Structural and functional characterizations of infectivity and immune evasion of SARS-CoV-2 Omicron.

The SARS-CoV-2 Omicron variant with increased fitness is spreading rapidly worldwide. Analysis of cryo-EM structures of the spike (S) from Omicron reveals amino acid substitutions forging interactions that stably maintain an active conformation for receptor recognition. The relatively more compact domain organization confers improved stability and enhances attachment but compromises the efficiency of the viral fusion step. Alterations in local conformation, charge, and hydrophobic microenvironments underpin the modulation of the epitopes such that they are not recognized by most NTD- and RBD-antibodies, facilitating viral immune escape. Structure of the Omicron S bound with human ACE2, together with the analysis of sequence conservation in ACE2 binding region of 25 sarbecovirus members, as well as heatmaps of the immunogenic sites and their corresponding mutational frequencies, sheds light on conserved and structurally restrained regions that can be used for the development of broad-spectrum vaccines and therapeutics.

Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants.

Omicron (B.1.1.529), the most heavily mutated SARS-CoV-2 variant so far, is highly resistant to neutralizing antibodies, raising concerns about the effectiveness of antibody therapies and vaccines1,2. Here we examined whether sera from individuals who received two or three doses of inactivated SARS-CoV-2 vaccine could neutralize authentic Omicron. The seroconversion rates of neutralizing antibodies were 3.3% (2 out of 60) and 95% (57 out of 60) for individuals who had received 2 and 3 doses of vaccine, respectively. For recipients of three vaccine doses, the geometric mean neutralization antibody titre for Omicron was 16.5-fold lower than for the ancestral virus (254). We isolated 323 human monoclonal antibodies derived from memory B cells in triple vaccinees, half of which recognized the receptor-binding domain, and showed that a subset (24 out of 163) potently neutralized all SARS-CoV-2 variants of concern, including Omicron. Therapeutic treatments with representative broadly neutralizing monoclonal antibodies were highly protective against infection of mice with SARS-CoV-2 Beta (B.1.351) and Omicron. Atomic structures of the Omicron spike protein in complex with three classes of antibodies that were active against all five variants of concern defined the binding and neutralizing determinants and revealed a key antibody escape site, G446S, that confers greater resistance to a class of antibodies that bind on the right shoulder of the receptor-binding domain by altering local conformation at the binding interface. Our results rationalize the use of three-dose immunization regimens and suggest that the fundamental epitopes revealed by these broadly ultrapotent antibodies are rational targets for a universal sarbecovirus vaccine.

Functionalized dual modification of covalent organic framework for efficient and rapid trace heavy metals removal from drinking water.

A key challenge in trace heavy metals removal from drinking water by adsorption technology is to achieve high adsorption capacity and rapid uptake speed of adsorbent. Herein, we report a functionalized double modified covalent organic framework (DMTD-COF-SH) bearing high-density sulfur and nitrogen chelating groups provided simultaneously by 2,5-dimercapto-1,3,4-thiadiazole (DMTD) and 1,2-ethanedithiol, which was prepared via a facile one-pot thiol-ene "click" reaction. PXRD, FTIR, XPS, SEM, BET and 13C MAS NMR confirmed their successful graft, and DMTD was found to be more easily grafted on the COF surface layer than 1,2-ethanedithiol. The as-prepared DMTD-COF-SH showed remarkable adsorption capacity and ultrafast uptake dynamics to trace heavy metals owing to the synergistic effects resulting from densely populated sulfur and nitrogen chelating groups within ordered COF mesopores and at the COF surface. On the basis of the drinking water treatment units standard NSF/ANSI 53-2020, when the adsorbent dosage was 10 mg/30 mL and 20 mg L-1 calcium ions coexisted, the lead concentration decreased from initial 150 µg L-1 to 2.89 µg L-1 within 10 s, far below the allowable limit of world health organization (WHO) drinking water standard (10 µg L-1), and the maximum adsorption capacity meeting the standard attained 14.22 mg g-1. The adsorbent also exhibited excellent stability, wide applicable pH range and outstanding adsorption performance for coexisting trace lead, mercury, cadmium, chromium (VI) and copper in tap water, indicating that the DMTD-COF-SH material has excellent application prospect for trace heavy metals removal from drinking water.

