Stabilization of the Dimeric State of SARS-CoV-2 Main Protease by GC376 and Nirmatrelvir.

The main protease (Mpro or 3CLpro) is an enzyme that is evolutionarily conserved among different genera of coronaviruses. As it is essential for processing and maturing viral polyproteins, Mpro has been identified as a promising target for the development of broad-spectrum drugs against coronaviruses. Like SARS-CoV and MERS-CoV, the mature and active form of SARS-CoV-2 Mpro is a dimer composed of identical subunits, each with a single active site. Individual monomers, however, have very low or no catalytic activity. As such, inhibition of Mpro can be achieved by molecules that target the substrate binding pocket to block catalytic activity or target the dimerization process. In this study, we investigated GC376, a transition-state analog inhibitor of the main protease of feline infectious peritonitis coronavirus, and Nirmatrelvir (NMV), an oral, bioavailable SARS-CoV-2 Mpro inhibitor with pan-human coronavirus antiviral activity. Our results show that both GC376 and NMV are capable of strongly binding to SARS-CoV-2 Mpro and altering the monomer-dimer equilibrium by stabilizing the dimeric state. This behavior is proposed to be related to a structured hydrogen-bond network established at the Mpro active site, where hydrogen bonds between Ser1' and Glu166/Phe140 are formed in addition to those achieved by the latter residues with GC376 or NMV.

14th International Conference on Synchrotron Radiation Instrumentation (SRI 2021), 28 March to 1 April 2022

The International Conference on Synchrotron Radiation Instrumentation (SRI) is a unique and significant international forum held every three years in the community of synchrotron radiation (SR) and free electron lasers (FEL). It is the prime forum for fostering connections between cutting-edge synchrotron radiation instrumentation, science, and the requirements of the user community. The SRI 2021 had originally been scheduled to take place in Hamburg in summer 2021. Due to the COVID-19 pandemic, it was postponed to 2022 and held as an online event.More than 1160 international participants from 25 countries met virtually at the SRI 2021. In nearly 290 talks and 450 posters, latest results were presented. Although it was an online-only conference, lively discussions took place in the nearly 40 parallel sessions, and the eight poster sessions were also very well attended.The main topics of the SRI conference were: new SR and FEL facilities, update plans of these facilities, and recent developments in various instrumentation areas like beamline design, X-ray optics, sample environments, detectors and spectrometers, data acquisition, and data analysis techniques or automation. These innovations contributed to new results for a wide range of experimental techniques and scientific applications such as X-ray scattering and spectroscopy, bio- and scanning imaging, structural biology crystallography, coherent techniques, or in-situ/operando methods. A dedicated session concerned industrial applications of synchrotron radiation.The field of synchrotron radiation instrumentation is currently seeing very active development due to various factors. Firstly, the number of SR sources world-wide is increasing significantly, with new sources in particular in Europe and in Asia. Secondly, a new generation of storage rings with new multi-bend achromat lattices are being implemented at a growing number of existing facilities. These facilities offer a significant increase of brilliance and coherence and thereby lead to new and improved applications of synchrotron radiation, in particular in the areas of imaging and high spatial resolution. Thirdly, the increase of soft and hard X-ray FEL sources worldwide and the maturation of their experimental techniques and scientific applications is the background for a strongly increasing number of developments for ultrafast time-resolved investigations of dynamic behaviour of materials and reactions. Most of the keynote speakers and many invited and contributed talks or posters at the conference showed new results directly related to these three major developments.Lists of International Advisory Committee (listed by facility), Scientific Programme Committee (listed by facility), Local Organising Committee (listed by facility) are available in this PDF.

Adopting Intrinsic Hydrophilic Thermoplastic Starch Composites to Fabricate Antifogging Sustainable Films with High Antibiosis and Transparency

