Structure-Based Identification of Organoruthenium Compounds as Nanomolar Antagonists of Cannabinoid Receptors.

Metal complexes exhibit a diverse range of coordination geometries, representing novel privileged scaffolds with convenient click types of preparation inaccessible for typical carbon-centered organic compounds. Herein, we explored the opportunity to identify biologically active organometallic complexes by reverse docking of a rigid, minimum-size octahedral organoruthenium scaffold against thousands of protein-binding pockets. Interestingly, cannabinoid receptor type 1 (CB1) was identified based on the docking scores and the degree of overlap between the docked organoruthenium scaffold and the hydrophobic scaffold of the cocrystallized ligand. Further structure-based optimization led to the discovery of organoruthenium complexes with nanomolar binding affinities and high selectivity toward CB2. Our work indicates that octahedral organoruthenium scaffolds may be advantageous for targeting the large and hydrophobic binding pockets and that the reverse docking approach may facilitate the discovery of novel privileged scaffolds, such as organometallic complexes, for exploring chemical space in lead discovery.

Natural Product-Inspired Chiral Ligand Design: Aloperine and N-Substituted Aloperines-Induced Pd-Catalyzed Asymmetric Hydroarylation of Ketimines.

A naturally occurring alkaloid aloperine was utilized as a chiral skeleton for the development of new ligands/catalysts in asymmetric synthesis. A number of N-substituted aloperines have been prepared, and a Pd-catalyzed asymmetric hydroarylation of ketimines using these chiral 1,3-diamine ligands was reported. A range of chiral sulfonyl amides were prepared in high yields and enantioselectivities. The stereoselectivity and structure relationships of aloperines have been studied. In addition, preliminary studies on the desymmetrization of meso-anhydride have also shown that these diamines have good potential in organocatalysis. These discoveries would provide a new future development for natural product-inspired chiral ligand design and developments.

Construction of aziridine, azetidine, indole and quinoline-like heterocycles via Pd-mediated C-H activation/annulation strategies.

N-Heterocycles can be found in natural products and drug molecules and are indispensable components in the area of organic synthesis, medicinal chemistry and materials science. The construction of these N-containing heterocycles by traditional methods usually requires the preparation of reactive intermediates. In the past decades, with the rapid growth of transition metal catalysed coupling reactions, syntheses of heterocycles from precursors with inert chemical bonds have become a challenge. More recently, in the field of transition metal associated C-H direct functionalization, efficient methods have been developed for the syntheses of N-heterocyclic compounds such as aziridines, azetidines, indoles and quinolines under the click type of reaction mode. In this review, representative synthetic methodologies developed in the recent 10 years for the preparation of this small class of N-heterocycles via the Pd-catalysed C-H activation and C-N bond formation pathway are discussed. We hope this article will provide new insights from the strategies highlighted into future molecular design, synthesis and applications in medical and materials sciences.

Cinchonine induces apoptosis of HeLa and A549 cells through targeting TRAF6.

BACKGROUND: Cancer cells are known to over-express TRAF6 that is critical for both AKT and TAK1 activations. The Really Interesting New Gene (RING) domain of TRAF6 is believed to be responsible for the E3 ligase activity, ZINC fingers of TRAF6 provide critical support for the activity of the RING domain which is critical for both AKT and TAK1 activations. METHODS: We employed computational docking program to identify small molecules that could effectively and competitively bind with the RING domain of TRAF6, which is believed to be responsible for its E3 ligase activity. MTT assay and flow cytometry were employed to analyze apoptosis of cancer cells. Signaling pathways were detected using immunoprecipitation and western blotting, and immunofluorescence was pursued to assess the nature of binding of cinchonine to TRAF6. We also performed animal experiments to test effect of cinchonine in vivo. RESULTS: Cinchonine, a naturally occurring Cinchona alkaloid identified from the docking study, could bind to TRAF6 in HeLa and A549 cells and induce apoptosis of these cancer cells. We found that AKT ubiquitination and phosphorylation as well as phosphorylation of TAK1 were decreased. These activities would lead to subsequent suppression anti-apoptotic protein Bcl-2, while elevating pro-apoptotic protein Bax. Immunofluorescence staining unambiguously demonstrated the binding of cinchonine specifically at the RING domain of TRAF6 in cells, thereby validating the computational modeling. Animal experiments showed that cinchonine could suppress tumor growth in mice without showing significant acute toxicity. CONCLUSION: These investigations suggest that through competitive binding with the RING domain of TRAF6, cinchonine could induce apoptosis via inhibiting AKT and TAK1 signaling pathways.

Mechanistic Study of Human Glucose Transport Mediated by GLUT1.