A highly immunogenic live-attenuated vaccine candidate prevents SARS-CoV-2 infection and transmission in hamsters.

The highly pathogenic and readily transmissible SARS-CoV-2 has caused a global coronavirus pandemic, urgently requiring effective countermeasures against its rapid expansion. All available vaccine platforms are being used to generate safe and effective COVID-19 vaccines. Here, we generated a live-attenuated candidate vaccine strain by serial passaging of a SARS-CoV-2 clinical isolate in Vero cells. Deep sequencing revealed the dynamic adaptation of SARS-CoV-2 in Vero cells, resulting in a stable clone with a deletion of seven amino acids (N679SPRRAR685) at the S1/S2 junction of the S protein (named VAS5). VAS5 showed significant attenuation of replication in multiple human cell lines, human airway epithelium organoids, and hACE2 mice. Viral fitness competition assays demonstrated that VAS5 showed specific tropism to Vero cells but decreased fitness in human cells compared with the parental virus. More importantly, a single intranasal injection of VAS5 elicited a high level of neutralizing antibodies and prevented SARS-CoV-2 infection in mice as well as close-contact transmission in golden Syrian hamsters. Structural and biochemical analysis revealed a stable and locked prefusion conformation of the S trimer of VAS5, which most resembles SARS-CoV-2-3Q-2P, an advanced vaccine immunogen (NVAX-CoV2373). Further systematic antigenic profiling and immunogenicity validation confirmed that the VAS5 S trimer presents an enhanced antigenic mimic of the wild-type S trimer. Our results not only provide a potent live-attenuated vaccine candidate against COVID-19 but also clarify the molecular and structural basis for the highly attenuated and super immunogenic phenotype of VAS5.

An ultrapotent pan-ß-coronavirus lineage B (ß-CoV-B) neutralizing antibody locks the receptor-binding domain in closed conformation by targeting its conserved epitope.

New threats posed by the emerging circulating variants of SARS-CoV-2 highlight the need to find conserved neutralizing epitopes for therapeutic antibodies and efficient vaccine design. Here, we identified a receptor-binding domain (RBD)-binding antibody, XG014, which potently neutralizes ß-coronavirus lineage B (ß-CoV-B), including SARS-CoV-2, its circulating variants, SARS-CoV and bat SARSr-CoV WIV1. Interestingly, antibody family members competing with XG014 binding show reduced levels of cross-reactivity and induce antibody-dependent SARS-CoV-2 spike (S) protein-mediated cell-cell fusion, suggesting a unique mode of recognition by XG014. Structural analyses reveal that XG014 recognizes a conserved epitope outside the ACE2 binding site and completely locks RBD in the non-functional "down" conformation, while its family member XG005 directly competes with ACE2 binding and position the RBD "up". Single administration of XG014 is effective in protection against and therapy of SARS-CoV-2 infection in vivo. Our findings suggest the potential to develop XG014 as pan-ß-CoV-B therapeutics and the importance of the XG014 conserved antigenic epitope for designing broadly protective vaccines against ß-CoV-B and newly emerging SARS-CoV-2 variants of concern.

Structure of the HRV-C 3C-Rupintrivir Complex Provides New Insights for Inhibitor Design.

Human rhinoviruses (HRVs) are the predominant infectious agents for the common cold worldwide. The HRV-C species cause severe illnesses in children and are closely related to acute exacerbations of asthma. 3C protease, a highly conserved enzyme, cleaves the viral polyprotein during replication and assists the virus in escaping the host immune system. These key roles make 3C protease an important drug target. A few structures of 3Cs complexed with an irreversible inhibitor rupintrivir have been determined. These structures shed light on the determinants of drug specificity. Here we describe the structures of HRV-C15 3C in free and inhibitor-bound forms. The volume-decreased S1' subsite and half-closed S2 subsite, which were thought to be unique features of enterovirus A 3C proteases, appear in the HRV-C 3C protease. Rupintrivir assumes an "intermediate" conformation in the complex, which might open up additional avenues for the design of potent antiviral inhibitors. Analysis of the features of the three-dimensional structures and the amino acid sequences of 3C proteases suggest new applications for existing drugs.

The neuroprotective effect of schisandrol A on 6-OHDA-induced PD mice may be related to PI3K/AKT and IKK/IκBα/NF-κB pathway.

