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Design, synthesis and biological evaluation of stereo- and regioisomers of amino aryl esters as multidrug resistance (MDR) reversers. Eur J Med Chem 2019; 182:111655. [DOI: 10.1016/j.ejmech.2019.111655] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 12/23/2022]
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Cicaloni V, Trezza A, Pettini F, Spiga O. Applications of in Silico Methods for Design and Development of Drugs Targeting Protein-Protein Interactions. Curr Top Med Chem 2019; 19:534-554. [PMID: 30836920 DOI: 10.2174/1568026619666190304153901] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 01/02/2019] [Accepted: 01/25/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Identification of Protein-Protein Interactions (PPIs) is a major challenge in modern molecular biology and biochemistry research, due to the unquestionable role of proteins in cells, biological process and pathological states. Over the past decade, the PPIs have evolved from being considered a highly challenging field of research to being investigated and examined as targets for pharmacological intervention. OBJECTIVE Comprehension of protein interactions is crucial to known how proteins come together to build signalling pathways, to carry out their functions, or to cause diseases, when deregulated. Multiplicity and great amount of PPIs structures offer a huge number of new and potential targets for the treatment of different diseases. METHODS Computational techniques are becoming predominant in PPIs studies for their effectiveness, flexibility, accuracy and cost. As a matter of fact, there are effective in silico approaches which are able to identify PPIs and PPI site. Such methods for computational target prediction have been developed through molecular descriptors and data-mining procedures. RESULTS In this review, we present different types of interactions between protein-protein and the application of in silico methods for design and development of drugs targeting PPIs. We described computational approaches for the identification of possible targets on protein surface and to detect of stimulator/ inhibitor molecules. CONCLUSION A deeper study of the most recent bioinformatics methodologies for PPIs studies is vital for a better understanding of protein complexes and for discover new potential PPI modulators in therapeutic intervention.
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Affiliation(s)
- Vittoria Cicaloni
- Department of Biotechnology, Chemistry and Pharmacy (Dept. of Excellence 2018-2022), University of Siena, via A. Moro 2, 53100 Siena, Italy.,Toscana Life Sciences Foundation, via Fiorentina 1, 53100 Siena, Italy
| | - Alfonso Trezza
- Department of Biotechnology, Chemistry and Pharmacy (Dept. of Excellence 2018-2022), University of Siena, via A. Moro 2, 53100 Siena, Italy
| | - Francesco Pettini
- Department of Biotechnology, Chemistry and Pharmacy (Dept. of Excellence 2018-2022), University of Siena, via A. Moro 2, 53100 Siena, Italy
| | - Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy (Dept. of Excellence 2018-2022), University of Siena, via A. Moro 2, 53100 Siena, Italy
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3
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Kandeel M, Al-Taher A, Li H, Schwingenschlogl U, Al-Nazawi M. Molecular dynamics of Middle East Respiratory Syndrome Coronavirus (MERS CoV) fusion heptad repeat trimers. Comput Biol Chem 2018; 75:205-212. [PMID: 29803965 PMCID: PMC7106505 DOI: 10.1016/j.compbiolchem.2018.05.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 05/13/2018] [Accepted: 05/16/2018] [Indexed: 12/23/2022]
Abstract
Virus-membrane fusion proteins have vital role in MERS CoV replication. Both trimers and monomers were found in both of virus and cell membranes. Changes in MERS CoV heptad repeat domains monomers and trimers were resolved by MD simulation. Monomer was unstable, having high RMSDs with major drifts above 8 Å. Trimer is more dynamically stable with very low RMSD.
