Solution phase synthesis of short oligoribonucleotides on a precipitative tetrapodal support

• Alejandro Gimenez Molina,
• Amit M. Jabgunde,
• Pasi Virta and
• Harri Lönnberg

Beilstein J. Org. Chem. 2014, 10, 2279–2285, doi:10.3762/bjoc.10.237

• , dynamics of chain invasion and recognition by small molecular entities [6][7][8][9][10]. The quantities of short RNA sequences required for such studies are often larger than what can easily be obtained by lab-scale solid phase synthesis. In other words, there seems to be a need for a straightforward

Synthesis and optical properties of pyrrolidinyl peptide nucleic acid carrying a clicked Nile red label

• Nattawut Yotapan,
• Chayan Charoenpakdee,
• Pawinee Wathanathavorn,
• Boonsong Ditmangklo,
• Hans-Achim Wagenknecht and
• Tirayut Vilaivan

Beilstein J. Org. Chem. 2014, 10, 2166–2174, doi:10.3762/bjoc.10.224

• under different sequence context, were successfully synthesized and characterized by MALDI–TOF MS (Figure 1 and Table 1). Isolated yields in the range of 6–18% were obtained (0.5 μmol scale), which are typical for solid phase synthesis, whereby the majority of material loss occurred during HPLC

Second generation silver(I)-mediated imidazole base pairs

• Susanne Hensel,
• Nicole Megger,
• Kristina Schweizer and
• Jens Müller

Beilstein J. Org. Chem. 2014, 10, 2139–2144, doi:10.3762/bjoc.10.221

• shows silver(I)-mediated methylimidazole homo base pairs involving either 2-methylimidazole (top) or 4-methylimidazole (bottom), resulting in a shielded access to the silver(I) ions from the minor and major groove, respectively. The phosphoramidites required for automated DNA solid-phase synthesis were

• the two hydroxy functions with the dimethoxytrityl and the 2-cyanoethyl-N,N-diisopropylphosphoramidite moieties, finally resulting in the formation of 4a/4b suitable for automated solid-phase oligonucleotide synthesis. The pKa values of the free nucleosides 2a/2b were determined by pD-dependent 1H NMR

• ) ions from minor and major groove, respectively. Synthesis of methylimidazole-based nucleosides and their corresponding phosphoramidites required for automated solid-phase DNA synthesis. a) 1. NaH, 2. Hoffer’s chloro sugar, CH3CN, 0 °C to ambient temperature, 3 h; b) aqueous NH3 (25%), CH3OH, ambient

Synthesis of phosphoramidites of isoGNA, an isomer of glycerol nucleic acid

• Keunsoo Kim,
• Venkateshwarlu Punna,
• Phaneendrasai Karri and
• Ramanarayanan Krishnamurthy

Beilstein J. Org. Chem. 2014, 10, 2131–2138, doi:10.3762/bjoc.10.220

• triethylamine·HF complex instead of TBAF was preferable at room temperature. The free alcohols 12, 18, 21 and 24 were phosphitylated under standard conditions to obtain the phosphoramidites suitable for the automated solid phase synthesis. Conclusion We have described herein improvements to and the optimization of

Synthesis of a bifunctional cytidine derivative and its conjugation to RNA for in vitro selection of a cytidine deaminase ribozyme

• Nico Rublack and
• Sabine Müller

Beilstein J. Org. Chem. 2014, 10, 1906–1913, doi:10.3762/bjoc.10.198

• confirmed by successful conjugation to the 3'-terminus of a model RNA, as analyzed by HPLC and MALDI–MS. This set-up is going to be used for selection of a cytidine deaminase ribozyme supporting the conversion of uridine to cytidine. Active molecules will be cleaved from the solid phase and released into

Convergent synthetic methodology for the construction of self-adjuvanting lipopeptide vaccines using a novel carbohydrate scaffold

• Vincent Fagan,
• Istvan Toth and
• Pavla Simerska

Beilstein J. Org. Chem. 2014, 10, 1741–1748, doi:10.3762/bjoc.10.181

• previously reported carbohydrate-based vaccine constructs [11] were prepared by a divergent approach, where the carbohydrate core was coupled to the resin-bound LCP adjuvanting moiety, followed by stepwise synthesis of the B cell epitopes using solid-phase peptide synthesis (SPPS). Using this divergent

