SARS-CoV-2(2019-nCoV)emerged in 2019 and proliferated rapidly across the globe.Scientists are attempting to investigate antivirals specific to COVID-19 treatment.The 2019-nCoV and SARS-CoV utilize the same receptor of...SARS-CoV-2(2019-nCoV)emerged in 2019 and proliferated rapidly across the globe.Scientists are attempting to investigate antivirals specific to COVID-19 treatment.The 2019-nCoV and SARS-CoV utilize the same receptor of the host which is COVID-19 of the main protease(Mpro).COVID-19 caused by SARS-CoV-2 is burdensome to overcome by presently acquired antiviral candidates.So the objective and purpose of this work was to investigate the plants with reported potential antiviral activity.With the aid of in silico techniques such as molecular docking and druggability studies,we have proposed several natural active compounds including glycyrrhizin,bicylogermecrene,tryptanthrine,β-sitosterol,indirubin,indican,indigo,hesperetin,crysophanic acid,rhein,berberine andβ-caryophyllene which can be encountered as potential herbal candidate exhibiting anti-viral activity against SARS-CoV-2.Promising docking outcomes have been executed which evidenced the worthy of these selected herbal remedies for future drug development to combat coronavirus disease.展开更多
Coronaviruses caused an outbreak pandemic disease characterized by a severe acute respiratory distress syndrome leading to the infection of more than 200 million patients and the death of more than 4 million individua...Coronaviruses caused an outbreak pandemic disease characterized by a severe acute respiratory distress syndrome leading to the infection of more than 200 million patients and the death of more than 4 million individuals.The primary treatment is either supportive or symptomatic.Natural products have an important role in the development of various drugs.Thus,screening of natural compounds with reported antiviral activities can lead to the discovery of potential inhibitory entities against coronaviruses.In the current study,an in-silico molecular docking experiment was conducted on the effects of some of these natural antiviral phytoconstituents,(e.g.,procyanidin B2,theaflavin,quercetin,ellagic acid,caffeoylquinic acid derivatives,berginin,eudesm-1β,6α,11-triol and arbutin),on the crystal structure of SARS-CoV-2 main protease(PDB ID:6w63)using AutoDock-Vina software.Many of the docked compounds revealed good binding affinity,with procyanidin B2(–8.6 Kcal/mol)and theaflavin(–8.5 Kcal/mol)showing a better or similar binding score as the ligand(–8.5 Kcal/mol).Molecular dynamics simulations were carried out at 100 ns and revealed that procyanidin B2 forms a more stable complex with SARS-CoV-2 main protease than theaflavin.Procyanidin B2,theaflavin,and 4,5-dicaffeoylquinic acid were evaluated for toxicity by ProTox-II webserver and were non-toxic according to the predicted LD50 values and safe on different organs and pathways.Additionally,these phytoconstituents showed good ADME properties and acceptable lipophilicity,as evaluated using WLOGP.Amongst the tested compounds,procyanidin B2 showed the highest lipophilic value.It is worth mentioning that these natural inhibitiors of SARS-CoV-2 main protease are components of green and black tea that can be used as a supporting supplement for COVID patients or as potential nuclei for further drug design and development campaigns.展开更多
Background:Since the emergence of coronavirus disease 2019 to date,there is no available approved drug or definitive treatment for coronavirus disease 2019 viral infection,and the identification of novel hits against ...Background:Since the emergence of coronavirus disease 2019 to date,there is no available approved drug or definitive treatment for coronavirus disease 2019 viral infection,and the identification of novel hits against therapeutic targets has become a global emergency.Echinacea purpurea is a traditional herb utilized to treat cough,fever,sore throat,respiratory tract infection,and so on as an immune stimulant.In this study,in silico molecular docking approach was used to screen phytocompounds from E.purpurea against severe acute respiratory syndrome coronavirus 2 main protease 3C-like protease(3CLpro)and severe acute respiratory syndrome coronavirus main peptidase(96%sequence similarity)to blunt the viral gene expression and viral replication.Methods:Initially,we screened phytocompounds for their druggability and ADMET property.Furthermore,x-ray crystallographic structures of main proteases 3CLpro and main peptidase having Protein Data Bank ID 6LU7 and 2GTB were used as protein targets for the identification of potential drug candidates.We performed docking using AutoDock Vina by PyRx 0.8 software.BIOVIA Discovery Studio Visualizer v2019 was used to analyze ligand-protein complex.The probable protein targets of the selected compound were predicted by BindingDB(P≥0.7).STRING and Kyoto Encyclopedia of Genes and Genomes pathways are utilized to identify the molecular pathways modulated by the predicted targets(FDR≤0.05),and the network interaction between compounds and protein pathways was constructed by Cytoscape 3.6.1.Results:Among all the compounds,chlorogenic acid showed druggable characteristics and scored the lowest binding energy with main protease and main peptidase via interacting with active site 1 domain amino acid residues.Interestingly,chlorogenic acid interacted with Phe140 main protease 3CLpro,which is potentially involved in the dimerization.Enrichment analysis identified chlorogenic acid to modulate insulin resistance,necroptosis,interleukin-17,tumor necrosis factor signaling pathway,legionellosis,T helper 17 cell differentiation,advanced glycation end products and receptor for advanced glycation end products,mitogen-activated protein kinase,Ras,estrogen,vascular endothelial growth factor,B-cell receptor,nuclear factor kappa B,Rap1,hypoxia inducible factor-1,phosphatidylinositide 3-kinase-Akt,insulin,mechanistic target of rapamycin,p53,retinoic acid inducible gene I like receptor,and ErbB signaling pathways.Conclusion:Chlorogenic acid may act as a potent main protease 3CLpro inhibitor and may also inhibit the severe acute respiratory syndrome coronavirus 2 dimerization,viral gene expression,and replication within the lung epithelium.Chlorogenic acid may go a long way in finding one of the multipronged solutions to tackle coronavirus disease 2019 viral infection in the future.展开更多
