Advances in methods and algorithms in a modern quantum chemistry program package

C-Geranylated flavanone diplacone enhances in vitro antiproliferative and anti-inflammatory effects in its copper(II) complexes

Two copper(II) complexes containing diplacone (H4dipl), a naturally occurring C-geranylated flavanone derivative, in combination with bathophenanthroline (bphen) or 1,10-phenanthroline (phen) with the composition [Cu3(bphen)3(Hdipl)2]⋅2H2O (1) and {[Cu(phen)(H2dipl)2]⋅1.25H2O}n (2) were prepared and characterized. As compared to diplacone, the complexes enhanced in vitro cytotoxicity against A2780 and A2780R human ovarian cancer cells (IC50 ≈ 0.4-1.2 μM), human lung carcinoma (A549, with IC50 ≈ 2 μM) and osteosarcoma (HOS, with IC50 ≈ 3 μM). Cellular effects of the complexes in A2780 cells were studied using flow cytometry, covering studies concerning cell-cycle arrest, induction of cell death and autophagy and induction of intracellular ROS/superoxide production. These results uncovered a possible mechanism of action characterized by the G2/M cell cycle arrest. The studies on human endothelial cells revealed that complexes 1 and 2, as well as their parental compound diplacone, do possess anti-inflammatory activity in terms of NF-κB inhibition. As for the effects on PPARα and/or PPARγ, complex 2 reduced the expression of leukocyte adhesion molecules VCAM-1 and E-selectin suggesting its dual anti-inflammatory capacity. A wide variety of Cu-containing coordination species and free diplacone ligand were proved by mass spectrometry studies in water-containing media, which might be responsible for multimodal effect of the complexes.

Separation of isotopologues of amphetamine with various degree of deuteration on achiral and polysaccharide-based chiral columns in high-performance liquid chromatography

Hydrogen/deuterium (H/D) isotope effects are not unusual in chromatography and such phenomena have been observed in both gas- and liquid-phase separations. Despite the numerous reports on this topic, the understanding of mechanisms and the underlying noncovalent interactions at play remains rather challenging. In our recent study, we reported baseline separation of isotopologoues of some amphetamine (AMP) derivatives on achiral and polysaccharide-based chiral columns, as well as some correlations between the degree of separation of enantiomers and isotopologues on (the same) polysaccharide-based chiral column(s). Following our previous findings on isotope effects in high-performance liquid chromatography, we report herein a comparative study on the isotope effects observed with AMP and methamphetamine (MET). The impact of some pivotal factors such as the number of deuterium atoms part of AMP isotopologues, the structure of its isotopomers, the chemical structure of the achiral and chiral stationary phases used in this study, and the use of methanol- vs acetonitrile-containing mobile phases on the isotope effects was examined and discussed. Quantitative correlations between the observed isotope effects and the enantioselectivity of the chiral columns used are also shortly discussed. Furthermore, considering the chromatographic results as benchmark experimental data, we attempted to elucidate the molecular bases of the observed phenomena using quantum mechanics calculations.

Ether-Diol Ambiguity: An Inconspicuous Issue in the Structure Elucidation of Oxygenated Natural Products

Tertiary and allylic hydroxyl groups readily eliminate water during positive ion mode mass spectrometry and may show similar NMR spectra to their corresponding ethers. In a routine structure elucidation workflow, these factors can cause researchers to incorrectly assign diol moieties as ethers or vice versa, leading to inaccurate chemical structures. After facing this problem during our work on oxygenated sesquiterpenoids from a Fusarium sp. fungal strain, we became aware of this challenging issue. We examined the literature for oxygenated natural products bearing these functional groups, and with the aid of density functional calculations of NMR chemical shifts, we now report the structures of 15 natural products that should be revised. We further establish that derivatizing sub-micromolar amounts of alcohols to their sulfates can be used to distinguish these from their corresponding ethers using liquid chromatography negative ion mode mass spectrometry. Finally, we isolated lignoren/cyclonerodiol from the Fusarium sp. culture extract and supported its revised identity as cyclonerodiol using this sulfation approach. Our results suggest that ether-diol ambiguity could be a prevalent issue affecting the structure elucidation of oxygenated natural products and highlight the importance of using complementary techniques, such as sulfation with LC-(-)-ESI-MS or density functional calculations of NMR chemical shifts.

Sesquiterpenoids from Carpesium abrotanoides and their anti-inflammatory activity both in vitro and in vivo

Twenty-nine sesquiterpenoids, including pseudoguaiane-type (1-11), eudesmane-type (12-23), and carabrane-type (24-29), have been identified from the plant Carpesium abrotanoides. Of them, compounds 1-4, 12-15, and 24-27, namely carpabrotins A-L, are twelve previously undescribed ones. Compound 3 possessed a pseudoguaiane backbone with a rearrangement modification at C-11, C-12 and C-13, while compound 4 suffered a carbon bond break between the C-4 and C-5 to form a rare 4,5-seco-pseudoguaiane lactone. Compounds 1-3, 5, 13-16 and 25-27 exhibited anti-inflammatory activity by inhibiting NO production in LPS-induced RAW264.7 macrophages with IC50 values less than 40 μM, while compounds 1, 2, 5, 13, 14, 16, and 25-27 showed significant inhibitory activity comparable to that of dexamethasone. The anti-atopic dermatitis (AD) effects of compounds 5 and 16 were tested according to 2,4-dinitrochlorobenzene (DNCB)-induced AD-like skin lesions in KM mice, and the results revealed that the major products 5 and 16 improved the histological features of AD-like skin lesions and mast cell infiltration in mice. This study suggested that sesquiterpenoids in C. abrotanoides should play a key role in its anti-inflammatory use.

Regulation of NS5B Polymerase Activity of Hepatitis C Virus by Target Specific Phytotherapeutics: An In-Silico Molecular Dynamics Approach

Chronic hepatitis caused by the hepatitis C virus (HCV) is closely linked with the advancement of liver disease. The research hypothesis suggests that the NS5B enzyme (non-structural 5B protein) of HCV plays a pivotal role in facilitating viral replication within host cells. Hence, the objective of the present investigation is to identify the binding interactions between the structurally diverse phytotherapeutics and those of the catalytic residue of the target NS5B polymerase protein. Results of our docking simulations reveal that compounds such as arjunolic acid, sesamin, arjungenin, astragalin, piperic acid, piperidine, piperine, acalyphin, adhatodine, amyrin, anisotine, apigenin, cuminaldehyde, and curcumin exhibit a maximum of three interactions with the catalytic residues (Asp 220, Asp 318, and Asp 319) present on the Hepatitis C virus NS5B polymerase of HCV. Molecular dynamic simulation, particularly focusing on the best binding lead compound, arjunolic acid (-8.78 kcal/mol), was further extensively analyzed using RMSD, RMSF, Rg, and SASA techniques. The results of the MD simulation confirm that the NS5B-arjunolic acid complex becomes increasingly stable from 20 to 100 ns. The orientation of both arjunolic acid and sofosbuvir triphosphate (standard) within the active site was investigated through DCCM, PCA, and FEL analysis, indicating highly stable interactions of the lead arjunolic acid with the catalytic region of the NS5B enzyme. The findings of our current investigation suggest that bioactive therapeutics like arjunolic acid could serve as promising candidates for limiting the NS5B polymerase activity of the hepatitis C virus, offering hope for the future of HCV treatment.

Screened optimally tuned range separated hybrid functional for solvated low bandgap molecular systems

The description of electronic properties of low bandgap molecular system is often performed by using density functional theory (DFT) and time dependent (TD) DFT calculations with the optimally tuned range-separated hybrid (OT-RSH) functional, as it contains the necessary ingredients to reliably predict charge transfer excitations. However, the range separating parameter (ω) is system-dependent and its optimization, including the chemical environment, is intricate. Refaely-Abramson et al. demonstrated that the gap renormalization in molecular crystals, a ground state property, can be represented by an OT-RSH functional screened by ɛstatic [Phys. Rev. B 88, 081204(R) (2013)], the zero frequency scalar dielectric constant. In this study, we propose the use of an OT-RSH functional screened by the scalar dielectric constant in the high frequency limit (OT-sRSH), ɛ∞, an appropriate constraint for vertical ionization energies or excitations in a dielectric environment. We have performed calculations for S,N-heteroacene derivatives in tetrahydrofuran and dichloromethane. The "unscreened" OT-RSH functional tends to underestimate experimental ionization potentials (IPs) and optical gaps (Egs) by up to 1.5 and 0.5 eV, respectively. In contrast, OT-sRSH functional calculations underestimate IPs and Egs by only 0.4 and 0.2 eV. We also compared the OT-sRSH results to explicitly solvated OT-RSH functional calculations for oligothiophenes in dioxane, benzene in ammonia, and methylene blue in water. We observe that both the approaches perform similarly for weakly interacting intermolecular systems and deviate for solvent-solute interacting systems, as expected. In conclusion, the OT-sRSH functional can describe molecular systems with environmental polarization effects accurately, a step toward describing realistic molecular systems.

