High-resolution cryo-EM of the human CDK-activating kinase for structure-based drug design.

Rational design of next-generation therapeutics can be facilitated by high-resolution structures of drug targets bound to small-molecule inhibitors. However, application of structure-based methods to macromolecules refractory to crystallization has been hampered by the often-limiting resolution and throughput of cryogenic electron microscopy (cryo-EM). Here, we use high-resolution cryo-EM to determine structures of the CDK-activating kinase, a master regulator of cell growth and division, in its free and nucleotide-bound states and in complex with 15 inhibitors at up to 1.8 Å resolution. Our structures provide detailed insight into inhibitor interactions and networks of water molecules in the active site of cyclin-dependent kinase 7 and provide insights into the mechanisms contributing to inhibitor selectivity, thereby providing the basis for rational design of next-generation therapeutics. These results establish a methodological framework for the use of high-resolution cryo-EM in structure-based drug design.

Syntheses and Characterization of Main Group, Transition Metal, Lanthanide, and Actinide Complexes of Bidentate Acylpyrazolone Ligands.

The synthesis of acylpyrazolone salts and their complexes of main group elements, transition metals, lanthanides, and actinides are described and characterized inter alia by means of single-crystal X-ray crystallography, NMR, and IR spectroscopies. The complexes consist of two, three, or four acylprazolone ligands bound to the metal atom, resulting in a structurally diverse set of coordination complexes with (distorted) octahedral, pentagonal-bipyramidal, or antiprismatic arrangements. Several complexes proved to be polymeric in the solid state including heterobimetallic sodium/lanthanide coordination polymers. A selection of the polymeric compounds was analyzed via TG/DTA measurements to establish their stability. The ligands, in turn, were readily synthesized in good yields from commercially available hydrazine hydrochloride salts. These findings demonstrate that acylpyrazolone ligands can form complexes with metals of varying ionic radii, highlighted by their utility in other areas such as analytical and metal organic framework chemistry.

Agrochemical Lessons for Infectious Disease Research: New Resistance Breaking Antifungal Hits against Candida auris.

Analysis of the history of the invention of the block-buster antifungal drug Fluconazole underscores the importance of agrochemical research on drug discovery and development. The multidrug resistant fungal pathogen Candida auris is now responsible for serious morbidity and mortality among immuno-compromised and long-term resident hospital patients globally. New drugs against C. auris are urgently needed. A focused screening of 1487 fungicides from the BASF agrochemical collection gave several potent inhibitors of C. auris with yet noncommercialized modes of action. The hits showed only minor activity loss against the azole-resistant C. auris strain CDC 0385 and low to moderate cytotoxicity to human HepG2 cells. Aminopyrimidine 4 showed high activity against resistant strains and selectivity in a HepG2 cells assay and is a potential hit candidate for further optimization.

Pyrimidine Nucleosides Syntheses by Late-Stage Base Heterocyclization Reactions.

An efficient two-step procedure for the syntheses of pyrimidine nucleosides is presented. A series of glycosyl 5-(aminomethylene)-1,3-dioxane-4,6-dione derivatives were prepared from ß-anomeric isonitriles by reaction with Meldrum's acid or by allowing aminomethylene Meldrum's acid to react with an 1-aldofuranosyl halide or acetate. The resultant 5-(aminomethylene)-1,3-dioxane-4,6-dione derivatives underwent reaction with benzyl- or 2,4-dimethoxybenzyl isocyanate via transacylation to provide uridine-5-carboxylic acid derivatives and related nucleosides. These nucleoside carboxylic acids were converted into other C-5 derivatives by bromo-decarboxylation with N-bromosuccinimide.

Superalkali-Alkalide Interactions and Ion Pairing in Low-Polarity Solvents.

The nature of anionic alkali metals in solution is traditionally thought to be "gaslike" and unperturbed. In contrast to this noninteracting picture, we present experimental and computational data herein that support ion pairing in alkalide solutions. Concentration dependent ionic conductivity, dielectric spectroscopy, and neutron scattering results are consistent with the presence of superalkali-alkalide ion pairs in solution, whose stability and properties have been further investigated by DFT calculations. Our temperature dependent alkali metal NMR measurements reveal that the dynamics of the alkalide species is both reversible and thermally activated suggesting a complicated exchange process for the ion paired species. The results of this study go beyond a picture of alkalides being a "gaslike" anion in solution and highlight the significance of the interaction of the alkalide with its complex countercation (superalkali).

