Biodegradation of Herbicides by a Plant Nonheme Iron Dioxygenase: Mechanism and Selectivity of Substrate Analogues

Aryloxyalkanoate dioxygenases are unique herbicide biodegrading nonheme iron enzymes found in plants and hence, from environmental and agricultural point of view they are important and valuable. However, they often are substrate specific and little is known on the details of the mechanism and the substrate scope. To this end, we created enzyme models and calculate the mechanism for 2,4-dichlorophenoxyacetic acid biodegradation and 2-methyl substituted analogues by density functional theory. The work shows that the substrate binding is tight and positions the aliphatic group close to the metal center to enable a chemoselective reaction mechanism to form the C²-hydroxy products, whereas the aromatic hydroxylation barriers are well higher in energy. Subsequently, we investigated the metabolism of R- and S-methyl substituted inhibitors and show that these do not react as efficiently as 2,4-dichlorophenoxyacetic acid substrate due to stereochemical clashes in the active site and particularly for the R-isomer give high rebound barriers.     

Structure and Functional Differences of Cysteine and 3-Mercaptopropionate Dioxygenases: A Computational Study

Thiol dioxygenases are important enzymes for human health; they are involved in the detoxification and catabolism of toxic thiol-containing natural products such as cysteine. As such, these enzymes have relevance to the development of Alzheimer's and Parkinson's diseases in the brain. Recent crystal structure coordinates of cysteine and 3-mercaptopropionate dioxygenase (CDO and MDO) showed major differences in the second-coordination spheres of the two enzymes. To understand the difference in activity between these two analogous enzymes, we created large, active-site cluster models. We show that CDO and MDO have different iron(III)-superoxo-bound structures due to differences in ligand coordination. Furthermore, our studies show that the differences in the second-coordination sphere and particularly the position of a positively charged Arg residue results in changes in substrate positioning, mobility and enzymatic turnover. Furthermore, the substrate scope of MDO is explored with cysteinate and 2-mercaptosuccinic acid and their reactivity is predicted.     

Quantum Mechanics/Molecular Mechanics Studies on the Mechanism of Action of Cofactor Pyridoxal 5′‐Phosphate in Ornithine 4,5‐Aminomutase

A computational study was performed on the experimentally elusive cyclisation step in the cofactor pyridoxal 5′‐phosphate (PLP)‐dependent D ‐ornithine 4,5‐aminomutase (OAM)‐catalysed reaction. Calculations using both model systems and a combined quantum mechanics/molecular mechanics approach suggest that regulation of the cyclic radical intermediate is achieved through the synergy of the intrinsic catalytic power of cofactor PLP and the active site of the enzyme. The captodative effect of PLP is balanced by an enzyme active site that controls the deprotonation of both the pyridine nitrogen atom (N1) and the Schiff‐base nitrogen atom (N2). Furthermore, electrostatic interactions between the terminal carboxylate and amino groups of the substrate and Arg297 and Glu81 impose substantial “strain” energy on the orientation of the cyclic intermediate to control its trajectory. In addition the “strain” energy, which appears to be sensitive to both the number of carbon atoms in the substrate/analogue and the position of the radical intermediates, may play a key role in controlling the transition of the enzyme from the closed to the open state. Our results provide new insights into several aspects of the radical mechanism in aminomutase catalysis and broaden our understanding of cofactor PLP‐dependent reactions.     

Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs

Nature has developed large groups of enzymatic catalysts with the aim to transfer substrates into useful products, which enables biosystems to perform all their natural functions. As such, all biochemical processes in our body (we drink, we eat, we breath, we sleep, etc.) are governed by enzymes. One of the problems associated with research on biocatalysts is that they react so fast that details of their reaction mechanisms cannot be obtained with experimental work. In recent years, major advances in computational hardware and software have been made and now large (bio)chemical systems can be studied using accurate computational techniques. One such technique is the quantum mechanics/molecular mechanics (QM/MM) technique, which has gained major momentum in recent years. Unfortunately, it is not a black‐box method that is easily applied, but requires careful set‐up procedures. In this work we give an overview on the technical difficulties and caveats of QM/MM and discuss work‐protocols developed in our groups for running successful QM/MM calculations.     

