Vibrational spectroscopic encoding of polystyrene-based resin beads: converting the encoding peaks into barcodes

A detailed approach is described for the vibrational spectroscopic encoding of polystyrene-based resin beads by converting the infrared absorption peaks suitable for encoding (encoding peaks) into barcodes. Based on combining the FT-IR measurements and the quantum-chemical computations, the vibrational characteristics of p-tert-butylstyrene monomer, polystyrene and poly(p-tert-butylstyrene) resin beads are analyzed, which are helpful for the selection of encoding peaks. The vibrational spectroscopic encoding of polystyrene-based resin beads could be obtained by converting the wavenumber, intensity and full width at half maximum (FWHM) of the encoding peaks into barcodes automatically through a computer program designed in our laboratory.     

Computational combinatorial ligand design: Application to human α-thrombin

Summary A new method is presented for computer-aided ligand design by combinatorial selection of fragments that bind favorably to a macromolecular target of known three-dimensional structure. Firstly, the multiple-copy simultaneous-search procedure (MCSS) is used to exhaustively search for optimal positions and orientations of functional groups on the surface of the macromolecule (enzyme or receptor fragment). The MCSS minima are then sorted according to an approximated binding free energy, whose solvation component is expressed as a sum of separate electrostatic and nonpolar contributions. The electrostatic solvation energy is calculated by the numerical solution of the linearized Poisson-Boltzmann equation, while the nonpolar contribution to the binding free energy is assumed to be proportional to the loss in solvent-accessible surface area. The program developed for computational combinatorial ligand design (CCLD) allows the fast and automatic generation of a multitude of highly diverse compounds, by connecting in a combinatorial fashion the functional groups in their minimized positions. The fragments are linked as two atoms may be either fused, or connected by a covalent bond or a small linker unit. To avoid the combinatorial explosion problem, pruning of the growing ligand is performed according to the average value of the approximated binding free energy of its fragments. The method is illustrated here by constructing candidate ligands for the active site of human -thrombin. The MCSS minima with favorable binding free energy reproduce the interaction patterns of known inhibitors. Starting from these fragments, CCLD generates a set of compounds that are closely related to high-affinity thrombin inhibitors. In addition, putative ligands with novel binding motifs are suggested. Probable implications of the MCSS-CCLD approach for the evolving scenario of drug discovery are discussed.     

Antimicrobial and anticancer activities of Schiff base ligand and its transition metal mixed ligand complexes with heterocyclic base

A new Schiff base ligand (HL) was prepared via a condensation reaction of quinoline‐2‐carboxaldhyde with 2‐aminophenol in a molar ratio of 1:1. Its transition metal mixed ligand complexes with 1,10‐phenanthroline (1,10‐phen) as co‐ligand were also synthesized in a 1:1:1 ratio. HL and its mixed ligand complexes were characterized using elemental analysis, infrared, ¹H NMR, mass and UV–visible spectroscopies, molar conductance, magnetic measurements, solid reflectance, thermal analysis, electron spin resonance and X‐ray diffraction. Molar conductance measurements showed that all complexes have an electrolytic nature, except Cd(II) complex. From elemental and spectral data, the formulae [M(L)(1,10‐phen)(H₂O)]Cl_x?nH₂O (where M = Cr(III) (x = n = 2), Mn(II) and Ni(II) (x = 1, n = 2), Fe(III) (x = n = 2), Co(II), Cu(II) and Zn(II) (x = 1, n = 2)) and [Cd(L)(1,10‐phen)Cl]?3H₂O for the metal complexes have been proposed. The geometric structures of complexes were found to be octahedral. Powder X‐ray diffraction reflected the crystalline nature of the complexes; however, the Schiff base is amorphous. HL and its mixed ligand complexes were screened against Gram‐positive bacteria (Streptococcus pneumoniae and Bacillus subtilis) and Gram‐negative bacteria (Pseudomonas aeruginosa and Escherichia coli). Antifungal activity was determined against Aspergillus fumigatus and Candida albicans, the data showing that most complexes had activity less than that of the Schiff base while Mn(II), Fe(III) and Ni(II) complexes showed no significant antifungal activity. The anticancer activity of HL and its metal complexes was also studied against breast and colon cell lines. The metal complexes showed IC₅₀ higher than that of HL, especially the Cu(II) complex which showed the highest IC₅₀ against breast cell line.     

Detection and recognition of cancer cells in vivo

A fundamentally new recognition method of bio-objects (e.g., cancer cells as the most important case of them) that escape the immune system supervision control is suggested. It is proposed to use a unified complex consisting of several molecular groups (e.g., antibodies or their fragments) bound with each other. Binding targets are localized on the surface of this bio-object. The choice of the targets is determined by antigen profiling being expressed on the surface of these bio-objects. The recognition efficiency appears to be notably higher than in a situation when molecular groups do not form a unified complex and act separately.     

