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.

Cobalt-Catalyzed Bis-Borylation of Quinolines: The Importance of the Cobalt Triplet State.

We report herein a mild stereo- and regioselective dearomatization of quinolines using the simple low valent HCo(N2 )(PPh3 )3 complex that exhibits labile ligands. Conditions to form selectively, at room temperature, high-valued 1,4-bis-borylated tetrahydroquinolines from simple starting heteroaromatic compounds have been developed. The efficient and selective functionalization of a large scope of quinolines bearing various electron-donating or electron-withdrawing substituents is presented, as well as the post-modification of the resulting C-B bond. NMR and labelling studies are consistent with a cascade mechanism pathway, starting from an in situ generated paramagnetic bis-quinoline cobalt(I) hydride complex. A first quinoline dearomatization followed by a cobalt(I)-catalyzed Markovnikov hydroboration of the remaining double bond allows the introduction of the boronic ester group only at C4 position. DFT calculations particularly highlight the importance of the cobalt triplet state throughout the reaction pathway, and bring some rationalization for the observed C4 selective borylation.

Gold-Catalyzed Addition of Propargyl Acetates to Olefins via O-Acyl Migration/Cyclopropanation Sequence: Insight into the Diastereoselective Formation of the Alkene.

This article discloses a study on the well-known addition of propargyl acetates to olefins via an O-acyl migration/cyclopropanation sequence. Herein, we show that the stereochemical outcome of the olefin is strongly dependent on the gold catalyst and reaction parameters (concentration, temperature, and alkene partner equivalents); the E- and Z-isomers can be selectively formed by the judicious choice of reaction conditions.

Hydrido-Cobalt Complexes for the Chemo- and Regioselective 1,2-Silylative Dearomatization of N-Heteroarenes.

We describe an efficient regio- and chemoselective dearomatization of N-heteroarenes using hydrido-cobalt catalysts. Reactions were performed under mild conditions on a wide range of N-heteroarenes leading exclusively to the silyl-1,2-dihydroheteroarene. Various quinolines and pyridines bearing electron-donating and electron-withdrawing substituents are compatible with this methodology. DFT calculations, NMR spectroscopic studies, and X-ray diffraction analysis underlined the importance of a second silane for the final step of the reaction.

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.

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.

Chiral Phosphate in Rhodium-Catalyzed Asymmetric [2+2+2] Cycloaddition: Ligand, Counterion, or Both?

Investigations based on NMR spectroscopy, mass spectrometry, and DFT calculations shed light on the metallic species generated in the rhodium-catalyzed asymmetric [2+2+2] cycloaddition reaction between diynes and isocyanates with the chiral phosphate TRIP. The catalytic mixture comprising [{Rh(cod)Cl}2 ], 1,4-diphenylphosphinobutane (dppb), and Ag(S)-TRIP actually gives rise to two species, both having an effect on the stereoselectivity. One is a rhodium(I) complex in which TRIP is a weakly coordinating counterion, whereas the other is a bimetallic Rh/Ag complex in which TRIP is a strongly coordinating X-type ligand.

Double-Stereodifferentiation in Rhodium-Catalyzed [2 + 2 + 2] Cycloaddition: Chiral Ligand/Chiral Counterion Matched Pair.

The first enantioselective metal-catalyzed [2 + 2 + 2] cycloaddition involving a double asymmetric induction has been devised. It relies on the use of an in situ generated chiral cationic rhodium(I) catalyst with a matched chiral ligand/chiral counterion pair. Careful optimization of the catalytic system, as well as of the reaction conditions, led to atroposelective [2 + 2 + 2] pyridone cycloadducts with high ee's up to 96%. This strategy outperformed those previously described involving a chiral ligand only or a chiral counterion only.

Atroposelective [2+2+2] cycloadditions catalyzed by a rhodium(I)-chiral phosphate system.

Enantioselective cationic Rh(I)-catalyzed [2+2+2] cycloaddition reactions between diynes and isocyanates relying on the chiral anion strategy have been devised. In the presence of [Rh(cod)Cl]2, 1,4-bis(diphenylphosphino)butane, and the silver phosphate salt Ag(S)-TRIP as the unique source of chirality, axially chiral pyridones were isolated with ees up to 82%. This approach is novel in the field of chiral anion-mediated asymmetric catalysis since atroposelective transformations have so far remained unprecedented. It also proves to be complementary to the classical strategy based on chiral L-type ligands.