Multicomponent reactions in nucleoside chemistry

• Mariola Koszytkowska-Stawińska and
• Włodzimierz Buchowicz

Beilstein J. Org. Chem. 2014, 10, 1706–1732, doi:10.3762/bjoc.10.179

• ). Complete deprotection of 43 was accomplished in methanolic HCl to yield products 44 as mixtures of diastereoisomers. The Ugi reaction has been often used in solid-phase synthesis of compound libraries [83]. Suda et al. developed the optimal reaction conditions of the solid-phase Ugi reaction involving Rink

• (IC50 = 4.78 µM) was significantly lower than that of nikkomycin Z (IC50 = 0.06 µM). The remaining compounds 46 were inactive toward Candida albicans chitin synthase 2. Another approach to the solid-phase synthesis of nucleoside analogs was developed by Sun and Lee (Scheme 19) [85]. The library of 1344

• -nucleoside substrates, the ones dealing with the construction of a non-natural nucleobase predominated (18 examples). Interestingly, a combinatorial solid-phase approach has not been extensively exploited (2 examples). The findings concerning the syntheses of nucleoside antibiotic analogs or 1'-aza-analogs

Photoswitchable precision glycooligomers and their lectin binding

• Daniela Ponader,
• Sinaida Igde,
• Marko Wehle,
• Katharina Märker,
• Mark Santer,
• David Bléger and
• Laura Hartmann

Beilstein J. Org. Chem. 2014, 10, 1603–1612, doi:10.3762/bjoc.10.166

• & Bio-Systems, Research Campus Golm, 14424 Potsdam, Germany Humboldt University, Department of Chemistry, Brook-Taylor-Str. 2, 12489 Berlin, Germany 10.3762/bjoc.10.166 Abstract The synthesis of photoswitchable glycooligomers is presented by applying solid-phase polymer synthesis and functional

• the combination of solid phase polymer synthesis and tailor-made building blocks [7][8][9]. Through a stepwise assembly of our functional building blocks, we can now control the kind, number, and spacing of sugar ligands along a monodisperse scaffold. Thus, our precision glycomacromolecules allow for

• azobenzene functionalized with an Fmoc-protected aminomethyl group and a carboxylic acid both para to the N=N bond was used as one building block during solid-phase polymer synthesis of precision glycomacromolecules (see AZO, Figure 1) [19][20][21][22]. The benzylamine fragment was favored over the

Orthogonal dual thiol–chloroacetyl and thiol–ene couplings for the sequential one-pot assembly of heteroglycoclusters

• Michele Fiore,
• Gour Chand Daskhan,
• Baptiste Thomas and
• Olivier Renaudet

Beilstein J. Org. Chem. 2014, 10, 1557–1563, doi:10.3762/bjoc.10.160

• 3000+ Bruker Daltonics in positive mode. General procedure for solid-phase peptide synthesis. Assembly of all protected peptides was carried out on a synthesizer (Syro II, Biotage) using the Fmoc/t-Bu strategy and the Fmoc-Gly-SasrinTM resin. Coupling reactions were performed using, relative to the

Synthesis and solvodynamic diameter measurements of closely related mannodendrimers for the study of multivalent carbohydrate–protein interactions

• Yoann M. Chabre,
• Alex Papadopoulos,
• Alexandre A. Arnold and
• René Roy

Beilstein J. Org. Chem. 2014, 10, 1524–1535, doi:10.3762/bjoc.10.157

• precipitation of the complexes [30][31]. Alternatively, the application of surface plasmon resonance (SPR) also creates artificial situations not sufficiently related to the natural cellular events, thus requiring complex mathematical algorithms [32]. Most solid-phase immunoassays (ELLA, ELISA) also fall under

Bis(β-lactosyl)-[60]fullerene as novel class of glycolipids useful for the detection and the decontamination of biological toxins of the Ricinus communis family

• Hirofumi Dohi,
• Takeru Kanazawa,
• Akihiro Saito,
• Keita Sato,
• Hirotaka Uzawa,
• Yasuo Seto and
• Yoshihiro Nishida

