Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling

• Mateusz Marcisz,
• Sebastian Anila,
• Margrethe Gaardløs,
• Martin Zacharias and
• Sergey A. Samsonov

Beilstein J. Org. Chem. 2023, 19, 1933–1946, doi:10.3762/bjoc.19.144

• surface and in the extracellular matrix [4]. Due to their charged nature, they bind a large amount of water [5]. Although GAGs were previously considered just an inert glue surrounding the cell, GAG research in the past few decades has illustrated the crucial role in cell signaling processes, including

Synthesis of ether lipids: natural compounds and analogues

• Marco Antônio G. B. Gomes,
• Alicia Bauduin,
• Chloé Le Roux,
• Romain Fouinneteau,
• Wilfried Berthe,
• Mathieu Berchel,
• Hélène Couthon and
• Paul-Alain Jaffrès

Beilstein J. Org. Chem. 2023, 19, 1299–1369, doi:10.3762/bjoc.19.96

• noted that ELs are essential players of cell signaling [25]. Together, all these studies point out that ELs are essential for a multitude of biological functions [26] despite their mode of action is not yet fully understood. From a molecular point of view, the ether function present in alkenyl ELs

Revisiting the bromination of 3β-hydroxycholest-5-ene with CBr₄/PPh₃ and the subsequent azidolysis of the resulting bromide, disparity in stereochemical behavior

• Christian Schumacher,
• Jas S. Ward,
• Kari Rissanen,
• Carsten Bolm and
• Mohamed Ramadan El Sayed Aly

Beilstein J. Org. Chem. 2023, 19, 91–99, doi:10.3762/bjoc.19.9

• acts as fluidity buffer, permeability switch, and consequently in cell signaling pathways. Physiologically, cholesterol is the substrate for the biosynthesis of steroidal hormones, vitamin D and bile acids [1][2]. Although cholesterol can adopt 256 stereoisomeric structures, biological significances

Synthesis of the biologically important dideuterium-labelled adenosine triphosphate analogue ApppI(d₂)

• Petri A. Turhanen

Beilstein J. Org. Chem. 2022, 18, 1466–1470, doi:10.3762/bjoc.18.153

• little is still known about this class of compounds: a recent search of the structure of ApppI on SciFinder led to only 18 references. It is not a whole truth, but it can be said that this is a very underexplored area of research. Interestingly, it has been reported that BP-based ATP analogs inhibit cell

• signaling pathways and that ApppI has a role in pain relief [17][18]. It can be proposed that some NBPs might represent a significant lead for the treatment of problematic chronic pain. Perhaps the main reason for the lack of research results on ApppI and ApppD is that these molecules are not commercially

Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups

• Neda Rafieiolhosseini,
• Matthias Killa,
• Thorben Neumann,
• Niklas Tötsch,
• Jean-Noël Grad,
• Alexander Höing,
• Thies Dirksmeyer,
• Jochen Niemeyer,
• Christian Ottmann,
• Shirley K. Knauer,
• Michael Giese,
• Jens Voskuhl and
• Daniel Hoffmann

Beilstein J. Org. Chem. 2022, 18, 1322–1331, doi:10.3762/bjoc.18.137

• enormous number of interactions with other proteins. Currently, more than 200 interacting proteins are known. 14-3-3 proteins play a significant role in cell signaling [2][3] and they were found to be essential in processes such as differentiation, apoptosis, or migration [4]. 14-3-3 proteins also play a

GlycoBioinformatics

• Kiyoko F. Aoki-Kinoshita,
• Frédérique Lisacek,
• Niclas Karlsson,
• Daniel Kolarich and
• Nicolle H. Packer

Beilstein J. Org. Chem. 2021, 17, 2726–2728, doi:10.3762/bjoc.17.184

• be detected when comparing similar glycomes by this method. The articles by Groth et al. [12] and by Bagdonas et al. [13] illustrate how glycoinformation can be harvested and integrated from available -omics databases, with the former paper identifying putative cell signaling molecules and

A systems-based framework to computationally describe putative transcription factors and signaling pathways regulating glycan biosynthesis

• Theodore Groth,
• Rudiyanto Gunawan and
• Sriram Neelamegham

Beilstein J. Org. Chem. 2021, 17, 1712–1724, doi:10.3762/bjoc.17.119

• relate cell-signaling pathways to TFs and cellular glycosylation state. Whereas analysis results are presented for all 29 cancer types, specific focus is placed on human luminal and basal breast cancer disease progression. Overall, the article presents a computational approach to describe TF–glycogene

