Photo‐Cross‐Linked Small‐Molecule Microarrays as Chemical Genomic Tools for Dissecting Protein–Ligand Interactions

We have developed a unique photo‐cross‐linking approach for immobilizing a variety of small molecules in a functional‐group‐independent manner. Our approach depends on the reactivity of the carbene species generated from trifluoromethylaryldiazirine upon UV irradiation. It was demonstrated in model experiments that the photogenerated carbenes were able to react with every small molecule tested, and they produced multiple conjugates in most cases. It was also found in on‐array immobilization experiments that various small molecules were immobilized, and the immobilized small molecules retained their ability to interact with their binding proteins. With this approach, photo‐cross‐linked microarrays of about 2000 natural products and drugs were constructed. This photo‐cross‐linked microarray format was found to be useful not merely for ligand screening but also to study the structure–activity relationship, that is, the relationship between the structural motif (or pharmacophore) found in small molecules and its binding affinity toward a protein, by taking advantage of the nonselective nature of the photo‐cross‐linking process.     

Synthesis of Δ-OPC-8:0 and OPC-6:0

CuCN-catalyzed reaction of the (1R)-isomer of 4-cyclopentene-1,3-diol monoacetate with TBDPSO(CH₂)₆MgCl produced an S_N2-type product regioselectively in high yield. Mitsunobu inversion of the product and subsequent Claisen rearrangement furnished aldehyde with the two side chains, from which the title compounds were synthesized efficiently.     

Synthesis of poly(epsilon-lysine)-grafted dextrans and their pH- and thermosensitive hydrogelation with cyclodextrins.

To give pH sensitivity to a thermoreversible supramolecular-structured hydrogel system, poly(epsilon-lysine) (PL), as a cationic polymer, was grafted to dextran and used for inclusion complexation with alpha-cyclodextrins (alpha-CDs). The synthesized graft copolymer was characterized by 1H NMR spectroscopy, and the hydrogel formation was confirmed by X-ray diffraction and solid-state 13C NMR analysis. The hydrogelation was induced from a phase-separated structure of hydrated dextrans and hydrophobically aggregated inclusion complexes in buffer solution at pH 10.0. The prepared hydrogels showed thermoreversible gel-sol transitions as well as pH-sensitive phase transitions, which were recorded by the changes in UV/Vis transmittance. A rapid phase transition from gel to sol was observed upon decreasing the pH value to 4.0, which resulted from the dissociation process between the protonated guest polymer and alpha-CDs. The stimuli-responsive physical properties of the hydrogels were improved by modulating the degree of substitution of the grafted PL and the combination with alpha-CDs.     

On the radiation-induced polyaddition of bisperfluoroisopropenyl terephthalate with 1,4-dioxane

Radical polyaddition of bis(α-trifluoromethyl-β,β-difluorovinyl)terephthalate [CF₂C(CF₃)OCOC₆H₄COOC(CF₃)CF₂] (BFP) with 1,4-dioxane (DOX) afforded higher molecular weight polymers under γ-rays radiation from a source when compared to those yielded by benzoyl peroxide initiation. More detailed study on the radiation-induced polyaddition of BFP with DOX and optimization of the reaction conditions were carried out. It was necessary to irradiate with doses of 2000, 1500, and 750 kGy, to obtain quantitative conversion of BFP at the feed molar ratios DOX/BFP of 8.0, 16, and 32, respectively. Step-growth polymerization mechanism was suggested by the measurements of molecular weights of the polymers obtained with several irradiation doses. It was concluded that the molecular weight of the polymer could be controlled by the feed molar ratio of DOX/BFP and irradiation doses. The steep increase of molecular weight was observed at the feed molar ratio of DOX/BFP of 8.0 with the irradiation doses above 2000 kGy and the polymer with the weight-average molecular weight of 2.36×10⁴ was obtained with the dose of 3000 kGy. The reaction between polymers might take place after the quantitative conversion of BFP. Radiation-induced radical polyaddition mechanism of BFP with DOX was proposed.     

Synthesis of Diblock Copolymers With Cellulose Derivatives. 2. Characterization and Thermal Properties of Cellulose Triacetate-Block-Oligoamide-15

Well-defined A-block-B type cellulose derivatives consisting of cellulose triacetate (CTA) and oligoamide-15 were synthesized. Chemical structures of the diblock copolymers were characterized by MALDI-TOF MS, ¹H-NMR, and GPC. Influence of length of CTA and oligoamide-15 segments on their thermal properties was investigated by means of differential scanning calorimetry (DSC). All diblock copolymers displayed T _g, T _c, and T _m transition temperatures. Their T _g and T _m values increased with the increase of molecular weight of CTA segment. The crystallinity of diblock copolymers increased after isothermal crystallization at 200 °C. Its X-ray analysis revealed that the diblock copolymer had CTA II crystal structure. Thermal analysis supported microphase separation between CTA and oligoamide-15 segments at room temperature, because T _g and T _m values of polyamide-15 are −7 °C and 170–180 °C, respectively.     

Stereochemical revision of communiols D and H through synthesis

Based on the previously revised stereochemistries for communiols A-C, the ent-8-epi- and ent-6-epi-stereoisomers of the original structures proposed for communiols D and H, respectively, were synthesized as highly probable candidates for their genuine structures by using the Sharpless asymmetric dihydroxylation as the source of chirality. Complete accord in spectral properties between each synthetic candidate and the corresponding natural material as well as the fact that communiols A-D and H were all isolated from the same fungal source, led us to the conclusion that the stereochemistries of communiols D and H should also be revised to their (3S,5S,7R,8S,11R)- and (5S,7R,8S)-forms, respectively.     

