Thomas Eiland Nielsen

Synthesis of Heterocycles through a Ruthenium‐Catalyzed Tandem Ring‐Closing Metathesis/Isomerization/N‐Acyliminium Cyclization Sequence

Olefin metathesis is an extremely powerful and general method for carbon–carbon bond formation in organic synthesis. For example, ruthenium alkylidene catalyzed metathesis has been widely used to construct a variety of alkenes for applications in chemistry, materials science, and chemical biology. A key asset of the metathesis process is the unique olefin functional group selectivity mediated by robust and well-defined catalytic systems. Over the years, however, unexpected nonmetathetic reactions have been observed under metathesis conditions. Although these reactions typically are highly substrate dependent, associated with specific reaction conditions, and possibly caused by ill-defined metal-catalytic species, they represent a unique opportunity for the development of tandem processes. It is well recognized that tandem reactions offer major advantages in the synthesis of valuable target compounds. In this context, metathesis mediated by ruthenium alkylidene catalysts 1 e and 1k (Grubbs firstand second-generation catalysts; Figure 1) has successfully been coupled to nonmetathetic transformations, such as double-bond isomerization, hydrogenation, cyclopropanation, dihydroxylation, 12] keto-hydroxylation, and Kharasch addition reactions. Only a few reports have dealt with the tandem ringclosing metathesis (RCM)/ double-bond isomerization. Notable works by the groups of Snapper and Schmidt have independently shown how cyclic allyl ethers can isomerize into 2,3-dihydropyrans. Schmidt and co-workers have also shown the beneficial effect of added hydride to favor the isomerization step. Inspired by the work of Fustero et al. (RCM/isomerization), and P rez-Castells and co-workers (RCM/isomerization/cyclopropanation), we speculated that enamides generated in the event of a RCM/isomerization sequence could be further isomerized into reactive Nacyliminium intermediates (Scheme 1). The presence of a suitably tethered nucleophile could then bring about a second cyclization step.

N‐acyliminium intermediates in solid‐phase synthesis

N‐Acyliminium ions are powerful intermediates in synthetic organic chemistry. Examples of their use are numerous in solution‐phase synthesis, but there are unmerited few reports on these highly reactive electrophiles in solid‐phase synthesis. The present review covers the literature to date and illustrates the methods used to generate N‐acyliminium intermediates on solid support and their further elaboration to a range of pharmacologically interesting peptidomimetics, heterocycles, and other small molecules.

Synthesis of tetrahydro-β-carbolines via isomerization of N-allyltryptamines: a metal-catalyzed variation on the Pictet–Spengler theme

An efficient and broadly applicable alternative to the classical Pictet-Spengler synthesis of tetrahydro-β-carbolines is presented. The method relies on metal-catalyzed isomerization of allylic amines to form reactive iminium intermediates which can be trapped by a tethered indole nucleophile.

Comparative Systems Biology Analysis To Study the Mode of Action of the Isothiocyanate Compound Iberin on Pseudomonas aeruginosa

ABSTRACT Food is now recognized as a natural resource of novel antimicrobial agents, including those that target the virulence mechanisms of bacterial pathogens. Iberin, an isothiocyanate compound from horseradish, was recently identified as a quorum-sensing inhibitor (QSI) of the bacterial pathogen Pseudomonas aeruginosa. In this study, we used a comparative systems biology approach to unravel the molecular mechanisms of the effects of iberin on QS and virulence factor expression of P. aeruginosa. Our study shows that the two systems biology methods used (i.e., RNA sequencing and proteomics) complement each other and provide a thorough overview of the impact of iberin on P. aeruginosa. RNA sequencing-based transcriptomics showed that iberin inhibits the expression of the GacA-dependent small regulatory RNAs RsmY and RsmZ; this was verified by using gfp-based transcriptional reporter fusions with the rsmY or rsmZ promoter regions. Isobaric tags for relative and absolute quantitation (iTRAQ) proteomics showed that iberin reduces the abundance of the LadS protein, an activator of GacS. Taken together, the findings suggest that the mode of QS inhibition in iberin is through downregulation of the Gac/Rsm QS network, which in turn leads to the repression of QS-regulated virulence factors, such as pyoverdine, chitinase, and protease IV. Lastly, as expected from the observed repression of small regulatory RNA synthesis, we also show that iberin effectively reduces biofilm formation. This suggests that small regulatory RNAs might serve as potential targets in the future development of therapies against pathogens that use QS for controlling virulence factor expression and assume the biofilm mode of growth in the process of causing disease.

Ralph F. Hirschmann award address 2009: Merger of organic chemistry with peptide diversity

A huge unleashed potential lies hidden in the large and diverse pool of encoded and particularly nonencoded chiral α‐, β‐, and γ‐amino acids available today. Although these have been extensively exploited in peptide science, the community of organic chemistry has only used this source of diversity in a quite focused and targeted manner. The properties and behavior of peptides as functional molecules in biology are well documented and based on the ability of peptides to adapt a range of discrete conformers at a minimal entropic penalty and therefore ideally fitting their endogenous targets. The development of new organic reactions and chemistries that in a general and quantitative way transform peptides into new functional molecules, preferably on solid support, is a source of completely new classes of molecules with important and advantageous functional properties. The peptide diversity and the ability to perform chemistry on solid support add tremendously to the combinatorial scope of such reactions in pharmaceutical and materials screening scenario. In recent years, the need for “click” reactions to shape complex molecular architecture has been realized mainly with a basis in the world of peptides and DNA, and in polymer chemistry where connection of highly functionalized biologically active substances or property bearing fragments are assembled as molecular LEGO® using quantitative and orthogonal click chemistries. In this article, three such new reactions originating in the Carlsberg Laboratory over the last decade taking advantage of organic transformations in the peptide framework is presented. Initially, the click reaction between azide and terminal alkynes catalyzed by Cu(1) (CuAAC‐reaction) is described. This CuAAC “click” reaction was observed first at Carlsberg Laboratory in reactions of azido acid chlorides with alkynes on solid support. Second, the Electrophilic Aromatic Substitution Cyclization–Intramolecular Click‐Cascade (EASCy‐ICC) reaction will be presented. This quantitative stereo‐selective cascade reaction provides a highly diverse set of interesting novel scaffolds from peptides. Finally, we describe the preparation of solid phase peptide phosphine‐ and carbene‐based green catalysts (organozymes), which upon complex formation with transition metal perform with high turnovers under aqueous conditions. These catalysts thrive from the peptide folding and diversity, while phosphines and carbenes in the backbone provide for bidental complex formation with transition metals in a format providing an excellent entry into combinatorial catalyst chemistry.

