Substituent effects on the reactivity of benzoquinone derivatives with thiols

Highly efficient site-specific protein modification using tyrosinase from Streptomyces avermitilis: Structural insight

Tyrosinase-mediated protein conjugation has recently drawn attention as a site-specific protein modification tool under mild conditions. However, the tyrosinases reported to date act only on extremely exposed tyrosine residues, which limits where the target tyrosine can be located. Herein, we report a tyrosinase from Streptomyces avermitilis (SaTYR), that exhibits a much higher activity against tyrosine residues on the protein surface than other tyrosinases. We determined the crystal structure of SaTYR and revealed that the enzyme has a relatively flat and shallow substrate-binding pocket to accommodate a protein substrate. We demonstrated SaTYR-mediated fluorescence dye tagging and PEGylation of a surface tyrosine residue that was unreacted by other tyrosinases with an approximately 95.2 % conjugation yield in 1 h. We also present a structural rationale that considers the steric hindrance from adjacent residues and surrounding structures along with the extent of solvent exposure of residues, as necessary when determining the optimal positions for introducing target tyrosine residues in SaTYR-mediated protein modification. The study demonstrated that the novel tyrosinase, SaTYR, extends the scope of tyrosinase-mediated protein modification, and we propose that site-specific tyrosine conjugation using SaTYR is a promising strategy for protein bioconjugation in various applications.

Formation of adducts during digestion triggered dietary protein for alleviating cytotoxicity of 2-tert-butyl-1,4-benzoquinone

2-tert-butyl-1,4-benzoquinone (TBBQ), a degradation product of lipid antioxidant Tert-Butylhydroquinone (TBHQ), is a new hazardous compound in foods. This study investigated whether co-ingestion of dietary protein and TBBQ can alleviate the toxicity of TBBQ. The results indicated that soy protein isolate, whey protein isolate, and rice protein significantly reduced the residual amount of TBBQ during simulated gastrointestinal digestion. This result was attributed to the excellent elimination capacity of the released amino acids for TBBQ through formation of adducts. Among 20 amino acids, histidine, lysine, glycine, and cysteine showed better elimination capacity for TBBQ; they can eliminate 92.1%, 89.4%, 86.1%, and almost 100%, respectively, in 5 min at pH 8.0. Further study indicated that amino acids with lower ionization constant exhibited greater TBBQ elimination capacity. In addition, incubation of the cells with 50 μM TBBQ for 12 h decreased the cell viability to 28.95 ± 3.25%; while amino acids intervention was involved in the alleviation of TBBQ cytotoxicity via decreasing ROS. Particularly, cysteine showed 100 times more TBBQ detoxifying capacity than other amino acids. This work could provide a theoretical basis for the potential application of amino acids for detoxifying TBBQ in the food industry.

Activation of PTP1B/EGFR signaling and cytotoxicity during combined exposure to ambient electrophiles in A431 cells

Chemical modification of the thiol group on protein tyrosine phosphatase (PTP) 1B triggers an activation of epidermal growth factor receptor (EGFR) signaling that is mimicked by environmental electrophiles through S-modification of PTP1B. While activation of PTP1B/EGFR by a single exposure to an electrophile has been established, the effects of combined exposure to electrophiles are unknown. Here, we examined the activation of EGFR signaling by combined exposure to ambient electrophiles in human epithelial carcinoma A431 cells. Simultaneous exposure to 1,2- and 1,4-naphthoquinone (NQ) augmented the S-modification of endogenous and recombinant human PTP1B (hPTP1B). Combined exposure of hPTP1B or A431 cells to 1,2- and 1,4-NQ escalated the inactivation of PTP compared with individual exposure. Phosphorylation of EGFR and its downstream kinase extracellular signal-regulated kinase (ERK) 1/2 by 1,2-NQ exposure was facilitated by simultaneous exposure to 1,2-NQ with 10 µM 1,4-NQ. An EGFR inhibitor diminished the phosphorylation of ERK1/2, indicating that ERK was phosphorylated following EGFR activation by the NQ cocktail. The combined exposure to NQs also accelerated cell death in A431 cells compared with each NQ alone. While no EGFR/ERK activation was seen following 1,4-benzoquinone (BQ) treatment, exposure to 1,4-NQ in the presence of 1,4-BQ increased 1,4-NQ-mediated activation of EGFR. This suggests that the enhancement of 1,4-NQ-dependent EGFR activation by 1,4-BQ is caused by a different mechanism than 1,2-NQ with 1,4-NQ. These results suggest that combined exposure to ambient electrophiles, even at low concentrations, can induce stronger activation of redox signaling than individual exposure. Our findings indicate that combining different electrophiles may produce unexpected effects.

