Sugar-Derived Amidines and Congeners: Structures, Glycosidase Inhibition and Applications

Glycosidases, the enzymes responsible for the breakdown of glycoconjugates including di-, oligo- and polysaccharides are ubiquitous through all kingdoms of life. The extreme chemical stability of the glycosidic bond combined with the catalytic rates achieved by glycosidases makes them among the most proficient of all enzymes. Given their multitude of roles in vivo, inhibition of these enzymes is highly attractive with potential in the treatment of a vast array of pathologies ranging from lysosomal storage and diabetes to viral infections. Therefore great efforts have been invested in the last three decades to design and synthesize inhibitors of glycosidases leading to a number of drugs currently on the market. Amongst the vast array of structures that have been disclosed, sugars incorporating an amidine moiety have been the focus of many research groups around the world because of their glycosidase transition state-like structure. In this review we report and discuss the structure, the inhibition profile and the use of these molecules including related structural congeners as transition state analogs.

Efficient biosynthesis of nucleoside cytokinin angustmycin A containing an unusual sugar system

Angustmycin A has anti-mycobacterial and cytokinin activities, and contains an intriguing structure in which an unusual sugar with C5′-C6′ dehydration is linked to adenine via an N-glycosidic bond. However, the logic underlying the biosynthesis of this molecule has long remained obscure. Here, we address angustmycin A biosynthesis by the full deciphering of its pathway. We demonstrate that AgmD, C, A, E, and B function as d-allulose 6-phosphate 3-epimerase, d-allulose 6-phosphate pyrophosphokinase, adenine phosphoallulosyltransferase, phosphoribohydrolase, and phosphatase, respectively, and that these collaboratively catalyze the relay reactions to biosynthesize angustmycin C. Additionally, we provide evidence that AgmF is a noncanonical dehydratase for the final step to angustmycin A via a self-sufficient strategy for cofactor recycling. Finally, we have reconstituted the entire six-enzyme pathway in vitro and in E. coli leading to angustmycin A production. These results expand the enzymatic repertoire regarding natural product biosynthesis, and also open the way for rational and rapid discovery of other angustmycin related antibiotics.

High-temperature decomposition of amorphous and crystalline cellulose: reactive molecular simulations

We study the thermal decomposition of cellulose using molecular simulations based on the ReaxFF reactive force field. Our analysis focuses on the mechanism and kinetics of chain scission, and their sensitivity on the condensed phase environment. For this purpose, we simulate the thermal decomposition of amorphous and partially crystalline cellulose at various heating rates. We find that thermal degradation begins with depolymerization via glycosidic bond cleavage, and that the order of events corresponds to a randomly initiated chain reaction. Depolymerization is followed by ring fragmentation reactions that lead to the formation of a number of light oxygenates. Water is formed mainly in intermolecular dehydration reactions at a later stage. The reaction rate of glycosidic bond cleavage follows a sigmoidal reaction model, with an apparent activation energy of 166 ± 4 kJ/mol. Neither the condensed phase environment nor the heating programme have appreciable effects on the reactions. We make several observations that are compatible with mechanisms proposed for cellulose fast pyrolysis. However, due to the absence of anhydrosugar forming reactions, the simulations offer limited insight for conditions of industrial interest. It remains unclear whether this is a natural consequence of the reaction conditions, or a shortcoming of the force field or its parameter set. Graphic abstract

A self-immolative linker for heparanase activatable probe

Substrate-based probes utilize known substrate specificity parameters to create a probe that can be activated by a target enzyme. In developing probes for heparanase, an endo-beta-glucuronidase, we previously reported that small, inactive substrate-based probes could be electronically tuned by incorporating electron-withdrawing atoms on the aromatic aglycone fluorophore, ortho- to the cleaved glycosidic bond. However, the installation of electron-withdrawing groups directly onto established fluorophores or other reporters complicates the synthesis of new heparanase probes. In this work we report a new design strategy to expand the toolkit of heparanase imaging probes, in which the installation of an electronically tuned benzyl alcohol linker restored the activity of a previously inactive heparanase probe using 4-methylumbelliferone as the fluorescent reporter, suggesting such a linker can provide a scaffold for facile development of activatable heparanase probes bearing a variety of imaging moieties.

Structural elements determining the transglycosylating activity of glycoside hydrolase family 57 glycogen branching enzymes

Glycoside hydrolase family 57 glycogen branching enzymes (GH57GBE) catalyze the formation of an α-1,6 glycosidic bond between α-1,4 linked glucooliogosaccharides. As an atypical family, a limited number of GH57GBEs have been biochemically characterized so far. This study aimed at acquiring a better understanding of the GH57GBE family by a systematic sequence-based bioinformatics analysis of almost 2,500 gene sequences and determining the branching activity of several native and mutant GH57GBEs. A correlation was found between a very low or even no branching activity with the absence of a flexible loop, a tyrosine at the loop tip, and two β-sheets.

Ekstraksi Glukomanan dari Umbi Gembili (Dioscorea esculenta L.)

Gembili bulbs (Dioscorea esculenta L.) have a fairly high carbohydrate content, so they can potentially be a new source of glucomannan compounds. This study aims to determine the yield and glucomannan characteristics of Gembili bulbs at different extraction times and temperatures. Glucomannan was obtained by extraction with water at temperatures of 45, 60, 75, 90, and 105oC for 45, 60, 75, 90, and 105 minutes, and precipitated with isopropyl alcohol. The results showed that the highest yield was obtained at the extraction time of 90 minutes and a temperature of 105oC of 53.09%. The glucomannan of Gembili bulb has a molecular weight of 1,865 x 104 g/mol with ash and water content values of 0.866% and 10.45%, respectively. The results of identification of functional groups with an FTIR spectrophotometer showed that there was a functional group stretching vibration of glucomannan compounds, including the –OH group at a wavenumber of 3431 cm-1 and -C-O-C (glycosidic bond) at a wavenumber of 1020.34 cm-1 and bending vibration of -CH functional groups on wavenumber of 850.61 cm-1.