Machine learning prediction of 3CLpro SARS-CoV-2 docking scores.

Molecular docking results of two training sets containing 866 and 8,696 compounds were used to train three different machine learning (ML) approaches. Neural network approaches according to Keras and TensorFlow libraries and the gradient boosted decision trees approach of XGBoost were used with DScribe's Smooth Overlap of Atomic Positions molecular descriptors. In addition, neural networks using the SchNetPack library and descriptors were used. The ML performance was tested on three different sets, including compounds for future organic synthesis. The final evaluation of the ML predicted docking scores was based on the ZINC in vivo set, from which 1,200 compounds were randomly selected with respect to their size. The results obtained showed a consistent ML prediction capability of docking scores, and even though compounds with more than 60 atoms were found slightly overestimated they remain valid for a subsequent evaluation of their drug repurposing suitability.

Mass spectrometrical and quantum-chemical study of pentafluorophenylhydrazones.

Twenty-one pentafluorphenylhydrazones have been analyzed by means of tandem mass spectrometry (ESI MS/MS) conditions to compare their fragmentations with those ones obtained from quantum-chemical calculations of the hydrazone moiety depending on the substitution from the aldehyde site. The hydrazone N-N bond is disrupted under such conditions, and these results are in accordance with the facts that an electron-rich particle, such as an anion and or radical in a solution, can cause this disruption and simultaneous defluorination in para-position of the hydrazone part of the molecule.

Synthesis and Anticancer Activity of Novel 9-O-Substituted Berberine Derivatives.

Berberine is a bioactive isoquinoline alkaloid derived from many plants. Although berberine has been shown to inhibit growth and induce apoptosis of several tumor cell lines, its poor absorption and moderate activity hamper its full therapeutic potential. Here, we describe the synthesis of a series of 9-O-substituted berberine derivatives with improved antiproliferative and apoptosis-inducing activities. An analysis of novel berberine derivatives by EPR spectroscopy confirmed their similar photosensitivity and analogous behavior upon UVA irradiation as berberine, supporting their potential to generate ROS. Improved antitumor activity of novel berberine derivatives was revealed by MTT assay, by flow cytometry and by detection of apoptotic DNA fragmentation and caspase-3 activation, respectively. We showed that novel berberine derivatives are potent inhibitors of growth of HeLa and HL-60 tumor cell lines with IC50 values ranging from 0.7 to 16.7 µM for HL-60 cells and 36 to >200 µM for HeLa cells after 48 h treatment. Further cell cycle analysis showed that the observed inhibition of growth of HL-60 cells treated with berberine derivatives was due to arresting these cells in the G2/M and S phases. Most strikingly, we found that berberine derivative 3 (9-(3-bromopropoxy)-10-methoxy-5,6-dihydro-[1,3]dioxolo[4,5-g]isoquino[3,2-a] isoquinolin-7-ylium bromide) possesses 30-fold superior antiproliferative activity with an IC50 value of 0.7 µM and 6-fold higher apoptosis-inducing activity in HL-60 leukemia cells compared to berberine. Therefore, further studies are merited of the antitumor activity in leukemia cells of this berberine derivative.

Interaction of DNA and mononucleotides with theophylline investigated using electrochemical biosensors and biosensing.