Structural studies related to Middle East Respiratory Syndrome Coronavirus (MERS CoV) infection process are so limited. In this study, molecular dynamics (MD) simulations were carried out to unravel changes in the MERS CoV heptad repeat domains (HRs) and factors affecting fusion state HR stability. Results indicated that HR trimer is more rapidly stabilized, having stable system energy and lower root mean square deviations (RMSDs). While trimers were the predominant active form of CoVs HRs, monomers were also discovered in both of viral and cellular membranes. In order to find the differences between S2 monomer and trimer molecular dynamics, S2 monomer was modelled and subjected to MD simulation. In contrast to S2 trimer, S2 monomer was unstable, having high RMSDs with major drifts above 8 Å. Fluctuation of HR residue positions revealed major changes in the C-terminal of HR2 and the linker coil between HR1 and HR2 in both monomer and trimer. Hydrophobic residues at the a and d positions of HR helices stabilize the whole system, with minimal changes in RMSD. The global distance test and contact area difference scores support instability of MERS CoV S2 monomer. Analysis of HR1-HR2 inter-residue contacts and interaction energy revealed three energy scales along HR helices. Two strong interaction energies were identified at the start of the HR2 helix and at the C-terminal of HR2. The identified critical residues by MD simulation and residues at the a and d positions of HR helix were strong stabilizers of HR recognition.
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Affiliation(s)
- Mahmoud Kandeel
- Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa, Saudi Arabia; Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelshikh University, Kafrelshikh, Egypt.
| | - Abdulla Al-Taher
- Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa, Saudi Arabia
| | - Huifang Li
- Physical Science and Engineering Division (PSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Udo Schwingenschlogl
- Physical Science and Engineering Division (PSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Mohamed Al-Nazawi
- Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa, Saudi Arabia
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4
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Jarvis MC, Lam HC, Zhang Y, Wang L, Hesse RA, Hause BM, Vlasova A, Wang Q, Zhang J, Nelson MI, Murtaugh MP, Marthaler D. Genomic and evolutionary inferences between American and global strains of porcine epidemic diarrhea virus. Prev Vet Med 2016; 123:175-184. [PMID: 26611651 PMCID: PMC7114344 DOI: 10.1016/j.prevetmed.2015.10.020] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 09/29/2015] [Accepted: 10/22/2015] [Indexed: 02/07/2023]
Abstract
Porcine epidemic diarrhea virus (PEDV) has caused severe economic losses both recently in the United States (US) and historically throughout Europe and Asia. Traditionally, analysis of the spike gene has been used to determine phylogenetic relationships between PEDV strains. We determined the complete genomes of 93 PEDV field samples from US swine and analyzed the data in conjunction with complete genome sequences available from GenBank (n=126) to determine the most variable genomic areas. Our results indicate high levels of variation within the ORF1 and spike regions while the C-terminal domains of structural genes were highly conserved. Analysis of the Receptor Binding Domains in the spike gene revealed a limited number of amino acid substitutions in US strains compared to Asian strains. Phylogenetic analysis of the complete genome sequence data revealed high rates of recombination, resulting in differing evolutionary patterns in phylogenies inferred for the spike region versus whole genomes. These finding suggest that significant genetic events outside of the spike region have contributed to the evolution of PEDV.
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Affiliation(s)
- Matthew C Jarvis
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Ham Ching Lam
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Yan Zhang
- Animal Disease Diagnostic Laboratory, Ohio Department of Agriculture, Reynoldsburg, OH, USA
| | - Leyi Wang
- Animal Disease Diagnostic Laboratory, Ohio Department of Agriculture, Reynoldsburg, OH, USA
| | - Richard A Hesse
- Kansas State Veterinary Diagnostic Laboratory and Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Ben M Hause
- Kansas State Veterinary Diagnostic Laboratory and Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Anastasia Vlasova
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, Ohio Agricultural Research and Development Center, College of Food Agriculture and Environmental Sciences, The Ohio State University, Wooster, OH, USA
| | - Qiuhong Wang
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, Ohio Agricultural Research and Development Center, College of Food Agriculture and Environmental Sciences, The Ohio State University, Wooster, OH, USA
| | - Jianqiang Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Martha I Nelson
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Michael P Murtaugh
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Douglas Marthaler
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA.
