Structural characterisation and pH-dependent preference of pyrrole cross-link isoforms from reactions of oxoenal with cysteine and lysine side chains as model systems.

In this study, we subjected 5,5-diethoxy-4-oxopent-2-enal (DOPE), a model amino acids cross-linking reagent, to reactions with N-acetylcysteine (Ac-Cys) and Nα-acetyllysine (Ac-Lys), and identified three pyrrole cross-links. The compounds were isolated and their structures were rigorously determined by spectrometric and spectroscopic methods, including 2D NMR experiments. The use of 2D NMR spectroscopy was crucial to determine the position of the substituents in the pyrrole rings. The products were identified as 2,4-, 2,3-, and 2,5-substituted pyrroles. The data obtained from their structural characterisation can help similar studies on amino acids modifications induced by analogous bifunctional carbonyl compounds. Our results show that the study of pathways in which model electrophiles modify amino acids may be helpful for similar studies dealing with identification of structural changes in cysteine- and lysine-containing proteins associated with oxidative stress.

Study of protonated dimers of cytosine, cytidine, and deoxycytidine using survival yield method and quantum mechanics calculations.

RATIONALE: Cytosine and its conjugates are prone to form protonated, triply-bonded dimers. Therefore, the nucleic-acid cytosine-rich sequence forms the four-stranded noncanonical secondary structure known as the intercalated motif (i-motif). This process has resulted in studies on cytosine protonated dimers. This communication focuses on the protonated dimers of cytosine and its nucleoside using the survival yield (SY) method and quantum mechanics calculations. METHODS: To obtain the precursor ion fragmentation curve, the plot of SY against Ecomδ , the product ion spectra of the protonated dimers were obtained using a Waters/Micromass Q-TOF Premier mass spectrometer. Quantum mechanics calculations were performed using GAUSSIAN 16, and full geometry optimizations and energy calculations were performed within the density functional theory framework at B3LYP/6-31G(d,p). RESULTS: The precursor ion fragmentation curve allowed the rating of the gas-phase stabilities of the analyzed protonated dimers. Substitution of sugar moiety at N1 cytosine atom decreased the gas-phase stabilities of the protonated dimers. The deoxycytidine dimer was found to be more stable than the cytidine dimer and cytidine-deoxycytidine dimer. Quantum chemical calculations indicated that cytosine aminohydroxy tautomer may be involved in the formation of protonated cytosine-cytosine nucleoside dimers but not in the formation of cytosine dimers. CONCLUSIONS: The results obtained for nucleoside dimers indicated that the SY method may reflect the i-motif stabilities observed under physiological conditions. Therefore, the analysis of other protonated dimers of variously substituted cytosine-cytosine nucleoside using the SY method may be important to study the effect of cytosine substitution on the i-motif stabilities. Cytosine tautomer containing C2-OH… N(2H)-C4 moiety may be involved in the formation of protonated cytosine-cytosine nucleoside dimers.

Neural Networks in the Design of Molecules with Affinity to Selected Protein Domains.

Drug design with machine learning support can speed up new drug discoveries. While current databases of known compounds are smaller in magnitude (approximately 108), the number of small drug-like molecules is estimated to be between 1023 and 1060. The use of molecular docking algorithms can help in new drug development by sieving out the worst drug-receptor complexes. New chemical spaces can be efficiently searched with the application of artificial intelligence. From that, new structures can be proposed. The research proposed aims to create new chemical structures supported by a deep neural network that will possess an affinity to the selected protein domains. Transferring chemical structures into SELFIES codes helped us pass chemical information to a neural network. On the basis of vectorized SELFIES, new chemical structures can be created. With the use of the created neural network, novel compounds that are chemically sensible can be generated. Newly created chemical structures are sieved by the quantitative estimation of the drug-likeness descriptor, Lipinski's rule of 5, and the synthetic Bayesian accessibility classifier score. The affinity to selected protein domains was verified with the use of the AutoDock tool. As per the results, we obtained the structures that possess an affinity to the selected protein domains, namely PDB IDs 7NPC, 7NP5, and 7KXD.

