Alexander Shivanyuk

Reversible encapsulation by self-assembling resorcinarene subunits

Encapsulation complexes are assemblies in which a reversibly formed host more or less completely surrounds guest molecules. Host structures held together by hydrogen bonds have lifetimes in organic solvents of milliseconds to hours, long enough to directly observe the encapsulated guest by NMR spectroscopy. We describe here the action of alkyl ammonium compounds as guests that gather up to six molecules of the host module to form encapsulation complexes. The stoichiometry of the complexes—the largest hydrogen-bonded host capsules to date—is determined by the size and concentration of the guest.

A low molecular weight mimic of the Toll/IL-1 receptor/resistance domain inhibits IL-1 receptor-mediated responses

Toll-like receptors (TLRs) and the type I IL-1 receptor (IL-1RI) are key components of the innate immune system activated by microbial infections and inflammation. The signaling cascade from agonist-occupied TLRs and IL-1Rs involves recruitment of the small cytosolic adapter protein MyD88 that binds to IL-1RI via homotypic interactions mediated by Toll/IL-1R/resistance (TIR) domains. Dominant negative forms and null mutations of MyD88 have recently been shown to preclude bacterial product or IL-1-mediated activation of NF-κB pathways, demonstrating that MyD88 is an essential component of the Toll receptor signaling. Here, we report the synthesis and pharmacological effects of a low molecular weight MyD88 mimic, hydrocinnamoyl-l-valyl pyrrolidine (compound 4a), modeled on a tripeptide sequence of the BB-loop [(F/Y)-(V/L/I)-(P/G)] of the TIR domain. Results are presented showing that compound 4a interferes with the interactions between mouse MyD88 and IL-1RI at the TIR domains. Compound 4a inhibited IL-1β-induced phosphorylation of the mitogen-activated protein kinase p38 in EL4 thymoma cells and in freshly isolated murine lymphocytes in a concentration-dependent manner. In vivo, compound 4a produced a significant attenuation of the IL-1β-induced fever response (200 mg/kg, i.p.). Inhibition of the TIR domain-mediated MyD88/IL1-RI interaction by a low molecular weight, cell-penetrating TIR domain mimic suggests an intracellular site for antiinflammatory drug action.

Guest-Controlled Formation of a Hydrogen-Bonded Molecular Capsule.

The dimerization of the self-complementary resorcarene tetraesters is triggered by the entrapment of a tropylium cation in the pi-basic cavity. Eight intermolecular OH small middle dot small middle dot small middle dotOC hydrogen bonds together with host-guest interactions such as charge transfer and C-H small middle dot small middle dot small middle dotpi bonding are responsible for the high stability of this assembly (see picture). Hereby neither the host-guest interaction nor the interaction of two resorcarene molecules through hydrogen bonds is sufficient by itself to form the complex.

Induced-Fit Molecular Recognition with Water-Soluble Cavitands

Synthesis of novel water-soluble cavitands 1 and 2 and their complexes--the caviplexes--is described. The solubility in water derives from four primary ammonium groups on the lower rim and eight secondary amide groups on the upper rim. Cavitands 1 and 2 exist as D2d velcraplex dimers in aqueous solution but the addition of lipophilic guests 15-24 induces conformational changes to the vase-like structures. The internal cavity dimensions are 8 x 10 A, and the exchange rates of guests in the caviplexes are slow on the NMR time-scale (room temperature and 600 MHz). The direct observation of bound species and the stoichiometry of the complexes is reported. The association constants (Ka) between 0.4 x 10(-1) (-deltaG295= 0.7 kcalmol(-1)) and 1.4 x 10(2)M(-1) (-deltaG295=2.9 kcalmol(-1)) in D2O and 1.4 x 10(1)(-deltaG295= 1.7 kcalmol(-1)) and 2.8 x 10(4)M(-1)(-deltaG295=6.0 kcalmol(-1)) in [D4]methanol for aliphatic guests 16-24 were determined. Guest exchange rates of the new hosts 1 and 2 are considerably slower than rates observed for typical open-ended cavities in aqueous solution.

Drug- and Lead-likeness, Target Class, and Molecular Diversity Analysis of 7.9 Million Commercially Available Organic Compounds Provided by 29 Suppliers

A database of 7.9 million compounds commercially available from 29 suppliers in 2008-2009 was assembled and analyzed. 5.2 million structures of this database were identified to be unique and were subjected to an assessment of physical and biological properties and estimation of molecular diversity. The rules of Lipinski and Veber were applied to the molecular weight, the calculated water/n-octanol partition coefficients (Clog P), the calculated aqueous solubility (log S), the numbers of hydrogen-bond donors and acceptors, and the calculated Caco-2 membrane permeability to identify the drug-like compounds, whereas the toxicity/reactivity filters were used to remove the structures with biologically undesired functional groups. This filtering resulted in 2.0 million (39%) structures perfectly suitable for high-throughput screening of biological activity. Modified filters applied to identify lead-like structures revealed that 16% of the unique compounds could be potential leads. Assessment of the biological activities, the analysis of diversity, and the sizes of exclusive sets of compounds are presented.