The glucose transporter 1 (GLUT1) belongs to the major facilitator superfamily (MFS) and is responsible for the constant uptake of glucose. However, the molecular mechanism of sugar transport remains obscure. In this study, homology modeling and molecular dynamics (MD) simulations in lipid bilayers were performed to investigate the combination of the alternate and multisite transport mechanism of glucose with GLUT1 in atomic detail. To explore the substrate recognition mechanism, the outward-open state human GLUT1 homology model was generated based on the template of xylose transporter XylE (PDB ID: 4GBZ), which shares up to 29% sequence identity and 49% similarity with GLUT1. Through the MD simulation study of glucose across lipid bilayer with both the outward-open GLUT1 and the GLUT1 inward-open crystal structure, we investigated six different conformational states and identified four key binding sites in both exofacial and endofacial loops that are essential for glucose recognition and transport. The study further revealed that four flexible gates consisting of W65/Y292/Y293-M420/TM10b-W388 might play important roles in the transport cycle. The study showed that some side chains close to the central ligand binding site underwent larger position changes. These conformational interchanges formed gated networks within an S-shaped central channel that permitted staged ligand diffusion across the transporter. This study provides new inroads for the understanding of GLUT1 ligand recognition paradigm and configurational features which are important for molecular, structural, and physiological research of the MFS members, especially for GLUT1-targeted drug design and discovery.

2-Deoxyglucose conjugated platinum (II) complexes for targeted therapy: design, synthesis, and antitumor activity.

Malignant neoplasms exhibit an elevated rate of glycolysis over normal cells. To target the Warburg effect, we designed a new series of 2-deoxyglucose (2-DG) conjugated platinum (II) complexes for glucose transporter 1 (GLUT1)-mediated anticancer drug delivery. The potential GLUT1 transportability of the complexes was investigated through a comparative molecular docking analysis utilizing the latest GLUT1 protein crystal structure. The key binding site for 2-DG as GLUT1's substrate was identified with molecular dynamics simulation, and the docking study demonstrated that the 2-DG conjugated platinum (II) complexes can be recognized by the same binding site as potential GLUT1 substrate. The conjugates were synthesized and evaluated for in vitro cytotoxicity study with seven human cancer cell lines. The results of this study revealed that 2-DG conjugated platinum (II) complexes are GLUT1 transportable substrates and exhibit improved cytotoxicities in cancer cell lines that over express GLUT1 when compared to the clinical drug, Oxaliplatin. The correlation between GLUT1 expression and antitumor effects are also confirmed. The study provides fundamental information supporting the potential of the 2-DG conjugated platinum (II) complexes as lead compounds for further pharmaceutical R&D.

A Comparison of Biological Activity of B Lymphocyte Stimulator (BLyS) Antagonist Peptibodies and the Elucidation of Possible BLyS Binding Sites.

B lymphocyte stimulator (BLyS) overexpression is associated with autoimmune diseases such as rheumatoid arthritis and lupus. BLyS antagonists are new effective therapeutic strategies that have been studied extensively. BLyS-binding peptides, BC originated from computer-aided drug design (CADD), 814 selected from the phage display library, as well as the 3-copy of BC (3-BC), were fused with human IgG1 Fc to constitute peptide-Fc fusion proteins, referred as peptibodies. BP-Fc, a peptibody possessing the identical sequence as BC-Fc but a His tag, was also constructed. The biological activities of these peptibodies were assessed by Enzyme-Linked Immuno Sorbent Assay (ELISA). Furthermore, the potential interacting orientations of BP and 814 with BLyS were studied. At 100 µg/ml, BC-Fc, BP-Fc, 814-Fc and 3-BC-Fc could distinctly inhibit 64 %, 50 %, 73 % and 56 % of the interaction of B cell maturation antigen (BCMA) with BLyS respectively. BP-Fc demonstrated 15 % higher binding ratio with BLyS than BC-Fc at 100 µg/ml. However, 814-Fc displayed at least 39 % higher BLyS-binding activity than BP-Fc at different concentrations. The binding capacity of 3-BC-Fc was slightly superior to BC-Fc. In addition, 814 and BP shared the identical domain on the surface of BLyS which involves in binding with BCMA, but owned the detached orientations. The discovery of possible locations of the BLyS-targeted peptides lays the foundation for the development of novel antagonists. Both BP-Fc and 3-BC-Fc fusion proteins could bind to BLyS in a dose-dependent manner and inhibit BLyS biological activity significantly, which might act as candidate agents for autoimmune disease therapy.

Molecular Mechanism of the Affinity Interactions between BAFF and Its Peptides by Molecular Simulations.

B-cell activating factor (BAFF) belonging to the TNF family, plays an important role in the proliferation and differentiation of B cells which renders it an attractive target for autoimmune diseases. Some peptides have been designed to target BAFF for the treatment of autoimmune diseases. Our previous studies suggested that peptides TA and DX-814 had competitive bioactivities compared to the natural peptide trans-membrane activator and calcium modulator and cyclophilin ligand interactor (TACI) in different binding orientations. In this study, we carried out molecular modeling and dynamics and molecular docking calculations to explore the structural and chemical features responsible for the binding affinities of these peptides. Binding free energy calculations, mutational analyses were also conducted to validate our findings. The result showed that hydrophobic and electrostatic interactions are the dominant forces for binding. DX-814 had a similar binding orientation with BCMA in a conserved hydrophobic pocket and formed electrostatic interaction with conserved arginine residues on the BAFF surface, compared with TA which might interact with a sub-pocket of BAFF in a different orientation. These results provide a thorough understanding of the binding mode between BAFF and its peptide inhibitors at the molecular level and further guide inhibitor design.