A T5 Exonuclease-Based Assay for DNA Topoisomerases and DNA Intercalators

DNA topoisomerases, essential enzymes to all living organisms, are important targets of certain antibiotics and anticancer drugs. Although efforts have been taken to identify new inhibitors targeting DNA topoisomerases, limited high throughput screening (HTS) studies have been conducted since a widely accessible HTS assay is not available. We report here the establishment of a fluorescence-based, low-cost HTS assay to identify topoisomerase inhibitors. This HTS assay is based on a unique property of T5 exonuclease that can completely digest supercoiled plasmid pAB1 containing an "AT" hairpin structure and spare relaxed pAB1 and has been validated by screening a small library that contains 50 compounds for various topoisomerases. This T5 exonuclease-based HTS assay can also be used to identify DNA intercalators, the major false positives for identifying topoisomerase inhibitors using this HTS assay. Additionally, we found a new compound that potently inhibits human and bacterial DNA topoisomerase I.

Nucleophilic Reactivities of Thiophenolates

The nucleophilic reactivities of substituted thiophenolates were determined by following the kinetics of their reactions with a series of quinone methides (reference electrophiles) in DMSO at 20 °C. The experimentally determined second-order rate constants were analyzed according to the Mayr-Patz equation log k = s_N(N + E) to derive the nucleophile-specific reactivity parameters N and s_N for ten thiophenolate ions.

Computational studies reveal mechanism by which quinone derivatives can inhibit SARS-CoV-2. Study of embelin and two therapeutic compounds of interest, methyl prednisolone and dexamethasone

Background

Quinones are reactive to proteins containing cysteine residues and the main protease in Covid-19 contains an active site that includes Cys145. Embelin, a quinone natural product, is known to have antiviral activity against influenza and hepatitis B. Preliminary studies by our group also indicate its ability to inhibit HSV-1 in cultured cells.

Methods

Docking and DFT methods applied to the protease target.

Results

a mechanism for this inhibition of the SARS-CoV-2 Mpro protease is described, specifically due to formation of a covalent bond between S(Cys145) and an embelin C(carbonyl). This is assisted by two protein amino acids (1) N(imidazole-His41) which is able to capture H[S(Cys145)] and (2) HN(His163), which donates a proton to embelin O(carbonyl) forming an OH moiety that results in inhibition of the viral protease. A similar process is also seen with the anti-inflammatory drugs methyl prednisolone and dexamethasone, used for Covid-19 patients. Methyl prednisolone and dexamethasone are methide quinones, and possess only one carbonyl moiety, instead of two for embelin. Additional consideration was given to another natural product, emodin, recently patented against Covid-19, as well as some therapeutic quinones, vitamin K, suspected to be involved in Covid-19 action, and coenzyme Q10. All show structural similarities with embelin, dexamethasone and methyl prednisolone results.

Conclusions

Our data on embelin and related quinones indicate that these natural compounds may represent a feasible, strategic tool against Covid-19.

Effect of methyl substituent on the solubility of 1,4-benzoquinone derivatives in n-octanol/water system

The solubility of the compound is a crucial task for new drug design. Quinone is a promising candidate to develop as a new drug. In this research, the synthesis of 1,4-benzoquinone derivatives, that is, 2-(5-bromoamyl)-3,5-dimethyl-1,4-benzoquinone (2a) and 2-(5-bromoamyl)-5-methyl-1,4-benzoquinone (2b) were carried out by decarboxylation and insertion reaction of alkyl bromides. The product 2a and 2b are purified using SiO2 gel column chromatography and analyzed by UV-Visible, FT-IR, and NMR. The yield of 2a is 13.75%, and 2b is 4.04%. The solubility of 2a and 2b, expressed by log P, is measured in the n-octanol/water (3:7 (v/v)) system by the shake flask method. The log P of 2a and 2b are 2.99 and 1.36, respectively. It is showed that the log P of 2a is higher compared to 2b. The presence of two methyl substituents on the quinone ring of 2a supports the increase of hydrophobicity of the compound in the n-octanol/water system.

