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Zhang Q, Jeppesen DK, Higginbotham JN, Franklin JL, Crowe JE, Coffey RJ. Angiotensin-converting Enzyme 2-containing Small Extracellular Vesicles and Exomeres Bind the Severe Acute Respiratory Syndrome Coronavirus 2 Spike Protein. Gastroenterology 2021; 160:958-961.e3. [PMID: 33022277 PMCID: PMC7832655 DOI: 10.1053/j.gastro.2020.09.042] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 01/19/2023]
Key Words
- ace2, angiotensin-converting enzyme 2
- cov, coronavirus
- covid-19, coronavirus disease 2019
- dpp4, dipeptidyl peptidase 4
- mers, middle east respiratory syndrome
- rbd, receptor-binding domain
- sars, severe acute respiratory syndrome
- sev, small extracellular vesicle
- tace, tnf-α converting enzyme
- tmprss, transmembrane serine protease
- tnf-α, tumor necrosis factor-α
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Affiliation(s)
- Qin Zhang
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Dennis K Jeppesen
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - James N Higginbotham
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jeffrey L Franklin
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - James E Crowe
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee; Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Robert J Coffey
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.
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2
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Nuzzo A, Tan CO, Raskar R, DeSimone DC, Kapa S, Gupta R. Universal Shelter-in-Place Versus Advanced Automated Contact Tracing and Targeted Isolation: A Case for 21st-Century Technologies for SARS-CoV-2 and Future Pandemics. Mayo Clin Proc 2020; 95:1898-1905. [PMID: 32861334 PMCID: PMC7306713 DOI: 10.1016/j.mayocp.2020.06.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/29/2020] [Accepted: 06/16/2020] [Indexed: 11/22/2022]
Abstract
OBJECTIVE To model and compare effect of digital contact tracing versus shelter-in-place on severe acute respiratory syndrome - coronavirus 2 (SARS-CoV-2) spread. METHODS Using a classical epidemiologic framework and parameters estimated from literature published between February 1, 2020, and May 25, 2020, we modeled two non-pharmacologic interventions - shelter-in-place and digital contact tracing - to curb spread of SARS-CoV-2. For contact tracing, we assumed an advanced automated contact tracing (AACT) application that sends alerts to individuals advising self-isolation based on individual exposure profile. Model parameters included percentage population ordered to shelter-in-place, adoption rate of AACT, and percentage individuals who appropriately follow recommendations. Under influence of these variables, the number of individuals infected, exposed, and isolated were estimated. RESULTS Without any intervention, a high rate of infection (>10 million) with early peak is predicted. Shelter-in-place results in rapid decline in infection rate at the expense of impacting a large population segment. The AACT model achieves reduction in infected and exposed individuals similar to shelter-in-place without impacting a large number of individuals. For example, a 50% AACT adoption rate mimics a shelter-in-place order for 40% of the population and results in a greater than 90% decrease in peak number of infections. However, as compared to shelter-in-place, with AACT significantly fewer individuals would be isolated. CONCLUSION Wide adoption of digital contact tracing can mitigate infection spread similar to universal shelter-in-place, but with considerably fewer individuals isolated.
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Affiliation(s)
| | - Can Ozan Tan
- Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital, Boston, MA; Neuroradiology, Department of Radiology, Massachusetts General Hospital, Boston, MA
| | - Ramesh Raskar
- Media Lab, Massachusetts Institute of Technology, Boston, MA
| | - Daniel C DeSimone
- Division of Infectious Disease, Mayo Clinic, Rochester, MN; Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Suraj Kapa
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Rajiv Gupta
- Neuroradiology, Department of Radiology, Massachusetts General Hospital, Boston, MA
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3
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Ding S, Liang TJ. Is SARS-CoV-2 Also an Enteric Pathogen With Potential Fecal-Oral Transmission? A COVID-19 Virological and Clinical Review. Gastroenterology 2020; 159:53-61. [PMID: 32353371 PMCID: PMC7184994 DOI: 10.1053/j.gastro.2020.04.052] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 04/24/2020] [Indexed: 02/07/2023]
Abstract
In as few as 3 months, coronavirus disease 2019 (COVID-19) has spread and ravaged the world at an unprecedented speed in modern history, rivaling the 1918 flu pandemic. Severe acute respiratory syndrome coronavirus-2, the culprit virus, is highly contagious and stable in the environment and transmits predominantly among humans via the respiratory route. Accumulating evidence suggest that this virus, like many of its related viruses, may also be an enteric virus that can spread via the fecal-oral route. Such a hypothesis would also contribute to the rapidity and proliferation of this pandemic. Here we briefly summarize what is known about this family of viruses and literature basis of the hypothesis that severe acute respiratory syndrome coronavirus-2 is capable of infecting the gastrointestinal tract and shedding in the environment for potential human-to-human transmission.
