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Ho WY, Shen ZH, Chen Y, Chen TH, Lu X, Fu YS. Therapeutic implications of quercetin and its derived-products in COVID-19 protection and prophylactic. Heliyon 2024; 10:e30080. [PMID: 38765079 PMCID: PMC11098804 DOI: 10.1016/j.heliyon.2024.e30080] [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: 12/01/2023] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 05/21/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel human coronavirus, which has triggered a global pandemic of the coronavirus infectious disease 2019 (COVID-19). Outbreaks of emerging infectious diseases continue to challenge human health worldwide. The virus conquers human cells through the angiotensin-converting enzyme 2 receptor-driven pathway by mostly targeting the human respiratory tract. Quercetin is a natural flavonoid widely represented in the plant kingdom. Cumulative evidence has demonstrated that quercetin and its derivatives have various pharmacological properties including anti-cancer, anti-hypertension, anti-hyperlipidemia, anti-hyperglycemia, anti-microbial, antiviral, neuroprotective, and cardio-protective effects, because it is a potential treatment for severe inflammation and acute respiratory distress syndrome. Furthermore, it is the main life-threatening condition in patients with COVID-19. This article provides a comprehensive review of the primary literature on the predictable effectiveness of quercetin and its derivatives docked to multi-target of SARS-CoV-2 and host cells via in silico and some of validation through in vitro, in vivo, and clinically to fight SARS-CoV-2 infections, contribute to the reduction of inflammation, which suggests the preventive and therapeutic latency of quercetin and its derived-products against COVID-19 pandemic, multisystem inflammatory syndromes (MIS), and long-COVID.
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Affiliation(s)
- Wan-Yi Ho
- Department of Anatomy, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Zi-Han Shen
- Department of Clinical Medicine, Xiamen Medical College, Xiamen, 361023, Fujian, China
| | - Yijing Chen
- Department of Dentisty, Xiamen Medical College, Xiamen, 361023, Fujian, China
| | - Ting-Hsu Chen
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - XiaoLin Lu
- Anatomy Section, Department of Basic Medical Science, Xiamen Medical College, Xiamen, 361023, Fujian, China
| | - Yaw-Syan Fu
- Institute of Respiratory Disease, Department of Basic Medical Science, Xiamen Medical College, Xiamen, 361023, Fujian, China
- Anatomy Section, Department of Basic Medical Science, Xiamen Medical College, Xiamen, 361023, Fujian, China
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2
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Bharadwaj A, Kaur R, Gupta S. Emerging Treatment Approaches for COVID-19 Infection: A Critical Review. Curr Mol Med 2024; 24:435-448. [PMID: 37070448 DOI: 10.2174/1566524023666230417112543] [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: 09/02/2022] [Revised: 02/04/2023] [Accepted: 02/07/2023] [Indexed: 04/19/2023]
Abstract
In the present scenario, the SARS-CoV-2 virus has imposed enormous damage on human survival and the global financial system. It has been estimated that around 111 million people all around the world have been infected, and about 2.47 million people died due to this pandemic. The major symptoms were sneezing, coughing, cold, difficulty breathing, pneumonia, and multi-organ failure associated 1with SARS-CoV-2. Currently, two key problems, namely insufficient attempts to develop drugs against SARSCoV-2 and the lack of any biological regulating process, are mostly responsible for the havoc caused by this virus. Henceforth, developing a few novel drugs is urgently required to cure this pandemic. It has been noticed that the pathogenesis of COVID-19 is caused by two main events: infection and immune deficiency, that occur during the pathological process. Antiviral medication can treat both the virus and the host cells. Therefore, in the present review, the major approaches for the treatment have been divided into "target virus" and "target host" groups. These two mechanisms primarily rely on drug repositioning, novel approaches, and possible targets. Initially, we discussed the traditional drugs per the physicians' recommendations. Moreover, such therapeutics have no potential to fight against COVID-19. After that, detailed investigation and analysis were conducted to find some novel vaccines and monoclonal antibodies and conduct a few clinical trials to check their effectiveness against SARSCoV- 2 and mutant strains. Additionally, this study presents the most successful methods for its treatment, including combinatorial therapy. Nanotechnology was studied to build efficient nanocarriers to overcome the traditional constraints of antiviral and biological therapies.
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Affiliation(s)
- Alok Bharadwaj
- Department of Biotechnology, GLA University, Mathura, 281406, UP, India
| | - Rasanpreet Kaur
- Department of Biotechnology, GLA University, Mathura, 281406, UP, India
| | - Saurabh Gupta
- Department of Biotechnology, GLA University, Mathura, 281406, UP, India
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3
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Zhang R, Qin H, Prasad R, Fu R, Zhou HX, Cross TA. Dimeric Transmembrane Structure of the SARS-CoV-2 E Protein. Commun Biol 2023; 6:1109. [PMID: 37914906 PMCID: PMC10620413 DOI: 10.1038/s42003-023-05490-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 10/19/2023] [Indexed: 11/03/2023] Open
Abstract
The SARS-CoV-2 E protein is a transmembrane (TM) protein with its N-terminus exposed on the external surface of the virus. At debate is its oligomeric state, let alone its function. Here, the TM structure of the E protein is characterized by oriented sample and magic angle spinning solid-state NMR in lipid bilayers and refined by molecular dynamics simulations. This protein was previously found to be a pentamer, with a hydrophobic pore that appears to function as an ion channel. We identify only a front-to-front, symmetric helix-helix interface, leading to a dimeric structure that does not support channel activity. The two helices have a tilt angle of only 6°, resulting in an extended interface dominated by Leu and Val sidechains. While residues Val14-Thr35 are almost all buried in the hydrophobic region of the membrane, Asn15 lines a water-filled pocket that potentially serves as a drug-binding site. The E and other viral proteins may adopt different oligomeric states to help perform multiple functions.
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Affiliation(s)
- Rongfu Zhang
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306, USA
- National High Magnetic Field Laboratory, Tallahassee, FL, 32310, USA
| | - Huajun Qin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306, USA
| | - Ramesh Prasad
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Tallahassee, FL, 32310, USA
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, 60607, USA.
- Department of Physics, University of Illinois Chicago, Chicago, IL, 60607, USA.
| | - Timothy A Cross
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306, USA.
- National High Magnetic Field Laboratory, Tallahassee, FL, 32310, USA.
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306, USA.
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Alsaiari AA, Hakami MA, Alotaibi BS, Alkhalil SS, Alkhorayef N, Khan K, Jalal K. Delineating multi-epitopes vaccine designing from membrane protein CL5 against all monkeypox strains: a pangenome reverse vaccinology approach. J Biomol Struct Dyn 2023:1-22. [PMID: 37599459 DOI: 10.1080/07391102.2023.2248301] [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: 05/29/2023] [Accepted: 08/02/2023] [Indexed: 08/22/2023]
Abstract
The recently identified monkeypox virus (MPXV or mpox) is a zoonotic orthopox virus that infects humans and causes diseases with traits like smallpox. The world health organization (WHO) estimates that 3-6% of MPXV cases result in death. As it might impact everyone globally, like COVID, and become the next pandemic, the cure for this disease is important for global public health. The high incidence and disease ratio of MPXV necessitates immediate efforts to design a unique vaccine candidate capable of addressing MPXV diseases. Here, we used a computational pan-genome-based vaccine design strategy for all currently reported 19 MPXV strains acquired from different regions of the world. Thus, this study's objective was to develop a new and safe vaccine candidate against MPXV by targeting the membrane CL5 protein; identified after the pangenome analysis. Proteomics and reverse vaccinology have covered up all of the MPXV epitopes that would usually stimulate robust host immune responses. Following this, only two mapped (MHC-I, MHC-II, and B-cell) epitopes were observed to be extremely effective that can be used in the construction of CL5 protein vaccine candidates. The suggested vaccine (V5) candidate from eight vaccine models was shown to be antigenic, non-allergenic, and stable (with 213 amino acids). The vaccine's candidate efficacy was evaluated by using many in silico methods to predict, improve, and validate its 3D structure. Molecular docking and molecular dynamics simulations further reveal that the proposed vaccine candidate ensemble has a high interaction energy with the HLAs and TRL2/4 immunological receptors under study. Later, the vaccine sequence was used to generate an expression vector for the E. coli K12 strain. Further study uncovers that V5 was highly immunogenic because it produced robust primary, secondary, and tertiary immune responses. Eventually, the use of computer-aided vaccine designing may significantly reduce costs and speed up the process of developing vaccines. Although, the results of this research are promising, however, more research (experimental; in vivo, and in vitro studies) is needed to verify the biological efficacy of the proposed vaccine against MPXV.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ahad Amer Alsaiari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al- Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Bader S Alotaibi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al- Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Samia S Alkhalil
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al- Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Nada Alkhorayef
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al- Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Kanwal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Khurshid Jalal
- HEJ Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
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5
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Tabibzadeh A, Karbalaie Niya MH, Keyvani H, Karampoor S, Yousefi P, Razizadeh MH, Mousavizadeh L, Esghaei M. A survey of ORF8 sequence and immunoinformatics features during alpha, delta, and wild type peaks of the SARS-CoV-2 pandemic in Iran. Malawi Med J 2023; 35:101-105. [PMID: 38264170 PMCID: PMC10731532 DOI: 10.4314/mmj.v35i2.5] [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] [Indexed: 01/25/2024] Open
Abstract
Background The Coronavirus disease 2019 (COVID-19) pandemic influences all around the world. The SARS-CoV-2 ORF8 accessory gene represents multiple functions in virus-host interaction. The current study aimed to compare the ORF8 substitutions and epitope features of these substitutions in the various SARS-CoV-2 outbreaks including delta, alpha, and wild type variants in Iran from 2020 to 2022. In addition, we evaluate B cell, HLA I and II epitopes, by in-silico approach to ORF8 binding site prediction. Methods The samples were collected from patients diagnosed with SARS-CoV-2 infection via a real-time PCR assay. Then, a conventional PCR was carried out for ORF8 mutations analysis and further Sanger sequencing. Possible important alterations in epitope features of the ORF8 were evaluated by epitope mapping. B cell, HLA class I and II epitopes, evaluated by online databases ABCpred, NetMHCpan-4.1, and NetMHCIIpan-3.2, respectively. Results The current study results could not represent novel variations in seven full-length ORF8 sequences or major ORF8 deletions in 80 evaluated samples. In addition, we could not find any ORF8 A382 during each outbreak of variants. Epitope mapping represents differences between the Alpha and other variants, especially in B cell potential epitopes and HLA I. Conclusion The immunoinformatic evaluation of ORF8 suggested epitopes represent major differences for the Alpha variant in comparison with other variants. In addition, having mild pathogenesis of the Omicron variant does not seem to be associated with ORF8 alteration by phylogenetic evaluation. Future in-vitro studies for a clear conclusion about the epitope features of ORF8 are required.
