Design and Synthesis of Eugenol Derivatives Bearing a 1,2,3-Triazole Moiety for Papaya Protection against Colletotrichum gloeosporioides.

A series of 19 novel eugenol derivatives containing a 1,2,3-triazole moiety was synthesized via a two-step process, with the key step being a copper(I)-catalyzed azide-alkyne cycloaddition reaction. The compounds were assessed for their antifungal activities against Colletotrichum gloeosporioides, the causative agent of papaya anthracnose. Triazoles 2k, 2m, 2l, and 2n, at 100 ppm, were the most effective, reducing mycelial growth by 88.3, 85.5, 82.4, and 81.4%, respectively. Molecular docking calculations allowed us to elucidate the binding mode of these derivatives in the catalytic pocket of C. gloeosporioides CYP51. The best-docked compounds bind closely to the heme cofactor and within the channel access of the lanosterol (LAN) substrate, with crucial interactions involving residues Tyr102, Ile355, Met485, and Phe486. From such studies, the antifungal activity is likely attributed to the prevention of substrate LAN entry by the 1,2,3-triazole derivatives. The triazoles derived from natural eugenol represent a novel lead in the search for environmentally safe agents for controlling C. gloeosporioides.

Leishmanicidal activity and 4D quantitative structure-activity relationship and molecular docking studies of vanillin-containing 1,2,3-triazole derivatives.

Aim: The assessment of the antileishmanial potential of 22 vanillin-containing 1,2,3-triazole derivatives against Leishmania braziliensis is reported. Materials & methods: Initial screening was performed against the parasite promastigote form. The most active compound, 4b, targeted parasites within amastigotes (IC50 = 4.2 ± 1.0 µmol l-1), presenting low cytotoxicity and a selective index value of 39. 4D quantitative structure-activity relationship and molecular docking studies provided insights into structure-activity and biological effects. Conclusion: A vanillin derivative with significant antileishmanial activity was identified. Enhanced activity was linked to increased electrostatic and Van der Waals interactions near the benzyl ring of the derivatives. Molecular docking indicated the inhibition of the Leishmania amazonensis sterol 14α-demethylase, using Leishmania infantum sterol 14α-demethylase as a model, without affecting the human isoform. Inhibition was active site competition with lanosterol.

Synthesis of vanillin derivatives with 1,2,3-triazole fragments and evaluation of their fungicide and fungistatic activities.

Vanillin is the main component of natural vanilla extract and is responsible for its flavoring properties. Besides its well-known applications as an additive in food and cosmetics, it has also been reported that vanillin can inhibit fungi of clinical interest, such as Candida spp., Cryptococcus spp., Aspergillus spp., as well as dermatophytes. Thus, the present work approaches the synthesis of a series of vanillin derivatives with 1,2,3-triazole fragments and the evaluation of their antifungal activities against Candida albicans, Candida glabrata, Candida parapsilosis, Candida tropicalis, Cryptococcus neoformans, Cryptococcus gattii, Trichophyton rubrum, and Trichophyton interdigitale strains. Twenty-two vanillin derivatives were obtained, with yields in the range of 60%-91%, from copper(I)-catalyzed alkyne-azide cycloaddition (CuAAC) click reaction between two terminal alkynes prepared from vanillin and different benzyl azides. In general, the evaluated compounds showed moderate activity against the microorganisms tested, with minimum inhibitory concentration (MIC) values ranging from 32 to >512 µg mL-1 . Except for compound 3b against the C. gattii R265 strain, all vanillin derivatives showed fungicidal activity for the yeasts tested. The predicted physicochemical and ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties for the compounds indicated favorable profiles for drug development. In addition, a four-dimensional structure-activity relationship (4D-SAR) analysis was carried out and provided useful insights concerning the structures of the compounds and their biological profile. Finally, molecular docking calculations showed that all compounds bind favorably at the lanosterol 14α-demethylase enzyme active site with binding energies ranging from -9.1 to -12.2 kcal/mol.

Quantitative NMR Interpretation without Reference.

As has been documented numerous times over the years, nuclear magnetic resonance (NMR) experiments are intrinsically quantitative. Still, quantitative NMR methods have not been widely adopted or largely introduced into pharmacopoeias. Here, we describe the quantitative interpretation of the 1D proton NMR experiment using only absolute signal intensities with the variation of common experimental parameters and their application.

