Specific CLK inhibitors from a novel chemotype for regulation of alternative splicing

There is a growing recognition of the importance of protein kinases in the control of alternative splicing. To define the underlying regulatory mechanisms, highly selective inhibitors are needed. Here, we report the discovery and characterization of the dichloroindolyl enaminonitrile KH-CB19, a potent and highly specific inhibitor of the CDC2-like kinase isoforms 1 and 4 (CLK1/CLK4). Cocrystal structures of KH-CB19 with CLK1 and CLK3 revealed a non-ATP mimetic binding mode, conformational changes in helix αC and the phosphate binding loop and halogen bonding to the kinase hinge region. KH-CB19 effectively suppressed phosphorylation of SR (serine/arginine) proteins in cells, consistent with its expected mechanism of action. Chemical inhibition of CLK1/CLK4 generated a unique pattern of splicing factor dephosphorylation and had at low nM concentration a profound effect on splicing of the two tissue factor isoforms flTF (full-length TF) and asHTF (alternatively spliced human TF).     

Geometrothermodynamics of higher dimensional black holes

We study the thermodynamics and geometrothermodynamics of different black hole configurations in more than four spacetime dimensions. We use the response functions to find the conditions under which second order phase transitions occur in higher-dimensional static Reissner–Nordström and stationary Kerr black holes. Our results indicate that the equilibrium manifold of all these black hole configurations is in general curved and that curvature singularities appear exactly at those places where second order phase transitions occur.     

On the Diastereoselectivity of the Aqueous-Acid-Catalyzed Intramolecular Aldol Condensation of 3-Oxocyclohexaneacetaldehydes

The factors responsible for the diastereoselective formation of the 6-endo-hydroxybicyclo[2.2.2]octan-2-one by acid-catalyzed intramolecular aldol reaction of 3-oxocyclohexaneacetaldehydes have been investigated. This study, carried out on (1SR,4RS,6RS)-6-hydroxybicyclo[2.2.2]octan-2-one 1a , (1SR,4RS,6SR)-6-hydroxybicyclo[2.2.2]octan-2-one 1b , and 3,3-(ethylenedioxy)cyclohexaneacetaldehyde 2a , allowed to demonstrate the absence of intramolecular H-bonding in 1a as a stabilizing factor, and to ascertain the presence of unfavorable steric interactions in 1b .     

Synthesis and target identification of hymenialdisine analogs

Hymenialdisine (HMD) is a sponge-derived natural product kinase inhibitor with nanomolar activity against CDKs, Mek1, GSK3beta, and CK1 and micromolar activity against Chk1. In order to explore the broader application of the pyrrolo[2,3-c]azepine skeleton of HMD as a general kinase inhibitory scaffold, we searched for additional protein targets using affinity chromatography in conjunction with the synthesis of diverse HMD analogs and profiled HMD against a panel of 60 recombinant enzymes. This effort has led to nanomolar to micromolar inhibitors of 11 new targets including p90RSK, KDR, c-Kit, Fes, MAPK1, PAK2, PDK1, PKCtheta, PKD2, Rsk1, and SGK. The synthesis of HMD analogs has resulted in the identification of compounds with enhanced and/or dramatically altered selectivities relative to HMD (28n) and in molecules with antiproliferative activities 30-fold higher than HMD (28p).     

Hydrogenation of the ansa-Chain of Rifamycins. X-ray crystal structure of (16S)-16,17,18,19-tetrahydrorifamycin S

The catalytic hydrogenation of rifamycin S ( 2 ) over Pd/C, followed by oxidation with K₃[Fe(CN)₆], generates a pair of 16,17,18,19-tetrahydrorifamycins S ( 3/4 ), epimeric at C (16). The use of PtO₂ as catalyst leads to the hydrogenation also of the C(28)?C(29) bond giving, after oxidation by K₃[Fe(CN)₆], a mixture of the epimers (16R)- and (16S)-16,17,18,19,28,29-hexahydrorifamycins S ( 5/6 ). Furthermore, we synthesized the (16R)- and (16S)-3-bromo derivatives 7/8 and (16R)- and (16S)-3-(piperidin-1-yl) derivatives 9/10 . The determination of the X-ray crystal structure of the most abundant epimer 4 of the tetrahydrorifamycins allowed the assignment of the absolute configuration at C(16) of all derivative. A Structure-activity relationship study showed that in general the (16R)-epimers are more potent inhibitors of bacterial RNA polymerase than the (16S)-epimers.     

