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Search for "extracellular matrix" in Full Text gives 17 result(s) in Beilstein Journal of Organic Chemistry.
Origami with small molecules: exploiting the C–F bond as a conformational tool
- Patrick Ryan,
- Ramsha Iftikhar and
- Luke Hunter
Beilstein J. Org. Chem. 2025, 21, 680–716, doi:10.3762/bjoc.21.54
Graphical Abstract
Figure 1: Fundamental characteristics of the C–F bond.
Figure 2: Incorporation of fluorine at the end of an alkyl chain.
Figure 3: Incorporation of fluorine into the middle of a linear alkyl chain.
Figure 4: Incorporation of fluorine across much, or all, of a linear alkyl chain.
Figure 5: Incorporation of fluorine into cycloalkanes.
Figure 6: Conformational effects of introducing fluorine into an ether (geminal to oxygen).
Figure 7: Conformational effects of introducing fluorine into an ether (vicinal to oxygen).
Figure 8: Effects of introducing fluorine into alcohols (and their derivatives).
Figure 9: Controlling the ring pucker of sugars through fluorination.
Figure 10: Controlling bond rotations outside the sugar ring through fluorination.
Figure 11: Effects of incorporating fluorine into amines.
Figure 12: Effects of incorporating fluorine into amine derivatives, such as amides and sulfonamides.
Figure 13: Effects of incorporating fluorine into organocatalysts.
Figure 14: Effects of incorporating fluorine into carbonyl compounds, focusing on the “carbon side.”
Figure 15: Fluoroproline-containing peptides and proteins.
Figure 16: Further examples of fluorinated linear peptides (besides fluoroprolines). For clarity, sidechains a...
Figure 17: Fluorinated cyclic peptides.
Figure 18: Fluorine-derived conformational control in sulfur-containing compounds.
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
Graphical Abstract
Figure 1: Graphical representation of ligands (in licorice, hydrogen atoms not shown) used in this study. Lig...
Figure 2: RMSD values obtained using the cpptraj script from AMBER suite for 1BFC (basic fibroblast factor) c...
Figure 3: Graphical representation of the ligands’ starting (in red, licorice) and final (in blue, licorice) ...
Figure 4: Graphical representation of the ligand’s starting (in red, licorice) and final (in blue, licorice) ...
Figure 5: Graphical representation of the ligand 4 starting (in red, licorice) and final (in blue, licorice) ...
Figure 6: Comparison of the last frame of the US simulation (orange, licorice) with the chondroitin sulfate l...
Figure 7: The X-ray conformation of bFGF-HP dp6 (PDB ID: 1BFC) and windows 5 and 10 and windows 6, 8, 10 in t...
Insight into oral amphiphilic cyclodextrin nanoparticles for colorectal cancer: comprehensive mathematical model of drug release kinetic studies and antitumoral efficacy in 3D spheroid colon tumors
- Sedat Ünal,
- Gamze Varan,
- Juan M. Benito,
- Yeşim Aktaş and
- Erem Bilensoy
Beilstein J. Org. Chem. 2023, 19, 139–157, doi:10.3762/bjoc.19.14
- extracellular matrix in 3D cultures of colorectal cancer cell lines prepared using polymer-based scaffolds. Murine or human colon cancer cells were seeded on poly-HEMA-coated cell plates prepared as described in the methods section, and the plates were centrifuged. The cells were found to be collected in the
Graphical Abstract
Figure 1: In vitro release profile of CPT from nanoparticle formulations (n = 3, ± SD).
Figure 2: Results for release kinetics obtained automatically by the DDSolver software for SGF release medium...
Figure 3: Results for release kinetics obtained automatically by the DDSolver software for SIF release medium...
Figure 4: Results for release kinetics obtained automatically by the DDSolver software for SCoF release mediu...
Figure 5: Anticancer effect of blank or CPT-loaded CD nanoparticles and camptothecin solution against 2D CT26...
Figure 6: Live/dead analysis of CT26 and HT29 cells using double staining with calcein AM and ethidium homodi...
Figure 7: Murine (CT26) and human (HT29) colon cancer spheroid was formed by scaffold-based method, and the m...
Figure 8: Anticancer effect of blank or drug-loaded cyclodextrin nanoparticles and CPT solution against 3D CT...
Figure 9: Chemical structures of 6-O-capro-β-CD, poly-β-CD-C6, and chitosan.
Cryogels: recent applications in 3D-bioprinting, injectable cryogels, drug delivery, and wound healing
- Luke O. Jones,
- Leah Williams,
- Tasmin Boam,
- Martin Kalmet,
- Chidubem Oguike and
- Fiona L. Hatton
Beilstein J. Org. Chem. 2021, 17, 2553–2569, doi:10.3762/bjoc.17.171
- produce them from biocompatible materials make these materials ideal for cell culture and tissue engineering [12][16][38][42]. Furthermore, post-synthesis modifications can be performed to enhance attachment from certain objects, for example proteins from the extracellular matrix (ECM) in tissue
Graphical Abstract
Figure 1: Schematic representation of the process of aqueous cryogel formation, using (a) monomers/small mole...
Figure 2: Microarchitecture of gelatin cryogels. (A) Surface and cross-sectional SEM micrographs of highly po...
Figure 3: Principle of 3D-cryogel printing. A) Illustration of 3D-printing of cryogels. B) Illustration of th...
Figure 4: Illustration of the production of the injectable multifunctional composite, comprised of alginate c...
Figure 5: Digital and SEM photographs of PETEGA cryogel at 20 °C (top) and 50 °C (bottom), synthesised via UV...
Figure 6: Cell morphology of T47D breast cancer cells cultured in HA cryogels. (A) Schematic representation o...
Figure 7: Preparation of PDMA/β-CD cryogel via cryogenic treatment and photochemical crosslinking in frozen s...
Figure 8: (A) Healing rate of wounds treated with autoclaved CG11 cryogels and those treated with 70% ethanol...
Figure 9: In vivo haemostatic capacity evaluation of the cryogels. Blood loss (a) and haemostatic time (b) in...