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Affiliation(s)
- Alireza Tabibzadeh
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Hadi Karbalaie Niya
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Hossein Keyvani
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Sajad Karampoor
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Parastoo Yousefi
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | | | - Leila Mousavizadeh
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Esghaei
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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6
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Zhang R, Qin H, Prasad R, Fu R, Zhou HX, Cross TA. Dimeric Transmembrane Structure of the SARS-CoV-2 E Protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.07.539752. [PMID: 37214926 PMCID: PMC10197518 DOI: 10.1101/2023.05.07.539752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The SARS-CoV-2 E protein is a transmembrane (TM) protein with its N-terminus exposed on the external surface of the virus. Here, the TM structure of the E protein is characterized by oriented sample and magic angle spinning solid-state NMR in lipid bilayers and refined by molecular dynamics simulations. This protein has been found to be a pentamer, with a hydrophobic pore that appears to function as an ion channel. We identified only a symmetric helix-helix interface, leading to a dimeric structure that does not support channel activity. The two helices have a tilt angle of only 6°, resulting in an extended interface dominated by Leu and Val sidechains. While residues Val14-Thr35 are almost all buried in the hydrophobic region of the membrane, Asn15 lines a water-filled pocket that potentially serves as a drug-binding site. The E and other viral proteins may adopt different oligomeric states to help perform multiple functions.
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Affiliation(s)
- Rongfu Zhang
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306
- National High Magnetic Field Laboratory, Tallahassee, FL 32310
- Contributed equally to this work
| | - Huajun Qin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306
- Contributed equally to this work
| | - Ramesh Prasad
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Tallahassee, FL 32310
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607
- Department of Physics, University of Illinois Chicago, Chicago, IL 60607
| | - Timothy A. Cross
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306
- National High Magnetic Field Laboratory, Tallahassee, FL 32310
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306
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7
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Tan X, Cai K, Li J, Yuan Z, Chen R, Xiao H, Xu C, Hu B, Qin Y, Ding B. Coronavirus subverts ER-phagy by hijacking FAM134B and ATL3 into p62 condensates to facilitate viral replication. Cell Rep 2023; 42:112286. [PMID: 36952345 PMCID: PMC9998290 DOI: 10.1016/j.celrep.2023.112286] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 02/07/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
ER-phagy is a form of autophagy that is mediated by ER-phagy receptors and selectively degrades endoplasmic reticulum (ER). Coronaviruses have been shown to use the ER as a membrane source to establish their double-membrane vesicles (DMVs). However, whether viruses modulate ER-phagy to drive viral DMV formation and its underlying molecular mechanisms remains largely unknown. Here, we demonstrate that coronavirus subverts ER-phagy by hijacking the ER-phagy receptors FAM134B and ATL3 into p62 condensates, resulting in increased viral replication. Mechanistically, we show that viral protein ORF8 binds to and undergoes condensation with p62. FAM134B and ATL3 interact with homodimer of ORF8 and are aggregated into ORF8/p62 liquid droplets, leading to ER-phagy inhibition. ORF8/p62 condensates disrupt ER-phagy to facilitate viral DMV formation and activate ER stress. Together, our data highlight how coronavirus modulates ER-phagy to drive viral replication by hijacking ER-phagy receptors.
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Affiliation(s)
- Xuan Tan
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Kun Cai
- Institute of Health Inspection and Testing, Hubei Provincial Center for Disease Control and Prevention, Wuhan, Hubei 430079, China
| | - Jiajia Li
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Zhen Yuan
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Ruifeng Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Hurong Xiao
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Chuanrui Xu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Bing Hu
- Institute of Health Inspection and Testing, Hubei Provincial Center for Disease Control and Prevention, Wuhan, Hubei 430079, China
| | - Yali Qin
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China.
| | - Binbin Ding
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Cell Architecture Research Institute, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China.
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8
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Zhou S, Lv P, Li M, Chen Z, Xin H, Reilly S, Zhang X. SARS-CoV-2 E protein: Pathogenesis and potential therapeutic development. Biomed Pharmacother 2023; 159:114242. [PMID: 36652729 PMCID: PMC9832061 DOI: 10.1016/j.biopha.2023.114242] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a devastating global pandemic, which has seriously affected human health worldwide. The discovery of therapeutic agents is extremely urgent, and the viral structural proteins are particularly important as potential drug targets. SARS-CoV-2 envelope (E) protein is one of the main structural proteins of the virus, which is involved in multiple processes of the virus life cycle and is directly related to pathogenesis process. In this review, we present the amino acid sequence of the E protein and compare it with other two human coronaviruses. We then explored the role of E protein in the viral life cycle and discussed the pathogenic mechanisms that E protein may be involved in. Next, we summarize the potential drugs against E protein discovered in the current studies. Finally, we described the possible effects of E protein mutation on virus and host. This established a knowledge system of E protein to date, aiming to provide theoretical insights for mitigating the current COVID-19 pandemic and potential future coronavirus outbreaks.
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Affiliation(s)
- Shilin Zhou
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China.
| | - Panpan Lv
- Clinical Laboratory, Minhang Hospital, Fudan University, Shanghai, China.
| | - Mingxue Li
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China.
| | - Zihui Chen
- School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Hong Xin
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China.
| | - Svetlana Reilly
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
| | - Xuemei Zhang
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China.
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Waisner H, Grieshaber B, Saud R, Henke W, Stephens EB, Kalamvoki M. SARS-CoV-2 Harnesses Host Translational Shutoff and Autophagy To Optimize Virus Yields: the Role of the Envelope (E) Protein. Microbiol Spectr 2023; 11:e0370722. [PMID: 36622177 PMCID: PMC9927098 DOI: 10.1128/spectrum.03707-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/07/2022] [Indexed: 01/10/2023] Open
Abstract
The SARS-CoV-2 virion is composed of four structural proteins: spike (S), nucleocapsid (N), membrane (M), and envelope (E). E spans the membrane a single time and is the smallest, yet most enigmatic of the structural proteins. E is conserved among coronaviruses and has an essential role in virus-mediated pathogenesis. We found that ectopic expression of E had deleterious effects on the host cell as it activated stress responses, leading to LC3 lipidation and phosphorylation of the translation initiation factor eIF2α that resulted in host translational shutoff. During infection E is highly expressed, although only a small fraction is incorporated into virions, suggesting that E activity is regulated and harnessed by the virus to its benefit. Consistently, we found that proteins from heterologous viruses, such as the γ1 34.5 protein of herpes simplex virus 1, prevented deleterious effects of E on the host cell and allowed for E protein accumulation. This observation prompted us to investigate whether other SARS-CoV-2 structural proteins regulate E. We found that the N and M proteins enabled E protein accumulation, whereas S did not. While γ1 34.5 protein prevented deleterious effects of E on the host cells, it had a negative effect on SARS-CoV-2 replication. The negative effect of γ1 34.5 was most likely associated with failure of SARS-CoV-2 to divert the translational machinery and with deregulation of autophagy. Overall, our data suggest that SARS-CoV-2 causes stress responses and subjugates these pathways, including host protein synthesis (phosphorylated eIF2α) and autophagy, to support optimal virus replication. IMPORTANCE In late 2019, a new β-coronavirus, SARS-CoV-2, entered the human population causing a pandemic that has resulted in over 6 million deaths worldwide. Although closely related to SARS-CoV, the mechanisms of SARS-CoV-2 pathogenesis are not fully understood. We found that ectopic expression of the SARS-CoV-2 E protein had detrimental effects on the host cell, causing metabolic alterations, including shutoff of protein synthesis and mobilization of cellular resources through autophagy activation. Coexpression of E with viral proteins known to subvert host antiviral responses such as autophagy and translational inhibition, either from SARS-CoV-2 or from heterologous viruses, increased cell survival and E protein accumulation. However, such factors were found to negatively impact SARS-CoV-2 infection, as autophagy contributes to formation of viral membrane factories and translational control offers an advantage for viral gene expression. Overall, SARS-CoV-2 has evolved mechanisms to harness host functions that are essential for virus replication.