• analysis of studies that link TFs to glycosylation pathways and glycan structures. Results TF–glycogene interaction map and relation to cell signaling pathways The article follows a workflow shown in Figure 2. It mines TF–glycosylation pathway relationships from the Cistrome Cancer DB [14], which involves

• potential signaling pathways. This resulted in a relationship between cell signaling, TF activity regulation, and glycan structure changes (Supporting Information File 3, Tables S4 and S5). The data are presented as alluvial plots for the 29 cancer types (Supporting Information File 1). Here, the TFs were

Simulating the enzymes of ganglioside biosynthesis with Glycologue

• Andrew G. McDonald and
• Gavin P. Davey

Beilstein J. Org. Chem. 2021, 17, 739–748, doi:10.3762/bjoc.17.64

• then to subsequent ceramide-linked glycoconjugate acceptors, before transport and eventual incorporation into the plasma membrane via vesicular fusion. Gangliosides, which function as antigenic determinants [4], may play a role in membrane organization [5], cell signaling [6], apoptosis [7], and in

Encrypting messages with artificial bacterial receptors

• Pragati Kishore Prasad,
• Naama Lahav-Mankovski,
• Leila Motiei and
• David Margulies

Beilstein J. Org. Chem. 2020, 16, 2749–2756, doi:10.3762/bjoc.16.225

• [2]. Although it will take some time until artificial receptors will be able to engage in cell signaling pathways, this work shows an alternative way by which artificial cell surface receptors can process information. Specifically, it shows that fluorescence signals generated by such systems can be

1,2,3-Triazolium macrocycles in supramolecular chemistry

• Mastaneh Safarnejad Shad,
• Pulikkal Veettil Santhini and
• Wim Dehaen

Beilstein J. Org. Chem. 2019, 15, 2142–2155, doi:10.3762/bjoc.15.211

• reduced cavity. These conformational changes are reversible in solution with switching pH. 4.3. A multivalent catenane and its motion in diverse pH media Cell signaling, energy transduction, and cargo delivery are some of functions of very complicatedly assembled biomolecular machines. Multivalent

Host–guest interactions in nor-seco-cucurbit[10]uril: novel guest-dependent molecular recognition and stereoisomerism

• Xiaodong Zhang,
• Wei Wu,
• Zhu Tao and
• Xin-Long Ni

Beilstein J. Org. Chem. 2019, 15, 1705–1711, doi:10.3762/bjoc.15.166

• importance in the study of enzymatic catalysis and allosteric regulation of cell signaling, as well as in the design of efficient drugs that utilize host–guest interactions [1]. Cucurbit[n]urils (Q[n]s or CB[n]s) [2][3] having been viewed to have high potential use in host–guest chemistry in aqueous solution

Stereo- and regioselective hydroboration of 1-exo-methylene pyranoses: discovery of aryltriazolylmethyl C-galactopyranosides as selective galectin-1 inhibitors

• Alexander Dahlqvist,
• Axel Furevi,
• Niklas Warlin,
• Hakon Leffler and
• Ulf J. Nilsson

Beilstein J. Org. Chem. 2019, 15, 1046–1060, doi:10.3762/bjoc.15.102

• /bjoc.15.102 Abstract Galectins are carbohydrate recognition proteins that bind carbohydrates containing galactose and are involved in cell signaling and cellular interactions, involving them in several diseases. We present the synthesis of (aryltriazolyl)methyl galactopyranoside galectin inhibitors

• uptake and breakdown, respectively. The association of galectins to cell signaling and adhesion gives them roles in several different pathological processes, such as pulmonary fibrosis [6][10], pathological lymphangiogenesis [11], inflammation [12] and cancer [13], with galectin inhibitors demonstrated

A chemoenzymatic synthesis of ceramide trafficking inhibitor HPA-12

• Seema V. Kanojia,
• Sucheta Chatterjee,
• Subrata Chattopadhyay and
• Dibakar Goswami

Beilstein J. Org. Chem. 2019, 15, 490–496, doi:10.3762/bjoc.15.42

• ]. Once formed, ceramide transport protein (CERT), a 68 kDa cytosolic protein, delivers the compound to the Golgi apparatus for further conversion to sphingomyelins, which play important roles in cell-signaling pathways [2]. In the last few years, the downregulation of CERT-mediated ceramide transfer from

Non-native autoinducer analogs capable of modulating the SdiA quorum sensing receptor in Salmonella enterica serovar Typhimurium

