Structure and Replication of yDNA: A Novel Genetic Set Widened by Benzo‐Homologation

In a functioning genetic system, the information‐encoding molecule must form a regular self‐complementary complex (for example, the base‐paired double helix of DNA) and it must be able to encode information and pass it on to new generations. Here we study a benzo‐widened DNA‐like molecule (yDNA) as a candidate for an alternative genetic set, and we explicitly test these two structural and functional requirements. The solution structure of a 10 bp yDNA duplex is measured by using 2D‐NMR methods for a simple sequence composed of T–yA/yA–T pairs. The data confirm an antiparallel, right‐handed, hydrogen‐bonded helix resembling B‐DNA but with a wider diameter and enlarged base‐pair size. In addition to this, the abilities of two different polymerase enzymes (Klenow fragment of DNA pol I (Kf) and the repair enzyme Dpo4) to synthesize and extend the yDNA pairs T–yA, A–yT, and G–yC are measured by steady‐state kinetics studies. Not surprisingly, insertion of complementary bases opposite yDNA bases is inefficient due to the larger base‐pair size. We find that correct pairing occurs in several cases by both enzymes, but that common and relatively efficient mispairing involving T–yT and T–yC pairs interferes with fully correct formation and extension of pairs by these polymerases. Interestingly, the data show that extension of the large pairs is considerably more efficient with the flexible repair enzyme (Dpo4) than with the more rigid Kf enzyme. The results shed light on the properties of yDNA as a candidate for an alternative genetic information‐encoding molecule and as a tool for application in basic science and biomedicine.     

Making Epothilones Fluoresce: Design,Synthesis, and Biological Characterization of a Fluorescent N12‐Aza‐Epothilone (Azathilone)

A green fluorescent 12‐aza‐epothilone (azathilone) derivative has been prepared through the attachment of the 4‐nitro‐2,1,3‐benzoxadiazole (NBD) fluorophore to the 12‐nitrogen atom of the azamacrolide core structure. While less potent than natural epothilones or different N12‐acylated azathilone derivatives, NBD‐azathilone ( 3 ) promotes tubulin assembly, inhibits cancer cell proliferation in vitro and arrests the cell cycle at the G2/M transition. Most significantly, the binding of 3 to cellular microtubules (MTs) could be directly visualized by confocal fluorescence microscopy. Based on competition binding experiments with laulimalide‐stabilized MTs in vitro, the N12‐Boc substituted azathilone 1 , Epo A, and NBD‐azathilone ( 3 ) all interact with the same tubulin‐binding site. Computational studies provided a structural model of the complexes between β‐tubulin and 1 or 3 , respectively, in which the NBD moiety of 3 or the BOC moiety of 1 directly and specifically contribute to MT binding. Collectively, these data demonstrate that the cellular effects of 3 and, by inference, also of other azathilones are the result of their interactions with the cellular MT network.     

Inhibition of HSP90 with Pochoximes: SAR and Structure‐Based Insights

The pochoximes, based on the radicicol pharmacophore, are potent inhibitors of heat shock protein 90 (HSP90) that retain their activity in vivo. Herein we report an extended library that broadly explores the structure–activity relationship (SAR) of the pochoximes with four points of diversity. Several modifications were identified that afford improved cellular efficacy, new opportunities for conjugation, and further diversifications. Cocrystal structures of pochoximes A and B with HSP90 show that pochoximes bind to a different conformation of HSP90 than radicicol and provide a rationale for the enhanced affinity of the pochoximes relative to radicicol and the pochonins.     

Potent Inhibition of Acid Sphingomyelinase by Phosphoinositide Analogues

The different mammalian sphingomyelinases are involved in cell regulation, apoptosis and inflammatory events. Recent reports suggest pharmacological potential especially for inhibitors of the acid sphingomyelinase. Phosphatidyl inositol‐3,5bisphosphate (PtdIns3,5P₂) is the most potent selective acid sphingomyelinase inhibitor known to date. In the present study, we synthesized analogues of PtdIns3,5P₂ for initial structure–activity‐relationship (SAR) studies. We identified an inhibitor that is easy to synthesize, that has superior chemical and biophysical properties when compared to PtdIns3,5P₂ and that should be stable against virtually all phospholipases. Last but not least, the new inhibitor partially protected cells from dexamethasone‐induced cell death.