1School of Life Sciences, Shanghai University, Shanghai, 200444, China 2Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China 3Beijing You’an Hospital, Capital Medical University, Beijing, China 4Department of Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China 5Department of Orthopaedics, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China 6Institute of Stem Cell and Regeneration Medicine, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China 7Department of Orthopaedics, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China 8Department of Neurosurgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China 9The Executive Committee on Anti-aging and Disease Prevention in the framework of Science and Technology, Pharmacology and Medicine Themes under an Interactive Atlas along the Silk Roads, UNESCO, Paris, France 10International Society on Aging and Disease (ISOAD), Fort Worth, Texas, USA 11The Geriatric Medical Center “Shmuel Harofe”, Beer Yaakov, affiliated to Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel 12University of North Texas Health Science Center, Fort Worth, TX, USA 13School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China 14Institute of Chinese Medical Science, University of Macau, Taipa, Macau, China 15Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Center of Russian Academy of Sciences, Syktyvkar, Russia 16Department of Pediatrics, Obstetrics and Gynecology, University of Valencia, Valencia, Spain 17Department of Biochemistry, Maharishi Markandeshwar University, Kolkata, India
18Institute of Medical Science, University of Toronto, Toronto, Canada 19Department of Biological Sciences, Inha University, Incheon, South Korea 20Centre of Human & Aerospace Physiological Sciences & Centre for Stem Cells and Regenerative Medicine, Faculty of Life Sciences & Medicine, King’s College London, London, UK 21Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neuroscience and Advanced Diagnostics, University of Palermo, Palermo, Italy
#These authors contributed equally to this work
*Corresponding authors: Robert Chunhua Zhao, M.D. & Ph.D., Professor, School of Life Sciences, Shanghai University, Shanghai 200444, China. Email: email@example.com
Kunlin Jin, M.D. & Ph.D., Professor, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA. kunlin.Jin@unthsc.edu
Ronghua Jin, M.D. & Ph.D., Professor, You’an Hospital, Capital Medical University, Beijing, China. Email: firstname.lastname@example.org
Hongjian Liu, M.D. & Ph.D., Professor, Department of Orthopaedics, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China. Email: email@example.com
A coronavirus (HCoV-19) has caused the novel coronavirus disease (COVID-19) outbreak in Wuhan, China, Preventing and reversing the cytokine storm may be the key to save the patients with severe COVID-19 pneumonia. Mesenchymal stem cells (MSCs) have been shown to possess a comprehensive powerful immunomodulatory function. This study aims to investigate whether MSC transplantation improve the outcome of 7 enrolled patients with COVID-19 pneumonia in Beijing YouAn Hospital, China from Jan 23, 2020. to Feb 16, 2020. The clinical outcomes, as well as changes of inflammatory and immune function levels and adverse effects of 7 enrolled patients were assessed for 14 days after MSC injection. MSCs could cure or significantly improve the functional outcomes of seven patients with COVID-19 pneumonia in 14 days without observed adverse effect. The pulmonary function and symptoms of all patients with COVID-19 pneumonia were significantly improved in 2 days after MSC transplantation. Among them, two common and one severe patient were recovered and discharged in 10 days after treatment. After treatment, the peripheral lymphocytes were increased and the overactivated cytokine-secreting immune cells CXCR3+CD4+ T cells, CXCR3+CD8+ T cells, and CXCR3+ NK cells were disappeared in 3-6 days. And a group of CD14+CD11c+CD11bmid regulatory DC cell population dramatically increased. Meanwhile, the level TNF-α is significantly decreased while IL-10 increased in MSC treatment group compared to the placebo control group. Furthermore, the gene expression profile showed MSCs were ACE2- and TMPRSS2- which indicated MSCs are free from COVID-19 infection. Thus, the intravenous transplantation of MSCs was safe and effective for treatment in patients with COVID-19 pneumonia, especially for the patients in critically severe condition.
The novel coronavirus disease 2019 (COVID-19) has grown to be a global public health emergency since patients were first detected in Wuhan, China, in December 2019. Since then, the number of COVID-19 confirmed patients have sharply increased not only in China, but also worldwide, including Germany, South Korea, Vietnam, Singapore, and USA. Currently, no specific drugs or vaccines are available to cure the patients with COVID-19 infection. Hence, there is a large unmet need for a safe and effective treatment for COVID-19 infected patients, especially the severe cases.
Several reports demonstrated that the first step of the HCoV-19 pathogenesis is that the virus specifically recognizes the angiotensin I converting enzyme 2 receptor (ACE2) by its spike protein[2-4]. ACE2-positive cells are infected by the HCoV-19, like SARS-2003[5,6]. In addition, a research team from Germany revealed that the cellular serine protease TMPRSS2 for HCoV-19 Spike protein priming is also essential for the host cell entry and spread, like
the other coronavirus (i.e. SARS-2003)[8,9]. Unfortunately, the ACE2 receptor is widely distributed on the human cells surface, especially the alveolar type II cells (AT2) and capillary endothelium, and the AT2 cells highly express TMPRSS2. However, in the bone marrow, lymph nodes, thymus, and the spleen, immune cells, such as T and B lymphocytes, and macrophages are consistently negative for ACE2. The findings suggest that immunological therapy may be used to treat the infected patients. However, the immunomodulatory capacity may be not strong enough, if only one or two immune factors were used, as the virus can stimulate a terrible cytokine storm in the lung, such as IL-2, IL-6, IL-7, GSCF, IP10, MCP1, MIP1A, and TNFα, followed by the edema, dysfunction of the air exchange, acute respiratory distress syndrome, acute cardiac injury and the secondary infection, which may led to death. Therefore, avoiding the cytokine storm may be the key for the treatment of HCoV-19 infected patients. MSCs, owing to their powerful immunomodulatory ability, may have beneficial effects on preventing or attenuating the cytokine storm.
MSCs have been widely used in cell-based therapy, from basic research to clinical trials[12,13]. Safety and effectiveness have been clearly documented in many clinical trials, especially in the immune-mediated inflammatory diseases, such as graft versus-host disease (GVHD) and systemic lypus erythematosus (SLE). MSCs play a positive role mainly in two ways, namely immunomodulatory effects and differentiation abilities. MSCs can secrete many types of cytokines by paracrine secretion or make direct interactions with immune cells, leading to immunomodulation. The immunomodulatory effects of MSCs are triggered further by the activation of TLR receptor in MSCs, which is stimulated by pathogen-associated molecules such as LPS or double-stranded RNA from virus[18,19], like the HCoV-19.
Here we conducted an MSC transplantation pilot study to explore their therapeutic potential for HCoV-19 infected patients. In addition, we also explored the underlying mechanisms using a 10× Genomics high throughput RNA sequencing clustering analysis on MSCs and mass cytometry.
Materials and Methods Study design A pilot trial of intravenous MSC transplantation was performed on seven patients with COVID-19 infected pneumonia. The study was conducted in Beijing YouAn Hospital, Capital Medical University, China, and approved by the ethics committee of the hospital (LL-2020- 013-K). The safety and scientific validity of this study “Clinical trials of mesenchymal stem cells for the treatment of pneumonitis caused by novel coronavirus” from Shanghai University/ PUMC have been reviewed by the scientific committee at International Society on Aging and Disease (ISOAD) and issued in Chinese Clinical Trial Registry (ChiCTR2000029990). The Patients The patients were enrolled from Jan 23, 2020 to Jan 31, 2020. All enrolled patients were
confirmed by the real-time reverse transcription polymerase chain reaction (RT-PCR) assay of HCoV-19 RNA in Chinese Center for Disease Control and Prevention using the protocol as described previously[11,20]. The sequences were as follows: forward primer 5′-
TCAGAATGCCAATCTCCCCAAC-3′; reverse AAAGGTCCACCCGATACATTGA-3′; andCTAGTTACACTAGCCATCCTTACTGC-3′BHQ1. We initially enrolled patients with COVID-19 (age 18–95 years) according to the guidance of National Health and Health Commission of China (Table 1).
If no improvement signs were observed under the standard treatments, the patient would be suggested to receive the MSC transplantation. Patients were ineligible if they had been diagnosed with any kind of cancers or the doctor declared the situation to belong to the critically severe condition. We excluded patients who were participating in other clinical trials or who have participated in other clinical trials within 3 months.
Cell preparation and transplantation
The clinical grade MSCs were supplied, for free, by Shanghai University, Qingdao Co-orient Watson Biotechnology group co. LTD and the Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences. The cell product has been certified by the National Institutes for Food and Drug Control of China (authorization number: 2004L04792，2006L01037，CXSB1900004). Before the intravenous drip, MSCs were suspended in 100 ml of normal saline, and the total number of transplanted cells was calculated by 1 × 106 cells per kilogram of weight. The window period for cell transplantation was defined as the time when symptoms or/and signs still were getting worse even as the expectant treatments were being conducted. The injection was performed about forty minutes with a speed of ~40 drops per minute.
The patients were assessed by the investigators through the 14-day observation after receiving the investigational product. The clinical, laboratory, and radiological outcomes were recorded and certified by a trained group of doctors. The detailed record included primary safety data (infusional and allergic reactions, secondary infection and life-threatening adverse events) and the primary efficacy data (the level of the cytokines variation, the level of C-reactive protein in plasma and the oxygen saturation). The secondary efficacy outcomes mainly included the total lymphocyte count and subpopulations, the chest CT, the respiratory rate, and the patient symptoms (especially the fever and shortness of breath). In addition, the therapeutic measures (i.e. antiviral medicine and respiratory support) and outcomes were also examined.
MIMICS 21.0 (Interactive medical image control system of Materialise, Belgium) was used to evaluate the chest CT data. The analysis of Mass cytometry of the peripheral blood mononuclear cells is described in Supplementary Material 1. The analysis of the 10 x RNA-seq survey is described in Supplementary Material 2. Data were analyzed by SPSS software (SPSS 22.0). Differences between two groups were assessed using unpaired two-tailed t tests. Data
primer 5′- the probe 5′CY5-
involving more than two groups were assessed by analysis of variance (ANOVA). P values <0.05 indicated statistical significance.
Results MSC treatment procedure and general patient information This study was conducted from Jan 23, 2020, to Feb 16, 2020. Seven confirmed COVID-19 patients, including 1 critically severe type (patient 1), 4 severe types (patient 2, 3, 6, 7) and 2 common types (patient 4, 6) were enrolled. The timepoint of MSC transplantation for each patient is as shown in Figure 1. The general information of the 7 patients is listed in Table 1. Hitherto, the critically severe patient had completed the MSC treatment. This patient had a 10- year medical history of hypertension with the highest-level of 180/90 mmHg recorded. All the treatment information of the patients was collected.
Figure 1. The flow chart of the cell transplantation treatment
The primary safety outcome
Before the MSC transplantation, the patients had symptoms of high fever (38.5°C ± 0.5°C), weakness, shortness of breath, and low oxygen saturation. However, 2~4 days after transplantation, all the symptoms were disappeared in all the patients, the oxygen saturations rose to ≥ 95% at rest, without or with oxygen uptake (5 liters per minute). In addition, no acute infusion-related or allergic reactions were observed within two hours after transplantation. Similarly, no delayed hypersensitivity or secondary infections were detected after treatment. The detailed diagnosis and treatment procedures of the critically severe patient are shown in Supplementary Material 3. The main symptoms and signs are shown in Table 3.
The efficacy outcome
The immunomodulating function of MSCs contributed to the main efficacy outcome and the transplantation of MSCs showed impressive positive results (Table 3). For the primary outcome in the critically severe patient 1, the plasma C-reaction protein level decreased from 105.5 g/L (Jan 30) to 10.1 g/L (Feb 13), which reached the highest level of 191.0 g/L on Feb 1, indicating that the inflammation status was alleviating quickly. The oxygen saturation, without Supplementary oxygen, rose from 89% (Jan 31) to 98% (Feb 13), which indicated the pulmonary alveoli regained the air-change function.
