Combinatorial chemistry: oh what a decade or two can do

High-Throughput Purification in Drug Discovery: Scaling New Heights of Productivity

With the "low hanging fruit" of early drug discovery gone, pharmaceutical companies are increasingly turning to developing high-throughput synthetic platforms capable of greatly shortening the design-make-test cycle of new drugs. Purification has long been considered the bottleneck of this procedure; however, new technologies and systems are now being integrated into these high-throughput synthetic workflows, providing compounds of high purity capable of being used directly in biological screening.

Deep Eutectic Solvent (DES)-Mediated One-Pot Multicomponent Green Approach for Naphthalimide-Centered Acridine-1,8-dione Derivatives and Their Photophysical Properties

An efficient and green methodology to assemble various functionalized naphthalimide-centered acridine-1,8-dione derivatives involving a one-pot multicomponent protocol has successfully been developed. Herein, a variety of aromatic aldehydes, 1,3-diketones, 1,8-naphthanoic anhydride, and hydrazine hydrate have been condensed under a reusable, inexpensive, and biodegradable deep eutectic solvent (DES) of N,N'-dimethyl urea and l-(+)-tartaric acid to obtain the desired targets under operationally mild reaction conditions with outstanding conversions. Strikingly, in this strategy, the DES plays a dual role of a catalyst and solvent and was recycled efficiently in four consecutive runs with no substantial drop in the yield of the desired product. Interestingly, the easy recovery and high reusability of the DES make this simple yet efficient protocol environmentally desirable. Moreover, the preliminary photophysical properties of thus-prepared valuable molecules have also been investigated by ultraviolet-visible (UV-vis) and fluorescence spectroscopy.

Mo@GAA-Fe3O4 MNPs: a highly efficient and environmentally friendly heterogeneous magnetic nanocatalyst for the synthesis of polyhydroquinoline derivatives

Polyhydroquinolines were efficiently obtained from a sequential four-component reaction between dimedone or 1,3-cyclohexandione, ethyl acetoacetate, or methyl acetoacetate as a β-ketoester, aldehydes, and ammonium acetate, under the catalysis of Mo@GAA-Fe3O4 MNPs as a green, effective, recyclable, and environmentally friendly nanocatalyst. Due to its magnetic nature the prepared catalyst can be easily separated from the reaction mixture by an external magnet and reused several times without significant changes in catalytic activity and reaction efficiency. The catalyst was characterized using energy dispersive X-ray spectroscopy (EDX), X-ray diffraction (XRD), thermogravimetric analysis (TGA), Fourier transform infrared spectroscopy (FTIR), vibrating sample magnetometry (VSM), scanning electron microscopy (SEM), and transmission electron microscopy (TEM).

A review on multicomponent reactions catalysed by zero-dimensional/one-dimensional titanium dioxide (TiO2) nanomaterials: Promising green methodologies in organic chemistry

Heterogeneous catalysis has currently become an emerging tool for the design and development of sustainable manufacturing processes in order to obtain advanced intermediates, fine chemicals, and bioactive molecules. This field has been considered efficient and eco-friendly, as it investigates the utilization of non-hazardous metals for atom-economical reactions. Nanomaterials have created a significant impact on scientific and engineering advancements due to their tunable properties with superior performance over their massive counterparts. Due to the increased demand for heterogeneous catalysts in industries and academia, different transition metal oxides have been made into substantial nanostructures. Among them, titanium dioxide (TiO₂) nanomaterials have received more attention on account of their chemical stability, low cost, dual acid-base properties, good oxidation rate and refractive index. Different modifications of TiO₂ extend their applications as active catalysts or catalyst supports in diverse catalytic processes, such as photovoltaics, lithium batteries, pigments and others. One-dimensional (1-D) TiO₂ nanostructures such as nanotubes, nanowires and nanorods have achieved greater importance owing to the unique properties of improved porosity, decreased inter-crystalline contacts, large surface-to-volume ratio, superior dispersibility, amplified accessibility of hydroxyl (-OH) groups and presence of good concentrations of Brønsted/Lewis acid sites. Since the discovery, 1-D TiO₂ nanostructures have served good photocatalytic applications, but were less explored in organic transformations. While many articles and reviews have covered the applications of 0-D and 1-D TiO₂ nanostructured materials (NSMs) in photoelectrochemical reactions and solar cells, there are other interesting applications of these as well. In contrast to the conventional multi-step processes that utilise the stepwise formation of individual bonds, one-pot conversions based on multicomponent reactions (MCRs) have acquired much significance in contemporary organic synthesis. This paper presents a critical review on history, classification, design and synthetic utility of titania-based nanostructures, which could be used as robust solid-acid catalysts and catalyst supports for MCRs. Further, to put ideas into perspective, the introduction and applications of MCRs for various organic transformations have been discussed.

