A fluorescence-based assay for p38α recruitment site binders: identification of rooperol as a novel p38α kinase inhibitor

Profiling MAP kinase cysteines for targeted covalent inhibitor design

Mitogen-activated protein kinases (MAPK) are important therapeutic targets, and yet no inhibitors have advanced to the market. Here we applied the GPU-accelerated continuous constant pH molecular dynamics (CpHMD) to calculate the pK a's and profile the cysteine reactivities of all 14 MAPKs for assisting the targeted covalent inhibitor design. The simulations not only recapitulated but also rationalized the reactive cysteines in the front pocket of JNK1/2/3 and the extended front pocket of p38α. Interestingly, the DFG - 1 cysteine in the DFG-in conformation of ERK1/ERK2 was found somewhat reactive or unreactive; however, simulations of MKK7 showed that switching to the DFG-out conformation makes the DFG - 1 cysteine reactive, suggesting the advantage of type II covalent inhibitors. Additionally, the simulations prospectively predicted several druggable cysteine and lysine sites, including the αH head cysteine in JNK1/3 and DFG + 6 cysteine in JNK2, corroborating the chemical proteomic screening data. Given the low cost and the ability to offer physics-based rationales, we envision CpHMD simulations to complement the chemo-proteomic platform for systematic profiling cysteine reactivities for targeted covalent drug discovery.

Synthesis of 1,4-enynes via nickel-catalyzed cross-coupling of allylic alcohols with alkynylzinc reagents

Synthesis of 1,4-enynes was performed via nickel-catalyzed cross-coupling of allylic alcohols with alkynylzinc reagents. The reaction features high regio- and E/Z-selectivity when aryl-substituted allylic alcohols were employed. The method also exhibits a wide scope of substrates and good compatibility of functional groups.

Assessment of anti-inflammatory-like, antioxidant activities and molecular docking of three alkynyl-substituted 3-ylidene-dihydrobenzo[d]isothiazole 1,1-dioxide derivatives

The presence of enyne and benzoisothiazole functions in the molecular architecture of compounds 1, 2 and 3 were expected to provide biochemical activities. In the present work, we first examined the molecular surface contact of three alkynyl-substituted 3-ylidenedihydrobenzo[d] isothiazole 1,1-dioxides. The analysis of the Hirshfeld surfaces reveals that only compound 3 exhibited a well-defined red spots, indicating intermolecular interactions identified as S-O⋯H, C-H⋯O and C-O⋯H contacts. Comparative fingerprint histograms of the three compounds show that close pair interactions are dominated by C-H⋯H-C contact. By UV-visible analysis, compound 1 showed the most intense absorbances at 407 and 441 nm, respectively. The radical scavenging activity explored in the DPPH test, shows that only 1 exhibited low anti-radical activity. Furthermore, cellular antioxidant capacity of benzoisothiazoles 1-3 was investigated with PMA-activated HL-60 cells using chemiluminescence and fluorescence techniques in the presence of L-012 and Amplex Red probe, respectively. Results highlight that compound 1 exhibited moderate anti-ROS capacity while compounds 2 and 3 enhanced ROS production. The cytotoxicity test performed on HL-60 cells, using the MTS assay, confirmed the lack of toxicity of the tested benzoisothiazole 1 compared to 2 and 3 which show low cytotoxicity (≤30%). Anti-catalytic activity was evaluated by following the inhibitory potential of the benzoisothiazoles on MPO activity and depicted benzoisothiazoles-MPO interactions by docking. Both SIEFED and docking studies demonstrated an anti-catalytic activity of the tested benzoisothiazoles towards MPO with the best activity for compound 2.

