Aqueous semisynthesis of C-glycoside glycamines from agarose

• Juliana C. Cunico Dallagnol,
• Alexandre Orsato,
• Diogo R. B. Ducatti,
• Miguel D. Noseda,
• Maria Eugênia R. Duarte and
• Alan G. Gonçalves

Beilstein J. Org. Chem. 2017, 13, 1222–1229, doi:10.3762/bjoc.13.121

• aminomonosaccharides 9 and 13 are interesting moieties, regarding their resemblance with the bioactive (+)-muscarine 14 (Figure 2). Indeed, ongoing docking and molecular dynamics experiments revealed the amino-AnGal moiety as a promising platform to launch the design of new mAChR modulators [11]. The differences in

Strategies in megasynthase engineering – fatty acid synthases (FAS) as model proteins

• Manuel Fischer and
• Martin Grininger

Beilstein J. Org. Chem. 2017, 13, 1204–1211, doi:10.3762/bjoc.13.119

• in ACP docking and acyl-moiety binding, and allowed catching an initial glimpse of the dynamic process of ACP substrate delivery. Also the interaction of ACP VinL and the acyltransferase VinK, involved in loading a PKS megasynthase, was recently resolved in structure [38]. It is reasonable to assume

• shown for clarity. Each ACP acts in cis for substrate elongation (see Figure 2b) and in trans for substrate translocation. Strategies of megasynthase engineering. a) Mix-and-match approach: A hypothetical chimeric PKS is assembled module by module from a pool of available PKS. In such approach, docking

Synthesis of spiro[isoindole-1,5’-isoxazolidin]-3(2H)-ones as potential inhibitors of the MDM2-p53 interaction

• Salvatore V. Giofrè,
• Santa Cirmi,
• Raffaella Mancuso,
• Francesco Nicolò,
• Giuseppe Lanza,
• Laura Legnani,
• Agata Campisi,
• Maria A. Chiacchio,
• Michele Navarra,
• Bartolo Gabriele and
• Roberto Romeo

Beilstein J. Org. Chem. 2016, 12, 2793–2807, doi:10.3762/bjoc.12.278

• be linked to the inhibition of the protein–protein p53-MDM2 interaction. Docking measurements support the biological data. Keywords: antitumor agents; DFT studies; 1,3-dipolar cycloaddition; docking studies; spiro-compounds; Introduction The p53 tumor suppressor protein is a transcriptional factor

• -ethynylbenzamides 1 [35]. The rationale of our choice is based on molecular docking data. Using the published structure of the MDM2–p53 binding site, we have employed computational methods and focused library synthesis based on the isoindolinone template, to develop compounds with inhibitory activity. These studies

•  11c). These set of experiments demonstrate that the exposure of SH-SY5Y cancer cell lines to 10 µM 6e for 72 h was able to activate the apoptotic pathway. Docking studies To support the suggested interaction of synthesized compounds with MDM2, docking studies were applied, starting from the X-ray

Chemical probes for competitive profiling of the quorum sensing signal synthase PqsD of Pseudomonas aeruginosa

• Michaela Prothiwa,
• Dávid Szamosvári,
• Sandra Glasmacher and
• Thomas Böttcher

Beilstein J. Org. Chem. 2016, 12, 2784–2792, doi:10.3762/bjoc.12.277

• decrease in the production of the virulence factors pyocyanine and pyoverdine [32]. So far only laborious enzyme-based assays, docking studies or modelling resulted in new scaffolds. We were thus interested, if our probes could be applied as a simple tool to discover novel scaffolds or chemical PqsD

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

• methods are discussed. Advances in virtual high-throughput screening, protein structure prediction methods, protein–ligand docking, pharmacophore modeling and QSAR techniques are reviewed. Keywords: ADME; computer-aided drug design; docking; free energy; high-throughput screening; LBDD; lead optimization

• it possible to use structure-based tools such as virtual high-throughput screening and direct docking methods on targets and possible drug molecules. The affinity of molecules to targets can be evaluated by computing various estimates of binding free energies. Further filtering and optimization of