Introduction of Succinimide as A Green and Sustainable Organo-Catalyst for the Synthesis of Arylidene Malononitrile and Tetrahydrobenzo[b] pyran Derivatives

AIM AND OBJECTIVE

In this work, we tried to introduce a non-toxic and stable organic compound named succinimide as a green and efficient organo-catalyst for the promotion of the synthesis of arylidene malononitrile and tetrahydrobenzo[b]pyran derivatives. Using this method led to a clean procedure to achieve these types of bioactive compounds without a specific purification step. The rate and yield of the reactions were excellent, and also succinimide showed acceptable reusability as the catalyst.

MATERIALS AND METHODS

In a 25 mL round-bottom flask, [A: a mixture of aromatic aldehyde (1 mmol), malononitrile (1.1 mmol) and B: a mixture of aromatic aldehyde (1.0 mmol), malononitrile (1.1 mmol)] and succinimide (0.2 mmol) in H2O/ EtOH [5 mL (1:1)] was stirred at 80 °C for an appropriate time. After completion of the reaction, which was monitored by TLC [n-hexane-EtOAc (7:3)], the mixture was cooled to room temperature, and the solid product was filtered, washed several times with cold distilled water to obtain the corresponding pure product.

RESULTS

After the optimization of the conditions and amount of the catalyst, a series of aromatic aldehydes containing either-electron-donating or electron-withdrawing substituents were successfully used for both of the reactions. The reactions rates and yields under the selected conditions were excellent. The nature and electronic properties of the substituents had no obvious effect on the rate and yield of the reaction. Meanwhile, the catalyst showed acceptable reusability for these two reactions.

CONCLUSION

In this work, we have introduced Succinimide as a green and safe organo-catalyst for the efficient synthesis arylidene malononitrile and tetrahydrobenzo[b]pyran derivatives. The results showed that the catalyst had excellent efficiency in green aqueous media and also the reusability of the catalyst was good.

Enzymatic Ugi Reaction with Amines and Cyclic Imines

The application of the Ugi reaction to the construction of new peptide scaffolds is an important goal of organic chemistry. To date, there are no examples of the Ugi reaction being performed with a cyclic imine and amine simultaneously. The application of 2-substituted cyclic imines in an enzymatic three-component Ugi-type reaction provides an elegant and attractive synthesis of substituted pyrrolidine and piperidine derivatives in up to 60 % yield. Results on studies of the selection of an enzyme, amount of water, and solvent used in a novel three-component Ugi reaction and the limitations thereof are reported herein. The presented methodology exploiting enzyme promiscuity in the multicomponent reaction fulfills the requirements associated with green chemistry. Several methods, such as isotope labeling and enzyme inhibition, were used to probe the possible mechanism of this complex synthesis. This research is the first example of an enzyme-catalyzed Ugi-type reaction with an imine, amine, and isocyanide.

Getting the most out of PubChem for virtual screening

INTRODUCTION

With the emergence of the 'big data' era, the biomedical research community has great interest in exploiting publicly available chemical information for drug discovery. PubChem is an example of public databases that provide a large amount of chemical information free of charge.

AREAS COVERED

This article provides an overview of how PubChem's data, tools, and services can be used for virtual screening and reviews recent publications that discuss important aspects of exploiting PubChem for drug discovery.

EXPERT OPINION

PubChem offers comprehensive chemical information useful for drug discovery. It also provides multiple programmatic access routes, which are essential to build automated virtual screening pipelines that exploit PubChem data. In addition, PubChemRDF allows users to download PubChem data and load them into a local computing facility, facilitating data integration between PubChem and other resources. PubChem resources have been used in many studies for developing bioactivity and toxicity prediction models, discovering polypharmacologic (multi-target) ligands, and identifying new macromolecule targets of compounds (for drug-repurposing or off-target side effect prediction). These studies demonstrate the usefulness of PubChem as a key resource for computer-aided drug discovery and related area.

