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El-Megharbel SM, Qahl SH, Albogami B, Hamza RZ. Chemical and spectroscopic characterization of (Artemisinin/Querctin/ Zinc) novel mixed ligand complex with assessment of its potent high antiviral activity against SARS-CoV-2 and antioxidant capacity against toxicity induced by acrylamide in male rats. PeerJ 2024; 12:e15638. [PMID: 38188145 PMCID: PMC10768679 DOI: 10.7717/peerj.15638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 11/03/2023] [Indexed: 01/09/2024] Open
Abstract
A novel Artemisinin/Quercetin/Zinc (Art/Q/Zn) mixed ligand complex was synthesized, tested for its antiviral activity against coronavirus (SARS-CoV-2), and investigated for its effect against toxicity and oxidative stress induced by acrylamide (Acy), which develops upon cooking starchy foods at high temperatures. The synthesized complex was chemically characterized by performing elemental analysis, conductance measurements, FT-IR, UV, magnetic measurements, and XRD. The morphological surface of the complex Art/Q/Zn was investigated using scanning and transmission electron microscopy (SEM and TEM) and energy dispersive X-ray analysis (XRD). The in vitro antiviral activity of the complex Art/Q/Zn against SARS-CoV-2 and its in vivo activity against Acy-induced toxicity in hepatic and pulmonary tissues were analyzed. An experimental model was used to evaluate the beneficial effects of the novel Art/Q/Zn novel complex on lung and liver toxicities of Acy. Forty male rats were randomly divided into four groups: control, Acy (500 mg/Kg), Art/Q/Zn (30 mg/kg), and a combination of Acy and Art/Q/Zn. The complex was orally administered for 30 days. Hepatic function and inflammation marker (CRP), tumor necrosis factor, interleukin-6 (IL-6), antioxidant enzyme (CAT, SOD, and GPx), marker of oxidative stress (MDA), and blood pressure levels were investigated. Histological and ultrastructure alterations and caspase-3 variations (immunological marker) were also investigated. FT-IR spectra revealed that Zn (II) is able to chelate through C=O and C-OH (Ring II) which are the carbonyl oxygen atoms of the quercetin ligand and carbonyl oxygen atom C=O of the Art ligand, forming Art/Q/Zn complex with the chemical formula [Zn(Q)(Art)(Cl)(H2O)2]⋅3H2O. The novel complex exhibited a potent anti-SARS-CoV-2 activity even at a low concentration (IC50 = 10.14 µg/ml) and was not cytotoxic to the cellular host (CC50 = 208.5 µg/ml). Art/Q/Zn may inhibit the viral replication and binding to the angiotensin-converting enzyme-2 (ACE2) receptor and the main protease inhibitor (MPro), thereby inhibiting the activity of SARS-CoV-2 and this proved by the molecular dynamics simulation. It alleviated Acy hepatic and pulmonary toxicity by improving all biochemical markers. Therefore, it can be concluded that the novel formula Art/Q/Zn complex is an effective antioxidant agent against the oxidative stress series, and it has high inhibitory effect against SARS-CoV-2.
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Affiliation(s)
- Samy M. El-Megharbel
- Department of Chemistry, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Safa H. Qahl
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Bander Albogami
- Biology Department, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Reham Z. Hamza
- Biology Department, College of Sciences, Taif University, Taif, Saudi Arabia
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Sanders C, Dzelamonyuy A, Ntemafack A, Alatoom N, Nchinda G, Georgiadis MM, Bopda Waffo A. Mapping immunological and host receptor binding determinants of SARS-CoV spike protein utilizing the Qubevirus platform. J Biol Chem 2023; 299:105460. [PMID: 37977224 PMCID: PMC10750099 DOI: 10.1016/j.jbc.2023.105460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/25/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
The motifs involved in tropism and immunological interactions of SARS-CoV spike (S) protein were investigated utilizing the Qubevirus platform. We showed that separately, 14 overlapping peptide fragments representing the S protein (F1-14 of 100 residues each) could be inserted into the C terminus of A1 on recombinant Qubevirus without affecting its viability. Additionally, recombinant phage expression resulted in the surface exposure of different engineered fragments in an accessible manner. The F6 from S425-525 was found to contain the binding determinant of the recombinant human angiotensin-converting enzyme 2, with the shortest active binding motif situated between residues S437-492. Upstream, another fragment, F7, containing an overlapping portion of F6 would not bind to recombinant human angiotensin-converting enzyme 2, confirming that a contiguous stretch of residues could adopt the appropriate structural orientation of F6 as an insertion within the Qubevirus. The F6 (S441-460) and other inserts, including F7/F8 (S601-620) and F10 (S781-800), were demonstrated to contain important immunological determinants through recognition and binding of S protein specific (anti-S) antibodies. An engineered chimeric insert bearing the fusion of all three anti-S reactive epitopes improved substantially the recognition and binding to their cognate antibodies. These results provide insights into humoral immune relevant epitopes and tropism characteristics of the S protein with implications for the development of subunit vaccines or other biologics against SARS-CoV.
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Affiliation(s)
- Carrie Sanders
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Disease, Center for Disease Control, Atlanta, Georgia, USA
| | - Aristide Dzelamonyuy
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Augustin Ntemafack
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Nadia Alatoom
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Godwin Nchinda
- Department of Immunology, Laboratory of Vaccinology and Biobanking, Yaoundé, Cameroon
| | - Millie M Georgiadis
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Alain Bopda Waffo
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA.
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Liu Y, Chen D, Wang Y, Li X, Qiu Y, Zheng M, Song Y, Li G, Song C, Liu T, Zhang Y, Guo JT, Lin H, Zhao X. Characterization of CCoV-HuPn-2018 spike protein-mediated viral entry. J Virol 2023; 97:e0060123. [PMID: 37676001 PMCID: PMC10537617 DOI: 10.1128/jvi.00601-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 07/25/2023] [Indexed: 09/08/2023] Open
Abstract
Canine coronavirus-human pneumonia-2018 (CCoV-HuPn-2018) was recently isolated from a child with pneumonia. This novel human pathogen resulted from cross-species transmission of a canine coronavirus. It has been known that CCoV-HuPn-2018 uses aminopeptidase N (APN) from canines, felines, and porcines, but not humans, as functional receptors for cell entry. The molecular mechanism of cell entry in CCoV-HuPn-2018 remains poorly understood. In this study, we demonstrated that among the nine APN orthologs tested, the APN of the Mexican free-tailed bat could also efficiently support CCoV-HuPn-2018 spike (S) protein-mediated entry, raising the possibility that bats may also be an alternative host epidemiologically important for the transmission of this virus. The glycosylation at residue N747 of canine APN is critical for its receptor activity. The gain of glycosylation at the corresponding residues in human and rabbit APNs converted them to functional receptors for CCoV-HuPn-2018. Interestingly, the CCoV-HuPn-2018 spike protein pseudotyped virus infected multiple human cancer cell lines in a human APN-independent manner, whereas sialic acid appeared to facilitate the entry of the pseudotyped virus into human cancer cells. Moreover, while host cell surface proteases trypsin and TMPRSS2 did not promote the entry of CCoV-HuPn-2018, endosomal proteases cathepsin L and B are required for the entry of CCoV-HuPn-2018 in a pH-dependent manner. IFITMs and LY6E are host restriction factors for the CCoV-HuPn-2018 entry. Our results thus suggest that CCoV-HuPn-2018 has not yet evolved to be an efficient human pathogen. Collectively, this study helps us understand the cell tropism, receptor usage, cross-species transmission, natural reservoir, and pathogenesis of this potential human coronavirus. IMPORTANCE Viral entry is driven by the interaction between the viral spike protein and its specific cellular receptor, which determines cell tropism and host range and is the major constraint to interspecies transmission of coronaviruses. Aminopeptidase N (APN; also called CD13) is a cellular receptor for HCoV-229E, the newly discovered canine coronavirus-human pneumonia-2018 (CCoV-HuPn-2018), and many other animal alphacoronaviruses. We examined the receptor activity of nine APN orthologs and found that CCoV-HuPn-2018 utilizes APN from a broad range of animal species, including bats but not humans, to enter host cells. To our surprise, we found that CCoV-HuPn-2018 spike protein pseudotyped viral particles successfully infected multiple human hepatoma-derived cell lines and a lung cancer cell line, which is independent of the expression of human APN. Our findings thus provide mechanistic insight into the natural hosts and interspecies transmission of CCoV-HuPn-2018-like coronaviruses.
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Affiliation(s)
- Yongmei Liu
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Danying Chen
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Yuanyuan Wang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Peking University Ditan Teaching Hospital, Beijing, China
| | - Xinglin Li
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Yaruo Qiu
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Peking University Ditan Teaching Hospital, Beijing, China
| | - Mei Zheng
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Yanjun Song
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Guoli Li
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Chuan Song
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Tingting Liu
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Yuanyuan Zhang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Ju-Tao Guo
- Baruch S. Blumberg Institute, Hepatitis B Foundation, Doylestown, Pennsylvania, USA
| | - Hanxin Lin
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
- Molecular Genetics Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
| | - Xuesen Zhao
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
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Khan SS, Ullah A. Comparative genomics of spike, envelope, and nucleocapsid protein of severe acute respiratory syndrome coronavirus 2. Afr Health Sci 2023; 23:384-399. [PMID: 38357143 PMCID: PMC10862604 DOI: 10.4314/ahs.v23i3.45] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024] Open
Abstract
Background Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) upsurge sprang up in Wuhan, China, in late December 2019. Objectives Due to the exceptionally high mutation frequency, comparative genomics of viruses isolated throughout time and in various geographical locations are crucial. To better understand how SARS-CoV-2 heterogeneity has changed around the globe, this research was conducted. Methods Nucleotide and protein sequences of SARS-CoV-2, SARS-CoV, and bat SARS-like CoV were extracted from the NCBI Virus database. The Wuhan SARS-CoV-2 variant was used as a reference. Molecular Evolutionary Genetics Study performed the phylogenetic analysis, while the Genome Detective Coronavirus Typing Tool performed the mutational analysis. Results The evolutionary research has revealed that bats are the primary host for coronavirus evolution and the origin of the formation of SARS-CoV and SARS-CoV-2. Numerous mutations have been discovered in the spike, envelope, and nucleocapsid protein. Conclusions The current research findings may have an implication that facilitates the development of prospective immunization candidates/small pharmacological compounds targeting COVID-19.
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Affiliation(s)
- Sufyan Sohail Khan
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Anwar Ullah
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
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Chattopadhyay A, Jailani AAK, Mandal B. Exigency of Plant-Based Vaccine against COVID-19 Emergence as Pandemic Preparedness. Vaccines (Basel) 2023; 11:1347. [PMID: 37631915 PMCID: PMC10458178 DOI: 10.3390/vaccines11081347] [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: 06/20/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/29/2023] Open
Abstract
After two years since the declaration of COVID-19 as a pandemic by the World Health Organization (WHO), more than six million deaths have occurred due to SARS-CoV-2, leading to an unprecedented disruption of the global economy. Fortunately, within a year, a wide range of vaccines, including pathogen-based inactivated and live-attenuated vaccines, replicating and non-replicating vector-based vaccines, nucleic acid (DNA and mRNA)-based vaccines, and protein-based subunit and virus-like particle (VLP)-based vaccines, have been developed to mitigate the severe impacts of the COVID-19 pandemic. These vaccines have proven highly effective in reducing the severity of illness and preventing deaths. However, the availability and supply of COVID-19 vaccines have become an issue due to the prioritization of vaccine distribution in most countries. Additionally, as the virus continues to mutate and spread, questions have arisen regarding the effectiveness of vaccines against new strains of SARS-CoV-2 that can evade host immunity. The urgent need for booster doses to enhance immunity has been recognized. The scarcity of "safe and effective" vaccines has exacerbated global inequalities in terms of vaccine coverage. The development of COVID-19 vaccines has fallen short of the expectations set forth in 2020 and 2021. Furthermore, the equitable distribution of vaccines at the global and national levels remains a challenge, particularly in developing countries. In such circumstances, the exigency of plant virus-based vaccines has become apparent as a means to overcome supply shortages through fast manufacturing processes and to enable quick and convenient distribution to millions of people without the reliance on a cold chain system. Moreover, plant virus-based vaccines have demonstrated both safety and efficacy in eliciting robust cellular immunogenicity against COVID-19 pathogens. This review aims to shed light on the advantages and disadvantages of different types of vaccines developed against SARS-CoV-2 and provide an update on the current status of plant-based vaccines in the fight against the COVID-19 pandemic.