On the Moisture Absorption Capability of Ionic Liquids

Due to their many attractive physicochemical properties, ionic liquids (ILs) have received extensive attention with numerous applications proposed in various fields of science and technology. Despite this, the molecular origins of many of their properties, such as the moisture absorption capability, are still not well understood. For insight into this, we systematically synthesized 24 types of ILs by the combination of the dimethyl phosphate anion with various types of alkyl group-substituted cyclic cations─imidazolium, pyrazolium, 1,2,3-triazolium, and 1,2,4-triazolium cations─and performed a detailed analysis of the dehumidification properties of these ILs and their aqueous solutions. It was found that these IL systems have a high dehumidification capability (DC). Among the monocationic ILs, the best performance was obtained with 1-cyclohexylmethyl-4-methyl-1,2,4-triazolium dimethyl phosphate, whose DC (per mol) value is 14 times higher than that of popular solid desiccants like CaCl2 and silica gel. Dicationic ILs, such as 1,1'-(propane-1,3-diyl)bis(4-methyl-1,2,4-triazolium) bis(dimethyl phosphate), showed an even better moisture absorption, with a DC (per mol) value about 20 times higher than that of CaCl2. Small- and wide-angle X-ray scattering measurements of eight types of 1,2,4-triazolium dimethyl phosphate ILs were performed and revealed that the majority of these ILs form nanostructures. Such nanostructures, which vary with the identity of the IL and the water content, fall into three main categories: bicontinuous microemulsions, hexagonal cylinders, and micelle-like structures. Water in the solutions exists primarily in polar regions in the nanostructures; these spaces function as water pockets at relatively low water concentrations. Since the structure and stability of the aggregated forms of the ILs are mainly governed by the interactions of nonpolar groups, the alkyl side chains of the cations play an important role in the DC and temperature-dependent equilibrium water vapor pressure of the IL solutions. Our experimental findings and molecular dynamics simulation results shed light on the moisture absorption mechanism of the IL aqueous solutions from a molecular perspective.

Iodinated 4,4'-Bipyridines with Antiproliferative Activity Against Melanoma Cell Lines

In the last decade, biological processes involving halogen bond (HaB) as a leading interaction attracted great interest. However, although bound iodine atoms are considered powerful HaB donors, few iodinated new drugs were reported so far. Recently, iodinated 4,4'-bipyridines showed interesting properties as HaB donors in solution and in the solid state. In this paper, a study on the inhibition activity of seven halogenated 4,4'-bipyridines against malignant melanoma (MM) cell proliferation is described. Explorative dose/response proliferation assays were first performed with three 4,4'-bipyridines by using four MM cell lines and the normal BJ fibroblast cell line as control. Among them, the A375 MM cell line was the most sensitive, as determined by MTT assays, which was selected to evaluate the antiproliferative activity of all 4,4'-bipyridines. Significantly, the presence of an electrophilic iodine impacted the biological activity of the corresponding compounds. The 3,3',5,5'-tetrachloro-2-iodo-4,4'-bipyridine showed significant antiproliferation activity against the A375 cell line, and lower toxicity on BJ fibroblasts. Through in silico studies, the stereoelectronic features of possible sites determining the bioactivity were explored. These results pave the way for the utilization of iodinated 4,4'-bipyridines as templates to design new promising HaB-enabled inhibitors of MM cell proliferation.

Harzianic acids and oxazolidinone from the endophytic fungus Ilyonectria sp. and their cytotoxicity activity

Four undescribed compounds including three harzianic acids (1, 3 and 4) and one oxazolidinone (2), along with three known ones (5-7) were isolated from the solid fermented product of endophytic fungus Ilyonectria sp., their structures were elucidated as 1-amino-harzianic acid (1), ilyonectria-oxazolidinone (2),10'-nor- isoharzianic acid (3), isohomoharzianic acid (4), harzianic acid (5), isoharzianic acid (6), homoharzianic acid (7) by means of detailed chemical evidences and spectroscopic data analysis. All the compounds were evaluated for cytotoxicity against SMMC-7721 human cancer cell lines by MTS assay. Among the seven tested compounds, 1-amino-harzianic acid (1) demonstrated well cytotoxic activity against SMMC-7721 with IC50 value of 26.84 μM. The results of molecular docking indicated that compound exhibited moderate anti-tumor activity may through binding to apoptosis related proteins.

Four lathyrane diterpenoids from the seeds of Euphorbia lathyris

Four new diterpenoids, including three secolathyrane diterpenoids (1-3) and one lathyrane diterpenoid (4), together with seven known diterpenoids, were obtained in the shelled seeds of Euphorbia lathyris. In particular, 1-3 possess a rare split ring structure, and currently only one compound with the same skeleton has been identified in E. lathyris. Compound 4 furnishes an unprecedented oxygen bridge structure. The structures were identified using various spectral techniques, including NMR, HR-ESI-MS, single-crystal X-ray diffraction and calculated electronic circular dichroism (ECD). The biosynthetic pathway of 1-4 was inferred. Furthermore, the cytotoxic activities of all compounds (1-11) were measured on three human tumor cells. New compounds 2 and 3 showed moderate cytotoxic activities against U937 cells with IC50 values of 22.18 and 25.41 μM, respectively.

An Eutectic Mixture in the Tetrabutylammonium Bromide-Octanol System: Macroscopic and Microscopic Points of View

An eutectic mixture of tetrabutylammonium bromide and octanol in the molar ratio 1-10 exhibited a melting point of -17 °C. This system was investigated by means of infrared spectroscopy, in the liquid and in the solid state. Classical molecular dynamics was performed to study the fine details of the hydrogen bond interactions established in the mixture. Both octanol and the mixtures displayed an almost featureless far-infrared spectrum in the liquid state but it becomes highly structured in the solid phase. DFT calculations suggest that new vibrational modes appearing in the mixture at low temperatures may be related to the population of the higher energy conformers of the alcohol. Mid-infrared spectroscopy measurements evidenced no shift of the CH stretching bands in the mixture compared to the starting materials, while the OH stretching are blue shifted by a few cm-1. Consistently, molecular dynamics provides a picture of the mixture in which part of the hydrogen bonds (HB) of pure octanol is replaced by weaker HB formed with the Br anion. Due to these interactions the ionic couple becomes more separated. In agreement with this model, the lengths of all HB are much larger than those observed in mixtures containing acids reported in previous studies.

Quantum Interference Enhancement of the Spin-Dependent Thermoelectric Response

We investigate the influence of quantum interference (QI) and broken spin-symmetry on the thermoelectric response of node-possessing junctions, finding a dramatic enhancement of the spin-thermopower (Ss), figure-of-merit (ZsT), and maximum thermodynamic efficiency (ηsmax) caused by destructive QI. Using many-body and single-particle methods, we calculate the response of 1,3-benzenedithiol and cross-conjugated molecule-based junctions subject to an applied magnetic field, finding nearly universal behavior over a range of junction parameters with Ss, ZsT, and reaching peak values of 2 π / 3 ( k / e ) , 1.51, and 28% of Carnot efficiency, respectively. We also find that the quantum-enhanced spin-response is spectrally broad, and the field required to achieve peak efficiency scales with temperature. The influence of off-resonant thermal channels (e.g., phonon heat transport) on this effect is also investigated.

Harnessing the anti-cancer potential of linamarin: A computational study on design and hydrolysis mechanisms of its derivatives

Cassava extracts containing cyanogenic compounds demonstrate anticancer properties. The cyanogenic glucoside linamarin found abundantly in cassava can release hydrogen cyanide (HCN) upon hydrolysis, a potent cytotoxin. However, linamarin's hydrolysis mechanism by human enzymes is poorly delineated and constitutes a bottleneck for therapeutic development. This study aimed to investigate linamarin's hydrolysis mechanism by human β-glucosidase and identify structural derivatives with enhanced hydrolytic potential using density functional theory calculations. Results revealed α-anomeric derivatives as promising, with leaving group ability and steric bulk strongly governing hydrolysability. We identified several linamarin analogs with predicted rapid hydrolysis kinetics that may enable swift cytotoxic HCN release against cancer cells. This investigation enriches understanding of cyanogenic glycoside reactivity to facilitate their development as targeted antineoplastic agents. The identified derivatives set the groundwork for experimental evaluation of enhanced linamarin-inspired compounds as innovative cancer therapeutics.

