Experimental and time-dependent density functional theory characterization of the UV-visible spectra of monomeric and μ-oxo dimeric ferriprotoporphyrin IX

Cell-free hemoglobin and hemin catalyzing triclosan oxidative coupling in plasma: A novel exogenous phenolic pollutants coupling pathway

Previous studies reported that hemoprotein CYP450 catalyzed triclosan coupling is an "uncommon" metabolic pathway that may enhance toxicity, raising concerns about its environmental and health impacts. Hemoglobin, a notable hemoprotein, can catalyze endogenous phenolic amino acid tyrosine coupling reactions. Our study explored the feasibility of these coupling reactions for exogenous phenolic pollutants in plasma. Both hemoglobin and hemin were found to catalyze triclosan coupling in the presence of H₂O₂. This resulted in the formation of five diTCS-2 H, two diTCS-Cl-3 H, and twelve triTCS-4 H in phosphate buffer, with a total of nineteen triclosan coupling products monitored using LC-QTOF. In plasma, five diTCS-2 H, two diTCS-Cl-3 H, and two triTCS-4 H were detected in hemoglobin-catalyzed reactions. Hemin showed a weaker catalytic effect on triclosan transformation compared to hemoglobin, likely due to hemin dimerization and oxidative degradation by H₂O₂, which limits its catalytic efficiency. Triclosan transformation in the human plasma-like medium still occurs with high H₂O₂, despite the presence of antioxidant proteins that typically inhibit such transformations. In plasma, free H₂O₂ was depleted within 40 minutes when 800 µM H₂O₂ was added, suggesting a rapid consumption of H₂O₂ in these reactions. Antioxidative species, or hemoglobin/hemin scavengers such as bovine serum albumin, may inhibit but not completely terminate the triclosan coupling reactions. Previous studies reported that diTCS-2 H showed higher hydrophobicity and greater endocrine-disrupting effects compared to triclosan, which further underscores the potential health risks. This study indicates that hemoglobin and heme in human plasma might significantly contribute to phenolic coupling reactions, potentially increasing health risks.

Ferric heme b in aqueous micellar and vesicular systems: state-of-the-art and challenges

Ferric heme b (= ferric protoporphyrin IX = hemin) is an important prosthetic group of different types of enzymes, including the intensively investigated and widely applied horseradish peroxidase (HRP). In HRP, hemin is present in monomeric form in a hydrophobic pocket containing among other amino acid side chains the two imidazoyl groups of His170 and His42. Both amino acids are important for the peroxidase activity of HRP as an axial ligand of hemin (proximal His170) and as an acid/base catalyst (distal His42). A key feature of the peroxidase mechanism of HRP is the initial formation of compound I under heterolytic cleavage of added hydrogen peroxide as a terminal oxidant. Investigations of free hemin dispersed in aqueous solution showed that different types of hemin dimers can form, depending on the experimental conditions, possibly resulting in hemin crystallization. Although it has been recognized already in the 1970s that hemin aggregation can be prevented in aqueous solution by using micelle-forming amphiphiles, it remains a challenge to prepare hemin-containing micellar and vesicular systems with peroxidase-like activities. Such systems are of interest as cheap HRP-mimicking catalysts for analytical and synthetic applications. Some of the key concepts on which research in this fascinating and interdisciplinary field is based are summarized, along with major accomplishments and possible directions for further improvement. A systematic analysis of the physico-chemical properties of hemin in aqueous micellar solutions and vesicular dispersions must be combined with a reliable evaluation of its catalytic activity. Future studies should show how well the molecular complexity around hemin in HRP can be mimicked by using micelles or vesicles. Because of the importance of heme b in virtually all biological systems and the fact that porphyrins and hemes can be obtained under potentially prebiotic conditions, ideas exist about the possible role of heme-containing micellar and vesicular systems in prebiotic times.

