A group of SARS-like coronaviruses(SL-CoV)have been identified in horseshoe bats.Despite SL-CoVs and SARS-CoV share identical genome structure and high-level sequence similarity,SL-CoV does not bind to the same cellul...A group of SARS-like coronaviruses(SL-CoV)have been identified in horseshoe bats.Despite SL-CoVs and SARS-CoV share identical genome structure and high-level sequence similarity,SL-CoV does not bind to the same cellular receptor as for SARS-CoV and the N-terminus of the S proteins only share 64%amino acid identity,suggesting there are fundamental differences between these two groups of coronaviruses.To gain insight into the basis of this difference,we established a recombinant adenovirus system expressing the S protein from SL-CoV(rAd-Rp3-S)to investigate its immune characterization.Our results showed that immunized mice generated strong humoral immune responses against the SL-CoV S protein.Moreover,a strong cellular immune response demonstrated by elevated IFN-γand IL-6 levels was also observed in these mice.However,the induced antibody from these mice had weaker cross-reaction with the SARS-CoV S protein,and did not neutralize HIV pseudotyped with SARS-CoV S protein.These results demonstrated that the immunogenicity of the SL-CoV S protein is distinct from that of SARS-CoV,which may cause the immunological differences between human SARS-CoV and bat SL-CoV.Furthermore,the recombinant virus could serve as a potential vaccine candidate against bat SL-CoV infection.展开更多
Objective:To identify the safe and effective natural inhibitors of spike glycoprotein and main protease 3CLpro using potential natural antiviral compounds which are studied under various animal models and viral cell l...Objective:To identify the safe and effective natural inhibitors of spike glycoprotein and main protease 3CLpro using potential natural antiviral compounds which are studied under various animal models and viral cell lines.Methods:First,compounds were retrieved from the Pub Chem database and predicted for their druggability using the Mol Soft web server,and compounds having drug-like property were predicted for major adverse drug reactions like cardiotoxicity,hepatotoxicity,arrhythmia,myocardial infarction,and nephrotoxicity using ADVERpred.Docking of nontoxic antiviral compounds with spike glycoprotein and main protease 3CLpro was performed using Auto Dock vina by PyRx 0.8 version.The stability of compoundprotein interactions was checked by molecular dynamic(MD)simulation using Schrodinger Desmond software.Results:Based on the druggable and nontoxic profile,nine compounds were selected.Among them,Withanone from Withania somnifera showed the highest binding affinity and best fit at active sites 1 of spike glycoprotein(glycosylation site)and main protease 3CLpro via interacting with active site amino acid residues before and after MD simulation at 50 ns.Withanone,which may reduce the glycosylation of SARS-CoV-2 via interacting with Asn343 and inhibit viral replication.Conclusion:The current study reports Withanone as a non-toxic antiviral against SARS-CoV-2 and serve as a potential lead hit for further experimental validation.展开更多
As severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)continues to disperse globally with worrisome speed,identifying amino acid variations in the virus could help to understand the characteristics of it.Here,...As severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)continues to disperse globally with worrisome speed,identifying amino acid variations in the virus could help to understand the characteristics of it.Here,we studied 489 SARS-CoV-2 genomes obtained from 32 countries from the Nextstrain database and performed phylogenetic tree analysis by clade,country,and genotype of the surface spike glycoprotein(S protein)at site 614.We found that virus strains from China's Mainland were mostly distributed in Clade B and Clade undefined in the phylogenetic tree,with very few found in Clade A.In contrast,Clades A2(one case)and A2a(112 cases)predominantly contained strains from European regions.Moreover,Clades A2 and A2a differed significantly from those of China's Mainland in age of infected population(P Z 0.0071,mean age 40.24 to 46.66),although such differences did not exist between the US and China's Mainland.Further analysis demonstrated that the variation of the Sprotein at site 614(QHD43416.1:p.614D>G)was a characteristic of stains in Clades A2 and A2a.Importantly,this variation was predicted to have neutral or benign effects on the function of the S protein.In addition,global quality estimates and 3D protein structures tended to be different between the two S proteins.In summary,we identified different genomic epidemiology among SARS-CoV-2 strains in different clades,especially in an amino acid variation of the S protein at 614,revealing potential viral genome divergence in SARS-CoV-2 strains.展开更多
