An orally bioavailable SARS-CoV-2 main protease inhibitor exhibits improved affinity and reduced sensitivity to mutations.

Inhibitors of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro) such as nirmatrelvir (NTV) and ensitrelvir (ETV) have proven effective in reducing the severity of COVID-19, but the presence of resistance-conferring mutations in sequenced viral genomes raises concerns about future drug resistance. Second-generation oral drugs that retain function against these mutants are thus urgently needed. We hypothesized that the covalent hepatitis C virus protease inhibitor boceprevir (BPV) could serve as the basis for orally bioavailable drugs that inhibit SARS-CoV-2 Mpro more efficiently than existing drugs. Performing structure-guided modifications of BPV, we developed a picomolar-affinity inhibitor, ML2006a4, with antiviral activity, oral pharmacokinetics, and therapeutic efficacy similar or superior to those of NTV. A crucial feature of ML2006a4 is a derivatization of the ketoamide reactive group that improves cell permeability and oral bioavailability. Last, ML2006a4 was found to be less sensitive to several mutations that cause resistance to NTV or ETV and occur in the natural SARS-CoV-2 population. Thus, anticipatory design can preemptively address potential resistance mechanisms to expand future treatment options against coronavirus variants.

Photoswitchable binders enable temporal dissection of endogenous protein function.

General methods for spatiotemporal control of specific endogenous proteins would be broadly useful for probing protein function in living cells. Synthetic protein binders that bind and inhibit endogenous protein targets can be obtained from nanobodies, designed ankyrin repeat proteins (DARPins), and other small protein scaffolds, but generalizable methods to control their binding activity are lacking. Here, we report robust single-chain photoswitchable DARPins (psDARPins) for bidirectional optical control of endogenous proteins. We created topological variants of the DARPin scaffold by computer-aided design so fusion of photodissociable dimeric Dronpa (pdDronpa) results in occlusion of target binding at baseline. Cyan light induces pdDronpa dissociation to expose the binding surface (paratope), while violet light restores pdDronpa dimerization and paratope caging. Since the DARPin redesign leaves the paratope intact, the approach was easily applied to existing DARPins for GFP, ERK, and Ras, as demonstrated by relocalizing GFP-family proteins and inhibiting endogenous ERK and Ras with optical control. Finally, a Ras-targeted psDARPin was used to determine that, following EGF-activation of EGFR, Ras is required for sustained EGFR to ERK signaling. In summary, psDARPins provide a generalizable strategy for precise spatiotemporal dissection of endogenous protein function.

Kinase-Modulated Bioluminescent Indicators Enable Noninvasive Imaging of Drug Activity in the Brain.

Aberrant kinase activity contributes to the pathogenesis of brain cancers, neurodegeneration, and neuropsychiatric diseases, but identifying kinase inhibitors that function in the brain is challenging. Drug levels in blood do not predict efficacy in the brain because the blood-brain barrier prevents entry of most compounds. Rather, assessing kinase inhibition in the brain requires tissue dissection and biochemical analysis, a time-consuming and resource-intensive process. Here, we report kinase-modulated bioluminescent indicators (KiMBIs) for noninvasive longitudinal imaging of drug activity in the brain based on a recently optimized luciferase-luciferin system. We develop an ERK KiMBI to report inhibitors of the Ras-Raf-MEK-ERK pathway, for which no bioluminescent indicators previously existed. ERK KiMBI discriminates between brain-penetrant and nonpenetrant MEK inhibitors, reveals blood-tumor barrier leakiness in xenograft models, and reports MEK inhibitor pharmacodynamics in native brain tissues and intracranial xenografts. Finally, we use ERK KiMBI to screen ERK inhibitors for brain efficacy, identifying temuterkib as a promising brain-active ERK inhibitor, a result not predicted from chemical characteristics alone. Thus, KiMBIs enable the rapid identification and pharmacodynamic characterization of kinase inhibitors suitable for treating brain diseases.

A red fluorescent protein with improved monomericity enables ratiometric voltage imaging with ASAP3.

