Alkyl Derivatives of Perylene Photosensitizing Antivirals: Towards Understanding the Influence of Lipophilicity.

Amphipathic perylene derivatives are broad-spectrum antivirals against enveloped viruses that act as fusion inhibitors in a light-dependent manner. The compounds target the lipid bilayer of the viral envelope using the lipophilic perylene moiety and photogenerating singlet oxygen, thereby causing damage to unsaturated lipids. Previous studies show that variation of the polar part of the molecule is important for antiviral activity. Here, we report modification of the lipophilic part of the molecule, perylene, by the introduction of 4-, 8-, and 12-carbon alkyls into position 9(10) of the perylene residue. Using Friedel-Crafts acylation and Wolff-Kishner reduction, three 3-acetyl-9(10)-alkylperylenes were synthesized from perylene and used to prepare 9 nucleoside and 12 non-nucleoside amphipathic derivatives. These compounds were characterized as fluorophores and singlet oxygen generators, as well as tested as antivirals against herpes virus-1 (HSV-1) and vesicular stomatitis virus (VSV), both known for causing superficial skin/mucosa lesions and thus serving as suitable candidates for photodynamic therapy. The results suggest that derivatives with a short alkyl chain (butyl) have strong antiviral activity, whereas the introduction of longer alkyl substituents (n = 8 and 12) to the perylenyethynyl scaffold results in a dramatic reduction of antiviral activity. This phenomenon is likely attributable to the increased lipophilicity of the compounds and their ability to form insoluble aggregates. Moreover, molecular dynamic studies revealed that alkylated perylene derivatives are predominately located closer to the middle of the bilayer compared to non-alkylated derivatives. The predicted probability of superficial positioning correlated with antiviral activity, suggesting that singlet oxygen generation is achieved in the subsurface layer of the membrane, where the perylene group is more accessible to dissolved oxygen.

Membrane-Targeting Perylenylethynylphenols Inactivate Medically Important Coronaviruses via the Singlet Oxygen Photogeneration Mechanism.

Perylenylethynyl derivatives have been recognized as broad-spectrum antivirals that target the lipid envelope of enveloped viruses. In this study, we present novel perylenylethynylphenols that exhibit nanomolar or submicromolar antiviral activity against Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) and feline infectious peritonitis virus (FIPV) in vitro. Perylenylethynylphenols incorporate into viral and cellular membranes and block the entry of the virus into the host cell. Furthermore, these compounds demonstrate an ability to generate singlet oxygen when exposed to visible light. The rate of singlet oxygen production is positively correlated with antiviral activity, confirming that the inhibition of fusion is primarily due to singlet-oxygen-induced damage to the viral envelope. The unique combination of a shape that affords affinity to the lipid bilayer and the capacity to generate singlet oxygen makes perylenylethynylphenols highly effective scaffolds against enveloped viruses. The anticoronaviral activity of perylenylethynylphenols is strictly light-dependent and disappears in the absence of daylight (under red light). Moreover, these compounds exhibit negligible cytotoxicity, highlighting their significant potential for further exploration of the precise antiviral mechanism and the broader scope and limitations of this compound class.

Antiviral activity of singlet oxygen-photogenerating perylene compounds against SARS-CoV-2: Interaction with the viral envelope and photodynamic virion inactivation.

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has prompted great interest in novel broad-spectrum antivirals, including perylene-related compounds. In the present study, we performed a structure-activity relationship analysis of a series of perylene derivatives, which comprised a large planar perylene residue, and structurally divergent polar groups connected to the perylene core by a rigid ethynyl or thiophene linker. Most of the tested compounds did not exhibit significant cytotoxicity towards multiple cell types susceptible to SARS-CoV-2 infection, and did not change the expressions of cellular stress-related genes under normal light conditions. These compounds showed nanomolar or sub-micromolar dose-dependent anti-SARS-CoV-2 activity, and also suppressed the in vitro replication of feline coronavirus (FCoV), also termed feline infectious peritonitis virus (FIPV). Perylene compounds exhibited high affinity for liposomal and cellular membranes, and efficiently intercalated into the envelopes of SARS-CoV-2 virions, thereby blocking the viral-cell fusion machinery. Furthermore, the studied compounds were demonstrated to be potent photosensitizers, generating reactive oxygen species (ROS), and their anti-SARS-CoV-2 activities were considerably enhanced after irradiation with blue light. Our results indicated that photosensitization is the major mechanism underlying the anti-SARS-CoV-2 activity of perylene derivatives, with these compounds completely losing their antiviral potency under red light. Overall, perylene-based compounds are broad-spectrum antivirals against multiple enveloped viruses, with antiviral action based on light-induced photochemical damage (ROS-mediated, likely singlet oxygen-mediated), causing impairment of viral membrane rheology.