The understanding of DNA-drug interaction mechanism is among the important aspects of biological studies for drug design, discovery and pharmaceutical development processes. Published rather detailed FTIR and UV-visible spectroscopic studies on the interactions of theophylline, theobromine and caffeine with calf thymus DNA have shown effective binding of these methylxanthine derivatives to DNA and RNA involving H-bonds. However, to our knowledge, there is no such investigation using electrochemical approach. As a novelty of the study, in this paper the bioelectrochemical approach has been chosen for the investigation of an interaction of low molecular salmon sperm dsDNA, ssDNA and mononucleotides with theophylline (TP) in aqueous phosphate buffered medium using DNA-based electrochemical biosensors and biosensing in solution phase. Exploitation of the electrochemical approach via changes in square wave voltammetric responses of deoxyguanosine (dGuo) and deoxyadenosine (dAdo) provided a new indication on preferential association of TP with dGuo in the case of double helical dsDNA structure which was not reported previously. Moreover, an attachment of TP molecules outside DNA was found in the presence of high concentration of 3.3 × 10-4 M TP in solution which diminishes the electron transfer and leads to the difficulties in quantitative evaluation of the TP and dGuo voltammetric responses. The changes in UV-vis and FTIR spectra obtained in the same medium confirmed the association interaction of TP with both nucleobases. Utilizing the model and the published energies of hydrogen bonding stabilization, the formation of a DNA-TP complex was predicted through the intermolecular H-bonds between TP and the NH-CO moiety of guanine and the N-NH2 moiety of adenine.

Immunobiological efficacy and immunotoxicity of novel synthetically prepared fluoroquinolone ethyl 6-fluoro-8-nitro-4-oxo-1,4-dihydroquinoline-3-carboxylate.

The present study examined the cytotoxicity, anti-cancer reactivity, and immunomodulatory properties of new synthetically prepared fluoroquinolone derivative 6-fluoro-8-nitro-4-oxo-1,4-dihydroquinoline-3-carboxylate (6FN) in vitro. The cytotoxicity/toxicity studies (concentrations in the range 1-100µM) are focused on the cervical cancer cells HeLa, murine melanoma cancer cells B16, non-cancer fibroblast NIH-3T3 cells and reconstructed human epidermis tissues EpiDerm™. The significant growth inhibition of cancer cells HeLa and B16 was detected. The cytotoxicity was mediated via apoptosis-associated with activation of caspase-9 and -3. After 72h of treatment, the two highest 6FN concentrations (100 and 50µM) induced toxic effect on epidermis tissue EpiDerm™, even the structural changes in tissue were observed with concentration of 100µM. The effective induction of RAW 264.7 macrophages cell-release of pro- and anti-inflammatory TH1, TH2 and TH17 cytokines, with anti-cancer and/or anti-infection activities, respectively, has been revealed even following low-dose exposition.

Assessment of Immunomodulatory Activities and in vitro Toxicity of New Quinolone 7-ethyl 9-ethyl-6-oxo-6,9-dihydro[1,2,5]selenadiazolo[3,4-h]quinoline-7-carboxylate.

Our previous studies on leukemia cells L1210 and cervical cancer HeLa cells revealed cytotoxic effects of the 7-ethyl 9-ethyl-6-oxo-6,9-dihydro[1,2,5]selenadiazolo[3,4-h]quinoline-7-carboxylate (E2h), a new synthetically prepared quinolone derivative, toward selected cancer cell lines. The aim of the present study was to examine the cytotoxicity of E2h toward next cell lines and tissues; that is, human cancer HL-60 and A549 cells, human non-cancer fibroblast BHNF-1 cells, and reconstructed human epidermis tissues. Further we investigated the immunomodulatory activity of E2h on murine macrophage RAW 264.7 cells. Selenadiazoloquinolone E2h induced specific antiproliferative/cytotoxic activity against leukemia HL-60 cells and is the potent inducer of apoptotic cell death. Quinolone derivative demonstrated the immunomodulatory activities on RAW 264.7 cell line murine macrophages. The immunobiological studies revealed time- and concentration-dependent effective immunomodulation of pro- and anti-inflammatory cytokines' release and antiproliferative/cytotoxic effect following exposure of RAW 264.7 cells to E2h. ABBREVIATIONS: DMEM, Dulbecco's modified eagle medium; DMSO, Dimethylsulfoxide; EtBr, Ethidium bromide; PI, Propidium iodide; E2h, 7-ethyl 9-ethyl-6-oxo-6,9-dihydro[1,2,5]selenadiazolo[3,4-h]quinoline-7-carboxylate.