Mechanism of Silylation of Vinyl Arenes by Hydrodisiloxanes Driven by Stoichiometric Amounts of Sodium Triethylborohydride-A Combined DFT and Experimental Study.

The reactions of vinyl arenes with hydrodisiloxanes in the presence of sodium triethylborohydride were studied using experimental and computational methods. The expected hydrosilylation products were not detected because triethylborohydrides did not exhibit the catalytic activity observed in previous studies; instead, the product of formal silylation with dimethylsilane was identified, and triethylborohydride was consumed in stoichiometric amounts. In this article, the mechanism of the reaction is described in detail, with due consideration given to the conformational freedom of important intermediates and the two-dimensional curvature of the potential energy hypersurface cross sections. A simple way to reestablish the catalytic character of the transformation was identified and explained with reference to its mechanism. The reaction presented here is an example of the application of a simple transition-metal-free catalyst in the synthesis of silylation products, with flammable gaseous reagents replaced by a more convenient silane surrogate.

Artificial Intelligence in Decrypting Cytoprotective Activity under Oxidative Stress from Molecular Structure.

Artificial intelligence (AI) is widely explored nowadays, and it gives opportunities to enhance classical approaches in QSAR studies. The aim of this study was to investigate the cytoprotective activity parameter under oxidative stress conditions for indole-based structures, with the ultimate goal of developing AI models capable of predicting cytoprotective activity and generating novel indole-based compounds. We propose a new AI system capable of suggesting new chemical structures based on some known cytoprotective activity. Cytoprotective activity prediction models, employing algorithms such as random forest, decision tree, support vector machines, K-nearest neighbors, and multiple linear regression, were built, and the best (based on quality measurements) was used to make predictions. Finally, the experimental evaluation of the computational results was undertaken in vitro. The proposed methodology resulted in the creation of a library of new indole-based compounds with assigned cytoprotective activity. The other outcome of this study was the development of a validated predictive model capable of estimating cytoprotective activity to a certain extent using molecular structure as input, supported by experimental confirmation.

Vibration Suppression with Use of Input Shaping Control in Machining.

This article discusses the problem of vibrations during machining. The manufacturing process of generator turbine blades is highly complex. Machining using Computerized Numerical Control (CNC) requires low cutting parameters in order to avoid vibration problems. However, even under these conditions, the surface quality and accuracy of the manufactured objects suffer from high levels of vibrations. Hence, the aim of this research is to counteract this phenomenon. Basic issues related to vibration problems will also be also discussed and a short review of currently available solutions for both active and passive vibration monitoring during machining will be presented. The authors developed a method which does not require any additional equipment other than modified CNC code. The proposed method can be applied to any CNC machine, and is especially suitable for lathes. The method seeks to eradicate the phenomenon of vibrations by providing enhanced control through Input Shaping Control (ISC). For this purpose, the authors present a method for modeling the machining process and design an ISC filter; the model is then implemented in the Matlab and Simulink environment. The last part of the article presents the results, together with a discussion, and includes a brief summary.

Naphthalene vs. Benzene as a Transmitting Moiety: Towards the More Sensitive Trifluoromethylated Molecular Probes for the Substituent Effects.

The application of DFT computational method (B3LYP/6-311++G(d,p)) to mono- and poly(CF3)substituted naphthalene derivatives helps to study changes in the electronic properties of these compounds under the influence of 11 substituents (-Br, -CF3, -CH3, -CHO, -Cl, -CN, -F, -NH2, -NMe2, -NO2, and -OH) to confront substituent effects in naphthalene with an analogous situation in benzene. This paper shows the dependencies of theoretically calculated SESE (Substituent Effect Stabilization Energy) values on empirically determined, well-defined Hammett-type constants (σp, σm, R, and F). Described poly(CF3)substituted derivatives of naphthalene are, so far, the most sensitive molecular probes for the substituent effects in the aromatic system. The presence of the trifluoromethyl groups of such an expressive nature significantly increases the sensitivity of the SESE to changes caused by another substitution. Further, the more -CF3 groups are attached to the naphthalene ring, the more sensitive the probe is. Certain groups of probes show additivity of sensitivity: the obtained sensitivity relates to the sum of the sensitivities of the mono(CF3)substituted probes.