Beilstein J. Org. Chem. 2014, 10, 1504–1512, doi:10.3762/bjoc.10.155

• undertook an alternative way by means of the SDS-PAGE. The results summarized in Table 1 show that the ricin protein was partitioned into two phases, i.e., solid phase (precipitates) and liquid phase (supernatants), after the sedimentation. Its distribution (%) in the solid phase increased with the

• multivalent protein–lactose interactions, prompted us to apply this glycolipid as a tool for the rapid detection and the decontamination of ricin and other biological toxins. By using an SDS-PAGE analysis, we successfully quantified distributions (%) of ricin in the aqueous and the solid phase. With this

Pyrene-modified PNAs: Stacking interactions and selective excimer emission in PNA₂DNA triplexes

• Alex Manicardi,
• Lucia Guidi,
• Alice Ghidini and
• Roberto Corradini

Beilstein J. Org. Chem. 2014, 10, 1495–1503, doi:10.3762/bjoc.10.154

• using standard Fmoc-based manual solid phase protocol. The crude products were purified by RP-HPLC and characterized by HPLC–UV–MS (Supporting Information File 1, Figures S6–S11). Thermal stability of PNA:DNA complexes The introduction of a modification in a PNA stand can lead to different effects

Design, automated synthesis and immunological evaluation of NOD2-ligand–antigen conjugates

• Marian M. J. H. P. Willems,
• Gijs G. Zom,
• Nico Meeuwenoord,
• Ferry A. Ossendorp,
• Herman S. Overkleeft,
• Gijsbert A. van der Marel,
• Jeroen D. C. Codée and
• Dmitri V. Filippov

Beilstein J. Org. Chem. 2014, 10, 1445–1453, doi:10.3762/bjoc.10.148

• incorporated SIINFEKL epitope on MHC-I molecules. However, stimulation of the NOD2 receptor in DCs was not sufficient to provide a strong immunostimulatory signal. Keywords: automated synthesis; glycopeptide; innate immunity; muramyl dipeptide; NOD2 receptor; solid phase synthesis; Introduction In recent

• . We here describe the assembly of MDP building blocks, suitable for automated solid phase peptide synthesis (SPPS), their use in the assembly of the four MDP-antigen conjugates 2–5 and the immunological evaluation of the constructs. Results and Discussion Synthesis of the conjugates The MDP-antigen

• conjugates 2–5 were prepared using an automated solid-phase peptide synthesis (SPPS) protocol. In all these syntheses commercially available Tentagel S RAM resin and amino acids were applied. The synthesis of the required MDP building blocks 10 and 16 is depicted in Scheme 1. The 3-azidopropanol spacer was

Biantennary oligoglycines and glyco-oligoglycines self-associating in aqueous medium

• Svetlana V. Tsygankova,
• Alexander A. Chinarev,
• Alexander B. Tuzikov,
• Nikolai Severin,
• Alexey A. Kalachev,
• Juergen P. Rabe,
• Alexandra S. Gambaryan and
• Nicolai V. Bovin

Beilstein J. Org. Chem. 2014, 10, 1372–1382, doi:10.3762/bjoc.10.140

• the structure PG II [12]. Spectra were recorded for the samples in solid phase. Model of the formation of tectomer layers by biantennary oligoglycines on a mica surface. The heights are given for Н-Gly4NH(СН2)10NHGly4-Н. Growth of the tectomer formed by the peptide Н-Gly4-NH(СН2)10-NHGly4-Н

Molecular recognition of surface-immobilized carbohydrates by a synthetic lectin

• Melanie Rauschenberg,
• Eva-Corrina Fritz,
• Christian Schulz,
• Tobias Kaufmann and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2014, 10, 1354–1364, doi:10.3762/bjoc.10.138

• lectins on the immobilized carbohydrates provides insight into the affinity and selectivity of lectin–carbohydrate interaction. Results and Discussion The synthetic lectin HisHis was prepared by air oxidation of the tripeptide Cys-Hys-Cys (synthesized by solid phase peptide synthesis) as described

