The Red Color of Life Transformed - Synthetic Advances and Emerging Applications of Protoporphyrin IX in Chemical Biology

Molecular Symmetry and Art: Visualizing the Near-Symmetry of Molecules in Piet Mondrian's De Stijl

Symmetry and shape are essential aspects of molecular structure and how we interpret molecules and their properties. We, as chemists, are comfortable with pictorial representations of structure, in which some nuance is lost-investigating molecular shape numerically by looking at how closely it fits a reference, such as a plane, or a set of vectors or coordinates, is informative, though far from engaging. Often relationships between chemical structure and derived values are obscured. Taking our inspiration from Piet Mondrian's Compositions, we have depicted the symmetry information encoded within 3D data as blocks of color, to show clearly how chemical arguments and resultant molecular distortion may contribute to symmetry. Great art gives us a new perspective on the world; as a pastiche, this art may allow us to look at familiar molecules, such as porphyrins, in a new light, understanding how their shape and properties are intertwined.

Porphyrin-based covalent organic frameworks from design, synthesis to biological applications

Covalent organic frameworks (COFs) constitute a class of highly functional porous materials composed of lightweight elements interconnected by covalent bonds, characterized by structural order, high crystallinity, and large specific surface area. The integration of naturally occurring porphyrin molecules, renowned for their inherent rigidity and conjugate planarity, as building blocks in COFs has garnered significant attention. This strategic incorporation addresses the limitations associated with free-standing porphyrins, resulting in the creation of well-organized porous crystal structures with molecular-level directional arrangements. The unique optical, electrical, and biochemical properties inherent to porphyrin molecules endow these COFs with diversified applications, particularly in the realm of biology. This review comprehensively explores the synthesis and modulation strategies employed in the development of porphyrin-based COFs and delves into their multifaceted applications in biological contexts. A chronological depiction of the evolution from design to application is presented, accompanied by an analysis of the existing challenges. Furthermore, this review offers directional guidance for the structural design of porphyrin-based COFs and underscores their promising prospects in the field of biology.

Nonadiabatic Charge Transfer within Photoexcited Nickel Porphyrins

Metalloporphyrins with open d-shell ions can drive biochemical energy cycles. However, their utilization in photoconversion is hampered by rapid deactivation. Mapping the relaxation pathways is essential for elaborating strategies that can favorably alter the charge dynamics through chemical design and photoexcitation conditions. Here, we combine transient optical absorption spectroscopy and transient X-ray emission spectroscopy with femtosecond resolution to probe directly the coupled electronic and spin dynamics within a photoexcited nickel porphyrin in solution. Measurements and calculations reveal that a state with charge-transfer character mediates the formation of the thermalized excited state, thereby advancing the description of the photocycle for this important representative molecule. More generally, establishing that intramolecular charge-transfer steps play a role in the photoinduced dynamics of metalloporphyrins with open d-shell sets a conceptual ground for their development as building blocks capable of boosting nonadiabatic photoconversion in functional architectures through "hot" charge transfer down to the attosecond time scale.

Recent Progress on Peroxidase Modification and Application

Peroxdiase is one of the member of oxireductase super family, which has a broad substrate range and a variety of reaction types, including hydroxylation, epoxidation or halogenation of unactivated C-H bonds, and aromatic group or biophenol compounds. Here, we summarized the recently discovered enzymes with peroxidation activity, and focused on the special structures, sites, and corresponding strategies that can change the peroxidase catalytic activity, stability, and substrate range. The comparison of the structural differences between these natural enzymes and the mimic enzymes of binding nanomaterials and polymer materials is helpful to expand the application of peroxidase in industry. In addition, we also reviewed the catalytic application of peroxidase in the synthesis of important organic molecules and the degradation of pollutants.

Spatio-temporal distribution characteristics and influencing factors of protoporphyrin IX in the estuarine-coastal ecosystems

Protoporphyrin IX (PPIX), a key precursor for the synthesis of chlorophyll and heme, is fundamental to photosynthetic eukaryotic cells and participates in light absorption, energy transduction, and numerous other cellular metabolic activities. Along with the application of genetic and biochemical techniques over the past few years, our understanding of the formation of PPIX has been largely advanced, especially regarding possible metabolic pathways. However, the ecological role and function of PPIX in natural ecosystems remains unclear. We have previously established a method for quantifying PPIX in marine ecosystems. Here, our results provide evidence that PPIX is not only subtly linked to nutrient uptake but also triggers phytoplankton productivity. PPIX and its derivatives are dynamic spatiotemporally in direct response to increased nutrient availability. Using 16 S rRNA gene amplicon sequencing, PPIX was revealed to interact strongly with many microorganisms, indicating that PPIX serves as a critical metabolite in maintaining microbial metabolism and community development. In summary, we observed that PPIX is linearly related to nutrient availability and microbial diversity. The levels of microbial PPIX reflect ecological health, and the availability of PPIX and nutrients jointly affect microbial community composition.