Design and Synthesis of New α-hydroxy ß-fluoro/ß-trifluoromethyl and Unsaturated Phosphonates from Carbohydrate-Derived Building Blocks via Pudovik and Horner-Wadsworth-Emmons Reactions.

Herein, we present the application of fluorinated carbohydrate-derived building blocks for α-hydroxy ß-fluoro/ß-trifluoromethyl and unsaturated phosphonates synthesis. Pudovik and Horner-Wadsworth-Emmons reactions were applied to achieve this goal. The proposed pathway of the key reactions is supported by the experimental results, as well as quantum chemical calculations. The structure of the products was established by spectroscopic (1D, 2D NMR) and spectrometric (MS) techniques. Based on our data received, we claim that the progress of the Pudovik and HWE reactions is significantly influenced by the acidic protons present in the molecules as assessed by pKa values of the reagent.

Mechanochemical Synthesis of Fluorinated Imines.

A number of imines, including 12 new compounds, previously not reported in the literature, derived from variously fluorinated benzaldehydes and different anilines or chiral benzylamines were synthesized by a solvent-free mechanochemical method, which was based on the manual grinding of equimolar amounts of the substrates at the room temperature. In a very short reaction time of only 15 min, the method produced the expected products with good-to-excellent yields. The yields were comparable or significantly higher than those reported in the literature for the imines synthesized by other methods. Importantly, the conditions used for the reactions with aniline derivatives also resulted in the high yields of imines obtained from chiral benzylamines, and can be extended to the synthesis with other similar amines. Structures of all imines were confirmed by NMR spectroscopy: 1H, 13C and 19F. For four compounds, X-ray structures were also obtained. The synthetic approach presented in this paper contributes to the prevention of environmental pollution and can be easily extended for larger-scale syntheses. The mechanochemical solvent-free method provides a convenient strategy particularly useful for the preparation of fluorinated imines being versatile intermediates or starting material in the synthesis of drugs and other fine chemicals.

Catalytic and non-catalytic hydroboration of carbonyls: quantum-chemical studies.

The addition of hydroboranes across several unsaturated moieties is a universal synthetic tool for the reduction or functionalization of unsaturated moieties. Given the sustainable nature of this process, the development of more environmentally-benign approaches (main-group catalysis or uncatalysed approaches) for hydroboration has gained considerable recent momentum. The present paper examines both catalyst-free and KF-mediated hydroboration of carbonyl compounds with the use of quantum-chemical methods. The results of computations for several potential reaction pathways are juxtaposed with experiment-based calculations, which leads to stepwise mechanisms and energy profiles for the reactions of pinacolborane with benzaldehyde and acetophenone (in the presence of KF). For each step of these reactions, we provide an accurate description of the geometric and electronic structures of corresponding stationary points. Five different levels of theory are employed to select the most applicable theoretical approach and develop a computational protocol for further research. Upon selection of the best-performing methods, larger molecular systems are studied to explore possible more complex pathways at the M06-2X/6-311++G(2d,p) and ωB97XD/6-311++G(2d,p) levels of theory, which brings up multi-pathway, overlapping catalytic cycles. The mechanism of solvent-free, catalyst-free hydroboration of aldehydes is also revisited through the prism of the elaborated methodology, which leads to a whole new perspective on the pathways of this and similar reactions, with a multimolecular cascade of hydride transfers being more energetically favoured than a four-membered transition state.

Effect of ß-Ketoiminato Ancillary Ligand Modification on Emissive Properties of New Iridium Complexes.

