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Stilbene urea derivatives as a novel and competitive class of non-glycosidic α-glucosidase inhibitors are effective for the treatment of type II diabetes and obesity. The main purposes of our molecular modeling study are to explore the most suitable binding poses of stilbene derivatives with analyzing the binding affinity differences and finally to develop a pharmacophore model which would represents critical features responsible for α-glucosidase inhibitory activity. Three-dimensional structure of S. cerevisiae α-glucosidase was built by homology modeling method and the structure was used for the molecular docking study to find out the initial binding mode of compound 12, which is the most highly active one. The initial structure was subjected to molecular dynamics (MD) simulations for protein structure adjustment at compound 12-bound state. Based on the adjusted conformation, the more reasonable binding modes of the stilbene urea derivatives were obtained from molecular docking and MD simulations. The binding mode of the derivatives was validated by correlation analysis between experimental Ki value and interaction energy. Our results revealed that the binding modes of the potent inhibitors were engaged with important hydrogen bond, hydrophobic, and π-interactions. With the validated compound 12-bound structure obtained from combining approach of docking and MD simulation, a proper four featured pharmacophore model was generated. It was also validated by comparison of fit values with the Ki values. Thus, these results will be helpful for understanding the relationship between binding mode and bioactivity and for designing better inhibitors from stilbene derivatives.

Soybean leaves are eaten as seasonal edible greens in Korea. Analysis of the ethyl acetate extract of these leaves showed that it exhibited potent and selective neuraminidase inhibition, which began at the R3 stage and peaked at R7. Ten pterocarpans, including the new 6a-hydroxypterocarpan 10, were isolated from soybean leaves and their inhibition activities tested against a range of glycosidases. The relationship between structure and enzyme inhibition was investigated: 6a-hydroxypterocarpans exhibited much higher inhibition against neuraminidase (IC(50) = 2.4-89.4 μM) than α-glucosidase (IC(50) = 90.4- >100 μM). Glyceollin VII (7) displayed 40-fold greater activity (IC(50) = 2.4 μM) against neuraminidase than α-glucosidase (IC(50) = 90.4 μM). On the other hand, coumestanes (1-3) were good α-glucosidase inhibitors (IC(50) = 6.0-42.6 μM). In kinetic analysis, the most potent neuraminidase inhibitors (5-10) were noncompetitive. HPLC analysis indicated that most pterocarpan synthesis began from the R3 stage, and a rapid change of pterocarpan concentrations was observed between the R4 and R7 stages.

Neuraminidase is a proven target in anti-viral drug development. It also appears to be important for infection by certain pathogenic bacteria and has been implicated in biofilm formation. Based on activity-guided fractionation, the acetone extract of Amorpha fruticosa roots gave four flavanones 1-4 and three rotenoids 5-7 which were identified as amoradicin (1), amorisin (2), isoamoritin (3), amoricin (4), amorphigeni (5), dalbinol (6), and 6-ketodehydroamorphigenin (7), respectively. All isolated inhibitors showed strong neuraminidase inhibition with IC₅₀s between 0.12 and 22.03 μM. In particular, amorisin 2 exhibited 120 nM IC(₅₀, which is 30-fold more potent than the positive control, quercetin. In addition, this is the first report detailing rotenoids (IC₅₀ = 8.34-16.74 μM) exhibiting neuraminidase inhibition. Kinetic analysis revealed that all inhibitors were noncompetitive. The most active neuraminidase inhibitors (2, 3, 5, 6) were proven to be present in the native root in high quantities by HPLC. Finally, at concentrations where no toxicity was observed, 3 and 6 inhibited Pseudomonas aeruginosa biofilm production. 29.7% and 21.0% inhibition respectively was observed at 25 μΜ., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

Competitive glycosidase inhibitors are generally sugar mimics that are costly and tedious to obtain because they require challenging and elongated chemical synthesis, which must be stereo- and regiocontrolled. Here, we show that readily accessible achiral (E)-1-phenyl-3-(4-strylphenyl)ureas are potent competitive α-glucosidase inhibitors. A systematic synthesis study shows that the 1-phenyl moiety on the urea is critical for ensuring competitive inhibition, and substituents on both terminal phenyl groups contribute to inhibition potency. The most potent inhibitor, compound 12 (IC(50)=8.4 μM, K(i)=3.2 μM), manifested a simple slow-binding inhibition profile for α-glucosidase with the kinetic parameters k(3)=0.005256 μM(-1) min(-1), k(4)=0.003024 min(-1), and K(i)(app) =0.5753 μM.

The structural characteristics of flavonoids (1-3 and 6-8) from the root of Cudrania tricuspidata required for neuraminidase inhibition were studied and compared with commercially available flavonoids (4, 5, and 9-12). Alkylated flavanones (1-3) display better inhibition than the corresponding parent compound 4. Importantly, flavanone 1 bearing a C-8 hydrated prenyl group showed extremely high inhibition with IC(50) of 380 nM. On the other hand, the parent flavone 5 was more effective than alkylated analogues (6-8). Isolated inhibitors (1-3 and 6-8) showed noncompetitive inhibition in kinetic studies. The binding affinity of flavanones (1-4) for neuraminidase in in silico docking experiments correlated well with their IC(50) values and noncompetitive inhibition mode.

Natural polyphenolic compounds generally transpire to show relatively low inhibition against glycosidase including neuraminidase. In addition the inhibition modes of such compounds are rarely competitive. In this manuscript, a series of xanthone derivatives from Cudrania tricuspidata are shown to display nanomolar inhibitor activity against neuraminidase (EC 3.2.1.18) as well as competitive inhibition modes. Compound 8 bearing vicinal dihydroxy group on the A-ring displays nanomolar activity (IC(50)=0.08+/-0.01 microM), a 200-fold increase in activity relative to that of the first reported xanthone-derived neuraminidase inhibitor, mangiferin (IC(50)=16.2+/-4.2 microM). The 6,7-vicinal dihydroxy group plays a crucial role for inhibitory activity because compound 4, which has one of these hydroxyl groups prenylated was inactive (33% at 200 microM), whereas other compounds (1-3 and 6-8) showed nanomolar activity (0.08-0.27 microM) and competitive inhibition modes. Interestingly all inhibitors manifested enzyme isomerization inhibition against neuraminidase. The most potent inhibitor, compound 8 showed similar interaction with a transition-state analogue of neuraminic acid in active site.

Abstract: Bacterial neuraminidase has been highlighted as a key enzyme for pathogenic infection and sepsis. Six pterocarpans displaying significant levels of neuraminidase inhibitory activity were isolated from the root bark of Lespedeza bicolor. The isolated compounds were identified as three new pterocarpans (1−3) together with known compounds erythrabyssin II (4), lespebuergine G4 (5), and 1-methoxyerythrabyssin II (6). The new compounds were characterized as bicolosin A (1), bicolosin B (2), and bicolosin C (3). All compounds inhibited bacterial neuraminidase in a dose-dependent manner with significant inhibition (IC50 =0.09–3.25μM). All neuraminidase inhibitors screened were found to exhibit noncompetitive kinetics. The three most potent neuraminidase inhibitors (1, 3 and 6) feature a methoxy substitution on C-1. [Copyright &y& Elsevier]