Sampling CASE Application for the Quality Control of Published Natural Product Structures.

Structure elucidation with NMR correlation data is dicey, as there is no way to tell how ambiguous the data set is and how reliably it will define a constitution. Many different software tools for computer assisted structure elucidation (CASE) have become available over the past decades, all of which could ensure a better quality of the elucidation process, but their use is still not common. Since 2011, WebCocon has integrated the possibility to generate theoretical NMR correlation data, starting from an existing structural proposal, allowing this theoretical data then to be used for CASE. Now, WebCocon can also read the recently presented NMReDATA format, allowing for uncomplicated access to CASE with experimental data. With these capabilities, WebCocon presents itself as an easily accessible Web-Tool for the quality control of proposed new natural products. Results of this application to several molecules from literature are shown and demonstrate how CASE can contribute to improve the reliability of Structure elucidation with NMR correlation data.

Incorporation of 4J-HMBC and NOE Data into Computer-Assisted Structure Elucidation with WebCocon.

Over the past decades, different software programs have been developed for the Computer-Assisted Structure Elucidation (CASE) with NMR data using with various approaches. WebCocon is one of them that has been continuously improved over the past 20 years. Here, we present the inclusion of 4JCH correlations (4J-HMBC) in the HMBC interpretation of Cocon and NOE data in WebCocon. The 4J-HMBC data is used during the structure generation process, while the NOE data is used in post-processing of the results. The marine natural product oxocyclostylidol was selected to demonstrate WebCocon's enhanced HMBC data processing capabilities. A systematic study of the 4JCH correlations of oxocyclostylidol was performed. The application of NOEs in CASE is demonstrated using the NOE correlations of the diterpene pyrone asperginol A known from the literature. As a result, we obtained a conformation that corresponds very well to the existing X-ray structure.

NMReDATA: Tools and applications.

The nuclear magnetic resonance extracted data (NMReDATA) format has been proposed as a way to store, exchange, and disseminate nuclear magnetic resonance (NMR) data and physical and chemical metadata of chemical compounds. In this paper, we report on analytical workflows that take advantage of the uniform and standardized NMReDATA format. We also give access to a repository of sample data, which can serve for validating software packages that encode or decode files in NMReDATA format.

Two new usnic acid derivatives from the endophytic fungus Mycosphaerella sp.

The endophytic fungus Mycosphaerella sp. (UFMGCB2032) was isolated from the healthy leaves of Eugenia bimarginata, a plant from the Brazilian savanna. Two novel usnic acid derivatives, mycousfuranine (1) and mycousnicdiol (2), were isolated from the ethyl acetate extract, and their structure was elucidated by NMR and MS analyses. Compounds 1 and 2 exhibited moderate antifungal activities against Cryptococcus neoformans and Cryptococcus gattii, each with minimum inhibitory concentration values of 50.0 µg/mL and 250.0 µg/mL, respectively.

Statistical filtering for NMR based structure generation.

The constitutional assignment of natural products by NMR spectroscopy is usually based on 2D NMR experiments like COSY, HSQC, and HMBC. The difficulty of a structure elucidation problem depends more on the type of the investigated molecule than on its size. Saturated compounds can usually be assigned unambiguously by hand using only COSY and 13C-HMBC data, whereas condensed heterocycles are problematic due to their lack of protons that could show interatomic connectivities. Different computer programs were developed to aid in the structural assignment process, one of them COCON. In the case of unsaturated and substituted molecules structure generators frequently will generate a very large number of possible solutions. This article presents a "statistical filter" for the reduction of the number of results. The filter works by generating 3D conformations using smi23d, a simple MD approach. All molecules for which the generation of constitutional restraints failed were eliminated from the result set. Some structural elements removed by the statistical filter were analyzed and checked against Beilstein. The automatic removal of molecules for which no MD parameter set could be created was included into WEBCOCON. The effect of this filter varies in dependence of the NMR data set used, but in no case the correct constitution was removed from the resulting set.

Theoretical NMR correlations based Structure Discussion.