Heterogeneous Reactions of Phenol on Different Components of Mineral Dust Aerosol: Formation of Oxidized Organic and Nitro-Phenolic Compounds

Phenol, a common semi-volatile compound associated with different emissions including from plants and biomass burning, as well as anthropogenic emissions and its derivatives, are important components of secondary organic aerosols (SOAs). Gas and aqueous phase reactions of phenol, in the presence of photochemical drivers, are fairly well understood. However, despite observations showing aromatic content within SOA size and mass increases during dust episodes, the heterogeneous reactions of phenol with mineral dusts are poorly understood. In the current study, surface reactions of phenol at the gas/solid interface with different components of mineral dust including SiO2, α-Fe2O3, and TiO2 have been investigated. Whereas reversible surface adsorption of phenol occurs on SiO2 surfaces, for both α-Fe2O3 and TiO2 surfaces, phenol reacts to form a wide range of OH substituted aromatic products. For α-Fe2O3 surfaces that have been nitrated by gas-phase reactions of nitric acid prior to exposure to phenol, unique compounds form on the surface including nitro-phenolic compounds. Moreover, additional surface chemistry was observed when adsorbed nitro-phenolic products were exposed to gas-phase SO2 as a result of the formation of adsorbed nitrite from nitrate redox chemistry with adsorbed SO2. Overall, this study reveals the extensive chemistry as well as the complexity of reactions of prevalent organic compounds leading to the formation of SOA on mineral surfaces.

Speciation of Technetium Dibutylphosphate in the Third Phase Formed in the TBP/HNO3 Solvent Extraction System

The speciation of technetium in the nitric acid/dibutylphosphoric acid (HDBP)-n-dodecane system was studied by extended X-ray absorption fine structure (EXAFS) spectroscopy and theoretical methods. Tetravalent technetium, produced by the hydrazine reduction of TcO4- in 3 M HNO3, was extracted by HDBP in n-dodecane (30% by volume). During extraction, the splitting of the organic phase into a heavy phase and a light phase was observed. EXAFS analysis is consistent with the presence of Tc(NO3)3(DBP)(HDBP)2 in the light phase and Tc(NO3)2(DBP)2(HDBP)2 in the heavy phase. Density functional theory calculations at the B3LYP/6-31G* level confirm the stability of the proposed species and indicate that stereoisomers -mer- and fac-Tc(NO3)3(DBP)(HDBP)2 for the light phase and cis- and trans-Tc(NO3)2(DBP)2(HDBP)2 for the heavy phase] could coexist in the system (in the n-dodecane solution). Mechanisms of formation of Tc(NO3)3(DBP)(HDBP)2 and Tc(NO3)2(DBP)2(HDBP)2 are proposed.

Insights into the effect of glucose on the binding between human serum albumin and the nonsteroidal anti-inflammatory drug nimesulide

Glucose interacts with human serum albumin (HSA, the main protein responsible for the biodistribution of drugs in the bloodstream) and consequently affects the binding capacity of exogenous compounds. Thus, in this work, the interactive profile between HSA and the anti-inflammatory drug nimesulide (NMD, used mainly by patients with diabetic neuropathy to relieve acute or chronic pains) was characterized in nonglycemic, normoglycemic (80 mg/dL), and hyperglycemic (320 mg/dL) conditions by biophysics techniques. There is a spontaneous and ground-state association HSA:NMD under physiological conditions. Therefore, the Stern-Volmer constant (Ksv) can also be used to estimate the binding affinity. The Ksv values for nonglycemic, normoglycemic, and hyperglycemic conditions are around 104 M-1, indicating a moderate affinity of NMD to albumin that was slightly improved by glucose levels. Additionally, the binding is enthalpically and entropically driven mainly into subdomains IIA or IIIA. The binding perturbs weakly the α-helix content of albumin, however, glucose potentially stabilizes the tertiary structure, decreasing the structural perturbation upon NMD binding and improves the complex HSA:NMD stability. Overall, the biophysical characterization indicated that glucose levels might slightly positively impact the pharmacokinetic profile of NMD, allowing NMD to achieve its therapeutical potential without affecting drastically its effective dosages.

2,4-disubstituted 6-fluoroquinolines as potent antiplasmodial agents: QSAR, homology modeling, molecular docking and ADMET studies

Objective

This work was designed to study 2,4-disubstituted 6-fluoroquinolines as antiplasmodial agents by using in silico techniques, to aid in the design of novel analogs with high potency against malaria and high inhibition of Plasmodium falciparum translation elongation factor 2 (PfeEF2), a novel drug target.

Methods

Quantitative structure-activity relationships (QSAR) of 2,4-disubstituted 6-fluoroquinolines were studied with the genetic function approximation technique in Material Studio software. The 3D structure of PfeEF2 was modeled in the SWISS-MODEL workspace through homology modeling. A molecular docking study of the modeled PfeEF2 and 2,4-disubstituted 6-fluoroquinolines was conducted with Autodock Vina in Pyrx software. Furthermore, the in silico pharmacokinetic properties of selected compounds were investigated.

Results

A robust, reliable and predictive QSAR model was developed that related the chemical structures of 2,4-disubstituted 6-fluoroquinolines to their antiplasmodium activities. The model had an internal squared correlation coefficient R2 of 0.921, adjusted squared correlation coefficient R2adj of 0.878, leave-one-out cross-validation coefficient Q2cv of 0.801 and predictive squared correlation coefficient R2pred of 0.901. The antiplasmodium activity of 6-fluoroquinolines was found to depend on the n5Ring, GGI9, TDB7u, TDB8u and RDF75i physicochemical properties: n5Ring, TDB8u and RDF75i were positively associated, whereas GGI9 and TDB7u were negatively associated, with the antiplasmodium activity of the compounds. Stable complexes formed between the compounds and modeled PfeEF2, with binding affinity ranging from -8.200 to -10.700 kcal/mol. Compounds 5, 11, 16, 22 and 24 had better binding affinities than quinoline-4-carboxamide (DDD107498), as well as good pharmacokinetic properties, and therefore may be better inhibitors of this novel target.

Conclusion

QSAR and docking studies provided insight into designing novel 2,4-disubstituted 6-fluoroquinolines with high antiplasmodial activity and good structural properties for inhibiting a novel antimalarial drug target.

Current Perspectives on Biological Screening of Newly Synthetised Sulfanilamide Schiff Bases as Promising Antibacterial and Antibiofilm Agents

Growing resistance to antimicrobials, combined with pathogens that form biofilms, presents significant challenges in healthcare. Modifying current antimicrobial agents is an economical approach to developing novel molecules that could exhibit biological activity. Thus, five sulfanilamide Schiff bases were synthesized under microwave irradiation and characterized spectroscopically and in silico. They were evaluated for their antimicrobial and antibiofilm activities against both Gram-positive and Gram-negative bacterial strains. Their cytotoxic potential against two cancer cell lines was also determined. Gram-positive bacteria were susceptible to the action of these compounds. Derivatives 1b and 1d inhibited S. aureus's growth (MIC from 0.014 mg/mL) and biofilm (IC from 0.029 mg/mL), while compound 1e was active against E. faecalis's planktonic and sessile forms. Two compounds significantly reduced cell viability at 5 μg/mL after 24 h of exposure (1d-HT-29 colorectal adenocarcinoma cells, 1c-LN229 glioblastoma cells). A docking study revealed the increased binding affinities of these derivatives compared to sulfanilamide. Hence, these Schiff bases exhibited higher activity compared to their parent drug, with halogen groups playing a crucial role in both their antimicrobial and cytotoxic effects.