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Affiliation(s)
- Siyuan Ding
- Department of Molecular Microbiology, Washington University in St Louis, St Louis, Missouri.
| | - T. Jake Liang
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland,Correspondence Address correspondence to: T. Jake Liang, MD, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg10-9B16, 10 Center Drive, Bethesda, MD
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4
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DeMuri GP, Gern JE, Moyer SC, Lindstrom MJ, Lynch SV, Wald ER. Clinical Features, Virus Identification, and Sinusitis as a Complication of Upper Respiratory Tract Illness in Children Ages 4-7 Years. J Pediatr 2016; 171:133-9.e1. [PMID: 26787374 PMCID: PMC4808614 DOI: 10.1016/j.jpeds.2015.12.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 11/06/2015] [Accepted: 12/11/2015] [Indexed: 12/04/2022]
Abstract
OBJECTIVE To determine the rate of sinusitis complicating upper respiratory tract illnesses (URIs) in children. We prospectively identified the clinical, virologic, and epidemiologic characteristics of URIs in a population of 4- to 7-year-old children followed for 1 year. STUDY DESIGN This was an observational cohort study in 2 primary care pediatric practices in Madison, Wisconsin. Nasal samples were obtained during 4 asymptomatic surveillance visits and during symptomatic URIs. A polymerase chain reaction-based assay for 9 respiratory viruses was performed on nasal samples. A diagnosis of sinusitis was based on published criteria. RESULTS Two hundred thirty-six children ages 48-96 months were enrolled. A total of 327 URIs were characterized. The mean number of URIs per child was 1.3 (range 0-9) per year. Viruses were detected in 81% of URIs; rhinovirus (RV) was most common. Seventy-two percent of URIs were resolved clinically by the 10th day. RV-A and RV-C were detected more frequently at URI visits; RV-B was detected at the same rate for both asymptomatic surveillance visits and URI visits. Sinusitis was diagnosed in 8.8% of symptomatic URIs. Viruses were detected frequently (33%) in samples from asymptomatic children. CONCLUSIONS Sinusitis occurred in 8.8% of symptomatic URIs in our study. The virus most frequently detected with URIs in children was RV; RV-A and RV-C detection but not RV-B detection were associated with illness. Viruses, especially RV, are detected frequently in asymptomatic children. Most URIs have improved or resolved by the 10th day after onset. Children experienced a mean of 1.3 URIs per year, which was lower than expected.
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Key Words
- adv, adenovirus
- cov, coronavirus
- ev, enterovirus
- flu, influenza virus
- gee, generalized estimating equation
- hbov, human bocavirus
- hmpv, human metapneumovirus
- piv, parainfluenza virus
- rsv, respiratory syncytial virus
- rv, rhinovirus
- uri, upper respiratory tract illness
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Affiliation(s)
- Gregory P. DeMuri
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - James E. Gern
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Stacey C. Moyer
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Mary J. Lindstrom
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Susan V. Lynch
- Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Ellen R. Wald
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI
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Park JY, Kim JH, Kwon JM, Kwon HJ, Jeong HJ, Kim YM, Kim D, Lee WS, Ryu YB. Dieckol, a SARS-CoV 3CL(pro) inhibitor, isolated from the edible brown algae Ecklonia cava. Bioorg Med Chem 2013; 21:3730-7. [PMID: 23647823 PMCID: PMC7126891 DOI: 10.1016/j.bmc.2013.04.026] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 04/11/2013] [Accepted: 04/12/2013] [Indexed: 12/11/2022]
Abstract
SARS-CoV 3CL(pro) plays an important role in viral replication. In this study, we performed a biological evaluation on nine phlorotannins isolated from the edible brown algae Ecklonia cava. The nine isolated phlorotannins (1-9), except phloroglucinol (1), possessed SARS-CoV 3CL(pro) inhibitory activities in a dose-dependently and competitive manner. Of these phlorotannins (1-9), two eckol groups with a diphenyl ether linked dieckol (8) showed the most potent SARS-CoV 3CL(pro) trans/cis-cleavage inhibitory effects (IC(50)s = 2.7 and 68.1 μM, respectively). This is the first report of a (8) phlorotannin chemotype significantly blocking the cleavage of SARS-CoV 3CL(pro) in a cell-based assay with no toxicity. Furthermore, dieckol (8) exhibited a high association rate in the SPR sensorgram and formed extremely strong hydrogen bonds to the catalytic dyad (Cys145 and His41) of the SARS-CoV 3CL(pro).