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Affiliation(s)
- Hope Waisner
- University of Kansas Medical Center, Department of Microbiology, Molecular Genetics, and Immunology, Kansas City, Kansas, USA
| | - Brandon Grieshaber
- University of Kansas Medical Center, Department of Microbiology, Molecular Genetics, and Immunology, Kansas City, Kansas, USA
| | - Rabina Saud
- University of Kansas Medical Center, Department of Microbiology, Molecular Genetics, and Immunology, Kansas City, Kansas, USA
| | - Wyatt Henke
- University of Kansas Medical Center, Department of Microbiology, Molecular Genetics, and Immunology, Kansas City, Kansas, USA
| | - Edward B. Stephens
- University of Kansas Medical Center, Department of Microbiology, Molecular Genetics, and Immunology, Kansas City, Kansas, USA
| | - Maria Kalamvoki
- University of Kansas Medical Center, Department of Microbiology, Molecular Genetics, and Immunology, Kansas City, Kansas, USA
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10
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In Silico Screening of Drugs That Target Different Forms of E Protein for Potential Treatment of COVID-19. Pharmaceuticals (Basel) 2023. [DOI: 10.3390/ph16020296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Recently the E protein of SARS-CoV-2 has become a very important target in the potential treatment of COVID-19 since it is known to regulate different stages of the viral cycle. There is biochemical evidence that E protein exists in two forms, as monomer and homopentamer. An in silico screening analysis was carried out employing 5852 ligands (from Zinc databases), and performing an ADMET analysis, remaining a set of 2155 compounds. Furthermore, docking analysis was performed on specific sites and different forms of the E protein. From this study we could identify that the following ligands showed the highest binding affinity: nilotinib, dutasteride, irinotecan, saquinavir and alectinib. We carried out some molecular dynamics simulations and free energy MM–PBSA calculations of the protein–ligand complexes (with the mentioned ligands). Of worthy interest is that saquinavir, nilotinib and alectinib are also considered as a promising multitarget ligand because it seems to inhibit three targets, which play an important role in the viral cycle. On the other side, saquinavir was shown to be able to bind to E protein both in its monomeric as well as pentameric forms. Finally, further experimental assays are needed to probe our hypothesis derived from in silico studies.
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11
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Rizwan T, Kothidar A, Meghwani H, Sharma V, Shobhawat R, Saini R, Vaishnav HK, Singh V, Pratap M, Sihag H, Kumar S, Dey JK, Dey SK. Comparative analysis of SARS-CoV-2 envelope viroporin mutations from COVID-19 deceased and surviving patients revealed implications on its ion-channel activities and correlation with patient mortality. J Biomol Struct Dyn 2022; 40:10454-10469. [PMID: 34229570 DOI: 10.1080/07391102.2021.1944319] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
One major obstacle in designing a successful therapeutic regimen to combat COVID-19 pandemic is the frequent occurrence of mutations in the SARS-CoV-2 resulting in patient to patient variations. Out of the four structural proteins of SARS-CoV-2 namely, spike, envelope, nucleocapsid and membrane, envelope protein governs the virus pathogenicity and induction of acute-respiratory-distress-syndrome which is the major cause of death in COVID-19 patients. These effects are facilitated by the viroporin (ion-channel) like activities of the envelope protein. Our current work reports metagenomic analysis of envelope protein at the amino acid sequence level through mining all the available SARS-CoV-2 genomes from the GISAID and coronapp servers. We found majority of mutations in envelope protein were localized at or near PDZ binding motif. Our analysis also demonstrates that the acquired mutations might have important implications on its structure and ion-channel activity. A statistical correlation between specific mutations (e.g. F4F, R69I, P71L, L73F) with patient mortalities were also observed, based on the patient data available for 18,691 SARS-CoV-2-genomes in the GISAID database till 30 April 2021. Albeit, whether these mutations exist as the cause or the effect of co-infections and/or co-morbid disorders within COVID-19 patients is still unclear. Moreover, most of the current vaccine and therapeutic interventions are revolving around spike protein. However, emphasizing on envelope protein's (1) conserved epitopes, (2) pathogenicity attenuating mutations, and (3) mutations present in the deceased patients, as reported in our present study, new directions to the ongoing efforts of therapeutic developments against COVID-19 can be achieved by targeting envelope viroporin.
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Affiliation(s)
- Tayyeba Rizwan
- Department of Biochemistry, University of Delhi South Campus, New Delhi, Delhi, India
| | - Akansha Kothidar
- Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Himanshu Meghwani
- Aab Cardiovascular Research Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - Vaibhav Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, Delhi, India
| | - Rahul Shobhawat
- Department of Bioscience and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, Maharashtra, India
| | - Rajpal Saini
- Department of Statistics, Faculty of Mathematical Sciences, University of Delhi, New Delhi, Delhi, India
| | - Hemendra Kumar Vaishnav
- Operations Management, Quantitative Methods and Information Systems Area, Indian Institute of Management Udaipur, Udaipur, Rajasthan, India
| | - Vikramaditya Singh
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, Delhi, India
| | - Mukut Pratap
- Department of Biochemistry, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Hitaishi Sihag
- Department of Biochemistry, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Shakti Kumar
- Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Joy Kumar Dey
- Central Council for Research in Homoeopathy, Ministry of AYUSH, Govt. of India, New Delhi, Delhi, India
| | - Sanjay Kumar Dey
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, New Delhi, Delhi, India
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12
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Chromosome-scale haplotype-resolved pangenomics. Trends Genet 2022; 38:1103-1107. [PMID: 35817620 DOI: 10.1016/j.tig.2022.06.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/14/2022] [Accepted: 06/16/2022] [Indexed: 01/24/2023]
Abstract
Complete pangenomics is crucial for understanding genetic diversity and evolution across the tree of life. Chromosome-scale, haplotype-resolved pangenomics allows complex structural variations, long-range interactions, and associated functions to be discerned in species populations. We explore the need for high-resolution pangenomes, discuss computational strategies for their development, and describe applications in biodiversity and human health.
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13
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Yang R, Wu S, Wang S, Rubino G, Nickels JD, Cheng X. Refinement of SARS-CoV-2 envelope protein structure in a native-like environment by molecular dynamics simulations. Front Mol Biosci 2022; 9:1027223. [PMID: 36299297 PMCID: PMC9589232 DOI: 10.3389/fmolb.2022.1027223] [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: 08/24/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
COVID-19 has become an unprecedented threat to human health. The SARS-CoV-2 envelope (E) protein plays a critical role in the viral maturation process and pathogenesis. Despite intensive investigation, its structure in physiological conditions remains mysterious: no high-resolution full-length structure is available and only an NMR structure of the transmembrane (TM) region has been determined. Here, we present a refined E protein structure, using molecular dynamics (MD) simulations to investigate its structure and dynamics in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer system. Our initial homology model based upon the SARS-CoV E protein structure is shown to be unstable in the lipid bilayer, and the H3 helices tend to move away from the membrane center to the membrane-water interface. A more stable model was developed by replacing all H3 helices with the fully equilibrated H3 structure sampled in the MD simulations. This refined model exhibited more favorable contacts with lipids and water than the original homology model and induced local membrane curvature, decreasing local lipid order. Interestingly, the pore radius profiles showed that the channel in both homology and refined models remained in a closed state throughout the simulations. We also demonstrated the utility of this structure to develop anti-SARS-CoV-2 drugs by docking a library of FDA-approved, investigational, and experimental drugs to the refined E protein structure, identifying 20 potential channel blockers. This highlights the power of MD simulations to refine low-resolution structures of membrane proteins in a native-like membrane environment, shedding light on the structural features of the E protein and providing a platform for the development of novel antiviral treatments.
