Crystalline Sponge Method: X-ray Structure Analysis of Small Molecules by Post-Orientation within Porous Crystals-Principle and Proof-of-Concept Studies.

This Review discusses, along with the historical background, the principles as well as proof-of-concept studies of the crystalline sponge (CS) method, a new single-crystal X-ray diffraction (SCXRD) method for the analysis of the structures of small molecules without sample crystallization. The method uses single-crystalline porous coordination networks (crystalline sponges) that can absorb small guest molecules within their pores. The absorbed guest molecules are ordered in the pores through molecular recognition and become observable by conventional SCXRD analysis. The complex {[(ZnI2 )3 (tpt)2 ]⋅x(solvent)}n (tpt=tris(4-pyridyl)-1,3,5-triazine) was first proposed as a crystalline sponge and has been most generally used. Crystalline sponges developed later are also discussed here. The principle of the CS method can be described as "post-crystallization" of the absorbed guest, whose ordering is templated by the pre-latticed cavities. The method has been widely applied to synthetic chemistry as well as natural product studies, for which proof-of-concept examples will be shown here.

X-ray Structure Analysis of Ozonides by the Crystalline Sponge Method.

The crystalline sponge method was used for the X-ray structure analysis of ozonide compounds. As this new technique requires only microgram quantities of the samples, structural analysis can be conducted without product isolation, isomer separation, or crystallization and most importantly without any risk of explosion.

In†Situ Observation of Thiol Michael Addition to a Reversible Covalent Drug in a Crystalline Sponge.

A reversible Michael addition reaction between thiol nucleophiles and cyanoenones has been previously postulated to be the mechanism-of-action of a new family of reversible covalent drugs. However, the hypothetical Michael adducts in this mechanism have only been detected by spectroscopic methods in solution. Herein, the crystallographic observation of reversible Michael addition with a potent cyanoenone drug candidate by means of the crystalline-sponge method is reported. After inclusion of the cyanoenone substrate, the sponge crystal was treated with a thiol solution. Subsequent crystallographic analysis confirmed the single-crystal-to-single-crystal transformation of the substrate into the impermanent Michael adduct.

Undeniable Confirmation of the syn-Addition Mechanism for Metal-Free Diboration by Using the Crystalline Sponge Method.

The stereochemical outcome of the recently developed metal-free 1,2-diboration of aliphatic alkenes has, until now, only been elucidated by indirect means (e.g. derivatization). This is because classical conformational analysis of the resulting 1,2-diboranes is not viable; in the (1)H NMR spectrum the relevant (1)H resonances are broadened by (11)B, and the occurrence of the products as oily compounds precludes X-ray crystallographic analysis. Herein, the crystalline sponge method is used to display the crystal structures of the diboronic esters formed from internal E and Z olefins, evidencing the stereospecific syn addition mechanism of the reaction, which is fully consistent with the prediction from DFT calculations.

Contractile and extensible molecular figures-of-eight.

Two large rings, 66- (m-66) and 78-membered (m-78) rings, each one incorporating two pairs of transition-metal-complexing units, have been prepared. The coordinating fragments are alternating bi- and tridentate chelating groups, namely, 2,9-diphenyl-1,10-phenanthroline (dpp) and 2,2',2',6''-terpyridine (terpy) respectively. Both macrocycles form molecular figures-of-eight in the presence of Fe(II) , affording a classical bis-terpy complex as the central core. The larger m-78 ring can accommodate a four-coordinate Cu(I) center with the formation of a {Cu(dpp)2 }(+) central complex and a highly twisted figure-of-eight backbone, whereas m-66 is too small to coordinate Cu(I) . Macrocycle m-78 thus affords stable complexes with both Fe(II) and Cu(I) ; the ligand around the metal changes from (terpy)2 to (dpp)2 . This bimodal coordination situation allows for a large amplitude rearrangement of the organic backbone. When coordinated to preferentially octahedrally coordinated Fe(II) or Cu(II) , the height of the molecule along the coordinating axis of the tridentate terpy ligands is only about 11 Å, whereas the height of the molecule along the same vertical axis is several times as large for the tetrahedral Cu(I) complex. Chemically or electrochemically driven contraction and extension motions along a defined axis make this figure-of-eight particularly promising as a new class of molecular machine prototype for use as a constitutive element in muscle-like dynamic systems.

