Chemistry in Fungal Bioluminescence: A Theoretical Study from Luciferin to Light Emission

Inspired by nature: Bioluminescent systems for bioimaging applications

Bioluminescence is a natural process where biological organisms produce light through chemical reactions. These reactions predominantly occur between small-molecule substrates and luciferase within bioluminescent organisms. Bioluminescence imaging (BLI) has shown significant potential in biomedical research owing to its non-invasive, real-time observation and quantification. In this review, we introduced the chemical mechanism of bioluminescent systems and categorized several strategies that successfully addressed the native limitations, including improvements on the chemical structures of luciferase-luciferin bioluminescence system and bioluminescence resonance energy transfer (BRET) methods. In addition, we also reviewed and summarized recent advances in bioimaging applications. We hope that this review can provide effective guidance for the development and application of bioluminescent systems in the field of bioimaging.

Investigation of the Chemiluminescent Reaction of a Fluorinated Analog of Marine Coelenterazine

Bioluminescence (BL) and chemiluminescence (CL) are remarkable processes in which light is emitted due to (bio)chemical reactions. These reactions have attracted significant attention for various applications, such as biosensing, bioimaging, and biomedicine. Some of the most relevant and well-studied BL/CL systems are that of marine imidazopyrazine-based compounds, among which Coelenterazine is a prime example. Understanding the mechanisms behind efficient chemiexcitation is essential for the optimization and development of practical applications for these systems. Here, the CL of a fluorinated Coelenterazine analog was studied using experimental and theoretical approaches to obtain insight into these processes. Experimental analysis revealed that CL is more efficient under basic conditions than under acidic ones, which could be attributed to the higher relative chemiexcitation efficiency of an anionic dioxetanone intermediate over a corresponding neutral species. However, theoretical calculations indicated that the reactions of both species are similarly associated with both electron and charge transfer processes, which are typically used to explain efficiency chemiexcitation. So, neither process appears to be able to explain the relative chemiexcitation efficiencies observed. In conclusion, this study provides further insight into the mechanisms behind the chemiexcitation of imidazopyrazinone-based systems.

Theoretical investigation on triphenylamine coelenteramide for bioinspired OLED application using thiophene rings in π-bridge

As light emitter of most marine organisms bioluminescence, coelenteramide (CLM) received much attention due to some exciting application in the field of bioinspired organic light-emitting devices (OLED). Nevertheless, native CLM only emit bright blue light. In order to obtain light of different colors, two CLM analogues, TPA-CLM and TPA-TP-CLM were designed by introduction of triphenylamine group and (thiophene) π-bridge. On the other hand, because the light emitter, CLM was produced by the chemical reaction which originates from the oxidation of bioluminescent substrate, coelenterazine (CLZ), it must be evaluated if and how substituent group tune the chemiluminescent (CL) reaction mechanism, firstly. In this article, the complete chemiluminescent reaction mechanism of TPA-CLZ and TPA-TP-CLZ and the photophysical properties of light emitters, TPA-CLM and TPA-TP-CLM were investigated by (time-dependent) density functional theory, (TD) DFT calculations. The calculations indicate that the introduction of triphenylamine and π-bridge minimally affect the complete reaction process. For the light emitters, TPA-CLM and TPA-TP-CLM, the calculation results indicate that the injection abilities of hole and electron can be largely improved by introduction of triphenylamine and π-bridge. The absorption and emission spectra appeared at longer wavelengths than native CLM. These results illustrate that TPA-CLM and TPA-TP-CLM are good candidates for bioinspired OLED application.

Chemical Mechanism of Fireworm Bioluminescence - A Theoretical Proposition

Odontosyllis undecimdonta is a marine worm, commonly known as a fireworm, that exhibits bluish-green bioluminescence (BL). The luciferin (L) and oxyluciferin (OL) during fireworm BL have been experimentally identified in vitro. The L and OL are the respective starting point and ending point of a series of complicated chemical reactions in the BL. However, the chemical mechanism of the fireworm BL remains largely unknown. Before the experiments provided strong evidence for the mechanism, based on our previously successful studies on several bioluminescent systems, we theoretically proposed the chemical mechanism of the fireworm BL in this article. By means of the spin-flip and time-dependent density functional calculations, we clearly described the complete process from L to OL: under the catalysis of luciferase, L undergoes deprotonation and reacts with 3O2 to form a dioxetanone anion via the single-electron transfer mechanism; the dioxetanone anion decomposes into the OL at the first singlet excited state (S1) by the gradually reversible charge-transfer-induced luminescence mechanism; and the S1-OL emits light and deexcites to OL in the ground state.

