Insights into Hildebrand Solubility Parameters - Contributions from Cohesive Energies or Electrophilicity Densities?

We introduce certain concepts and expressions from conceptual density functional theory (DFT) to study the properties of the Hildebrand solubility parameter. The original form of the Hildebrand solubility parameter is used to qualitatively estimate solubilities for various apolar and aprotic substances and solvents and is based on the square root of the cohesive energy density. Our results show that a revised expression allows the replacement of cohesive energy densities by electrophilicity densities, which are numerically accessible by simple DFT calculations. As an extension, the reformulated expression provides a deeper interpretation of the main contributions and, in particular, emphasizes the importance of charge transfer mechanisms. All calculated values of the Hildebrand parameters for a large number of common solvents are compared with experimental values and show good agreement for non- or moderately polar aprotic solvents in agreement with the original formulation of the Hildebrand solubility parameters. The observed deviations for more polar and protic solvents define robust limits from the original formulation which remain valid. Likewise, we show that the use of machine learning methods leads to only slightly better predictability.

Investigating sensitization activity of azobenzene disperse dyes via the Direct Peptide Reactivity Assay (DPRA)

Azobenzene disperse dyes are the fastest-growing category of commercial dyestuffs and have been found in indoor house dust and in children's polyester apparel. Azobenzene disperse dyes are implicated as potentially allergenic; however, little experimental data is available on allergenicity of these dyes. Here, we examine the binding of azobenzene disperse dyes to nucleophilic peptide residues as a proxy for their potential reactivity as electrophilic allergenic sensitizers. The Direct Peptide Reactivity Assay (DPRA) was utilized via both a spectrophotometric method and a high-performance liquid chromatography (HPLC) method. We tested dyes purified from commercial dyestuffs as well as several known transformation products. All dyes were found to react with nucleophilic peptides in a dose-dependent manner with pseudo-first order kinetics (rate constants as high as 0.04 h-1). Rates of binding reactivity were also found to correlate to electrophilic properties of dyes as measured by Hammett constants and electrophilicity indices. Reactivities of polyester shirt extracts were also tested for DPRA activity and the shirt extracts with high measured abundances of azobenzene disperse dyes were observed to induce greater peptide reactivity. Results suggest that azobenzene disperse dyes may function as immune sensitizers, and that clothing containing these dyes may pose risks for skin sensitization.

Synthesis and biological evaluation of 2-(Tetrazol-5-yl)sulfonylacetamides as inhibitors of Mycobacterium tuberculosis and Mycobacterium marinum

A series of 2-(tetrazol-5-yl)sulfonylacetamide derivatives were synthesized and evaluated for their in vitro inhibitory activity against Mycobacterium tuberculosis (Mtb) and Mycobacterium marinum (Mm). The most active compounds exhibited in vitro MIC90 values of 1.25 μg/mL against Mtb, but they were less effective against Mm (MIC90 ≥ 10 μg/mL). Despite the most active compounds having favourable physicochemical properties and one of them having a half-life of ∼3 h when incubated with mouse liver microsomes, two representative highly active compounds showed strong chemical reactivity to cysteine derivatives, as surrogate in vivo sulfur-centred nucleophiles, indicating excessive electrophilicity, and therefore, likely indiscriminate chemical reactivity in vivo, representing an unacceptably high risk of general toxicity, and low likelihood of being therapeutically effective.

Prediction of Nucleophilicity and Electrophilicity Based on a Machine Learning Approach

Nucleophilicity and electrophilicity dictate the reactivity of polar organic reactions. In the past decades, Mayr et al. established a quantitative scale for nucleophilicity (N) and electrophilicity (E), which proved to be useful tools for the rationalization of chemical reactivity. In this study, a holistic prediction model was developed through a machine-learning approach. rSPOC, an ensemble molecular representation with structural, physicochemical and solvent features, was developed for this purpose. With 1115 nucleophiles, 285 electrophiles, and 22 solvents, the dataset was currently the largest one for reactivity prediction. The rSPOC model trained with the Extra Trees algorithm showed high accuracy in predicting Mayr's N and E parameters with R2 of 0.92 and 0.93, MAE of 1.45 and 1.45, respectively. Furthermore, the practical applications of the model, for instance, nucleophilicity prediction of NAD(P)H and a series of enamines showed potential in predicting molecules with unknown reactivity within seconds. An online prediction platform (http://isyn.luoszgroup.com/) was constructed based on the current model, which is available free to the scientific community.