A series of new bis(benzo[h]quinolinato) Ir(III) complexes with modified ß-ketoiminato ancillary ligands were synthesized, and their electrochemical, photophysical properties were determined with the support of theoretical calculations. Moreover, all the synthesized heteroleptic Ir(III) complexes were examined as dopants of the host-guest type emissive layers in solution-processed phosphorescent organic light emitting diodes (PhOLEDs) of a simple structure. As expected on the basis of voltammetry measurements as well as DFT calculations, all the compounds appeared to be green emitters. Their examination showed that alteration of ß-ketoiminato ligand structure causes frontier orbitals' energy levels to be slightly changed, while significantly affecting photoluminescence and electroluminescence efficiencies of iridium phosphors containing these ligands. It was also found that modification of ancillary ligands might enhance charge trapping on the dopant, thus increasing its efficiency, especially in electroluminescence. From among the iridium complexes studied, the compound bearing 1-naphthyl group bonded to the nitrogen atom of the ancillary ligand proved to be the most efficient emitter. The PhOLED fabricated on the basis of this dopant has reached a luminance level of 16000 cd/m2, current efficiency close to 12 cd/A, and an external quantum efficiency around 3.2%.

Carbazole Derivatives' Binding to c-KIT G-Quadruplex DNA.

The binding affinities of three carbazole derivatives to the intramolecular G-quadruplex (GQ) DNA formed by the sequence 5'-AGGGAGGGCGCTGGGAGGAGGG-3', derived from the c-KIT 1 oncogene region, were investigated. All carbazole cationic ligands that differed in the substituents on the nitrogen atom were able to stabilize G-quadruplex, as demonstrated using UV-Vis, fluorescence and CD spectroscopic techniques as well as molecular modeling. The spectrophotometric titration results showed spectral features characteristic of these ligands-bathochromic shifts and initial hypochromicity followed by hyperchromicity at higher GQ concentrations. All free carbazole ligands exhibited modest fluorescent properties, but after binding to the DNA the fluorescence intensity increased significantly. The binding affinities of carbazole ligands to the c-KIT 1 DNA were comparable showing values in the order of 105 M−1. Molecular modeling highlights the differences in interactions between each particular ligand and studied G-quadruplex, which potentially influenced binding strength. Obtained results relevant that all three investigated ligands have stabilization properties on studied G-quadruplex.

Selectivity of major isoquinoline alkaloids from Chelidonium majus towards telomeric G-quadruplex: A study using a transition-FRET (t-FRET) assay.

BACKGROUND: Natural bioproducts are invaluable resources in drug discovery. Isoquinoline alkaloids of Chelidonium majus constitute a structurally diverse family of natural products that are of great interest, one of them being their selectivity for human telomeric G-quadruplex structure and telomerase inhibition. METHODS: The study focuses on the mechanism of telomerase inhibition by stabilization of telomeric G-quadruplex structures by berberine, chelerythrine, chelidonine, sanguinarine and papaverine. Telomerase activity and mRNA levels of hTERT were estimated using quantitative telomere repeat amplification protocol (q-TRAP) and qPCR, in MCF-7 cells treated with different groups of alkaloids. The selectivity of the main isoquinoline alkaloids of Chelidonium majus towards telomeric G-quadruplex forming sequences were explored using a sensitive modified thermal FRET-melting measurement in the presence of the complementary oligonucleotide CT22. We assessed and monitored G-quadruplex topologies using circular dichroism (CD) methods, and compared spectra to previously well-characterized motifs, either alone or in the presence of the alkaloids. Molecular modeling was performed to rationalize ligand binding to the G-quadruplex structure. RESULTS: The results highlight strong inhibitory effects of chelerythrine, sanguinarine and berberine on telomerase activity, most likely through substrate sequestration. These isoquinoline alkaloids interacted strongly with telomeric sequence G-quadruplex. In comparison, chelidonine and papaverine had no significant interaction with the telomeric quadruplex, while they strongly inhibited telomerase at transcription level of hTERT. Altogether, all of the studied alkaloids showed various levels and mechanisms of telomerase inhibition. CONCLUSIONS: We report on a comparative study of anti-telomerase activity of the isoquinoline alkaloids of Chelidonium majus. Chelerythrine was most effective in inhibiting telomerase activity by substrate sequesteration through G-quadruplex stabilization. GENERAL SIGNIFICANCE: Understanding structural and molecular mechanisms of anti-cancer agents can help in developing new and more potent drugs with fewer side effects. Isoquinolines are the most biologically active agents from Chelidonium majus, which have shown to be telomeric G-quadruplex stabilizers and potent telomerase inhibitors.

Experimental and theoretical studies on fluvastatin primary photoproduct formation.