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Canine enteric coronaviruses: emerging viral pathogens with distinct recombinant spike proteins. Viruses 2014; 6:3363-76. [PMID: 25153347 PMCID: PMC4147700 DOI: 10.3390/v6083363] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 08/11/2014] [Accepted: 08/15/2014] [Indexed: 12/16/2022] Open
Abstract
Canine enteric coronavirus (CCoV) is an alphacoronavirus infecting dogs that is closely related to enteric coronaviruses of cats and pigs. While CCoV has traditionally caused mild gastro-intestinal clinical signs, there are increasing reports of lethal CCoV infections in dogs, with evidence of both gastrointestinal and systemic viral dissemination. Consequently, CCoV is now considered to be an emerging infectious disease of dogs. In addition to the two known serotypes of CCoV, novel recombinant variants of CCoV have been found containing spike protein N-terminal domains (NTDs) that are closely related to those of feline and porcine strains. The increase in disease severity in dogs and the emergence of novel CCoVs can be attributed to the high level of recombination within the spike gene that can occur during infection by more than one CCoV type in the same host.
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Belouzard S, Millet JK, Licitra BN, Whittaker GR. Mechanisms of coronavirus cell entry mediated by the viral spike protein. Viruses 2012; 4:1011-33. [PMID: 22816037 PMCID: PMC3397359 DOI: 10.3390/v4061011] [Citation(s) in RCA: 890] [Impact Index Per Article: 74.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 06/13/2012] [Accepted: 06/14/2012] [Indexed: 12/12/2022] Open
Abstract
Coronaviruses are enveloped positive-stranded RNA viruses that replicate in the cytoplasm. To deliver their nucleocapsid into the host cell, they rely on the fusion of their envelope with the host cell membrane. The spike glycoprotein (S) mediates virus entry and is a primary determinant of cell tropism and pathogenesis. It is classified as a class I fusion protein, and is responsible for binding to the receptor on the host cell as well as mediating the fusion of host and viral membranes—A process driven by major conformational changes of the S protein. This review discusses coronavirus entry mechanisms focusing on the different triggers used by coronaviruses to initiate the conformational change of the S protein: receptor binding, low pH exposure and proteolytic activation. We also highlight commonalities between coronavirus S proteins and other class I viral fusion proteins, as well as distinctive features that confer distinct tropism, pathogenicity and host interspecies transmission characteristics to coronaviruses.
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Affiliation(s)
- Sandrine Belouzard
- Center for Infection and Immunity of Lille, CNRS UMR8204, INSERM U1019, Institut Pasteur de Lille, Université Lille Nord de France, 59000 Lille, France;
| | - Jean K. Millet
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA; (J.K.M.); (B.N.L.)
| | - Beth N. Licitra
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA; (J.K.M.); (B.N.L.)
| | - Gary R. Whittaker
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA; (J.K.M.); (B.N.L.)
- Author to whom correspondence should be addressed; ; Tel.: +1-607-253-4021; Fax: +1-607-253-3384
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Madu IG, Belouzard S, Whittaker GR. SARS-coronavirus spike S2 domain flanked by cysteine residues C822 and C833 is important for activation of membrane fusion. Virology 2009; 393:265-71. [PMID: 19717178 PMCID: PMC3594805 DOI: 10.1016/j.virol.2009.07.038] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 05/27/2009] [Accepted: 07/30/2009] [Indexed: 01/04/2023]
Abstract
The S2 domain of the coronavirus spike (S) protein is known to be responsible for mediating membrane fusion. In addition to a well-recognized cleavage site at the S1–S2 boundary, a second proteolytic cleavage site has been identified in the severe acute respiratory syndrome coronavirus (SARS-CoV) S2 domain (R797). C-terminal to this S2 cleavage site is a conserved region flanked by cysteine residues C822 and C833. Here, we investigated the importance of this well conserved region for SARS-CoV S-mediated fusion activation. We show that the residues between C822–C833 are well conserved across all coronaviruses. Mutagenic analysis of SARS-CoV S, combined with cell–cell fusion and pseudotyped virion infectivity assays, showed a critical role for the core-conserved residues C822, D830, L831, and C833. Based on available predictive models, we propose that the conserved domain flanked by cysteines 822 and 833 forms a loop structure that interacts with components of the SARS-CoV S trimer to control the activation of membrane fusion.