Multiple diguanylate cyclase‐coordinated regulation of pyoverdine synthesis in Pseudomonas aeruginosa

The nucleotide signalling molecule bis-(3-5)-cyclic dimeric guanosine monophosphate (c-di-GMP) plays an essential role in regulating microbial virulence and biofilm formation. C-di-GMP is synthesized by diguanylate cyclase (DGC) enzymes and degraded by phosphodiesterase (PDE) enzymes. One intrinsic feature of c-di-GMP signalling is the abundance of DGCs and PDEs encoded by many bacterial species. It is unclear whether the different DGCs or PDEs coordinately establish the c-di-GMP regulation or function independently of each other. Here, we provide evidence that multiple DGCs are involved in regulation of c-di-GMP on synthesis of the major iron siderophore pyoverdine in Pseudomonas aeruginosa. Constitutive expression of the WspG or YedQ DGC in P.u2009aeruginosa is able to induce its pyoverdine synthesis. Induction of pyoverdine synthesis by high intracellular c-di-GMP depends on the synthesis of exopolysaccharides and another two DGCs, SiaD and SadC. SiaD was found to boost the c-di-GMP synthesis together with constitutively expressing YedQ. The exopolysaccharides and the SiaD DGC were found to modulate the expression of the RsmY/RsmZ ncRNAs. Induction of the RsmY/RsmZ ncRNAs might enhance the pyoverdine synthesis through SadC. Our study sheds light on a novel multiple DGC-coordinated c-di-GMP regulatory mechanism of bacteria.

Enzymatic resolution to (-)-ormeloxifene intermediates from their racemates using immobilized Candida rugosa lipase.

In the synthesis of (-)-ormeloxifene, a drug candidate recently under development, enzymatic resolution of potential intermediates can be carried out using a simple, practical method. Five commercially available lipases, Candida rugosa lipase, Candida antarctica lipase B, Mucor miehei lipase, Pseudomonas cepacia lipase, and Humicola lanuginosa lipase, all immobilized on Accurel(R), were initially screened in combination with four different substrates belonging to the class of phenyl esters. Excellent stereoselectivity was observed using C. rugosa lipase with an acetate as substrate, but low reaction rates were observed in scale-up experiments. However, by changing the acyl part of the ester into a hexanoyl moiety and subjecting this substrate to enzymatic hydrolysis in aqueous acetonitrile at room temperature by C. rugosa lipase, it became possible to run the reaction to a 50% conversion on a 10 g scale within a period of 4 h, obtaining a phenolic product of more than 95% ee that could be converted to the target molecule, (-)-ormeloxifene, in two synthetic steps. Simple recovery of the immobilized enzyme by filtration allowed multiple recycling of the catalyst without significant loss of enzymatic activity. Capillary electrophoresis with sulfobutyl ether beta-cyclodextrin as a chiral buffer additive and acetonitrile as an organic modifier was demonstrated to provide an excellent chiral analytical tool for monitoring the enzymatic reactions.

An Improved Protocol for the Synthesis of 1-(Mesitylenesulfonyl)-3-nitro-1,2,4-triazole (MSNT)

Since the pioneering work of Merrifield,1–5 solid-phase synthesis has become a key technology for the rapid parallel synthesis of polypeptides and other oligomeric compounds for drug discovery and chemical biology research. With an increasing number of peptide and peptide mimetic drug candidates in the pipelines of large pharmaceutical companies, solidphase synthesis will likely continue to have a major impact on pharmaceutical chemistry. For solid-phase synthesis, it is essential that all transformations on the solid support proceed in a quantitative fashion. Until the final step of a synthetic sequence, reaction products remain covalently bound to the support and can only be purified by simple washings and filtrations, rendering any incomplete reaction step along the way a source of decreased yields of products. Solid-phase synthesis typically involves the creation of amideor ester bonds, either as part of the linkage strategy, or to build the final product. In this context, a multitude of coupling reagents has been developed. For example, reagents for esterification on solid support include N,N ′-dicyclohexylcarbodiimide (DCC) in conjunction with 4-(N,N-dimethylamino)pyridine (DMAP)6 or 1-hydroxybenzotriazole (HOBt),7 2,6-dichlorobenzoyl chloride,8 and diethyl azodicarboxylate–triphenylphosphine.9 However, these activators generally result in inferior conversions and product yields. 1-(Mesitylenesulfonyl)-3-nitro-1,2,4-triazole (MSNT) has most often been used for the formation of phosphateand phosphorothiolate esters in oligonucleotide synthesis,10–18 and, to a limited extent for amide-bond formation in peptide synthesis.19,20 Another important application of MSNT is its usefulness to anchor the C-terminal of amino acids to hydroxyl-functionalized supports.21–23 MSNT-based esterification protocols generally proceed with minimal racemization in high yields, and have therefore frequently been