Exploring the mechanism of action of licorice in the treatment of COVID-19 through bioinformatics analysis and molecular dynamics simulation.

Purpose: The rapid worldwide spread of Corona Virus Disease 2019 (COVID-19) has become not only a global challenge, but also a lack of effective clinical treatments. Studies have shown that licorice can significantly improve clinical symptoms such as fever, dry cough and shortness of breath in COVID-19 patients with no significant adverse effects. However, there is still a lack of in-depth analysis of the specific active ingredients of licorice in the treatment of COVID-19 and its mechanism of action. Therefore, we used molecular docking and molecular dynamics to explore the mechanism of action of licorice in the treatment of COVID-19. Methods: We used bioinformatics to screen active pharmaceutical ingredients and potential targets, the disease-core gene target-drug network was established and molecular docking was used for verification. Molecular dynamics simulations were carried out to verify that active ingredients were stably combined with protein targets. The supercomputer platform was used to measure and analyze stability of protein targets at the residue level, solvent accessible surface area, number of hydrogen bonds, radius of gyration and binding free energy. Results: Licorice had 255 gene targets, COVID-19 had 4,628 gene targets, the intersection gene targets were 101. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene ontology (GO) analysis showed that licorice played an important role mainly through the signaling pathways of inflammatory factors and oxidative stress. Molecular docking showed that Glycyrol, Phaseol and Glyasperin F in licorice may playe a role in treating COVID-19 by acting on STAT3, IL2RA, MMP1, and CXCL8. Molecular dynamics were used to demonstrate and analyze the binding stability of active ingredients to protein targets. Conclusion: This study found that Phaseol in licorice may reduce inflammatory cell activation and inflammatory response by inhibiting the activation of CXCL8 and IL2RA; Glycyrol may regulate cell proliferation and survival by acting on STAT3. Glyasperin F may regulate cell growth by inhibiting the activation of MMP1, thus reducing tissue damage and cell death caused by excessive inflammatory response and promoting the growth of new tissues. Therefore, licorice is proposed as an effective candidate for the treatment of COVID-19 through STAT3, IL2RA, MMP1, and CXCL8.

Exploring the mechanism of action of licorice in the treatment of COVID-19 through bioinformatics analysis and molecular dynamics simulation

The mechanisms analysis of licorice in the treatment of COVID-19.

Development, manufacturing, and preliminary validation of a reusable half-face respirator during the COVID-19 pandemic.

INTRODUCTION: The COVID-19 pandemic has led to widespread shortages of N95 respirators and other personal protective equipment (PPE). An effective, reusable, locally-manufactured respirator can mitigate this problem. We describe the development, manufacture, and preliminary testing of an open-hardware-licensed device, the "simple silicone mask" (SSM). METHODS: A multidisciplinary team developed a reusable silicone half facepiece respirator over 9 prototype iterations. The manufacturing process consisted of 3D printing and silicone casting. Prototypes were assessed for comfort and breathability. Filtration was assessed by user seal checks and quantitative fit-testing according to CSA Z94.4-18. RESULTS: The respirator originally included a cartridge for holding filter material; this was modified to connect to standard heat-moisture exchange (HME) filters (N95 or greater) after the cartridge showed poor filtration performance due to flow acceleration around the filter edges, which was exacerbated by high filter resistance. All 8 HME-based iterations provided an adequate seal by user seal checks and achieved a pass rate of 87.5% (N = 8) on quantitative testing, with all failures occurring in the first iteration. The overall median fit-factor was 1662 (100 = pass). Estimated unit cost for a production run of 1000 using distributed manufacturing techniques is CAD $15 in materials and 20 minutes of labor. CONCLUSION: Small-scale manufacturing of an effective, reusable N95 respirator during a pandemic is feasible and cost-effective. Required quantities of reusables are more predictable and less vulnerable to supply chain disruption than disposables. With further evaluation, such devices may be an alternative to disposable respirators during public health emergencies. The respirator described above is an investigational device and requires further evaluation and regulatory requirements before clinical deployment. The authors and affiliates do not endorse the use of this device at present.

Virus-Host Interactome and Proteomic Survey Reveal Potential Virulence Factors Influencing SARS-CoV-2 Pathogenesis.

