An evaluation of indirubin analogues as phosphorylase kinase inhibitors

Phosphorylase kinase (PhK) has been linked with a number of conditions such as glycogen storage diseases, psoriasis, type 2 diabetes and more recently, cancer (Camus S. et al., Oncogene 2012, 31, 4333). However, with few reported structural studies on PhK inhibitors, this hinders a structure based drug design approach. In this study, the inhibitory potential of 38 indirubin analogues have been investigated. 11 of these ligands had IC50 values in the range 0.170 – 0.360 µM, with indirubin-3’-acetoxime (1c) the most potent. 7-bromoindirubin-3’-oxime (13b), an antitumor compound which induces caspase-independent cell-death (Ribas J. et al., Oncogene, 2006, 25, 6304) is revealed as a specific inhibitor of PhK (IC50 = 1.8 µM). Binding assay experiments performed using both PhK-holo and PhK-γtrnc confirmed the inhibitory effects to arise from binding at the kinase domain (γ subunit). High level computations using QM/MM-PBSA binding free energy calculations were in good agreement with experimental binding data, as determined using statistical analysis, and support binding at the ATP-binding site. The value of a QM description for the binding of halogenated ligands exhibiting -hole effects is highlighted. A new statistical metric, the ‘sum of the modified logarithm of ranks’ (SMLR), has been defined which measures performance of a model for both the “early recognition” (ranking earlier/higher) of active compounds and their relative ordering by potency. Through a detailed structure activity relationship analysis considering other kinases (CDK2, CDK5 and GSK-3α/β), 6’(Z) and 7(L) indirubin substitutions have been identified to achieve selective PhK inhibition. The key PhK binding site residues involved can also be targeted using other ligand scaffolds in future work

Nonclassical Hydrophobic Effect in Micellization: Molecular Arrangement of Non-Amphiphilic Structures

Micellization brought about by nonclassical hydrophobic effect invokes enthalpy as the driving force. Thus, the underlying molecular phenomena differ from the entropically dominated hydrophobic effect. In quest for a molecular-scale understanding, we report on the molecular arrangement of nonamphiphilic structures of an anionic boron cluster compound, COSAN. We synergistically combine experimental (NMR and calorimetry) and theoretical (molecular dynamics and quantum chemical calculations) approaches. The experimental data support the mechanism of closed association of COSAN, where the self-assembly is driven by the enthalpy contribution to the free energy. Molecular dynamics simulations in explicit solvent show that water molecules form a patchy network around COSAN molecules, giving rise to the strong hydrophobic self-association. In the second solvation shell, water forms a slightly hydrophilic “spot” close to the C-H segments of the cluster. The simulations further show a counterintuitive short-range [COSAN]−∙∙∙[COSAN]− attraction and Na+∙∙∙[COSAN]− repulsion. Quantum chemical calculations reveal a major role of solvation in stabilizing the contact pairs. Further, the calculations show the parallel/X-shape geometrical arrangements of COSAN dimers as the most preferred. Lastly, dihydrogen bonding are found to influence the structure of micelles. In summary, we provide a molecular view of nonclassical micellization that can be extended to other amphiphiles like boranes

Bromination Mechanism of closo-1,2-C2 B10 H12 and the Structure of the Resulting 9-Br-closo-1,2-C2 B10 H11 Determined by Gas Electron Diffraction.

Holub J, Vishnevskiy Y, Fanfrlik J, et al. Bromination Mechanism of closo-1,2-C2 B10 H12 and the Structure of the Resulting 9-Br-closo-1,2-C2 B10 H11 Determined by Gas Electron Diffraction. ChemPlusChem. 2020;85(12):2606-2610.9-Br-closo-1,2-C2 B10 H11 has been prepared and its gas-phase structure has been examined by means of gas electron diffraction. The structure of the carbaborane core is similar to the structure of the parent compound, which is of C2v symmetry. A DFT-based search for the corresponding reaction pathway of the bromination of closo-1,2-C2 B10 H12 revealed that the catalytic amount of aluminum reduces the barrier of the initial attack of the bromination agent toward the negatively charged part of the icosahedral carbaborane, i.e., the first transition state, from about 40 to about 27 kcalmol-1 . The Br-Br bond is weakened by an intermediate binding to the large pi-hole on the aluminum atom of AlBr3 , which is the driving force for the AlBr3 -catalyzed bromination. © 2020 Wiley-VCH GmbH

Structural and Functional Studies of Phosphoenolpyruvate Carboxykinase from Mycobacterium tuberculosis

Tuberculosis, the second leading infectious disease killer after HIV, remains a top public health priority. The causative agent of tuberculosis, Mycobacterium tuberculosis (Mtb), which can cause both acute and clinically latent infections, reprograms metabolism in response to the host niche. Phosphoenolpyruvate carboxykinase (Pck) is the enzyme at the center of the phosphoenolpyruvate-pyruvate-oxaloacetate node, which is involved in regulating the carbon flow distribution to catabolism, anabolism, or respiration in different states of Mtb infection. Under standard growth conditions, Mtb Pck is associated with gluconeogenesis and catalyzes the metal-dependent formation of phosphoenolpyruvate. In non-replicating Mtb, Pck can catalyze anaplerotic biosynthesis of oxaloacetate. Here, we present insights into the regulation of Mtb Pck activity by divalent cations. Through analysis of the X-ray structure of Pck-GDP and Pck-GDP-Mn2+ complexes, mutational analysis of the GDP binding site, and quantum mechanical (QM)-based analysis, we explored the structural determinants of efficient Mtb Pck catalysis. We demonstrate that Mtb Pck requires presence of Mn2+ and Mg2+ cations for efficient catalysis of gluconeogenic and anaplerotic reactions. The anaplerotic reaction, which preferably functions in reducing conditions that are characteristic for slowed or stopped Mtb replication, is also effectively activated by Fe2+ in the presence of Mn2+ or Mg2+ cations. In contrast, simultaneous presence of Fe2+ and Mn2+ or Mg2+ inhibits the gluconeogenic reaction. These results suggest that inorganic ions can contribute to regulation of central carbon metabolism by influencing the activity of Pck. Furthermore, the X-ray structure determination, biochemical characterization, and QM analysis of Pck mutants confirmed the important role of the Phe triad for proper binding of the GDP-Mn2+ complex in the nucleotide binding site and efficient catalysis of the anaplerotic reaction