Aminooxy Click Modification of a Periodate-Oxidized Immunoglobulin G: A General Approach to Antibody-Drug Conjugates with Dye-Mediated Expeditious Stoichiometry Control.

A universal approach to the construction of antibody-drug conjugates (ADCs) has been developed. It relies on periodate oxidation of naturally present glycans of immunoglobulin G, followed by oxime ligation and, optionally, copper(I)-catalyzed alkyne-azide cycloaddition for conjugation with a toxic payload. The introduction of highly absorbing cyanine dyes into the linker allows for facile determination of the drug-antibody ratio. We applied this methodology to the synthesis of cytotoxic conjugates of an antibody against the tumor-associated antigen PRAME with doxorubicin and monomethyl auristatin E (MMAE). The resultant conjugates retained their affinity to a large extent, yet their cytotoxicity in vitro varied dramatically: while the doxorubicin-based conjugate did not produce any effect on cells, the MMAE-based one demonstrated specific activity against PRAME-expressing cancer cell lines. Importantly, the latter conjugate constitutes the first reported example of a PRAME-targeting ADC.

Branched Linkers for Site-Specific Fluorescent Labeling of Antibodies.

Fluorescent antibodies have proved to be an invaluable tool for molecular biology and diagnostics. They are routinely produced by modification of lysine residues, which leads to high heterogeneity. As such, their affinity may be compromised if the antigen-binding site is affected, the probability of which increases along with the degree of labeling. In this work, we propose a methodology for the synthesis of site-specific antibody-dye conjugates with a high degree of labeling. To this end, we synthesized two oxyamine-based branched triazide linkers and coupled them with a periodate-oxidized anti-PRAME antibody 6H8; two oxyamine-based linear monoazide linkers of similar structure were used as controls. The azide-labeled antibodies were subsequently conjugated with fluorescent dyes via SPAAC, a copper-free click reaction. Compared to their counterparts made with linear linkers, the branched conjugates possessed a higher degree of labeling. The utility of the methodology was demonstrated in the detection of the PRAME protein on the surface of the cell by flow cytometry.

5-(Perylen-3-ylethynyl)uracil as an antiviral scaffold: Potent suppression of enveloped virus reproduction by 3-methyl derivatives in vitro.

Amphipathic nucleoside and non-nucleoside derivatives of pentacyclic aromatic hydrocarbon perylene are known as potent non-cytotoxic broad-spectrum antivirals. Here we report 3-methyl-5-(perylen-3-ylethynyl)-uracil-1-acetic acid and its amides, a new series of compounds based on a 5-(perylen-3-ylethynyl)-uracil scaffold. The compounds demonstrate pronounced in vitro activity against arthropod-borne viruses, namely tick-borne encephalitis virus (TBEV) and yellow fever virus (YFV), in plaque reduction assays with EC50 values below 1.9 and 1.3 nM, respectively, and Chikungunya virus (CHIKV) in cytopathic effect inhibition test with EC50 values below 3.2 µM. The compounds are active against respiratory viruses as well: severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) in cytopathic effect inhibition test and influenza A virus (IAV) in virus titer reduction experiments are inhibited - EC50 values below 51 nM and 2.2 µM, respectively. The activity stems from the presence of a hydrophobic perylene core, and all of the synthesized compounds exhibit comparable 1O2 generation rates. Nonetheless, activity can vary by orders of magnitude depending on the hydrophilic part of the molecule, suggesting a complex mode of action. A time-of-addition experiment and fluorescent imaging indicate that the compounds inhibit viral fusion in a dose-dependent manner. The localization of the compound in the lipid bilayers and visible damage to the viral envelope suggest the membrane as the primary target. Dramatic reduction of antiviral activity with limited irradiation or under treatment with antioxidants further cements the idea of photoinduced ROS-mediated viral envelope damage being the mode of antiviral action.

Near-Infrared Dyes: Towards Broad-Spectrum Antivirals.