Profiling the Interaction between Human Serum Albumin and Clinically Relevant HIV Reverse Transcriptase Inhibitors

Tenofovir (TFV) is the active form of the prodrugs tenofovir disoproxil fumarate (TDF) and tenofovir alafenamide (TAF), both clinically prescribed as HIV reverse transcriptase inhibitors. The biophysical interactions between these compounds and human serum albumin (HSA), the primary carrier of exogenous compounds in the human bloodstream, have not yet been thoroughly characterized. Thus, the present study reports the interaction profile between HSA and TFV, TDF, and TAF via UV-Vis, steady-state, and time-resolved fluorescence techniques combined with isothermal titration calorimetry (ITC) and in silico calculations. A spontaneous interaction in the ground state, which does not perturb the microenvironment close to the Trp-214 residue, is classified as weak. In the case of HSA/TFV and HSA/TDF, the binding is both enthalpically and entropically driven, while for HSA/TAF, the binding is only entropically dominated. The binding constant (Ka) and thermodynamic parameters obtained via ITC assays agree with those obtained using steady-state fluorescence quenching measurements, reinforcing the reliability of the data. The small internal cavity known as site I is probably the main binding pocket for TFV due to the low steric volume of the drug. In contrast, most external sites (II and III) can better accommodate TAF due to the high steric volume of this prodrug. The cross-docking approach corroborated experimental drug-displacement assays, indicating that the binding affinity of TFV and TAF might be impacted by the presence of different compounds bound to albumin. Overall, the weak binding capacity of albumin to TFV, TDF, and TAF is one of the main factors for the low residence time of these antiretrovirals in the human bloodstream; however, positive cooperativity for TAF and TDF was detected in the presence of some drugs, which might improve their residence time (pharmacokinetic profile).

Separation of undeuterated and partially deuterated enantioisotopologues of some amphetamine derivatives on achiral and polysaccharide-based chiral columns in high-performance liquid chromatography

The different behavior of enantiomers of chiral compounds in non-isotropic environments (among them in living organism) is well known. On the other hand, the importance of a kinetic isotope effect in the biomedical field has become evident during past few decades. Thus, separation of both, enantiomers and isotopologues is now critical. Only very few published studies have attempted the simultaneous separation of enantioisotopologues. In this article we report baseline separation of partially deuterated isotopologues of a few amphetamine derivatives in high-performance liquid chromatography (HPLC) using achiral columns. In addition, the simultaneous separations of enantiomers and isotopologues (i.e. enantioisotopologues) were attempted on polysaccharide-based chiral columns. For several compounds the isotope effect was tunable and could be switched from a "normal" to "inverse" by making changes to the mobile-phase composition. A stronger isotope effect was observed in acetonitrile-containing mobile phases compared to methanol-containing ones with both chiral and achiral columns. In a separation system where both "normal" and "inverse" isotope effects were observed the "normal" isotope effect was favored in polar organic solvents while increasing content of the aqueous component in the reversed-phase (RP) mobile phase favored an "inverse" isotope effect. This observation indicates that polar, hydrogen bonding-type noncovalent interactions are involved in the "normal" isotope effect, while apolar hydrophobic-type interactions are mostly responsible for the "inverse" isotope effect.

Electron beam-induced demetallation of Fe, Co, Ni, Cu, Zn, Pd, and Pt metalloporphyrins: insights in e-beam chemistry and metal cluster formations

Electron beams are versatile tools for nanoscale fabrication processes, however, the underlying e-beam chemistry remains in its infancy. Through operando transmission electron microscopy investigations, we elucidate a redox-driven cargo release of individual metal atoms triggered by electron beams. The chosen organic delivery molecule, tetraphenylporphyrin (TPP), proves highly versatile, forming complexes with nearly all metals from the periodic table and being easily processed in solution. A comprehensive cinematographic analysis of the dynamics of single metal atoms confirms the nearly instantaneous ejection of complexed metal atoms under an 80 kV electron beam, underscoring the system's broad versatility. Providing mechanistic insights, we employ density functional theory to support the proposed reductive demetallation pathway facilitated by secondary electrons, contributing novel perspectives to electron beam-mediated chemical reaction mechanisms. Lastly, our findings demonstrate that all seven metals investigated form nanoclusters once ejected from TPP, highlighting the method's potential for studying and developing sustainable single-atom and nanocluster catalysts.

Dinuclear copper(II) complexes with a bridging bis(chalcone) ligand reveal considerable in vitro cytotoxicity on human cancer cells and enhanced selectivity

A bis(chalcone) molecule (H2L) was synthesized via Aldol's condensation from terephthalaldehyde and 2'-hydroxyacetophenone and it was used as bridging ligand for the preparation of five dinuclear copper(II) complexes of the composition [Cu(NN)(μ-L)Cu(NN)](NO3)2⋅nH2O (n = 0-2) (1-5), where NN stands for a bidentate N-donor ligand such as phen (1,10-phenanthroline, 1), bpy (2,2'-bipyridine, 2), mebpy (5,5'-dimethyl-2,2'-dipyridine, 3), bphen (bathophenanthroline, 4) and nphen (5-nitro-1,10-phenanthroline, 5). The compounds were characterized by different suitable techniques to confirm their purity, composition, and structure. Moreover, the products were evaluated for their in vitro cytotoxicity on a panel of human cancer cell lines: ovarian (A2780), ovarian resistant to cisplatin (A2780R), prostate (PC3), osteosarcoma (HOS), breast (MCF7) and lung (A549), and normal fibroblasts (MRC-5), showing significant cytotoxicity in most cases, with IC50 ≈ 0.35-7.8 μM. Additionally, the time-dependent cytotoxicity and cellular uptake of copper, together with flow cytometric studies concerning cell-cycle arrest, induction of cell death and autophagy and induction of intracellular ROS/superoxide production in A2780 cells, were also performed. The results of biological testing on A2780 cells pointed out a possible mechanism of action characterized by the G2/M cell cycle arrest and induction of apoptosis by triggering the intrinsic signalling pathway associated with the damage of mitochondrial structure and depletion of mitochondrial membrane potential. SYNOPSIS: Dinuclear Cu(II) complexes bearing a bridging bis(chalcone) ligand revealed high in vitro cytotoxicity, initiated A2780 cell arrest at G2/M phase and efficiently triggered intrinsic pathway of apoptosis.

Integrating multiscale and machine learning approaches towards the SAMPL9 log P challenge

The partition coefficient (log P) is an important physicochemical property that provides information regarding a molecule's pharmacokinetics, toxicity, and bioavailability. Methods to accurately predict the partition coefficient have the potential to accelerate drug design. In an effort to test current methods and explore new computational techniques, the statistical assessment of the modeling of proteins and ligands (SAMPL) has established a blind prediction challenge. The ninth iteration challenge was to predict the toluene-water partition coefficient (log Ptol/w) of sixteen drug molecules. Herein, three approaches are reported broadly under the categories of quantum mechanics (QM), molecular mechanics (MM), and data-driven machine learning (ML). The three blind submissions yield mean unsigned errors (MUE) ranging from 1.53-2.93 log Ptol/w units. The MUEs were reduced to 1.00 log Ptol/w for the QM methods. While MM and ML methods outperformed DFT approaches for challenge molecules with fewer rotational degrees of freedom, they suffered for the larger molecules in this dataset. Overall, DFT functionals paired with a triple-ζ basis set were the simplest and most effective tool to obtain quantitatively accurate partition coefficients.

Solution and Solvent-Free Stopper Exchange Reactions for the Preparation of Pillar[5]arene-containing [2] and [3]Rotaxanes

Diamine reagents have been used to functionalize a [2]rotaxane building block bearing an activated pentafluorophenyl ester stopper. Upon a first acylation, an intermediate host-guest complex with a terminal amine function is obtained. Dissociation of the intermediate occurs in solution and acylation of the released axle generates a [2]rotaxane with an elongated axle subunit. In contrast, the corresponding [3]rotaxane can be obtained if the reaction conditions are appropriate to stabilize the inclusion complex of the mono-amine intermediate and the pillar[5]arene. This is the case when the stopper exchange is performed under mechanochemical solvent-free conditions. Alternatively, if the newly introduced terminal amide group is large enough to prevent the dissociation, the second acylation provides exclusively a [3]rotaxane. On the other hand, detailed conformational analysis has been also carried out by variable temperature NMR investigations. A complete understanding of the shuttling motions of the pillar[5]arene subunit along the axles of the rotaxanes reported therein has been achieved with the help of density functional theory calculations.

Identification of estrogen receptor agonists among hydroxylated polychlorinated biphenyls using classification-based quantitative structure-activity relationship models

Identification of estrogen receptor (ER) agonists among environmental toxicants is essential for assessing the potential impact of toxicants on human health. Using 2D autocorrelation descriptors as predictor variables, two binary logistic regression models were developed to identify active ER agonists among hydroxylated polychlorinated biphenyls (OH-PCBs). The classifications made by the two models on the training set compounds resulted in accuracy, sensitivity and specificity of 95.9 %, 93.9 % and 97.6 % for ERα dataset and 91.9 %, 90.9 % and 92.7 % for ERβ dataset. The areas under the ROC curves, constructed with the training set data, were found to be 0.985 and 0.987 for the two models. Predictions made by models I and II correctly classified 84.0 % and 88.0 % of the test set compounds and 89.8 % and 85.8% of the cross-validation set compounds respectively. The two classification-based QSAR models proposed in this paper are considered robust and reliable for rapid identification of ERα and ERβ agonists among OH-PCB congeners.