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Affiliation(s)
- Rui Yang
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Sijin Wu
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, United States
- *Correspondence: Sijin Wu, ; Jonathan D. Nickels, ; Xiaolin Cheng,
| | - Shen Wang
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Grace Rubino
- Department of Chemical and Biomolecular Engineering, College of Engineering, The Ohio State University, Columbus, OH, United States
| | - Jonathan D. Nickels
- Department of Chemical and Environmental Engineering, The University of Cincinnati, Cincinnati, OH, United States
- *Correspondence: Sijin Wu, ; Jonathan D. Nickels, ; Xiaolin Cheng,
| | - Xiaolin Cheng
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, United States
- Translational Data Analytics Institute (TDAI), The Ohio State University, Columbus, OH, United States
- *Correspondence: Sijin Wu, ; Jonathan D. Nickels, ; Xiaolin Cheng,
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14
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Schoeman D, Cloete R, Fielding BC. The Flexible, Extended Coil of the PDZ-Binding Motif of the Three Deadly Human Coronavirus E Proteins Plays a Role in Pathogenicity. Viruses 2022; 14:v14081707. [PMID: 36016329 PMCID: PMC9416557 DOI: 10.3390/v14081707] [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: 06/13/2022] [Revised: 07/22/2022] [Accepted: 07/29/2022] [Indexed: 02/04/2023] Open
Abstract
The less virulent human (h) coronaviruses (CoVs) 229E, NL63, OC43, and HKU1 cause mild, self-limiting respiratory tract infections, while the more virulent SARS-CoV-1, MERS-CoV, and SARS-CoV-2 have caused severe outbreaks. The CoV envelope (E) protein, an important contributor to the pathogenesis of severe hCoV infections, may provide insight into this disparate severity of the disease. We, therefore, generated full-length E protein models for SARS-CoV-1 and -2, MERS-CoV, HCoV-229E, and HCoV-NL63 and docked C-terminal peptides of each model to the PDZ domain of the human PALS1 protein. The PDZ-binding motif (PBM) of the SARS-CoV-1 and -2 and MERS-CoV models adopted a more flexible, extended coil, while the HCoV-229E and HCoV-NL63 models adopted a less flexible alpha helix. All the E peptides docked to PALS1 occupied the same binding site and the more virulent hCoV E peptides generally interacted more stably with PALS1 than the less virulent ones. We hypothesize that the increased flexibility of the PBM in the more virulent hCoVs facilitates more stable binding to various host proteins, thereby contributing to more severe disease. This is the first paper to model full-length 3D structures for both the more virulent and less virulent hCoV E proteins, providing novel insights for possible drug and/or vaccine development.
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Affiliation(s)
- Dewald Schoeman
- Molecular Biology and Virology Research Laboratory, Department of Medical Biosciences, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa;
| | - Ruben Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa;
| | - Burtram C. Fielding
- Molecular Biology and Virology Research Laboratory, Department of Medical Biosciences, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa;
- Correspondence:
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15
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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16
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Ahmadi K, Zahedifard F, Mafakher L, Einakian MA, Ghaedi T, Kavousipour S, Faezi S, Karmostaji A, Sharifi-Sarasiabi K, Gouklani H, Hassaniazad M. Active site-based analysis of structural proteins for drug targets in different human Coronaviruses. Chem Biol Drug Des 2021; 99:585-602. [PMID: 34914204 DOI: 10.1111/cbdd.14004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/03/2021] [Accepted: 12/09/2021] [Indexed: 11/30/2022]
Abstract
Seven types of Coronaviruses (CoVs) have been identified that can cause infection in humans, including HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1, SARS-CoV, HCoV-MERS, and SARS-CoV-2. In this study, we investigated the genetic structure, the homology of the structural protein sequences, as well as the investigation of the active site of structural proteins. The active site of structural proteins was determined based on the previous studies, and the homology of their amino acid sequences and structure was compared. Multiple sequence alignment of Spike protein of HCoVs showed that the receptor-binding domain of SARS-CoV-2, SARS-CoV, and MERS-CoV was located at a similar site to the S1 subunit. The binding motif of PDZ (postsynaptic density- 95/discs large/zona occludens-1) of the envelope protein, was conserved in SARS-CoV and SARS-CoV-2 according to multiple sequence alignment but showed different changes in the other HCoVs. Overall, Spike protein showed the most variation in its active sites, but the other structural proteins were highly conserved. In this study, for the first time, the active site of all structural proteins of HCoVs as a drug target was investigated. The binding site of these proteins can be suitable targets for drugs or vaccines among HCoVs.
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Affiliation(s)
- Khadijeh Ahmadi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Farnaz Zahedifard
- Drug discovery and Evaluation unit, Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ladan Mafakher
- Thalassemia & Hemoglobinopathy Research center, Health research institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Ali Einakian
- Food Health Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Tayebeh Ghaedi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Soudabeh Kavousipour
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Sobhan Faezi
- Department of Microbiology, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Afsaneh Karmostaji
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Khojasteh Sharifi-Sarasiabi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Hamed Gouklani
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mehdi Hassaniazad
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
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17
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Emrani J, Ahmed M, Jeffers-Francis L, Teleha JC, Mowa N, Newman RH, Thomas MD. SARS-COV-2, infection, transmission, transcription, translation, proteins, and treatment: A review. Int J Biol Macromol 2021; 193:1249-1273. [PMID: 34756970 PMCID: PMC8552795 DOI: 10.1016/j.ijbiomac.2021.10.172] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/21/2021] [Indexed: 01/18/2023]
Abstract
In this review, we describe the key molecular entities involved in the process of infection by SARS-CoV-2, while also detailing how those key entities influence the spread of the disease. We further introduce the molecular mechanisms of preventive and treatment strategies including drugs, antibodies, and vaccines.
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Affiliation(s)
- Jahangir Emrani
- Department of Chemistry, North Carolina A&T State University, Greensboro, NC 27411, United States of America.
| | - Maryam Ahmed
- Department of Biology, Appalachian State University, Boone, NC 28608, United States of America
| | - Liesl Jeffers-Francis
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, United States of America
| | - John C Teleha
- Department of Reference and Instruction, North Carolina A&T State University, Greensboro, NC 27411, United States of America
| | - Nathan Mowa
- Department of Biology, Appalachian State University, Boone, NC 28608, United States of America
| | - Robert H Newman
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, United States of America
| | - Misty D Thomas
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, United States of America
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18
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Pinheiros LBP, Aversi-Ferreira TA. Blood-brain barrier and the virus diseases. Dement Neuropsychol 2021; 15:419-420. [PMID: 34630932 PMCID: PMC8485643 DOI: 10.1590/1980-57642021dn15-030016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/11/2021] [Indexed: 11/25/2022] Open
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19
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Hutchison JM, Capone R, Luu DD, Shah KH, Hadziselimovic A, Van Horn WD, Sanders CR. Recombinant SARS-CoV-2 envelope protein traffics to the trans-Golgi network following amphipol-mediated delivery into human cells. J Biol Chem 2021; 297:100940. [PMID: 34237302 PMCID: PMC8256659 DOI: 10.1016/j.jbc.2021.100940] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/29/2021] [Accepted: 07/02/2021] [Indexed: 11/16/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 envelope protein (S2-E) is a conserved membrane protein that is important for coronavirus (CoV) assembly and budding. Here, we describe the recombinant expression and purification of S2-E in amphipol-class amphipathic polymer solutions, which solubilize and stabilize membrane proteins, but do not disrupt membranes. We found that amphipol delivery of S2-E to preformed planar bilayers results in spontaneous membrane integration and formation of viroporin cation channels. Amphipol delivery of the S2-E protein to human cells results in plasma membrane integration, followed by retrograde trafficking to the trans-Golgi network and accumulation in swollen perinuclear lysosomal-associated membrane protein 1-positive vesicles, likely lysosomes. CoV envelope proteins have previously been proposed to manipulate the luminal pH of the trans-Golgi network, which serves as an accumulation station for progeny CoV particles prior to cellular egress via lysosomes. Delivery of S2-E to cells will enable chemical biological approaches for future studies of severe acute respiratory syndrome coronavirus 2 pathogenesis and possibly even development of "Trojan horse" antiviral therapies. Finally, this work also establishes a paradigm for amphipol-mediated delivery of membrane proteins to cells.
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Affiliation(s)
- James M Hutchison
- Chemical and Physical Biology Graduate Program, Vanderbilt University, Nashville, Tennessee, USA; Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Ricardo Capone
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Dustin D Luu
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA; The Biodesign Institute Centers for Personalized Diagnostics and Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA
| | - Karan H Shah
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA; The Biodesign Institute Centers for Personalized Diagnostics and Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA
| | - Arina Hadziselimovic
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Wade D Van Horn
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA; The Biodesign Institute Centers for Personalized Diagnostics and Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA.
| | - Charles R Sanders
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA.
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20
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Kulmanov M, Zhapa-Camacho F, Hoehndorf R. DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web. Nucleic Acids Res 2021; 49:W140-W146. [PMID: 34019664 PMCID: PMC8262746 DOI: 10.1093/nar/gkab373] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/18/2021] [Accepted: 04/26/2021] [Indexed: 11/24/2022] Open
Abstract
Understanding the functions of proteins is crucial to understand biological processes on a molecular level. Many more protein sequences are available than can be investigated experimentally. DeepGOPlus is a protein function prediction method based on deep learning and sequence similarity. DeepGOWeb makes the prediction model available through a website, an API, and through the SPARQL query language for interoperability with databases that rely on Semantic Web technologies. DeepGOWeb provides accurate and fast predictions and ensures that predicted functions are consistent with the Gene Ontology; it can provide predictions for any protein and any function in Gene Ontology. DeepGOWeb is freely available at https://deepgo.cbrc.kaust.edu.sa/.
