Modified Building Blocks Research Articles

Synthesis of biobased poly(ether-ester) from potentially bioproduced betulin and p-coumaric acid

For a more sustainable future, innovative polymer materials synthesized from biobased molecules are currently a key trend, in the frame of the bioeconomy. In this study, new renewable macromolecular architectures poly(ether-esters) has been synthesized from betulin and para-coumaric acid, two plant-based building blocks, poorly valorized till now, and potentially bioproduced by white biotechnologies. To date, these are the first synthesized polymers with such a reported architecture. In a first step, different chemical modifications were carried out on these biomolecules to increase their reactivities. Betulin hydroxyl groups were esterified with aliphatic acids of carbon chain lengths C6, C8 and C10 terminated by a bromine, with good yields (79–85%). P-coumaric acid was dimerized by [2 + 2] cycloaddition, and then esterified with ethanol, butanol or isobutanol with excellent yields (92–96%). These modified building blocks were finally copolymerized by Williamson polyetherification reaction, leading to various analogous materials with molar masses ranging from 9700 to 15500 g mol−1. Different thermal characterizations have been then performed. TGA results show that these poly(ether-esters) displayed high thermal stabilities (up to 336 °C). Besides, DSC analyses revealed Tg ranging from 38 to 81 °C, depending on the length of the aliphatic carbon chain and the nature of the pendant ester groups for a large range of potential applications.

Development of 4′-Oxo-MLN4924 as potential neddylation inhibitors: Design, synthesis, anti-HCMV evaluation, and molecular docking

MLN4924 (1), a neddylation inhibitor, has shown promising anticancer and antiviral properties. In this study, we designed and synthesized new derivatives of 4′-oxo-MLN4924, inspired by the structures of MLN4924 and another known neddylation inhibitor, referred to as compound 2. Like compound 2, we used a specific type of sugar molecule but incorporated a modified building block known as 7-deazapurine for the nucleobase part. Additionally, we arranged the sulfamate and 2′-hydroxyl as key functional groups. We found that the 2′-OH group is essential for activity against human cytomegalovirus (HCMV) using luciferase reporter assay. Molecular docking and molecular dynamics (MD) studies revealed that the conformation of the sugar moiety plays a crucial role in protein–ligand interactions. These studies suggest that derivatives with a bulky aromatic ring at the 6-position of the nucleobase are likely to have enhanced binding, which is supported by experimental findings.

The Effect of a Low Degree of Fluorine Substitution on Cotton Fiber Properties

AbstractCellulose modification often employs chemical processes to tailor its properties and functionalities to fit the demands of a wide range of applications, maximizing its potential as a versatile and sustainable material. From both synthetic and environmental standpoints, one of the ultimate goals is to achieve significant modifications to enhance the end properties of the cellulose while minimizing the number of modified building blocks. The current study demonstrates that a synthetic glucose derivative, 6‐deoxy‐6‐fluoro‐glucose (6F‐Glc), fed into the fertilized cotton ovules, resulted in the accumulation of fluorine inside the cotton fibers with no apparent alteration to their morphology or development. These fibers exhibited a degree of substitution of 0.006, which is 170 times lower than that reported for chemical methods for cellulose modification. However, the physical characterization of the modified fibers showed a surprisingly large impact of this low‐level modification on the cellulose structure (e.g., hydrogen bonding network rearrangement) and a modest increase in the mechanical properties of the fibers. The obtained results exemplify the use of biological systems to introduce low quantities of new functionalities while maximizing the impact on fiber properties.

Bifunctional Lipid-Derived Affinity-Based Probes (AfBPs) for Analysis of Lipid-Protein Interactome.