Pro-apoptotic effect of new quinolone 7- ethyl 9-ethyl-6-oxo-6,9-dihydro[1,2,5]selenadiazolo [3,4-h]quinoline-7-carboxylate on cervical cancer cell line HeLa alone/with UVA irradiation.

7- ethyl 9-ethyl-6-oxo-6,9-dihydro[1,2,5]selenadiazolo [3,4-h]quinoline-7-carboxylate (E2h) is a new synthetically prepared quinolone derivative, which in our primary study showed cytotoxic effects towards tumor cells. The aim of the present study was to examine the antiproliferative and apoptosis inducing activities of E2h towards human cervical cancer cell line HeLa with/without the presence of UVA irradiation. Further, the molecular mechanism involved in E2h-induced apoptosis in HeLa cells was investigated. Our results showed that both non-photoactivated and photoactivated E2h caused morphological changes and inhibited the cell growth of HeLa cells in a time- and dose-dependent manner. Irradiation increased the sensitivity of HeLa cells to E2h. Quinolone induced S and G2/M arrest and apoptosis in HeLa cells, as characterized by DNA fragmentation and flow cytometry. In addition, E2h elevated the level of reactive oxygen species and activated caspases 3. In conclusions, E2h alone/in combination with UVA irradiation induced apoptosis in HeLa cells through the ROS-mitochondrial/caspase 3-dependent pathway.

Study of the cytotoxic/toxic potential of the novel anticancer selenodiazoloquinolone on fibroblast cells and 3D skin model.

The new synthetically prepared quinolone derivative 7-ethyl 9-ethyl-6-oxo-6,9-dihydro[1,2,5]selenadiazolo [3,4-h]quinoline-7-carboxylate (E2h) showed in our previous study cytotoxic effects towards tumor cells and immunomodulatory activities on RAW 264.7 cell line murine macrophages. E2h may have a potential use as a novel chemotherapeutic agent with immunomodulatory properties and the ability to induce apoptotic death of cancer cells. The aim of the present study was to examine the antiproliferative/cytotoxic activities of E2h on human non-cancer fibroblast BHNF-1 cells and reconstructed human epidermis EpiDerm™. Further the effects of E2h on tissue structure and morphology were examined. Cytotoxic/toxic studies showed that selenadiazoloquinolone is not toxic on normal human fibroblast cells BHNF-1 and dimensional skin constructs EpiDerm™. Evaluation of morphological changes in EpiDerm™ showed no change in the construction and morphology of skin tissue treated by E2h compared to control.

Copper(II) complexes with new fluoroquinolones: Synthesis, structure, spectroscopic and theoretical study, DNA damage, cytotoxicity and antiviral activity.

Copper(II) complexes with fluoroquinolones in the presence of the nitrogen donor heterocyclic ligands 1,10-phenanthroline have been considered in detail. The phenanthroline moiety was introduced into the ligand environment with the aim to determine whether the nuclease activity is feasible. All suitable X-ray structures of the complexes under study reveal a distorted square pyramidal coordination geometry for Cu(II) atom. The conformational and spectroscopic (FT-IR and UV-visible) behavior has been analyzed and has been interpreted with respect to B3LYP/6-311G* calculations including molecular dynamics. The ability of the complexes to cleave DNA was studied by agarose gel electrophoresis with plasmid DNA pBSK+. The results have confirmed that the complexes under study behave as the chemical nucleases. Nuclease like activity in the absence of hydrogen peroxide allows us to deduce an interaction of the complexes with the DNA resulting in the conversion of supercoiled circular DNA to the nicked form. The DNA cleavage activity enhanced by the presence of hydrogen peroxide demonstrates the participation of reactive oxygen species, such as superoxide radical anions and hydroxyl radicals which presence was confirmed independently using the standard radical scavenging agents. It has been suggested that the radical formation through the Fenton/Haber-Weiss reaction is mediated by the redox cycling mechanisms with the participation of cupric/cuprous ions. Cytotoxic activity was evaluated as the 50% cytotoxic concentration (CC50). The potential effects of tested compounds on replication of murine gammaherpesvirus 68 (MHV-68) under in vitro conditions were also evaluated. However, no antiviral activity against MHV-68 was observed.

