Experimental determination and calculations of redox potential descriptors of compounds directed against retroviral zinc fingers: Implications for rational drug design

Electrophilicity index revisited

This review aims to be a comprehensive, authoritative, critical, and accessible review of general interest to the chemistry community; because the electrophilicity index is a very useful global reactivity descriptor defined within a conceptual density functional theory framework. Our group has also introduced electrophilicity based new global and local reactivity descriptors and also new associated electronic structure principles, which are important indicators of structure, stability, bonding, reactivity, interactions, and dynamics in a wide variety of physico-chemical systems and processes. This index along with its local counterpart augmented by the associated electronic structure principles could properly explain molecular vibrations, internal rotations and various types of chemical reactions. The concept of the electrophilicity index has been extended to dynamical processes, excited states, confined environment, spin-dependent and temperature-dependent situations, biological activity, site selectivity, aromaticity, charge removal and acceptance, presence of external perturbation through solvents, external electric and magnetic fields, and so forth. Although electrophilicity and its local variant can adequately interpret the behavior of a wide variety of systems and different physico-chemical processes involving them, their predictive potential remains to be explored. An exhaustive review on all these aspects will set the tone of the future research in that direction.

Prediction of the standard potentials for one-electron oxidation of N,N,N',N' tetrasubstituted p-phenylenediamines by calculation

The formal potentials for the reversible one-electron oxidation of N,N,N',N' tetrasubstituted p-phenylenediamines in acetonitrile have been applied as a test set for benchmarking computational methods for a series of compounds with only small structural differences. The aim of the study is to propose a simple method for calculating the standard oxidation potentials, and therefore, the protocol is progressively developed by adding more terms in the energy expression. In addition, the effect of including implicit solvation models (IEFPCM, CPCM, and SMD), larger basis sets, and correlation methods are investigated. The oxidation potentials calculated using the G3MP2B3 approach with IEFPCM resulted in the best fit (R² = 0.9624), but the slope of the correlation line, 0.74, is far from the optimal value, 1.00. B3LYP/6-311++G(d,p) and TPSSh/6-311++G(2d,p) yielded only slightly less consistent data (R² = 0.9388 and R² = 0.9425), but with much better slopes, 1.00 and 0.94, respectively. We conclude that it is important to investigate the basis set size and treatment of electron correlation when calculating oxidation potentials for N,N,N',N' tetrasubstituted p-phenylenediamines.

Tailored Design of Electrochemically Degradable Anthraquinone Functionality toward Organic Cathodes

In efforts to design organic cathode materials for rechargeable batteries, a fundamental understanding of the redox properties of diverse non-carbon-based functionalities incorporated into 9,10-anthraquinone is lacking despite their potential impact. Herein, a preliminary investigation of the potential of anthraquinones with halogenated nitrogen-based functionalities reveals that the Li-triggered structural collapse observed in the early stage of discharging can be ascribed to the preference toward the strong Lewis acid-base interaction of N-Li-X (X = F or Cl) over the repulsive interaction of the electron-rich N-X bond. A further study of three solutions (i.e., substitution of NX₂ with (i) BX₂, (ii) NH₂, and (iii) BH₂) to the structural decomposition issue highlights four conclusive remarks. First, the replacement of N and/or X with electron-deficient atom(s), such as B and/or H, relieves the repulsive force on the N-X bond without the assistance of Li, and thus, no structural decomposition occurs. Second, the incorporation of BH₂ is verified to be the most beneficial for improving the theoretical performance. Third, all the redox properties are better correlated with electron affinity and solvation energy than the electronegativity of functionality, implying that these key parameters cooperatively contribute to the electrochemical redox potential; additionally, solvation energy plays a crucial role in determining cathodic deactivation. Fourth, the improvement to the Li storage capability of anthraquinone using the third solution can primarily be ascribed to solvation energy remaining at a negative value even after the binding of more Li atoms than the other derivatives.