Hemin-catalyzed oxidative oligomerization of p-aminodiphenylamine (PADPA) in the presence of aqueous sodium dodecylbenzenesulfonate (SDBS) micelles

In a previous report on the enzymatic synthesis of the conductive emeraldine salt form of polyaniline (PANI-ES) in aqueous solution using PADPA (p-aminodiphenylamine) as monomer, horseradish peroxidase isoenzyme C (HRPC) was applied as a catalyst at pH = 4.3 with H₂O₂ as a terminal oxidant. In that work, anionic vesicles were added to the reaction mixture for (i) guiding the reaction to obtain poly(PADPA) products that resemble PANI-ES, and for (ii) preventing product precipitation (known as the “template effect”). In the work now presented, instead of native HRPC, only its prosthetic group ferric heme b (= hemin) was utilized as a catalyst, and micelles formed from SDBS (sodium dodecylbenzenesulfonate) served as templates. For the elaborated optimal reaction conditions, complementary UV/vis/NIR, EPR, and Raman spectroscopy measurements clearly showed that the reaction mixture obtained after completion of the reaction contained PANI-ES-like products as dominating species, very similar to the products formed with HRPC as catalyst. HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonate) was found to have a positive effect on the reaction rate as compared to dihydrogenphosphate. This work is the first on the template-assisted formation of PANI-ES type products under mild, environmentally friendly conditions using hemin as a cost-effective catalyst.

Polyaniline emeraldine salt-type products were synthesized under mild, environmentally friendly conditions using hemin as a cost-effective catalyst, p-aminodiphenylamine (PADPA) as a monomer, and micelles formed from SDBS as templates.

A first principle study of heme molecule as an active adsorbent for halogenated hydrocarbons

Heme, a biomolecule with complex structure and unique properties and strong adsorption of oxygen, is utilized as an adsorbing material for haloalkene gas molecules. It has been systematically investigated employing density functional theory. Among the haloalkene gases chosen in the present study, the interaction energy is maximum for CDFM (-10.66 kcal/mol) and lowest for TFM (-5.02 kcal/mol). The calculated bond stabilization energy for heme-haloalkene complexes correlates with findings of interaction energy. The noncovalent interaction between heme and haloalkenes is confirmed from the topological analysis. The energy gap values decrease on adsorption of haloalkenes along with a decrease in reactivity of the complexes.

Characterization of the UV-Visible absorption spectra of manganese(III) porphyrins with time-dependent density functional theory calculations

Mn(III) porphyrins display a unique UV–Vis spectrum: compared to the free-base and other metalloporphyrins, a strong red shift of the Soret-band and several extra bands can be observed in their spectra. To understand this behavior, we have recorded the UV–Vis spectra of differently substituted water-soluble Mn(III) porphyrins and conducted extensive theoretical investigations using time-dependent density functional theory. The calculated optical transitions, using the O3LYP functional, agree well with the measured absorption bands. According to the spectral interpretation, the Soret-band involves a mixture of L–L and ligand-to-metal charge transfer excitations, while the Q-bands and the higher-energy bands in the UV region correspond to pure LMCT as well as to ligand to metal-ligand mixed orbital excitations. The impact of the explicit and implicit water solvent on the spectral features is also discussed.

Heme Detoxification in the Malaria Parasite: A Target for Antimalarial Drug Development

