Metal-assisted red light-induced DNA cleavage by ternary l-methionine copper(ii) complexes of planar heterocyclic bases

Antimicrobial screening involving Helicobacter pylori of nano-therapeutic compounds based on the amoxicillin antibiotic drug

Nano-structure Cu(II) complex [Cu(AMAB)2 ]Cl2 with Schiff base (AMAB) derived from the condensation between 4-(dimethylamino)benzaldehyde and amoxicillin trihydrate was prepared. (AMAB) Schiff base and its Cu(II) complex were identified and confirmed by different physicochemical techniques. The Schiff base (AMAB) was coordinated to copper ion through carbonyl oxygen and imine nitrogen donor sites. X-ray powder diffraction shows a cubic crystal system of the Cu(II) complex. The density functional theory was used to optimize the structure geometries of the investigated compounds. The molecular docking of the active amino acids of the investigated proteins' interactions with the tested compounds was evaluated. The bactericidal or bacteriostatic effect of the compounds was screened against some bacterial strains. The activity of Cu-chelate against Gram-negative bacteria was mainly more effective than its (AMAB) ligand and vice versa in the case of Gram-positive bacteria. The biological activity of the prepared compounds with biomolecules calf thymus DNA (CT-DNA) was determined by electronic absorption spectra and DNA gel electrophoresis technique. All studies revealed that the Cu-chelate derivative exhibited better binding affinity to both CT-DNA than the AMAB and amoxicillin itself. The anti-inflammatory effect of the designed compounds was determined by testing their protein denaturation inhibitory activity spectrophotometrically. All obtained data supported that the designed nano-Cu(II) complex with Schiff base (AMAB) is a potent bactericide against H. pylori, and exhibits anti-inflammatory activity. The dual inhibition effects of the designed compound represent a modern therapeutic approach with extended spectrum of action. Therefore, it can act as good drug target in antimicrobial and anti-inflammtory therapies. Finally, H. pylori resistance to amoxicillin is absent or rare in many countries, thus amoxicillin nanoparticles may be beneficial for countries where amoxicillin resistance is reported.

Reusable nano-catalyzed green protocols for the synthesis of quinoxalines: an overview

Heterocyclic compounds are very widely distributed in nature and are essential for life activities. They play a vital role in the metabolism of all living cells, for example, vitamins and co-enzyme precursors thiamine, riboflavin etc. Quinoxalines are a class of N-heterocycles that are present in a variety of natural and synthetic compounds. The distinct pharmacological activities of quinoxalines have attracted medicinal chemists considerably over the past few decades. Quinoxaline-based compounds possess extensive potential applications as medicinal drugs, presently; more than fifteen drugs are available for the treatment of different diseases. Diverse synthetic protocols have been developed via a one-pot approach using efficient catalysts, reagents, and nano-composites/nanocatalysts etc. But the use of homogeneous and transition metal-based catalysts suffers some demerits such as low atom economy, recovery of catalysts, harsh reaction conditions, extended reaction period, expensive catalysts, the formation of by-products, and unsatisfactory yield of products as well as toxic solvents. These drawbacks have shifted the attention of chemists/researchers to develop green and efficient protocols for synthesizing quinoxaline derivatives. In this context, many efficient methods have been developed for the synthesis of quinoxalines using nanocatalysts or nanostructures. In this review, we have summarized the recent progress (till 2023) in the nano-catalyzed synthesis of quinoxalines using condensation of o-phenylenediamine with diketone/other reagents with plausible mechanistic details. With this review, we hope that some more efficient ways of synthesizing quinoxalines can be developed by synthetic chemists.