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Affiliation(s)
- Ji-Young Park
- Infection Control Research Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 580-185, Republic of Korea
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Park JY, Kim JH, Kim YM, Jeong HJ, Kim DW, Park KH, Kwon HJ, Park SJ, Lee WS, Ryu YB. Tanshinones as selective and slow-binding inhibitors for SARS-CoV cysteine proteases. Bioorg Med Chem 2012; 20:5928-35. [PMID: 22884354 PMCID: PMC7127169 DOI: 10.1016/j.bmc.2012.07.038] [Citation(s) in RCA: 160] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 07/23/2012] [Accepted: 07/23/2012] [Indexed: 11/24/2022]
Abstract
In the search for anti-SARS-CoV, tanshinones derived from Salvia miltiorrhiza were found to be specific and selective inhibitors for the SARS-CoV 3CL(pro) and PL(pro), viral cysteine proteases. A literature search for studies involving the seven isolated tanshinone hits showed that at present, none have been identified as coronaviral protease inhibitors. We have identified that all of the isolated tanshinones are good inhibitors of both cysteine proteases. However, their activity was slightly affected by subtle changes in structure and targeting enzymes. All isolated compounds (1-7) act as time dependent inhibitors of PL(pro), but no improved inhibition was observed following preincubation with the 3CL(pro). In a detail kinetic mechanism study, all of the tanshinones except rosmariquinone (7) were identified as noncompetitive enzyme isomerization inhibitors. However, rosmariquinone (7) showed a different kinetic mechanism through mixed-type simple reversible slow-binding inhibition. Furthermore, tanshinone I (5) exhibited the most potent nanomolar level inhibitory activity toward deubiquitinating (IC(50)=0.7 μM). Additionally, the inhibition is selective because these compounds do not exert significant inhibitory effects against other proteases including chymotrysin, papain, and HIV protease. These findings provide potential inhibitors for SARS-CoV viral infection and replication.
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Key Words
- ic50, the inhibitor concentration leading to 50% activity loss
- ki, inhibition constant
- kiapp, apparent ki
- k, rate constant
- vmax, maximum velocity
- km, michaelis-menten constant
- kobs, apparent first-order rate constant for the transition from vi to vs
- vi, initial velocity
- vs, steady-state rate
- sars, severe acute respiratory syndrome
- cov, coronavirus
- tanshinone
- sars-cov
- 3clpro
- plpro
- slow-binding inhibitor
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Affiliation(s)
- Ji-Young Park
- Infection Control Research Center, Korea Research Institute of Bioscience and Biotechnology, KRIBB, Jeongeup 580-185, Republic of Korea
- School of Biological Science and Biotechnology, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Jang Hoon Kim
- Infection Control Research Center, Korea Research Institute of Bioscience and Biotechnology, KRIBB, Jeongeup 580-185, Republic of Korea
| | - Young Min Kim
- Infection Control Research Center, Korea Research Institute of Bioscience and Biotechnology, KRIBB, Jeongeup 580-185, Republic of Korea
| | - Hyung Jae Jeong
- Infection Control Research Center, Korea Research Institute of Bioscience and Biotechnology, KRIBB, Jeongeup 580-185, Republic of Korea
| | - Dae Wook Kim
- Division of Applied Life Science (BK 21 Program, IALS), Graduate School of Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Ki Hun Park
- Division of Applied Life Science (BK 21 Program, IALS), Graduate School of Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Hyung-Jun Kwon
- Infection Control Research Center, Korea Research Institute of Bioscience and Biotechnology, KRIBB, Jeongeup 580-185, Republic of Korea
| | - Su-Jin Park
- Infection Control Research Center, Korea Research Institute of Bioscience and Biotechnology, KRIBB, Jeongeup 580-185, Republic of Korea
| | - Woo Song Lee
- Infection Control Research Center, Korea Research Institute of Bioscience and Biotechnology, KRIBB, Jeongeup 580-185, Republic of Korea
| | - Young Bae Ryu
- Infection Control Research Center, Korea Research Institute of Bioscience and Biotechnology, KRIBB, Jeongeup 580-185, Republic of Korea
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7
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Chiu CY, Urisman A, Greenhow TL, Rouskin S, Yagi S, Schnurr D, Wright C, Drew WL, Wang D, Weintrub PS, DeRisi JL, Ganem D. Utility of DNA microarrays for detection of viruses in acute respiratory tract infections in children. J Pediatr 2008; 153:76-83. [PMID: 18571541 PMCID: PMC3174048 DOI: 10.1016/j.jpeds.2007.12.035] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Revised: 11/09/2007] [Accepted: 12/18/2007] [Indexed: 11/06/2022]