ConspectusAlthough lipids are not genetically encoded, they are fundamental building blocks of cell membranes and essential components of cell metabolites. Lipids regulate various biological processes, including energy storage, membrane trafficking, signal transduction, and protein secretion; therefore, their metabolic imbalances cause many diseases. Approximately 47 000 lipid species with diverse structures have been identified, but little is known about their crucial roles in cellular systems. Particularly the structural, metabolic, and signaling functions of lipids often arise from interactions with proteins. Lipids attach to proteins not only by covalent bonds but also through noncovalent interactions, which also influence protein functions and localization. Therefore, it is important to explore this lipid-protein "interactome" to understand its roles in health and disease, which may further provide insight for medicinal development. However, lipid structures are generally quite complicated, rendering the systematic characterization of lipid-protein interactions much more challenging.Chemoproteomics is a well-known chemical biology platform in which small-molecule chemical probes are utilized in combination with high-resolution, quantitative mass spectrometry to study protein-ligand interactions in living cells or organisms, and it has recently been applied to the study of protein-lipid interactions as well. The study of these complicated interactions has been advanced by the development of bifunctional lipid probes, which not only enable probes to form covalent cross-links with lipid-interacting proteins under UV irradiation, but are also capable of enriching these proteins through bioorthogonal reactions.In this Account, we will discuss recent developments in bifunctional lipid-derived, affinity-based probes (AfBP)s that have been developed to investigate lipid-protein interactions in live cell systems. First, we will give a brief introduction of fundamental techniques based on AfBPs which are related to lipid research. Then, we will focus on three aspects, including probes developed on the basis of lipidation, lipid-derived probes with different modification positions (e.g., hydrophobic or hydrophilic parts of a lipid), and, finally, in situ biosynthesis of probes through intrinsic metabolic pathways by using chemically modified building blocks. We will present some case studies to describe these probes' design principles and cellular applications. At the end, we will also highlight key limitations of current approaches so as to provide inspirations for future improvement. The lipid probes that have been constructed are only the tip of the iceberg, and there are still plenty of lipid species that have yet to be explored. We anticipate that AfBP-based chemoproteomics and its further advancement will pave the way for a deep understanding of lipid-protein interactions in the future.

Photodynamic Antimicrobial Cellulosic Material Through Covalent Linkage of Protoporphyrin IX onto Lyocell Fibers

Here, we report the preparation of porphyrin-functionalized Lyocell fibers according to an azide-alkyne click concept. First, azido-modified Lyocell fibers and alkynylated protoporphyrin building blocks were prepared through alkoxysilane chemistry and Steglich esterification, respectively. Lyocell fibers were pre-activated by swelling in organic solvents in order to increase the accessibility of hydroxyl groups in the subsequent silanization process. The azide-equipped cellulosic matrix reacted with the propargyl groups of the protoporphyrin IX derivative in a copper-catalyzed azide-alkyne cycloaddition reaction (CuAAC), by which protoporphyrin IX was introduced onto the surface of the Lyocell fibers. The modified building blocks and the final functionalized cellulosic materials were comprehensively characterized by FTIR, NMR, UV/Vis spectroscopy and elemental analysis. Photo-bactericidal activity of modified fibers against 2 gram-positive bacteria strains, including Staphylococcus aureus and Bacillus subtilis, were investigated and compared to those of unmodified and azido-modified Lyocell fibers. The results confirmed the photo-antibacterial activity of the synthesized fibers against both bacteria strains.

3D Noble Metal-Based Porous Materials Self-Assembled By Atomically Modified Building Blocks As Electrocatalysts Boosting Small Molecule Electro-Oxidation or Reduction