The constitutional assignment of natural products by NMR spectroscopy is usually based on 2D NMR experiments like COSY, HSQC, and HMBC. The actual difficulty of the structure elucidation problem depends more on the type of the investigated molecule than on its size. The moment HMBC data is involved in the process or a large number of heteroatoms is present, a possibility of multiple solutions fitting the same data set exists. A structure elucidation software can be used to find such alternative constitutional assignments and help in the discussion in order to find the correct solution. But this is rarely done. This article describes the use of theoretical NMR correlation data in the structure elucidation process with WEBCOCON, not for the initial constitutional assignments, but to define how well a suggested molecule could have been described by NMR correlation data. The results of this analysis can be used to decide on further steps needed to assure the correctness of the structural assignment. As first step the analysis of the deviation of carbon chemical shifts is performed, comparing chemical shifts predicted for each possible solution with the experimental data. The application of this technique to three well known compounds is shown. Using NMR correlation data alone for the description of the constitutions is not always enough, even when including 13C chemical shift prediction.

TAR-RNA recognition by a novel cyclic aminoglycoside analogue.

The formation of the Tat-protein/TAR-RNA complex is a crucial step in the regulation of human immunodeficiency virus (HIV)-gene expression. To obtain full-length viral transcripts the Tat/TAR complex has to recruit the positive transcription elongation factor complex (P-EFTb), which interacts with TAR through its cyclin T1 (CycT1) component. Mutational studies identified the TAR hexanucleotide loop as a crucial region for contacting CycT1. Interfering with the interaction between the Tat/CycT1 complex and the TAR-RNA is an attractive strategy for the design of anti-HIV drugs. Positively charged molecules, like aminoglycosides or peptidomimetics, bind the TAR-RNA, disrupting the Tat/TAR complex. Here, we investigate the complex between the HIV-2 TAR-RNA and a neooligoaminodeoxysaccharide by NMR spectroscopy. In contrast to other aminoglycosides, this novel aminoglycoside analogue contacts simultaneously the bulge residues required for Tat binding and the A35 residue of the hexanucleotide loop. Upon complex formation, the loop region undergoes profound conformational changes. The novel binding mode, together with the easy accessibility of derivatives for the neooligoaminodeoxysaccharide, could open the way to the design of a new class of TAR-RNA binders, which simultaneously inhibit the formation of both the Tat/TAR binary complex and the Tat/TAR/CycT1 ternary complex by obstructing both the bulge and loop regions of the RNA.

Two new chiral EDTA-based metal chelates for weak alignment of proteins in solution.

[structure: see text] A short synthesis of EDTA-based metal chelates that can be attached to the cysteine residue of a protein via a disulfide bond is described. The complexes were used after coordination of lanthanides to align trigger factor and apo-calmodulin in solution to yield residual dipolar couplings and pseudocontact shifts. Alignment tensors for the new tags are linearly independent compared to those of previously published tags.

The NMR structure of the sensory domain of the membranous two-component fumarate sensor (histidine protein kinase) DcuS of Escherichia coli.

The structure of the water-soluble, periplasmic domain of the fumarate sensor DcuS (DcuS-pd) has been determined by NMR spectroscopy in solution. DcuS is a prototype for a sensory histidine kinase with transmembrane signal transfer. DcuS belongs to the CitA family of sensors that are specific for sensing di- and tricarboxylates. The periplasmic domain is folded autonomously and shows helices at the N and the C terminus, suggesting direct linking or connection to helices in the two transmembrane regions. The structure constitutes a novel fold. The nearest structural neighbor is the Per-Arnt-Sim domain of the photoactive yellow protein that binds small molecules covalently. Residues Arg107, His110, and Arg147 are essential for fumarate sensing and are found clustered together. The structure constitutes the first periplasmic domain of a two component sensory system and is distinctly different from the aspartate sensory domain of the Tar chemotaxis sensor.

Validation of structural proposals by substructure analysis and 13C NMR chemical shift prediction.

The 2D NMR-guided computer program COCON can be extremely valuable for the constitutional analysis of unknown compounds, if its results are evaluated by neural network-assisted 13C NMR chemical shift and substructure analyses. As instructive examples, data sets of four differently complex marine natural products were thoroughly investigated. As a significant step towards a true automated structure elucidation, it is shown that the primary COCON output can be safely diminished to less than 1% of its original size without losing the correct structural proposal.