The secondary outcomes were also improved (Table 4). Considering, for example, the critically severe patient 1, the lymphopenia was significantly improved after the cell transplantation. The patient was isolated in the hospital isolation ward with a history of hypertension and blood pressure reaching grade 3 hypertension. On Feb 1, biochemical indicators in the blood test showed that aspartic aminotransferase, creatine kinase activity and myoglobin increased sharply to 57 U/L, 513 U/L, and 138 ng/ml, respectively, indicating severe damage to the liver and myocardium. However, the levels of these functional biochemical indicators were decreased to normal reference values in 2~4 days after treatment (Table 4). On February 13, all the indexes reached to normal levels, namely 19 U/L, 40 U/L, and 43 ng/ml, respectively. The respiratory rate was decreased to the normal range on the 4th day after MSC transplantation. Both fever and shortness of breath disappeared on the 4th day after MSCs transplantation. Chest CT imaging showed that the ground-glass opacity and pneumonia infiltration had largely reduced on the 9th day after MSC transplantation (Figure 2).
Figure 2. Chest computerized tomography (CT) images of the critically severe COVID-19 patient. On Jan 23, no pneumonia performance was observed. On Jan 30, ground-glass opacity and pneumonia infiltration occurred in multi-lobes of the double sides. Cell transplantation was performed on Jan 31. On Feb 2, the pneumonia invaded all through the whole lung. On Feb 9, the pneumonia infiltration faded away very much. On Feb 15, only little ground-glass opacity was residual in local.
HCoV-19 nucleic acid detection
RT-PCR analysis of HCoV-19 nucleic acid was performed before and after MSC transplantation. For the critically severe patient, before transplantation (Jan 23) and 6 days after transplantation (Feb 6), HCoV-19 nucleic acid was positive. 13 days after transplantation (Feb 13), HCoV-19 nucleic acid turned to be negative. The patient 3, 4,5 also turned to be negative result of HCoV- 19 nucleic acid until this report date.
Mass cytometry (CyTOF) analysis of the patients’ peripheral blood
To investigate the profile of the immune system constitution during MSC transplantation, we performed the CyTOF to analyze immune cells in the patients’ peripheral blood before and after transplantation. CyTOF revealed that there was nearly no increase of regulatory T cells (CXCR3-) or dendritic cells (DC, CXCR3-) for the two patients of common type (Patient 4 and 5). But in the severe patients, both the regulatory T cells and DC increased after the cell therapy, especially for the critically severe patient. Notably, no significant CXCR3- DC enhanced after placebo treatment in three severe control patients. Moreover, for the critically severe patient, before the MSC transplantation the percentage of CXCR3+CD4+ T cells, CXCR3+CD8+ T cells, and CXCR3+ NK cells in the patient’s PBMC were remarkably increased compared to the healthy control, which caused the inflammatory cytokine storm. However, 6 days after MSC transplantation, the overactivated T cells and NK cells nearly disappeared and the numbers of the other cell subpopulations were almost restored to the normal levels, especially the CD14+CD11c+CD11bmid regulatory dendritic cell population (Figure 3).
Figure 3. The mass cytometry results of peripheral blood mononuclear cells of the enrolled patients (A, B) and the critically severe patient (C). No increase of regulatory T cells (CXCR3-) or dendritic cells (DC, CXCR3-) for the two patients of common type (Patient 4 and 5, Figrue 3A). But in the severe patients, both the regulatory T cells and DC increased after the cell therapy, especially for the critical severe patient 1 (Figure 3B). Moreover, for the critically severe patient 1, before the MSC transplantation the percentage of overactivated CXCR3+CD4+ T cells (#9), CXCR3+CD8+ T cells (#17), and CXCR3+ NK cells (#12) in the patient’s PBMC were remarkably increased compared to the healthy control (Figure 3C). However, 6 days after MSC transplantation, the overactivated T cells and NK cells nearly disappeared and the numbers of the other cell subsets were almost reversed to the normal levels, especially the CD14+CD11c+CD11bmid DC (#20) population. Normal: health individuals, MSCs: mesenchymal stem cells transplant group, Ctrl: placebo control group.
Serum Cytokine/Chemokine/Growth Factor Analysis
After intravenous injection of MSCs, the decrease ratio of pro-inflammatory cytokine in serum TNF-α before and after MSC treatment was significant (p<0.05). Meanwhile, the increase ratio of anti-inflammatory IL-10 (p<0.05) also showed remarkably in the MSC treatment group. The
serum levels of chemokines like IP-10 and growth factor VEGF were both increased, though not significantly (Figure 4).
Figure 4. The ratio of serum cytokines IL-10 (A), growth factor VEGF (B), the chemokine IP-10 (C) and TNF-α (D) before and after MSCs treatment were detected in severe patients compared with the control group without MSCs by panel assay analysis, respectively. Ctrl: placebo control group. P-values were determined using the student’s t-test. *P < 0.05.
10 x RNA-seq analysis for transplanted MSCs
To further elucidate the mechanisms underlying MSC-mediated protection for COVID-19 infected patients, we performed the 10 x RNA-seq survey for transplanted MSCs. The 10 x RNA-seq survey captured 12,500 MSCs which were then sequenced with 881,215,280 raw reads totally (Supplementary Material 4). The results revealed that MSCs are ACE2 or TMPRSS2 negative, indicating that MSCs are free from COVID-19 infection. Moreover, anti- inflammatory and trophic factors like TGF-β, HGF, LIF, GAL, NOA1, FGF, VEGF, EGF, BDNF, and NGF were highly expressed in MSCs, further demonstrating the immunomodulatory function of MSCs. Moreover, SPA and SPC were highly expressed in MSCs, indicating that MSCs might differentiate to AT2 cells (Figure 5). KEGG pathway analysis showed that MSCs were closely involved in the antiviral pathways (Supplementary Material 4).
Figure 5. The 10 x RNA-seq survey of MSCs genes expression: Both ACE2 (A) and TMPRSS2 (B) were rarely expressed. TGF-β (C), HGF (D), LIF (E), GAL (F), NOA1 (G), FGF (H), VEGF (I), EGF (J), BDNF (K), and NGF (L) were highly expressed, indicating the immunomodulatory function of MSCs. SPA (M) and SPC (N) were highly expressed, indicating MSCs owned the ability to differentiate into the alveolar epithelial cells II. One point represented one cell, and red and gray color showed high expression and low expression,
Both the novel coronavirus and SARS-2003 could enter the host cell by binding the S protein on the viral surface to the ACE2 on the cell surface[3,5]. In addition to the lung, ACE2 is widely expressed in human tissues, including the heart, liver, kidney, and digestive organs. In fact, almost all endothelial cells and smooth muscle cells in organs express ACE2, therefore once the virus enters the blood circulation, it spreads widely. All tissues and organs expressing ACE2 could be the battlefield of novel coronavirus and immune cells. This explains why not only all infected ICU patients are suffering from acute respiratory distress syndrome, but also complications such as acute myocardial injury, arrhythmia, acute kidney injury, shock, and death of multiple organ dysfunction syndrome(Figure 6). Moreover, the HCoV-19 is more likely to affect older males with comorbidities and can result in severe and even fatal respiratory diseases such as acute respiratory distress syndrome, like the critically severe case here. However, the cure of COVID-2019 is essentially dependent on the patient’s own immune system. When the overactivated immune system kills the virus, it produces a large amount of inflammatory factors, leading to the severe cytokine storms. It suggests that the main reason of these organs damage may be due to virus-induced cytokine storm. Older subjects may be much easier to be affected due to immunosenescence.
Figure 6. ACE2- MSCs benefit the COVID-19 patients via immunoregulatory function
Our 10x scRNA-seq survey shows that MSCs are ACE2- and TMPRSS2- (to the best of our knowledge, it is the first time to be reported) and secrete anti-inflammatory factors to prevent the cytokine storm. They have the natural immunity to the HCoV-19. According to the mass
cytometry streaming results, the virus infection caused a total function failure of the lymphocytes, even of the whole immune system. MSCs played the vital immune modulation roles to reverse the lymphocyte subsets mainly through dendritic cells. Our previous study showed that co-culture with MSCs could decrease the differentiation of cDC from human CD34+ cells, while increasing the differentiation of pDC through PGE2. Furthermore, the induction of IL-10–dependent regulatory dendritic cells and IRF8-controlled regulatory dendritic cells from HSC were also reported in rats[23,24]. MSCs could also induce mature dendritic cells into a novel Jagged-2-dependent regulatory dendritic cell population. All these interactions with different dendritic cells led to a shift of the immune system from Th1 toward Th2 responses.
Several reports also focused on lymphopenia and high levels of C-reactive protein in COVID- 19 patients[20,21]. C-reactive protein is a biomarker with high-sensitivity for inflammation and host response to the production of cytokines, particularly TNFα, IL-6, MCP1 and IL-8 secreted by T cells. However, most mechanistic studies suggest that C-reactive protein itself is unlikely to be a target for intervention. C-reactive protein is also a biomarker of myocardial damage.
MSC therapy can inhibit the overactivation of the immune system and promote endogenous repair by improving the microenvironment. After entering the human body through intravenous infusion, part of the MSCs accumulate in the lung, which could improve the pulmonary microenvironment, protect alveolar epithelial cells, prevent pulmonary fibrosis and improve lung function.
As reported by Cao’s team, the levels of serum IL-2, IL-7, G-SCF, IP10, MCP-1, MIP-1A and TNF-α in ICU patients were higher than those of normal patients. The cytokine release syndrome caused by abnormally activated immune cells deteriorated the patient’s states which may cause disabled function of endothelial cells, the capillary leakage, the mucus block in lung and finally the respiratory failure. And they could cause even an inflammatory cytokine storm lead to multiple organ failure. The administration of intravenous injection of MSCs significantly improved the inflammation situation in severe COVID-19 patients. Due to its unique immunosuppression capacity, the serum levels of pro-inflammatory cytokines and chemokines were reduced dramatically which attracted less mononuclear/macrophages to fragile lung, while induced more regulatory dendric cells to the inflammatory tissue niche. Moreover, the increased IL-10 and VEGF promoted the lung’s repair. Ultimately, the patients with severe COVID-19 pneumonia survived the worst condition and recovery.
Therefore, the fact that transplantation of MSCs improved the outcome of COVID-2019 patients may be through regulating inflammatory response and promoting tissue repair and regeneration.
This work was supported by the National Key Research and Development Program of China
(2016YFA0101000, 2018YFE0114200), CAMS Innovation Fund for Medical Sciences (2017- I2M-3-007) and the 111 Project (B18007), National Natural Science Foundation of China (81971324, 81672313, 81700782, 81972523, 81771349).
Conflicts of interest
We have no conflicts of interest.