Hydrogen-Bonding Effects in Calix[4]arene Capsules

The synthesis and spectroscopic characterization of self-assembling calix[4]arene based capsules 1a.1a and 1b.1b are described. These compounds feature four urea substituents at the upper rims and four secondary amide fragments at the lower rims that can participate in inter- and intramolecular hydrogen bonding in apolar solution. Communication between the calixarene rims in 1a, b influences the self-assembled cavitys size and shape. Specifically. dimerization results in a perfect cone conformation of the calixarene skeleton in 1a, b and stabilizes a seam of intramolecular amide C=O...H-N hydrogen bonds at the lower rim. This seam is cycloenantiomeric, with either clockwise or counterclockwise arrangements of the head-to-tail amides. Complexation of Na+-cation breaks hydrogen bonds at the lower rim but maintains the capsular assembly. Encapsulation properties of 1a.1a and 1b.1b were studied in nonpolar solvents and their binary mixtures as well as through heterodimerization experiments. The presence of amide groups at the lower rim causes notable differences in the capsules binding affinities when compared to the corresponding tetraester capsules 1c.1c and 1d.1d. In the monomeric state calixarenes 1a, b are in a pinched cone conformation. The solid state X-ray crystallographic studies with monomeric 1a reveal only two intramolecular C=O...H-N hydrogen bonds between the adjacent amides at the lower rim, and an extensive network of intermolecular hydrogen bonds between urea groups at the upper rim.

Resorcarenes in the boat conformation as building blocks for hydrogen-bonded assemblies including two ammonium cations.

Crystal structures are reported for various co-crystals of rccc-resorcarenes with triethylammonium chloride. Usually, two molecules of a C2v-symmetric tetraester 2 in the boat conformation are linked through four hydrogen-bonded chloride anions to give dimeric assemblies. Two of the chloride anions may be replaced by four hydrogen-bonded ethanol molecules in an otherwise similar structure. These assemblies, which consist of six or eight components, posses voluminous, negatively charged chambers in which two triethylammionium cations, 3+, are included as guests by strong electrostatic and hydrogen-bonding interactions. The host-guest N-H...Cl hydrogen bonds were clearly detected at 173 K. These are the first examples of hydrogen-bonded, solid-state capsules trapping two ions of the same charge in close proximity. In the 1:2 complex with 3+ Cl-, the molecule of the parent resorcarene 1 also adopts a boat conformation whose cavity is considerably extended by four hydrogen-bonded chloride anions. The pocket formed in this way again includes two 3+ ions as a result of electrostatic and hydrogen bonding host-guest interactions. All these structures show that the boat conformers of resorcarenes can be used as a novel motif for the construction of hydrogen-bonded assemblies capable of molecular inclusion and encapsulation.

Synthesis, Conformation, and Binding Properties of Resorcarene Tetrasulfonates. Asymmetric Reorganization of Pendant Sulfonyl Groups via Intramolecular SO- - -H−O Hydrogen Bonds

The regioselective reaction of resorcarene octaols 1 with 4 equiv of arylsulfonyl chlorides and Et3N in MeCN gives in 30−60% yield the C2v symmetrical tetrasulfonates 3. The mild electrophilic substitution (aminomethylation, bromination) of resorcarene tetrasulfonates 3 and tetraphosphates 2 takes place only in the 2-positions of unsubstituted resorcinol rings yielding distally disubstituted resorcarenes 4. The acylation of hydroxy groups in compounds 2 and 3 gives C2v symmetrical octaesters 5 including large resorcarene tetracrown-ethers. In the minimized boat conformation of tetrasulfonates 3 the two unsubstituted resorcinol rings are vertical and the sulfonyl fragments are arranged in a C2 symmetrical manner via intramolecular SO- - -H−O hydrogen bonds. This structure is proved by NMR and IR spectroscopy. In the case of tetrasulfonate 3c the two enantiomeric conformations interconvert in CDCl3 with ΔG* = 11.6 kcal/mol. This is in agreement with the ΔE* value predicted by molecular mechanics in vacuo.

Hydrogen bond-stabilised N-alkylammonium resorcinarene halide cavitands

A family of hydrogen bond-stabilised N-alkylammonium resorcinarene chloride and bromide cavitands were synthesised and characterised with 1H NMR and ESI mass spectrometry. The seven compounds exhibit interestingly either self-inclusion or guest complexation in the solid state evidenced by single crystal X-ray diffraction. The four dimers show self-inclusion of the upper rim propyl chains and consist of two hydrogen-bonded resorcinarene tetracations and six halide anions, while the remaining two halide anions are located in between the dimers linking them via hydrogen bonding. Small solvent molecules such as dichloromethane, methanol, n-butanol or chloroform are complexed into the resorcinarene cavity in three 1:1 or 1:2 host–guest complexes. While included, the methanol and butanol molecules are simultaneously hydrogen bonded to the halide anion enhancing the complex formation. The complementary self-inclusion results in a nearly perfect cone conformation of the resorcinarene core in the dimers, while the host–guest complexes are much more distorted.

Reversible encapsulation of multiple, neutral guests in hexameric resorcinarene hosts

A variety of aromatic guest molecules are co-encapsulated with Bu4SbBr in an assembly of six resorcinarene subunits.