsed, and retrieved. The annotations are stored on a standardized Web annotation server (Annotea), which has been extended to support 3D macromolecular structures. Finally, the system is embedded within a security framework that is capable of authenticating users and restricting access only to trusted colleagues.     

2D spatially periodic architectures via the drying of 1D holographically photopatterned polymer solutions

We demonstrate an efficient and versatile method for selectively generating 1D and 2D periodic polymer structures in the submicron to tens of micron range by the directed drying of 1D photopatterned polymer solutions. Ultraviolet (UV) holographic lithography (Xia et al. Chem. Rev. 1999, 99, 1823-1848) is initially used to create 1D periodic cross-link and density variations in the polymer/volatile solvent solutions. These variations act as anisotropic barriers (walls) that direct the subsequent solvent evaporation process. Somewhat akin to directional drying (Allain and Limat Phys. Rev. Lett. 1995, 74, 2981-2984) and directional solidification (Pelc, P. Dynamics of Curved Fronts; Academic Press: San Diego, CA, 1988) experiments, the drying exhibits channel-like interface propagation behavior. The combination of the instabilities and minimization of the interface area during drying can be effectively used to produce larger scale 2D pseudohexagonal polymer-strut structures, or by the addition of a monomeric component to the polymer solution, the instabilities can be suppressed, resulting in the formation of 1D linear gratings.     

Sunbeds as Vitamin D Sources

The objectives of this work were: (1) To determine whether repeated exposures to small doses from a commercial sun bed (Wolff Solarium Super Plus 100 W) over 5 weeks gave less vitamin D than repeated exposures to twice as large, but still nonerythemogenic, doses. (2) To investigate whether the contribution to the vitamin D status from such sessions of exposures was dependent on the baseline status before the start of the sessions. (3) To determine the decay rate of the induced increment of vitamin D. The sun bed sessions raised the 25-hydroxyvitamin D levels from typical winter values to typical summer values. The mean value after exposure being 80 n m (±14) and the increase being 15 n m on average. Persons with the lowest initial levels got the largest increase. The level in this group was back to the pre-exposure level after 2–4 weeks. To maintain a summer level through the winter, when no vitamin D is produced by the sun in northern countries, one should consider increasing the recommended intake of vitamin D intake significantly, or encouraging the population to get moderate, nonerythemal sun bed exposures.     

Amine-controlled assembly of metal-sulfite architecture from 1D chains to 3D framework

Whereas open-framework materials have been made in a variety of chemical compositions, few are known in which 3-connected SO3(2)- anions serve as basic building units. Here, we report four new metal-sulfite polymeric structures, (ZnSO3)Py (1, py = pyridine), (ZnSO3)2(2,2'-bipy)H2O (2, 2,2'-bipy = 2,2'-bipyridine), (ZnSO3)2(TMDPy) (3, TMDPy = 4,4'-trimethylenedipyridine), and (MnSO3)2en (4, en = ethylenediamine) that have been synthesized hydrothermally and structurally characterized. In these compounds, low-dimensional 1D and 2D inorganic subunits are assembled into higher 2D or 3D covalent frameworks by organic ligands. In addition to the structure-directing effect of organic ligands, the flexible coordination chemistry of Zn2+ and SO3(2)- also contributes to the observed structural diversity. In compounds 1-3, Zn2+ sites alternate with trigonal pyramidal SO3(2)- anions to form three types of [ZnSO3]n chains, whereas in compound 4, a 2D-corrugated [MnSO3]n layer is present. Compound 1 features a rail-like chain with pendant pyridine rings. The pi-pi interaction between 2,2'-bipy ligands is found between adjacent chains in compound 2, resulting in 2D sheets that are further stacked through interlayer hydrogen bonds. Compound 3 exhibits a very interesting inorganic [(ZnSO3)2]n chain constructed from two chairlike subunits, and such chains are bridged by TMDPy ligands into a 2D sheet. In compound 4, side-by-side helical chains permeate through 2D-corrugated [MnSO3]n layers, which are pillared by neutral ethylenediamine molecules into a 3D framework that can be topologically represented as a (3,6)-connected net. The results presented here illustrate the rich structural chemistry of metal-sulfites and the potential of sulfite anions as a unique structural building block for the construction of novel open-framework materials, in particular, those containing polymeric inorganic subunits that may have interesting physical properties such as low-dimensional magnetism or electronic properties.