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Table 1: Clinical classification of the COVID-19 released by the National Health and Health Commission of China
Table 4: The laboratory results of the critically severe patient. Red: the value was above the normal. Blue: the value was below the normal. NA: Not Available
C-reactive protein (ng/mL)
Absolute lymphocyte count (× 109 per liter)
White-cell count (× 109 per liter)
Absolute neutrophil count (× 109 per liter)
Absolute monocyte count (× 109 per liter)
Red-cell count (× 1012 per liter)
Platelet count (× 109 per liter)
Absolute eosinophil count (× 109 per liter)
Absolute basophilic count (× 109 per liter)
Total bilirubin (μmol/L)
Aspartate amino transferase (U/L)
Creatine kinase isoenzymes (ng/mL)
Creatine kinase (U/L)
Glomerular filtration rate (ml/min)
Supplementary Materials: Supplementary 1: The method of Mass Cytometry of peripheral blood mononuclear cells (PBMC) Sample preparation for mass cytometry PBMC samples were collected from COVID-19 infected patients treated with MSCs transplantation at baseline and on Day 6, and PBMC from a healthy donor were set as the control group. All samples were cultured with 2 μM cisplatin (195-Pt, Fluidigm) for 2 minutes before quenching with CSB (Fluidigm) to identify the viability using mass cytometry analysis. A Fix-I buffer (Fluidigm) was then used to fix cells for 15 min at room temperature, followed by washing three times with phosphate buffer solution (PBS). Mass cytometry antibody staining and CD45 barcoding Three samples from the healthy donor, the patient at baseline and Day 6 were stained with CD45 antibodies that were labeled with different metal tags (89, 141 and 172) to minimize internal cross reaction between samples. MaxPar × 8 Polymer Kits (Fluidigm) were used to conjugate with purified antibodies (listed in Supplemental Table 1). All metal-conjugated antibodies were titrated for optimal concentrations before use. Cells were counted and diluted into 1× 106 cells per milliliter in PBS and underwent permeabilization with 80% methanol for 15 minutes at 0°C. After triple washes in CSB, cells were cultured with antibodies in a total 50 μL CSD for 30 min in RT, triple washed in CSB and incubated with 0.125 μm intercalator in fix and perm buffer (Fluidigm) at 4 °C overnight. Data acquisition in Helios After cultured with intercalator, cells were washed three times with ice cold PBS and three times with deionized water. Prior to acquisition, samples were resuspended in deionized water containing 10% EQ 4 Element Beads (Fluidigm) and cell concentrations were adjusted to 1×106 cell/ml. Data acquisition was performed on a Helios mass cytometer (Fluidigm). The original FCS data were normalized and .fcs files for everyone were collected. CyTOF Data Analysis All .fcs files were uploaded into Cytobank, data cleaning and populations of single living cells were exported as .fcs files for further analysis. Files were loaded into R (http://www.rstudio.com), arcsinh transform was performed to signal intensities of all channels. PhenoGraph analysis was performed.
Supplementary 2: The method of the 10 x RNA-seq survey Materials and reagents All supplies and reagents were of the highest grade commercially available. The 0.20 μm-filters, dishes and tubes were purchased from Corning (NY, USA). CD105, CD90, CD44 and CD45 antibodies for the flow cytometry were purchased from Miltenyi Biotec (Bergisch gladbach, Germany). DMEM/F12, fetal bovine serum (FBS), GlutaMAXTM-I, TrypLETM Express, and penicillin and streptomycin antibiotics were purchased from Gibco (California, USA). All other reagents were analytical grade and required no further purification.
Supplemental Table 1: Antibodies used in the Mass cytometry analysis.
The mesenchymal stem cells were cultured in DMEM/F12 medium supplemented with 2% FBS, 2%
GlutaMAXTM-I, 1% antibiotics and 2 mM GlutaMAXTM-I at 37°C with 5% CO2. After three passages, MSCs were immune-phenotyped by flow cytometry for the following surface markers: CD105, CD90, CD73, CD29, HLA-DR, CD44, CD14 and CD45 (all antibodies from BD Pharmingen, San Jose, USA). And MSCs were tested for adipogenic, chondrogenic and osteogenic differentiation to identify their characters.
Cell preparation and Library construction
Cell count and viability were examined by microscope after 0.4% trypan blue coloring. When the viability was no lower than 80%, the library construction was performed. Library was constructed using the Chromium controller (10 x Genomics, Pleasanton, CA). Briefly, single cells, reagents and Gel Beads containing barcoded oligonucleotides were encapsulated into nanoliter-sized GEMs (Gel Bead in Emulsion) using the GemCode technology. Lysis and barcoded reverse transcription of polyadenylated mRNA from single cells were performed inside every GEM. Post RT-GEMs were cleaned up and cDNA were amplified. cDNA was fragmented and fragment ends were repaired, as well as A-tailing was added to the 3’ end. The adaptors were ligated to fragments which were double sided SPRI selected. Another double sided SPRI selecting was carried out after sample index PCR. Quality control-pass libraries were sequenced. The final library was quantitated in two ways: determining the average molecule length using the Agilent 2100 bioanalyzer instrument; and quantifying the library by real-time quantitative PCR.
Analysis of single-cell transcriptomics data
The reads were demultiplexed by using the Cell Ranger Single Cell Software Suite (v3.1.0, 10 x Genomics) and R package Seurat (v3.1.0). The number of genes, unique molecule identifier (UMI) counts and percentage of mitochondrial genes were examined to identify outliers. Principal component analysis was used for dimensionality reduction. U-MAP was then used for two- dimensional visualization of the results. DEGs were identified with the FindConservedMarkers function in Seurat by parameters of logfc.threshold >0.25, minPct>0.25 and Padj≤0.05. KEGG pathways with FDR ≤0.05 were considered to be significantly enriched.
Supplementary 3: The detailed diagnosis and treatment procedures for the critically severe patient On the evening of January 22, 2020, a 65-year-old man presented to the emergency department of Beijing YouAn Hospital, Beijing, with a 2-day history of cough, sputum and subjective fever. The patient wore a mask in the hospital. He disclosed to the physician that he had traveled in Wuhan, China, from December 31, 2019 to January 20, 2020 and returned to Beijing on January 20. Apart from a 10-year history of hypertension with the highest blood pressure of 180/90 mmHg ever, the patient had no other specific medical history. The physical examination showed a body temperature of 37.8, blood pressure of 138/85 mmHg, pulse of 85 beats per minute, respiratory rate of 19 breaths per minute. Lung auscultation revealed rhonchi. A blood routine examination was arranged urgently, and the result revealed that the white-cell count and absolute lymphocyte count were 4.9 × 109/L (reference range (3.5~9.5) × 109/L) and 0.94 × 109/L (reference range (1.1~3.2) × 109/L),
respectively (Table 1). According to the COVID-19 guidance released by the National Health Commission of China, the physician gave him a diagnosis of a suspected COVID-19 case and asked him to undergo medical isolation observation in the hospital. Meantime, the doctor collected his oropharyngeal swab specimen.
On January 23, 2020, the RT-PCR assay confirmed that the patient’s specimen tested positive for HCoV-19. Then the patient was admitted to an airborne-isolation unit in Beijing YouAn Hospital for clinical observation. He had no dyspnea. His consciousness was clear, and the diet and sleep were normal since he became sick. A chest computed tomography (CT) was reported as showing no evidence of infiltrates or abnormalities. The admitting diagnoses were new coronary pneumonia (common type) and hypertension III. The patient received no special care except the irbesartan, which was taken all through the treatment period.
On January 24 to January 29, the patient’s vital physical signs remained largely stable, apart from the development of intermittent fevers and shortness of breath. During this time, the patient received antipyretic therapy including 15 ml of ibuprofen suspension every 6 hours and 650 mg of acetaminophen every 6 hours. From January 26, the patient also received antiviral therapy including lopinavir and ritonavir twice a day, with the amount of 400 mg and 100 mg each time, respectively. On January 30, the patient felt severe shortness of breath and appeared fatigued. The oxygen saturation values measured by pulse oximetry decreased to as low as 91% while he was breathing ambient air. Auscultation rhonchi became worse in the middle of the double sides of the lung. An urgent chest CT clearly showed evidence of pneumonia, ground-glass opacity, in the middle lobes of the right and left lung. The other positive results of laboratory tests included the C-reactive protein rise to 105.5 g/L (reference range < 3 g/L), but the absolute lymphocyte count decreased to 0.60 × 109/L. The potassium concentration went down to 2.74 mmol/L (reference range 3.5-5.5 mmol/L). The doctors decided to change the diagnosis to COVID-19 (critically severe type), and the patient was admitted to ICU unit. More treatments were conducted consisting of mask oxygen supplementation (5 liters per minute), electrocardiograph monitoring, potassium chloride sustained release tablets (oral, 500 mg per time, 3 times per day) and more glucose and amino acid injection. Finally, the discomfort was released, and the oxygen saturation increased to 95%.
On January 31, the shortness of breath even got worse under the oxygen supplementation. The doctor speeded up the oxygen airflow to 10 liters per minute. After the patient signed an agreement to perform the MSCs transplantation, 100 ml of normal saline including 6 × 107 MSCs was intravenously injected into the patient, and no adverse events were observed in association with the infusion.
On February 1 and 2, the patient did not feel better. The third chest CT revealed that the pneumonia got worse. On February 1, the levels of C-reactive protein were 191.0 g/L, and the absolute lymphocyte count decreased badly to 0.23 × 109/L. The laboratory results showed that his liver and myocardium were very likely to be affected. The electrocardiograph monitoring showed the blood pressure, heart rate, respiratory rate and oxygen saturation were 138/80 mmHg, 95 bpm, 33 bpm and 93% under the mask oxygen supplementation of 10 liters per minute. The doctors informed the
patient’s families of a critical condition. However, the patient felt better on February 3, for instance, the shortness of breath was significantly recovering. On February 4, the C-reactive protein decreased to 13.6 g/L, and the absolute lymphocyte count rose to 0.58 × 109/L, which indicated that the patient was recovering rapidly. The indexes of liver and myocardium function recovered. Both fever and shortness of breath disappeared on February 5. He was rolled out of ICU. On February 9, the fourth chest CT confirmed that the pneumonia was disappearing. On February 13, the C-reactive protein concentration was 10.1 g/L, and the absolute lymphocyte count was 0.93 × 109/L. Up to now, the patient felt much better.
Supplementary 4: More results of the 10 x RNA-seq surevey Flow cytometry analysis The PI staining results showed that 91.60% of the total cell population was alive, and the cells were: CD105+, CD90+, CD73+, CD44+, CD29+, CD14- and CD45- (Supplemental Figure 1).
Supplemental Figure 1. Flow cytometry evaluation of transplanted MSCs (A) Single cells (87%) were gated firstly. (B) Live cells (91% of the single cells) were enrolled. (C-F) 99% of selected cells were CD105+, CD90+, CD73+, CD44+, CD29+, CD14- and CD45-.
The overview of the survey
A deep transcriptional states map of MSCs and gene expression at single-cell level was generated after the performance of 10× Genomics high throughput of RNA sequencing. The 12,500 cells were acquired in the survey, leading to 881,215,280 raw reads totally. The median number of genes and UMIs detected per cell were 4,099 and 23,971, respectively (Supplemental Figure 2). The sequencing saturation rate was 72.9%, which met the scRNA-seq requirements.
Supplemental Figure 2. In the 10 x RNA-seq survey, the median number of genes and UMIs detected per cell were 4,099 (A) and 23,971 (B) as showed in the violin distribution.
MSCs marker genes expression
The scRNA-seq showed that the MSCs highly expressed ENG (CD105), THY1 (CD90), and NT5E (CD73). However, the expression of PTPRC (CD45), CD34, CD14, CD19, and HLA-DR was nearly undetected in the cells (CD45 was the only one shown in Supplemental Figure 3). The results were in accordance with the flow cytometry analysis. In Supplemental Figure 3, one point meant one cell, and red and gray color represented high expression and low expression, respectively.
Supplemental Figure 3. MSCs marker genes expression by 10 x scRNA-seq analysis. (A) CD105+, (B) CD90+, (C) CD73+, and (D) CD45-
ACE2 gene expression and DEGs between ACE2+ MSC and ACE2– MSC
Only one of the 12,500 cells was ACE2+ as shown in Supplemental Figure 4A. Furthermore, the top 60 DEGs between the ACE2+ MSC and the other nearby ACE2- MSC were shown in Supplemental Figure 4B. It is revealed that the ACE2+ MSC tended to generate pro-inflammatory function by
secreting IL-8, IL-6 and so on, while ACE2- MSC tended to generate anti-inflammatory effect by secreting BDNF and other factors.
Supplemental Figure 4. (A) ACE2 gene expression in MSCs. (B) top 60 DEGs between one ACE2+ MSC and one ACE2- MSC
TMPRSS2 gene expression and DEGs between TMPRSS2 + MSC and TMPRSS2 – MSC
Only seven of the 12,500 cells were TMPRSS2+ as shown in Supplemental Figure 5A. Furthermore, the top 60 DEGs between the TMPRSS2+ MSC and the other seven nearby TMPRSS2- MSC were shown in Supplemental Figure 5B.