Abstract
OBJECTIVE To assess the utility of a panviral DNA microarray platform (Virochip) in the detection of viruses associated with pediatric respiratory tract infections (RTIs). STUDY DESIGN The Virochip was compared with conventional direct fluorescent antibody (DFA)- and polymerase chain reaction (PCR)-based testing for the detection of respiratory viruses in 278 consecutive nasopharyngeal aspirate samples from 222 children. RESULTS The Virochip was superior in performance to DFA, showing a 19% increase in the detection of 7 respiratory viruses included in standard DFA panels, and was similar to virus-specific PCR (sensitivity, 85% to 90%; specificity, >/=99%; positive predictive value, 94% to 96%; negative predictive value, 97% to 98%) in the detection of respiratory syncytial virus, influenza A, and rhinoviruses/enteroviruses. The Virochip also detected viruses not routinely tested for or missed by DFA and PCR, as well as double infections and infections in critically ill patients that DFA failed to detect. CONCLUSIONS Given its favorable sensitivity and specificity profile and expanded spectrum for detection, microarray-based viral testing holds promise for clinical diagnosis of pediatric RTIs.
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Key Words
- adv, adenovirus
- cov, coronavirus
- dfa, direct fluorescent antibody
- ev, enterovirus
- flua/b, influenza a/b
- hmpv, human metapneumovirus
- hpiv, human parainfluenza virus
- npa, nasopharyngeal aspirate
- pcr, polymerase chain reaction
- rsv, respiratory syncytial virus
- rt, reverse-transcriptase
- rti, respiratory tract infection
- rv, rhinovirus
- ucsf, university of california san francisco
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Affiliation(s)
- Charles Y. Chiu
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA,Department of Medicine, University of California San Francisco, San Francisco, CA,Division of Infectious Diseases, University of California San Francisco, San Francisco, CA
| | - Anatoly Urisman
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA,Department of Medicine, University of California San Francisco, San Francisco, CA
| | - Tara L. Greenhow
- Department of Pediatric Infectious Diseases, Children's Hospital and Research Center, Oakland, CA
| | - Silvi Rouskin
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA
| | - Shigeo Yagi
- Viral and Rickettsial Disease Laboratory, California Department of Health Services, Richmond, CA
| | - David Schnurr
- Viral and Rickettsial Disease Laboratory, California Department of Health Services, Richmond, CA
| | - Carolyn Wright
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
| | - W. Lawrence Drew
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA,Department of Medicine, University of California San Francisco, San Francisco, CA,Division of Infectious Diseases, University of California San Francisco, San Francisco, CA
| | - David Wang
- Departments of Microbiology and Pathology and Immunology, Washington University, St. Louis, MO
| | - Peggy S. Weintrub
- Department of Pediatrics, University of California San Francisco, San Francisco, CA,Division of Infectious Diseases, University of California San Francisco, San Francisco, CA
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA,Department of Medicine, University of California San Francisco, San Francisco, CA,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA
| | - Don Ganem
- Department of Microbiology, University of California San Francisco, San Francisco, CA,Department of Medicine, University of California San Francisco, San Francisco, CA,Division of Infectious Diseases, University of California San Francisco, San Francisco, CA,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA,Reprint requests: Dr Don Ganem, Medicine/Microbiology and Immunology, University of California San Francisco, 513 Parnassus Ave, Room HSW 1522, Box 0552, San Francisco, CA 94143
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Kuhn D, Weskamp N, Schmitt S, Hüllermeier E, Klebe G. From the similarity analysis of protein cavities to the functional classification of protein families using cavbase. J Mol Biol 2006; 359:1023-44. [PMID: 16697007 PMCID: PMC7094329 DOI: 10.1016/j.jmb.2006.04.024] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2006] [Revised: 03/31/2006] [Accepted: 04/06/2006] [Indexed: 02/05/2023]
Abstract