Progress and challenges in the synthesis of sequence controlled polysaccharides
- Giulio Fittolani,
- Theodore Tyrikos-Ergas,
- Denisa Vargová,
- Manishkumar A. Chaube and
- Martina Delbianco
Beilstein J. Org. Chem. 2021, 17, 1981–2025, doi:10.3762/bjoc.17.129
Graphical Abstract
Figure 1: Overview of the methods available for the synthesis of polysaccharides. For each method, advantages...
Figure 2: Overview of the classes of polysaccharides discussed in this review. Each section deals with polysa...
Scheme 1: Enzymatic and chemical polymerization approaches provide cellulose oligomers with a non-uniform dis...
Scheme 2: AGA of a collection of cellulose analogues obtained using BBs 6–9. Specifically placed modification...
Figure 3: Chemical structure of the different branches G, X, L, F commonly found in XGs. Names are given foll...
Scheme 3: AGA of XG analogues with defined side chains. The AGA cycle includes coupling (TMSOTf), Fmoc deprot...
Figure 4: Synthetic strategies and issues associated to the formation of the β(1–3) linkage.
Scheme 4: Convergent synthesis of β(1–3)-glucans using a regioselective glycosylation strategy.
Scheme 5: DMF-mediated 1,2-cis glycosylation. A) General mechanism and B) examples of α-glucans prepared usin...
Scheme 6: Synergistic glycosylation strategy employing a nucleophilic modulation strategy (TMSI and Ph3PO) in...
Scheme 7: Different approaches to produce xylans. A) Polymerization techniques including ROP, and B) enzymati...
Scheme 8: A) Synthesis of arabinofuranosyl-decorated xylan oligosaccharides using AGA. Representative compoun...
Scheme 9: Chemoenzymatic synthesis of COS utilizing a lysozyme-catalyzed transglycosylation reaction followed...
Scheme 10: Synthesis of COS using an orthogonal glycosylation strategy based on the use of two different LGs.
Scheme 11: Orthogonal N-PGs permitted the synthesis of COS with different PA.
Scheme 12: AGA of well-defined COS with different PA using two orthogonally protected BBs. The AGA cycle inclu...
Scheme 13: A) AGA of β(1–6)-N-acetylglucosamine hexasaccharide and dodecasaccharide. AGA includes cycles of co...
Figure 5: ‘Double-faced’ chemistry exemplified for ᴅ-Man and ʟ-Rha. Constructing β-Man linkages is considerab...
Figure 6: Implementation of a capping step after each glycosylation cycle for the AGA of a 50mer oligomannosi...
Scheme 14: AGA enabled the synthesis of a linear α(1–6)-mannoside 100mer 93 within 188 h and with an average s...
Scheme 15: The 151mer branched polymannoside was synthesized by a [30 + 30 + 30 + 30 + 31] fragment coupling. ...
Figure 7: PG stereocontrol strategy to obtain β-mannosides. A) The mechanism of the β-mannosylation reaction ...
Scheme 16: A) Mechanism of 1,2-cis stereoselective glycosylation using ManA donors. Once the ManA donor is act...
Figure 8: A) The preferred 4H3 conformation of the gulosyl oxocarbenium ion favors the attack of the alcohol ...
Scheme 17: AGA of type I rhamnans up to 16mer using disaccharide BB 115 and CNPiv PG. The AGA cycle includes c...
Figure 9: Key BBs for the synthesis of the O-antigen of Bacteroides vulgatus up to a 128mer (A) and the CPS o...
Figure 10: Examples of type I and type II galactans synthesized to date.
Figure 11: A) The DTBS PG stabilizes the 3H4 conformation of the Gal oxocarbenium ion favoring the attack of t...
Figure 12: Homogalacturonan oligosaccharides synthesized to date. Access to different patterns of methyl-ester...
Figure 13: GlfT2 from Mycobacterium tuberculosis catalyzes the sequential addition of UPD-Galf donor to a grow...
Figure 14: The poor reactivity of acceptor 137 hindered a stepwise synthesis of the linear galactan backbone a...
Scheme 18: AGA of a linear β(1–5) and β(1–6)-linked galactan 20mer. The AGA cycle includes coupling (NIS/TfOH)...
Figure 15: The 92mer arabinogalactan was synthesized using a [31 + 31 + 30] fragment coupling between a 31mer ...
Scheme 19: Synthesis of the branched arabinofuranose fragment using a six component one-pot synthesis. i) TTBP...
Figure 16: A) Chemical structure and SNFG of the representative disaccharide units forming the GAG backbones, ...
Figure 17: Synthetic challenges associated to the H/HS synthesis.
Scheme 20: Degradation of natural heparin and heparosan generated valuable disaccharides 150 and 151 that can ...
Scheme 21: A) The one-step conversion of cyanohydrin 156 to ʟ-iduronamide 157 represent the key step for the s...
Scheme 22: A) Chemoenzymatic synthesis of heparin structures, using different types of UDP activated natural a...
Scheme 23: Synthesis of the longest synthetic CS chain 181 (24mer) using donor 179 and acceptor 180 in an iter...
Scheme 24: AGA of a collection of HA with different lengths. The AGA cycle includes coupling (TfOH) and Lev de...
Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement
- Vladimir Kubyshkin,
- Rebecca Davis and
- Nediljko Budisa
Beilstein J. Org. Chem. 2021, 17, 439–460, doi:10.3762/bjoc.17.40
- extracellular matrix in higher animals. When introduced at a certain position in the structure, R-Flp and S-Flp exhibit prominent effects on the thermal stability of the protein. The effect originates from the stabilization of the pyrrolidine ring puckers, which has an effect on the packing of the triple helix
Graphical Abstract
Figure 1: The structures of the fluoroprolines discussed herein.
Figure 2: The distinction between “the alanine and the proline worlds”. While the polyalanine backbone leads ...
Figure 3: Molecular volume for 20 coded amino acids and fluoroprolines. The COSMO volume was calculated for a...
Figure 4: Comparative analysis of the electrostatic potential for proline and fluoroprolines (electrostatic p...
Figure 5: Experimental logP data for methyl esters of N-acetylamino acids.
Figure 6: The conformational dependence of the proline ring on the fluorination at position 4.
Figure 7: Rotation around the peptidyl-prolyl fragments in polypeptide structures is important for correct ov...
