This study aims to investigate the potential impact of inhibitors targeting the papain-like protease(PLpro)of SARS-CoV-2 on viral replication and the host immune response.A mathematical model was developed to simulate...This study aims to investigate the potential impact of inhibitors targeting the papain-like protease(PLpro)of SARS-CoV-2 on viral replication and the host immune response.A mathematical model was developed to simulate the interaction among susceptible cells,infected cells,PLpro,and immune cells,incorporating data on PLpro inhibition.Through numerical simulations using MATLAB,the model parameters were estimated based on available statistical data.The results indicate that strategically positioned inhibitors could impede the virus’s access to host cellular machinery,thereby enhancing the immune response and gradually reducing susceptible and infected cells over time.The dynamics of the viral enzyme PLpro showed reduced activity with the introduction of the inhibitor,leading to a decline in viral replication.Moreover,the immune cell population exhibited functional recovery as the inhibitor suppressed PLpro activity.These findings suggest that inhibitors targeting PLpro may serve as therapeutic interventions against SARS-CoV-2 by inhibiting viral replication and bolstering the immune response.展开更多
The pandemic of coronavirus disease 2019(COVID-19)is changing the world like never before.This crisis is unlikely contained in the absence of effective therapeutics or vaccine.The papain-like protease(PLpro)of severe ...The pandemic of coronavirus disease 2019(COVID-19)is changing the world like never before.This crisis is unlikely contained in the absence of effective therapeutics or vaccine.The papain-like protease(PLpro)of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)plays essential roles in virus replication and immune evasion,presenting a charming drug target.Given the PLpro proteases of SARS-CoV-2 and SARS-CoV share significant homology,inhibitor developed for SARS-CoV PLpro is a promising starting point of therapeutic development.In this study,we sought to provide structural frameworks for PLpro inhibitor design.We determined the unliganded structure of SARS-CoV-2 PLpro mutant C111 S,which shares many structural features of SARS-CoV PLpro.This crystal form has unique packing,high solvent content and reasonable resolution 2.5 A°,hence provides a good possibility for fragment-based screening using crystallographic approach.We characterized the protease activity of PLpro in cleaving synthetic peptide harboring nsp2/nsp3 juncture.We demonstrate that a potent SARS-CoV PLpro inhibitor GRL0617 is highly effective in inhibiting protease activity of SARSCoV-2 with the IC50 of 2.2?0.3 mmol/L.We then determined the structure of SARS-CoV-2 PLpro complexed by GRL0617 to 2.6 A°,showing the inhibitor accommodates the S3 e S4 pockets of the substrate binding cleft.The binding of GRL0617 induces closure of the BL2 loop and narrows the substrate binding cleft,whereas the binding of a tetrapeptide substrate enlarges the cleft.Hence,our results suggest a mechanism of GRL0617 inhibition,that GRL0617 not only occupies the substrate pockets,but also seals the entrance to the substrate binding cleft hence prevents the binding of the LXGG motif of the substrate.展开更多
Acute respiratory infection caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)had caused a global pandemic since 2019,and posed a serious threat to global health security.Traditional Chinese medicin...Acute respiratory infection caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)had caused a global pandemic since 2019,and posed a serious threat to global health security.Traditional Chinese medicine(TCM)has played an indispensable role in the battle against the epidemic.Many components originated from TCMs were found to inhibit the production of SARS-CoV-23C-like protease(3CLpro)and papain-like protease(PLpro),which are two promising therapeutic targets to inhibit SARS-CoV-2.This study describes a systematic investigation of the roots and rhizomes of Sophora tonkinensis,which results in the characterization of 12 new flavonoids,including seven prenylated flavanones(1−7),one prenylated flavonol(8),two prenylated chalcones(9−10),one isoflavanone(11),and one isoflavan dimer(12),together with 43 known compounds(13−55).Their structures including the absolute configurations were elucidated by comprehensive analysis of MS,1D and 2D NMR data,and time-dependent density functional theory electronic circular dichroism(TDDFT ECD)calculations.Compounds 12 and 51 exhibited inhibitory effects against SARS-CoV-23CLpro with IC_(50) values of 34.89 and 19.88μmol·L^(−1),repectively while compounds 9,43 and 47 exhibited inhibitory effects against PLpro with IC_(50) values of 32.67,79.38,and 16.74μmol·L^(−1),respectively.展开更多