A ratiometric genetically encoded voltage indicator (GEVI) would be desirable for tracking transmembrane voltage changes in the presence of sample motion. We performed combinatorial multi-site mutagenesis on a cyan-excitable red fluorescent protein to create the bright and monomeric mCyRFP3, which proved to be uniquely non-perturbing when fused to the GEVI ASAP3. The green/red ratio from ASAP3-mCyRFP3 (ASAP3-R3) reported voltage while correcting for motion artifacts, allowing the visualization of membrane voltage changes in contracting cardiomyocytes and throughout the cell cycle of motile cells.

Stable Transfection of the Singlet Oxygen Photosensitizing Protein SOPP3: Examining Aspects of Intracellular Behavior.

Protein-encased chromophores that photosensitize the production of reactive oxygen species, ROS, have been the center of recent activity in studies of oxidative stress. One potential attribute of such systems is that the local environment surrounding the chromophore, and that determines the chromophore's photophysics, ideally remains constant and independent of the global environment into which the system is placed. Therefore, a protein-encased sensitizer localized in the mitochondria would arguably have the same photophysics as that protein-encased sensitizer at the plasma membrane, for example. One thus obtains a useful tool to study processes modulated by spatially localized ROS. One ROS of interest is singlet oxygen, O2 (a1 Δg ). We recently developed a singlet oxygen photosensitizing protein, SOPP, in which flavin mononucleotide, FMN, is encased in a re-engineered light-oxygen-voltage protein. One goal was to ascertain how a version of this system, SOPP3, which selectively makes O2 (a1 Δg ), in vitro, behaves in a cell. We now demonstrate that SOPP3 undergoes exacerbated irradiation-mediated bleaching when expressed at either the plasma membrane or mitochondria in stable cell lines. We find that the environment around the SOPP3 system affects the bleaching rate, which argues against one of the key suppositions in support of a protein-encased chromophore.

Photophysics of a protein-bound derivative of malachite green that sensitizes the production of singlet oxygen.

Genetically encodable proteins that photosensitize the production of singlet oxygen, O2(a1Δg), will play an increasingly important role in elucidating mechanisms of cellular processes modulated by reactive oxygen species, ROS, and changes in redox balance. In the development of such tools, it is essential to characterize the oxygen-dependent photophysics of the protein-encased chromophore. Of the O2(a1Δg)-photosensitizing systems recently developed, a protein-bound derivative of Malachite Green has several desirable features: (1) it absorbs light at wavelengths longer than those typically absorbed by endogenous molecules, and (2) the chromophore becomes a viable sensitizer only when bound to the activating protein. However, we now demonstrate that the photophysics of this Malachite Green system is not simple. Our data indicate that, with an increase in the concentration of ground-state oxygen, O2(X3Σg-), the yield of O2(a1Δg) does not increase in a proportional manner. Moreover, the lifetime of O2(a1Δg) decreases as the O2(X3Σg-) concentration is increased. One mechanism that could account for our observations involves the concomitant photo-initiated formation of O2(a1Δg) and the superoxide radical anion. We propose that the superoxide ion acts as a dynamic diffusion-dependent quencher to influence the O2(a1Δg) lifetime and as a static quencher within the protein enclosure to influence the measured O2(a1Δg) yield. Thus, in the least, caution should be exercised when using this Malachite Green system to probe mechanisms of ROS-mediated processes. Our results contribute to a better understanding of the general photophysics of protein-bound O2(a1Δg) sensitizers which, in turn, facilitates the further development of these useful mechanistic tools.

Single mutation in a novel bacterial LOV protein yields a singlet oxygen generator.

Mr4511 from Methylobacterium radiotolerans is a 164 amino acid protein built of a flavin mononucleotide (FMN) binding, blue-light responsive LOV (Light, Oxygen, Voltage) core domain plus flanking regions. In contrast to the majority of LOV domains, Mr4511 lacks a tryptophan residue that was previously identified as a major quencher for the FMN triplet state in photosensitizers for singlet oxygen (SO) engineered from these photoreceptors. Here we show that for Mr4511 it is sufficient to only mutate the reactive cysteine responsible for the photocycle (Cys71) in the native protein to generate an efficient SO photosensitizer: both C71S and C71G variants exhibit SO quantum yields of formation, ΦΔ, around 0.2 in air-saturated solutions. Under oxygen saturated conditions, ΦΔ reaches ∼0.5 in deuterated buffer. The introduction of Trp112 in the canonical position for LOV domains dramatically lowers ΦΔ to values comparable to miniSOG, one of the early FMN binding proteins touted as a SO sensitizer. Besides its SO properties, Mr4511 is also exceedingly robust against denaturation with urea and is more photostable than free FMN.