Fogging on transparent surfaces such as goggles causes a series of hazards to users. To fabricate antifogging and low-haze transparent renewable polymer materials, intrinsic hydrophilicity with high water adsorption capability of thermoplastic starch (TPS) had been adopted. Strikingly, when benzoic acid (BA) was blended with thermoplastic starch (TPS-BA), the haze of TPS-BA was only 7.8% when it suffered the cold and warm method of antifogging measurement with 87% transmittance. Simultaneously, TPS-BA achieved an 18 mm inhibition zone for Staphylococcus aureus. To reveal the antifogging mechanism of TPS-BA films, the surficial and interior structure features were evaluated by three-dimensional optical scanner, scanning electron microscopy (SEM), contact angle testing, small-angle X-ray scattering (SAXS), X-ray diffraction (XRD), temperature-dependent Fourier transform infrared (FTIR), dynamic mechanical analysis (DMA), and so on. The incorporation of BA resulted in the roughness (Rq), water contact angle (WCA), and crystallinity of the TPS-BA film decreasing from 6.5 to 0.68 μm, 65.1 to 39.9°, and 13.6 to 6.3%, respectively. The amorphous matrix and smooth surface reduced the scattered light, allowing the TPS-BA film to achieve low haze performance and high transmittance. Importantly, the diversified and weakened hydrogen bonds formed among starch, BA, and glycerol could inhibit the formation of starch crystalline regions and allowed hydroxyl groups to quickly bond with water. Thus, when TPS-BA is placed in a high-humidity surrounding, an "expressway"is constructed for water molecules diffusing into the TPS-BA matrix. This novel low-haze, antifogging, sustainable, and facilely fabricated TPS with antibacterial properties is a promising candidate in disposable medical goggles to fight against COVID-19. © 2021 American Chemical Society. All rights reserved.

Fully automated measurement system for temperature-dependent X-ray total scattering at beamline BL04B2 at SPring-8.

Data-driven approaches in materials science demand the collection of large amounts of data on the target materials at synchrotron beamlines. To accurately gather suitable experimental data, it is essential to establish fully automated measurement systems to reduce the workload of the beamline staff. Moreover, the recent COVID-19 pandemic has further emphasized the necessity of automated and/or remote measurements at synchrotron beamlines. Here, the installation of a new sample changer combined with a high-temperature furnace and a fully automated alignment system on beamline BL04B2 at SPring-8 is reported. The system allows X-ray total scattering measurements of up to 21 samples at different temperatures (from room temperature to 1200°C) to be conducted without any human assistance.

Hyaluronic Acid-Dexamethasone Nanoparticles for Local Adjunct Therapy of Lung Inflammation.

The delivery of a dexamethasone formulation directly into the lung appears as an appropriate strategy to strengthen the systemic administration, reducing the dosage in the treatment of lung severe inflammations. For this purpose, a hyaluronic acid-dexamethasone formulation was developed, affording an inhalable reconstituted nanosuspension suitable to be aerosolized. The physico-chemical and biopharmaceutical properties of the formulation were tested: size, stability, loading of the spray-dried dry powder, reconstitution capability upon redispersion in aqueous media. Detailed structural insights on nanoparticles after reconstitution were obtained by light and X-ray scattering techniques. (1) The size of the nanoparticles, around 200 nm, is in the proper range for a possible engulfment by macrophages. (2) Their structure is of the core-shell type, hosting dexamethasone nanocrystals inside and carrying hyaluronic acid chains on the surface. This specific structure allows for nanosuspension stability and provides nanoparticles with muco-inert properties. (3) The nanosuspension can be efficiently aerosolized, allowing for a high drug fraction potentially reaching the deep lung. Thus, this formulation represents a promising tool for the lung administration via nebulization directly in the pipe of ventilators, to be used as such or as adjunct therapy for severe lung inflammation.

Structural deformability induced in proteins of potential interest associated with COVID-19 by binding of homologues present in ivermectin: Comparative study based in elastic networks models.

The COVID-19 pandemic has accelerated the study of the potential of multi-target drugs (MTDs). The mixture of homologues called ivermectin (avermectin-B1a + avermectin-B1b) has been shown to be a MTD with potential antiviral activity against SARS-CoV-2 in vitro. However, there are few reports on the effect of each homologue on the flexibility and stiffness of proteins associated with COVID-19, described as ivermectin targets. We observed that each homologue was stably bound to the proteins studied and was able to induce detectable changes with Elastic Network Models (ENM). The perturbations induced by each homologue were characteristic of each compound and, in turn, were represented by a disruption of native intramolecular networks (interactions between residues). The homologues were able to slightly modify the conformation and stability of the connection points between the Cα atoms of the residues that make up the structural network of proteins (nodes), compared to free proteins. Each homologue was able to modified differently the distribution of quasi-rigid regions of the proteins, which could theoretically alter their biological activities. These results could provide a biophysical-computational view of the potential MTD mechanism that has been reported for ivermectin.

Cationic Liposomes as Vectors for Nucleic Acid and Hydrophobic Drug Therapeutics.

