Noninnocent effect of axial ligand on the heme degradation process: a theoretical approach to hydrolysis pathway of verdoheme to biliverdin

Theoretical investigation of five-coordinated manganese(III) oxophlorin with different axial ligands at various spin states using different DFT methods

The Mn(III)-oxophlorin complexes with imidazole, pyridine and t-butylcyanide as axial ligands have been studied using B3LYP, Bv86p, and M06-2X methods. All of the possible optimized geometries are specified, while the M06-2X is employed. Results obtained show that the isomers of Mn(III)-oxophlorin with imidazole or pyridine are the most stable at quintet state, compared to singlet and triplet spin states. Besides, there are two and four [Formula: see text]-electrons on manganese in each of these complexes at triplet and quintet states, respectively. Also, Mn(III)-oxophlorin with t-butylcyanide as axial ligand is only stable at singlet state. Non-specific solvent effects show that dispersion and London forces have the basic role in stability of complexes in a solvent. Note that latter interactions can occur in medium with dielectric constant ([Formula: see text]) of [Formula: see text]8, such as [Formula: see text] for position of oxophlorin in heme oxygenase enzyme. NBO analysis show that there is no degeneracy between d orbitals of Mn in the five-coordinated Mn(III)-oxophlorin at singlet and triplet spin states, but two d orbitals of manganese are degenerated in latter complexes at quintet state. Such degeneracy of d orbitals is observed in a complex with square pyramid structure. Then five-coordinated Mn(III)-oxophlorin with imidazole or pyridine is the most stable at quintet spin state, because of its geometry corresponding to square pyramid configuration of atoms. Also, nonbounding interaction between Mn and the ring of oxophlorin or Mn and ligand are more effective in Mn(III)-oxophlorin with imidazole as axial ligand, compared to pyridine and t-butylcyanide.

Investigation of different substitutions, structure, charge and multiplicity spin of the iron verdoheme-rat heme oxygenase complex: a DFT study

Heme oxygenase-1 (HO-1) is an inducible stress protein that degrades heme to carbon monoxide, iron and biliverdin, which subsequently reduces to bilirubin. Many parameters of verdoheme–rat heme oxygenase complex structure and their role and function on heme degradation were unknown. In this work the structure of iron verdoheme in complex with rat heme oxygenase was studied by density functional theory based B3LYP method and 6-31G basis set. The main goal is to obtain structural and energetic information for various transition states and intermediates on reaction pathways. The charge of verdoheme and iron as the central metal, electron distribution, spin multiplicity of the molecule and proximal substituents effect on the verdoheme ring stabilization and their arrangement are discussed. Gas phase computation has shown that the central metal of the five coordinated rat-verdohemeas ferrous (Fe[Formula: see text] (from 1a-1i) and ferric (Fe[Formula: see text] (from 1j–1q). The Mulliken and NBO charge and spin calculation show that iron is considered as ferrous in all of the optimized structures. Assessment results can gain valuable chemical insight into the electronic reorganization during the reactions.

Theoretical study of OH− nucleophilic attack on cobalt(II)-verdoheme complex

OH[Formula: see text] attack on a four, five and six-coordinated cobalt(II)-verdoheme-coordinated with imidazole (1 M) while the axial ligand was studied using B3LYP method. Different spin multiplicities were considered, namely doublet, quartet, and sextet. Results show the most positive charge to be concentrated at the cobalt and carbon atoms adjacent to the oxygen in the cobalt(II)-verdoheme complex. Data obtained show that a stable intermediate was formed by a nucleophilic attack on one of the latter carbon atoms. The intermediate is initially formed by a nucleophilic attack on one of the aforementioned carbon atoms. This intermediate is then directly converted to a helical open-ring complex by passing it through a transition state. It is specified that if every nucleophilic attack is considered separately, then the OH[Formula: see text] attack on cobalt(II)-verdoheme occurred at all spin multiplicity and coordination states, from a thermodynamics and kinetics point of view, all except an OH[Formula: see text] attack on five-coordinated cobalt(II)-verdoheme at quartet state. However, comparison of reaction paths with different spin in the same coordination show that such a nucleophilic attack is not proceeded, while the reactant is a four and six-coordinated cobalt(II)-verdoheme because the latter reaction spin state is not conserved. It is clear that OH[Formula: see text] attack on five-inatedcoordinated Co(II)-verdoheme at doublet spin multiplicity is the most stable reaction path. Moreover, these findings were confirmed by NBO analysis and molecular orbital calculations.