A titrant for the SARS-CoV-2 main protease(M^(pro))was developed that enables,for the first time,the exact determination of the concentration of the enzymatically active M^(pro) by active-site titration.The covalent b...A titrant for the SARS-CoV-2 main protease(M^(pro))was developed that enables,for the first time,the exact determination of the concentration of the enzymatically active M^(pro) by active-site titration.The covalent binding mode of the tetrapeptidic titrant was elucidated by the determination of the crystal structure of the enzyme–titrant complex.Four fluorogenic substrates of M^(pro),including a prototypical,internally quenched Dabcyl-EDANS peptide,were compared in terms of solubility under typical assay conditions.By exploiting the new titrant,key kinetic parameters for the M^(pro)-catalyzed cleavage of these substrates were determined.展开更多
The rapid evolution of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)mainly due to its high mutation rate and rapid viral replication,has led to new variants resistant to the available vaccines and monocl...The rapid evolution of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)mainly due to its high mutation rate and rapid viral replication,has led to new variants resistant to the available vaccines and monoclonal antibodies.In contrast,oral clinical drugs targeting viral protease and RNA polymerase remain effective against Omicron variants[1].Main protease(Mpro)plays a crucial role in the maturation and replication of viral strains,making it an attractive target for developing antiviral drugs.Nirmatrelvir(NTV)is the first-in-class Mpro peptidomimetic covalent inhibitor known as“Paxlovid”approved in 2021 by the Food and Drug Administration[2].Nevertheless,NTV-resistant Mpro mutants particularly the E166V mutation,have been characterized in the Global Initiative on Sharing Avian Influenza Data(GISAID)database[3]and reported in COVID-19 patients[4,5].展开更多
During the continuing evolution of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the Omicron variant of concern emerged in the second half of 2021 and has been dominant since November of that year.Along ...During the continuing evolution of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the Omicron variant of concern emerged in the second half of 2021 and has been dominant since November of that year.Along with its sublineages,it has maintained a prominent role ever since.The Nsp5 main protease(Mpro)of the Omicron virus is characterized by a single dominant mutation,P132H.Here we determined the X-ray crystal structures of the P132H mutant(or O-Mpro)as a free enzyme and in complex with the Mpro inhibitor,the alpha-ketoamide 13b-K,and we conducted enzymological,biophysical,as well as theoretical studies to characterize the O-Mpro.We found that O-Mpro has a similar overall structure and binding with 13b-K;however,it displays lower enzymatic activity and lower thermal stability compared to the WT-Mpro(with“WT”referring to the prototype strain).Intriguingly,the imidazole ring of His132 and the carboxylate plane of Glu240 are in a stacked configuration in the X-ray structures determined here.Empirical folding free energy calculations suggest that the O-Mpro dimer is destabilized relative to the WT-Mpro due to less favorable van der Waals interactions and backbone conformations in the individual protomers.All-atom continuous constant-pH molecular dynamics(MD)simulations reveal that His132 and Glu240 display coupled titration.At pH 7,His132 is predominantly neutral and in a stacked configuration with respect to Glu240 which is charged.In order to examine whether the Omicron mutation eases the emergence of further Mpro mutations,we also analyzed the P132H+T169S double mutant,which is characteristic of the BA.1.1.2 lineage.However,we found little evidence of a correlation between the two mutation sites.展开更多
SARS-CoV-2 main protease(M^(pro))is one of the most extensively exploited drug targets for COVID-19.Structurally disparate compounds have been reported as M^(pro) inhibitors,raising the question of their target specif...SARS-CoV-2 main protease(M^(pro))is one of the most extensively exploited drug targets for COVID-19.Structurally disparate compounds have been reported as M^(pro) inhibitors,raising the question of their target specificity.To elucidate the target specificity and the cellular target engagement of the claimed M^(pro) inhibitors,we systematically characterize their mechanism of action using the cell-free FRET assay,the thermal shift-binding assay,the cell lysate Protease-Glo luciferase assay,and the cell-based FlipGFP assay.Collectively,our results have shown that majority of the M^(pro) inhibitors identified from drug repurposing including ebselen,carmofur,disulfiram,and shikonin are promiscuous cysteine inhibitors that are not specific to M^(pro),while chloroquine,oxytetracycline,montelukast,candesartan,and dipyridamole do not inhibit M^(pro) in any of the assays tested.Overall,our study highlights the need of stringent hit validation at the early stage of drug discovery.展开更多