Supplemental Figure 5. (A) TMPRSS2 gene expression in MSCs. (B) top 60 DEGs between seven TMPRSS2+ MSCs and seven TMPRSS2- MSCs
Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis
KEGG pathway analysis demonstrated diseases mainly related to viral infectious diseases, cancers and endocrine and metabolic disorders (1727 genes, 1605 genes and 1384 genes, respectively). Organismal systems mainly related to endocrine and immune systems (1578 genes and 748 genes, respectively) (Supplemental Figure 6). Four enriched KEGG pathways were also involved in viral infection (Supplemental Figure 7).
Supplemental Figure 6. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that many gene expressions of MSCs were related with endocrine and immune systems.
Supplemental Figure 7. Four enriched KEGG pathways were also involved in viral infection.
Furin, a potential therapeutic target for COVID-19
Canrong WU,a,1Yueying YANG,b,1Yang LIU,bPeng ZHANG,bYaliWANG,bQiqi WANG, b Yang XU,bMingxue LI,bMengzhu ZHENG,a,* Lixia CHEN,b,* &Hua LIa,b,*
aHubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China bWuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
1 These authors contributed equally to this work. *Corresponding author: Hua Li (E-mail: firstname.lastname@example.org).
A novel coronavirus (SARS-CoV-2) infectious disease has broken out in Wuhan, Hubei Province since December 2019, and spread rapidly from Wuhan to other areas, which has been listed as an international concerning public health emergency. We compared the Spike proteins from four sources, SARS-CoV-2, SARS-CoV, MERS-CoV and Bat-CoVRaTG13, and found that the SARS-CoV-2 virus sequence had redundant PRRA sequences. Through a series of analyses, we propose the reason why SARS-CoV-2is more infectious than other coronaviruses. And through structure based virtual ligand screening, we foundpotentialfurin inhibitors, which might be used in the treatment of new coronary pneumonia.
In December 2019, a series of acute respiratory diseases occurred in Wuhan, Hubei Province, China and then spread rapidly from Wuhan to other areas. As of February 17, 2020, a total of 71,444 patients have been diagnosed and 1,775 have died worldwide. This is caused by a novel coronavirus, which was named as “2019-nCoV” by the World Health Organization, and diseases caused by 2019-nCoV was COVID-19. 2019-nCoV, as a close relative of SARS-CoV, was classified as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses (ICTV) on February 11, 2020.
Coronaviruses (CoVs) are mainly composed of four structural proteins, including Spike (S), membrane (M), envelope (E) and nucleocapsid (N) . Spike, a trimeric glycoprotein of CoVs, determines diversity of CoVs and host tropism, and mediates CoVs binding to host cells surface-specific receptors and virus-cell membrane fusion . Current research found that SARS-CoV-2 belongs to the beta coronavirus genus, and speculated that it may interact with angiotensin-converting enzyme 2 (ACE2) on the surface of human cells through Spike protein, thereby infecting human respiratory epithelium cell . Letko M and Munster Vthen identified the receptor for SARS-CoV-2 entry into human cells to be ACE2 .
Coronavirus Spike protein plays a key role in the early stages of viral infection, with the S1 domain responsible for receptor binding and the S2 domain mediating membrane fusion . The process of SARS-CoV infecting the host involves two indispensable cleaving processes which affect the infectious capacity of SARS-CoV. First, Spike was cleaved into receptor-bound N-terminal S1 subunit and membrane-fusion C-terminal S2 subunit by host proteases at S1/S2 cleavage site (such as type II transmembrane serine protease (TMPRSS2), cathepsins B and L) [6,7]. Second, after CoVs are endocytosed by the host, the lysosomal protease mediates cleavage of S2 subunit (S2’ cleavage site) and releases the hydrophobic fusion peptide to fuse with the host cell membrane .
Furin, a kind of proprotein convertases (PCs), is located in the trans-Golgi network (TGN) and activated by acid pH . Furin can cleave precursor proteins with specific motifs to produce mature proteins with biological activity. The first (P1) and fourth (P4) amino acids at the N-terminus of the substrate cleavage site must be arginine “Arg-X-X-Arg ↓” (R-X-X-R，X: any amino acid, ↓:cleavage site). If the P2 position is basic lysine or arginine, the cleavage efficiency
can be improved by about 10 times . Kibler KV et al. demonstrated that the Spike protein S1/S2 and S2′ cleavage sites of the infectious bronchitis virus (IBVs) Beaudette strain can be recognized by fruin, which is a distinctive feature of IBV-Beaudette with other IBVs and has stronger infection ability [11,12]. Based on the characteristics of furin’s recognition substrate sequence, some short peptide inhibitors have been developed, such as Decanoyl-Arg-Val-Lys-Arg-chloromethylketone (Dec-RVKR-CMK) and modified α1-antitrypsin Portland (α1-PDX). However, the non-specific and irreversible inhibitory effects on all members of the PC family limit their application [10, 13]. No small molecule inhibitor of furin with good effect and high specificity has been found so far.
The epidemiological observations showed the infectious capacity of SARS-CoV-2 is stronger than SARS-CoV, so there are likely to be other mechanisms to make the infection of SARS-CoV-2 easier. We suppose the main possibilities as follows, first, SARS-CoV-2 RBD combining with ACE2 may have other conformations; second, the SARS-CoV-2 Spike protein can also bind to other receptors besides ACE2; third, Spike is more easily cleaved by host enzymes and easily fuses with host cell membrane. We compared the Spike proteins from four sources, SARS-CoV-2, SARS-CoV, MERS-CoV and Bat-CoVRaTG13, and found that the SARS-CoV-2 virus sequence had redundant PRRA sequences. Through a series of analyses, this study propose that one of the important reasons for the high infectivity of SARS-CoV-2 is a redundant furin cut site in its Spike protein.And through structure based virtual ligand screening, we proposed possible furin inhibitors, which might be potentially used in the treatment of COVID-19.
2. Methodology 2.1 Homology Spike protein blast and sequence alignment.
The Spike protein of(GB:QHR63250.1) was downloaded from NCBI nucleotide database. The protein sequence were aligned with whole database using BLASTp to search for homology viral Spike protein (Alogorithm parameters, Max target sequences: 1000, Expect threshold: 10). Multiple-sequence alignment was conducted in BLASTp online and analysis with DNAMAN and Jalview. The evolutionary history was inferred using the Neighbor-Joining method in MEGA 7 software package. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test wasdetermined by 500 replicates. The Spike protein sequence analyses were
conducted in snapgene view.
2.2 Furin cleavage site prediction
The prediction of furin cleavage sites were carried out in ProP 1.0 Server (http://www.cbs.dtu.dk/services/ProP/). 2.3 Compounds database
Approved drug database was from the subset of ZINC database, ZDD (ZINC drug database) containing 2924 compounds . Natural products database was constructed by ourselves, containing 1066 chemicals separated from traditional Chinese herbals in own lab and natural-occurring potential antiviral components and derivatives. Antiviral compounds library contains 78 known antiviral drugs and reported antiviral compounds through literature search.
2.4 Homology modeling and molecular docking
Corresponding homology models predicted by Fold and Function Assignment System server for each target protein were downloaded from Protein Data Bank (www.rcsb.org). Alignment of two protein sequences and subsequent homology modeling were performed by bioinformatics module of ICM 3.7.3 modeling software on an Intel i7 4960 processor (MolSoft LLC, San Diego, CA). For the structure-based virtual screening, ligands were continuously resiliently made to dock with the targetthat was represented in potential energy maps by ICM 3.7.3 software, to identify possible drug candidates. 3D compounds of each database were scored according to the internal coordinate mechanics (Internal Coordinate Mechanics, ICM). Based on Monte Carlo method, stochastic global optimization procedure and pseudo-Brownian positional/torsional steps, the position of intrinsic molecular was optimized. By visually inspecting, compounds outside the active site, as well as those weakly fitting to the active site were eliminated. Compounds with Scores less than -30 or mfScores less than -100 (generally represents strong interactions) have priority to be selected. Protein-protein docking procedure was performed according to the ICM-Pro manual.
3. Results 3.1 Bioinformatics analysis reveals furin cut site in Spike protein of SARS-CoV-2
By sequence alignment of Spike protein sequence of SARS-CoV-2 with its highly homologous sequences, it was found that cleavage site Spike of SARS-CoV-2 had 4 redundant
amino acids-PRRA, and these were not found in those of high homology coronavirus, which formed a furin-like restriction site as RRAR(Figure S1). Through prediction in ProP 1.0 Server, it was found the sequence was indeed easily digested by furin(Figure S2). In order to explore the evolution of this sequence, we used the BLASTp method to find 1,000 homologous Spike sequences with homology from 100% to 31%, which all from beta CoVs. Multiple sequence alignments were performed on these thousands of Spike sequences. One sequence was selected from each highly homologous class (homology greater than 98.5%) for further sequence alignment, and about 155 sequences were finally selected. A homologous multiple sequence alignment was performed on these 155 sequences, and then a phylogenetic tree was constructed(Figure 1). It is found from the phylogenetic tree that the Spike of SARS-CoV-2 exhibited the closest linkage to those of Bat-SL-CoV and SARS-CoV, and far from those of MERS-CoV, HCoV-HKU1, HCoV-OC43. In general, most of the Spike protein in α-CoV does not have a furin cleavage site, most of that in gama-CoV has a furin cleavage site, and that in beta-CoV with or without furin cleavage site are common.
We performed furin digestion site prediction on the sequence of each type of coronavirus Spikethrough online software. It was found that all Spike with a SARS-CoV-2 Spike sequence homology greater than 40% did not have a furin cleavage site (Figure 1, Table 1), including Bat-CoV RaTG13 and SARS-CoV (with sequence identity as 97.4% and 78.6%, respectively). The furin cleavage site “RRAR” in SARS-CoV-2 is unique in its family, rendering by its unique insert of “PRRA”. The furin cleavage site of SARS-CoV-2 is unlikely to have evolved from MERS, HCoV-HKU1, and so on. From the currently available sequences in databases, it is difficult for us to find the source. Perhaps there are still many evolutionary intermediate sequences waiting to be discovered.
By analysis of the SARS -CoV-2 Spike protein sequence, it was found that most features are similar to SARS-CoV. It has an N-terminal signal peptide and is divided into two parts, S1 and S2. Among them, S1 contains N-terminal domain and receptor binding region. And S2 is mainly responsible for membrane fusion. The C-terminal region of S2 is S2′, containing a fusion peptide, Hetad repeat1, Hetad repeat 2, and a transmembrane domain(Figure 2). There are two cleavage sites between S1 and S2 ‘, named CS1 and CS2. However, there are some differences in this two cleavage sites.
Unlike SARS-CoV, SARS-CoV-2 contains polybasic amino acids (RRAR) at the CS1 digestion site, and trypsin digestion efficiency will be significantly improved here. More importantly, as mentioned above, this site can be recognized and cleaved by the furin enzyme. The cleavage of Spike protein promotes structural rearrangements of RBD for the adaptation to receptor, thus increasing the affinity. More importantly, the digestion of Spike is an indispensable for membrane fusion of S2 part. In this case, the efficiency of the SARS-CoV-2Spike protein cleavage is significantly higher than that of SARS-CoV, and the SARS-CoV-2Spike protein could be cut during the process of virus maturation (Figure 3). The receptor affinity and membrane fusion efficiency of SARS-CoV-2 would be significantly enhanced compared to that of SARS-CoV. The membrane fusion of SARS-CoV-2Spike protein is more likely to occur during endocytosis process. This may explains the current strong infectious capacity of SARS-CoV-2. So, the development of furin inhibitors may be a promising approach to block its transmissibility.
Figure1.Evolutionary relationships of taxa.The evolutionary history was inferred using the Neighbor-Joining method. The bootstrap consensus tree inferred from 500 replicates is taken to represent the evolutionary history of the taxa analyzed. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. The evolutionary distances were
computed using the Poisson correction method and in the units of the number of amino acid substitutions per site. The analysis involved 155 amino acid sequences. All positions containing gaps and missing data were eliminated. There are a total of 711 positions in the final dataset. Evolutionary analyses were conducted in MEGA7. Those painted in red mean containing cleavage site in sequences and those painted in yellow mean no cleavage site in sequences.