On the Regio- and Stereospecificity of Arachidonic Acid Peroxidation Catalyzed by Mammalian 15-Lypoxygenases: A Combined Molecular Dynamics and QM/MM Study

15-Lipoxygenases (15-LOs) catalyse the peroxidation reaction of arachidonic acid (AA) in mammals with remarkable regio- and stereospecificity. This positional-specific peroxidation is of paramount importance because it determines the nature and biological functions of the final metabolites generated by each LO as a result of the oxidative metabolism of AA. Although several hypotheses have been formulated concerning the regio- and stereospecificity of LOs, the molecular basis of such behaviour is still unclear. Herein, we combined quantum mechanics/molecular mechanics calculations with molecular dynamics simulations of the complete rabbit 15-LO/AA solvated model to examine the most accepted hypotheses for the regio- and stereospecificity of LOs. We have found that the clue to explain this specificity is the oxygen-targeting hypothesis through steric shielding of specific residues (mainly Leu597, Gln548 and Phe175, as well as the AA tail itself). Our deductions are based primarily on the analysis of the energy barrier heights from the oxygen addition reaction profiles.     

Molecular Switching Behavior in Isosteric DNA Base Pairs

The structures and proton‐coupled behavior of adenine–thymine (A‐T) and a modified base pair containing a thymine isostere, adenine–difluorotoluene (A‐F), are studied in different solvents by dispersion‐corrected density functional theory. The stability of the canonical Watson–Crick base pair and the mismatched pair in various solvents with low and high dielectric constants is analyzed. It is demonstrated that A‐F base pairing is favored in solvents with low dielectric constant. The stabilization and conformational changes induced by protonation are also analyzed for the natural as well as the mismatched base pair. DNA sequences capable of changing their sequence conformation on protonation are used in the construction of pH‐based molecular switches. An acidic medium has a profound influence in stabilizing the isostere base pair. Such a large gain in stability on protonation leads to an interesting pH‐controlled molecular switch, which can be incorporated in a natural DNA tract.     

New Insights into the Nature of Observable Reaction Intermediates in Cytochrome P450 NO Reductase by Using a Combination of Spectroscopy and Quantum Mechanics/Molecular Mechanics Calculations

Cytochrome P450 NO reductase is an unusual member of the cytochrome P450 superfamily. It catalyzes the reduction of nitric oxide to nitrous oxide. The reaction intermediates were studied in detail by a combination of experimental and computational methods. They have been characterized experimentally by UV/Vis, EPR, Mössbauer, and MCD spectroscopy. In conjunction with quantum mechanics/molecular mechanics (QM/MM) calculations, we sought to characterize the resting state and the two detectable intermediates in detail and to elucidate the nature of the key intermediate I of the reaction. Six possible candidates were taken into account for the unknown key intermediate in the computational study, differing in protonation state and electronic structure. Two out of the six candidates could be identified as putative intermediates I with the help of the spectroscopic data: singlet diradicals Fe^III‐NHO ^{. ?} and Fe^III‐NHOH ^. . In a companion publication (C. Riplinger, F. Neese, ChemPhysChem­ 2011, 12, 3192 ) we have used QM/MM models based on these structures and performed a kinetic simulation. The combination of these two studies shows the nature of the key intermediate to be the singlet diradical, Fe^III‐NHOH ^. .     