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Affiliation(s)
- Anirudha Chattopadhyay
- Pulses Research Station, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar 385506, India;
| | - A. Abdul Kader Jailani
- Department of Plant Pathology, North Florida Research and Education Center, University of Florida, Quincy, FL 32351, USA
| | - Bikash Mandal
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India
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Sanders C, Dzelamonyuy A, Ntemafack A, Alatoom N, Nchinda G, Georgiadis M, Waffo AB. Mapping immunological and host receptor binding determinants of SARS-CoV spike protein utilizing the Qubevirus platform. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.27.550841. [PMID: 37546816 PMCID: PMC10402108 DOI: 10.1101/2023.07.27.550841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The motifs involved in tropism and immunological interactions of SARS-CoV spike (S) protein were investigated utilizing the Qubevirus platform. We showed that separately, 14 overlapping peptide fragments representing the S protein (F1-14 of 100 residues each) could be inserted into the C-terminus of A1 on recombinant Qubevirus without affecting its viability. Additionally, recombinant phage expression resulted in the surface exposure of different engineered fragments in an accessible manner. The F6 from S 425-525 , was found to contain the binding determinant of the recombinant human angiotensin converting enzyme 2 (rhACE2), with the shortest active binding motif situated between residues S 437-492 . Upstream, another fragment, F7, containing an overlapping portion of F6 would not bind to rhACE2, confirming not just only that residues were linear but equally also the appropriate structural orientation of F6 upon the Qubevirus. The F6 (S 441-460 ) and other inserts, including F7/F8 (S 601-620 ) and F10 (S 781-800 ), were demonstrated to contain important immunological determinants through recognition and binding of S protein specific (anti-S) antibodies. An engineered chimeric insert bearing the fusion of all three anti-S reactive epitopes, improved substantially the recognition and binding to their cognate antibodies. These results provide insights into humoral immune relevant epitopes and tropism characteristics of the S protein with implications for the development of subunit vaccines or other biologics against SARS-CoV. Significance Mapping epitopes within the receptor binding domains of viruses which are essential for viral tropism is critical for developing antiviral agents and subunit vaccines. In this study we have engineered the surface of Qubevirus to display a peptide library derived from the SARS-CoV S protein. In biopanning with S protein antibodies, we have identified three peptide fragments (EP1, EP2 and EP3) which reacted selectively with antibodies specific to the S protein. We demonstrated that all recombinant phage displayed peptide fragments both individually and as chimera exposed important immunological epitopes to their cognate antibodies. A peptide fragment F6 situated at S 425-525 , was found containing the binding determinant of the recombinant human angiotensin converting enzyme 2 (rhACE2), with the shortest active binding motif situated between residues S 437-492 . The platform is rapidly to identify epitopes and receptor binding sites within viral receptors found in target host cell. Thus, this platform holds great significance.
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Singh R, Malik P, Kumar M, Kumar R, Alam MS, Mukherjee TK. Secondary fungal infections in SARS-CoV-2 patients: pathological whereabouts, cautionary measures, and steadfast treatments. Pharmacol Rep 2023:10.1007/s43440-023-00506-z. [PMID: 37354313 DOI: 10.1007/s43440-023-00506-z] [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: 02/09/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023]
Abstract
The earliest documented COVID-19 case caused by the SARS-CoV-2 coronavirus occurred in Wuhan, China, in December 2019. Since then, several SARS-CoV-2 mutants have rapidly disseminated as exemplified by the community spread of the recent omicron variant. The disease already attained a pandemic status with ever-dwindling mortality even after two and half years of identification and considerable vaccination. Aspergillosis, candidiasis, cryptococcosis and mucormycosis are the prominent fungal infections experienced by the majority of SARS-CoV-2 high-risk patients. In its entirety, COVID-19's nexus with these fungal infections may worsen the intricacies in the already beleaguered high-risk patients, making this a topic of substantial clinical concern. Thus, thorough knowledge of the subject is necessary. This article focuses on the concomitant fungal infection(s) in COVID-19 patients, taking into account their underlying causes, the screening methods, manifested drug resistance, and long-term effects. The information and knowledge shared herein could be crucial for the management of critically ill, aged, and immunocompromised SARS-CoV-2 patients who have had secondary fungal infections (SFIs).
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Affiliation(s)
- Raj Singh
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala, Haryana, 133207, India
| | - Parth Malik
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India
| | - Mukesh Kumar
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala, Haryana, 133207, India
| | - Raman Kumar
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala, Haryana, 133207, India
| | - Md Shamshir Alam
- Department of Pharmacy Practice, College of Pharmacy, National University of Science and Technology, PO Box 620, 130, Bosher-Muscat, Sultanate of Oman
| | - Tapan Kumar Mukherjee
- Amity Institute of Biotechnology, Amity University, Sector-125, Noida, UP, India.
- Department of Biotechnology, Amity University, Major Arterial Road, Action Area II, Rajarhat, New Town, Kolkata, West Bengal, 700135, India.
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Al-Salmi FA, El-Megharbel SM, Hamza RZ. Synthesis and spectroscopic study of novel mixed ligand formula "Artemisinin/Zn" and assessment of its inhibitory effect against "SARS-CoV-2″. Heliyon 2023; 9:e17177. [PMID: 37366527 PMCID: PMC10277259 DOI: 10.1016/j.heliyon.2023.e17177] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 06/28/2023] Open
Abstract
Background Herein, a newly synthesised mixed ligand artemisinin/zinc (Art/Zn) is chemically characterised and examined against SARS-CoV-2. Methods The synthesised complex was thoroughly characterised using various spectroscopic methods (FT-IR, UV and XRD). Its surface morphology and chemical purity were investigated using transmission electron microscopy (TEM), scanning electron microscopy (SEM) and energy-dispersive X-ray (EDX) analysis. The synthesised Art/Zn complex was tested for its inhibitory effects against SARS-CoV-2 using inhibitory concentration 50 (IC50) and cytotoxicity concentration 50 (CC50). Results The results reveal that the Art/Zn complex exhibits a moderate in vitro inhibitory effects against SARS-CoV-2, with a CC50 index of 213.6 μg/ml and an IC50 index of 66.79 μg/ml. Notably, it exhibits the inhibitory effect (IC50 = 66.79 μg/ml) at a very low concentration without any observable cytotoxic effects on host cells (CC50 = 213.6 μg/ml). Its mode of action against SARS-CoV-2 involves inhibiting the viral replication. The predicted target classes that Art/Zn may affect include kinases, which can regulate and inhibit the viral replication and binding to the angiotensin-converting enzyme-2 (ACE2) receptor and the main protease inhibitor (MPro), thereby inhibiting the activity of SARS-CoV-2 and proved by the molecular dynamics simulation. Conclusion We recommend using the Art/Zn complex owing to its moderate inhibitory and antiviral effects against the SARS-CoV-2 with a low cytotoxic effect on host (Vero E6) cells. We suggest conducting further prospective studies to investigate the biological effects of Art/Zn in animal models at different concentrations for testing its clinical efficacy and safety in inhibiting SARS-CoV-2 activities.
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Affiliation(s)
- Fawziah A Al-Salmi
- Department of Biology, College of Sciences, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Samy M El-Megharbel
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
- Department of Chemistry, Zagazig University, P.O. Box 44519, Zagazig, 44519, Egypt
| | - Reham Z Hamza
- Department of Biology, College of Sciences, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
- Department of Zoology, Zagazig University, P.O. Box 44519, Zagazig, 44519, Egypt
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Haseeb M, Amir A, Ikram A. In Silico Analysis of SARS-CoV-2 Spike Proteins of Different Field Variants. Vaccines (Basel) 2023; 11:vaccines11040736. [PMID: 37112648 PMCID: PMC10145761 DOI: 10.3390/vaccines11040736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/04/2023] [Accepted: 03/07/2023] [Indexed: 03/29/2023] Open
Abstract
Coronaviruses belong to the group of RNA family of viruses that trigger diseases in birds, humans, and mammals, which can cause respiratory tract infections. The COVID-19 pandemic has badly affected every part of the world. Our study aimed to explore the genome of SARS-CoV-2, followed by in silico analysis of its proteins. Different nucleotide and protein variants of SARS-CoV-2 were retrieved from NCBI. Contigs and consensus sequences were developed to identify these variants using SnapGene. Data of the variants that significantly differed from each other was run through Predict Protein software to understand the changes produced in the protein structure. The SOPMA web server was used to predict the secondary structure of the proteins. Tertiary structure details of the selected proteins were analyzed using the web server SWISS-MODEL. Sequencing results showed numerous single nucleotide polymorphisms in the surface glycoprotein, nucleocapsid, ORF1a, and ORF1ab polyprotein while the envelope, membrane, ORF3a, ORF6, ORF7a, ORF8, and ORF10 genes had no or few SNPs. Contigs were used to identify variations in the Alpha and Delta variants of SARS-CoV-2 with the reference strain (Wuhan). Some of the secondary structures of the SARS-CoV-2 proteins were predicted by using Sopma software and were further compared with reference strains of SARS-CoV-2 (Wuhan) proteins. The tertiary structure details of only spike proteins were analyzed through the SWISS-MODEL and Ramachandran plots. Through the Swiss-model, a comparison of the tertiary structure model of the SARS-CoV-2 spike protein of the Alpha and Delta variants was made with the reference strain (Wuhan). Alpha and Delta variants of the SARS-CoV-2 isolates submitted in GISAID from Pakistan with changes in structural and nonstructural proteins were compared with the reference strain, and 3D structure mapping of the spike glycoprotein and mutations in the amino acids were seen. The surprisingly increased rate of SARS-CoV-2 transmission has forced numerous countries to impose a total lockdown due to an unusual occurrence. In this research, we employed in silico computational tools to analyze the SARS-CoV-2 genomes worldwide to detect vital variations in structural proteins and dynamic changes in all SARS-CoV-2 proteins, mainly spike proteins, produced due to many mutations. Our analysis revealed substantial differences in the functionality, immunological, physicochemical, and structural variations in the SARS-CoV-2 isolates. However, the real impact of these SNPs can only be determined further by experiments. Our results can aid in vivo and in vitro experiments in the future.
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Bertran O, Martí D, Torras J, Turon P, Alemán C. Computer simulations on oxidative stress-induced reactions in SARS-CoV-2 spike glycoprotein: a multi-scale approach. Mol Divers 2022; 26:3143-3155. [PMID: 35179698 PMCID: PMC8854484 DOI: 10.1007/s11030-021-10373-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/21/2021] [Indexed: 11/30/2022]
Abstract
Oxidative stress, which occurs when an organism is exposed to an adverse stimulus that results in a misbalance of antioxidant and pro-oxidants species, is the common denominator of diseases considered as a risk factor for SARS-CoV-2 lethality. Indeed, reactive oxygen species caused by oxidative stress have been related to many virus pathogenicity. In this work, simulations have been performed on the receptor binding domain of SARS-CoV-2 spike glycoprotein to study what residues are more susceptible to be attacked by ·OH, which is one of the most reactive radicals associated to oxidative stress. The results indicate that isoleucine (ILE) probably plays a crucial role in modification processes driven by radicals. Accordingly, QM/MM-MD simulations have been conducted to study both the ·OH-mediated hydrogen abstraction of ILE residues and the induced modification of the resulting ILE radical through hydroxylation or nitrosylation reactions. All in all, in silico studies show the importance of the chemical environment triggered by oxidative stress on the modifications of the virus, which is expected to help for foreseeing the identification or development of antioxidants as therapeutic drugs.
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Affiliation(s)
- Oscar Bertran
- Departament de Física EETAC, Universitat Politècnica de Catalunya, c/Esteve Terrades, 7, 08860, Castelldefels, Spain.
| | - Didac Martí
- Departament d'Enginyeria Química (DEQ) and Barcelona Research Center in Multiscale Science and Engineering, EEBE, Universitat Politècnica de Catalunya (UPC), C/Eduard Maristany 10-14, 08019, Barcelona, Spain
| | - Juan Torras
- Departament d'Enginyeria Química (DEQ) and Barcelona Research Center in Multiscale Science and Engineering, EEBE, Universitat Politècnica de Catalunya (UPC), C/Eduard Maristany 10-14, 08019, Barcelona, Spain.
| | - Pau Turon
- B. Braun Surgical, S.A.U. Carretera de Terrasa 121, 08191, Rubí, Barcelona, Spain.
| | - Carlos Alemán
- Departament d'Enginyeria Química (DEQ) and Barcelona Research Center in Multiscale Science and Engineering, EEBE, Universitat Politècnica de Catalunya (UPC), C/Eduard Maristany 10-14, 08019, Barcelona, Spain.
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028, Barcelona, Spain.
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11
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Zhou X, Zhao J, Qiu Y, Jia R. Sequence difference of angiotensin-converting enzyme 2 between nonhuman primates affects its binding-affinity with SARS-CoV-2 S receptor binding domain. BIOSAFETY AND HEALTH 2022; 4:293-298. [PMID: 36105891 PMCID: PMC9461283 DOI: 10.1016/j.bsheal.2022.09.001] [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: 06/27/2022] [Revised: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 11/24/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused many deaths and contributed to a tremendous public health concern worldwide since 2020. Angiotensin-converting enzyme 2 (ACE2) binds to the SARS-CoV-2 virus as a receptor. The challenge of different nonhuman primate (NHP) species by SARS-CoV-2 virus demonstrated different effects on virus replication and disease pathology. This study characterizes differences between host ACE2 sequences of three NHP species: Macaca mulatta, Macaca fascicularis, and Chlorocebus sabaeus. In addition, the binding affinity between the ACE2 ectodomain and the SARS-CoV-2 S receptor-binding domain (RBD) was analyzed. Variation of ACE2 sequence among NHP species and the binding affinity may account for different susceptibility and responses to SARS-CoV-2 infection.