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Affiliation(s)
- Ikenna G Madu
- C4127 Veterinary Medical Center, Department of Microbiology and Immunology, Cornell University, Ithaca NY 14853, USA
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Characterization of a highly conserved domain within the severe acute respiratory syndrome coronavirus spike protein S2 domain with characteristics of a viral fusion peptide. J Virol 2009; 83:7411-21. [PMID: 19439480 DOI: 10.1128/jvi.00079-09] [Citation(s) in RCA: 203] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many viral fusion proteins are primed by proteolytic cleavage near their fusion peptides. While the coronavirus (CoV) spike (S) protein is known to be cleaved at the S1/S2 boundary, this cleavage site is not closely linked to a fusion peptide. However, a second cleavage site has been identified in the severe acute respiratory syndrome CoV (SARS-CoV) S2 domain (R797). Here, we investigated whether this internal cleavage of S2 exposes a viral fusion peptide. We show that the residues immediately C-terminal to the SARS-CoV S2 cleavage site SFIEDLLFNKVTLADAGF are very highly conserved across all CoVs. Mutagenesis studies of these residues in SARS-CoV S, followed by cell-cell fusion and pseudotyped virion infectivity assays, showed a critical role for residues L803, L804, and F805 in membrane fusion. Mutation of the most N-terminal residue (S798) had little or no effect on membrane fusion. Biochemical analyses of synthetic peptides corresponding to the proposed S2 fusion peptide also showed an important role for this region in membrane fusion and indicated the presence of alpha-helical structure. We propose that proteolytic cleavage within S2 exposes a novel internal fusion peptide for SARS-CoV S, which may be conserved across the Coronaviridae.
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Severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection. Clin Microbiol Rev 2007; 20:660-94. [PMID: 17934078 DOI: 10.1128/cmr.00023-07] [Citation(s) in RCA: 657] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Before the emergence of severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) in 2003, only 12 other animal or human coronaviruses were known. The discovery of this virus was soon followed by the discovery of the civet and bat SARS-CoV and the human coronaviruses NL63 and HKU1. Surveillance of coronaviruses in many animal species has increased the number on the list of coronaviruses to at least 36. The explosive nature of the first SARS epidemic, the high mortality, its transient reemergence a year later, and economic disruptions led to a rush on research of the epidemiological, clinical, pathological, immunological, virological, and other basic scientific aspects of the virus and the disease. This research resulted in over 4,000 publications, only some of the most representative works of which could be reviewed in this article. The marked increase in the understanding of the virus and the disease within such a short time has allowed the development of diagnostic tests, animal models, antivirals, vaccines, and epidemiological and infection control measures, which could prove to be useful in randomized control trials if SARS should return. The findings that horseshoe bats are the natural reservoir for SARS-CoV-like virus and that civets are the amplification host highlight the importance of wildlife and biosecurity in farms and wet markets, which can serve as the source and amplification centers for emerging infections.