Proteolytic processing of viral polyproteins is indispensible for the lifecycle of coronaviruses.The main protease(M^(pro))of SARS-CoV is an attractive target for anti-SARS drug development as it is essential for the ...Proteolytic processing of viral polyproteins is indispensible for the lifecycle of coronaviruses.The main protease(M^(pro))of SARS-CoV is an attractive target for anti-SARS drug development as it is essential for the polyprotein processing.M^(pro) is initially produced as part of viral polyproteins and it is matured by autocleavage.Here,we report that,with the addition of an N-terminal extension peptide,M^(pro) can form a domain-swapped dimer.After complete removal of the extension peptide from the dimer,the mature M^(pro) self-assembles into a novel super-active octamer(AO-M^(pro)).The crystal structure of AO-M^(pro) adopts a novel fold with four domainswapped dimers packing into four active units with nearly identical conformation to that of the previously reported M^(pro) active dimer,and 3D domain swapping serves as a mechanism to lock the active conformation due to entanglement of polypeptide chains.Compared with the previously well characterized form of M^(pro),in equilibrium between inactive monomer and active dimer,the stable AO-M^(pro) exhibits much higher proteolytic activity at low concentration.As all eight active sites are bound with inhibitors,the polyvalent nature of the interaction between AO-M^(pro) and its polyprotein substrates with multiple cleavage sites,would make AO-M^(pro) functionally much more superior than the M^(pro) active dimer for polyprotein processing.Thus,during the initial period of SARS-CoV infection,this novel active form AOM^(pro) should play a major role in cleaving polyproteins as the protein level is extremely low.The discovery of AOM^(pro) provides new insights about the functional mechanism of M^(pro) and its maturation process.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
The main protease (Mpro) of SARS-CoV plays an essential role in the extensive proteolytic processing of the viral polyproteins (pp1a and pp1ab), and it is an important target
Despite the global decline in the severity of the coronavirus disease 2019 (COVID-19) cases, the disease stillrepresents a major concern to the relevant scientific and medical communities. The primary concern of drug ...Despite the global decline in the severity of the coronavirus disease 2019 (COVID-19) cases, the disease stillrepresents a major concern to the relevant scientific and medical communities. The primary concern of drug scientists,virologists, and other concerned specialists in this respect is to find ready-to-use suitable and potent anticoronaviraltherapies that are broadly effective against the different species/strains of the coronaviruses in general, not only againstthe current and previous coronaviruses (e.g., the recently-appeared severe acute respiratory syndrome coronavirus 2“SARS-CoV-2”), i.e., effective antiviral agents for treatment and/or prophylaxis of any coronaviral infections, includingthose of the coming ones from the next species and strains (if any). As an expert in this field, I tried, in this up-to-dateperspective “viewpoint” article, to evaluate the suitability and applicability of using the currently-availableanticoronaviral agents for the next coronavirus diseases (COVIDs) and coronaviral pandemics, highlighting the mostimportant general guidelines that should be considered in the next pandemics from the therapeutic points of view.展开更多
Virtual screening can be a helpful approach to propose treatments for COVID-19 by developing inhibitors for blocking the attachment of the virus to human cells. This study uses molecular docking, recovery time and dyn...Virtual screening can be a helpful approach to propose treatments for COVID-19 by developing inhibitors for blocking the attachment of the virus to human cells. This study uses molecular docking, recovery time and dynamics to analyze if potential inhibitors of main protease (M<sup>pro</sup>) of SARS-CoV-2 can interfere in the attachment of nanobodies, specifically Nb20, in the receptor binding domain (RBD) of SARS-CoV-2. The potential inhibitors are four compounds previously identified in a fluorescence resonance energy transfer (FRET)-based enzymatic assay for the SARS-CoV-2 M<sup>pro</sup>: Boceprevir, Calpain Inhibitor II, Calpain Inhibitor XII, and GC376. The findings reveal that Boceprevir has the higher affinity with the RBD/Nb20 complex, followed by Calpain Inhibitor XII, GC376 and Calpain Inhibitor II. The recovery time indicates that the RBD/Nb20 complex needs a relatively short time to return to what it was before the presence of the ligands. For the RMSD the Boceprevir and Calpain Inhibitor II have the shortest interaction times, while Calpain Inhibitor XII shows slightly more interaction, but with significant pose fluctuations. On the other hand, GC376 remains stably bound for a longer duration compared to the other compounds, suggesting that they can potentially interfere with the neutralization process of Nb20.展开更多
The main protease(M^(pro))of SARS-CoV-2 is an attractive target in anti-COVID-19 therapy for its high conservation and major role in the virus life cycle.The covalent M^(pro)inhibitor nirmatrelvir(in combination with ...The main protease(M^(pro))of SARS-CoV-2 is an attractive target in anti-COVID-19 therapy for its high conservation and major role in the virus life cycle.The covalent M^(pro)inhibitor nirmatrelvir(in combination with ritonavir,a pharmacokinetic enhancer)and the non-covalent inhibitor ensitrelvir have shown efficacy in clinical trials and have been approved for therapeutic use.Effective antiviral drugs are needed to fight the pandemic,while non-covalent M^(pro)inhibitors could be promising alternatives due to their high selectivity and favorable druggability.Numerous non-covalent M^(pro)inhibitors with desirable properties have been developed based on available crystal structures of M^(pro).In this article,we describe medicinal chemistry strategies applied for the discovery and optimization of non-covalent M^(pro)inhibitors,followed by a general overview and critical analysis of the available information.Prospective viewpoints and insights into current strategies for the development of non-covalent M^(pro)inhibitors are also discussed.展开更多
