Multiple redox switches of the SARS-CoV-2 main protease in vitro provide opportunities for drug design.

Besides vaccines, the development of antiviral drugs targeting SARS-CoV-2 is critical for preventing future COVID outbreaks. The SARS-CoV-2 main protease (Mpro), a cysteine protease with essential functions in viral replication, has been validated as an effective drug target. Here, we show that Mpro is subject to redox regulation in vitro and reversibly switches between the enzymatically active dimer and the functionally dormant monomer through redox modifications of cysteine residues. These include a disulfide-dithiol switch between the catalytic cysteine C145 and cysteine C117, and generation of an allosteric cysteine-lysine-cysteine SONOS bridge that is required for structural stability under oxidative stress conditions, such as those exerted by the innate immune system. We identify homo- and heterobifunctional reagents that mimic the redox switching and inhibit Mpro activity. The discovered redox switches are conserved in main proteases from other coronaviruses, e.g. MERS-CoV and SARS-CoV, indicating their potential as common druggable sites.

Mechanisms of Cysteine-Lysine Covalent Linkage-The Role of Reactive Oxygen Species and Competition with Disulfide Bonds.

Recently, a new naturally occurring covalent linkage was characterised, involving a cysteine and a lysine, bridged through an oxygen atom. The latter was dubbed as the NOS bond, reflecting the individual atoms involved in this uncommon bond which finds little parallel in lab chemistry. It is found to form under oxidising conditions and is reversible upon addition of reducing agents. Further studies have identified the bond in crystal structures across a variety of systems and organisms, potentially playing an important role in regulation, cellular defense and replication. Not only that, double NOS bonds have been identified and even found to be competitive in relation to the formation of disulfide bonds. This raises several questions about how this exotic bond comes to be, what are the intermediates involved in its formation and how it competes with other pathways of sulfide oxidation. With this objective in mind, we revisited our first proposed mechanism for the reaction with model electronic structure calculations, adding information about the reactivity with alternative reactive oxygen species and other potential competing products of oxidation. We present a network with more than 30 reactions which provides one of the most encompassing pictures for cysteine oxidation pathways to date.

Modulating Secondary Structure Motifs Through Photo-Labile Peptide Staples.

Peptide-protein interactions (PPIs) are facilitated by the well-defined three-dimensional structure of bioactive peptides, interesting compounds for the development of new therapeutic agents. Their secondary structure and thus their propensity to engage in PPIs can be influenced by the introduction of peptide staples on the side chains. In particular, light-controlled staples based on azobenzene photoswitches and their structural influence on helical peptides have been studied extensively. In contrast, photolabile staples bearing photocages as a structural key motif, have mainly been used to block supramolecular interactions. Their influence on the secondary structure of the target peptide is under-investigated. Thus, in this study we use a combination of spectroscopic techniques and in silico simulations to systematically study a series of helical peptides with varying length of the photo-labile staple to obtain a detailed insight into the structure-property relationship in such photoresponsive biomolecules.

Anesthetic Management of Adults With Epidermolysis Bullosa.

Epidermolysis bullosa (EB) is a group of rare, inherited diseases characterized by skin fragility and multiorgan system involvement that presents many anesthetic challenges. Although the literature regarding anesthetic management focuses primarily on the pediatric population, as life expectancy improves, adult patients with EB are more frequently undergoing anesthesia in nonpediatric hospital settings. Safe anesthetic management of adult patients with EB requires familiarity with the complex and heterogeneous nature of this disease, especially with regard to complications that may worsen during adulthood. General, neuraxial, and regional anesthetics have all been used safely in patients with EB. A thorough preoperative evaluation is essential. Preoperative testing should be guided by EB subtype, clinical manifestations, and extracutaneous complications. Advanced planning and multidisciplinary coordination are necessary with regard to timing and operative plan. Meticulous preparation of the operating room and education of all perioperative staff members is critical. Intraoperatively, utmost care must be taken to avoid all adhesives, shear forces, and friction to the skin and mucosa. Special precautions must be taken with patient positioning, and standard anesthesia monitors must be modified. Airway management is often difficult, and progressive airway deterioration can occur in adults with EB over time. A smooth induction, emergence, and postoperative course are necessary to minimize blister formation from excess patient movement. With careful planning, preparation, and precautions, adult patients with EB can safely undergo anesthesia.

