Automating multistep flow synthesis: approach and challenges in integrating chemistry, machines and logic

• Chinmay A. Shukla and
• Amol A. Kulkarni

Beilstein J. Org. Chem. 2017, 13, 960–987, doi:10.3762/bjoc.13.97

• ][16][17][18][19][20][21][22][23][24]. Several integrated protocols have been developed for generating a library of compounds [12][25][26][27]. In-line separators like scavenging columns [22][25][26][27][28], liquid–liquid extractors (based on gravity or membrane) [3][23][29], distillation [30], etc

• operations like filtration, evaporation, membrane separation, liquid–liquid extraction, etc. We have also suggested some guidelines for these multistep syntheses for transforming these lab scale chemistries to automated pilot scale processes. At pilot or production scale, automation is largely employed for

• exchangers, evaporators, membrane extractors, etc. However, similar control strategies can also be employed for other chemistries/processes which are not included in the present case studies. Each case study is transformed in the form of a Piping and Instrument Diagram (P&ID) that makes a process engineer

Expression, purification and structural analysis of functional GABA transporter 1 using the baculovirus expression system

• Jing Hu,
• Chris Weise,
• Christoph Böttcher,
• Hua Fan and
• Jian Yin

Beilstein J. Org. Chem. 2017, 13, 874–882, doi:10.3762/bjoc.13.88

• protein, GAT1, is a potential drug target. The exact three-dimensional structure of GAT1 protein could provide more information for pharmaceutical research. The structural analysis of most membrane proteins is challenging since significant protein yields are required and because eukaryotic membrane

• proteins should be in a native and functional conformation during expression and purification. The natural abundance of most membrane proteins is typically not high enough for the isolation of sufficient quantities for functional and structural studies. In this work, the baculovirus expression system was

• but not the terminal trimming of N-glycans is involved in the regulation of the correct membrane glycoprotein folding since the inhibition of N-glycosylation processing by 1-deoxymannojirimycin (dMM) results in a mannose-rich type of N-glycan that does not affect either the protein stability or

Opportunities and challenges for the sustainable production of structurally complex diterpenoids in recombinant microbial systems

• Katarina Kemper,
• Max Hirte,
• Markus Reinbold,
• Monika Fuchs and
• Thomas Brück

Beilstein J. Org. Chem. 2017, 13, 845–854, doi:10.3762/bjoc.13.85

• oxidoreductases requires significant enzyme modifications. Specifically, codon optimization and the truncation of distinct domains which are responsible for, e.g., membrane localization can improve the enzyme activity. To date, identifying the necessary sequence segment for soluble expression in the bacterial

Lipids: fatty acids and derivatives, polyketides and isoprenoids

• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2017, 13, 793–794, doi:10.3762/bjoc.13.78

• Jeroen S. Dickschat Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, D-53121 Bonn, Germany 10.3762/bjoc.13.78 Keywords: fatty acids; isoprenoids; polyketides; Lipids fulfill various functions in life as membrane

• in addition to that in eukaryotic organisms membranes are of utmost importance also for cell compartmentation, i.e., the inner structure of a cell. A large portion of these membranes is composed of steroids that influence membrane properties, such as fluidity and permeability, but have a

• fundamentally different biosynthetic origin from fatty acids since they are made via terpene biosynthetic pathways. Nevertheless, steroids are highly apolar yet may contain a polar headgroup such as a 3-hydroxy function (as in lanosterol). Besides membrane formation, the highly apolar character of lipids has

Membrane properties of hydroxycholesterols related to the brain cholesterol metabolism

• Malte Hilsch,
• Ivan Haralampiev,
• Peter Müller,
• Daniel Huster and
• Holger A. Scheidt

Beilstein J. Org. Chem. 2017, 13, 720–727, doi:10.3762/bjoc.13.71

• Abstract Compared to cholesterol, hydroxycholesterols contain an additional hydroxy group in the alkyl chain and are able to efficiently cross the brain–blood barrier. Therefore, they are responsible for the sterol transfer between brain and circulation. The current study compares the membrane properties