Figure 8: The complex fate of a protein-encoded amino acid in the cell (EF-Tu – elongation factor thermo unst...
Figure 9: Metabolic routes for proline in E. coli. A) Synthesis of proline and B) degradation of proline.
Figure 10: A complete flowchart for the proline incorporation into proteins during ribosomal biosynthesis. A) ...
Figure 11: Amide bond formation capacities of fluoroprolines compared to some coded amino acids measured on ri...
Figure 12: Ribbon representation of the X-ray crystal structures of proteins containing fluoroprolines. A) Enh...
Figure 13: Problems and phenomena associated with the production of a protein-containing proline-to-fluoroprol...
Figure 14: Effects of fluoroprolines on recombinant protein expression using the auxotrophic expression host E...
Figure 15: A) Experimental setup for the incorporation of fluoroprolines into proteins. B) Adaptive laboratory...
UV resonance Raman spectroscopy of the supramolecular ligand guanidiniocarbonyl indole (GCI) with 244 nm laser excitation
- Tim Holtum,
- Vikas Kumar,
- Daniel Sebena,
- Jens Voskuhl and
- Sebastian Schlücker
Beilstein J. Org. Chem. 2020, 16, 2911–2919, doi:10.3762/bjoc.16.240
- extracellular matrix. Results and Discussion Figure 1 (left) displays the absorption spectra of GCP ethyl amide and GCI ethyl amide at 200 µM concentration in buffer solution. The GCP ethyl amide [9] shows a strong electronic absorption covering the entire spectral region below ca. 325 nm with two peaks at 298
Graphical Abstract
Figure 1: UV–vis absorption spectra of GCP ethyl amide [9] (in grey) and GCI ethyl amide (in green) at 200 µM co...
Figure 2: UVRR spectra of a 1 mM solution of toluene in acetonitrile acquired with 240, 258, and 266 nm laser...
Figure 3: The UVRR spectra of a 200 µM solution of GCP ethyl amide in 6 mM BisTris buffer solution at pH 6 ac...
Figure 4: The UVRR spectra of GCI ethyl amide at a 200 µM concentration in 6 mM BisTris buffer solution at pH...
Figure 5: The computed Raman spectrum of GCI ethyl amide in the fingerprint region 800–1800 cm−1, calculated ...
Figure 6: The DFT computed eigenvectors of GCI ethyl amide of selected normal modes (cf. Figure 5) at (a) 1035 cm−1, ...
Figure 7: The UVRR spectra obtained with 244 nm laser excitation: GCI and a 1:1 mixture of ‘GCI and BA’ (bott...
Figure 8: The UVRR spectra obtained with 244 nm laser excitation: GCI and a 1:1 mixture of ‘GCI and RGD’ (bot...
Repurposing the anticancer drug cisplatin with the aim of developing novel Pseudomonas aeruginosa infection control agents
- Mingjun Yuan,
- Song Lin Chua,
- Yang Liu,
- Daniela I. Drautz-Moses,
- Joey Kuok Hoong Yam,
- Thet Tun Aung,
- Roger W. Beuerman,
- May Margarette Santillan Salido,
- Stephan C. Schuster,
- Choon-Hong Tan,
- Michael Givskov,
- Liang Yang and
- Thomas E. Nielsen
Beilstein J. Org. Chem. 2018, 14, 3059–3069, doi:10.3762/bjoc.14.284
- biofilms are encased by an extracellular matrix, which protects them from antimicrobial treatment and the host’s immune clearance [5]. Clinical P. aeruginosa isolates are mostly multidrug-resistant (MDR) strains [6], with robust ability to form biofilms [7]. P. aeruginosa also secretes virulence factors
Graphical Abstract
Figure 1: Structures and MICs of Pt-based compounds against P. aeruginosa PAO1.
Figure 2: Transcriptomic analysis of control and cisplatin-treated PAO1 cultures. Heatmap comparing the trans...
Figure 3: Function enrichment of differentially expressed genes from the transcriptomic analysis. A dot-lot f...
Figure 4: Cisplatin fast-kill assay against the P. aeruginosa PAO1, ΔrecA mutant and the ΔrecACOM strain. P. ...
Figure 5: Cisplatin treatment represses T3SS associated virulence. (A) Cisplatin treatment downregulated the ...
Figure 6: P. aeruginosa biofilm killing assay by cisplatin, tobramycin and their combinations. P. aeruginosa ...
Figure 7: Cisplatin treatment attenuates P. aeruginosa infections. CFU mL−1 of PAO1 obtained from corneas wit...
One hundred years of benzotropone chemistry
- Arif Dastan,
- Haydar Kilic and
- Nurullah Saracoglu
Beilstein J. Org. Chem. 2018, 14, 1120–1180, doi:10.3762/bjoc.14.98
- yield, whereas the treatment with 42% aq HBF4 of the compounds 65 and 66 regenerated 61+.BF4− in good yields. Integrins are transmembrane α/β heterodimers that bind to extracellular matrix ligands, cell-surface ligands, and soluble ligands [72]. Perron-Sierra’s group prepared substituted benzo[7
Graphical Abstract
Scheme 1: Tropone (1), tropolone (2) and their resonance structures.
Figure 1: Natural products containing a tropone nucleus.
Figure 2: Possible isomers 11–13 of benzotropone.
Scheme 2: Synthesis of benzotropones 11 and 12.
Scheme 3: Oxidation products of benzotropylium fluoroborate (16).
Scheme 4: Oxidation of 7-bromo-5H-benzo[7]annulene (22).
Scheme 5: Synthesis of 4,5-benzotropone (11) using o-phthalaldehyde (27).
Scheme 6: Synthesis of 4,5-benzotropone (11) starting from oxobenzonorbornadiene 31.
Scheme 7: Acid-catalyzed cleavage of oxo-bridge of 34.
Scheme 8: Synthesis of 4,5-benzotropone (11) from o-xylylene dibromide (38).
Scheme 9: Synthesis of 4,5-benzotropone (11) via the carbene adduct 41.
Scheme 10: Heck coupling strategy for the synthesis of 11.
Scheme 11: Synthesis of benzofulvalenes via carbonyl group of 4,5-benzotropone (11).
