Mitsunobu Doi

Fumiquinazolines A–G, novel metabolites of a fungus separated from a Pseudolabrus marine fish

Seven new fumiquinazolines (FQs) A–G have been isolated from a strain of Aspergillus fumigatus originally separated from the marine fish Pseudolabrus japonicus, and their stereostructures and conformations have been established on the basis of spectral and X-ray analyses and some chemical transformations. All the compounds exhibited moderate cytotoxicity against cultured P388 cells.

Imidazole-4-acetic Acid–Picric Acid (1/1) Complex

In the crystal structure of 4-(carboxymethyl)imidazol-3-ium picrate, C 5 H 7 N 2 O 2 + .C 6 H 2 N 3 O 7 - , the imidazole N3 atom is protonated and contacts the deprotonated phenol and nitro O atoms of the picrate anion through a bifurcated hydrogen bond. The carboxy group of the 4-(carboxymethyl)imidazolium cation is in a neutral state and participates in dimer formation between centrosymmetrically related molecules through O...H-O hydrogen bonds. No significant stacking interaction is observed between the aromatic rings of the two molecules, indicating the superiority of the hydrogen-bonding ability of imidazole-4-acetic acid over the π-donating ability of picric acid.

Conformational change of ascidiacyclamide caused by asymmetric modification for an isoleucine residue: structural analyses of [Gly], [Leu], and [Phe]ascidiacyclamides by x-ray diffraction and NMR spectroscopy.

Ascidiacyclamide, a cytotoxic cyclic peptide from tunicate, is composed of unusual amino acids and has a repeated sequence, c[-thiazole-D-Val-oxazoline-L-Ile-]2 ([Ile]ASC). The symmetric chemical structure has been assumed to be correlated with the cytotoxicity, and it is reasonable to consider that the disturbance of its structure from the C2 symmetry results in the changes of conformation and activity. In order to quantitatively estimate the molecular conformation-activity relationship, an isoleucine residue was substituted by Gly, Leu, or Phe to disturb the C2 symmetry. The conformations of three derivatives were examined by nmr spectroscopy and the crystal structure of [Leu]ASC was also analyzed by x-ray diffraction method. The 1H-nmr experiments and the constrained molecular dynamics simulations showed the twisted figure 8 conformers for [Gly] and [Phe]ASCs and the square conformer for [Leu]ASC in the DMSO solution. The x-ray crystal analysis of [Leu]ASC also revealed the square form similar to the solution structure. On the other hand, their cytotoxic activities were measured using L1210 leukemia cells and were related with the bulkiness and/or hydrophobicity of the side chain of the substituted amino acid; [Phe] > or = [Ile] > [Leu] >> [Gly]ASCs. As an attempt to consider the correlation between the activity and conformer, the accessible surface area (ASA) was calculated for each derivative to estimate the size or bulkiness of its conformation. Although the ASAs of nmr structures were not directly related to the type of conformer (figure 8 or square form), it was an important probe to consider the cytotoxicity of each derivative.

A possible recognition mode of mRNA cap terminal structure by peptide: Cooperative stacking and hydrogen-bond pairing interactions between m7GpppA and Trp-Leu-Glu

1H-NMR and fluorescence spectroscopic studies on the interaction between the Trp-Leu-Glu and m7GpppA have shown a specific binding mode, in which the pi-pi stacking interaction of the Trp indole ring and the hydrogen-bond pairing of Glu carboxyl side group with 7-methylguanine base are simultaneously formed.

Cooperative stacking and hydrogen bond pairing interactions of fragment peptide in cap binding protein with mRNA cap structure

The stacking and hydrogen bonding abilities of Trp-(Gly)n-Glu (n = 0 approximately 3) for the interaction with 7-methylguanine (m7G) base were examined by fluorescence and 1H-NMR methods, and it was shown that they correlate with the distance between the Trp and Glu residues, and become most significant when both residues are separated from each other by two Gly residues (n = 2). Based on this insight, the sequence conserved between the human and yeast cap binding proteins (CBPs) was surveyed, and the sequence of Trp-Glu-Asp-Glu (No. 102-105 in human CBP) was selected as a probable site for the binding with mRNA cap structure. Thus, the stacking and hydrogen bonding abilities of Trp-Glu-Asp-Glu with m7G cap structure were examined by comparative experiments using its analogous peptides. The results showed that the fourth Glu residue is important not only for the construction of hydrogen bond pairing with m7G base but also for strengthening the stacking interaction between the Trp indole ring and m7G base. Taking account of the recognition analysis using the mutant CBP proteins by site-directed mutagenesis (Ueda, H., Iyo, H., Doi, M., Inoue, M., Ishida, T., Morioka, H., Tanaka, T., Nishikawa, S. and Uesugi, S. (1991) FEBS Lett. 280, 207-210), this cooperative interaction could be important for the recognition of mRNA cap structure.