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Affiliation(s)
- Xiaojun Zhou
- Department of Biosafety, China Biotechnology Co.LTD, Beijing 100025, China
| | - Jingjing Zhao
- Department of Infectious Diseases, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100043, China
| | - Yefeng Qiu
- Laboratory Animal Center, Academy of Military Medical Sciences, Beijing 100071, China,Corresponding authors: Laboratory Animal Center, Academy of Military Medical Sciences, Beijing 100071, China (Y. Qiu); Department of Biosafety, China Biotechnology Co.LTD, Beijing 100025, China (R. Jia)
| | - Rui Jia
- Department of Biosafety, China Biotechnology Co.LTD, Beijing 100025, China,Corresponding authors: Laboratory Animal Center, Academy of Military Medical Sciences, Beijing 100071, China (Y. Qiu); Department of Biosafety, China Biotechnology Co.LTD, Beijing 100025, China (R. Jia)
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12
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Duhen R, Beymer M, Jensen SM, Abbina S, Abraham S, Jain N, Thomas A, Geall AJ, Hu HM, Fox BA, Weinberg AD. OX40 agonist stimulation increases and sustains humoral and cell-mediated responses to SARS-CoV-2 protein and saRNA vaccines. Front Immunol 2022; 13:896310. [PMID: 36238275 PMCID: PMC9551348 DOI: 10.3389/fimmu.2022.896310] [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: 03/14/2022] [Accepted: 09/08/2022] [Indexed: 12/01/2022] Open
Abstract
To prevent SARS-CoV-2 infections and generate long-lasting immunity, vaccines need to generate strong viral-specific B and T cell responses. Previous results from our lab and others have shown that immunizations in the presence of an OX40 agonist antibody lead to higher antibody titers and increased numbers of long-lived antigen-specific CD4 and CD8 T cells. Using a similar strategy, we explored the effect of OX40 co-stimulation in a prime and boost vaccination scheme using an adjuvanted SARS-CoV-2 spike protein vaccine in C57BL/6 mice. Our results show that OX40 engagement during vaccination significantly increases long-lived antibody responses to the spike protein. In addition, after immunization spike protein-specific proliferation was greatly increased for both CD4 and CD8 T cells, with enhanced, spike-specific secretion of IFN-γ and IL-2. Booster (3rd injection) immunizations combined with an OX40 agonist (7 months post-prime) further increased vaccine-specific antibody and T cell responses. Initial experiments assessing a self-amplifying mRNA (saRNA) vaccine encoding the spike protein antigen show a robust antigen-specific CD8 T cell response. The saRNA spike-specific CD8 T cells express high levels of GrzmB, IFN-γ and TNF-α which was not observed with protein immunization and this response was further increased by the OX40 agonist. Similar to protein immunizations the OX40 agonist also increased vaccine-specific CD4 T cell responses. In summary, this study compares and contrasts the effects and benefits of both protein and saRNA vaccination and the extent to which an OX40 agonist enhances and sustains the immune response against the SARS-CoV-2 spike protein.
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Affiliation(s)
- Rebekka Duhen
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, OR, United States
- *Correspondence: Rebekka Duhen,
| | - Michael Beymer
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, OR, United States
| | - Shawn M. Jensen
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, OR, United States
| | | | | | - Nikita Jain
- Precision NanoSystems Inc, Vancouver, BC, Canada
| | | | | | - Hong-Ming Hu
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, OR, United States
| | - Bernard A. Fox
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, OR, United States
| | - Andrew D. Weinberg
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, OR, United States
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13
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Yang Y, Murray J, Haverstick J, Tripp RA, Zhao Y. Silver nanotriangle array based LSPR sensor for rapid coronavirus detection. SENSORS AND ACTUATORS. B, CHEMICAL 2022; 359:131604. [PMID: 35221531 PMCID: PMC8857771 DOI: 10.1016/j.snb.2022.131604] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/28/2022] [Accepted: 02/18/2022] [Indexed: 05/06/2023]
Abstract
A rapid, portable, and cost-effective method to detect the infection of SARS-CoV-2 is fundamental toward mitigating the current COVID-19 pandemic. Herein, a human angiotensin-converting enzyme 2 protein (ACE2) functionalized silver nanotriangle (AgNT) array localized surface plasmon resonance (LSPR) sensor is developed for rapid coronavirus detection, which is validated by SARS-CoV-2 spike RBD protein and CoV NL63 virus with high sensitivity and specificity. A linear shift of the LSPR wavelength versus the logarithm of the concentration of the spike RBD protein and CoV NL63 is observed. The limits of detection for the spike RBD protein, CoV NL63 in buffer and untreated saliva are determined to be 0.83 pM, 391 PFU/mL, and 625 PFU/mL, respectively, while the detection time is found to be less than 20 min. Thus, the AgNT array optical sensor could serve as a potential rapid point-of-care COVID-19 diagnostic platform.
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Affiliation(s)
- Yanjun Yang
- School of Electrical and Computer Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Jackelyn Murray
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - James Haverstick
- Department of Physics and Astronomy, The University of Georgia, Athens, GA 30602, USA
| | - Ralph A Tripp
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Yiping Zhao
- Department of Physics and Astronomy, The University of Georgia, Athens, GA 30602, USA
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14
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Carta M, Marinello I, Cappelletti A, Rodolfi A, Cerrito E, Bernasconi C, Gottardo M, Dal Lago F, Rizzetto D, Barzon E, Giavarina D. Comparison of Anti-SARS-CoV-2 S1 Receptor-Binding Domain Antibody Immunoassays in Health Care Workers Before and After the BNT162b2 mRNA Vaccine. Am J Clin Pathol 2022; 157:212-218. [PMID: 34463321 PMCID: PMC8499837 DOI: 10.1093/ajcp/aqab107] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/19/2021] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES The Pfizer-BioNTech BNT162b2 vaccine against SARS-CoV-2 infection is now available. This vaccine induces antibody production against the receptor-binding domain (RBD) of the spike glycoprotein S1 (S1-RBD). This study evaluated the performance of new immunoassays to measure this type of antibody. METHODS Blood samples were collected at t0 (prime dose), after 21 days (t1, booster dose), and then after another 15 days (t2) from 70 health care professionals who had tested negative for previous SARS-CoV-2 infection and underwent vaccination with BNT162b2. RESULTS Antibodies against S1-RBD were measured using 4 commercial assays. At t0, t1, and t2, the median antibody concentrations (interquartile range) were, respectively, 0.2 (0.1-0.4), 49.5 (19.1-95.7), and 888.0 (603.6-1,345.8) U/mL by Maglumi SARS-CoV-2 S-RBD immunoglobulin G (IgG) (Shenzen New Industries Biomedical Engineering, Snibe Diagnostics); 0.0 (0.0-0.0), 7.9 (4.2-15.6), and 112.3 (76.4-205.6) U/mL by Atellica IM SARS-CoV-2 IgG assay (Siemens Healthineers); 0.0 (0.0-0.0), 59.9 (18.3-122.0), and 2,646.0 (1,351.2-4,124.0) U/mL by Elecsys Anti-SARS-CoV-2 S assay (Roche Diagnostics); and 1.8 (1.8-1.8), 184 (94-294), and 1,841.0 (1,080.0-2,900.0) AU/mL by LIAISON SARS-CoV-2 TrimericS IgG assay (DiaSorin). The differences between medians at t0, t1, and t2 were all statistically significant (P < .001). CONCLUSIONS Antibodies against nucleocapsid proteins (N) were also measured using Maglumi 2019-nCoV IgG assay, which showed all negative results. All the considered anti-RBD methods detected response to the vaccine, while the method directed against anti-N failed to show response.
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Affiliation(s)
- Mariarosa Carta
- Laboratory Medicine Department, St Bortolo Hospital, AULSS 8 Berica, Vicenza, Italy
| | - Irene Marinello
- Laboratory Medicine Department, St Bortolo Hospital, AULSS 8 Berica, Vicenza, Italy
| | - Anna Cappelletti
- Laboratory Medicine Department, St Bortolo Hospital, AULSS 8 Berica, Vicenza, Italy
| | - Alessandra Rodolfi
- Laboratory Medicine Department, St Bortolo Hospital, AULSS 8 Berica, Vicenza, Italy
| | - Erica Cerrito
- Laboratory Medicine Department, St Bortolo Hospital, AULSS 8 Berica, Vicenza, Italy
| | - Camilla Bernasconi
- Laboratory Medicine Department, St Bortolo Hospital, AULSS 8 Berica, Vicenza, Italy
| | - Marlene Gottardo
- Laboratory Medicine Department, St Bortolo Hospital, AULSS 8 Berica, Vicenza, Italy
| | - Francesca Dal Lago
- Laboratory Medicine Department, St Bortolo Hospital, AULSS 8 Berica, Vicenza, Italy
| | - Daniele Rizzetto
- Laboratory Medicine Department, St Bortolo Hospital, AULSS 8 Berica, Vicenza, Italy
| | - Elena Barzon
- Laboratory Medicine Department, St Bortolo Hospital, AULSS 8 Berica, Vicenza, Italy
| | - Davide Giavarina
- Laboratory Medicine Department, St Bortolo Hospital, AULSS 8 Berica, Vicenza, Italy
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15
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Biswas S, Mahmud S, Mita MA, Afrose S, Hasan MR, Sultana Shimu MS, Saleh MA, Mostafa-Hedeab G, Alqarni M, Obaidullah AJ, Batiha GES. Molecular Docking and Dynamics Studies to Explore Effective Inhibitory Peptides Against the Spike Receptor Binding Domain of SARS-CoV-2. Front Mol Biosci 2022; 8:791642. [PMID: 35187069 PMCID: PMC8851422 DOI: 10.3389/fmolb.2021.791642] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/24/2021] [Indexed: 01/15/2023] Open
Abstract
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a pandemic due to the high transmission and mortality rate of this virus. The world health and economic sectors have been severely affected by this deadly virus, exacerbated by the lack of sufficient efficient vaccines. The design of effective drug candidates and their rapid development is necessary to combat this virus. In this study, we selected 23 antimicrobial peptides from the literature and predicted their structure using PEP-FOLD 3.5. In addition, we docked them to the SARS-CoV-2 spike protein receptor-binding domain (RBD) to study their capability to inhibit the RBD, which plays a significant role in virus binding, fusion and entry into the host cell. We used several docking programs including HDOCK, HPEPDOCK, ClusPro, and HawkDock to calculate the binding energy of the protein-peptide complexes. We identified four peptides with high binding free energy and docking scores. The docking results were further verified by molecular dynamics (MD) simulations to characterize the protein-peptide complexes in terms of their root-mean-square fluctuation (RMSF), root-mean-square deviation (RMSD), radius of gyration (Rg), solvent-accessible surface area (SASA), and hydrogen bond formation. Allergenicity and toxicity predictions suggested that the peptides we identified were non-allergenic and non-toxic. This study suggests that these four antimicrobial peptides could inhibit the RBD of SARS-CoV-2. Future in vitro and in vivo studies are necessary to confirm this.
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Affiliation(s)
- Suvro Biswas
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Shafi Mahmud
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Mohasana Akter Mita
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Shamima Afrose
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Robiul Hasan
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | | | - Md. Abu Saleh
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Gomaa Mostafa-Hedeab
- Pharmacology Department and Health Research Unit-medical College, Jouf University, Jouf, Saudi Arabia
- Pharmacology Department, Faculty of Medicine, Beni-Suef University, Beni Suef, Egypt
| | - Mohammed Alqarni
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Ahmad J. Obaidullah
- Drug Exploration and Development Chair (DEDC), Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
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16
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Angiotensin-Converting Enzyme 2 (ACE2) As a Novel Biorecognition Element in A Cell-Based Biosensor for the Ultra-Rapid, Ultra-Sensitive Detection of the SARS-CoV-2 S1 Spike Protein Antigen. CHEMOSENSORS 2021. [DOI: 10.3390/chemosensors9120341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Antigen screening for the SARS-CoV-2 S1 spike protein is among the most promising tools for the mass monitoring of asymptomatic carriers of the virus, especially in limited resource environments. Herewith, we report on the possible use of the angiotensin-converting enzyme 2 (ACE2), the natural receptor and entry point of the virus, as a biorecognition element for the detection of the S1 antigen combined with an established bioelectric biosensor based on membrane-engineered cells. The working principle of our approach is based on the measurable change of the electric potential of membrane-engineered mammalian cells bearing ACE2 after attachment of the respective viral protein. We demonstrate that sensitive and selective detection of the S1 antigen is feasible in just three min, with a limit of detection of 20 fg/mL. In a preliminary clinical application, positive patient-derived samples were identified with a 87.9% score compared to RT-PCR. No cross-reactivity was observed against a wide range of nucleocapsid protein concentrations. The novel biosensor is embedded in a commercially ready-to-use testing platform, complete with the consumable immobilized cell–electrode interface and a portable read-out device operable through smartphone or tablet. In addition, the possible application of the system for the high throughput screening of potential pharmacological inhibitors of the ACE2 receptor-S1 RBD interaction is discussed.
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17
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Prediction of suitable T and B cell epitopes for eliciting immunogenic response against SARS-CoV-2 and its mutant. NETWORK MODELING AND ANALYSIS IN HEALTH INFORMATICS AND BIOINFORMATICS 2021; 11:1. [PMID: 34849327 PMCID: PMC8619655 DOI: 10.1007/s13721-021-00348-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 08/21/2021] [Accepted: 11/12/2021] [Indexed: 12/23/2022]
Abstract
Spike glycoprotein of SARS-CoV-2 is mainly responsible for the recognition and membrane fusion within the host and this protein has an ability to mutate. Hence, T cell and B cell epitopes were derived from the spike glycoprotein sequence of wild SARS-CoV-2. The proposed T cell and B cell epitopes were found to be antigenic and conserved in the sequence of SARS-CoV-2 mutant (B.1.1.7). Thus, the proposed epitopes are effective against SARS-CoV-2 and its B.1.1.7 mutant. MHC-I that best interacts with the proposed T cell epitopes were found, using immune epitope database. Molecular docking and molecular dynamic simulations were done for ensuring a good binding between the proposed MHC-I and T cell epitopes. The finally proposed T cell epitope was found to be antigenic, non-allergenic, non-toxic and stable. Further, the finally proposed B cell epitopes were also found to be antigenic. The population conservation analysis has ensured the presence of MHC-I molecule (respective to the finally proposed T cell) in human population of most affected countries with SARS-CoV-2. Thus the proposed T and B cell epitope could be effective in designing an epitope-based vaccine, which is effective on SARS-CoV-2 and its B.1.1.7mutant. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13721-021-00348-w.