Figure 3: Some cycloheptatrienylium cations.
Scheme 12: Synthesis of condensation product 63 and its subsequent oxidative cyclization products.
Figure 4: A novel series of benzo[7]annulenes prepared from 4,5-benzotropone (11).
Scheme 13: Preparation of substituted benzo[7]annulene 72 using the Mukaiyama-Michael reaction.
Figure 5: Possible benzo[7]annulenylidenes 73–75.
Scheme 14: Thermal and photochemical decomposition of 7-diazo-7H-benzo[7]annulene (76) and the trapping of int...
Scheme 15: Synthesis of benzoheptafulvalene 86.
Scheme 16: Synthesis of 7-(diphenylmethylene)-7H-benzo[7]annulene (89).
Scheme 17: Reaction of 4,5-benzotropone (11) with dimethyl diazomethane.
Scheme 18: Synthesis of dihydrobenzomethoxyazocine 103.
Scheme 19: Synthesis and reducibility of benzo-homo-2-methoxyazocines.
Scheme 20: Synthesis of 4,5-benzohomotropones 104 and 115 from 4,5-benzotropones 11 and 113.
Scheme 21: A catalytic deuterogenation of 4,5-benzotropone (11) and synthesis of 5-monosubstituted benzo[7]ann...
Scheme 22: Synthesis of methyl benzo[7]annulenes 131 and 132.
Scheme 23: Ambident reactivity of halobenzo[7]annulenylium cations 133a/b.
Scheme 24: Preparation of benzo[7]annulenylidene–iron complexes 147.
Scheme 25: Synthesis of 1-ethynylbenzotropone (150) and the etheric compound 152 from 4,5-benzotropone (11) wi...
Scheme 26: Thermal decomposition of 4,5-benzotropone (11).
Scheme 27: Reaction of 4,5-benzotropone (11) with 1,2-ethanediol and 1,2-ethanedithiol.
Scheme 28: Conversions of 1-benzosuberone (162) to 2,3-benzotropone (12).
Scheme 29: Synthesis strategies for 2,3-bezotropone (12) using 1-benzosuberones.
Scheme 30: Oxidation-based synthesis of 2,3-benzotropone (12) via 1-benzosuberone (162).
Scheme 31: Synthesis of 2,3-benzotropone (12) from α-tetralone (171) via ring-expansion.
Scheme 32: Preparation of 2,3-benzotropone (12) by using of benzotropolone 174.
Figure 6: Benzoheptafulvenes as condensation products of 2,3-benzotropone (12).
Scheme 33: Conversion of 2,3-benzotropone (12) to tosylhydrazone salt 182 and gem-dichloride 187.
Figure 7: Benzohomoazocines 191–193 and benzoazocines 194–197.
Scheme 34: From 2,3-benzotropone (12) to carbonium ions 198–201.
Scheme 35: Cycloaddition reactions of 2,3-benzotropone (12).
Scheme 36: Reaction of 2,3-benzotropone (12) with various reagents and compounds.
Figure 8: 3,4-Benzotropone (13) and its resonance structure.
Scheme 37: Synthesis of 6,7-benzobicyclo[3.2.0]hepta-3,6-dien-2-one (230).
Figure 9: Photolysis and thermolysis products of 230.
Figure 10: Benzotropolones and their tautomeric structures.
Scheme 38: Synthesis strategies of 4,5-benzotropolone (238).
Scheme 39: Synthesis protocol for 2-hydroxy-4,5-benzotropone (238) using oxazole-benzo[7]annulene 247.
Figure 11: Some quinoxaline and pyrazine derivatives 254–256 prepared from 4,5-benzotropolone (238).
Scheme 40: Nitration product of 4,5-benzotropolone (238) and its isomerization to 1-nitro-naphthoic acid (259)....
Scheme 41: Synthesis protocol for 6-hydroxy-2,3-benzotropone (239) from benzosuberone (162).
Scheme 42: Various reactions via 6-hydroxy-2,3-benzotropone (239).
Scheme 43: Photoreaction of 6-hydroxy-2,3-benzotropone (239).
Scheme 44: Synthesis of 7-hydroxy-2,3-benzotropone (241) from benzosuberone (162).
Scheme 45: Synthesis strategy for 7-hydroxy-2,3-benzotropone (241) from ketone 276.
Scheme 46: Synthesis of 7-hydroxy-2,3-benzotropone (241) from β-naphthoquinone (280).
Scheme 47: Synthesis of 7-hydroxy-2,3-benzotropone (241) from bicyclic endoperoxide 213.
Scheme 48: Synthesis of 7-hydroxy-2,3-benzotropone (241) by ring-closing metathesis.
Figure 12: Various monosubstitution products 289–291 of 7-hydroxy-2,3-benzotropone (241).
Scheme 49: Reaction of 7-hydroxy-2,3-benzotropone (241) with various reagents.
Scheme 50: Synthesis of 4-hydroxy-2,3-benzotropones 174 and 304 from diketones 300/301.
Scheme 51: Catalytic hydrogenation of diketones 300 and 174.
Scheme 52: Synthesis of halo-benzotropones from alkoxy-naphthalenes 306, 307 and 310.
Figure 13: Unexpected byproducts 313–315 during synthesis of chlorobenzotropone 309.
Figure 14: Some halobenzotropones and their cycloadducts.
Scheme 53: Multisep synthesis of 2-chlorobenzotropone 309.
Scheme 54: A multistep synthesis of 2-bromo-benzotropone 26.
Scheme 55: A multistep synthesis of bromo-2,3-benzotropones 311 and 316.
Scheme 56: Oxidation reactions of 8-bromo-5H-benzo[7]annulene (329) with some oxidants.
Scheme 57: Synthesis of 2-bromo-4,5-benzotropone (26).
Scheme 58: Synthesis of 6-chloro-2,3-benzotropone (335) using LiCl and proposed intermediate 336.
Scheme 59: Reaction of 7-bromo-2,3-benzotropone (316) with methylamine.
Scheme 60: Reactions of bromo-2,3-benzotropones 26 and 311 with dimethylamine.
Scheme 61: Reactions of bromobenzotropones 311 and 26 with NaOMe.
