Enlightening epigenetics: optochemical tools illuminate the path.

Optochemical tools have become potent instruments for understanding biological processes at the molecular level, and the past decade has witnessed their use in epigenetics and epitranscriptomics (also known as RNA epigenetics) for deciphering gene expression regulation. By using photoresponsive molecules such as photoswitches and photocages, researchers can achieve precise control over when and where specific events occur. Therefore, these are invaluable for studying both histone and nucleotide modifications and exploring disease-related mechanisms. We systematically report and assess current examples in the field, and identify open challenges and future directions. These outstanding proof-of-concept investigations will inspire other chemical biologists to participate in these emerging fields given the potential of photochromic molecules in research and biomedicine.

New challenges for photopharmacology and computational modeling.

Mous et al. recently reported the molecular mechanism of chloride transport through a light-activated pumping rhodopsin, a key process involved in a range of cellular functions. Their results open exciting new challenges for photopharmacology and computational modeling that should be addressed in the coming years.

Optogenetic Tools for Regulating RNA Metabolism and Functions.

RNA molecules play a vital role in linking genetic information with various cellular processes. In recent years, a variety of optogenetic tools have been engineered for regulating cellular RNA metabolism and functions. These highly desirable tools can offer non-intrusive control with spatial precision, remote operation, and biocompatibility. Here, we would like to review these currently available approaches that can regulate RNAs with light: from non-genetically encodable chemically modified oligonucleotides to genetically encoded RNA aptamers that recognize photosensitive small-molecule or protein ligands. Some key applications of these optogenetic tools will also be highlighted to illustrate how they have been used for regulating all aspects of the RNA life cycle: from RNA synthesis, maturation, modification, and translation to their degradation, localization, and phase separation control. Some current challenges and potential practical utilizations of these RNA optogenetic tools will also be discussed.

Synthesis of Styrylbenzazole Photoswitches and Evaluation of their Photochemical Properties.

Styrylbenzazoles form a promising yet under-represented class of photoswitches that can perform a light-driven E-Z isomerization of the central alkene double bond without undergoing irreversible photocyclization, typical of the parent stilbene. In this work, we report the synthesis and photochemical study of 23 styrylbenzazole photoswitches. Their thermal stabilities, quantum yields, maximum absorption wavelengths and photostationary state (PSS) distributions can be tuned by changing the benzazole heterocycle and the substitution pattern on the aryl ring. In particular, we found that push-pull systems show large redshifts of the maximum absorption wavelengths and the highest quantum yields, whereas ortho-substituted styrylbenzazole photoswitches exhibit the most favorable PSS ratios. Taking advantage of both design principles, we produced 2,6-dimethyl-4-(dimethylamino)-styrylbenzothiazole, a thermally stable and efficient P-type photoswitch which displays negative photochromism upon irradiation with visible light up to 470 nm to obtain a near-quantitative isomerization with a very high quantum yield of 59 %. Furthermore, 4-hydroxystyrylbenzoxazole was demonstrated to be a pH-sensitive switch which exhibits a 100 nm redshift upon deprotonation. Ortho-methylation of its benzothiazole analogue improved the obtained PSS ratio in its deprotonated state from E : Z=53 : 47 to E : Z=18 : 82. We anticipate that this relatively unexplored class of photoswitches will form a valuable expansion of the current family of photoswitches.

Pyrene Functionalized Norbornadiene-Quadricyclane Fluorescent Photoswitches: Characterization of their Spectral Properties and Application in Imaging of Amyloid Beta Plaques.