Over the last century, malaria deaths have decreased by more than 85%. Nonetheless, there were 405 000 deaths in 2018, mostly resulting from Plasmodium falciparum infection. In the 21st century, much of the advance has arisen from the deployment of insecticide-treated bed nets and artemisinin combination therapy. However, over the past few decades parasites with a delayed artemisinin clearance phenotype have appeared in Southeast Asia, threatening further gains. The effort to find new drugs is thus urgent. A prominent process in blood stage malaria parasites, which we contend remains a viable drug target, is hemozoin formation. This crystalline material consisting of heme can be readily seen when parasites are viewed microscopically. The process of its formation in the parasite, however, is still not fully understood.In early work, we recognized hemozoin formation as a biomineralization process. We have subsequently investigated the kinetics of synthetic hemozoin (β-hematin) crystallization catalyzed at lipid-aqueous interfaces under biomimetic conditions. This led us to the use of neutral detergent-based high-throughput screening (HTS) for inhibitors of β-hematin formation. A good hit rate against malaria parasites was obtained. Simultaneously, we developed a pyridine-based assay which proved successful in measuring the concentrations of hematin not converted to β-hematin.The pyridine assay was adapted to determine the effects of chloroquine and other clinical antimalarials on hemozoin formation in the cell. This permitted the determination of the dose-dependent amounts of exchangeable heme and hemozoin in P. falciparum for the first time. These studies have shown that hemozoin inhibitors cause a dose-dependent increase in exchangeable heme, correlated with decreased parasite survival. Electron spectroscopic imaging (ESI) showed a relocation of heme iron into the parasite cytoplasm, while electron microscopy provided evidence of the disruption of hemozoin crystals. This cellular assay was subsequently extended to top-ranked hits from a wide range of scaffolds found by HTS. Intriguingly, the amounts of exchangeable heme at the parasite growth IC₅₀ values of these scaffolds showed substantial variation. The amount of exchangeable heme was found to be correlated with the amount of inhibitor accumulated in the parasitized red blood cell. This suggests that heme-inhibitor complexes, rather than free heme, lead to parasite death. This was supported by ESI using a Br-containing compound which showed the colocalization of Fe and Br as well as by confocal Raman microscopy which confirmed the presence of a complex in the parasite. Current evidence indicates that inhibitors block hemozoin formation by surface adsorption. Indeed, we have successfully introduced molecular docking with hemozoin to find new inhibitors. It follows that the resulting increase in free heme leads to the formation of the parasiticidal heme-inhibitor complex. We have reported crystal structures of heme-drug complexes for several aryl methanol antimalarials in nonaqueous media. These form coordination complexes but most other inhibitors interact noncovalently, and the determination of their structures remains a major challenge.It is our view that key future developments will include improved assays to measure cellular heme levels, better in silico approaches for predicting β-hematin inhibition, and a concerted effort to determine the structure and properties of heme-inhibitor complexes.

Unravelling the mechanisms controlling heme supply and demand

In addition to heme's role as the prosthetic group buried inside many different proteins that are ubiquitous in biology, there is new evidence that heme has substantive roles in cellular signaling and regulation. This means that heme must be available in locations distant from its place of synthesis (mitochondria) in response to transient cellular demands. A longstanding question has been to establish the mechanisms that control the supply and demand for cellular heme. By fusing a monomeric heme-binding peroxidase (ascorbate peroxidase, mAPX) to a monomeric form of green-fluorescent protein (mEGFP), we have developed a heme sensor (mAPXmEGFP) that can respond to heme availability. By means of fluorescence lifetime imaging, this heme sensor can be used to quantify heme concentrations; values of the mean fluorescence lifetime (τ_Mean) for mAPX-mEGFP are shown to be responsive to changes in free (unbound) heme concentration in cells. The results demonstrate that concentrations are typically limited to one molecule or less within cellular compartments. These miniscule amounts of free heme are consistent with a system that sequesters the heme and is able to buffer changes in heme availability while retaining the capability to mobilize heme when and where it is needed. We propose that this exchangeable supply of heme can operate using mechanisms for heme transfer that are analogous to classical ligand-exchange mechanisms. This exquisite control, in which heme is made available for transfer one molecule at a time, protects the cell against the toxic effect of excess heme and offers a simple mechanism for heme-dependent regulation in single-molecule steps.

Computational insights into the inhibition of β-haematin crystallization by antimalarial drugs