Visible-Light-Mediated Modification and Manipulation of Biomacromolecules

Chemically modified biomacromolecules-i.e., proteins, nucleic acids, glycans, and lipids-have become crucial tools in chemical biology. They are extensively used not only to elucidate cellular processes but also in industrial applications, particularly in the context of biopharmaceuticals. In order to enable maximum scope for optimization, it is pivotal to have a diverse array of biomacromolecule modification methods at one's disposal. Chemistry has driven many significant advances in this area, and especially recently, numerous novel visible-light-induced photochemical approaches have emerged. In these reactions, light serves as an external source of energy, enabling access to highly reactive intermediates under exceedingly mild conditions and with exquisite spatiotemporal control. While UV-induced transformations on biomacromolecules date back decades, visible light has the unmistakable advantage of being considerably more biocompatible, and a spectrum of visible-light-driven methods is now available, chiefly for proteins and nucleic acids. This review will discuss modifications of native functional groups (FGs), including functionalization, labeling, and cross-linking techniques as well as the utility of oxidative degradation mediated by photochemically generated reactive oxygen species. Furthermore, transformations at non-native, bioorthogonal FGs on biomacromolecules will be addressed, including photoclick chemistry and DNA-encoded library synthesis as well as methods that allow manipulation of the activity of a biomacromolecule.

Insights into the crystal structure of two newly synthesized quinoxalines derivatives as potent inhibitor for c-Jun N-terminal kinases

Two new compounds namely, ethyl (2E)-3-(dimethylamino)-2-(3-methoxyquinoxalin-2-yl)propen-2-enoate (II) and ethyl 2-(3-oxo-4-(prop-2-yn-1-yl)-3,4-dihydroquinoxalin-2-yl)-3-phenylpropanoate (III) have been synthesized from ethyl 2-(oxo-3,4-dihydroquinoxalin-2-yl) acetate (I). The compounds were characterized using NMR (¹H and ¹³C), Fourier transform infrared and confirmed by single crystal X-ray diffraction studies. The quinoxaline portion of II is almost planar with the substituent containing the dimethylamino and carboxyethyl groups rotated well out of its mean plane. In the crystal, C-H···O and C-H···N hydrogen bonds as well as C-H···π(ring) interactions form chains having a U-shaped cross-section and running along the c-axis direction. Two sets of pair-wise C-H···O hydrogen bonds connect the chains into corrugated sheets. In III, the three substituents on the dihydroquinoxaline moiety are rotated well out of its mean plane. Three sets of C-H···O hydrogen bonds as well as C-H···π(ring) and π-π-stacking interactions form layers approximately parallel to [001]. These are associated along the c-axis direction by additional C-H···π(ring) interactions. Additionally, the Hirshfeld surface analyses showed that the H···H contact is the most important interaction for both II and III. In addition to this, molecular docking and dynamics studies were carried for these two compounds with the c-Jun N-terminal kinases (JNK1) molecule.Communicated by Ramaswamy H. Sarma.

DNA Cleavage Properties, Antimicrobial and Cytotoxic Activity and 4D-QSAR Analysis of Some Pyrazole Derivatives

Background:

An extensive study of 19 pyrazole derivatives were carried out based on the evaluation of DNA cleavage properties, antimicrobial and cytotoxic activities and 4D-QSAR analysis including pharmacophore modelling and bioactivity prediction by the Electron Conformational-Genetic Algorithm (EC-GA) method.

Methods:

The pyrazole derivatives were tested for their antimicrobial activity against certain human pathogenic organisms using the agar diffusion procedure. Binding of compounds with DNA was studied by gel electrophoresis using plasmid pBR322 DNA. The compounds were investigated for their properties as cytotoxic agents by brine shrimp lethality bioassay. To identify the pharmacophoric elements and find out the most important molecular properties which govern cytotoxic activity, multiple conformations of the compounds were used.

Results:

The urea derivatives of pyrazole had higher antibacterial activities against Gram-negative bacteria than against Gram-positive bacteria. Many of the compounds were found to cleave plasmid pBR322 DNA from the supercoiled form to the nicked circular. The cytotoxicity values of the compounds ranged from 13.87 to 84.1 µg/mL. The generated QSAR model was evaluated through the use of the Leave-One-Out Cross Validation (LOO-CV) method. A statistically significant and considerably predictive QSAR model was obtained with 4- descriptors resulting in R2 training =0.8223, R2 test =0.9346, q2=0.6201, q2 ext1=0.8672, q2 ext2= 0.8662 and q2 ext3=0.9511.

Discussion:

The generated model demonstrates that geometrical parameters are more correlated with cytotoxic activity. The resulting EC-GA model would provide benefits to design novel bioactive pyrazole derivatives which are more potent and have less side effects.