The pandemic of novel coronavirus disease 2019(COVID-19)has rampaged the world,with more than 58.4 million confirmed cases and over 1.38 million deaths across the world by 23 November 2020.There is an urgent need to i...The pandemic of novel coronavirus disease 2019(COVID-19)has rampaged the world,with more than 58.4 million confirmed cases and over 1.38 million deaths across the world by 23 November 2020.There is an urgent need to identify effective drugs and vaccines to fight against the virus.Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)belongs to the family of coronaviruses consisting of four structural and 16 non-structural proteins(NSP).Three non-structural proteins,main protease(Mpro),papain-like protease(PLpro),and RNAdependent RNA polymerase(RdRp),are believed to have a crucial role in replication of the virus.We applied computational ligand-receptor binding modeling and performed comprehensive virtual screening on FDA-approved drugs against these three SARS-CoV-2 proteins using AutoDock Vina,Glide,and rDock.Our computational studies identified six novel ligands as potential inhibitors against SARS-CoV-2,including antiemetics rolapitant and ondansetron for Mpro;labetalol and levomefolic acid for PLpro;and leucal and antifungal natamycin for RdRp.Molecular dynamics simulation confirmed the stability of the ligand-protein complexes.The results of our analysis with some other suggested drugs indicated that chloroquine and hydroxychloroquine had high binding energy(low inhibitory effect)with all three proteins—Mpro,PLpro,and RdRp.In summary,our computational molecular docking approach and virtual screening identified some promising candidate SARS-CoV-2 inhibitors that may be considered for further clinical studies.展开更多
文摘This study aims to investigate the potential impact of inhibitors targeting the papain-like protease(PLpro)of SARS-CoV-2 on viral replication and the host immune response.A mathematical model was developed to simulate the interaction among susceptible cells,infected cells,PLpro,and immune cells,incorporating data on PLpro inhibition.Through numerical simulations using MATLAB,the model parameters were estimated based on available statistical data.The results indicate that strategically positioned inhibitors could impede the virus’s access to host cellular machinery,thereby enhancing the immune response and gradually reducing susceptible and infected cells over time.The dynamics of the viral enzyme PLpro showed reduced activity with the introduction of the inhibitor,leading to a decline in viral replication.Moreover,the immune cell population exhibited functional recovery as the inhibitor suppressed PLpro activity.These findings suggest that inhibitors targeting PLpro may serve as therapeutic interventions against SARS-CoV-2 by inhibiting viral replication and bolstering the immune response.
基金supported by the National Key Research and Development Program of China(2016YFD0500300)National Science and Technology Major Project(2018ZX10101001,China)+3 种基金National Natural Science Foundation of China(Grant Nos.81572005,81772207,81971985,11775308 and 81802057)Beijing Municipal Natural Science Foundation(Grant Nos.7182117 and 7174288,China)Chinese Academy of Medical Sciences(CAMS)Innovation Fund for Medical Sciences(Grant Nos.2017I2M-1-014 and 2016-I2M-1-013,China)Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences(Grant Nos.2018PT51009 and 2017PT31049,China)
文摘The pandemic of coronavirus disease 2019(COVID-19)is changing the world like never before.This crisis is unlikely contained in the absence of effective therapeutics or vaccine.The papain-like protease(PLpro)of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)plays essential roles in virus replication and immune evasion,presenting a charming drug target.Given the PLpro proteases of SARS-CoV-2 and SARS-CoV share significant homology,inhibitor developed for SARS-CoV PLpro is a promising starting point of therapeutic development.In this study,we sought to provide structural frameworks for PLpro inhibitor design.We determined the unliganded structure of SARS-CoV-2 PLpro mutant C111 S,which shares many structural features of SARS-CoV PLpro.This crystal form has unique packing,high solvent content and reasonable resolution 2.5 A°,hence provides a good possibility for fragment-based screening using crystallographic approach.We characterized the protease activity of PLpro in cleaving synthetic peptide harboring nsp2/nsp3 juncture.We demonstrate that a potent SARS-CoV PLpro inhibitor GRL0617 is highly effective in inhibiting protease activity of SARSCoV-2 with the IC50 of 2.2?0.3 mmol/L.We then determined the structure of SARS-CoV-2 PLpro complexed by GRL0617 to 2.6 A°,showing the inhibitor accommodates the S3 e S4 pockets of the substrate binding cleft.The binding of GRL0617 induces closure of the BL2 loop and narrows the substrate binding cleft,whereas the binding of a tetrapeptide substrate enlarges the cleft.Hence,our results suggest a mechanism of GRL0617 inhibition,that GRL0617 not only occupies the substrate pockets,but also seals the entrance to the substrate binding cleft hence prevents the binding of the LXGG motif of the substrate.