During the red blood cell phase of their life cycle, malaria parasites digest their host's haemoglobin, with concomitant release of potentially toxic iron(iii) protoporphyrin IX (FePPIX). The parasites' strategy for detoxification of FePPIX involves its crystallization to haemozoin, such that the build-up of free haem in solution is avoided. Antimalarial drugs of both historical importance and current clinical use are known to be capable of disrupting the growth of crystals of β-haematin, which is the synthetic equivalent of haemozoin. Hence, the disruption of haemozoin crystal growth is implicated as a possible mode of action of such drugs. However, the details of β-haematin crystal poisoning at the molecular level have yet to be fully elucidated. In this study, we have used a combination of density functional theory (DFT) and molecular modelling to examine the possible modes of action of ten different antimalarial drugs, including quinine-type aliphatic alcohols, amodiaquine-type phenols, and chloroquine-type aliphatic diamines. The DFT calculations indicate that each of the drugs can form at least one molecular complex with FePPIX. These complexes have 1 : 1 or 2 : 1 FePPIX : drug stoichiometries and all of them incorporate Fe-O bonds, formed either by direct coordination of a zwitterionic form of the drug, or by deprotonation of water. Most of the drugs can form more than one such complex. We have used the DFT model structures to explore the possible formation of a monolayer of each drug-haem complex on four of the β-haematin crystal faces. In all cases, the drug complexes can form a monolayer on the fast-growing {001} and {011} faces, but not on the slower growing {010} and {100} faces. Additional modelling of the chloroquine and quinidine complexes shows that individual molecules of these species can also obstruct the growth of new layers on other crystal faces. The implications of these observations for antimalarial drug development are discussed.

Charge Transfer and π to π* Transitions in the Visible Spectra of Sulfheme Met Isomeric Structures

Since the 1863 discovery of a new green hemoglobin derivative called "sulfhemoglobin", the nature of the characteristic 618 nm absorption band has been the subject of several hypotheses. The experimental spectra are a function of the observation time and interplay between two major sulfheme isomer concentrations (a three- and five-membered ring adduct), with the latter being the dominant isomer at longer times. Thus, time-dependent density functional theory (TDDFT) was used to calculate the sulfheme excited states and visualize the highest occupied molecular orbitals (HOMOs) and lowest unoccupied MOs (LUMOs) of both isomers in order to interpret the transitions between them. These two isomers have distinguishable a_1u and a_2u HOMO energies. Formation of the three-membered ring S_A isomeric structure decreases the energy of the HOMO a_1u and a_2u orbitals compared to the unmodified heme due to the electron-withdrawing, sulfur-containing, three-membered ring. Conversely, formation of the S_C isomeric structure decreases the energy of the HOMO a_1u and a_2u orbitals due to the electron-withdrawing, sulfur-containing, five-membered ring. The calculations reveal that the absorption spectrum within the 700 nm region arises from a mixture of MOs but can be characterized as π to π* transitions, while the 600 nm region is characterized by π to d_π (d _yz, d _xz) transitions having components of a deoxy-like derivative.

A mechanism for CO regulation of ion channels

Despite being highly toxic, carbon monoxide (CO) is also an essential intracellular signalling molecule. The mechanisms of CO-dependent cell signalling are poorly defined, but are likely to involve interactions with heme proteins. One such role for CO is in ion channel regulation. Here, we examine the interaction of CO with K_ATP channels. We find that CO activates K_ATP channels and that heme binding to a CXXHX₁₆H motif on the SUR2A receptor is required for the CO-dependent increase in channel activity. Spectroscopic and kinetic data were used to quantify the interaction of CO with the ferrous heme-SUR2A complex. The results are significant because they directly connect CO-dependent regulation to a heme-binding event on the channel. We use this information to present molecular-level insight into the dynamic processes that control the interactions of CO with a heme-regulated channel protein, and we present a structural framework for understanding the complex interplay between heme and CO in ion channel regulation.

Ultrafast dynamics of hemin aggregates

The effects of solvents on the conformation of hemin and their implications on the dynamics of the complex have been studied using the time-resolved optical Kerr effect (OKE) with 35 fs laser pulses (at a central wavelength of 800 nm). The OKE enabled estimation to be made of the third-order nonlinear electronic susceptibility (χ⁽³⁾) of hemin solutions: it was found to be significantly smaller than that in hemin thin films. The real and imaginary components of χ⁽³⁾ were negative in both the solvents, suggesting that one-photon as well as two-photon absorption processes contribute to the nonlinear electronic susceptibility of hemin. Our study of the ultrafast heme dynamics not only unveils the instantaneous electronic response related to electronic susceptibility but also brings to the fore a novel libration process that has hitherto remained undetected. The hindered rotation in the femtosecond domain that may be responsible for this libration process possibly stems from π-π hemin oligomers formed in aqueous solution. The present results provide new insights into the conformational dynamics in the self-assembly of heme oligomers that may also be significant in certain pathogenic conditions where free heme is formed in biological systems.