Scheme 62: Reactions of bromobenzotropones 26 and 312 with t-BuOK in the presence of DPIBF.
Scheme 63: Cobalt-catalyzed reductive cross-couplings of 7-bromo-2,3-benzotropone (316) with cyclic α-bromo en...
Figure 15: Cycloadduct 357 and its di-π-methane rearrangement product 358.
Scheme 64: Catalytic hydrogenation of 2-chloro-4,5-benzotropone (311).
Scheme 65: Synthesis of dibromo-benzotropones from benzotropones.
Scheme 66: Bromination/dehydrobromination of benzosuberone (162).
Scheme 67: Some transformations of isomeric dibromo-benzotropones 261A/B.
Scheme 68: Transformations of benzotropolone 239B to halobenzotropolones 369–371.
Figure 16: Bromobenzotropolones 372–376 and 290 prepared via bromination/dehydrobromination strategy.
Scheme 69: Synthesis of some halobenzotropolones 289, 377 and 378.
Figure 17: Bromo-chloro-derivatives 379–381 prepared via chlorination.
Scheme 70: Synthesis of 7-iodo-3,4-benzotropolone (382).
Scheme 71: Hydrogenation of bromobenzotropolones 369 and 370.
Scheme 72: Debromination reactions of mono- and dibromides 290 and 375.
Figure 18: Nitratation and oxidation products of some halobenzotropolenes.
Scheme 73: Azo-coupling reactions of some halobenzotropolones 294, 375 and 378.
Figure 19: Four possible isomers of dibenzotropones 396–399.
Figure 20: Resonance structures of tribenzotropone (400).
Scheme 74: Two synthetic pathways for tribenzotropone (400).
Scheme 75: Synthesis of tribenzotropone (400) from dibenzotropone 399.
Scheme 76: Synthesis of tribenzotropone (400) from 9,10-phenanthraquinone (406).
Scheme 77: Synthesis of tribenzotropone (400) from trifluoromethyl-substituted arene 411.
Figure 21: Dibenzosuberone (414).
Figure 22: Reduction products 415 and 416 of tribenzotropone (400).
Figure 23: Structures of tribenzotropone dimethyl ketal 417 and 4-phenylfluorenone (412) and proposed intermed...
Figure 24: Structures of benzylidene- and methylene-9H-tribenzo[a,c,e][7]annulenes 419 and 420 and chiral phos...
Figure 25: Structures of tetracyclic alcohol 422, p-quinone methide 423 and cation 424.
Figure 26: Structures of host molecules 425–427.
Scheme 78: Synthesis of non-helical overcrowded derivatives syn/anti-431.
Figure 27: Hexabenzooctalene 432.
Figure 28: Structures of possible eight isomers 433–440 of naphthotropone.
Scheme 79: Synthesis of naphthotropone 437 starting from 1-phenylcycloheptene (441).
Scheme 80: Synthesis of 10-hydroxy-11H-cyclohepta[a]naphthalen-11-one (448) from diester 445.
Scheme 81: Synthesis of naphthotropone 433.
Scheme 82: Synthesis of naphthotropones 433 and 434 via cycloaddition reaction.
Scheme 83: Synthesis of naphthotropone 434 starting from 452.
Figure 29: Structures of tricarbonyl(tropone)irons 458, and possible cycloadducts 459.
Scheme 84: Synthesis of naphthotropone 436.
Scheme 85: Synthesis of precursor 465 for naphthotropone 435.
Scheme 86: Generation of naphthotropone 435 from 465.
Figure 30: Structures of tropylium cations 469 and 470.
Figure 31: Structures of tropylium ions 471+.BF4−, 472+.BF4−, and 473+.BF4−.
Scheme 87: Synthesis of tropylium ions 471+.BF4− and 479+.ClO4−.
Scheme 88: Synthesis of 1- and 2-methylanthracene (481 and 482) via carbene–carbene rearrangement.
Figure 32: Trapping products 488–490.
Scheme 89: Generation and chemistry of a naphthoannelated cycloheptatrienylidene-cycloheptatetraene intermedia...
Scheme 90: Proposed intermediates and reaction pathways for adduct 498.
Scheme 91: Exited-state intramolecular proton transfer of 505.
Figure 33: Benzoditropones 506 and 507.
Scheme 92: Synthesis of benzoditropone 506e.
Scheme 93: Synthetic approaches for dibenzotropone 507 via tropone (1).
Scheme 94: Formation mechanisms of benzoditropone 507 and 516 via 515.
Scheme 95: Synthesis of benzoditropones 525 and 526 from pyromellitic dianhydride (527).
Figure 34: Possible three benzocyclobutatropones 534–536.
Scheme 96: Synthesis of benzocyclobutatropones 534 and 539.
Scheme 97: Synthesis attempts for benzocyclobutatropone 545.
Scheme 98: Generation and trapping of symmetric benzocyclobutatropone 536.
Scheme 99: Synthesis of chloro-benzocyclobutatropone 552 and proposed mechanism of fluorenone derivatives.
Scheme 100: Synthesis of tropolone analogue 559.
Scheme 101: Synthesis of tropolones 561 and 562.
Figure 35: o/p-Tropoquinone rings (563 and 564) and benzotropoquinones (565–567).
Scheme 102: Synthesis of benzotropoquinone 566.
Scheme 103: Synthesis of benzotropoquinone 567 via a Diels–Alder reaction.
Figure 36: Products 575–577 through 1,2,3-benzotropoquinone hydrate 569.
Scheme 104: Structures 578–582 prepared from tropoquinone 567.
Figure 37: Two possible structures 583 and 584 for dibenzotropoquinone, and precursor compound 585 for 583.
Scheme 105: Synthesis of saddle-shaped ketone 592 using dibenzotropoquinone 584.
On the design principles of peptide–drug conjugates for targeted drug delivery to the malignant tumor site
- Eirinaios I. Vrettos,
- Gábor Mező and
- Andreas G. Tzakos
Beilstein J. Org. Chem. 2018, 14, 930–954, doi:10.3762/bjoc.14.80
- general, the ‘integrin’ nomenclature was first used in 1987 to describe a family of receptors, appearing as heterodimers of noncovalently associated α and β subunits, able to link the extracellular matrix (ECM) with the intracellular cytoskeleton to mediate cell adhesion, migration and proliferation [42
Graphical Abstract
Figure 1: Conventional chemotherapy versus targeted chemotherapy. Black color = Solid malignant tumor; red = ...