• of several hydroxycholesterols with those of cholesterol using 2H NMR spectroscopy, a membrane permeability assay, and fluorescence microscopy experiments. It is shown that hydroxycholesterols do not exert the unique impact on membrane properties characteristic for cholesterol with regard to the

• influence on lipid chain order, membrane permeability and formation of lateral domains. Keywords: cholesterol; fluorescence; hydroxycholesterol; membrane structure; NMR; Introduction Cholesterol is a major component of mammalian cell membranes with various biological functions. It plays a key role in

How and why kinetics, thermodynamics, and chemistry induce the logic of biological evolution

• Addy Pross and
• Robert Pascal

Beilstein J. Org. Chem. 2017, 13, 665–674, doi:10.3762/bjoc.13.66

• of nucleic acid duplexes as well as that of phospholipids to form a bilayer membrane). On the other hand, even though the Second Law must always remain an inescapable constraint, a simple drift towards the equilibrium state is not sufficient to account for the evolutionary changes of life. More

Fast and efficient synthesis of microporous polymer nanomembranes via light-induced click reaction

• Qi An,
• Youssef Hassan,
• Xiaotong Yan,
• Peter Krolla-Sidenstein,
• Tawheed Mohammed,
• Mathias Lang,
• Stefan Bräse and
• Manuel Tsotsalas

Beilstein J. Org. Chem. 2017, 13, 558–563, doi:10.3762/bjoc.13.54

• membrane separation has been limited due to their insoluble nature when synthesized as bulk material. To make full use of the beneficial properties of CMPs for membrane applications, their synthesis and functionalization on surfaces become increasingly important. In this respect, we recently introduced the

• -methylpropan-1-one), iodine and potassium iodide were purchased from Sigma-Aldrich. TPM-SH [30] and TPM-alkyne [31] were synthesized as described in the literature. Substrates: The sacrificial substrate consists of a 150 nm gold film on mica. For analytical measurements, we transferred the membrane to a Si(100

• environment, washed thoroughly with dry THF and ethanol and dried using a nitrogen stream. Transfer of CMP nanomembranes: To obtain freestanding nanomembranes, the CMP-films were grown on sacrificial substrates using the above-described procedure. The membrane was then obtained by following a procedure

Novel β-cyclodextrin–eosin conjugates

• Gábor Benkovics,
• Damien Afonso,
• András Darcsi,
• Szabolcs Béni,
• Sabrina Conoci,
• Éva Fenyvesi,
• Lajos Szente,
• Milo Malanga and
• Salvatore Sortino

Beilstein J. Org. Chem. 2017, 13, 543–551, doi:10.3762/bjoc.13.52

• mechanism of their action and their fate inside living cells. The fluorescent labeling of CDs enables their tracking and visualization in biological media and provides useful information about their cell-membrane-penetration ability [2][3]. Besides, fluorophore-appended CDs have been extensively studied and

• diffuses in the cellular environment over short distances (few tens of nm) resulting in negligible systemic side effects. For PDT applications CDs have been conjugated with porphyrin [7] and protoporphyrin (5-aminolevulinic acid) [8] in order to enhance the membrane penetration of the PS (or its prodrug

Synthesis of multi-lactose-appended β-cyclodextrin and its cholesterol-lowering effects in Niemann–Pick type C disease-like HepG2 cells

• Keiichi Motoyama,
• Rena Nishiyama,
• Yuki Maeda,
• Taishi Higashi,
• Yoichi Ishitsuka,
• Yuki Kondo,
• Tetsumi Irie,
• Takumi Era and
• Hidetoshi Arima

Beilstein J. Org. Chem. 2017, 13, 10–18, doi:10.3762/bjoc.13.2

• NPC-like HepG2 cells via asialoglycoprotein receptor (ASGPR)-mediated endocytosis. Keywords: asialoglycoprotein receptor; cholesterol; cyclodextrin; lactose; Niemann–Pick type C disease; Introduction The Niemann–Pick type C (NPC) disease is a lipid storage disorder with the accumulation of membrane

