Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding

• Christopher B. Barnett,
• Tharindu Senapathi and
• Kevin J. Naidoo

Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206

• . and others [14][16] provides a foundation for further investigation into the binding of glycopeptide antigens to antibodies using computational modeling. Molecular dynamics (MD) simulations and analysis thereof are a well-known ingredient of the in-silico process for mechanistic screening of

• breast cancer [11][13]. We use MD simulations to investigate the conformational behavior of (glyco)peptide antigens bound to the AR20.5 antibody and to investigate the hypothesis that the glycan modulates the conformation of the peptide portion of the antigen. Primarily showcasing a structural analytics

• approach, we aim to use the tools and workflows available as part of the Galaxy project to analyze MD simulations to find out if the sugar moiety of the Tn-antigen binds directly to the antibody. Further, if the sugar does not bind directly (as found previously), then we will use these analyses to observe

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

• oligosaccharides containing additional groups like sulfates, phosphates etc. [24] Generally used force fields for the Molecular Mechanics (MD) simulation of carbohydrates are CHARMM [25], GLYCAM [26], and GROMOS [27]. The structural complexity increases the computational cost, which makes simulations of large

• GIF format. GLYCAM-web- Carbohydrate Builder can be used to prepare the system for MD simulation as it solvates the glycans and also generates the topology and coordinate files. In addition to its carbohydrate builder, Glycam-web consists of additional tools like glycoprotein builder and

• information. Alternatively, it can also read a glycan sequence (GRS format) to generate a 3D model and input files for MD simulation of the carbohydrate-only system. GRS carbohydrate sequences can be made through a straightforward interface: monosaccharides (20+ options) and their linkages are added

How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates

• Carl A. Fogarty,
• Aoife M. Harbison,
• Amy R. Dugdale and
• Elisa Fadda

Beilstein J. Org. Chem. 2020, 16, 2046–2056, doi:10.3762/bjoc.16.171

• undetected because of their intrinsic structural disorder. In this work we use molecular dynamics (MD) simulations to provide insight into N-glycans’ 3D structure by analysing the effects of a set of very specific modifications found in plants and invertebrate N-glycans, which are immunogenic in humans. We

• glycans sequence can alter their 3D structure and conformational dynamics, ultimately regulating recognition [19]. In this work we use molecular dynamics (MD) simulations to analyse the effects of the inclusion of motifs typically found in plants and invertebrates N-glycans and immunogenic in mammals [20

• interesting feature, through the cumulative 3 μs MD sampling, the xylose ring repeatedly inverts its conformation from the all equatorial 4C1 chair, to the 1C4 chair, where all hydroxy groups are axial, see Figure 3. This transition may be energetically facilitated by the hydrogen bonding interaction xylose

A cyclopeptide and three oligomycin-class polyketides produced by an underexplored actinomycete of the genus Pseudosporangium

• Shun Saito,
• Kota Atsumi,
• Tao Zhou,
• Keisuke Fukaya,
• Daisuke Urabe,
• Naoya Oku,
• Md. Rokon Ul Karim,
• Hisayuki Komaki and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 1100–1110, doi:10.3762/bjoc.16.97

• Shun Saito Kota Atsumi Tao Zhou Keisuke Fukaya Daisuke Urabe Naoya Oku Md. Rokon Ul Karim Hisayuki Komaki Yasuhiro Igarashi Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan Biological Resource Center

Towards the total synthesis of chondrochloren A: synthesis of the (Z)-enamide fragment

• Jan Geldsetzer and
• Markus Kalesse

Beilstein J. Org. Chem. 2020, 16, 670–673, doi:10.3762/bjoc.16.64

• of the molecule was elucidated by a combination of NMR, UV and IR spectroscopy and molecular dynamics calculations (MD, MM2) [12]. However, its (Z)-enamide motif and the polyoxygenated middle segment are synthetically challenging. Results and Discussion Synthesis of amide 3 Here we report our

Synthesis of triphenylene-fused phosphole oxides via C–H functionalizations

• Md. Shafiqur Rahman and
• Naohiko Yoshikai

Beilstein J. Org. Chem. 2020, 16, 524–529, doi:10.3762/bjoc.16.48

• Md. Shafiqur Rahman Naohiko Yoshikai Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore 10.3762/bjoc.16.48 Abstract The synthesis of triphenylene-fused phosphole oxides has been achieved

Ultrafast processes triggered by one- and two-photon excitation of a photochromic and luminescent hydrazone

• Alessandro Iagatti,
• Baihao Shao,
• Alberto Credi,
• Barbara Ventura,
• Ivan Aprahamian and
• Mariangela Di Donato

