Chemical–biological characterization of a cruzain inhibitor reveals a second target and a mammalian off-target

• Jonathan W. Choy,
• Clifford Bryant,
• Claudia M. Calvet,
• Patricia S. Doyle,
• Shamila S. Gunatilleke,
• Siegfried S. F. Leung,
• Kenny K. H. Ang,
• Steven Chen,
• Jiri Gut,
• Juan A. Oses-Prieto,
• Jonathan B. Johnston,
• Michelle R. Arkin,
• Alma L. Burlingame,
• Jack Taunton,
• Matthew P. Jacobson,
• James M. McKerrow,
• Larissa M. Podust and
• Adam R. Renslo

Beilstein J. Org. Chem. 2013, 9, 15–25, doi:10.3762/bjoc.9.3

• -based probe derived from 1 was used to identify mammalian cathepsin B as a potentially important off-target of 1 and 4. Computational docking studies and the evaluation of truncated analogues of 4 reveal structural determinants for TcCYP51 binding, information that will be useful in further optimization

• hypothesis that the 4-pyridyl ring in 4 is involved in binding TcCYP51. The 2-pyridyl ring system in 3 is presumably unable to chelate heme in TcCYP51 due to steric hindrance from the immediately adjacent amide linkage. Computational docking studies We next employed computational docking and a model derived

• from the crystal structure of TcCYP51 to compare predicted binding modes of 4 and (R)-5. The two ligands were docked by using the induced-fit docking protocol with Glide XP [34], and the models were further refined by minimizing the energies of the ligand and surrounding residues (within 5 Å of ligand

Synthesis and in silico screening of a library of β-carboline-containing compounds

• Kay M. Brummond,
• John R. Goodell,
• Matthew G. LaPorte,
• Lirong Wang and
• Xiang-Qun Xie

Beilstein J. Org. Chem. 2012, 8, 1048–1058, doi:10.3762/bjoc.8.117

• them are in accordance with Lipinski’s rules. Virtual docking and ligand-based target evaluations were performed for the β-carboline library compounds and selected synthetic intermediates to assess the therapeutic potential of these small organic molecules. These compounds have been deposited into the

• (PDB) and ChEMBL, it is possible to map new compounds into existing chemical space and to predict protein targets for new compounds, for which there are two complementary strategies that can be implemented. One is a structure-based docking strategy, in which a query compound is fit into a series of

• predict potential targets of the newly synthesized library of β-carboline-containing compounds. High-throughput docking studies for protein-target prediction of newly synthesized compounds Molecular docking studies were performed with the 34 newly synthesized compounds, represented by scaffolds 1, 2, 3

The use of glycoinformatics in glycochemistry

• Thomas Lütteke

Beilstein J. Org. Chem. 2012, 8, 915–929, doi:10.3762/bjoc.8.104

• CHARMM [97] input files from PDB files that contain carbohydrates. Various tools to predict the occupancy state of potential glycosylation sites from protein sequence data are available as well (Table 5). If a protein–carbohydrate complex is to be modeled, generally available docking tools such as

• AutoDock [113] can be used to identify the binding position. These tools, however, often do not sufficiently consider the peculiarities of protein–carbohydrate complexes, such as CH–π interactions [13]. Therefore, BALLDock/SLICK has been developed specifically for protein–carbohydrate docking [92][93]. One

• of the major problems of docking algorithms in general is the identification of the correct conformation among the potential binding modes [100]. Therefore, computational docking approaches are frequently combined with wet-lab experiments, such as saturation transfer difference NMR (STD NMR) or

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

• , revealed specific docking of GSF to the same binding site as the natural peptidic ligands of this integrin. The sulfate in the molecule coordinated with one manganese ion in the binding site. These studies show that this chemically easily accessible molecule GSF, synthesized in three steps from 3,4-bis

• (hydroxymethyl)furan and benzoylated galactose imidate, is nontoxic and antagonizes cell physiological processes in vitro that are important for the dissemination and growth of tumor cells in vivo. Keywords: angiogenesis; biomimetic synthesis; carbohydrates; in silico blind docking; melanoma cells

• interaction of GSF with integrins. To find possible binding sites for GSF, we used a “blind docking” approach to screen the protein surface of the extracellular domain of αvβ3, the crystal structure of which was published by Xiong et al. [26]. In an initial validation study, we performed multiple blind

Oxalyl retro-peptide gelators. Synthesis, gelation properties and stereochemical effects

