Large Computational Survey of Intrinsic Reactivity of Aromatic Carbon Atoms with Respect to a Model Aldehyde Oxidase

Aldehyde oxidase (AOX) and other related molybdenum-containing enzymes are known to oxidize the C-H bonds of aromatic rings. This process contributes to the metabolism of pharmaceutical compounds and, therefore, is of vital importance to drug pharmacokinetics. The present work describes an automated computational workflow and its use for the prediction of intrinsic reactivity of small aromatic molecules toward a minimal model of the active site of AOX. The workflow is based on quantum chemical transition state searches for the underlying single-step oxidation reaction, where the automated protocol includes identification of unique aromatic C-H bonds, creation of three-dimensional reactant and product complex geometries via a templating approach, search for a transition state, and validation of reaction end points. Conformational search on the reactants, products, and the transition states is performed. The automated procedure has been validated on previously reported transition state barriers and was used to evaluate the intrinsic reactivity of nearly three hundred heterocycles commonly found in approved drug molecules. The intrinsic reactivity of more than 1000 individual aromatic carbon sites is reported. Stereochemical and conformational aspects of the oxidation reaction, which have not been discussed in previous studies, are shown to play important roles in accurate modeling of the oxidation reaction. Observations on structural trends that determine the reactivity are provided and rationalized.

Revisiting the HO●-initiated oxidation of L-proline amino acid in the aqueous phase: influence of transition metal ions

The oxidation of L-proline (Pro) by HO^● radical in water and the influence of transition metal ions on this process has been revisited by using the density functional theory (DFT) method at the M05-2X/6-311 + + G(3df,3pd)//M05-2X/6-311 + + G(d,p) level of theory at the temperature of 298.15 K. The main reactive sites of the HO^●-initiated oxidation of Pro via hydrogen atom transfer (HAT) reactions are at the β- and γ-carbon, with the branching ratios being 44.6% and 39.5%, respectively. The overall rate constant at 298.15 K is 6.04 × 10⁸ M^-1 s^-1. In addition, Pro tends to form stable complexes with both Fe and Cu ions via the -COO functional group of dipole-salt form. The most stable Cu(II)-Pro complexes have high oxidant risks in enhancing the HO^● formation in the presence of reducing agents. Besides this, the high oxidation state metal complexes, i.e. Fe(III)-Pro and Cu(II)-Pro, may be oxidized by HO^● radical via HAT reactions but with a lower rate constant than that of free-Pro. By contrast, the low oxidation state metal complexes (i.e. Fe(II)-Pro and Cu(I)-Pro) have higher oxidation risks than the free ligands, and thus, the complexation enhances the oxidation of Pro amino acid.

CADMA-Chem: A Computational Protocol Based on Chemical Properties Aimed to Design Multifunctional Antioxidants

A computational protocol aimed to design new antioxidants with versatile behavior is presented. It is called Computer-Assisted Design of Multifunctional Antioxidants and is based on chemical properties (CADMA-Chem). The desired multi-functionality consists of in different methods of antioxidant protection combined with neuroprotection, although the protocol can also be used to pursue other health benefits. The dM38 melatonin derivative is used as a study case to illustrate the protocol in detail. This was found to be a highly promising candidate for the treatment of neurodegeneration, in particular Parkinson's and Alzheimer's diseases. This also has the desired properties of an oral-drug, which is significantly better than Trolox for scavenging free radicals, and has chelates redox metals, prevents the ●OH production, via Fenton-like reactions, repairs oxidative damage in biomolecules (lipids, proteins, and DNA), and acts as a polygenic neuroprotector by inhibiting catechol-O-methyl transferase (COMT), acetylcholinesterase (AChE) and monoamine oxidase B (MAOB). To the best of our best knowledge, CADMA-Chem is currently the only protocol that simultaneously involves the analyses of drug-like behavior, toxicity, manufacturability, versatile antioxidant protection, and receptor-ligand binding affinities. It is expected to provide a starting point that helps to accelerate the discovery of oral drugs with the potential to prevent, or slow down, multifactorial human health disorders.

Oxidation of l-leucine amino acid initiated by hydroxyl radical: are transition metal ions an enhancement factor?

Hydroxyl radical (HO·) formation initiated by the Fenton-type reactions of Fe and Cu complexes of l-leucine (Leu) amino acid as well as its oxidation reaction by HO· was computationally investigated by using the density functional theory method at the M05-2X/6-311++G(3df,2pd)//M05-2X/6-311++G(d,p) level of theory in the aqueous phase. The results showed that dipole-salt is the main form of Leu in the physiological condition. Leu exhibits high chelating potential towards both Fe(III)/Fe(II) and Cu(II)/Cu(I) ions with the most favourable coordinating positions at two oxygen atoms of the -COO functional group. Furthermore, the Leu-ions complexes show a high risk of HO· formation via Fenton-like reactions, especially when ascorbate anion exists in the environment as a reducing agent. Finally, the oxidation reaction of l-leucine by HO· demonstrated a relatively high overall apparent reaction rate, k _overall, being 1.18 × 10⁹ M^-1 s^-1, in which formal hydrogen transfer reactions of the dipole-salt form occur as the primary mechanism. Consequently, the Leu oxidation by HO· radical can be promoted by the Fenton reaction enhancement of its transition metal complexes.