Solid-State NMR-Driven Crystal Structure Prediction of Molecular Crystals: The Case of Mebendazole

Among all possible NMR crystallography approaches for crystal-structure determination, crystal structure prediction – NMR crystallography (CSP-NMRX) has recently turned out to be a powerful method. In the latter, the original procedure exploited solid-state NMR (SSNMR) information during the final steps of the prediction. In particular, it used the comparison of computed and experimental chemical shifts for the selection of the correct crystal packing. Still, the prediction procedure, generally carried out with DFT methods, may require important computational resources and be quite time-consuming, especially if there are no available constraints to use at the initial stage. Herein, the successful application of this combined prediction method, which exploits NMR information also in the input step to reduce the search space of the predictive algorithm, is presented. Herein, this method was applied on mebendazole, which is characterized by desmotropism. The use of SSNMR data as constraints for the selection of the right tautomer and the determination of the number of independent molecules in the unit cell led to a considerably faster process, reducing the number of calculations to be performed. In this way, the crystal packing was successfully predicted for the three known phases of mebendazole. To evaluate the quality of the predicted structures, these were compared to the experimental ones. The crystal structure of phase B of mebendazole, in particular, was determined de novo by powder diffraction and is presented for the first time in this paper.     

Tethered particle motion as a diagnostic of DNA tether length

The tethered particle motion (TPM) technique involves an analysis of the Brownian motion of a bead tethered to a slide by a single DNA molecule. We describe an improved experimental protocol with which to form the tethers, an algorithm for analyzing bead motion visualized using differential interference contrast microscopy, and a physical model with which we have successfully simulated such DNA tethers. Both experiment and theory show that the statistics of the bead motion are quite different from those of a free semiflexible polymer. Our experimental data for chain extension versus tether length fit our model over a range of tether lengths from 109 to 3477 base pairs, using a value for the DNA persistence length that is consistent with those obtained under similar solution conditions by other methods. Moreover, we present the first experimental determination of the full probability distribution function of bead displacements and find excellent agreement with our theoretical prediction. Our results show that TPM is a useful tool for monitoring large conformational changes such as DNA looping.     

Contact symmetries and Hamiltonian thermodynamics

It has been shown that contact geometry is the proper framework underlying classical thermodynamics and that thermodynamic fluctuations are captured by an additional metric structure related to Fisher’s Information Matrix. In this work we analyse several unaddressed aspects about the application of contact and metric geometry to thermodynamics. We consider here the Thermodynamic Phase Space and start by investigating the role of gauge transformations and Legendre symmetries for metric contact manifolds and their significance in thermodynamics. Then we present a novel mathematical characterization of first order phase transitions as equilibrium processes on the Thermodynamic Phase Space for which the Legendre symmetry is broken. Moreover, we use contact Hamiltonian dynamics to represent thermodynamic processes in a way that resembles the classical Hamiltonian formulation of conservative mechanics and we show that the relevant Hamiltonian coincides with the irreversible entropy production along thermodynamic processes. Therefore, we use such property to give a geometric definition of thermodynamically admissible fluctuations according to the Second Law of thermodynamics. Finally, we show that the length of a curve describing a thermodynamic process measures its entropy production.     

X-Ray Crystal Structure of 25-O-Deacetyl-27, 28-didehydro-27-demthoxy-11-deoxo-11, 29-epoxy-28,29-dihydro-21,23-O-isopropylidenerifamycin S

In search of new types of semisynthetic derivatives of the natural antibiotic rifamycin S ( 1 ), we synthesized 25-O-deacetyl-27,28-didehydro-27-demethoxy-11-deoxo-11,29-epoxy-28, 29-dihydro-21,23-O-isopropyli-denerifamycin S ( 3 ). Its X-ray crystal structure shows a new type of ansa-chain with an 11,29-epoxy moiety, the loss of the MeO group on C(27), and the shift of the C?C bond from C(28),C(29) to C(27),C(28). These modifications result in a conformational rearrangement of the whole ansa-chain, nonetheless the overall spatial shape of the molecule is still close to that of most rifamycins. As found in other 11-deoxo-11-hydroxyrifamycin-S derivatives, the chromophore rings of 3 give rise to π-π association in the crystal.     

A Stereoselective Total Synthesis of (±)-Maritimol, (±)-2-Deoxystemodinone, (±)-Stemodinone,and (±)-Stemodin

A simple and stereoselective total synthesis of (±)-maritimol ( 2d ) and its conversion into the other title compounds (±)-( 2a ), ((±)- 2b ), and ((±)- 2c ) is described. The unique bicyclo[3.2.1]octane moiety, constituting their C/D-ring system, is stereospecifically obtained by solvolytic rearrangement of the methanesulfonate 23 .