Structure-Reactivity Relationships in the Adsorption and Degradation of Substituted Phenylarsonic Acids on Birnessite (δ-MnO2)

Phenylarsonic acid compounds could be oxidized by manganese oxides in surface soils, resulting in quick release of inorganic arsenic. This study investigated the structure-reactivity relationships in the adsorption and oxidative degradation of six substituted phenylarsonic acids on the surface of a major type of manganese oxides, birnessite (δ-MnO₂), using batch experiments conducted under acidic to neutral conditions. The initial adsorption rates of the substituted phenylarsonic acids on δ-MnO₂ decreased in the order of phenylarsonic acid (PAA) > 4-aminophenylarsonic acid (p-ASA) ≈ 2-aminophenylarsonic acid (2-APAA) > 4-hydroxyphenylarsonic acid (4-HPAA) > 2-nitrophenylarsonic acid (2-NPAA) > 4-hydroxy-3-nitrophenylarsonic acid (ROX), which could be attributed to steric hindrance of the substituents and the hydrophobicity of these compounds. The oxidation rates of these structural analogues by δ-MnO₂ decreased in the order of p-ASA ≈ 2-APAA > 4-HPAA > ROX, while 2-NPAA and PAA were nonreactive because of the lack of electron-donating substituents on their aromatic rings. The redox reactivity of these compounds agrees well with the electron density at C₁, which is determined by the types and position of the substituents on the aromatic ring. Although cleavage of the arsonic acid group from the aromatic ring was the predominant transformation pathway, a range of adduct products also formed through cross-coupling of the radicals and radical substitution. The contribution of radical coupling and substitution in overall degradation decreased in the order of p-ASA > 2-APAA > 4-HPAA > ROX, which results from the varying reactivity and steric hindrance of the substituents. These insights could help better understand and predict the fate of substituted phenylarsonic acids in manganese oxide-rich surface soils and the associated environmental risk of arsenic pollution.

TRP channels in oxygen physiology: distinctive functional properties and roles of TRPA1 in O2 sensing

Transient Receptor Potential (TRP) proteins form cation channels characterized by a wide variety of activation triggers. Here, we overview a group of TRP channels that respond to reactive redox species to transduce physiological signals, with a focus on TRPA1 and its role in oxygen physiology. Our systematic evaluation of oxidation sensitivity using cysteine-selective reactive disulphides with different redox potentials reveals that TRPA1 has the highest sensitivity to oxidants/electrophiles among the TRP channels, which enables it to sense O₂. Proline hydroxylation by O₂-dependent hydroxylases also regulates the O₂-sensing function by inhibiting TRPA1 in normoxia; TRPA1 is activated by hypoxia through relief from the inhibition and by hyperoxia through cysteine oxidation that overrides the inhibition. TRPA1 enhances neuronal discharges induced by hyperoxia and hypoxia in the vagus to underlie respiratory adaptation to changes in O₂ availability. This importance of TRPA1 in non-carotid body O₂ sensors can be extended to the universal significance of redox-sensitive TRP channels in O₂ adaptation.

Estimation of Mayr electrophilicity with a quantitative structure-property relationship approach using empirical and DFT descriptors

Quantitative structure-property relationships (QSPRs) were investigated for the estimation of the Mayr electrophilicity parameter using a data set of 64 compounds, all currently available uncharged electrophiles in Mayr's Database of Reactivity Parameters. Three collections of empirical descriptors were employed, from Dragon, Adriana.Code, and CDK. Models were built with multilinear regressions, k nearest neighbors, model trees, random forests, support vector machines (SVMs), associative neural networks, and counterpropagation neural networks. Quantum chemical descriptors were calculated with density functional theory (DFT) methods and incorporated in QSPR models. The best results were achieved with SVM using seven empirical and DFT descriptors; an R(2) of 0.92 was obtained for the test set (21 compounds). The final seven descriptors were the Parr electrophilicity index, ε(LUMO), hardness, and four CDK descriptors (FNSA-3, ATSc5, Kier2, and nAtomLAC). Screening of correlations between individual descriptors and Mayr electrophilicity revealed the highest absolute value of correlation for DFT ε(LUMO) (R = -0.82) and comparable correlations for some empirical descriptors, e.g., Dragon's folding degree index (R = -0.80), Kier flexibility index (R = -0.78), and Kier S2K index (R = -0.78). High correlations were observed in the training set between reactivity descriptors calculated by the PM6 semiempirical and DFT methods (R = 0.96 for ε(LUMO) and 0.94 for the electrophilicity index).

