Enhanced target cell specificity and uptake of lipid nanoparticles using RNA aptamers and peptides

• Roslyn M. Ray,
• Anders Højgaard Hansen,
• Maria Taskova,
• Bernhard Jandl,
• Jonas Hansen,
• Citra Soemardy,
• Kevin V. Morris and
• Kira Astakhova

Beilstein J. Org. Chem. 2021, 17, 891–907, doi:10.3762/bjoc.17.75

• lipid, 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), cholesterol, and PEG-lipid, each with an essential role in the design (Figure 1). These lipids promote the effective distribution of the LNP in vivo as well as aid in effective cargo release from the endosome [1][37]. To this end, we herein

• mixture of DLin-MC3-DMA, DSPC, cholesterol, and 1,2-dimyristoyl-rac-glycero-3-methoxypolyethylene glycol-2000 (DMG-PEG 2000). Lipids were first extruded and then complexed with negatively charged aptamers annealed with fluorescently tagged complementary DNA oligonucleotides (GP160:A-1 or CCR5:G-3) to

• through stimulating the retinoic acid-inducible gene 1 (RIG-1) pathway, and it may thus be prudent to assess type-I interferons (IFN-α and IFN-β) in the future [32][59]. Importantly, the LNP B9 formulation alone had no effect on cell viability, suggesting that the ratio of cationic and ionizable lipids is

Synthesis and physicochemical evaluation of fluorinated lipopeptide precursors of ligands for microbubble targeting

• Masayori Hagimori,
• Estefanía E. Mendoza-Ortega and
• Marie Pierre Krafft

Beilstein J. Org. Chem. 2021, 17, 511–518, doi:10.3762/bjoc.17.45

• occurrence of side reactions due to reactive groups introduced during PEG to lipids (or peptides) connecting reactions [23][24][25]. In particular, the PEG layer grafted on the surface of certain nanocarriers restricts the exposure of functional peptides [26][27]. Novel ligand-grafted lipids have been

• step by washing. The human epidermal growth factor receptor-2 (HER2)-targeting KCCYSL peptide–(SG)n–lipids in which the (SG)n (n = 3, 5, 7) sequence was used as a spacer allowed the reduction of the steric hindrance when compared to the conventional PEG2000 spacer [28]. Liposomes containing these

• peptide ligands dramatically increased cellular association in HER2-positive cells. Other lipids grafted to the RGD peptide and SG spacer were integrated in PEGylated liposomes and were efficiently associated with integrin αvβ3-expressing Colon-26 cells [25]. One of our general objectives is to synthesize

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

Beilstein J. Org. Chem. 2020, 16, 2971–2982, doi:10.3762/bjoc.16.247

• important biomolecules including nucleotides, DNA, proteins, lipids etc. in aqueous media. Fluorescent peptides have also been used for specific organelles such as lysosomes tracking. In this review, it is summarized Schmuck group’s tremendous effort in developing fluorescent peptide-based probes for

• for the turn on fluorescent detection of LPS in mixed solvent (DMSO/TBS buffer, 1:4) (Figure 10A) [59]. The liposomes are created by mixing two lipids in a ratio of 9:1. First lipid 12 is designed by attaching 10,12-tricosadiyonic acid to a penta-lysine oligopeptide bearing an aminonaphthalimide

Easy access to a carbohydrate-based template for stimuli-responsive surfactants

• Thomas Holmstrøm,
• Daniel Raydan and
• Christian Marcus Pedersen

Beilstein J. Org. Chem. 2020, 16, 2788–2794, doi:10.3762/bjoc.16.229

• surfactants are triggered, thereby releasing the cargo [8]. Guo and co-workers have earlier succeeded with the use of pH-sensitive surfactants and even introduced the term “flipids” for such pH-responsive lipids [7][8]. This term could also describe compounds where the binding of a guest molecule is able to

• -responsive lipids [11]. The three compounds reluctance to adopt a 1C4 conformation may be due to a steric clash between the methylene group at C5 and the anomeric substituent when both of these groups are in axial orientation. To further study the scope and versatility of building block 5, we decided to