Beilstein J. Org. Chem. 2019, 15, 2438–2446, doi:10.3762/bjoc.15.236

• a previously reported procedure [29]. Its UV–vis spectra were recorded on a Shimadzu UV-1800 UV–vis spectrophotometer. A Photon Technology International QuantaMaster 4 spectrofluorometer outfitted with a LPS-100 lamp power supply and Xenon arc lamp housing, ASOC-10 electronics interface, MD-4 motor

Analysis of sesquiterpene hydrocarbons in grape berry exocarp (Vitis vinifera L.) using in vivo-labeling and comprehensive two-dimensional gas chromatography–mass spectrometry (GC×GC–MS)

• Philipp P. Könen and
• Matthias Wüst

Beilstein J. Org. Chem. 2019, 15, 1945–1961, doi:10.3762/bjoc.15.190

• International Ltd, Llantrisant, RCT, UK; version 1.2). First, a dynamic background compensation (dbc) was performed with a peak width of 2 s. The genuine sesquiterpene hydrocarbons were identified using the NIST Mass Spectral Search Program (NIST, Gaithersburg, MD, U.S.A.; version 2.2) by comparing the recorded

Archangelolide: A sesquiterpene lactone with immunobiological potential from Laserpitium archangelica

• Silvie Rimpelová,
• Michal Jurášek,
• Lucie Peterková,
• Jiří Bejček,
• Vojtěch Spiwok,
• Miloš Majdl,
• Michal Jirásko,
• Miloš Buděšínský,
• Juraj Harmatha,
• Eva Kmoníčková,
• Pavel Drašar and
• Tomáš Ruml

Beilstein J. Org. Chem. 2019, 15, 1933–1944, doi:10.3762/bjoc.15.189

• , the potent SERCA inhibitors, manual docking of compound 1 into SERCA followed by MD simulation (1–10 ns) was performed. For this simulation, four different complexes of SERCA and SL were chosen: i) compound 1 positioned correspondingly to the orientation of DTB in the SERCA binding cavity (simulation

• pure product (37 mg, 0.04 mmol) as a slightly yellowish solid in 64% yield with Rf = 0.25 in hexanes/AcOEt, 1:1. For analytical data, see Supporting Information File 1, sections 2–4. Computational studies MD Simulations of compound 1 and 2 with sarco/endoplasmic reticular calcium ATPase For docking and

Water inside β-cyclodextrin cavity: amount, stability and mechanism of binding

• Stiliyana Pereva,
• Valya Nikolova,
• Silvia Angelova,
• Tony Spassov and
• Todor Dudev

Beilstein J. Org. Chem. 2019, 15, 1592–1600, doi:10.3762/bjoc.15.163

• details Different molecular modeling methods (quantum mechanics (QM), molecular dynamics (MD), docking and quantitative structure activity relationships (QSARs)) can be applied in studying the structure, dynamics, and energetics of the host CD systems. However, the results from different modeling (or

Transient and intermediate carbocations in ruthenium tetroxide oxidation of saturated rings

• Manuel Pedrón,
• Laura Legnani,
• Maria-Assunta Chiacchio,
• Pierluigi Caramella,
• Tomás Tejero and
• Pedro Merino

Beilstein J. Org. Chem. 2019, 15, 1552–1562, doi:10.3762/bjoc.15.158

• , the proposed asynchronous concerted mechanism. A deeper analysis of the full path of the reaction using MD calculations [29] would be needed in order to assess the synchronicity and life time of transient species [30]. The recent use of MD simulations has demonstrated that a single transition state

• some chemical behavior. Indeed, further theoretical studies on MD simulations would be needed to elucidate the lifetime of the transient carbocation [34][35]. These results demonstrate the one-step-two-stage character [42] of the ruthenium oxidations of alkanes in which H transfer and O–C bond

Host–guest interactions between p-sulfonatocalix[4]arene and p-sulfonatothiacalix[4]arene and group IA, IIA and f-block metal cations: a DFT/SMD study

• Valya K. Nikolova,
• Cristina V. Kirkova,
• Silvia E. Angelova and
• Todor M. Dudev

Beilstein J. Org. Chem. 2019, 15, 1321–1330, doi:10.3762/bjoc.15.131

• anchoring points for the positively charged guests. Cation–π interactions between the monoatomic cations and p-sulfonatocalix[4]arene in water are supposed (but not proven) to take part in the inclusion complex formation [31]. Mendes et al. have carried out molecular dynamics (MD) simulations of association