Enzymatic-related network of catalysis, polyamine, and tumors for acetylpolyamine oxidase: from calculation to experiment

The regulation of enzymes and development of polyamine analogs capable of controlling the dynamics of endogenous polyamines to achieve anti-tumor effects is one of the biggest challenges in polyamine research. However, the root of the problem remains unsolved. This study represents a significant milestone as it unveils, for the first time, the comprehensive catalytic map of acetylpolyamine oxidase that includes chemical transformation and product release kinetics, by utilizing multiscale simulations with over six million dynamical snapshots. The transportation of acetylspermine is strongly exothermic, and high binding affinity of enzyme and reactant is observed. The transfer of hydride from polyamine to FAD is the rate-limiting step, via an H-shift coupled electron transfer mechanism. The two products are released in a detour stepwise mechanism, which also impacts the enzymatic efficiency. Inspired by these mechanistic insights into enzymatic catalysis, we propose a novel strategy that regulates the polyamine level and catalytic progress through the action of His64. Directly suppressing APAO by mutating His64 further inhibited growth and migration of tumor cells and tumor tissue in vitro and in vivo. Therefore, the network connecting microcosmic and macroscopic scales opens up new avenues for designing polyamine compounds and conducting anti-tumor research in the future.

Excited state hydrogen or proton transfer pathways in microsolvated n-cyanoindole fluorescent probes

The sensitivity of the fluorescence properties of n-cyanoindole (n-CNI) fluorescent probes to the microenvironment makes them potential reporters of protein conformation and hydration. The fluorescence intensity of 5-CNI, 6-CNI, and 7-CNI is quenched when exposed to water solvent whereas substitution on position 4 of indoles dramatically increases it. A potential mechanism for this sensitivity to water may be similar to that found in indole. The fluorescence of indole is found to be quenched when interacting with water and ammonia solvent molecules via radiationless decay through an S1 (πσ*)/S0 conical intersection caused by excited state proton or hydrogen transfer to the solvent molecules. In this study we examine this fluorescence quenching mechanism along the N-H bond stretch of n-CNI probes using water cluster models and quantum mechanical calculations of the excited states. We find that n-CNI-(H2O)1-2 clusters form cyclic or non-cyclic structures via hydrogen bonds which lead to different photochemical reaction paths that can potentially quench the fluorescence by undergoing internal conversion from S1 to S0. However, the existence of a high energy barrier along the potential energy surface of the S1 state in most cases prevents this from occurring. We show that substitution on position 4 leads to the highest energy barrier that prevents the fluorophore from accessing these non-radiative channels, in agreement with its high intensity. We also find that the energy barrier in the S1 state of non-cyclic 5-CNI-(H2O)1-2 excited complexes decreases as the number of water molecules increases, which suggests great sensitivity of the fluorescence quenching on the aqueous environment.

Binary Mixtures of Choline Acetate and Tetrabutylammonium Acetate with Natural Organic Acids by Vibrational Spectroscopy and Molecular Dynamics Simulations

We present a study of several mixtures obtained by the mixing of two organic acetate-based salts (choline acetate, ChAc, or tetrabutylammonium acetate, TBAAc) with three different natural organic acids (ascorbic acid, AA, citric acid, CA, and maleic acid, MA). The structures of the starting materials and of the mixtures were characterized by infrared spectroscopy (FT-IR) and classic molecular dynamics simulations (MD). The thermal behavior was characterized by differential scanning calorimetry (DSC) and thermogravimetry analysis (TGA). The obtained mixtures, especially the ChAc-based ones, strongly tend to vitrify at low temperatures and are stable up to 100-150 °C. The FTIR measurements suggest the formation of a strong H-bond network: the coordination between acids and ChAc or TBAAc takes place by the donation of the H-bond by the acids to the oxygen of the acetate anion, which acts as an acceptor (HBA). The comparison with MD analysis indicates that acids predominantly exploit their more acidic hydrogens. In particular, we observe the progressive shift of νC═O and νOH when the ratios of acids increase. The structural differences between the two studied cations influence the spatial distribution of the components in the mixture bulk phases. In particular, the analysis of the theoretical structure function I(q) of the TBAAc-based systems shows the presence of important prepeaks at low q, a sign of the formation of apolar domain, due to the nanosegregation of the alkyl chains.

Effects of intramolecular hydrogen bonding on nuclear magnetic resonance, electron paramagnetic resonance and molecular docking studies: Mexiletine molecule

CONTEXT

In this study, the molecular structure of the mexiletine molecule was investigated. Since the Mexiletine molecule is a drug active ingredient, its molecular structure and spectroscopic properties are important. The effects of intramolecular hydrogen bonding on Nuclear Magnetic Resonance Parameters (NMR), Electron Paramagnetic Resonance (EPR) parameters and molecular docking studies were examined in the mexiletine molecule. The effects of intramolecular hydrogen bonding on EPR parameters and molecular docking studies are the most important steps for this study.

METHOD

Conformational space scanning required for molecular structure calculations was carried out with the Molecular Mechanic Force Field method. DFT method with 6-311 +  + G(d,p) basis set level was used to obtain the most stable structure among the conformations. NMR parameters (1H and 13C chemical shift values) were also performed using the same basis set as the DFT method. The radicals created to calculate the Electron Paramagnetic Resonance parameters were modeled using the DFT/B3LYP/6-311 +  + G(d,p) method basis set level. Molecular Docking studies were carried out with the Autodock vina program.

Doubly Bridged Anthracenes: Blue Emitters for OLEDs

The photooxidative stability of a series of doubly bridged anthracenes was evaluated after their preparation via twofold macrocyclization of a bis(resorcinyl)anthracene. Lightfastness correlates with the energy levels of the highest occupied molecular orbital (HOMO), resulting in superior stability of the tetraesters compared to the tetraethers. The lengths and steric demand of the linker only plays a minor role for the ester-based compounds, which can be prepared in reasonable yields and thus tested in proof-of-concept organic light-emitting diodes. Double ester-bridging allows deep blue electro-luminescence, highlighting the importance of the choice of the functional groups used for macrocyclization.

Stereogenic Harmony Fabricated Mechanoresponsive Homochiral Triphenylalanine Analogues with Synergistic Antibacterial Performances: A Potential Weapon for Dermal Wound Management

The wound recovery phenomenon remains as one of the long challenging concerns worldwide. In search of user-friendly dressing materials, in this report, we fabricated a rational combinatorial strategy utilizing stereogenic harmony in a triphenylalanine fragment and appending it to δ-amino valeric acid at the N-terminus (hydrogelators I-VII) such that a potential scaffold could be fished out from the design. Our investigations revealed that all the hydrogelators displayed not only excellent self-healing performance as well as high mechanical strength at physiological pH but also mechanical stress-triggered gel-sol-gel transition properties. The structural and morphological investigation confirmed the presence of β-sheet-like assemblies stabilized by intermolecular H-bonding and π-π interactions. Moreover, these scaffolds showed substantial antibacterial as well as antifungal efficacy against common wound pathogens, i.e, four Gram-positive bacteria (Staphylococcus aureus, Streptococcus mutans, B. subtilis, E. fecalis), four Gram-negative bacteria (Escherichia coli, Klebsiella pneumonia, P. aerugonosa, Proteus spp.), and two fungal strains (C. albicans and A. niger). The manifestation of consistent antioxidant properties might be due to the enhancement of amphiphilicity in hydrogelators, which has led to the generation of reactive oxygen species (ROS) in a facile manner, a probable mechanism to damage the microbial membrane, the driving force behind the antimicrobial efficacy. Also, the constructs exhibited proteolytic resistance and remarkable biocompatibility toward mammalian cells. Thus, based on the above benchmarks, the homochiral hydrogelator IV was seived out from a pool of seven, and we proceeded toward its in vivo evaluation using full-thickness excisional wounds in Wister rats. The scaffolds also accentuated the re-epithelialization as well in comparison to the negative control, thereby facilitating the wound closure process in a very short span of time (10 days). Overall, our in vitro and in vivo analysis certifies hydrogelator IV as an ideal dressing material that might hold immense promise for future wound care management.