A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR)

• Benjamin P. Kellman,
• Yujie Zhang,
• Emma Logomasini,
• Eric Meinhardt,
• Karla P. Godinez-Macias,
• Austin W. T. Chiang,
• James T. Sorrentino,
• Chenguang Liang,
• Bokan Bao,
• Yusen Zhou,
• Sachiko Akase,
• Isami Sogabe,
• Thukaa Kouka,
• Elizabeth A. Winzeler,
• Iain B. H. Wilson,
• Matthew P. Campbell,
• Sriram Neelamegham,
• Frederick J. Krambeck,
• Kiyoko F. Aoki-Kinoshita and
• Nathan E. Lewis

Beilstein J. Org. Chem. 2020, 16, 2645–2662, doi:10.3762/bjoc.16.215

• recommended preserving this symbol use since it is human and computer-readable and does not overlap with any notation in the original Linear Code. Recommendation 3 – “Number.” “ # ” was defined to combine glycans with glycosides other than amino acids and lipids (Table 3: GR1). Krambeck et al. use it to

Computational tools for drawing, building and displaying carbohydrates: a visual guide

• Kanhaya Lal,
• Rafael Bermeo and
• Serge Perez

Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199

• together either linearly or branched); (ii) polysaccharides (for glycan chains composed of more than ten monosaccharides); (iii) glycoconjugates (where the glycan chains are covalently linked to proteins (glycoproteins), lipids (glycolipids). The complexity of glycans is a consequence of their branched

• assembles data resources ranging from glycoscience standard ontologies to pathologies associated with glycans. GlyCosmos is recognized as the official portal of the Japanese Society for Carbohydrate Research and provides information about genes, proteins, lipids, pathways and diseases. GlyTouCan (Figure 5

The B & B approach: Ball-milling conjugation of dextran with phenylboronic acid (PBA)-functionalized BODIPY

• Patrizia Andreozzi,
• Lorenza Tamberi,
• Elisamaria Tasca,
• Gina Elena Giacomazzo,
• Marta Martinez,
• Mirko Severi,
• Marco Marradi,
• Stefano Cicchi,
• Sergio Moya,
• Giacomo Biagiotti and
• Barbara Richichi

Beilstein J. Org. Chem. 2020, 16, 2272–2281, doi:10.3762/bjoc.16.188

• range of biomolecules: amino acids [8], peptides [9], glycosides [10], nucleosides/nucleotides [11], and lipids [12]. Also, protein-based nano-bio-conjugates [13] have been prepared by ball milling, retaining the native properties of the proteins after mechanochemical synthesis. Boronic acids and their

Tools for generating and analyzing glycan microarray data

• Akul Y. Mehta,
• Jamie Heimburg-Molinaro and
• Richard D. Cummings

Beilstein J. Org. Chem. 2020, 16, 2260–2271, doi:10.3762/bjoc.16.187

• structural informatics tools. Keywords: data analysis; glycan binding; glycan microarray; glycomics; informatics; Introduction Glycans represent a major type of biomolecule in all living things, along with DNA, RNA, lipids and proteins [1]. In mammals, glycans commonly occur as post-translational

• modifications of proteins (glycoproteins), but they are also linked to lipids (glycolipids) and occur as free molecules. Such glycomolecules have vital roles in a wide range of physiological functions and also participate in many pathologic conditions [2]. Some classic examples of important glycans include the

One-pot synthesis of oxazolidinones and five-membered cyclic carbonates from epoxides and chlorosulfonyl isocyanate: theoretical evidence for an asynchronous concerted pathway

• Esra Demir,
• Ozlem Sari,
• Yasin Çetinkaya,
• Ufuk Atmaca,
• Safiye Sağ Erdem and
• Murat Çelik

Beilstein J. Org. Chem. 2020, 16, 1805–1819, doi:10.3762/bjoc.16.148

• natural products ranging from small molecules, such as sugars, lipids and amino acids to huge molecules [56]. Computational results A detailed mechanistic investigation of the synthesis of oxazolidinone and five-membered cyclic carbonate derivatives by the reaction between epoxide 7f and CSI has been