The Chinese herb Ephedra(also known as Mahuang)has been extensively utilized for the prevention and treatment of coronavirus-induced diseases,including coronavirus disease 2019(COVID-19).However,the specific anti-SARS...The Chinese herb Ephedra(also known as Mahuang)has been extensively utilized for the prevention and treatment of coronavirus-induced diseases,including coronavirus disease 2019(COVID-19).However,the specific anti-SARS-CoV-2 compounds and mechanisms have not been fully elucidated.The main protease(M^(pro))of SARS-CoV-2 is a highly conserved enzyme responsible for proteolytic processing during the viral life cycle,making it a critical target for the development of antiviral therapies.This study aimed to identify naturally occurring covalent inhibitors of SARS-CoV-2 M^(pro)from Ephedra and to investigate their covalent binding sites.The results demonstrated that the non-alkaloid fraction of Ephedra(ENA)exhibited a potent inhibitory effect against the SARS-CoV-2 M^(pro)effect,whereas the alkaloid fraction did not.Subsequently,the chemical constituents in ENA were identified,and the major constituents'anti-SARS-CoV-2 M^(pro)effects were evaluated.Among the tested constituents,herbacetin(HE)and gallic acid(GA)were found to inhibit SARS-CoV-2 M^(pro)in a time-and dose-dependent manner.Their combination displayed a significant synergistic effect on this key enzyme.Additionally,various techniques,including inhibition kinetic assays,chemoproteomic methods,and molecular dynamics simulations,were employed to further elucidate the synergistic anti-M^(pro)mechanisms of the combination of HE and GA.Overall,this study deciphers the naturally occurring covalent inhibitors of SARS-CoV-2 M^(pro)from Ephedra and characterizes their synergistic anti-M^(pro)synergistic effect,providing robust evidence to support the anti-coronavirus efficacy of Ephedra.展开更多
Coronaviruses(CoVs) can cause highly prevalent diseases in humans and animals. The fatal outbreak of severe acute respiratory syndrome(SARS) and Middle East respiratory syndrome(MERS) highlights the threat posed by th...Coronaviruses(CoVs) can cause highly prevalent diseases in humans and animals. The fatal outbreak of severe acute respiratory syndrome(SARS) and Middle East respiratory syndrome(MERS) highlights the threat posed by this unique virus subfamily. However, no specific drugs have been approved to treat CoV-associated diseases to date. The CoV proteases, which play pivotal roles in viral gene expression and replication through a highly complex cascade involving the proteolytic processing of replicase polyproteins, are attractive targets for drug design. This review summarizes the recent advances in biological and structural studies, together with the development of inhibitors targeting CoV proteases, particularly main proteases(M^(pro)s), which could help develop effective treatments to prevent CoV infection.展开更多
Artemisia annua and its phytocompounds have a rich history in the research and treatment of malaria,rheumatoid arthritis, systemic lupus erythematosus, and other diseases. Currently, the World Health Organization reco...Artemisia annua and its phytocompounds have a rich history in the research and treatment of malaria,rheumatoid arthritis, systemic lupus erythematosus, and other diseases. Currently, the World Health Organization recommends artemisinin-based combination therapy as the first-line treatment for multi-drug-resistant malaria. Due to the various research articles on the use of antimalarial drugs to treat coronaviruses, a question is raised: would A. annua and its compounds provide anti-severe acute respiratory syndrome coronavirus-2(SARS-CoV-2) properties? PubMed/MEDLINE, Scopus, and Google Scholar were searched for peer-reviewed articles that investigated the antiviral effects and mechanisms of A. annua and its phytochemicals against SARS-CoVs. Particularly, articles that evidenced the herb’s role in inhibiting the coronavirus-host proteins were favored. Nineteen studies were retrieved. From these,fourteen in silico molecular docking studies demonstrated potential inhibitory properties of artemisinins against coronavirus-host proteins including 3 CL^(PRO), S protein, N protein, E protein, cathepsin-L, helicase protein, nonstructural protein 3(nsp3), nsp10, nsp14, nsp15, and glucose-regulated protein 78 receptor.Collectively, A. annua constituents may impede the SARS-CoV-2 attachment, membrane fusion, internalization into the host cells, and hinder the viral replication and transcription process. This is the first comprehensive overview of the application of compounds from A. annua against SARS-CoV-2/coronavirus disease 2019(COVID-19) describing all target proteins. A. annua’s biological properties, the signaling pathways implicated in the COVID-19, and the advantages and disadvantages for repurposing A. annua compounds are discussed. The combination of A. annua’s biological properties, action on different signaling pathways and target proteins, and a multi-drug combined-therapy approach may synergistically inhibit SARS-CoV-2 and assist in the COVID-19 treatment. Also, A. annua may modulate the host immune response to better fight the infection.展开更多
文摘SARS-CoV-2(2019-nCoV)emerged in 2019 and proliferated rapidly across the globe.Scientists are attempting to investigate antivirals specific to COVID-19 treatment.The 2019-nCoV and SARS-CoV utilize the same receptor of the host which is COVID-19 of the main protease(Mpro).COVID-19 caused by SARS-CoV-2 is burdensome to overcome by presently acquired antiviral candidates.So the objective and purpose of this work was to investigate the plants with reported potential antiviral activity.With the aid of in silico techniques such as molecular docking and druggability studies,we have proposed several natural active compounds including glycyrrhizin,bicylogermecrene,tryptanthrine,β-sitosterol,indirubin,indican,indigo,hesperetin,crysophanic acid,rhein,berberine andβ-caryophyllene which can be encountered as potential herbal candidate exhibiting anti-viral activity against SARS-CoV-2.Promising docking outcomes have been executed which evidenced the worthy of these selected herbal remedies for future drug development to combat coronavirus disease.