Differences and Comparisons of the Properties and Reactivities of Iron(III)–hydroperoxo Complexes with Saturated Coordination Sphere

Heme and nonheme monoxygenases and dioxygenases catalyze important oxygen atom transfer reactions to substrates in the body. It is now well established that the cytochrome P450 enzymes react through the formation of a high‐valent iron(IV)–oxo heme cation radical. Its precursor in the catalytic cycle, the iron(III)–hydroperoxo complex, was tested for catalytic activity and found to be a sluggish oxidant of hydroxylation, epoxidation and sulfoxidation reactions. In a recent twist of events, evidence has emerged of several nonheme iron(III)–hydroperoxo complexes that appear to react with substrates via oxygen atom transfer processes. Although it was not clear from these studies whether the iron(III)–hydroperoxo reacted directly with substrates or that an initial O?O bond cleavage preceded the reaction. Clearly, the catalytic activity of heme and nonheme iron(III)–hydroperoxo complexes is substantially different, but the origins of this are still poorly understood and warrant a detailed analysis. In this work, an extensive computational analysis of aromatic hydroxylation by biomimetic nonheme and heme iron systems is presented, starting from an iron(III)–hydroperoxo complex with pentadentate ligand system (L₅²). Direct C?O bond formation by an iron(III)–hydroperoxo complex is investigated, as well as the initial heterolytic and homolytic bond cleavage of the hydroperoxo group. The calculations show that [(L₅²)Fe^III(OOH)]²⁺ should be able to initiate an aromatic hydroxylation process, although a low‐energy homolytic cleavage pathway is only slightly higher in energy. A detailed valence bond and thermochemical analysis rationalizes the differences in chemical reactivity of heme and nonheme iron(III)–hydroperoxo and show that the main reason for this particular nonheme complex to be reactive comes from the fact that they homolytically split the O?O bond, whereas a heterolytic O?O bond breaking in heme iron(III)–hydroperoxo is found.     

Binding of Cationic and Neutral Phenanthridine Intercalators to a DNA Oligomer Is Controlled by Dispersion Energy: Quantum Chemical Calculations and Molecular Mechanics Simulations

Correlated ab initio as well as semiempirical quantum chemical calculations and molecular dynamics simulations were used to study the intercalation of cationic ethidium, cationic 5‐ethyl‐6‐phenylphenanthridinium and uncharged 3,8‐diamino‐6‐phenylphenanthridine to DNA. The stabilization energy of the cationic intercalators is considerably larger than that of the uncharged one. The dominant energy contribution with all intercalators is represented by dispersion energy. In the case of the cationic intercalators, the electrostatic and charge‐transfer terms are also important. The ΔG of ethidium intercalation to DNA was estimated at ?4.5 kcal mol^?1 and this value agrees well with the experimental result. Of six contributions to the final free energy, the interaction energy value is crucial. The intercalation process is governed by the non‐covalent stacking (including charge‐transfer) interaction while the hydrogen bonding between the ethidium amino groups and the DNA backbone is less important. This is confirmed by the evaluation of the interaction energy as well as by the calculation of the free energy change. The intercalation affects the macroscopic properties of DNA in terms of its flexibility. This explains the easier entry of another intercalator molecule in the vicinity of an existing intercalation site.     

Mechanistic Insights into the Regio- and Stereoselectivities of Testosterone and Dihydrotestosterone Hydroxylation Catalyzed by CYP3A4 and CYP19A1

The hydroxylation of nonreactive C−H bonds can be easily catalyzed by a variety of metalloenzymes, especially cytochrome P450s (P450s). The mechanism of P450 mediated hydroxylation has been intensively studied, both experimentally and theoretically. However, understanding the regio- and stereoselectivities of substrates hydroxylated by P450s remains a great challenge. Herein, we use a multi-scale modeling approach to investigate the selectivity of testosterone (TES) and dihydrotestosterone (DHT) hydroxylation catalyzed by two important P450s, CYP3A4 and CYP19A1. For CYP3A4, two distinct binding modes for TES/DHT were predicted by dockings and molecular dynamics simulations, in which the experimentally identified sites of metabolism of TES/DHT can access to the catalytic center. The regio- and stereoselectivities of TES/DHT hydroxylation were further evaluated by quantum mechanical and ONIOM calculations. For CYP19A1, we found that sites 1β, 2β and 19 can access the catalytic center, with the intrinsic reactivity 2β>1β>19. However, our ONIOM calculations indicate that the hydroxylation is favored at site 19 for both TES and DHT, which is consistent with the experiments and reflects the importance of the catalytic environment in determining the selectivity. Our study unravels the mechanism underlying the selectivity of TES/DHT hydroxylation mediated by CYP3A4 and CYP19A1 and is helpful for understanding the selectivity of other substrates that are hydroxylated by P450s.     