Probing the Thermochemistry Properties and Rate Kinetics of Trimethyl Phosphate (TMP): An H-Atom Abstraction (HAA) Reactions Perspective

Trimethyl Phosphate (TMP), an organophosphorus liquid compound, is valued for its versatile qualities and applications in various fields. In modern chemical research and industry, processes involving Trimethyl Phosphate are optimized for minimal negative environmental impact, and scientific advancement is driven by adherence to stringent regulations to provide sustainable solutions and resource preservation. Thermochemical insights enhance our understanding of monomer incorporation, initiation, and propagation energetics. This study comprehensively investigates the thermochemistry and rate kinetics that govern H-atom abstractions in TMP through advanced computational techniques. The theoretical framework encompasses methodologies for conducting conformer searches, exploring transition states, and performing energy calculations. This study calculates rate constants for eight H-atom abstraction reactions involving TMP with stable species, O2 (oxygen), H (hydrogen), and radicals [ȮH (hydroxyl), ĊH3 (methyl), CH3Ȯ (methoxy), HȮ2 (hydroperoxyl), ṄH2 (amino), and ĊN (cyano)], and further analogies are related to barrier heights. Bond dissociation energies are also determined, highlighting TMP's susceptibility to various reaction pathways. The discussion and findings elucidate the need for further experimental validation for practical applications of TMP in chemical synthesis, combustion, flame-retardant technologies, environmental processes, and pharmaceutical research.

Photoactive glycoconjugates with a very large Stokes shift: synthesis, photophysics, and copper(II) and BSA sensing

This study presents the synthesis of novel glycoconjugates by connecting benzazole and carbohydrate units with a 1,2,3-triazole linker. A simple synthetic route employing a copper(I) catalyzed azide-alkyne 1,3-dipolar cycloaddition (CuAAC) was utilized. The synthesized compounds exhibit excited-state intramolecular proton transfer (ESIPT), resulting in longer wavelength emission with a significantly large Stokes shift (∼10 000 cm-1). These compounds show potential as chemical sensors due to their ability to detect Cu2+ ions, causing a decrease in fluorescence emission (turn-off effect). Additionally, they demonstrate strong interaction with proteins, exemplified by their interaction with bovine serum albumin (BSA) as a model protein.

Assessing Squarates as Amine-Reactive Probes

Probes that covalently label protein targets facilitate the identification of ligand-binding sites. Lysine residues are prevalent in the proteome, making them attractive substrates for covalent probes. However, identifying electrophiles that undergo amine-specific, regioselective reactions with binding site lysine residues is challenging. Squarates can engage in two sequential conjugate addition-elimination reactions with amines. Nitrogen donation reduces the second reaction rate, making the mono squaramide a mild electrophile. We postulated that this mild electrophilicity would demand a longer residence time near the amine, affording higher selectivity for binding site lysines. Therefore, we compared the kinetics of squarate and monosquaramide amine substitution to alternative amine bioconjugation handles. The data revealed that N-hydroxy succinimidyl esters react 4 orders of magnitude faster, consistent with their labeling promiscuity. Squarate reactivity can be tuned by a substitution pattern. Electron-withdrawing groups on the vinylogous ester or amide increase reaction rates. Dithionosquarates react more rapidly than squarates, while vinylogous thioester analogs, dithiosquarates, react more slowly. We assessed squarate selectively using the UDP-sugar processing enzyme GlfT2 from Mycobacterium tuberculosis, which possesses 21 surface-exposed lysines. The reaction predominately modified one lysine proximal to a binding site to afford covalent inhibition. These findings demonstrate the selectivity of squaric esters and squaramides, which is a critical feature for affinity-based chemoproteomic probes.

Anti-Proliferative Potential of Cynaroside and Orientin-In Silico (DYRK2) and In Vitro (U87 and Caco-2) Studies

Luteolin derivates are plant compounds with multiple benefits for human health. Stability to heat and acid hydrolysis and high resistance to (auto)oxidation are other arguments for the laden interest in luteolin derivates today. The present study was designed to compare the in silico and in vitro anti-proliferative potential of two luteolin derivates, luteolin-7-O-glucoside/cynaroside (7-Lut) and luteolin-8-C-glucoside/orientin (8-Lut). In silico investigations were carried out on the molecular target, namely, the human dual specificity tyrosine phosphorylation-regulated kinase 2 (DYRK2) in association with its natural ligand, curcumin (PDB ID: 5ZTN), by CLC Drug Discovery Workbench v. 1.5.1. software and Molegro Virtual Docker (MVD) v. MVD 2019.7.0. software. In vitro studies were performed on two human tumor cell lines, glioblastoma (U87) and colon carcinoma (Caco-2), respectively. Altogether, docking studies have revealed 7-Lut and 8-Lut as effective inhibitors of DYRK2, even stronger than the native ligand curcumin; in vitro studies indicated the ability of both luteolin glucosides to inhibit the viability of both human tumor cell lines, up to 85% at 50 and 100 µg/mL, respectively; the most augmented cytotoxic and anti-proliferative effects were obtained for U87 exposed to 7-Lut (IC50 = 26.34 µg/mL). The results support further studies on cynaroside and orientin to create drug formulas targeting glioblastoma and colon carcinoma in humans.

Cu(I)-thioether coordination complexes based on a chiral cyclic β-amino acid ligand

Coordination complexes, particularly metalloproteins, highlight the significance of metal-sulfur bonds in biological processes. Their unique attributes inspire efforts to synthetically reproduce these intricate metal-sulfur motifs. Here, we investigate the synthesis and characterization of copper(I)-thioether coordination complexes derived from copper(I) halides and the chiral cyclic β-amino acid trans-4-aminotetrahydrothiophene-3-carboxylic acid (ATTC), which present distinctive structural properties and ligand-to-metal ratios. By incorporating ATTC as the ligand, we generated complexes that feature a unique chiral conformation and the capacity for hydrogen bonding, facilitating the formation of distinct geometric structures. Through spectroscopic analyses and density functional theory (DFT) calculations, we studied the complexes' optical properties, including their emission bands and variable second-harmonic generation (SHG) efficiencies, which vary based on the halide used. Our findings underscore the potential of the ATTC ligand in creating unusual coordination complexes and pave the way for further investigations into their potential applications, particularly within materials science.

Hexakis-TIPS-Alkynylated Nonacenes: Persistent and Processible

Four substituted nonacenes were prepared and characterized by UV-vis and EPR spectroscopy and X-ray crystallography. The compounds are the most stable and soluble nonacenes to date - due to six strategically placed triisopropylsilyl(TIPS)-ethynyl groups. They are stable for several weeks in the solid state. In dilute solution their half-life is 5-9 h. Crystal structure analyses of two nonacenes prove their structures. A nonacene derivative was tested in a solution-processed transistor and exhibits ambipolar charge transport (μe =0.007 cm2 /Vs; μh =0.023 cm2 /Vs).

Structural and vibrational investigations and molecular docking studies of a vinca alkoloid, vinorelbine

Vinorelbine, a vinca alkaloid, is an antimitotic drug that inhibits polymerisation process of tubulins to microtubules, and is widely used in cancer chemotherapy. Due to the importance of the structure-activity relationship, in this work the conformational preferences of the vinorelbine molecule were surched by PM3 method. The obtained lowest energy conformer was then optimized at DFT/B3LYP/6-31G(d,p) level of theory and the structural characteristics were determined. Frontier orbital (HOMO, LUMO) and molecular electrostatic potential (MEP) analyses were performed for the optimized structure. The experimental FT-IR, Raman and UV-VIS spectral data of vinorelbine along with the theoretical DFT/B3LYP/6-31G(d,p) calculations were investigated in detail. The vibrational wavenumbers were assigned based on the calculated potential energy distribution (PED) of the vibrational modes. To shed light into the anticancer property of vinorelbine as microtubule destabilizer, the most favourable binding mode and the interaction details between vinorelbine and tubulin were revealed by molecular docking studies of vinorelbine into the α,β-tubulin (PDB IDs: 4O2B; 1SA0; 7CNN) and binding free energies were calculated by the combination of Molecular Mechanics/Generalized Born Surface Area (MMGBSA) and Molecular Mechanics/Poisson-Boltzmann Surface Area (MM-PBSA) methods {MM/PB(GB)SA}. The calculated vinorelbine-7CNN binding free energy, using by MM/PB(GB)SA approach, was found to be the best (-50.39 kcal/mol), and followed by vinorelbine-4O2B (-28.5 kcal/mol) and vinorelbine-1SA0 (-17.59 kcal/mol) systems. Moreover, the interaction of vinorelbine with the cytochrome P450 enzymes (CYP), which are known to help in the metabolism of many drugs in the body, was investigated by docking studies against CYP2D6 and CYP3A4 targets.Communicated by Ramaswamy H. Sarma.

