Photocontrol of the β-Hairpin Polypeptide Structure through an Optimized Azobenzene-Based Amino Acid Analogue

A family of neurodegenerative diseases, including Huntington's disease (HD) and spinocerebellar ataxias, are associated with an abnormal polyglutamine (polyQ) expansion in mutant proteins that become prone to form amyloid-like aggregates. Prior studies have suggested a key role for β-hairpin formation as a driver of nucleation and aggregation, but direct experimental studies have been challenging. Toward such research, we set out to enable spatiotemporal control over β-hairpin formation by the introduction of a photosensitive β-turn mimic in the polypeptide backbone, consisting of a newly designed azobenzene derivative. The reported derivative overcomes the limitations of prior approaches associated with poor photochemical properties and imperfect structural compatibility with the desired β-turn structure. A new azobenzene-based β-turn mimic was designed, synthesized, and found to display improved photochemical properties, both prior and after incorporation into the backbone of a polyQ polypeptide. The two isomers of the azobenzene-polyQ peptide showed different aggregate structures of the polyQ peptide fibrils, as demonstrated by electron microscopy and solid-state NMR (ssNMR). Notably, only peptides in which the β-turn structure was stabilized (azobenzene in the cis configuration) closely reproduced the spectral fingerprints of toxic, β-hairpin-containing fibrils formed by mutant huntingtin protein fragments implicated in HD. These approaches and findings will enable better deciphering of the roles of β-hairpin structures in protein aggregation processes in HD and other amyloid-related neurodegenerative diseases.

From a bistable adsorbate to a switchable interface: tetrachloropyrazine on Pt(111)

Virtually all organic (opto)electronic devices rely on organic/inorganic interfaces with specific properties. These properties are, in turn, inextricably linked to the interface structure. Therefore, a change in structure can introduce a shift in function. If this change is reversible, it would allow constructing a switchable interface. We accomplish this with tetrachloropyrazine on Pt(111), which exhibits a double-well potential with a chemisorbed and a physisorbed minimum. These minima have significantly different adsorption geometries allowing the formation of switchable interface structures. Importantly, these structures facilitate different work function changes and coherent fractions (as would be obtained from X-ray standing wave measurements), which are ideal properties to read out the interface state. We perform surface structure search using a modified version of the SAMPLE approach and account for thermodynamic conditions using ab initio thermodynamics. This allows investigating millions of commensurate as well as higher-order commensurate interface structures. We identify three different classes of structures exhibiting different work function changes and coherent fractions. Using temperature and pressure as handles, we demonstrate the possibility of reversible switching between those different classes, creating a dynamic interface for potential applications in organic electronics.

Hypothesis-Driven, Structure-Based Design in Photopharmacology: The Case of eDHFR Inhibitors

Photopharmacology uses light to regulate the biological activity of drugs. This precise control is obtained through the incorporation of molecular photoswitches into bioactive molecules. A major challenge for photopharmacology is the rational design of photoswitchable drugs that show light-induced activation. Computer-aided drug design is an attractive approach toward more effective, targeted design. Herein, we critically evaluated different structure-based approaches for photopharmacology with Escherichia coli dihydrofolate reductase (eDHFR) as a case study. Through the iterative examination of our hypotheses, we progressively tuned the design of azobenzene-based, photoswitchable eDHFR inhibitors in five design–make–switch–test–analyze cycles. Targeting a hydrophobic subpocket of the enzyme and a specific salt bridge only with the thermally metastable cis-isomer emerged as the most promising design strategy. We identified three inhibitors that could be activated upon irradiation and reached potencies in the low-nanomolar range. Above all, this systematic study provided valuable insights for future endeavors toward rational photopharmacology.