Conformational, spectroscopic, and molecular dynamics DFT study of precursors for new potential antibacterial fluoroquinolone drugs.

Biological activity, functionality, and synthesis of (fluoro)quinolones is closely related to their precursors (for instance 3-fluoroanilinoethylene derivatives) (i.e., their functional groups, conformational behavior, and/or electronic structure). Herein, the theoretical study of 3-fluoroanilinoethylene derivatives is presented. Impact of substituents (acetyl, methyl ester, and ethyl ester) on the conformational analysis and the spectral behavior is investigated. The B3LYP/6-311++G** computational protocol is utilized. It is found that the intramolecular hydrogen bond N-H···O is responsible for the energetic preference of anti (a) conformer (anti position of 3-fluoroanilino group with respect to the C═C double bond). The Boltzmann ratios of the conformers are related to the differences of the particular dipole moments and/or their dependence on the solvent polarity. The studied acetyl, ethyl ester, and methyl ester substituted fluoroquinolone precursors prefer in the solvent either EZa, ZZa, or both conformers equally, respectively. In order to understand the degree of freedom of rotation of the trans ethyl ester group, B3LYP/6-311G** molecular dynamic simulations were carried out. Vibrational frequencies, electron transitions, as well as NMR spectra are analyzed with respect to conformational analysis, including the effect of the substituent. X-ray structures of the precursors are presented and compared with the results of the conformational analysis.

Fused-ring derivatives of quinoxalines: spectroscopic characterization and photoinduced processes investigated by EPR spin trapping technique.

10-Ethyl-7-oxo-7,10-dihydropyrido[2,3-f]quinoxaline derivatives, synthesized as promising biologically/photobiologically active compounds were characterized by UV/vis, FT-IR and fluorescent spectroscopy. Photoinduced processes of these derivatives were studied by EPR spectroscopy, monitoring in situ the generation of reactive intermediates upon UVA (λmax=365 nm) irradiation. The formation of reactive oxygen species and further oxygen- and carbon-centered radical intermediates was detected and possible reaction routes were suggested. To quantify the investigated processes, the quantum yields of the superoxide radical anion spin-adduct and 4-oxo-2,2,6,6-tetramethylpiperidine N-oxyl generation were determined, reflecting the activation of molecular oxygen by the excited state of the quinoxaline derivative.

Use of activated enol ethers in the synthesis of pyrazoles: reactions with hydrazine and a study of pyrazole tautomerism.

Activated enol ethers derived from esters or the dinitrile of malonic acid, or from pentane-2,4-dione were treated with hydrazine hydrate. The structures of the obtained products - pyrazoles 5 - were studied with a focus on tautomerism and supramolecular structure. A reverse addition of the reagents led to the isolation of two novel products, namely bis-enehydrazines 6 with an unsymmetrical arrangement of the formally equivalent subunits.

Oxidation of quinolones with peracids (an in situ EPR study).

4-Oxoquinoline derivatives (quinolones) represent heterocyclic compounds with a variety of biological activities, along with interesting chemical reactivity. The quinolone derivatives possessing secondary amino hydrogen at the nitrogen of the enaminone system are oxidized with 3-chloroperbenzoic acid to nitroxide radicals in the primary step while maintaining their 4-pyridone ring. Otherwise, N-methyl substituted quinolones also form nitroxide radicals coupled with the opening of the 4-pyridone ring in a gradual oxidation of the methyl group via the nitrone-nitroxide spin-adduct cycle. This was confirmed in an analogous oxidation using N,N-dimethylaniline as a model compound. N-Ethyl quinolones in contrast to its N-methyl analog form only one nitroxide radical without a further degradation.