Characterization of the second conserved domain in the heme uptake protein HtaA from Corynebacterium diphtheriae

HtaA is a heme-binding protein that is part of the heme uptake system in Corynebacterium diphtheriae. HtaA contains two conserved regions (CR1 and CR2). It has been previously reported that both domains can bind heme; the CR2 domain binds hemoglobin more strongly than the CR1 domain. In this study, we report the biophysical characteristics of HtaA-CR2. UV-visible spectroscopy and resonance Raman experiments are consistent with this domain containing a single heme that is bound to the protein through an axial tyrosine ligand. Mutants of conserved tyrosine and histidine residues (Y361, H412, and Y490) have been studied. These mutants are isolated with very little heme (≤5%) in comparison to the wild-type protein (~20%). Reconstitution after removal of the heme with butanone gave an alternative form of the protein. The HtaA-CR2 fold is very stable; it was necessary to perform thermal denaturation experiments in the presence of guanidinium hydrochloride. HtaA-CR2 unfolds extremely slowly; even in 6.8M GdnHCl at 37°C, the half-life was 5h. In contrast, the apo forms of WT HtaA-CR2 and the aforementioned mutants unfolded at much lower concentrations of GdnHCl, indicating the role of heme in stabilizing the structure and implying that heme transfer is effected only to a partner protein in vivo.

Quantum dots-hemin: Preparation and application in the absorption of heme iron

The absorption mechanism of heme iron remains unclear due to the limit of labeling techniques. Quantum dots (QDs) are powerful fluorescent probes resistant to photobleaching, however, there is no data about the application of QDs in heme iron absorption. Herein, we prepared hemin-coated CdSe/ZnS (QDs-hemin), and studied their absorption in vitro and in vivo. Results showed that QDs-hemin had uniform particle sizes, physiological stability and high joint efficiency. Moreover, QDs-hemin could be successfully absorbed gradually into the duodenum with the time using synchrotron radiation micro X-ray fluorescence and confocal laser scanning microscopy. Furthermore, QDs-hemin were observed to degrade in lysosomes, and their absorption was blocked by Heme Carrier Protein 1 (HCP1) antibody and HCP1 siRNA. All the results demonstrate that QDs can be a good tracer for heme iron and that HCP1 pathway is critical and predominant over the endocytosis pathway in the absorption mechanism.

Insights into the initial stages of lipid-mediated haemozoin nucleation

Lipid-mediated haemozoin nucleation, as probed by molecular dynamics, proceeds via aggregation of ferrihaem π–π dimers at a lipid–aqueous interface.

Solution structures of chloroquine-ferriheme complexes modeled using MD simulation and investigated by EXAFS spectroscopy

The interaction of chloroquine (CQ) and the μ-oxo dimer of iron(III) protoporphyrin IX (ferriheme) in aqueous solution was modeled using molecular dynamics (MD) simulations. Two models of the CQ-(μ-oxo ferriheme) complex were investigated, one involving CQ π-stacked with an unligated porphyrin face of μ-oxo ferriheme and the other in which CQ was docked between the two porphyrin rings. The feasibility of both models was tested by fitting computed structures to the experimental extended X-ray absorption fine structure (EXAFS) spectrum of the CQ-(μ-oxo ferriheme) complex in frozen aqueous solution. The docked model produced better agreement with experimental data, suggesting that this is the more likely structure in aqueous solution. The EXAFS fit indicated a longer than expected Fe-O bond of 1.87Å, accounting for the higher than expected magnetic moment of the complex. As a consequence, the asymmetric Fe-O-Fe stretch shifts much lower in frequency and was identified in the precipitated solid at 744cm(-1) with the aid of the O(18) isomer shift. Three important CQ-ferriheme interactions were identified in the docked structure. These were a hydrogen bond between the oxide bridge of μ-oxo ferriheme and the protonated quinolinium nitrogen atom of CQ; π-stacking between the quinoline ring of CQ and the porphyrin rings; and a close contact between the 7-chloro substituent of CQ and the porphyrin methyl hydrogen atoms. These interactions can be used to rationalize previously observed structure-activity relationships for quinoline-ferriheme association.