Molecular photoswitches in aqueous environments

Molecular photoswitches enable dynamic control of processes with high spatiotemporal precision, using light as external stimulus, and hence are ideal tools for different research areas spanning from chemical biology to smart materials. Photoswitches are typically organic molecules that feature extended aromatic systems to make them responsive to (visible) light. However, this renders them inherently lipophilic, while water-solubility is of crucial importance to apply photoswitchable organic molecules in biological systems, like in the rapidly emerging field of photopharmacology. Several strategies for solubilizing organic molecules in water are known, but there are not yet clear rules for applying them to photoswitchable molecules. Importantly, rendering photoswitches water-soluble has a serious impact on both their photophysical and biological properties, which must be taken into consideration when designing new systems. Altogether, these aspects pose considerable challenges for successfully applying molecular photoswitches in aqueous systems, and in particular in biologically relevant media. In this review, we focus on fully water-soluble photoswitches, such as those used in biological environments, in both in vitro and in vivo studies. We discuss the design principles and prospects for water-soluble photoswitches to inspire and enable their future applications.

Rational design of a photoswitchable DNA glue enabling high regulatory function and supramolecular chirality transfer

Short, complementary DNA single strands with mismatched base pairs cannot undergo spontaneous formation of duplex DNA (dsDNA). Mismatch binding ligands (MBLs) can compensate this effect, inducing the formation of the double helix and thereby acting as a molecular glue. Here, we present the rational design of photoswitchable MBLs that allow for reversible dsDNA assembly by light. Careful choice of the azobenzene core structure results in excellent band separation of the E and Z isomers of the involved chromophores. This effect allows for efficient use of light as an external control element for duplex DNA formation and for an in-depth study of the DNA-ligand interaction by UV-Vis, SPR, and CD spectroscopy, revealing a tight mutual interaction and complementarity between the photoswitchable ligand and the mismatched DNA. We also show that the configuration of the switch reversibly dictates the conformation of the DNA strands, while the dsDNA serves as a chiral clamp and translates its chiral information onto the ligand inducing a preference in helical chirality of the Z isomer of the MBLs.

Bioorthogonal Reactions of Triarylphosphines and Related Analogues

Bioorthogonal phosphines were introduced in the context of the Staudinger ligation over 20 years ago. Since that time, phosphine probes have been used in myriad applications to tag azide-functionalized biomolecules. The Staudinger ligation also paved the way for the development of other phosphorus-based chemistries, many of which are widely employed in biological experiments. Several reviews have highlighted early achievements in the design and application of bioorthogonal phosphines. This review summarizes more recent advances in the field. We discuss innovations in classic Staudinger-like transformations that have enabled new biological pursuits. We also highlight relative newcomers to the bioorthogonal stage, including the cyclopropenone-phosphine ligation and the phospha-Michael reaction. The review concludes with chemoselective reactions involving phosphite and phosphonite ligations. For each transformation, we describe the overall mechanism and scope. We also showcase efforts to fine-tune the reagents for specific functions. We further describe recent applications of the chemistries in biological settings. Collectively, these examples underscore the versatility and breadth of bioorthogonal phosphine reagents.

Synthesis and properties of photoswitchable diphosphines and gold(I) complexes derived from azobenzenes

Diphosphines displaying azobenzene scaffolds and the corresponding bis-gold chloride complexes have been prepared and fully characterized by photophysical, spectroscopic and X-ray diffraction studies. DFT calculations provide complementary information on their electronic, structural and spectroscopic properties. Comparative investigations have been carried out on compounds featuring phosphorus functions in the meta- and para-positions, respectively, with respect to the azo functions, as well as on diphosphines with an ortho-tetrafluoro substituted azobenzene core. The effects of the substitution patterns on structural and spectroscopic properties are discussed.

Photoresponsive molecular tools for emerging applications of light in medicine

Light-based therapeutic and imaging modalities, which emerge in clinical applications, rely on molecular tools, such as photocleavable protecting groups and photoswitches that respond to photonic stimulus and translate it into a biological effect. However, optimisation of their key parameters (activation wavelength, band separation, fatigue resistance and half-life) is necessary to enable application in the medical field. In this perspective, we describe the applications scenarios that can be envisioned in clinical practice and then we use those scenarios to explain the necessary properties that the photoresponsive tools used to control biological function should possess, highlighted by examples from medical imaging, drug delivery and photopharmacology. We then present how the (photo)chemical parameters are currently being optimized and an outlook is given on pharmacological aspects (toxicity, solubility, and stability) of light-responsive molecules. With these interdisciplinary insights, we aim to inspire the future directions for the development of photocontrolled tools that will empower clinical applications of light.

