Pattern enrichment analysis for phage selection of stapled peptide ligands

Phage display is the most widely used technique to discover de novo peptides that bind to target proteins. However, it is associated with some challenges such as compositional bias. In this study, to overcome these difficulties, we devised a ‘pattern enrichment analysis.’ In this method, two samples (one obtained by affinity selection, the other simply amplified without selection) are prepared, and the two sequence datasets read on next-generation sequencer are compared to find the three-residue pattern most enriched in the selected sample. This allows us to compare two sequence datasets with high coverage and facilitates the identification of peptide sequences and the key residues for binding. We also demonstrated that this approach in the combination with structured peptide libraries allowed spatial mapping of the enriched sequence patterns. Here, we prepared a phage library displaying chemically stapled helical peptides with the X₁C₂X₃X₄X₅X₆X₇X₈C₉X₁₀ sequence, where X is any amino acid. To validate our method, we performed screening against the HDM2 protein. The results showed that the hydrophobic residues (Phe, Tyr, Trp and Leu) that are key to interactions with HDM2 were clearly identified by the pattern enrichment analysis. We also performed selection targeting the SARS-CoV-2 spike RBD in the same manner. The results showed that similar patterns were enriched among the hit peptides that inhibited the protein–protein interaction.

To effectively identify helical peptide binders from a phage library, we developed “pattern enrichment analysis,” which finds the enriched three-residue patterns by comparison with a control sample.     

Pseudo-Binary Phase Diagram of LiNH2-MH (M = Na,K) Eutectic Mixture

The hunt for a cleaner energy carrier leads us to consider a source that produces no toxic byproducts. One of the targeted alternatives in this approach is hydrogen energy, which, unfortunately, suffers from a lack of efficient storage media. Solid-state hydrogen absorption systems, such as lithium amide (LiNH₂) systems, may store up to 6.5 weight percent hydrogen. However, the temperature of hydrogenation and dehydrogenation is too high for practical use. Various molar ratios of LiNH₂ with sodium hydride (NaH) and potassium hydride (KH) have been explored in this paper. The temperature of hydrogenation for LiNH₂ combined with KH and NaH was found to be substantially lower than the temperature of individual LiNH₂. This lower temperature operation of both LiNH₂-NaH and LiNH₂-KH systems was investigated in depth, and the eutectic melting phenomenon was observed. Systematic thermal studies of this amide-hydride system in different compositions were carried out, which enabled the plotting of a pseudo-binary phase diagram. The occurrence of eutectic interaction increased atomic mobility, which resulted in the kinetic modification followed by an increase in the reactivity of two materials. For these eutectic compositions, i.e., 0.15LiNH₂-0.85NaH and 0.25LiNH₂-0.75KH, the lowest melting temperature was found to be 307 °C and 235 °C, respectively. Morphological studies were used to investigate and present the detailed mechanism linked with this phenomenon.     

Enantioselective Protonation of Cyclic Carbonyl Ylides by Chiral Lewis Acid Assisted Alcohols

Chiral Lewis acid-catalyzed asymmetric alcohol addition reactions to cyclic carbonyl ylides generated from N-(α-diazocarbonyl)-2-oxazolidinones featuring a dual catalytic system are reported. Construction of a chiral quaternary heteroatom-substituted carbon center was accomplished in which the unique heterobicycles were obtained in good yields with high stereoselection. The alcohol adducts were successfully converted to optically active oxazolidine-2,4-diones by hydrolysis. Mechanistic studies by DFT calculations revealed that alcohols could be activated by Lewis acids, enabling enantioselective protonation of the carbonyl ylides.     

Evaluation of interfacial toughness curve of bimaterial in submicron scale

A novel method combining the experimental data at only two different mixed mode fractures and an empirical interface toughness function has been proposed to establish the interfacial toughness function of a bimaterial in submicron scale. The modified four-point bend specimen was used in experiment to evaluate the first type of mixed mode fracture, while the sandwiched cantilever specimen was employed to get the second one. An empirical interface toughness function reflecting quite accurately the delamination behavior was adopted as a typical one. The obtained results investigated that the proposed method could be used to calibrate not only the interfacial fracture criteria at pure modes but also at any mixed mode fracture of bimaterials in submicron scale.     

