Biomedical subjects
Publications and source records attributed to Kentaro Yamaguchi.
Bowl-shaped superstructures have been constructed by intra-clipping of resorcin[4]arene derivatives with two equivalents of (en)Pd(NO3)2 in water. The binding phenomena of the aromatic carboxylates were proven to be both enthalpically and entropically favoured.
[reaction: see text] Introduction of an electron-withdrawing group on the aromatic ring of N-methylacetanilide decreased the ratio of the cis conformer, and the ratio correlates well with the Hammett sigma values of the substituents. These steric properties can be applied to achieve amide conformational switching by protonation at the aromatic substituent of 4-[bis(dimethylamino)]-N-methylacetanilide or N-[p-(dimethylamino)phenyl]-N-phenylacetamide.
A resorcin[4]arene-based ligand 2 a with four pyrimidine substituents at the upper rim was synthesized, and the generation of different metal-mediated superstructures from the same ligand and metal ions utilizing the unfavorable incorporation of the third and fourth Pd(II) ions to ligand 2 a was investigated. The supramolecular bowl 3 a, which comes from a 1:2 combination of ligand 2 a and [Pd(en)(NO(3))(2)], was obtained in water even though excess of Pd(II) complexes were employed. By adding methanol, the supramolecular pot 4 gradually formed, which was the major product when the ratio of mixed solvent reached methanol/water=5:1 (v/v). Host-guest complexation phenomena of 3 a toward several aromatic carboxylates were demonstrated by isothermal titration calorimetry (ITC) and by (1)H NMR spectroscopy; both the enthalpy gain from electrostatic and hydrophobic interactions, and the entropy gain from desolvation cooperatively contribute to the binding of anionically charged guests. The crystal structure of supramolecular pot 4 shows direct evidence for the hydrogen bonding between water and the aromatic pi electrons in the solid state. The modulation between supramolecular bowl 3 a and pot 4 was also made possible by changing the metal/ligand ratios in aqueous methanol solution as well as by varying the water content of the mixed solvent.
With an aim to disclose the convergency and flexibility of our previously explored synthetic route to natural himbacine 1, and moreover, to clarify some novel aspects of the structure-activity relationships of 1, we prepared various structural types of novel himbacine congeners, 3-demethylhimbacine (3-norhimbacine) 2 and 4-epi-3-demethylhimbacine (4-epi-3-norhimbacine) 4-epi-2 and their enantiomers (ent-2 and ent-4-epi-2), 11-methylhimbacine 3, and 3-epihimbacine 4 in optically pure forms by employing our methodology. All of the synthesized congeners correspond to the compounds modified at the C-3 position of gamma-lactone moiety involved in 1. Among these congeners, 3-demethylhimbacine (3-norhimbacine) 2 was found to exhibit more potent muscarinic M(2) receptor binding affinity than natural 1.
[reaction: see text] Helical capsule-like assembly of [1(2).2(3)] shows a strong Cotton effect from the chirality transfer of the tartaric acid unit to tris(imidazoline) base through charged hydrogen bonds in aqueous solvent.
The dynamic solution behavior during formation of the 2'-deoxyguanosine tetrad (G-quartet) upon addition of alkali metal cations and destruction of the G-quartet upon addition of the guanine-guanine mismatch recognition molecule naphthyridine dimer was observed by cold-spray ionization mass spectrometry.
The crystal structures for three types of three-dimensional (3-D) hydrogen-bonded networks of hexakis(4-carbamoylphenyl)benzene (1), the network morphologies of which depend greatly on crystallization conditions, have been determined. When this compound is crystallized from hot DMSO, the resulting crystals, 1.12DMSO (orthorhombic, Pca2(1)), showed a 3-D hydrogen-bonded porous network (type A) via 1-D catemer chains as a hydrogen-bonding motif of six primary amide groups. The type A network creates chambers surrounded by six molecules of 1 and channels along the c axis to give the highest porosity among the network polymorphs of 1 investigated here. Crystallization from a boiling mixture of n-PrOH and water gave 1.6n-PrOH (monoclinic, P2(1)/c), which exhibits another type of 3-D hydrogen-bonded porous network (type B) via cyclic dimers as another hydrogen-bonding motif of six primary amide groups. The type B network leads to triangle-like channels along the a axis having a cross section of ca. 9.2 x 9.7 x 9.7 A (including van der Waals radii). The crystal structure of 1.H(2)O (monoclinic, P2(1)/c), which was produced under hydrothermal conditions, showed a nonporous 3-D hydrogen-bonded network chain of amide groups (type C) composed of a mixed hydrogen bonding motif of helical catemer chains/cyclic dimer/catemer. Solvent-induced topological isomerism of these 3-D hydrogen-bonded networks of 1 arises from (i) the guest inclusion ability based on a radially functionalized hexagonal structure of 1, (ii) the correlation between the hydrogen bond donor ability of the syn and anti protons of the primary amide group in host 1 and the hydrogen bond acceptor ability of the oxygen atoms of 1 and guest solvents, and (iii) the polarity of the bulk crystallization solvents.