Regulation of mRNA translation by a photoriboswitch

Optogenetic tools have revolutionized the study of receptor-mediated processes, but such tools are lacking for RNA-controlled systems. In particular, light-activated regulatory RNAs are needed for spatiotemporal control of gene expression. To fill this gap, we used in vitro selection to isolate a novel riboswitch that selectively binds the trans isoform of a stiff-stilbene (amino-tSS)-a rapidly and reversibly photoisomerizing small molecule. Structural probing revealed that the RNA binds amino-tSS about 100-times stronger than the cis photoisoform (amino-cSS). In vitro and in vivo functional analysis showed that the riboswitch, termed Werewolf-1 (Were-1), inhibits translation of a downstream open reading frame when bound to amino-tSS. Photoisomerization of the ligand with a sub-millisecond pulse of light induced the protein expression. In contrast, amino-cSS supported protein expression, which was inhibited upon photoisomerization to amino-tSS. Reversible photoregulation of gene expression using a genetically encoded RNA will likely facilitate high-resolution spatiotemporal analysis of complex RNA processes.

Strategies and considerations of G-protein-coupled receptor photopharmacology

G-protein-coupled receptor (GPCR) pharmacology tends to be complex and at times poorly understood. This has led to the development of GPCR-targeting agents that often demonstrate poor pharmacokinetic properties and poor selectivity for their target receptors. One approach that is emerging as a means of addressing these limitations is the use of molecules whose activity can be controlled by light. Photopharmacology involves the incorporation of a photoswitch into the structure of a given compound, cage or linker and following irradiation with light, undergoes a structural rearrangement, which changes its biological activity. The use of light-regulated ligands offers the opportunity to modulate and understand GPCR signaling in a more spatiotemporal manner than classical pharmacological approaches. In this chapter we will discuss some of the advancements that have been made in photopharmacology, particularly in developing photoswitchable ligands that target class A GPCRs, e.g., muscarinic acetylcholine receptors, class B GPCRs, e.g., glucagon-like peptide-1 receptor, and class C GPCRs, e.g., metabotrobic glutamate receptors. Given the intricacy of GPCR pharmacology, this chapter will also discuss some of the challenges the field faces when designing photopharmacological tools. Furthermore, it will propose that it is with a full appreciation of the spectrum of pharmacological and pharmacokinetic properties of photoswitchable ligands that research will be better placed to develop ligands with a reduced risk of failure during preclinical progression. This will likely enable photopharmacological approaches to continue to find novel applications and offer new perspectives in understanding (patho)physiology to ultimately inform future GPCR drug discovery efforts.

Reversible Photocontrolled Nanopore Assembly

Self-assembly is a fundamental feature of biological systems, and control of such processes offers fascinating opportunities to regulate function. Fragaceatoxin C (FraC) is a toxin that upon binding to the surface of sphingomyelin-rich cells undergoes a structural metamorphosis, leading to the assembly of nanopores at the cell membrane and causing cell death. In this study we attached photoswitchable azobenzene pendants to various locations near the sphingomyelin binding pocket of FraC with the aim of remote controlling the nanopore assembly using light. We found several constructs in which the affinity of the toxin for biological membranes could be activated or deactivated by irradiation, thus enabling reversible photocontrol of pore formation. Notably, one construct was completely inactive in the thermally adapted state; it however induced full lysis of cultured cancer cells upon light irradiation. Selective irradiation also allowed isolation of individual nanopores in artificial lipid membranes. Photocontrolled FraC might find applications in photopharmacology for cancer therapeutics and has potential to be used for the fabrication of nanopore arrays in nanopore sensing devices, where the reconstitution, with high spatiotemporal precision, of single nanopores must be controlled.

