Highly sensitive in vitro selections for DNA-linked synthetic small molecules with protein binding affinity and specificity

We have developed in vitro selections for DNA-linked synthetic small molecules with protein binding affinity and specificity. These selections require only generally accessible equipment, offer high degrees of enrichment of active molecules from mixtures of predominantly inactive species, can be applied to a variety of unrelated proteins, and require approximately 108-fold less material than existing synthetic molecule screening methods. Iterating these selections multiplies the net enrichment of active molecules, enabling enormous overall enrichment factors exceeding 106 to be achieved. Further, the selections can be adapted to select for binding specificity in addition to binding affinity. The application of methods described in this work may play a key role in the discovery of desired molecules from DNA-templated synthetic libraries.     

Highly sensitive detection of protein and small molecules based on aptamer-modified electrochemiluminescence nanoprobe

Amplified optical detection of biomolecules using nanoparticle as the carrier has attracted considerable interest in the scientific community. In this study, a promising aptasensor was developed for highly sensitive detection of protein and small molecules based on the construction of aptamer-modified electrochemiluminescence (ECL) nanoprobe. Specifically, thrombin and ATP serve as the examples for detection. By taking advantage of sandwich binding of two affinity aptamers for high specificity, tris-(2,2'-bipyridyl)ruthenium (TBR)-cysteamine loaded in gold nanoparticle (GNP) as barcodes for signal amplification, and micromagnetic particles (MMPs) based ECL technology for rapid detection, a novel assay for biomolecules quantification was developed. The sandwich complex containing targets could be selectively captured by MMPs and then quantified by ECL intensity. We have demonstrated that the detection limits of human thrombin and ATP are 1 pM and 10 pM, respectively, with high specificity. The proposed technology is expected to become a powerful tool for biomolecule analysis.     

Comparison of structure fingerprint and molecular interaction field based methods in explaining biological similarity of small molecules in cell-based screens

In this work, we calculated the pair wise chemical similarity for a subset of small molecules screened against the NCI60 cancer cell line panel. Four different compound similarity calculation methods were used: Brutus, GRIND, Daylight and UNITY. The chemical similarity scores of each method were related to the biological similarity data set. The same was done also for combinations of methods. In the end, we had an estimate of biological similarity for a given chemical similarity score or combinations thereof. The data from above was used to identify chemical similarity ranges where combining two or more methods (data fusion) led to synergy. The results were also applied in ligand-based virtual screening using the DUD data set. In respect to their ability to enrich biologically similar compound pairs, the ranking of the four methods in descending performance is UNITY, Daylight, Brutus and GRIND. Combining methods resulted always in positive synergy within a restricted range of chemical similarity scores. We observed no negative synergy. We also noted that combining three or four methods had only limited added advantage compared to combining just two. In the virtual screening, using the estimated biological similarity for ranking compounds produced more consistent results than using the methods in isolation.     

RGB small molecules based on a bipolar molecular design for highly efficient solution-processed single-layer OLEDs

In this paper, we describe a bipolar molecular design for small molecule solution-processed organic light emitting diodes (OLEDs). Combining the rigidity of the conjugated emissive cores and the flexibility of the peripheral alkyl-linked carbazole groups, two series of highly efficient bipolar RGB (red, green, blue) emitters have been synthesized and characterized. The emissive cores are composed of electron-withdrawing groups; the carbazole groups endow the materials electron-donating units. Such bipolar structures are advantageous for the carrier injection and balance. Four peripheral carbazole groups are introduced in T-series materials (TCDqC, TCSoC, TCBzC, TCNzC), and another four in O-series materials (OCDqC, OCSoC, OCBzC, OCNzC). With the single-layer device configuration of ITO/PEDOT:PSS/emitting layer/CsF/Al, two green devices exhibited excellent performance with a maximum luminescence efficiency of over 6.4 cd A(-1), and a high maximum luminance of more than 6700 cd m(-2). In addition, compared with the T-series, the luminescence efficiency of blue and red devices based on O-series materials increased from 1.6 to 2.8 cd A(-1) and 0.2 to 1.3 cd A(-1), respectively. To our knowledge, the performance of the blue device based on OCSoC is among the best of the blue small-molecule solution-processed single-layer devices reported so far.     