Heterogeneous photocatalysis in flow chemical reactors

• Christopher G. Thomson,
• Ai-Lan Lee and
• Filipe Vilela

Beilstein J. Org. Chem. 2020, 16, 1495–1549, doi:10.3762/bjoc.16.125

Steroid diversification by multicomponent reactions

• Leslie Reguera,
• Cecilia I. Attorresi,
• Javier A. Ramírez and
• Daniel G. Rivera

Beilstein J. Org. Chem. 2019, 15, 1236–1256, doi:10.3762/bjoc.15.121

• two different steroidal scaffolds [65], but it failed for the ligation of larger peptides to steroids due to the poor solubility of the former ones. In this sense, Rivera’s group introduced a solid-phase multicomponent procedure enabling the conjugation of steroids and lipids to peptides longer than

• conjugation at the N-terminus required microwave irradiation due to the bulkier character of the amino component. Besides steroids, the method worked well with varied boronic acids, including those bearing fluorescent labels, lipids and PEG chains, thus providing a new class of biomolecular conjugates showing

Towards the preparation of synthetic outer membrane vesicle models with micromolar affinity to wheat germ agglutinin using a dialkyl thioglycoside

• Dimitri Fayolle,
• Nathalie Berthet,
• Bastien Doumeche,
• Olivier Renaudet,
• Peter Strazewski and
• Michele Fiore

Beilstein J. Org. Chem. 2019, 15, 937–946, doi:10.3762/bjoc.15.90

• Lipids (Alabaster, AL, USA). 2,3,4,6-Tetra-O-acetyl-α--glucopyranosyl bromide and N-acetyl--glucosamine were from Carbosynth (San Diego, CA, USA). Wheat germ agglutinin (WGA), horseradish peroxidase-labelled WGA (WGA-HRP), bovine serum albumin (BSA) and SIGMA FAST O-phenylenediamine dihydrochloride (OPD

• : Giant vesicles (GVs) were prepared by the natural swelling method [23]. Lipids (mixture of commercial POPC and n-alkyl thioglycosides 5 or 8) were dissolved in methanol (typically, 2 mL) in a 10 mL round-bottom flask. The solvent was completely evaporated under reduced pressure using a rotatory

• . a–e) POPC/8, 9:1 molar ratio; f and g) pure 8; h) 5/8, 1:1 molar ratio; i) pure 5; All the samples were prepared with 1 mM lipids and stained with NileRed® (1 mM in EtOH, 1 µL, λ[excit] = 561 nm) before the microscopic observation. Red arrows are used to indicate small GVs. The scale bar is 20 µm

Synthesis of acylglycerol derivatives by mechanochemistry

• Karen J. Ardila-Fierro,
• Andrij Pich,
• Marc Spehr,
• José G. Hernández and
• Carsten Bolm

Beilstein J. Org. Chem. 2019, 15, 811–817, doi:10.3762/bjoc.15.78

• , mechanosynthesis of lipids by ball milling techniques has remained essentially unexplored. In this work, a multistep synthetic route to access mono- and diacylglycerol derivatives by mechanochemistry has been realized, including the synthesis of diacylglycerol-coumarin conjugates. Keywords: ball mill; coumarin

• ; diacylglycerols; lipids; mechanochemistry; Introduction In addition to being guided by chemical signals, cells respond to mechanical cues by sensing and transducing external mechanical inputs into biochemical and electrical signals [1]. Consequently, every time a cell is subjected to mechanical loads, the

• relevant building blocks with mechanochemistry has further been shown by the recent mechanochemical protocols to transform nucleoside and nucleotide substrates (Figure 1) [18][19]. On the other hand, reports on mechanochemical protocols for the synthesis or derivatization of lipids are scarce [20][21