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18
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Parkhe P, Verma S. Evolution, Interspecies Transmission, and Zoonotic Significance of Animal Coronaviruses. Front Vet Sci 2021; 8:719834. [PMID: 34738021 PMCID: PMC8560429 DOI: 10.3389/fvets.2021.719834] [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: 06/03/2021] [Accepted: 09/07/2021] [Indexed: 12/18/2022] Open
Abstract
Coronaviruses are single-stranded RNA viruses that affect humans and a wide variety of animal species, including livestock, wild animals, birds, and pets. These viruses have an affinity for different tissues, such as those of the respiratory and gastrointestinal tract of most mammals and birds and the hepatic and nervous tissues of rodents and porcine. As coronaviruses target different host cell receptors and show divergence in the sequences and motifs of their structural and accessory proteins, they are classified into groups, which may explain the evolutionary relationship between them. The interspecies transmission, zoonotic potential, and ability to mutate at a higher rate and emerge into variants of concern highlight their importance in the medical and veterinary fields. The contribution of various factors that result in their evolution will provide better insight and may help to understand the complexity of coronaviruses in the face of pandemics. In this review, important aspects of coronaviruses infecting livestock, birds, and pets, in particular, their structure and genome organization having a bearing on evolutionary and zoonotic outcomes, have been discussed.
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Affiliation(s)
| | - Subhash Verma
- Department of Veterinary Microbiology, DGCN College of Veterinary and Animal Sciences, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, India
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19
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Rodrigues JSM, Rodrigues AM, do Nascimento Souza D, de Novais ERP, Rodrigues AM, de Oliveira GCA, de Lima Ferreira Novais A. DFT calculations to investigate silver ions as a virucide from SARS-CoV-2. J Mol Model 2021; 27:323. [PMID: 34643800 PMCID: PMC8510886 DOI: 10.1007/s00894-021-04941-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/29/2021] [Indexed: 01/18/2023]
Abstract
The world has face the COVID-19 pandemic which has already caused millions of death. Due to the urgency in fighting the virus, we study five residues of free amino acids present in the structure of the SARS-CoV-2 spike protein (S). We investigated the spontaneous interaction between amino acids and silver ions (Ag+), considering these ions as a virucide chemical agent for SARS-CoV-2. The amino acid-Ag+ systems were investigated in a gaseous medium and a simulated water environment was described with a continuum model (PCM) the calculations were performed within the framework of density functional theory (DFT). Calculations related to the occupied orbitals of higher energy showed that Ag+ has a tendency to interact with the nitrile groups (-NH). The negative values of the Gibbs free energies show that the interaction process between amino acids-Ag+ in both media occurs spontaneously. There is a decrease in Gibbs free energy from the amino acid-Ag+ interactions immersed in a water solvation simulator.
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20
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Saadi F, Pal D, Sarma JD. Spike Glycoprotein Is Central to Coronavirus Pathogenesis-Parallel Between m-CoV and SARS-CoV-2. Ann Neurosci 2021; 28:201-218. [PMID: 35341224 PMCID: PMC8948335 DOI: 10.1177/09727531211023755] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 03/24/2021] [Indexed: 01/04/2023] Open
Abstract
Coronaviruses (CoVs) are single-stranded, polyadenylated, enveloped RNA of positive polarity with a unique potential to alter host tropism. This has been exceptionally demonstrated by the emergence of deadly virus outbreaks of the past: Severe Acute Respiratory Syndrome (SARS-CoV) in 2003 and Middle East Respiratory Syndrome (MERS-CoV) in 2012. The 2019 outbreak by the new cross-species transmission of SARS-CoV-2 has put the world on alert. CoV infection is triggered by receptor recognition, membrane fusion, and successive viral entry mediated by the surface Spike (S) glycoprotein. S protein is one of the major antigenic determinants and the target for neutralizing antibodies. It is a valuable target in antiviral therapies because of its central role in cell-cell fusion, viral antigen spread, and host immune responses leading to immunopathogenesis. The receptor-binding domain of S protein has received greater attention as it initiates host attachment and contains major antigenic determinants. However, investigating the therapeutic potential of fusion peptide as a part of the fusion core complex assembled by the heptad repeats 1 and 2 (HR1 and HR2) is also warranted. Along with receptor attachment and entry, fusion mechanisms should also be explored for designing inhibitors as a therapeutic intervention. In this article, we review the S protein function and its role in mediating membrane fusion, spread, tropism, and its associated pathogenesis with notable therapeutic strategies focusing on results obtained from studies on a murine β-Coronavirus (m-CoV) and its associated disease process.
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Affiliation(s)
- Fareeha Saadi
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Kolkata, West Bengal, India
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Jayasri Das Sarma
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Kolkata, West Bengal, India
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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21
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Cell Entry of Animal Coronaviruses. Viruses 2021; 13:v13101977. [PMID: 34696406 PMCID: PMC8540712 DOI: 10.3390/v13101977] [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: 09/10/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 01/11/2023] Open
Abstract
Coronaviruses (CoVs) are a group of enveloped positive-sense RNA viruses and can cause deadly diseases in animals and humans. Cell entry is the first and essential step of successful virus infection and can be divided into two ongoing steps: cell binding and membrane fusion. Over the past two decades, stimulated by the global outbreak of SARS-CoV and pandemic of SARS-CoV-2, numerous efforts have been made in the CoV research. As a result, significant progress has been achieved in our understanding of the cell entry process. Here, we review the current knowledge of this essential process, including the viral and host components involved in cell binding and membrane fusion, molecular mechanisms of their interactions, and the sites of virus entry. We highlight the recent findings of host restriction factors that inhibit CoVs entry. This knowledge not only enhances our understanding of the cell entry process, pathogenesis, tissue tropism, host range, and interspecies-transmission of CoVs but also provides a theoretical basis to design effective preventive and therapeutic strategies to control CoVs infection.
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22
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Aminu S, Ibrahim MA, Sallau AB. Interaction of SARS-CoV-2 spike protein with angiotensin converting enzyme inhibitors and selected compounds from the chemical entities of biological interest. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2021; 10:48. [PMID: 34458381 PMCID: PMC8386153 DOI: 10.1186/s43088-021-00138-3] [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: 11/24/2020] [Accepted: 08/13/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Recent COVID-19 outbreak has prompted the search of novel therapeutic agents to treat the disease. The initial step of the infection involves the binding of the virus through the viral spike protein with the host angiotensin converting enzyme 2 (ACE2). In this study, the interaction of some ACE or ACE2 inhibitors and their analogues as well as selected compounds with the viral spike protein as a strategy to hinder viral-ACE2 interaction were investigated. SARS-CoV-2 spike protein as well as the ligands were retrieved from protein databank and ChEBI database respectively. The molecules were prepared before initiating the virtual screening using PyRx software. Discovery studio was used to further visualize the binding interactions between the compounds and the protein. RESULTS The ACE inhibitors and their analogues fosinopril (1-), fosinopril and moexipril have the best binding affinity to the protein with binding energies < - 7.0 kcal/mol while non-flavonoid stilben-4-ol binds with free binding energy of - 7.1 kcal/mol. Others compounds which belong to either the flavonoids, terpenes and alkaloid classes also have binding energies < - 7.0 kcal/mol. Such high binding energies were enhanced via hydrogen bond (h-bond) interactions in addition to other interactions observed between the compounds and the amino acid residues of the protein. CONCLUSIONS The ACE inhibitors and their analogues as well as the selected compounds could serve as inhibitors of the spike protein as well as lead in drug discovery processes to target the SARS-CoV-2 virus.
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Affiliation(s)
- Suleiman Aminu
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
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Starshinova A, Malkova A, Zinchenko U, Kudlay D, Glushkova A, Dovgalyk I, Yablonskiy P, Shoenfeld Y. Efficacy of Different Types of Therapy for COVID-19: A Comprehensive Review. Life (Basel) 2021; 11:753. [PMID: 34440497 PMCID: PMC8400016 DOI: 10.3390/life11080753] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 01/08/2023] Open
Abstract
A new coronavirus disease (COVID-19) has already affected millions of people in 213 countries. The possibilities of treatment have been reviewed in recent publications but there are many controversial results and conclusions. An analysis of the studies did not reveal a difference in mortality level between people treated with standard therapy, such as antiviral drugs and dexamethasone, and new antiviral drugs/additional immune therapy. However, most studies describe clinical improvement and a decrease in mortality among patients with severe and critical conditions, with the early initiation of additional immune therapy. Possible new targets based on viral life cycles were considered. Unfortunately, the data analysis on the efficacy of different medicine and therapy regimens among patients with COVID-19, showed little success in decreasing the mortality rate in all treatment methods. Some efficacy has been shown with an immunosuppressive therapy in small patient samples, but when a larger number of patients were analyzed the data did not differ significantly from the control groups.
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Affiliation(s)
- Anna Starshinova
- Almazov National Medical Research Centre, Head of the Research Department, 2 Akkuratov Str., 197341 Saint-Petersburg, Russia
| | - Anna Malkova
- Medical Department, Saint Petersburg State University, 199034 Saint-Petersburg, Russia; (A.M.); (P.Y.); (Y.S.)
| | - Ulia Zinchenko
- St. Petersburg Research Institute of Phthisiopulmonology, 199034 Saint-Petersburg, Russia; (U.Z.); (I.D.)
| | - Dmitry Kudlay
- NRC Institute of Immunology FMBA of Russia, 115478 Moscow, Russia;
- Medical Department, I.M. Sechenov First Moscow State Medical University, 119435 Moscow, Russia
| | - Anzhela Glushkova
- V.M. Bekhterev National Research Medical Center for Psychiatry and Neurology, 192019 Saint Petersburg, Russia;
| | - Irina Dovgalyk
- St. Petersburg Research Institute of Phthisiopulmonology, 199034 Saint-Petersburg, Russia; (U.Z.); (I.D.)
| | - Piotr Yablonskiy
- Medical Department, Saint Petersburg State University, 199034 Saint-Petersburg, Russia; (A.M.); (P.Y.); (Y.S.)
- St. Petersburg Research Institute of Phthisiopulmonology, 199034 Saint-Petersburg, Russia; (U.Z.); (I.D.)
| | - Yehuda Shoenfeld
- Medical Department, Saint Petersburg State University, 199034 Saint-Petersburg, Russia; (A.M.); (P.Y.); (Y.S.)
- Ariel University, Kiryat HaMada 3, Ariel 40700, Israel
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer 5265601, Israel
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24
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Recent advance of ACE2 and microbiota dysfunction in COVID-19 pathogenesis. Heliyon 2021; 7:e07548. [PMID: 34296023 PMCID: PMC8270732 DOI: 10.1016/j.heliyon.2021.e07548] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/08/2021] [Accepted: 07/07/2021] [Indexed: 02/07/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the coronavirus disease 2019 (COVID-19) and has become the world's most pressing public health threat. Although not as common as respiratory symptoms, a substantial proportion of patients with COVID-19 presented the gastrointestinal symptoms. ACE2, as the receptor of SARS-CoV and SARS-CoV-2, is highly expressed in the epithelia of the epithelium cells in lung and intestine. In addition, ACE2 is essential for the innate immunity, amino acid transportation and the homeostasis of intestinal microecology. The composition of gut microbiota in COVID-19 patients was altered and concordant with inflammatory, which may explain the gastrointestinal symptoms in patients. Here we reviewed and discussed the evolving role for ACE2 and gut microbiota in SARS-CoV-2 infection which might provide innovative approaches to targeting ACE2 and gut microbiota for the COVID-19 therapy.
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25
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Siemers M, Bondar AN. Interactive Interface for Graph-Based Analyses of Dynamic H-Bond Networks: Application to Spike Protein S. J Chem Inf Model 2021; 61:2998-3014. [PMID: 34133162 DOI: 10.1021/acs.jcim.1c00306] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Dynamic hydrogen-bond networks are key determinants of protein conformational dynamics. In the case of macromolecular protein complexes, which can have a large number of hydrogen bonds giving rise to extensive hydrogen-bond networks, efficient algorithms are required to analyze interactions that could be important for the dynamics and biological function of the complex. We present here a highly efficient, standalone interface designed for analyses of dynamical hydrogen-bond networks of biomolecules and macromolecular complexes. To facilitate a comprehensive description of protein dynamics, the interface includes analyses of hydrophobic interactions. We illustrate the usefulness and workflow of the interface by dissecting the dynamics of the ectodomain of SARS-CoV-2 protein S in its closed conformation. We find that protein S contains numerous local clusters of dynamic hydrogen bonds and identify hydrogen bonds that are sampled persistently. The receptor binding domain of the spike protein hosts only a handful of persistent hydrogen-bond clusters, suggesting structural plasticity. Our data analysis interface is released here for open use.
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Affiliation(s)
- Malte Siemers
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
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26
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Feng Y, Jiang H, Qiu M, Liu L, Zou S, Li Y, Guo Q, Han N, Sun Y, Wang K, Lu L, Zhuang X, Zhang S, Chen S, Mo F. Multi-Epitope Vaccine Design Using an Immunoinformatic Approach for SARS-CoV-2. Pathogens 2021; 10:pathogens10060737. [PMID: 34208061 PMCID: PMC8230658 DOI: 10.3390/pathogens10060737] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 06/04/2021] [Accepted: 06/08/2021] [Indexed: 12/14/2022] Open
Abstract
Through 4 June 2021, COVID-19 has caused over 172.84 million cases of infection and 3.71 million deaths worldwide. Due to its rapid dissemination and high mutation rate, it is essential to develop a vaccine harboring multiple epitopes and efficacious against multiple variants to prevent the immune escape of SARS-CoV-2. An in silico approach based on the viral genome was applied to identify 19 high-immunogenic B-cell epitopes and 499 human leukocyte antigen (HLA)-restricted T-cell epitopes. Thirty multi-epitope peptide vaccines were designed by iNeo-Suite and manufactured by solid-phase synthesis. Docking analysis confirmed stable hydrogen bonds of epitopes with their corresponding HLA alleles. When four peptide candidates derived from the spike protein of SARS-CoV-2 were selected to immunize mice, a significantly larger amount of total IgG in serum, as well as an increase of CD19+ cells in the inguinal lymph nodes, were observed in the peptide-immunized mice compared to the control. The ratios of IFN-γ-secreting lymphocytes in CD4+ or CD8+ T-cells in the peptide-immunized mice were higher than those in the control mice. There were also a larger number of IFN-γ-secreting T-cells in the spleens of peptide-immunized mice. The peptide vaccines in this study successfully elicited antigen-specific humoral and cellular immune responses in mice. To further validate the safety and efficacy of this vaccine, animal studies using a primate model, as well as clinical trials in humans, are required.