Conclusion:

It is believed that the generated QSAR model gives insight into developing new more potent pyrazole derivative drugs.

DNA binding affinity of a macrocyclic copper(II) complex: Spectroscopic and molecular docking studies

The interaction of a novel macrocyclic copper(II) complex, ([CuL(ClO₄)₂] that L is 1,3,6,10,12,15-hexaazatricyclo[13.3.1.1^6,10]eicosane) with calf thymus DNA (ct-DNA) was investigated by various physicochemical techniques and molecular docking at simulated physiological conditions (pH = 7.4). The absorption spectra of the Cu(II) complex with ct-DNA showed a marked hyperchroism with 10 nm blue shift. The intrinsic binding constant (K_b) was determined as 1.25 × 10⁴ M^-1, which is more in keeping with the groove binding with DNA. Furthermore, competitive fluorimetric studies with Hoechst33258 have shown that Cu(II) complex exhibits the ability to displace the ct-DNA-bound Hoechst33258 indicating that it binds to ct-DNA in strong competition with Hoechst33258 for the groove binding. Also, no change in the relative viscosity of ct-DNA and fluorescence intensity of ct-DNA-MB complex in the present of Cu(II) complex is another evidence to groove binding. The thermodynamic parameters are calculated by van't Hoff equation, which demonstrated that hydrogen bonds and van der Waals interactions played major roles in the binding reaction. The experimental results were in agreement with the results obtained via molecular docking study.

Mechanism of synergistic DNA damage induced by the hydroquinone metabolite of brominated phenolic environmental pollutants and Cu(II): Formation of DNA-Cu complex and site-specific production of hydroxyl radicals

2,6-Dibromohydroquinone (2,6-DBrHQ) has been identified as an reactive metabolite of many brominated phenolic environmental pollutants such as tetrabromobisphenol-A (TBBPA), bromoxynil and 2,4,6-tribromophenol, and was also found as one of disinfection byproducts in drinking water. In this study, we found that the combination of 2,6-DBrHQ and Cu(II) together could induce synergistic DNA damage as measured by double strand breakage in plasmid DNA and 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) formation, while either of them alone has no effect. 2,6-DBrHQ/Cu(II)-induced DNA damage could be inhibited by the Cu(I)-specific chelating agent bathocuproine disulfonate and catalase, but not by superoxide dismutase, nor by the typical hydroxyl radical (•OH) scavengers such as DMSO and mannitol. Interestingly, we found that Cu(II)/Cu(I) could be combined with DNA to form DNA-Cu(II)/Cu(I) complex by complementary application of low temperature direct ESR, circular dichroism, cyclic voltammetry and oxygen consumption methods; and the highly reactive •OH were produced synergistically by DNA-bound-Cu(I) with H₂O₂ produced by the redox reactions between 2,6-DBrHQ and Cu(II), which then immediately attack DNA in a site-specific manner as demonstrated by both fluorescent method and by ESR spin-trapping studies. Further DNA sequencing investigations provided more direct evidence that 2,6-DBrHQ/Cu(II) caused preferential cleavage at guanine, thymine and cytosine residues. Based on these data, we proposed that the synergistic DNA damage induced by 2,6-DBrHQ/Cu(II) might be due to the synergistic and site-specific production of •OH near the binding site of copper and DNA. Our findings may have broad biological and environmental implications for future research on the carcinogenic polyhalogenated phenolic compounds.

New Bio-Based Cu(II) Complexes and Study of their Anti-Cancer Activities

Two new Cu(II) complexes with Picolinic acid and Tryptophan [Cu(II)(DPTR)(H2O)2](1:1) (1) and [Cu(II)(DPTR)(Phen)] (1:1:1) (2) were synthesized, characterized and studied their DNA binding, cleavage, docking and anti-cancer properties. The molecular modeling studies were carried out with energy minimized structures of metal complexes. CT-DNA binding studies revealed that the complexes bind through an intercalative mode and show good binding propensity. The docking study also confirms the intercalative mode of binding. The hydrolytic DNA cleavage activity of these complexes has been studied using gel electrophoresis. Complex 2 shows better efficiency than 1. Cell viability experiments indicated that the ligand, complexes show significant dose dependent cytotoxicity in selected cell lines. Graphical Abstract Two new Cu(II) complexes with Picolinic acid and Tryptophan, [Cu(II)(DPTR)(H2O)2](1:1) (1) and [Cu(II)(DPTR)(Phen)] (1:1:1) (2) were synthesized, characterized and studied their DNA binding, cleavage, docking and anti-cancer properties.