Transnasal Humidified Rapid-Insufflation Ventilatory Exchange for Difficult Airway Management in Adults With Recessive Dystrophic Epidermolysis Bullosa: A Case Series.

Airway management of adult patients with recessive dystrophic epidermolysis bullosa presents significant challenges associated with tissue fragility and distortion of airway anatomy. This retrospective case series describes 11 adult patients with recessive dystrophic epidermolysis bullosa and difficult airways undergoing 24 general anesthetics in which transnasal humidified rapid-insufflation ventilatory exchange was used for preoxygenation and apneic oxygenation. Despite an average time to intubation of over 6 minutes, transnasal humidified rapid-insufflation ventilatory exchange provided oxygenation before endotracheal intubation without the need for bag-mask ventilation or supraglottic airway ventilation, facilitating smooth and atraumatic flexible scope intubation. There were no major adverse events.

Ultrafast Charge Transfer and Structural Dynamics Following Outer-Valence Ionization of a Halogen-Bonded Dimer.

We study the temporal evolution of the CH2O···ClF halogen-bonded dimer following vertical ionization out of outer-valence molecular orbitals on a femtosecond time scale, employing mixed quantum-classical molecular dynamics simulations. The charge density pattern in the ground state that is suitable for the formation of the ground-state halogen bond can be changed upon ionization. Depending on the molecular orbital that gets ionized, the change in the charge density transiently strengthens or weakens the halogen bond through altering the electrostatic interaction. A transient increase in the halogen bond strength is observed if the ionization enhances the positive charge on the halogen atom provided that the electron donor site possesses some negative charge. The evolution of the system following ionization is driven by energetic stabilization through transferring the electronic charge from the halogen bond acceptor/electron donor (CH2O) to the halogen bond donor/electron acceptor (ClF). The charge transfer oscillations are at the same time governed by the covalent bond vibrations.

Challenges in XUV Photochemistry Simulations: A Case Study on Ultrafast Fragmentation Dynamics of the Benzene Radical Cation.

The challenges of simulating extreme ultraviolet (XUV)-induced dissociation dynamics of organic molecules on a multitude of coupled potential energy surfaces are discussed for the prototypical photoionization of benzene. The prospects of Koopmans' theorem-based electronic structure calculations in combination with classical trajectories and Tully's fewest switches surface hopping are explored. It is found that a Koopmans' theorem-based approach overestimates the CH dissociation barrier and thus underestimates the fragmentation yield. However, the nonadiabatic population dynamics are in good agreement with previous approaches, indicating that the Koopmans' theorem based potentials are well described around the Franck-Condon point. This is explicitly tested for the ground state potential of the benzene cation employing CASPT2 calculations, for which very good agreement is found. This work highlights the need for efficient electronic structure approaches that can treat medium-sized organic molecules with a multitude of coupled excited states and several dissociation channels.

Anion-π Interactions in Flavoproteins Involve a Substantial Charge-Transfer Component.

Anion-π interactions have been shown to stabilize flavoproteins and to regulate the redox potential of the flavin cofactor. They are commonly attributed to electrostatic forces. Herein we show that anion-flavin interactions can have a substantial charge-transfer component. Our conclusion emanates from a multi-approach theoretical analysis and is backed by previously reported observations of absorption bands, originating from charge transfer between oxidized flavin and proximate cysteine thiolate groups. This partial covalency of anion-flavin contacts renders classical simulations of flavoproteins questionable.

Lone-pair-π interactions: analysis of the physical origin and biological implications.