Biomimetic Syntheses of Analogs of Hongoquercin A and B by Late-Stage Derivatization.

The hongoquercins are tetracyclic meroterpenoid natural products with the trans-transoid decalin-dihydrobenzopyran ring system, which display a range of different bioactivities. In this study, the syntheses of a range of hongoquercins using gold-catalyzed enyne cyclization reactions and further derivatization are described. The parent enyne resorcylate precursors were synthesized biomimetically from the corresponding dioxinone keto ester via regioselective acylation, Tsuji-Trost allylic decarboxylative rearrangement, and aromatization. The dioxinone keto ester 12 was prepared in 6 steps from geraniol using allylic functionalization and alkyne synthesis.

Meroterpenoid Synthesis via Sequential Polyketide Aromatization and Radical Anion Cascade Triene Cyclization: Biomimetic Total Syntheses of Austalide Natural Products.

The first total synthesis of five austalide natural products, (±)-17 S-dihydroaustalide K, (±)-austalide K, (±)-13-deacetoxyaustalide I, (±)-austalide P, and (±)-13-deoxyaustalide Q acid, was accomplished via a series of biomimetic transformations. Key steps involved polyketide aromatization of a trans, trans-farnesol-derived ß,δ-diketodioxinone into the corresponding ß-resorcylate, followed by titanium(III)-mediated reductive radical cyclization of an epoxide to furnish the drimene core. Subsequent phenylselenonium ion induced diastereoselective cyclization of the drimene completed the essential carbon framework of the austalides to access (±)-17 S-dihydroaustalide K, (±)-austalide K, and (±)-13-deacetoxyaustalide I via sequential oxidations. Furthermore, (±)-13-deacetoxyaustalide I could serve as a common intermediate to be derivatized into other related natural products, (±)-austalide P and (±)-13-deoxyaustalide Q acid, by functionalizing the cyclic lactone moiety.

Meroterpenoid Synthesis via Sequential Polyketide Aromatization and Cationic Polyene Cyclization: Total Syntheses of (+)-Hongoquercin A and B and Related Meroterpenoids.

(+)-Hongoquercin A and B were synthesized from commercially available trans, trans-farnesol in six and eleven steps, respectively, using dual biomimetic strategies with polyketide aromatization and subsequent polyene functionalization from a common farnesyl-resorcylate intermediate. Key steps involve Pd(0)-catalyzed decarboxylative allylic rearrangement of a dioxinone ß,δ-diketo ester to a ß,δ-diketo dioxinone, which was readily aromatized into the corresponding resorcylate, and subsequent polyene cyclization via enantioselective protonation or regioselective terminal alkene oxidation and cationic cyclization of enantiomerically enriched epoxide to furnish the tetracyclic natural product cores. Analogues of the hongoquercin were synthesized via halonium-induced polyene cyclizations, and the meroterpenoid could be further functionalized via saponification, hydrolytic decarboxylation, reduction, and amidation reactions.

Bidirectional Synthesis of Di- tert-butyl (2 S,6 S,8 S)- and (2 R,6 R,8 R)-1,7-Diazaspiro[5.5]undecane-2,8-dicarboxylate and Related Spirodiamines.

Efficient syntheses of both enantiomers of a spirodiamine diester from (l)- and (d)-aspartic acid are described. The key transformation was the conversion of Boc-protected tert-butyl aspartate into the derived aldehyde, two-directional Horner-Wadsworth-Emmons olefination, hydrogenation, and selective acid-catalyzed Boc-deprotection and spirocyclization. An alternative, two-directional approach to derivatives of 1,7-diazaspiro[5.5]undecane is described.

ICEC0942, an Orally Bioavailable Selective Inhibitor of CDK7 for Cancer Treatment.

