Protein crystallization remains a serious bottleneck to structure determination by X-ray diffraction methods. Compounds acting as “molecular glue” provide a promising strategy to overcome this bottleneck. Such molecules interact via noncovalent bonds with two or more protein surfaces to promote lattice formation. Here, we report a 1.5 Å resolution crystal structure of lysine-rich cytochrome c complexed with p-phosphonatomethyl-calix­[4]­arene (pmclx 4 ). Evidence for complex formation in solution was provided by NMR studies. Similar to p-sulfonato-calix­[4]­arene (sclx 4 ), the cavity of pmclx 4 entrapped a single lysine side chain. Interesting features of protein recognition by the phosphonate substituents were identified in the crystal structure. A new calixarene binding site was identified at Lys54. The electron density at this site indicated two distinct calixarene conformers, suggesting a degree of ligand mobility. The role of pmclx 4 in protein crystal packing (molecular glue and patchy particle model) as well as differences in protein-binding with respect to sclx 4 are discussed.

A cone-calix[4]arene derivative, featuring a guanidinium group and a Cu(II) ion ligated to a 1,4,7-triazacyclononane (TACN) ligand at the 1,3-distal positions of the upper rim, effectively catalyzes the cleavage of 2-hydroxypropyl p-nitrophenyl phosphate (HPNP) and a number of diribonucleoside 3',5'-monophosphates (NpN'). Kinetic and potentiometric measurements support the operation of a general-base/general-acid mechanism and demonstrate that the hydroxo form of the ligated Cu(II) ion is the sole catalytically active species. Rate enhancements relative to the background hydrolysis reaction at 1 mM catalyst concentration are 6 × 10(5)-fold for HPNP and cluster around 10(7)-fold with the most favorable catalyst-NpN' combinations.

The catalytic activity of an artificial phosphodiesterase that combines a ligated metal ion (Cu(II), Zn(II)) with a guanidinium unit connected by a 1,2-vicinal calix[4]arene spacer was investigated in the transesterification of RNA models HPNP and four diribonucleoside 3',5'-monophosphates. Comparison with previous data related to the 1,3-distal regioisomeric metal complexes confirms the superiority of the Cu(II) complexes over the Zn(II) analogs and shows that in the reactions of HPNP, GpU, and UpU, the catalytic efficiency depends very little on whether the substitution pattern is 1,2-vicinal or 1,3-distal. On the other hand, CpA turned out to be a good substrate for the Cu(II) complex of the 1,2-vicinal catalyst and a bad substrate for the corresponding 1,3-distal regioisomer, whereas the opposite holds for GpA. Extension of the investigation to the cleavage of the DNA model BNPP showed that both Zn(II) and Cu(II) complexes exhibit good catalytic efficiency, with a superiority of the 1,2-vicinal catalyst in both cases. The data reported in this work show that rate accelerations over background for the best catalyst-substrate combinations at 0.5 mM catalyst concentration are 3.6 × 10(5)-fold for HPNP, 1.1 × 10(6)-fold for BNPP, and range from 1.3 × 10(6)- to 1.3 × 10(7)-fold for diribonucleoside monophosphates.

In contrast to sulfonato-calix[4]arene (sclx4), which mediates close-packed assemblies, the higher charge carboxylate-containing sclx4mc induced a crystalline framework of cytochrome c.

The number of applications of peptide nucleic acids (PNAs)—oligonucleotide analogs with a polyamide backbone—is continuously increasing in both in vitro and cellular systems and, parallel to this, delivery systems able to bring PNAs to their targets have been developed. This review is intended to give to the readers an overview on the available carriers for these oligonucleotide mimics, with a particular emphasis on newly developed multi-component- and multifunctional vehicles which boosted PNA research in recent years. The following approaches will be discussed: (a) conjugation with carrier molecules and peptides; (b) liposome formulations; (c) polymer nanoparticles; (d) inorganic porous nanoparticles; (e) carbon based nanocarriers; and (f) self-assembled and supramolecular systems. New therapeutic strategies enabled by the combination of PNA and proper delivery systems are discussed.