Three-dimensional (3D) noble metal-based electrocatalysts are currently being intensively studied due to their unique hybrid porous architectures that could effectively enlarge their active sites, favor the mass and electron transfer rate, avoid the corrosion issues of carbon support and so on. Modifying building blocks is also of great importance for constructing the self-assembled 3D porous electrocatalysts with significantly improved electrochemical performances. However, the synthesis strategies for tailoring the structures and morphologies from atomic scale are still challenging and the mass activity (MA) and stability are still far from sufficient toward small molecule (i.e., ethanol, oxygen) electro-oxidation or reduction. Here, we rationally designed a series of 3D architectures by finely tailoring the morphologies, compositions, and surface atomic configurations etc. of building blocks for boosting their electrocatalytic performances. Core-shell structures are very popular because of their ligands effects, ensemble effects and electronic effects, which are related to charge transfer and structure constraints that could favor desorption of oxygen-containing intermediates from the Pt active sites. Therefore, we firstly synthesized Au@Pt3Pd ternary metallic aerogels via a one-pot gelation strategy employing the dendritic core-shell structured Au@Pt3Pd nanoparticles (NPs) with size of about 24.5 nm as the building block. The as-obtained Au@Pt3Pd metallic hydrogels exhibited an improved MA of 0.812 A/mgPt+Pd and enhanced stability of showing 11.8 mV of half-potential shift after ADT test compared to commercial Pt/C toward oxygen reduction reaction (ORR). Both macro- and micro-structures contributed to the enhanced catalytic performances, like the high porosity for fast mass diffusion, cross-linked nanowires for rapid electron transfer, dendritic surface for providing more active sites, core-shell structure for offering synergistic effect and so on.Compared to disordered alloyed structures, intermetallic nanocrystals (IM-NCs) possesses specific atomic structures with predictable electronic and geometric effect, high selectivity achieved through reducing the homoatomic coordination number of active sites, and stable chemical structures realized by the more negative enthalpy for generation of intermetallics compared to that of alloys. In order to improve the MA, selectivity and durability of the electrocatalysts toward ORR, for the first time, we successfully synthesized 3D IM-Pd3Pb nanowire networks (NNs) using ethylene glycol as the solvent and PVP as the surfactant at 170 ℃ for 1 h. The MA of IM-Pd3Pb NNs increased to be 1.06 A/mg and showed a half-potential shift of only 8 mV after 10000 potential cycles test. Besides, IM-Pd3Pb NNs displayed negligible current changes with addition of methanol while commercial Pt/C showed significant oxidation peak of methanol, indicating a high selectivity of oxygen as the cathode electrocatalysts. What’s more, IM-Pd3Pb NNs also shows a MA of 3.2 A/mg, which was two times higher than commercial Pd black toward ethanol oxidation.Well established is the knowledge that catalytic activities leapt via downsizing the NPs to nanoclusters or single atoms, which is attributed to the remarkably increased active sites along with the altered surface defects, atomic and electronic structure. The as-resulted geometric and electronic/synergistic effects are all beneficial for boosting catalytic activities in electrochemical reactions. As for the ethanol oxidation, it had been revealed that Pd ensembles rather than isolated Pd atoms that serve as highly activated sites toward ethanol oxidation. Based on this principle, we successfully anchored Pd ensembles on the surface of the core-shell structured Au2Cu metallic hydrogels (denoted as Au2Cu@Pd) via galvanic displacement reaction under ice bath and achieved a MA of 22.1 A/mg toward ethanol oxidation, which is 15.8 times higher than Pd black. Also it suffers only 10 % degradation after 300 potential cycle test. The MA and long-term durability of Au2Cu@Pd exhibited remarkable improvement due to the modified surface composition and atomic configuration, core-shell structured NNs, 3D porous structures and so on. All in all, the high porosity and interconnected architecture of 3D porous materials are significant for electrocatalysts because they provide free paths and open channels for electron and mass transfer. However, the modification of the building blocks by optimizing the compositions and structures, tailoring the surface atomic configurations also hold a key for boosting the electrocatalytic performances due to the as-resulted electronic and geometric effect from the atomic scale.

In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids?

Synthetic analogs of natural nucleotides have long been utilized for structural studies of canonical and noncanonical nucleic acids, including the extensively investigated polymorphic G-quadruplexes (GQs). Dependence on the sequence and nucleotide modifications of the folding landscape of GQs has been reviewed by several recent studies. Here, an overview is compiled on the thermodynamic stability of the modified GQ folds and on how the stereochemical preferences of more than 70 synthetic and natural derivatives of nucleotides substituting for natural ones determine the stability as well as the conformation. Groups of nucleotide analogs only stabilize or only destabilize the GQ, while the majority of analogs alter the GQ stability in both ways. This depends on the preferred syn or anti N-glycosidic linkage of the modified building blocks, the position of substitution, and the folding architecture of the native GQ. Natural base lesions and epigenetic modifications of GQs explored so far also stabilize or destabilize the GQ assemblies. Learning the effect of synthetic nucleotide analogs on the stability of GQs can assist in engineering a required stable GQ topology, and exploring the in vitro action of the single and clustered natural base damage on GQ architectures may provide indications for the cellular events.