Figure 2.Sequence analysis of Spike protein in SARS-CoV-2. It contains an N-terminal signal peptide, S1 and S2. S1 contains N-terminal domain and receptor binding region. And S2 is mainly responsible for membrane fusion. The C-terminal region of S2 is S2′, it contains a fusion peptide, HR1, HR2, and a transmembrane domain, the amino acid sequence numbers of every domain are annotated below them. Cleavage sites contained in SARS-CoV and SARS-CoV-2 are marked by rhombus.
Figure 3.A schematic diagram of the process of SARS-CoV and SARS-CoV-2 infecting host cells.Those protease are presented by sector in different colors. Furin can cleaveSpike in the process of viral maturation.
Table 1.Furin cleavage probability of Spike sequence homology
aScores are predicted by ProP 1.0 Server. Scores above 0.5 mean furin cleavable. bIdentities compared with SARS-CoV-2 Spike protein.
3.2 Homology modeling and protein-protein docking calculation
In our previous studies (accepted by ActaPharmaceuticaSinica B), both SARS and SARS-CoV-2 spike RBD structures have been docked with human ACE2 to calculate their binding free energy. In that time, the complex structure of SARS-CoV-2 RBD with ACE2 was not available.Its energy was calculated based on the homology model generated from
SARS_RBD-ACE2 complex. The binding energy between the SARS-CoV-2 spike RBD and human ACE2 was -33.72 kJ mol-1, and that between SARS-CoV spike RBD and ACE2 was -49.22 KJ mol-1.This means the binding affinity between SARS-CoV-2 spike and ACE2 is weaker than that of SARS spike. During this manuscript was prepared, the structure of SARS-CoV-2 spike RBD-ACE2 complex was disclosed. Based on this new real structure of SARS-CoV-2 spike RBD-ACE2 complex, we re-did the calculation and found that the binding free energy between SARS-CoV-2 spike RBD and ACE2 was -50.13 KJ mol-1 (Figure S3). This means the binding affinity between SARS-CoV-2 spike and ACE2 is slightly stronger than that of SARS spike.By inspecting the crystal structure of SARS-CoV-2 RBD-ACE2 complex and SARS RBD-ACE2 complex, one can find that one key loop of SARS-CoV-2 RBD in the complex interface had very different conformation compared to that of SARS RBD and previous modeled SARS-CoV-2 RBD (Figure S4).
In order to further explore the possible mechanism how furin cleaves SARS-CoV-2 Spike, we perform protein-protein docking for furin and Spike. Although a Cryo-EM structure of SARS-CoV-2 Spike has been published in bioRxiv during this manuscript was prepared, the PDB coordinate was still not available so far. We already built a homology model of SARS-CoV-2 Spike in our previous paper submitted to another regular journal. SARS-CoV-2 Spike structure was built by using the SARS-CoVSpike structure as the temple (PDB code: 5X58). By superimposing the SARS-CoVSpike with the SARS-CoV-2 Spike, we can find that the major conformation differences between two structures are RBD domain, Arg685/677 loop region(furin/trypsin/TMPRSS2 cut site) and S2 loop region just after fusion peptide (Figure 4A).The trypsin/TMPRSS2 cut site of SARS-CoV was disordered and missing from the original Cryo-EM structure possibly due to its flexibility and without electro density. The “PRRA” inserting in SARS-CoV-2 in this region apparently generate the more flexible loop region and accessible cut site for protease. We performed protein-protein docking by setting SARS-CoV-2 Spikefurincleavage loop as the receptor, and furin active pocket as the ligand. The protein-protein docking results showed that furin acidic/negative active pocket can be well fitted onto the SARS-CoV-2 Spikebasic/positive S1/S2 protease cleavage loop with low energy (-18.43 Kcal/mol). This implies that the extra “PRRAR” loop of SARS-CoV-2 Spike renders it more fragile to the protease. And this may allow this site to be cut during the maturation, efficiently
enhancing the infection efficiency.
Figure 4.Protein-protein docking model of SARS-CoV-2 Spike with furin. (A) Superimposition of SARS-CoVSpike and SARS-CoV-2 Spike. Two S1/S2 protease cleavage sites and fusion peptide were shown as electrostatic surface mode. (B) Furin was docked onto the putative furin cut site (Arg685) of SARS-CoV-2 Spike. Both domains are shown as electrostatic surface mode.
3.3. Virtual ligand screening of furin protein
Structure-based virtual ligand screening method was used to screen potential furin protein inhibitors through ICM 3.7.3 modeling software (MolSoft LLC, San Diego, CA) from a ZINC Drug Database (2924 compounds), a small in-house database of natural products (including reported common antiviral components from traditional Chinese medicine) and derivatives (1066 compounds), and an antiviral compounds library contains 78 known antiviral drugs and reported antiviral compounds. Compounds with lower calculated binding energies (being expressed with scores and mfscores) are considered to have higher binding affinities with the target protein.
The screening results for the ZINC Drug Database (Table 2) showed that anti-tumor drugs Aminopterin, Fludarabine phosphate and Irinotecan, antibacterial drugs Sulfoxone,Lomefloxacinand Cefoperazone,antifungaldrug Hydroxystilbamidine, antivirus drugValganciclovir,hepatoprotective drugSilybin,folic acid supplementFolinic acid have higher binding affinity to furin with mfscores lower than -100 or Scores lower than -30.
Here, we show one example of screen hits, Hydroxystilbamidine, which was predicted to bind in the active site of furin with low binding energy. In the generated docking model, Hydroxystilbamidine was well fitted into the binding pocket of the substrate and adopted similar conformation as substrate analogous inhibitor MI-52 in PDB model 5JXH,occupied two arms’ position of MI-52 (Figure 5A). Asp159, Asp259 and Asp306 were predicted to form three hydrogen bonds with imine groups of compounds (Figure 5B). It looks like that Hydroxystilbamidine mimic at least two arginines. Weak hydrophobic interaction between His194, Leu227, the backbone of Trp254 and Asn295 with the compound may further stabilize its conformation.
Table 2. Potential furin inhibitors from ZINC drug database
Vitamin B9, necessary material for the growth and reproduction of body cells
Antineoplastic, antirheumatic effects
Treatment of Parkinson’s disease
Folic acid supplement
Intermediate for serine synthesis
Treatment of nausea and vomiting induced by chemotherapy
Treatment of gastrohelcosis
Figure 5.Low-energy binding conformations of Hydroxystilbamidine bound to furin generated by molecular docking. (A) Hydroxystilbamidinewas fitted well in the active pocket of human furin, and furin was shown as electrostatic surface model. Hydroxystilbamidine (yellow) was overlapped with substrate analogue inhibitor MI-52 (purple).(B) Detailed view of Hydroxystilbamidinebinding in the activepocket of furin.
Another example was anticancer drug Imatinib. It was also predicted to bind in the active site of furin. In the generated docking model, Imatinib was fitted well in the binding pocket, and occupied the top two arms’ position of MI-52 (Figure 6A). Two hydrogen bonds were predicted to form between the compound with Glu236 and Gly255. Weak hydrophobic interaction between Val231, Pro256, Trp254 and Gly294 and the compound was found (Figure 6B).
Figure 6. Low-energy binding conformations of Imatinibto furin generated by molecular docking. (A) Imatinibwas fitted well in the active pocket of human furin, and furin was shown as electrostatic surface model. Imatinib (yellow) was overlapped with substrate analogue inhibitor MI-52 (purple).(B) Detailed view of Imatinibbinding in the activepocket of furin.
Table 3.Potential furin inhibitors from in-house natural product database
Antioxidation, anti-tumor, treatment of depression
For the natural products (Table 3), a series of compounds with antivirus and anti-inflammation effects, such as (-)-Epigallocatechin gallateand Theaflavin 3,3′-di-O-gallatefromCamellia sinensis,Biorobin from Ficusbenjamina, Andrographolide and 14-deoxy-11,12-didehydroandrographiside from Andrographispaniculata, one Andrographolide derivative (1S,2R,4aS,5R,8aS)-1- formamido-1,4a-dimethyl-6-methylene-5-((E)-2-(2-oxo-2,5-dihydrofuran-3-yl)ethenyl)decahydro
naphthalen-2-yl 5-((R)-1,2-dithiolan-3-yl)pentanoate, 3,4-seco-friedelolactone-27-lactone from Viola G7fromPhyllanthusemblica, xanthones2-[[2-O-(6-deoxy-α-L-mannopyranosyl)-β-D-xylopyranosyl]oxy]-1,8-dihydroxy-6-meth oxy-9H-xanthen-9-one, Kouitchenside J and Kouitchenside Ffrom Swertiakouitchensisexhibited high binding affinity to furin protein (mfscores< -100), suggesting the potential utility of these compounds in the treatment of SARS-CoV-2.
(-)-Epigallocatechin gallate (EGCG) was predicted to bind in the active site of furin, as Imatinib, it occupied the top two arms’ position of MI-52 (Figure 7A). Two hydrogen bonds were predicted formed between the compound with Asp258 and Ala292. Weak hydrophobic interactions between Pro256, Trp254 and Gly294 and the compound were predicted (Figure 7B).
2β,30β-dihydroxy- Phyllaemblicin three
Figure 7. Low-energy binding conformations of ECCG to furin generated by molecular docking. (A) ECCGwas fitted well in the active pocket of human furin, and furin was shown as electrostatic surface model. ECCG (yellow) was overlapped with substrate analogue inhibitor MI-52 (purple).(B) Detailed view of ECCG binding in the activepocket of furin.
The database of 78 antiviral drugs including compounds already on the market and currently undergoing clinical trials to treat SARS-CoV-2 infections was further screened. The results were shown in Table 4. DNA topoisomerase II inhibitorSuramin treating hand-foot-and-mouth disease exhibited the highest affinity with furin (mfscore = 190.406). A series HIV-1 therapeutic drugs, such as Indinavir, Tenofoviralafenamide, TenofovirDisoproxil and Dolutegravir, and hepatitis C therapeutic drugs, Boceprevir and Telaprevir also have high binding affinity to furin.
Suramin was predicted to bind in the active site of furin with high binding mfScores. From generated docking model, Suramin occupied the top right arm and bottom arm positions of MI-52, it extended more to another adjacent pocket and covered almost all the surface areas for furin substrate binding (Figure 8A). Asp154, Asp228, Gly229, Ser253, Asp264, Glu271, Ile312, Lys449,
Arg490 and Asp530 were predicted to form 10 hydrogen bonds with the compound. Weak hydrophobic interactions may form between His194, Leu227, Tyr308, Trp531 and A532 with the compound (Figure 8B).
Table 4.Potential furin inhibitors from the common antiviral drugs database
DNA topoisomerase II inhibitor
Human immunodeficiency virus Protease (HIV PR)
Hepatitis C virus Serine protease NS3/4A (HCV NS3/4A) Modulator
Hepatitis C virus Serine protease NS3/4A (HCV NS3/4A) Modulator
Human immunodeficiency virus Integrase (HIV IN)
1.C-C chemokine receptor type 5 (CCR5) 2.CCR5 messenger RNA(CCR5 mRNA)
Inhibitor of cytochrome P450 3A (CYP3A) enzymes
Nucleoside analogue reverse transcriptase inhibitor used in the treatment of HIV infection
Figure 8.Low-energy binding conformations of Suraminto furin generated by molecular docking. (A) Suraminwas fitted well in the active pocket of human furin, and furin was shown as electrostatic surface model. Suramin (yellow) was overlapped with substrate analogue inhibitor MI-52 (purple).(B) Detailed view of Suraminbinding in the activepocket of furin.