Diversifying the functions of heme proteins with non-porphyrin cofactors

Heme proteins perform diverse biochemical functions using a single iron porphyrin cofactor. This versatility makes them attractive platforms for the development of new functional proteins. While directed evolution and metal substitution have expanded the properties, reactivity, and applications of heme proteins, the incorporation of porphyrin analogs remains an underexplored approach. This review discusses the replacement of heme with non-porphyrin cofactors, such as porphycene, corrole, tetradehydrocorrin, phthalocyanine, and salophen, and the attendant properties of these conjugates. While structurally similar, each ligand exhibits distinct optical and redox properties, as well as unique chemical reactivity. These hybrids serve as model systems to elucidate the effects of the protein environment on the electronic structure, redox potentials, optical properties, or other features of the porphyrin analog. Protein encapsulation can confer distinct chemical reactivity or selectivity of artificial metalloenzymes that cannot be achieved with the small molecule catalyst alone. Additionally, these conjugates can interfere with heme acquisition and uptake in pathogenic bacteria, providing an inroad to innovative antibiotic strategies. Together, these examples illustrate the diverse functionality that can be achieved by cofactor substitution. The further expansion of this approach will access unexplored chemical space, enabling the development of superior catalysts and the creation of heme proteins with emergent properties.

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.

Characterization of the interaction of metal-protoporphyrins photosensitizers with β- lactoglobulin

We investigated the interaction of a series of metal-protoporphyrins (PPIXs) with bovine β- lactoglobulin (BLG) using a combination of optical spectroscopy and computational simulations. Unlike other studies, the simulations were not merely used to rationalize the experimental data but were employed to refine the experimental data itself. The study was carried out at two pH values, 5 and 9, where BLG is known to have different conformation dictated by the so-called Tanford transition which occurs near pH 7.5. The transition is postulated to regulate access to the interior binding cavity of the protein, thus the pH variation was used as a parameter to investigate whether PPIXs access the central cavity of BLG. The results of our study show that indeed binding increases significantly at alkaline pH, however, the increased affinity is not due to the accessibility of the central cavity. Instead, binding appears to be determined by the tendency of PPIXs to form large inhomogeneous aggregates at acidic pH which hinders interactions with proteins. The binding site determined through a combination of experimental and computational methods is located at the interface between two BLG monomers where the long α-helix segment of the protein face each other. This region is rich in positively charged Lys residues that interact with the propionic acid chains of the protoporphyrins. Establishing the modality of binding between protoporphyrins and BLG would have important consequences for the use of BLG:PPIX complexes in applications such as artificial photoreceptors, artificial metallo-enzymes, delivery of photosensitizers for phototherapy and even solar energy conversion.

Recent developments of sonodynamic therapy in antibacterial application

The rapid emergence of pathogenic bacteria poses a serious threat to global health. Notably, traditional antibiotic therapies suffer from the risk of strengthening bacterial drug resistance. Sonodynamic therapy (SDT) combining sonosensitizers and low-intensity ultrasound (US) has broadened the way towards treating drug-resistant bacteria. The allure of this therapy emerges from the capacity to focus the US energy on bacterial infection sites buried deep in tissues, locally activating the sonosensitizers to produce cytotoxic reactive oxygen species (ROS) with the ability to induce bacterial death. The past decade has witnessed the rapid development of antibacterial SDT owing to their excellent penetration, favorable biocompatibility and specific targeting ability. This review summarizes available sonosensitizers for antibacterial SDT, and digs into innovative biotechnologies to improve SDT efficiency, such as enhancing the targeting ability of sonosensitizers, image-guided assisted SDT, improvement of hypoxia and combination of SDT with other therapies. Finally, we conclude with the present challenges and provide insights into the future research of antibacterial SDT.

