Investigating the role of c-Jun N-terminal kinases in the proliferation of Werner syndrome fibroblasts using diaminopyridine inhibitors

Fibroblasts derived from the progeroid Werner syndrome show reduced replicative lifespan and a "stressed" morphology, both alleviated using the MAP kinase inhibitor SB203580. However, interpretation of these data is problematical because although SB203580 has the stress-activated kinases p38 and JNK1/2 as its preferred targets, it does show relatively low overall kinase selectivity. Several lines of data support a role for both p38 and JNK1/2 activation in the control of cellular proliferation and also the pathology of diseases of ageing, including type II diabetes, diseases to which Werner Syndrome individuals are prone, thus making the use of JNK inhibitors attractive as possible therapeutics. We have thus tested the effects of the widely used JNK inhibitor SP600125 on the proliferation and morphology of WS cells. In addition we synthesised and tested two recently described aminopyridine based inhibitors. SP600125 treatment resulted in the cessation of proliferation of WS cells and resulted in a senescent-like cellular phenotype that does not appear to be related to the inhibition of JNK1/2. In contrast, use of the more selective aminopyridine CMPD 6o at concentrations that fully inhibit JNK1/2 had a positive effect on cellular proliferation of immortalised WS cells, but no effect on the replicative lifespan of primary WS fibroblasts. In addition, CMPD 6o corrected the stressed WS cellular morphology. The aminopyridine CMPD 6r, however, had little effect on WS cells. CMDP 6o was also found to be a weak inhibitor of MK2, which may partially explain its effects on WS cells, since MK2 is known to be involved in regulating cellular morphology via HSP27 phosphorylation, and is thought to play a role in cell cycle arrest. These data suggest that total JNK1/2 activity does not play a substantial role in the proliferation control in WS cells

Novel Allosteric Sites on Ras for Lead Generation

Aberrant Ras activity is a hallmark of diverse cancers and developmental diseases. Unfortunately, conventional efforts to develop effective small molecule Ras inhibitors have met with limited success. We have developed a novel multi-level computational approach to discover potential inhibitors of previously uncharacterized allosteric sites. Our approach couples bioinformatics analysis, advanced molecular simulations, ensemble docking and initial experimental testing of potential inhibitors. Molecular dynamics simulation highlighted conserved allosteric coupling of the nucleotide-binding switch region with distal regions, including loop 7 and helix 5. Bioinformatics methods identified novel transient small molecule binding pockets close to these regions and in the vicinity of the conformationally responsive switch region. Candidate binders for these pockets were selected through ensemble docking of ZINC and NCI compound libraries. Finally, cell-based assays confirmed our hypothesis that the chosen binders can inhibit the downstream signaling activity of Ras. We thus propose that the predicted allosteric sites are viable targets for the development and optimization of new drugs

Methods of using click chemistry in the discovery of enzyme inhibitors

10.1038/nprot.2007.323Nature protocols2112655-266

Expression and Purification of Intrinsically Disordered Aβ Peptide and Setup of Reproducible Aggregation Kinetics Experiment

High purity and sequence homogeneity of intrinsically disordered proteins are prerequisites for reproducible studies of the kinetics and equilibrium of their self-assembly reactions. Starting from the pure state enables quantitative studies of intrinsic and extrinsic factors in the process to understand its molecular determinants. Here we outline detailed protocols for recombinant expression and purification of ultra-pure amyloid β peptide (Aβ) in sequence homogeneous form, which allows for the setup of reproducible kinetic self-assembly experiments

Theoretical approaches to identify the potent scaffold for human sirtuin1 activator: Bayesian modeling and density functional theory

Bayesian and pharmacophore modeling approaches were utilized to identify the fragments and critical chemical features of small molecules that enhance sirtuin1 (SIRT1) activity. Initially, 48 Bayesian models (BMs) were developed by exploring 12 different fingerprints (ECFC, ECFP, EPFC, EPFP, FPFC, FPFP, FCFC, FCFP, LCFC, LCFP, LPFC, and LPLP) with diameters of 4, 6, 8, and 10. Among them the BM1 model was selected as the best model based on its good statistical parameters including total accuracy: 0.98 and positive recalls: 0.95. Additionally, BM1 showed good predictive power for the test set (total accuracy: 0.87 and positive recall: 0.87). In addition, 10 qualitative pharmacophore models were generated using 6 well-known SIRT1 activators. Hypothesis2 (Hypo2) was selected as best hypothesis, among 10 Hypos, based on its discriminant ability between the highly active and least/moderately active SIRT1 activators. The best models, BM1 and Hypo2 were used as a query in virtual screens of a drug-like database and the hit molecules were sorted based on Bayesian score and fit value, respectively. In addition, the highest occupied molecular orbital, lowest unoccupied molecular orbital, and energy gap values were calculated for the selected virtual screening hits using density functional theory. Finally, 16 compounds were selected as leads based on their energy gap values, which represent the high reactivity of molecules. Thus, our results indicated that the combination of two-dimensional (2D) and 3D approaches are useful for the discovery and development of specific and potent SIRT1 activators, and will benefit medicinal chemists focused on designing novel lead compounds that activate SIRT1