Synthesis of acylhydrazino-peptomers, a new class of peptidomimetics, by consecutive Ugi and hydrazino-Ugi reactions

• Angélica de Fátima S. Barreto,
• Veronica Alves dos Santos and
• Carlos Kleber Z. Andrade

Beilstein J. Org. Chem. 2016, 12, 2865–2872, doi:10.3762/bjoc.12.285

• peptoids the side chain of the Cα is bound to the nitrogen atom. Due to the consequent lack of the polar N–H bonds, their lipophilicity is increased, which may result in improved membrane permeability [16][17]. Furthermore, peptoids have also found utility in supra- and macromolecular engineering [18] and

Benzothiadiazole oligoene fatty acids: fluorescent dyes with large Stokes shifts

• Lukas J. Patalag and
• Daniel B. Werz

Beilstein J. Org. Chem. 2016, 12, 2739–2747, doi:10.3762/bjoc.12.270

• ; membrane; Stokes shift; Introduction The membrane of living cells consists of a variety of lipids. More than 40 years ago, biological membranes were first described as Fluid Mosaic in which proteins were embedded [1]. During recent decades it became more and more clear that such a simple model is not

• sufficient to understand membrane dynamics and function. Often membrane domains are formed in which certain lipids, glycolipids or proteins are enriched [2][3][4]. Such domains – also called lipid rafts – do not only differ in their chemical composition, but also show different physical properties (e.g

• ., differences in membrane thickness and stiffness, different diffusion coefficients etc.) [5][6]. Tools to investigate lipid membranes are multifaceted; however, all optical methods are hampered by the missing absorption and fluorescence properties of natural occurring lipid components. Therefore, indirect

Computational methods in drug discovery

• Sumudu P. Leelananda and
• Steffen Lindert

Beilstein J. Org. Chem. 2016, 12, 2694–2718, doi:10.3762/bjoc.12.267

• membrane proteins where membrane permeability is considered to be important for drugs to be useful [10][11]. Successes have been reported for SBDD and it has contributed to many compounds reaching clinical trials and get FDA approvals to go into the market [12]. HIV-1 (Human Immunodeficiency Virus I

• experimental challenges. X-ray crystallography is only possible if the target protein can be crystallized. Some proteins, for example membrane proteins which account for about 60% of the approved drug targets today [19], are usually difficult to crystallize, thus experimental methods are not always successful

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

• based on the ability of CDs to extract lipids from the cell membrane. The objective of this contribution is to focus on the potential use of natural and chemically modified CDs in the vast array of medical and biological applications. Review Cyclodextrins: synthesis, structure and physicochemical

• their hemolytic activities. Indeed, several in vitro studies reported erythrocyte lysis although the toxicological implication in vivo is negligible. The lysis mechanism is related to their capacity to draw phospholipids and cholesterol out of the biological membrane (see below). Based on this, the

• conditions (isotonic solution with similar incubation time and temperature), the observed hemolysis is in the order γ-CD < α-CD < β-CD. This different effect, observed for native CDs, has been explained by Ohtani et al. in 1989 [58]. As the membrane of erythrocytes is composed of proteins (43%) associated

A self-assembled cyclodextrin nanocarrier for photoreactive squaraine

• Ulrike Kauscher and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2016, 12, 2535–2542, doi:10.3762/bjoc.12.248

• 30 µM (since approximately 50% of the amphiphilic cyclodextrins reside at the interior surface of the CDV and AdSq is too large and too polar to pass the membrane), saturation is reached at a six-fold excess of host to guest, even though both are present in micromolar concentrations only. The binding

• . The images taken show GUVs with a red luminescent membrane due to the squaraines bound to the GUV surface (Figure 4). Thus, fluorescence microscopy provided direct evidence for the immobilization of AdSq on the CDV. After the immobilization of AdSq on the surface of CDV was demonstrated, we