TRPA1 underlies a sensing mechanism for O2

Oxygen (O(2)) is a prerequisite for cellular respiration in aerobic organisms but also elicits toxicity. To understand how animals cope with the ambivalent physiological nature of O(2), it is critical to elucidate the molecular mechanisms responsible for O(2) sensing. Here our systematic evaluation of transient receptor potential (TRP) cation channels using reactive disulfides with different redox potentials reveals the capability of TRPA1 to sense O(2). O(2) sensing is based upon disparate processes: whereas prolyl hydroxylases (PHDs) exert O(2)-dependent inhibition on TRPA1 activity in normoxia, direct O(2) action overrides the inhibition via the prominent sensitivity of TRPA1 to cysteine-mediated oxidation in hyperoxia. Unexpectedly, TRPA1 is activated through relief from the same PHD-mediated inhibition in hypoxia. In mice, disruption of the Trpa1 gene abolishes hyperoxia- and hypoxia-induced cationic currents in vagal and sensory neurons and thereby impedes enhancement of in vivo vagal discharges induced by hyperoxia and hypoxia. The results suggest a new O(2)-sensing mechanism mediated by TRPA1.

Theoretical design of a specific DNA-Zinc-finger protein interaction with semi-empirical quantum chemical methods

The interactions of a zinc-finger (ZF) protein with DNA containing the specific recognition site of the ZF and with a non-specific DNA were studied with the semi-empirical quantum chemical method of PM6/Mozyme. The ZF protein (1MEY)-DNA complex structures were generated by docking calculations. The complex structures were reoptimized with the PM6/Mozyme method with implicit solvation in water. The structures were also calculated in the gas phase. The interaction enthalpies between the protein and DNA within the complexes obtained in the PM6/Mozyme with solvation optimized structures were calculated with the single-point PM6-DH2/Mozyme method (PM6 with dispersion, H-bond correction and Mozyme) with solvation. The results supported the specific and non-specific interactions in the complexes obtained from the docking experiments. The binding enthalpies of the specific and non-specific DNA binding to the protein differed significantly. The interactions between the nucleic acid strands in duplexes were also evaluated; these interactions between the base pairs were different because of the different "G…C:A…T" ratios in the DNA molecules studied. The stacking interactions between the nucleic bases were also characterized in the DNA duplexes.

HIV-1 inactivation by 4-vinylpyridine is enhanced by dissociating Zn(2+) from nucleocapsid protein

Selective inactivation of critical cysteine residues in human immunodeficiency virus type one (HIV-1) was observed after treatment with 4-vinylpyridine (4-VP), with and without the membrane-permeable metal chelator N,N,N',N'-tetrakis(2-pyridylmethyl)-ethylenediamine (TPEN). Chromatographic analysis showed that cysteines contained within nucleocapsid zinc fingers, in the context of whole virus or purified protein, were essentially unreactive, but became reactive when a chelator was included. Virus treated with 4-VP showed only a modest decrease in infectivity; after TPEN addition, nearly complete inactivation of HIV-1 occurred. Similarly, quantitation of viral DNA products from 4-VP-treated virus infections showed no significant effects on reverse transcription, but did show a 14-fold reduction in proviruses; when TPEN was added, a 10(5)-fold decrease in late reverse transcription products was observed and no proviruses were detected. Since 4-VP effectiveness was greatly enhanced by TPEN, this strongly suggests that modification of nucleocapsid zinc fingers is necessary and sufficient for HIV-1 inactivation by sulfhydryl reagents.