Automated solid-phase peptide synthesis to obtain therapeutic peptides

• Veronika Mäde,
• Sylvia Els-Heindl and
• Annette G. Beck-Sickinger

Beilstein J. Org. Chem. 2014, 10, 1197–1212, doi:10.3762/bjoc.10.118

• their respective targets have led to tremendous progress for therapeutic applications in the last years. In order to increase the drugability of these frequently unstable and rapidly cleared molecules, chemical modifications are of great interest. Automated solid-phase peptide synthesis (SPPS) offers a

• : automated synthesis; automation; lipidation; PEGylation; peptide drugs; solid-phase peptide synthesis; therapeutic peptides; Introduction Peptides and proteins are involved in a large variety of biochemical processes and physiological functions. Peptides can consist of up to 50 amino acids and have

• intravenous) application, have prompted further research in this field [14]. Therefore, methods to prolong peptide stability are of great interest. Here, we highlight the importance of automated solid-phase peptide synthesis (SPPS) in the process of peptide modification. Principles of chemical synthesis of

Atherton–Todd reaction: mechanism, scope and applications

• Stéphanie S. Le Corre,
• Mathieu Berchel,
• Hélène Couthon-Gourvès,
• Jean-Pierre Haelters and
• Paul-Alain Jaffrès

Beilstein J. Org. Chem. 2014, 10, 1166–1196, doi:10.3762/bjoc.10.117

• solid phase by forming a thermal barrier between the solid phase and the gaseous phase. This charring process results from the formation of polyphosphoric acid derivatives. Interestingly, the association of phosphorus and nitrogen-based flame retardants proved to be efficient probably due to synergic

Solid-phase-supported synthesis of morpholinoglycine oligonucleotide mimics

• Tatyana V. Abramova,
• Sergey S. Belov,
• Yulia V. Tarasenko and
• Vladimir N. Silnikov

Beilstein J. Org. Chem. 2014, 10, 1151–1158, doi:10.3762/bjoc.10.115

• efficient solid-phase-supported peptide synthesis (SPPS) of morpholinoglycine oligonucleotide (MorGly) mimics has been developed. The proposed strategy includes a novel specially designed labile linker group containing the oxalyl residue and the 2-aminomethylmorpholino nucleoside analogues as first subunits

• . Keywords: labile linker; morpholino oligomers; oligonucleotide mimics; solid-phase-supported peptide synthesis (SPPS); Introduction The phosphorodiamidate morpholino oligomers (PMO) and peptide conjugated PMO (PPMO) are currently promising candidates for antisense therapy of a number of infectious and

• nucleobases can be performed simultaneously by treatment with aqueous ammonia as in the solid phase synthesis of native oligonucleotides (ODN) [21]. The oxalyl-mediated attachment of the growing chain to the solid support is usual in the synthesis of base sensitive ODN derivatives [22]. Figure 3 indicates the

Amino acid motifs in natural products: synthesis of O-acylated derivatives of (2S,3S)-3-hydroxyleucine

• Oliver Ries,
• Martin Büschleb,
• Markus Granitzka,
• Dietmar Stalke and
• Christian Ducho

Beilstein J. Org. Chem. 2014, 10, 1135–1142, doi:10.3762/bjoc.10.113

• derivatization as well as for solid-phase peptide synthesis. With respect to according motifs occurring in natural products, we have converted these building blocks into 3-O-acylated structures. Utilizing an esterification and cross-metathesis protocol, (2S,3S)-3-hydroxyleucine derivatives were synthesized, thus

• -Fmoc-protected building blocks potentially suitable for solid-phase peptide synthesis (SPPS). It is well established that O-acylated β-hydroxy-α-amino acids can be used in Fmoc-strategy peptide syntheses without migration of the acyl unit [37][38][39]. Based on these findings, we have desired to

• (2S,3S)-3-hydroxyleucine building blocks employing stereoisomerically pure amino alcohol 5 [32]. Applying different protecting group strategies, we were able to prepare (2S,3S)-3-hydroxyleucine derivatives suitable for further modification both at the carboxy and the amino moiety, as well as for solid

A new building block for DNA network formation by self-assembly and polymerase chain reaction

• Holger Bußkamp,
• Sascha Keller,
• Marta Robotta,
• Malte Drescher and
• Andreas Marx