A theoretical study on the reaction pathways of peroxynitrite formation and decay at nonheme iron centers

A computational study based on density functional theory was undertaken to identify possible reaction pathways for the formation and decomposition of peroxynitrite at models of the active sites of the nonheme superoxide scavenging enzymes superoxide reductase (SOR) and iron superoxide dismutase (FeSOD). Two peroxynitrite isomers and their possible protonated states were investigated, namely Fe? OONO^?, Fe? N(O)OO^?, Fe? OONOH, and Fe? N(O)OOH. Peroxynitrite formation at the active sites was assumed by either the interaction of a peroxynitrite cis/trans anion with the pentacoordinated iron active site or the interaction between a nitric oxide bound adduct and superoxide; both scenarios were found to be facile for all models investigated. The ferrous adducts of the Fe? OONO^?isomer were found to undergo instant heterolytic cleavage of the O? ONO bond to yield nitrite, whereas for the ferric adducts, the homolytic cleavage of the O? ONO bond to yield nitrogen dioxide was found to be energetically facile. For the Fe? N(O)OO^? isomer, the active site models of FeSOD and SOR were only able to accommodate the cis isomer of peroxynitrite. Ferric adducts of the cis Fe? OONO^? isomer were found to be energetically more stable than their trans counterparts and were also more stable than the cis adducts of the Fe? N(O)OO^? isomer; conversely, the protonated forms of all adducts of the Fe? OONOH isomer were found to be lower in energy than their equivalent Fe? N(O)OOH adducts. Multiple reaction pathways for the decomposition of the formed peroxynitrite adducts (whether the anions or the protonated forms) were proposed and explored. The energy requirements for the decomposition processes ranged from exothermic to highly demanding depending on the peroxynitrite isomer, the type of model (whether an SOR or FeSOD active site), and the oxidation state of iron. © 2014 Wiley Periodicals, Inc.     

Quantum Chemical Study of the Enzymatic Repair of T(6‐4)C/C(6‐4)T UV‐Photolesions by DNA Photolyases

Several strategies have evolved to repair one of the abundant UV radiation‐induced damages caused to DNA, namely the mutagenic pyrimidine (6‐4) pyrimidone photolesions. DNA (6‐4)‐photolyases are enzymes repairing these lesions by a photoinitiated electron transfer. An important aspect of a possible repair mechanism is its generality and transferability to different (6‐4) lesions. Therefore, previously suggested mechanisms for the repair of the T(6‐4)T lesion are here transferred to the T(6‐4)C and C(6‐4)T lesions and investigated theoretically using quantum chemical methods. Despite the different functional groups of the pyrimidine bases involved, a general valid molecular mechanism was identified, in which the initial step is an electron transfer coupled to a proton transfer from the protonated HIS365 to the N3^′ nitrogen of the 3^′ pyrimidine, followed by an intramolecular OH/NH₂ transfer in one concerted step, which does not require an oxetane/azetidine or isolated water/ammonia intermediate.     

The Effect of Solvation on the Radiation Damage Rate Constants for Adenine

It is well known that water plays an important part in almost all biological systems and that inclusion of solvation effects might therefore be of utmost importance in studies of radiation damage to DNA. In the present investigation, we have studied the effect of different solvation models in calculations of Gibbs free energies and reaction rates for the reaction between the OH radical and the DNA nucleobase adenine by conducting density functional theory calculations at the ωB97X‐D/6‐311++G(2df,2pd) level with the Eckart tunnelling correction. The solvent, water, was included through either the implicit polarizable continuum model (PCM) or through explicit modelling of micro‐solvation by a single water molecule at the site of reaction as well as by the combination of both. Scrutiny of the thermodynamics and kinetics of the individual sub‐reactions suggests that the qualitative differences introduced by the solvation models do not significantly alter the conclusions made based solely on simple gas‐phase calculations. Abstraction of the amine hydrogen atoms H₆₁ and H₆₂ and addition onto C₈ remain the most likely reaction pathways.     