<strong>Aims:</strong> The outbreak of the novel coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is still accountable for millions of deaths wor...<strong>Aims:</strong> The outbreak of the novel coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is still accountable for millions of deaths worldwide and declared as a global pandemic by the World Health Organisation. Despite efforts, there is still limited evidence available on a successful potent inhibitor with a low toxicity profile that can aid in the prevention and/or treatment of COVID-19. This study will focus on four main aspects: 1) screening 19 Food Drug and Administration (FDA) approved drugs using computational molecular docking;2) assessing drug toxicity profiles using biological data;3) recommending potential therapies against COVID-19 and 4) supplementing currently used therapies. <strong>Methods:</strong> 19 FDA approved drugs were investigated against the crystal structure of SARS-CoV-2 protease (6LU7) and SARS-CoV-2 glycoprotein (6VXX) using a computational molecular docking software, Molecular Operating Environment (MOE). Separately, on MOE, 6LU7 and 6VXX were loaded, prepared, and the binding pockets located. The drug’s canonical SMILES were imported, minimised, and docked on the prepared proteins using a search algorithm to establish the highest stability conformation. Drugs were ranked depending on binding properties and biological data to assess safety;steric clashes and voids in the binding site were also analysed. <strong>Results and discussion:</strong> Out of the nineteen (19) FDA approved drugs, 18 inhibited 6LU7 and 13 inhibited 6VXX. High-ranked drugs based on binding properties for 6LU7 were hydroxychloroquine, dexamethasone, naproxen, etoricoxib, and ibuprofen. For 6VXX were hydroxychloroquine, celecoxib, etoricoxib, meloxicam, and parecoxib. Considering safety profile, the top 3 drugs in descending order for 6LU7 were etoricoxib, naproxen and dexamethasone and for 6VXX were etoricoxib, meloxicam, and parecoxib. Compared to the literature, the results were consistent for dexamethasone which was effective against 6LU7. However, for hydroxychloroquine and ibuprofen, there was conflicting literature regarding safety and efficacy. <strong>Conclusion and future work:</strong> The findings suggest that against COVID-19 etoricoxib might be effective as a therapeutic and prophylactic measure. Naproxen and dexamethasone would be more effective as treatment only while meloxicam and parecoxib as prophylaxis. However, future studies are needed to validate these findings. Compared to previous literature, the findings in this study also support the use of dexamethasone over hydroxychloroquine and ibuprofen for COVID-19 based on the binding and safety properties. Despite this, future research should explore the impressive binding properties displayed by hydroxychloroquine and ibuprofen to aid in developing a new drug against COVID-19.展开更多
运用ADME/T预测进行首轮筛选中药数据库TCMSP(Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform)中的化学成分,然后分别以(刺突糖蛋白,Spike glycoprotein,简称S蛋白)和ACE2蛋白(血管紧张素转化酶2,A...运用ADME/T预测进行首轮筛选中药数据库TCMSP(Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform)中的化学成分,然后分别以(刺突糖蛋白,Spike glycoprotein,简称S蛋白)和ACE2蛋白(血管紧张素转化酶2,Angiotensin Converting Enzyme 2,ACE2)为靶点,采用YASARA和AutoDock VINA进行第二轮虚拟筛选,最后基于靶点与药物相互作用位点对候选药物分子进行相互作用分析.从TCMSP数据库中筛选出425个候选中药成分,以S蛋白为靶点,筛选出中药成分有12个,包含在青蒿、丹参、黄芩、半夏、甘草、柴胡等;以ACE2为靶点,筛选出中药成分有77个,包含在丹参、甘草、黄芩、麻黄、杏仁、柴胡等,并最终找到潜在的抑制剂分子鼠尾草酚酮和二氢丹参内酯.展开更多
Severe acute respiratory syndrome coronavirus (SARS-CoV-2) is a newly identified member of the coronavirus family that has caused the coronavirus disease 2019 (COVID-19) pandemic. This rapidly evolving and unrelenting...Severe acute respiratory syndrome coronavirus (SARS-CoV-2) is a newly identified member of the coronavirus family that has caused the coronavirus disease 2019 (COVID-19) pandemic. This rapidly evolving and unrelenting SARS-CoV-2has disrupted the lives and livelihoods of millions worldwide. As of 23 August 2021, a total of 211,373,303 COVID-19cases have been confirmed globally with a death toll of 4,424,341. A strong understanding of the infection pathway of SARS-CoV-2, and how our immune system responds to the virus is highly pertinent for guiding the development and improvement of effective treatments. In this review, we discuss the current understanding of neutralising antibodies(NAbs) and their implications in clinical practice. The aspects include the pathophysiology of the immune response,particularly humoral adaptive immunity and the roles of NAbs from B cells in infection clearance. We summarise the onset and persistence of IgA, IgM and IgG antibodies, and we explore their roles in neutralising SARS-CoV-2, their persistence in convalescent individuals, and in reinfection. Furthermore, we also review the applications of neutralising antibodies in the clinical setting—from predictors of disease severity to serological testing to vaccinations, and finally in therapeutics such as convalescent plasma infusion.展开更多
