Switching the Switch: Ligand Induced Disulfide Formation in HDAC8

Human histone deacetylase 8 is a well-recognized target for T-cell lymphoma and particularly childhood neuroblastoma. PD-404,182 was shown to be a selective covalent inhibitor of HDAC8 that forms mixed disulfides with several cysteine residues and is also able to transform thiol groups to thiocyanates. Moreover, HDAC8 was shown to be regulated by a redox switch based on the reversible formation of a disulfide bond between cysteines Cys₁₀₂ and Cys₁₅₃. This study on the distinct effects of PD-404,182 on HDAC8 reveals that this compound induces the dose-dependent formation of intramolecular disulfide bridges. Therefore, the inhibition mechanism of HDAC8 by PD-404,182 involves both, covalent modification of thiols as well as ligand mediated disulfide formation. Moreover, this study provides a deep molecular insight into the regulation mechanism of HDAC8 involving several cysteines with graduated capability to form reversible disulfide bridges.     

Hybridorubrins A–D: Azaphilone Heterodimers from Stromata of Hypoxylon fragiforme and Insights into the Biosynthetic Machinery for Azaphilone Diversification

The diversity of azaphilones in stromatal extracts of the fungus Hypoxylon fragiforme was investigated and linked to their biosynthetic machineries by using bioinformatics. Nineteen azaphilone-type compounds were isolated and characterized by NMR spectroscopy and mass spectrometry, and their absolute stereoconfigurations were assigned by using Mosher ester analysis and electronic circular dichroism spectroscopy. Four unprecedented bis-azaphilones, named hybridorubrins A–D, were elucidated, in addition to new fragirubrins F and G and various known mitorubrin derivatives. Only the hybridorubrins, which are composed of mitorubrin and fragirubrin moieties, exhibited strong inhibition of Staphylococcus aureus biofilm formation. Analysis of the genome of H. fragiforme revealed the presence of two separate biosynthetic gene clusters (BGCs) hfaza1 and hfaza2 responsible for azaphilone formation. While the hfaza1 BGC likely encodes the assembly of the backbone and addition of fatty acid moieties to yield the (R)-configured series of fragirubrins, the hfaza2 BGC contains the necessary genes to synthesise the widely distributed (S)-mitorubrins. This study is the first example of two distant cross-acting fungal BGCs collaborating to produce two families of azaphilones and bis-azaphilones derived therefrom.     

Tunable Probes with Direct Fluorescence Signals for the Constitutive and Immunoproteasome

Electrophiles are commonly used for the inhibition of proteases. Notably, inhibitors of the proteasome, a central determinant of cellular survival and a target of several FDA‐approved drugs, are mainly characterized by the reactivity of their electrophilic head groups. We aimed to tune the inhibitory strength of peptidic sulfonate esters by varying the leaving groups. Indeed, proteasome inhibition correlated well with the pK_a of the leaving group. The use of fluorophores as leaving groups enabled us to design probes that release a stoichiometric fluorescence signal upon reaction, thereby directly linking proteasome inactivation to the readout. This principle could be applicable to other sulfonyl fluoride based inhibitors and allows the design of sensitive probes for enzymatic studies.     

Towards Photochromic Azobenzene-Based Inhibitors for Tryptophan Synthase

Light regulation of drug molecules has gained growing interest in biochemical and pharmacological research in recent years. In addition, a serious need for novel molecular targets of antibiotics has emerged presently. Herein, the development of a photocontrollable, azobenzene-based antibiotic precursor towards tryptophan synthase (TS), an essential metabolic multienzyme complex in bacteria, is presented. The compound exhibited moderately strong inhibition of TS in its E configuration and five times lower inhibition strength in its Z configuration. A combination of biochemical, crystallographic, and computational analyses was used to characterize the inhibition mode of this compound. Remarkably, binding of the inhibitor to a hitherto-unconsidered cavity results in an unproductive conformation of TS leading to noncompetitive inhibition of tryptophan production. In conclusion, we created a promising lead compound for combatting bacterial diseases, which targets an essential metabolic enzyme, and whose inhibition strength can be controlled with light.     

An improved ensemble learning machine for biological activity prediction of tyrosine kinase inhibitors

Boosting is one of the most important strategies in ensemble learning because of its ability to improve the stability and performance of weak learners. It is nonparametric, multivariate, fast and interpretable but is not robust against outliers. To enhance its prediction accuracy as well as immunize it against outliers, a modified version of a boosting algorithm (AdaBoost R2) was developed and called AdaBoost R3. In the sampling step, extremum samples were added to the boosting set. In the robustness step, a modified Huber loss function was applied to overcome the outlier problem. In the output step, a deterministic threshold was used to guarantee that bad predictions do not participate in the final output. The performance of the modified algorithm was investigated with two anticancer data sets of tyrosine kinase inhibitors, and the mechanism of inhibition was studied using the relative weighted variable importance procedure. Investigating the effect of base learner's strength reveals that boosting is only successful using the classification and regression tree method (a weak to moderate learner) and does not have a significant effect using the radial basis functions partial least square method (a strong base learners). Copyright © 2015 John Wiley & Sons, Ltd.     

CONFORMATIONAL PREFERENCES ABOUT Cpy-S BONDS IN DI-2-PYRIDYL DISULFIDE

Abstract

The total energy, dipole moment and electron densities for each possible rotational conformation about the C_py-S bonds of di-2-pyridyl disulfide were evaluated by using the semi-quantitative CNDO/2 method. The conformations in which the pyridine rings are coplanar with the valency plane of the bonded sulfur atom (cis-cis, cis-trans and trans-trans) were predicted to be the most favored ones.

Results of the theoretical study, when compared to some experimental determinations such as dipole moment and variable temperature pmr spectra, provided evidence that easy interconversion between these conformations can occur.