LBVS: an online platform for ligand-based virtual screening using publicly accessible databases

Abundant data on compound bioactivity and publicly accessible chemical databases increase opportunities for ligand-based drug discovery. In order to make full use of the data, an online platform for ligand-based virtual screening (LBVS) using publicly accessible databases has been developed. LBVS adopts Bayesian learning approach to create virtual screening models because of its noise tolerance, speed, and efficiency in extracting knowledge from data. LBVS currently includes data derived from BindingDB and ChEMBL. Three validation approaches have been employed to evaluate the virtual screening models created from LBVS. The tenfold cross validation results of twenty different LBVS models demonstrate that LBVS achieves an average AUC value of 0.86. Our internal and external testing results indicate that LBVS is predictive for lead identifications. LBVS can be publicly accessed at http://rcdd.sysu.edu.cn/lbvs.     

Strategies for the synthesis of novel indole alkaloid-based screening libraries for drug discovery

A series of diverse indole-based chemotypes were synthesized from -tetrahydrocarboline (-THC) scaffolds prepared from commercially and readily available tryptamines and -ketoesters. Diversity can be generated within these chemotypes through the following strategies: (a) appendage of substituents to the -THC scaffold, prepared in situ or as a template, through further elaboration and (b) skeletal modifications to the -THC scaffold via ring forming or ring breaking reactions. The strategies described here are amenable to high throughput solution-phase parallel synthesis, providing access to novel indole-based screening libraries for drug discovery.Dedicated to Professor Spyros P. Perlepes     

Combinatorial chemistry and high-throughput screening in drug discovery: Different strategies and formats

Different strategies for the discovery of novel leadsinteracting with therapeutically relevant targets are thoroughlypresented and discussed, using also three recent examples.Emphasis is given to approaches which do not require extensiveresources and budgets, but rather prove how cleverness andcreativity can provide active compounds in drug discovery.     

Self-organized synthesis of silver dendritic nanostructures via an electroless metal deposition method

Unique silver dendritic nanostructures, with stems, branches, and leaves, were synthesized with self-organization via a simple electroless metal deposition method in a conventional autoclave containing aqueous HF and AgNO₃ solution. Their growth mechanisms are discussed in detail on the basis of a self-assembled localized microscopic electrochemical cell model. A process of diffusion-limited aggregation is suggested for the formation of the silver dendritic nanostructures. This nanostructured material is of great potential to be building blocks for assembling mini-functional devices of the next generation. PACS 61.46.+w; 68.70.+w; 81.65.Cf     

Polymer resin library and the discovery of highly efficient polymer supported reagents and scavengers

Summary This paper is focused on the preparation of a library of highly efficient, tailor made, macroporous resins as supports for reagents and scavengers. From this library a macroporous resin, prepared with 40% cross-linking and with a porogen level of 300% in toluene gave a material superior to those presently available, and was shown to be highly efficient in the preparation of novel highly reactive polymer supported reagents, including scavengers and oxidants.     

Photo-chemical synthesis and deposition of noble metal nanoparticles

Highly dispersed nanoparticles of transition and noble metals are utilized for hydrocarbon reactions and rearrangements important to the chemical industry. The need to obtain 1 to 3 nm particles with narrow size distributions has prompted the development of alternative processing methods. In this paper, a novel, dry method to synthesize nanoparticles from a frozen salt solution is reported. Pd nanoparticles were synthesized by photo-chemical decomposition of palladium acetate (PdAc) within a host matrix of chloroform using an excimer laser operating at 248 nm. Frozen composite targets were ablated at fluences ranging from 0.25 J/cm² to 0.75 J/cm² at a processing pressure of 10 mTorr. The ejected nanoparticles were deposited on continuous carbon coated and lacey carbon transmission electron microscopy (TEM) grids at ambient temperature. Characterization was performed by transmission electron microscopy (TEM) and energy dispersive X-ray spectroscopy (EDXS). High-resolution TEM analysis showed definitive evidence that the size distributions of the nanoparticles were narrow, exhibiting mean diameters ranging from 2.15 nm to 2.62 nm. PACS 81.15.Fg; 68.37.Lp; 81.07.Wx; 81.07.Bc; 81.10.Dn     

Integrating sampling techniques and inverse virtual screening: toward the discovery of artificial peptide-based receptors for ligands