• structure prediction tools that are routinely used in structure-based drug discovery, widely used docking algorithms, scoring functions, virtual high-throughput screening, lead optimization and methods of assessment of ADME properties of drugs. Review Structure-based drug discovery (SBDD) If the three

Beta-hydroxyphosphonate ribonucleoside analogues derived from 4-substituted-1,2,3-triazoles as IMP/GMP mimics: synthesis and biological evaluation

• Tai Nguyen Van,
• Audrey Hospital,
• Corinne Lionne,
• Lars P. Jordheim,
• Charles Dumontet,
• Christian Périgaud,
• Laurent Chaloin and
• Suzanne Peyrottes

Beilstein J. Org. Chem. 2016, 12, 1476–1486, doi:10.3762/bjoc.12.144

• -containing derivatives are biologically interesting (Figure 1) [7]. In addition, molecular docking studies have been performed and highlighted the importance of three binding areas within the active site of the protein: a hydrophobic clamp (Phe157, His209 and Tyr210) interacting with the nucleobase, a

• which they block the enzyme activity. For this purpose, a SAR study was carried out by molecular docking. Attempts to make a direct correlation between the inhibitory activity and the gold-computed docking score (Table 2) were unsuccessful. Indeed, all compounds exhibited a similar score with a value

• substituent varies mainly in size, the docking score was normalized by dividing it by the number of heavy atoms (NHA, non-hydrogen atoms). By this mean and in respect to IMP (used as a control as it is the natural substrate of cN-II) one group of derivatives is predicted as good binder (1n, 1o, 1p and 1q

Discovery of an inhibitor of the production of the Pseudomonas aeruginosa virulence factor pyocyanin in wild-type cells

• Bernardas Morkunas,
• Balint Gal,
• Warren R. J. D. Galloway,
• James T. Hodgkinson,
• Brett M. Ibbeson,
• Yaw Sing Tan,
• Martin Welch and
• David R. Spring

Beilstein J. Org. Chem. 2016, 12, 1428–1433, doi:10.3762/bjoc.12.137

• order to further explore the possibility that compound 4 may act as a LasR antagonist, it was subjected to molecular docking studies against the P. aeruginosa LasR ligand–binding domain (LBD) [31]. Specifically, both OdDHL and 4 were docked into the OdDHL binding pocket of two LasR LBD structures, one

• with a bridging water molecule, which is known to be involved in a hydrogen bonding between OdDHL and Arg61 (Figure 3a) [32], and one without. In addition, both rigid and flexible conformations of LasR LBD were used in the docking runs. Tyr47 and Arg61 exhibit considerable variation in their side-chain

• conformations in various crystal structures of LasR LBD complexes and hence, they were made flexible in the flexible receptor docking runs. The best score for OdDHL (−9.1 kcal/mol) was obtained from the rigid receptor docking run with water. The docked and crystallographic conformations of OdDHL agree closely

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

• ” was a zinc-containing cyclase, and the “D-protein” possesses ATPase activity. The requirement for ATP turnover during cyclisation led to the hypothesis that the D-protein was a docking protein that regulates heterocyclase activity [33], while the presence of zinc in the C-protein pointed towards a

Is conformation a fundamental descriptor in QSAR? A case for halogenated anesthetics

• Maria C. Guimarães,
• Mariene H. Duarte,
• Josué M. Silla and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2016, 12, 760–768, doi:10.3762/bjoc.12.76

• ], but these are mostly complementary and are aimed at corroborating and/or rationalizing the results provided by the regression models, since the docking methodology itself provides intermolecular energies and docking scores that correlate with bioactivity. On the other hand, despite not encoding

Biosynthesis of α-pyrones

• Till F. Schäberle

Beilstein J. Org. Chem. 2016, 12, 571–588, doi:10.3762/bjoc.12.56

• of PpyS, docking studies of the substrates onto the catalytic cysteine were performed. The resulting model suggested that a glutamate residue, which reaches into the catalytic cavity of the respectively other homodimer, acts as a base by forming a hydrogen bond with the α-carbon of the covalently

Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic–ribosome complex supervised by experiment and electronic structure methods