文摘Coronaviruses caused an outbreak pandemic disease characterized by a severe acute respiratory distress syndrome leading to the infection of more than 200 million patients and the death of more than 4 million individuals.The primary treatment is either supportive or symptomatic.Natural products have an important role in the development of various drugs.Thus,screening of natural compounds with reported antiviral activities can lead to the discovery of potential inhibitory entities against coronaviruses.In the current study,an in-silico molecular docking experiment was conducted on the effects of some of these natural antiviral phytoconstituents,(e.g.,procyanidin B2,theaflavin,quercetin,ellagic acid,caffeoylquinic acid derivatives,berginin,eudesm-1β,6α,11-triol and arbutin),on the crystal structure of SARS-CoV-2 main protease(PDB ID:6w63)using AutoDock-Vina software.Many of the docked compounds revealed good binding affinity,with procyanidin B2(–8.6 Kcal/mol)and theaflavin(–8.5 Kcal/mol)showing a better or similar binding score as the ligand(–8.5 Kcal/mol).Molecular dynamics simulations were carried out at 100 ns and revealed that procyanidin B2 forms a more stable complex with SARS-CoV-2 main protease than theaflavin.Procyanidin B2,theaflavin,and 4,5-dicaffeoylquinic acid were evaluated for toxicity by ProTox-II webserver and were non-toxic according to the predicted LD50 values and safe on different organs and pathways.Additionally,these phytoconstituents showed good ADME properties and acceptable lipophilicity,as evaluated using WLOGP.Amongst the tested compounds,procyanidin B2 showed the highest lipophilic value.It is worth mentioning that these natural inhibitiors of SARS-CoV-2 main protease are components of green and black tea that can be used as a supporting supplement for COVID patients or as potential nuclei for further drug design and development campaigns.
文摘Background:Since the emergence of coronavirus disease 2019 to date,there is no available approved drug or definitive treatment for coronavirus disease 2019 viral infection,and the identification of novel hits against therapeutic targets has become a global emergency.Echinacea purpurea is a traditional herb utilized to treat cough,fever,sore throat,respiratory tract infection,and so on as an immune stimulant.In this study,in silico molecular docking approach was used to screen phytocompounds from E.purpurea against severe acute respiratory syndrome coronavirus 2 main protease 3C-like protease(3CLpro)and severe acute respiratory syndrome coronavirus main peptidase(96%sequence similarity)to blunt the viral gene expression and viral replication.Methods:Initially,we screened phytocompounds for their druggability and ADMET property.Furthermore,x-ray crystallographic structures of main proteases 3CLpro and main peptidase having Protein Data Bank ID 6LU7 and 2GTB were used as protein targets for the identification of potential drug candidates.We performed docking using AutoDock Vina by PyRx 0.8 software.BIOVIA Discovery Studio Visualizer v2019 was used to analyze ligand-protein complex.The probable protein targets of the selected compound were predicted by BindingDB(P≥0.7).STRING and Kyoto Encyclopedia of Genes and Genomes pathways are utilized to identify the molecular pathways modulated by the predicted targets(FDR≤0.05),and the network interaction between compounds and protein pathways was constructed by Cytoscape 3.6.1.Results:Among all the compounds,chlorogenic acid showed druggable characteristics and scored the lowest binding energy with main protease and main peptidase via interacting with active site 1 domain amino acid residues.Interestingly,chlorogenic acid interacted with Phe140 main protease 3CLpro,which is potentially involved in the dimerization.Enrichment analysis identified chlorogenic acid to modulate insulin resistance,necroptosis,interleukin-17,tumor necrosis factor signaling pathway,legionellosis,T helper 17 cell differentiation,advanced glycation end products and receptor for advanced glycation end products,mitogen-activated protein kinase,Ras,estrogen,vascular endothelial growth factor,B-cell receptor,nuclear factor kappa B,Rap1,hypoxia inducible factor-1,phosphatidylinositide 3-kinase-Akt,insulin,mechanistic target of rapamycin,p53,retinoic acid inducible gene I like receptor,and ErbB signaling pathways.Conclusion:Chlorogenic acid may act as a potent main protease 3CLpro inhibitor and may also inhibit the severe acute respiratory syndrome coronavirus 2 dimerization,viral gene expression,and replication within the lung epithelium.Chlorogenic acid may go a long way in finding one of the multipronged solutions to tackle coronavirus disease 2019 viral infection in the future.
基金The authors acknowledge support by Dr.Carina Lemke and Marion Schneider.Christa E.Müller and Michael Gütschow were supported by the Volkswagen Foundation(9A894)Rabea Voget,Christian Steinebach,Christa E.Müller and Michael Gütschow by the German Research Foundation(RTG 2873)Norbert Sträter by the Volkswagen Foundation(9A850).We acknowledge DESY(Hamburg,Germany),a member of the Helmholtz Association HGF,and the EMBL for the provision of experimental facilities at synchrotron beamlines P13 and P14 and the MX Laboratory at the Helmholtz Zentrum Berlin(BESSY II)for beam time.We would like to thank Selina Storm for assistance in using the EMBL beamlines.