Light-controlled inhibition of BRAFV600E kinase

Metastatic melanoma is amongst the most difficult types of cancer to treat, with current therapies mainly relying on the inhibition of the BRAF^V600E mutant kinase. However, systemic inhibition of BRAF by small molecule drugs in cancer patients results - paradoxically - in increased wild-type BRAF activity in healthy tissue, causing side-effects and even the formation of new tumors. Here we show the development of BRAF^V600E kinase inhibitors of which the activity can be switched on and off reversibly with light, offering the possibility to overcome problems of systemic drug activity by selectively activating the drug at the desired site of action. Based on a known inhibitor, eight photoswitchable effectors containing an azobenzene photoswitch were designed, synthesized and evaluated. The most promising inhibitor showed an approximately 10-fold increase in activity upon light-activation. This research offers inspiration for the development of therapies for metastatic melanoma in which tumor tissue is treated with an active BRAF^V600E inhibitor with high spatial and temporal resolution, thus limiting the damage to other tissues.

A molecular engineering toolbox for the structural biologist

Exciting new technological developments have pushed the boundaries of structural biology, and have enabled studies of biological macromolecules and assemblies that would have been unthinkable not long ago. Yet, the enhanced capabilities of structural biologists to pry into the complex molecular world have also placed new demands on the abilities of protein engineers to reproduce this complexity into the test tube. With this challenge in mind, we review the contents of the modern molecular engineering toolbox that allow the manipulation of proteins in a site-specific and chemically well-defined fashion. Thus, we cover concepts related to the modification of cysteines and other natural amino acids, native chemical ligation, intein and sortase-based approaches, amber suppression, as well as chemical and enzymatic bio-conjugation strategies. We also describe how these tools can be used to aid methodology development in X-ray crystallography, nuclear magnetic resonance, cryo-electron microscopy and in the studies of dynamic interactions. It is our hope that this monograph will inspire structural biologists and protein engineers alike to apply these tools to novel systems, and to enhance and broaden their scope to meet the outstanding challenges in understanding the molecular basis of cellular processes and disease.

N,O π-Conjugated 4-Substituted 1,3-Thiazole BF2 Complexes: Synthesis and Photophysical Properties

A series of 1,3-thiazole-based organoboron complexes has been designed and synthesized by acylation of 2-amino 4-subsituted 1,3-thiazoles with (4-dimethylamino)benzoyl chloride and the subsequent BF₂ complexation reaction. The influence of substituents in position 4 of the thiazole ring on photophysical properties of the complexes has been investigated. Synthesized thiazolo[3,2-c][1,3,5,2]oxadiazaborinines mainly showed intensive fluorescence in solutions. Complex with a 4,5-unsubstituted thiazole unit demonstrated an aggregation induced emission (AIE) effect and a very high fluorescent quantum yield (94%) in the solid state because of the inhibition of π-π/π-n interactions in the molecular packing.

Bimetallic gold(i) complexes of photoswitchable phosphines: synthesis and uses in cooperative catalysis

The first photoswitchable bimetallic gold catalysts based on an azobenzene backbone have been synthesized and their catalytic properties have been investigated.

Photo-enhanced Aqueous Solubilization of an Azo-compound

We previously showed that disruption of intermolecular interactions, e.g., by lowering the molecular planarity and/or introducing bent structures, improves the aqueous solubility of compounds, and based upon that work, we hypothesized that azobenzene trans-to-cis photoswitching could also be utilized to enhance the aqueous solubility of compounds. Here, we demonstrate that UV/visible light irradiation can reversibly switch the aqueous solubilization of an anti-cancer candidate drug, a low-molecular-weight kinase inhibitor bearing an azobenzene moiety. The increase of solubilization associated with UV-induced trans-to-cis conversion may have clinical relevance, because the time-scale of thermal cis-to-trans reversion at 37 °C is longer than that of oral absorption.