Figure 2: A. General structural architecture of the ideal navigated drug delivery system [31]. B. General structu...
Figure 3: Binding and penetration mechanism of iRGD. The iRGD peptide is accumulated on the surface of αv int...
Figure 4: Representative examples of anticancer drugs utilized for the construction of PDCs. The most usual c...
Figure 5: Illustration of the drug release mechanism from the self-immolative spacer PABC conjugated to a tum...
Figure 6: Structures of the PDCs named AN-152 and AN-207.
Figure 7: Structure of the PDC named AN-238.
Figure 8: Chemical structure and synthetic scheme for the PDC ANG1005. (A) ANG1005 is composed of three molec...
Figure 9: Structure of oxime linked Dau–GnRH-III conjugate with or without cathepsin B labile spacer and thei...
Figure 10: Synthesis of the most effective GnRH-III–Dau conjugate with two drug molecules [153].
Figure 11: Structures of the four different PDCs of D-Lys6-GnRH-I and gemcitabine (GSG, GSG2, 3G, 3G2) [19].
Figure 12: Structures of (A) native sunitinib; (B) SAN1 analog of sunitinib and (C) assembled PDC named SAN1GS...
Figure 13: Synthetic scheme for the formation of GSG and the unexpected side product [156].
Figure 14: Illustration of uncharted guanidinium peptide coupling reagent side reactions during PDCs synthesis ...
Figure 15: Putative mechanism for the formation of the uronium side product [156].
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
- . Glycosaminoglycan–protein complexes: As members of the proteoglycan family, glycosaminoglycans (GAGs) are linear polysaccharides, constituted by 40 to 100 repeating disaccharide units, which are usually found to be linked to core proteins. These polysaccharides are components of the peri- and extracellular matrix
- of the later, many sources of structural micro-heterogeneities occur as the epimerization at the C-5 position of uronic acids, and N- and O-sulfation. Of paramount interest is the elucidation of the role of GAGs in their interactions with such important proteins as extracellular matrix proteins
Graphical Abstract
Figure 1: Complementarity of synchrotron radiation and neutron sources to investigate the structure of matter....
Figure 2: A representation of a synchrotron storage ring, including linear accelerator, booster and two beaml...
Figure 3: Schematic representation of a sector of a storage ring. Bending magnets and insertion devices are a...
Figure 4: Structural features of the resin glycoside tricolorin A. (a) Extracted from the Mexican variety of ...
Figure 5: Powder diffractogram measured on a synthetic pentasaccharide from heparin, at ESRF beamline ID31, λ...
Figure 6: Three dimensional ribbon representation of a heavily N-glycosylated Aspergilllus sp. Family GH3 β-D...
Figure 7: Histogram of the number of deposited crystal structures of glycan-binding proteins deposited over t...
Figure 8: Ribbon diagram representations of prototypical members of the GT-A and GT-B super-family fold, resp...
Figure 9: Representation of the FUT1 structure determined in complex with the acceptor (carbon atoms in green...
Figure 10: Representation of the seven folds most commonly found in glycoside hydrolases. From the classificat...
Figure 11: The multivalent carbohydrate binding features of lectins from X-ray structures. (a) Monovalent. E-s...
Figure 12: Three-dimensional depiction of the ternary complex formed by a heparin mimetic in interaction with ...
Figure 13: 3D representation of different sugar transporter structures: (left to right, top to down) lactose p...
Figure 14: Kinetic crystallography. Protein crystals are soaked with the cage compound (Step 1) followed by fl...
Figure 15: Reconstruction of the full three-dimensional structure of the soluble lectin (BC2L-C) from the oppo...
Figure 16: Characterization by synchrotron X-ray reflectometry of the transverse structures of a model membran...
Figure 17: Complementary use of X-ray synchrotron and neutron fiber diffraction to unravel the three-dimension...
Figure 18: Scanning electron micrograph of high-quality micrometer-sized A-amylose microcrystals grown from sh...
Figure 19: Cartography of distribution and orientation of cellulose in wood using a 3 µm X-ray beam. The scann...
Figure 20: Structural micro-diffraction scanning of a starch granule from Phajus grandifolius with dimensions ...
Fluorescent carbon dots from mono- and polysaccharides: synthesis, properties and applications
- Stephen Hill and
- M. Carmen Galan
Beilstein J. Org. Chem. 2017, 13, 675–693, doi:10.3762/bjoc.13.67
- -glucosamine units and which forms the core of complex proteoglycan aggregates found in the extracellular matrix [57]. The team of Du and Shao et al. reported the synthesis of N-doped hyaluronic acid-derived CDs and their application as drug delivery vectors [59]. Following standard hydrothermal synthetic
Graphical Abstract
Scheme 1: Microwave-driven reaction of glucose in the presence of PEG-200 to afford blue-emissive CDs.
Scheme 2: Two-step synthesis of TTDDA-coated CDs generated from acid-refluxed glucose.
Scheme 3: Glucose-derived CDs using KH2PO4 as a dehydrating agent to both form and tune CD’s properties.
Scheme 4: Ultrasonic-mediated synthesis of glucose-derived CDs in the presence of ammonia.
Scheme 5: Tryptophan-derived CDs used for the sensing of peroxynitrite in serum-fortified cell media.
Scheme 6: Glucose-derived CDs conjugated with methotrexate for the treatment of H157 lung cancer cells.
Scheme 7: Boron-doped blue-emissive CDs used for sensing of Fe3+ ion in solution.
Scheme 8: N/S-doped CDs with aggregation-induced fluorescence turn-off to temperature and pH stimuli.
Scheme 9: N/P-doped hollow CDs for efficient drug delivery of doxorubicin.
Scheme 10: N/P-doped CDs applied to the sensing of Fe3+ ions in mammalian T24 cells.
Scheme 11: Comparative study of CDs formed from glucose and N-doped with TTDDA and dopamine.