Boerechalasins A-G, cytochalasans from the fungus Boeremia exigua with anti-inflammatory and cytotoxic activities

Seven previously undescribed cytochalasans, namely, boerechalasins A-G, together with one analogue, were characterized from the solid culture of the fungus Boeremia exigua. Their structures and absolute configurations were elucidated on the basis of extensive spectroscopic analysis as well as electronic circular dichroism calculations. Remarkably, boerechalasin F possessed an unusual sulfoxide moiety that might be derived from methionine, while boerechalasin G had an unusual 5-methylcyclohexane-1,2,3-triol substituent at N-2 position. Boerechalasins A and E exhibited inhibitory activities against nitric oxide production in LPS-induced RAW264.7 macrophages with IC50 values of 21.9 and 5.7 μM, respectively. Boerechalasin F displayed cytotoxicity against human MCF‒7 cells with an IC50 value of 22.8 μM.

How to read optical properties of matter via the Kubo-Greenwood approach

Substances with a complex electronic structure exhibit non-Drude optical properties that are challenging to interpret experimentally and theoretically. In our recent paper [Phys. Rev. E 105, 035307 (2022)2470-004510.1103/PhysRevE.105.035307], we offered a computational method based on the continuous Kubo-Greenwood formula, which expresses dynamic conductivity as an integral over the electron spectrum. In this Letter, we propose a methodology to analyze the complex conductivity using liquid Zr as an example to explain its nontrivial behavior. To achieve this, we apply the continuous Kubo-Greenwood formula and extend it to include the imaginary part of the complex conductivity into the analysis. Our method is suitable for a wide range of substances, providing an opportunity to explain optical properties from ab initio calculations of any difficulty.

Dose-dependent binding behavior of anthraquinone derivative purpurin interacting with tau-derived peptide protofibril

Alzheimer's disease is hallmarked by microtubule-associated protein tau tangles and amyloid-β plaques. The β-structure propensity of tau inclusions is closely related to the hexapeptide motif VQIVYK (termed PHF6), and disruption of this motif prevents tau aggregation. Small-molecule inhibitors are considered a promising therapeutic strategy, but the molecular mechanisms underlying the correlation between dose and inhibitory effects are still unclear. In this work, we investigated the dose-induced influence of purpurin, an anthraquinone derivative, on the structural stability of the PHF6 fibrillar nucleus by performing microsecond all-atom molecular dynamics simulations in explicit water. The stability of PHF6 protofibrils of different sizes was first examined, and it was found that the structural stability of fibrillar oligomers increases with oligomer size, and that the octamer is the minimal stable nucleus for fibril formation. When purpurin molecules were added to the protofibril octamer at a low purpurin/peptide ratio, they bound to the octamer with different coupling states, and the different states may transition to each of the other states through an uncoupling state or directly through a short-time transition. With increasing purpurin/peptide ratio, purpurins tend to self-aggregate rather than bind to the protein surface. Interestingly, the contacts between individual purpurins and the octamer as a function of the purpurin number show a power-law behavior, which may serve as a useful indicator to reflect the binding efficiency of ligands to proteins in drug screening. The interaction analysis reveals that purpurin prefers to bind to the hydrophilic and aromatic Tyr and has the lowest probability with the hydrophobic Val located in the middle of PHF6. Aromatic stacking plays a key role in the octamer-purpurin interaction, in which the three aromatic rings of purpurin have different contributions. In addition, purpurin shows a remarkable disruptive effect on the protofibril octamer when the molar ratio of purpurin to peptide is 1 : 2; above this ratio, the binding mode and disruption effect of purpurin do not change significantly. Our work provides a detailed picture of the dynamics and interactions of purpurin binding to the PHF6 protofibril and expands the understanding of the dose-induced inhibitory mechanism.

Time-resolved imaging and analysis of the electron beam-induced formation of an open-cage metallo-azafullerene

The visualization of single-molecule reactions provides crucial insights into chemical processes, and the ability to do so has grown with the advances in high-resolution transmission electron microscopy. There is currently a limited mechanistic understanding of chemical reactions under the electron beam. However, such reactions may enable synthetic methodologies that cannot be accessed by traditional organic chemistry methods. Here we demonstrate the synthetic use of the electron beam, by in-depth single-molecule, atomic-resolution, time-resolved transmission electron microscopy studies, in inducing the formation of a doubly holed fullerene-porphyrin cage structure from a well-defined benzoporphyrin precursor deposited on graphene. Through real-time imaging, we analyse the hybrid's ability to host up to two Pb atoms, and subsequently probe the dynamics of the Pb-Pb binding motif in this exotic metallo-organic cage structure. Through simulation, we conclude that the secondary electrons, which accumulate in the periphery of the irradiated area, can also initiate chemical reactions. Consequently, designing advanced carbon nanostructures by electron-beam lithography will depend on the understanding and limitations of molecular radiation chemistry.

The anti-infective crotalicidin peptide analog RhoB-Ctn[1-9] is harmless to bovine oocytes and able to induce parthenogenesis in vitro

Crotalicidin is a cathelicidin-related anti-infective (antimicrobial) peptide expressed in the venom glands of the South American rattlesnake Crotalus durissus terrificus. Congener peptides of crotalicidin, named vipericidins, are found in other pit vipers inhabiting South America. Crotalicidin is active against bacteria and pathogenic yeasts and has anti-proliferative activity for some cancer cells. The structural dissection of crotalicidin produced fragments (e.g., Ctn [15-34]) with multiple biological functionalities that mimic the native peptide. Another structural characteristic of crotalidicin and congeners is a unique repetitive stretch of amino acid sequences in tandem embedded in their primary structures. One of the encrypted vipericidn peptides (Ctn [1-9]) was synthesized, and the analog covalently conjugated with rhodamine B (RhoB-Ctn [1-9]) displayed considerable antimicrobial activity and selective cytotoxicity. Methods to evaluate antimicrobial peptides' toxicity include lysis of red blood cells (hemolysis) in vitro and cytotoxicity of healthy cultured cells (e.g., fibroblasts). Here, as a non-conventional model of toxicity, the bovine oocytes were exposed to two standardized concentrations of RhoB-Ctn [1-9], and embryo viability and development at its first stage of cleavage (division of cells) and blastocyst formation were evaluated. Oocytes treated with peptide at 10 and 40 μM induced cleavage rates of 44.94% and 51.53%, resulting in the formation of blastocysts of 7.07% and 11.73%, respectively. Light sheet microscopy and in silico prediction analysis indicated that RhoB-Ctn [1-9] peptide interacts with zona pellucida and internalizes into bovine oocytes and developing embryos. The ADMET prediction estimated good bioavailability of RhoB-Ctn [1-9]. In conclusion, the peptide appeared harmless to bovine oocytes and, remarkably, activated the parthenogenesis in vitro.

Influence of Protonation on the Norepinephrine Inhibiting α-Synuclein 71-82 Oligomerization

The pathogenesis of Parkinson's disease (PD) is closely linked to the massive presence of Lewy vesicles and Lewy axons in the cytoplasm of neurons, mainly consisting of α-synuclein (αS). Norepinephrine (NE), whose secretion can be increased by exercise, has been demonstrated to prevent the fibrillation of αS and to break down the mature αS fibrils. In this work, we focus on the influence of protonation on the inhibitory ability of NE by using amyloid core fragment αS71-82 as a template. All-atom replica-exchange molecular dynamics simulations (accumulating to 33.6 μs) in explicit water were performed to explore the inhibitory effect of protonated and nonprotonated NE on αS oligomerization. Our results show that NE/NE+ can lead to a significant decrease in β-sheet content with increasing temperature, while isolated αS maintains relatively higher β-sheet conformations until 363 K, implying that both NE and NE+ can lower the critical temperature required for αS fibril decomposition. NE and NE+ also lead to the formation of less compact αS oligomers by preventing the backbone hydrogen bonds and the side-chain packing. The protonation would affect the binding affinity, interaction modes, and binding intensity of NE with αS. Interesting, NE and NE+ have a distinct binding free energy in the electrostatic and solvation terms, which mostly counter each other and produce a weak binding intensity with αS. Our work contributes to a better understanding of the inhibitory mechanism of NE and NE+ on αS oligomerization relevant to PD pathogenesis, which may provide clues for the design of antiamyloid medicine.

