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Islam S, Parves MR, Islam MJ, Ali MA, Efaz FM, Hossain MS, Ullah MO, Halim MA. Structural and functional effects of the L84S mutant in the SARS-COV-2 ORF8 dimer based on microsecond molecular dynamics study. J Biomol Struct Dyn 2024; 42:5770-5787. [PMID: 37403295 DOI: 10.1080/07391102.2023.2228919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 06/17/2023] [Indexed: 07/06/2023]
Abstract
The L84S mutation has been observed frequently in the ORF8 protein of SARS-CoV-2, which is an accessory protein involved in various important functions such as virus propagation, pathogenesis, and evading the immune response. However, the specific effects of this mutation on the dimeric structure of ORF8 and its impacts on interactions with host components and immune responses are not well understood. In this study, we performed one microsecond molecular dynamics (MD) simulation and analyzed the dimeric behavior of the L84S and L84A mutants in comparison to the native protein. The MD simulations revealed that both mutations caused changes in the conformation of the ORF8 dimer, influenced protein folding mechanisms, and affected the overall structural stability. In particular, the 73YIDI76 motif has found to be significantly affected by the L84S mutation, leading to structural flexibility in the region connecting the C-terminal β4 and β5 strands. This flexibility might be responsible for virus immune modulation. The free energy landscape (FEL) and principle component analysis (PCA) have also supported our investigation. Overall, the L84S and L84A mutations affect the ORF8 dimeric interfaces by reducing the frequency of protein-protein interacting residues (Arg52, Lys53, Arg98, Ile104, Arg115, Val117, Asp119, Phe120, and Ile121) in the ORF8 dimer. Our findings provide detail insights for further research in designing structure-based therapeutics against the SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shafiqul Islam
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Rimon Parves
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Jahirul Islam
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Ackas Ali
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Faiyaz Md Efaz
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Shahadat Hossain
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - M Obayed Ullah
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Mohammad A Halim
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
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2
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Yazdani Z, Rafiei A, Momenizadeh M, Abediankenari S, Yazdani M, Lagzian M. Designing novel peptides for detecting the Omicron variant, specifying SARS-CoV-2, and simultaneously screening coronavirus infections. J Biomol Struct Dyn 2024; 42:4759-4768. [PMID: 37306566 DOI: 10.1080/07391102.2023.2222821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 06/02/2023] [Indexed: 06/13/2023]
Abstract
In this study in silico a candidate diagnostic peptide-based tool was designed in four stages including diagnosis of coronavirus diseases, simultaneously identifying of COVID-19 and SARS from other members of this family, specific identification of SARS-CoV2, and diagnosis of COVID-19 Omicron. Designed candidate peptides consist of four immunodominant peptides from the proteins of the SARS-CoV-2 spike (S) and membrane (M). The tertiary structure of each peptide was predicted. The stimulation ability of the humoral immunity for each peptide was evaluated. Finally, in silico cloning was performed to develop an expression strategy for each peptide. These four peptides have suitable immunogenicity, appropriate construct, and the ability to be expressed in E.coli. These results must be experimentally validated in vitro and in vivo to ensure the immunogenicity of the kit.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zahra Yazdani
- Department of Immunology, Molecular and Cell Biology Research Center, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Students Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - Alireza Rafiei
- Department of Immunology, Molecular and Cell Biology Research Center, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mahdi Momenizadeh
- Students Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - Saeid Abediankenari
- Immunogenetics Research Center, Department of Immunology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | | | - Milad Lagzian
- Department of Biology, Faculty of Sciences, University of Sistan and Baluchestan, Zahedan, Iran
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3
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Wang R, Lu S, Deng F, Wu L, Yang G, Chong S, Liu Y. Enhancing the understanding of SARS-CoV-2 protein with structure and detection methods: An integrative review. Int J Biol Macromol 2024; 270:132237. [PMID: 38734351 DOI: 10.1016/j.ijbiomac.2024.132237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 05/07/2024] [Indexed: 05/13/2024]
Abstract
As the rapid and accurate screening of infectious diseases can provide meaningful information for outbreak prevention and control, as well as owing to the existing limitations of the polymerase chain reaction (PCR), it is imperative to have new and validated detection techniques for SARS-CoV-2. Therefore, the rationale for outlining the techniques used to detect SARS-CoV-2 proteins and performing a comprehensive comparison to serve as a practical benchmark for future identification of similar viral proteins is clear. This review highlights the urgent need to strengthen pandemic preparedness by emphasizing the importance of integrated measures. These include improved tools for pathogen characterization, optimized societal precautions, the establishment of early warning systems, and the deployment of highly sensitive diagnostics for effective surveillance, triage, and resource management. Additionally, with an improved understanding of the virus' protein structure, considerable advances in targeted detection, treatment, and prevention strategies are expected to greatly improve our ability to respond to future outbreaks.
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Affiliation(s)
- Ruiqi Wang
- Shenyang University of Chemical Technology, Shenyang 110142, China; National Institute of Metrology, Beijing 100029, China
| | - Song Lu
- National Institute of Metrology, Beijing 100029, China
| | - Fanyu Deng
- National Institute of Metrology, Beijing 100029, China; North University of China, Taiyuan 030051, China
| | - Liqing Wu
- National Institute of Metrology, Beijing 100029, China
| | - Guowu Yang
- Shenzhen Academy of Metrology and Quality Inspection, Shenzhen 518055, China
| | - Siying Chong
- Shenyang University of Chemical Technology, Shenyang 110142, China
| | - Yahui Liu
- National Institute of Metrology, Beijing 100029, China.
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4
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Peixoto VP, Prudêncio C, Vieira M, Sousa SF. Evaluation of the impact of two C5 genetic variants on C5-eculizumab complex stability at the molecular level. J Biomol Struct Dyn 2024:1-10. [PMID: 38529903 DOI: 10.1080/07391102.2024.2331091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/11/2024] [Indexed: 03/27/2024]
Abstract
Complement C5 is the target of the monoclonal antibody eculizumab, used in complement dysregulating disorders, like the rare disease Paroxysmal Nocturnal Hemoglobinuria (PNH). PNH is an acquired hematopoietic stem cell condition characterized by aberrant destruction of erythrocytes, chronic hemolytic anemia, and thromboembolism propensity. C5 is a protein component of the complement system which is part of the immune system of the body and plays a prominent role in the destruction of red blood cells, misidentifying them as a threat. This work describes the application of molecular dynamics simulations to the study of the underlying interactions between complement C5 and eculizumab. This study also reveals the importance of single nucleotide polymorphisms on C5 protein concerning the effective inhibition of the mAB, involving the mechanistic events taking place at the interface spots of the complex. The predicted conformational change in the C5 Arg885/His/Cys mutation has implications on the protein's interaction with eculizumab, compromising their compatibility. The acquired insights into the conformational changes, dynamics, flexibility, and interactions shed light on the knowledge of the function of this biomolecule providing answers about the poor response to the treatment in PNH patient carriers of the mutations. By investigating the intricate dynamics, significant connections between C5 and eculizumab can be uncovered. Such insights may aid in the creation of novel compounds or lead to the enhancement of eculizumab's efficacy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vanda P Peixoto
- Chemical and Biomolecular Sciences, School of Health, Polytechnic Institute of Porto, Porto, Portugal
- Center for Translational Health and Medical Biotechnology Research (TBIO), Polytechnic Institute of Porto, Porto, Portugal
- LAQV/REQUIMTE, BioSIM - Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, Porto, Portugal
| | - Cristina Prudêncio
- Chemical and Biomolecular Sciences, School of Health, Polytechnic Institute of Porto, Porto, Portugal
- Center for Translational Health and Medical Biotechnology Research (TBIO), Polytechnic Institute of Porto, Porto, Portugal
- Institute for Research and Innovation in Health (i3S), University of Porto, Porto, Portugal
| | - Mónica Vieira
- Chemical and Biomolecular Sciences, School of Health, Polytechnic Institute of Porto, Porto, Portugal
- Center for Translational Health and Medical Biotechnology Research (TBIO), Polytechnic Institute of Porto, Porto, Portugal
- Institute for Research and Innovation in Health (i3S), University of Porto, Porto, Portugal
| | - Sérgio F Sousa
- LAQV/REQUIMTE, BioSIM - Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, Porto, Portugal
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5
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Fakih TM, Darusman F, Apriliani R, Prahayati S, Ramadhan DSF, Fikri Hidayat A, Rizkita AD, Yuniarta TA. Predicting anti-COVID-19 potential: in silico analysis of Mauritine compound from Ziziphus-spina christi as a promising papain-like protease (PLpro) inhibitor. J Biomol Struct Dyn 2024:1-12. [PMID: 38529845 DOI: 10.1080/07391102.2024.2322627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/19/2024] [Indexed: 03/27/2024]
Abstract
The COVID-19 pandemic caused by the SARS-CoV-2 virus, recognized by the World Health Organization (WHO), has led to 164,523,894 confirmed cases and 3,412,032 deaths globally as of May 20, 2021. SARS-CoV-2 encodes crucial proteases for its replication cycle, including the papain-like protease (PLpro), presenting a potential target for developing COVID-19 treatments. Mauritine, a cyclopeptide alkaloid found in the Ziziphus-spina christi plant, exhibits antiviral properties and was investigated for its affinity and toxicity towards PLpro using molecular docking through MGLTools 1.5.6 with Autodock Tools 4.2. Preceding this, toxicity and ADME prediction were performed via Toxtree 3.1.0 software and SwissADME servers. Results from molecular docking revealed free binding energy values of -8.58; -7.73; -8.36; -6.07; -6.67; -7.83; -7.67; -7.40; and -6.87 Kcal/mol for Mauritine-A, Mauritine-B, Mauritine-C, Mauritine-D, Mauritine-F, Mauritine-H, Mauritine-J, Mauritine-L, and Mauritine-M, respectively. Correspondingly, inhibition constants were 0.51724; 2.14; 0.7398; 35.43; 12.95; 1.83; 2.38; 3.80; and 9.17 µM, respectively. Interactions observed included hydrogen bonds, hydrophobic interactions, and electrostatic interactions between the Mauritine compounds and the receptor. Mauritine-A and Mauritine-C emerged as a promising anti-COVID-19 candidate due to its superior affinity compared to other derivatives, as indicated by research findings. Interestingly, Mauritine-A and Mauritine-C exhibits notable stability as depicted by the RMSD and RMSF graphs, along with a considerable MM-PBSA binding free energy value of -162.431 and -137.500 kJ/mol, respectively.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Taufik Muhammad Fakih
