Single-Step Formation of Pyrimido[4,5‑<i>d</i>]pyridazines by a Pyrimidine-Tetrazine Tandem Reaction

A straightforward synthesis of pyrimido­[4,5-<i>d</i>]­pyridazines from pyrimidines and tetrazines under basic conditions is reported. Deprotonated, substituted 5-halopyrimidines readily react with variously substituted tetrazines in a highly regioselective manner via a complex reaction pathway, which was supported by DFT calculations. This mechanism leads to the empirically observed regioisomers without going through the conceivable hetaryne intermediate. These results on 5-halopyrimidines led to development of the methodology for preparation of opposite regioisomers based on 6-halopyrimidines

Control of α/β Anomer Formation by a 2′,5′ Bridge: Toward Nucleoside Derivatives Locked in the South Conformation

We describe a novel stereoselective synthesis of nucleoside derivatives with the ribose ring locked in the South conformation by a bridge between C2′ and C5′. Despite the intrinsic constraints of the bicyclic structure, we demonstrate that their synthesis can be achieved by ring closing metathesis of readily accessible precursors. The obtained ribose derivatives are, however, very poor substrates for further installation of the nucleobases, and even simple nucleophiles, such as azido or cyano anions, react with unexpected stereo- or regioselectivity under standard glycosylation conditions. Here we explain this behavior by employing density functional theory (DFT) computations and devise an alternative approach resulting in isomers with the desired orientation of the nucleobase

Benchmark Theoretical and Experimental Study on ¹⁵N NMR Shifts of Oxidatively Damaged Guanine

The ¹⁵N NMR shifts of 9-ethyl-8-oxoguanine (OG) were calculated and measured in liquid DMSO and in crystal. The OG molecule is a model for oxidatively damaged 2′-deoxyguanosine that occurs owing to oxidative stress in cell. The DNA lesion is repaired with human 8-oxoguanine glycosylase 1 (hOGG1) base-excision repair enzyme, however, the exact mechanism of excision of damaged nucleobase with hOGG1 is currently unknown. This benchmark study on ¹⁵N NMR shifts of OG aims their accurate structural interpretation and calibration of the calculation protocol utilizable in future studies on mechanism of hOGG1 enzyme. The effects of NMR reference, DFT functional, basis set, solvent, structure, and dynamics on calculated ¹⁵N NMR shifts were first evaluated for OG in crystal to calibrate the best performing calculation method. The effect of large-amplitude motions on ¹⁵N NMR shifts of OG in liquid was calculated employing molecular dynamics. The B3LYP method with Iglo-III basis used for B3LYP optimized geometry with 6-311++G­(d,p) basis and including effects of solvent and molecular dynamic was the calculation protocol used for calculation of ¹⁵N NMR shifts of OG. The NMR shift of N9 nitrogen of OG was particularly studied because the atom is involved in an N-glycosidic bond that is cleaved with hOGG1. The change of N9 NMR shift owing to oxidation of 9-ethylguanine (G) measured in liquid was −27.1 ppm. The calculated N9 NMR shift of OG deviated from experiment in crystal and in liquid by 0.45 and 0.65 ppm, respectively. The calculated change of N9 NMR shift owing to notable N9-pyramidalization of OG in one previously found polymorph was 20.53 ppm. We therefore assume that the pyramidal geometry of N9 nitrogen that could occur for damaged DNA within hOGG1 catalytic site might be detectable with ¹⁵N NMR spectroscopy. The calculation protocol can be used for accurate structural interpretation of ¹⁵N NMR shifts of oxidatively damaged guanine DNA residue

Selective Inhibitors of Cyclin G Associated Kinase (GAK) as Anti-Hepatitis C Agents

Cyclin G associated kinase (GAK) emerged as a promising drug target for the treatment of viral infections. However, no potent and selective GAK inhibitors have been reported in the literature to date. This paper describes the discovery of isothiazolo­[5,4-<i>b</i>]­pyridines as selective GAK inhibitors, with the most potent congeners displaying low nanomolar binding affinity for GAK. Cocrystallization experiments revealed that these compounds behaved as classic type I ATP-competitive kinase inhibitors. In addition, we have demonstrated that these compounds exhibit a potent activity against hepatitis C virus (HCV) by inhibiting two temporally distinct steps in the HCV life cycle (i.e., viral entry and assembly). Hence, these GAK inhibitors represent chemical probes to study GAK function in different disease areas where GAK has been implicated (including viral infection, cancer, and Parkinson’s disease)

Highly Selective Phosphatidylinositol 4‑Kinase IIIβ Inhibitors and Structural Insight into Their Mode of Action

Phosphatidylinositol 4-kinase IIIβ is a cellular lipid kinase pivotal to pathogenesis of various RNA viruses. These viruses hijack the enzyme in order to modify the structure of intracellular membranes and use them for the construction of functional replication machinery. Selective inhibitors of this enzyme are potential broad-spectrum antiviral agents, as inhibition of this enzyme results in the arrest of replication of PI4K IIIβ-dependent viruses. Herein, we report a detailed study of novel selective inhibitors of PI4K IIIβ, which exert antiviral activity against a panel of single-stranded positive-sense RNA viruses. Our crystallographic data show that the inhibitors occupy the binding site for the adenine ring of the ATP molecule and therefore prevent the phosphorylation reaction

Linguistic analysis of protein folding

Folding of nascent chains resembles the decoding of spoken language in that information is emitted as a unidirectional, one-dimensional string of elements, with higher structures and long-distance interactions emerging with time. Applying a ‘pseudolinguistic’ analysis of structure to a set of all 36 possible six-stranded antiparallel β-sandwich topologies reveals new order principles and reduces the complexity of this family significantly. The simple connectivity diagrams (‘linguistic trees’) proposed here allow predictions of the speed and cooperativity of β-sheet folding and help understanding the cotranslational folding from the N-terminus.Copyright 1996 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. Re-use of this article is permitted in accordance with the Terms and Conditions set out at http://www.elsevier.com/open-access/userlicense/1.0