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Affiliation(s)
- Maxat Kulmanov
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences & Engineering Division, King Abdullah University of Science and Technology, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Fernando Zhapa-Camacho
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences & Engineering Division, King Abdullah University of Science and Technology, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Robert Hoehndorf
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences & Engineering Division, King Abdullah University of Science and Technology, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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21
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Duart G, García-Murria MJ, Mingarro I. The SARS-CoV-2 envelope (E) protein has evolved towards membrane topology robustness. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2021; 1863:183608. [PMID: 33771486 PMCID: PMC7987508 DOI: 10.1016/j.bbamem.2021.183608] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 12/15/2022]
Abstract
Single-spanning SARS-CoV-2 envelope (E) protein topology is a major determinant of protein quaternary structure and function. Charged residues distribution in E protein sequences from highly pathogenic human coronaviruses (i.e., SARS-CoV, MERS-CoV and SARS-CoV-2) stabilize Ntout-Ctin membrane topology. E protein sequence could have evolved to ensure a more robust membrane topology from MERS-CoV to SARS-CoV and SARS-CoV-2.
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Affiliation(s)
- Gerard Duart
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Maria J García-Murria
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Ismael Mingarro
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain.
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22
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Anand U, Jakhmola S, Indari O, Jha HC, Chen ZS, Tripathi V, Pérez de la Lastra JM. Potential Therapeutic Targets and Vaccine Development for SARS-CoV-2/COVID-19 Pandemic Management: A Review on the Recent Update. Front Immunol 2021; 12:658519. [PMID: 34276652 PMCID: PMC8278575 DOI: 10.3389/fimmu.2021.658519] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/07/2021] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a highly pathogenic novel virus that has caused a massive pandemic called coronavirus disease 2019 (COVID-19) worldwide. Wuhan, a city in China became the epicenter of the outbreak of COVID-19 in December 2019. The disease was declared a pandemic globally by the World Health Organization (WHO) on 11 March 2020. SARS-CoV-2 is a beta CoV of the Coronaviridae family which usually causes respiratory symptoms that resemble common cold. Multiple countries have experienced multiple waves of the disease and scientific experts are consistently working to find answers to several unresolved questions, with the aim to find the most suitable ways to contain the virus. Furthermore, potential therapeutic strategies and vaccine development for COVID-19 management are also considered. Currently, substantial efforts have been made to develop successful and safe treatments and SARS-CoV-2 vaccines. Some vaccines, such as inactivated vaccines, nucleic acid-based, and vector-based vaccines, have entered phase 3 clinical trials. Additionally, diverse small molecule drugs, peptides and antibodies are being developed to treat COVID-19. We present here an overview of the virus interaction with the host and environment and anti-CoV therapeutic strategies; including vaccines and other methodologies, designed for prophylaxis and treatment of SARS-CoV-2 infection with the hope that this integrative analysis could help develop novel therapeutic approaches against COVID-19.
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Affiliation(s)
- Uttpal Anand
- Department of Life Sciences, National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Shweta Jakhmola
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Omkar Indari
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Hem Chandra Jha
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, NY, United States
| | - Vijay Tripathi
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India
| | - José M. Pérez de la Lastra
- Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones científicas (CSIS), Santa Cruz de Tenerife, Spain
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23
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A computational analysis of molecular evolution for virulence genes of zoonotic novel coronavirus (COVID-19). Comput Biol Chem 2021; 93:107532. [PMID: 34171504 PMCID: PMC8213524 DOI: 10.1016/j.compbiolchem.2021.107532] [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: 06/05/2020] [Revised: 06/04/2021] [Accepted: 06/16/2021] [Indexed: 11/21/2022]
Abstract
Zoonotic Novel coronavirus disease 2019 (COVID-19) is highly pathogenic and transmissible considered as emerging pandemic disease. The virus belongs from a large virus Coronaviridae family affect respiratory tract of animal and human likely originated from bat and homology to SARA-CoV and MERS-CoV. The virus consists of single-stranded positive genomic RNA coated by nucleocapsid protein. The rate of mutation in any virulence gene may influence the phenomenon of host radiation. We have studied the molecular evolution of selected virulence genes (HA, N, RdRP and S) of novel COVID-19. We used a site-specific comparison of synonymous (silent) and non-synonymous (amino acid altering) nucleotide substitutions. Maximum Likelihood genealogies based on differential gamma distribution rates were used for the analysis of null and alternate hypothesis. The null hypothesis was found more suitable for the analysis using Likelihood Ratio Test (LRT) method, confirming higher rate of substitution. The analysis revealed that RdRP gene had the fastest rate evolution followed by HA gene. We have also reported the new motifs for different virulence genes, which are further useful to design new detection and diagnosis kit for COVID -19.
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24
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Cao H, Xu H, Ning C, Xiang L, Ren Q, Zhang T, Zhang Y, Gao R. Multi-Omics Approach Reveals the Potential Core Vaccine Targets for the Emerging Foodborne Pathogen Campylobacter jejuni. Front Microbiol 2021; 12:665858. [PMID: 34248875 PMCID: PMC8265506 DOI: 10.3389/fmicb.2021.665858] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/06/2021] [Indexed: 11/30/2022] Open
Abstract
Campylobacter jejuni is a leading cause of bacterial gastroenteritis in humans around the world. The emergence of bacterial resistance is becoming more serious; therefore, development of new vaccines is considered to be an alternative strategy against drug-resistant pathogen. In this study, we investigated the pangenome of 173 C. jejuni strains and analyzed the phylogenesis and the virulence factor genes. In order to acquire a high-quality pangenome, genomic relatedness was firstly performed with average nucleotide identity (ANI) analyses, and an open pangenome of 8,041 gene families was obtained with the correct taxonomy genomes. Subsequently, the virulence property of the core genome was analyzed and 145 core virulence factor (VF) genes were obtained. Upon functional genomics and immunological analyses, five core VF proteins with high antigenicity were selected as potential core vaccine targets for humans. Furthermore, functional annotations indicated that these proteins are involved in important molecular functions and biological processes, such as adhesion, regulation, and secretion. In addition, transcriptome analysis in human cells and pig intestinal loop proved that these vaccine target genes are important in the virulence of C. jejuni in different hosts. Comprehensive pangenome and relevant animal experiments will facilitate discovering the potential core vaccine targets with improved efficiency in reverse vaccinology. Likewise, this study provided some insights into the genetic polymorphism and phylogeny of C. jejuni and discovered potential vaccine candidates for humans. Prospective development of new vaccines using the targets will be an alternative to the use of antibiotics and prevent the development of multidrug-resistant C. jejuni in humans and even other animals.
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Affiliation(s)
- Hengchun Cao
- School of Mathematics and Statistics, Shandong University, Weihai, China
| | - Hanxiao Xu
- School of Mathematics and Statistics, Shandong University, Weihai, China
| | - Chunhui Ning
- School of Mathematics and Statistics, Shandong University, Weihai, China
| | - Li Xiang
- School of Mathematics and Statistics, Shandong University, Weihai, China
| | - Qiufang Ren
- School of Mathematics and Statistics, Shandong University, Weihai, China
| | - Tiantian Zhang
- School of Mathematics and Statistics, Shandong University, Weihai, China
| | - Yusen Zhang
- School of Mathematics and Statistics, Shandong University, Weihai, China
| | - Rui Gao
- School of Control Science and Engineering, Shandong University, Jinan, China
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Shepley-McTaggart A, Sagum CA, Oliva I, Rybakovsky E, DiGuilio K, Liang J, Bedford MT, Cassel J, Sudol M, Mullin JM, Harty RN. SARS-CoV-2 Envelope (E) protein interacts with PDZ-domain-2 of host tight junction protein ZO1. PLoS One 2021; 16:e0251955. [PMID: 34106957 PMCID: PMC8189464 DOI: 10.1371/journal.pone.0251955] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/06/2021] [Indexed: 12/31/2022] Open
Abstract
Newly emerged SARS-CoV-2 is the cause of an ongoing global pandemic leading to severe respiratory disease in humans. SARS-CoV-2 targets epithelial cells in the respiratory tract and lungs, which can lead to amplified chloride secretion and increased leak across epithelial barriers, contributing to severe pneumonia and consolidation of the lungs as seen in many COVID-19 patients. There is an urgent need for a better understanding of the molecular aspects that contribute to SARS-CoV-2-induced pathogenesis and for the development of approaches to mitigate these damaging pathologies. The multifunctional SARS-CoV-2 Envelope (E) protein contributes to virus assembly/egress, and as a membrane protein, also possesses viroporin channel properties that may contribute to epithelial barrier damage, pathogenesis, and disease severity. The extreme C-terminal (ECT) sequence of E also contains a putative PDZ-domain binding motif (PBM), similar to that identified in the E protein of SARS-CoV-1. Here, we screened an array of GST-PDZ domain fusion proteins using either a biotin-labeled WT or mutant ECT peptide from the SARS-CoV-2 E protein. Notably, we identified a singular specific interaction between the WT E peptide and the second PDZ domain of human Zona Occludens-1 (ZO1), one of the key regulators of TJ formation/integrity in all epithelial tissues. We used homogenous time resolve fluorescence (HTRF) as a second complementary approach to further validate this novel modular E-ZO1 interaction. We postulate that SARS-CoV-2 E interacts with ZO1 in infected epithelial cells, and this interaction may contribute, in part, to tight junction damage and epithelial barrier compromise in these cell layers leading to enhanced virus spread and severe dysfunction that leads to morbidity. Prophylactic/therapeutic intervention targeting this virus-host interaction may effectively reduce airway and/or gastrointestinal barrier damage and mitigate virus spread.