Broad antiviral activity in vitro is known for many organic photosensitizers generating reactive oxygen species under irradiation with visible light. Low tissue penetration of visible light prevents further development of antiviral therapeutics based on these compounds. One possible solution to this problem is the development of photosensitizers with near-infrared absorption (NIR dyes). These compounds found diverse applications in the photodynamic therapy of tumors and bacterial infections, but they are scarcely mentioned as antivirals. In this account, we aimed to evaluate the therapeutic prospects of various NIR-absorbing and singlet oxygen-generating chromophores for the development of broad-spectrum photosensitizing antivirals.

Sensitive Immunofluorescent Detection of the PRAME Antigen Using a Practical Antibody Conjugation Approach.

Bioconjugation of antibodies with various payloads has diverse applications across various fields, including drug delivery and targeted imaging techniques. Fluorescent immunoconjugates provide a promising tool for cancer diagnostics due to their high brightness, specificity, stability and target affinity. Fluorescent antibodies are widely used in flow cytometry for fast and sensitive identification and collection of cells expressing the target surface antigen. Nonetheless, current approaches to fluorescent labeling of antibodies most often use random modification, along with a few rather sophisticated site-specific techniques. The aim of our work was to develop a procedure for fluorescent labeling of immunoglobulin G via periodate oxidation of antibody glycans, followed by oxime ligation with fluorescent oxyamines. Here, we report a novel technique based on an in situ oxime ligation of ethoxyethylidene-protected aminooxy compounds with oxidized antibody glycans. The approach is suitable for easy modification of any immunoglobulin G, while ensuring that antigen-binding domains remain intact, thus revealing various possibilities for fluorescent probe design. The technique was used to label an antibody to PRAME, a cancer-testis protein overexpressed in a number of cancers. A 6H8 monoclonal antibody to the PRAME protein was directly modified with protected-oxyamine derivatives of fluorescein-type dyes (FAM, Alexa488, BDP-FL); the stoichiometry of the resulting conjugates was characterized spectroscopically. The immunofluorescent conjugates obtained were applied to the analysis of bone marrow samples from patients with oncohematological diseases and demonstrated high efficiency in flow cytometry quantification. The approach can be applied for the development of various immunofluorescent probes for detection of diagnostic and prognostic markers, which can be useful in anticancer therapy.

Photosensitizing Antivirals.

Antiviral action of various photosensitizers is already summarized in several comprehensive reviews, and various mechanisms have been proposed for it. However, a critical consideration of the matter of the area is complicated, since the exact mechanisms are very difficult to explore and clarify, and most publications are of an empirical and "phenomenological" nature, reporting a dependence of the antiviral action on illumination, or a correlation of activity with the photophysical properties of the substances. Of particular interest is substance-assisted photogeneration of highly reactive singlet oxygen (1O2). The damaging action of 1O2 on the lipids of the viral envelope can probably lead to a loss of the ability of the lipid bilayer of enveloped viruses to fuse with the lipid membrane of the host cell. Thus, lipid bilayer-affine 1O2 photosensitizers have prospects as broad-spectrum antivirals against enveloped viruses. In this short review, we want to point out the main types of antiviral photosensitizers with potential affinity to the lipid bilayer and summarize the data on new compounds over the past three years. Further understanding of the data in the field will spur a targeted search for substances with antiviral activity against enveloped viruses among photosensitizers able to bind to the lipid membranes.

Ultrastrong photon-to-magnon coupling in multilayered heterostructures involving superconducting coherence via ferromagnetic layers.

The critical step for future quantum industry demands realization of efficient information exchange between different-platform hybrid systems that can harvest advantages of distinct platforms. The major restraining factor for the progress in certain hybrids is weak coupling strength between the elemental particles. In particular, this restriction impedes a promising field of hybrid magnonics. In this work, we propose an approach for realization of on-chip hybrid magnonic systems with unprecedentedly strong coupling parameters. The approach is based on multilayered microstructures containing superconducting, insulating, and ferromagnetic layers with modified photon phase velocities and magnon eigenfrequencies. The enhanced coupling strength is provided by the radically reduced photon mode volume. Study of the microscopic mechanism of the photon-to-magnon coupling evidences formation of the long-range superconducting coherence via thick strong ferromagnetic layers in superconductor/ferromagnet/superconductor trilayer in the presence of magnetization precession. This discovery offers new opportunities in microwave superconducting spintronics for quantum technologies.