Our previous study(accepted by ActaPharmaceuticaSinica B) analyzed the amino acid composition of the RBD domain of the ACE2 receptor of SARS-CoV-2 and Bat-CoVRaTG13. We found that several key amino acids determining binding were mutated in SARS-CoV-2, which are more similar tothat of SARS-CoV.The calculation results show that in the same conformation as the SARS-CoV protein, the binding energy of SARS-CoV-2 and ACE2 receptors was a litter higher, but this result cannot fully explain the epidemiologically high contagion, so we speculate (1)the RBD domain of SARS-CoV-2 may have other conformations; (2) there may be other receptors; and (3) there are other mechanisms that enhance infectivity. During this manuscript was prepared, the Cryo-EM structure of SARS-CoV-2 Spike was solved. Comparing thestructure of SARS-CoV-2 with the Spike structure of SARS-CoV, combined with biophysical detection, they found that SARS-CoV-2 binds more strongly to cellular ACE2 receptors. Furthermore, the just disclosed crystal structure of SARS-CoV-2 RBD-ACE2 complex showed a distinct conformational change in the key loop of complex binding interface. And the binding free energy calculation indicated a slightly stronger binding for SARS-CoV-2 RBD compared to that of SARS RBD. These results confirm our guess that the conformational change of the RBD domain of SARS-CoV-2 leads to stronger binding. However, stronger receptor binding still can’t fully explain the more infectious problem.
So we put forward these hypotheses: (1) SARS-CoV-2 can also bind to other receptors; (2) the lung may not be the earliest infection site; (3) SARS-CoV-2 is easier to cut and more easily fuse with cell membranes. Published in the Pubmed database, researchers performed RNA-seq analysis on tissue samples from 95 individuals’ 27 different tissues. The results showed that ACE2 protein was highly expressed in the small intestine and duodenum, but the expression level in lung tissue is low (Figure S5). However, we analyzed the expression of furin and found that it is distributed in various organs with little difference in expression level. Combined with the possible infection mechanism of SARS-CoV-2, the widespread distribution of furin increases the SARS-CoV-2 infection of other organs. The possibility of other organ attack is consistent with the multiple symptoms observed in clinic of COVID-19.
Based on these three conjectures, we compared the Spike sequences from SARS-CoV-2, SARS-CoV, MERS-CoV and Bat-CoVRaTG13, and found that anextra “PRRA”insert near the
S1/S2 cleavage site. The “PRRA”insert and subsequent arginine (R) constitute a RRAR sequence that can be recognized and cleaved by furin-like proteases, which may be the reason why SARS-CoV-2 infection is stronger than SARS-CoV. What’s more, we performed a homologous alignment and phylogenetic analysis of the SARS-CoV-2 sequence, and found that “PRRA”insert did not appear at any other close relatives of SARS-CoV-2, indicating that this insertwas completely novel in this genus virus. The existence of such a motif may allow Spikes to be cut into S1 and S2 by furin-like proteases before maturity, but not separated, which provides S1 with the flexibility to change the conformation to better fit the host receptor. According to Simmons G et al. studies, overexpression of furin can increase the activity of SARS-CoVSpike, but it will not cause Spike to be cleaved .This is consistent with our prediction.
Furthermore, Glowacka Ietal.and Simmons Get al.studies have demonstrated that SARS-CoVSpikes can be activated by cleavage in two ways, including proteolytic activation by cathepsins B and L in host cells . In addition, SARS-CoVSpike can be activated by TMPRSS2 cleavage on the host cell surface.What’s more, MERA-CoV, S1/S1 and S2’ cleavage sites cannot be cut by fruin.So we speculated that the activation of SARS-CoV-2 Spike can be through different protease cleavage pathways and these pathways can occur simultaneously in host cells. SARS-CoV-2 Spike can utilize host protease diversity to activate, which may explain the strong infectious capacity of SARS-CoV-2. As we can see in Figure 2, the Spike protein of SARS-CoV-2 can be cleaved at multiple stages, which greatly increases the efficiency of fusion. It is likely that the virus will fuse with the cell during endocytosis and release the genome. In addition, the binding ability of the cleaved Spike to the ACE2 receptor is also greatly enhanced .
According to our study, furin-like proteases may be potential drug targets for anti-SARS-CoV-2 treatment. At present, some peptide inhibitors have been developed and have good effects [27, 28]. To search potential inhibitors of furin-like proteases, we screened potential compounds from a ZINC drug database (2924 compounds), a small in-house database of natural products (1066 compounds), and existing antiviral drugs library (78 compounds) withfurinby virtual ligand screening. From the ZINC Drug Database, we found a series of anti-tumor, antibacterial, antivirus,hepatoprotective drugs, such as Aminopterin, Fludarabinephosphate,Sulfoxone,Irinotecan, Hydroxystilbamidine, Lomefloxacin, Cefoperazone, Valganciclovir,Imatinib, etc. might be used as furin inhibitors. For the natural products, some
flavonoids, diterpenoids, and steroids with antivirus and anti-inflammation effects, such as ECCG, Biorobin, Phyllaemblicin G7, Andrographolide and its derivatives, and xanthonesfrom the Swertiagenus, etc.exhibited high binding affinity to furin protein. From the database of 78 antiviral drugs, a series of HIV-1, hepatitis C, and hand-foot-and-mouth disease therapeutic drugs, such as Indinavir, Tenofoviralafenamide, Tenofovir, Disoproxil, Dolutdegravir, Boceprevir, Telaprevir and Suraminalso showed high binding affinity to furin. These potentialfurin inhibitors and medicinal plants containing these compounds as major constituents might be useful for the treatment COVID-19. The further experiments to verify their efficiency in viro and in vivo will be carried out in our future studies. What’s more, combined administration of targeting different SARS-CoV-2 proteases with furin inhibitors may be an effective therapeutic strategy.
We acknowledge support from National Mega-project for Innovative Drugs (grant number 2019ZX09721001-004-007), National Natural Science Foundation of China (NSFC) (grant number No.U1803122, 81773637, 81773594, U1703111).
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Furin, a potential therapeutic target for COVID-19 Supplementary information
Figure S1. Multiple sequence alignment of 1000 Spike proteins. These 156 proteins were ranked according to their homology with SARS-2.The sequence corresponding to PRRA in SARS-CoV-2 in each sequence is marked in the red box.
Figure S2. Result of furin cleavage site pridiction of Spike protein in SARS-CoV-2, which predicted by online method ProP 1.0 Server.
Figure S3. Protein-protein dockingcalculation model of SARS-CoV-2 spike RBD (light blue) with human ACE2 (yellow), original RBD conformation was shown in orange. The calculated free energy is -50.13 Kcal/mol.
Figure S4. Comparison of SARS-CoV-2 spike RBD (orange) and SARS spike RBD (yellow). The complex with ACE2 (left part, yellow) was shown. The homology model of SARS-CoV-2 spike RBDbuilt from SARS spike RBD was shown as blue.
Figure S5. Expression levels of Furin, ACE2 and TMPRSS2 in various tissues. The data is from pubmed [1-3].
 Angiotensin I converting enzyme 2 (ACE2) expression level in human tissues using HPA RNA-seq method. [DB/OL].(2020-02-03) [2020-02-17]. https://www.ncbi.nlm.nih.gov/gene/59272/?report=expression.  Furin, paired basic amino acid cleaving enzyme (Fruin) expression level in human tissues using HPA RNA-seq method. [DB/OL].(2019-12-21) [2020-02-17]. https://www.ncbi.nlm.nih.gov/gene/5045/?report=expression.
 Transmembrane serine protease 2 (TMPRSS2) expression level in human tissues using HPA RNA-seq method. [DB/OL].(2019-12-21) [2020-02-17]. https://www.ncbi.nlm.nih.gov/gene/7113?report=expression.
Potential treatment of Chinese and Western Medicine targeting nsp14 of 2019-nCoV
Chao Liu 1, Xiaoxiao Zhu 1, Yiyao Lu 1, Xu Jia 1*, Tai Yang 2*
1 Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, China
2 School of Pharmacy, Chengdu Medical College, Chengdu, Sichuan, China *Correspondence to: Xu Jia: email@example.com
Tai Yang: firstname.lastname@example.org
2019 novel coronavirus (2019-nCoV) caused severe, large-scale acute respiratory disease outbreak in Wuhan, China. The 2019-nCoV has spread to other regions and countries around the world, which is seriously threatening human health. There is an urgent need to develop drugs for the prevention and treatment of 2019-nCoV. 2019- nCoV nonstructural protein 14 (NSP14) carrying RNA cap guanine N7- methyltransferase and 3′-5′ exoribonuclease activities could be a potential drug target for intervention. NSP14 of 2019-nCoV shared 98.7% similarity with the one (PDB ID: 5nfy) of acute respiratory syndrome (SARS) Coronavirus. Then, the 2019-nCoV NSP14 structures were modelled by using SARS NSP14 (PDB ID: 5nfy) as template for virtual screening. Based on the docking score, 18 small molecule drugs were selected for further evaluation. The compounds, including Saquinavir, Hypericin, Baicalein and Bromocriptine, could bind the N-terminus and C-terminus of the homology model of the 2019-nCoV Nsp14, thus providing as a candidate drug against 2019-nCoV for further study.
In December 2019, a large scale, severe acute respiratory disease named as “2019 novel coronavirus (2019-nCoV)” occurred in Wuhan, China, and has already spread to other regions of China and other countries around the world in the following one month, seriously threatening human health. There is an urgent demand to develop drugs for the prevention and treatment of 2019-nCoV. Coronavirus NSP plays an important role in the virus’ genome replication and transcription 1,2, and it is generally conserved as an important functional protein in the coronavirus family. Among the family, NSP14 protein has both exonuclease and methyltransferase functions, which is important for replication and transcription of SARS and other coronavirus, thus providing attractive target for drug designs 3-5.
The amino acid sequence alignment revealed that the NSP14 of 2019-nCoV shared 98.7% similarity with the one (PDB ID: 5nfy) of SARS (Figure 1). Thus, the 2019- nCoV NSP14 structures were modelled by using SARS NSP14 (PDB ID: 5nfy) as template. The N-terminus and C-terminus of 2019-nCoV NSP14 were designated as active sites for screening drugs. A total of 7496 drugs obtained in the ZINC database were subjected to the binding screening. Among them, 2100 drugs were approved by FDA, 4264 drugs were approved by other regulatory agencies besides FDA (world-not- FDA) and 1132 drugs are undergoing clinical trials but not yet approved (investigational-only). The docking was carried out using AutoDock Vina1.1.2. Ten top compounds showed the lowest negative vina score in a range of -8.6 to -9.7 kcal/mol were selected from the N-terminal domain of homology model (Table. 1), and eight top compounds with lowest negative vina score in a range of -8.7 to -9.7 kcal/mol were achieved from the C-terminal domain of homology model (Table. 2). More importantly, the compounds, including Saquinavir, Hypericin, Baicalein and Bromocriptine, not only could bind the N-terminus and C-terminus of the homology model (Figure 1. A, B), but also could bind the N- terminal and C-terminal active pockets of the 2019-nCoV Nsp14 (Figure 1. C, D).
2. Materials and Methods 2.1 Docking method
The SARS NSP14 amino acid sequence was downloaded from the PDB protein structure database (PDB ID: 5nfy). The 2019-nCoV amino acid sequence (Accession number: MN908947) was obtained from database of the National Center for Biotechnology Information (NCBI). The homology of above amino acid sequence was aligned using ClustalW. Homology model of the target protein was constructed and optimized by Modeller9.18 using crystal structure of SARS NSP14 (PDB ID: 5nfy) as template. A total of 100 independent structures were constructed, and the one with best DOPE score was selected for further energy minimization by Amber.
The ligands were downloaded from the ZINC database (FDA, world-not-FDA, investigational-only, http://zinc.docking.org/substances/subsets/). The 2D structure of the compound was then converted into the corresponding 3D coordinates using the Babel server (http://openbabel.sf.net). Then the model was converted to pdbqt format by prepare_receptor4.py script with assigning atom type and partial charge. All rotatable bonds in the ligand were set as flexible for flexible docking. Vina1.1.2 was used for molecular docking. The docking boxes were selected at the N-terminal exonuclease domain (aa: 62-290) and C-termimal transmethylase domain (aa: 291-527) of 2019-nCoV NSP14 respectively.