Functionalized Celluloses with Regular Substitution Pattern by Glycosynthase-Catalyzed Polymerization.

Control of the monomer sequence in polymers is extraordinarily difficult by chemical synthesis, though Nature routinely exerts such control, including in the biosynthesis of polysaccharides. This inability has prevented us from being able to match the exquisite structure-activity control exhibited in biosynthesis of bioactive natural polysaccharides. We here address a powerful approach, whereby enzyme-catalyzed polymerization of properly modified building blocks is introduced as a simple route affording polysaccharides with controlled sequence and functionalization pattern. Targeting cellulose as a versatile scaffold for novel biomaterials, we describe the preparation of a perfectly alternating polysaccharide with repeat unit 6'-azido-6'-deoxycellobiose by a glycosynthase-catalyzed polymerization using the Humicola insolens cellulase Cel7B E197A mutant, and its further functionalization to give novel modified cellulose derivatives with a regular substitution pattern.

Recombinant messenger RNA technology and its application in cancer immunotherapy, transcript replacement therapies, pluripotent stem cell induction, and beyond.

In recent years, the interest in using messenger RNA (mRNA) as a therapeutic means to tackle different diseases has enormously increased. This holds true not only for numerous preclinical studies, but mRNA has also entered the clinic to fight cancer. The advantages of using mRNA compared to DNA were recognized very early on, e.g., the lack of risk for genomic integration, or the expression of the encoded protein in the cytoplasm without the need to cross the nuclear membrane. However, it was generally assumed that mRNA is just not stable enough to give rise to sufficient expression of the encoded protein. Yet, an initially small group of mRNA aficionados could demonstrate that the stability of mRNA and the efficiency, by which the encoded protein is translated, can be significantly increased by selecting the right set of cis-acting structural elements (including the 5'-cap, 5'- and 3'-untranslated regions, poly(A)-tail, and modified building blocks). In parallel, significant advances in RNA packaging and delivery have been made, extending the potential for this molecule. This paved the way for further work to prove mRNA as a promising therapeutic for multiple diseases. Here, we review the developments to optimize mRNA regarding stability, translational efficiency, and immune-modulating properties to enhance its functionality and efficacy as a therapeutic. Furthermore, we summarize the current status of preclinical and clinical studies that use mRNA for cancer immunotherapy, for the expression of functional proteins as so-called transcript (or protein) replacement therapy, as well as for induction of pluripotent stem cells.

Liquid chromatography–diode array detection–mass spectrometry for compositional analysis of low molecular weight heparins

Low molecular weight heparins (LMWHs) are important artificial preparations from heparin polysaccharide and are widely used as anticoagulant drugs. To analyze the structure and composition of LMWHs, identification and quantitation of their natural and modified building blocks are indispensable. We have established a novel reversed-phase high-performance liquid chromatography–diode array detection–electrospray ionization–mass spectrometry approach for compositional analysis of LMWHs. After being exhaustively digested and labeled with 2-aminoacridone, the structural motifs constructing LMWHs, including 17 components from dalteparin and 15 components from enoxaparin, were well separated, identified, and quantified. Besides the eight natural heparin disaccharides, many characteristic structures from dalteparin and enoxaparin, such as modified structures from the reducing end and nonreducing end, 3-O-sulfated tetrasaccharides, and trisaccharides, have been unambiguously identified based on their retention time and mass spectra. Compared with the traditional heparin compositional analysis methods, the approach described here is not only robust but also comprehensive because it is capable of identifying and quantifying nearly all components from lyase digests of LMWHs.

Complex Small‐Molecule Architectures Regulate Phenotypic Plasticity in a Nematode

Chemistry the worm's way: The nematode Pristionchus pacificus constructs elaborate small molecules from modified building blocks of primary metabolism, including an unusual xylopyranose-based nucleoside (see scheme). These compounds act as signaling molecules to control adult phenotypic plasticity and dauer development and provide examples of modular generation of structural diversity in metazoans.

RNA nanoparticles come of age

RNA nanoparticles come of age

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.

The Chiron Approach to Pironetins: Synthesis of the δ‐Lactonic Fragment and Modified Building Blocks from D‐Glucal.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.