Fluvastatin (FLV) belongs to the group of compounds referred to as statins, also known as 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase inhibitors. Statins act as cholesterol-lowering agents and are among the most frequently prescribed drugs. They upregulate low-density lipoprotein receptors in the liver by binding to the active site of HMG-CoA reductase, which is the key enzyme in cholesterol biosynthesis. Statins have been detected as contaminants in natural waters and are susceptible to degradation upon exposure to light. Fluvastatin is extremely sensitive to light; upon irradiation it forms a range of photoproducts. In this study the fluvastatin molar absorption coefficient and the quantum yield of the drug photodegradation were determined. The FLV photodegradation quantum yield value determined in this work (Φ = 0.13 ± 0.02) was found to be significantly larger than that previously reported in the literature. Our results also showed that the generation of singlet oxygen is not involved in the drug photodecomposition indicating that the excited triplet state of fluvastatin is not populated efficiently. Moreover, experimental methods and DFT calculations were applied to get insight into the possible mechanisms of fluvastatin primary photoproduct formation. Using the transient absorption spectroscopy technique, the transient species formed immediately after the drug excitation were followed, and the scheme for fluvastatin primary photochemistry was suggested. The primary photoproducts were identified on the basis of spectroscopic and spectrometric methods. A new mechanism for photooxygenation leading to the formation of one of the identified photoproducts (FP2) was proposed and a new approach to the formation of the other photoproduct (FP1) was provided. The theoretical mechanistic explanation of the photoproduct formation is in excellent agreement with the experimental data.

Naphthalimides Selectively Inhibit the Activity of Bacterial, Replicative DNA Ligases and Display Bactericidal Effects against Tubercle Bacilli.

The DNA ligases, enzymes that seal breaks in the backbones of DNA, are essential for all organisms, however bacterial ligases essential for DNA replication use ß-nicotinamide adenine dinucleotide as their co-factor, whereas those that are essential in eukaryotes and viruses use adenosine-5'-triphosphate. This fact leads to the conclusion that NAD⁺-dependent DNA ligases in bacteria could be targeted by their co-factor specific inhibitors. The development of novel alternative medical strategies, including new drugs, are a top priority focus areas for tuberculosis research due to an increase in the number of multi-drug resistant as well as totally drug resistant tubercle bacilli strains. Here, through the use of a virtual high-throughput screen and manual inspection of the top 200 records, 23 compounds were selected for in vitro studies. The selected compounds were evaluated in respect to their Mycobacterium tuberculosis NAD⁺ DNA ligase inhibitory effect by a newly developed assay based on Genetic Analyzer 3500 Sequencer. The most effective agents (e.g., pinafide, mitonafide) inhibited the activity of M. tuberculosis NAD⁺-dependent DNA ligase A at concentrations of 50 µM. At the same time, the ATP-dependent (phage) DNA LigT4 was unaffected by the agents at concentrations up to 2 mM. The selected compounds appeared to also be active against actively growing tubercle bacilli in concentrations as low as 15 µM.

Synthesis and anticancer activity of some 5-fluoro-2'-deoxyuridine phosphoramidates.

Two series of novel 4-chlorophenyl N-alkyl phosphoramidates of 3'-O-(t-butoxycarbonyl)-5-fluoro-2'-deoxyuridine (3'-BOC-FdU) (9a-9j) and 5-fluoro-2'-deoxyuridine (FdU) (10a-10j) were synthesized by means of phosphorylation of 3'-BOC-FdU (4) with 4-chlorophenyl phosphoroditriazolide (7), followed by a reaction with the appropriate amine. Phosphoramidates 9a-9j were converted to the corresponding 10a-10j by removal of the 3'-t-butoxycarbonyl protecting group (BOC) under acidic conditions. The synthesized phosphoramidates 9a-9j and 10a-10j were evaluated for their cytotoxic activity in five human cancer cell lines: cervical (HeLa), nasopharyngeal (KB), breast (MCF-7), liver (HepG2), osteosarcoma (143B) and normal human dermal fibroblast cell line (HDF) using the sulforhodamine B (SRB) assay. Two phosphoramidates 9b and 9j with the N-ethyl and N-(methoxy-(S)-alaninyl) substituents, respectively, displayed remarkable activity in all the investigated cancer cells, and the activity was considerably higher than that of the parent nucleoside 4 and FdU. Among phosphoramidates 10a-10j compound 10c with the N-(2,2,2-trifluoroethyl) substituent showed the highest activity. Phosphoramidate 10c was more active than the FdU in all the cancer cell lines tested.