• upon binding has been noted [31]. A model of hydrated, by an average number of 10 water molecules, La3+ cation has already been used by Mendes et al. in the MD simulations of p-sulfonatocalix[4]arene association with rare-earth metal cations and organic cations in aqueous solutions [32]. The effect of

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

• the weaker affinity by the corresponding 2-fluorophenyltriazole analogue 1d, because in the favored complex geometry of 1b introduction of a 2-fluoro atom would lead to this atom being close to either the Glu71 carboxylate or the triazole N3 lone pair. MD simulations with 1b positioned in a similar

Adhesion, forces and the stability of interfaces

• Robin Guttmann,
• Johannes Hoja,
• Christoph Lechner,
• Reinhard J. Maurer and
• Alexander F. Sax

Beilstein J. Org. Chem. 2019, 15, 106–129, doi:10.3762/bjoc.15.12

Synthesis, biophysical properties, and RNase H activity of 6’-difluoro[4.3.0]bicyclo-DNA

• Sibylle Frei,
• Adam K. Katolik and
• Christian J. Leumann

Beilstein J. Org. Chem. 2019, 15, 79–88, doi:10.3762/bjoc.15.9

• as the 6’F-bc4,3-DNA. Furthermore, duplexes of a 6’F-bc4,3-modified strand paired to RNA unveiled in the MD simulations a flexible minor groove distance [37]. This flexibility is thought to play a crucial role for the fitting of the duplex into the DNA-binding channel and the phosphate-binding pocket

• of the enzyme. Furthermore, the phosphate-binding pocket requires a large distortion of the backbone angle α in order that the phosphate group of the AON can be positioned in it [50][51]. The 6’F-bc4,3-DNA containing strand also complied with this requirement according to the MD simulations [37

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

• Katharina Kolbe Sri Kumar Veleti Norbert Reiling Thisbe K. Lindhorst Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, 33 North Drive, Bethesda, 20892, MD, United States Microbial Interface Biology, Research

6’-Fluoro[4.3.0]bicyclo nucleic acid: synthesis, biophysical properties and molecular dynamics simulations

• Sibylle Frei,
• Andrei Istrate and
• Christian J. Leumann

Beilstein J. Org. Chem. 2018, 14, 3088–3097, doi:10.3762/bjoc.14.288

• . Nevertheless, the MD simulations pointed to a flexible minor groove for the modified oligonucleotides hybridized to RNA, indicating together with the preferred Southern conformation of the modified unit, that this modification might be a substrate for RNase H. Chemical structure of selected nucleic acid

MoO₃ on zeolites MCM-22, MCM-56 and 2D-MFI as catalysts for 1-octene metathesis

• Hynek Balcar,
• Martin Kubů,
• Naděžda Žilková and
• Mariya Shamzhy

Beilstein J. Org. Chem. 2018, 14, 2931–2939, doi:10.3762/bjoc.14.272

• weights of alkenes from C9 to C14; md, mt and Md, Mt are weight amounts and molecular weights of octene dimers and trimers, respectively; mC8 is weight amount of octene (all isomers) and MC8 is the molecular weight of octene. For comparison, the conversion curve over 6MoO3/SBA-15 is added in Figure 2

The mechanochemical synthesis of quinazolin-4(3H)-ones by controlling the reactivity of IBX

• Md Toufique Alam,
• Saikat Maiti and
• Prasenjit Mal

Beilstein J. Org. Chem. 2018, 14, 2396–2403, doi:10.3762/bjoc.14.216

• Md Toufique Alam Saikat Maiti Prasenjit Mal School of Chemical Sciences, National Institute of Science Education and Research (NISER), HBNI, Bhubaneswar, PO Bhimpur-Padanpur, Via Jatni, District Khurda, Odisha 752050, India; Tel: +919439613856 10.3762/bjoc.14.216 Abstract Performing any synthesis

Non-metal-templated approaches to bis(borane) derivatives of macrocyclic dibridgehead diphosphines via alkene metathesis

• Tobias Fiedler,
• Michał Barbasiewicz,
• Michael Stollenz and
• John A. Gladysz

Beilstein J. Org. Chem. 2018, 14, 2354–2365, doi:10.3762/bjoc.14.211

• -Nürnberg, Henkestraße 42, 91054 Erlangen, Germany Present address: Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warszawa, Poland Present address: Department of Chemistry and Biochemistry, Kennesaw State University, 370 Paulding Building NW, MD#1203, Kennesaw, Georgia 30144, USA 10.3762

Synthesis and photophysical studies of a multivalent photoreactive Ru^II-calix[4]arene complex bearing RGD-containing cyclopentapeptides

