Quantum mechanical calculations on phosphate hydrolysis reactions

Multiple biological processes are regulated by kinases and phosphatases. This study aims to provide nonenzymatic models for phosphorylation and dephosphorylation of serine, threonine, and tyrosine phosphate using ab initio guantum mechanical calculations. We reduce the problem to methyl phosphate hydrolysis to model serine/threonine, and the hydrolysis of phenyl phosphate to model the tyrosine. HF, B3LYP, and MP2 calculations with a 6‐31+G(d) basis set were employed. The effect of water as a catalyst was also analyzed. As expected, the activation energy barrier is lowered. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 43–51, 2000     

Jusanin,a New Flavonoid from Artemisia commutata with an In Silico Inhibitory Potential against the SARS-CoV-2 Main Protease

A new flavonoid, Jusanin, (1) has been isolated from the aerial parts of Artemisia commutata. The chemical structure of Jusanin has been elucidated using 1D, 2D NMR, and HR-Ms spectroscopic methods to be 5,2′,4′-trihydroxy-6,7,5′-trimethoxyflavone. Being new in nature, the inhibition potential of 1 has been estimated against SARS-CoV-2 using different in silico techniques. Firstly, molecular similarity and fingerprint studies have been conducted for Jusanin against co-crystallized ligands of eight different SARS-CoV-2 essential proteins. The studies indicated the similarity between 1 and X77, the co-crystallized ligand SARS-CoV-2 main protease (PDB ID: 6W63). To confirm the obtained results, a DFT study was carried out and indicated the similarity of (total energy, HOMO, LUMO, gap energy, and dipole moment) between 1 and X77. Accordingly, molecular docking studies of 1 against the target enzyme have been achieved and showed that 1 bonded correctly in the protein’s active site with a binding energy of −19.54 Kcal/mol. Additionally, in silico ADMET in addition to the toxicity evaluation of Jusanin against seven models have been preceded and indicated the general safety and the likeness of Jusanin to be a drug. Finally, molecular dynamics simulation studies were applied to investigate the dynamic behavior of the M^pro-Jusanin complex and confirmed the correct binding at 100 ns. In addition to 1, three other metabolites have been isolated and identified to be сapillartemisin A (2), methyl-3-[S-hydroxyprenyl]-cumarate (3), and β-sitosterol (4).     

Aqueous Stable Gold Nanostar/ZIF‐8 Nanocomposites for Light‐Triggered Release of Active Cargo Inside Living Cells

A plasmonic core–shell gold nanostar/zeolitic‐imidazolate‐framework‐8 (ZIF‐8) nanocomposite was developed for the thermoplasmonic‐driven release of encapsulated active molecules inside living cells. The nanocomposites were loaded, as a proof of concept, with bisbenzimide molecules as functional cargo and wrapped with an amphiphilic polymer that prevents ZIF‐8 degradation and bisbenzimide leaking in aqueous media or inside living cells. The demonstrated molecule‐release mechanism relies on the use of near‐IR light coupled to the plasmonic absorption of the core gold nanostars, which creates local temperature gradients and thus, bisbenzimide thermodiffusion. Confocal microscopy and surface‐enhanced Raman spectroscopy (SERS) were used to demonstrate bisbenzimide loading/leaking and near‐IR‐triggered cargo release inside cells, thereby leading to DNA staining.     

Analysis of amino acids in latent fingerprint residue by capillary electrophoresis‐mass spectrometry

The analysis of the chemical composition of fingerprints is important for the development and improvement of existing fingerprint enhancement techniques. This study demonstrates the first analysis of a latent fingerprint sample, using an optimized CE‐MS method. In total 12 amino acids were detected in the fingerprint sample. MS/MS fragmentation was used to provide additional identity confirmation, for which eight of the twelve detected amino acids generated confirmatory product ions. Nine amino acids were quantified and their relative abundances were consistent with previous studies with serine and glycine being the most abundant. The successful detection of amino acids from latent fingerprints demonstrates that CE‐MS is a potential future technique for further study of such compounds in fingerprint samples.     

A Conformationally Flexible Dinuclear PtII Complex with Differential Behavior of its Two States toward Quadruplex DNA

The reaction of tetrakis(pyridine‐2‐yl)pyrazine (tppz) with 2 equiv of (2,2′‐bpy)Pt^II in water yields two isomeric dinuclear cations, [{Pt(2,2′‐bpy)}₂(tppz)]⁴⁺, in which Pt coordination exclusively takes place through the two pairs of pyridine‐2‐yl nitrogen atoms. The two conformational isomers differ in their overall shape, with the formation of “Z” and “U” shapes, which are formed at 40 °C (Z isomer, 1 ) and under reflux conditions (U isomer, 2 ), respectively. X‐ray crystal‐structure analyses of the Z isomer, [{Pt(2,2′‐bpy)}₂(tppz)](PF₆)₄ ? 3 CHCl₃ ? 4 H₂O ( 1 a ), and of the U isomer, [{Pt(2,2′‐bpy)}₂](PF₆)₄ ? 2 CH₃CN ? 1.5 H₂O ( 2 a ), were carried out. Co‐crystallization of compound 2 with PtCl₂(2,2′‐bpy) yielded [{Pt(2,2′‐bpy)}₂(tppz)](BF₄)₄?[PtCl₂(2,2′‐bpy)] ? 4.5 H₂O ( 3 ), in which the PtCl₂(2,2′‐bpy) entity was sandwiched between the two 2,2′‐bpy faces of the U‐shaped cation ( 2 ). Quantum chemical calculations revealed that the U isomer was more stable than the Z isomer, both in the gas phase and in an aqueous environment. These two isomers display different affinities toward duplex DNA and human telomeric quadruplex DNA (Htelo), as concluded from CD spectroscopy and FID assays. Thus, the U isomer binds significantly more strongly to quadruplex DNA (DC₅₀=0.38 μM ) than the Z isomer (DC₅₀=8.50 μM ).     

Synthesis and characterization of chiral polyamides derived from glycine and (S)-5-amino-4-methoxypentanoic acid

Stereoregular, enantiomerically pure, chiral polyamides of the –AB– type, containing a natural (glycine) and a synthetic [(S)-5-amino-4-methoxypentanoic acid (AMP)] component have been prepared by the active ester polycondensation method. Thus, polyamide 7 was obtained by polycondensation of the conveniently activated H₂NGly–AMPCO₂R unit ( 6 ). In this reaction, 7 appeared accompanied by a considerable amount of cyclic (Gly–AMP)₂ ( 8 ), which makes the isolation and purification of 7 difficult. The formation of cyclic byproducts could be avoided by preparing and polymerizing the oligoamide H₂NGly–AMP–AMPCO₂R ( 11 ), which has the terminal carboxyl group activated as the pentachlorophenyl ester. The resulting polyamide ( 12 ) was obtained in 85% yield and free of macrolactams, such as 8 . The new polyamides 7 and 12 were characterized by elemental analysis and infrared and ¹H- and ¹³C-nuclear magnetic resonance spectroscopies. Thermal studies revealed that 12 is crystalline and yields films with spherulitic texture by slow evaporation of formic acid solutions. © 1998 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 36: 2741–2748, 1998