Specific pupylation as IDEntity reporter (SPIDER) for the identification of protein-biomolecule interactions.

Protein-biomolecule interactions play pivotal roles in almost all biological processes. For a biomolecule of interest, the identification of the interacting protein(s) is essential. For this need, although many assays are available, highly robust and reliable methods are always desired. By combining a substrate-based proximity labeling activity from the pupylation pathway of Mycobacterium tuberculosis and the streptavidin (SA)-biotin system, we developed the Specific Pupylation as IDEntity Reporter (SPIDER) method for identifying protein-biomolecule interactions. Using SPIDER, we validated the interactions between the known binding proteins of protein, DNA, RNA, and small molecule. We successfully applied SPIDER to construct the global protein interactome for m6A and mRNA, identified a variety of uncharacterized m6A binding proteins, and validated SRSF7 as a potential m6A reader. We globally identified the binding proteins for lenalidomide and CobB. Moreover, we identified SARS-CoV-2-specific receptors on the cell membrane. Overall, SPIDER is powerful and highly accessible for the study of protein-biomolecule interactions.

Single-wing extended tribenzotriquinacenes via bowl-shaped dehydrobenzene and isobenzofuran tribenzotriquinacene derivatives.

Monoaryne and monoisobenzofuran analogues of a C(3v)-symmetrical tribenzotriquinacene (TBTQ) were generated in situ and trapped with various dienes and dienophiles, respectively. In this way, a series of single-wing extended TBTQ derivatives bearing the bowl-shaped TBTQ unit in different topographical expositions have become accessible. This includes some novel tribenzotriquinacene "dimers", in which two TBTQ bowls are attached in syn- or anti-orientation at the terminal positions of rigid linker units. Several of these compounds have been characterized by both spectroscopy and X-ray structural analysis. The efficient access to the TBTQ "dimers" may lay a useful foundation for further studies of novel container compounds and supramolecular architectures.

Tribenzotriquinacenes based on regioselective bis-formylation: optical resolution and absolute configuration of inherently chiral derivatives and synthesis of the first cyclophane-type tribenzotriquinacene dimers.

Enantiomerically pure tribenzotriquinacenes (TBTQs) bearing two monofunctionalized aromatic nuclei were synthesized for the first time and their optical properties and absolute configuration determined. A remarkably regioselective bis-formylation of the fully bridgehead methylated parent TBTQ hydrocarbon with MeOCHCl(2)/TiCl(4) afforded a mixture of two C(s)-symmetrical (achiral) difunctionalized derivatives together with one C(1)-symmetrical (chiral) isomer. Reduction and subsequent column chromatography furnished the three respective benzylic TBTQ dialcohols. Optical resolution of the racemic 2,6-bis(hydroxymethyl) derivative was achieved via the diastereomeric (R)-1,1'-bi-2-naphthol ethers and the absolute configuration of the enantiomers was determined by CD exciton model analysis. The electronic circular dichroism (ECD) spectra and the specific rotation of the enantiomers were found to agree with the results of DFT calculations. Among the C(s)-symmetrical isomers, the "proximal" 2,11-dialdehyde and the corresponding benzylic dialcohol were identified by 2D NMR spectroscopy and X-ray crystallographic analysis, respectively, and used as the starting point for the synthesis of several novel dithiametacyclophanes. These include the first "dimeric" tribenzotriquinacene-based cyclophanes bearing the bowls of the two TBTQ units attached to each other in a syn (concave-concave) or anti (convex-concave) configuration. The usefulness of such thiacyclophanes as fluorescent chemosensors for different metal ions is also demonstrated.

Synthesis and optical resolution of inherently chiral difunctionalized tribenzotriquinacenes.

The synthesis of several inherently chiral tribenzotriquinacenes (TBTQs) bearing one single mono- or difunctionalized aromatic nucleus and the optical resolution of one of these derivatives, a TBTQ-based salicylic acid (11), are described for the first time. Efficient access to enantiopure, inherently chiral tribenzotriquinacenes may lay a foundation for studies of novel container compounds, supramolecular aggregation, chiral recognition, and asymmetric catalysis.