A straightforward approach to antibodies recognising cancer specific glycopeptidic neoepitopes

Aberrantly truncated immature O-glycosylation in proteins occurs in essentially all types of epithelial cancer cells, which was demonstrated to be a common feature of most adenocarcinomas and strongly associated with cancer proliferation and metastasis. Although extensive efforts have been made toward the development of anticancer antibodies targeting MUC1, one of the most studied mucins having cancer-relevant immature O-glycans, no anti-MUC1 antibody recognises carbohydrates and the proximal MUC1 peptide region, concurrently. Here we present a general strategy that allows for the creation of antibodies interacting specifically with glycopeptidic neoepitopes by using homogeneous synthetic MUC1 glycopeptides designed for the streamlined process of immunization, antibody screening, three-dimensional structure analysis, epitope mapping and biochemical analysis. The X-ray crystal structure of the anti-MUC1 monoclonal antibody SN-101 complexed with the antigenic glycopeptide provides for the first time evidence that SN-101 recognises specifically the essential epitope by forming multiple hydrogen bonds both with the proximal peptide and GalNAc linked to the threonine residue, concurrently. Remarkably, the structure of the MUC1 glycopeptide in complex with SN-101 is identical to its solution NMR structure, an extended conformation induced by site-specific glycosylation. We demonstrate that this method accelerates dramatically the development of a new class of designated antibodies targeting a variety of “dynamic neoepitopes” elaborated by disease-specific O-glycosylation in the immunodominant mucin domains and mucin-like sequences found in intrinsically disordered regions of many proteins.

We developed new class of designated antibodies targeting of “dynamic neoepitopes” elaborated by disease-specific O-glycosylation at the immunodominant mucin domains.     

Dynamic and static nature of activated interactions in transition states as elucidated by quantum theory of atoms-in-molecules dual functional analysis: A case of ligand exchange at the N of sulfonylimino-λ3-bromanes

A method to elucidate the dynamic and static natures of the activated interactions in transition states (TSs) is proposed using quantum theory of atoms-in-molecules (QTAIM) dual functional analysis (QTAIM-DFA). The natures are determined for the ligand exchange at the N of sulfonylimino-λ³-bromanes, RBr-*-N(SO₂CF₃)-*-X′R′ (R, R′ = Me or Ph, X′ = Br′ or I′). Asterisks (*) emphasize the presence of bond critical points within the interactions in question. While data from the optimized structures of TSs correspond to the static nature, those from the perturbed and optimized structures represent the dynamic nature. The nature of the interactions in Br-*-N-*-X′ calculated with QTAIM-DFA, using the perturbed structures generated using the normal coordinates for the imaginary frequencies (NIV), was very similar to that in trigonal bipyramidal adduct formation through charge transfer. The results with NIV were precisely the same as those obtained based on intrinsic reaction coordinate (IRC). The high applicability of QTAIM-DFA is demonstrated when analyzing the activated interactions in TSs.     

Fluidic shear-assisted formation of actuating multilamellar lipid tubes using microfabricated nozzle array device

Molecular self-assemblies exhibiting automatic motions have received much attention as potential artificial models of living organisms. We have developed a microfluidic picolitre nozzle-array device to form multilamellar lipid tubes (MLTs) under fluidic shear stress, which transformed into different two patterns (yarn-balls and double-helixes) and also exhibited unique self-actuation behaviors.     

Detection of interfacial phenomena with osteoblast-like cell adhesion on hydroxyapatite and oxidized polystyrene by the quartz crystal microbalance with dissipation

The adhesion process of osteoblast-like cells on hydroxyapatite (HAp) and oxidized polystyrene (PSox) was investigated using a quartz crystal microbalance with dissipation (QCM-D), confocal laser scanning microscope (CLSM), and atomic force microscope (AFM) techniques in order to clarify the interfacial phenomena between the surfaces and cells. The interfacial viscoelastic properties (shear viscosity (η(ad)), elastic shear modulus (μ(ad)), and tan δ) of the preadsorbed protein layer and the interface layer between the surfaces and cells were estimated using a Voigt-based viscoelastic model from the measured frequency (Δf) and dissipation shift (ΔD) curves. In the ΔD-Δf plots, the cell adhesion process on HAp was classified as (1) a mass increase only, (2) increases in both mass and ΔD, and (3) slight decreases in mass and ΔD. On PSox, only ΔD increases were observed, indicating that the adhesion behavior depended on the surface properties. The interfacial μ(ad) value between the material surfaces and cells increased with the number of adherent cells, whereas η(ad) and tanδ decreased slightly, irrespective of the surface. Thus, the interfacial layer changed the elasticity to viscosity with an increase in the number. The tan δ values on HAp were higher than those on PSox and exceeded 1.0. Furthermore, the pseudopod-like structures of the cells on HAp had periodic stripe patterns stained with a type I collagen antibody, whereas those on PSox had cell-membrane-like structures unstained with type I collagen. These results indicate that the interfacial layers on PSox and HAp exhibit elasticity and viscosity, respectively, indicating that the rearrangements of the extracellular matrix and cytoskeleton changes cause different cell-surface interactions. Therefore, the different cell adhesion process, interfacial viscoelasticity, and morphology depending on the surfaces were successfully monitored in situ and evaluated by the QCM-D technique combined with other techniques.     