Biomimetic synthesis and HPLC–ECD analysis of the isomers of dracocephins A and B

• Viktor Ilkei,
• András Spaits,
• Anita Prechl,
• Áron Szigetvári,
• Zoltán Béni,
• Miklós Dékány,
• Csaba Szántay Jr,
• Judit Müller,
• Árpád Könczöl,
• Ádám Szappanos,
• Attila Mándi,
• Sándor Antus,
• Ana Martins,
• Attila Hunyadi,
• György Tibor Balogh,
• György Kalaus (†),
• Hedvig Bölcskei,
• László Hazai and
• Tibor Kurtán

Beilstein J. Org. Chem. 2016, 12, 2523–2534, doi:10.3762/bjoc.12.247

• lowest acidic pKa values are predominant in physiological environment, which is also indicated by the difference of log D values between pH 7.4 and pH 6.5. The blood–brain barrier (BBB) specific penetration of dracocephins isomers has also been studied by the PAMPA (parallel artificial membrane

Enduracididine, a rare amino acid component of peptide antibiotics: Natural products and synthesis

• Darcy J. Atkinson,
• Briar J. Naysmith,
• Daniel P. Furkert and
• Margaret A. Brimble

Beilstein J. Org. Chem. 2016, 12, 2325–2342, doi:10.3762/bjoc.12.226

• to be delivered to an individual chamber where it can grow. The chambers are covered with a semi-permeable membrane and placed into the microbe’s natural environment where nutrients can diffuse into each chamber. This method gives access to cultures of microbes which were previously unobtainable

• which involves binding to Lipid II, inhibiting one of the membrane-associated steps of peptidoglycan biosynthesis [43][44]. Analogues of teixobactin (17) have undergone biological testing and results show that the L-allo-enduracididine (3, blue, Figure 7) residue is important for potent antibacterial

Tunable microwave-assisted method for the solvent-free and catalyst-free peracetylation of natural products

• Manuela Oliverio,
• Paola Costanzo,
• Monica Nardi,
• Carla Calandruccio,
• Raffaele Salerno and
• Antonio Procopio

Beilstein J. Org. Chem. 2016, 12, 2222–2233, doi:10.3762/bjoc.12.214

• molecules to pass the cell membrane [5] and, once inside the cells, acetyl groups can be removed by intracellular esterases thus resulting in an augmented dose of active principle [2][3]. Moreover, peracetylation affects the pharmacokinetics by prolonging the half-life of the unprotected molecules whose

Synthesis and NMR studies of malonyl-linked glycoconjugates of N-(2-aminoethyl)glycine. Building blocks for the construction of combinatorial glycopeptide libraries

• Markus Nörrlinger,
• Sven Hafner and
• Thomas Ziegler

Beilstein J. Org. Chem. 2016, 12, 1939–1948, doi:10.3762/bjoc.12.183

• animal and many bacterial cells. It is covalently bound to the surface of the cell membrane through glycoproteins and plays a major role in numerous biologically important recognition mechanisms like cell–cell recognition, signal transduction and immunological processes [1][2][3][4]. Therefore

Potent triazine-based dehydrocondensing reagents substituted by an amido group

• Munetaka Kunishima,
• Daiki Kato,
• Nobu Kimura,
• Masanori Kitamura,
• Kohei Yamada and
• Kazuhito Hioki

Beilstein J. Org. Chem. 2016, 12, 1897–1903, doi:10.3762/bjoc.12.179

• ], a crown-ether-based cyclotransferase [8], membrane fusion of small unilamellar vesicles to form giant unilamellar vesicles [9], modular methods for the affinity labeling of targeting proteins [10][11][12], and reaction acceleration on micelle interfaces [13][14]. Thus, various types of molecular

Organic chemistry meets polymers, nanoscience, therapeutics and diagnostics

• Vincent M. Rotello

Beilstein J. Org. Chem. 2016, 12, 1638–1646, doi:10.3762/bjoc.12.161

• uptake would result in identical rates of uptake, leading us to surmise that uptake occurred through a membrane fusion process. Driven by the desire to deliver biological payloads directly to the cytosol, we tested our system for the very challenging goal of protein delivery using green fluorescent