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Affiliation(s)
- Ariel Shepley-McTaggart
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Cari A. Sagum
- Department of Epigenetics & Molecular Carcinogenesis, M.D. Anderson Cancer Center, University of Texas, Smithville, Texas, United States of America
| | - Isabela Oliva
- The Wistar Cancer Center for Molecular Screening, The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - Elizabeth Rybakovsky
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania, United States of America
| | - Katie DiGuilio
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania, United States of America
| | - Jingjing Liang
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Mark T. Bedford
- Department of Epigenetics & Molecular Carcinogenesis, M.D. Anderson Cancer Center, University of Texas, Smithville, Texas, United States of America
| | - Joel Cassel
- The Wistar Cancer Center for Molecular Screening, The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - Marius Sudol
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - James M. Mullin
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania, United States of America
| | - Ronald N. Harty
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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26
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Cao Y, Yang R, Lee I, Zhang W, Sun J, Wang W, Meng X. Characterization of the SARS-CoV-2 E Protein: Sequence, Structure, Viroporin, and Inhibitors. Protein Sci 2021; 30:1114-1130. [PMID: 33813796 PMCID: PMC8138525 DOI: 10.1002/pro.4075] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 12/19/2022]
Abstract
The COVID-19 epidemic is one of the most influential epidemics in history. Understanding the impact of coronaviruses (CoVs) on host cells is very important for disease treatment. The SARS-CoV-2 envelope (E) protein is a small structural protein involved in many aspects of the viral life cycle. The E protein promotes the packaging and reproduction of the virus, and deletion of this protein weakens or even abolishes the virulence. This review aims to establish new knowledge by combining recent advances in the study of the SARS-CoV-2 E protein and by comparing it with the SARS-CoV E protein. The E protein amino acid sequence, structure, self-assembly characteristics, viroporin mechanisms and inhibitors are summarized and analyzed herein. Although the mechanisms of the SARS-CoV-2 and SARS-CoV E proteins are similar in many respects, specific studies on the SARS-CoV-2 E protein, for both monomers and oligomers, are still lacking. A comprehensive understanding of this protein should prompt further studies on the design and characterization of effective targeted therapeutic measures.
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Affiliation(s)
- Yipeng Cao
- Tianjin Medical University Cancer Institute and HospitalKey Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinPeople's Republic of China
- National Supercomputer Center in TianjinTEDA‐Tianjin Economic‐Technological Development AreaTianjinPeople's Republic of China
| | - Rui Yang
- Department of Infection and ImmunityTianjin Union Medical Center, Nankai University Affiliated HospitalTianjinPeople's Republic of China
| | - Imshik Lee
- College of PhysicsNankai UniversityTianjinPeople's Republic of China
| | - Wenwen Zhang
- Tianjin Medical University Cancer Institute and HospitalKey Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinPeople's Republic of China
| | - Jiana Sun
- Tianjin Medical University Cancer Institute and HospitalKey Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinPeople's Republic of China
| | - Wei Wang
- Tianjin Medical University Cancer Institute and HospitalKey Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinPeople's Republic of China
| | - Xiangfei Meng
- National Supercomputer Center in TianjinTEDA‐Tianjin Economic‐Technological Development AreaTianjinPeople's Republic of China
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27
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Jelinek HF, Mousa M, Alefishat E, Osman W, Spence I, Bu D, Feng SF, Byrd J, Magni PA, Sahibzada S, Tay GK, Alsafar HS. Evolution, Ecology, and Zoonotic Transmission of Betacoronaviruses: A Review. Front Vet Sci 2021; 8:644414. [PMID: 34095271 PMCID: PMC8173069 DOI: 10.3389/fvets.2021.644414] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/25/2021] [Indexed: 12/18/2022] Open
Abstract
Coronavirus infections have been a part of the animal kingdom for millennia. The difference emerging in the twenty-first century is that a greater number of novel coronaviruses are being discovered primarily due to more advanced technology and that a greater number can be transmitted to humans, either directly or via an intermediate host. This has a range of effects from annual infections that are mild to full-blown pandemics. This review compares the zoonotic potential and relationship between MERS, SARS-CoV, and SARS-CoV-2. The role of bats as possible host species and possible intermediate hosts including pangolins, civets, mink, birds, and other mammals are discussed with reference to mutations of the viral genome affecting zoonosis. Ecological, social, cultural, and environmental factors that may play a role in zoonotic transmission are considered with reference to SARS-CoV, MERS, and SARS-CoV-2 and possible future zoonotic events.
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Affiliation(s)
- Herbert F. Jelinek
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Center of Heath Engineering Innovation, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Mira Mousa
- Nuffield Department of Women's and Reproduction Health, Oxford University, Oxford, United Kingdom
| | - Eman Alefishat
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Pharmacology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biopharmaceutics and Clinical Pharmacy, School of Pharmacy, The University of Jordan, Amman, Jordan
| | - Wael Osman
- Department of Chemistry, College of Arts and Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Ian Spence
- Discipline of Pharmacology, University of Sydney, Sydney, NSW, Australia
| | - Dengpan Bu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Samuel F. Feng
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Mathematics, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Jason Byrd
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Paola A. Magni
- Discipline of Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, WA, Australia
- Murdoch University Singapore, King's Centre, Singapore, Singapore
| | - Shafi Sahibzada
- Antimicrobial Resistance and Infectious Diseases Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Guan K. Tay
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Division of Psychiatry, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, WA, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Habiba S. Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Genetics and Molecular Biology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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28
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Hu CAA, Murphy I, Klimaj S, Reece J, Chand HS. SARS-CoV-2, Inflammatory Apoptosis, and Cytokine Storm Syndrome. ACTA ACUST UNITED AC 2021. [DOI: 10.2174/2666958702101010022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2), a novel and currently intensively studied beta coronavirus, is the causing agent of COVID-19 (Coronavirus Disease 2019), a highly contagious and devastating disease that has killed more than 2 million human beings since December 2019. Building on what has already been understood from studying SARS-CoV, a closely related single-strand RNA virus that set off SARS in 2002 and 2003, researchers began to learn how SARS-CoV-2 operates its vicious effects on the host cells. In essence, COVID-19 patients display hyperinflammatory and dysregulated cell death phenotypes that give a spectrum of symptoms ranging from mild to moderate upper-respiratory tract illnesses. However, SARS-CoV-2 can elicit serious pathologies, such as acute respiratory distress syndrome, sepsis-like multi-organ failure and even death, depending on the individual and their pre-existing condition(s). As viruses cannot reproduce independently, they hijack the machinery within the host cells and enslave them for the purpose of propagation. SARS-CoV-2 RNA genome harbors the genes that produce the protein products for manipulating host cell, viral replication, and repeating the vicious viral cycle. For counteracting the viral invasion, human cells have developed layers of defense mechanisms, such as restriction factors, Regulated Cell Death (RCD) pathways, interferon production, inflammatory response, and innate and adaptive immunity that are used to recognize and thwart viral infection. Unfortunately, some coronavirus encoded proteins are capable of attacking the host anti-viral system to achieve parasitic advantages. We reviewed the proteins of SARS-CoV and SARS-CoV-2 that possess manipulating effects on the host cell and cause tissue damage, immune cascade, cytokine production and release. We also discuss the means to restore the homeostatic balance between inflammatory response and RCD pathways and the potential targeted interventions that can be used to treat and/or prevent COVID-19.