Synthesis and bioactivity evaluation of eugenol hybrids obtained by Mannich and 1,3 dipolar cycloaddition reactions

Design, synthesis, and bioactivity evaluation of novel mannich bases ( 2a-2j ) and triazole-chalcone derivatives ( 7a-7k ) of Eugenol 1 were reported. Among all the derivatives tested for antiproliferative activity, di-amine manich derivative 2b (32.92 μM), and 4-methoxy chalcone triazole derivative 7d (33.05 μM) significantly inhibited HepG2 cell lines when compared to the standard doxorubicin (37.29 μM). Whereas most of the compounds such as diethylamine 2a (17.75 μM), (aminomethyl) methane diamine 2b (17.02 μM), and bis (chloromethyl) amine 2c (20.12 μM) showed moderate to better inhibition towards MCF-7 cell lines. The synthesized analogues were also tested for antidiabetic and antiobesity potentials. Compounds 2f (55.50%), 2c (54.34%), 7g (55.5%), and 2a (55.5%) have shown moderate inhibitory potentials toward intestinal α-glucosidase enzyme when compared to the standard Acarbose (72.86%). Likewise, compounds 7d (82.95%), 7f (76.19%), 7g (74.81%), 7e (74.81%), and 2g (72.50%) have shown significant to moderate inhibitory potentials toward Pancreatic lipase enzyme when compared to the standard orlistat (91.10%). ROS induces life-threatening diseases like diabetes, cancer, etc., and antioxidants play a major role in controlling their production. Compounds 2c (99.81%), 2i (99.80%), 2d (99.26%), 2g (98.79%), and 2f (98.42%) have shown significant antioxidant profiles in ABTS assay when compared to the standard Trolox (99.07%). Further, In silico Molecular docking and pharmacokinetic screening of the eugenol derivatives complemented the in vitro results indicating the drug likeness of the obtained active compounds.     

Silver(I)‐N‐heterocyclic carbene complexes of bis‐imidazol‐2‐ylidenes having different aromatic‐spacers: synthesis,crystal structure,and in vitro antimicrobial and anticancer studies

A series of Ag(I) complexes ( 6 , 7 , 8 , 9 ) derived from imidazol‐2‐ylidenes was synthesized by reacting Ag₂O with an o‐, m‐, p‐xylyl or 1,3,5‐triazine‐linked imidazolium salts ( 1 , 2 , 3 , 4 ) and then characterizing these using various spectro‐analytical techniques. Additionally, triazine‐linked bis‐imidazolium salt 5 was characterized using the single‐crystal X‐ray diffraction method. Complexes 6–9 were formed from the N‐heterocyclic carbene ligand precursors 1–3 as PF₆^‐ salts in good yields. Conversely, salt 5 does not form Ag(I) complex even under various reaction conditions. Using ampicillin as a standard, complexes 6–9 were tested against bacteria strains Escherichia coli and Staphylococcus aureus as Gram‐negative and Gram‐positive bacteria, respectively, showing potent antimicrobial activities against the tested bacteria even at minimum inhibition concentration and bacterial concentration levels. Furthermore, the potential anticancer activities of the reported complexes were evaluated against the human colorectal cancer (HCT 116) cell lines, using 5‐fluorouracil as a standard drug. The highest anticancer activities were observed for complex 8 with an IC₅₀ value of 3.4 μm , whereas the lowest was observed for complex 9 with an IC₅₀ value of 18.1 μm . Copyright © 2013 John Wiley & Sons, Ltd.     

Effect of deuteron density distribution on the deduction of screening potential from the D(d,p)T reaction in Be metals

The D(d,p)T reaction in Be metal environments has been measured to investigate the electron screening effect in metals in an energy region of from 5.5 keV to 10 keV in a center of mass system(CMS)at a temperature of 121 K.The depth distribution of deuteron density in Be metals has an impact on the observed reaction yields.A model of deuteron density distribution in metal has been proposed to obtain the original yields.A screening energy of(116±46)eV has been obtained with the assumed deuteron density distribution model.     

stk: A python toolkit for supramolecular assembly

A tool for the automated assembly, molecular optimization and property calculation of supramolecular materials is presented. stk is a modular, extensible and open‐source Python library that provides a simple Python API and integration with third party computational codes. stk currently supports the construction of linear polymers, small linear oligomers, organic cages in multiple topologies and covalent organic frameworks (COFs) in multiple framework topologies, but is designed to be easy to extend to new, unrelated, supramolecules or new topologies. Extension to metal–organic frameworks (MOFs), metallocycles or supramolecules, such as catenanes, would be straightforward. Through integration with third party codes, stk offers the user the opportunity to explore the potential energy landscape of the assembled supramolecule and then calculate the supramolecule's structural features and properties. stk provides support for high‐throughput screening of large batches of supramolecules at a time. The source code of the program can be found at https://github.com/supramolecular-toolkit/stk . © 2018 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.     

A mixed-ligand approach for building a N-rich porous metal-organic framework for drug release and anticancer activity against oral squamous cell carcinoma

Abstract

A new Zn(II) metal-organic framework (MOFs), [Zn(BTC)(HME)]·(DMAc)(H₂O) (1, H₃BTC =1,3,5-benzenetricarboxylic acid, HME?=?protonated melamine, DMAc?=?N,N-dimethylacetamide), has been synthesized under solvothermal conditions. In the structure of 1, the four-coordinate Zn(II) ions are connected by BTC^3? ligands into a 3-D framework with (3)-connected utg-type topology. This MOF shows permanent porosity after lattice solvent removal with a calculated pore size distribution around 0.72?nm. With abundant N-donor sites and suitable pore size, the desolvated 1 (1a) was used as a drug carrier for the loading of anticancer drug 5-fluorouracil (5-Fu) molecules. Moderate 5-Fu loading capacity and long drug release time were observed for 1a. The computational simulation results reveal that strong H-bond interactions between the 5-Fu molecules and the nitrogen sites allow slow release of the drug 1a. In addition, the in vitro cytotoxicity of 1 and 5-Fu loaded 1a were also evaluated using MTT assays against human oral squamous cell carcinoma (SCC-251 and HSC-4).