文摘A titrant for the SARS-CoV-2 main protease(M^(pro))was developed that enables,for the first time,the exact determination of the concentration of the enzymatically active M^(pro) by active-site titration.The covalent binding mode of the tetrapeptidic titrant was elucidated by the determination of the crystal structure of the enzyme–titrant complex.Four fluorogenic substrates of M^(pro),including a prototypical,internally quenched Dabcyl-EDANS peptide,were compared in terms of solubility under typical assay conditions.By exploiting the new titrant,key kinetic parameters for the M^(pro)-catalyzed cleavage of these substrates were determined.
基金National Key Research and Development Program of China,Grant/Award Number:2023YFA0913900National Natural Science Foundation of China,Grant/Award Numbers:31971354,32100146,32170672,32271501。
文摘The rapid evolution of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)mainly due to its high mutation rate and rapid viral replication,has led to new variants resistant to the available vaccines and monoclonal antibodies.In contrast,oral clinical drugs targeting viral protease and RNA polymerase remain effective against Omicron variants[1].Main protease(Mpro)plays a crucial role in the maturation and replication of viral strains,making it an attractive target for developing antiviral drugs.Nirmatrelvir(NTV)is the first-in-class Mpro peptidomimetic covalent inhibitor known as“Paxlovid”approved in 2021 by the Food and Drug Administration[2].Nevertheless,NTV-resistant Mpro mutants particularly the E166V mutation,have been characterized in the Global Initiative on Sharing Avian Influenza Data(GISAID)database[3]and reported in COVID-19 patients[4,5].
基金Financial support from the German Center for Infection Research(DZIFproject FF 01.905,to R.H.)+1 种基金the National Institutes of Health(R35GM148261 to J.S.)is gratefully acknowledged.R.H.is also supported by the Government of Schleswig-Holstein through its StructureExcellence Fund as well as by a close partnership between the Possehl Foundation(Lübeck)and the University of Lübeck.
文摘During the continuing evolution of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the Omicron variant of concern emerged in the second half of 2021 and has been dominant since November of that year.Along with its sublineages,it has maintained a prominent role ever since.The Nsp5 main protease(Mpro)of the Omicron virus is characterized by a single dominant mutation,P132H.Here we determined the X-ray crystal structures of the P132H mutant(or O-Mpro)as a free enzyme and in complex with the Mpro inhibitor,the alpha-ketoamide 13b-K,and we conducted enzymological,biophysical,as well as theoretical studies to characterize the O-Mpro.We found that O-Mpro has a similar overall structure and binding with 13b-K;however,it displays lower enzymatic activity and lower thermal stability compared to the WT-Mpro(with“WT”referring to the prototype strain).Intriguingly,the imidazole ring of His132 and the carboxylate plane of Glu240 are in a stacked configuration in the X-ray structures determined here.Empirical folding free energy calculations suggest that the O-Mpro dimer is destabilized relative to the WT-Mpro due to less favorable van der Waals interactions and backbone conformations in the individual protomers.All-atom continuous constant-pH molecular dynamics(MD)simulations reveal that His132 and Glu240 display coupled titration.At pH 7,His132 is predominantly neutral and in a stacked configuration with respect to Glu240 which is charged.In order to examine whether the Omicron mutation eases the emergence of further Mpro mutations,we also analyzed the P132H+T169S double mutant,which is characteristic of the BA.1.1.2 lineage.However,we found little evidence of a correlation between the two mutation sites.
基金This research was supported by the National Institute of Allergy and Infectious Diseasess at the National Instiute of Health(NIH,USA,grants AI147325,AI157046,and AI158775)the Arizona Biomedical Research Centre Young Investigator grant(ADHS18-198859,USA)to Jun Wang.
文摘SARS-CoV-2 main protease(M^(pro))is one of the most extensively exploited drug targets for COVID-19.Structurally disparate compounds have been reported as M^(pro) inhibitors,raising the question of their target specificity.To elucidate the target specificity and the cellular target engagement of the claimed M^(pro) inhibitors,we systematically characterize their mechanism of action using the cell-free FRET assay,the thermal shift-binding assay,the cell lysate Protease-Glo luciferase assay,and the cell-based FlipGFP assay.Collectively,our results have shown that majority of the M^(pro) inhibitors identified from drug repurposing including ebselen,carmofur,disulfiram,and shikonin are promiscuous cysteine inhibitors that are not specific to M^(pro),while chloroquine,oxytetracycline,montelukast,candesartan,and dipyridamole do not inhibit M^(pro) in any of the assays tested.Overall,our study highlights the need of stringent hit validation at the early stage of drug discovery.
基金This work was supported by Grant No.2003CB514104 from the National Basic Research Program(973 Program)Grant No.30125009 from National Natural Science Foundation of China to Bin Xia+1 种基金Grant No.2006AA02A323 from the National Programs for High Technology Research and Development Program(863 Program)to Changwen JinGrant No.2009ZX09311-001 to Zhiyong Lou from the National Major Projects of China.