In this contribution, the classification of protein binding sites using the physicochemical properties exposed to their pockets is presented. We recently introduced Cavbase, a method for describing and comparing protein binding pockets on the basis of the geometrical and physicochemical properties of their active sites. Here, we present algorithmic and methodological enhancements in the Cavbase property description and in the cavity comparison step. We give examples of the Cavbase similarity analysis detecting pronounced similarities in the binding sites of proteins unrelated in sequence. A similarity search using SARS M(pro) protease subpockets as queries retrieved ligands and ligand fragments accommodated in a physicochemical environment similar to that of the query. This allowed the characterization of the protease recognition pockets and the identification of molecular building blocks that can be incorporated into novel antiviral compounds. A cluster analysis procedure for the functional classification of binding pockets was implemented and calibrated using a diverse set of enzyme binding sites. Two relevant protein families, the alpha-carbonic anhydrases and the protein kinases, are used to demonstrate the scope of our cluster approach. We propose a relevant classification of both protein families, on the basis of the binding motifs in their active sites. The classification provides a new perspective on functional properties across a protein family and is able to highlight features important for potency and selectivity. Furthermore, this information can be used to identify possible cross-reactivities among proteins due to similarities in their binding sites.
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Key Words
- protein binding pockets
- classification of protein binding pockets
- cluster analysis of protein binding pockets
- protein kinases
- sars protease
- sam, s-adenosyl-methionine
- fad, flavine adenine dinucleotide
- sars, severe acute respiratory syndrome
- cov, coronavirus
- tgev, transmissible gastroenteritis virus
- ca, carbonic anhydrase
- cml, chronic myelogenous leukemia
- map, mitogen-activated protein kinases
- cdks, cyclin-dependent protein kinases
- hb, hydrogen bond
- rmsd, root-mean-square deviations
- upgma, unweighted pair group method with arithmetic mean
- ec, enzyme classification
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Affiliation(s)
- Daniel Kuhn
- Department of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
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9
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Guarino LA, Bhardwaj K, Dong W, Sun J, Holzenburg A, Kao C. Mutational analysis of the SARS virus Nsp15 endoribonuclease: identification of residues affecting hexamer formation. J Mol Biol 2005; 353:1106-17. [PMID: 16216269 PMCID: PMC7094243 DOI: 10.1016/j.jmb.2005.09.007] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2005] [Revised: 08/30/2005] [Accepted: 09/03/2005] [Indexed: 11/29/2022]
Abstract
The severe acute respiratory syndrome (SARS) coronavirus virus non-structural protein 15 is a Mn2+-dependent endoribonuclease with specificity for cleavage at uridylate residues. To better understand structural and functional characteristics of Nsp15, 22 mutant versions of Nsp15 were produced in Escherichia coli as His-tagged proteins and purified by metal-affinity and ion-exchange chromatography. Nineteen of the mutants were soluble and were analyzed for enzymatic activity. Six mutants, including four at the putative active site, were significantly reduced in endoribonuclease activity. Two of the inactive mutants had unusual secondary structures compared to the wild-type protein, as measured by circular dichroism spectroscopy. Gel-filtration analysis, velocity sedimentation ultracentrifugation, and native gradient pore electrophoresis all showed that the wild-type protein exists in an equilibrium between hexamers and monomers in solution, with hexamers dominating at micromolar protein concentration, while native gradient pore electrophoresis also revealed the presence of trimers. A mutant in the N terminus of Nsp15 was impaired in hexamer formation and had low endoribonuclease activity, suggesting that oligomerization is required for endoribonuclease activity. This idea was supported by titration experiments showing that enzyme activity was strongly concentration-dependent, indicating that oligomeric Nsp15 is the active form. Three-dimensional reconstruction of negatively stained single particles of Nsp15 viewed by transmission electron microscopic analysis suggested that the six subunits were arranged as a dimer of trimers with a number of cavities or channels that may constitute RNA binding sites.
