Discovery and optimization of narrow spectrum inhibitors of Tousled like kinase 2 (TLK2) using quantitative structure activity relationships.

The oxindole scaffold has been the center of several kinase drug discovery programs, some of which have led to approved medicines. A series of two oxindole matched pairs from the literature were identified where TLK2 was potently inhibited as an off-target kinase. The oxindole has long been considered a promiscuous kinase inhibitor template, but across these four specific literature oxindoles TLK2 activity was consistent, while the kinome profile was radically different ranging from narrow to broad spectrum kinome coverage. We synthesized a large series of analogues, utilizing quantitative structure-activity relationship (QSAR) analysis, water mapping of the kinase ATP binding sites, kinome profiling, and small-molecule x-ray structural analysis to optimize TLK2 inhibition and kinome selectivity. This resulted in the identification of several narrow spectrum, sub-family selective, chemical tool compounds including 128 (UNC-CA2-103) that could enable elucidation of TLK2 biology.

SGC-CLK-1: A chemical probe for the Cdc2-like kinases CLK1, CLK2, and CLK4.

Small molecule modulators are important tools to study both basic biology and the complex signaling of protein kinases. The cdc2-like kinases (CLK) are a family of four kinases that have garnered recent interest for their involvement in a diverse set of diseases such as neurodegeneration, autoimmunity, and many cancers. Targeted medicinal chemistry around a CLK inhibitor hit identified through screening of a kinase inhibitor set against a large panel of kinases allowed us to identify a potent and selective inhibitor of CLK1, 2, and 4. Here, we present the synthesis, selectivity, and preliminary biological characterization of this compound - SGC-CLK-1 (CAF-170). We further show CLK2 has the highest binding affinity, and high CLK2 expression correlates with a lower IC50 in a screen of multiple cancer cell lines. Finally, we show that SGC-CLK-1 not only reduces serine arginine-rich (SR) protein phosphorylation but also alters SR protein and CLK2 subcellular localization in a reversible way. Therefore, we anticipate that this compound will be a valuable tool for increasing our understanding of CLKs and their targets, SR proteins, at the level of phosphorylation and subcellular localization.

Mechanistic interpretation of orders in catalyst greater than one.

Orders in catalyst greater than one can be attributed to several different reaction mechanisms. Differentiating among these possibilities requires careful analysis of their rate laws, rational experiment design and accurate measurement of the progress of the reactions. We have compiled the most popular mechanisms proposed for reactions with an order in catalyst greater than one and derived their steady-state rate laws. We have analysed the rate laws and proposed experiments to discern between mechanisms. Finally, we have examined 100 case studies that showcase good practices to propose robust mechanisms and to avoid common pitfalls.

Discovery and Optimization of Narrow Spectrum Inhibitors of Tousled Like Kinase 2 (TLK2) Using Quantitative Structure Activity Relationships.

The oxindole scaffold has been the center of several kinase drug discovery programs, some of which have led to approved medicines. A series of two oxindole matched pairs from the literature were identified where TLK2 was a potent off-target kinase. The oxindole has long been considered a promiscuous inhibitor template, but across these 4 specific literature oxindoles TLK2 activity was consistent, while the kinome profile was radically different from narrow to broad spectrum coverage. We synthesized a large series of analogues and through quantitative structure-activity relationship (QSAR) analysis, water mapping of the kinase ATP binding sites, small-molecule x-ray structural analysis and kinome profiling, narrow spectrum, sub-family selective, chemical tool compounds were identified to enable elucidation of TLK2 biology.

A computational tool to accurately and quickly predict 19F NMR chemical shifts of molecules with fluorine-carbon and fluorine-boron bonds.

We report the evaluation of density-functional-theory (DFT) based procedures for predicting 19F NMR chemical shifts at modest computational cost for a range of molecules with fluorine bonds, to be used as a tool for assisting the characterisation of reaction intermediates and products and as an aid to identifying mechanistic pathways. The results for a balanced learning set of molecules were then checked using two further testing sets, resulting in the recommendation of the ωB97XD/aug-cc-pvdz DFT method and basis set as having the best combination of accuracy and computational time, with a RMS error of 3.57 ppm. Cationic molecules calculated without counter-anion showed normal errors, whilst anionic molecules showed somewhat larger errors. The method was applied to the prediction of the conformationally averaged 19F chemical shifts of 2,2,3,3,4,4,5,5-octafluoropentan-1-ol, in which gauche stereoelectronic effects involving fluorine dominate and to determining the position of coordination equilibria of fluorinated boranes as an aid to verifying the relative energies of intermediate species involved in catalytic amidation reactions involving boron catalysts.

Temozolomide-induced guanine mutations create exploitable vulnerabilities of guanine-rich DNA and RNA regions in drug-resistant gliomas.

Temozolomide (TMZ) is a chemotherapeutic agent that has been the first-line standard of care for the aggressive brain cancer glioblastoma (GBM) since 2005. Although initially beneficial, TMZ resistance is universal and second-line interventions are an unmet clinical need. Here, we took advantage of the known mechanism of action of TMZ to target guanines (G) and investigated G-rich G-quadruplex (G4) and splice site changes that occur upon TMZ resistance. We report that TMZ-resistant GBM has guanine mutations that disrupt the G-rich DNA G4s and splice sites that lead to deregulated alternative splicing. These alterations create vulnerabilities, which are selectively targeted by either the G4-stabilizing drug TMPyP4 or a novel splicing kinase inhibitor of cdc2-like kinase. Last, we show that the G4 and RNA binding protein EWSR1 aggregates in the cytoplasm in TMZ-resistant GBM cells and patient samples. Together, our findings provide insight into targetable vulnerabilities of TMZ-resistant GBM and present cytoplasmic EWSR1 as a putative biomarker.