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Universitas Islam Bandung, Bandung, Indonesia
| | - Fitrianti Darusman
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Universitas Islam Bandung, Bandung, Indonesia
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Universitas Padjadjaran, Bandung, Indonesia
| | - Riry Apriliani
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Universitas Islam Bandung, Bandung, Indonesia
| | - Syifa Prahayati
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Universitas Islam Bandung, Bandung, Indonesia
| | | | - Aulia Fikri Hidayat
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Universitas Islam Bandung, Bandung, Indonesia
| | - Aden Dhana Rizkita
- Department of Pharmacy, Sekolah Tinggi Ilmu Kesehatan (STIKES) Bogor Husada, Bogor, Indonesia
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Tegar Achsendo Yuniarta
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Surabaya, Surabaya, Indonesia
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6
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Drogalin A, Monteiro LS, Alves MJ, Castro TG. Golgi α-mannosidase: opposing structures of Drosophila melanogaster and novel human model using molecular dynamics simulations and docking at different pHs. J Biomol Struct Dyn 2024; 42:2714-2725. [PMID: 37158092 DOI: 10.1080/07391102.2023.2209184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/19/2023] [Indexed: 05/10/2023]
Abstract
The search for Golgi α-mannosidase II (GMII) potent and specific inhibitors has been a focus of many studies for the past three decades since this enzyme is a key target for cancer treatment. α-Mannosidases, such as those from Drosophila melanogaster or Jack bean, have been used as functional models of the human Golgi α-mannosidase II (hGMII) because mammalian mannosidases are difficult to purify and characterize experimentally. Meanwhile, computational studies have been seen as privileged tools able to explore assertive solutions to specific enzymes, providing molecular details of these macromolecules, their protonation states and their interactions. Thus, modelling techniques can successfully predict hGMII 3D structure with high confidence, speeding up the development of new hits. In this study, Drosophila melanogaster Golgi mannosidase II (dGMII) and a novel human model, developed in silico and equilibrated via molecular dynamics simulations, were both opposed for docking. Our findings highlight that the design of novel inhibitors should be carried out considering the human model's characteristics and the enzyme operating pH. A reliable model is evidenced, showing a good correlation between Ki/IC50 experimental data and theoretical ΔGbinding estimations in GMII, opening the possibility of optimizing the rational drug design of new derivatives.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Artem Drogalin
- Chemistry Centre, School of Sciences, University of Minho, Braga, Portugal
| | - Luís S Monteiro
- Chemistry Centre, School of Sciences, University of Minho, Braga, Portugal
| | - Maria José Alves
- Chemistry Centre, School of Sciences, University of Minho, Braga, Portugal
| | - Tarsila G Castro
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS -Associate Laboratory, Braga/Guimarães, Portugal
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7
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Zhang Y, Anbir S, McTiernan J, Li S, Worcester M, Mishra P, Colvin ME, Gopinathan A, Mohideen U, Zandi R, Kuhlman TE. Synthesis, insertion, and characterization of SARS-CoV-2 membrane protein within lipid bilayers. SCIENCE ADVANCES 2024; 10:eadm7030. [PMID: 38416838 PMCID: PMC10901468 DOI: 10.1126/sciadv.adm7030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/25/2024] [Indexed: 03/01/2024]
Abstract
Throughout history, coronaviruses have posed challenges to both public health and the global economy; nevertheless, methods to combat them remain rudimentary, primarily due to the absence of experiments to understand the function of various viral components. Among these, membrane (M) proteins are one of the most elusive because of their small size and challenges with expression. Here, we report the development of an expression system to produce tens to hundreds of milligrams of M protein per liter of Escherichia coli culture. These large yields render many previously inaccessible structural and biophysical experiments feasible. Using cryo-electron microscopy and atomic force microscopy, we image and characterize individual membrane-incorporated M protein dimers and discover membrane thinning in the vicinity, which we validated with molecular dynamics simulations. Our results suggest that the resulting line tension, along with predicted induction of local membrane curvature, could ultimately drive viral assembly and budding.
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Affiliation(s)
- Yuanzhong Zhang
- Department of Physics and Astronomy, University of California, Riverside, Riverside, CA 92521, USA
| | - Sara Anbir
- Biophysics Program, University of California, Riverside, Riverside, CA 92521, USA
| | - Joseph McTiernan
- Department of Physics, University of California, Merced, Merced, CA 95340, USA
| | - Siyu Li
- Department of Physics and Astronomy, University of California, Riverside, Riverside, CA 92521, USA
| | - Michael Worcester
- Department of Physics and Astronomy, University of California, Riverside, Riverside, CA 92521, USA
| | - Pratyasha Mishra
- Department of Biochemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Michael E. Colvin
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA 95340, USA
| | - Ajay Gopinathan
- Department of Physics, University of California, Merced, Merced, CA 95340, USA
| | - Umar Mohideen
- Department of Physics and Astronomy, University of California, Riverside, Riverside, CA 92521, USA
- Biophysics Program, University of California, Riverside, Riverside, CA 92521, USA
| | - Roya Zandi
- Department of Physics and Astronomy, University of California, Riverside, Riverside, CA 92521, USA
- Biophysics Program, University of California, Riverside, Riverside, CA 92521, USA
| | - Thomas E. Kuhlman
- Department of Physics and Astronomy, University of California, Riverside, Riverside, CA 92521, USA
- Biophysics Program, University of California, Riverside, Riverside, CA 92521, USA
- Microbiology Program, University of California, Riverside, Riverside, CA 92521, USA
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8
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Kumar V, Shepard Bryan J, Rojewski A, Manzo C, Pressé S. Learning Continuous 2D Diffusion Maps from Particle Trajectories without Data Binning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582378. [PMID: 38464131 PMCID: PMC10925201 DOI: 10.1101/2024.02.27.582378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Diffusion coefficients often vary across regions, such as cellular membranes, and quantifying their variation can provide valuable insight into local membrane properties such as composition and stiffness. Toward quantifying diffusion coefficient spatial maps and uncertainties from particle tracks, we use a Bayesian method and place Gaussian Process (GP) Priors on the maps. For the sake of computational efficiency, we leverage inducing point methods on GPs arising from the mathematical structure of the data giving rise to non-conjugate likelihood-prior pairs. We analyze both synthetic data, where ground truth is known, as well as data drawn from live-cell single-molecule imaging of membrane proteins. The resulting tool provides an unsupervised method to rigorously map diffusion coefficients continuously across membranes without data binning.
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Affiliation(s)
- Vishesh Kumar
- Center for Biological Physics, Arizona State University, USA
- Department of Physics, Arizona State University, USA
| | - J. Shepard Bryan
- Center for Biological Physics, Arizona State University, USA
- Department of Physics, Arizona State University, USA
| | - Alex Rojewski
- Center for Biological Physics, Arizona State University, USA
- Department of Physics, Arizona State University, USA
| | - Carlo Manzo
- Facultat de Ciéncies, Tecnologia i Enginyeries, Universitat de Vic – Universitat Central de Catalunya (UVic-UCC), C. de la Laura,13, 08500 Vic, Barcelona, Spain
- Institut de Recerca i Innovació en Ciències de la Vida i de la Salut a la Catalunya Central (IRIS-CC), 08500 Vic, Barcelona, Spain
| | - Steve Pressé
- Center for Biological Physics, Arizona State University, USA
- Department of Physics, Arizona State University, USA
- School of Molecular Sciences, Arizona State University
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9
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Ferreira P, Soares R, López-Fernández H, Vazquez N, Reboiro-Jato M, Vieira CP, Vieira J. Multiple Lines of Evidence Support 199 SARS-CoV-2 Positively Selected Amino Acid Sites. Int J Mol Sci 2024; 25:2428. [PMID: 38397104 PMCID: PMC10889775 DOI: 10.3390/ijms25042428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/03/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
SARS-CoV-2 amino acid variants that contribute to an increased transmissibility or to host immune system escape are likely to increase in frequency due to positive selection and may be identified using different methods, such as codeML, FEL, FUBAR, and MEME. Nevertheless, when using different methods, the results do not always agree. The sampling scheme used in different studies may partially explain the differences that are found, but there is also the possibility that some of the identified positively selected amino acid sites are false positives. This is especially important in the context of very large-scale projects where hundreds of analyses have been performed for the same protein-coding gene. To account for these issues, in this work, we have identified positively selected amino acid sites in SARS-CoV-2 and 15 other coronavirus species, using both codeML and FUBAR, and compared the location of such sites in the different species. Moreover, we also compared our results to those that are available in the COV2Var database and the frequency of the 10 most frequent variants and predicted protein location to identify those sites that are supported by multiple lines of evidence. Amino acid changes observed at these sites should always be of concern. The information reported for SARS-CoV-2 can also be used to identify variants of concern in other coronaviruses.
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Affiliation(s)
- Pedro Ferreira
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (P.F.); (R.S.); (C.P.V.)
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), Porto University, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Ricardo Soares
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (P.F.); (R.S.); (C.P.V.)
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), Porto University, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
- Faculdade de Ciências da Universidade do Porto (FCUP), Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Hugo López-Fernández
- CINBIO, Department of Computer Science, ESEI—Escuela Superior de Ingeniería Informática, Universidade de Vigo, 32004 Ourense, Spain; (H.L.-F.); (M.R.-J.)
- CINBIO, SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36213 Vigo, Spain
| | - Noé Vazquez
- CINBIO, Department of Computer Science, ESEI—Escuela Superior de Ingeniería Informática, Universidade de Vigo, 32004 Ourense, Spain; (H.L.-F.); (M.R.-J.)
- CINBIO, SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36213 Vigo, Spain
| | - Miguel Reboiro-Jato
- CINBIO, Department of Computer Science, ESEI—Escuela Superior de Ingeniería Informática, Universidade de Vigo, 32004 Ourense, Spain; (H.L.-F.); (M.R.-J.)
- CINBIO, SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36213 Vigo, Spain
| | - Cristina P. Vieira
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (P.F.); (R.S.); (C.P.V.)
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Jorge Vieira
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (P.F.); (R.S.); (C.P.V.)