Synthesis, liquid-crystalline properties, and supramolecular nanostructures of dendronized poly(isocyanide)s and their precursors

A series of novel dendronized pi-conjugated poly(isocyanide)s were synthesized successfully by using a Pd-Pt mu-ethynediyl dinuclear complex ([ClPt{P(C2H5)3}2C[triple bond]CPt{P(C2H5)3}2Cl]) as the initiator. The polymerizations of the dendronized monomers follow first-order kinetics, indicating that living polymerization takes place. The obtained polymers exhibit narrow polydispersities in the range of 1.03-1.20. Thermal properties of the poly(isocyanide)s as well as their isocyanide monomers and precursors with formamido (HCONH-) moieties as apexes were investigated by using differential scanning calorimetry (DSC), polarized optical microscopy (POM) and wide-angle X-ray diffraction (WAXD). Both the peripheries and the apex groups of the dendrons affect the formation of supramolecular column and/or cubic phases of the precursors and monomers. The formamido precursor forms a liquid-crystalline phase due to intermolecular hydrogen bonding. The isocyanide monomer lacks this hydrogen-bonding ability and does not display an organized mesophase. All of the rigid poly(isocyanide)s with the monodendrons exhibit columnar liquid-crystalline phases. Interestingly, cylindrical structures of a poly(isocyanide) were directly visualized by using transmission electron microscopy (TEM).     

Effect of chlorosilanes on the radical polymerization of styrene and methyl methacrylate

Styrene (St) and methyl methacrylate (MMA) were polymerized by azobisisobutyronitrile at 50°C. in the presence of silanes such as tetramethylsilane, trimethylcholorosilane, dimethyldichlorosilane, methyltrichlorosilane, and tetrachlorosilane. The polymerization rates of both St and MMA in the presence of silanes were nearly equal to those in the absence of silanes. On the other hand, the molecular weights decreased gradually as the concentration of chlorosilane increased. The chain transfer constants of all the silanes in the polymerization of St and MMA at 50°C. were calculated by Mayo's equation. The chain transfer constants of Me₄Si, Me₃SiCl, Me₂SiCl, MeSiCl₃, and SiCl₄ were 0.31 × 10^?3, 1.25 × 10^?3, 1.78 × 10^?3, 1.92 × 10^?3, and 2.0 × 10^?3, for St and 0.13 × 10^?3, 0.22 × 10^?3, 0.245 × 10^?3, 0.27 × 10^?3, and 0.30 × 10^?3, for MMA, respectively. From these results, it was found that the Si? Cl bond was radically cleaved. The Q_tr values of the silanes, in the same order as above, were found to be 1.03 × 10^?4, 2.33 × 10^?4, 2.83 × 10^?4, 3.10 × 10^?4, and 3.35 × 10^?4, respectively and the e_tr values were +0.58, +1.30, +1.50, +1.48, and +1.43, respectively.     

Ab initio quantum mechanical study of the binding energies of human estrogen receptor alpha with its ligands: an application of fragment molecular orbital method

We have theoretically examined the relative binding affinities (RBA) of typical ligands, 17beta-estradiol (EST), 17alpha-estradiol (ESTA), genistein (GEN), raloxifene (RAL), 4-hydroxytamoxifen (OHT), tamoxifen (TAM), clomifene (CLO), 4-hydroxyclomifene (OHC), diethylstilbestrol (DES), bisphenol A (BISA), and bisphenol F (BISF), to the alpha-subtype of the human estrogen receptor ligand-binding domain (hERalpha LBD), by calculating their binding energies. The ab initio fragment molecular orbital (FMO) method, which we have recently proposed for the calculations of macromolecules such as proteins, was applied at the HF/STO-3G level. The receptor protein was primarily modeled by 50 amino acid residues surrounding the ligand. The number of atoms in these model complexes is about 850, including hydrogen atoms. For the complexes with EST, RAL, OHT, and DES, the binding energies were calculated again with the entire ERalphaLBD consisting of 241 residues or about 4000 atoms. No significant difference was found in the calculated binding energies between the model and the real protein complexes. This indicates that the binding between the protein and its ligands is well characterized by the model protein with the 50 residues. The calculated binding energies relative to EST were very well correlated with the experimental RBA (the correlation coefficient r=0.837) for the ligands studied in this work. We also found that the charge transfer between ER and ligands is significant on ER-ligand binding. To our knowledge, this is the first achievement of ab initio quantum mechanical calculations of large molecules such as the entire ERalphaLBD protein.     

Crystallization of carboxylic acid salts in poly(ethylene oxide) oligomers at higher temperatures

Many alkali metal carboxylates when dissolved in poly(ethylene oxide) (PEO) oligomers, are phaseseparated by heating. These were revealed to be the crystals of the initially dissolved corresponding salts from the X-ray diffraction patterns. Some acetate salts achieve the lower limit of the lattice energy for phase separation of ordinary inorganic salts by heating in PEO oligomers. These carboxylate salts were therefore expected to show crystallization behavior in PEO oligomers by heating. The effects of cation size, alkyl chain length and molecular weight of PEO on the solubility are summarized. Negative temperature dependence of solubility of these acetate salts is seen in the PEO oligomers only when the salts have long alkyl chains. The salts containing larger cations needed a longer chain length of PEOs for crystallization by heating. These salts with longer alkyl chains showed positive temperautred dependence in lower molecular weight polyethers, but negative temperature dependence in solubility in PEO with molecular weights higher than 400. In PEO₄₀₀, all the carboxylates with longer alkyl chains were phase separated by heating.