Multiplicity spin, structure, and charge of iron-verdohemeoxygenase complex: A comparison study by the DFT method

Recently the three-dimensional structure of verdoheme heme oxygenase complex was revealed. However, many parameters of verdoheme heme oxygenase’s complex structure and their role and function on Heme degradation were unknown. In this work the structure of iron verdoheme in complex with heme oxygenase was compared by the density functional theory (DFT)-based B3LYP method using the 6-31G basis set. Many parameters such as charge of verdoheme and iron as central metal, electron distribution, spin multiplicity of the molecule and proximal substituents effects on verdoheme ring stabilization and their arrangement are discussed and compared for twelve different conformations of the molecules to find the most energetically stable states.

Theoretical kinetics and thermodynamics study: Peripheral substituent effects on the hydrolysis of verdoheme

The heme oxygenase (HO) enzyme is a free heme protein that binds to heme in the body. Heme acts as both a cofactor and a substrate in this enzyme. The catabolism of heme into biliverdin, monoxide carbon, and free-iron, catalyzed by heme oxygenase via three consecutive oxygenation steps, in which the heme group functions as the prosthetic group as well as the substrate. Investigations of the reactions of the peripheral substituent on the heme ring with 5-oxaporphyrin iron complexes (verdohemes) have been assumed to provide models and largely unknown for the primary step in the hydrolysis of verdohemes. In this work, a theoretical kinetics and thermodynamics study of the degradation reactions of verdohemes was performed, and calculations show that the [Formula: see text] in the hydrolysis of verdohemes with non-peripheral substituents is more negative than hydrolysis of verdohemes with peripheral substituents. In other words, the hydrolysis of verdohemes with non-peripheral substituents is more energy-efficient than verdohemes with a peripheral substituents. Equilibrium constant calculations show that hydrolysis of verdohemes with non-peripheral substituents is much faster than that of verdohemes with peripheral substituents, which is due to a more convenient nucleophilic attack on the cationic ring than the anionic ring. To acquire a good molecular understanding, peripheral substituent effects on the hydrolysis of verdoheme’s inhibitory role was studied using the DFT method.

Theoretical study of first row transitional metals effects on stabilization of verdoheme analogues

Heme catabolism is an important physiological process that converts heme to biliverdin in the presence of heme oxygenase which has an essential role in destroying unwanted heme. Verdohemes, the green iron (II) complexes of the 5-oxaporphyrin macrocycle are produced by oxidative destruction of heme. The main goal of this study is clarification of the central metal effect on stabilization of metal 5-oxaporphyrin molecules. To investigate the role of central metal on geometric and electronic properties of five coordinated verdoheme analogues, the first row transitional metals, including Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu and Zn, as the central metal of five-coordinated metal 5-oxaporphyrins were systematically calculated without any symmetry constraint by using the B3LYP as DFT method and the 6-31G basis set in gas and solvent phases. According to the results, the stabilization energy of metal 5-oxaporphyrins increases with atomic mass in the solvent phase more than in the gas phase. By reviewing the properties such as the computed frontier orbital energy, HOMO and LUMO gap energy [Formula: see text], hardness [Formula: see text], chemical potential [Formula: see text], softness (s) and electrophilicity [Formula: see text], the pharmaceutical use of this compound can be discussed.

Density functional theory studies on the conversion of hydroxyheme to iron-verdoheme in the presence of dioxygen