A novel heuristic using an iterative select-and-purge strategy is proposed. It combines statistical techniques for sampling and classification by rigid molecular docking through an inverse virtual screening scheme. This approach aims to the de novo discovery of short peptides that may act as docking receptors for small target molecules when there are no data available about known association complexes between them. The algorithm performs an unbiased stochastic exploration of the sample space, acting as a binary classifier when analyzing the entire peptides population. It uses a novel and effective criterion for weighting the likelihood of a given peptide to form an association complex with a particular ligand molecule based on amino acid sequences. The exploratory analysis relies on chemical information of peptides composition, sequence patterns, and association free energies (docking scores) in order to converge to those peptides forming the association complexes with higher affinities. Statistical estimations support these results providing an association probability by improving predictions accuracy even in cases where only a fraction of all possible combinations are sampled. False positives/false negatives ratio was also improved with this method. A simple rigid-body docking approach together with the proper information about amino acid sequences was used. The methodology was applied in a retrospective docking study to all 8000 possible tripeptide combinations using the 20 natural amino acids, screened against a training set of 77 different ligands with diverse functional groups. Afterward, all tripeptides were screened against a test set of 82 ligands, also containing different functional groups. Results show that our integrated methodology is capable of finding a representative group of the top-scoring tripeptides. The associated probability of identifying the best receptor or a group of the top-ranked receptors is more than double and about 10 times higher, respectively, when compared to classical random sampling methods.     

Preparation of Bi:TiO2 thin films by an hybrid deposition configuration: pulsed laser deposition and thermal evaporation

The aim of this work was to report the application of an hybrid deposition configuration to deposit Titanium dioxide (TiO₂) thin films modified with different amounts of bismuth (Bi:TiO₂). The samples were synthesized combining a TiO₂ laser ablation plasma with a flux of vapor of bismuth produced by thermal evaporation. By varying the deposition rate of Bi it was possible to control the amount of Bi incorporated in the film and consequently the film properties. A detailed compositional, structural, and optical characterization by XPS, RBS, Raman spectroscopy, and UV–Vis spectrometry techniques is discussed. Photocatalytic response of the deposited thin films was studied through the degradation of a malachite green solution.     

On the industrial applications of MCRs: molecular diversity in drug discovery and generic drug synthesis

During the last decades, multicomponent chemistry has gained much attention in pharmaceutical research, especially in the context of lead finding and optimization. Here, in particular, the main advantages of multicomponent reactions (MCRs) like ease of automation and high diversity generation were utilized. In consequence of these beneficial properties, a plethora of new MCRs combined with appropriate classical reaction sequences have been published, the accessible chemical space was extended steadily. In the meantime, the desired high diversity became a challenge itself, because by now the systematic use of this huge and unmanageable space for drug discovery was limited by the lack of suitable computational tools. Therefore, this article provides an insight for the rational use of this enormous chemical space in drug discovery and generic drug synthesis. In this context, a short overview of the applied chemo informatics, necessary for the virtual screening of the biggest available chemical space, is given. Furthermore, some examples for recently developed multicomponent sequences are presented.     

Catalysis of nucleophilic aromatic substitutions in the 2,6,8-trisubstituted purines and application in the synthesis of combinatorial libraries

The following paper summarizes our work on compound libraries of 2,6,8-trisubstituted purines. This synthesis route on a polystyrene support begins with 2,6-dichloro purine making extensive use of catalysis. During the synthesis the polymer bound purines were brominated selectively on C8. The substitution reaction of C6-Cl by amines was found to be acid catalyzed. The substitution of C2-Cl by amines and aryls, as well as the substitution of a C8-Br by aryls, alkenyl and alkynyl groups can be catalyzed by transition metals. Under some bromination conditions novel selective oxidative transformations of 2-amino groups in 2,6-diamino purines have been found.     

Efficient library synthesis of imidazoles using a multicomponent reaction and microwave irradiation

Optimization of Radziszewski's four-component reaction employing a microwave-assisted protocol, led to a small library of 48 imidazoles with a success rate of 65% (conversion > 45%). All three diversity points of the four-component reaction were varied. Aromatic and aliphatic inputs were successfully implemented and mono-, di-, tri- and tetrasubstituted imidazoles with various substitution patterns were synthesized. Furthermore, unsymmetrical diketones could successfully be used which improved the intrinsic diversity of the method significantly. If the unsymmetrical diketone 1,2-phenylpropanedione (R¹ and R²) was used two regioisomers were formed. Depending on the type of amine (R⁴) and aldehyde (R³) applied, regioselectivity was modest to good. Based on these results, a reaction mechanism is proposed.     

Influence of the synthesis conditions of silicon nanodots in an industrial low pressure chemical vapor deposition reactor

Experiments conducted in an industrial tubular low pressure chemical vapor deposition (LPCVD) reactor have demonstrated the reproducibility and spatial uniformity of silicon nanodots (NDs) area density and mean radius. The wafer to wafer uniformity was satisfactory (density and radius standard deviations <10%) for the whole conditions tested except for low silane flow rates, high silane partial pressures and short run durations (<20 s). Original synthesis conditions have then been searched to reach both excellent wafer to wafer uniformities along the industrial load of wafers and high NDs densities. From previous results, it was deduced that the key was to markedly increase run duration in decreasing temperature and in increasing silane pressure. At 773 K, run durations as long as 180 and 240 s have thus allowed to reach NDs densities respectively equal to 9 × 10¹¹ and 6.5 × 10¹¹ NDs/cm² for the two highest silane pressures tested in the range 60-150 Pa.     