Star-shaped and linear π-conjugated oligomers consisting of a tetrathienoanthracene core and multiple diketopyrrolopyrrole arms for organic solar cells

• Hideaki Komiyama,
• Chihaya Adachi and
• Takuma Yasuda

Beilstein J. Org. Chem. 2016, 12, 1459–1466, doi:10.3762/bjoc.12.142

• mL), followed by baking at 200 °C for 10 min under air. The photoactive layer was then prepared by spin-coating from a chloroform solution containing the donor material and PC71BM, after passing through a 0.45 μm PTFE membrane filter. Finally, a 6 nm thick MoO3 layer and a 100 nm-thick Ag layer were

Artificial Diels–Alderase based on the transmembrane protein FhuA

• Hassan Osseili,
• Daniel F. Sauer,
• Klaus Beckerle,
• Marcus Arlt,
• Tomoki Himiyama,
• Tino Polen,
• Akira Onoda,
• Ulrich Schwaneberg,
• Takashi Hayashi and
• Jun Okuda

Beilstein J. Org. Chem. 2016, 12, 1314–1321, doi:10.3762/bjoc.12.124

• : artificial Diels-Alderase; biohybrid catalysis; copper enyzme; membrane protein; Introduction So-called artificial metalloenzymes have attracted attention over the last decade [1][2][3][4][5][6][7][8][9]. Incorporation of an organometallic cofactor into proteins offers new possibilities to expand the

• hydroxamate uptake protein component A (FhuA) as host for defined Cu(I) NHC or Cu(II) terpyridyl complexes with a maleimide moiety. By covalently bonding these copper complexes to the protein artificial Diels–Alderases based on a membrane protein have been obtained. Results and Discussion Synthesis of the

• absence of any enantioselectivity suggests that no preferential orientation of the substrate at the active site within the barrel structure is possible. Notably, no protein precipitated during catalysis, showing the advantageous feature of membrane proteins in terms of robustness as compared to soluble

Cyclisation mechanisms in the biosynthesis of ribosomally synthesised and post-translationally modified peptides

• Andrew W. Truman

Beilstein J. Org. Chem. 2016, 12, 1250–1268, doi:10.3762/bjoc.12.120

• pathway is that the leader peptide removal and cyclisation could be catalysed by membrane associated proteins (perhaps as a complex), which hinders biochemical characterisation. Alternatively, these biosynthetic proteins may exist elsewhere in the Enterococcus genome. Defensins Mammals produce various

Stimuli-responsive HBPS-g-PDMAEMA and its application as nanocarrier in loading hydrophobic molecules

• Yongsheng Chen,
• Li Wang,
• Haojie Yu,
• Zain-Ul-Abdin,
• Ruoli Sun,
• Guanghui Jing,
• Rongbai Tong and
• Zheng Deng

Beilstein J. Org. Chem. 2016, 12, 939–949, doi:10.3762/bjoc.12.92

• a 0.45 μm micro-filtration membrane. Figure 7A,B shows UV–vis data below 25 °C. It was observed that the intensity of the peak attributed to pyrene around 337 nm was increased with the increase in the concentration of HBPS-g-PDMAEMA, which indicated that pyrene was transported to the aqueous

1H-Imidazol-4(5H)-ones and thiazol-4(5H)-ones as emerging pronucleophiles in asymmetric catalysis

• Antonia Mielgo and
• Claudio Palomo

Beilstein J. Org. Chem. 2016, 12, 918–936, doi:10.3762/bjoc.12.90

• therapeutical candidates because of their high lipophilicity and membrane permeability [44][51]. A major catalytic entry to α,α-disubstituted (quaternary) amino acids is the α-functionalization of an appropriate template as, for instance, an α-imino ester or lactone, followed by hydrolysis [49][52][53]; but