Scheme 12: Formation of blue-emissive CDs from the microwave irradiation of glycerol, TTDDA and phosphate.
Scheme 13: Xylitol-derived N-doped CDs with excellent photostability demonstrating the importance of Cl incorp...
Scheme 14: Base-mediated synthesis of CDs with nanocrystalline cores, from fructose and maltose, without forci...
Scheme 15: N/P-doped green-emissive CDs working in tandem with hyaluronic acid-coated AuNPs to monitor hyaluro...
Scheme 16: Three-minute microwave synthesis of Cl/N-doped CDs from glucosamine hydrochloride and TTDDA to affo...
Scheme 17: Mechanism for the formation of N/Cl-doped CDs via key aldehyde and iminium intermediates, monitored...
Scheme 18: Phosphoric acid-mediated synthesis of orange-red emissive CDs from sucrose.
Scheme 19: Proposed HMF dimer, and its formation mechanism, that upon aggregations bestows orange-red emissive...
Scheme 20: Different polysaccharide-derived CDs in the presence of PEG-200 and how the starting material compo...
Scheme 21: Tetracycline release profiles for differentially-decorated CDs.
Scheme 22: Hyaluronic acid (HA) and glycine-derived CDs, suspected to be decorated in unreacted HA, allowing r...
Scheme 23: Cyclodextrin-derived CDs used for detection of Ag+ ions in solution, based on the formal reduction ...
Scheme 24: Cyclodextrin and OEI-derived CDs, coated with hyaluronic acid and DOX, to produce an effective lung...
Scheme 25: Cellulose and urea-derived N-doped CDs with green-emissive fluorescence.
Regulation of integrin and growth factor signaling in biomaterials for osteodifferentiation
- Qiang Wei,
- Theresa L. M. Pohl,
- Anja Seckinger,
- Joachim P. Spatz and
- Elisabetta A. Cavalcanti-Adam
Beilstein J. Org. Chem. 2015, 11, 773–783, doi:10.3762/bjoc.11.87
- extracellular matrix (ECM) is the essential component the in stem cell niche, in which both integrin ligands and growth factors are important regulators to directly or indirectly modulate the cell behavior. In this review, we summarize the current knowledge about the potential of integrin ligands and growth
- , chondrocytes, adipocytes, and reticular cells (Figure 1) [3]. Osteogenic differentiation is especially valuable in regenerative medicine approaches [4]. It has been proven that stem cell fate can be regulated from the specific microenvironment known as stem cell niche. The extracellular matrix (ECM), which
Graphical Abstract
Figure 1: Differentiation potential of mesenchymal stem cells (MSCs) in bone marrow. MSCs can differentiate i...
Figure 2: (a) The structure of the integrin heterodimeric receptors with α and β subunits. (b) The major inte...
Figure 3: The chemical structure of the α5β1-selective (left) and the αvβ3-selective (right) peptidomimetics....
Figure 4: When the distance between two neighboring integrin ligands is <70 nm, the focal adhesions and contr...
Figure 5: (a) BMP-2 homodimer. 3D-Structure of a BMP-2 homodimer (blue and pink) with cysteine residues, high...
Figure 6: Growth factors, e.g., BMP-2, can be immobilized on the substrates to mimic the matrix-bound form (l...
Synthesis of a hexasaccharide partial sequence of hyaluronan for click chemistry and more
- Marina Bantzi,
- Stephan Rigol and
- Athanassios Giannis
Beilstein J. Org. Chem. 2015, 11, 604–607, doi:10.3762/bjoc.11.67
- : azide; click chemistry; extracellular matrix; hexasaccharide; hyaluronan; multivalency; Introduction Much effort has been exerted during the last years to refine current knowledge about the biology of the extracellular matrix (ECM) [1]. While in the past, it was only regarded as a “space filler” among
Graphical Abstract
Scheme 1: Synthesis of hexasaccharide 10. Conditions: a) TfOH, NIS, 4 Å molecular sieves, DCM, 0 °C to rt; b)...
Application of cyclic phosphonamide reagents in the total synthesis of natural products and biologically active molecules
- Thilo Focken and
- Stephen Hanessian
Beilstein J. Org. Chem. 2014, 10, 1848–1877, doi:10.3762/bjoc.10.195
- contributes significantly more towards PTP1B affinity [68]. MMP inhibitors (2001) The matrix metalloproteinases (MMPs) are a family of structurally-related, zinc-containing enzymes that play a critical role in the degradation and remodelling of extracellular matrix. Over expression of MMPs has been associated
Graphical Abstract
Figure 1: Examples of phosphonamide reagents used in stereoselective synthesis.
Figure 2: Natural products and bioactive molecules synthesized using phosphonamide-based chemistry (atoms, bo...
Scheme 1: Olefination with cyclic phosphonamide anions, mechanistic rationale, and selected examples 27a–d [18].
Scheme 2: Asymmetric olefination with chiral phosphonamide anions and selected examples 31a–d [1,22].
Scheme 3: Synthesis of α-substituted phosphonic acids 33a–e by asymmetric alkylation of chiral phosphonamide ...
Scheme 4: Asymmetric conjugate additions of C2-symmetric chiral phosphonamide anions to cyclic enones, lacton...
Scheme 5: Asymmetric conjugate additions of P-chiral phosphonamide anions generated from 40a and 44a to cycli...
Scheme 6: Asymmetric cyclopropanation with chiral chloroallyl phosphonamide 47, mechanistic rationale, and se...
Scheme 7: Asymmetric cyclopropanation with chiral chloromethyl phosphonamide 28d [59].
Scheme 8: Stereoselective synthesis of cis-aziridines 57 from chiral chloroallyl phosphonamide 47a [62].
Scheme 9: Synthesis of phosphonamides by (A) Arbuzov reaction, (B) condensation of diamines with phosphonic a...
Figure 3: Original and revised structure of polyoxin A (69) [24-26].
Scheme 10: Synthesis of (E)-polyoximic acid (9) [24-26].
Figure 4: Key assembly strategy of acetoxycrenulide (10) [41,42].
Scheme 11: Total synthesis of (+)-acetoxycrenulide (10) [41,42].