Chemical repair of damaged leucine and tryptophane by thiophenols at close to diffusion-controlled rates: Mechanisms and kinetics

Thiophenols are chemical species with multiple desirable biological properties, including their primary and secondary antioxidant capacity. In this work, the repairing antioxidant activity of eight different thiophenols has been investigated for damaged leucine and tryptophane. The investigation was carried out employing quantum mechanical and transition state methods to calculate the thermodynamic and kinetic data of the reactions involved, while simulating the biological conditions at physiological pH and aqueous and lipidic medium. The analysis of the atomic charges and the spin densities at each of the points on the potential energy surface was the tool that allowed the elucidation of the reaction mechanisms through which thiophenols repair the oxidative damage caused to the amino acids leucine and tryptophan. It was found that thiophenols can repair leucine via a hydrogen atom transfer mechanism in a manner which is similar to the one used by glutathione to repair the carbon-centered radicals of guanosine. In addition, thiophenols can also restore tryptophane, a nitrogen-centered radical, via proton-coupled electron transfer and single electron transfer mechanisms. Moreover, both processes occur at close to diffusion-controlled rates.

Theoretical Study of the Reactivity and Selectivity of Various Free Radicals with Cysteine Residues

Radicals in biochemical environments can lead to protein damage. Theoretical studies can help us to understand the observed radical selectivity. In this work, the kinetics and thermodynamics of the hydrogen-transfer (HT) and single-electron transfer (SET) reactions between a cysteine derivative and 17 free radicals of biological significance have been theoretically investigated in aqueous and lipid media. With the exception of the reaction with •OCCl3, all SET reactions in aqueous medium have rate constants in the diffusion-limited regime. The γ site of cysteine was found to be the most reactive for the HT reactions with all the radicals, with rate constants in the diffusion limit for •OH, •OCHCl2, and •OCCl3. The HT reactions from the α and γ positions have very similar ΔG° values and even though the β position is the least thermodynamically favored, when the HT from β is exergonic it is a more reactive site than α. The results obtained confirm that the Bell-Evans-Polanyi principle does not apply to the reactions between amino acid residues and free radicals and that reactivity comparisons demand proper kinetic calculations.

Comprehensive Investigation of the Antioxidant and Pro-oxidant Effects of Phenolic Compounds: A Double-Edged Sword in the Context of Oxidative Stress?

Oxidative stress (OS) is a health-threatening process that is involved, at least partially, in the development of several diseases. Although antioxidants can be used as a chemical defense against OS, they might also exhibit pro-oxidant effects, depending on environmental conditions. In this work, such a dual behavior was investigated for phenolic compounds (PhCs) within the framework of the density functional theory and based on kinetic data. Multiple reaction mechanisms were considered in both cases. The presence of redox metals, the pH, and the possibility that PhCs might be transformed into benzoquinones were identified as key aspects in the antioxidant versus pro-oxidant effects of these compounds. The main virtues of PhCs as antioxidants are their radical trapping activity, their regeneration under physiological conditions, and their behavior as OH-inactivating ligands. The main risks of PhCs as pro-oxidants are predicted to be the role of phenolate ions in the reduction of metal ions, which can promote Fenton-like reactions, and the formation of benzoquinones that might cause protein arylation at cysteine sites. Although the benefits seem to overcome the hazards, to properly design chemical strategies against OS using PhCs, it is highly recommended to carefully explore their duality in this context.

Interaction of bisphenol A 3,4-quinone metabolite with glutathione and ribonucleosides/deoxyribonucleosides in vitro

Bisphenol A is a monomer used in the manufacture of polycarbonate plastic products, epoxy resin-based food can liners and flame retardants. To determine the genotoxic potential of bisphenol A, the mechanism of the reactions between the reactive electophilic bisphenol A 3,4-quinone (BPAQ) with glutathione and ribonucleosides/deoxyribonucleosides were studied. The obtained results demonstrated that BPAQ reacted with 2'-deoxyguanosine (dG)/guanosine (G), 2'-deoxyadenosine (dA)/adenosine (A), but not with 2'-deoxycytidine (dC)/cytidine (C) and thymidine (T)/uridine (U) in aqueous acetic acid. The reactions were accompanied by loss of deoxyribose, and the rate of depurination by deoxyribonucleoside adducts were faster than that of ribonucleoside adducts. In mixtures of ribonucleosides and deoxyribonucleosides treated with BPAQ, reactions occurred more readily with dG/G than dA/A. The structures of the modified bases were confirmed by electrospray ionization tandem mass spectrometry (ESI-MS/MS). We also found that BPAQ reacted readily with glutathione (GSH) in aqueous acetic acid, and characterized the BPAQ-GSH conjugate by ESI-MS/MS. The in vitro data of depurinating DNA/RNA adducts and BPAQ-GSH adducts may provide appropriate reference for the identification of BPAQ adducts in environmental and biological systems.

Modelling the chemical repair of protein carbon-centered radicals formed via oxidative damage with dihydrolipoic acid

Dihydrolipoic acid repairs carbon-centred radicals at diffusion-controlled rates via HAT mechanism.