Porphyrin substituted phosphoramidites: new building blocks for porphyrin-oligonucleotide syntheses

Thymidine phosphoramidites containing trispyridylphenyl and tetraphenylporphyrin chromophores attached via a short amide linker in the 3'-position have been synthesized and used as building blocks in solid-phase synthesis of self-complementary 8-mer oligonucleotides 3'-T-5'-GCGCGCA-3' and 5'-ACGCGCGT-3'. To our knowledge, these are the first porphyrin-oligonucleotide conjugates carrying the porphyrin chromophores in the 3'-position. Chain assembly was achieved by automated solid-phase synthesis and by inexpensive straightforward 'in flask' modification of commercially available solid supported oligonucleotides. This approach allows the synthesis of modified oligonucleotides without using costly instrumentation for automated DNA synthesis. Porphyrin-containing self-complementary oligonucleotides are expected to be a valuable model for drug binding studies and determination of conformational changes in DNA sequences using circular dichroism.     

Synthesis of multiply 13C-labeled furofuran lignans using 13C-labeled cinnamyl alcohols as building blocks

Plant lignans are currently being widely studied for their potential benefits for human health as their consumption has been correlated with lower risks for developing chronic diseases, such as breast cancer and coronary heart disease. However, studies of some classes of lignans, in particular the furofurans, are hampered by the lack of suitable standards to allow accurate analysis. Herein, we report the syntheses of two racemic (13)C-labeled furofuran lignans [7,8,9-(13)C(3)]medioresinol and [7,8,9-(13)C(3)]sesamin as internal standards for LC-MS analysis. The labeled furofuran lignans were constructed from triply labeled cinnamyl alcohols, using a radical cyclization method.     

White biotechnology for green chemistry: fermentative 2-oxocarboxylic acids as novel building blocks for subsequent chemical syntheses

Functionalized compounds, which are difficult to produce by classical chemical synthesis, are of special interest as biotechnologically available targets. They represent useful building blocks for subsequent organic syntheses, wherein they can undergo stereoselective or regioselective reactions. "White Biotechnology" (as defined by the European Chemical Industry [ http://www.europabio.org/white_biotech.htm ], as part of a sustainable "Green Chemistry,") supports new applications of chemicals produced via biotechnology. Environmental aspects of this interdisciplinary combination include: Use of renewable feedstock Optimization of biotechnological processes by means of: New "high performance" microorganisms On-line measurement of substrates and products in bioreactors Alternative product isolation, resulting in higher yields, and lower energy demand In this overview we describe biotechnologically produced pyruvic, 2-oxopentaric and 2-oxohexaric acids as promising new building blocks for synthetic chemistry. In the first part, the microbial formation of 2-oxocarboxylic acids (2-OCAs) in general, and optimization of the fermentation steps required to form pyruvic acid, 2-oxoglutaric acid, and 2-oxo-D-gluconic acid are described, highlighting the fundamental advantages in comparison to chemical syntheses. In the second part, a set of chemical formula schemes demonstrate that 2-OCAs are applicable as building blocks in the chemical synthesis of, e.g., hydrophilic triazines, spiro-connected heterocycles, benzotriazines, and pyranoic amino acids. Finally, some perspectives are discussed.     

White biotechnology for green chemistry: fermentative 2-oxocarboxylic acids as novel building blocks for subsequent chemical syntheses

Functionalized compounds, which are difficult to produce by classical chemical synthesis, are of special interest as biotechnologically available targets. They represent useful building blocks for subsequent organic syntheses, wherein they can undergo stereoselective or regioselective reactions. “White Biotechnology” (as defined by the European Chemical Industry [http://www.europabio.org/white_biotech.htm], as part of a sustainable “Green Chemistry,”) supports new applications of chemicals produced via biotechnology. Environmental aspects of this interdisciplinary combination include:

• Use of renewable feedstock

• Optimization of biotechnological processes by means of:

  • New “high performance” microorganisms

  • On-line measurement of substrates and products in bioreactors

  • Alternative product isolation, resulting in higher yields, and lower energy demand

In this overview we describe biotechnologically produced pyruvic, 2-oxopentaric and 2-oxohexaric acids as promising new building blocks for synthetic chemistry. In the first part, the microbial formation of 2-oxocarboxylic acids (2-OCAs) in general, and optimization of the fermentation steps required to form pyruvic acid, 2-oxoglutaric acid, and 2-oxo-d-gluconic acid are described, highlighting the fundamental advantages in comparison to chemical syntheses. In the second part, a set of chemical formula schemes demonstrate that 2-OCAs are applicable as building blocks in the chemical synthesis of, e.g., hydrophilic triazines, spiro-connected heterocycles, benzotriazines, and pyranoic amino acids. Finally, some perspectives are discussed.