Combining the Advantages of Alkene and Azo E-Z Photoisomerizations: Mechanistic Insights into Ketoimine Photoswitches

We carried out CASPT2//(TD)DFT and CASPT2//CASSCF studies on the working mechanism of imine switches, including a camphorquinone-derived ketoimine (shortened as k-Imine) switch designed by Lehn as well as a model camphorquinone alkene-imine (a-Imine) proposed in this study. Under the experimental conditions (light irradiation with 455 and 365 nm for E and Z, respectively), k-Imine is excited to the S₁:(n_N,π*) state and then decays toward a perpendicular intermediate following the C═N bond rotation coordinate. During the bond rotation, a mild energy barrier caused by the strong interaction of S₁:(n_N,π*) and S₂:(n_O,π*) states will more or less slow down the rotation speed of k-Imine. The large difference in irradiation light wavelength supports k-Imine as a two-way photoswitch. The photoisomerization of a-Imine obeys a similar but fully barrierless pattern while requiring a higher excitation energy to reach the (n_N,π*) state. The good directionality of thermal isomerization toward E(a-Imine), plus the barrierless photoisomerization, allows for the design of a thermal and photo-operated switch. For both imines, a minimal-energy crossing point (MECI) located at the perpendicular region, with low relative energy and close to the rotary path, ensures the directionality of C═N bond rotation and confirms imines as optimal candidates for photoswitches and motors.

Processing and surface modification of polymer nanofibers for biological scaffolds: a review

Polymeric fibrous constructs possess high surface area-to-volume ratios when compared with solid substrates and are quite commonly used as tissue engineering and cell growth scaffolds. An overview of important design and material considerations for fibrous scaffolds as well as an outline of both established and emerging solution- and melt-based fabrication techniques is provided. Innovative post-process surface modification avenues using "click" chemistry with both single and dual active cues as well as gradient cues, which maintain the fibrous structure are described. By combining process parameters with post-process surface modification, researchers have been able to selectively tune cellular response after seeding and culturing on fibrous constructs.

Orthogonal photoswitching in a multifunctional molecular system

The wavelength-selective, reversible photocontrol over various molecular processes in parallel remains an unsolved challenge. Overlapping ultraviolet-visible spectra of frequently employed photoswitches have prevented the development of orthogonally responsive systems, analogous to those that rely on wavelength-selective cleavage of photo-removable protecting groups. Here we report the orthogonal and reversible control of two distinct types of photoswitches in one solution, that is, a donor-acceptor Stenhouse adduct (DASA) and an azobenzene. The control is achieved by using three different wavelengths of irradiation and a thermal relaxation process. The reported combination tolerates a broad variety of differently substituted photoswitches. The presented system is also extended to an intramolecular combination of photoresponsive units. A model application for an intramolecular combination of switches is presented, in which the DASA component acts as a phase-transfer tag, while the azobenzene moiety independently controls the binding to α-cyclodextrin.

Direct P-functionalization of azobenzene by a cationic phosphidozirconocene complex

Cooperation between zirconium and phosphorus enables the direct synthesis of a new PNN ligand via a spectrosopically characterized σ^H adduct.

Azobenzenes and catalysis

Azobenzene is the most extensively used class of chromophore in a large variety of applications.

Light-Controlled Histone Deacetylase (HDAC) Inhibitors: Towards Photopharmacological Chemotherapy

Cancer treatment suffers from limitations that have a major impact on the patient's quality of life and survival. In the case of chemotherapy, the systemic distribution of cytotoxic drugs reduces their efficacy and causes severe side effects due to nonselective toxicity. Photopharmacology allows a novel approach to address these problems because it employs external, local activation of chemotherapeutic agents by using light. The development of photoswitchable histone deacetylase (HDAC) inhibitors as potential antitumor agents is reported herein. Analogues of the clinically used chemotherapeutic agents vorinostat, panobinostat, and belinostat were designed with a photoswitchable azobenzene moiety incorporated into their structure. The most promising compound exhibits high inhibitory potency in the thermodynamically less stable cis form and a significantly lower activity for the trans form, both in terms of HDAC activity and proliferation of HeLa cells. This approach offers a clear prospect towards local photoactivation of HDAC inhibition to avoid severe side effects in chemotherapy.