基金This work was supported from the National Natural Science Foundation of China(Nos.82173696 and 21920102003)the Science and Technology Commission of Shanghai Municipality(Nos.20431900200 and 20430780300)+1 种基金the Strategic Priority Research Program of Chinese Academy of Sciences(Nos.SIMM010110 and SIMM040302)the Sustainable Development of Precious Traditional Chinese Medicine Resources(No.2060302-2001-01).
文摘Acute respiratory infection caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)had caused a global pandemic since 2019,and posed a serious threat to global health security.Traditional Chinese medicine(TCM)has played an indispensable role in the battle against the epidemic.Many components originated from TCMs were found to inhibit the production of SARS-CoV-23C-like protease(3CLpro)and papain-like protease(PLpro),which are two promising therapeutic targets to inhibit SARS-CoV-2.This study describes a systematic investigation of the roots and rhizomes of Sophora tonkinensis,which results in the characterization of 12 new flavonoids,including seven prenylated flavanones(1−7),one prenylated flavonol(8),two prenylated chalcones(9−10),one isoflavanone(11),and one isoflavan dimer(12),together with 43 known compounds(13−55).Their structures including the absolute configurations were elucidated by comprehensive analysis of MS,1D and 2D NMR data,and time-dependent density functional theory electronic circular dichroism(TDDFT ECD)calculations.Compounds 12 and 51 exhibited inhibitory effects against SARS-CoV-23CLpro with IC_(50) values of 34.89 and 19.88μmol·L^(−1),repectively while compounds 9,43 and 47 exhibited inhibitory effects against PLpro with IC_(50) values of 32.67,79.38,and 16.74μmol·L^(−1),respectively.
基金The study was partially supported by the American Heart Association(AHA)(grant No.18IPA34170301)and the National Institutes of Health(NIH)(grant No.R01/HD088039).
文摘The pandemic of novel coronavirus disease 2019(COVID-19)has rampaged the world,with more than 58.4 million confirmed cases and over 1.38 million deaths across the world by 23 November 2020.There is an urgent need to identify effective drugs and vaccines to fight against the virus.Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)belongs to the family of coronaviruses consisting of four structural and 16 non-structural proteins(NSP).Three non-structural proteins,main protease(Mpro),papain-like protease(PLpro),and RNAdependent RNA polymerase(RdRp),are believed to have a crucial role in replication of the virus.We applied computational ligand-receptor binding modeling and performed comprehensive virtual screening on FDA-approved drugs against these three SARS-CoV-2 proteins using AutoDock Vina,Glide,and rDock.Our computational studies identified six novel ligands as potential inhibitors against SARS-CoV-2,including antiemetics rolapitant and ondansetron for Mpro;labetalol and levomefolic acid for PLpro;and leucal and antifungal natamycin for RdRp.Molecular dynamics simulation confirmed the stability of the ligand-protein complexes.The results of our analysis with some other suggested drugs indicated that chloroquine and hydroxychloroquine had high binding energy(low inhibitory effect)with all three proteins—Mpro,PLpro,and RdRp.In summary,our computational molecular docking approach and virtual screening identified some promising candidate SARS-CoV-2 inhibitors that may be considered for further clinical studies.