Chemistry in Fungal Bioluminescence: Theoretical Studies on Biosynthesis of Luciferin from Caffeic Acid and Regeneration of Caffeic Acid from Oxidized Luciferin

Fungal bioluminescence is widely distributed in the terrestrial environment. At a specific stage of growth, luminescent fungi shine green light at the fruiting body or mycelium. From the viewpoint of chemistry, fungal bioluminescence involves an in vivo cycle of caffeic acid. The complete cycle is composed of three stages: biosynthesis of luciferin from caffeic acid, luminescence process from luciferin to oxidized luciferin, and regeneration of caffeic acid from oxidized luciferin. Experimental studies roughly proposed this cycle but not the detailed reaction process and mechanism. Our previous theoretical study clearly described the mechanism of the middle stage. The present article attempts to describe the reaction processes and mechanisms of the other two stages by theoretical calculations. A complete theoretical study on the chemistry in the entire process of fungal bioluminescence is helpful to deeply understand fungal bioluminescence.

The application and trend of ultra-weak photon emission in biology and medicine

Ultra-weak bioluminescence, also known as ultra-weak photon emission (UPE), is one of the functional characteristics of biological organisms, characterized by specialized, low-energy level luminescence. Researchers have extensively studied UPE for decades, and the mechanisms by which UPE is generated and its properties have been extensively investigated. However, there has been a gradual shift in research focus on UPE in recent years toward exploring its application value. To better understand the application and trend of UPE in biology and medicine, we have conducted a review of relevant articles in recent years. Among the several topics covered in this review is UPE research in biology and medicine (including traditional Chinese medicine), primarily focused on UPE as a promising non-invasive tool for diagnosis and oxidative metabolism monitoring as well as a potential tool for traditional Chinese medicine research.

Conical Intersection in Chemiluminescence of Cyclic Peroxides

Chemiluminescence (CL) utilizing chemiexcitation for energy transformation is one of the most highly sensitive and useful analytical techniques. The chemiexcitation is a chemical process of a ground-state reactant producing an excited-state product, in which a nonadiabatic event is facilitated by conical intersections (CIs), the specific molecular geometries where electronic states are degenerated. Cyclic peroxides, especially 1,2-dioxetane/dioxetanone derivatives, are the iconic chemiluminescent substances. In this Perspective, we concentrated on the CIs in the CL of cyclic peroxides. We first present a computational overview on the role of CIs between the ground (S₀) state and the lowest singlet excited (S₁) state in the thermolysis of cyclic peroxides. Subsequently, we discuss the role of the S₀/S₁ CI in the CL efficiency and point out misunderstandings in some theoretical studies on the singlet chemiexcitations of cyclic peroxides. Finally, we address the challenges and future prospects in theoretically calculating S₀/S₁ CIs and simulating the dynamics and chemiexcitation efficiency in the CL of cyclic peroxides.

Tuning the Intramolecular Chemiexcitation of Neutral Dioxetanones by Interaction with Ionic Species

The intramolecular chemiexcitation of high-energy peroxide intermediates, such as dioxetanones, is an essential step in different chemi- and bioluminescent reactions. Here, we employed the Time-Dependent Density Functional Theory (TD-DFT) methodology to evaluate if and how external stimuli tune the intramolecular chemiexcitation of model dioxetanones. More specifically, we evaluated whether the strategic placement of ionic species near a neutral dioxetanone model could tune its thermolysis and chemiexcitation profile. We found that these ionic species allow for the “dark” catalysis of the thermolysis reaction by reducing the activation barrier to values low enough to be compatible with efficient chemi- and bioluminescent reactions. Furthermore, while the inclusion of these species negatively affected the chemiexcitation profile compared with neutral dioxetanones, these profiles appear to be at least as efficient as anionic dioxetanones. Thus, our results demonstrated that the intramolecular chemiexcitation of neutral dioxetanones can be tuned by external stimuli in such a way that their activation barriers are decreased. Thus, these results could help to reconcile findings that neutral dioxetanones could be responsible for efficient chemi-/bioluminescence, while being typically associated with high activation parameters.

Theoretical Study of the Thermolysis Reaction and Chemiexcitation of Coelenterazine Dioxetanes

Coelenterazine and other imidazopyrazinones are important bioluminescent substrates widespread in marine species and can be found in eight phyla of luminescent organisms. Light emission from these systems is caused by the formation and subsequent thermolysis of a dioxetanone intermediate, whose decomposition allows for efficient chemiexcitation to singlet excited states. Interestingly, some studies have also reported the involvement of unexpected dioxetane intermediates in the chemi- and bioluminescent reactions of Coelenterazine, albeit with little information on the underlying mechanisms of these new species. Herein, we have employed a theoretical approach based on density functional theory to study for the first time the thermolysis reaction and chemiexcitation profile of two Coelenterazine dioxetanes. We have found that the thermolysis reactions of these species are feasible but with relevant energetic differences. More importantly, we found that the singlet chemiexcitation profiles of these dioxetanes are significantly less efficient than the corresponding dioxetanones. Furthermore, we identified triplet chemiexcitation pathways for the Coelenterazine dioxetanes. Given this, the chemiexcitation of these dioxetanes should lead only to minimal luminescence. Thus, our theoretical investigation of these systems indicates that the thermolysis of these dioxetanes should only provide "dark" pathways for the formation of nonluminescent degradation products of the chemi- and bioluminescent reactions of Coelenterazine and other imidazopyrazinones.