Proteasome inhibitors with photocontrolled activity

Proteasome inhibitors are widely used in cancer treatment as chemotherapeutic agents. However, their employment often results in severe side effects, due to their non-specific cytotoxicity towards healthy tissue. This problem might be overcome by using a photopharmacological approach, that is, by attaining external, dynamic, spatiotemporal photocontrol over the activity of a cytotoxic agent, achieved by the introduction of a photoswitchable moiety into its molecular structure. Here we describe the design, synthesis, and activity of photoswitchable proteasome inhibitors. Substantial differences in proteasome inhibitory activity in cell extracts were observed before and after irradiation with light. The presented results show potential for the development of chemotherapeutic agents that can be switched on and off with light, constituting a new strategy for spatiotemporally modulating proteasomal activity.

Molecular switches from benzene derivatives adsorbed on metal surfaces

Transient precursor states are often experimentally observed for molecules adsorbing on surfaces. However, such precursor states are typically rather short-lived, quickly yielding to more stable adsorption configurations. Here we employ first-principles calculations to systematically explore the interaction mechanism for benzene derivatives on metal surfaces, enabling us to selectively tune the stability and the barrier between two metastable adsorption states. In particular, in the case of the tetrachloropyrazine molecule, two equally stable adsorption states are identified with a moderate and conceivably reversible barrier between them. We address the feasibility of experimentally detecting the predicted bistable behaviour and discuss its potential usefulness in a molecular switch.

Short-lived precursors typically occur before molecules chemisorb on surfaces. Liu et al. predict that for benzene derivatives on metal surfaces, the precursors can be long-lived and the transition to chemisorption states can be reversible, which may be useful in molecular switch applications.

Kinetics studies of rapid strain-promoted [3+2] cycloadditions of nitrones with bicyclo[6.1.0]nonyne

Strain-promoted alkyne−nitrone cycloaddition (SPANC) reactions represent a bioorthogonal labeling strategy that is both very rapid and at the same time efficient and selective. Nitrones provide increased reaction rates as well as greater susceptibility toward stereoelectronic modification when compared with organic azides. We find that strain-promoted cycloadditions of cyclic nitrones with bicyclo[6.1.0]nonyne react with second-order rate constants as large as 1.49 L mol−1 s−1 at 25 °C. These reactions display rate constants that are up to 37-fold greater than those of the analogous reactions of benzyl azide with bicyclo[6.1.0]nonyne. We observed that reactions of nitrones with bicyclo[6.1.0]nonyne showed a stronger dependence on substituent effect for the reaction, as evidenced by a larger Hammett ρ value, than that for biaryl-aza-cyclooctanone. We demonstrate the ability to stereoelectronically tune the reactivity of nitrones towards different cyclooctynes in SPANC reactions. This ability to introduce selectivity into different SPANC reactions through substituent provides the opportunity to perform multiple SPANC reactions in one reaction vessel and opens up potential applications in multiplex labeling.

Photo-controlled deactivation of immobilised lipase

Immobilization of lipase on a quartz surface using a photoswitchable linker permits to control the deactivation of the enzyme by irradiation with light.

Chemical methods for peptide and protein production

Since the invention of solid phase synthetic methods by Merrifield in 1963, the number of research groups focusing on peptide synthesis has grown exponentially. However, the original step-by-step synthesis had limitations: the purity of the final product decreased with the number of coupling steps. After the development of Boc and Fmoc protecting groups, novel amino acid protecting groups and new techniques were introduced to provide high quality and quantity peptide products. Fragment condensation was a popular method for peptide production in the 1980s, but unfortunately the rate of racemization and reaction difficulties proved less than ideal. Kent and co-workers revolutionized peptide coupling by introducing the chemoselective reaction of unprotected peptides, called native chemical ligation. Subsequently, research has focused on the development of novel ligating techniques including the famous click reaction, ligation of peptide hydrazides, and the recently reported α-ketoacid-hydroxylamine ligations with 5-oxaproline. Several companies have been formed all over the world to prepare high quality Good Manufacturing Practice peptide products on a multi-kilogram scale. This review describes the advances in peptide chemistry including the variety of synthetic peptide methods currently available and the broad application of peptides in medicinal chemistry.