Azologization of serotonin 5-HT₃ receptor antagonists

• Karin Rustler,
• Galyna Maleeva,
• Piotr Bregestovski and
• Burkhard König

Beilstein J. Org. Chem. 2019, 15, 780–788, doi:10.3762/bjoc.15.74

• restoration [53][54][55], the respiratory chain [56] and lipids [57][58]. Owing to the reported serotonin antagonists’ chemical structures, the use of azobenzene as photochromic scaffold in the presented work seemed axiomatic. Therefore, the primary design of our photochromic derivatives is based on the

Lectins of Mycobacterium tuberculosis – rarely studied proteins

• Katharina Kolbe,
• Sri Kumar Veleti,
• Norbert Reiling and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2019, 15, 1–15, doi:10.3762/bjoc.15.1

• cells exhibit a diverse array of glycoconjugates on their cell surfaces, together known as the glycocalyx (Figure 2). Carbohydrate moieties of the eukaryotic glycocalyx mainly exist in the form of oligosaccharide chains covalently linked to proteins or lipids. The most prevalent oligosaccharide

• modifications of glycocalyx proteins are N-glycans (asparagine-linked) and O-glycans (serine- or threonine-linked), while glycosphingolipids are the major subclass of glycosylated lipids in the cell membrane of human cells (Figure 2). While many core elements of glycocalyx oligosaccharides are conserved between

Learning from B₁₂ enzymes: biomimetic and bioinspired catalysts for eco-friendly organic synthesis

• Keishiro Tahara,
• Ling Pan,
• Toshikazu Ono and
• Yoshio Hisaeda

Beilstein J. Org. Chem. 2018, 14, 2553–2567, doi:10.3762/bjoc.14.232

• vesicles composed of synthetic lipids and alkylated complexes of heptapropyl cobyrinate (Scheme 3) [32][33]. The alkylated B12 model complexes were introduced into the vesicle in aqueous solutions through non-covalent hydrophobic interactions and irradiated with a 500 W tungsten lamp to result in the

Artificial bioconjugates with naturally occurring linkages: the use of phosphodiester

• Takao Shoji,
• Hiroki Fukutomi,
• Yohei Okada and
• Kazuhiro Chiba

Beilstein J. Org. Chem. 2018, 14, 1946–1955, doi:10.3762/bjoc.14.169

• the current conjugation approach, we then turned our attention to the use of relatively longer peptides, sugars, and lipids as biomolecules (Table 2) [76][77]. When pentapeptide 6 was used instead (see Scheme S4 in Supporting Information File 1 for preparation of pentapeptide 6), however, the

• phosphodiester bond can be an effective linkage not only to construct oligonucleotides but also to conjugate them to various biomolecules, including peptides, sugars, and lipids. The development of a method to activate the supported 5’-terminus, affording useful stable phosphoramidites that are compatible with

Latest development in the synthesis of ursodeoxycholic acid (UDCA): a critical review

• Fabio Tonin and
• Isabel W. C. E. Arends

Beilstein J. Org. Chem. 2018, 14, 470–483, doi:10.3762/bjoc.14.33

• for this multistep synthesis will be discussed. Review Precursor availability Bile acids The most important active ingredients of bile are the bile acids. Together with their salts, they allow the emulsification of lipids, a fundamental step for their absorption and digestion. Bile acids are 24-carbon

Recent applications of click chemistry for the functionalization of gold nanoparticles and their conversion to glyco-gold nanoparticles

• Vivek Poonthiyil,
• Thisbe K. Lindhorst,
• Vladimir B. Golovko and
• Antony J. Fairbanks

Beilstein J. Org. Chem. 2018, 14, 11–24, doi:10.3762/bjoc.14.2

• types of carbohydrate–protein interactions, it is therefore essential to present carbohydrates in a multivalent fashion. For that purpose, different scaffolds, such as peptides, proteins, lipids, and synthetic polymers, have all been used [7]. The search for better scaffolds for the presentation of

2-Methyl-2,4-pentanediol (MPD) boosts as detergent-substitute the performance of ß-barrel hybrid catalyst for phenylacetylene polymerization