Cationic liposomes (CLs) are effective carriers of a variety of therapeutics. Their applications as vectors of nucleic acids (NAs), from long DNA and mRNA to short interfering RNA (siRNA), have been pursued for decades to realize the promise of gene therapy, with approvals of the siRNA therapeutic patisiran and two mRNA vaccines against COVID-19 as recent milestones. The long-term goal of developing optimized CL-based NA carriers for a broad range of medical applications requires a comprehensive understanding of the structure of these vectors and their interactions with cell membranes and components that lead to the release and activity of the NAs within the cell. Structure-activity relationships of lipids for CL-based NA and drug delivery must take into account that these lipids act not individually but as components of an assembly of many molecules. This review summarizes our current understanding of how the choice of the constituting lipids governs the structure of their CL-NA self-assemblies, which constitute distinct liquid crystalline phases, and the relation of these structures to their efficacy for delivery. In addition, we review progress toward CL-NA nanoparticles for targeted NA delivery in vivo and close with an outlook on CL-based carriers of hydrophobic drugs, which may eventually lead to combination therapies with NAs and drugs for cancer and other diseases.

Structure and Function of N-Terminal Zinc Finger Domain of SARS-CoV-2 NSP2.

SARS-CoV-2 has become a global pandemic threatening human health and safety. It is urgent to find effective therapeutic agents and targets with the continuous emergence of novel mutant strains. The knowledge of the molecular basis and pathogenesis of SARS-CoV-2 in host cells requires to be understood comprehensively. The unknown structure and function of nsp2 have hindered our understanding of its role in SARS-CoV-2 infection. Here, we report the crystal structure of the N-terminal of SARS-CoV-2 nsp2 to a high resolution of 1.96 Å. This novel structure contains three zinc fingers, belonging to the C2H2, C4, and C2HC types, respectively. Structure analysis suggests that nsp2 may be involved in binding nucleic acids and regulating intracellular signaling pathways. The binding to single or double-stranded nucleic acids was mainly through the large positively charged region on the surface of nsp2, and K111, K112, K113 were key residues. Our findings lay the foundation for a better understanding of the relationship between structure and function for nsp2. It is helpful to make full use of nsp2 as further research and development of antiviral targets and drug design.

Surfactants - Compounds for inactivation of SARS-CoV-2 and other enveloped viruses.

We provide here a general view on the interactions of surfactants with viruses, with a particular emphasis on how such interactions can be controlled and employed for inhibiting the infectivity of enveloped viruses, including coronaviruses. The aim is to provide to interested scientists from different fields, including chemistry, physics, biochemistry, and medicine, an overview of the basic properties of surfactants and (corona)viruses, which are relevant to understanding the interactions between the two. Various types of interactions between surfactant and virus are important, and they act on different components of a virus such as the lipid envelope, membrane (envelope) proteins and nucleocapsid proteins. Accordingly, this cannot be a detailed account of all relevant aspects but instead a summary that bridges between the different disciplines. We describe concepts and cover a selection of the relevant literature as an incentive for diving deeper into the relevant material. Our focus is on more recent developments around the COVID-19 pandemic caused by SARS-CoV-2, applications of surfactants against the virus, and on the potential future use of surfactants for pandemic relief. We also cover the most important aspects of the historical development of using surfactants in combatting virus infections. We conclude that surfactants are already playing very important roles in various directions of defence against viruses, either directly, as in disinfection, or as carrier components of drug delivery systems for prophylaxis or treatment. By designing tailor-made surfactants, and consequently, advanced formulations, one can expect more and more effective use of surfactants, either directly as antiviral compounds or as part of more complex formulations.

Rigid monoclonal antibodies improve detection of SARS-CoV-2 nucleocapsid protein.

Monoclonal antibodies (mAbs) are the basis of treatments and diagnostics for pathogens and other biological phenomena. We conducted a structural characterization of mAbs against the N-terminal domain of nucleocapsid protein (NPNTD) from SARS-CoV-2 using small-angle X-ray scattering and transmission electron microscopy. Our solution-based results distinguished the mAbs' flexibility and how this flexibility affects the assembly of multiple mAbs on an antigen. By pairing two mAbs that bind different epitopes on the NPNTD, we show that flexible mAbs form a closed sandwich-like complex. With rigid mAbs, a juxtaposition of the antigen-binding fragments is prevented, enforcing a linear arrangement of the mAb pair, which facilitates further mAb polymerization. In a modified sandwich enzyme-linked immunosorbent assay, we show that rigid mAb-pairings with linear polymerization led to increased NPNTD detection sensitivity. These enhancements can expedite the development of more sensitive and selective antigen-detecting point-of-care lateral flow devices, which are critical for early diagnosis and epidemiological studies of SARS-CoV-2 and other pathogens.