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Zhao GP. SARS molecular epidemiology: a Chinese fairy tale of controlling an emerging zoonotic disease in the genomics era. Philos Trans R Soc Lond B Biol Sci 2007; 362:1063-81. [PMID: 17327210 PMCID: PMC2435571 DOI: 10.1098/rstb.2007.2034] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome (SARS) was the first natural disaster that challenged the Chinese people at the beginning of the twenty-first century. It was caused by a novel animal coronavirus, never recognized or characterized before. This SARS coronavirus (SARS-CoV) exploited opportunities provided by 'wet markets' in southern China to adapt to the palm civet and human. Under the positive selection pressure of human host, certain mutated lineages of the virus became readily transmissible between humans and thus caused the epidemic of 2002-2003. This review will provide first-hand information, particularly from Guangdong, China, about the initial epidemiology, the identification of the aetiological agent of the disease, the molecular evolution study of the virus, the finding of SARS-like CoV in horseshoe bats and the mechanistic analysis for the cross-host tropism transition. The substantial scientific contributions made by the Chinese scientists towards understanding the virus and the disease will be emphasized. Along with the description of the scientific discoveries and analyses, the significant impact of these researches upon the public health measurement or regulations will be highlighted. It is aimed to appreciate the concerted and coordinated global response that controlled SARS within a short period of time as well as the research strategy and methodology developed along with this process, which can be applied in response to other public health challenges, particularly the future emerging/re-merging infectious diseases.
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Affiliation(s)
- Guo-ping Zhao
- Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Building 1, 250 Bi-Bo Road, Zhangjiang HiTech Park, Pudong, Shanghai 201203, People's Republic of China.
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Zhang CY, Wei JF, He SH. Adaptive evolution of the spike gene of SARS coronavirus: changes in positively selected sites in different epidemic groups. BMC Microbiol 2006; 6:88. [PMID: 17020602 PMCID: PMC1609170 DOI: 10.1186/1471-2180-6-88] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2006] [Accepted: 10/04/2006] [Indexed: 12/28/2022] Open
Abstract
Background It is believed that animal-to-human transmission of severe acute respiratory syndrome (SARS) coronavirus (CoV) is the cause of the SARS outbreak worldwide. The spike (S) protein is one of the best characterized proteins of SARS-CoV, which plays a key role in SARS-CoV overcoming species barrier and accomplishing interspecies transmission from animals to humans, suggesting that it may be the major target of selective pressure. However, the process of adaptive evolution of S protein and the exact positively selected sites associated with this process remain unknown. Results By investigating the adaptive evolution of S protein, we identified twelve amino acid sites (75, 239, 244, 311, 479, 609, 613, 743, 765, 778, 1148, and 1163) in the S protein under positive selective pressure. Based on phylogenetic tree and epidemiological investigation, SARS outbreak was divided into three epidemic groups: 02–04 interspecies, 03-early-mid, and 03-late epidemic groups in the present study. Positive selection was detected in the first two groups, which represent the course of SARS-CoV interspecies transmission and of viral adaptation to human host, respectively. In contrast, purifying selection was detected in 03-late group. These indicate that S protein experiences variable positive selective pressures before reaching stabilization. A total of 25 sites in 02–04 interspecies epidemic group and 16 sites in 03-early-mid epidemic group were identified under positive selection. The identified sites were different between these two groups except for site 239, which suggests that positively selected sites are changeable between groups. Moreover, it was showed that a larger proportion (24%) of positively selected sites was located in receptor-binding domain (RBD) than in heptad repeat (HR)1-HR2 region in 02–04 interspecies epidemic group (p = 0.0208), and a greater percentage (25%) of these sites occurred in HR1–HR2 region than in RBD in 03-early-mid epidemic group (p = 0.0721). These suggest that functionally different domains of S protein may not experience same positive selection in each epidemic group. In addition, three specific replacements (F360S, T487S and L665S) were only found between 03-human SARS-CoVs and strains from 02–04 interspecies epidemic group, which reveals that selective sweep may also force the evolution of S genes before the jump of SARS-CoVs into human hosts. Since certain residues at these positively selected sites are associated with receptor recognition and/or membrane fusion, they are likely to be the crucial residues for animal-to-human transmission of SARS-CoVs, and subsequent adaptation to human hosts. Conclusion The variation of positive selective pressures and positively selected sites are likely to contribute to the adaptive evolution of S protein from animals to humans.