Discovery of natural naphthoquinones as sortase A inhibitors and potential anti-infective solutions against Staphylococcus aureus

Three natural naphthoquinones were screened to find new anti-virulence agents as inhibitors against sortase A from Staphylococcus aureus (SaSrtA) by quantifying the increase in fluorescence intensity upon substrate cleavage at various concentrations. The 5-hydroxy-1,4-naphthalenedione derivatives, juglone and plumbagin, demonstrated a potent inhibitory effect, with IC₅₀ values of 1.78 μM, respectively, 16.71 μM. The related 2-hydroxy-1,4-naphthalenedione derivative, lawsone, demonstrated the selectivity of the chemical scaffold having no significant effect on SaSrtA. The experimental assay was reinforced by molecular docking experiments, antimicrobial, and toxicological studies. Molecular docking studies and the electrophilic character analysis suggest bonding to the enzyme active cysteine residue by a Michael addition reaction. None of the compounds had a significant effect on the concentration of total thiol proteins in the Daphnia magna toxicological assay after 24 hr exposure. Juglone and plumbagin moderately inhibited biofilm formation with no significant effect on bacterial growth of S. aureus, Enterococcus faecalis, and Staphylococcus epidermidis, indicating a selective anti-virulence profile.

Correlating the structure and reactivity of a contact allergen, DNCB, and its analogs to sensitization potential

We report a study that seeks to find a correlation between the overall sensitization potential quantified by the expression of IL-8 by stimulated monocytes and the chemical structure of a model contact allergen, 2,4-dinitrochlorobenzene (DNCB). We show that structure and reactivity of the chemical compounds play an important role in activation of the monocytes and subsequent inflammation in tissue. However, we observed a non-linear correlation between the rate of reaction and biological activity indicating a required balance of stability and reactivity.

Benzoquinone, a leukemogenic metabolite of benzene, catalytically inhibits the protein tyrosine phosphatase PTPN2 and alters STAT1 signaling

Protein tyrosine phosphatase, nonreceptor type 2 (PTPN2) is mainly expressed in hematopoietic cells, where it negatively regulates growth factor and cytokine signaling. PTPN2 is an important regulator of hematopoiesis and immune/inflammatory responses, as evidenced by loss-of-function mutations of PTPN2 in leukemia and lymphoma and knockout mice studies. Benzene is an environmental chemical that causes hematological malignancies, and its hematotoxicity arises from its bioactivation in the bone marrow to electrophilic metabolites, notably 1,4-benzoquinone, a major hematotoxic benzene metabolite. Although the molecular bases for benzene-induced leukemia are not well-understood, it has been suggested that benzene metabolites alter topoisomerases II function and thereby significantly contribute to leukemogenesis. However, several studies indicate that benzene and its hematotoxic metabolites may also promote the leukemogenic process by reacting with other targets and pathways. Interestingly, alterations of cell-signaling pathways, such as Janus kinase (JAK)/signal transducer and activator of transcription (STAT), have been proposed to contribute to benzene-induced malignant blood diseases. We show here that 1,4-benzoquinone directly impairs PTPN2 activity. Mechanistic and kinetic experiments with purified human PTPN2 indicated that this impairment results from the irreversible formation (k _inact = 645 m^-1·s^-1) of a covalent 1,4-benzoquinone adduct at the catalytic cysteine residue of the enzyme. Accordingly, cell experiments revealed that 1,4-benzoquinone exposure irreversibly inhibits cellular PTPN2 and concomitantly increases tyrosine phosphorylation of STAT1 and expression of STAT1-regulated genes. Our results provide molecular and cellular evidence that 1,4-benzoquinone covalently modifies key signaling enzymes, implicating it in benzene-induced malignant blood diseases.

Reaction of quinones with proteins: Kinetics of adduct formation, effects on enzymatic activity and protein structure, and potential reversibility of modifications

Quinones are a common motif in many biological compounds, and have been linked to tissue damage as they can undergo redox cycling to generate radicals, and/or act as Michael acceptors with nucleophiles, such as protein Cys residues, with consequent adduct formation. The kinetics and consequences of these Michael reactions are poorly characterized. In this study we hypothesized that adduction of protein Cys residues with quinones would be rapid, structure-dependent, quantitatively-significant, and result in altered protein structure and function. Multiple quinones were incubated with glyceraldehyde-3-phosphate dehydrogenase (GAPDH), creatine kinase (CK), papain, bovine (BSA) and human (HSA) serum albumins, with the kinetics of adduction and effects on protein structure and activity determined. Adduction rate constants at Cys residues, which were dependent on the quinone and protein structure, and thiol pK_a, are in the range 10²-10⁵ M^-1 s^-1. p-Benzoquinone (BQ) induced dimerization of GAPDH and CK (but not BSA, HSA, or papain) in a dose- and time-dependent manner. Incubation of purified proteins, or cell lysates, with quinones resulted in a rapid loss of GAPDH and CK activity; this loss correlated well with the rate constant for Cys adduction. Glutathione (GSH) reacts competitively with quinones, and could reverse the loss of activity and dimerization of GAPDH and CK. Mass spectrometry peptide mass mapping provided evidence for BQ adduction to GAPDH to specific Cys residues (Cys149, Cys244), whereas all Cys residues in CK were modified. These data suggested that quinones can induce biological effects by rapid and selective formation of adducts with Cys residues in proteins.

