Analysis of serum from type II diabetes mellitus and diabetic complication using surface-enhanced Raman spectra (SERS)

In this paper, we show surface-enhanced Raman spectra (SERS) of serums from type II diabetes mellitus and diabetic complication (coronary disease, glaucoma and cerebral infarction), and analyze the SERS through the multivariate statistical methods of principal component analysis (PCA). In particular, we find that there exist many adenines in these serums, which maybe come from DNA (RNA) damage. The relative intensity of the band at 725±2 cm⁻¹ assigned to adenine is higher for patients than for the healthy volunteers; therefore, it can be used as an important ‘fingerprint’ in order to diagnose these diseases. It is also shown that serums from type II diabetes mellitus group, diabetic complication group and healthy volunteers group can be discriminated by PCA.     

Study of relaxation processes in polyethylene and polystyrene by positron annihilation

Relaxation processes in polyethylene (PE) and polystyrene (PS) were studied by positron annihilation technique. For PE, above the glass transition temperature, T_g, the size of free volumes and its concentration were increased by the micro-Brownian motion of molecules. For PS, local motions of molecules in backbone chains were found to start above 260 K. However, these local motions were suppressed by an interphenyl correlation. For both PE and PS, below 250–260 K, the formation probability of positronium atoms increased with decreasing temperature. This fact was assigned to the freezing in of the local motions of molecules. For PS, an onset of the local motions of molecules was observed above 100 K. These motions were expected to be associated with liberation of phenyl groups. © 1996 John Wiley & Sons, Inc.     

Fluorescent P-Hydroxyphosphole for Peptide Labeling through P-N Bond Formation

Synthesis of fluorescent P-hydroxybinaphtylphosphole-oxide or -sulfide was achieved by trapping a binaphtyl dianion with methyl dichlorophosphite or P-(N,N-diethylamino)dichlorophosphine, followed by oxidation or sulfuration of the P-center. After saponification or acid hydrolysis, the P-hydroxyphospholes were coupled to peptides using the coupling agent BOP, under the conditions required for the synthesis in solution or on a solid support. This new method was illustrated by the labeling of the JMV2959, a potent antagonist of the Growth Hormone Secretagogue Receptor type 1a (GHS−R1a). The labeled conjugates were used to characterize GHSR ligands by competition assays, based on Fluorescence Resonance Energy Transfer (FRET). Such P-hydroxyphosphole-oxide or -sulfide constitute a promising new class of compact fluorophores with large Stokes shift, for labeling biomolecules by grafting through the phosphorus atom.     

Nanoscale imaging of oxidized copper foil covered with chemical vapor deposition-grown graphene layers

Characterization of the geometrical and structural characteristics of oxidized Cu area in high resolution is crucial for tracking the change in morphology, exploring interactions between graphene layers and Cu substrates and revealing the mechanism for the orientation-dependent oxidation of Cu. Here, we reported experimental results on nanoscale imaging of natural oxidation of the polycrystalline Cu substrate coated by partial-coverage chemical vapor deposition (CVD)-grown graphene stored in dryer under ambient conditions for up to 10 months. Scanning electron microscope (SEM), together with atomic force microscope (AFM), Raman, and X-ray photoelectron spectroscopy (XPS), was used for systematically studying the morphological and compositional changes at nanoscale during oxidation. The appearance of oxidized Cu substrates could be unambiguously distinguished from the unoxidized regions based on their distinctly different morphologies in SEM images, and the underlying mechanism was discussed in detail. By analyzing a millimeter-seized polycrystalline Cu substrate, we found that the oxidation of polycrystalline Cu substrate depends sensitively on both orientation of graphene layers and Cu substrates. Furthermore, the time-dependent oxidation evolution of Cu substrate was also established, and the oxidation rate was readily determined. The findings reported here will have important implications for developing protection coatings for Cu.     

Reaction of α-haloester having internal double bond with the low-valent metal complex

The α-haloester having an internal double bond was allowed to react with a catalytic amount of Pd(PPh₃)₄ to afford a cyclized product in a fairly good yield and the same product was obtained by treatment with Pd(OAc)₂ to ketene silyl acetal.     

Molecular Recognition of Nucleic Acid Bases in Water by Hydrogen Bonding of Poly(vinyldiaminotriazine)

Poly(2-vinyl-4,6-diamino-1,3,5-triazine) efficiently binds nucleic acid bases and nucleosides in water by using complementary hydrogen bonding. The binding activity decreases in the order: U, T > A C, G. The corresponding monomer shows virtually no activity, indicating a predominant role of polymer effect for the molecular recognition in water.     

Comparison of Ferroptosis-Inhibitory Mechanisms between Ferrostatin-1 and Dietary Stilbenes (Piceatannol and Astringin)

Synthetic arylamines and dietary phytophenolics could inhibit ferroptosis, a recently discovered regulated cell death process. However, no study indicates whether their inhibitory mechanisms are inherently different. Herein, the ferroptosis-inhibitory mechanisms of selected ferrostatin-1 (Fer-1) and two dietary stilbenes (piceatannol and astringin) were compared. Cellular assays suggested that the ferroptosis-inhibitory and electron-transfer potential levels decreased as follows: Fer-1 >> piceatannol > astringin; however, the hydrogen-donating potential had an order different from that observed by the antioxidant experiments and quantum chemistry calculations. Quantum calculations suggested that Fer-1 has a much lower ionization potential than the two stilbenes, and the aromatic N-atoms were surrounded by the largest electron clouds. By comparison, the C4′O-H groups in the two stilbenes exhibited the lowest bond disassociation enthalpies. Finally, the three were found to produce corresponding dimer peaks through ultra-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry analysis. In conclusion, Fer-1 mainly depends on the electron transfer of aromatic N-atoms to construct a redox recycle. However, piceatannol and astringin preferentially donate hydrogen atoms at the 4′-OH position to mediate the conventional antioxidant mechanism that inhibits ferroptosis, and to ultimately form dimers. These results suggest that dietary phytophenols may be safer ferroptosis inhibitors for balancing normal and ferroptotic cells than arylamines with high electron-transfer potential.     

Automated discovery of noncovalent inhibitors of SARS-CoV-2 main protease by consensus Deep Docking of 40 billion small molecules

Recent explosive growth of ‘make-on-demand’ chemical libraries brought unprecedented opportunities but also significant challenges to the field of computer-aided drug discovery. To address this expansion of the accessible chemical universe, molecular docking needs to accurately rank billions of chemical structures, calling for the development of automated hit-selecting protocols to minimize human intervention and error. Herein, we report the development of an artificial intelligence-driven virtual screening pipeline that utilizes Deep Docking with Autodock GPU, Glide SP, FRED, ICM and QuickVina2 programs to screen 40 billion molecules against SARS-CoV-2 main protease (Mpro). This campaign returned a significant number of experimentally confirmed inhibitors of Mpro enzyme, and also enabled to benchmark the performance of twenty-eight hit-selecting strategies of various degrees of stringency and automation. These findings provide new starting scaffolds for hit-to-lead optimization campaigns against Mpro and encourage the development of fully automated end-to-end drug discovery protocols integrating machine learning and human expertise.

Deep learning-accelerated docking coupled with computational hit selection strategies enable the identification of inhibitors for the SARS-CoV-2 main protease from a chemical library of 40 billion small molecules.