Zinc coordination environments in proteins as redox sensors and signal transducers

Zinc/cysteine coordination environments in proteins are redox-active. Oxidation of the sulfur ligands mobilizes zinc, while reduction of the oxidized ligands enhances zinc binding, providing redox control over the availability of zinc ions. Some zinc proteins are redox sensors, in which zinc release is coupled to conformational changes that control varied functions such as enzymatic activity, binding interactions, and molecular chaperone activity. Whereas the released zinc ion in redox sensors has no known function, the redox signal is transduced to specific and sensitive zinc signals in redox transducers. Released zinc can bind to sites on other proteins and modulate signal transduction, generation of metabolic energy, mitochondrial function, and gene expression. The paradigm of such redox transducers is the zinc protein metallothionein, which, together with its apoprotein, thionein, functions at a central node in cellular signaling by redistributing cellular zinc, presiding over the availability of zinc, and interconverting redox and zinc signals. In this regard, the transduction of nitric oxide (NO) signals into zinc signals by metallothionein has received particular attention. It appears that redox-inert zinc has been chosen to control some aspects of cellular thiol/disulfide redox metabolism. Tight control of zinc is essential for redox homeostasis because both increases and decreases of cellular zinc elicit oxidative stress. Depending on its availability, zinc can be cytoprotective as a pro-antioxidant or cytotoxic as a pro-oxidant. Any condition with acute or chronic oxidative stress is expected to perturb zinc homeostasis.

Elimination of retroviral infectivity by N-ethylmaleimide with preservation of functional envelope glycoproteins

The zinc finger motifs in retroviral nucleocapsid (NC) proteins are essential for viral replication. Disruption of these Cys-X2-Cys-X4-His-X4-Cys zinc-binding structures eliminates infectivity. To determine if N-ethylmaleimide (NEM) can inactivate human immunodeficiency virus type 1 (HIV-1) or simian immunodeficiency virus (SIV) preparations by alkylating cysteines of NC zinc fingers, we treated infectious virus with NEM and evaluated inactivation of infectivity in cell-based assays. Inactivation was rapid and proportional to the NEM concentration. NEM treatment of HIV-1 or SIV resulted in extensive covalent modification of NC and other internal virion proteins. In contrast, viral envelope glycoproteins, in which the cysteines are disulfide bonded, remained intact and functional, as assayed by high-performance liquid chromatography, fusion-from-without analyses, and dendritic cell capture. Quantitative PCR assays for reverse transcription intermediates showed that NEM and 2,2'-dipyridyl disulfide (aldrithiol-2), a reagent which inactivates retroviruses through oxidation of cysteines in internal virion proteins such as NC, blocked HIV-1 reverse transcription prior to the formation of minus-strand strong-stop products. However, the reverse transcriptase from NEM-treated virions remained active in exogenous template assays, consistent with a role for NC in reverse transcription. Since disruption of NC zinc finger structures by NEM blocks early postentry steps in the retroviral infection cycle, virus preparations with modified NC proteins may be useful as vaccine immunogens and probes of the role of NC in viral replication.

Metal and redox modulation of cysteine protein function

In biological systems, the amino acid cysteine combines catalytic activity with an extensive redox chemistry and unique metal binding properties. The interdependency of these three aspects of the thiol group permits the redox regulation of proteins and metal binding, metal control of redox activity, and ligand control of metal-based enzyme catalysis. Cysteine proteins are therefore able to act as "redox switches," to sense concentrations of oxidative stressors and unbound zinc ions in the cytosol, to provide a "storage facility" for excess metal ions, to control the activity of metalloproteins, and to take part in important regulatory and signaling pathways. The diversity of cysteine's multiple roles in vivo is equally as fascinating as it is promising for future biochemical and pharmacological research.