Engineering piperlongumine-inspired analogs as Nrf2-dependent neuroprotectors against oxidative damage by an electrophilicity-based strategy

Oxidative stress contributes significantly to the development of neurodegenerative diseases, thus developing nuclear factor erythroid 2-related factor 2 (Nrf2)-dependent neuroprotectors is highly required for either prevention or treatment of these diseases. This work highlights an electrophilicity-based strategy that allows finding more active Nrf2-dependent neuroprotectors than natural piperlongumine (PL). Electrophilic modification was applied on both the exocylic and endocyclic Michael acceptors of PL, which includes placement of an electron-withdrawing trifluoromethyl group on its aromatic ring in the ortho, meta, or para position to the exocyclic olefin, and further introduction of an electron-withdrawing α-chlorine on its lactam ring. From a panel of PL analogs, we identified PLCl-4CF₃, characterized by the presence of p-trifluoromethyl group and α-chlorine, to be significantly superior to the parent PL in protecting PC12 cells from oxidative damage induced by 6-hydroxydopamine hydrochloride. Mechanistic studies reveal that the increased electrophilicity of PLCl-4CF₃ in its two Michael acceptors allows its ability to covalently modify Cys-151 at Keap1, facilitating inhibition against Nrf2 ubiquitination, translocation of Nrf2 into the nucleus, induction of phase 2 enzymes and final protection of PC12 cells from oxidative damage.

Theoretical prediction on the hydrolysis rate of the new types of nerve agents: A density functional study

Although the hydrolysis mechanism of the nerve agents, which is the main decontamination pathway, has been studied experimentally and theoretically, the reliable theoretical prediction method for the hydrolysis rate is not studied yet. Furthermore, after the CWC (Chemical Warfare Agent) list is updated, Novichok candidate structures can be more than 10,000 structures, for which it is not possible to perform the experiment for all of them for synthesizing and getting the hydrolysis rate. Therefore, developing a reliable theoretical method for hydrolysis rate prediction is crucial to prepare for the forthcoming usage of new types of nerve agents. Herein, by using DFT (Density Functional Theory), we successfully developed a new method of predicting the hydrolysis rate on nerve agents by investigating the electrophilicity index (EI) of the various A-, V-, and G-series nerve agents and found a suitable correlation with the experimental hydrolysis rate. Among the several DFT methods, wb97xD predicts the EI with the lowest % deviation of the studied nerve agents. Our results show that EI can be a good indicator to predict the hydrolysis rate of the anticipated nerve agents. Based on the result, we predicted the hydrolysis rate on another type of Novichok candidates, which could be the firm basis for developing a decontaminant and antidote with much fewer experimental efforts on new types of nerve agents.

Investigation of fused remote N-heterocyclic silylenes (frNHSis), at DFT

We compared and contrasted the ΔΕ_s-t, band gap (ΔΕ_HOMO-LUMO), aromaticity, charge distribution, and reactivity of singlet (s) and triplet (t) benzopyridine-4-ylidene as the fused remote N-heterocyclic carbene (frNHC) and frNHSis with different fused aromatic rings, at (U)B3LYP/AUG-cc-pVTZ and (U)M06-2X/AUG-cc-pVTZ levels of theory. In this investigation, we found (1) all s and t divalent states appear as minimum structures, for having no negative force constant. Nonetheless, only singlets present more thermodynamic stability than their triplet analogous; (2) the trend of ΔΕ_s-t in kcal/mol is ortho-pyrrole (52.94) > ortho-furan (51.84) > ortho-thiophene (50.38) > para-furan (49.36) > para-pyrrole (49.00) > para-phosphole (48.67) ≥ para-thiophene (48.64) > benzene (44.33) > ortho-phosphole frNHSi (27.50), while ΔΕ_s-t of frNHC is 15.65 kcal/mol; (3) apart from phosphole frNHSis, the order of ΔΕ_s-t in a "ortho position or zigzag array" about 1.8-4.0 kcal/mol is more than that of in a "para position or chair array"; (4) the highest ΔΕ_HOMO-LUMO is demonstrated by ortho-pyrrole frNHSi (95.65 kcal/mol) while the lowest ΔΕ_HOMO-LUMO is verified by the reference frNHC (63.44 kcal/mol); (5) in contradiction of frNHC, all singlet frNHSis reveal higher band gap and lower global reactivity than their triplet congeners; (6) charge distribution along with MEP maps indicate differentially electronic cloud in middle of rings frNHSis vs. frNHC; (7) we anticipate higher nucleophilicity and lower electrophilicity of triplet frNHSis than singlet congeners, will make them worthy of synthetic surveys.