Plate-based diversity subset screening: an efficient paradigm for high throughput screening of a large screening file

The screening files of many large companies, including Pfizer, have grown considerably due to internal chemistry efforts, company mergers and acquisitions, external contracted synthesis, or compound purchase schemes. In order to screen the targets of interest in a cost-effective fashion, we devised an easy-to-assemble, plate-based diversity subset (PBDS) that represents almost the entire computed chemical space of the screening file whilst comprising only a fraction of the plates in the collection. In order to create this file, we developed new design principles for the quality assessment of screening plates: the Rule of 40 (Ro40) and a plate selection process that insured excellent coverage of both library chemistry and legacy chemistry space. This paper describes the rationale, design, construction, and performance of the PBDS, that has evolved into the standard paradigm for singleton (one compound per well) high-throughput screening in Pfizer since its introduction in 2006.     

Hole-doped semiconductor nanowire on top of an s-wave superconductor: a new and experimentally accessible system for Majorana fermions

Majorana fermions were envisioned by Majorana in 1935 to describe neutrinos. Recently, it has been shown that they can be realized even in a class of electron-doped semiconductors, on which ordinary s-wave superconductivity is proximity induced, provided the time reversal symmetry is broken by an external Zeeman field above a threshold. Here we show that in a hole-doped semiconductor nanowire the threshold Zeeman field for Majorana fermions can be very small for some magic values of the hole density. In contrast to the electron-doped systems, smaller Zeeman fields and much stronger spin-orbit coupling and effective mass of holes allow the hole-doped systems to support Majorana fermions in a parameter regime which is routinely realized in current experiments.     

Ring opening cross-metathesis on solid support: a combinatorial library synthesis of highly functionalized cyclopentanes

Ruthenium catalyzed ring opening cross-metathesis of resin-bound bicyclic alkenes with terminal aryl olefins was utilized for the construction of a combinatorial library containing highly functionalized cyclopentane derivatives. The technology described herein represents a convergent method for the diastereospecific synthesis of unique cyclopentane molecular scaffolds useful for exploratory medicinal chemistry. This revised version was published online in August 2006 with corrections to the Cover Date.     

Synthesis,characterization, and antimicrobial evaluation of a small library of ferrocene-containing acetoacetates and phenyl analogs: the discovery of a potent anticandidal agent

A library of 16 2-substituted methyl acetoacetates containing ferrocenyl or phenyl units was designed to disclose differences in the antimicrobial activity of ferrocene-containing compounds and their phenyl analogs. Two methyl acetoacetates, whose structures do not contain an aromatic nucleus, were also included in order to probe the inherent activity of the scaffold itself. The acetoacetates were synthesized (low-to-good yields) and fully characterized by spectral (MS, IR, UV–Vis, 1D and 2D NMR) and electrochemical (cyclic voltammetry) techniques. Single-crystal X-ray analysis has been performed for methyl 2-acetyl-2-(ferrocenylmethyl)-5-methylhex-4-enoate. All compounds have demonstrated in vitro antimicrobial activity against six bacterial (three Gram-positive and three Gram-negative) and two fungal strains with minimal inhibitory concentration values of 0.0050–20.6  \(\upmu \hbox {mol mL}^{-1}\) . The most active compound was 2-acetyl-2-(ferrocenylmethyl)-4-methylpent-4-enoate whose activity was comparable to that of nystatin against the yeast Candida albicans. Agglomerative hierarchical clustering statistical analysis of the antimicrobial assay data demonstrated that ferrocene-containing compounds have statistically different and greater antimicrobial activity when compared to their phenyl analogs.     

Electronic and software systems of an automated portable static mass spectrometer

Technical Physics - The electronic systems of a small high-sensitivity static mass spectrometer and software and hardware tools, which allow one to determine trace concentrations of gases and...     

Parallel and automated library synthesis of 2-long alkyl chain benzoazoles and azole[4,5-<Emphasis Type="BoldItalic">b</Emphasis>]pyridines under microwave irradiation

Summary A versatile route to 40-membered library of 2-long alkyl chain substituted benzoazoles (1 and 2) and azole[4,5-b]pyridines (3 and 4) via microwave-assisted combinatorial synthesis was developed. The reactions were carried out in both monomode and multimode microwave oven. With the latter, all reactions were performed in high-throughput experimental settings consisting of an 8×5 combinatorial library designed to synthesize 40 compounds. Each step, from the addition of reagents to the recovery of final products, was automated. The microwave-assisted N-long chain alkylation reactions of 2-alkyl-1H-benzimidazole (1) and 2-alkyl-1H-benzimidazole[4,5-b] pyridines (3) were also studied.