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29
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Hassan SS, Aljabali AAA, Panda PK, Ghosh S, Attrish D, Choudhury PP, Seyran M, Pizzol D, Adadi P, Abd El-Aziz TM, Soares A, Kandimalla R, Lundstrom K, Lal A, Azad GK, Uversky VN, Sherchan SP, Baetas-da-Cruz W, Uhal BD, Rezaei N, Chauhan G, Barh D, Redwan EM, Dayhoff GW, Bazan NG, Serrano-Aroca Á, El-Demerdash A, Mishra YK, Palu G, Takayama K, Brufsky AM, Tambuwala MM. A unique view of SARS-CoV-2 through the lens of ORF8 protein. Comput Biol Med 2021; 133:104380. [PMID: 33872970 PMCID: PMC8049180 DOI: 10.1016/j.compbiomed.2021.104380] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 01/07/2023]
Abstract
Immune evasion is one of the unique characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) attributed to its ORF8 protein. This protein modulates the adaptive host immunity through down-regulation of MHC-1 (Major Histocompatibility Complex) molecules and innate immune responses by surpassing the host's interferon-mediated antiviral response. To understand the host's immune perspective in reference to the ORF8 protein, a comprehensive study of the ORF8 protein and mutations possessed by it have been performed. Chemical and structural properties of ORF8 proteins from different hosts, such as human, bat, and pangolin, suggest that the ORF8 of SARS-CoV-2 is much closer to ORF8 of Bat RaTG13-CoV than to that of Pangolin-CoV. Eighty-seven mutations across unique variants of ORF8 in SARS-CoV-2 can be grouped into four classes based on their predicted effects (Hussain et al., 2021) [1]. Based on the geo-locations and timescale of sample collection, a possible flow of mutations was built. Furthermore, conclusive flows of amalgamation of mutations were found upon sequence similarity analyses and consideration of the amino acid conservation phylogenies. Therefore, this study seeks to highlight the uniqueness of the rapidly evolving SARS-CoV-2 through the ORF8.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, 721140, India
| | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University-Faculty of Pharmacy, Irbid, 566, Jordan
| | - Pritam Kumar Panda
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20, Uppsala, Sweden
| | - Shinjini Ghosh
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, 700009, West Bengal, India
| | - Diksha Attrish
- Dr. B. R. Ambedkar Centre for Biomedical Research (ACBR), University of Delhi (North Campus), Delhi, 110007, India
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, Kolkata, 700108, West Bengal, India
| | - Murat Seyran
- Doctoral Studies in Natural and Technical Sciences (SPL 44), University of Vienna, Austria
| | - Damiano Pizzol
- Italian Agency for Development Cooperation - Khartoum, Sudan Street 33, Al Amarat, Sudan
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin, 9054, New Zealand
| | - Tarek Mohamed Abd El-Aziz
- Zoology Department, Faculty of Science, Minia University, El-Minia, 61519, Egypt; Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229-3900, USA
| | - Antonio Soares
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229-3900, USA
| | - Ramesh Kandimalla
- CSIR-Indian Institute of Chemical Technology Uppal Road, Tarnaka, Hyderabad, 500007, Telangana State, India
| | | | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA, 70112, USA
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Bruce D Uhal
- Department of Physiology, Michigan State University, East Lansing, MI, 48824, USA
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran and Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Stockholm, Sweden
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501, Sur, 64849, Monterrey, NL, Mexico Tecnológico De Monterrey, Campus Monterrey, Monterrey, Nuevo León, Mexico
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), PatnaPatna, India
| | - Elrashdy M Redwan
- King Abdulazizi University, Faculty of Science, Department of Biological Science, Saudi Arabia
| | - Guy W Dayhoff
- Department of Chemistry, College of Art and Sciences, University of South Florida, Tampa, FL, 33620, USA
| | - Nicolas G Bazan
- Neuroscience Center of Excellence, School of Medicine, Louisiana State University Health New Orleans, New Orleans, LA, 70112, USA
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Translational Research Centre San Alberto Magno, Catholic University of Valencia San Vicente Mártir, C/Guillem de Castro 94, 46001, Valencia, Spain
| | - Amr El-Demerdash
- Natural Products and Medicinal Chemistry Department, Institute de Chimie des Substances Naturelles, Gif-sur-Yvette, France
| | - Yogendra K Mishra
- University of Southern Denmark, Mads Clausen Institute, NanoSYD, Alsion 2, 6400 Sønderborg, Denmark
| | - Giorgio Palu
- Department of Molecular Medicine, University of Padova, Italy
| | - Kazuo Takayama
- Center for IPS Cell Research and Application, Kyoto University, Kyoto, 606-8397, Japan
| | - Adam M Brufsky
- University of Pittsburgh School of Medicine, Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Murtaza M Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK.
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30
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UMAP-assisted K-means clustering of large-scale SARS-CoV-2 mutation datasets. Comput Biol Med 2021; 131:104264. [PMID: 33647832 PMCID: PMC7897976 DOI: 10.1016/j.compbiomed.2021.104264] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/05/2021] [Accepted: 02/06/2021] [Indexed: 12/16/2022]
Abstract
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a worldwide devastating effect. Understanding the evolution and transmission of SARS-CoV-2 is of paramount importance for controlling, combating and preventing COVID-19. Due to the rapid growth in both the number of SARS-CoV-2 genome sequences and the number of unique mutations, the phylogenetic analysis of SARS-CoV-2 genome isolates faces an emergent large-data challenge. We introduce a dimension-reduced K-means clustering strategy to tackle this challenge. We examine the performance and effectiveness of three dimension-reduction algorithms: principal component analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE), and uniform manifold approximation and projection (UMAP). By using four benchmark datasets, we found that UMAP is the best-suited technique due to its stable, reliable, and efficient performance, its ability to improve clustering accuracy, especially for large Jaccard distanced-based datasets, and its superior clustering visualization. The UMAP-assisted K-means clustering enables us to shed light on increasingly large datasets from SARS-CoV-2 genome isolates.
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31
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Barrantes FJ. Structural biology of coronavirus ion channels. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:391-402. [PMID: 33825700 DOI: 10.1107/s2059798321001431] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/08/2021] [Indexed: 01/08/2023]
Abstract
Viral infection compromises specific organelles of the cell and readdresses its functional resources to satisfy the needs of the invading body. Around 70% of the coronavirus positive-sense single-stranded RNA encodes proteins involved in replication, and these viruses essentially take over the biosynthetic and transport mechanisms to ensure the efficient replication of their genome and trafficking of their virions. Some coronaviruses encode genes for ion-channel proteins - the envelope protein E (orf4a), orf3a and orf8 - which they successfully employ to take control of the endoplasmic reticulum-Golgi complex intermediate compartment or ERGIC. The E protein, which is one of the four structural proteins of SARS-CoV-2 and other coronaviruses, assembles its transmembrane protomers into homopentameric channels with mild cationic selectivity. Orf3a forms homodimers and homotetramers. Both carry a PDZ-binding domain, lending them the versatility to interact with more than 400 target proteins in infected host cells. Orf8 is a very short 29-amino-acid single-passage transmembrane peptide that forms cation-selective channels when assembled in lipid bilayers. This review addresses the contribution of biophysical and structural biology approaches that unravel different facets of coronavirus ion channels, their effects on the cellular machinery of infected cells and some structure-functional correlations with ion channels of higher organisms.
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Affiliation(s)
- Francisco J Barrantes
- Biomedical Research Institute (BIOMED), Catholic University of Argentina (UCA) - National Scientific and Technical Research Council (CONICET), C1107AFF Buenos Aires, Argentina
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32
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Kadam SB, Sukhramani GS, Bishnoi P, Pable AA, Barvkar VT. SARS-CoV-2, the pandemic coronavirus: Molecular and structural insights. J Basic Microbiol 2021; 61:180-202. [PMID: 33460172 PMCID: PMC8013332 DOI: 10.1002/jobm.202000537] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 12/12/2022]
Abstract
The outbreak of a novel coronavirus associated with acute respiratory disease, called COVID-19, marked the introduction of the third spillover of an animal coronavirus (CoV) to humans in the last two decades. The genome analysis with various bioinformatics tools revealed that the causative pathogen (SARS-CoV-2) belongs to the subgenus Sarbecovirus of the genus Betacoronavirus, with highly similar genome as bat coronavirus and receptor-binding domain (RBD) of spike glycoprotein as Malayan pangolin coronavirus. Based on its genetic proximity, SARS-CoV-2 is likely to have originated from bat-derived CoV and transmitted to humans via an unknown intermediate mammalian host, probably Malayan pangolin. Further, spike protein S1/S2 cleavage site of SARS-CoV-2 has acquired polybasic furin cleavage site which is absent in bat and pangolin suggesting natural selection either in an animal host before zoonotic transfer or in humans following zoonotic transfer. In the current review, we recapitulate a preliminary opinion about the disease, origin and life cycle of SARS-CoV-2, roles of virus proteins in pathogenesis, commonalities, and differences between different corona viruses. Moreover, the crystal structures of SARS-CoV-2 proteins with unique characteristics differentiating it from other CoVs are discussed. Our review also provides comprehensive information on the molecular aspects of SARS-CoV-2 including secondary structures in the genome and protein-protein interactions which can be useful to understand the aggressive spread of the SARS-CoV-2. The mutations and the haplotypes reported in the SARS-CoV-2 genome are summarized to understand the virus evolution.