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Affiliation(s)
- Chi-Yu Zhang
- Department of Biochemistry and Molecular Biology, Jiangsu University School of Medical Technology, Zhenjiang, Jiangsu 212001, China
| | - Ji-Fu Wei
- The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210026, China
| | - Shao-Heng He
- The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210026, China
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He ML, Zheng BJ, Chen Y, Wong KL, Huang JD, Lin MC, Peng Y, Yuen KY, Sung JJ, Kung HF. Kinetics and synergistic effects of siRNAs targeting structural and replicase genes of SARS-associated coronavirus. FEBS Lett 2006; 580:2414-20. [PMID: 16638566 PMCID: PMC7094648 DOI: 10.1016/j.febslet.2006.03.066] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2006] [Revised: 03/14/2006] [Accepted: 03/24/2006] [Indexed: 12/23/2022]
Abstract
SARS‐associated coronavirus was identified as the etiological agent of severe acute respiratory syndrome and a large virus pool was identified in wild animals. Virus generates drug resistance through fast mutagenesis and escapes antiviral treatment. siRNAs targeting different genes would be an alternative for overcoming drug resistance. Here, we report effective siRNAs targeting structural genes (i.e., spike, envelope, membrane, and nucleocapsid) and their antiviral kinetics. We also showed the synergistic effects of two siRNAs targeting different functional genes at a very low dose. Our findings may pave a way to develop cost effective siRNA agents for antiviral therapy in the future.
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Affiliation(s)
- Ming-Liang He
- The Center for Emerging Infectious, Li Ka-Shing Medical Institute, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Bo-jian Zheng
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Ying Chen
- The Center for Emerging Infectious, Li Ka-Shing Medical Institute, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Kin-Ling Wong
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Jian-Dong Huang
- Department of Biochemistry, The University of Hong Kong, Hong Kong
| | - Marie C. Lin
- Department of Chemistry, The University of Hong Kong, Hong Kong
| | - Ying Peng
- The Department of Neurology, The Second Affiliated Hospital, Sun Yat-san University, Guangzhou, China
| | - Kwok Y. Yuen
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Joseph J.Y. Sung
- The Center for Emerging Infectious, Li Ka-Shing Medical Institute, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Hsiang-fu Kung
- The Center for Emerging Infectious, Li Ka-Shing Medical Institute, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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Duan J, Ji X, Feng J, Han W, Zhang P, Cao W, Guo X, Qi C, Yang D, Jin G, Gao G, Yan X. A Human Neutralizing Antibody against a Conformational Epitope Shared by Oligomeric Sars S1 Protein. Antivir Ther 2006. [DOI: 10.1177/135965350601100101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
An antibody phage-display library was constructed from the B cells of convalescent severe acute respiratory syndrome (SARS) patients and screened using inactivated SARS coronavirus (CoV) virions as antigens. More than 80 positive clones were isolated from the library and one of them, scFv H12, was extensively characterized. scFv H12 bound to SARS-CoV with high affinity (equilibrium dissociation constant, Kd=73.5 nM), and neutralized SARS virions in vitro. The facts that scFv H12 bound to the SARS-S1 protein under non-reducing conditions and that it did not bind to monomeric S1 protein under reducing conditions strongly suggest that scFv H12 recognizes a conformational epitope shared by oligomeric S1 proteins. This study should aid in the manufacture of neutralizing antibody, provide a better understanding the immunological characteristics of SARS protein and facilitate the design of a SARS vaccine.