Detailed insight into the second step of heme degradation by heme oxygenase, oxophlorin to verdoheme and biliverdin, is presented. Density functional theory methods are reported for the conversion of oxophlorin to verdoheme. Since it is currently unclear whether dioxygen binding to iron oxophlorin is followed by a reduction or not, in this work we have focused on the difference in reactivity between [(Im)(O₂˙)Fe^III(PO˙)] (PO˙ is the oxophlorin dianion radical) and [(Im)(O₂˙)Fe^III(PO)]^- (PO is the oxophlorin trianion). Thus, we have shown that in [(Im)(O₂˙)Fe^III(PO˙)] and [(Im)(O₂˙)Fe^III(PO)]^-, the mechanisms are stepwise with an initial C-O bond activation to form a ring-structure where the oxophlorin is distorted from planarity. This is followed by homolytic dioxygen bond breaking that directly leads to iron-oxo verdoheme products. The [(Im)(O₂˙)Fe^III(PO˙)] mechanism proceeds via two-state-reactivity patterns on the adjacent doublet and quartet spin state surfaces, whereas the [(Im)(O₂˙)Fe^III(PO)]^- route shows single-state-reactivity on a triplet spin state surface. In both, the rate determining step is the C-O bond activation, with substantially lower barriers on the [(Im)(O₂˙)Fe^III(PO˙)] surface of 12.15 kcal mol^-1 in the gas phase compared to 22.55 kcal mol^-1 for the intermediate-spin of [(Im)(O₂˙)Fe^III(PO)]^-. The complete active space self-consistent-field wave functions with second-order multi-reference perturbation theory were also studied. Finally, the effects of the solvent and the medium on the reaction barriers were tested and shown to be considerable.

Unusual diheme conformation of the heme-degrading protein from Mycobacterium tuberculosis

Heme degradation plays a pivotal role in the availability of the essential nutrient, iron, in pathogenic bacteria. A previously unannotated protein from Mycobacterium tuberculosis, Rv3592, which shares homology to heme-degrading enzymes, has been identified. Biochemical analyses confirm that Rv3592, which we have termed MhuD (mycobacterial heme utilization, degrader), is able to bind and degrade heme. Interestingly, contrary to previously reported stoichiometry for the Staphylococcus aureus heme degraders, iron-regulated surface determinant (Isd)G and IsdI, MhuD has the ability to bind heme in a 1:2 protein-to-heme ratio, although the MhuD-diheme complex is inactive. Furthermore, the 1.75-A crystal structure of the MhuD-diheme complex reveals two stacked hemes forming extensive contacts with residues in the active site. In particular, the solvent-exposed heme is axially liganded by His75 and is stacked planar upon the solvent-protected heme. The solvent-protected heme is coordinated by a chloride ion, which is, in turn, stabilized by Asn7. Structural comparison between MhuD-diheme and inactive IsdG and IsdI bound to only one highly distorted metalloporphyrin ring reveals that several residues located in alpha-helix 2 and the subsequent loop appear to be responsible for heme stoichiometric differences and suggest open and closed conformations for substrate entry and product exit.

Theoretical investigations on the hydrolysis pathway of tin verdoheme complexes: elucidation of tin's ring opening inhibition role

In order to obtain a better molecular understanding of inhibitory role of tin metal in the verdoheme ring opening process, hydrolysis of three possibly six, five, and four coordinate verdoheme complexes of tin(IV) and (II) have been studied using DFT method. The results of calculations indicate that, in excellent accord with experimental reports, hydrolysis of different possibly coordinated tin(IV) and (II) verdohemes does not lead to the opening of the macrocycle. Contrary to iron and zinc verdohemes, in five and four coordinate verdoheme complexes of tin(IV) and (II), formation of open ring helical complexes of tin are unfavorable both thermodynamically and kinetically. In these pathways, coordination of hydroxide nucleophile to tin metal due to the highly charged, exclusive oxophilicity nature of the Sn center, and high affinity of Sn to increase coordination state are proposed responsible as inhibiting roles of tin via the ring opening. While, in saturated six coordinate tin(IV) and (II) verdoheme complexes the ring opening of tin verdohemes is possible thermodynamically, but it is not predicted to occur from a kinetics point of view. In the six coordinate pathway, tin plays no coordination role and direct addition of hydroxide nucleophile to the positive oxo-carbon centers and formation of closed ring hydroxy compounds is proposed for preventing the verdoheme ring opening. These key points and findings have been corroborated by the results obtained from atomic charge analysis, geometrical parameters, and molecular orbital calculations. In addition, the results of inhibiting ring opening reaction of tin verdoheme complexes could support the great interest of tin porphyrin analogues as pharmacologic means of chemoprevention of neonatal jaundice by the competitive inhibitory action of tin porphyrins on heme oxygenase.