     

Identification of side arm-modified DOTA scaffolds as multi-site binding ligands for cancer cells over normal cells

The metal-chelated 1,4,7,10-tetraazacyclododecan-1,4,7,10-tetraacetic acid-tetraamide (DOTA) scaffold has been widely used as a contrast agent for diagnostic purposes in positron emission tomography (PET) and magnetic resonance imaging (MRI), but not as a biomarker targetable ligand. While the oxygen atoms at the stem of the four arms of the DOTA scaffold are needed for metal chelation, we previously introduced various physiochemical properties to extend these arms in a chemical library fashion to enhance the imaging contrast mechanism. We developed two such on-bead libraries, with 80 and 76 DOTA derivatives, where one arm was used to attach the DOTA scaffold onto resin beads and the other three arms were chemically modified. We now hypothesized that the chemical moieties used to modify these three arms can also recognize biomarkers on a cell surface. Therefore in this current study, we used such 76 derivatives of DOTA library to screen against HeLa cervical cancer cells. We found that two of the four ‘hits’ identified displayed higher binding towards HeLa cells than the unmodified parent DOTA. Furthermore, one of those ‘hits’ displayed better binding towards cervical and prostate cancer cells than lung and breast cancer cells and normal HBEC-3KT and RWPE1 cells. This indicates that this derivative can recognize a biomarker specific for certain types of cancer cells. If the compound has intrinsic activity, this can be used as a theranostic agent for real time therapy monitoring applications in the future. We believe that our DOTA derivative-based library approach can be applied to other types of cell and protein screens on various disease types in the future.     

New building blocks for the dendritic spine

Two recent studies by Sheng and associates (Pak et al., 2001; Sala et al., 2001) provide an elegant molecular analysis of the role of a spine-specific protein, SPAR, and the synaptic proteins Shank and Homer, in regulating dendritic spine morphology, and the possible functional consequences of this regulation.     

Engineering building blocks for self-assembling protein nanoparticles

Like natural viruses, manmade protein cages for drug delivery are to be ideally formed by repetitive subunits with self-assembling properties, mimicking viral functions and molecular organization. Naturally formed nanostructures (such as viruses, flagella or simpler protein oligomers) can be engineered to acquire specific traits of interest in biomedicine, for instance through the addition of cell targeting agents for desired biodistribution and specific delivery of associated drugs. However, fully artificial constructs would be highly desirable regarding finest tuning and adaptation to precise therapeutic purposes. Although engineering of protein assembling is still in its infancy, arising principles and promising strategies of protein manipulation point out the rational construction of nanoscale protein cages as a feasible concept, reachable through conventional recombinant DNA technologies and microbial protein production.     

Robust building blocks for inorganic crystal engineering

We have prepared two ligands, 4- and 5-carboxylic acid pyrimidine, and synthesized and crystallographically characterized seven coordination complexes thereof. The need for potentially structurally disruptive counterions is eliminated by deprotonation of the carboxylic acid moieties; the carboxylates present in each structure act as counterions and balance the charge on the divalent metal ions leading to charge-neutral complex ions. The four new M(II)-complexes with 4-carboxylic acid pyrimidine (M = Ni, Cu, Zn, and Co) are isostructural as are the three M(II) complexes with 3-carboxylic acid pyrimidine (M = Ni, Cu, and Zn), indicating robust and reliable coordination modes for both ligands.     

Microbial modification of sugars as building blocks for chemicals

Summary Investigations on the microbial modification of sucrose to the corresponding 3-keto-derivative were carried out with resting cells of Agrobacterium tumefaciens NCPPB 396. This highly specific oxidation to yield the 3-keto-derivative has been analysed kinetically with varying substrate and cell mass concentrations. The formation of the corresponding 3-keto-derivative depended strongly on the reaction time and the aeration rate, and was maximal at aeration rates up to 11.5 volume air/cultivation volume per minute with resting cells. The product formation increased with increasing substrate concentrations. However, the product yield was maximal at substrate concentrations below 20 g/l. Data pertaining to the production of active cell mass as well as for maximal 3-keto-derivative formation are presented in this paper. Also included are some applications for these derivatives.     