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Affiliation(s)
- Linda A Guarino
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, USA.
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10
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Lee TW, Cherney MM, Huitema C, Liu J, James KE, Powers JC, Eltis LD, James MNG. Crystal structures of the main peptidase from the SARS coronavirus inhibited by a substrate-like aza-peptide epoxide. J Mol Biol 2005; 353:1137-51. [PMID: 16219322 PMCID: PMC7094542 DOI: 10.1016/j.jmb.2005.09.004] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2005] [Revised: 09/02/2005] [Accepted: 09/05/2005] [Indexed: 12/05/2022]
Abstract
The main peptidase (M(pro)) from the coronavirus (CoV) causing severe acute respiratory syndrome (SARS) is one of the most attractive molecular targets for the development of anti-SARS agents. We report the irreversible inhibition of SARS-CoV M(pro) by an aza-peptide epoxide (APE; k(inact)/K(i) = 1900(+/-400) M(-1) s(-1)). The crystal structures of the M(pro):APE complex in the space groups C2 and P2(1)2(1)2(1) revealed the formation of a covalent bond between the catalytic Cys145 S(gamma) atom of the peptidase and the epoxide C3 atom of the inhibitor, substantiating the mode of action of this class of cysteine-peptidase inhibitors. The aza-peptide component of APE binds in the substrate-binding regions of M(pro) in a substrate-like manner, with excellent structural and chemical complementarity. In addition, the crystal structure of unbound M(pro) in the space group C2 revealed that the "N-fingers" (N-terminal residues 1 to 7) of both protomers of M(pro) are well defined and the substrate-binding regions of both protomers are in the catalytically competent conformation at the crystallization pH of 6.5, contrary to the previously determined crystal structures of unbound M(pro) in the space group P2(1).
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Affiliation(s)
- Ting-Wai Lee
- Canadian Institute of Health Research Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alta., Canada T6G 2H7
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Du QS, Wang SQ, Zhu Y, Wei DQ, Guo H, Sirois S, Chou KC. Polyprotein cleavage mechanism of SARS CoV Mpro and chemical modification of the octapeptide. Peptides 2004; 25:1857-64. [PMID: 15501516 PMCID: PMC7115412 DOI: 10.1016/j.peptides.2004.06.018] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2004] [Revised: 06/18/2004] [Accepted: 06/22/2004] [Indexed: 11/26/2022]
Abstract
The cleavage mechanism of severe acute respiratory syndrome (SARS) coronavirus main proteinase (M(pro) or 3CL(pro)) for the octapeptide AVLQSGFR is studied using molecular mechanics (MM) and quantum mechanics (QM). The catalytic dyad His-41 and Cys-145 in the active pocket between domain I and II seem to polarize the pi-electron density of the peptide bond between Gln and Ser in the octapeptide, leading to an increase of positive charge on C(CO) of Gln and negative charge on N(NH) of Ser. The possibility of enhancing the chemical bond between Gln and Ser based on the "distorted key" theory [Anal. Biochem. 233 (1996) 1] is examined. The scissile peptide bond between Gln and Ser is found to be solidified through "hybrid peptide bond" by changing the carbonyl group CO of Gln to CH(2) or CF(2). This leads to a break of the pi-bond system for the peptide bond, making the octapeptide (AVLQSGFR) a "distorted key" and a potential starting system for the design of anti SARS drugs.