This study presents the synthesis and characterization of two fluorescent norbornadiene (NBD) photoswitches, each incorporating two conjugated pyrene units. Expanding on the limited repertoire of reported photoswitchable fluorescent NBDs, we explore their properties with a focus on applications in bioimaging of amyloid beta (Aß) plaques. While the fluorescence emission of the NBD decreases upon photoisomerization, aligning with what has been previously reported, for the first time we observed luminescence after irradiation of the quadricyclane (QC) isomer. We deduce how the observed emission is induced by photoisomerization to the excited state of the parent isomer (NBD) which is then the emitting species. Thorough characterizations including NMR, UV-Vis, fluorescence, X-ray structural analysis and density functional theory (DFT) calculations provide a comprehensive understanding of these systems. Notably, one NBD-QC system exhibits exceptional durability. Additionally, these molecules serve as effective fluorescent stains targeting Aß plaques in situ, with observed NBD/QC switching within the plaques. Molecular docking simulations explore NBD interactions with amyloid, unveiling novel binding modes. These insights mark a crucial advancement in the comprehension and design of future photochromic NBDs for bioimaging applications and beyond, emphasizing their potential in studying and addressing protein aggregates.

Norbornadiene-Quadricyclane Photoswitches with Enhanced Solar Spectrum Match.

Herein, we report monomeric and dimeric norbornadiene-quadricyclane molecular photoswitch systems intended for molecular solar thermal applications. A series of six new norbornadiene derivatives conjugated with benzothiadiazole as the acceptor unit and dithiafulvene as the donor unit were synthesized and fully characterized. The photoswitches were evaluated by experimentally and theoretically measuring optical absorption profiles and thermal conversion of quadricyclane to norbornadiene. Computational insight by density functional theory calculations at the M06-2X/def2-SVPD level of theory provided geometries, storage energies, UV-vis absorption spectra, and HOMO-LUMO levels that are used to describe the function of the molecular systems. The studied molecules exhibit absorption onset ranging from 416 nm to 595 nm due to a systemic change in their donor-acceptor character. This approach was advantageous due to the introduction of benzothiadiazole and the dimeric nature of molecular structures. The best-performing system has a half-life of 3 days with quantum yields over 50 %.

Photopharmacology of Protease Inhibitors: Current Status and Perspectives.

Proteases are involved in many essential biological processes. Dysregulation of their activity underlies a wide variety of human diseases. Photopharmacology, as applied on various classes of proteins, has the potential to assist protease research by enabling spatiotemporal control of protease activity. Moreover, it may be used to decrease side-effects of protease-targeting drugs. In this review, we discuss the current status of the chemical design of photoactivatable proteases inhibitors and their biological application. Additionally, we give insight into future possibilities for further development of this field of research.

Geometry-Induced Oligomerization of Fluorine-Substituted Phenylazothiazole Photoswitches.

Photoswitches are molecules that can absorb light of specific wavelengths and undergo a reversible transformation between their trans and cis isomeric forms. In phenylazo photoswitches, it is common for the less stable cis (Z) isomer to convert back to the more stable trans (E) isomer either through photochemical or thermal means. In this research, we designed new derivatives of phenylazothiazole (PAT) photoswitches, PAT-Fn, which feature fluorine substituents on their phenyl component. These derivatives can reversibly isomerize under visible light exposure with the enrichment of E and Z isomers at photostationary state (PSS). Surprisingly, we observed an unconventional phenomenon when these PAT-Fn (n≧2) photoswitches were in their cis isomeric state in the absence of light. Instead of the anticipated transformation from cis to trans isomer, these compounds converted to an oligomeric compound. Our detailed experimental investigation and theoretical calculations, indicated the crucial role of fluorine substituents and the distinctive geometric arrangement of the cis isomer in driving the unexpected oligomerization process originating from the cis isomeric state.

Calamitic Liquid Crystals for Reversible Light-Modulated Phase Regulation Based on Arylazopyrazole Photoswitches.

The design of responsive liquid crystals enables a diversity of technological applications. Especially photochromic liquid crystals gained a lot of interest in recent years due to the excellent spatiotemporal control of their phase transitions. In this work we present calamitic light responsive mesogens based on a library of arylazopyrazole photoswitches. These compounds show liquid-crystalline behavior as shown by differential scanning calorimetry, grazing incidence X-ray diffraction and polarized optical microscopy. UV-vis spectroscopy and NMR analysis confirmed the excellent photophysical properties in solution and thin film. Additionally, polarized optical microscopy studies of the pristine compounds show reversible phase transition upon irradiation with light. Moreover, as a dopant in the commercially available liquid crystal 4-cyano-4'-pentylbiphenyl (5CB), the temperature range was reduced to ambient temperatures while preserving the photophysical properties. Remarkably, this co-assembled system shows reversible liquid-crystalline to isotropic phase transition upon irradiation with light of different wavelengths. The spatiotemporal control of the phase transition of the liquid crystals offers opportunities in the development of optical devices.