Eliminating Quantum Phase Slips in Superconducting Nanowires.

In systems with reduced dimensions, quantum fluctuations have a strong influence on the electronic conduction, even at very low temperatures. In superconductors, this is especially interesting, since the coherent state of the superconducting electrons strongly interacts with these fluctuations and therefore is a sensitive tool to study them. In this paper, we report on comprehensive measurements of superconducting nanowires in the quantum phase slip regime. Using an intrinsic electromigration process, we have developed a method to lower the nanowire's resistance in situ and therefore eliminate quantum phase slips in small consecutive steps. We observe critical (Coulomb) blockade voltages and superconducting critical currents, in good agreement with theoretical models. Between these two regimes, we find a continuous transition displaying a nonlinear metallic-like behavior. The reported intrinsic electromigration technique is not limited to low temperatures, as we find a similar change in resistance that spans over 3 orders of magnitude also at room temperature. Aside from superconducting quantum circuits, such a technique to reduce the resistance may also have applications in modern electronic circuits.

Toehold-Mediated Selective Assembly of Compact Discrete DNA Nanostructures.

Production of small discrete DNA nanostructures containing covalent junctions requires reliable methods for the synthesis and assembly of branched oligodeoxynucleotide (ODN) conjugates. This study reports an approach for self-assembly of hard-to-obtain primitive discrete DNA nanostructures-"nanoethylenes", dimers formed by double-stranded oligonucleotides using V-shaped furcate blocks. We scaled up the synthesis of V-shaped oligonucleotide conjugates using pentaerythritol-based diazide and alkyne-modified oligonucleotides using copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) and optimized the conditions for "nanoethylene" formation. Next, we designed nanoethylene-based "nanomonomers" containing pendant adapters. They demonstrated smooth and high-yield spontaneous conversion into the smallest cyclic product, DNA tetragon aka "nano-methylcyclobutane". Formation of DNA nanostructures was confirmed using native polyacrylamide gel electrophoresis (PAGE) and atomic force microscopy (AFM) and additionally studied by molecular modeling. The proposed facile approach to discrete DNA nanostructures using precise adapter-directed association expands the toolkit for the realm of DNA origami.

Postsynthetic On-Column 2' Functionalization of RNA by Convenient Versatile Method.

We report a universal straightforward strategy for the chemical synthesis of modified oligoribonucleotides containing functional groups of different structures at the 2' position of ribose. The on-column synthetic concept is based on the incorporation of two types of commercial nucleotide phosphoramidites containing orthogonal 2'-O-protecting groups, namely 2'-O-thiomorpholine-carbothioate (TC, as "permanent") and 2'-O-tert-butyl(dimethyl)silyl (tBDMS, as "temporary"), to RNA during solid-phase synthesis. Subsequently, the support-bound RNA undergoes selective deprotection and follows postsynthetic 2' functionalization of the naked hydroxyl group. This convenient method to tailor RNA, utilizing the advantages of solid phase approaches, gives an opportunity to introduce site-specifically a wide range of linkers and functional groups. By this strategy, a series of RNAs containing diverse 2' functionalities were synthesized and studied with respect to their physicochemical properties.

Publisher Correction: Resolving the positions of defects in superconducting quantum bits.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Current-Resistance Effects Inducing Nonlinear Fluctuation Mechanisms in Granular Aluminum Oxide Nanowires.

The unusual superconducting properties of granular aluminum oxide have been recently investigated for application in quantum circuits. However, the intrinsic irregular structure of this material requires a good understanding of the transport mechanisms and, in particular, the effect of disorder, especially when patterned at the nanoscale level. In view of these aspects, electric transport and voltage fluctuations have been investigated on thin-film based granular aluminum oxide nanowires, in the normal state and at temperatures between 8 and 300 K. The nonlinear resistivity and two-level tunneling fluctuators have been observed. Regarding the nature of the noise processes, the experimental findings give a clear indication in favor of a dynamic random resistor network model, rather than the possible existence of a local ordering of magnetic origin. The identification of the charge carrier fluctuations in the normal state of granular aluminum oxide nanowires is very useful for improving the fabrication process and, therefore, reducing the possible sources of decoherence in the superconducting state, where quantum technologies that are based on these nanostructures should work.

Simplistic perylene-related compounds as inhibitors of tick-borne encephalitis virus reproduction.