文摘Proteolytic processing of viral polyproteins is indispensible for the lifecycle of coronaviruses.The main protease(M^(pro))of SARS-CoV is an attractive target for anti-SARS drug development as it is essential for the polyprotein processing.M^(pro) is initially produced as part of viral polyproteins and it is matured by autocleavage.Here,we report that,with the addition of an N-terminal extension peptide,M^(pro) can form a domain-swapped dimer.After complete removal of the extension peptide from the dimer,the mature M^(pro) self-assembles into a novel super-active octamer(AO-M^(pro)).The crystal structure of AO-M^(pro) adopts a novel fold with four domainswapped dimers packing into four active units with nearly identical conformation to that of the previously reported M^(pro) active dimer,and 3D domain swapping serves as a mechanism to lock the active conformation due to entanglement of polypeptide chains.Compared with the previously well characterized form of M^(pro),in equilibrium between inactive monomer and active dimer,the stable AO-M^(pro) exhibits much higher proteolytic activity at low concentration.As all eight active sites are bound with inhibitors,the polyvalent nature of the interaction between AO-M^(pro) and its polyprotein substrates with multiple cleavage sites,would make AO-M^(pro) functionally much more superior than the M^(pro) active dimer for polyprotein processing.Thus,during the initial period of SARS-CoV infection,this novel active form AOM^(pro) should play a major role in cleaving polyproteins as the protein level is extremely low.The discovery of AOM^(pro) provides new insights about the functional mechanism of M^(pro) and its maturation process.
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.
文摘The main protease (Mpro) of SARS-CoV plays an essential role in the extensive proteolytic processing of the viral polyproteins (pp1a and pp1ab), and it is an important target
文摘Despite the global decline in the severity of the coronavirus disease 2019 (COVID-19) cases, the disease stillrepresents a major concern to the relevant scientific and medical communities. The primary concern of drug scientists,virologists, and other concerned specialists in this respect is to find ready-to-use suitable and potent anticoronaviraltherapies that are broadly effective against the different species/strains of the coronaviruses in general, not only againstthe current and previous coronaviruses (e.g., the recently-appeared severe acute respiratory syndrome coronavirus 2“SARS-CoV-2”), i.e., effective antiviral agents for treatment and/or prophylaxis of any coronaviral infections, includingthose of the coming ones from the next species and strains (if any). As an expert in this field, I tried, in this up-to-dateperspective “viewpoint” article, to evaluate the suitability and applicability of using the currently-availableanticoronaviral agents for the next coronavirus diseases (COVIDs) and coronaviral pandemics, highlighting the mostimportant general guidelines that should be considered in the next pandemics from the therapeutic points of view.
文摘Virtual screening can be a helpful approach to propose treatments for COVID-19 by developing inhibitors for blocking the attachment of the virus to human cells. This study uses molecular docking, recovery time and dynamics to analyze if potential inhibitors of main protease (M<sup>pro</sup>) of SARS-CoV-2 can interfere in the attachment of nanobodies, specifically Nb20, in the receptor binding domain (RBD) of SARS-CoV-2. The potential inhibitors are four compounds previously identified in a fluorescence resonance energy transfer (FRET)-based enzymatic assay for the SARS-CoV-2 M<sup>pro</sup>: Boceprevir, Calpain Inhibitor II, Calpain Inhibitor XII, and GC376. The findings reveal that Boceprevir has the higher affinity with the RBD/Nb20 complex, followed by Calpain Inhibitor XII, GC376 and Calpain Inhibitor II. The recovery time indicates that the RBD/Nb20 complex needs a relatively short time to return to what it was before the presence of the ligands. For the RMSD the Boceprevir and Calpain Inhibitor II have the shortest interaction times, while Calpain Inhibitor XII shows slightly more interaction, but with significant pose fluctuations. On the other hand, GC376 remains stably bound for a longer duration compared to the other compounds, suggesting that they can potentially interfere with the neutralization process of Nb20.
基金We gratefully acknowledge financial support from Major Basic Research Project of Shandong Provincial Natural Science Foundation(ZR2021ZD17,China)Science Foundation for Outstanding Young Scholars of Shandong Province(ZR2020JQ31,China)+4 种基金Foreign Cultural and Educational Experts Project(GXL20200015001,China)Guangdong Basic and Applied Basic Research Foundation(2021A1515110740,China)China Postdoctoral Science Foundation(2021M702003)This work was supported in part by the Ministry of Science and Innovation of Spain through grant PID2019-104176RBI00/AEI/10.13039/501100011033 awarded to Luis Menéndez-AriasAn institutional grant of the Fundación Ramón Areces(Madrid,Spain)to the CBMSO is also acknowledged.Luis Menéndez-Arias is member of the Global Virus Network.
文摘The main protease(M^(pro))of SARS-CoV-2 is an attractive target in anti-COVID-19 therapy for its high conservation and major role in the virus life cycle.The covalent M^(pro)inhibitor nirmatrelvir(in combination with ritonavir,a pharmacokinetic enhancer)and the non-covalent inhibitor ensitrelvir have shown efficacy in clinical trials and have been approved for therapeutic use.Effective antiviral drugs are needed to fight the pandemic,while non-covalent M^(pro)inhibitors could be promising alternatives due to their high selectivity and favorable druggability.Numerous non-covalent M^(pro)inhibitors with desirable properties have been developed based on available crystal structures of M^(pro).In this article,we describe medicinal chemistry strategies applied for the discovery and optimization of non-covalent M^(pro)inhibitors,followed by a general overview and critical analysis of the available information.Prospective viewpoints and insights into current strategies for the development of non-covalent M^(pro)inhibitors are also discussed.