Dissecting cellular processes using small molecules: identification of colchicine-like, taxol-like and other small molecules that perturb mitosis

BACKGROUND: Understanding the molecular mechanisms of complex cellular processes requires unbiased means to identify and to alter conditionally gene products that function in a pathway of interest. Although random mutagenesis and screening (forward genetics) provide a useful means to this end, the complexity of the genome, long generation time and redundancy of gene function have limited their use with mammalian systems. We sought to develop an analogous process using small molecules to modulate conditionally the function of proteins. We hoped to identify simultaneously small molecules that may serve as leads for the development of therapeutically useful agents. RESULTS: We report the results of a high-throughput, phenotype-based screen for identifying cell-permeable small molecules that affect mitosis of mammalian cells. The predominant class of compounds that emerged directly alters the stability of microtubules in the mitotic spindle. Although many of these compounds show the colchicine-like property of destabilizing microtubules, one member shows the taxol-like property of stabilizing microtubules. Another class of compounds alters chromosome segregation by novel mechanisms that do not involve direct interactions with microtubules. CONCLUSIONS: The identification of structurally diverse small molecules that affect the mammalian mitotic machinery from a large library of synthetic compounds illustrates the use of chemical genetics in dissecting an essential cellular pathway. This screen identified five compounds that affect mitosis without directly targeting microtubules. Understanding the mechanism of action of these compounds, along with future screening efforts, promises to help elucidate the molecular mechanisms involved in chromosome segregation during mitosis.     

Conformational searching methods for small molecules. II. Genetic algorithm approach

We demonstrate the use of a genetic algorithm (GA) search procedure for finding low-energy conformations of small to medium organic molecules (1–12 rotatable bonds). GAS are in a class of biologically motivated optimization methods that evolve a population of individuals where individuals who are more “fit” have a higher probability of surviving into subsequent generations. Here, an individual is a conformation of a given molecule and the fitness is the molecule's conformational energy. In the course of a simulated evolution, the population produces conformations having increasingly lower energy. We test the GA method on a suite of 72 molecules and compare the performance against the CSEARCH algorithm in Sybyl. For molecules with more than eight rotatable bonds, the GA method is more efficient computationally and as the number of rotatable bonds increases the relative efficiency of the GA method grows. The GA method also found energies equal to or lower than the energy of the relaxed crystal structure in the large majority of cases. © John Wiley & Sons, Inc.     

Cellular delivery of dinucleotides by conjugation with small molecules: targeting translation initiation for anticancer applications

Targeting cap-dependent translation initiation is one of the experimental approaches that could lead to the development of novel anti-cancer therapies. Synthetic dinucleoside 5′,5′-triphosphates cap analogs are potent antagonists of eukaryotic translation initiation factor 4E (eIF4E) in vitro and could counteract elevated levels of eIF4E in cancer cells; however, transformation of these compounds into therapeutic agents remains challenging – they do not easily penetrate into cells and are susceptible to enzymatic cleavage. Here, we tested the potential of several small molecule ligands – folic acid, biotin, glucose, and cholesterol – to deliver both hydrolyzable and cleavage-resistant cap analogs into cells. A broad structure–activity relationship (SAR) study using model fluorescent probes and cap–ligand conjugates showed that cholesterol greatly facilitates uptake of cap analogs without disturbing the interactions with eIF4E. The most potent cholesterol conjugate identified showed apoptosis-mediated cytotoxicity towards cancer cells.

Ligand assisted cellular delivery of negatively charged dinucleotides, which are potential antagonists of the protooncogenic protein eIF4E.     

Developments in the production of biological and synthetic binders for immunoassay and sensor-based detection of small molecules

The need for chemical and biological entities of predetermined selectivity and affinity towards target analytes is greater than ever, in applications such as environmental monitoring, bioterrorism detection and analysis of natural toxin contaminants in the food chain.In this review, we focus on advances in the production of specific binders, in terms of both natural entities (e.g., antibodies) and synthetic binders (e.g., molecularly-imprinted polymers). We discuss the potential of emerging technologies for integration into immunoassay and sensing techniques. We place special emphasis on use of these technologies in bioanalytical applications.     

基于小分子的核酸结构探针最新研究进展

本文主要综述了基于小分子的核酸结构探针的最新研究进展.所探索的核酸结构主要有四链核酸（包括G-四链体以及i-motif）结构、三链核酸结构、左手螺旋DNA结构以及不规则核酸结构（包括突起结构以及环状结构）等;所探索的小分子包括过渡金属配合物、大环共轭化合物、环肽以及寡糖抗生素等.     

一维有机微纳米光功能材料研究进展

近年来,一维有机小分子微纳材料因为其新颖的光学性能和在未来小型化器件中的广泛应用,受到了人们越来越多的关注.相比于传统无机半导体材料,有机小分子材料具有结构多样性、功能可设计性、易大量制备、易机械加工等显著优势.本文将从一维有机小分子纳米材料的制备方法、形貌调控、光学性能(如光波导、受激发射、电致发光等),及其在光学器件上的应用出发,对近十年来的相关研究进展及成果进行总结和介绍.     