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Affiliation(s)
| | | | | | - Anupama A. Pable
- Department of MicrobiologySavitribai Phule Pune UniversityPuneIndia
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33
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Characterizing genomic variants and mutations in SARS-CoV-2 proteins from Indian isolates. GENE REPORTS 2021; 25:101044. [PMID: 33623833 PMCID: PMC7893251 DOI: 10.1016/j.genrep.2021.101044] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/25/2020] [Accepted: 01/29/2021] [Indexed: 12/17/2022]
Abstract
SARS-CoV-2 is mutating and creating divergent variants by altering the composition of essential constituent proteins. Pharmacologically, it is crucial to understand the diverse mechanism of mutations for stable vaccine or anti-viral drug design. Our current study concentrates on all the constituent proteins of 469 SARS-CoV-2 genome samples, derived from Indian patients. However, the study may easily be extended to the samples across the globe. We perform clustering analysis towards identifying unique variants in each of the SARS-CoV-2 proteins. A total of 536 mutated positions within the coding regions of SARS-CoV-2 proteins are detected among the identified variants from Indian isolates. We quantify mutations by focusing on the unique variants of each SARS-CoV-2 protein. We report the average number of mutation per variant, percentage of mutated positions, synonymous and non-synonymous mutations, mutations occurring in three codon positions and so on. Our study reveals the most susceptible six (06) proteins, which are ORF1ab, Spike (S), Nucleocapsid (N), ORF3a, ORF7a, and ORF8. Several non-synonymous substitutions are observed to be unique in different SARS-CoV-2 proteins. A total of 57 possible deleterious amino acid substitutions are predicted, which may impact on the protein functions. Several mutations show a large decrease in protein stability and are observed in putative functional domains of the proteins that might have some role in disease pathogenesis. We observe a good number of physicochemical property change during above deleterious substitutions.
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Hutchison JM, Capone R, Luu DD, Hadziselimovic A, Van Horn WD, Sanders CR. Delivery of recombinant SARS-CoV-2 envelope protein into human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.18.431684. [PMID: 33619482 PMCID: PMC7899446 DOI: 10.1101/2021.02.18.431684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
SARS-CoV-2 envelope protein (S2-E) is a conserved membrane protein that is essential to coronavirus assembly and budding. Here, we describe the recombinant expression and purification of S2-E into amphipol-class amphipathic polymer solutions. The physical properties of amphipols underpin their ability to solubilize and stabilize membrane proteins without disrupting membranes. Amphipol delivery of S2-E to pre-formed planar bilayers results in spontaneous membrane integration and formation of viroporin ion channels. Amphipol delivery of the S2-E protein to human cells results in membrane integration followed by retrograde trafficking to a location adjacent to the endoplasmic reticulum-to-Golgi intermediate compartment (ERGIC) and the Golgi, which are the sites of coronavirus replication. Delivery of S2-E to cells enables both chemical biological approaches for future studies of SARS-CoV-2 pathogenesis and development of "Trojan Horse" anti-viral therapies. This work also establishes a paradigm for amphipol-mediated delivery of membrane proteins to cells.
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Affiliation(s)
- James M. Hutchison
- Chemical and Physical Biology Graduate Program, Vanderbilt University, Nashville, TN, 37240 USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240 USA
| | - Ricardo Capone
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240 USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN, 37240 USA
| | - Dustin D. Luu
- School of Molecular Sciences, Arizona State University,Tempe, AZ 85287 USA
- The Biodesign Institute Centers for Personalized Diagnostics and Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281 USA
| | - Arina Hadziselimovic
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240 USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN, 37240 USA
| | - Wade D. Van Horn
- School of Molecular Sciences, Arizona State University,Tempe, AZ 85287 USA
- The Biodesign Institute Centers for Personalized Diagnostics and Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281 USA
| | - Charles R. Sanders
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240 USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN, 37240 USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232 USA
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Shepley-McTaggart A, Sagum CA, Oliva I, Rybakovsky E, DiGuilio K, Liang J, Bedford MT, Cassel J, Sudol M, Mullin JM, Harty RN. SARS-CoV-2 Envelope (E) Protein Interacts with PDZ-Domain-2 of Host Tight Junction Protein ZO1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.12.22.422708. [PMID: 33398268 PMCID: PMC7781303 DOI: 10.1101/2020.12.22.422708] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Newly emerged SARS-CoV-2 is the cause of an ongoing global pandemic leading to severe respiratory disease in humans. SARS-CoV-2 targets epithelial cells in the respiratory tract and lungs, which can lead to amplified chloride secretion and increased leak across epithelial barriers, contributing to severe pneumonia and consolidation of the lungs as seen in many COVID-19 patients. There is an urgent need for a better understanding of the molecular aspects that contribute to SARS-CoV-2 induced pathogenesis and for the development of approaches to mitigate these damaging pathologies. The multifunctional SARS-CoV-2 Envelope (E) protein contributes to virus assembly/egress, and as a membrane protein, also possesses viroporin channel properties that may contribute to epithelial barrier damage, pathogenesis, and disease severity. The extreme C-terminal (ECT) sequence of E also contains a putative PDZ-domain binding motif (PBM), similar to that identified in the E protein of SARS-CoV-1. Here, we screened an array of GST-PDZ domain fusion proteins using either a biotin-labeled WT or mutant ECT peptide from the SARS-CoV-2 E protein. Notably, we identified a singular specific interaction between the WT E peptide and the second PDZ domain of human Zona Occludens-1 (ZO1), one of the key regulators of TJ formation/integrity in all epithelial tissues. We used homogenous time resolve fluorescence (HTRF) as a second complementary approach to further validate this novel modular E-ZO1 interaction. We postulate that SARS-CoV-2 E interacts with ZO1 in infected epithelial cells, and this interaction may contribute, in part, to tight junction damage and epithelial barrier compromise in these cell layers leading to enhanced virus spread and severe respiratory dysfunction that leads to morbidity. Prophylactic/therapeutic intervention targeting this virus-host interaction may effectively reduce airway barrier damage and mitigate virus spread.
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Affiliation(s)
- Ariel Shepley-McTaggart
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Cari A. Sagum
- Department of Epigenetics & Molecular Carcinogenesis, M.D. Anderson Cancer Center, University of Texas, Smithville, Texas, USA
| | - Isabela Oliva
- The Wistar Cancer Center for Molecular Screening, The Wistar Institute, Philadelphia, PA, USA
| | | | - Katie DiGuilio
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania, USA
| | - Jingjing Liang
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mark T. Bedford
- Department of Epigenetics & Molecular Carcinogenesis, M.D. Anderson Cancer Center, University of Texas, Smithville, Texas, USA
| | - Joel Cassel
- The Wistar Cancer Center for Molecular Screening, The Wistar Institute, Philadelphia, PA, USA
| | - Marius Sudol
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - James M. Mullin
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania, USA
| | - Ronald N. Harty
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Khan JY, Khondaker MTI, Hoque IT, Al-Absi HRH, Rahman MS, Guler R, Alam T, Rahman MS. Toward Preparing a Knowledge Base to Explore Potential Drugs and Biomedical Entities Related to COVID-19: Automated Computational Approach. JMIR Med Inform 2020; 8:e21648. [PMID: 33055059 PMCID: PMC7674141 DOI: 10.2196/21648] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/23/2020] [Accepted: 09/06/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Novel coronavirus disease 2019 (COVID-19) is taking a huge toll on public health. Along with the non-therapeutic preventive measurements, scientific efforts are currently focused, mainly, on the development of vaccines and pharmacological treatment with existing drugs. Summarizing evidences from scientific literatures on the discovery of treatment plan of COVID-19 under a platform would help the scientific community to explore the opportunities in a systematic fashion. OBJECTIVE The aim of this study is to explore the potential drugs and biomedical entities related to coronavirus related diseases, including COVID-19, that are mentioned on scientific literature through an automated computational approach. METHODS We mined the information from publicly available scientific literature and related public resources. Six topic-specific dictionaries, including human genes, human miRNAs, diseases, Protein Databank, drugs, and drug side effects, were integrated to mine all scientific evidence related to COVID-19. We employed an automated literature mining and labeling system through a novel approach to measure the effectiveness of drugs against diseases based on natural language processing, sentiment analysis, and deep learning. We also applied the concept of cosine similarity to confidently infer the associations between diseases and genes. RESULTS Based on the literature mining, we identified 1805 diseases, 2454 drugs, 1910 genes that are related to coronavirus related diseases including COVID-19. Integrating the extracted information, we developed the first knowledgebase platform dedicated to COVID-19, which highlights potential list of drugs and related biomedical entities. For COVID-19, we highlighted multiple case studies on existing drugs along with a confidence score for their applicability in the treatment plan. Based on our computational method, we found Remdesivir, Statins, Dexamethasone, and Ivermectin could be considered as potential effective drugs to improve clinical status and lower mortality in patients hospitalized with COVID-19. We also found that Hydroxychloroquine could not be considered as an effective drug for COVID-19. The resulting knowledgebase is made available as an open source tool, named COVID-19Base. CONCLUSIONS Proper investigation of the mined biomedical entities along with the identified interactions among those would help the research community to discover possible ways for the therapeutic treatment of COVID-19.
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Affiliation(s)
- Junaed Younus Khan
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Md Tawkat Islam Khondaker
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Iram Tazim Hoque
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Hamada R H Al-Absi
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | - Mohammad Saifur Rahman
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Reto Guler
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town, South Africa
- Division of Immunology and South African Medical Research Council Immunology of Infectious Diseases, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Tanvir Alam
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | - M Sohel Rahman
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
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