The Chiron Approach to Pironetins: Synthesis of the δ‐Lactonic Fragment and Modified Building Blocks from D‐Glucal

The synthesis of the δ‐lactonic fragment of pironetin (1), a natural product with outstanding antimitotic properties, is reported. The synthesis was achieved from commercially available tri‐O‐acetyl‐D‐glucal (6) that was employed as starting material for the preparation of ethyl ketone 4, through a synthetic sequence that included a Ferrier rearrangement of 6 and suitable functional group manipulations of the resulting O‐glycoside 7 to obtain the 4‐ethyl glycoside 11, together with a series of 4‐C‐alkyl modified derivatives. The completion of the synthesis of 4 was performed via chain elongation at C‐6 by the introduction of a nitrile group and subsequent reduction, nucleophilic attack with ethyl magnesium bromide, and, finally, oxidation of the resulting alcohol 20.

DNA containing phenanthroline- and phenanthrene-derived, non-nucleosidic base surrogates

Simple, non-nucleosidic phenanthroline- and phenanthrene derivatives have been synthesised and incorporated into oligodeoxynucleotides. Complementary strands containing the modified building blocks in opposite positions form stable hybrids. Thermal denaturation experiments show that the double strands containing the phenanthroline derivatives are more stable than the ones with the corresponding phenanthrenes. Furthermore, it was found that duplex stability is considerably decreased if the linkers of the modified building blocks are too short.

Accounting for Auger yield energy loss for improved determination of molecular orientation using soft x-ray absorption spectroscopy

Partial (Auger) yield near edge x-ray absorption fine structure (NEXAFS) is a structural analytical technique that has been primarily used to measure the spatial orientation and chemical bonding of small molecules on solid (i.e., inorganic or semiconductor) surfaces. In this article we demonstrate that the building block (BB) scheme proposed by Outka and co-workers [Phys. Rev. Lett. 59, 1321 (1987)] for analyzing NEXAFS spectra can be applied to model the molecular orientation of larger molecules, provided one accounts properly for kinetic energy losses of the Auger electrons traversing through the sample and hence the attenuation in measured Auger yield. We test the applicability of the proposed “modified” BB (MBB) model by measuring the orientation of a self-assembled monolayer (SAM) of –O1.5Si–(CH2)2–(CF2)8F, SF–SAM (SiOx), deposited on top of SiOx-covered silicon wafer as a function of the entrance grid bias (EGB) of the channeltron photoelectron detector. Our measurements of the EGB-dependent electron escape depth reveal that a crude depth profiling within the top ≈5 nm of the sample is possible by increasing the negative EGB on the channeltron detector, at the highest bias thus selecting only the Auger electrons, which have suffered negligible energy loss. In addition, we discuss how the order parameter method introduced recently by Stöhr and Samant [J. Electron Spectrosc. Relat. Phenom. 98–99, 189 (1989)] can be used to determine the molecular orientation of large organic molecules on surfaces. We also show that by accounting for energy losses of the NEXAFS Auger electrons (attenuation of measured Auger yield), the corrected order parameter (COP) approach gives good estimates of the orientation of molecules. We present a comparison between the MBB and COP models using experimental data collected from NEXAFS experiments from semifluorinated (SF) mesogens, –(CH2)x(CF2)yF, which are attached to: (1) the isoprene backbone of polyisoprene or a styrene–isoprene diblock copolymer and (2) a SiOx-covered solid substrate. We show that on both surfaces, the SF groups are oriented and on average are tilted by an angle 〈τF-helix〉 from the sample normal. We show that at higher 〈τF-helix〉 the results from the COP approach agree almost quantitatively with those extracted using the MBB model.

Chemical synthesis and biochemical properties of oligonucleotides that contain the (5'S,5S,6S)-5',6-cyclo-5-hydroxy-5,6-dihydro-2'-deoxyuridine DNA lesion.