Nickel(II) Complexes of Pentadentate N5 Ligands as Catalysts for Alkane Hydroxylation by Using m‐CPBA as Oxidant: A Combined Experimental and Computational Study

A new family of nickel(II) complexes of the type [Ni(L)(CH₃CN)](BPh₄)₂, where L=N‐methyl‐N,N′,N′‐tris(pyrid‐2‐ylmethyl)‐ethylenediamine (L1, 1 ), N‐benzyl‐N,N′,N′‐tris(pyrid‐2‐yl‐methyl)‐ethylenediamine (L2, 2 ), N‐methyl‐N,N′‐bis(pyrid‐2‐ylmethyl)‐N′‐(6‐methyl‐pyrid‐2‐yl‐methyl)‐ethylenediamine (L3, 3 ), N‐methyl‐N,N′‐bis(pyrid‐2‐ylmethyl)‐N′‐(quinolin‐2‐ylmethyl)‐ethylenediamine (L4, 4 ), and N‐methyl‐N,N′‐bis(pyrid‐2‐ylmethyl)‐N′‐imidazole‐2‐ylmethyl)‐ethylenediamine (L5, 5 ), has been isolated and characterized by means of elemental analysis, mass spectrometry, UV/Vis spectroscopy, and electrochemistry. The single‐crystal X‐ray structure of [Ni(L3)(CH₃CN)](BPh₄)₂ reveals that the nickel(II) center is located in a distorted octahedral coordination geometry constituted by all the five nitrogen atoms of the pentadentate ligand and an acetonitrile molecule. In a dichloromethane/acetonitrile solvent mixture, all the complexes show ligand field bands in the visible region characteristic of an octahedral coordination geometry. They exhibit a one‐electron oxidation corresponding to the Ni^II/Ni^III redox couple the potential of which depends upon the ligand donor functionalities. The new complexes catalyze the oxidation of cyclohexane in the presence of m‐CPBA as oxidant up to a turnover number of 530 with good alcohol selectivity (A/K, 7.1–10.6, A=alcohol, K=ketone). Upon replacing the pyridylmethyl arm in [Ni(L1)(CH₃CN)](BPh₄)₂ by the strongly σ‐bonding but weakly π‐bonding imidazolylmethyl arm as in [Ni(L5)(CH₃CN)](BPh₄)₂ or the sterically demanding 6‐methylpyridylmethyl ([Ni(L3)(CH₃CN)](BPh₄)₂ and the quinolylmethyl arms ([Ni(L4)(CH₃CN)](BPh₄)₂, both the catalytic activity and the selectivity decrease. DFT studies performed on cyclohexane oxidation by complexes 1 and 5 demonstrate the two spin‐state reactivity for the high‐spin [(N5)Ni^II?O^.] intermediate (ts1_hs, ts2_doublet), which has a low‐spin state located closely in energy to the high‐spin state. The lower catalytic activity of complex 5 is mainly due to the formation of thermodynamically less accessible m‐CPBA‐coordinated precursor of [Ni^II(L5)(OOCOC₆H₄Cl)]⁺ ( 5 a ). Adamantane is oxidized to 1‐adamantanol, 2‐adamantanol, and 2‐adamantanone (3°/2°, 10.6–11.5), and cumene is selectively oxidized to 2‐phenyl‐2‐propanol. The incorporation of sterically hindering pyridylmethyl and quinolylmethyl donor ligands around the Ni^II leads to a high 3°/2° bond selectivity for adamantane oxidation, which is in contrast to the lower cyclohexane oxidation activities of the complexes.