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Affiliation(s)
- Jinzhu Duan
- National Laboratory of Biomacromolecules, and Centre for Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xin Ji
- National Laboratory of Biomacromolecules, and Centre for Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jing Feng
- National Laboratory of Biomacromolecules, and Centre for Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Wei Han
- National Laboratory of Biomacromolecules, and Centre for Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Panhe Zhang
- Department of Epidemiology, Institute of Microbiology and Epidemiology, Beijing, China
| | - Wuchun Cao
- Department of Epidemiology, Institute of Microbiology and Epidemiology, Beijing, China
| | - Xueming Guo
- National Laboratory of Biomacromolecules, and Centre for Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Cai Qi
- National Laboratory of Biomacromolecules, and Centre for Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Dongling Yang
- National Laboratory of Biomacromolecules, and Centre for Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Gang Jin
- National Laboratory of Biomacromolecules, and Centre for Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Guangxia Gao
- National Laboratory of Biomacromolecules, and Centre for Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xiyun Yan
- National Laboratory of Biomacromolecules, and Centre for Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
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14
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Qu XX, Hao P, Song XJ, Jiang SM, Liu YX, Wang PG, Rao X, Song HD, Wang SY, Zuo Y, Zheng AH, Luo M, Wang HL, Deng F, Wang HZ, Hu ZH, Ding MX, Zhao GP, Deng HK. Identification of Two Critical Amino Acid Residues of the Severe Acute Respiratory Syndrome Coronavirus Spike Protein for Its Variation in Zoonotic Tropism Transition via a Double Substitution Strategy. J Biol Chem 2005; 280:29588-95. [PMID: 15980414 PMCID: PMC8740630 DOI: 10.1074/jbc.m500662200] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV) is a recently identified human coronavirus. The extremely high homology of the viral genomic sequences between the viruses isolated from human (huSARS-CoV) and those of palm civet origin (pcSARS-CoV) suggested possible palm civet-to-human transmission. Genetic analysis revealed that the spike (S) protein of pcSARS-CoV and huSARS-CoV was subjected to the strongest positive selection pressure during transmission, and there were six amino acid residues within the receptor-binding domain of the S protein being potentially important for SARS progression and tropism. Using the single-round infection assay, we found that a two-amino acid substitution (N479K/T487S) of a huSARS-CoV for those of pcSARS-CoV almost abolished its infection of human cells expressing the SARS-CoV receptor ACE2 but no effect upon the infection of mouse ACE2 cells. Although single substitution of these two residues had no effects on the infectivity of huSARS-CoV, these recombinant S proteins bound to human ACE2 with different levels of reduced affinity, and the two-amino acid-substituted S protein showed extremely low affinity. On the contrary, substitution of these two amino acid residues of pcSARS-CoV for those of huSRAS-CoV made pcSARS-CoV capable of infecting human ACE2-expressing cells. These results suggest that amino acid residues at position 479 and 487 of the S protein are important determinants for SARS-CoV tropism and animal-to-human transmission.
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Affiliation(s)
- Xiu-Xia Qu
- Department of Cell Biology and Genetics, College of Life Sciences, Peking University, Beijing, China
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15
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Zheng BJ, Guan Y, He ML, Sun H, Du L, Zheng Y, Wong KL, Chen H, Chen Y, Lu L, Tanner JA, Watt RM, Niccolai N, Bernini A, Spiga O, Woo PCY, Kung HF, Yuen KY, Huang JD. Synthetic Peptides outside the Spike Protein Heptad Repeat Regions as Potent Inhibitors of Sars-Associated Coronavirus. Antivir Ther 2005. [DOI: 10.1177/135965350501000301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A novel severe acute respiratory syndrome (SARS)-associated coronavirus (SARS-CoV) has been identified as the aetiological agent of SARS. We previously isolated and characterized SARS-CoV and SARS-CoV-like viruses from human and animals, respectively, suggesting that SARS could be transmitted from wild/farmed animals to humans. Comparison of the viral genomes indicated that sequence variation between animal and human isolates existed mainly in the spike (S) gene. We hypothesized that these variations may underlie a change of binding specificity of the S protein to the host cells, permitting viral transmission from animals to humans. Here we report that four 20-mer synthetic peptides (S protein fragments), designed to span these sequence variation otspots, exhibited significant antiviral activities in a cell line. SARS-CoV infectivity was reduced over 10 000-fold through pre-incubation with two of these peptides, while it was completely inhibited in the presence of three peptides. Molecular modelling of the SARS-CoV peplomer suggests that three of these antiviral peptides map to the interfaces between the three monomers of the trimeric peplomer rather than the heptad repeat region from which short peptides are known to inhibit viral entry. Our results revealed novel regions in the spike protein that can be targeted to inhibit viral infection. The peptides identified in this study could be further developed into antiviral drugs.