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen 208, 4200-135 Porto, Portugal
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10
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Wulf J, Lewit N, Akter S, K Bwambok D, Anum D, Alonge T, Kuedukey C, Bolton B, Dassow B, Halim MA, O Fakayode S. Evaluating binding and interaction of selected pesticides with serum albumin proteins by Raman, 1H NMR, mass spectrometry and molecular dynamics simulation. J Biomol Struct Dyn 2024:1-14. [PMID: 38197596 DOI: 10.1080/07391102.2024.2302344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 11/23/2023] [Indexed: 01/11/2024]
Abstract
Addressing the acute pesticide poisoning and toxicity to humans, is a global challenge of top priority. Serum albumin is the most abundant plasma protein, capable of binding with herbicide and pesticide residues. This study reports multifaceted approaches for in-depth and robust investigation of the molecular interactions of selected pesticides, including propanil (PPL), bromoxynil (BXL), metolachlor (MLR) and glyphosate (GPE) with bovine serum albumin (BSA) proteins using experimental (Raman and FTIR spectroscopy, native mass spectrometry and high field 1H NMR), molecular dynamics (MD) simulation and principal component analysis (PCA). The binding of pesticides with BSA resulted in BSA amide I and amide II Raman spectral shifts. PCA of Raman spectra of serum-pesticide complexes showed the grouping of pesticides on the score plot based on the similarities and differences in pesticides' chemical structures. Native mass spectrometry results revealed strong adduct formation of the pesticides with the protein. The observed changes in chemical shifts, peak broadening or peak disappearance of characteristic proton signals of the pesticides, indicated altered chemical environments due to binding BSA-pesticides interactions. The results of MD simulation conducted for over 500 ns revealed strong pesticides interaction with LEU197, LEU218, LEU237, TRP213, SER286 and ILE289 residues to the site I of BSA. Free energy landscapes provided insights into the conformational changes in BSA on the binding of pesticides. Overall, the experimental and computational results are in consonant and indicate the binding of pesticides into the site I and site II (sub-domain IIA) of the BSA via hydrogen bonding, non-covalent and hydrophobic interactions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Josefa Wulf
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Noam Lewit
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Shaila Akter
- Division of Quantum Chemistry, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - David K Bwambok
- Department of Chemistry, Ball State University, Muncie, IN, USA
| | - Davis Anum
- Department of Chemistry, Ball State University, Muncie, IN, USA
| | - Temitope Alonge
- Department of Chemistry, Ball State University, Muncie, IN, USA
| | | | - Brinkley Bolton
- Department of Chemistry, Physics & Astronomy, Georgia College & State University, Milledgeville, GA, USA
| | - Bailey Dassow
- Department of Chemistry, Physics & Astronomy, Georgia College & State University, Milledgeville, GA, USA
| | - Mohammad A Halim
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Sayo O Fakayode
- Department of Chemistry, Physics & Astronomy, Georgia College & State University, Milledgeville, GA, USA
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11
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Gissot L, Fontaine F, Kelemen Z, Dao O, Bouchez I, Deruyffelaere C, Winkler M, Costa AD, Pierre F, Meziadi C, Faure JD, Froissard M. E and M SARS-CoV-2 membrane protein expression and enrichment with plant lipid droplets. Biotechnol J 2024; 19:e2300512. [PMID: 37986207 DOI: 10.1002/biot.202300512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 11/22/2023]
Abstract
Plants are gaining traction as a cost-effective and scalable platform for producing recombinant proteins. However, expressing integral membrane proteins in plants is challenging due to their hydrophobic nature. In our study, we used transient and stable expression systems in Nicotiana benthamiana and Camelina sativa respectively to express SARS-CoV-2 E and M integral proteins, and target them to lipid droplets (LDs). LDs offer an ideal environment for folding hydrophobic proteins and aid in their purification through flotation. We tested various protein fusions with different linkers and tags and used three dimensional structure predictions to assess their effects. E and M mostly localized in the ER in N. benthamiana leaves but E could be targeted to LDs in oil accumulating tobacco when fused with oleosin, a LD integral protein. In Camelina sativa seeds, E and M were however found associated with purified LDs. By enhancing the accumulation of E and M within LDs through oleosin, we enriched these proteins in the purified floating fraction. This strategy provides an alternative approach for efficiently producing and purifying hydrophobic pharmaceuticals and vaccines using plant systems.
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Affiliation(s)
- Lionel Gissot
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Florent Fontaine
- SAS Core Biogenesis, 850 Bd Sébastien Brant BioParc 3, 67400, Illkirch-Graffenstaden, France
| | - Zsolt Kelemen
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Ousmane Dao
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Isabelle Bouchez
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Carine Deruyffelaere
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Michèle Winkler
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Anais Da Costa
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Fabienne Pierre
- SAS Core Biogenesis, 850 Bd Sébastien Brant BioParc 3, 67400, Illkirch-Graffenstaden, France
| | - Chouaib Meziadi
- SAS Core Biogenesis, 850 Bd Sébastien Brant BioParc 3, 67400, Illkirch-Graffenstaden, France
| | - Jean-Denis Faure
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Marine Froissard
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
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12
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Biswas S, Hossen MR, Akter S, Ali MA, Halim MA, Ullah MO. Structural dynamics and functional analysis of Saprolegnia parasitica chitin synthases 5 in a phospholipid bilayer. J Biomol Struct Dyn 2024; 42:461-474. [PMID: 36995127 DOI: 10.1080/07391102.2023.2193993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 03/15/2023] [Indexed: 03/31/2023]
Abstract
Saprolegnia parasitica is an oomycete responsible for a fish disease called saprolegniosis, which poses an economic and environmental burden on aquaculture production. In Saprolegnia, CHS5 of S. parasitica (SpCHS5) contains an N-terminal domain, a catalytic domain of the glycosyltransferase -2 family containing a GT-A fold, and a C-terminal transmembrane domain. No three-dimensional structure of SpCHS5 is reported yet disclosing the structural details of this protein. We have developed a structural model of full-length SpCHS5 and validated it by molecular dynamics simulation technique. From the 1 microsecond simulations, we retrieved the stable RoseTTAFold model SpCHS5 protein to explain characteristics and structural features. Furthermore, from the analysis of the movement of chitin in the protein cavity, we assumed that ARG 482, GLN 527, PHE 529, PHE 530, LEU 540, SER 541, TYR 544, ASN 634, THR 641, TYR 645, THR 641, ASN 772 residues as a main cavity lining site. In SMD analysis, we investigated the opening of the transmembrane cavity required for chitin translocation. The pulling of chitin from the internal cavity to the extracellular region was observed through steered molecular dynamics simulations. A comparison of the initial and final structures of chitin complex showed that there's a transmembrane cavity opening in the simulations. Overall, this present work will help us understand the structural and functional basis of CHS5 and design inhibitors against SpCHS5.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sourav Biswas
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
- Department of Chemistry, Clemson University, Clemson, SC, USA
| | - Md Rubel Hossen
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Shaila Akter
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Ackas Ali
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Mohammad A Halim
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - M Obayed Ullah
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
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13
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Yuan C, Ma Z, Xie J, Li W, Su L, Zhang G, Xu J, Wu Y, Zhang M, Liu W. The role of cell death in SARS-CoV-2 infection. Signal Transduct Target Ther 2023; 8:357. [PMID: 37726282 PMCID: PMC10509267 DOI: 10.1038/s41392-023-01580-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 06/09/2023] [Accepted: 07/31/2023] [Indexed: 09/21/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), showing high infectiousness, resulted in an ongoing pandemic termed coronavirus disease 2019 (COVID-19). COVID-19 cases often experience acute respiratory distress syndrome, which has caused millions of deaths. Apart from triggering inflammatory and immune responses, many viral infections can cause programmed cell death in infected cells. Cell death mechanisms have a vital role in maintaining a suitable environment to achieve normal cell functionality. Nonetheless, these processes are dysregulated, potentially contributing to disease pathogenesis. Over the past decades, multiple cell death pathways are becoming better understood. Growing evidence suggests that the induction of cell death by the coronavirus may significantly contributes to viral infection and pathogenicity. However, the interaction of SARS-CoV-2 with cell death, together with its associated mechanisms, is yet to be elucidated. In this review, we summarize the existing evidence concerning the molecular modulation of cell death in SARS-CoV-2 infection as well as viral-host interactions, which may shed new light on antiviral therapy against SARS-CoV-2.
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Affiliation(s)
- Cui Yuan
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Zhenling Ma
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Jiufeng Xie
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wenqing Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Lijuan Su
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Guozhi Zhang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Jun Xu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yaru Wu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Min Zhang
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Wei Liu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China.
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14
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Muhammad Rehman H, Rehman HM, Naveed M, Khan MT, Shabbir MA, Aslam S, Bashir H. In Silico Investigation of a Chimeric IL24-LK6 Fusion Protein as a Potent Candidate Against Breast Cancer. Bioinform Biol Insights 2023; 17:11779322231182560. [PMID: 37377793 PMCID: PMC10291407 DOI: 10.1177/11779322231182560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Targeted delivery of therapeutic anticancer chimeric molecules enhances the efficacy of drug by improving cellular uptake and circulation time. Engineering the molecules to facilitate the specific interaction between chimeric protein and its receptor is critical to elucidate biological mechanism as well as accuracy in modeling of complexes. A theoretically designed novel protein-protein interfaces can serve as a bottom-up method for comprehensive understanding of interacting protein residues. This study was aimed for in silico analyses of a chimeric fusion protein against breast cancer. The amino acid sequences of the interleukin 24 (IL-24) and LK-6 peptide were used to design the chimeric fusion protein via a rigid linker. The secondary and tertiary structures along with physicochemical properties by ProtParam and solubility were predicted using online software. The validation and quality of the fusion protein was confirmed by Rampage and ERRAT2. The newly designed fusion construct has a total length of 179 amino acids. The top-ranked structure from alpha fold2 showed 18.1 KD molecular weight by ProtParam, quality factor of 94.152 by ERRAT, and a valid structure by a Ramachandran plot with 88.5% residues in the favored region. Finally, the docking and simulation studies were performed using HADDOCK and Desmond module of Schrodinger. The quality, validity, interaction analysis, and stability of the fusion protein depict a functional molecule. The fusion gene IL24-LK6 after cloning and expression in a suitable prokaryotic cell might be a useful candidate for developing a novel anticancer therapy.
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Affiliation(s)
- Hafiz Muhammad Rehman
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
- University Institute of Medical Lab Technology, Faculty of Allied Health Sciences, The University of Lahore, Pakistan
| | - Hafiz Muzzammel Rehman
- School of Biochemistry & Biotechnology, University of the Punjab, Lahore, Pakistan
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore, Pakistan
| | - Muhammad Naveed
- Department of Biotechnology, Faculty of Science & Technology, University of Central Punjab, Lahore, Pakistan
| | - Muhammad Tahir Khan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Aqib Shabbir
- Department of Biotechnology, Faculty of Science & Technology, University of Central Punjab, Lahore, Pakistan
| | - Shakira Aslam
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
| | - Hamid Bashir
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
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15
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Yang T, Wang SC, Ye L, Maimaitiyiming Y, Naranmandura H. Targeting viral proteins for restraining SARS-CoV-2: focusing lens on viral proteins beyond spike for discovering new drug targets. Expert Opin Drug Discov 2023; 18:247-268. [PMID: 36723288 DOI: 10.1080/17460441.2023.2175812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Emergence of highly infectious SARS-CoV-2 variants are reducing protection provided by current vaccines, requiring constant updates in antiviral approaches. The virus encodes four structural and sixteen nonstructural proteins which play important roles in viral genome replication and transcription, virion assembly, release , entry into cells, and compromising host cellular defenses. As alien proteins to host cells, many viral proteins represent potential targets for combating the SARS-CoV-2. AREAS COVERED Based on literature from PubMed and Web of Science databases, the authors summarize the typical characteristics of SARS-CoV-2 from the whole viral particle to the individual viral proteins and their corresponding functions in virus life cycle. The authors also discuss the potential and emerging targeted interventions to curb virus replication and spread in detail to provide unique insights into SARS-CoV-2 infection and countermeasures against it. EXPERT OPINION Our comprehensive analysis highlights the rationale to focus on non-spike viral proteins that are less mutated but have important functions. Examples of this include: structural proteins (e.g. nucleocapsid protein, envelope protein) and extensively-concerned nonstructural proteins (e.g. NSP3, NSP5, NSP12) along with the ones with relatively less attention (e.g. NSP1, NSP10, NSP14 and NSP16), for developing novel drugs to overcome resistance of SARS-CoV-2 variants to preexisting vaccines and antibody-based treatments.