A peptide & peptide nucleic acid synthesis technology for transporter molecules and theranostics--the SPPS

Advances in imaging diagnostics using magnetic resonance tomography (MRT), positron emission tomography (PET) and fluorescence imaging including near infrared (NIR) imaging methods are facilitated by constant improvement of the concepts of peptide synthesis. Feasible patient-specific theranostic platforms in the personalized medicine are particularly dependent on efficient and clinically applicable peptide constructs. The role of peptides in the interrelations between the structure and function of proteins is widely investigated, especially by using computer-assisted methods. Nowadays the solid phase synthesis (SPPS) chemistry emerges as a key technology and is considered as a promising methodology to design peptides for the investigation of molecular pharmacological processes at the transcriptional level. SPPS syntheses could be carried out in core facilities producing peptides for large-scale scientific implementations as presented here.

PubChem3D: Biologically relevant 3-D similarity

Background

The use of 3-D similarity techniques in the analysis of biological data and virtual screening is pervasive, but what is a biologically meaningful 3-D similarity value? Can one find statistically significant separation between "active/active" and "active/inactive" spaces? These questions are explored using 734,486 biologically tested chemical structures, 1,389 biological assay data sets, and six different 3-D similarity types utilized by PubChem analysis tools.

Results

The similarity value distributions of 269.7 billion unique conformer pairs from 734,486 biologically tested compounds (all-against-all) from PubChem were utilized to help work towards an answer to the question: what is a biologically meaningful 3-D similarity score? The average and standard deviation for the six similarity measures ST^ST-opt, CT^ST-opt, ComboT^ST-opt, ST^CT-opt, CT^CT-opt, and ComboT^CT-opt were 0.54 ± 0.10, 0.07 ± 0.05, 0.62 ± 0.13, 0.41 ± 0.11, 0.18 ± 0.06, and 0.59 ± 0.14, respectively. Considering that this random distribution of biologically tested compounds was constructed using a single theoretical conformer per compound (the "default" conformer provided by PubChem), further study may be necessary using multiple diverse conformers per compound; however, given the breadth of the compound set, the single conformer per compound results may still apply to the case of multi-conformer per compound 3-D similarity value distributions. As such, this work is a critical step, covering a very wide corpus of chemical structures and biological assays, creating a statistical framework to build upon.

The second part of this study explored the question of whether it was possible to realize a statistically meaningful 3-D similarity value separation between reputed biological assay "inactives" and "actives". Using the terminology of noninactive-noninactive (NN) pairs and the noninactive-inactive (NI) pairs to represent comparison of the "active/active" and "active/inactive" spaces, respectively, each of the 1,389 biological assays was examined by their 3-D similarity score differences between the NN and NI pairs and analyzed across all assays and by assay category types. While a consistent trend of separation was observed, this result was not statistically unambiguous after considering the respective standard deviations. While not all "actives" in a biological assay are amenable to this type of analysis, e.g., due to different mechanisms of action or binding configurations, the ambiguous separation may also be due to employing a single conformer per compound in this study. With that said, there were a subset of biological assays where a clear separation between the NN and NI pairs found. In addition, use of combo Tanimoto (ComboT) alone, independent of superposition optimization type, appears to be the most efficient 3-D score type in identifying these cases.

Conclusion

This study provides a statistical guideline for analyzing biological assay data in terms of 3-D similarity and PubChem structure-activity analysis tools. When using a single conformer per compound, a relatively small number of assays appear to be able to separate "active/active" space from "active/inactive" space.

e-LEA3D: a computational-aided drug design web server

e-LEA3D web server integrates three complementary tools to perform computer-aided drug design based on molecular fragments. In drug discovery projects, there is a considerable interest in identifying novel and diverse molecular scaffolds to enhance chances of success. The de novo drug design tool is used to invent new ligands to optimize a user-specified scoring function. The composite scoring function includes both structure- and ligand-based evaluations. The de novo approach is an alternative to a blind virtual screening of large compound collections. A heuristic based on a genetic algorithm rapidly finds which fragments or combination of fragments fit a QSAR model or the binding site of a protein. While the approach is ideally suited for scaffold-hopping, this module also allows a scan for possible substituents to a user-specified scaffold. The second tool offers a traditional virtual screening and filtering of an uploaded library of compounds. The third module addresses the combinatorial library design that is based on a user-drawn scaffold and reactants coming, for example, from a chemical supplier. The e-LEA3D server is available at: http://bioinfo.ipmc.cnrs.fr/lea.html.