Chemogenomics and cancer chemotherapy: cell-based assays to screen for small molecules that impair microtubule dynamics

Microtubules are still a promising target for new therapeutic agents. Thus, there is a continuous interest for compounds able to modify microtubule assembly, either by interacting directly with tubulin, or by interacting with microtubules regulators. Because of its dynamic characteristics, the microtubule cytoskeleton is a suitable target for small molecules that rapidly diffuse in the cell cytoplasm. Moreover, compounds targeting the microtubule cytoskeleton have proved to be valuable tools for basic research in cell biology. In this paper, after a short presentation of the apparent molecular pathways involved in the anticancer effect of agents that interfere with microtubules functions, the potentials and impact of chemogenomics and cell-based assays in the discovery of new therapeutic compounds and of new regulators of the microtubule cytoskeleton are described.     

Design, synthesis, and operation of small molecules that walk along tracks

The synthesis and system dynamics of a series of small-molecule walker-track conjugates, 3,4-C(n) (n = 2, 3, 4, 5, and 8), based on dynamic covalent linkages between the "feet" of the walkers and the "footholds" of the track, is described. Each walker has one acyl hydrazide and one sulfur-based foot separated by a spacer chain of "n" methylene groups, while the track consists of four footholds of alternating complementary functionalities (aldehydes and masked thiols). Upon repeatedly switching between acid and base, the walker moiety can be exchanged between the footholds on the track, primarily through a "passing-leg gait" mechanism, until a steady state, minimum energy, distribution is reached. The introduction of a kinetically controlled step in the reaction sequence (redox-mediated breaking and reforming of the disulfide linkages) can cause a directional bias in the distribution of the walker on the track. The different length walker molecules exhibit very different walking behaviors: Systems n = 2 and 3 cannot actually "walk" along the track because their stride lengths are too short to bridge the internal footholds. The walkers with longer spacers (n = 4, 5, and 8) do step up and down the track repeatedly, but a directional bias under the acid-redox conditions is only achieved for the C(4) and C(5) systems, interestingly in opposite directions (the C(8) walker has insufficient ring strain with the track). Although they are extremely rudimentary systems, the C(4) and C(5) walker-track conjugates exhibit four of the essential characteristics of linear molecular motor dynamics: processive, directional, repetitive, and progressive migration of a molecular unit up and down a molecular track.     

Reorientation and translation of individual dye molecules in a polymer matrix

The orientational and translational motion of individual dye molecules embedded in a polymer matrix is studied in the temperature regime above the glass transition. The rotational diffusion close to the glass transition is heterogeneous on the single molecule level and few sudden changes in the reorientational speed of single molecules are found. The exchange between these reorientational speeds is found to be one order of magnitude slower than the reorientational time constant of the molecules. Translational motion can be clearly identified at about 1.2 T_g. However, the translational diffusion shows no signs of heterogeneity on the timescale of our experiments, from which we conclude, that the timescale of the exchange process between microenvironments has become too fast or that no heterogeneity exists at the temperatures above 1.2 T_g.     

Genetic and genomic approaches to identify and study the targets of bioactive small molecules

Natural and synthetic bioactive small molecules form the backbone of modern therapeutics. These drugs primarily exert their effect by targeting cellular host or foreign proteins that are critical for the progression of disease. Therefore, a crucial step in the process of recognizing valuable new drug leads is identification of their protein targets; this is often a time consuming and difficult task. This report is intended to provide a comprehensive review of recent developments in genetic and genomic approaches to overcome the hurdle of discovering the protein targets of bioactive small molecules.     

Chemisorption and reactions of small molecules on small gold particles

The activity of supported gold particles for a number of oxidations and hydrogenations starts to increase dramatically as the size falls below ~3 nm. This is accompanied by an increased propensity to chemisorption, especially of oxygen and hydrogen. The explanation for these phenomena has to be sought in kinetic analysis that connects catalytic activity with the strength and extent of chemisorption of the reactants, the latter depending on the electronic structure of the gold atoms constituting the active centre. Examination of the changes to the utilisation of electrons as particle size is decreased points to loss of metallic character at about 3 nm, as energy bands are replaced by levels, and a band gap appears. Detailed consideration of the Arrhenius parameters (E and ln A) for CO oxidation points clearly to a step-change in activity at the point where metallic character is lost, as opposed to there being a monotonic dependence of rate on a physical property such as the fraction of atoms at corners or edges of particles. The deplorable scarcity of kinetic information on other reactions makes extension of this analysis difficult, but non-metallic behaviour is an unavoidable property of very small gold particles, and therefore cannot be ignored when seeking to explain their exceptional activity.     

Monolithic columns based on a poly(styrene-divinylbenzene-methacrylic acid) copolymer for capillary liquid chromatography of small organic molecules

A very simple and readily performed method is described for the preparation of poly(styrene-divinylbenzene-methacrylic acid) monolithic columns for capillary liquid chromatography. The effect of the methacrylic acid content on the morphological and chromatographic properties has been investigated. Methacrylic acid is shown to be essential for isocratic separations of small organic analytes by capillary liquid chromatography. Column efficiencies of about 28,000 theoretical plates/m have been obtained for all the test compounds. The batch-to-batch and run-to-run repeatability of the retention times is better than 1.5%.