• Matthew J. Styles and
• Helen E. Blackwell

Beilstein J. Org. Chem. 2018, 14, 2651–2664, doi:10.3762/bjoc.14.243

• , host colonization, and biofilm formation at high population densities. This cell–cell signaling process is regulated by N-acyl L-homoserine lactone (AHL) signals, or autoinducers, and LuxR-type receptors in Gram-negative bacteria. SdiA is an orphan LuxR-type receptor found in Escherichia, Salmonella

A stereoselective and flexible synthesis to access both enantiomers of N-acetylgalactosamine and peracetylated N-acetylidosamine

• Bettina Riedl and
• Walther Schmid

Beilstein J. Org. Chem. 2018, 14, 856–860, doi:10.3762/bjoc.14.71

• pivotal role in cell–cell interaction and receptor induced cell signaling. Herein, we present a synthetic route in which two of the four stereogenic centers present in the target compound are derived from enantiopure tartaric acid being selectively converted to epoxy alcohols. The key step is the Pd

An uracil-linked hydroxyflavone probe for the recognition of ATP

• Márton Bojtár,
• Péter Zoltán Janzsó-Berend,
• Dávid Mester,
• Dóra Hessz,
• Mihály Kállay,
• Miklós Kubinyi and
• István Bitter

Beilstein J. Org. Chem. 2018, 14, 747–755, doi:10.3762/bjoc.14.63

• ; nucleotide recognition; Introduction Nucleotides play essential roles in various physiological processes, such as energy transportation [1], DNA synthesis [2] and cell signaling events [3]. Especially, adenosine-5’-triphosphate (ATP) is vital, since it is the main energy source in living systems [4]. The

Versatile synthesis of the signaling peptide glorin

• Robert Barnett,
• Daniel Raszkowski,
• Thomas Winckler and
• Pierre Stallforth

Beilstein J. Org. Chem. 2017, 13, 247–250, doi:10.3762/bjoc.13.27

• intraspecies interactions will give insight into the fundamentals of cell signaling and access to a rich source of novel natural products. We describe a practical synthesis of the modified dipeptide glorin (1, Figure 1), the assumed acrasin for many of the early-diverged species of social amoebae. While

Interactions between cyclodextrins and cellular components: Towards greener medical applications?

• Loïc Leclercq

Beilstein J. Org. Chem. 2016, 12, 2644–2662, doi:10.3762/bjoc.12.261

• are composed of lipids. Lipids also provide various other biological functions, including cell signaling and storage of metabolic energy by lipogenesis. Biological lipids are basically due to two types of compounds acting as “building blocks”: ketoacyl groups and isoprene units. From this point of

Synthesis of isoprenoid bisphosphonate ethers through C–P bond formations: Potential inhibitors of geranylgeranyl diphosphate synthase

• Xiang Zhou,
• Jacqueline E. Reilly,
• Kathleen A. Loerch,
• Raymond J. Hohl and
• David F. Wiemer

Beilstein J. Org. Chem. 2014, 10, 1645–1650, doi:10.3762/bjoc.10.171

• should reduce cellular levels of GGPP and thus diminish protein geranylgeranylation, one might expect that inhibitors of this enzyme would interfere with essential cell signaling pathways and demonstrate antiproliferative activity. Several years ago we reported the synthesis of digeranyl bisphosphonate

Biosynthesis of rare hexoses using microorganisms and related enzymes

• Zijie Li,
• Yahui Gao,
• Hideki Nakanishi,
• Xiaodong Gao and
• Li Cai

Beilstein J. Org. Chem. 2013, 9, 2434–2445, doi:10.3762/bjoc.9.281

• well aiming to reduce the cost by employing the one-pot four-enzyme system as described before (also see Scheme 3 and Scheme 7) and obtained an overall isolated yield of 66% on a preparative scale [48][57]. 1-Deoxy-L-fructose Deoxy sugars play significant roles in central metabolism [62], cell

• signaling, immunological recognition and host–pathogen interactions [63][64]. Gullapalli et al. demonstrated an effective way of obtaining deoxy L-fructose by combining chemical and biotechnological approaches (Scheme 10) [8]. Hydrogenation of 6-deoxy-L-mannose (L-rhamnose) produced 6-deoxy-L-mannitol (L

A chemist and biologist talk to each other about caged neurotransmitters

• Graham C.R. Ellis-Davies

Beilstein J. Org. Chem. 2013, 9, 64–73, doi:10.3762/bjoc.9.8

• between the two communities to further the creative development and application of these powerful optical probes. Keywords: caged compounds; cell signaling; electrophysiology; neuronal currents; photolabile neurotransmitters; rates of reaction; receptor antagonism; Introduction The first biologically