The first chemical synthesis of (5'S,5S,6S)-5',6-cyclo-5-hydroxy-5,6-dihydro-2'-deoxyuridine [(5'S,5S,6S)-cyclo-5-OH-dHdU], a radiation-induced decomposition product of 2'-deoxycytidine in aerated solution, is reported. Subsequently, 2'-deoxycytidine was incorporated into oligodeoxyribonucleotides with defined sequences by using an optimized system of protection that takes into account the reactivity and stability of the modified building blocks. After deprotection and purification, the chemical composition of the modified DNA fragments was assessed by enzymatic digestions and mass spectrometry measurements. The MS analyses confirmed the presence and integrity of the lesion within the synthesized DNA fragments. In vitro replication and repair studies showed that (5'S,5S,6S)-cyclo-5-OH-dHdU acts as a block for DNA polymerases when inserted into DNA oligomers and is not excised by any of the tested DNA N-glycosylases. Therefore, (5'S,5S,6S)-cyclo-5-OH-dHdU may represent a potential lethal lesion within the cell if it is not removed by the nucleotide excision repair machinery.

C-F...H-C hydrogen bonds in ribonucleic acids.

We report the synthesis of 1'-deoxy-1'-(benzimidazol-1-yl)-beta-D-ribofuranose 7 and 1'-deoxy-1'-phenyl-beta-D-ribofuranose 2. With these two ribonucleoside analogues we have a set of nine different RNA building blocks in hand, which are isostere to the natural bases. Now it is possible to investigate their duplex stabilizing forces. These forces are hydrogen bonds, base stacking, and solvation. The phosphoramidites of all building blocks were incorporated into a 12mer RNA, and the resulting RNA duplexes were investigated by UV- and CD-spectroscopy. We found that some of the RNA analogues are universal bases. The best universal bases with the lowest destabilization and the smallest discrimination between the natural bases are 1 (B) and 9 (E). On the basis of UV measurements we determined the melting points and the thermodynamic data. We were able to show that there are no hydrogen bonds between the natural bases and the RNA analogues. From thermodynamic data we calculated the contributions for base stacking and solvation of all modified building blocks. Comparison of calculated and measured data of double modified base pairs in 12mer RNA duplexes showed a further duplex stabilizing force in base pairs containing fluorine atoms at the Watson-Crick binding site. This stabilizing force can be defined as C-F.H-C hydrogen bond as is observed in crystal structures of 1'-deoxy-1'-(4-fluorophenyl)-beta-D-ribofuranose.

Structural Aspects of Nucleic Acid Analogs and Antisense Oligonucleotides

AbstractHybridization of complementary oligonucleotides is essential to highly valuable research tools in many fields including genetics, molecular biology, and cell biology. For example, an antisense molecule for a particular segment of sense messenger RNA allows gene expression to be selectively turned off, and the polymerase chain reaction requires complementary primers in order to proceed. It is hoped that the antisense approach may lead to therapeutics for treatment of various diseases including cancer. Areas of active research in the antisense field focus on the mechanisms of cellular uptake of antisense molecules and their delivery to specific cell sites, an improved understanding of how these molecules inhibit the production of proteins, as well as the optimization of the chemical stability of antisense molecules and the thermodynamic stability of the duplexes they form with the mRNA targets. The last two issues in particular have prompted chemists to launch an extensive search for oligonucleotide analogs with improved binding properties for hybridization with RNA and higher resistance toward nuclease degradation. During the last years this research has resulted in a flurry of new chemical analogs of DNA and RNA with modifications in the sugar–phosphate backbone as well as in the nucleobase sites. However, to date little effort has been directed toward uncovering the exact origins of the gain or loss in stability when nucleic acid analogs bind to RNA. Although large amounts of thermodynamic data have been collected, the structural perturbations induced by the modifications in hybrid duplexes are only poorly understood. For many modified oligonucleotides the compatibility of protection, coupling, and deprotection chemistry with standard DNA and RNA synthesis protocols makes it now possible to generate modified nucleic acid fragments or mixed oligonucleotides containing modifications at selected sites in quantities suitable for three‐dimensional structure investigations. Such studies should reveal the structural origins of the observed changes in affinity and specificity of binding for particular modifications and may guide the development of second‐and third‐generation antisense molecules. In addition, the availability of a previously unimaginable variety of modified building blocks and the investigation of their structures provides the basis for a deeper understanding of the native DNA and RNA structures. This contribution will summarize the results of X‐ray crystallographic structure determinations of modified nucleic acid fragments conducted in our laboratory during the last three years and the insights gained from them.