• Sofia Kajouj,
• Lionel Marcelis,
• Alice Mattiuzzi,
• Adrien Grassin,
• Damien Dufour,
• Pierre Van Antwerpen,
• Didier Boturyn,
• Eric Defrancq,
• Mathieu Surin,
• Julien De Winter,
• Pascal Gerbaux,
• Ivan Jabin and
• Cécile Moucheron

Beilstein J. Org. Chem. 2018, 14, 1758–1768, doi:10.3762/bjoc.14.150

• presented in Figure 2, as issued from a molecular dynamics (MD) simulations. The ruthenium complex and the RGD units are spatially well-separated thanks to their grafting on opposite faces of the rigid calixarene-based platform. In this conformation, the distances between the Ru atom and each of the nearest

• carbon atoms of RGDfK units exceed 30 Å. Along the MD simulations, we noticed that the Ru complex remained far from the cyclic pentapeptides. This is due to the fact that the linkers of each arm are smaller than the size of the calixarene platform, preventing contacts between the Ru complex and the RGDfK

• units. The global structure has an average radius of gyration Rg of 1.25 nm ± 0.1 nm. Noteworthy, the distance between the RGDfK units largely varies along the MD simulations, ranging from 10 Å to 24 Å (average at 17 Å), as estimated from the distance between equivalent carbon atoms crossing the linker

Drug targeting to decrease cardiotoxicity – determination of the cytotoxic effect of GnRH-based conjugates containing doxorubicin, daunorubicin and methotrexate on human cardiomyocytes and endothelial cells

• Livia Polgár,
• Eszter Lajkó,
• Pál Soós,
• Orsolya Láng,
• Marilena Manea,
• Béla Merkely,
• Gábor Mező and
• László Kőhidai

Beilstein J. Org. Chem. 2018, 14, 1583–1594, doi:10.3762/bjoc.14.136

• image in the graphical abstract is derived from the image ”Heart anterior exterior view” by Patrick J. Lynch, illustrator, and C. Carl Jaffe, MD, cardiologist, an image published under a Creative Commons Attribution 2.5 license.

Synthetic avenues towards a tetrasaccharide related to Streptococcus pneumonia of serotype 6A

• Aritra Chaudhury,
• Mana Mohan Mukherjee and
• Rina Ghosh

Beilstein J. Org. Chem. 2018, 14, 1095–1102, doi:10.3762/bjoc.14.95

• : Laboratory of Bioorganic Chemistry, NIH, NIDDK, Bethesda, MD, USA 10.3762/bjoc.14.95 Abstract Streptococcus pneumonia (SPn) is a Gram-positive bacterium which causes life threatening diseases. The bacteria protect themselves against non-specific host defence by an external polysaccharide (PS) capsule which

Crystal structure of the inclusion complex of cholesterol in β-cyclodextrin and molecular dynamics studies

• Elias Christoforides,
• Andreas Papaioannou and
• Kostas Bethanis

Beilstein J. Org. Chem. 2018, 14, 838–848, doi:10.3762/bjoc.14.69

• crystalline state comprise the asymmetric unit of the structure. The dimers are arranged in an intermediate (IM) channel packing mode in the crystal. Moreover, MD simulations, at 300 and 340 K, based on the crystallographically determined coordinates of the complex show that the formed cholesterol/β-CD

• characterization of the cholesterol/β-CD inclusion complex [22], its binding affinity [23][24][25], the inclusion mode of the complex [26] and its dynamic behavior through MD simulations [27][28][29] but its crystal structure is absent. In this work, the structure of CHL/β-CD is determined by X-ray crystallography

• and its geometrical features are examined thoroughly. In order to examine the stability of the crystallographically determined model excluding the crystal contacts observed in the crystalline state, MD simulations of the inclusion complex in aqueous environment were performed. The starting set of

Recent advances in synthetic approaches for medicinal chemistry of C-nucleosides

• Kartik Temburnikar and
• Katherine L. Seley-Radtke

Beilstein J. Org. Chem. 2018, 14, 772–785, doi:10.3762/bjoc.14.65

• Kartik Temburnikar Katherine L. Seley-Radtke Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 N. Wolfe St. Baltimore, MD 21205, United States Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle

• , Baltimore, MD 21250, United States 10.3762/bjoc.14.65 Abstract C-nucleosides have intrigued biologists and medicinal chemists since their discovery in 1950's. In that regard, C-nucleosides and their synthetic analogues have resulted in promising leads in drug design. Concurrently, advances in chemical