Parkinson's disease is the second most common neurodegenerative disease. Its main pathological feature is the substantial nigra-striatum dopaminergic neuronal dysfunction, which causes insufficient release of DA, induces motor symptoms, and is accompanied by nonmotor symptoms. Schisandrol A belongs to lignan components and has anti-inflammatory, antioxidant and neuroprotective effects. In this experiment, we injected 6-OHDA into medial forebrain bundle of C57BL/6J male mice to establish the model. The motor function of mice was examined by open field test and pole test, the depression-like behavior of mice was examined by sucrose preference test and the memory function was examined by Y maze. We found that schisandrol A (20 mg/kg/d) could significantly improve the motor symptoms, and alleviate the depression-like symptoms and memory dysfunction of PD mice induced by 6-OHDA. Then we studied the neuroprotective mechanism of schisandrol A by H.E., ELISA assay kits and Western blot. Results showed that schisandrol A may enhance the PI3K/AKT pathway, inhibit the IKK/IκBα/NF-κB pathway, reduce neuronal inflammation and oxidative stress, and enhance the survival of DA neurons in the brain of mice. These results indicate that schisandrol A is expected to be a potential drug for improving Parkinson's disease.

Polysaccharide of Schisandra Chinensis Fructus ameliorates cognitive decline in a mouse model of Alzheimer's disease.

ETHNOPHARMACOLOGICAL RELEVANCE: Polysaccharides is an important ingredient of Schisandra Chinensis Fructus which often appears in ancient prescriptions for forgetfulness or dementia. AIM OF THE STUDY: The purpose of our study is to investigate the effects of polysaccharides of Schisandra Chinensis Fructus (SCP) on animal model of Alzheimer's disease (AD), which is a common disease of dementia, to elucidate the traditional medical theories with modern pharmacological methods and provide a reference for further clarifying its active mechanisms. MATERIALS AND METHODS: Hydrolysates of SCP were analyzed by HPLC. Y-maze, Morris water maze (MWM) were used for evaluating cognition processes of mice. Immunohistochemistry (IHC) was used to detect the deposition of Aß. The levels of cytokine expression including Tumor Necrosis Factor α (TNF-α), interleukin-1ß (IL-1ß) and interleukin-6 (IL-6) in the hippocampus were detected by ELISA kits. Activation of astrocytes and microglia was assessed by immunofluorescence labeling GFAP and Iba-1. The phosphorylated state of various mitogen-activated protein kinase (MAPKs) signaling molecules (p38 MAPK, ERK 1/2, and JNK) and activation of nuclear factor κB (NF-κB) was studied by western blot. Histopathological changes were observed by H.E. straining. RESULTS: SCP could significantly improve the cognition and histopathological changes of AD mice, reduce the deposition of Aß, downregulate the expression of pro-inflammatory cytokines and the activation of glial cells in the hippocampus. Further, SCP decreased nuclear displacement of NF-κB and MAPKs phosphorylation. CONCLUSIONS: SCP could improve the cognition of mice, and it may play an anti-AD role by activating the NF-κB/MAPK pathway to alleviate neuroinflammation.

Protective effects of Alpinae Oxyphyllae Fructus extracts on lipopolysaccharide-induced animal model of Alzheimer's disease.