Main Strategies for the Synthesis of meso-Arylporphyrins

meso-Arylporphyrins as most accessible tetrapyrrole macroheterocycles have always been the focus of attention from researchers concerned with practically useful properties of these compounds. The first syn­theses of meso-arylporphyrins date back to about 90 years ago. Up to now, the yields of these compounds have been improved from 5 to 80%. The present review analyzes different ways and strategies for the synthesis of meso-aryl-substituted porphyrins. The most efficient methods that can be scaled up to an industrial level have been identified.

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.

Enhancing the Cellular Uptake of Macromolecules via Enzyme-Instructed Self-Assembly

Poor solubility, low cellular uptake, and poor cell selectivity are the main obstacles hampering the therapeutic potential and clinic application of macromolecules. To overcome these limitations, here we propose a chemical modification strategy of macromolecules based on enzyme-instructed self-assembly (EISA). By using protoporphyrin IX (PpIX) and its metal complex Zn-PpIX as the modification objects, we demonstrated that the integration of enzymatic transformation and molecular self-assembly of macromolecules successfully improved the solubility of macromolecules, enhancing their intracellular uptake selectively against cancer cells. The proposed strategy is potentially applicable as a general tool for the development of macromolecule-based nanomedicine.

Syntheses, Rearrangements, and Structural Analyses of Unsaturated Nitrogen Donor Ligands Derived from Diphenyldiazomethane and the Chiral Rhenium Lewis Acid [(η5-C5H5)Re(NO)(PPh3)]+

Diphenyldiazomethane and a labile chlorobenzene complex of [(η5-C5H5)Re(NO)(PPh3)]+ BF4– react to give the η1 adduct [(η5-C5H5)Re(NO)(PPh3)(NNCPh2)]+ BF4– (73%). When this is con-ducted in the presence of copper powder, a 3-phenyl-1H-indazole...

Corrole–protein interactions in H-NOX and HasA

Mutagenesis was utilised to reveal corrole–protein interactions in H-NOX and HasA. The key interaction is a hydrogen bond between the PO unit of the corrole and a protonated histidine residue.

Steric Repulsion Induced Conformational Switch in Supramolecular Structures

Inspired by the rigidified architecture of ‘picket‐fence’ systems, we propose a strategy utilizing strain to impose intramolecular tension in already peripherally overcrowded structures leading to selective atropisomeric conversion. Employing this approach, tuneable shape‐persistent porphyrin conformations were acquired exhibiting distinctive supramolecular nanostructures based on the orientation of the peripheral groups. The intrinsic assemblies driven by non‐covalent bonding interactions form supramolecular polymers while encapsulating small molecules in parallel channels or solvent‐accessible voids. The developed molecular strain engineering methodologies combined with synthetic approaches have allowed the introduction of the pivalate units creating a highly strained molecular skeleton. Changes in the absorption spectrum indicated the presence of severe steric repulsions between the peripheral groups which were confirmed by single crystal X‐ray analysis. To release the steric strain introduced by the peripheral units, thermal equilibration strategies were used to selectively convert the most abundant atropisomer to the desirable minor one.

A Coumarin-Porphyrin FRET Break-Apart Probe for Heme Oxygenase-1

Heme oxygenase-1 (HO-1) is a vital enzyme in humans that primarily regulates free heme concentrations. The overexpression of HO-1 is commonly associated with cardiovascular and neurodegenerative diseases including atherosclerosis and ischemic stroke. Currently, there are no known chemical probes to detect HO-1 activity, limiting its potential as an early diagnostic/prognostic marker in these serious diseases. Reported here are the design, synthesis, and photophysical and biological characterization of a coumarin-porphyrin FRET break-apart probe to detect HO-1 activity, Fe-L1. We designed Fe-L1 to "break-apart" upon HO-1-catalyzed porphyrin degradation, perturbing the efficient FRET mechanism from a coumarin donor to a porphyrin acceptor fluorophore. Analysis of HO-1 activity using Escherichia coli lysates overexpressing hHO-1 found that a 6-fold increase in emission intensity at 383 nm was observed following incubation with NADPH. The identities of the degradation products following catabolism were confirmed by MALDI-MS and LC-MS, showing that porphyrin catabolism was regioselective at the α-position. Finally, through the analysis of Fe-L2, we have shown that close structural analogues of heme are required to maintain HO-1 activity. It is anticipated that this work will act as a foundation to design and develop new probes for HO-1 activity in the future, moving toward applications of live fluorescent imaging.