• Jörg Grunenberg and
• Giuseppe Licari

Beilstein J. Org. Chem. 2016, 12, 415–428, doi:10.3762/bjoc.12.45

• aureus), VRE and Hi (Haemophilus influenzae) bacterial strains, it is currently undergoing clinical trials. An earlier docking study of 7 by Shaw et al. [47] postulated an increased potency mediated by additional interactions between the ribosomal active site and the pyridine and tetrazole rings from 7

Dynamic behavior of rearranging carbocations – implications for terpene biosynthesis

• Stephanie R. Hare and
• Dean J. Tantillo

Beilstein J. Org. Chem. 2016, 12, 377–390, doi:10.3762/bjoc.12.41

• proceed without becoming “trapped” in an intermediate energy well. For some conformers of the bisabolyl cation, many trajectories proceeded to the cedryl cation without significant delay in the regions of the homobisabolyl and acorenyl cations. Subsequent automated docking calculations of carbocations

Determination of formation constants and structural characterization of cyclodextrin inclusion complexes with two phenolic isomers: carvacrol and thymol

• Miriana Kfoury,
• David Landy,
• Steven Ruellan,
• Lizette Auezova,
• Hélène Greige-Gerges and
• Sophie Fourmentin

Beilstein J. Org. Chem. 2016, 12, 29–42, doi:10.3762/bjoc.12.5

• conformations was carried out by a conformational Monte Carlo research method using the MMFFs force field in the presence of water (GB/SA implicit model) with the generation of 5000 conformations (FMNR conjugate gradient minimization convergence fixed to 0.01 kJ Å−1 mol−1). Prior to docking and simulations, the

A novel and widespread class of ketosynthase is responsible for the head-to-head condensation of two acyl moieties in bacterial pyrone biosynthesis

• Darko Kresovic,
• Florence Schempp,
• Zakaria Cheikh-Ali and
• Helge B. Bode

Beilstein J. Org. Chem. 2015, 11, 1412–1417, doi:10.3762/bjoc.11.152

• covalent binding of the fatty acid precursor, as well as amino acids present at the dimer interface (Figure S3, Supporting Information File 1). Using this model we performed docking studies by covalently docking 14 and 16 (Figure 2) into the active site C129, revealing that the binding cavity of modeled

• , Supporting Information File 1) and docking experiments (Figure S9, Supporting Information File 1) with the proposed substrate 17 and intermediate 19 to the active site C124 also confirmed the glutamic acid inside the binding pocket as catalytically important suggesting a biosynthesis model (Scheme S1

Are D-manno-configured Amadori products ligands of the bacterial lectin FimH?

• Tobias-Elias Gloe,
• Insa Stamer,
• Cornelia Hojnik,
• Tanja M. Wrodnigg and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2015, 11, 1096–1104, doi:10.3762/bjoc.11.123

• E. coli bacteria by means of molecular docking and bacterial adhesion studies. It turns out that Amadori rearrangement products have a limited activity as inhibitors of bacterial adhesion because the β-C-glycosidically linked aglycone considerably hampers complexation within the carbohydrate binding

• site of the type 1-fimbrial lectin FimH. Keywords: Amadori rearrangement; bacterial adhesion; C-mannosides; docking studies; FimH ligands; Introduction The Amadori rearrangement (AR) is the reaction in which aldohexoses react with suitable amines under acidic catalysis to 1-amino-1-deoxyketohexoses

• the FimH CRD might be possible and that Amadori products could indeed function as antagonists of natural FimH. Docking of Amadori products 9 and 10 into the carbohydrate binding site of FimH In order to visualise the complexation of Amadori rearrangement products 9 and 10, respectively, inside the

Discrete multiporphyrin pseudorotaxane assemblies from di- and tetravalent porphyrin building blocks

• Mirko Lohse,
• Larissa K. S. von Krbek,
• Sebastian Radunz,
• Suresh Moorthy,
• Christoph A. Schalley and
• Stefan Hecht

Beilstein J. Org. Chem. 2015, 11, 748–762, doi:10.3762/bjoc.11.85

• significant attention mediated in particular by the desire to understand biological phenomena, such as virus docking to cells [27], toxin inhibition [28], or leucocyte recruitment in inflammation processes of the endothelium [29]. Multivalency has also inspired synthetic supramolecular architecture as it not

