Variation of a Theme: Crystal Structure with Four Octakis(2,3,6-tri-O-methyl)-γ-cyclodextrin Molecules Hydrated Differently by a Total of 19.3 Water,

Supramolecular Complexes of β-Cyclodextrin with Clomipramine and Doxepin: Effect of the Ring Substituent and Component of Drugs on Their Inclusion Topologies and Structural Flexibilities

Depression is a global threat. Tricyclic antidepressants (TCAs) are still efficacious in treating depression, albeit with more side effects. Cyclodextrins (CDs) with a suitable nanocavity are potential drug carriers and can enhance the drug bioavailability. Aiming for an atomistic understanding of the CD encapsulation facilitating the improvement of drug stability and the reduction of side effects, a comprehensive study series of the β-CD-TCA inclusion complexes through single crystal X-ray diffraction and density functional theory (DFT) calculation was undertaken. This work reports the supramolecular complexes of β-CD with two pivotal TCAs, clomipramine (CPM; 1) and doxepin (DXP; 2). The different inclusion topologies of the β-CD-TCA complexes were notable. X-ray analysis revealed that, in 1, the CPM B-ring (without chloro group) was entrapped in the β-CD cavity, whereas, in 2, the E-DXP A-ring and the Z-DXP B-ring were disordered in the cavity, yielding energetically favorable complexes primarily maintained by intermolecular C-H⋯π interactions, as indicated by DFT calculation. Because both wings of TCAs were similar, an alternative inclusion scenario of the A-ring was evidenced crystallographically in four other TCA complexes. The enhanced TCA thermodynamic stabilities via CD inclusion complexation helped to reduce the side effects and to increase the bioavailability. Moreover, the scrutinization of six TCAs in different lattice circumstances revealed the greater TCA structural flexibilities for their optimum pharmacological activity while binding with proteins.

Linkage and pyranosyl ring twisting in cyclodextrins

Acylated beta-cyclodextrins (beta-CDs) were studied to gain perspective on maltose octapropanoate, the crystal structure of which was reported in the preceding paper in this issue. Acylated beta-CDs are distorted so we looked at other CDs and gained increased understanding of distortion in CDs and possibly, shapes in starch. Classic CDs have six to eight glucose residues in a doughnut shape that is stabilized by a ring of inter-residue O3,,,O2' hydrogen bonds. On a phi,psi energy map for a maltose analog that does not form hydrogen bonds, classic CD linkages have higher energies than structures that are stabilized by the exo-anomeric effect. In distorted beta-CDs, which lack hydrogen bonding, some linkages attain low-energies from the exo-anomeric effect and acyl stacking. Those linkages result in left-handed helical geometry so other linkages are forced by the CD macrocycle to have counter-balancing right-handed character. Permethylated gamma-CDs have two 'flipping' linkages as do some larger native CDs. Flipping linkages allow two left-handed segments to join into a macrocycle, thus avoiding the higher-energy, right-handed forms. Some glucose rings in derivatized beta-CDs have substantial positive twists of the pseudo torsion angle O1-C1...C4-O4, adding right-handed character to balance the left-handed linkages. In substituted gamma-CD, all residues have negative twists, giving extra left-handed character to the short, pseudo-helical segments. In non-macrocyclic molecules the twists ranged from -14 degrees to +2 degrees , averaging -6.1 degrees. In these beta- and gamma-CDs, the twists ranged from -22 degrees to +16 degrees for (4)C(1) rings, and the (O)S(2) ring in acetylated beta-CD has a twist of +34 degrees . Glucose residues in other CDs were less twisted.

New synthesis of (Z,E)-2,7-bis(4-cyanobenzylidene)cycloheptan-1-one under stereospecific constraints induced by host-guest interactions

A selective, efficient, and fast access to (Z,E)-2,7-bis(4-cyanobenzylidene)cycloheptan-1-one (BCBCH), precursor of the synthetic antagonist of tissue-plasminogen activator (t-PA), is reported using a solid/solid aldolisation-crotonisation reaction on a supramolecular complex under microwave irradiation. The underlying mechanism is investigated from the crystal structure of the intermediate host-guest complex formed between permethylated gamma-cyclodextrin and (Z)-2-(4-cyanobenzylidene)cycloheptan-1-one.

Metal-capped alpha-cyclodextrins: squaring the circle

This report describes the four-step synthesis of 6A,6D-diamino-6A,6D-dideoxy-2(A),2(B),2(C),2(D),2(E),2(F),3(A),3(B),3(C),3(D),3(E),3(F), 6(B),6(C),6(E),6(F)-hexadeca-O-methylcyclomaltohexaose (5), a methylated alpha-CD that bears two -CH(2)NH(2) ligands located on diametrically opposed glucopyranose rings. Reaction of 5 with K(2)PtCl(4) afforded the water-soluble chelate complex [PtCl(2)(5)] where the metal center is bonded to cis-arranged nitrogen atoms. A single-crystal X-ray structure of the latter reveals the high distortion imposed on the CD structure by the short metallo-organic cap. The cyclodextrin core adopts an unprecedented elongated, almost rectangular shape, the shortest and longest O(4)(n). O(4)(n+3) distances being respectively 5.44 and 9.98 A. Two opposing glucose rings are no longer in the usual (4)C(1) chair conformation, but adopt an elongated (O)S(2) skew-boat structure. The observed CD-flattening produces a highly preorganized hydrophilic pocket that complexes through multiple hydrogen bonding a single water molecule. Complex [PtCl(2)(5)] and the corresponding synthetic intermediates were characterized by elemental analysis, MS, and IR and NMR spectroscopy.

Crystal structure of octakis(2,3,6-tri-O-methyl)-gamma-cyclodextrin x 4.5 H2O: evidence for conformational flexibility of permethylated cyclodextrins

Octakis(2,3,6-tri-O-methyl)-gamma-CD (TRIMEG) cocrystallized at 18 degrees C with 4.5 water molecules in the orthorhombic space group P2(1)2(1)2(1), unit cell dimensions a = 10.7879(3), b = 29.0580(9), c = 32.2909(11) A. The TRIMEG macrocycle is in a 'round' form with all glucose units oriented syn, and one O-6-CH3 methoxy group points 'toward' the molecular cavity. The TRIMEG x 4.5 H2O molecules are stacked to form infinite cylinders with the central cavities aligned into channels filled for each TRIMEG by 4.5 water molecules distributed over 15 partially occupied sites. This structure differs from the two known structures of TRIMEG in which two diametrically opposed glucoses are oriented anti to yield an 'elliptical' form, and their O-6-CH3 groups are directed 'toward' the cavity and close it at this side to form a bowl-shaped molecule.

Advances in direct methods for protein crystallography

Recent advances in ab initio direct methods have enabled the solution of crystal structures of small proteins from native X-ray data alone, that is, without the use of fragments of known structure or the need to prepare heavy-atom or selenomethionine derivatives, provided that the data are available to atomic resolution. These methods are also proving to be useful for locating the selenium atoms or other anomalous scatterers in the multiple wavelength anomalous diffraction phasing of larger proteins at lower resolution.