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Affiliation(s)
- Tao Yang
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Si Chun Wang
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Linyan Ye
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yasen Maimaitiyiming
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Zhejiang Province Key Laboratory of Haematology Oncology Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Department of Neurobiology, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Brain Science and Brain Medicine, and MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Hua Naranmandura
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Zhejiang Province Key Laboratory of Haematology Oncology Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
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16
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Abbasian MH, Mahmanzar M, Rahimian K, Mahdavi B, Tokhanbigli S, Moradi B, Sisakht MM, Deng Y. Global landscape of SARS-CoV-2 mutations and conserved regions. J Transl Med 2023; 21:152. [PMID: 36841805 PMCID: PMC9958328 DOI: 10.1186/s12967-023-03996-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/15/2023] [Indexed: 02/27/2023] Open
Abstract
BACKGROUND At the end of December 2019, a novel strain of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) disease (COVID-19) has been identified in Wuhan, a central city in China, and then spread to every corner of the globe. As of October 8, 2022, the total number of COVID-19 cases had reached over 621 million worldwide, with more than 6.56 million confirmed deaths. Since SARS-CoV-2 genome sequences change due to mutation and recombination, it is pivotal to surveil emerging variants and monitor changes for improving pandemic management. METHODS 10,287,271 SARS-CoV-2 genome sequence samples were downloaded in FASTA format from the GISAID databases from February 24, 2020, to April 2022. Python programming language (version 3.8.0) software was utilized to process FASTA files to identify variants and sequence conservation. The NCBI RefSeq SARS-CoV-2 genome (accession no. NC_045512.2) was considered as the reference sequence. RESULTS Six mutations had more than 50% frequency in global SARS-CoV-2. These mutations include the P323L (99.3%) in NSP12, D614G (97.6) in S, the T492I (70.4) in NSP4, R203M (62.8%) in N, T60A (61.4%) in Orf9b, and P1228L (50.0%) in NSP3. In the SARS-CoV-2 genome, no mutation was observed in more than 90% of nsp11, nsp7, nsp10, nsp9, nsp8, and nsp16 regions. On the other hand, N, nsp3, S, nsp4, nsp12, and M had the maximum rate of mutations. In the S protein, the highest mutation frequency was observed in aa 508-635(0.77%) and aa 381-508 (0.43%). The highest frequency of mutation was observed in aa 66-88 (2.19%), aa 7-14, and aa 164-246 (2.92%) in M, E, and N proteins, respectively. CONCLUSION Therefore, monitoring SARS-CoV-2 proteomic changes and detecting hot spots mutations and conserved regions could be applied to improve the SARS-CoV-2 diagnostic efficiency and design safe and effective vaccines against emerging variants.
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Affiliation(s)
- Mohammad Hadi Abbasian
- Department of Medical Genetics, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
| | - Mohammadamin Mahmanzar
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, 96813, USA
| | - Karim Rahimian
- Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Bahar Mahdavi
- Department of Computer Science, Tarbiat Modares University, Tehran, Iran
| | - Samaneh Tokhanbigli
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, Australia
| | - Bahman Moradi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mahsa Mollapour Sisakht
- Department of Biochemistry, Erasmus University Medical Center, 2040, 3000 CA, Rotterdam, The Netherlands
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, 96813, USA.
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17
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Chaturvedi A, Borkar K, Priyakumar UD, Vinod P. PREHOST: Host prediction of coronaviridae family using machine learning. Heliyon 2023; 9:e13646. [PMID: 36816252 PMCID: PMC9922161 DOI: 10.1016/j.heliyon.2023.e13646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 02/05/2023] [Accepted: 02/06/2023] [Indexed: 02/13/2023] Open
Abstract
Coronavirus, a zoonotic virus capable of transmitting infections from animals to humans, emerged as a pandemic recently. In such circumstances, it is essential to understand the virus's origin. In this study, we present a novel machine-learning pipeline PreHost for host prediction of the family, Coronaviridae. We leverage the complete viral genome and sequences at the protein level (spike protein, membrane protein, and nucleocapsid protein). Compared with the current state-of-the-art approaches, the random forest model attained high accuracy and recall scores of 99.91% and 0.98, respectively, for genome sequences. In addition to the spike protein sequences, our study shows membrane and nucleocapsid protein sequences can be utilized to predict the host of viruses. We also identified important sites in the viral sequences that help distinguish between different host classes. The host prediction pipeline PreHost will cater as a valuable tool to take effective measures to govern the transmission of future viruses.
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18
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Tang M, Zhang X, Huang Y, Cheng W, Qu J, Gui S, Li L, Li S. Peptide-based inhibitors hold great promise as the broad-spectrum agents against coronavirus. Front Microbiol 2023; 13:1093646. [PMID: 36741878 PMCID: PMC9893414 DOI: 10.3389/fmicb.2022.1093646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/08/2022] [Indexed: 01/20/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), Middle East Respiratory Syndrome (MERS), and the recent SARS-CoV-2 are lethal coronaviruses (CoVs) that have caused dreadful epidemic or pandemic in a large region or globally. Infections of human respiratory systems and other important organs by these pathogenic viruses often results in high rates of morbidity and mortality. Efficient anti-viral drugs are needed. Herein, we firstly take SARS-CoV-2 as an example to present the molecular mechanism of CoV infection cycle, including the receptor binding, viral entry, intracellular replication, virion assembly, and release. Then according to their mode of action, we provide a summary of anti-viral peptides that have been reported in peer-reviewed publications. Even though CoVs can rapidly evolve to gain resistance to the conventional small molecule drugs, peptide-based inhibitors targeting various steps of CoV lifecycle remain a promising approach. Peptides can be continuously modified to improve their antiviral efficacy and spectrum along with the emergence of new viral variants.
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Affiliation(s)
- Mingxing Tang
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China,Department of Otolaryngology, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China,School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Xin Zhang
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Yanhong Huang
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China,School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Wenxiang Cheng
- Center for Translational Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jing Qu
- Department of Pathogen Biology, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Shuiqing Gui
- Department of Critical Care Medicine, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China,*Correspondence: Shuiqing Gui, ✉
| | - Liang Li
- School of Medicine, Southern University of Science and Technology, Shenzhen, China,Liang Li, ✉
| | - Shuo Li
- Department of Otolaryngology, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China,Shuo Li, ✉
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19
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Jahirul Islam M, Nawal Islam N, Siddik Alom M, Kabir M, Halim MA. A review on structural, non-structural, and accessory proteins of SARS-CoV-2: Highlighting drug target sites. Immunobiology 2023; 228:152302. [PMID: 36434912 PMCID: PMC9663145 DOI: 10.1016/j.imbio.2022.152302] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 10/30/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, is a highly transmittable and pathogenic human coronavirus that first emerged in China in December 2019. The unprecedented outbreak of SARS-CoV-2 devastated human health within a short time leading to a global public health emergency. A detailed understanding of the viral proteins including their structural characteristics and virulence mechanism on human health is very crucial for developing vaccines and therapeutics. To date, over 1800 structures of non-structural, structural, and accessory proteins of SARS-CoV-2 are determined by cryo-electron microscopy, X-ray crystallography, and NMR spectroscopy. Designing therapeutics to target the viral proteins has several benefits since they could be highly specific against the virus while maintaining minimal detrimental effects on humans. However, for ongoing and future research on SARS-CoV-2, summarizing all the viral proteins and their detailed structural information is crucial. In this review, we compile comprehensive information on viral structural, non-structural, and accessory proteins structures with their binding and catalytic sites, different domain and motifs, and potential drug target sites to assist chemists, biologists, and clinicians finding necessary details for fundamental and therapeutic research.
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Affiliation(s)
- Md. Jahirul Islam
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka 1215, Bangladesh
| | - Nafisa Nawal Islam
- Department of Biotechnology and Genetic Engineering, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Md. Siddik Alom
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Mahmuda Kabir
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Mohammad A. Halim
- Department of Chemistry and Biochemistry, Kennesaw State University, 370 Paulding Avenue NW, Kennesaw, GA 30144, USA,Corresponding author
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20
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Pacheco-Olvera DL, Saint Remy-Hernández S, García-Valeriano MG, Rivera-Hernández T, López-Macías C. Bioinformatic Analysis of B- and T-cell Epitopes from SARS-CoV-2 Structural Proteins and their Potential Cross-reactivity with Emerging Variants and other Human Coronaviruses. Arch Med Res 2022; 53:694-710. [PMID: 36336501 PMCID: PMC9633039 DOI: 10.1016/j.arcmed.2022.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 08/23/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
Background The mutations in SARS-CoV-2 variants of concern (VOC) facilitate the virus’ escape from the neutralizing antibodies induced by vaccines. However, the protection from hospitalization and death is not significantly diminished. Both vaccine boosters and infection improve immune responses and provide protection, suggesting that conserved and/or cross-reactive epitopes could be involved. While several important T- and B-cell epitopes have been identified, mainly in the S protein, the M and N proteins and their potential cross-reactive epitopes with other coronaviruses remain largely unexplored. Aims To identify and map new potential B- and T-cell epitopes within the SARS-CoV-2 S, M and N proteins, as well as cross-reactive epitopes with human coronaviruses. Methods Different bioinformatics tools were used to: i) Identify new and compile previously-reported B-and T-cell epitopes from SARS-CoV-2 S, M and N proteins; ii) Determine the mutations in S protein from VOC that affect B- and T-cell epitopes, and; iii) Identify cross-reactive epitopes with coronaviruses relevant to human health. Results New, potential B- and T-cell epitopes from S, M and N proteins as well as cross-reactive epitopes with other coronaviruses were found and mapped within the proteins’ structures. Conclusion Numerous potential B- and T-cell epitopes were found in S, M and N proteins, some of which are conserved between coronaviruses. VOCs present mutations within important epitopes in the S protein; however, a significant number of other epitopes remain unchanged. The epitopes identified here may contribute to augmenting the protective response to SARS-CoV-2 and its variants induced by infection and/or vaccination, and may also be used for the rational design of novel broad-spectrum coronavirus vaccines.