Beilstein J. Org. Chem. 2014, 10, 1037–1046, doi:10.3762/bjoc.10.104

• 4 [42] yielding 5 in acceptable yields (Scheme 1). Finally, compound 5 was transformed into 6 by phosphitylation resulting in a building block that bears protection groups and reactive groups that are standard in solid phase DNA oligonucleotide synthesis. Synthesis of branched oligonucleotides. DNA

• that was successfully used in solid phase DNA synthesis. In thermal denaturation studies Y-shaped bDNA indicates comparable behavior to the linear non-branched counterpart, thus forming a B-DNA conformation. Furthermore, the branched DNA self assembles into stable networks when short self-complimentary

• °C, 84%. Stepwise solid-phase synthesis for branched oligonucleotides. (I): The first oligonucleotide branch is synthesized in 3'–5' direction using standard phosphoramidites. (II): Incorporation of the branching point by usage of 6. (III): Simultaneous synthesis of the two remaining oligonucleotide

Molecular architecture with carbohydrate functionalized β-peptides adopting 3₁₄-helical conformation

• Nitin J. Pawar,
• Navdeep S. Sidhu,
• George M. Sheldrick,
• Dilip D. Dhavale and
• Ulf Diederichsen

Beilstein J. Org. Chem. 2014, 10, 948–955, doi:10.3762/bjoc.10.93

• for carbohydrate and peptide chemistry. Therefore, sugar units are introduced by side-chain ligation and labeling strategies on the peptide scaffold or were established by incorporation of sugar-β-amino acids by solid-phase peptide synthesis (SPPS) [36][37]. Sugar amino acid building blocks have

Asymmetric total synthesis of a putative sex pheromone component from the parasitoid wasp Trichogramma turkestanica

• Danny Geerdink,
• Jeffrey Buter,
• Teris A. van Beek and
• Adriaan J. Minnaard

Beilstein J. Org. Chem. 2014, 10, 761–766, doi:10.3762/bjoc.10.71

• that only virgin females are able to trigger casting behavior in males, which has led to the assumption that virgin females of Trichogramma turkestanica produce a sex pheromone. Analysis of headspace volatiles of virgin females, collected via solid-phase microextraction, showed the presence of two sex

Isocyanide-based multicomponent reactions towards cyclic constrained peptidomimetics

• Gijs Koopmanschap,
• Eelco Ruijter and
• Romano V.A. Orru

Beilstein J. Org. Chem. 2014, 10, 544–598, doi:10.3762/bjoc.10.50

• tautomerizes, the authors proposed a plausible mechanism, in which tautomer 113 undergoes cyclization via an intramolecular Michael reaction to give intermediate 114. The next step involves cleavage of the dimethylamine group to afford the thiazole structures 115. In 2003, the same group also described a solid

• -phase approach with either thioacetic acid or thiobenzoic acid to obtain the 2-acylaminomethylthiazoles [104]. Deprotection of the resin onto the amide, resulted in compound 117 (Scheme 36). As an extension, Dömling and co-workers designed thiazole-based dipeptide mimics with an additional β-lactam

Continuous flow nitration in miniaturized devices

• Amol A. Kulkarni

Beilstein J. Org. Chem. 2014, 10, 405–424, doi:10.3762/bjoc.10.38

• heterogeneous (immiscible) with only 24% for homogeneous systems. Most of the remaining examples involve the substrate in solid phase. Only very rarely is the nitration of gases reported in the literature. Thus, suitable devices and equipment for nitrations are determined by the phases involved and their

Boron-substituted 1,3-dienes and heterodienes as key elements in multicomponent processes

• Ludovic Eberlin,
• Fabien Tripoteau,
• François Carreaux,
• Andrew Whiting and
• Bertrand Carboni

Beilstein J. Org. Chem. 2014, 10, 237–250, doi:10.3762/bjoc.10.19

• these results obtained in the liquid phase, Hall and co-workers also examined the suitability of a solid-phase strategy. Finally, due to problems of purity encountered with an N-arylmaleidobenzoic acid-functionalized resin [70], or availability of the supported aldehyde partner, a four-component variant