Rational design of genetically encoded singlet oxygen photosensitizing proteins.

Reactive oxygen species (ROS), such as the superoxide anion, the hydroxyl radical and singlet oxygen, can influence cellular processes in many ways. However, the molecular mechanisms of ROS action in cells are still poorly understood. As such, we need to develop tools that can better elucidate ROS behavior in the dynamic environment of a cell. Optogenetics provides one approach to this end. Using a genetically encoded protein-encased photosensitizer, one could produce a given ROS with a controllable yield in a specific intracellular domain or compartment. A palette of ROS sensitizing protein derivatives has emerged and, in this review, we use information gleaned from recent studies to discuss properties that define a 'good' singlet oxygen photosensitizing protein.

Uric Acid: A Less-than-Perfect Probe for Singlet Oxygen.

Uric acid and/or its monoanion has long been used as chemical-trapping agents to demonstrate the presence of singlet oxygen, O2 (a1 Δg ), in aqueous systems. "Oxidative bleaching" of uric acid, generally monitored through changes in the uric acid absorption spectrum, is often used in support of claims for the intermediacy of O2 (a1 Δg ). The bleaching of uric acid has also been used to quantify photosensitized O2 (a1 Δg ) yields in selected systems. Unfortunately, experiments performed to these ends often neglect processes and phenomena that can influence the results obtained. For the present study, we experimentally examined the behavior of uric acid under a variety of conditions relevant to the photoinitiated creation and subsequent removal of O2 (a1 Δg ). Although the oxidative destruction of uric acid can indeed be a useful tool in some cases, we conclude that caution must be exercised such as not to incorrectly interpret the data obtained.

No Photon Wasted: An Efficient and Selective Singlet Oxygen Photosensitizing Protein.

Optogenetics has been, and will continue to be, a boon to mechanistic studies of cellular processes. Genetically encodable proteins that sensitize the production of reactive oxygen species (ROS) are expected to play an increasingly important role, particularly in elucidating mechanisms of temporally and spatially dependent cell signaling. However, a substantial challenge in developing such photosensitizing proteins has been to funnel the optical excitation energy into the initial selective production of only one ROS. Singlet molecular oxygen, O2(a1Δg), is a ROS known to have a wide range of effects on cell function. Nevertheless, mechanistic details of singlet oxygen's behavior in a cell are lacking. On the basis of the rational optimization of a LOV-derived flavoprotein, we now report the development and photophysical characterization of a protein-encased photosensitizer that efficiently and selectively produces singlet oxygen at the expense of other ROS, especially ROS that derive from photoinduced electron transfer reactions. These results set the stage for a plethora of new experiments to elucidate ROS-mediated events in cells.

Singlet Oxygen Photophysics in Liquid Solvents: Converging on a Unified Picture.