BACKGROUND: The ongoing coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a global public health concern due to relatively easy person-to-person transmission and the current lack of effective antiviral therapy. However, the exact molecular mechanisms of SARS-CoV-2 pathogenesis remain largely unknown. METHODS: Genome-wide screening was used to establish intraviral and viral-host interactomes. Quantitative proteomics was used to investigate the peripheral blood mononuclear cell (PBMC) proteome signature in COVID-19. FINDINGS: We elucidated 286 host proteins targeted by SARS-CoV-2 and >350 host proteins that are significantly perturbed in COVID-19-derived PBMCs. This signature in severe COVID-19 PBMCs reveals a significant upregulation of cellular proteins related to neutrophil activation and blood coagulation, as well as a downregulation of proteins mediating T cell receptor signaling. From the interactome, we further identified that non-structural protein 10 interacts with NF-κB-repressing factor (NKRF) to facilitate interleukin-8 (IL-8) induction, which potentially contributes to IL-8-mediated chemotaxis of neutrophils and the overexuberant host inflammatory response observed in COVID-19 patients. CONCLUSIONS: Our study not only presents a systematic examination of SARS-CoV-2-induced perturbation of host targets and cellular networks but it also reveals insights into the mechanisms by which SARS-CoV-2 triggers cytokine storms, representing a powerful resource in the pursuit of therapeutic interventions. FUNDING: National Key Research and Development Project of China, National Natural Science Foundation of China, National Science and Technology Major Project, Program for Professor of Special Appointment (Eastern Scholar) at Shanghai Institutions of Higher Learning, Shanghai Science and Technology Commission, Shanghai Municipal Health Commission, Shanghai Municipal Key Clinical Specialty, Innovative Research Team of High-level Local Universities in Shanghai, Interdisciplinary Program of Shanghai Jiao Tong University, SII Challenge Fund for COVID-19 Research, Chinese Academy of Sciences (CAS) Large Research Infrastructure of Maintenance and Remolding Project, and Chinese Academy of Sciences Key Technology Talent Program.

Subject validation of reusable N95 stop-gap filtering facepiece respirators in COVID-19 pandemic.

INTRODUCTION: The COVID-19 pandemic has unveiled widespread shortages of personal protective equipment including N95 respirators. Several centers are developing reusable stop-gap respirators as alternatives to disposable N95 respirators during public health emergencies, using techniques such as 3D-printing, silicone moulding and plastic extrusion. Effective sealing of the mask, combined with respiratory filters should achieve 95% or greater filtration of particles less than 1um. Quantitative fit-testing (QNFT) data from these stop-gap devices has not been published to date. Our team developed one such device, the "SSM", and evaluated it using QNFT. METHODS: Device prototypes were iteratively evaluated for comfort, breathability and communication, by team members wearing them for 15-30min. The fit and seal were assessed by positive and negative pressure user seal checks. The final design was then formally tested by QNFT, according to CSA standard Z94.4-18 in 40 volunteer healthcare providers. An overall fit-factor >100 is the passing threshold. Volunteers were also tested by QNFT on disposable N95 masks which had passed qualitative fit testing (QLFT) by institutional Occupational Health and Safety Department. RESULTS: The SSM scored 3.5/5 and 4/5 for comfort and breathability. The median overall harmonic mean fit-factors of disposable N95 and SSM were 137.9 and 6316.7 respectively. SSM scored significantly higher than disposable respirators in fit-test runs and overall fit-factors (p <0.0001). Overall passing rates in disposable and SSM respirators on QNFT were 65% and 100%. During dynamic runs, passing rates in disposable and SSM respirators were 68.1% and 99.4%; harmonic means were 73.7 and 1643. CONCLUSIONS: We present the design and validation of a reusable N95 stop-gap filtering facepiece respirator that can match existent commercial respirators. This sets a precedence for adoption of novel stop-gap N95 respirators in emergency situations.

Spike protein-based epitopes predicted against SARS-CoV-2 through literature mining.

BACKGROUND: With the diffusion of SARS-CoV-2 around the world, human health is being threatened. As there is no effective vaccine yet, the development of the vaccine is urgently in progress. MATERIALS AND METHODS: Immunoinformatics methods were applied to predict epitopes from the Spike protein through mining literature associated with B- and T-cell epitopes prediction published or preprinted since the outbreak of the virus till June 1, 2020. 3D structure of the Spike protein were obtained (PDB ID: 6VSB) for prediction of discontinuous B-cell epitopes and localization of epitopes in the hotspot regions. RESULTS: Methods provided by the Immune Epitope Database (IEDB) server were the most frequently used to predict epitopes. Sequence alignment of the epitopes extracted from literature with the Spike protein demonstrated that the epitopes in different studies converged to multiple short hotspot regions. There were three hotspot regions found in RBD of the Spike protein harboring B-cell linear epitopes ('RQIAPGQTGKIADYNYKLPD', 'SYGFQPTNGVGYQ' and 'YAWNRKRISNCVA') predicted to have high antigenicity score. Two T-cell epitopes ('KPFERDISTEIYQ' and 'NYNYLYRLFR') predicted to be highly antigenic in the original studies were discovered in the hotspot region. Toxicity and allergenicity analysis confirmed all the five epitopes are of non-toxin, and four of them are of non-allergen. The five epitopes identified in hotspot regions of RBD were found fully exposed based on the 3D structure of the Spike protein. CONCLUSION: The five epitopes we discovered from literature mining may be potential candidates for diagnostics and vaccine development against SARS-CoV-2.