Full details of our newly developed catalyses with asymmetric zinc complexes as mimics of class II zinc-containing aldolase are described. A Et(2)Zn/(S,S)-linked-BINOL complex was developed and successfully applied to direct catalytic asymmetric aldol reactions of hydroxyketones. A Et(2)Zn/(S,S)-linked-BINOL 1 = 2/1 system was initially developed, which efficiently promoted the direct aldol reaction of 2-hydroxy-2'-methoxyacetophenone (7d). Using 1 mol % of (S,S)-linked-BINOL 1 and 2 mol % of Et(2)Zn, we obtained 1,2-dihydroxyketones syn-selectively in high yield (up to 95%), good diastereomeric ratio (up to 97/3), and excellent enantiomeric excess (up to 99%). Mechanistic investigation of Et(2)Zn/(S,S)-linked-BINOL 1, including X-ray analysis, NMR analysis, cold spray ionization mass spectrometry (CSI-MS) analysis, and kinetic studies, provided new insight into the active oligomeric Zn/(S,S)-linked-BINOL 1/ketone 7d active species. On the basis of mechanistic investigations, a modified second generation Et(2)Zn/(S,S)-linked-BINOL 1 = 4/1 with molecular sieves 3A (MS 3A) system was developed as a much more effective catalyst system for the direct aldol reaction. As little as 0.1 mol % of (S,S)-linked-BINOL 1 and 0.4 mol % of Et(2)Zn promoted the direct aldol reaction smoothly, using only 1.1 equiv of 7d as a donor (substrate/ligand = 1000). This is the most efficient, in terms of catalyst loading, asymmetric catalyst for the direct catalytic asymmetric aldol reaction. Moreover, the Et(2)Zn/(S,S)-linked-BINOL 1 = 4/1 system was effective in the direct catalytic asymmetric aldol reaction of 2-hydroxy-2'-methoxypropiophenone (12), which afforded a chiral tetrasubstituted carbon center (tert-alcohol) in good yield (up to 97%) and ee (up to 97%), albeit in modest syn-selectivity. Newly developed (S,S)-sulfur-linked-BINOL 2 was also effective in the direct aldol reaction of 12. The Et(2)Zn/(S,S)-sulfur-linked-BINOL 2 = 4/1 system gave aldol adducts anti-selectively in good ee (up to 93%). Transformations of the aldol adducts into synthetically versatile intermediates were also described.
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Irradiation of a benzene solution of 3-cyano-2,6-dimethoxypyridine in the presence of ethyl vinyl ether (EVE) gave 1:1 photoadducts, 3-cyano-5-ethoxy-2,8-dimethoxy-4,5-dihydroazocine, in good yields, whose structure was established by X-ray single-crystal analysis. The photoadduct was produced via cycloaddition between the C3-C4 position of the pyridine derivatives and an alkene chromophore. On the other hand, 3-cyano-2,6-dimethoxy-4-methylpyridine cycloadds to EVE at the C2-C3 position of the pyridine ring upon irradiation. The difference is explained on the basis of the steric effect.
The construction of chirally twisted porphyrin-based molecular capsule 6 and polymeric capsule 8 was investigated by means of scanning electron microscopy (SEM) and (1)H NMR, UV-visible, and CD spectroscopic observations. Molecular capsule 6 and polymeric capsule 8 were constructed by the reaction of chiral cis-Pd(II) complex 4 bearing a (R)-(+)-2,2'-bis(diphenylphosphino)-1,1'-binaphthyl (BINAP) ligand with porphyrin 1 bearing four pyridyl groups and porphyrin 2 bearing eight pyridyl groups, respectively. The peak-splitting pattern of the beta-pyrrole protons in the (1)H NMR spectrum and the specific CD spectral pattern bearing an exciton coupling band indicate that both molecular capsule 6 and polymeric capsule 8 are chirally twisted. Moreover, it was found that the CD intensity of the polymeric capsule plotted against [4]/([4] + [3]) shows a sigmoidal curvature, reflecting a unique cooperativity among the ligand groups; that is, the ligand existing in excess over the other dominates the twisting direction. These results consistently demonstrate that "chirality" in these molecular assembly systems is conveniently controlled by the use of chiral ligands.