Cooperative and Orthogonal Switching in the Solid State Enabled by Metal-Organic Framework Confinement Leading to a Thermo-Photochromic Platform

Cooperative behavior and orthogonal responses of two classes of coordinatively integrated photochromic molecules towards distinct external stimuli were demonstrated on the first example of a photo-thermo-responsive hierarchical platform. Synergetic and orthogonal responses to temperature and excitation wavelength are achieved by confining the stimuli-responsive moieties within a metal-organic framework (MOF), leading to the preparation of a novel photo-thermo-responsive spiropyran-diarylethene based material. Synergistic behavior of two photoswitches enables the study of stimuli-responsive resonance energy transfer as well as control of the photoinduced charge transfer processes, milestones required to advance optoelectronics development. Spectroscopic studies in combination with theoretical modeling revealed a nonlinear effect on the material electronic structure arising from the coordinative integration of photoresponsive molecules with distinct photoisomerization mechanisms. Thus, the reported work covers multivariable facets of not only fundamental aspects of photoswitch cooperativity, but also provides a pathway to modulate photophysics and electronics of multidimensional functional materials exhibiting thermo-photochromism.

Role of Inner Molecular Orbitals in High-Harmonic Generation Spectra of Aligned Uracil

In this work, we decompose the high-harmonic generation (HHG) signal of aligned gas-phase uracil into single molecular-orbital (MO) contributions. We compute HHG spectra for a pulse linearly polarized perpendicular to the molecular plane, with an intensity of 0.6 and 0.85 × 1014 W/cm2 and a wavelength of 800 nm. We use the real-time time-dependent Configuration Interaction with singles method, coupled to a Gaussian-based representation of the time-dependent wavefunction. The strong-field dynamics is affected by the energy of the ionization/recombination channels and by the coupling between the orbital symmetry and laser polarization. In the configuration studied here, we expect that π-type MOs favorably couple with the incoming pulse and play a substantial role in generating the HHG spectrum. Indeed, we show that HOMO, HOMO - 1, and HOMO - 4, which all are π-like, determine the intensity of harmonic peaks at different energies, while HOMO - 2 and HOMO - 3 provide a smaller contribution. It is worth mentioning that HOMO - 4 produces a stronger signal than that from HOMO - 1, even though the corresponding ionization energy, in an one-electron picture, is around 2.5 eV larger and more than 4 eV larger than the HOMO one.

Deciphering the Inhibitory Mechanism of Naphthoquinone-Dopamine on the Aggregation of Tau Core Fragments PHF6* and PHF6

The formation of neurofibrillary tangles by abnormal aggregation of tau protein is considered to be an important pathological characteristic of tauopathies, including Alzheimer's disease and chronic traumatic encephalopathy. Two hexapeptides 275VQIINK280 and 306VQIVYK311 in the microtubule binding region, named PHF6* and PHF6, are known to be aggregation-prone and responsible for tau fibrillization. Previous experiments reported that naphthoquinone-dopamine (NQDA) could effectively inhibit the aggregation of PHF6* and PHF6 and disrupt the fibrillar aggregates into nontoxic species, displaying a dual effect on the amyloid aggregation. However, the underlying molecular mechanism remains mostly elusive. Herein, we performed all-atom molecular dynamics (MD) simulations for 114 μs in total to systematically investigate the impacts of NQDA on the oligomerization of PHF6* and PHF6. The conformational ensembles of PHF6* and PHF6 peptides generated by replica exchange MD simulations show that NQDA could effectively prevent the hydrogen bond formation, reduce the ability of peptides to self-assemble into long β-strand and large β-sheets, and induce peptides to form a loosely packed and coil-rich oligomer. The interaction analysis shows that the binding of NQDA to PHF6* is mainly through hydrophobic interactions with residue I277 and hydrogen bonding interactions with Q276; for the PHF6 peptides, NQDA displays a strong π-π stacking interaction with residue Y310, thus impeding the Y310-Y310 π-π stacking and I308-Y310 CH-π interactions. The DA group of NQDA displays a stronger cation-π interaction than the NQ group, while the NQ group exhibits a stronger π-π stacking interaction. MD simulations demonstrate that NQDA prevents the conformational conversion to β-sheet-rich aggregates and displays an inhibitory effect on the oligomerization dynamics of PHF6* and PHF6. Our results provide a complete picture of inhibitory mechanisms of NQDA on PHF6* and PHF6 oligomerization, which may pave the way for designing drug candidates for the treatment of tauopathies.

Molecular modeling of Mannich phenols as reactivators of human acetylcholinesterase inhibited by A-series nerve agents

The A-series is the most recent generation of chemical warfare nerve agents (CWA) which act directly on the inhibition of the human acetylcholinesterase (HssAChE) enzyme. These compounds lack accurate experimental data on their physicochemical properties, and there is no evidence that traditional antidotes effectively reactivate HssAChE inhibited by them. In the search for potential antidotes, we employed virtual screening, molecular docking, and molecular dynamics (MD) simulations for the theoretical assessment of the performance of a library of Mannich phenols as potential reactivators of HssAChE inhibited by the Novichok agents A-230, A-232, and A-234, in comparison with the commercial oximes pralidoxime (2-PAM), asoxime (HI-6), trimedoxime (TMB-4), and obidoxime. Following the near-attack conformation (NAC) approach, our results suggest that the compounds assessed would face difficulties in triggering the proposed nucleophilic in-line displacement mechanism. Despite this, it was observed that certain Mannich phenols presented similar or superior results to those obtained by reference oximes against A-232 and A-234 model, suggesting that these compounds can adopt more favourable conformations. Additional binding energy calculations confirmed the stability of the model/ligands complexes and the reactivating potential observed in the molecular docking and MD studies. Our findings indicate that the Mannich phenols could be alternative antidotes and that their efficacy should be evaluated experimentally against the A-series CWA.

cis-Decalin-containing tetramic acids as inhibitors of insect steroidogenic glutathione S-transferase Noppera-bo

Decalin-containing tetramic acid is a bioactive scaffold primarily produced by filamentous fungi. The structural diversity of this group of compounds is generated by characteristic enzymes of fungal biosynthetic pathways, including polyketide synthase/nonribosomal peptide synthetase hybrid enzymes and decalin synthase, which are responsible for the construction of a linear polyenoyl tetramic acid structure and stereoselective decalin formation via the intramolecular Diels-Alder reaction, respectively. Compounds that differed only in the decalin configuration were collected from genetically engineered mutants derived from decalin-containing tetramic acid-producing fungi and used for a structure-activity relationship study. Our evaluation of biological activities, such as cytotoxicity against several cancer cell lines and antibacterial, antifungal, antimalarial, and mitochondrial inhibitory activities, demonstrated that the activity for each assay varies depending on the decalin configurations. In addition to these known biological activities, we revealed that the compounds showed inhibitory activity against the insect steroidogenic glutathione S-transferase Noppera-bo. Engineering the decalin configurations would be useful not only to find derivatives with better biological activities but also to discover overlooked biological activities.

Aggregation in Aqueous Solutions of 2-(Tetrafluoro(trifluoromethyl)-λ6-sulfanyl-ethan-1-ol (CF3SF4-ethanol)): A Comparison with Aqueous Trifluoroethanol and Hexafluoroisopropanol Using Molecular Dynamics Simulations and Dynamic Light Scattering Experiments

2-Tetrafluoro(trifluoromethyl)-λ6-sulfanylethan-1-ol (CF3SF4-ethanol) combines the polar hydrophobicity of tetrafluoro(trifluoromethyl)-λ6-sulfanyl (CF3SF4) group with the polarity of simple alcohols. The properties of aqueous solutions of the well-known fluorinated alcohols 2,2,2-trifluoroethanol (TFE) and 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) were compared with those of aqueous solutions of the novel CF3SF4-ethanol. Those properties were computed using all atom molecular dynamics simulations with OPLS-compatible parameters. DFT ab initio calculations were used to accurately describe the nonsymmetrical, hypervalent sulfur in CF3SF4-ethanol. Although the molecular and conformational characteristics of CF3SF4-ethanol are like those of both TFE and HFIP, the greater hydrophobicity and lower polarity of CF3SF4-ethanol resulted in solution phase aggregation at a much lower concentration. The properties computed for TFE and HFIP in this work were consistent with published computational and experimental studies. CF3SF4-ethanol is predicted to be environmentally benign and hence an excellent green solvent candidate while possessing many of the same properties as TFE or HFIP.