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Affiliation(s)
- Bo-Jian Zheng
- Department of Microbiology, University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Yi Guan
- Department of Microbiology, University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Ming-Liang He
- Institute of Molecular Biology, University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Centre for Emerging Infectious Diseases, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hongzhe Sun
- Department of Chemistry and Open Laboratory of Chemical Biology, University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Lanying Du
- Department of Microbiology, University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Ying Zheng
- Department of Microbiology, University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Kin-Ling Wong
- Department of Microbiology, University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Honglin Chen
- Department of Microbiology, University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Ying Chen
- Department of Microbiology, University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Linyu Lu
- Department of Biochemistry, University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Julian A Tanner
- Department of Biochemistry, University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Rory M Watt
- Department of Chemistry and Open Laboratory of Chemical Biology, University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Department of Biochemistry, University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Neri Niccolai
- Biomolecular Structure Research Centre, University of Siena, Siena, Italy
| | - Andrea Bernini
- Biomolecular Structure Research Centre, University of Siena, Siena, Italy
| | - Ottavia Spiga
- Biomolecular Structure Research Centre, University of Siena, Siena, Italy
| | - Patrick CY Woo
- Department of Microbiology, University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Hsiang-fu Kung
- Institute of Molecular Biology, University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Centre for Emerging Infectious Diseases, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kwok-Yung Yuen
- Department of Microbiology, University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Jian-Dong Huang
- Department of Biochemistry, University of Hong Kong, Pokfulam, Hong Kong SAR, China
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16
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Song HD, Tu CC, Zhang GW, Wang SY, Zheng K, Lei LC, Chen QX, Gao YW, Zhou HQ, Xiang H, Zheng HJ, Chern SWW, Cheng F, Pan CM, Xuan H, Chen SJ, Luo HM, Zhou DH, Liu YF, He JF, Qin PZ, Li LH, Ren YQ, Liang WJ, Yu YD, Anderson L, Wang M, Xu RH, Wu XW, Zheng HY, Chen JD, Liang G, Gao Y, Liao M, Fang L, Jiang LY, Li H, Chen F, Di B, He LJ, Lin JY, Tong S, Kong X, Du L, Hao P, Tang H, Bernini A, Yu XJ, Spiga O, Guo ZM, Pan HY, He WZ, Manuguerra JC, Fontanet A, Danchin A, Niccolai N, Li YX, Wu CI, Zhao GP. Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human. Proc Natl Acad Sci U S A 2005; 102:2430-5. [PMID: 15695582 PMCID: PMC548959 DOI: 10.1073/pnas.0409608102] [Citation(s) in RCA: 511] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genomic sequences of severe acute respiratory syndrome coronaviruses from human and palm civet of the 2003/2004 outbreak in the city of Guangzhou, China, were nearly identical. Phylogenetic analysis suggested an independent viral invasion from animal to human in this new episode. Combining all existing data but excluding singletons, we identified 202 single-nucleotide variations. Among them, 17 are polymorphic in palm civets only. The ratio of nonsynonymous/synonymous nucleotide substitution in palm civets collected 1 yr apart from different geographic locations is very high, suggesting a rapid evolving process of viral proteins in civet as well, much like their adaptation in the human host in the early 2002-2003 epidemic. Major genetic variations in some critical genes, particularly the Spike gene, seemed essential for the transition from animal-to-human transmission to human-to-human transmission, which eventually caused the first severe acute respiratory syndrome outbreak of 2002/2003.
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Affiliation(s)
- Huai-Dong Song
- State Key Laboratory for Medical Genomics/Pôle Sino-Français de Recherche en Sciences du Vivant et Génomique, Ruijin Hospital Affiliated to Shanghai Second Medical University, 197 Rui Jin Road II, Shanghai 200025, China
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