2.2 Binding free energy calculation
Each simulation system was immersed in a cubic box of TIP3P water with 10 Å distance from the solute. The Na+ or Cl- was applied to neutralize the system. General Amber force field (GAFF) 15 and Amber ff14SB force field were used to parameterize the ligand and protein respectively. 10,000 steps of minimization with constraints (10 kcal/mol/Å2) on heavy atoms of complex, including 5,000 steps of steepest descent minimization and 5,000 steps of conjugate gradient minimization, was used to optimize each system. Then each system was heated to 300 K within 0.2 ns followed by 0.1 ns equilibration in NPT ensemble. Finally, 5 ns MD simulation on each system at 300 K
was performed. The minimization, heating and equilibrium are performed with sander program in Amber18. The 5 ns production run was performed with pmemd.cuda. Based on the 5 ns MD simulation trajectory, binding free energy (ΔG) was calculated with MM/GBSA method according to the following equation: ΔGcal=ΔH- TΔS=ΔEvdw+ΔEele+ΔGgb+ΔGnp-TΔS, where ΔEele and ΔEVDW refer to electrostatic and van der Waals energy terms respectively. ΔGgb and ΔGnp refer to polar and non-polar solvation free energies respectively. Conformational entropy (TΔS) was not calculated for saving time. Besides, the ligands were compared based on the same target, so it is reasonable to ignore the entropy.
3. Results and Discussion
3.1 Docking results of Saquinavir against 2019-nCoV NSP14 model
Saquinavir, as the first FDA-approved HIV protease inhibitor, has been used in the treatment of patients with human immunodeficiency virus (HIV) infection since 1995 6. Our docking results showed that five of the hydrogen bonds involving ASP-273, ASN-252, ASP-90, and LEU-253 were maintained upon the binding of Saquinavir and N terminus of 2019-nCoV NSP14 (Fig. 1A). Meanwhile hydrogen bonds involving ASN-386, GLN-313, GLY-333 and THR-428 maintained upon the binding of Saquinavir and C terminus of 2019-nCoV NSP14 (Fig. 1C). Saquinavir could bind to the N- and C-terminal active pockets of the 2019-nCoV NSP14 (Fig. 1B, D). The recent study from a drug-target interaction deep learning model showed that Saquinavir can bind to 2019-nCoV RNA-dependent RNA polymerase to inhibit the enzyme activity7. Our simulation results showed that Saquinavir can bind two active sites of NSP14, thus Saquinavir could be as a candidate drug against 2019-nCoV for further research.
3.2 Docking results of Hypericin against 2019-nCoV NSP14 model
Hypericin as a main ingredient in traditional Chinese medicine- Hypericum perforatum L. (St. John’s wort) has been demonstrated activity against RNA viruses in
vitro by inhibiting viral replication 8. The present docking results showe that three of the hydrogen bonds involving ASN-252, GLY-93, and HIS-268 are maintained upon the binding of Hypericin and N-terminus of 2019-nCoV NSP14 (Fig. 2A). The six hydrogen bonds involving ASN-306, ARG-310, ASN-422 and LY-336 are maintained upon the binding of Hypericin and C-terminus of it (Fig. 2C). Hypericin can bind to the N- and C-terminal active pockets of the 2019-nCoV Nsp14 (Fig. 2B, D). Hypericin has been proven to have inhibitory effects on human hepatitis C virus (HCV) and human immunodeficiency virus (HIV)9. Combined the present study, Hypericin may have potential antiviral effect against 2019-NcoV. The traditional Chinese medicine- Hypericum perforatum L as main composition of Shuanghuanglian oral liquid has been widely used for the treatment of viral influenza. However, Shuanghuanglian oral solution has been suggested for the treatment of 2019-nCoV, triggering a huge crisis of public trust in Chinese scientists. We suggested that anti-2019-nCoV effects of Hypericin should be detected in cell culture models of 2019-nCoV infection. This will help us have a good understanding whether it is a good method to use Chinese medicines for the treatment of 2019-nCoV or not.
3.3 Docking results of Baicalein against 2019-nCoV NSP14 model
Baicalein, a flavonoid compound isolated from the root of Scutellaria baicalensis Georgi (Huang Qin in Chinese), inhibit viral replication of parainfluenza, influenza A, hepatitis B, HIV-1, and SARS coronavirus 10-12. The present docking results showed that six of the hydrogen bonds involving ASN-266, ASP-273, GLY-93, GLU-92, and HIS-268 were maintained upon the binding of Hypericin and N-terminus of 2019-nCoV NSP14 (Fig. 2A). Four hydrogen bonds involving ASN-386, ASP-331, and GLN-313 are maintained upon the binding of Hypericin and C-terminus of it (Fig. 2C). Baicalein can also bind to the N- and C-terminal active pockets of the 2019-nCoV NSP14 (Fig. 2B, D). The previous study showed that Baicalein as a novel chemical inhibitor could inhibit ATPase activity of NSP13 protein of SARS coronavirus 13. The present data suggests that Baicalin may bind to NSP14 protein to exert anti-2019-nCoV activity.
Therefore, we suspect that the anti-2019-nCoV activity induced by the Baicalein could be valuable for further study.
3.4 Docking results of Bromocriptine against 2019-nCoV NSP14 model
Bromocriptine, a specific dopamine receptor agonist for the hypothalamus and pituitary, has inhibitory effect on replication the Dengue virus with low cytotoxicity (half maximal effective concentration, EC50=0.8-1.6 μM; and half maximal cytotoxicity concentration, CC50=53.6 μM) 14. Moreover, Bromocriptine inhibited Zika virus protease activities and exhibited synergistic effects with interferon-α2b against Zika virus replications15. It is interesting to find that Bromocriptine can bind to the N- and C-terminal active pockets of the 2019-nCoV NSP14 from our molecular docking results (Fig. 4B, D). The present results showed that three of the hydrogen bonds involving ASN-104, ASP-273 and GLN-145 were maintained upon the binding of hypericin and N terminus of 2019-nCoV NSP14 (Fig. 4A). There was one bond involving THR-428 maintained upon the binding of hypericin and C terminus of it (Fig. 4C).
3.5 The calculation of binding free energy
Based on the 5 ns MD simulation trajectory, binding free energy (ΔG) was calculated by MM/GBSA method. The calculated binding free energies of Saquinavir, Hypericin, Baicalein and Bromocriptine for the N-terminus of the homology model were -37.2711±3.2160, -30.1746±3.1914, -23.8953±4.4800, -34.1350±4.3683 kcal/mol, respectively (Table 3), while the calculated binding free energies were – 60.2757±4.7708, -30.9955±2.9975, -46.3099±3.5689, -59.8104±3.5389 respectively, when binding to the C-terminus (Table 4). Taken together, the results demonstrated that Saquinavir had the strong binding free energy.
2019-nCoV NSP14, a bifunctional enzyme carrying RNA cap guanine N7-
methyltransferase and 3′-5′ exoribonuclease activities could be a potential drug target for intervention. 2019-nCoV NSP 14 shares 98.7% sequence similarity with the corresponding one in SARS. Thus, the homology models of 2019-nCoV NSP14 was structured for virtual screening. Based on the docking score, 18 drugs were selected for further evaluations. Four drugs (Saquinavir, Hypericin, Baicalein and Bromocriptine) could bind to the N-terminal and C-terminal domains of 2019-nCoV NSP 14. Combined the anti-viral function of above four drugs reported by the published literatures, we suggest the anti-2019-nCoV effects of above four drugs should be evaluated in the cell culture models of 2019-nCoV infection.
This work was supported by grants from the National Natural Science Foundation of China (NO. 31870135, 31600116) and the “1000 Talent Plan” of Sichuan Province (NO. 980).
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Figure and Table legends
Figure 1. The binding model of Saquinavir against 2019-nCoV NSP14. (A) Interactions between Saquinavir (cyan) and associated residues (off-white) in the N-terminus of the homology model for 2019-nCoV; (B) Binding models of Saquinavir (cyan) in the 2019-nCoV NSP14 protein N-terminus pocket (white surface); (C) Interactions between Saquinavir (cyan) and associated residues (off- white) in the C-terminus of the homology model for 2019-nCoV; (D) Binding models of Saquinavir (cyan) in the 2019-nCoV NSP14 protein C-terminus pocket (white surface). Numbers accompanying dashed yellow lines represents the interaction distance (Å).
Figure 2. The binding model of Hypericin against 2019-nCoV NSP14. (A) Interactions between Hypericin (cyan) and associated residues (off-white) in the N-terminus of the homology model for 2019-nCoV; (B) Binding models of Hypericin (cyan) in the 2019-nCoV NSP14 protein N-terminus pocket (white surface); (C) Interactions between Hypericin (cyan) and associated residues (off- white) in the C-terminus of the homology model for 2019-nCoV; (D) Binding models of Hypericin (cyan) in the 2019-nCoV NSP14 protein C-terminus pocket (white surface). Numbers accompanying dashed yellow lines represents the interaction distance (Å).
Figure 3. The binding model of Baicalein against 2019-nCoV NSP14. (A) Interactions between Baicalein (cyan) and associated residues (off-white) in the N-terminus of the homology model for 2019-nCoV; (B) Binding models of Baicalein (cyan) in the 2019-nCoV NSP14 protein N-terminus pocket (white surface); (C) Interactions between Baicalein (cyan) and associated residues (off-white) in the C-terminus of the homology model for 2019-nCoV; (D) Binding models of Baicalein (cyan) in the 2019-nCoV NSP14 protein C-terminus pocket (white surface). Numbers accompanying dashed yellow lines represents the interaction distance (Å).
Figure 4. The binding model of Bromocriptine against 2019-nCoV NSP14. (A) Interactions between Bromocriptine (cyan) and associated residues (off-white) in the N-terminus of the homology model for 2019-nCoV; (B) Binding models of Bromocriptine (cyan) in the 2019-nCoV NSP14 protein N- terminus pocket (white surface); (C) Interactions between Bromocriptine (cyan) and associated residues (off-white) in the C-terminus of the homology model for 2019-nCoV; (D) Binding models of Bromocriptine (cyan) in the 2019-nCoV NSP14 protein C-terminus pocket (white surface).
Numbers accompanying dashed yellow lines represents the interaction distance (Å).
Table 1 –Ten drugs selected from the N-terminal domain of homology model
Table 1 –Ten drugs selected from the N-terminal domain of homology model
1 Department of Critical Care Medicine, Baoshan People’s Hospital, Baoshan 678000, China
2 Intervention and Cell Therapy Center, Peking University Shenzhen Hosptial, Shenzhen 518035, China
3 Yunnan Yasheng Medical Technology Co., Ltd., Kunming 650021, China
4 Emergency Department of the First Affiliated Hospital of Kunming Medical University, EICU/MICU, Kunming 650032, China
5 Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases & Yunnan Stem Cell Translational Research Center, Kunming University, Kunming 650214, China
6 Department of Neonatology, Baoshan People’s Hospital, Baoshan, 678000, China
7 School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 517108, China
8 Yunnan Jici Institute for Regenerative Medicine co., Ltd., Kunming 650106, China
# These authors contribute equally.
* Correspondence to: E-mail: email@example.com (Hu M.); firstname.lastname@example.org (Qian
C.); email@example.com (Gao Y.)
The COVID-19 cases increased very fast in the last two months. The mortality among critically ill patients, especially the elder ones, was relatively high. Considering that most of the dead patients were caused by severe inflammation response, it is very urgent to develop effective therapeutic agents and strategies for these patients. The human umbilical cord mesenchymal stem cells (hUCMSCs) have shown very good capability to modulate immune response and repair the injured tissue with good safety.
Here, we reported the treatment process and clinical outcome of a 65-year-old female critically ill COVID-19 patient infected with 2019-nCoV (now called SARS-CoV-2). The significant clinical outcome and well tolerance was observed by the adoptive transfer of allogenic hUCMSCs.
Our results suggested that the adoptive transfer therapy of hUCMSCs might be an ideal choice to be used or combined with other immune modulating agents to treat the critically ill COVID- 19 patients.