基金supported by the National Key Research and Development Program of China(No.2022YFC-3502000)the Basic Public Welfare Research Program of Zhejiang Province(No.LGF22H280012)+4 种基金Zhejiang Provincial TCM Science and Technology Plan Project(Nos.2023ZR064,GZY-ZJ-KJ-24004,2024ZL007 and 2022ZB017)the Medical Science and Technology Project of Zhejiang Province(Nos.2022495401,2021KY040 and2022KY069)Zhejiang Provincial Key Projects in Chinese Medicine(Nos.2020ZZ003 and 2021ZZ001)Shanghai Science and Technology Innovation Action Plans(Nos.21S21900600)Zhejiang Province"Ten Thousand People Plan"Science and Technology Innovation Leading Talents Project(No.2020R52029)。
文摘The Chinese herb Ephedra(also known as Mahuang)has been extensively utilized for the prevention and treatment of coronavirus-induced diseases,including coronavirus disease 2019(COVID-19).However,the specific anti-SARS-CoV-2 compounds and mechanisms have not been fully elucidated.The main protease(M^(pro))of SARS-CoV-2 is a highly conserved enzyme responsible for proteolytic processing during the viral life cycle,making it a critical target for the development of antiviral therapies.This study aimed to identify naturally occurring covalent inhibitors of SARS-CoV-2 M^(pro)from Ephedra and to investigate their covalent binding sites.The results demonstrated that the non-alkaloid fraction of Ephedra(ENA)exhibited a potent inhibitory effect against the SARS-CoV-2 M^(pro)effect,whereas the alkaloid fraction did not.Subsequently,the chemical constituents in ENA were identified,and the major constituents'anti-SARS-CoV-2 M^(pro)effects were evaluated.Among the tested constituents,herbacetin(HE)and gallic acid(GA)were found to inhibit SARS-CoV-2 M^(pro)in a time-and dose-dependent manner.Their combination displayed a significant synergistic effect on this key enzyme.Additionally,various techniques,including inhibition kinetic assays,chemoproteomic methods,and molecular dynamics simulations,were employed to further elucidate the synergistic anti-M^(pro)mechanisms of the combination of HE and GA.Overall,this study deciphers the naturally occurring covalent inhibitors of SARS-CoV-2 M^(pro)from Ephedra and characterizes their synergistic anti-M^(pro)synergistic effect,providing robust evidence to support the anti-coronavirus efficacy of Ephedra.
基金supported by the Tianjin University Undergraduate Research FoundationTianjin University-Hainan University Collaborative Foundation+1 种基金National Natural Science Foundation of China (No.31300150)Tianjin Marine Science and Technology Program (No.KJXH2014-16)
文摘Coronaviruses(CoVs) can cause highly prevalent diseases in humans and animals. The fatal outbreak of severe acute respiratory syndrome(SARS) and Middle East respiratory syndrome(MERS) highlights the threat posed by this unique virus subfamily. However, no specific drugs have been approved to treat CoV-associated diseases to date. The CoV proteases, which play pivotal roles in viral gene expression and replication through a highly complex cascade involving the proteolytic processing of replicase polyproteins, are attractive targets for drug design. This review summarizes the recent advances in biological and structural studies, together with the development of inhibitors targeting CoV proteases, particularly main proteases(M^(pro)s), which could help develop effective treatments to prevent CoV infection.
文摘Artemisia annua and its phytocompounds have a rich history in the research and treatment of malaria,rheumatoid arthritis, systemic lupus erythematosus, and other diseases. Currently, the World Health Organization recommends artemisinin-based combination therapy as the first-line treatment for multi-drug-resistant malaria. Due to the various research articles on the use of antimalarial drugs to treat coronaviruses, a question is raised: would A. annua and its compounds provide anti-severe acute respiratory syndrome coronavirus-2(SARS-CoV-2) properties? PubMed/MEDLINE, Scopus, and Google Scholar were searched for peer-reviewed articles that investigated the antiviral effects and mechanisms of A. annua and its phytochemicals against SARS-CoVs. Particularly, articles that evidenced the herb’s role in inhibiting the coronavirus-host proteins were favored. Nineteen studies were retrieved. From these,fourteen in silico molecular docking studies demonstrated potential inhibitory properties of artemisinins against coronavirus-host proteins including 3 CL^(PRO), S protein, N protein, E protein, cathepsin-L, helicase protein, nonstructural protein 3(nsp3), nsp10, nsp14, nsp15, and glucose-regulated protein 78 receptor.Collectively, A. annua constituents may impede the SARS-CoV-2 attachment, membrane fusion, internalization into the host cells, and hinder the viral replication and transcription process. This is the first comprehensive overview of the application of compounds from A. annua against SARS-CoV-2/coronavirus disease 2019(COVID-19) describing all target proteins. A. annua’s biological properties, the signaling pathways implicated in the COVID-19, and the advantages and disadvantages for repurposing A. annua compounds are discussed. The combination of A. annua’s biological properties, action on different signaling pathways and target proteins, and a multi-drug combined-therapy approach may synergistically inhibit SARS-CoV-2 and assist in the COVID-19 treatment. Also, A. annua may modulate the host immune response to better fight the infection.