The electrophilic character of quinones is essential for the suppression of Bach1

The activation of nuclear factor erythroid 2-related factor 2 (Nrf2) is the most important cellular defense mechanisms against oxidative attack. BTB and CNC homology-1 (Bach1), like Kelch-like ECH-associated protein 1 (Keap1), is one of a negative regulator of Nrf2 that control antioxidant response elements (ARE)-dependent gene expressions. In the current study, we found that quinones show greater capacity than hydroquinones in nuclear Bach1 export, as well as ubiquitin-dependent Bach1 degradation in our experimental time frame. Consistently, quinones are easier than hydroquinones in Nrf2 activation and ARE-driven antioxidant protein expressions. Considering the redox cycling potential of quinone-hydroquinone couple, we investigated the effect of transit metal oxidation on the regulation of Nrf2 activity. As shown, Fe³⁺ enhanced hydroquinone-induced Nrf2 activation and ARE-driven gene expressions, suggesting quinones rather than hydroquinone activate Nrf2 through Bach1 arylation. Taking together, our investigation illustrated that the electrophilic character of quinones ensure their conjugation with Bach1, which is important for the downregulation of Bach1 and the upregulation of Nrf2 signaling.

Covalent Modifiers: A Chemical Perspective on the Reactivity of α,β-Unsaturated Carbonyls with Thiols via Hetero-Michael Addition Reactions

Although Michael acceptors display a potent and broad spectrum of bioactivity, they have largely been ignored in drug discovery because of their presumed indiscriminate reactivity. As such, a dearth of information exists relevant to the thiol reactivity of natural products and their analogues possessing this moiety. In the midst of recently approved acrylamide-containing drugs, it is clear that a good understanding of the hetero-Michael addition reaction and the relative reactivities of biological thiols with Michael acceptors under physiological conditions is needed for the design and use of these compounds as biological tools and potential therapeutics. This Perspective provides information that will contribute to this understanding, such as kinetics of thiol addition reactions, bioactivities, as well as steric and electronic factors that influence the electrophilicity and reversibility of Michael acceptors. This Perspective is focused on α,β-unsaturated carbonyls given their preponderance in bioactive natural products.

Reactivity measurement in estimation of benzoquinone and benzoquinone derivatives' allergenicity

Benzoquinone (BQ) and benzoquinone derivatives (BQD) are used in the production of dyes and cosmetics. While BQ, an extreme skin sensitizer, is an electrophile known to covalently modify proteins via Michael Addition (MA) reaction whilst halogen substituted BQD undergo nucleophilic vinylic substitution (SNV) mechanism onto amine and thiol moieties on proteins, the allergenic effects of adding substituents on BQ have not been reported. The effects of inserting substituents on the BQ ring has not been studied in animal assays. However, mandated reduction/elimination of animals used in cosmetics testing in Europe has led to an increased need for alternatives for the prediction of skin sensitization potential. Electron withdrawing and electron donating substituents on BQ were assessed for effects on BQ reactivity toward nitrobenzene thiol (NBT). The NBT binding studies demonstrated that addition of EWG to BQ as exemplified by the chlorine substituted BQDs increased reactivity while addition of EDG as in the methyl substituted BQDs reduced reactivity. BQ and BQD skin allerginicity was evaluated in the murine local lymph node assay (LLNA). BQD with electron withdrawing groups had the highest chemical potency followed by unsubstituted BQ and the least potent were the BQD with electron donating groups. The BQD results demonstrate the impact of inductive effects on both BQ reactivity and allergenicity, and suggest the potential utility of chemical reactivity data for electrophilic allergen identification and potency ranking.

Theoretical study on homolytic C(sp2)–O cleavage in ethers and phenols

The C(sp²)–O BDEs and the substituent effect of ethers/phenols were investigated in detail by the wB97 method.

p-Benzoquinone adsorption–separation, sensing and its photoinduced transformation within a robust Cd(ii)-MOF in a SC–SC fashion

p-Benzoquinone (Q) adsorption–separation, sensing and its photoinduced transformation within a robust Cd(ii)-MOF (1) is reported.