New syntheses of 5,6- and 7,8-diaminoquinolines.

The synthesis of 5,6- and 7,8-diaminoquinoline derivatives starting from angularly annelated selenadiazoloquinolones is presented. Simple chlorination of the pyridone ring followed by reductive deselenation of the 1,2,5-selenadiazole ring afforded novel 4-chloro-o-diaminoquinolines. Dechlorination of 4-chloro-7,8-diaminoquinoline gave 7,8-diaminoquinoline hydrochloride which was successfully employed as starting material in the synthesis of condensed nitrogen heterocycles.

[Warfarin - its synthesis and properties in a twenty-year retrospective*]. / Warfarín - jeho syntéza a vlastnosti v dvadsatrocnej retrospektíve*

The review paper deals with some aspects of warfarin history and its use, at the beginning as a rodenticide and later as an anticoagulant. It describes its principal physical-chemical properties and it analyzes schematically the possibilities of its preparation by both selective and non-selective synthesis from coumarin derivatives. A survey of syntheses and its results are tabulated, including the literary references, and the paper is concluded with an evaluation of the prospects of this agent in comparison with alternative anticoagulants and its advantages, disadvantages and prospects.

Stable radical trianions from reversibly formed sigma-dimers of selenadiazoloquinolones studied by in situ EPR/UV-vis spectroelectrochemistry and quantum chemical calculations.

The redox behavior of the series of 7-substituted 6-oxo-6,9-dihydro[1,2,5]selenadiazolo[3,4-h]quinolines and 8-substituted 9-oxo-6,9-dihydro[1,2,5]selenadiazolo[3,4-f]quinolines with R(7), R(8) = H, COOC(2)H(5), COOCH(3), COOH, COCH(3), and CN has been studied by in situ EPR and EPR/UV-vis spectroelectrochemistry in dimethylsulfoxide. All selenadiazoloquinolones undergo a one-electron reduction process to form the corresponding radical anions. Their stability strongly depends on substitution at the nitrogen atom of the 4-pyridone ring. The primary generated radical anions from N-ethyl-substituted quinolones are stable, whereas for the quinolones with imino hydrogen, the initial radical anions rapidly dimerize to produce unusually stable sigma-dimer (σ-dimer) dianions. These are reversibly oxidized to the initial compounds at potentials considerably less negative than the original reduction process in the back voltammetric scan. The dimer dianion can be further reduced to the stable paramagnetic dimer radical trianion in the region of the second reversible reduction step. The proposed complex reaction mechanism was confirmed by in situ EPR/UV-vis cyclovoltammetric experiments. The site of the dimerization in the σ-dimer and the mapping of the unpaired spin density both for radical anions and σ-dimer radical trianions with unusual unpaired spin distribution have been assigned by means of density functional theory calculations.

Ethyl 1-ethyl-7-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylate: X-ray and DFT studies.

The basic building unit in the structure of the title compound, C(14)H(14)FNO(3), is pairs of molecules arranged in an antiparallel fashion, enabling weak C-H···O interactions. Each molecule is additionally involved in π-π interactions with neighbouring molecules. The pairs of molecules formed by the C-H···O hydrogen bonds and π-π interactions form ribbon-like chains running along the c axis. Theoretical calculations based on these pairs showed that, although the main intermolecular interaction is electrostatic, it is almost completely compensated by an exchange-repulsion contribution to the total energy. As a consequence, the dominating force is a dispersion interaction. The F atoms form weak C-F···H-C interactions with the H atoms of the neighbouring ethyl groups, with H···F separations in the range 2.59-2.80 Å.

Anodic oxidation of selenadiazoloquinolones in alkaline media.