Identification of conjugation positions of urinary glucuronidated vitamin D3 metabolites by LC/ESI–MS/MS after conversion to MS/MS‐fragmentable derivatives

A liquid chromatography/electrospray ionization–tandem mass spectrometry‐based method was developed for the identification of the conjugation positions of the monoglucuronides of 25‐hydroxyvitamin D₃ [25(OH)D₃] and 24,25‐dihydroxyvitamin D₃ [24,25(OH)₂D₃] in human urine. The method employed derivatization with 4‐(4‐dimethylaminophenyl)‐1,2,4‐triazoline‐3,5‐dione to convert the glucuronides into fragmentable derivatives, which provided useful product ions for identifying the conjugation positions during the MS/MS. The derivatization also enhanced the assay sensitivity and specificity for urine sample analysis. The positional isomeric monoglucuronides, 25(OH)D₃‐3‐ and ‐25‐glucuronides, or 24,25(OH)₂D₃‐3‐, ‐24‐ and ‐25‐glucuronides, were completely separated from each other under the optimized LC conditions. Using this method, the conjugation positions were successfully determined to be the C3 and C24 positions for the glucuronidated 25(OH)D₃ and 24,25(OH)₂D₃, respectively. The 3‐glucuronide was not present for 24,25(OH)₂D₃, unlike 25(OH)D₃, thus we found that selective glucuronidation occurs at the C24‐hydroxy group for 24,25(OH)₂D₃.     

Combinatorial and approximative analyses in a spatially random division process

For a spatial characteristic, there exist commonly fat-tail frequency distributions of fragment-size and -mass of glass, areas enclosed by city roads, and pore size/volume in random packings. In order to give a new analytical approach for the distributions, we consider a simple model which constructs a fractal-like hierarchical network based on random divisions of rectangles. The stochastic process makes a Markov chain and corresponds to directional random walks with splitting into four particles. We derive a combinatorial analytical form and its continuous approximation for the distribution of rectangle areas, and numerically show a good fitting with the actual distribution in the averaging behavior of the divisions.     

Alloyed Tetranuclear Metal Chains of Pd4−nPtn (n=0–3) Scaffolded by a New Linear Tetraphosphine Containing a PNP Bridge

A new linear tetraphosphine containing a PNP phosphazane bridge, rac-bis[(diphenylphosphinomethyl)phenylphosphino]phenylamine (rac-dpmppan), was synthesized and utilized to support a series of Pd/Pt mixed metal tetranuclear chains, [Pd_4−nPt_n(μ-rac-dpmppan)₂(XylNC)₂](PF₆)₂ (XylNC=xylyl isocyanide; n=0: Pd₄ ( 1 ), 1: PtPd₃ ( 2 ), 2: PtPd₂Pt ( 3 ), 2: Pt₂Pd₂ ( 4 ), 3: Pt₂PdPt ( 5 )), in which the number and positions of additional Pt atoms were successfully controlled depending on the respective synthetic procedures using transformations from 1 to 3 through 2 and from 4 to 5 by redox-coupled exchange reactions. The ³¹P{¹H} NMR and ESI mass spectra and X-ray diffraction analyses revealed almost identical tetranuclear structures, with slight contraction of metal-metal bonds according to incorporation of Pt atoms. The electronic absorption spectra of 1 – 5 exhibited characteristic bands at 635–510 nm with an energy propensity depending on the number and positions of Pt centres, which were assigned to HOMO (dσ*σσ*) to LUMO (dσ*σ*σ*) transition by theoretical calculations. The present results demonstrated that the electronic structures of Pd/Pt mixed-metal tetranuclear complexes are finely tuned as orbital-overlapping alloyed metal chains by atomically precise Pt incorporation in the Pd₄ chain.