Kinase Atlas: Druggability Analysis of Potential Allosteric Sites in Kinases

The inhibition of kinases has been pursued by the pharmaceutical industry for over 20 years. While the locations of the sites that bind type II and III inhibitors at or near the adenosine 5'-triphosphate binding sites are well defined, the literature describes 10 different regions that were reported as regulatory hot spots in some kinases and thus are potential target sites for type IV inhibitors. Kinase Atlas is a systematic collection of binding hot spots located at the above ten sites in 4910 structures of 376 distinct kinases available in the Protein Data Bank. The hot spots are identified by FTMap, a computational analogue of experimental fragment screening. Users of Kinase Atlas ( https://kinase-atlas.bu.edu ) may view summarized results for all structures of a particular kinase, such as which binding sites are present and how druggable they are, or they may view hot spot information for a particular kinase structure of interest.

Preparation and Utility of N-Alkynyl Azoles in Synthesis

Heteroatom-substituted alkynes have attracted a significant amount of interest in the synthetic community due to the polarized nature of these alkynes and their utility in a wide range of reactions. One specific class of heteroatom-substituted alkynes combines this utility with the presence of an azole moiety. These N-alkynyl azoles have been known for nearly 50 years, but recently there has been a tremendous increase in the number of reports detailing the synthesis and utility of this class of compound. While much of the chemistry of N-alkynyl azoles mirrors that of the more extensively studied N-alkynyl amides (ynamides), there are notable exceptions. In addition, as azoles are extremely common in natural products and pharmaceuticals, these N-alkynyl azoles have high potential for accessing biologically important compounds. In this review, the literature reports of N-alkynyl azole synthesis, reactions, and uses have been assembled. Collectively, these reports demonstrate the growth in this area and the promise of exploiting N-alkynyl azoles in synthesis.

Progress with covalent small-molecule kinase inhibitors

With reduced risk of toxicity and high selectivity, covalent small-molecule kinase inhibitors (CSKIs) have emerged rapidly. Through the lens of structural system pharmacology, here we review this rapid progress by considering design strategies and the challenges and opportunities offered by current CSKIs.

Determining Cysteines Available for Covalent Inhibition Across the Human Kinome

Covalently bound protein kinase inhibitors have been frequently designed to target noncatalytic cysteines at the ATP binding site. Thus, it is important to know if a given cysteine can form a covalent bond. Here we combine a function-site interaction fingerprint method and DFT calculations to determine the potential of cysteines to form a covalent interaction with an inhibitor. By harnessing the human structural kinome, a comprehensive structure-based binding site cysteine data set was assembled. The orientation of the cysteine thiol group indicates which cysteines can potentially form covalent bonds. These covalent inhibitor easy-available cysteines are located within five regions: P-loop, roof of pocket, front pocket, catalytic-2 of the catalytic loop, and DFG-3 close to the DFG peptide. In an independent test set these cysteines covered 95% of covalent kinase inhibitors. This study provides new insights into cysteine reactivity and preference which is important for the prospective development of covalent kinase inhibitors.

Pd-catalyzed decarboxylative allylic coupling of acetates of Baylis–Hillman alcohols with propiolic acids: a highly regio- and stereoselective synthesis of 1,5-diarylpent-1-en-4-yne derivatives

Pd-catalyzed decarboxylative allylic coupling of acetates of Baylis–Hillman alcohols with alkynyl carboxylic acids leading to the formation of 1,5-diarylpent-1-en-4-ynes in a highly regio- and stereoselective manner has been developed.

Pseudo-four component synthesis of mono- and di-benzylated-1,2,3-triazoles derived from aniline

The pseudo-four component click synthesis of dibenzylated 1,2,3-triazoles derived from aniline is reported. The cycloaddition of sodium azide to N-(prop-2-ynyl)-benzenamine (I) in the presence of equimolar amounts of p-substituted benzyl derivatives, yields a mixture of mono- and dibenzylated 1,2,3-triazoles. When two equivalents of the benzyl derivative are added to the multicomponent reaction, the selective preparation of the dibenzylated compounds is achieved. The reactivity of the aniline N-H bond in monobenzylated 1,2,3-triazoles was tested by treatment with one equivalent of a p-substituted benzyl chloride at 40 °C, rendering the dibenzylated derivatives quantitatively.