Three‐dimensional structure of monoanionic methionine‐enkephalin: X‐ray structure of tert‐butyloxycarbonyl‐Tyr‐Gly‐Gly‐(4‐bromo)Phe‐Met‐OH

The conformation of tert‐butyloxycarbonyl‐Tyr‐Gly‐Gly‐(4‐bromo)Phe‐Met‐OH, as a monoanionic derivative of Met‐enkephalin, was elucidated by X‐ray crystal analysis. The molecule took an extended conformation which was bended at the Phe residue. The implication of the dimer formation caused by 4 intermolecular hydrogen bonds was discussed in the relation with the opiate receptor.

Dankasterone, a new class of cytotoxic steroid produced by a Gymnascella species from a marine sponge

Dankasterone, produced by a strain of Gymnascella dankaliensis from the marine sponge Halichondria japonica, is a novel class of steroid with significant cytotoxicity against tumour cells in culture.

Interaction of indole derivatives with biologically important aromatic compounds. Part 22. Importance of simultaneous co-operation of hydrogen-bond pairing and stacking interactions for recognition of guanine base by a peptide: X-ray crystal analysis of 7-methylguanosine-5′-phosphate–tryptophanylglutamic acid complex

As a model to investigate the mode of recognition of the base guanine by peptides and proteins, the crystal structure of the 7-methylguanosine-5′-phosphate–tryptophanylglutamic acid complex was analysed by X-ray diffraction; this is the first crystal structure determination of a peptide–nucleotide complex. The complex crystals are stabilized by extensive hydrogen-bond formation in which three independent water molecules per complex pair participate. Both molecules are joined by the coupled contributions of the triple hydrogen bonds between the guanine base and the peptide backbone chain and of the prominent stacking interactions between the guanine base and the tryptophan indole side-chain, suggesting the importance of the coupling of hydrogen bonding and stacking interactions for recognition of the base to occur.

Combination of Trp and Glu residues for recognition of mRNA cap structure : analysis of m7G base recognition site of human cap binding protein (IF-4E) by site-directed mutagenesis

Four mutants of the human cap binding protein (hCBP), in which Trp‐102, Glu‐103, Asp‐104 or Glu‐105 was changed to the aliphatic Leu or Ala, were prepared, and their cap binding abilities were examined. Cap binding abilities of two mutants. W102L (Trp‐102→Leu) and E105A (Glu‐105→Ala), were significantly decreased in comparison with the wild‐type hCBP. This result suggest that Trp‐102 and Glu‐105 are both necessary for the cap binding, and the most probable binding mode with the m7G of cap structure is the combination of the stacking by Trp‐102 and the hydrogen‐bond pairing by Glu‐105, as was already proposed from the model studies.

Prominent stacking interaction with aromatic amino acid by N-quarternization of nucleic acid base: X-ray crystallographic characteristics and biological implications

In order to investigate the mode of interaction between the N-quarternized cytosine base and the aromatic amino acid, the crystal structure of the 3-methyl-cytidine-5-monophosphate:tryptamine complex was analyzed by X-ray diffraction. The complex crystals were stabilized by extensive hydrogen bond formations in which eight independent water molecules per complex pair participated. A prominent stacking interaction, characterized by a parallel alignment of both rings with a separation distance of ca. 3.4 A, was observed between the cytosine base and the indole ring. Combining the present results with X-ray crystallographic data on the adenine--and guanine--aromatic amino acid interactions, we summarize the structural characteristics observed in the stacking interaction of the N-quarternized nucleic acid base with the aromatic amino acid and discuss their biological implications, especially in connection with the significance of N-protonation of nucleic acid base for selective recognition by protein.