Population study of sizes and components of self-reproducing giant multilamellar vesicles

Population analysis of a system of self-reproducing giant multilamellar vesicles (GMVs) was carried out by means of flow cytometry. The multidimensional distribution of forward light scattering (FS), side light scattering (SS), and fluorescence (FL) intensities originating from each GMV provided information about changes in a population composed of 104 vesicles. FS-FL dot plots indicated that, after the addition of the membrane precursor, the size distribution of the newly generated vesicles was nearly the same as that of the original, but the catalyst content was reduced. This result can be interpreted as evidence for the occurrence of the self-reproduction of GMVs. Moreover, the new GMVs recovered the amount of catalyst to the initial value, keeping their size distribution constant, when a solution of the catalyst was added to the new GMVs. These results are the first experimental evidence for a novel phenomenon on GMV size distribution during their self-reproducing cycle.     

Dinuclear macrocyclic palladium complexes having pincer coordinating groups and their catalytic properties in Mizoroki-Heck reactions

An improved synthetic method of palladium(II) dinuclear macrocyclic complexes have been described. Each of the two isomers of the complexes [Pd₂LBr₂] has a macrocyclic ligand L in which two 2,6-bis(diaminomethyl)phenyl units coordinate to the Pd(II) centers with N, C, N donor atoms. Substitution of the bromo ligands of one of the isomer of the complexes with acetonitrile ligands affords a new dinuclear complex. Catalytic activities of these complexes were studied for the Mizoroki-Heck type reactions of iodobenzene and styrene. High turnover number up to 30,000 was achieved using one of the isomer of the complexes.     

Multicomponent Molecular Orbital–Climbing Image–Nudged Elastic Band Method to Analyze Chemical Reactions Including Nuclear Quantum Effect

To analyze the H/D isotope effects on hydrogen transfer reactions in XHCHCHCHY?XCHCHCHYH (X, Y=O, NH, or CH₂) including the nuclear quantum effect of proton and deuteron, we propose a multicomponent molecular orbital‐climbing image‐nudged elastic band (MC_MO–CI–NEB) method. We obtain not only transition state structures but also minimum‐energy paths (MEPs) on the MC_MO effective potential energy surface by using MC_MO–CI–NEB method. We find that nuclear quantum effect affects not only stationary‐point geometries but also MEPs and electronic structures in the reactions. We clearly demonstrate the importance of including nuclear quantum effects for H/D isotope effect on rate constants (k_H/k_D).     

A series of luminescent Cu(I) mixed-ligand complexes containing 2,9-dimethyl-1,10-phenanthroline and simple diphosphine ligands

A series of Cu(I) mixed-ligand complexes containing dmp (2,9-dimethyl-1,10-phenanthroline) and one of simple diphosphine ligands (Ph2P(CH2)nPPh2) were prepared. Among the complexes, [Cu(dppp)(dmp)]PF6 (n=3) and [Cu2(dppb)2(dmp)2](PF6)2 (n=4) were characterized by X-ray structure analyses. The dppp complex has been characterized as a mononuclear complex, while [Cu2(dppb)2(dmp)2]2+ exists as a dinuclear complex in which two dppb ligands bridge between the two Cu(I) atoms. Although the distorted tetrahedral structures around the central metals of the two complexes are similar, the P-Cu-P angles are different between the two complexes. All of the series of complexes show photoluminescence in solution, and the intensity of the luminescence increases with n (n=2-4). The non-radiative rate constants of the complexes decrease markedly with n although radiative rate constants of the complexes are similar.     

Enhancement of Solar Hydrogen Evolution from Water by Surface Modification with CdS and TiO2 on Porous CuInS2 Photocathodes Prepared by an Electrodeposition–Sulfurization Method

Porous films of p‐type CuInS₂, prepared by sulfurization of electrodeposited metals, are surface‐modified with thin layers of CdS and TiO₂. This specific porous electrode evolved H₂ from photoelectrochemical water reduction under simulated sunlight. Modification with thin n‐type CdS and TiO₂ layers significantly increased the cathodic photocurrent and onset potential through the formation of a p–n junction on the surface. The modified photocathodes showed a relatively high efficiency and stable H₂ production under the present reaction conditions.     

Characterization of a mesophilic aliphatic-aromatic copolyester-degrading fungus

We isolated 5 mesophilic microorganisms that form clear zones around the colony on an opaque medium containing the aliphatic-aromatic copolyester poly(60 mol% butylene adipate-co-40 mol% butylene terephthalate) (PBAT). Among all strains, the fungal strain NKCM1712 degraded PBAT at the fastest rate (3.5 ± 0.3 μg cm⁻² h⁻¹). Genetic and morphological analyses revealed that this strain was closely related to Isaria fumosorosea (phylum Ascomycota). Mass spectroscopic analysis revealed that the degradation products were T, AB, TB, BAB, and ABT (T, terephthalic acid unit; A, adipic acid unit; B, 1,4-butanediol unit)] in the culture of the strain that used PBAT as the sole carbon source. Furthermore, the PBAT degradation ability of this strain in terms of BOD suggested that it could utilize the PBAT degradation products as growth substrates. This is the first report of a mesophilic strain that can mineralize an aliphatic-aromatic polyester into carbon dioxide on its own.