In December 2019, the outbreak of 2019 novel coronavirus (now called SARS-CoV-2) infected pneumonia (COVID-19) began in Wuhan, China. As of 22th Feb. 2020, 2019 novel coronavirus had infected 76392 people in China (among which 2348 were killed) and 1404 people in other twenty-seven countries and regions (among which twelve people were killed) . It was reported that the elder patients were inclined to get more severe symptom, and the ICU admission ratio of them was significantly than the younger. Including the ground glass opacity in the lung, the other typical diagnosis characteristic of the critically ill patients was significant decrease in lymphocytes along with the increase of neutrophils. The ICU admission patients have higher concentrations of IL-6, G-CSF, IP10, MCP-1, MIP1A, and TNF-α, indication the occurrence of cytokine storm [2, 3]. Persistence of cytokine storm will thus cause the severe organ injury and death . There are no good choice to overcome the cytokine storm, these critically ill patients were always treated with glucocorticoid. But in most cases, the treatment of glucocorticoid will cause severe side effects including osteoporosis and hypoimmunity, or even delay the clearance of the virus [2, 5]. Therefore, it is very urgent to discover novel strategies to treat these critically ill patients .
Mesenchymal stem cells (MSCs) have been widely used to treat type 2 diabetes, autoimmune disease, spinal cord injury, GVHD, and other diseases with very good safety [7, 8]. Among which, the umbilical cord mesenchymal stem cells (hUCMSCs) can be easily get and cultured. hUCMSCs have shown very significant immunomodulation and tissue repair effects with low immunogenicity, which makes them very ideal candidate to the allogenic adoptive transfer therapy. It was also suggested to be potential to treat the H5N1 infection induced acute lung injury, which showed similar inflammatory cytokine profile to that of COVID-19 . Up to now, the therapeutic effects of MSCs on COVID-19 have not been reported yet.
Here, we will introduce a critically ill elder female patient in China infected with 2019 novel coronavirus. The characteristics of the vital signs, CT images, clinical laboratory profiles, and major immune cell changes will be investigated. The clinical outcome of hUCMSCs adoptive transfer therapy will be also discussed.
On January 27, 2020, a 65-year-old woman felt fatigue and fever with a body temperature of 38.2oC, then cough with small amount of white bubble sputum. Considering that she had flown from Wuhan on January 21, 2020, she was immediately sent to the Longling People’s Hospital, and the throat swabs were collected. Then, antibiotics and phlegm reducing drugs were given for supportive treatment. On January 28, she had chest tightness with SPO2 of 81%, and blood pressure 160/91 mmHg. On the same day, the real-time RT-PCR result reported 2019 novel coronavirus positive, and X-ray examination showed ground glass opacity in the right lung. IFN-α inhalation treatment was performed. On January 29 morning, she felt chest tightness and more difficult to breathe, along with shortness of breath. In the afternoon, she was admitted to the infectious disease department of the Baoshan People’s Hospital (a tertiary hospital near Longling County) for better treatment.
On January 29, the clinical laboratory examination showed that the white blood cell count was in normal range, but the neutrophil percentage was increased to 87.9%, along with the lymphocyte percentage decreased to 9.8%. According to the guideline for the diagnosis and treatment of 2019 novel coronavirus infected pneumonia (Trial 4th Edition), the patient was treated with antiviral therapy of lopinavir/ritonavir, IFN-α inhalation and oseltamivir (oseltamivir was withdrawn after once administration), and also intravenous injection of moxifloxacin, Xuebijing, methylprednisolone, and immunoglobulin. To reduce hypoxia and prevent respiratory muscle fatigue of the patient, the non-invasive mechanical ventilator was used under the advice and guidance of hospital specialist group.
On January 30, the patient could breathe easily under the ventilator, along with normal body temperature but paroxysmal cough. Considering that she got a severe diarrhea from January 30 night to January 31 morning, electrolyte replacement and rehydration were given for supportive treatment. In case of reducing the blood glucose level (postprandial glucose level around 9.6- 14.6 mM), insulin was given intramuscularly. On January 31, the diarrhea symptom reduced significantly, but the patient showed severe electrolyte disturbance. The white blood cell count increased to 12.16×109/L, among which the neutrophil percentage increased to 92.4%. The C- reaction protein increased to 44.64mg/L, along with erythrocyte sedimentation rate increased to 88mm/h. Under the cooperation of multi-discipline team, the patient was diagnosed as
critically ill type COVID-19 along with acute respiratory failure and acute diarrhea. Diabetes
and hypertension remained to be further determined.
On February 1, the patient showed no diarrhea and no shortness of breath when stay calmly,
but with paroxysmal cough and small amount of white sputum. The white blood cell count continuously increased to 13.92×109/L, among which the neutrophil percentage increased to 95.1% and lymphocyte decreased to 2.9%. From February 1 evening to February 2 morning, the patient began to breathe fast with a respiratory rate of 35-44/min, which could not be improved by adjusting the parameter of the ventilator. The blood oxygen saturation was continuously lower than 86‒90%. Under the guidance of the COVID-19 specialist team, the patient was urgently transferred to the ICU, and invasive tracheal cannula was performed to decrease the respiratory distress.
From February 2 to 4, the white blood cell count slightly decreased, among which the percentage of neutrophil increased to 82.2% and lymphocyte to 12.5% (both were still abnormal). In the early morning of February 4, the patient got a gastrorrhagia with a liquid amount around 230mL. Considering the low levels of red blood cell count and hemoglobin, anemia symptom was shown which might be caused by immune or inflammation related hemolysis. To modulate immune cell ratio, thymosin α1 was given from February 3. Although a blood transfusion was performed on February 4, the red blood cell count (2.76×1012/L) and hemoglobin concentration (92.00g/L) were still very low on February 5. On February 6, the serum bilirubin continuously increased, with the concentrations of DBil to 43.8μM and I-Bil to 29.5μM, indicating liver injury possibility. The concentrations of CRP (82.69mg/L), PCT (0.102ng/mL), D-Dimer (4.76 μg/mL), and ProBNP (670.2pg/mL) were very high. Although the white cell count was in normal range (8.38×109/L), but the neutrophil percentage began to increase again to a very high level (92.4%). All these results indicated that the anti- inflammatory effects of glucocorticoid, antiviral drugs and antibiotics might not work very well, and the gastrorrhagia was suspected to be caused by the side effects of glucocorticoid.
On February 7, considering the severe organ injury caused by inflammatory response and side effects, the glucocorticoid and antiviral therapy were withdrawn under the advice and guidance of the specialist group. The hUCMSCs adoptive transfer therapy was proposed. On February 8, the physical condition of the patient was re-evaluated. It was confirmed that she
was critically ill type COVID-19, with severe pneumonia (mixed type), acute respiratory
distress, multi-organ injury (liver, respiratory system, and blood), moderate anemia, hypertension, type 2 diabetes, electrolyte disturbance, immunosuppression, acute gastrointestinal bleeding, and other symptoms. The family member and patient agreed to try hUCMSCs adoptive transfer therapy. The therapeutic scheme was then discussed and approved by the ethics committee of the hospital and consent forms were signed by the family member before the therapy.
As shown in Figure 1, the allogenic hUCMSCs produced under GMP condition were administrated intravenously for three times (5×107cells each time) on February 9, 12, and 15. During the therapy, antibiotics were given to prevent infection, and thymosin α1 was also given. After the first time adoptive transfer, no obvious side effects were observed, indicating it was well tolerated. As shown in Table 1, after the second administration, the serum bilirubin, CRP, and ALT/AST were gradually reduced, along with some other vital signs were also improved. The trachea cannula was also pulled off and the patient could ambulate on the ground from February 13 as well. As shown in Figure 2, after the second administration, the white blood cell count and neutrophil count decreased to the normal level, along with the lymphocyte count increased to normal level as well. More importantly, the counts of CD3+ T cell, CD4+ T cell, and CD8+ T cell were also remarkably increased to normal levels. It was also suggested that the immune modulating effects of thymosin α1 alone (From day 7 to day 12 in Figure 2) might be not very significant, indicating that hUCMSCs or combined with thymosin α1 could greatly reduce the inflammation response and help the recovery of antiviral immune cells and organs. Considering the characteristics of hUCMSCs, we speculated that they might homing to repair the injured tissues and neutralize the inflammatory cytokines (such as G-CSF and IL-6) by the expression of their receptors.
As shown in Figure 3, by comparing the chest CT images taken on January 29 to February 16 and February 21, it can be seen that the pneumonia was greatly relieved. On February 17, the patient was transferred out of ICU, and most of the vital signs and clinical laboratory indexes recovered to normal level. The throat swabs tests reported negative on both February 17 and February 19.
As a conclusion, we proposed that the adoptive transfer therapy of hUCMSCs might be an ideal choice to be used or combined with other immune modulating agents. Although only one case was shown here, it would also be very important to inspire more similar clinical practice to treat such critically ill COVID-19 patients.
Ethical Approval and Consent to participate
The study was approved by the Ethics Committee of the Baoshan People’s Hospital and informed consent was confirmed by the participants.
Consent for publication
Informed consent for publication was obtained from all authors and participants.
Availability of supporting data
The data supporting the results were included within the article.
All authors declare no competing interests.
This study was supported by the grants from Shenzhen Municipal Health Commission (SZSM201612071), the Ministry of Science and Technology of China (YCZYPT 03-1), and the Yunnan Science & Technology (2016RA093, 2018ZF007-03, 2019ZF002).
Liang B., Li T., and Hu M. had full access to all of the data in the study and take responsibility for the accuracy of the data. Chen J. Wu H. and Qian C. analyzed the data. Gao Y. wrote the manuscript. Yang W., Li Y., Li J., Nie F., Ma Z., Yang M., and Nie P. participated the study and help to collect the data.
We thank the grants supported by the Shenzhen Municipal Health Commission (SZSM201612071), the Ministry of Science and Technology of China (YCZYPT 03-1), and the Yunnan Science & Technology (2016RA093, 2018ZF007-03, 2019ZF002).
Bing Liang#, Wenjie Yang#, Jianchun Li, Fangang Nie, Mingxi Yang
Department of Critical Care Medicine, Baoshan People’s Hospital, Baoshan 678000, China Junhui Chen#, Congtao Yu
Intervention and Cell Therapy Center, Peking University Shenzhen Hosptial, Shenzhen 518035, China
Yunnan Yasheng Medical Technology Co., Ltd., Kunming 650021, China
Haiying Wu#, Chuanyun Qian*
Emergency Department of the First Affiliated Hospital of Kunming Medical University, EICU/MICU, Kunming 650032, China
Yanjiao Li, Zhaoxia Ma
Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases & Yunnan Stem Cell Translational Research Center, Kunming University, Kunming 650214, China
Department of Neonatology, Baoshan People’s Hospital, Baoshan, 678000, China
School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 517108, China; Intervention and Cell Therapy Center, Peking University Shenzhen Hosptial, Shenzhen 518035, China
Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases & Yunnan Stem Cell Translational Research Center, Kunming University, Kunming 650214, China; Intervention and
Cell Therapy Center, Peking University Shenzhen Hosptial, Shenzhen 518035, China; Yunnan
Jici Institute for Regenerative Medicine co., Ltd., Kunming 650106, China
# These authors contribute equally.
* Correspondence to: E-mail: firstname.lastname@example.org (Hu M.); email@example.com (Qian
C.); firstname.lastname@example.org (Gao Y.)
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Figure 1. The major symptoms and treatment of the critically ill COVID-19 patient
Table 1. The major clinical laboratory characteristics of the patient
Days after disease onset
range 3 6 8 10 12 13* 14 16* 17 19* 21
Figure 2. The dynamic changes of the immune cell counts of the patient. The arrows indicate the day of hUCMSCs therapy. To the white blood cell (normal range 3.5‒9.5×109/L) and neutrophil (normal range 1.8‒6.3×109/L), the dash line indicates upper threshold. While to the lymphocyte (normal range 1.1‒3.2×109/L) and T cell subsets, the dash line indicates lower threshold.