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Affiliation(s)
- Diana Laura Pacheco-Olvera
- Unidad de Investigación Médica en Inmunoquímica, Hospital de Especialidades del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Stephanie Saint Remy-Hernández
- Unidad de Investigación Médica en Inmunoquímica, Hospital de Especialidades del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - María Guadalupe García-Valeriano
- Unidad de Investigación Médica en Inmunoquímica, Hospital de Especialidades del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Tania Rivera-Hernández
- Unidad de Investigación Médica en Inmunoquímica, Hospital de Especialidades del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México,Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México,Address reprint requests to: Constantino López-Macías or Tania Rivera-Hern..ndez, UMAE, Hospital de Especialidades del Centro Médico Nacional Siglo XXI, IMSS, Av. Cuahutémoc 330, 06720, Ciudad de México, México; Phone: (+52) (55) 5627 6900 ext. 21476
| | - Constantino López-Macías
- Unidad de Investigación Médica en Inmunoquímica, Hospital de Especialidades del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México,Address reprint requests to: Constantino López-Macías or Tania Rivera-Hern..ndez, UMAE, Hospital de Especialidades del Centro Médico Nacional Siglo XXI, IMSS, Av. Cuahutémoc 330, 06720, Ciudad de México, México; Phone: (+52) (55) 5627 6900 ext. 21476
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21
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Sedegah M, Porter C, Goguet E, Ganeshan H, Belmonte M, Huang J, Belmonte A, Inoue S, Acheampong N, Malloy AMW, Hollis-Perry M, Jackson-Thompson B, Ramsey KF, Alcorta Y, Maiolatesi SE, Wang G, Reyes AE, Illinik L, Sanchez-Edwards M, Burgess TH, Broder CC, Laing ED, Pollett SD, Villasante E, Mitre E, Hollingdale MR. Cellular interferon-gamma and interleukin-2 responses to SARS-CoV-2 structural proteins are broader and higher in those vaccinated after SARS-CoV-2 infection compared to vaccinees without prior SARS-CoV-2 infection. PLoS One 2022; 17:e0276241. [PMID: 36251675 PMCID: PMC9576055 DOI: 10.1371/journal.pone.0276241] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/03/2022] [Indexed: 11/29/2022] Open
Abstract
Class I- and Class II-restricted epitopes have been identified across the SARS-CoV-2 structural proteome. Vaccine-induced and post-infection SARS-CoV-2 T-cell responses are associated with COVID-19 recovery and protection, but the precise role of T-cell responses remains unclear, and how post-infection vaccination ('hybrid immunity') further augments this immunity To accomplish these goals, we studied healthy adult healthcare workers who were (a) uninfected and unvaccinated (n = 12), (b) uninfected and vaccinated with Pfizer-BioNTech BNT162b2 vaccine (2 doses n = 177, one dose n = 1) or Moderna mRNA-1273 vaccine (one dose, n = 1), and (c) previously infected with SARS-CoV-2 and vaccinated (BNT162b2, two doses, n = 6, one dose n = 1; mRNA-1273 two doses, n = 1). Infection status was determined by repeated PCR testing of participants. We used FluoroSpot Interferon-gamma (IFN-γ) and Interleukin-2 (IL-2) assays, using subpools of 15-mer peptides covering the S (10 subpools), N (4 subpools) and M (2 subpools) proteins. Responses were expressed as frequencies (percent positive responders) and magnitudes (spot forming cells/106 cytokine-producing peripheral blood mononuclear cells [PBMCs]). Almost all vaccinated participants with no prior infection exhibited IFN-γ, IL-2 and IFN-γ+IL2 responses to S glycoprotein subpools (89%, 93% and 27%, respectively) mainly directed to the S2 subunit and were more robust than responses to the N or M subpools. However, in previously infected and vaccinated participants IFN-γ, IL-2 and IFN-γ+IL2 responses to S subpools (100%, 100%, 88%) were substantially higher than vaccinated participants with no prior infection and were broader and directed against nine of the 10 S glycoprotein subpools spanning the S1 and S2 subunits, and all the N and M subpools. 50% of uninfected and unvaccinated individuals had IFN-γ but not IL2 or IFN-γ+IL2 responses against one S and one M subpools that were not increased after vaccination of uninfected or SARS-CoV-2-infected participants. Summed IFN-γ, IL-2, and IFN-γ+IL2 responses to S correlated with IgG responses to the S glycoprotein. These studies demonstrated that vaccinations with BNT162b2 or mRNA-1273 results in T cell-specific responses primarily against epitopes in the S2 subunit of the S glycoprotein, and that individuals that are vaccinated after SARS-CoV-2 infection develop broader and greater T cell responses to S1 and S2 subunits as well as the N and M proteins.
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Affiliation(s)
- Martha Sedegah
- Agile Vaccines and Therapeutics, Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Chad Porter
- Translational Clinical Research Department, Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Emilie Goguet
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
| | - Harini Ganeshan
- Agile Vaccines and Therapeutics, Naval Medical Research Center, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
| | - Maria Belmonte
- Agile Vaccines and Therapeutics, Naval Medical Research Center, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
| | - Jun Huang
- Agile Vaccines and Therapeutics, Naval Medical Research Center, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
| | - Arnel Belmonte
- Agile Vaccines and Therapeutics, Naval Medical Research Center, Silver Spring, MD, United States of America
- General Dynamics Information Technology, Falls Church, VA, United States of America
| | - Sandra Inoue
- Agile Vaccines and Therapeutics, Naval Medical Research Center, Silver Spring, MD, United States of America
- General Dynamics Information Technology, Falls Church, VA, United States of America
| | - Neda Acheampong
- Agile Vaccines and Therapeutics, Naval Medical Research Center, Silver Spring, MD, United States of America
- General Dynamics Information Technology, Falls Church, VA, United States of America
| | - Allison M. W. Malloy
- Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States of America
| | - Monique Hollis-Perry
- Clinical Trials Center, Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Belinda Jackson-Thompson
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
| | - Kathy F. Ramsey
- General Dynamics Information Technology, Falls Church, VA, United States of America
- Clinical Trials Center, Naval Medical Research Center, Silver Spring, MD, United States of America
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States of America
| | - Yolanda Alcorta
- General Dynamics Information Technology, Falls Church, VA, United States of America
- Clinical Trials Center, Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Santina E. Maiolatesi
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
- Clinical Trials Center, Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Gregory Wang
- General Dynamics Information Technology, Falls Church, VA, United States of America
- Clinical Trials Center, Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Anatolio E. Reyes
- General Dynamics Information Technology, Falls Church, VA, United States of America
- Clinical Trials Center, Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Luca Illinik
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States of America
| | - Margaret Sanchez-Edwards
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States of America
| | - Timothy H. Burgess
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States of America
| | - Christopher C. Broder
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States of America
| | - Eric D. Laing
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States of America
| | - Simon D. Pollett
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States of America
| | - Eileen Villasante
- Agile Vaccines and Therapeutics, Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Edward Mitre
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States of America
| | - Michael R. Hollingdale
- Agile Vaccines and Therapeutics, Naval Medical Research Center, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
- * E-mail: ,
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22
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Patel RS, Agrawal B. Heterologous immunity induced by 1 st generation COVID-19 vaccines and its role in developing a pan-coronavirus vaccine. Front Immunol 2022; 13:952229. [PMID: 36045689 PMCID: PMC9420909 DOI: 10.3389/fimmu.2022.952229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/19/2022] [Indexed: 12/23/2022] Open
Abstract
Severe acute respiratory syndrome virus-2 (SARS-CoV-2), the causative infectious agent of the COVID-19 pandemic, has led to multiple (4-6) waves of infections worldwide during the past two years. The development of vaccines against SARS-CoV-2 has led to successful mass immunizations worldwide, mitigating the worldwide mortality due the pandemic to a great extent. Yet the evolution of new variants highlights a need to develop a universal vaccine which can prevent infections from all virulent SARS-CoV-2. Most of the current first generation COVID-19 vaccines are based on the Spike protein from the original Wuhan-hu-1 virus strain. It is encouraging that they still protect from serious illnesses, hospitalizations and mortality against a number of mutated viral strains, to varying degrees. Understanding the mechanisms by which these vaccines provide heterologous protection against multiple highly mutated variants can reveal strategies to develop a universal vaccine. In addition, many unexposed individuals have been found to harbor T cells that are cross-reactive against SARS-CoV-2 antigens, with a possible protective role. In this review, we will discuss various aspects of natural or vaccine-induced heterologous (cross-reactive) adaptive immunity against SARS-CoV-2 and other coronaviruses, and their role in achieving the concept of a pan-coronavirus vaccine.
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Affiliation(s)
| | - Babita Agrawal
- Department of Surgery, Faculty of Medicine and Dentistry, College of Health Sciences, University of Alberta, Edmonton, AB, Canada
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23
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Zhang Y, Wang K, Huang Q, Shu S. Molecular cloning and characterization of an alpha-amylase inhibitor (TkAAI) gene from Trichosanthes kirilowii Maxim. Biotechnol Lett 2022; 44:1127-1138. [PMID: 35925526 DOI: 10.1007/s10529-022-03277-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 06/21/2022] [Indexed: 12/01/2022]
Abstract
Trichosanthes kirilowii Maxim taxonomically belongs to the Cucurbitaceae family and Trichosanthes genus. Its whole fruit, fruit peel, seed and root are widely used in traditional Chinese medicines. A ribosome-inactivating protein with RNA N-glycosidase activity called Trichosanthrip was isolated and purified from the seeds of T. kirilowii in our recent previous research. To further explore the biological functions of Trichosanthrip, the cDNA of T. kirilowii alpha-amylase inhibitor (TkAAI) was cloned through rapid-amplification of cDNA ends and its sequence was analyzed. Also, the heterologous protein was expressed in Escherichia coli and its alpha-amylase activity was further measured under optimized conditions. The full-length cDNA of TkAAI was 613 bp. The speculated open reading frame sequence encoded 141 amino acids with a molecular weight of 16.14 kDa. Phylogenetic analysis demonstrated that the Alpha-Amylase Inhibitors Seed Storage domain sequence of TkAAI revealed significant evolutionary homology with the 2S albumin derived from the other plants in the Cucurbitaceae group. In addition, TkAAI was assembled into pET28a with eGFP to generate a prokaryotic expression vector and was induced to express in E. coli. The TkAAI-eGFP infusion protein was proven to exhibit alpha-amylase inhibitory activity against porcine pancreatic amylase in a suitable reaction system. Analysis of gene expression patterns proved that the relative expression level of TkAAI in seeds is highest. The results presented here forecasted that the TkAAI might play a crucial role during the development of T. kirilowii seeds and provided fundamental insights into the possibility of T. kirilowii derived medicine to treat diabetes related diseases.