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Affiliation(s)
- Ye Feng
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310001, China; (Y.F.); (S.Z.)
- Institute for Translational Medicine, Zhejiang University School of Medicine, Hangzhou 310002, China
| | - Haiping Jiang
- The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310007, China;
| | - Min Qiu
- Hangzhou Neoantigen Therapeutics Co., Ltd., Hangzhou 310058, China; (M.Q.); (L.L.); (Q.G.); (N.H.); (Y.S.); (K.W.); (L.L.); (S.Z.)
| | - Liang Liu
- Hangzhou Neoantigen Therapeutics Co., Ltd., Hangzhou 310058, China; (M.Q.); (L.L.); (Q.G.); (N.H.); (Y.S.); (K.W.); (L.L.); (S.Z.)
| | - Shengmei Zou
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310001, China; (Y.F.); (S.Z.)
- Institute for Translational Medicine, Zhejiang University School of Medicine, Hangzhou 310002, China
| | - Yun Li
- Zhejiang Forest Resources Monitoring Center, Hangzhou 310020, China;
| | - Qianpeng Guo
- Hangzhou Neoantigen Therapeutics Co., Ltd., Hangzhou 310058, China; (M.Q.); (L.L.); (Q.G.); (N.H.); (Y.S.); (K.W.); (L.L.); (S.Z.)
| | - Ning Han
- Hangzhou Neoantigen Therapeutics Co., Ltd., Hangzhou 310058, China; (M.Q.); (L.L.); (Q.G.); (N.H.); (Y.S.); (K.W.); (L.L.); (S.Z.)
| | - Yingqiang Sun
- Hangzhou Neoantigen Therapeutics Co., Ltd., Hangzhou 310058, China; (M.Q.); (L.L.); (Q.G.); (N.H.); (Y.S.); (K.W.); (L.L.); (S.Z.)
| | - Kui Wang
- Hangzhou Neoantigen Therapeutics Co., Ltd., Hangzhou 310058, China; (M.Q.); (L.L.); (Q.G.); (N.H.); (Y.S.); (K.W.); (L.L.); (S.Z.)
| | - Lantian Lu
- Hangzhou Neoantigen Therapeutics Co., Ltd., Hangzhou 310058, China; (M.Q.); (L.L.); (Q.G.); (N.H.); (Y.S.); (K.W.); (L.L.); (S.Z.)
| | - Xinlei Zhuang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China;
| | - Shanshan Zhang
- Hangzhou Neoantigen Therapeutics Co., Ltd., Hangzhou 310058, China; (M.Q.); (L.L.); (Q.G.); (N.H.); (Y.S.); (K.W.); (L.L.); (S.Z.)
- Zhejiang California International Nanosystems Institute, Zhejiang University, Hangzhou 310058, China
| | - Shuqing Chen
- Hangzhou Neoantigen Therapeutics Co., Ltd., Hangzhou 310058, China; (M.Q.); (L.L.); (Q.G.); (N.H.); (Y.S.); (K.W.); (L.L.); (S.Z.)
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China;
- Zhejiang California International Nanosystems Institute, Zhejiang University, Hangzhou 310058, China
- Correspondence: (S.C.); (F.M.); Tel.: +86-571-8820-8411 (S.C.); +86-571-8608-8519 (F.M.)
| | - Fan Mo
- Hangzhou Neoantigen Therapeutics Co., Ltd., Hangzhou 310058, China; (M.Q.); (L.L.); (Q.G.); (N.H.); (Y.S.); (K.W.); (L.L.); (S.Z.)
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China;
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC V6H 3Z6, Canada
- Hangzhou AI-Force Therapeutics Co., Ltd., Hangzhou 310000, China
- Correspondence: (S.C.); (F.M.); Tel.: +86-571-8820-8411 (S.C.); +86-571-8608-8519 (F.M.)
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Kurt-Jones EA, Dudek TE, Watanabe D, Mandell L, Che J, Zhou S, Cao L, Greenough T, Babcock GJ, Diaz F, Oh HS, Zhou C, Finberg RW, Knipe DM. Expression of SARS coronavirus 1 spike protein from a herpesviral vector induces innate immune signaling and neutralizing antibody responses. Virology 2021; 559:165-172. [PMID: 33930819 PMCID: PMC8058630 DOI: 10.1016/j.virol.2021.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 01/05/2023]
Abstract
SARS coronavirus 1 (SARS-CoV-1) causes a respiratory infection that can lead to acute respiratory distress characterized by inflammation and high levels of cytokines in the lung tissue. In this study we constructed a herpes simplex virus 1 replication-defective mutant vector expressing SARS-CoV-1 spike protein as a potential vaccine vector and to probe the effects of spike protein on host cells. The spike protein expressed from this vector is functional in that it localizes to the surface of infected cells and induces fusion of ACE2-expressing cells. In immunized mice, the recombinant vector induced antibodies that bind to spike protein in an ELISA assay and that show neutralizing activity. The spike protein expressed from this vector can induce the expression of cytokines in an ACE2-independent, MyD88-dependent process. These results argue that the SARS-CoV-1 spike protein intrinsically activates signaling pathways that induce cytokines and contribute directly to the inflammatory process of SARS.
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Affiliation(s)
- Evelyn A Kurt-Jones
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Timothy E Dudek
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Daisuke Watanabe
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Leisa Mandell
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jenny Che
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Shenghua Zhou
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - LuCheng Cao
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Thomas Greenough
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Gregory J Babcock
- MassBiologics, University of Massachusetts Medical School, Boston, MA, USA
| | - Fernando Diaz
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Hyung Suk Oh
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Changhong Zhou
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Robert W Finberg
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - David M Knipe
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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28
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Almofti YA, Abd-Elrahman KA, Eltilib EEM. Vaccinomic approach for novel multi epitopes vaccine against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). BMC Immunol 2021; 22:22. [PMID: 33765919 PMCID: PMC7992937 DOI: 10.1186/s12865-021-00412-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/10/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The spread of a novel coronavirus termed severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in China and other countries is of great concern worldwide with no effective vaccine. This study aimed to design a novel vaccine construct against SARS-CoV-2 from the spike S protein and orf1ab polyprotein using immunoinformatics tools. The vaccine was designed from conserved epitopes interacted against B and T lymphocytes by the combination of highly immunogenic epitopes with suitable adjuvant and linkers. RESULTS The proposed vaccine composed of 526 amino acids and was shown to be antigenic in Vaxigen server (0.6194) and nonallergenic in Allertop server. The physiochemical properties of the vaccine showed isoelectric point of 10.19. The instability index (II) was 31.25 classifying the vaccine as stable. Aliphatic index was 84.39 and the grand average of hydropathicity (GRAVY) was - 0.049 classifying the vaccine as hydrophilic. Vaccine tertiary structure was predicted, refined and validated to assess the stability of the vaccine via Ramachandran plot and ProSA-web servers. Moreover, solubility of the vaccine construct was greater than the average solubility provided by protein sol and SOLpro servers indicating the solubility of the vaccine construct. Disulfide engineering was performed to reduce the high mobile regions in the vaccine to enhance stability. Docking of the vaccine construct with TLR4 demonstrated efficient binding energy with attractive binding energy of - 338.68 kcal/mol and - 346.89 kcal/mol for TLR4 chain A and chain B respectively. Immune simulation significantly provided high levels of immunoglobulins, T-helper cells, T-cytotoxic cells and INF-γ. Upon cloning, the vaccine protein was reverse transcribed into DNA sequence and cloned into pET28a(+) vector to ensure translational potency and microbial expression. CONCLUSION A unique vaccine construct from spike S protein and orf1ab polyprotein against B and T lymphocytes was generated with potential protection against the pandemic. The present study might assist in developing a suitable therapeutics protocol to combat SARSCoV-2 infection.
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Affiliation(s)
- Yassir A Almofti
- Department of Molecular Biology and Bioinformatics, College of Veterinary Medicine, University of Bahri, Khartoum, Sudan.
| | - Khoubieb Ali Abd-Elrahman
- Department of Pharmaceutical Technology, College of Pharmacy, University of Medical Science and Technology (MUST), Khartoum, Sudan
| | - Elsideeq E M Eltilib
- Department of Molecular Biology and Bioinformatics, College of Veterinary Medicine, University of Bahri, Khartoum, Sudan
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29
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Frutos R, Serra-Cobo J, Pinault L, Lopez Roig M, Devaux CA. Emergence of Bat-Related Betacoronaviruses: Hazard and Risks. Front Microbiol 2021; 12:591535. [PMID: 33790874 PMCID: PMC8005542 DOI: 10.3389/fmicb.2021.591535] [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: 08/04/2020] [Accepted: 02/15/2021] [Indexed: 01/08/2023] Open
Abstract
The current Coronavirus Disease 2019 (COVID-19) pandemic, with more than 111 million reported cases and 2,500,000 deaths worldwide (mortality rate currently estimated at 2.2%), is a stark reminder that coronaviruses (CoV)-induced diseases remain a major threat to humanity. COVID-19 is only the latest case of betacoronavirus (β-CoV) epidemics/pandemics. In the last 20 years, two deadly CoV epidemics, Severe Acute Respiratory Syndrome (SARS; fatality rate 9.6%) and Middle East Respiratory Syndrome (MERS; fatality rate 34.7%), plus the emergence of HCoV-HKU1 which causes the winter common cold (fatality rate 0.5%), were already a source of public health concern. Betacoronaviruses can also be a threat for livestock, as evidenced by the Swine Acute Diarrhea Syndrome (SADS) epizootic in pigs. These repeated outbreaks of β-CoV-induced diseases raise the question of the dynamic of propagation of this group of viruses in wildlife and human ecosystems. SARS-CoV, SARS-CoV-2, and HCoV-HKU1 emerged in Asia, strongly suggesting the existence of a regional hot spot for emergence. However, there might be other regional hot spots, as seen with MERS-CoV, which emerged in the Arabian Peninsula. β-CoVs responsible for human respiratory infections are closely related to bat-borne viruses. Bats are present worldwide and their level of infection with CoVs is very high on all continents. However, there is as yet no evidence of direct bat-to-human coronavirus infection. Transmission of β-CoV to humans is considered to occur accidentally through contact with susceptible intermediate animal species. This zoonotic emergence is a complex process involving not only bats, wildlife and natural ecosystems, but also many anthropogenic and societal aspects. Here, we try to understand why only few hot spots of β-CoV emergence have been identified despite worldwide bats and bat-borne β-CoV distribution. In this work, we analyze and compare the natural and anthropogenic environments associated with the emergence of β-CoV and outline conserved features likely to create favorable conditions for a new epidemic. We suggest monitoring South and East Africa as well as South America as these regions bring together many of the conditions that could make them future hot spots.
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Affiliation(s)
- Roger Frutos
- Centre de coopération Internationale en Recherche Agronomique pour le Développement, UMR 17, Intertryp, Montpellier, France.,Institut d'Électronique et des Systèmes, UMR 5214, Université de Montpellier-CNRS, Montpellier, France
| | - Jordi Serra-Cobo
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Biodiversity Research Institute, Barcelona, Spain
| | - Lucile Pinault
- Aix Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Marc Lopez Roig
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Biodiversity Research Institute, Barcelona, Spain
| | - Christian A Devaux
- Aix Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France.,Centre National de la Recherche Scientifique, Marseille, France
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30
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Hasan A, Al-Ozairi E, Al-Baqsumi Z, Ahmad R, Al-Mulla F. Cellular and Humoral Immune Responses in Covid-19 and Immunotherapeutic Approaches. Immunotargets Ther 2021; 10:63-85. [PMID: 33728277 PMCID: PMC7955763 DOI: 10.2147/itt.s280706] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 12/22/2020] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 (Covid-19), caused by the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), can range in severity from asymptomatic to severe/critical disease. SARS-CoV-2 uses angiotensin-converting enzyme 2 to infect cells leading to a strong inflammatory response, which is most profound in patients who progress to severe Covid-19. Recent studies have begun to unravel some of the differences in the innate and adaptive immune response to SARS-CoV-2 in patients with different degrees of disease severity. These studies have attributed the severe form of Covid-19 to a dysfunctional innate immune response, such as a delayed and/or deficient type I interferon response, coupled with an exaggerated and/or a dysfunctional adaptive immunity. Differences in T-cell (including CD4+ T-cells, CD8+ T-cells, T follicular helper cells, γδ-T-cells, and regulatory T-cells) and B-cell (transitional cells, double-negative 2 cells, antibody-secreting cells) responses have been identified in patients with severe disease compared to mild cases. Moreover, differences in the kinetic/titer of neutralizing antibody responses have been described in severe disease, which may be confounded by antibody-dependent enhancement. Importantly, the presence of preexisting autoantibodies against type I interferon has been described as a major cause of severe/critical disease. Additionally, priorVaccine and multiple vaccine exposure, trained innate immunity, cross-reactive immunity, and serological immune imprinting may all contribute towards disease severity and outcome. Several therapeutic and preventative approaches have been under intense investigations; these include vaccines (three of which have passed Phase 3 clinical trials), therapeutic antibodies, and immunosuppressants.