• Janja Makarević,
• Milan Jokić,
• Leo Frkanec,
• Vesna Čaplar,
• Nataša Šijaković Vujičić and
• Mladen Žinić

Beilstein J. Org. Chem. 2010, 6, 945–959, doi:10.3762/bjoc.6.106

• close to trans-coplanar positioning of NH and Cα-H protons in both groups The low energy conformations of (S,R)-1b and (S,S)-1b were used for docking calculations to generate the hydrogen bonded dimers of extended gelator molecules involving both, the oxalamide and Leu-NH protons (Supporting Information

En route to photoaffinity labeling of the bacterial lectin FimH

• Thisbe K. Lindhorst,
• Michaela Märten,
• Andreas Fuchs and
• Stefan D. Knight

Beilstein J. Org. Chem. 2010, 6, 810–822, doi:10.3762/bjoc.6.91

• photoactive mannosides 1, 2, 3, and 5, we have performed computer-aided docking studies using FlexX [17][18][19] to get an idea about their binding to the bacterial lectin FimH, as reported earlier [20]. FlexX produces so-called scoring values for each docked ligand, which can be regarded as a rough estimate

• of its free binding energy. Low (more negative) scores correlate with high affinities, whilst higher scores reflect diminished binding potency (Table 1). Docking was based on two different X-ray structures. In the first case, crystals with an open tyrosine gate were taken as the basis [7], whilst in

• 5. Consequently, the synthetic photoactive mannosides are suited as ligands for the bacterial lectin FimH. Comparison of the measured IC50-values with the theoretical docking results, discloses a somewhat limited value of the computer-aided predictions in this case. Docking suggested that mannosides

A bivalent glycopeptide to target two putative carbohydrate binding sites on FimH

• Thisbe K. Lindhorst,
• Kathrin Bruegge,
• Andreas Fuchs and
• Oliver Sperling

Beilstein J. Org. Chem. 2010, 6, 801–809, doi:10.3762/bjoc.6.90

• lectin domain was probed by computational docking studies [16]. Three new potential carbohydrate binding cavities on the surface of the FimH lectin domain, in addition to the mannose pocket at the tip of the domain, were identified which have a marked preference for the same subset of high-mannose

• the known CRD at the tip of FimH and the suggested second binding site, which is a more extended region on the protein (Figure 1). Docking using FlexX [22][23][24] recommended a spacer of 10 to 15 amino acids to ligate the two different carbohydrate ligand portions of a bivalent glycoconjugate. This

• regulation of the ligand-receptor interaction. Experimental Docking studies Computer-aided modeling to estimate the spacer lengths of a bivalent glycopeptide ligand to allow bridging of two putative binding sites on FimH was carried out using FlexX flexible docking and consensus scoring, implemented in Sybyl

Dipyridodiazepinone derivatives; synthesis and anti HIV-1 activity

• Nisachon Khunnawutmanotham,
• Nitirat Chimnoi,
• Arunee Thitithanyanont,
• Patchreenart Saparpakorn,
• Kiattawee Choowongkomon,
• Pornpan Pungpo,
• Supa Hannongbua and
• Supanna Techasakul

Beilstein J. Org. Chem. 2009, 5, No. 36, doi:10.3762/bjoc.5.36

• groups in 7 and 8 led to diminished activity relative to that of 5 and 6. 10 and 11, 8-amino analogues of nevirapine, were found to be ineffective inhibitors. Molecular docking To understand the binding mode of the new potent derivatives 5, 6 and 9 were docked into the HIV-1 RT binding site by using the

Synthesis and enzymatic evaluation of 2- and 4-aminothiazole- based inhibitors of neuronal nitric oxide synthase

• Graham R. Lawton,
• Haitao Ji,
• Pavel Martásek,
• Linda J. Roman and
• Richard B. Silverman

Beilstein J. Org. Chem. 2009, 5, No. 28, doi:10.3762/bjoc.5.28

• -groups at the 5-position of 4 should allow us to probe the hydrophobic binding pocket defined by P565, A566, V567, and F584 in the substrate binding site and optimize this interaction. Figure 2 shows the docking mode for 3 and 4a in rat nNOS. Initially, attempts were made to construct 3 and 4 using

• -aminothiazole analogs 3 and 4a-c. A: The docking conformation of 3 in the active site of rat nNOS; B: The docking conformation of 4b in the active site of rat nNOS. Cofactors heme and H4B are shown in orange and purple, respectively. Attempts to open epoxide 5 with deprotonated aminothiazoles. i) n-BuLi, 2