Synthesis of glycolipopeptidic building blocks for carbohydrate receptor discovery

A class of glycolipopeptides for use as building blocks for a new type of dynamic combinatorial library is reported. The members of the library consist of a variable carbohydrate moiety, coded amino acids, and lipoamino acids in order to convert them into amphiphiles. Glycolipopeptidic amphiphiles interact through non-covalent bonding when mixed together in aqueous phase and form micelles in dynamic close-packed fluid mosaic arrays. The head groups of amphiphiles are exposed on the micelle surface, providing entities which could be screened in biological assays to find the most potent combination of building blocks in order to identify new bioactive carbohydrate ligands.     

Preparation of omega-functionalized eicosane-phosphate building blocks

New 1,20-substituted eicosanes carrying phosphate headgroups and readily derivatizable thiol, maleimido, and activated carboxylic ester moieties were prepared. The C20-backbone of these molecules was assembled by a halopolycarbon homologation from 1,8-dichlorooctane and 1,6-dibromohexane. 20-Mercapto- and 20-maleimido-icosylphosphates were synthesized via omega-bromo di-t-butyl protected icosylphosphate while 20-phosphonooxy-icosanoic acid N-hydroxysuccinimidoyl ester was prepared via omega-bromo dibenzyl protected icosylphosphate in multistep syntheses. These molecules can serve as model compounds for studying binding and structural organization on different surfaces with potential applications in the fields of biosensors.     

The building blocks and motifs of RNA architecture

RNA motifs can be defined broadly as recurrent structural elements containing multiple intramolecular RNA-RNA interactions, as observed in atomic-resolution RNA structures. They constitute the modular building blocks of RNA architecture, which is organized hierarchically. Recent work has focused on analyzing RNA backbone conformations to identify, define and search for new instances of recurrent motifs in X-ray structures. One current view asserts that recurrent RNA strand segments with characteristic backbone configurations qualify as independent motifs. Other considerations indicate that, to characterize modular motifs, one must take into account the larger structural context of such strand segments. This follows the biologically relevant motivation, which is to identify RNA structural characteristics that are subject to sequence constraints and that thus relate RNA architectures to sequences.     

Short self-assembling peptides as building blocks for modern nanodevices

Short, self-assembling peptides form a variety of stable nanostructures used for the rational design of functional devices. Peptides serve as organic templates for conjugating biorecognition elements, and assembling ordered nanoparticle arrays and hybrid supramolecular structures. We are witnessing the emergence of a new phase of bionanotechnology, particularly towards electronic, photonic and plasmonic applications. Recent advances include self-assembly of photoluminescent semiconducting nanowires and peptide-conjugated systems for sensing, catalysis and energy storage. Concurrently, methods and tools have been developed to control and manipulate the self-assembled nanostructures. Furthermore, there is growing knowledge on nanostructure properties such as piezoelectricity, dipolar electric field and stability. This review focuses on the emerging role of short, linear self-assembling peptides as simple and versatile building blocks for nanodevices.     

Synthesis of 2'-O-modified adenosine building blocks and application for RNA interference

RNA-interference has been recognized as a powerful tool to control gene function and has been used for gene silencing by knocking down mRNA. Chemically modified RNAs, especially 2'-O-modification, successfully improved their physicochemical and pharmaceutical properties such as stability, nuclease resistance and delivery. Here, we report the synthesis of adenosine building blocks with different 2'-tethered modifications like aminoethyl and guanidinoethyl and show that they are compatible with RNAi function. They enhance the half life of the siRNA in serum suggesting that these modifications can enhance the pharmacokinetic properties and knock down activity of siRNAs in vivo.     

The building blocks for basolateral vesicles in polarized epithelial cells

After the discovery of basolateral sorting signals for polarized delivery in epithelial cells in the early 1990s, it was only about a decade later that the epithelial-cell-specific sorting adaptor AP-1B was discovered. AP-1B decodes a subclass of basolateral sorting signals and localizes to the recycling endosomes as opposed to the trans-Golgi network, suggesting that this is its major site of action. Furthermore, AP-1B does not simply select its cargo but also facilitates the recruitment of the exocyst complex needed for subsequent fusion with the plasma membrane. This review discusses our current knowledge of AP-1B function in cargo sorting to the basolateral membrane and its impact on our understanding of the similarities and differences between AP-1B-minus fibroblasts and AP-1B-positive epithelial cells.     

Different strategies for the synthesis of 2'-O-aminoethyl adenosine building blocks

The chemical modification of the 2'-O-position of nucleosides proved to be of great importance for the RNA stability. Greater stability of RNA duplexes allows a longer half life in the cell and, therefore, a better effect of RNA Interference. Here we investigated the synthesis of 2'-O-aminoethyl adenosine as a cationic modified building block.