Can Google Searches Predict the Popularity and Harm of Psychoactive Agents?

BACKGROUND: Predicting the popularity of and harm caused by psychoactive agents is a serious problem that would be difficult to do by a single simple method. However, because of the growing number of drugs it is very important to provide a simple and fast tool for predicting some characteristics of these substances. We were inspired by the Google Flu Trends study on the activity of the influenza virus, which showed that influenza virus activity worldwide can be monitored based on queries entered into the Google search engine. OBJECTIVE: Our aim was to propose a fast method for ranking the most popular and most harmful drugs based on easily available data gathered from the Internet. METHODS: We used the Google search engine to acquire data for the ranking lists. Subsequently, using the resulting list and the frequency of hits for the respective psychoactive drugs combined with the word "harm" or "harmful", we estimated quickly how much harm is associated with each drug. RESULTS: We ranked the most popular and harmful psychoactive drugs. As we conducted the research over a period of several months, we noted that the relative popularity indexes tended to change depending on when we obtained them. This suggests that the data may be useful in monitoring changes over time in the use of each of these psychoactive agents. CONCLUSIONS: Our data correlate well with the results from a multicriteria decision analysis of drug harms in the United Kingdom. We showed that Google search data can be a valuable source of information to assess the popularity of and harm caused by psychoactive agents and may help in monitoring drug use trends.

Toward a physical interpretation of substituent effects: the case of fluorine and trifluoromethyl groups.

The application of ab initio and DFT computational methods at six different levels of theory (MP2/cc-pVDZ, MP2/aug-cc-pVTZ, B3LYP/cc-pVDZ, B3LYP/aug-cc-pVTZ, M06/cc-pVDZ, and M06/aug-cc-pVTZ) to meta- and para-substituted fluoro- and trifluoromethylbenzene derivatives and to 1-fluoro- and 1-trifluoromethyl-2-substituted trans-ethenes allowed the study of changes in the electronic and geometric properties of F- and CF3-substituted systems under the impact of other substituents (BeH, BF2, BH2, Br, CFO, CHO, Cl, CN, F, Li, NH2, NMe2, NO, NO2, OH, H, CF3, and CH3). Various parameters of these systems have been investigated, including homodesmotic reactions in terms of the substituent effect stabilization energy (SESE), the π and σ electron donor-acceptor indexes (pEDA and sEDA, respectively), the charge on the substituent active region (cSAR, known earlier as qSAR), and bond lengths, which have been regressed against Hammett constants, resulting mostly in an accurate correspondence except in the case of p-fluorobenzene derivatives. Moreover, changes in the characteristics of the ability of the substituent to attract or donate electrons under the impact of the kind of moiety to which the substituent is attached have been considered as the indirect substituent effect and investigated by means of the cSAR model. Regressions of cSAR(X) versus cSAR(Y) for any systems X and Y allow final results to be obtained on the same scale of magnitude.

Spectroscopic, potentiometric and quantum-mechanical studies of S-(-)-nicotine complexes with Cu(II) ion.

Copper(II)-nicotine complexes with chelating perchlorate, nitrate, acetate and formate ligands have been synthesized and characterized in solid state by elemental analysis and FT-IR spectroscopy. Coordination of Cu(II) by nicotine molecule has been also studied in water solution of various pH by potentiometry and spectroscopic (VIS, EPR and NMR) methods. Furthermore, quantum-mechanical calculations helped elucidate the experimental data as they provided some information on the energetic of the possible interaction modes of Cu(II) with nicotine. The studies showed that nicotine acts as a monodentate ligand utilizing for this purpose the pyridine nitrogen atom. In the Cu(II)/Nicotine system the MHL and ML type complexes were formed in 1:1 metal:ligand ratio.