Scheme 12: Synthesis squalene synthase inhibitor 19 by asymmetric sulfuration (A) and asymmetric alkylation (B...
Figure 5: Key assembly strategy of fumonisin B2 (20) and its tricarballylic acid fragment 105 [45,46].
Scheme 13: Final steps of the total synthesis of fumonisin B2 (20) [45,46].
Figure 6: Selected examples of two subclasses of β-lactam antibiotics – carbapenems (111 and 112) and trinems...
Scheme 14: Synthesis of tricyclic β-lactam antibiotic 123 [97].
Scheme 15: Total synthesis of (−)-anthoplalone (8) [56].
Figure 7: Protein tyrosine phosphatase (PTP) inhibitors 130, 131 and model compounds 16, 132 and 133 [68].
Scheme 16: Synthesis of model PTP inhibitors 16a,b [68].
Scheme 17: Synthesis of aziridine hydroxamic acid 17 as MMP inhibitor [63].
Scheme 18: Synthesis of methyl jasmonate (11) [48].
Figure 8: Structures of nudiflosides A (137) and D (13) [49].
Scheme 19: Total synthesis of the pentasubstituted cyclopentane core 159 of nudiflosides A (151) and D (13) an...
Figure 9: L-glutamic acid (161) and constrained analogues [57,124].
Scheme 20: Stereoselective synthesis of DCG-IV (162) [57].
Scheme 21: Stereoselective synthesis of mGluR agonist 21 [124].
Figure 10: Key assembly strategy of berkelic acid (15) [43].
Scheme 22: Total synthesis of berkelic acid (15) [43].
Figure 11: Key assembly strategy of jerangolid A (22) and ambruticin S (14) [27,28].
Scheme 23: Final assembly steps in the total synthesis of jerangolid A [27].
Scheme 24: Key assembly steps in the total synthesis of ambruticin S (14) [28].
Figure 12: General steroid construction strategy based on conjugate addition of 212 to cyclopentenone 48, exem...
Scheme 25: Total synthesis of estrone (12) [44].
Design and synthesis of multivalent neoglycoconjugates by click conjugations
- Feiqing Ding,
- Li Ji,
- Ronny William,
- Hua Chai and
- Xue-Wei Liu
Beilstein J. Org. Chem. 2014, 10, 1325–1332, doi:10.3762/bjoc.10.134
- and glycopeptides are the key constituents of the cellular membrane and extracellular matrix, and play a pivotal role in various key cellular events such as cell–cell recognition, host–pathogen or host–symbiont interactions, molecular recognition of antibodies and metastasis [1][2][3][4][5]. The
Graphical Abstract
Figure 1: Our reported strategy for quick access to 3-amino-2,3-dideoxysugars via regio- and stereoselective ...
Figure 2: Synthetic modification of α-GalNAc linked glycopeptides to 3-tosylamino-2,3-dideoxyneoglycoconjugat...
Figure 3: Our proposal for access to 3-tosylamino-2,3-dideoxyneoglycoconjugates via tandem hydroamination/gly...
Scheme 1: Synthesis of propargyl 3-tosylamino-2,3-dideoxy-α-D-allohexopyranoside (2a).
Scheme 2: Synthesis of divalent 3-tosylamino-2,3-dideoxyneoglycoconjugates 6a and 6b.
Scheme 3: Synthesis of trivalent 3-tosylamino-2,3-dideoxyneoglycoconjugate 6c.
An easily accessible sulfated saccharide mimetic inhibits in vitro human tumor cell adhesion and angiogenesis of vascular endothelial cells
- Grazia Marano,
- Claas Gronewold,
- Martin Frank,
- Anette Merling,
- Christian Kliem,
- Sandra Sauer,
- Manfred Wiessler,
- Eva Frei and
- Reinhard Schwartz-Albiez
Beilstein J. Org. Chem. 2012, 8, 787–803, doi:10.3762/bjoc.8.89
- microenvironment resulting in an increased malignancy. Schmidt’s imidate strategy offers an effective method to synthesize libraries of various oligosaccharide mimetics. With the aim to perturb interactions of tumor cells with extracellular matrix proteins and host cells, molecules with 3,4-bis(hydroxymethyl)furan
- ), inhibited the activation of matrix-metalloproteinase-2 (MMP-2) as well as migration of the human melanoma cells of the lines WM-115 and WM-266-4 in a two-dimensional migration assay. GSF inhibited completely the adhesion of WM-115 cells to the extracellular matrix (ECM) proteins, fibrinogen and fibronectin
- ; Introduction Adhesion of mammalian cells to the extracellular matrix (ECM) is mediated by protein–protein and protein–carbohydrate interactions. Alterations in the expression of cell-surface molecules lead to the dissemination of metastatic cells from tumor tissue [1][2]. Cell surface molecules in melanoma
Graphical Abstract
Scheme 1: Synthesis of (4-{[(β-D-galactopyranosyl)oxy]methyl}furan-3-yl)methyl hydrogen sulfate (GSF, 5) and ...
Figure 1: Effects of increasing concentrations of (4-{[(β-D-galactopyranosyl)oxy]methyl}furan-3-yl)methyl hyd...
Figure 2: Inhibition of adhesion of WM-115 cells to fibrinogen (A), or to fibronectin (B) with increasing con...
Figure 3: Inhibition of adhesion of melanoma cells WM-115 to fibronectin-coated plastic by 5 mM (4-{[(β-D-gal...
Figure 4: In silico blind-docking (A, B) and molecular dynamic simulations (C) of (4-{[(β-D-galactopyranosyl)...
Figure 5: Intact cell monolayers of WM-115 cells in 12-well plates were wounded with a 100 µL pipette tip and...
Figure 6: A: Zymograms (color inverted) of serum-free conditioned medium of melanoma cells treated with (4-{[...
Figure 7: Adhesion of HBMEC-60 to extracellular matrix proteins. Prior to the adhesion experiments, HBMEC-60 ...
Figure 8: Effect of (4-{[(β-D-galactopyranosyl)oxy]methyl}furan-3-yl)methyl hydrogen sulfate (GSF) on transmi...
Figure 9: Influence of saccharide mimetics on endothelial networking (matrigel-assay) (A) and tube formation ...