Binding mode and free energy prediction of fisetin/β-cyclodextrin inclusion complexes

• Bodee Nutho,
• Wasinee Khuntawee,
• Chompoonut Rungnim,
• Piamsook Pongsawasdi,
• Peter Wolschann,
• Alfred Karpfen,
• Nawee Kungwan and
• Thanyada Rungrotmongkol

Beilstein J. Org. Chem. 2014, 10, 2789–2799, doi:10.3762/bjoc.10.296

• to investigate the preferential binding mode and encapsulation of the flavonoid fisetin in the nano-pore of β-cyclodextrin (β-CD) at the molecular level using various theoretical approaches: molecular docking, molecular dynamics (MD) simulations and binding free energy calculations. The molecular

• docking suggested four possible fisetin orientations in the cavity through its chromone or phenyl ring with two different geometries of fisetin due to the rotatable bond between the two rings. From the multiple MD results, the phenyl ring of fisetin favours its inclusion into the β-CD cavity, whilst less

• understand the two flavonoids/β-CD complexes, hesperetin and naringenin complexes, in aqueous solution. The PM3 method was applied to calculate the energy regarding the antioxidant property of the flavonoid chysin in the complex with β-CD [32]. Interestingly, the molecular docking study on the fisetin/β-CD

Effect of cyclodextrin complexation on phenylpropanoids’ solubility and antioxidant activity

• Miriana Kfoury,
• David Landy,
• Lizette Auezova,
• Hélène Greige-Gerges and
• Sophie Fourmentin

Beilstein J. Org. Chem. 2014, 10, 2322–2331, doi:10.3762/bjoc.10.241

• most probable conformation of the β-CD/PP complexes and to give a meaningful 3D visualization of the complexes. Two docking strategies were used: i) inclusion into the CD cavity through the propenyl or allyl side chain of PP and ii) inclusion through the hydroxy or methoxy group. In both cases guests

• are allowed to penetrate the cavity through the wider rim of the CD. The computed complexation energies (ΔE) were calculated upon the docking of each PP into the β-CD cavity. The energy variation (ΔE) was used to find the most stable configurations of the inclusion complexes. The most stable

• conformations obtained from the two docking strategies and the corresponding energies (ΔE) are shown in Figure 4 in the case of 1 (see Supporting Information File 1, Table S1 for other compounds). No preferential inclusion mode was observed, the result being in agreement with previous NMR results [23

Multivalent scaffolds induce galectin-3 aggregation into nanoparticles

• Candace K. Goodman,
• Mark L. Wolfenden,
• Pratima Nangia-Makker,
• Anna K. Michel,
• Avraham Raz and
• Mary J. Cloninger

Beilstein J. Org. Chem. 2014, 10, 1570–1577, doi:10.3762/bjoc.10.162

• as a cellular docking site or a crosslinker for microorganisms binding to pathogens directly [20][21], and galectin-3 can act as a scaffold for the presentation of ligands such as lipopolysaccharides into an aggregate that stimulates cellular responses [19]. Binding affinities have been reported for

Studies toward bivalent κ opioids derived from salvinorin A: heteromethylation of the furan ring reduces affinity

• Thomas A. Munro,
• Wei Xu,
• Douglas M. Ho,
• Lee-Yuan Liu-Chen and
• Bruce M. Cohen

Beilstein J. Org. Chem. 2013, 9, 2916–2924, doi:10.3762/bjoc.9.328

• attachment point and linker for this second moiety would also be required. Docking 1 to an early rhodopsin-based homology model of κ-OR, Kane proposed a binding pose qualitatively similar to that of the HPP moiety of JDTic, placing the furan ring near Tyr3207.43 [8][18]. Indeed, at the time we commenced our

A unified approach to the important protein kinase inhibitor balanol and a proposed analogue