基金supported by the State Key Program for Basic Research Grant(2005CB523004)from the Chinese Ministry of Science and Technologythe Knowledge Innovation Program Key Project administered by the Chinese Academy of Sciences(KSCX1-YW-R-07)
文摘A group of SARS-like coronaviruses(SL-CoV)have been identified in horseshoe bats.Despite SL-CoVs and SARS-CoV share identical genome structure and high-level sequence similarity,SL-CoV does not bind to the same cellular receptor as for SARS-CoV and the N-terminus of the S proteins only share 64%amino acid identity,suggesting there are fundamental differences between these two groups of coronaviruses.To gain insight into the basis of this difference,we established a recombinant adenovirus system expressing the S protein from SL-CoV(rAd-Rp3-S)to investigate its immune characterization.Our results showed that immunized mice generated strong humoral immune responses against the SL-CoV S protein.Moreover,a strong cellular immune response demonstrated by elevated IFN-γand IL-6 levels was also observed in these mice.However,the induced antibody from these mice had weaker cross-reaction with the SARS-CoV S protein,and did not neutralize HIV pseudotyped with SARS-CoV S protein.These results demonstrated that the immunogenicity of the SL-CoV S protein is distinct from that of SARS-CoV,which may cause the immunological differences between human SARS-CoV and bat SL-CoV.Furthermore,the recombinant virus could serve as a potential vaccine candidate against bat SL-CoV infection.
文摘Objective:To identify the safe and effective natural inhibitors of spike glycoprotein and main protease 3CLpro using potential natural antiviral compounds which are studied under various animal models and viral cell lines.Methods:First,compounds were retrieved from the Pub Chem database and predicted for their druggability using the Mol Soft web server,and compounds having drug-like property were predicted for major adverse drug reactions like cardiotoxicity,hepatotoxicity,arrhythmia,myocardial infarction,and nephrotoxicity using ADVERpred.Docking of nontoxic antiviral compounds with spike glycoprotein and main protease 3CLpro was performed using Auto Dock vina by PyRx 0.8 version.The stability of compoundprotein interactions was checked by molecular dynamic(MD)simulation using Schrodinger Desmond software.Results:Based on the druggable and nontoxic profile,nine compounds were selected.Among them,Withanone from Withania somnifera showed the highest binding affinity and best fit at active sites 1 of spike glycoprotein(glycosylation site)and main protease 3CLpro via interacting with active site amino acid residues before and after MD simulation at 50 ns.Withanone,which may reduce the glycosylation of SARS-CoV-2 via interacting with Asn343 and inhibit viral replication.Conclusion:The current study reports Withanone as a non-toxic antiviral against SARS-CoV-2 and serve as a potential lead hit for further experimental validation.
基金This work was supported by the research-oriented clinician funding program of Tongji Medical College,Huazhong University of Science and Technology.The mentioned funding institutions played no role in the study design,data collection,and analysis,decision to publish,or preparation of the manuscript.We are grateful for the computational analysis tools of Nextstrain,SWISS-MODEL,PROVEAN(v1.1)and PolyPhen-2.We sincerely thank the work done by all anti-epidemic personnel.
文摘As severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)continues to disperse globally with worrisome speed,identifying amino acid variations in the virus could help to understand the characteristics of it.Here,we studied 489 SARS-CoV-2 genomes obtained from 32 countries from the Nextstrain database and performed phylogenetic tree analysis by clade,country,and genotype of the surface spike glycoprotein(S protein)at site 614.We found that virus strains from China's Mainland were mostly distributed in Clade B and Clade undefined in the phylogenetic tree,with very few found in Clade A.In contrast,Clades A2(one case)and A2a(112 cases)predominantly contained strains from European regions.Moreover,Clades A2 and A2a differed significantly from those of China's Mainland in age of infected population(P Z 0.0071,mean age 40.24 to 46.66),although such differences did not exist between the US and China's Mainland.Further analysis demonstrated that the variation of the Sprotein at site 614(QHD43416.1:p.614D>G)was a characteristic of stains in Clades A2 and A2a.Importantly,this variation was predicted to have neutral or benign effects on the function of the S protein.In addition,global quality estimates and 3D protein structures tended to be different between the two S proteins.In summary,we identified different genomic epidemiology among SARS-CoV-2 strains in different clades,especially in an amino acid variation of the S protein at 614,revealing potential viral genome divergence in SARS-CoV-2 strains.