Enantioselective Ir(I)-catalyzed carbocyclization of 1,6-enynes by the chiral counterion strategy.

Enantioenriched bicyclo[4.1.0]hept-2-enes were synthesized by Ir(I)-catalyzed carbocyclization of 1,6-enynes. No chiral ligands were used, CO and PPh(3) were the only ligands bound to iridium. Instead, the stereochemical information was localized on the counterion of the catalyst, generated in situ by reaction of Vaska's complex (trans-[IrCl(CO)(PPh(3))(2)]) with a chiral silver phosphate. Enantiomeric excesses up to 93% were obtained when this catalytic mixture was used. (31)P NMR and IR spectroscopy suggest that formation of the trans- [Ir(CO)(PPh(3))(2)](+) moiety occurs by chlorine abstraction. Moreover, density functional theory calculations support a 6-endo-dig cyclization promoted by this cationic moiety. The chiral phosphate anion (O-P*) controls the enantioselectivity through formation of a loose ion pair with the metal center and establishes a C-H···O-P* hydrogen bond with the substrate. This is a rare example of asymmetric counterion-directed transition-metal catalysis and represents the first application of such a strategy to a C-C bond-forming reaction.

Synthesis of 1,2-amino alcohols by sigmatropic rearrangements of 3-(N-tosylamino)allylic alcohol derivatives.

Sigmatropic rearrangements of 3-(N-tosylamino)allylic alcohol derivatives, a particular subclass of functionalized enamides, have been investigated. Whereas the presence of the nitrogen atom alters the stereochemical outcome of Ireland-Claisen rearrangements of glycolates derived from such substrates, [2,3]-Wittig rearrangements of α-allyloxy acetamides or propargylic ethers derivatives provide access to a wide variety of functionalized 1,2-amino alcohols usually with high levels of stereocontrol, as well as to heterocyclic compounds. The stereoselectivity issues of these rearrangements (1,2-diastereoselectivity, auxiliary-induced diastereoselection, chirality transfer, and double stereodifferentiation) were thoroughly investigated.

A novel pyrazolo[1,5-a]pyrimidine is a potent inhibitor of cyclin-dependent protein kinases 1, 2, and 9, which demonstrates antitumor effects in human tumor xenografts following oral administration.

Cyclin-dependent protein kinases (CDKs) are central to the appropriate regulation of cell proliferation, apoptosis, and gene expression. Abnormalities in CDK activity and regulation are common features of cancer, making CDK family members attractive targets for the development of anticancer drugs. Here, we report the identification of a pyrazolo[1,5-a]pyrimidine derived compound, 4k (BS-194), as a selective and potent CDK inhibitor, which inhibits CDK2, CDK1, CDK5, CDK7, and CDK9 (IC50= 3, 30, 30, 250, and 90 nmol/L, respectively). Cell-based studies showed inhibition of the phosphorylation of CDK substrates, Rb and the RNA polymerase II C-terminal domain, down-regulation of cyclins A, E, and D1, and cell cycle block in the S and G2/M phases. Consistent with these findings, 4k demonstrated potent antiproliferative activity in 60 cancer cell lines tested (mean GI50= 280 nmol/L). Pharmacokinetic studies showed that 4k is orally bioavailable, with an elimination half-life of 178 min following oral dosing in mice. When administered at a concentration of 25 mg/kg orally, 4k inhibited human tumor xenografts and suppressed CDK substrate phosphorylation. These findings identify 4k as a novel, potent CDK selective inhibitor with potential for oral delivery in cancer patients.

Total synthesis of amphidinolide J.

The marine natural product amphidinolide J has been synthesized according to a convergent strategy. The key steps of this synthesis include a B-alkyl Suzuki-Miyaura coupling and the addition of an alkynyllithium reagent to a Weinreb amide to build the C4-C5 and C12-C13 bonds, respectively, and a Yamaguchi macrolactonization.

Stereoselective synthesis of 1,2-aminoalcohols by [2,3]-wittig rearrangements.

[2,3]-Wittig rearrangements of (E)-3-aza-allylic alcohol derivatives can provide access to functionalized 1,2-aminoalcohols with high syn or anti diastereoselectivity depending on the anionic stabilizing group (amide or alkyne).