Synthesis and Development of Inverse-Type Nucleoside Diarylethene Photoswitches.

Nucleosidic diarylethenes (DAEs) have evolved from an emerging class of photochromes into a well-established option for integrating photochromic functionalities into biological systems. However, a comprehensive understanding of how chemical structure influences their photochromic properties remains essential. While structural features, such as an inverse connection between the aryl residues and the ethene bridge, are well-documented for classical DAEs, their application to nucleosidic DAEs has been underexplored. In this study, we address this gap by developing three distinct types of inverse nucleosidic DAEs-semi-inverse thiophenes, semi-inverse uridines and inverse uridines. We successfully synthesized these compounds and conducted comprehensive analyses of their photostationary states, thermal stability, reversibility, and reaction quantum yields. Additionally, we conducted an in-depth comparison of their photochromic properties with those of their normal-type counterparts. Among the synthesized compounds, seven semi-inverse thiophenes exhibited the most promising characteristics. Notably, these compounds demonstrated excellent fatigue resistance, with up to 96 % retention of photochromic activity over 40 switching cycles, surpassing the performance of all comparable nucleosidic DAEs reported to date. These findings hold significant promise for future applications in various fields.

Azopyridinium Ionic Photoswitches: Tuning Half-Lives of Z Isomers from Seconds to Days in Water.

Herein, we describe water-soluble heteroaryl azopyridinium ionic photoswitches (HAPIPs). We aim to combine variations in five-membered heterocycles, their substitutions, N-alkyl groups at pyridinium nitrogen, the position of pyridinium center relative to azo group, counterions, and solvents, in achieving better photoswitching. Through these studies, we successfully tuned the half-life of Z isomers of the resultant HAPIPs between seconds to days in water. Extensive spectroscopic studies and density functional theory (DFT) computations unravelled the factors responsible for thermal relaxation behavior. Considering the versatility of these photoswitches, the tunability of half-lives and photoswitching in aqueous medium allows the scope of applications in several fields.

Enhancing the Potential of Fused Heterocycle-Based Triarylhydrazone Photoswitches.

Triarylhydrazones represent an attractive class of photochromic compounds offering many interesting features including high molar absorptivity, good addressability, and extraordinary thermal stability. In addition, unlike most other hydrazone-based photoswitches, they effectively absorb light above 365 nm. However, previously prepared triaryhydrazones suffer from low quantum yields of the Z→E photoisomerization. Here, we have designed a new subclass of naphthoyl-benzothiazole hydrazones that balance the most beneficial features of previously reported naphthoyl-quinoline and benzoyl-pyridine triarylhydrazones. These preserve the attractive absorption characteristics, exhibit higher thermal stability of the metastable form than the former and enhance the rate of the Z→E photoisomerization compared to the later, as a result of the weakening of the intramolecular hydrogen bonding between the hydrazone hydrogen and the benzothiazole moiety. Introducing the benzothiazole motif extends the tunability of the photochromic behaviour of hydrazone-based switches.

Spiropyran-Based Photoisomerizable α-Amino Acid for Membrane-Active Peptide Modification.

Photoisomerizable peptides are promising drug candidates in photopharmacology. While azobenzene- and diarylethene-containing photoisomerizable peptides have already demonstrated their potential in this regard, reports on the use of spiropyrans to photoregulate bioactive peptides are still scarce. This work focuses on the design and synthesis of a spiropyran-derived amino acid, (S)-2-amino-3-(6'-methoxy-1',3',3'-trimethylspiro-[2H-1-benzopyran-2,2'-indolin-6-yl])propanoic acid, which is suitable for the preparation of photoisomerizable peptides. The utility of this amino acid is demonstrated by incorporating it into the backbone of BP100, a known membrane-active peptide, and by examining the photoregulation of the membrane perturbation by the spiropyran-containing peptides. The toxicity of the peptides (against the plant cell line BY-2), their bacteriotoxicity (E. coli), and actin-auxin oscillator modulation ability were shown to be significantly dependent on the photoisomeric state of the spiropyran unit.