Singlet oxygen, O2(a1Δg), the lowest excited electronic state of molecular oxygen, is an omnipresent part of life on earth. It is readily formed through a variety of chemical and photochemical processes, and its unique reactions are important not just as a tool in chemical syntheses but also in processes that range from polymer degradation to signaling in biological cells. For these reasons, O2(a1Δg) has been the subject of intense activity in a broad distribution of scientific fields for the past ∼50 years. The characteristic reactions of O2(a1Δg) kinetically compete with processes that deactivate this excited state to the ground state of oxygen, O2(X3Σg-). Moreover, O2(a1Δg) is ideally monitored using one of these deactivation channels: O2(a1Δg) → O2(X3Σg-) phosphorescence at 1270 nm. Thus, there is ample justification to study and control these competing processes, including those mediated by solvents, and the chemistry community has likewise actively tackled this issue. In themselves, the solvent-mediated radiative and nonradiative transitions between the three lowest-lying electronic states of oxygen [O2(X3Σg-), O2(a1Δg), and O2(b1Σg+)] are relevant to issues at the core of modern chemistry. In the isolated oxygen molecule, these transitions are forbidden by quantum-mechanical selection rules. However, solvent molecules perturb oxygen in such a way as to make these transitions more probable. Most interestingly, the effect of a series of solvents on the O2(X3Σg-)-O2(b1Σg+) transition, for example, can be totally different from the effect of the same series of solvents on the O2(X3Σg-)-O2(a1Δg) transition. Moreover, a given solvent that appreciably increases the probability of a radiative transition generally does not provide a correspondingly viable pathway for nonradiative energy loss, and vice versa. The ∼50 years of experimental work leading to these conclusions were not easy; spectroscopically monitoring such weak and low-energy transitions in time-resolved experiments is challenging. Consequently, results obtained from different laboratories often were not consistent. In turn, attempts to interpret molecular events were often simplistic and/or misguided. However, over the recent past, increasingly accurate experiments have converged on a base of credible data, finally forming a consistent picture of this system that is resonant with theoretical models. The concepts involved encompass a large fraction of chemistry's fundamental lexicon, e.g., spin-orbit coupling, state mixing, quantum tunneling, electronic-to-vibrational energy transfer, activation barriers, collision complexes, and charge-transfer interactions. In this Account, we provide an explanatory overview of the ways in which a given solvent will perturb the radiative and nonradiative transitions between the O2(X3Σg-), O2(a1Δg), and O2(b1Σg+) states.

Monitoring Interfacial Lipid Oxidation in Oil-in-Water Emulsions Using Spatially Resolved Optical Techniques.

The oxidation of lipids is an important phenomenon with ramifications for disciplines that range from food science to cell biology. The development and characterization of tools and techniques to monitor lipid oxidation are thus relevant. Of particular significance in this regard are tools that facilitate the study of oxidations at interfaces in heterogeneous samples (e.g., oil-in-water emulsions, cell membranes). In this article, we establish a proof-of-principle for methods to initiate and then monitor such oxidations with high spatial resolution. The experiments were performed using oil-in-water emulsions of polyunsaturated fatty acids (PUFAs) prepared from cod liver oil. We produced singlet oxygen at a point near the oil-water interface of a given PUFA droplet in a spatially localized two-photon photosensitized process. We then followed the oxidation reactions initiated by this process with the fluorescence-based imaging technique of structured illumination microscopy (SIM). We conclude that the approach reported herein has attributes well-suited to the study of lipid oxidation in heterogeneous samples.

Temperature Sensitive Singlet Oxygen Photosensitization by LOV-Derived Fluorescent Flavoproteins.

Optogenetic sensitizers that selectively produce a given reactive oxygen species (ROS) constitute a promising tool for studying cell signaling processes with high levels of spatiotemporal control. However, to harness the full potential of this tool for live cell studies, the photophysics of currently available systems need to be explored further and optimized. Of particular interest in this regard, are the flavoproteins miniSOG and SOPP, both of which (1) contain the chromophore flavin mononucleotide, FMN, in a LOV-derived protein enclosure, and (2) photosensitize the production of singlet oxygen, O2(a1Δg). Here we present an extensive experimental study of the singlet and triplet state photophysics of FMN in SOPP and miniSOG over a physiologically relevant temperature range. Although changes in temperature only affect the singlet excited state photophysics slightly, the processes that influence the deactivation of the triplet excited state are more sensitive to temperature. Most notably, for both proteins, the rate constant for quenching of 3FMN by ground state oxygen, O2(X3Σg-), increases ∼10-fold upon increasing the temperature from 10 to 43 °C, while the oxygen-independent channels of triplet state deactivation are less affected. As a consequence, this increase in temperature results in higher yields of O2(a1Δg) formation for both SOPP and miniSOG. We also show that the quantum yields of O2(a1Δg) production by both miniSOG and SOPP are mainly limited by the fraction of FMN triplet states quenched by O2(X3Σg-). The results presented herein provide a much-needed quantitative framework that will facilitate the future development of optogenetic ROS sensitizers.