ETHNOPHARMACOLOGICAL RELEVANCE: Alpinae Oxyphyllae Fructus (AOF) with warming and tonifying the kidney and spleen, anti-salivation, anti-polyuria and anti-diarrhea functions is the dried ripe fruits of Alpinia oxyphylla Miq. (Zingiberaceae). As a traditional Chinese medicine, its application history is very long. AIMS OF THE STUDY: The purpose of our study is to investigate the effects of different solvent extracts from AOF on lipopolysaccharide (LPS)-induced animal model of Alzheimer's disease (AD) to elucidate the traditional medical theories with modern pharmacological methods and provide a reference for further clarifying its active components and mechanisms. MATERIALS AND METHODS: The method of stepwise screening was adopted in this paper. The animals were divided into 9 groups, including control (CT) group, model (MD) group, donepezil (DPZ) group, total extract (TT) group, petroleum ether extract (PE) group, chloroform extract (CF) group, ethyl acetate extract (EA) group, n-butanol extract (NB) group and water extract (WT) group. The anti-amnesic effects of different solvent extracts from AOF were measured in LPS-induced memory deficits mice by Y maze test and Morris water maze (MWM) test. Hematoxylin eosin (HE) staining was applied to observe pathological changes in hippocampus and cerebral cortex tissue of different groups. Biochemical indicators including ionized calcium-binding adaptor molecule 1 (IBA-1), interleukin beta 1 (IL-1ß), Aß1-42 and hyperphosphorylated tau proteins (p-tau) in hippocampus and cortex after treatment with LPS were measured according to the manufacturer's instructions of ELISA kits. HPLC was used to evaluate the major components of different extracts. RESULTS: It was found that successive intragastric administration of AOF (360 mg/kg) extracts for 14 days showed different degrees of improvement on LPS-induced AD model as measured by Y-maze test, Morris water maze test, and Histopathological examination. Moreover, the results of ELISA suggested petroleum ether (PE) extracts were worth recommending for inhibiting the high level of IBA-1, IL-1ß, Aß1-42 and p-tau in hippocampus and cortex after treatment with LPS. CONCLUSIONS: The present study demonstrated for the first time that AOF attenuated LPS-induced learning and memory impairment, which may be associated with its inhibitory effect on neuroinflammation, amyloids-ß (Aß) deposition and p-tau. This research provided a theoretical basis for elucidating the traditional theory of AOF, and was also the stepping stone to the next step.

Ameliorating effect of Alpinia oxyphylla-Schisandra chinensis herb pair on cognitive impairment in a mouse model of Alzheimer's disease.

Alzheimer's disease (AD) is the most common cause of dementia. In our previous study, we found both Alpinia oxyphylla and Schisandra chinensis can improve the cognitive function of AD. To investigate whether the Alpinia oxyphylla - Schisandra chinensis herb pair (ASHP) has ameliorating effect on cognitive impairment, we used scopolamine to induce learning and memory impairments, as a mouse model of AD. Subsequently, we carried out Y-maze test and Morris water maze test to observe the behavior of mice. Finally, the level of Acetylcholine (Ach) and muscarinic receptor (M1) receptors, the activity of choline acetyltransferase (ChAT) and acetyl cholinesterase (AChE) were measured by commercial assay kits and ELISA kit. And we used hematoxylin-eosin (HE) staining to check the changes in cortex and the CA1 region of hippocampus. ASHP significantly protected against learning and memory impairments induced by scopolamine in Y-maze test and Morris water maze test. Besides, ASHP was able to increase the level of ACh and M1 receptors, and decrease the activity of AChE, but did not significantly affect the activity of ChAT. In addition, from the results of histopathological examination, we speculated ASHP may have neuroprotective effects. This study provided an experimental basis for further study of Alpinia oxyphylla - Schisandra chinensis herb pair in AD therapy.

Nootkatone, a neuroprotective agent from Alpiniae Oxyphyllae Fructus, improves cognitive impairment in lipopolysaccharide-induced mouse model of Alzheimer's disease.

Neuroinflammatory responses play a crucial role in the pathogenesis of Alzheimer's disease (AD). Our previous study demonstrated that petroleum ether extracts from Alpiniae Oxyphyllae Fructus(AOF) could attenuate lipopolysaccharide (LPS)-induced learning and memory impairment in mice, which could be associated with its inhibitory effect on neuroinflammation. Therefore, our present study is to investigate the potential therapeutic neuroprotective effects of nootkatone (NKT) on an AD mouse model induced by intracerebroventricular injection of LPS. We found that NKT (10 mg/kg) group showed good performance in behavior experiments including Y-maze test and Morris water maze test. The results of histopathological examination and immunohistochemical analysis showed that LPS induced degeneration of neurons and activation of microglia particularly in hippocampus and NKT (10 mg/kg) reversed these changes. Enzyme linked immunosorbent assay and western blot analysis also demonstrated that the model group had increased expression of IL-1ß, IL-6, TNF-α, NLRP3 and NF-κB p65, especially in hippocampus relative to sham-operated group, and NKT (10 mg/kg) decreased the high expression of these inflammatory cytokines. Collectively, these data indicated that LPS-induced learning and memory impairments in mice could be improved by NKT, which was associated with attenuating neuroinflammatory responses. Our study indicated that NKT could act as a potential therapeutic agent for the treatment of neuroinflammation and AD.