Acute in vitro effects on embryonic rat dorsal root ganglion (DRG) cultures by in silico predicted neurotoxic chemicals: Evaluations on cytotoxicity, neurite length, and neurophysiology

The Hard-Soft Acid and Base hypothesis can be used to predict the potential bio-reactivity (electrophilicity) of a chemical with intracellular proteins, resulting in neurotoxicity. Twelve chemicals predicted to be neurotoxic were evaluated in vitro in rat dorsal root ganglia (DRG) for effects on cytotoxicity (%LDH), neuronal structure (total neurite length/neuron, NLPN), and neurophysiology (mean firing rate, MFR). DRGs were treated acutely on days in vitro (DIV) 7 (1-100 μM) with test chemical; %LDH and NLPN were measured after 48 h. 4-cyclohexylhexanone (4-C) increased %LDH release at 50 (29%) and 100 μM (56%), citronellal (Cit) and 1-bromopropane increased %LDH at 100 μM (22% and 26%). 4-C, Cit, 2,5 Hexanedione (2,5Hex), phenylacetylaldehyde (PAA) and 2-ethylhexanal decreased mean NLPN at 48 h; 50 and 100 μM for 4-C (28% and 60%), 100 μM Cit (52%), 100 μM 2,5- Hex (37%) 100 μM PAA (41%) and 100 μM for 2-ethylhexanal (23%). Separate DRG cultures were treated on DIV 14 and changes in MFR measured. Four compounds decreased MFR at 50 or 100 μM: Acrylamide (-83%), 3,4-dichloro-1-butene (-93%), 4-C (-89%) and hexane (-79%, 50 μM). Changes in MFR and NLPN occurred in absence of cytotoxicity. While the current study showed little cytotoxicity, it gave insight to initial changes in MFR. Results provide insight for future chronic exposure experiments to evaluate neurotoxicity.

CF3-Containing para-Quinone Methides for Organic Synthesis

A new family of CF3-containing para-quinone methides (CF3-QMs) was systematically investigated for its suitability in organic synthesis. Addition of different nucleophiles gives access to target molecules with a benzylic CF3-containing stereogenic center straightforwardly. The electrophilicity parameter E of the prototypical CF3-QM 2,6-di-tert-butyl-4-(2,2,2-trifluoroethylidene)cyclohexa-2,5-dien-1-one was determined to be -11.68 according to the Mayr scale, making it one of the most reactive quinone methides known so far.

Developing piperlongumine-directed glutathione S-transferase inhibitors by an electrophilicity-based strategy

We report a case of successful design of glutathione S-transferase (GST) inhibitors via a natural product-inspired and electrophilicity-based strategy. Based on this strategy, a novel piperlongumine analog (PL-13) bearing a para-trifluoromethyl group and an α-chlorine on its aromatic and lactam rings, respectively, surfaced as a promising GST inhibitor, thereby overcoming cisplatin resistance in lung cancer A549 cells.

Designing piperlongumine-directed anticancer agents by an electrophilicity-based prooxidant strategy: A mechanistic investigation

Piperlongumine (PL), a natural electrophilic alkaloid bearing two α, β-unsaturated imides, is a promising anticancer molecule by targeting the stress response to reactive oxygen species (ROS). Considering that ROS generation depends on electrophilicity of PL, PL-CL was designed as its analog by introducing the α-substituent chlorine on the lactam ring to increase moderately its electrophilicity. In comparison with the parent molecule, this molecule was identified as a stronger ROS (O2(∙-) and H2O2) inducer and cytotoxic agent, and manifested more than 15-fold selectivity toward A549 cells over normal WI-38 cells. Mechanistic study uncovers for the first time that the selenoprotein thioredoxin reductase (TrxR) is one of the targets by which PL-CL promotes the ROS generation. Stronger intracellular TrxR inhibition and higher accumulation of ROS (O2(∙-) and H2O2) are responsible for more effective S-phase arrest and mitochondria-mediated apoptotic induction of A549 cells by PL-CL than PLvia p53-p21-cyclinA/CDK2 and ASK1-JNK/p38 signaling cascade pathways, respectively. This work provides an example of successfully designing PL-directed anticancer agent by an electrophilicity-based prooxidant (ROS-generating agent) strategy and gives added confidence for extending this strategy to other natural products.