Azadioxatriangulenium and Diazaoxatriangulenium: Quantum Yields and Fundamental Photophysical Properties.

Over the last decade, we have investigated and exploited the photophysical properties of triangulenium dyes. Azadioxatriangulenium (ADOTA) and diazaoxatriangulenium (DAOTA), in particular, have features that make them useful in various fluorescence-based technologies (e.g., bioimaging). Through our work with ADOTA and DAOTA, we became aware that the reported fluorescence quantum yields (ϕfl) for these dyes are lower than their actual values. We thus set out to further investigate the fundamental structure-property relationships in these unique conjugated cationic systems. The nonradiative processes in the systems were explored using transient absorption spectroscopy and time-resolved emission spectroscopy in combination with computational chemistry. The influence of molecular oxygen on the fluorescence properties was explored, and the singlet oxygen sensitization efficiencies of ADOTA and DAOTA were determined. We conclude that, for these dyes, the amount of nonradiative deactivation of the first excited singlet state (S1) of the azaoxa-triangulenium fluorophores is low, that the rate of such deactivation is slower than what is observed in common cationic dyes, that there are no observable radiative transitions occurring from the first excited triplet state (T1) of these dyes, and that the efficiency of sensitized singlet oxygen production is low (Ï•Δ ≤ 10%). These photophysical results provide a solid base upon which technological applications of these fluorescent dyes can be built.

A ligand substituted tungsten iodide cluster: luminescence vs. singlet oxygen production.

Octahedral tungsten iodide clusters equipped with apical ligands (L) are synthesized to implement substantial photophysical properties. The [W6I8(CF3COO)6]2- cluster reported herein is the first example of a family of ligand substituted [W6I8L6]2- clusters. Such compounds are expected to exhibit a rich photochemistry in which the apical ligands play a crucial role. The versatile solid state and solution phase photophysical properties of (TBA)2[W6I8(CF3COO)6] described herein parallel characteristics obtained in some photophysically active organic compounds, including a broad absorption in the UV/VIS region. Upon irradiation of this compound, a broad red emission is observed in the VIS/NIR region resulting from excited triplet states, and singlet oxygen (a1Δg) is generated in the presence of O2.

Solvent and Heavy-Atom Effects on the O2(X3Σg-) → O2(b1Σg+) Absorption Transition.

The effect of 16 liquid solvents on both the spectrum and molar absorption coefficient of the X3Σg- → b1Σg+ transition in molecular oxygen has been examined. The ability to monitor this weak transition using air or oxygen saturated samples at atmospheric pressure was facilitated by the rapid and efficient O2(b1Σg+) → O2(a1Δg) transition, which allowed the use of O2(a1Δg) phosphorescence as a sensitive probe of O2(b1Σg+) production. The results of these O2(a1Δg) phosphorescence experiments are consistent with the results of independent experiments in which the O2(a1Δg) thus produced was "trapped" via a chemical reaction. The data recorded were used to calculate rate constants for the O2(b1Σg+) → O2(X3Σg-) radiative transition, a parameter that is otherwise difficult to directly obtain from such a wide range of solvents using O2(b1Σg+) → O2(X3Σg-) phosphorescence. The data show that the response of the O2(b1Σg+) → O2(X3Σg-) radiative transition to solvent is not the same as that of the O2(b1Σg+) → O2(a1Δg) and O2(a1Δg) → O2(X3Σg-) radiative transitions, both of which have been extensively examined over the years. However, our data are consistent with a theoretical model proposed by Minaev for the effect of solvent on radiative transitions in oxygen and, as such, arguably provide one of the final chapters in describing a system that has challenged the scientific community for years.

Solvent-dependent singlet oxygen lifetimes: temperature effects implicate tunneling and charge-transfer interactions.