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Affiliation(s)
- Yipeng Zhang
- College of Plant Science and Technology, HUAZHONG Agricultural University, Shizishan Street 1#, Hongshan District, Wuhan, Hubei, People's Republic of China.
| | - Keyue Wang
- College of Plant Science and Technology, HUAZHONG Agricultural University, Shizishan Street 1#, Hongshan District, Wuhan, Hubei, People's Republic of China
| | - Qiyuan Huang
- College of Plant Science and Technology, HUAZHONG Agricultural University, Shizishan Street 1#, Hongshan District, Wuhan, Hubei, People's Republic of China
| | - Shaohua Shu
- College of Plant Science and Technology, HUAZHONG Agricultural University, Shizishan Street 1#, Hongshan District, Wuhan, Hubei, People's Republic of China
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24
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Troyano-Hernáez P, Reinosa R, Holguín Á. Evolution of SARS-CoV-2 in Spain during the First Two Years of the Pandemic: Circulating Variants, Amino Acid Conservation, and Genetic Variability in Structural, Non-Structural, and Accessory Proteins. Int J Mol Sci 2022; 23:ijms23126394. [PMID: 35742840 PMCID: PMC9223475 DOI: 10.3390/ijms23126394] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 02/04/2023] Open
Abstract
Monitoring SARS-CoV-2’s genetic diversity and emerging mutations in this ongoing pandemic is crucial to understanding its evolution and ensuring the performance of COVID-19 diagnostic tests, vaccines, and therapies. Spain has been one of the main epicenters of COVID-19, reaching the highest number of cases and deaths per 100,000 population in Europe at the beginning of the pandemic. This study aims to investigate the epidemiology of SARS-CoV-2 in Spain and its 18 Autonomous Communities across the six epidemic waves established from February 2020 to January 2022. We report on the circulating SARS-CoV-2 variants in each epidemic wave and Spanish region and analyze the mutation frequency, amino acid (aa) conservation, and most frequent aa changes across each structural/non-structural/accessory viral protein among the Spanish sequences deposited in the GISAID database during the study period. The overall SARS-CoV-2 mutation frequency was 1.24 × 10−5. The aa conservation was >99% in the three types of protein, being non-structural the most conserved. Accessory proteins had more variable positions, while structural proteins presented more aa changes per sequence. Six main lineages spread successfully in Spain from 2020 to 2022. The presented data provide an insight into the SARS-CoV-2 circulation and genetic variability in Spain during the first two years of the pandemic.
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25
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Patarroyo MA, Patarroyo ME, Pabón L, Alba MP, Bermudez A, Rugeles MT, Díaz-Arevalo D, Zapata-Builes W, Zapata MI, Reyes C, Suarez CF, Agudelo W, López C, Aza-Conde J, Melo M, Escamilla L, Oviedo J, Guzmán F, Silva Y, Forero M, Flórez-Álvarez L, Aguilar-Jimenez W, Moreno-Vranich A, Garry J, Avendaño C. SM-COLSARSPROT: Highly Immunogenic Supramutational Synthetic Peptides Covering the World's Population. Front Immunol 2022; 13:859905. [PMID: 35693819 PMCID: PMC9175637 DOI: 10.3389/fimmu.2022.859905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/19/2022] [Indexed: 12/02/2022] Open
Abstract
Fifty ~20-amino acid (aa)-long peptides were selected from functionally relevant SARS-CoV-2 S, M, and E proteins for trial B-21 and another 53 common ones, plus some new ones derived from the virus' main genetic variants for complementary trial C-21. Peptide selection was based on tremendous SARS-CoV-2 genetic variability for analysing them concerning vast human immunogenetic polymorphism for developing the first supramutational, Colombian SARS-protection (SM-COLSARSPROT), peptide mixture. Specific physicochemical rules were followed, i.e., aa predilection for polyproline type II left-handed (PPIIL) formation, replacing β-branched, aromatic aa, short-chain backbone H-bond-forming residues, π-π interactions (n→π* and π-CH), aa interaction with π systems, and molecular fragments able to interact with them, disrupting PPIIL propensity formation. All these modified structures had PPIIL formation propensity to enable target peptide interaction with human leukocyte antigen-DRβ1* (HLA-DRβ1*) molecules to mediate antigen presentation and induce an appropriate immune response. Such modified peptides were designed for human use; however, they induced high antibody titres against S, M, and E parental mutant peptides and neutralising antibodies when suitably modified and chemically synthesised for immunising 61 major histocompatibility complex class II (MHCII) DNA genotyped Aotus monkeys (matched with their corresponding HLA-DRβ1* molecules), predicted to cover 77.5% to 83.1% of the world's population. Such chemically synthesised peptide mixture represents an extremely pure, stable, reliable, and cheap vaccine for COVID-19 pandemic control, providing a new approach for a logical, rational, and soundly established methodology for other vaccine development.
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Affiliation(s)
- Manuel A. Patarroyo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Manuel E. Patarroyo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Laura Pabón
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Martha P. Alba
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Adriana Bermudez
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - María Teresa Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Diana Díaz-Arevalo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Wildeman Zapata-Builes
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - María Isabel Zapata
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - César Reyes
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Carlos F. Suarez
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - William Agudelo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Carolina López
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Jorge Aza-Conde
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Miguel Melo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Luis Escamilla
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Jairo Oviedo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Fanny Guzmán
- Núcleo de Biotecnología, Pontificia U. Católica de Valparaíso, Valparaíso, Chile
| | - Yolanda Silva
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Martha Forero
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Lizdany Flórez-Álvarez
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Wbeimar Aguilar-Jimenez
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Armando Moreno-Vranich
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Jason Garry
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Catalina Avendaño
- Facultad de Ciencias Agropecualrias, Universidad de Ciencias Aplicadas y Ambientales (UDCA), Bogotá, Colombia
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26
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Werner E. Strategies for the Production of Molecular Animations. FRONTIERS IN BIOINFORMATICS 2022; 2:793914. [DOI: 10.3389/fbinf.2022.793914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 04/14/2022] [Indexed: 11/13/2022] Open
Abstract
Molecular animations play an increasing role in scientific visualisation and science communication. They engage viewers through non-fictional, documentary type storytelling and aim at advancing the audience. Every scene of a molecular animation is to be designed to secure clarity. To achieve this, knowledge on design principles from various design fields is essential. The relevant principles help to draw attention, guide the eye, establish relationships, convey dynamics and/or trigger a reaction. The tools of general graphic design are used to compose a signature frame, those of cinematic storytelling and user interface design to choreograph the relative movement of characters and cameras. Clarity in a scientific visualisation is reached by simplification and abstraction where the choice of the adequate representation is of great importance. A large set of illustration styles is available to chose the appropriate detail level but they are constrained by the availability of experimental data. For a high-quality molecular animation, data from different sources can be integrated, even filling the structural gaps to show a complete picture of the native biological situation. For maintaining scientific authenticity it is good practice to mark use of artistic licence which ensures transparency and accountability. The design of motion requires knowledge from molecule kinetics and kinematics. With biological macromolecules, four types of motion are most relevant: thermal motion, small and large conformational changes and Brownian motion. The principles of dynamic realism should be respected as well as the circumstances given in the crowded cellular environment. Ultimately, consistent complexity is proposed as overarching principle for the production of molecular animations and should be achieved between communication objective and abstraction/simplification, audience expertise and scientific complexity, experiment and representation, characters and environment as well as structure and motion representation.
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27
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Vindeirinho JM, Pinho E, Azevedo NF, Almeida C. SARS-CoV-2 Diagnostics Based on Nucleic Acids Amplification: From Fundamental Concepts to Applications and Beyond. Front Cell Infect Microbiol 2022; 12:799678. [PMID: 35402302 PMCID: PMC8984495 DOI: 10.3389/fcimb.2022.799678] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
COVID-19 pandemic ignited the development of countless molecular methods for the diagnosis of SARS-CoV-2 based either on nucleic acid, or protein analysis, with the first establishing as the most used for routine diagnosis. The methods trusted for day to day analysis of nucleic acids rely on amplification, in order to enable specific SARS-CoV-2 RNA detection. This review aims to compile the state-of-the-art in the field of nucleic acid amplification tests (NAATs) used for SARS-CoV-2 detection, either at the clinic level, or at the Point-Of-Care (POC), thus focusing on isothermal and non-isothermal amplification-based diagnostics, while looking carefully at the concerning virology aspects, steps and instruments a test can involve. Following a theme contextualization in introduction, topics about fundamental knowledge on underlying virology aspects, collection and processing of clinical samples pave the way for a detailed assessment of the amplification and detection technologies. In order to address such themes, nucleic acid amplification methods, the different types of molecular reactions used for DNA detection, as well as the instruments requested for executing such routes of analysis are discussed in the subsequent sections. The benchmark of paradigmatic commercial tests further contributes toward discussion, building on technical aspects addressed in the previous sections and other additional information supplied in that part. The last lines are reserved for looking ahead to the future of NAATs and its importance in tackling this pandemic and other identical upcoming challenges.
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Affiliation(s)
- João M. Vindeirinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Eva Pinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Nuno F. Azevedo
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Carina Almeida
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
- Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
- *Correspondence: Carina Almeida,
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28
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Gonzalez Lomeli F, Elmaraghy N, Castro A, Osuna Guerrero CV, Newcomb LL. Conserved Targets to Prevent Emerging Coronaviruses. Viruses 2022; 14:v14030563. [PMID: 35336969 PMCID: PMC8949862 DOI: 10.3390/v14030563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 12/04/2022] Open
Abstract
Novel coronaviruses emerged as zoonotic outbreaks in humans in 2003 (SARS), 2012 (MERS), and notably in 2019 (SARS2), which resulted in the COVID-19 pandemic, causing worldwide health and economic disaster. Vaccines provide the best protection against disease but cannot be developed and engineered quickly enough to prevent emerging viruses, zoonotic outbreaks, and pandemics. Antivirals are the best first line of therapeutic defense against novel emerging viruses. Coronaviruses are plus sense, single stranded, RNA genome viruses that undergo frequent genetic mutation and recombination, allowing for the emergence of novel coronavirus strains and variants. The molecular life cycle of the coronavirus family offers many conserved activities to be exploited as targets for antivirals. Here, we review the molecular life cycle of coronaviruses and consider antiviral therapies, approved and under development, that target the conserved activities of coronaviruses. To identify additional targets to inhibit emerging coronaviruses, we carried out in silico sequence and structure analysis of coronavirus proteins isolated from bat and human hosts. We highlight conserved and accessible viral protein domains and residues as possible targets for the development of viral inhibitors. Devising multiple antiviral therapies that target conserved viral features to be used in combination is the best first line of therapeutic defense to prevent emerging viruses from developing into outbreaks and pandemics.
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29
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Le TB, Kim HK, Ahn MJ, Zanin M, Lo VT, Ling S, Jiang Z, Kang JA, Bae PK, Kim YS, Kim S, Wong SS, Jeong DG, Yoon SW. Diagnostic performance and clinical feasibility of a novel one-step RT-qPCR assay for simultaneous detection of multiple severe acute respiratory syndrome coronaviruses. Arch Virol 2022; 167:871-879. [PMID: 35137250 PMCID: PMC8885489 DOI: 10.1007/s00705-022-05383-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is an acute respiratory infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Other coronaviruses (CoVs) can also infect humans, although the majority cause only mild respiratory symptoms. Because early diagnosis of SARS-CoV-2 is critical for preventing further transmission events and improving clinical outcomes, it is important to be able to distinguish SARS-CoV-2 from other SARS-related CoVs in respiratory samples. Therefore, we developed and evaluated a novel reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay targeting the genes encoding the spike (S) and membrane (M) proteins to enable the rapid identification of SARS-CoV-2, including several new circulating variants and other emerging SARS-like CoVs. By analysis of in vitro-transcribed mRNA, we established multiplex RT-qPCR assays capable of detecting 5 × 10° copies/reaction. Using RNA extracted from cell culture supernatants, our multiple simultaneous SARS-CoV-2 assays had a limit of detection of 1 × 10° TCID50/mL and showed no cross-reaction with human CoVs or other respiratory viruses. We also validated our method using human clinical samples from patients with COVID-19 and healthy individuals, including nasal swab and sputum samples. This novel one-step multiplex RT-qPCR assay can be used to improve the laboratory diagnosis of human-pathogenic CoVs, including SARS-CoV-2, and may be useful for the identification of other SARS-like CoVs of zoonotic origin.