文摘<strong>Aims:</strong> The outbreak of the novel coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is still accountable for millions of deaths worldwide and declared as a global pandemic by the World Health Organisation. Despite efforts, there is still limited evidence available on a successful potent inhibitor with a low toxicity profile that can aid in the prevention and/or treatment of COVID-19. This study will focus on four main aspects: 1) screening 19 Food Drug and Administration (FDA) approved drugs using computational molecular docking;2) assessing drug toxicity profiles using biological data;3) recommending potential therapies against COVID-19 and 4) supplementing currently used therapies. <strong>Methods:</strong> 19 FDA approved drugs were investigated against the crystal structure of SARS-CoV-2 protease (6LU7) and SARS-CoV-2 glycoprotein (6VXX) using a computational molecular docking software, Molecular Operating Environment (MOE). Separately, on MOE, 6LU7 and 6VXX were loaded, prepared, and the binding pockets located. The drug’s canonical SMILES were imported, minimised, and docked on the prepared proteins using a search algorithm to establish the highest stability conformation. Drugs were ranked depending on binding properties and biological data to assess safety;steric clashes and voids in the binding site were also analysed. <strong>Results and discussion:</strong> Out of the nineteen (19) FDA approved drugs, 18 inhibited 6LU7 and 13 inhibited 6VXX. High-ranked drugs based on binding properties for 6LU7 were hydroxychloroquine, dexamethasone, naproxen, etoricoxib, and ibuprofen. For 6VXX were hydroxychloroquine, celecoxib, etoricoxib, meloxicam, and parecoxib. Considering safety profile, the top 3 drugs in descending order for 6LU7 were etoricoxib, naproxen and dexamethasone and for 6VXX were etoricoxib, meloxicam, and parecoxib. Compared to the literature, the results were consistent for dexamethasone which was effective against 6LU7. However, for hydroxychloroquine and ibuprofen, there was conflicting literature regarding safety and efficacy. <strong>Conclusion and future work:</strong> The findings suggest that against COVID-19 etoricoxib might be effective as a therapeutic and prophylactic measure. Naproxen and dexamethasone would be more effective as treatment only while meloxicam and parecoxib as prophylaxis. However, future studies are needed to validate these findings. Compared to previous literature, the findings in this study also support the use of dexamethasone over hydroxychloroquine and ibuprofen for COVID-19 based on the binding and safety properties. Despite this, future research should explore the impressive binding properties displayed by hydroxychloroquine and ibuprofen to aid in developing a new drug against COVID-19.
基金supported as the Key Medical Research Project for SARS Prevention sponsored by the Ministry of Science and Technology of China and by Guangdong Province
文摘运用ADME/T预测进行首轮筛选中药数据库TCMSP(Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform)中的化学成分,然后分别以(刺突糖蛋白,Spike glycoprotein,简称S蛋白)和ACE2蛋白(血管紧张素转化酶2,Angiotensin Converting Enzyme 2,ACE2)为靶点,采用YASARA和AutoDock VINA进行第二轮虚拟筛选,最后基于靶点与药物相互作用位点对候选药物分子进行相互作用分析.从TCMSP数据库中筛选出425个候选中药成分,以S蛋白为靶点,筛选出中药成分有12个,包含在青蒿、丹参、黄芩、半夏、甘草、柴胡等;以ACE2为靶点,筛选出中药成分有77个,包含在丹参、甘草、黄芩、麻黄、杏仁、柴胡等,并最终找到潜在的抑制剂分子鼠尾草酚酮和二氢丹参内酯.
基金supported by the National Medical Research Council,Singapore (NMRC COVID19RF2-0002)。
文摘Severe acute respiratory syndrome coronavirus (SARS-CoV-2) is a newly identified member of the coronavirus family that has caused the coronavirus disease 2019 (COVID-19) pandemic. This rapidly evolving and unrelenting SARS-CoV-2has disrupted the lives and livelihoods of millions worldwide. As of 23 August 2021, a total of 211,373,303 COVID-19cases have been confirmed globally with a death toll of 4,424,341. A strong understanding of the infection pathway of SARS-CoV-2, and how our immune system responds to the virus is highly pertinent for guiding the development and improvement of effective treatments. In this review, we discuss the current understanding of neutralising antibodies(NAbs) and their implications in clinical practice. The aspects include the pathophysiology of the immune response,particularly humoral adaptive immunity and the roles of NAbs from B cells in infection clearance. We summarise the onset and persistence of IgA, IgM and IgG antibodies, and we explore their roles in neutralising SARS-CoV-2, their persistence in convalescent individuals, and in reinfection. Furthermore, we also review the applications of neutralising antibodies in the clinical setting—from predictors of disease severity to serological testing to vaccinations, and finally in therapeutics such as convalescent plasma infusion.