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Affiliation(s)
- Qi-Shi Du
- Tianjin Normal University and Tianjin Institute of Bioinformatics and Drug Discovery (TIBDD), Tianjin 300074, China
- Institut Technologique de Montreal, Suite 168, 5253 Boul. Decarie, Montreal, Que., Canada H3W 3C3
| | - Shu-Qing Wang
- Tianjin Normal University and Tianjin Institute of Bioinformatics and Drug Discovery (TIBDD), Tianjin 300074, China
| | - Yu Zhu
- Tianjin Normal University and Tianjin Institute of Bioinformatics and Drug Discovery (TIBDD), Tianjin 300074, China
| | - Dong-Qing Wei
- Tianjin Normal University and Tianjin Institute of Bioinformatics and Drug Discovery (TIBDD), Tianjin 300074, China
- Institut Technologique de Montreal, Suite 168, 5253 Boul. Decarie, Montreal, Que., Canada H3W 3C3
- Center For Research in Molecular Modeling (CERMM), Concordia University, Montreal, Canada
| | - Hong Guo
- University of Tennessee, Department of Biochemistry, Cell and Molecular Biology, Knoxville, TN 37996-0840, USA
| | - Suzanne Sirois
- Institut Technologique de Montreal, Suite 168, 5253 Boul. Decarie, Montreal, Que., Canada H3W 3C3
| | - Kuo-Chen Chou
- Tianjin Normal University and Tianjin Institute of Bioinformatics and Drug Discovery (TIBDD), Tianjin 300074, China
- Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, Shanghai 200030, China
- Gordon Life Science Institute, San Diego, CA 92130, USA
- Corresponding author.
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Abstract
BACKGROUND AND AIMS Severe acute respiratory syndrome (SARS) is a recently emerged infection from a novel coronavirus (CoV). Apart from fever and respiratory complications, gastrointestinal symptoms are frequently observed in patients with SARS but the significance remains undetermined. Herein, we describe the clinical, pathologic, and virologic features of the intestinal involvement of this new viral infection. METHODS A retrospective analysis of the gastrointestinal symptoms and other clinical parameters of the first 138 patients with confirmed SARS admitted for a major outbreak in Hong Kong in March 2003 was performed. Intestinal specimens were obtained by colonoscopy or postmortem examination to detect the presence of coronavirus by electron microscopy, virus culture, and reverse-transcription polymerase chain reaction. RESULTS Among these 138 patients with SARS, 28 (20.3%) presented with watery diarrhea and up to 38.4% of patients had symptoms of diarrhea during the course of illness. Diarrhea was more frequently observed during the first week of illness. The mean number of days with diarrhea was 3.7 +/- 2.7, and most diarrhea was self-limiting. Intestinal biopsy specimens obtained by colonoscopy or autopsy showed minimal architectural disruption but the presence of active viral replication within both the small and large intestine. Coronavirus was also isolated by culture from these specimens, and SARS-CoV RNA can be detected in the stool of patients for more than 10 weeks after symptom onset. CONCLUSIONS Diarrhea is a common presenting symptom of SARS. The intestinal tropism of the SARS-CoV has major implications on clinical presentation and viral transmission.
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Affiliation(s)
- Wai K Leung
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong.
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Abstract
BACKGROUND AND AIMS Severe acute respiratory syndrome (SARS) is a recently emerged infection from a novel coronavirus (CoV). Apart from fever and respiratory complications, gastrointestinal symptoms are frequently observed in patients with SARS but the significance remains undetermined. Herein, we describe the clinical, pathologic, and virologic features of the intestinal involvement of this new viral infection. METHODS A retrospective analysis of the gastrointestinal symptoms and other clinical parameters of the first 138 patients with confirmed SARS admitted for a major outbreak in Hong Kong in March 2003 was performed. Intestinal specimens were obtained by colonoscopy or postmortem examination to detect the presence of coronavirus by electron microscopy, virus culture, and reverse-transcription polymerase chain reaction. RESULTS Among these 138 patients with SARS, 28 (20.3%) presented with watery diarrhea and up to 38.4% of patients had symptoms of diarrhea during the course of illness. Diarrhea was more frequently observed during the first week of illness. The mean number of days with diarrhea was 3.7 +/- 2.7, and most diarrhea was self-limiting. Intestinal biopsy specimens obtained by colonoscopy or autopsy showed minimal architectural disruption but the presence of active viral replication within both the small and large intestine. Coronavirus was also isolated by culture from these specimens, and SARS-CoV RNA can be detected in the stool of patients for more than 10 weeks after symptom onset. CONCLUSIONS Diarrhea is a common presenting symptom of SARS. The intestinal tropism of the SARS-CoV has major implications on clinical presentation and viral transmission.
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Affiliation(s)
- Wai K Leung
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong.
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