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Affiliation(s)
- Tran Bac Le
- Bio-nanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Bio-Analytical Science Division, University of Science and Technology, Daejeon, South Korea
| | - Hye Kwon Kim
- Chungbuk National University, Cheongju, South Korea
| | - Min-Ju Ahn
- Bio-nanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Bio-Analytical Science Division, University of Science and Technology, Daejeon, South Korea
| | - Mark Zanin
- State Key Laboratory for Respiratory Diseases, Guangzhou Medical University, Guangzhou, Guangdong Province, China.,School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Van Thi Lo
- Bio-nanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Bio-Analytical Science Division, University of Science and Technology, Daejeon, South Korea
| | - Shiman Ling
- State Key Laboratory for Respiratory Diseases, Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Zhanpeng Jiang
- State Key Laboratory for Respiratory Diseases, Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Jung-Ah Kang
- Bio-nanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Pan Kee Bae
- BioNano Health Guard Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Yeon-Sook Kim
- Chungnam National University School of Medicine, Daejeon, South Korea
| | | | - Sook-San Wong
- State Key Laboratory for Respiratory Diseases, Guangzhou Medical University, Guangzhou, Guangdong Province, China. .,School of Public Health, The University of Hong Kong, Hong Kong, China.
| | - Dae Gwin Jeong
- Bio-nanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea. .,Bio-Analytical Science Division, University of Science and Technology, Daejeon, South Korea.
| | - Sun-Woo Yoon
- Bio-nanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea. .,Bio-Analytical Science Division, University of Science and Technology, Daejeon, South Korea.
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30
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Yan W, Zheng Y, Zeng X, He B, Cheng W. Structural biology of SARS-CoV-2: open the door for novel therapies. Signal Transduct Target Ther 2022; 7:26. [PMID: 35087058 PMCID: PMC8793099 DOI: 10.1038/s41392-022-00884-5] [Citation(s) in RCA: 122] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 02/08/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the causative agent of the pandemic disease COVID-19, which is so far without efficacious treatment. The discovery of therapy reagents for treating COVID-19 are urgently needed, and the structures of the potential drug-target proteins in the viral life cycle are particularly important. SARS-CoV-2, a member of the Orthocoronavirinae subfamily containing the largest RNA genome, encodes 29 proteins including nonstructural, structural and accessory proteins which are involved in viral adsorption, entry and uncoating, nucleic acid replication and transcription, assembly and release, etc. These proteins individually act as a partner of the replication machinery or involved in forming the complexes with host cellular factors to participate in the essential physiological activities. This review summarizes the representative structures and typically potential therapy agents that target SARS-CoV-2 or some critical proteins for viral pathogenesis, providing insights into the mechanisms underlying viral infection, prevention of infection, and treatment. Indeed, these studies open the door for COVID therapies, leading to ways to prevent and treat COVID-19, especially, treatment of the disease caused by the viral variants are imperative.
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Affiliation(s)
- Weizhu Yan
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Yanhui Zheng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Xiaotao Zeng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Bin He
- Department of Emergency Medicine, West China Hospital of Sichuan University, 610041, Chengdu, China.
- The First People's Hospital of Longquanyi District Chengdu, 610100, Chengdu, China.
| | - Wei Cheng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China.
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31
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Targeting the Virus Capsid as a Tool to Fight RNA Viruses. Viruses 2022; 14:v14020174. [PMID: 35215767 PMCID: PMC8879806 DOI: 10.3390/v14020174] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 12/10/2022] Open
Abstract
Several strategies have been developed to fight viral infections, not only in humans but also in animals and plants. Some of them are based on the development of efficient vaccines, to target the virus by developed antibodies, others focus on finding antiviral compounds with activities that inhibit selected virus replication steps. Currently, there is an increasing number of antiviral drugs on the market; however, some have unpleasant side effects, are toxic to cells, or the viruses quickly develop resistance to them. As the current situation shows, the combination of multiple antiviral strategies or the combination of the use of various compounds within one strategy is very important. The most desirable are combinations of drugs that inhibit different steps in the virus life cycle. This is an important issue especially for RNA viruses, which replicate their genomes using error-prone RNA polymerases and rapidly develop mutants resistant to applied antiviral compounds. Here, we focus on compounds targeting viral structural capsid proteins, thereby inhibiting virus assembly or disassembly, virus binding to cellular receptors, or acting by inhibiting other virus replication mechanisms. This review is an update of existing papers on a similar topic, by focusing on the most recent advances in the rapidly evolving research of compounds targeting capsid proteins of RNA viruses.
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32
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Fanelli A, Sullivan ML. Tools for protein structure prediction and for molecular docking applied to enzyme active site analysis: A case study using a BAHD hydroxycinnamoyltransferase. Methods Enzymol 2022; 683:41-79. [PMID: 37087195 DOI: 10.1016/bs.mie.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Elucidating the structure of an enzyme and how substrates bind to the active site is an important step for understanding its reaction mechanism and function. Nevertheless, the methods available to obtain three-dimensional structures of proteins, such as x-ray crystallography and NMR, can be expensive and time-consuming. Considering this, an alternative is using structural bioinformatic tools to predict the tertiary structure of a protein from its primary sequence, followed by molecular docking of one or more substrates into the enzyme structure model. In the past few years, significant advances have been made in these computational tools, which can give useful information about the active site and enzyme-substrate interactions before the structure can be resolved using physical methods. Here, using common bean (Phaseolus vulgaris) hydroxycinnamoyl-coenzyme A:tetrahydroxyhexanedioic acid hydroxycinnamoyltransferase (HHHT) as an example, we describe methods and workflows for protein structure prediction and molecular docking that can be performed on a personal computer using only open-source tools.
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Affiliation(s)
- Amanda Fanelli
- US Dairy Forage Research Center, USDA Agricultural Research Service, Madison, WI, United States.
| | - Michael L Sullivan
- US Dairy Forage Research Center, USDA Agricultural Research Service, Madison, WI, United States
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33
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Ma Y, Ding TT, Liu YY, Zheng ZH, Sun SX, Zhang LS, Zhang H, Lu XH, Cheng XC, Wang RL. Design, synthesis, biological evaluation and molecular dynamics simulation studies of imidazolidine-2,4-dione derivatives as novel PTP1B inhibitors. Biochem Biophys Res Commun 2021; 579:40-46. [PMID: 34583194 DOI: 10.1016/j.bbrc.2021.09.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/10/2021] [Accepted: 09/19/2021] [Indexed: 12/14/2022]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is a member of the phosphotyrosine phosphatase family and plays an important role in the signal transduction of diabetes. Inhibition of PTP1B activity can increase insulin sensitivity and reduce blood sugar levels. Therefore, it is urgent to find compounds with novel structures that can inhibit PTP1B. This study designed imidazolidine-2,4-dione derivatives through the computer-aided drug design (CADD) strategy, and the Comp#10 showed outstanding inhibitory ability. (IC50 = 2.07 μM) and selectivity. The inhibitory mechanism at molecular level of Comp#10 on PTP1B was studied by molecular dynamics simulation. The results show that the catalytic region of PTP1B protein is more stable, which makes the catalytic sites unsuitable for exposure. Interestingly, the most obvious changes in the interaction between residues in the P-loop region (such as: His214, Cys215, and Ser216). In short, this study reported for the first time that imidazolidine-2,4-dione derivatives as novel PTP1B inhibitors had good inhibitory activity and selectivity, providing new ideas for the development of small molecule PTP1B inhibitors.
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Affiliation(s)
- Yangchun Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China; Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, 250012, China
| | - Ting-Ting Ding
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Ya-Ya Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Zhi-Hui Zheng
- New Drug Research & Development Center of North China Pharmaceutical Group Corporation, National Microbial Medicine Engineering & Research Center, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, Key Laboratory for New Drug Screening Technology of Shijiazhuang City, Shijiazhuang, 050015, Hebei, China
| | - Su-Xia Sun
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Li-Song Zhang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Hao Zhang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Xin-Hua Lu
- New Drug Research & Development Center of North China Pharmaceutical Group Corporation, National Microbial Medicine Engineering & Research Center, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, Key Laboratory for New Drug Screening Technology of Shijiazhuang City, Shijiazhuang, 050015, Hebei, China
| | - Xian-Chao Cheng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China.
| | - Run-Ling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China.
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34
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Mohammad T, Choudhury A, Habib I, Asrani P, Mathur Y, Umair M, Anjum F, Shafie A, Yadav DK, Hassan MI. Genomic Variations in the Structural Proteins of SARS-CoV-2 and Their Deleterious Impact on Pathogenesis: A Comparative Genomics Approach. Front Cell Infect Microbiol 2021; 11:765039. [PMID: 34722346 PMCID: PMC8548870 DOI: 10.3389/fcimb.2021.765039] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/16/2021] [Indexed: 12/23/2022] Open
Abstract
A continual rise in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection causing coronavirus disease (COVID-19) has become a global threat. The main problem comes when SARS-CoV-2 gets mutated with the rising infection and becomes more lethal for humankind than ever. Mutations in the structural proteins of SARS-CoV-2, i.e., the spike surface glycoprotein (S), envelope (E), membrane (M) and nucleocapsid (N), and replication machinery enzymes, i.e., main protease (Mpro) and RNA-dependent RNA polymerase (RdRp) creating more complexities towards pathogenesis and the available COVID-19 therapeutic strategies. This study analyzes how a minimal variation in these enzymes, especially in S protein at the genomic/proteomic level, affects pathogenesis. The structural variations are discussed in light of the failure of small molecule development in COVID-19 therapeutic strategies. We have performed in-depth sequence- and structure-based analyses of these proteins to get deeper insights into the mechanism of pathogenesis, structure-function relationships, and development of modern therapeutic approaches. Structural and functional consequences of the selected mutations on these proteins and their association with SARS-CoV-2 virulency and human health are discussed in detail in the light of our comparative genomics analysis.