Rigid amphipathic fusion inhibitors are potent broad-spectrum antivirals based on the perylene scaffold, usually decorated with a hydrophilic group linked via ethynyl or triazole. We have sequentially simplified these structures by removing sugar moiety, then converting uridine to aniline, then moving to perylenylthiophenecarboxylic acids and to perylenylcarboxylic acid. All these polyaromatic compounds, as well as antibiotic heliomycin, still showed pronounced activity against tick-borne encephalitis virus (TBEV) with limited toxicity in porcine embryo kidney (PEK) cell line. 5-(Perylen-3-yl)-2-thiophenecarboxylic acid (5a) showed the highest antiviral activity with 50% effective concentration of approx. 1.6 nM.

Resolving the positions of defects in superconducting quantum bits.

Solid-state quantum coherent devices are quickly progressing. Superconducting circuits, for instance, have already been used to demonstrate prototype quantum processors comprising a few tens of quantum bits. This development also revealed that a major part of decoherence and energy loss in such devices originates from a bath of parasitic material defects. However, neither the microscopic structure of defects nor the mechanisms by which they emerge during sample fabrication are understood. Here, we present a technique to obtain information on locations of defects relative to the thin film edge of the qubit circuit. Resonance frequencies of defects are tuned by exposing the qubit sample to electric fields generated by electrodes surrounding the chip. By determining the defect's coupling strength to each electrode and comparing it to a simulation of the field distribution, we obtain the probability at which location and at which interface the defect resides. This method is applicable to already existing samples of various qubit types, without further on-chip design changes. It provides a valuable tool for improving the material quality and nano-fabrication procedures towards more coherent quantum circuits.

Correlating Decoherence in Transmon Qubits: Low Frequency Noise by Single Fluctuators.

We report on long-term measurements of a highly coherent, nontunable superconducting transmon qubit, revealing low-frequency burst noise in coherence times and qubit transition frequency. We achieve this through a simultaneous measurement of the qubit's relaxation and dephasing rate as well as its resonance frequency. The analysis of correlations between these parameters yields information about the microscopic origin of the intrinsic decoherence mechanisms in Josephson qubits. Our results are consistent with a small number of microscopic two-level systems located at the edges of the superconducting film, which is further confirmed by a spectral noise analysis.

Ferromagnet/Superconductor Hybrid Magnonic Metamaterials.

In this work, a class of metamaterials is proposed on the basis of ferromagnet/superconductor hybridization for applications in magnonics. These metamaterials comprise of a ferromagnetic magnon medium that is coupled inductively to a superconducting periodic microstructure. Spectroscopy of magnetization dynamics in such hybrid evidences formation of areas in the medium with alternating dispersions for spin wave propagation, which is the basic requirement for the development of metamaterials known as magnonic crystals. The spectrum allows for derivation of the impact of the superconducting structure on the dispersion: it takes place due to a diamagnetic response of superconductors on the external and stray magnetic fields. In addition, the spectrum displays a dependence on the superconducting critical state of the structure: the Meissner and the mixed states of a type II superconductor are distinguished. This dependence hints toward nonlinear response of hybrid metamaterials on the magnetic field. Investigation of the spin wave dispersion in hybrid metamaterials shows formation of allowed and forbidden bands for spin wave propagation. The band structures are governed by the geometry of spin wave propagation: in the backward volume geometry the band structure is conventional, while in the surface geometry the band structure is nonreciprocal and is formed by indirect band gaps.

Granular aluminium as a superconducting material for high-impedance quantum circuits.

Superconducting quantum information processing machines are predominantly based on microwave circuits with relatively low characteristic impedance, about 100 Ω, and small anharmonicity, which can limit their coherence and logic gate fidelity1,2. A promising alternative is circuits based on so-called superinductors3-6, with characteristic impedances exceeding the resistance quantum RQ = 6.4 kΩ. However, previous implementations of superinductors, consisting of mesoscopic Josephson junction arrays7,8, can introduce unintended nonlinearity or parasitic resonant modes in the qubit vicinity, degrading its coherence. Here, we present a fluxonium qubit design based on a granular aluminium superinductor strip9-11. We show that granular aluminium can form an effective junction array with high kinetic inductance and be in situ integrated with standard aluminium circuit processing. The measured qubit coherence time [Formula: see text] illustrates the potential of granular aluminium for applications ranging from protected qubit designs to quantum-limited amplifiers and detectors.