Isolation of Taxol and Flavin-like fluorochrome from Endophytic Fungi of Mangifera indica

Scouting for novel and plant-derived biomolecules from endophytic microbial sources draws greater focus on the discovery of novel bioactive metabolites. With this rationale, we scouted the endophytic fungi for taxol, an anticancer diterpenoid and fluorescent biomolecules. In the present study, about 31 endophytic fungal isolates recovered from the Mangifera indica leaves were screened for taxol production in M1D medium. About five isolates were shortlisted based on the thin layer chromatographic analysis of the fungal extracts. Among them Colletotrichum sp. MIP-5 has been identified as a producer of fungal taxol based on UV, FTIR, TLC and HPLC analysis. The partially purified fungal taxol showed similar spectral and chromatographic features of commercially available paclitaxel. In addition to this, we also report the production of a fluorescent compound by Penicillium sp. MIP-3. The Flavin-like compound exhibited a bright greenish-yellow fluorescence with an emission maximum in the range of 505 – 545nm. GC-MS analysis showed the occurrence of Latia luciferin, primarily associated with the bioluminescence of freshwater limpet Latia neritoides. This is the first report of this compound from Penicillium sp. In addition, therapeutically active steroid (β-Sitosterol, Stigmasterol, Campesterol), quinones (Benzo[h]quinoline, 2,4-dimethyl-) and phloroglucinol (Aspidinol) derivatives were also identified from Penicillium sp. MIP-3 based on GC-MS analysis. These molecules could potentially be used in biological and pharmaceutical applications in future.

Luciferins Under Construction: A Review of Known Biosynthetic Pathways

Bioluminescence, or the ability of a living organism to generate visible light, occurs as a result of biochemical reaction where enzyme, known as a luciferase, catalyzes the oxidation of a small-molecule substrate, known as luciferin. This advantageous trait has independently evolved dozens of times, with current estimates ranging from the most conservative 40, based on the biochemical diversity found across bioluminescence systems (Haddock et al., 2010) to 100, taking into account the physiological mechanisms involved in the behavioral control of light production across a wide range of taxa (Davis et al., 2016; Verdes and Gruber, 2017; Bessho-Uehara et al., 2020a; Lau and Oakley, 2021). Chemical structures of ten biochemically unrelated luciferins and several luciferase gene families have been described; however, a full biochemical pathway leading to light emission has been elucidated only for two: bacterial and fungal bioluminescence systems. Although the recent years have been marked by extraordinary discoveries and promising breakthroughs in understanding the molecular basis of multiple bioluminescence systems, the mechanisms of luciferin biosynthesis for many organisms remain almost entirely unknown. This article seeks to provide a succinct overview of currently known luciferins’ biosynthetic pathways.

Three S0/S1 Conical Intersections Control Electron-Transfer-Catalyzed Chemiluminescence of 1,2-Dioxetanedione

Chemiluminescence (CL) utilizing four-membered cyclic peroxides is one of the most useful analytical techniques. Up to now, the CL mechanisms for nonketone (1,2-dioxetanes) and monoketone (1,2-dioxetanones) derivatives of four-membered cyclic peroxides have been intensively studied experimentally and theoretically in the past several decades, but no general mechanism has been concluded to rationalize the origin of high-efficiency singlet chemiexcitation. In contrast, as the only diketone derivative of four-membered cyclic peroxide, the electron-transfer (ET)-catalyzed CL of 1,2-dioxetanedione (DDO), which is most suggested as a critical step in the well-known peroxyoxalate CL (POCL), has never been theoretically investigated and uncovered yet. In this work, we theoretically investigated the rubrene-catalyzed decomposition of DDO for the first time, with a hybrid quantum mechanical/molecular mechanical model and nonadiabatic molecular dynamics simulation. The computation shows a stepwise ET-catalyzed decomposition and three S₀/S₁ conical intersection (CI)-controlled singlet chemiexcitation. The three universal S₀/S₁ CIs play different roles in the high-efficiency singlet chemiexcitation in ET-catalyzed CL of DDO and should be the true origin of the high-efficiency singlet CL. We believe that the current work could not only provide a further understanding for high-efficiency singlet CL but also provide some general clues to designed new high-efficient CL systems.