Classic highlights in porphyrin and porphyrinoid total synthesis and biosynthesis

Porphyrins feature prominently in nature, be it as enzymatic cofactors, electron and exciton shuffles, as photoactive dyes, or as signaling substances. Their involvement in the generation, storage and use of oxygen is pivotal to life, while their photochemical properties are central to the biochemical functioning of plants. When complexed to metals, porphyrins can engage in a multitude of contemporary applications ranging from solar energy generation to serving as catalysts for important chemical reactions. They are also able to function as useful theranostic agents, and as novel materials for a wide range of applications. As such, they are widely considered to be highly valuable molecules, and it almost goes without saying that synthetic organic chemistry has dramatically underpinned all the key advances made, by providing reliable access to them. In fact, strategies for the synthesis of functionalized porphyrins have now reached a state of refinement where pretty well any desired porphyrin can successfully be synthesized with the approaches that are available, including a cornucopia of related macrocycle-modified porphyrinoids. In this review, we are going to illustrate the development of this exciting field by discussing a number of classic syntheses of porphyrins. Our coverage will encompass the natural protoporphyrins and chlorophylls, while also covering general strategies for the synthesis of unsymmetrical porphyrins and chlorins. Various industrial syntheses of porphyrins will also be discussed, as will other routes of great practical importance, and avenues to key porphyrinoids with modified macrocycles. A range of selected examples of contemporary functionalization reactions will be highlighted. The various key syntheses will be described and analyzed from a traditional mechanistic organic chemistry perspective to help student readers, and those who are new to this area. The aim will be to allow readers to mechanistically appreciate and understand how many of these fascinating ring-systems are built and further functionalized.

Nucleophilic Aromatic Substitution (SNAr) and Related Reactions of Porphyrinoids: Mechanistic and Regiochemical Aspects

The nucleophilic substitution of aromatic moieties (SNAr) has been known for over 150 years and found wide use for the functionalization of (hetero)aromatic systems. Currently, several "types" of SNAr reactions have been established and notably the area of porphyrinoid macrocycles has seen many uses thereof. Herein, we detail the SNAr reactions of seven types of porphyrinoids with differing number and type of pyrrole units: subporphyrins, norcorroles, corroles, porphyrins, azuliporphyrins, N-confused porphyrins, and phthalocyanines. For each we analyze the substitution dependent upon: a) the type of nucleophile and b) the site of substitution (α, β, or meso). Along with this we evaluate this route as a synthetic strategy for the generation of unsymmetrical porphyrinoids. Distinct trends can be identified for each type of porphyrinoid discussed, regardless of nucleophile. The use of nucleophilic substitution on porphyrinoids is found to often be a cost-effective procedure with the ability to yield complex substituent patterns, which can be conducted in non-anhydrous solvents with easily accessible simple porphyrinoids.

Synthesis pathways for the preparation of the BODIPY analogues: aza-BODIPYs, BOPHYs and some other pyrrole-based acyclic chromophores

This mini-review summarizes the synthesis strategies for the preparation and post-functionalization of aza-BODIPYs, BOPHYs, “half-Pcs”, biliazines, MB-DIPYs, semihemiporphyrazines, BOIMPYs, BOPPYs, BOPYPYs, BOAHYs, and BOAPYs.

Learning from Nature: Bioinspired Chlorin-Based Photosensitizers Immobilized on Carbon Materials for Combined Photodynamic and Photothermal Therapy

Chlorophylls, which are chlorin-type photosensitizers, are known as the key building blocks of nature and are fundamental for solar energy metabolism during the photosynthesis process. In this regard, the utilization of bioinspired chlorin analogs as photosensitizers for photodynamic therapy constitutes an evolutionary topic of research. Moreover, carbon nanomaterials have been widely applied in photodynamic therapy protocols due to their optical characteristics, good biocompatibility, and tunable systematic toxicity. Herein, we review the literature related to the applications of chlorin-based photosensitizers that were functionalized onto carbon nanomaterials for photodynamic and photothermal therapies against cancer. Rather than a comprehensive review, we intended to highlight the most important and illustrative examples over the last 10 years.

Porphyrins as Colorimetric and Photometric Biosensors in Modern Bioanalytical Systems

Advances in porphyrin chemistry have provided novel materials and exciting technologies for bioanalysis such as colorimetric sensor array (CSA), photo-electrochemical (PEC) biosensing, and nanocomposites as peroxidase mimetics for glucose detection. This review highlights selected recent advances in the construction of supramolecular assemblies based on the porphyrin macrocycle that provide recognition of various biologically important entities through the unique porphyrin properties associated with colorimetry, spectrophotometry, and photo-electrochemistry.