Organocatalytic Enantioselective α-Bromination of Aldehydes with N-Bromosuccinimide.

Despite the wealth of existing organocatalytic, enantioselective transformations, the α-bromination of aldehydes remains a challenging reaction. The four examples reported to date require expensive, inconvenient brominating agents to achieve the desired products in excellent yields and enantioselectivities. The preferred brominating agent, N-bromosuccinimide (NBS), has been repeatedly discarded for these reactions because it results in low yields and relatively poor enantioselectivities. We describe a methodology that uses NBS and performs excellently with low catalyst loadings, short reaction times, and mild temperatures.

Mechanistically Guided Design of an Efficient and Enantioselective Aminocatalytic α-Chlorination of Aldehydes.

The enantioselective aminocatalytic α-chlorination of aldehydes is a challenging reaction because of its tendency to proceed through neutral intermediates in unselective pathways. Herein we report the rational shift to a highly selective reaction pathway involving charged intermediates using hexafluoroisopropanol as solvent. This change in mechanism has enabled us to match and improve upon the yields and enantioselectivities displayed by previous methods while using cheaper aminocatalysts and chlorinating agents, 80-95% less amount of catalyst, convenient temperatures, and shorter reaction times.

Understanding the Diastereopreference of Intermediates in Aminocatalysis: Application to the Chiral Resolution of Lactols.

Downstream intermediates are crucial for the reactivity and selectivity of aminocatalytic reactions. We present an analysis of the stereopreference in aminocatalytic downstream intermediates, which reveals an inconspicuous mechanism of chiral recognition between the catalyst and the rest of the molecule. We delineate a stereoelectronic model to rationalize the mode of chiral transmission. We also exploit it for the resolution of chiral lactols relevant in organic synthesis as well as in the flavor and fragrance industry.

Dual H-bond activation of NHC-Au(i)-Cl complexes with amide functionalized side-arms assisted by H-bond donor substrates or acid additives.

Novel approach with amide-tethered H-bond donor NHC ligands enabled Au(i)-catalysis via H-bonding. The plain NHC-Au(i)-Cl complex catalysed conversions of terminal N-propynamides to oxazolines, and enyne cycloisomerization with an acid additive, in DCM at RT. DFT calculations enlightened the function of the side-arm in the activation.

Metal Triflate-Promoted Allylic Substitution Reactions of Cinnamyl Alcohol in the Presence of Orthoesters and Acetals.

The product distribution of ethers formed from the reaction of cinnamyl alcohol with orthoesters in the presence of indium (III) triflate (InOTf)3 is dependent on both the reaction temperature and catalyst loading. Carrying out the reaction at room temperature under low loadings of the catalyst leads to a facile reaction generating the unexpected secondary allyl ether as the major product. In contrast, carrying out the reaction under higher catalyst loadings at elevated temperatures provides the expected primary linear ether in high yield and with excellent selectivity. The etherification reaction is also effective in the presence of acetals and ketals in place of orthoesters and allows for the development of the procedure to encompass a telescoped etherification protocol in which the acetal is generated in situ.

Kinetic Treatments for Catalyst Activation and Deactivation Processes based on Variable Time Normalization Analysis.

Progress reaction profiles are affected by both catalyst activation and deactivation processes occurring alongside the main reaction. These processes complicate the kinetic analysis of reactions, often directing researchers toward incorrect conclusions. We report the application of two kinetic treatments, based on variable time normalization analysis, to reactions involving catalyst activation and deactivation processes. The first kinetic treatment allows the removal of induction periods or the effect of rate perturbations associated with catalyst deactivation from kinetic profiles when the quantity of active catalyst can be measured. The second treatment allows the estimation of the activation or deactivation profile of the catalyst when the order of the reactants for the main reaction is known. Both treatments facilitate kinetic analysis of reactions suffering catalyst activation or deactivation processes.

Alkene Oxyamination Using Malonoyl Peroxides: Preparation of Pyrrolidines and Isoxazolidines.

Treatment of homoallylic N-tosyl amines or allylic N-tosyl hydroxylamines with 1.5 equiv of a malonoyl peroxide provides a stereoselective method to access functionalized pyrrolidines and isoxazolidines. This metal free alkene oxyamination proceeds in 50-85% yield and up to 13:1 trans-selectivity. In addition, the relative stereochemistry of the oxygen and nitrogen substituents can be inverted through an oxidation/reduction sequence or inverting the stereochemistry of the starting alkene. Mechanistic investigations show a higher reactivity for hydroxyl nucleophiles over sulfonamide nucleophiles revealing a preference for dioxygenation over oxyamination.

Alkene Dioxygenation with Malonoyl Peroxides: Synthesis of γ-Lactones, Isobenzofuranones, and Tetrahydrofurans.

Treatment of homoallylic alcohols or carboxylic acids with malonoyl peroxide 1 provides a stereoselective method for the preparation of tetrahydrofurans, γ-lactones, and isobenzofuranones in 44-82% yield and up to 27:1 trans selectivity. Application of this simple and effective heterocyclization in the synthesis of the antidepressant citalopram is also described.

Alkene anti-Dihydroxylation with Malonoyl Peroxides.

Malonoyl peroxide 1, prepared in a single step from the commercially available diacid, is an effective reagent for the anti-dihydroxylation of alkenes. Reaction of 1 with an alkene in the presence of acetic acid at 40 °C followed by alkaline hydrolysis leads to the corresponding diol (35-92%) with up to 13:1 anti-selectivity. A mechanism consistent with experimental findings is proposed that accounts for the selectivity observed.