• Tapan Saha,
• Ratnava Maitra and
• Shital K. Chattopadhyay

Beilstein J. Org. Chem. 2013, 9, 2910–2915, doi:10.3762/bjoc.9.327

• natural product. Based on the information [48][49] that balanol binds to the ATP-docking site of protein kinase, all the three distinct domains present in the natural product such as the benzophenone core [50][51][52], the azepine core [53][54][55][56][57][58][59] and the p-hydroxybenzamide [60][61] unit

Space filling of β-cyclodextrin and β-cyclodextrin derivatives by volatile hydrophobic guests

• Sophie Fourmentin,
• Anca Ciobanu,
• David Landy and
• Gerhard Wenz

Beilstein J. Org. Chem. 2013, 9, 1185–1191, doi:10.3762/bjoc.9.133

• contributor to the driving force of complex formation [15]. The accumulation of basic understanding is essential for the formulation of precise docking programs, which estimate and screen the binding of drug candidates for biological receptors [16][17]. Practical applications of native β-CD, such as drug

• by means of docking simulations. Measured binding free energies were plotted as a function of the simulated inclusion enthalpies (Figure 6), defined as the enthalpy differences between the inclusion compounds and the free species. A significant linear correlation was obtained, confirming that the

• simulations. The docking of each guest inside host 4 was realized by means of Monte Carlo searches, with the generation of 5000 conformations (Polak–Ribiere conjugate gradient minimization, convergence fixed to 0.05 kJ Å−1 mol−1). During the search, host 4 was kept rigid, while the guest was freely modified

Recent progress in the discovery of small molecules for the treatment of amyotrophic lateral sclerosis (ALS)

• Allison S. Limpert,
• Margrith E. Mattmann and
• Nicholas D. P. Cosford

Beilstein J. Org. Chem. 2013, 9, 717–732, doi:10.3762/bjoc.9.82

• compounds performed poorly, binding with higher affinity to blood proteins than to SOD1, suggesting that these compounds may have significant off-target activity [37]. Docking calculations were performed to model the inhibitors at the dimer interface and a database of small molecules was screened to

• identify molecules that satisfied the docking constraints [37]. Twenty new compounds were identified and analyzed for inhibition of SOD1 A4V aggregation as well as binding to SOD1 in the presence of human plasma. Six of these compounds (Figure 7) tested positively in these assays [37], indicating that they

Synthesis and evaluation of cell-permeable biotinylated PU-H71 derivatives as tumor Hsp90 probes

• Tony Taldone,
• Anna Rodina,
• Erica M. DaGama Gomes,
• Matthew Riolo,
• Hardik J. Patel,
• Raul Alonso-Sabadell,
• Danuta Zatorska,
• Maulik R. Patel,
• Sarah Kishinevsky and
• Gabriela Chiosis

Beilstein J. Org. Chem. 2013, 9, 544–556, doi:10.3762/bjoc.9.60

• [19], extensive SAR [20][21], and docking experiments [9], the N9-position of the purine scaffold was shown to be an ideal site for attachment since it is directed towards the solvent. Furthermore, the amino group of 1a or the desisopropyl analogue 1b provided a convenient handle with which to attach

Synthesis and testing of the first azobenzene mannobioside as photoswitchable ligand for the bacterial lectin FimH

• Vijayanand Chandrasekaran,
• Katharina Kolbe,
• Femke Beiroth and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2013, 9, 223–233, doi:10.3762/bjoc.9.26

• that of the standard inhibitor methyl mannoside. These findings could be rationalised on the basis of computer-aided docking studies. The properties of the new azobenzene mannobioside have qualified this glycoside to be eventually employed on solid support, in order to fabricate photoswitchable

• photochromic properties, and testing of mannobioside 2 as an inhibitor of type 1 fimbriae-mediated bacterial adhesion. Interpretation of the test results was supported by computer-aided docking studies. Results Synthesis of azobenzene mannobioside 2 For the preparation of azobenzene mannobioside 2, the

• computer-aided docking studies to get an idea of their interactions with the carbohydrate-recognition domain (CRD) of the lectin. Docking of azobenzene mannobioside 2 into the carbohydrate binding site of FimH To visualise complexation of the (E)- and (Z)-isomers of azobenzene mannobioside 2 within the CRD