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Affiliation(s)
- Amal Hasan
- Department of Immunology and Microbiology, Research Division, Dasman Diabetes Institute, Dasman, Kuwait City, Kuwait
| | - Ebaa Al-Ozairi
- Clinical Research Unit, Medical Division, Dasman Diabetes Institute, Dasman, Kuwait City, Kuwait
- Department of Medicine, Faculty of Medicine, Jabriya, Kuwait City, Kuwait
| | - Zahraa Al-Baqsumi
- Department of Immunology and Microbiology, Research Division, Dasman Diabetes Institute, Dasman, Kuwait City, Kuwait
| | - Rasheed Ahmad
- Department of Immunology and Microbiology, Research Division, Dasman Diabetes Institute, Dasman, Kuwait City, Kuwait
| | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Functional Genomics, Research Division, Dasman Diabetes Institute, Dasman, Kuwait City, Kuwait
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31
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Malkova A, Kudlay D, Kudryavtsev I, Starshinova A, Yablonskiy P, Shoenfeld Y. Immunogenetic Predictors of Severe COVID-19. Vaccines (Basel) 2021; 9:211. [PMID: 33802310 PMCID: PMC8001669 DOI: 10.3390/vaccines9030211] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 12/21/2022] Open
Abstract
According to an analysis of published data, only 20% of patients with the new coronavirus infection develop severe life-threatening complications. Currently, there are no known biomarkers, the determination of which before the onset of the disease would allow assessing the likelihood of its severe course. The purpose of this literature review was to analyze possible genetic factors characterizing the immune response to the new coronavirus infection that could be associated with the expression of angiotension-converting enzyme 2 (ACE-2) and related proteins as predictors of severe Corona virus disease 2019 (COVID-19). We analyzed original articles published in Medline, PubMed and Scopus databases from December 2019 to November 2020. For searching articles, we used the following keywords: New coronavirus infection, Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2), COVID-19, severe course, complications, thrombosis, cytokine storm, ACE-2, biomarkers. In total, 3714 publications were selected using the keywords, of which 8 were in congruence with all the criteria. The literature analysis of the association of immunogenic characteristics and the expression of ACE-2 and related proteins with the development of severe COVID-19 revealed following genetic factors: HLA-B*46:01 genotype, CXCR6 gene hypoexpression, CCR9 gene expression, TLR7, rs150892504 mutations in the ERAP2 gene, overexpression of wild-type ACE-2, TMPRSS2 and its different polymorphisms. Genes, associated with the severe course, are more common among men. According to the analysis data, it can be assumed that there are population differences. However, the diagnostic significance of the markers described must be confirmed with additional clinical studies.
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Affiliation(s)
- Anna Malkova
- St. Petersburg State University, Saint Petersburg 199034, Russia; (P.Y.); (Y.S.)
| | - Dmitriy Kudlay
- Sechenov First Moscow State Medical University, Moscow 119435, Russia;
- NRC Institute of Immunology FMBA of Russia, Moscow 115478, Russia
| | - Igor Kudryavtsev
- FSBI Institute of Experimental Medicine, St. Petersburg 197376, Russia;
- Far Eastern Federal University, Vladivostok 690091, Russia
| | - Anna Starshinova
- FSBI V.A. Almazov National Medical Research Center, Ministry of Health of Russia, St. Petersburg 197241, Russia;
| | - Piotr Yablonskiy
- St. Petersburg State University, Saint Petersburg 199034, Russia; (P.Y.); (Y.S.)
- St. Petersburg Research Institute of Phthisiopulmonology, Saint Petersburg 191036, Russia
| | - Yehuda Shoenfeld
- St. Petersburg State University, Saint Petersburg 199034, Russia; (P.Y.); (Y.S.)
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer 5265601, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
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Boklund A, Gortázar C, Pasquali P, Roberts H, Nielsen SS, Stahl K, Stegeman A, Baldinelli F, Broglia A, Van Der Stede Y, Adlhoch C, Alm E, Melidou A, Mirinaviciute G. Monitoring of SARS-CoV-2 infection in mustelids. EFSA J 2021; 19:e06459. [PMID: 33717355 PMCID: PMC7926496 DOI: 10.2903/j.efsa.2021.6459] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
American mink and ferret are highly susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but no information is available for other mustelid species. SARS-CoV-2 spreads very efficiently within mink farms once introduced, by direct and indirect contact, high within-farm animal density increases the chance for transmission. Between-farm spread is likely to occur once SARS-CoV-2 is introduced, short distance between SARS-CoV-2 positive farms is a risk factor. As of 29 January 2021, SARS-CoV-2 virus has been reported in 400 mink farms in eight countries in the European Union. In most cases, the likely introduction of SARS-CoV-2 infection into farms was infected humans. Human health can be at risk by mink-related variant viruses, which can establish circulation in the community, but so far these have not shown to be more transmissible or causing more severe impact compared with other circulating SARS-CoV-2. Concerning animal health risk posed by SARS-CoV-2 infection the animal species that may be included in monitoring plans are American mink, ferrets, cats, raccoon dogs, white-tailed deer and Rhinolophidae bats. All mink farms should be considered at risk of infection; therefore, the monitoring objective should be early detection. This includes passive monitoring (in place in the whole territory of all countries where animals susceptible to SARS-CoV-2 are bred) but also active monitoring by regular testing. First, frequent testing of farm personnel and all people in contact with the animals is recommended. Furthermore randomly selected animals (dead or sick animals should be included) should be tested using reverse transcriptase-polymerase chain reaction (RT-PCR), ideally at weekly intervals (i.e. design prevalence approximately 5% in each epidemiological unit, to be assessed case by case). Suspected animals (dead or with clinical signs and a minimum five animals) should be tested for confirmation of SARS-CoV-2 infection. Positive samples from each farm should be sequenced to monitor virus evolution and results publicly shared.
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Bhardwaj A, Sapra L, Saini C, Azam Z, Mishra PK, Verma B, Mishra GC, Srivastava RK. COVID-19: Immunology, Immunopathogenesis and Potential Therapies. Int Rev Immunol 2021; 41:171-206. [PMID: 33641587 PMCID: PMC7919479 DOI: 10.1080/08830185.2021.1883600] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/09/2020] [Accepted: 01/21/2021] [Indexed: 02/08/2023]
Abstract
The Coronavirus Disease-2019 (COVID-19) imposed public health emergency and affected millions of people around the globe. As of January 2021, 100 million confirmed cases of COVID-19 along with more than 2 million deaths were reported worldwide. SARS-CoV-2 infection causes excessive production of pro-inflammatory cytokines thereby leading to the development of "Cytokine Storm Syndrome." This condition results in uncontrollable inflammation that further imposes multiple-organ-failure eventually leading to death. SARS-CoV-2 induces unrestrained innate immune response and impairs adaptive immune responses thereby causing tissue damage. Thus, understanding the foremost features and evolution of innate and adaptive immunity to SARS-CoV-2 is crucial in anticipating COVID-19 outcomes and in developing effective strategies to control the viral spread. In the present review, we exhaustively discuss the sequential key immunological events that occur during SARS-CoV-2 infection and are involved in the immunopathogenesis of COVID-19. In addition to this, we also highlight various therapeutic options already in use such as immunosuppressive drugs, plasma therapy and intravenous immunoglobulins along with various novel potent therapeutic options that should be considered in managing COVID-19 infection such as traditional medicines and probiotics.
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Affiliation(s)
- Asha Bhardwaj
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Leena Sapra
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Chaman Saini
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Zaffar Azam
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Pradyumna K. Mishra
- Department of Molecular Biology, ICMR-NIREH, Nehru Hospital Building, Gandhi Medical College Campus, Bhopal, India
| | - Bhupendra Verma
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Gyan C. Mishra
- Lab # 1, National Centre for Cell Science (NCCS), Savitribai Phule Pune University Campus, Pune, India
| | - Rupesh K. Srivastava
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
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Devaux CA, Pinault L, Osman IO, Raoult D. Can ACE2 Receptor Polymorphism Predict Species Susceptibility to SARS-CoV-2? Front Public Health 2021; 8:608765. [PMID: 33643982 PMCID: PMC7902720 DOI: 10.3389/fpubh.2020.608765] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/23/2020] [Indexed: 12/16/2022] Open
Abstract
A novel severe acute respiratory syndrome coronavirus, SARS-CoV-2, emerged in China in December 2019 and spread worldwide, causing more than 1.3 million deaths in 11 months. Similar to the human SARS-CoV, SARS-CoV-2 shares strong sequence homologies with a sarbecovirus circulating in Rhinolophus affinis bats. Because bats are expected to be able to transmit their coronaviruses to intermediate animal hosts that in turn are a source of viruses able to cross species barriers and infect humans (so-called spillover model), the identification of an intermediate animal reservoir was the subject of intense researches. It was claimed that a reptile (Ophiophagus hannah) was the intermediate host. This hypothesis was quickly ruled out and replaced by the pangolin (Manis javanica) hypothesis. Yet, pangolin was also recently exonerated from SARS-CoV-2 transmission to humans, leaving other animal species as presumed guilty. Guided by the spillover model, several laboratories investigated in silico the species polymorphism of the angiotensin I converting enzyme 2 (ACE2) to find the best fits with the SARS-CoV-2 spike receptor-binding site. Following the same strategy, we used multi-sequence alignment, 3-D structure analysis, and electrostatic potential surface generation of ACE2 variants to predict their binding capacity to SARS-CoV-2. We report evidence that such simple in silico investigation is a powerful tool to quickly screen which species are potentially susceptible to SARS-CoV-2. However, possible receptor binding does not necessarily lead to successful replication in host. Therefore, we also discuss here the limitations of these in silico approaches in our quest on the origins of COVID-19 pandemic.
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Affiliation(s)
- Christian A. Devaux
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU–Méditerranée Infection, Marseille, France
- CNRS, Marseille, France
| | - Lucile Pinault
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU–Méditerranée Infection, Marseille, France
| | - Ikram Omar Osman
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU–Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU–Méditerranée Infection, Marseille, France
- Fondation IHU–Méditerranée Infection, Marseille, France
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Aryan H, Saxena A, Tiwari A. Correlation between bioactive lipids and novel coronavirus: constructive role of biolipids in curbing infectivity by enveloped viruses, centralizing on EPA and DHA. SYSTEMS MICROBIOLOGY AND BIOMANUFACTURING 2021; 1:186-192. [PMID: 38624677 PMCID: PMC7856852 DOI: 10.1007/s43393-020-00019-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 12/19/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) belongs to the family coronaviridae. It is spherical and possesses proteins called spikes, which can clamp onto the human cells. Once in close interaction with the human cells, these viruses undergo structural change and can fuse with the cell membrane. The virus enters the host and starts the process of translation and transcription in the cells and uncoated genome, respectively. Due to the rapid transmittable nature of the virus, extant actions should be taken. The fatty acids administrated orally, or intravenously, could help us gear things up in providing resistance and preventing infection. Hence, the multiplication of the virus could be hindered by arachidonic acid, eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA). In that context, the current review highlights the role of these unsaturated fatty acids and their derivatives such as lipoxins and resolvins in the inactivation of the enveloped coronavirus disease 2019 (COVID-19).
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Affiliation(s)
- Himani Aryan
- Diatoms Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201301 India
| | - Abhishek Saxena
- Diatoms Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201301 India
| | - Archana Tiwari
- Diatoms Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201301 India
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Mishra SK, Tripathi T. One year update on the COVID-19 pandemic: Where are we now? Acta Trop 2021; 214:105778. [PMID: 33253656 PMCID: PMC7695590 DOI: 10.1016/j.actatropica.2020.105778] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023]
Abstract
We are living through an unprecedented crisis with the rapid spread of the new coronavirus disease (COVID-19) worldwide within a short time. The timely availability of thousands of SARS-CoV-2 genomes has enabled the scientific community to study the origin, structures, and pathogenesis of the virus. The pandemic has spurred research publication and resulted in an unprecedented number of therapeutic proposals. Because the development of new drugs is time consuming, several strategies, including drug repurposing and repositioning, are being tested to treat patients with COVID-19. Researchers have developed several potential vaccine candidates that have shown promise in phase II and III trials. As of 12 November 2020, 164 candidate vaccines are in preclinical evaluation, and 48 vaccines are in clinical evaluation, of which four have cleared phase III trials (Pfizer/BioNTech's BNT162b2, Moderna's mRNA-1273, University of Oxford & AstraZeneca's AZD1222, and Gamaleya's Sputnik V vaccine). Despite the acquisition of a vast body of scientific information, treatment depends only on the clinical management of the disease through supportive care. At the pandemic's 1-year mark, we summarize current information on SARS-CoV-2 origin and biology, and advances in the development of therapeutics. The updated information presented here provides a comprehensive report on the scientific progress made in the past year in understanding of SARS-CoV-2 biology and therapeutics.
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Affiliation(s)
- Sanjay Kumar Mishra
- Department of Botany, Ewing Christian College, Prayagraj- 211003, Uttar Pradesh, India
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, Meghalaya, India,Corresponding author
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Li JY, Wang Q, Liao CH, Qiu Y, Ge XY. The 442th amino acid residue of the spike protein is critical for the adaptation to bat hosts for SARS-related coronaviruses. Virus Res 2021; 295:198307. [PMID: 33476695 PMCID: PMC7813513 DOI: 10.1016/j.virusres.2021.198307] [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: 09/08/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 11/24/2022]
Abstract
Bats carry diverse severe acute respiratory syndrome-related coronaviruses (SARSr-CoVs). The suspected interspecies transmission of SARSr-CoVs from bats to humans has caused two severe CoV pandemics, the SARS pandemic in 2003 and the recent COVID-19 pandemic. The receptor utilization of SARSr-CoV plays the key role in determining the host range and the interspecies transmission ability of the virus. Both SARS-CoV and SARS-CoV-2 use angiotensin-converting enzyme 2 (ACE2) as their receptor. Previous studies showed that WIV1 strain, the first living coronavirus isolated from bat using ACE2 as its receptor, is the prototype of SARS-CoV. The receptor-binding domain (RBD) in the spike protein (S) of SARS-CoV and WIV1 is responsible for ACE2 binding and medicates the viral entry. Comparing to SARS-CoV, WIV1 has three distinct amino acid residues (442, 472, and 487) in its RBD. This study aimed at exploring whether these three residues could alter the receptor utilization of SARSr-CoVs. We replaced the three residues in SARS-CoV (BJ01 strain) S with their counterparts in WIV1 S, and then evaluated the change of their utilization of bat, civet, and human ACE2s using a lentivirus-based pseudovirus infection system. To further validate the S-ACE2 interactions, the binding affinity between the RBDs of these S proteins and the three ACE2s were verified by flow cytometry. The results showed that the single amino acid substitution Y442S in the RBD of BJ01 S enhanced its utilization of bat ACE2 and its binding affinity to bat ACE2. On the contrary, the reverse substitution in WIV1 S (S442Y) significantly attenuated the pseudovirus utilization of bat, civet and human ACE2s for cell entry, and reduced its binding affinity with the three ACE2s. These results suggest that the S442 is critical for WIV1 adapting to bats as its natural hosts. These findings will enhance our understanding of host adaptations and cross-species infections of coronaviruses, contributing to the prediction and prevention of coronavirus epidemics.