Recent reports indicate that some cancer types are especially sensitive to transcription inhibition, suggesting that targeting the transcriptional machinery provides new approaches to cancer treatment. Cyclin-dependent kinase (CDK)7 is necessary for transcription, and acts by phosphorylating the C-terminal domain (CTD) of RNA polymerase II (PolII) to enable transcription initiation. CDK7 additionally regulates the activities of a number of transcription factors, including estrogen receptor (ER)-α. Here we describe a new, orally bioavailable CDK7 inhibitor, ICEC0942. It selectively inhibits CDK7, with an IC50 of 40 nmol/L; IC50 values for CDK1, CDK2, CDK5, and CDK9 were 45-, 15-, 230-, and 30-fold higher. In vitro studies show that a wide range of cancer types are sensitive to CDK7 inhibition with GI50 values ranging between 0.2 and 0.3 µmol/L. In xenografts of both breast and colorectal cancers, the drug has substantial antitumor effects. In addition, combination therapy with tamoxifen showed complete growth arrest of ER-positive tumor xenografts. Our findings reveal that CDK7 inhibition provides a new approach, especially for ER-positive breast cancer and identify ICEC0942 as a prototype drug with potential utility as a single agent or in combination with hormone therapies for breast cancer. ICEC0942 may also be effective in other cancers that display characteristics of transcription factor addiction, such as acute leukaemia and small-cell lung cancer. Mol Cancer Ther; 17(6); 1156-66. ©2018 AACR.

Discovery of the Antitumor Effects of a Porphyrazine Diol (Pz 285) in MDA-MB-231 Breast Tumor Xenograft Models in Mice.

A series of porphyrazines (Pzs) with chiral bis-acetal moieties in the ß-pyrrole positions ((2R,3R)-2,3-dimethyl-2,3-dimethoxy-1,4-diox-2-ene) have been synthesized and screened as antitumor agents in MDA-MB-231 breast tumor cells in vitro. The lead Pz 285 was further tested in a mouse tumor xenograft model with Td-tomato-luc2 fluorescent breast tumor cells (MDA-MB-231 LM24 Her2+) that are highly metastatic to the lungs. Pz 285 shows marked antitumor effects in vivo, with treated mice exhibiting longer median survival that we attribute to smaller primary tumor regrowth after resection and less occurrence of metastasis when compared to vehicle control groups. Pz 285 is further compared to the clinically approved chemotherapeutic doxorubicin (Dox). This report lays the groundwork for development of an understudied class of compounds for classical chemotherapy.

Inhibitor Selectivity for Cyclin-Dependent Kinase†7: A†Structural, Thermodynamic, and Modelling Study.

Deregulation of the cell cycle by mechanisms that lead to elevated activities of cyclin-dependent kinases (CDK) is a feature of many human diseases, cancer in particular. We identified small-molecule inhibitors that selectively inhibit CDK7, the kinase that phosphorylates cell-cycle CDKs to promote their activities. To investigate the selectivity of these inhibitors we used a combination of structural, biophysical, and modelling approaches. We determined the crystal structures of the CDK7-selective compounds ICEC0942 and ICEC0943 bound to CDK2, and used these to build models of inhibitor binding to CDK7. Molecular dynamics (MD) simulations of inhibitors bound to CDK2 and CDK7 generated possible models of inhibitor binding. To experimentally validate these models, we gathered isothermal titration calorimetry (ITC) binding data for recombinant wild-type and binding site mutants of CDK7 and CDK2. We identified specific residues of CDK7, notably Asp155, that are involved in determining inhibitor selectivity. Our MD simulations also show that the flexibility of the G-rich and activation loops of CDK7 is likely an important determinant of inhibitor specificity similar to CDK2.

Synthesis and Reactions of Benzannulated Spiroaminals: Tetrahydrospirobiquinolines.

An efficient two-step synthesis of symmetrical and unsymmetrical tetrahydrospirobiquinolines from o-azidobenzaldehydes is reported. A novel series of tetrahydrospirobiquinolines was prepared by sequential double-aldol condensation with acetone, cyclopentanone, and cyclohexanone to form the corresponding o,o'-diazido-dibenzylidene-acetone, -cyclopentanone, and -cyclohexanone derivatives, respectively, and hydrogenation-spirocyclization. The spirodiamines were further derivatized by electrophilic aromatic bromination, Suzuki coupling, and N-alkylation, all of which proceeded with preservation of the spirocyclic core.

Sequential Ketene Generation from Dioxane-4,6-dione-keto-dioxinones for the Synthesis of Terpenoid Resorcylates.

Trapping of the ketene generated from the thermolysis of 2-methyl-2-phenyl-1,3-dioxane-4,6-dione-keto-dioxinone at 50 °C with primary, secondary, or tertiary alcohols gave the corresponding dioxinone ß-keto-esters in good yield under neutral conditions. These intermediates were converted by palladium(0)-catalyzed decarboxylative allyl migration and aromatization into the corresponding ß-resorcylates. These transformations were applied to the syntheses of the natural products (±)-cannabiorcichromenic and (±)-daurichromenic acid.