Visible-Light Driven Control Over Triply and Quadruply Hydrogen-Bonded Supramolecular Assemblies.

Supramolecular polymers offer tremendous potential to produce new "smart" materials, however, there remains a need to develop systems that are responsive to external stimuli. In this work, visible-light responsive hydrogen-bonded supramolecular polymers comprising photoresponsive supramolecular synthons (I-III) consisting of two hydrogen bonding motifs (HBMs) connected by a central ortho-tetrafluorinated azobenzene have been characterized by DOSY NMR and viscometry. Comparison of different hydrogen-bonding motifs reveals that assembly in the low and high concentration regimes is strongly influenced by the strength of association between the HBMs. I, Incorporating a triply hydrogen-bonded heterodimer, was found to exhibit concentration dependent switching between a monomeric pseudo-cycle and supramolecular oligomer through intermolecular hydrogen bonding interactions between the HBMs. II, Based on the same photoresponsive scaffold, and incorporating a quadruply hydrogen-bonded homodimer was found to form a supramolecular polymer which was dependent upon the ring-chain equilibrium and thus dependent upon both concentration and photochemical stimulus. Finally, III, incorporating a quadruply hydrogen-bonded heterodimer represents the first photoswitchable AB type hydrogen-bonded supramolecular polymer. Depending on the concentration and photostationary state, four different assemblies dominate for both monomers II and III, demonstrating the ability to control supramolecular assembly and physical properties triggered by light.

Robust Red-Absorbing Donor-Acceptor Stenhouse Adduct Photoswitches.

Donor-Acceptor Stenhouse Adduct (DASA), a class of push-pull negative photochrome, has received large interest lately owing to its versatile synthesis, modularity and excellent photoswitching in solutions. From a technological perspective, it is imperative for this class of photoswitches to work robustly in solid state, e. g. thin films. We feature a molecular framework for the optimized design of DASAs by introducing a new thioindoline donor (D3) and assessing its performance against known 2nd generation indoline-based donors. The systematic structure-function investigations suggest that to achieve robust reversible photoswitching, a ground state with low charge separation is desired. DASAs with stronger electron donors and a larger charge separation in the ground state result in a low population of the photothermalstationary state (PTSS) and reduced photostability. The DASA with thioindoline donor (D3A3) seems to be a special case among the donor series as it causes a red shift (ca. 15 nm), however with less polarization of the ground state and marginally better photostability as compared to the unsubstituted 2-methyl indoline (D1A3). We also emphasize the consideration of the key additional factors that can modulate the red-light photoswitching properties of DASA chromophores in polymer thin films, which might not be dominant in homogenous solution state.

Synthesis, Characterization and Interconversion of p-Tolylsulfone-Functionalized Norbornadiene/Quadricyclane Couples.

We report the synthesis and characterization of library of new 2,3-disubstituted norbornadiene/quadricyclane couples. For the first time, the para-tolylsulfone moiety was employed as electron-withdrawing substituent in combination with a variety of different electron donors as counterparts. Comprehensive characterization was conducted for every interconversion couple. By comparison with structurally related molecules published previously we established the tosyl moiety as suitable alternative to previously investigated ester functionalities by providing similar photophysical properties. The photo-induced interconversion behavior was investigated via UV/Vis- and NMR-spectroscopy. The UV/Vis experiments were carried out exclusively in acetonitrile, whereas several solvents were investigated in the NMR studies. A detailed description and comparison of the isomerization behavior is provided, while examining relevant optical properties like λmax and λonset. Thereby, an enhanced red-shift up to λmax = 394 nm combined with an λonset value of 469 nm could be generated which is necessary for potential applications.

Heterocyclic Hemipiperazines: Multistimuli-Responsive Switches and Sensors for Zinc or Cadmium Ions.