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Affiliation(s)
- Jin-Yan Li
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan, 410012, China.
| | - Qiong Wang
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan, 410012, China.
| | - Ce-Heng Liao
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan, 410012, China.
| | - Ye Qiu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan, 410012, China.
| | - Xing-Yi Ge
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan, 410012, China.
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Fouladirad S, Bach H. Development of Coronavirus Treatments Using Neutralizing Antibodies. Microorganisms 2021; 9:microorganisms9010165. [PMID: 33451069 PMCID: PMC7828509 DOI: 10.3390/microorganisms9010165] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/09/2021] [Accepted: 01/11/2021] [Indexed: 12/19/2022] Open
Abstract
The Coronavirus disease 2019 (COVID-19), caused by the novel coronavirus SARS-CoV-2, was first reported in December 2019 in Wuhan, Hubei province, China. This virus has led to 61.8 million cases worldwide being reported as of December 1st, 2020. Currently, there are no definite approved therapies endorsed by the World Health Organization for COVID-19, focusing only on supportive care. Treatment centers around symptom management, including oxygen therapy or invasive mechanical ventilation. Immunotherapy has the potential to play a role in the treatment of SARS-CoV-2. Monoclonal antibodies (mAbs), in particular, is a relatively new approach in the world of infectious diseases and has the benefit of overcoming challenges with serum therapy and intravenous immunoglobulins preparations. Here, we reviewed the articles published in PubMed with the purpose of summarizing the currently available evidence for the use of neutralizing antibodies as a potential treatment for coronaviruses. Studies reporting in vivo results were summarized and analyzed. Despite promising data from some studies, none of them progressed to clinical trials. It is expected that neutralizing antibodies might offer an alternative for COVID-19 treatment. Thus, there is a need for randomized trials to understand the potential use of this treatment.
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Affiliation(s)
- Saman Fouladirad
- Department of Medicine, University of British Columbia, Vancouver, BC V6T 1Z, Canada;
| | - Horacio Bach
- Department of Medicine, University of British Columbia, Vancouver, BC V6T 1Z, Canada;
- Division of Infectious Diseases, University of British Columbia, Vancouver, BC V6T 1Z, Canada
- Correspondence: ; Tel.: +1-604-727-9719; Fax: +1-604-875-4013
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Lung adenocarcinoma patients have higher risk of SARS-CoV-2 infection. Aging (Albany NY) 2021; 13:1620-1632. [PMID: 33429366 PMCID: PMC7880402 DOI: 10.18632/aging.202375] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/30/2020] [Indexed: 12/26/2022]
Abstract
Both lung adenocarcinoma and coronavirus disease 2019 would cause pulmonary inflammation. Angiotensin-converting enzyme 2, the functional receptor of SARS-CoV-2, also plays a key role in lung adenocarcinoma. To study the risk of SARS-CoV-2 infection in lung adenocarcinoma patients, mRNA and microRNA profiles were obtained from The Cancer Genome Atlas and Gene Expression Omnibus followed by bioinformatics analysis. A network which regards angiotensin-converting enzyme 2 as the center was structured. In addition, via immunological analysis to explore the essential mechanism of SARS-CoV-2 susceptibility in lung adenocarcinoma. Compared with normal tissue, angiotensin-converting enzyme 2 was increased in lung adenocarcinoma patients. Furthermore, a total of 7 correlated differently expressed mRNAs (ACE2, CXCL9, MMP12, IL6, AZU1, FCN3, HYAL1 and IRAK3) and 5 correlated differently expressed microRNAs (miR-125b-5p, miR-9-5p, miR-130b-5p, miR-381-3p and miR-421) were screened. Interestingly, the most frequent toll-like receptor signaling pathway was enriched by mRNA (interlukin 6) and miRNA (miR-125b-5p) sets simultaneously. In conclusion, it was assumed that miR-125b-5p-ACE2-IL6 axis could alter the risk of SARS-CoV-2 infection in lung adenocarcinoma patients.
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Soleimanpour S, Yaghoubi A. COVID-19 vaccine: where are we now and where should we go? Expert Rev Vaccines 2021; 20:23-44. [PMID: 33435774 PMCID: PMC7898300 DOI: 10.1080/14760584.2021.1875824] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 01/11/2021] [Indexed: 01/12/2023]
Abstract
INTRODUCTION The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has currently caused the pandemic with a high progressive speed and has been considered as the global public health crisis in 2020. This new member of the coronavirus family has created a potentially fatal disease, called coronavirus disease-2019 (COVID-19). Despite the continuous efforts of researchers to find effective vaccines and drugs for COVID-19, there is still no success in this matter. AREAS COVERED Here, the literature regarding the COVID-19 vaccine candidates currently in the clinical trials, as well as main candidates in pre-clinical stages for development and research, were reviewed. These candidates have been developed under five different major platforms, including live-attenuated vaccine, mRNA-based vaccine, DNA vaccines, inactivated virus, and viral-vector-based vaccine. EXPERT OPINION There are several limitations in the field of the rapid vaccine development against SARS-CoV-2, and other members of the coronavirus family such as SARS-CoV and MERS-CoV. The key challenges of designing an effective vaccine within a short time include finding the virulence ability of an emerging virus and potential antigen, choosing suitable experimental models and efficient route of administration, the immune-response study, designing the clinical trials, and determining the safety, as well as efficacy.
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Affiliation(s)
- Saman Soleimanpour
- Antimicrobial Resistance Research Center, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Atieh Yaghoubi
- Antimicrobial Resistance Research Center, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Fahmi M, Kharisma VD, Ansori ANM, Ito M. Retrieval and Investigation of Data on SARS-CoV-2 and COVID-19 Using Bioinformatics Approach. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1318:839-857. [PMID: 33973215 DOI: 10.1007/978-3-030-63761-3_47] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Sudden emergence and a rapid outbreak of SARS-CoV-2 accompanied by a devastating impact on the economy and public health has driven extensive scientific mobilization to study and elucidate the various associated concerns about SARS-CoV-2. Bioinformatics plays a crucial role in addressing and providing solutions to questions about SARS-CoV-2. It helps shorten the duration for the vaccine development process and the discovery of potential clinical interventions through the simulation and information retrieval, and the development of well-ordered information hubs and resources, which are essential to derive data and meaningful findings from the current massive information about SARS-CoV-2. Advanced algorithms in this field also provide approaches that are essential to elucidate the relationship, origin, and evolutionary process of SARS-CoV-2. Here, we report essential bioinformatics entities, such as database and platform development, molecular evolution and phylogenetic analyses, and vaccine designs, that are useful to solve the SARS-CoV-2 conundrum.
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Affiliation(s)
- Muhamad Fahmi
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan.,Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Kusatsu, Japan
| | - Viol Dhea Kharisma
- Master Program in Biology, Department of Biology, Faculty of Mathematic and Natural Sciences, Universitas Brawijaya, Malang, Indonesia.,Computational Virology and Complexity Science Research Unit, Division of Molecular Biology and Genetics, Generasi Biologi Indonesia (GENBINESIA) Foundation, Gresik, Indonesia.,Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Malang, Indonesia
| | - Arif Nur Muhammad Ansori
- Doctoral Program in Veterinary Science, Faculty of Veterinary Medicine, Universitas Airlangga, Kampus C Universitas Airlangga, Surabaya, Indonesia.,Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Surabaya, Indonesia
| | - Masahiro Ito
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan. .,Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Kusatsu, Japan.
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Phytocompounds of Rheum emodi, Thymus serpyllum, and Artemisia annua Inhibit Spike Protein of SARS-CoV-2 Binding to ACE2 Receptor: In Silico Approach. CURRENT PHARMACOLOGY REPORTS 2021; 7:135-149. [PMID: 34306988 PMCID: PMC8279807 DOI: 10.1007/s40495-021-00259-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 05/24/2021] [Indexed: 02/07/2023]
Abstract
COVID-19, the disease caused by SARS-CoV-2, has been declared as a global pandemic. Traditional medicinal plants have long history to treat viral infections. Our in silico approach suggested that unique phytocompounds such as emodin, thymol and carvacrol, and artemisinin could physically bind SARS-CoV-2 spike glycoproteins (6VXX and 6VYB), SARS-CoV-2 B.1.351 South Africa variant of Spike glycoprotein (7NXA), and even with ACE2 and prevent the SARS-CoV-2 binding to the host ACE2, TMPRSS2 and neutrapilin-1 receptors. Since Chloroquine has been looked as potential therapy against COVID-19, we also compared the binding of chloroquine and artemisinin for its interaction with spike proteins (6VXX, 6VYB) and its variant 7NXA, respectively. Molecular docking study of phytocompounds and SARS-CoV-2 spike protein was performed by using AutoDock/Vina software. Molecular dynamics (MD) simulation was performed for 50ns. Among all the phytocompounds, molecular docking studies revealed lowest binding energy of artemisinin with 6VXX and 6VYB, with Etotal -10.5 KJ mol-1 and -10.3 KJ mol-1 respectively. Emodin showed the best binding affinity with 6VYB with Etotal -8.8 KJ mol-1and SARS-CoV-2 B.1.351 variant (7NXA) with binding energy of -6.4KJ mol-1. Emodin showed best interactions with TMPRSS 2 and ACE2 with Etotal of -7.1 and -7.3 KJ mol-1 respectively, whereas artemisinin interacts with TMPRSS 2 and ACE2 with Etotal of -6.9 and -7.4 KJ mol-1 respectively. All the phytocompounds were non-toxic and non-carcinogenic. MD simulation showed that artemisinin has more stable interaction with 6VYB as compared to 6VXX, and hence proposed as potential phytochemical to prevent SARS-CoV-2 interaction with ACE-2 receptor. GRAPHICAL ABSTRACT SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s40495-021-00259-4.
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Rolta R, Salaria D, Sharma P, Sharma B, Kumar V, Rathi B, Verma M, Sourirajan A, Baumler DJ, Dev K. Phytocompounds of Rheum emodi, Thymus serpyllum, and Artemisia annua Inhibit Spike Protein of SARS-CoV-2 Binding to ACE2 Receptor: In Silico Approach. CURRENT PHARMACOLOGY REPORTS 2021; 7:135-149. [PMID: 34306988 DOI: 10.21203/rs.3.rs-30938/v1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/24/2021] [Indexed: 05/21/2023]
Abstract
UNLABELLED COVID-19, the disease caused by SARS-CoV-2, has been declared as a global pandemic. Traditional medicinal plants have long history to treat viral infections. Our in silico approach suggested that unique phytocompounds such as emodin, thymol and carvacrol, and artemisinin could physically bind SARS-CoV-2 spike glycoproteins (6VXX and 6VYB), SARS-CoV-2 B.1.351 South Africa variant of Spike glycoprotein (7NXA), and even with ACE2 and prevent the SARS-CoV-2 binding to the host ACE2, TMPRSS2 and neutrapilin-1 receptors. Since Chloroquine has been looked as potential therapy against COVID-19, we also compared the binding of chloroquine and artemisinin for its interaction with spike proteins (6VXX, 6VYB) and its variant 7NXA, respectively. Molecular docking study of phytocompounds and SARS-CoV-2 spike protein was performed by using AutoDock/Vina software. Molecular dynamics (MD) simulation was performed for 50ns. Among all the phytocompounds, molecular docking studies revealed lowest binding energy of artemisinin with 6VXX and 6VYB, with Etotal -10.5 KJ mol-1 and -10.3 KJ mol-1 respectively. Emodin showed the best binding affinity with 6VYB with Etotal -8.8 KJ mol-1and SARS-CoV-2 B.1.351 variant (7NXA) with binding energy of -6.4KJ mol-1. Emodin showed best interactions with TMPRSS 2 and ACE2 with Etotal of -7.1 and -7.3 KJ mol-1 respectively, whereas artemisinin interacts with TMPRSS 2 and ACE2 with Etotal of -6.9 and -7.4 KJ mol-1 respectively. All the phytocompounds were non-toxic and non-carcinogenic. MD simulation showed that artemisinin has more stable interaction with 6VYB as compared to 6VXX, and hence proposed as potential phytochemical to prevent SARS-CoV-2 interaction with ACE-2 receptor. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s40495-021-00259-4.