Reported here for the first time are the synthesis and characterization of supramolecular complexes between diaryl-lambda(3)-iodanes and 18-crown-6 (18C6). Slow evaporation of solvents afforded 1:1 and 2:1 complexes between Ph(2)IBF(4) and 18C6 as stable crystals, depending on the conditions. X-ray crystal structures of these complexes indicated that each iodine atom contacts with the three adjacent oxygen atoms of 18C6 through two hypervalent secondary bonding and a weak interaction. (1)H NMR analyses and CSI-MS spectra showed that, in dichloromethane solution, Ph(2)IBF(4) exclusively forms the 1:1 complex with 18C6 (binding constant K(a), 1.02 x 10(3) M(-)(1)). The binding constants decrease with the increased solvent donor ability (Gutmann's DN). Changing the heteroatom ligand from BF(4) to the less nucleophilic PF(6) and AsF(6) increased the binding constant by about six times. Substitution of an electron-withdrawing group onto the para position of Ph(2)IBF(4) tends to increase in the complex stability. A linear Hammett relationship (rho = 0.59) between log K(a) and sigma(p)(+) values of substituents indicates that the diaryl-lambda(3)-iodanes with electropositive iodine(III) interact more efficiently with 18C6. Decreased binding magnitude was measured with 15C5, dibenzo-18C6, dibenzo-21C7, and dibenzo-30C10.
The binding of a dimeric form of the 2-amino-1,8-naphthyridine derivative (naphthyridine dimer) to a human telomeric sequence, TTAGGG, was investigated by UV melting, CD spectra, and CSI-MS measurements. Both the 9-mer d(TTAGGGTTA) and the 15-mer d(TTAGGGTTAGGGTTA) showed apparent melting temperatures (T(m)) of 45.6 and 63.6 degrees C, respectively, in the presence of naphthyridine dimer (30 microM) in sodium cacodylate buffer (50 mM, pH 7.0) containing 100 mM NaCl. The CD spectra at 235 and 255 nm of the 9-mer increased in intensity accompanied with strong induced CDs at 285 and 340 nm upon complex formation with naphthyridine dimer. UV titration of the binding of naphthyridine dimer to the 9-mer at 320 nm showed a hypochromism of the spectra. A Scatchard plot of the data showed the presence of multiple binding sites with different association constants. Cold spray ionization mass spectrometry of the complex between naphthyridine dimer and the 9-mer clearly showed that one to three molecules of the ligand bound to the dimer duplex of the 9-mer. Telomeric repeat elongation assay showed that the binding of naphthyridine dimer to the telomeric sequence inhibits the elongation of the sequence by telomerase.
The reversible cross-catenation of two different coordination rings (Pd(II)- and Pt(II)-linked rings) has been achieved by using the labile nature of the Pd-N interaction and efficient hydrophobic contact between the rings.
A direct solution analysis method, cold-spray ionization (CSI) mass spectrometry (MS), a variant of electrospray (ESI) MS operating at low temperature (ca -80 to 10 degrees C), allows the facile and precise characterization of labile organic species, especially those in which non-covalent bonding interactions are prominent. We applied this method to investigations of the solution structures of many labile organic species, including unstable reagents and reaction intermediates, asymmetric catalysts, supramolecules and even primary biomolecules. Remarkable analytical results were obtained for highly ordered supramolecules using the CSI method. Whereas conventional ESI is not applicable to these compounds because of their instability to heat and/or air, CSI affords multiply charged molecular ions with many solvent molecules attached. Investigation of the constitution of Grignard reagents in solution is extremely challenging, but CSI-MS allowed us to identify one of the key structures in THF solution. Recently, this method was adopted for investigations of the solution structures of primary biomolecules such as nucleosides, amino acids, sugars and lipids, revealing singly charged Na(+) adducts of large clusters (chain structures), presumably linked by non-covalent interactions, including hydrogen bonding and/or hydrophobic interactions. The principle of the CSI method and applications of the method to a wide variety of labile organic species and primary biomolecules in solution are described.
Ten new alkaloids, lycoposerramines-F (1), -G (2), -H (3), -I (4), -J (5), -K (6), -L (7), -M (8), -N (9), and -O (10), having lycopodine-related structures, were isolated from the club moss Lycopodium serratum THUNB. and their structures were elucidated on the basis of spectroscopic analysis and/or chemical transformation.
The crystal structure of inclusion complex between ursodeoxycholic acid (UDCA), and phenanthrene has been determined. UDCA molecules formed hydrogen bond network to provide the channel structure along b axis, and phenanthrene molecules were accommodated in the cavity with a stoichiometry of 1 : 1 molar ratio. The channel structure observed in the UDCA-phenanthrene complex was significantly different from that of inclusion complex previously reported for deoxycholic acid (DCA) and cholic acid (CA). Because of the mesh-like hydrogen bond network, channel framework of UDCA could have less flexibility than that of DCA and CA. The difference of molecular state of phenanthrene was clearly observed in solid-state fluorescence measurement.
Multidimensional T1rho-, diffusion-filtered and diffusion-ordered NOESY techniques were applied to identify segments of a ligand binding with a protein receptor. These experiments can easily provide intermolecular NOEs of the complex, which are of great significance for characterizing the binding epitopes of a ligand. This information cannot be obtained by high-throughput 1D NMR experiments, used for determining the binding affinity, although multidimensional NMR experiments require more experiment time. The present results indicate that the current experiments using T1rho- and diffusion-edited techniques are very suitable for identifying segments of a ligand binding with a protein receptor in the drug discovery process.