Interconversion between a vertically oriented transition metal-complexed figure-of-eight and a horizontally disposed one.

A large ring containing two pairs of transition metal-complexing fragments with alternating bi- and tridentate chelates has been shown to behave as a bimodal figure-of-eight. When coordinated to a preferentially octahedrally coordinated Fe(II) or Cu(II) center, the height of the molecule along the coordinating axis of the tridentate ligands (vertical on the drawing) is only ∼11 Å, whereas the height of the molecule along the same vertical axis is several times as large for the complex of the tetrahedrally coordinated copper(I) center. This new type of molecular machine-prototype could be used as constitutive element in muscle-like dynamic systems.

E3 ubiquitin-ligases and their target proteins during the regulation of plant innate immunity.

Reversible protein ubiquitination plays a crucial role during the regulation of plant immune signaling. E3 ubiquitin (Ub)-ligase enzymes, which are classified into different families depending on their structural and functional features, confer the specificity of substrate and are the best characterized components of the ubiquitination cascade. E3 Ub-ligases of different families have been shown to be involved in all steps of plant immune responses. Indeed, they have been involved in the first steps of pathogen perception, as they appear to modulate perception of pathogen-associated molecular patterns by pattern-recognition receptors at the plasma membrane and to regulate the accumulation of nucleotide-binding leucine-rich repeat-type intracellular immune receptors. In addition, E3 Ub-ligase proteins are also involved in the regulation of the signaling responses downstream of pathogen perception through targeting vesicle trafficking components or nuclear transcription factors, for instance. Finally, we also discuss the case of microbial effector proteins that are able to target host E3 Ub-ligases, or to act themselves as E3 Ub-ligases, in their attempt to subvert the host proteasome to promote disease.

Synthesis of sesquiterpene-inspired derivatives designed for covalent binding and their inhibition of the NF-κB pathway.

A significant portion of bioactive secondary metabolites are endowed with reactive functionalities that can engage in covalent interactions with their target. Sesquiterpene lactones in particular are rich in Michael acceptors that react with cysteines. Several polycyclic scaffolds derived from total synthesis or readily available polycyclic terpenes were used as the starting point in the synthesis of a library aiming to project mildly reactive functionalities (Michael acceptors or chloroacetates) with diverse geometries. Screening of the library for inhibition of the NF-κB pathway revealed several potent inhibitors that are chemically readily accessible.

Expanding the scope of PNA-encoded synthesis (PES): Mtt-protected PNA fully orthogonal to fmoc chemistry and a broad array of robust diversity-generating reactions.

Nucleic acid-encoded libraries are emerging as an attractive and highly miniaturized format for the rapid identification of protein ligands. An important criterion in the synthesis of nucleic acid encoded libraries is the scope of reactions that can be used to introduce molecular diversity and devise divergent pathways for diversity-oriented synthesis (DOS). To date, the protecting group strategies that have been used in peptide nucleic acid (PNA) encoded synthesis (PES) have limited the choice of reactions used in the library synthesis to just a few prototypes. Herein, we describe the preparation of PNA monomers with a protecting group combination (Mtt/Boc) that is orthogonal to Fmoc-based synthesis and compatible with a large palette of reactions that have been productively used in DOS (palladium cross-couplings, metathesis, reductive amination, amidation, heterocycle formation, nucleophilic addition, conjugate additions, Pictet-Spengler cyclization). We incorporate γ-modifications in the PNA backbone that are known to enhance hybridization and solubility. We demonstrate the robustness of this strategy with a library synthesis that is characterized by MALDI MS analysis at every step.