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Affiliation(s)
- Rajan Rolta
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Pin, Solan, Himachal Pradesh 173212 India
| | - Deeksha Salaria
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Pin, Solan, Himachal Pradesh 173212 India
| | - PremPrakash Sharma
- Laboratory for Translational Chemistry and Drug Discovery, Hansraj College University of Delhi, Delhi, 110007 India
| | - Bhanu Sharma
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Pin, Solan, Himachal Pradesh 173212 India
| | - Vikas Kumar
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Pin, Solan, Himachal Pradesh 173212 India
| | - Brijesh Rathi
- Laboratory for Translational Chemistry and Drug Discovery, Hansraj College University of Delhi, Delhi, 110007 India
| | - Mansi Verma
- Sri Venkateswara College, University of Delhi, New Delhi, 110021 India
| | - Anuradha Sourirajan
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Pin, Solan, Himachal Pradesh 173212 India
| | - David J Baumler
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN USA
| | - Kamal Dev
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Pin, Solan, Himachal Pradesh 173212 India
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44
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Schütz D, Ruiz-Blanco YB, Münch J, Kirchhoff F, Sanchez-Garcia E, Müller JA. Peptide and peptide-based inhibitors of SARS-CoV-2 entry. Adv Drug Deliv Rev 2020; 167:47-65. [PMID: 33189768 PMCID: PMC7665879 DOI: 10.1016/j.addr.2020.11.007] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/08/2020] [Accepted: 11/10/2020] [Indexed: 12/18/2022]
Abstract
To date, no effective vaccines or therapies are available against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative pandemic agent of the coronavirus disease 2019 (COVID-19). Due to their safety, efficacy and specificity, peptide inhibitors hold great promise for the treatment of newly emerging viral pathogens. Based on the known structures of viral proteins and their cellular targets, antiviral peptides can be rationally designed and optimized. The resulting peptides may be highly specific for their respective targets and particular viral pathogens or exert broad antiviral activity. Here, we summarize the current status of peptides inhibiting SARS-CoV-2 entry and outline the strategies used to design peptides targeting the ACE2 receptor or the viral spike protein and its activating proteases furin, transmembrane serine protease 2 (TMPRSS2), or cathepsin L. In addition, we present approaches used against related viruses such as SARS-CoV-1 that might be implemented for inhibition of SARS-CoV-2 infection.
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Affiliation(s)
- Desiree Schütz
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Yasser B Ruiz-Blanco
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, 45117 Essen, Germany.
| | - Janis A Müller
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany.
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45
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Silva LR, da Silva Santos-Júnior PF, de Andrade Brandão J, Anderson L, Bassi ÊJ, Xavier de Araújo-Júnior J, Cardoso SH, da Silva-Júnior EF. Druggable targets from coronaviruses for designing new antiviral drugs. Bioorg Med Chem 2020; 28:115745. [PMID: 33007557 PMCID: PMC7836322 DOI: 10.1016/j.bmc.2020.115745] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/26/2020] [Accepted: 08/29/2020] [Indexed: 01/18/2023]
Abstract
Severe respiratory infections were highlighted in the SARS-CoV outbreak in 2002, as well as MERS-CoV, in 2012. Recently, the novel CoV (COVID-19) has led to severe respiratory damage to humans and deaths in Asia, Europe, and Americas, which allowed the WHO to declare the pandemic state. Notwithstanding all impacts caused by Coronaviruses, it is evident that the development of new antiviral agents is an unmet need. In this review, we provide a complete compilation of all potential antiviral agents targeting macromolecular structures from these Coronaviruses (Coronaviridae), providing a medicinal chemistry viewpoint that could be useful for designing new therapeutic agents.
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Affiliation(s)
- Leandro Rocha Silva
- Chemistry and Biotechnology Institute, Federal University of Alagoas, Campus A.C. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil; Laboratory of Organic and Medicinal Synthesis, Federal University of Alagoas, Campus Arapiraca, Manoel Severino Barbosa Avenue, Arapiraca 57309-005, Brazil
| | | | - Júlia de Andrade Brandão
- IMUNOREG - Immunoregulation Research Group, Laboratory of Research in Virology and Immunology, Institute of Biological Sciences and Health, Federal University of Alagoas, Campus AC. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil
| | - Letícia Anderson
- IMUNOREG - Immunoregulation Research Group, Laboratory of Research in Virology and Immunology, Institute of Biological Sciences and Health, Federal University of Alagoas, Campus AC. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil; CESMAC University Center, Cônego Machado Street, Maceió 57051-160, Brazil
| | - Ênio José Bassi
- IMUNOREG - Immunoregulation Research Group, Laboratory of Research in Virology and Immunology, Institute of Biological Sciences and Health, Federal University of Alagoas, Campus AC. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil
| | - João Xavier de Araújo-Júnior
- Chemistry and Biotechnology Institute, Federal University of Alagoas, Campus A.C. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil; Laboratory of Medicinal Chemistry, Pharmaceutical Sciences Institute, Federal University of Alagoas, Campus A.C. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil
| | - Sílvia Helena Cardoso
- Laboratory of Organic and Medicinal Synthesis, Federal University of Alagoas, Campus Arapiraca, Manoel Severino Barbosa Avenue, Arapiraca 57309-005, Brazil
| | - Edeildo Ferreira da Silva-Júnior
- Chemistry and Biotechnology Institute, Federal University of Alagoas, Campus A.C. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil; Laboratory of Medicinal Chemistry, Pharmaceutical Sciences Institute, Federal University of Alagoas, Campus A.C. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil.
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46
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Karathanou K, Lazaratos M, Bertalan É, Siemers M, Buzar K, Schertler GFX, Del Val C, Bondar AN. A graph-based approach identifies dynamic H-bond communication networks in spike protein S of SARS-CoV-2. J Struct Biol 2020; 212:107617. [PMID: 32919067 PMCID: PMC7481144 DOI: 10.1016/j.jsb.2020.107617] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/03/2020] [Accepted: 09/06/2020] [Indexed: 02/07/2023]
Abstract
Corona virus spike protein S is a large homo-trimeric protein anchored in the membrane of the virion particle. Protein S binds to angiotensin-converting-enzyme 2, ACE2, of the host cell, followed by proteolysis of the spike protein, drastic protein conformational change with exposure of the fusion peptide of the virus, and entry of the virion into the host cell. The structural elements that govern conformational plasticity of the spike protein are largely unknown. Here, we present a methodology that relies upon graph and centrality analyses, augmented by bioinformatics, to identify and characterize large H-bond clusters in protein structures. We apply this methodology to protein S ectodomain and find that, in the closed conformation, the three protomers of protein S bring the same contribution to an extensive central network of H-bonds, and contribute symmetrically to a relatively large H-bond cluster at the receptor binding domain, and to a cluster near a protease cleavage site. Markedly different H-bonding at these three clusters in open and pre-fusion conformations suggest dynamic H-bond clusters could facilitate structural plasticity and selection of a protein S protomer for binding to the host receptor, and proteolytic cleavage. From analyses of spike protein sequences we identify patches of histidine and carboxylate groups that could be involved in transient proton binding.
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Affiliation(s)
- Konstantina Karathanou
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
| | - Michalis Lazaratos
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
| | - Éva Bertalan
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
| | - Malte Siemers
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
| | - Krzysztof Buzar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
| | - Gebhard F X Schertler
- Paul Scherrer Institut, Department of Biology and Chemistry, Laboratory of Biomolecular Research, CH-5303 Villigen-PSI, Switzerland; ETH Zürich, Department of Biology, 8093 Zürich, Switzerland
| | - Coral Del Val
- University of Granada, Department of Computer Science and Artificial Intelligence, E-18071 Granada, Spain; Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain; Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI Institute), 18014 Granada, Spain
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany.
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47
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Sharifkashani S, Bafrani MA, Khaboushan AS, Pirzadeh M, Kheirandish A, Yavarpour Bali H, Hessami A, Saghazadeh A, Rezaei N. Angiotensin-converting enzyme 2 (ACE2) receptor and SARS-CoV-2: Potential therapeutic targeting. Eur J Pharmacol 2020; 884:173455. [PMID: 32745604 PMCID: PMC7834210 DOI: 10.1016/j.ejphar.2020.173455] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/30/2020] [Accepted: 07/30/2020] [Indexed: 02/06/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a beta coronavirus that uses the human angiotensin-converting enzyme 2 (ACE2) receptor as a point of entry. The present review discusses the origin and structure of the virus and its mechanism of cell entry followed by the therapeutic potentials of strategies directed towards SARS-CoV2-ACE2 binding, the renin-angiotensin system, and the kinin-kallikrein system. SARS-CoV2-ACE2 binding-directed approaches mainly consist of targeting receptor binding domain, ACE2 blockers, soluble ACE2, and host protease inhibitors. In conclusion, blocking or manipulating the SARS-CoV2-ACE2 binding interface perhaps offers the best tactic against the virus that should be treated as a fundamental subject of future research.
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Affiliation(s)
- Sourena Sharifkashani
- Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Tehran, Iran; School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Melika Arab Bafrani
- Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Tehran, Iran; Students' Scientific Research Center (SSRC), Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Soltani Khaboushan
- Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Tehran, Iran; School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Marzieh Pirzadeh
- Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Tehran, Iran; Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Ali Kheirandish
- Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Tehran, Iran; Student Research Committee, School of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Hanie Yavarpour Bali
- Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Tehran, Iran; Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Amirhossein Hessami
- Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Tehran, Iran; Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Amene Saghazadeh
- Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Tehran, Iran; Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran; Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran.
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48
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Brandão SCS, Ramos JDOX, Dompieri LT, Godoi ETAM, Figueiredo JL, Sarinho ESC, Chelvanambi S, Aikawa M. Is Toll-like receptor 4 involved in the severity of COVID-19 pathology in patients with cardiometabolic comorbidities? Cytokine Growth Factor Rev 2020; 58:102-110. [PMID: 32988728 PMCID: PMC7505161 DOI: 10.1016/j.cytogfr.2020.09.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 09/09/2020] [Accepted: 09/14/2020] [Indexed: 02/06/2023]
Abstract
The severe form of COVID-19 is marked by an abnormal and exacerbated immunological host response favoring to a poor outcome in a significant number of patients, especially those with obesity, diabetes, hypertension, and atherosclerosis. The chronic inflammatory process found in these cardiometabolic comorbidities is marked by the overexpression of pro-inflammatory cytokines such as interleukin-6 (IL-6) and tumoral necrosis factor-alpha (TNF-α), which are products of the Toll-Like receptors 4 (TLR4) pathway. The SARS-CoV-2 initially infects cells in the upper respiratory tract and, in some patients, spread very quickly, needing respiratory support and systemically, causing collateral damage in tissues. We hypothesize that this happens because the SARS-CoV-2 spike protein interacts strongly with TLR4, causing an intensely exacerbated immune response in the host's lungs, culminating with the cytokine storm, accumulating secretions and hindering blood oxygenation, along with the immune system attacks the body, leading to multiple organ failure.
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Affiliation(s)
- Simone Cristina Soares Brandão
- Department of Medicine, Cardiology and Nuclear Imaging Division, Clinical Hospital, Federal University of Pernambuco, Recife, Pernambuco, Brazil.
| | | | | | | | - José Luiz Figueiredo
- Department of Surgery, Experimental Surgery Unit, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - Emanuel Sávio Cavalcanti Sarinho
- Department of Medicine, Allergy and Clinical Immunology Division, Clinical Hospital, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - Sarvesh Chelvanambi
- Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Masanori Aikawa
- Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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49
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Farrera-Soler L, Daguer JP, Barluenga S, Vadas O, Cohen P, Pagano S, Yerly S, Kaiser L, Vuilleumier N, Winssinger N. Identification of immunodominant linear epitopes from SARS-CoV-2 patient plasma. PLoS One 2020; 15:e0238089. [PMID: 32903266 PMCID: PMC7480855 DOI: 10.1371/journal.pone.0238089] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/10/2020] [Indexed: 01/09/2023] Open
Abstract
A novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) is the source of a current pandemic (COVID-19) with devastating consequences in public health and economic stability. Using a peptide array to map the antibody response of plasma from healing patients (12) and heathy patients (6), we identified three immunodominant linear epitopes, two of which correspond to key proteolytic sites on the spike protein (S1/S2 and S2') known to be critical for cellular entry. We show biochemical evidence that plasma positive for the epitope adjacent to the S1/S2 cleavage site inhibits furin-mediated proteolysis of spike.
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Affiliation(s)
- Lluc Farrera-Soler
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Jean-Pierre Daguer
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Sofia Barluenga
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Oscar Vadas
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Patrick Cohen
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Sabrina Pagano
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Sabine Yerly
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Laurent Kaiser
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
- Division of Infectious Diseases¸ Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Nicolas Vuilleumier
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
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50
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Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. PLoS One 2020; 15:e0238344. [PMID: 32881907 PMCID: PMC7470274 DOI: 10.1371/journal.pone.0238344] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/14/2020] [Indexed: 12/20/2022] Open
Abstract
A novel severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) causing COVID-19 pandemic in humans, recently emerged and has exported in more than 200 countries as a result of rapid spread. In this study, we have made an attempt to investigate the SARS-CoV-2 genome reported from 13 different countries, identification of mutations in major coronavirus proteins of these different SARS-CoV-2 genomes and compared with SARS-CoV. These thirteen complete genome sequences of SARS-CoV-2 showed high identity (>99%) to each other, while they shared 82% identity with SARS-CoV. Here, we performed a very systematic mutational analysis of SARS-CoV-2 genomes from different geographical locations, which enabled us to identify numerous unique features of this viral genome. This includes several important country-specific unique mutations in the major proteins of SARS-CoV-2 namely, replicase polyprotein, spike glycoprotein, envelope protein and nucleocapsid protein. Indian strain showed mutation in spike glycoprotein at R408I and in replicase polyprotein at I671T, P2144S and A2798V,. While the spike protein of Spain & South Korea carried F797C and S221W mutation, respectively. Likewise, several important country specific mutations were analyzed. The effect of mutations of these major proteins were also investigated using various in silico approaches. Main protease (Mpro), the therapeutic target protein of SARS with maximum reported inhibitors, was thoroughly investigated and the effect of mutation on the binding affinity and structural dynamics of Mpro was studied. It was found that the R60C mutation in Mpro affects the protein dynamics, thereby, affecting the binding of inhibitor within its active site. The implications of mutation on structural characteristics were determined. The information provided in this manuscript holds great potential in further scientific research towards the design of potential vaccine candidates/small molecular inhibitor against COVID19.
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