Advance in the design of molecular photoswitches - adapters that convert light into changes at molecular level - opens up exciting possibilities in preparing smart polymers, drugs photoactivated inside humans, or light-fueled nanomachines that might in the future operate in our bloodstream. Hemipiperazines are recently reported biocompatible molecular photoswitches based on cyclic dipeptides. Here we report a multistimuli-responsive hemipiperazine-based switch that reacts on light, solvents, acidity, or metal ions. Its photoequilibration is controlled by the intramolecular hydrogen bonding pattern. The compound can be used as a mid-nanomolar photoswitchable fluorescent sensor for zinc and cadmium ions, applicable to monitor environmental pollution in real time.

Exploring biocompatible chemistry to create stapled and photoswitchable variants of the antimicrobial peptide aurein 1.2.

Antibiotic resistance is an escalating global health threat. Due to their diverse mechanisms of action and evasion of traditional resistance mechanisms, peptides hold promise as future antibiotics. Their ability to disrupt bacterial membranes presents a potential strategy to combat drug-resistant infections and address the increasing need for effective antimicrobial treatments. Amphipathic α-helical peptides possess a distinctive molecular structure with both charged/hydrophilic and hydrophobic regions that interact with the bacterial cell membrane, disrupting its structural integrity. The α-helical amphipathic peptide aurein 1.2, secreted by the Australian frog Litoria aurea, is one of the shortest known antimicrobial peptides, spanning only 13 amino acids. The primary objective of this study was to investigate stapled and photoswitchable modifications of short helical peptides employing biocompatible chemistry, utilising aurein 1.2 as a model system. We developed various stapled versions of aurein 1.2 using biocompatible conjugation chemistry between dicyanopyridine and 1,2-aminothiols. While the commonly employed stapling pattern for longer staples is i, i + 7, we observed superior helicity in peptides stapled at positions i, i + 8. Molecular dynamics simulations confirmed both stapling patterns to support an α-helical peptide conformation. Additionally, we utilised a cysteine-selective photosensitive staple, perfluoro azobenzene, to explore photoswitchable variants of aurein 1.2. A double-cysteine variant stapled at i, i + 7 indeed exhibited a change in overall helicity induced by light. We further demonstrated the applicability of this staple to attach to cysteine residues in i, i + 7 positions of a helix in a model protein. While some of the stapled variants displayed substantial increase in helicity, minimal inhibitory concentration assays revealed that none of the stapled aurein 1.2 variants exhibited increased antimicrobial activity compared to the wildtype.

Unravelling Competitive Interactions between Polymer Side Chains and End Groups with ß-Cyclodextrin.

This study investigates unexpected competitive host-guest interactions of ß-cyclodextrin (ß-CD), which can occur with polymers in aqueous solution, using the examples of the two polymers poly(oligo(ethylene glycol) methyl ether methacrylate) and poly(glycerol mono methacrylate). Systematic structural modifications of the polymer provide insight into the host-guest interaction with ß-CD and the competition between side chains and end groups such as hydrophobic end groups remaining from reversible addition fragmentation chain transfer polymerization or intentionally implemented molecular recognition units such as arylazopyrazole photoswitches.

A Portrait of the Chromophore as a Young System-Quantum-Derived Force Field Unraveling Solvent Reorganization upon Optical Excitation of Cyclocurcumin Derivatives.

The study of fast non-equilibrium solvent relaxation in organic chromophores is still challenging for molecular modeling and simulation approaches, and is often overlooked, even in the case of non-adiabatic dynamics simulations. Yet, especially in the case of photoswitches, the interaction with the environment can strongly modulate the photophysical outcomes. To unravel such a delicate interplay, in the present contribution we resorted to a mixed quantum-classical approach, based on quantum mechanically derived force fields. The main task is to rationalize the solvent reorganization pathways in chromophores derived from cyclocurcumin, which are suitable for light-activated chemotherapy to destabilize cellular lipid membranes. The accurate and reliable decryption delivered by the quantum-derived force fields points to important differences in the solvent's reorganization, in terms of both structure and time scale evolution.