• Julia Kinzel,
• Daniel F. Sauer,
• Marco Bocola,
• Marcus Arlt,
• Tayebeh Mirzaei Garakani,
• Andreas Thiel,
• Klaus Beckerle,
• Tino Polen,
• Jun Okuda and
• Ulrich Schwaneberg

Beilstein J. Org. Chem. 2017, 13, 1498–1506, doi:10.3762/bjoc.13.148

• molecules start to cluster around the hydrophobic transmembrane region. Membrane proteins are normally stabilized by incorporation in a protecting membrane layer formed by ionic detergent molecules such as lipids, SDS or nonionic glycolipids. In contrast, in MD simulations with the two highest

Framing major prebiotic transitions as stages of protocell development: three challenges for origins-of-life research

• Ben Shirt-Ediss,
• Sara Murillo-Sánchez and
• Kepa Ruiz-Mirazo

Beilstein J. Org. Chem. 2017, 13, 1388–1395, doi:10.3762/bjoc.13.135

• first start to grow and divide in an unregulated and error-prone way, relying extensively on environmental conditions and external stimuli. (b) After a major prebiotic transition (blue arrow ‘MT’), the first self-producing protocells appeared, able to endogenously synthesise membrane lipids and other

Glycoscience@Synchrotron: Synchrotron radiation applied to structural glycoscience

• Serge Pérez and
• Daniele de Sanctis

Beilstein J. Org. Chem. 2017, 13, 1145–1167, doi:10.3762/bjoc.13.114

• the biosynthesis of glycosidic linkage requires the transfer of a sugar residue from a donor to an acceptor [35]. Acceptor substrates are carbohydrates, proteins, lipids, DNA, flavonol, antibiotics and steroids. In contrast, glycosyl donor substrates are mostly sugar nucleotides, such as UDP-GlcNAc

• average particle size, distribution and shape. Different kinds of samples beside soluble proteins can be studied by this technique including nucleic acids, protein-based complexes, lipids, membrane proteins and surfactants, glycoproteins, virus, polymers and colloids [78][79]. Proteins: SAXS applied to

From chemical metabolism to life: the origin of the genetic coding process

• Antoine Danchin

Beilstein J. Org. Chem. 2017, 13, 1119–1135, doi:10.3762/bjoc.13.111

• is not a fight against the second principle of thermodynamics), using the global distribution of water molecules as a driving force to order lipids into cell-like structures (of a considerable variety, even in bacteria [12]). Membranes also contain proteins as essential components. It took very long

• to understand the way proteins interact with membrane lipids, and our knowledge in the domain is still far from complete. There exist many models describing the operation (including ideas about the asymmetry of the bilayer, its local changes and lipid rafts). Work exploring the way proteins are

• that they split, fuse, get internalised and make complex internal networks [15]. Beside lipids, polypeptides form coacervates, which also allow for compartmentalisation [16]. A main difficulty to understand the process is that membrane proteins must fold within two-dimensional (2D) bilayers. This

Correlation of surface pressure and hue of planarizable push–pull chromophores at the air/water interface

• Frederik Neuhaus,
• Fabio Zobi,
• Gerald Brezesinski,
• Marta Dal Molin,
• Stefan Matile and
• Andreas Zumbuehl

Beilstein J. Org. Chem. 2017, 13, 1099–1105, doi:10.3762/bjoc.13.109

• were able to study the fundamental questions of surface pressure–hue correlation avoiding interfering effects from other lipids or solvents. The putative lateral organization of the hydrophobic part of the flipper probes was probed by grazing-incidence angle X-ray diffraction experiments (GIXD) [15][16

Glyco-gold nanoparticles: synthesis and applications

• Federica Compostella,
• Olimpia Pitirollo,
• Alessandro Silvestri and
• Laura Polito

Beilstein J. Org. Chem. 2017, 13, 1008–1021, doi:10.3762/bjoc.13.100

• diameter range can be obtained [4]. Moreover, this synthetic procedure allows to introduce different types of carbohydrates and other ligands (i.e., polyethylene chains, lipids, peptides, DNA, RNA or fluorescent dyes) in controlled ratios [4]. A modification of this technique consists in the application of