The effect of solvent on the lifetime of singlet oxygen, O2(a(1)Δg), particularly the pronounced H/D solvent isotope effect, has drawn the attention of chemists for almost 50 years. The currently accepted model for this phenomenon is built on a foundation in which the electronic excitation energy of O2(a(1)Δg) is transferred to vibrational modes in a solvent molecule, with oxygen returning to its ground electronic state, O2(X(3)Σg(-)). This model of electronic-to-vibrational (e-to-v) energy transfer specifically focusses on the solvent as a "sink" for the excitation energy of O2(a(1)Δg). On the basis of temperature-dependent changes in the solvent-mediated O2(a(1)Δg) lifetime, we demonstrate that this energy-sink-based model has limitations and needs to be re-formulated. We now show that the effect of solvent on the O2(a(1)Δg) lifetime is more reasonably interpreted by considering an activation barrier that reflects the extent to which a solvent molecule perturbs the forbidden O2(a(1)Δg) → O2(X(3)Σg(-)) transition. For a given solvent molecule, this barrier reflects contributions from (a) the oxygen-solvent charge transfer state that mediates nonradiative coupling between the O2(a(1)Δg) and O2(X(3)Σg(-)) states, and (b) vibrations of specific bonds in the solvent molecule. The latter establishes connectivity to the desirable features of the energy-sink-based model. Moreover, temperature-dependent H/D solvent isotope effects imply that tunneling through this barrier plays a role in the mechanism for O2(a(1)Δg) deactivation, even at room temperature. Although we focus on a long-standing problem involving O2(a(1)Δg), our results and interpretation touch fundamental issues of interest to chemists at large.

Exerting better control and specificity with singlet oxygen experiments in live mammalian cells.

Singlet molecular oxygen, O2(a1Δg), is a Reactive Oxygen Species, ROS, that acts as a signaling and/or perturbing agent in mammalian cells, influencing processes that range from cell proliferation to cell death. Although the importance of O2(a1Δg) in this regard is acknowledged, an understanding of the targets and mechanisms of O2(a1Δg) action is inadequate. Thus, methods that better facilitate studies of O2(a1Δg) in mammalian cells are highly desired. This is particularly important because, as a consequence of its chemistry in a cell, O2(a1Δg) can spawn the generation of other ROS (e.g., the hydroxyl radical) that, in turn, can have a unique influence on cell behavior and function. Therefore, exerting better control and specificity in O2(a1Δg) experiments ultimately reduces the number of variables in general studies to unravel the details of ROS-dependent cell dynamics. In this article, we summarize our recent efforts to produce O2(a1Δg) with increased control and selectivity in microscope-based single-cell experiments. The topics addressed include (1) two-photon excitation of a photosensitizer using a focused laser to create a spatially-localized volume of O2(a1Δg) with sub-cellular dimensions, (2) protein-encapsulated photosensitizers that can be localized in a specific cellular domain using genetic engineering, and (3) direct excitation of dissolved oxygen in sensitizer-free experiments to selectively produce O2(a1Δg) at the expense of other ROS. We also comment on our recent efforts to monitor O2(a1Δg) in cells and to monitor the cell's response to O2(a1Δg).

Intracellular singlet oxygen photosensitizers: on the road to solving the problems of sensitizer degradation, bleaching and relocalization.

Selected singlet oxygen photosensitizers have been examined from the perspective of obtaining a molecule that is sufficiently stable under conditions currently employed to study singlet oxygen behavior in single mammalian cells. Reasonable predictions about intracellular sensitizer stability can be made based on solution phase experiments that approximate the intracellular environment (e.g., solutions containing proteins). Nevertheless, attempts to construct a stable sensitizer based solely on the expected reactivity of a given functional group with singlet oxygen are generally not sufficient for experiments in cells; it is difficult to construct a suitable chromophore that is impervious to all of the secondary and/or competing degradative processes that are present in the intracellular environment. On the other hand, prospects are reasonably positive when one considers the use of a sensitizer encapsulated in a specific protein; the local environment of the chromophore is controlled, degradation as a consequence of bimolecular reactions can be mitigated, and genetic engineering can be used to localize the encapsulated sensitizer in a given cellular domain. Also, the option of directly exciting oxygen in sensitizer-free experiments provides a useful complementary tool. These latter systems bode well with respect to obtaining more accurate control of the "dose" of singlet oxygen used to perturb a cell; a parameter that currently limits mechanistic studies of singlet-oxygen-mediated cell signaling.