Ugi-based approaches to quinoxaline libraries

An expedient and concise Ugi-based unified approach for the rapid assembly of quinoxaline frameworks has been developed. This convergent and versatile method uses readily available commercial reagents, does not require advanced intermediates, and exhibits excellent bond-forming efficiency, thus exemplifying the operationally simple synthesis of quinoxaline libraries.

Effect of glucosamine conjugation to zinc(II) complexes of a bis-pyrazole ligand: syntheses, characterization and anticancer activity

The bis(3,5-dimethyl-1H- pyrazol-1yl)acetic acid (bdmpza) ligand was conjugated with tert-butyl-N-(2-aminoethyl) carbonate, methyl-2-amino-4-(methylthio)butanoate and 1,3,4,6-tetra-O-acetyl-β-d-glucosamine hydrochloride via amide coupling method to form three ligands L1-L3 which were then reacted with Zn(II) salts to form four zinc complexes (1-4). The complexes were characterized by (1)H NMR, (13)C NMR, electrospray ionization mass spectrometry (ESI-MS), FT-IR, CHN analyses. Complexes 1, 2 and 4 were also characterized by single crystal X-ray diffraction. It was found that Zn(II) salts could selectively remove the acetyl group from anomeric position leaving everything else intact. The cytotoxicity studies of the ligand and the complexes showed that the conjugation to acetylated glucosamine enhances cytotoxic ability although the complexes become more hydrophilic. Cytotoxicity studies in human breast adenocarcinoma (MCF-7), human cervical cancer (HeLa WT) and human lung adenocarcinoma (A549) showed that the acetylated glucosamine conjugation to the bis-pyrazole ligated Zn(II) complex led to 2-4 fold increase in cytotoxicity (IC50 values ca. 57-80μM) against HeLa WT and MCF-7 cell lines. The Zn(II) complex bearing the acetylated glucosamine inhibits the cell cycle in the G2/M phase of MCF-7 cell line. ICP-MS data shows more accumulation of Zn(II) inside the cell upon use of complex 4 as compared to Zn(II) salts or the other presented complexes. Further studies suggest that the mitochondrial transmembrane potential changes in the presence of complex 4 and caspase-7 is activated by Zn(II) salts but the activation is much more by complex 4 and hence there is apoptosis and dose dependent chromatin condensation/nuclear fragmentation as observed by microscopy.

Evaluation of DNA Binding, Cleavage, and Cytotoxic Activity of Cu(II), Co(II), and Ni(II) Schiff Base Complexes of 1-Phenylindoline-2,3-dione with Isonicotinohydrazide

One new series of Cu(II), Co(II), and Ni(II) Schiff base complexes was prepared through the condensation reaction between 1-phenylindoline-2,3-dione with isonicotinohydrazide followed by metalation, respectively. The Schiff base ligand(L), (E)-N'-(2-oxo-1-phenylindolin-3-lidene)isonicotinohydrazide, and its complexes were found soluble in DMF and DMSO solvents and characterized by using the modern analytical and spectral techniques such as elemental analysis, conductivity, magnetic moments, IR, NMR, UV-visible, Mass, CV, and EPR. The elemental analysis data of ligand and their complexes were well agreed with their calculated values in which metal and ligand stoichiometry ratio 1 : 2 was noted. Molar conductance values indicated that all the complexes were found to be nonelectrolytes. All the complexes showed octahedral geometry around the central metal ions. Herein, we better characterized DNA binding with the complexes by UV-visible and CD spectroscopy and cyclic voltammetry techniques. The DNA cleavage experiments were carried out by Agarose gel electrophoresis method and the cytotoxicity experiments by MTT assay method. Based on the DNA binding, cleavage, and cytotoxicity studies, Cu and Ni complexes were found to be good anticancer agents against AGS-human gastric cancer cell line.