Newly synthesized derivatives of 6-oxo-6,9-dihydro[1,2,5]selenadiazolo[3,4-h]quinoline variously substituted at position 7 (R = H, COOH, COCH(3), CN, COOC(2)H(5) and COOCH(3)) are established in strongly alkaline aqueous solutions (0.1 M NaOH; pH ∼ 13) as N(9)-deprotonated structures, but in less alkaline solutions (0.001 M NaOH; pH ∼ 11) the N(9)-protonated oxo tautomeric forms dominate. Upon their anodic oxidation in alkaline solutions, the selenadiazole ring is replaced, forming instead the paramagnetic species analogous to the ortho semiquinone radical anions as monitored by in situ EPR spectroscopy. The quantum chemical calculations for two representative selenadiazoloquinolones (R = H and COOH) and their anodic oxidation products presented are in agreement with experiments.

Photochemical and phototoxic properties of ethyl 1,4-dihydro-8-nitro-4-oxoquinoline-3-carboxylate, a new quinoline derivative.

The present study demonstrates photoinduced generation of superoxide radical anion and singlet oxygen upon UVA irradiation of ethyl 1,4-dihydro-8-nitro-4-oxoquinoline-3-carboxylate (DNQC), and its cytotoxic/phototoxic effects on murine leukemia L1210 cells. The formation of reactive oxygen species (ROS) was investigated by EPR spectroscopy using in situ spin trapping technique and 4-hydroxy-2,2,6,6-piperidine (TMP) for singlet oxygen ((1)O(2)) detection. The EPR spectra monitored upon photoexcitation of aerated solutions of DNQC in dimethylsulfoxide evidenced the efficient activation of molecular oxygen via Types I and II mechanisms. The cytotoxic/phototoxic effects of DNQC, analysis of cell cycle, induction of apoptosis/necrosis, DNA damage and molecular mechanism of apoptotic death of L1210 cells in dark and in the presence of UVA irradiation were compared. DNQC induced a different cytotoxic/phototoxic effect, which was concentration- and time-dependent. The four highest tested concentrations of non-photoactivated and photoactivated DNQC induced immediate cytotoxic/phototoxic effect after 24h cultivation of L1210 cells. This effect decreased with the time of treatment. The irradiation increased the sensitivity of leukemia cell line on DNQC, but the cell sensitivity decreased with time of processing. Quinolone derivative DNQC significantly induced direct DNA strand breaks in L1210 cells, which were increased with the irradiation of cells. The DNA damage generated by DNQC alone/with combination of UVA irradiation induced cell arrest in G(0)/G(1) and G(2)/M phases, decrease in the number of L1210 cells in Sphase and apoptotic cell death of certain part of cell population after 24 h of influence. DNQC alone/with combination of UVA irradiation induced apoptosis in L1210 cells through ROS-dependent mitochondrial pathway.

Photoinduced superoxide radical anion and singlet oxygen generation in the presence of novel selenadiazoloquinolones (an EPR Study).

Novel 7-substituted 6-oxo-6,9-dihydro[1,2,5]selenadiazolo[3,4-h]quinoline (SeQ(1-6)) and 8-substituted 9-oxo-6,9-dihydro[1,2,5]selenadiazolo[3,4-f ]quinoline derivatives (SeQN(1-5)) with R(7), R(8) =H, COOC(2) H(5), COOCH(3), COOH, COCH(3) or CN were synthesized and their spectral characteristics were obtained by UV/Vis spectroscopy. Ultraviolet A photoexcitation of the selenadiazoloquinolones in dimethylsulfoxide or acetonitrile resulted in the formation of paramagnetic species coupled with molecular oxygen activation generating the superoxide radical anion or singlet oxygen, evidenced by electron paramagnetic resonance spectroscopy. The cytotoxic/photocytotoxic impact of selenadiazoloquinolones on murine and human cancer cell lines was demonstrated using the derivative SeQ5 (with R(7)=COCH(3)).