An Outline of the Latest Crystallographic Studies on Inhibitor-Enzyme Complexes for the Design and Development of New Therapeutics against Tuberculosis

The elucidation of the structure of enzymes and their complexes with ligands continues to provide invaluable insights for the development of drugs against many diseases, including bacterial infections. After nearly three decades since the World Health Organization’s (WHO) declaration of tuberculosis (TB) as a global health emergency, Mycobacterium tuberculosis (Mtb) continues to claim millions of lives, remaining among the leading causes of death worldwide. In the last years, several efforts have been devoted to shortening and improving treatment outcomes, and to overcoming the increasing resistance phenomenon. The structural elucidation of enzyme-ligand complexes is fundamental to identify hot-spots, define possible interaction sites, and elaborate strategies to develop optimized molecules with high affinity. This review offers a critical and comprehensive overview of the most recent structural information on traditional and emerging mycobacterial enzymatic targets. A selection of more than twenty enzymes is here discussed, with a special emphasis on the analysis of their binding sites, the definition of the structure–activity relationships (SARs) of their inhibitors, and the study of their main intermolecular interactions. This work corroborates the potential of structural studies, substantiating their relevance in future anti-mycobacterial drug discovery and development efforts.     

An Intramolecular Hydroaminomethylation-Based Approach to Pyrrolizidine Alkaloids under Microwave-Assisted Heating

A general method for the synthesis of pyrrolizidine derivatives using an intramolecular hydroaminomethylation protocol (HAM) under microwave (MW) dielectric heating is reported. Starting from a 3,4-bis(benzyloxy)-2-[(benzyloxy)methyl]-5-vinylpyrrolidine, MW-assisted intramolecular HAM in the presence of gaseous H2 and CO gave the natural alkaloid hyacinthacine A2 protected as benzyl ether. The same approach gave a lentiginosine analogue starting from the corresponding vinyl N-hydroxypyrrolidine. The nature of the reaction products and the yields were strongly influenced by the relative stereochemistry of the starting pyrrolidines, as well as by the catalyst/ligand employed. The use of ethanol as a solvent provides environmentally friendly conditions, while the ligand/catalyst system can be recovered by separating the alkaloid product with an SCX column and recycling the ethanolic solution. HAM worked up to three times with the recycled catalyst solution without any significant impact on yield.     

The role of alkane dithiols in controlling polymer crystallization in small band gap polymer:Fullerene solar cells

The effect of the addition of 1,8‐octanedithiol (ODT) during processing on the microstructure of blend films of poly[2,6‐(4,4‐bis‐(2‐ethylhexyl)‐4H‐cyclopenta[2,1‐b;3,4‐b′]dithiophene)‐alt‐4,7(2,1,3‐benzothiadiazole)] (PCPDTBT) and [6,6]‐phenyl‐C₇₁ butyric acid methyl ester ([70]PCBM) is studied. Grazing incidence X‐ray diffraction and absorption spectroscopy show that the crystalline order of PCPDTBT increases when ODT is introduced in the solution phase either to neat polymer systems or to blends with [70]PCBM. The increased crystalline order is accompanied by less dispersive hole transport in the polymer, and leads to a more efficient formation of a percolating fullerene network within the blend. This contributes to an increase in photocurrent generation. However, the bimolecular recombination rate as determined from photovoltage transients increases upon addition of ODT, limiting the power conversion efficiency to values well below those expected from the energy levels of PCPDTBT. We propose some explanations for this increase in bimolecular recombination, based also on variable angle spectroscopic ellipsometry measurements. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011     

Glycoside and peptide clustering around the octasilsesquioxane scaffold via photoinduced free-radical thiol-ene coupling. The observation of a striking glycoside cluster effect

Two series of multivalent octasilsesquioxane glyco- and peptido-conjugates were synthesized using the photoinduced free-radical thiol-ene coupling (TEC). The first series was obtained by coupling C-glycosylpropyl thiols and cysteine containing peptides with the known octavinyl octasilsesquioxane while the second series was obtained by reacting glycosyl thiols with a new octasilsesquioxane derivative displaying eight PEGylated chains functionalized with terminal allyl groups. The evaluation of the binding properties of mannoside and glucoside clusters toward Concanavalin A by Enzyme-Linked Lectin Assay (ELLA) revealed a modest glycoside cluster effect. On the other hand, the PEGylated POSS-based glycocluster featuring eight N-acetyl-glucosamine residues showed high affinity toward Wheat Germ Agglutinin to give a measured IC(50) at 3 nM. The calculated relative potency per number of sugar unit (rp/n) was superior to a value of 10(6), thus revealing the occurrence of a striking glycoside cluster effect.     

Allergen microarrays on high-sensitivity silicon slides

We have recently introduced a silicon substrate for high-sensitivity microarrays, coated with a functional polymer named copoly(DMA-NAS-MAPS). The silicon dioxide thickness has been optimized to produce a fluorescence intensification due to the optical constructive interference between the incident and reflected lights of the fluorescent radiation. The polymeric coating efficiently suppresses aspecific interaction, making the low background a distinctive feature of these slides. Here, we used the new silicon microarray substrate for allergy diagnosis, in the detection of specific IgE in serum samples of subjects with sensitizations to inhalant allergens. We compared the performance of silicon versus glass substrates. Reproducibility data were measured. Moreover, receiver-operating characteristic (ROC) curves were plotted to discriminate between the allergy and no allergy status in 30 well-characterized serum samples. We found that reproducibility of the microarray on glass supports was not different from available data on allergen arrays, whereas the reproducibility on the silicon substrate was consistently better than on glass. Moreover, silicon significantly enhanced the performance of the allergen microarray as compared to glass in accurately identifying allergic patients spanning a wide range of specific IgE titers to the considered allergens.     

Free-radical hydrothiolation of glycals: a thiol-ene-based synthesis of S-disaccharides

A method for the synthesis of a new family of 1-deoxy S-disaccharides has been established via free-radical hydrothiolation of glycals by sugar thiols (thiol-ene coupling). The photoinduced coupling between four tri-O-acetyl-d-glycals and three different sugar thiols reveals that the reaction efficiency and stereoselectivity are highly dependent on the stereochemistry of the OAc groups at C3 and C4 of the glycal.     

Riboswitches Based on Kissing Complexes for the Detection of Small Ligands

Biosensors derived from aptamers were designed for which folding into a hairpin shape is triggered by binding of the cognate ligand. These aptamers (termed aptaswitches) thus switch between folded and unfolded states in the presence and absence of the ligand, respectively. The apical loop of the folded aptaswitch is recognized by a second hairpin called the aptakiss through loop–loop or kissing interactions, whereas the aptakiss does not bind the unfolded aptaswitch. Therefore, the formation of a kissing complex signals the presence of the ligand. Aptaswitches were designed that enable the detection of GTP and adenosine in a specific and quantitative manner by surface plasmon resonance when using a grafted aptakiss or in solution by anisotropy measurement with a fluorescently labeled aptakiss. This approach is generic and can potentially be extended to the detection of any molecule for which hairpin aptamers have been identified, as long as the apical loop is not involved in ligand binding.