ß-Keto-dioxinones and ß,δ-diketo-dioxinones in biomimetic resorcylate total synthesis.

Resorcylates are a large group of bioactive natural products that are biosynthesized from acetate and malonate units via the intermediacy of polyketides. These polyketides undergo cyclization reactions to introduce the aromatic core. The bioactivities of the resorcylates including resorcylate macrocyclic lactones include anticancer, antimalarial, mycotoxicity, antifungal, and antibiotic properties, and several compounds in the series are already in use in medicine. Examples are prodrugs derived from mycophenolic acid as immunosuppressants and the Hsp-90 inhibitor, AT13387, which is in phase-II clinical trials for the treatment of small cell lung cancer and melanoma. In consequence of these biological activities, methods for the concise synthesis of diverse resorcylates are of considerable importance. In natural product chemistry, biomimetic total synthesis can have significant advantages including functional group tolerance in key steps, the minimization of the use of protection and deprotection reactions and the shortening of the total number of synthetic steps. This Account provides a description of our adaption of the dioxinone chemistry of Hyatt, Clemens, and Feldman for the synthesis and retro-Diels-Alder reactions of diketo-dioxinones. Such dioxinones, which were synthesized by a range of C-acylation reactions, were found to undergo retro-Diels-Alder reactions on heating to provide the corresponding triketo-ketenes with the loss of acetone. The ketene reactive intermediates were rapidly trapped both inter- and intramolecularly with alcohols to provide the corresponding ß,δ,ζ-triketo-esters. These compounds, which consist of keto-enol mixtures, readily undergo cycloaromatization to produce resorcylate esters and macrocyclic lactones. We have established the use of diketo-dioxinones as key general intermediates for the synthesis of diverse resorcylate natural products and for the synthesis of new classes of compounds for the generation of medicinal chemistry lead structures. Many of the methods used were found to be tolerant of multiple sensitive functional groups. These include enolate C-acylations with acyl chlorides, 1-acyl-benzotriazoles, acyl imidazolides, or Weinreb amides to prepare diketo-dioxinones and their subsequent use to prepare ß,δ,ζ-triketo-esters and lactones and hence resorcylates. In addition, in most cases, phenol protection was avoided. As an alternative to the synthesis of ß,δ,ζ-triketo-esters, diketo-dioxinones were also found to undergo cycloaromatization with retention of the ketal entity via a nonketene pathway. Finally, diketo-dioxinones with an allyl, prenyl, geranyl, or other 2-alkenyl carboxylate esters at the γ-carbon underwent decarboxylative rearrangement with tetrakis(triphenylphosphine)palladium catalysis to produce α-substituted diketo-dioxinones and resorcylates with 3-allyl, prenyl, geranyl, or other 2-alkenyl groups. Such diketo-dioxinone chemistry was used in the total synthesis of natural products including aigialomycin, cruentaren A, and the oligomeric resorcylate antibiotics ent-W1278 A, B, and C. Additionally, tandem use of the decarboxylative rearrangement process and cycloaromatization was used in the total synthesis of natural products including the methyl ester of cristatic acid, mycophenolic acid, and hongoquercin B. The methodology was also applied to the synthesis of 9,10-anthraquinones, o-aminoalkyl resorcylates, dihydroxyisoindolinones, oligomers, and resorcinamides. The development of this methodology is described in this Account, showcasing its applicability and versatility for the synthesis of complex resorcylate products.

Heavier alkaline earth catalyzed ene-yne cyclizations: atom-efficient access to tetrahydroisoquinoline frameworks.

Tetrahydroisoquinoline frameworks may be accessed with 100% atom efficiency through the alkaline earth catalyzed addition of primary amines to ene-yne substrates through a sequence of intermolecular alkene and intramolecular alkyne hydroamination steps.

Cascade polyketide and polyene cyclizations: biomimetic total synthesis of hongoquercin B.

The total synthesis of hongoquercin B was carried out in 9 steps from trans,trans-farnesyl acetate using a palladium catalyzed decarboxylative π-farnesyl rearrangement of a diketo-dioxinone ester, aromatization and cationic diene-epoxide cyclization as key steps. This cascade tetracyclization simplifies the synthesis of terpenoid resorcylate natural products.