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Affiliation(s)
- Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Arunabh Choudhury
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Insan Habib
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Purva Asrani
- Department of Microbiology, University of Delhi, New Delhi, India
| | - Yash Mathur
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Mohd Umair
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Farah Anjum
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Alaa Shafie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Dharmendra Kumar Yadav
- Department of Pharmacy and Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Incheon, South Korea
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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35
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Abstract
COVID‑19, a new human respiratory disease that has killed nearly 3 million people in a year since the start of the pandemic, is a global public health challenge. Its infectious agent, SARS‑CoV‑2, differs from other coronaviruses in a number of structural features that make this virus more pathogenic and transmissible. In this review, we discuss some important characteristics of the main SARS‑CoV‑2 surface antigen, the spike (S) protein, such as (i) ability of the receptor-binding domain (RBD) to switch between the “standing-up” position (open pre-fusion conformation) for receptor binding and the “lying-down” position (closed pre-fusion conformation) for immune system evasion; (ii) advantage of a high binding affinity of the RBD open conformation to the human angiotensin-converting enzyme 2 (ACE2) receptor for efficient cell entry; and (iii) S protein preliminary activation by the intracellular furin-like proteases for facilitation of the virus spreading across different cell types. We describe interactions between the S protein and cellular receptors, co-receptors, and antagonists, as well as a hypothetical mechanism of the homotrimeric spike structure destabilization that triggers the fusion of the viral envelope with the cell membrane at physiological pH and mediates the viral nucleocapsid entry into the cytoplasm. The transition of the S protein pre-fusion conformation to the post-fusion one on the surface of virions after their treatment with some reagents, such as β-propiolactone, is essential, especially in relation to the vaccine production. We also compare the COVID‑19 pathogenesis with that of severe outbreaks of “avian” influenza caused by the A/H5 and A/H7 highly pathogenic viruses and discuss the structural similarities between the SARS‑CoV‑2 S protein and hemagglutinins of those highly pathogenic strains. Finally, we touch on the prospective and currently used COVID‑19 antiviral and anti-pathogenetic therapeutics, as well as recently approved conventional and innovative COVID‑19 vaccines and their molecular and immunological features.
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Affiliation(s)
- Larisa V Kordyukova
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Andrey V Shanko
- FORT LLC, R&D Department, Moscow, 119435, Russia.,Ivanovsky Institute of Virology, Gamaleya Federal Research Center for Epidemiology and Microbiology, Moscow, 123098, Russia
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36
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Chazal N. Coronavirus, the King Who Wanted More Than a Crown: From Common to the Highly Pathogenic SARS-CoV-2, Is the Key in the Accessory Genes? Front Microbiol 2021; 12:682603. [PMID: 34335504 PMCID: PMC8317507 DOI: 10.3389/fmicb.2021.682603] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/22/2021] [Indexed: 12/14/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), that emerged in late 2019, is the etiologic agent of the current "coronavirus disease 2019" (COVID-19) pandemic, which has serious health implications and a significant global economic impact. Of the seven human coronaviruses, all of which have a zoonotic origin, the pandemic SARS-CoV-2, is the third emerging coronavirus, in the 21st century, highly pathogenic to the human population. Previous human coronavirus outbreaks (SARS-CoV-1 and MERS-CoV) have already provided several valuable information on some of the common molecular and cellular mechanisms of coronavirus infections as well as their origin. However, to meet the new challenge caused by the SARS-CoV-2, a detailed understanding of the biological specificities, as well as knowledge of the origin are crucial to provide information on viral pathogenicity, transmission and epidemiology, and to enable strategies for therapeutic interventions and drug discovery. Therefore, in this review, we summarize the current advances in SARS-CoV-2 knowledges, in light of pre-existing information of other recently emerging coronaviruses. We depict the specificity of the immune response of wild bats and discuss current knowledge of the genetic diversity of bat-hosted coronaviruses that promotes viral genome expansion (accessory gene acquisition). In addition, we describe the basic virology of coronaviruses with a special focus SARS-CoV-2. Finally, we highlight, in detail, the current knowledge of genes and accessory proteins which we postulate to be the major keys to promote virus adaptation to specific hosts (bat and human), to contribute to the suppression of immune responses, as well as to pathogenicity.
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Affiliation(s)
- Nathalie Chazal
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS, Montpellier, France
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37
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Sanami S, Alizadeh M, Nosrati M, Dehkordi KA, Azadegan-Dehkordi F, Tahmasebian S, Nosrati H, Arjmand MH, Ghasemi-Dehnoo M, Rafiei A, Bagheri N. Exploring SARS-COV-2 structural proteins to design a multi-epitope vaccine using immunoinformatics approach: An in silico study. Comput Biol Med 2021; 133:104390. [PMID: 33895459 PMCID: PMC8055380 DOI: 10.1016/j.compbiomed.2021.104390] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 12/24/2022]
Abstract
In December 2019, a new virus called SARS-CoV-2 was reported in China and quickly spread to other parts of the world. The development of SARS-COV-2 vaccines has recently received much attention from numerous researchers. The present study aims to design an effective multi-epitope vaccine against SARS-COV-2 using the reverse vaccinology method. In this regard, structural proteins from SARS-COV-2, including the spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins, were selected as target antigens for epitope prediction. A total of five helper T lymphocytes (HTL) and five cytotoxic T lymphocytes (CTL) epitopes were selected after screening the predicted epitopes for antigenicity, allergenicity, and toxicity. Subsequently, the selected HTL and CTL epitopes were fused via flexible linkers. Next, the cholera toxin B-subunit (CTxB) as an adjuvant was linked to the N-terminal of the chimeric structure. The proposed vaccine was analyzed for the properties of physicochemical, antigenicity, and allergenicity. The 3D model of the vaccine construct was predicted and docked with the Toll-like receptor 4 (TLR4). The molecular dynamics (MD) simulation was performed to evaluate the stable interactions between the vaccine construct and TLR4. The immune simulation was also conducted to explore the immune responses induced by the vaccine. Finally, in silico cloning of the vaccine construct into the pET-28 (+) vector was conducted. The results obtained from all bioinformatics analysis stages were satisfactory; however, in vitro and in vivo tests are essential to validate these results.
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Affiliation(s)
- Samira Sanami
- Department of Medical Biotechnology, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Morteza Alizadeh
- Department of Tissue Engineering, School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Masoud Nosrati
- Department of Computer Science, Iowa State University, Ames, IA, USA
| | - Korosh Ashrafi Dehkordi
- Department of Molecular Medicine, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran.
| | - Fatemeh Azadegan-Dehkordi
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Shahram Tahmasebian
- Department of Medical Biotechnology, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Hamed Nosrati
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | | | - Maryam Ghasemi-Dehnoo
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Ali Rafiei
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Nader Bagheri
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran.
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38
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IgM and IgG Immunoreactivity of SARS-CoV-2 Recombinant M Protein. Int J Mol Sci 2021; 22:ijms22094951. [PMID: 34066920 PMCID: PMC8125631 DOI: 10.3390/ijms22094951] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/19/2021] [Accepted: 04/21/2021] [Indexed: 12/23/2022] Open
Abstract
Diagnostic evaluation of specific antibodies against the SARS-CoV-2 virus is mainly based on spike (S) and nucleocapsid (N) proteins. Despite the critical functions in virus infection and contribution to the pattern of immunodominance in COVID-19, exploitation of the most abundant membrane (M) protein in the SARS-CoV-2 serology tests is minimal. This study investigated the recombinant M protein's immunoreactivity with the sera from COVID-19 convalescents. In silico designed protein was created from the outer N-terminal part (19 aa) and internal C-terminal tail (101-222 aa) of the M protein (YP_009724393.1) and was recombinantly produced and purified. The designed M protein (16,498.74 Da, pI 8.79) revealed both IgM and IgG reactivity with serum samples from COVID-19 convalescents in Western blot. In ELISA, more than 93% (28/30) of COVID-19 sera were positive for IgM detection, and more than 96% (29/30) were positive for specific IgG detection to M protein. Based on the capacity to provoke an immune response and its strong antigenic properties, as shown here, and the fact that it is also involved in the virion entry into host cells, the M protein of the SARS-CoV-2 virus as a good antigen has the potential in diagnostic purposes and vaccine design.
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Zhang X, Liu Y, Liu J, Bailey AL, Plante KS, Plante JA, Zou J, Xia H, Bopp NE, Aguilar PV, Ren P, Menachery VD, Diamond MS, Weaver SC, Xie X, Shi PY. A trans-complementation system for SARS-CoV-2 recapitulates authentic viral replication without virulence. Cell 2021; 184:2229-2238.e13. [PMID: 33691138 PMCID: PMC7901297 DOI: 10.1016/j.cell.2021.02.044] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/11/2021] [Accepted: 02/19/2021] [Indexed: 12/25/2022]
Abstract
The biosafety level 3 (BSL-3) requirement to culture severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a bottleneck for research. Here, we report a trans-complementation system that produces single-round infectious SARS-CoV-2 that recapitulates authentic viral replication. We demonstrate that the single-round infectious SARS-CoV-2 can be used at BSL-2 laboratories for high-throughput neutralization and antiviral testing. The trans-complementation system consists of two components: a genomic viral RNA containing ORF3 and envelope gene deletions, as well as mutated transcriptional regulator sequences, and a producer cell line expressing the two deleted genes. Trans-complementation of the two components generates virions that can infect naive cells for only one round but does not produce wild-type SARS-CoV-2. Hamsters and K18-hACE2 transgenic mice inoculated with the complementation-derived virions exhibited no detectable disease, even after intracranial inoculation with the highest possible dose. Thus, the trans-complementation platform can be safely used at BSL-2 laboratories for research and countermeasure development.
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Affiliation(s)
- Xianwen Zhang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Yang Liu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jianying Liu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Adam L Bailey
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kenneth S Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Jessica A Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Jing Zou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Nathen E Bopp
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Patricia V Aguilar
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Ping Ren
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Michael S Diamond
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Scott C Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
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Zhang X, Liu Y, Liu J, Bailey AL, Plante KS, Plante JA, Zou J, Xia H, Bopp N, Aguilar P, Ren P, Menachery VD, Diamond MS, Weaver SC, Xie X, Shi PY. A trans -complementation system for SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33501436 DOI: 10.1101/2021.01.16.426970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The biosafety level-3 (BSL-3) requirement to culture severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a bottleneck for research and countermeasure development. Here we report a trans -complementation system that produces single-round infectious SARS-CoV-2 that recapitulates authentic viral replication. We demonstrate that the single-round infectious SARS-CoV-2 can be used at BSL-2 laboratories for high-throughput neutralization and antiviral testing. The trans -complementation system consists of two components: a genomic viral RNA containing a deletion of ORF3 and envelope gene, and a producer cell line expressing the two deleted genes. Trans- complementation of the two components generates virions that can infect naive cells for only one round, but does not produce wild-type SARS-CoV-2. Hamsters and K18-hACE2 transgenic mice inoculated with the complementation-derived virions exhibited no detectable disease, even after intracranial inoculation with the highest possible dose. The results suggest that the trans -complementation platform can be safely used at BSL-2 laboratories for research and countermeasure development.
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