Fingerprinting the reactive toxicity pathways of 50 drinking water disinfection by-products

A set of nine in vitro cellular bioassays indicative of different stages of the cellular toxicity pathway was applied to 50 disinfection by-products (DBPs) to obtain a better understanding of the commonalities and differences in the molecular mechanisms of reactive toxicity of DBPs. An Eschericia coli test battery revealed reactivity towards proteins/peptides for 64% of the compounds. 98% activated the NRf2-mediated oxidative stress response and 68% induced an adaptive stress response to genotoxic effects as indicated by the activation of the tumor suppressor protein p53. All DBPs reactive towards DNA in the E. coli assay and activating p53 also induced oxidative stress, confirming earlier studies that the latter could trigger DBP's carcinogenicity. The energy of the lowest unoccupied molecular orbital ELUMO as reactivity descriptor was linearly correlated with oxidative stress induction for trihalomethanes (r(2)=0.98) and haloacetamides (r(2)=0.58), indicating that potency of these DBPs is connected to electrophilicity. However, the descriptive power was poor for haloacetic acids (HAAs) and haloacetonitriles (r(2) (<) 0.06). For HAAs, we additionally accounted for speciation by including the acidity constant with ELUMO in a two-parameter multiple linear regression model. This increased r(2) to >0.80, indicating that HAAs' potency is connected to both, electrophilicity and speciation. Based on the activation of oxidative stress response and the soft electrophilic character of most tested DBPs we hypothesize that indirect genotoxicity-e.g., through oxidative stress induction and/or enzyme inhibition-is more plausible than direct DNA damage for most investigated DBPs. The results provide not only a mechanistic understanding of the cellular effects of DBPs but the effect concentrations may also serve to evaluate mixture effects of DBPs in water samples.

The chemical biology of hydropersulfides (RSSH): Chemical stability, reactivity and redox roles

Recent reports indicate the ubiquitous prevalence of hydropersulfides (RSSH) in mammalian systems. The biological utility of these and related species is currently a matter of significant speculation. The function, lifetime and fate of hydropersulfides will be assuredly based on their chemical properties and reactivity. Thus, to serve as the basis for further mechanistic studies regarding hydropersulfide biology, some of the basic chemical properties/reactivity of hydropersulfides was studied. The nucleophilicity, electrophilicity and redox properties of hydropersulfides were examined under biological conditions. These studies indicate that hydropersulfides can be nucleophilic or electrophilic, depending on the pH (i.e. the protonation state) and can act as good one- and two-electron reductants. These diverse chemical properties in a single species make hydropersulfides chemically distinct from other, well-known sulfur containing biological species, giving them unique and potentially important biological function.

Insights into the importance for designing curcumin-inspired anticancer agents by a prooxidant strategy: The case of diarylpentanoids

Developing anticancer agents by a prooxidant strategy has attracted increasing attention in recent years, although it is not conventional in medicinal chemistry and is completely opposite to antioxidant therapy. In this work, a panel of diarylpentanoids as the curcumin mono-carbonyl analogs were designed and synthesized, and their cytotoxic and proapoptotic mechanisms against human lung cancer A549 cells were investigated at the frontiers of chemistry and biology. It was found that compared with curcumin, the compounds (A1, B1, and C1) bearing two ortho substituents on the aromatic rings, especially A1, exhibit significantly increased cytotoxic and proapoptotic activities through a Michael acceptor unit-dependent prooxidant-mediated mechanism. The prooxidative ability is governed not only by their electrophilicity but also by their geometry, cellular uptake and metabolic stability, and TrxR-inhibitory activity. Mechanistic investigation reveals that the compound A1 could effectively and irreversibly modify the TrxR by virtue of the above optimal biochemical parameters, and convert this antioxidant enzyme into a reactive oxygen species (ROS) promoter, resulting in a burst of the intracellular ROS including H2O2 and O2(-)•. The ROS generation is associated with falling apart in the redox buffering system, and subsequently induces increases in Ca(2+) influx and oxidative stress, collapse of mitochondrial membrane potential, and activation of caspase-9 and caspase-3, ultimately leading to cell apoptosis. This work highlights the feasibility in designing curcumin-inspired anticancer agents by a prooxidant strategy, and gives us useful information on how to design them.