Molecular structures and solvation of free monomeric and dimeric ferriheme in aqueous solution: insights from molecular dynamics simulations and extended X-ray absorption fine structure spectroscopy

CHARMM force field parameters have been developed to model nonprotein bound five-coordinate ferriheme (ferriprotoporphyrin IX) species in aqueous solution. Structures and solvation were determined from molecular dynamics (MD) simulations at 298 K of monomeric [HO-ferriheme](2-), [H2O-ferriheme](-), and [H2O-ferriheme](0); π-π dimeric [(HO-ferriheme)2](4-), [(H2O-ferriheme)(HO-ferriheme)](3-), [(H2O-ferriheme)2](2-), and [(H2O-ferriheme)2](0); and μ-oxo dimeric [μ-(ferriheme)2O](4-). Solvation of monomeric species predominated around the axial ligand, meso-hydrogen atoms of the porphyrin ring (Hmeso), and the unligated face. Existence of π-π ferriheme dimers in aqueous solution was supported by MD calculations where such dimers remained associated over the course of the simulation. Porphyrin rings were essentially coplanar. In these dimers major and minor solvation was observed around the axial ligand and Hmeso positions, respectively. In μ-oxo ferriheme, strong solvation of the unligated face and bridging oxide ligand was observed. The solution structure of the μ-oxo dimer was investigated using extended X-ray absorption fine structure (EXAFS) spectroscopy. The EXAFS spectrum obtained from frozen solution was markedly different from that recorded on dried μ-oxo ferriheme solid. Inclusion of five solvent molecules obtained from spatial distribution functions in the structure generated from MD simulation was required to produce acceptable fits to the EXAFS spectra of the dimer in solution, while the solid was suitably fitted using the crystal structure of μ-oxo ferriheme dimethyl ester which included no solvent molecules.

Multiple spectroscopic and magnetic techniques show that chloroquine induces formation of the μ-oxo dimer of ferriprotoporphyrin IX

Interaction of the antimalarial chloroquine (CQ) with ferriprotoporphyrin IX, Fe(III)PPIX, was investigated in aqueous solution (pH7.4) and as a precipitate from aqueous medium at pH5.0. In solution, spectrophotometric titrations indicated strong association (logKobs 13.3±0.2) and a Job plot gave a stoichiometry of 1:2 CQ:Fe(III)PPIX. UV-visible absorbance and magnetic circular dichroism spectra of the complex were compared to various Fe(III)PPIX species. Close similarity to the spectra of the μ-oxo dimer, μ-[Fe(III)PPIX]2O, was revealed. The induction of this species by CQ was confirmed by magnetic susceptibility measurements using the Evans NMR method. The observed low-magnetic moment (2.25±0.02 μB) could only be attributed to antiferromagnetically coupled Fe(III) centers. The value was comparable to that of μ-[Fe(III)PPIX]2O (2.0±0.1 μB). In the solid-state, mass spectrometry confirmed the presence of CQ in the complex. Dissolution of this solid in aqueous solution (pH7.4) resulted in a solution with a UV-visible spectrum consistent with the same 1:2 stoichiometry observed in the Job plot. Magnetic susceptibility measurements made on the solid using an Evans balance produced a magnetic moment (2.3±0.1 μB) consistent with that in solution. Diffusion coefficients of CQ and its complex with Fe(III)PPIX were measured in aqueous solution (3.3±0.3 and 0.6±0.2×10(-10) m(2)·s(-1), respectively). The latter was used in conjunction with an empirical relationship between diffusion coefficient and molar volume to estimate the degree of aggregation. The findings suggest the formation of a 2:4 CQ:Fe(III)PPIX complex in aqueous solution at pH7.4.

A computational study of ligand binding affinities in iron(iii) porphine and protoporphyrin IX complexes

In the context of antimalarial drug development, density functional theory has been used to model the interactions between a diverse set of 31 small ligands and the iron(iii) centre of ferriprotoporphyrin IX, as well as key events in the crystallization of this molecule by the malaria parasite.