Lone-pair-π (lp-π) interactions have been suggested to stabilize DNA and protein structures, and to participate in the formation of DNA-protein complexes. To elucidate their physical origin, we have carried out a theoretical multi-approach analysis of two biologically relevant model systems, water-indole and water-uracil complexes, which we compared with the structurally similar chloride-tetracyanobenzene (TCB) complex previously shown to contain a strong charge-transfer (CT) binding component. We demonstrate that the CT component in lp-π interactions between water and indole/uracil is significantly smaller than that stabilizing the Cl(-)-TCB reference system. The strong lp(Cl(-))-π(TCB) orbital interaction is characterized by a small energy gap and an efficient lp-π* overlap. In contrast, in lp-π interactions between water and indole or uracil, the corresponding energy gap is larger and the overlap less efficient. As a result, water-uracil and water-indole interactions are weak forces composed by smaller contributions from all energy components: electrostatics, polarization, dispersion, and charge transfer. In addition, indole exhibits a negative electrostatic potential at its π-face, making lp-π interactions less favorable than O-Hπ hydrogen bonding. Consequently, some of the water-tryptophan contacts observed in X-ray structures of proteins and previously interpreted as lp-π interactions [Luisi, et al., Proteins, 2004, 57, 1-8], might in fact arise from O-Hπ hydrogen bonding.

Designing a New Class of Bases for Nucleic Acid Quadruplexes and Quadruplex-Active Ligands.

A new class of quadruplex nucleobases, derived from 3-deazaguanine, has been designed for various applications as smart quadruplex ligands as well as quadruplex-based aptamers, receptors, and sensors. An efficient strategy for modifying the guanine quadruplex core has been developed and tested by using quantum chemistry methods. Several potential guanine derivatives modified at the 3- or 8-position or both are analyzed, and the results compared to reference systems containing natural guanine. Analysis of the formation energies (BLYP-D3(BJ)/def2-TZVPP level of theory, in combination with the COSMO model for water) in model systems consisting of two and three stacked tetrads with Na(+) /K(+) ion(s) inside the internal channel indicates that the formation of structures with 3-halo-3-deazaguanine bases leads to a substantial gain in energy, as compared to the corresponding reference guanine complexes. The results cast light on changes in the noncovalent interactions (hydrogen bonding, stacking, and ion coordination) in a quadruplex stem upon modification of the guanine core. In particular, the enhanced stability of the modified quadruplexes was shown to originate mainly from increased π-π stacking. Our study suggests the 3-halo-3-deazaguanine skeleton as a potential building unit for quadruplex systems and smart G-quadruplex ligands.

The impact of protonation and deprotonation of 3-methyl-2'-deoxyadenosine on N-glycosidic bond cleavage.

The enzyme-substrate contacts that are believed to be involved in depurination by proton transfer have been modelled by protonation and deprotonation of 3-methyl-2'-deoxyadenosine (3-MDA) using quantum mechanical calculations in the gas-phase and solution media. The change in the charge distribution on the sugar ring and nucleobase that is introduced by the protonation and deprotonation strongly affects the N-glycosidic bond length. The unimolecular cleavage and hydrolysis of the N-glycosidic bond, involving D(N)*A(N) and A(N)D(N) pathways, have been considered at several levels of theory. The trend in the energy barriers is A(N)D(N) > cleavage > D(N)*A(N). All probable proton transfer reactions resulting from enzyme-substrate contacts do not facilitate the N-glycosidic bond cleavage of 3-MDA. The deprotonation of 3-MDA that may result from the interaction between H6 and enzyme do not facilitate bond cleavage. The protonation at N7 induces more positive charge on the sugar ring and further facilitates the depurination relative to the protonation at N1. The changes in the charges calculated on the ribose and nucleobase are in good relationship with the C1'-C2', C1'-O4', and N-glycosidic bond lengths along the cleavage. The change in energy barrier ΔE of glycosidic bond cleavage from the gas-phase to solution media strongly depends on the charge of the species.